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Journal of the Royal Society, Interface

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https://www.readbyqxmd.com/read/28100829/a-mathematical-model-of-tumour-angiogenesis-growth-regression-and-regrowth
#1
Guillermo Vilanova, Ignasi Colominas, Hector Gomez
Cancerous tumours have the ability to recruit new blood vessels through a process called angiogenesis. By stimulating vascular growth, tumours get connected to the circulatory system, receive nutrients and open a way to colonize distant organs. Tumour-induced vascular networks become unstable in the absence of tumour angiogenic factors (TAFs). They may undergo alternating stages of growth, regression and regrowth. Following a phase-field methodology, we propose a model of tumour angiogenesis that reproduces the aforementioned features and highlights the importance of vascular regression and regrowth...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28100828/an-integrated-modelling-framework-for-neural-circuits-with-multiple-neuromodulators
#2
Alok Joshi, Vahab Youssofzadeh, Vinith Vemana, T M McGinnity, Girijesh Prasad, KongFatt Wong-Lin
Neuromodulators are endogenous neurochemicals that regulate biophysical and biochemical processes, which control brain function and behaviour, and are often the targets of neuropharmacological drugs. Neuromodulator effects are generally complex partly owing to the involvement of broad innervation, co-release of neuromodulators, complex intra- and extrasynaptic mechanism, existence of multiple receptor subtypes and high interconnectivity within the brain. In this work, we propose an efficient yet sufficiently realistic computational neural modelling framework to study some of these complex behaviours...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28100827/insights-into-resource-consumption-cross-feeding-system-collapse-stability-and-biodiversity-from-an-artificial-ecosystem
#3
Yu Liu, David Sumpter
Community ecosystems at very different levels of biological organization often have similar properties. Coexistence of multiple species, cross-feeding, biodiversity and fluctuating population dynamics are just a few of the properties that arise in a range of ecological settings. Here we develop a bottom-up model of consumer-resource interactions, in the form of an artificial ecosystem 'number soup', which reflects basic properties of many bacterial and other community ecologies. We demonstrate four key properties of the number soup model: (i) communities self-organize so that all available resources are fully consumed; (ii) reciprocal cross-feeding is a common evolutionary outcome, which evolves in a number of stages, and many transitional species are involved; (iii) the evolved ecosystems are often 'robust yet fragile', with keystone species required to prevent the whole system from collapsing; (iv) non-equilibrium dynamics and chaotic patterns are general properties, readily generating rich biodiversity...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28100826/biomechanical-properties-of-wheat-grains-the-implications-on-milling
#4
James E Hourston, Michael Ignatz, Martin Reith, Gerhard Leubner-Metzger, Tina Steinbrecher
Millennia of continuous innovation have driven ever increasing efficiency in the milling process. Mechanically characterizing wheat grains and discerning the structure and function of the wheat bran layers can contribute to continuing innovation. We present novel shear force and puncture force testing regimes to characterize different wheat grain cultivars. The forces endured by wheat grains during the milling process can be quantified, enabling us to measure the impact of commonly applied grain pretreatments, such as microwave heating, extended tempering, enzyme and hormone treatments on grains of different 'hardness'...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28077764/antimicrobial-peptide-coatings-for-hydroxyapatite-electrostatic-and-covalent-attachment-of-antimicrobial-peptides-to-surfaces
#5
Leigh Townsend, Richard L Williams, Olachi Anuforom, Matthew R Berwick, Fenella Halstead, Erik Hughes, Artemis Stamboulis, Beryl Oppenheim, Julie Gough, Liam Grover, Robert A H Scott, Mark Webber, Anna F A Peacock, Antonio Belli, Ann Logan, Felicity de Cogan
The interface between implanted devices and their host tissue is complex and is often optimized for maximal integration and cell adhesion. However, this also gives a surface suitable for bacterial colonization. We have developed a novel method of modifying the surface at the material-tissue interface with an antimicrobial peptide (AMP) coating to allow cell attachment while inhibiting bacterial colonization. The technology reported here is a dual AMP coating. The dual coating consists of AMPs covalently bonded to the hydroxyapatite surface, followed by deposition of electrostatically bound AMPs...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28077763/a-simplified-mathematical-model-of-directional-dna-site-specific-recombination-by-serine-integrases
#6
Alexandra Pokhilko, Jia Zhao, W Marshall Stark, Sean D Colloms, Oliver Ebenhöh
Serine integrases catalyse site-specific recombination to integrate and excise bacteriophage genomes into and out of their host's genome. These enzymes exhibit remarkable directionality; in the presence of the integrase alone, recombination between attP and attB DNA sites is efficient and irreversible, giving attL and attR products which do not recombine further. However, in the presence of the bacteriophage-encoded recombination directionality factor (RDF), integrase efficiently promotes recombination between attL and attR to re-form attP and attB The DNA substrates and products of both reactions are approximately isoenergetic, and no cofactors (such as adenosine triphosphate) are required for recombination...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28077762/inverse-problems-in-reduced-order-models-of-cardiovascular-haemodynamics-aspects-of-data-assimilation-and-heart-rate-variability
#7
Sanjay Pant, Chiara Corsini, Catriona Baker, Tain-Yen Hsia, Giancarlo Pennati, Irene E Vignon-Clementel
Inverse problems in cardiovascular modelling have become increasingly important to assess each patient individually. These problems entail estimation of patient-specific model parameters from uncertain measurements acquired in the clinic. In recent years, the method of data assimilation, especially the unscented Kalman filter, has gained popularity to address computational efficiency and uncertainty consideration in such problems. This work highlights and presents solutions to several challenges of this method pertinent to models of cardiovascular haemodynamics...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28077761/on-the-autorotation-of-animal-wings
#8
Victor Manuel Ortega-Jimenez, Antonio Martín-Alcántara, Ramon Fernandez-Feria, Robert Dudley
Botanical samaras spin about their centre of mass and create vertical aerodynamic forces which slow their rate of descent. Descending autorotation of animal wings, however, has never been documented. We report here that isolated wings from Anna's hummingbirds, and also from 10 species of insects, can stably autorotate and achieve descent speeds and aerodynamic performance comparable to those of samaras. A hummingbird wing loaded at its base with the equivalent of 50% of the bird's body mass descended only twice as fast as an unloaded wing, and rotated at frequencies similar to those of the wings in flapping flight...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28077760/effective-delivery-of-volatile-biocides-employing-mesoporous-silicates-for-treating-biofilms
#9
Andrea C Chan, Marimar Bravo Cadena, Helen E Townley, Mark D Fricker, Ian P Thompson
Nanoparticulate delivery of biocides has the potential to decrease levels of exposure to non-target organisms, and miminize long-term exposure that can promote the development of resistance. Silica nanoparticles are an ideal vehicle since they are inert, biocompatible, biodegradable, and thermally and chemically stable. Encapsulation of biocides within nanoparticulates can improve their stability and longevity and maximize the biocidal potential of hydrophobic volatile compounds. Herein, we have shown that the plant secondary metabolites allyl isothiocyanate and cinnamaldehyde demonstrated increased antimicrobial activity against Escherichia coli in planktonic form, when packaged into mesoporous silica nanoparticles...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28077759/complex-responses-to-movement-based-disease-control-when-livestock-trading-helps
#10
Jamie C Prentice, Glenn Marion, Michael R Hutchings, Tom N McNeilly, Louise Matthews
Livestock disease controls are often linked to movements between farms, for example, via quarantine and pre- or post-movement testing. Designing effective controls, therefore, benefits from accurate assessment of herd-to-herd transmission. Household models of human infections make use of R*, the number of groups infected by an initial infected group, which is a metapopulation level analogue of the basic reproduction number R0 that provides a better characterization of disease spread in a metapopulation. However, existing approaches to calculate R* do not account for individual movements between locations which means we lack suitable tools for livestock systems...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28053113/stochastic-models-of-gene-transcription-with-upstream-drives-exact-solution-and-sample-path-characterization
#11
Justine Dattani, Mauricio Barahona
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells with time-varying (stochastic or deterministic) transcription and degradation rates. Such rates can be understood as upstream cellular drives representing the effect of different aspects of the cellular environment. We show that the full solution of the master equation contains two components: a model-specific, upstream effective drive, which encapsulates the effect of cellular drives (e...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28053112/modelling-and-parameter-inference-of-predator-prey-dynamics-in-heterogeneous-environments-using-the-direct-integral-approach
#12
Itai Dattner, Ezer Miller, Margarita Petrenko, Daniel E Kadouri, Edouard Jurkevitch, Amit Huppert
Most bacterial habitats are topographically complex in the micro scale. Important examples include the gastrointestinal and tracheal tracts, and the soil. Although there are myriad theoretical studies that explore the role of spatial structures on antagonistic interactions (predation, competition) among animals, there are many fewer experimental studies that have explored, validated and quantified their predictions. In this study, we experimentally monitored the temporal dynamic of the predatory bacterium Bdellovibrio bacteriovorus, and its prey, the bacterium Burkholderia stabilis in a structured habitat consisting of sand under various regimes of wetness...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28053111/evolutionary-interplay-between-structure-energy-and-epistasis-in-the-coat-protein-of-the-%C3%AF-x174-phage-family
#13
Rodrigo A F Redondo, Harold P de Vladar, Tomasz Włodarski, Jonathan P Bollback
Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28003530/the-stentable-in-vitro-artery-an-instrumented-platform-for-endovascular-device-development-and-optimization
#14
Elizabeth E Antoine, François P Cornat, Abdul I Barakat
Although vascular disease is a leading cause of mortality, in vitro tools for controlled, quantitative studies of vascular biological processes in an environment that reflects physiological complexity remain limited. We developed a novel in vitro artery that exhibits a number of unique features distinguishing it from tissue-engineered or organ-on-a-chip constructs, most notably that it allows deployment of endovascular devices including stents, quantitative real-time tracking of cellular responses and detailed measurement of flow velocity and lumenal shear stress using particle image velocimetry...
December 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28003529/managing-aquatic-parasites-for-reduced-drug-resistance-lessons-from-the-land
#15
Gregor F McEwan, Maya L Groner, Danielle L Burnett, Mark D Fast, Crawford W Revie
Atlantic salmon farming is one of the largest aquaculture industries in the world. A major problem in salmon farms is the sea louse ectoparasite Lepeophtheirus salmonis, which can cause stress, secondary infection and sometimes mortality in the salmon host. Sea lice have substantial impacts on farm economics and potentially nearby wild salmonid populations. The most common method of controlling sea louse infestations is application of chemicals. However, most farming regions worldwide have observed resistance to the small set of treatment chemicals that are available...
December 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28003528/behavioural-change-models-for-infectious-disease-transmission-a-systematic-review-2010-2015
#16
REVIEW
Frederik Verelst, Lander Willem, Philippe Beutels
We review behavioural change models (BCMs) for infectious disease transmission in humans. Following the Cochrane collaboration guidelines and the PRISMA statement, our systematic search and selection yielded 178 papers covering the period 2010-2015. We observe an increasing trend in published BCMs, frequently coupled to (re)emergence events, and propose a categorization by distinguishing how information translates into preventive actions. Behaviour is usually captured by introducing information as a dynamic parameter (76/178) or by introducing an economic objective function, either with (26/178) or without (37/178) imitation...
December 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28003527/ni%C3%A3-pce-bell-or-turing-how-to-test-odour-reproduction
#17
REVIEW
David Harel
Decades before the existence of anything resembling an artificial intelligence system, Alan Turing raised the question of how to test whether machines can think, or, in modern terminology, whether a computer claimed to exhibit intelligence indeed does so. This paper raises the analogous issue for olfaction: how to test the validity of a system claimed to reproduce arbitrary odours artificially, in a way recognizable to humans. Although odour reproduction systems are still far from being viable, the question of how to test candidates thereof is claimed to be interesting and non-trivial, and a novel method is proposed...
December 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28003526/differential-cell-matrix-responses-in-hypoxia-stimulated-aortic-versus-mitral-valves
#18
Matthew C Sapp, Varun K Krishnamurthy, Daniel S Puperi, Saheba Bhatnagar, Gabrielle Fatora, Neelesh Mutyala, K Jane Grande-Allen
Tissue oxygenation often plays a significant role in disease and is an essential design consideration for tissue engineering. Here, oxygen diffusion profiles of porcine aortic and mitral valve leaflets were determined using an oxygen diffusion chamber in conjunction with computational models. Results from these studies revealed the differences between aortic and mitral valve leaflet diffusion profiles and suggested that diffusion alone was insufficient for normal oxygen delivery in mitral valves. During fibrotic valve disease, leaflet thickening due to abnormal extracellular matrix is likely to reduce regional oxygen availability...
December 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28003525/correction-to-through-the-eyes-of-a-bird-modelling-visually-guided-obstacle-flight
#19
Huai-Ti Lin, Ivo G Ros, Andrew A Biewener
No abstract text is available yet for this article.
December 2016: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/27974578/variability-in-individual-activity-bursts-improves-ant-foraging-success
#20
Daniel Campos, Frederic Bartumeus, Vicenç Méndez, José S Andrade, Xavier Espadaler
Using experimental and computational methods, we study the role of behavioural variability in activity bursts (or temporal activity patterns) for individual and collective regulation of foraging in A. senilis ants. First, foraging experiments were carried out under special conditions (low densities of ants and food and absence of external cues or stimuli) where individual-based strategies are most prevalent. By using marked individuals and recording all foraging trajectories, we were then able to precisely quantify behavioural variability among individuals...
December 2016: Journal of the Royal Society, Interface
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