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Journal of the Royal Society, Interface

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https://www.readbyqxmd.com/read/29343635/combining-radiation-with-hyperthermia-a-multiscale-model-informed-by-in-vitro-experiments
#1
S Brüningk, G Powathil, P Ziegenhein, J Ijaz, I Rivens, S Nill, M Chaplain, U Oelfke, G Ter Haar
Combined radiotherapy and hyperthermia offer great potential for the successful treatment of radio-resistant tumours through thermo-radiosensitization. Tumour response heterogeneity, due to intrinsic, or micro-environmentally induced factors, may greatly influence treatment outcome, but is difficult to account for using traditional treatment planning approaches. Systems oncology simulation, using mathematical models designed to predict tumour growth and treatment response, provides a powerful tool for analysis and optimization of combined treatments...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29343634/fluttering-of-growing-leaves-as-a-way-to-reach-flatness-experimental-evidence-on-persea-americana
#2
Julien Derr, Renaud Bastien, Étienne Couturier, Stéphane Douady
Simple leaves show unexpected growth motions: the midrib of the leaves swings periodically in association with buckling events of the leaf blade, giving the impression that the leaves are fluttering. The quantitative kinematic analysis of this motion provides information about the respective growth between the main vein and the lamina. Our three-dimensional reconstruction of an avocado tree leaf shows that the conductor of the motion is the midrib, presenting continuous oscillations and inducing buckling events on the blade...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29343633/hydrogel-biomaterials-and-their-therapeutic-potential-for-muscle-injuries-and-muscular-dystrophies
#3
REVIEW
Rachel Lev, Dror Seliktar
Muscular diseases such as muscular dystrophies and muscle injuries constitute a large group of ailments that manifest as muscle weakness, atrophy or fibrosis. Although cell therapy is a promising treatment option, the delivery and retention of cells in the muscle is difficult and prevents sustained regeneration needed for adequate functional improvements. Various types of biomaterials with different physical and chemical properties have been developed to improve the delivery of cells and/or growth factors for treating muscle injuries...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29343632/correction-to-dynamics-of-phytoplankton-blooms-in-turbulent-vortex-cells
#4
Christian Lindemann, Andre Visser, Patrizio Mariani
No abstract text is available yet for this article.
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29343631/stochastic-resonances-in-a-distributed-genetic-broadcasting-system-the-nf%C3%AE%C2%BAb-i%C3%AE%C2%BAb-paradigm
#5
Zhipeng Wang, Davit A Potoyan, Peter G Wolynes
Gene regulatory networks must relay information from extracellular signals to downstream genes in an efficient, timely and coherent manner. Many complex functional tasks such as the immune response require system-wide broadcasting of information not to one but to many genes carrying out distinct functions whose dynamical binding and unbinding characteristics are widely distributed. In such broadcasting networks, the intended target sites are also often dwarfed in number by the even more numerous non-functional binding sites...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29343630/emergence-and-dynamics-of-self-producing-information-niches-as-a-step-towards-pre-evolutionary-organization
#6
Richard J Carter, Karoline Wiesner, Stephen Mann
As a step towards understanding pre-evolutionary organization in non-genetic systems, we develop a model to investigate the emergence and dynamics of proto-autopoietic networks in an interacting population of simple information processing entities (automata). Our simulations indicate that dynamically stable strongly connected networks of mutually producing communication channels emerge under specific environmental conditions. We refer to these distinct organizational steady states as information niches In each case, we measure the information content by the Shannon entropy, and determine the fitness landscape, robustness and transition pathways for information niches subjected to intermittent environmental perturbations under non-evolutionary conditions...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29343629/the-markov-blankets-of-life-autonomy-active-inference-and-the-free-energy-principle
#7
REVIEW
Michael Kirchhoff, Thomas Parr, Ensor Palacios, Karl Friston, Julian Kiverstein
This work addresses the autonomous organization of biological systems. It does so by considering the boundaries of biological systems, from individual cells to Home sapiens, in terms of the presence of Markov blankets under the active inference scheme-a corollary of the free energy principle. A Markov blanket defines the boundaries of a system in a statistical sense. Here we consider how a collective of Markov blankets can self-assemble into a global system that itself has a Markov blanket; thereby providing an illustration of how autonomous systems can be understood as having layers of nested and self-sustaining boundaries...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29343628/keeping-the-home-fires-burning-amp-activated-protein-kinase
#8
REVIEW
D Grahame Hardie
Living cells obtain energy either by oxidizing reduced compounds of organic or mineral origin or by absorbing light. Whichever energy source is used, some of the energy released is conserved by converting adenosine diphosphate (ADP) to adenosine triphosphate (ATP), which are analogous to the chemicals in a rechargeable battery. The energy released by the conversion of ATP back to ADP is used to drive most energy-requiring processes, including cell growth, cell division, communication and movement. It is clearly essential to life that the production and consumption of ATP are always maintained in balance, and the AMP-activated protein kinase (AMPK) is one of the key cellular regulatory systems that ensures this...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29343627/risk-ratios-for-contagious-outcomes
#9
Olga Morozova, Ted Cohen, Forrest W Crawford
Epidemiologists commonly use the risk ratio to summarize the relationship between a binary covariate and outcome, even when outcomes may be dependent. Investigations of transmissible diseases in clusters-households, villages or small groups-often report risk ratios. Epidemiologists have warned that risk ratios may be misleading when outcomes are contagious, but the nature of this error is poorly understood. In this study, we assess the meaning of the risk ratio when outcomes are contagious. We provide a mathematical definition of infectious disease transmission within clusters, based on the canonical stochastic susceptible-infective model...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29321271/incremental-distribution-of-strontium-and-zinc-in-great-ape-and-fossil-hominin-cementum-using-synchrotron-x-ray-fluorescence-mapping
#10
Christopher Dean, Adeline Le Cabec, Kathryn Spiers, Yi Zhang, Jan Garrevoet
Cementum and the incremental markings it contains have been widely studied as a means of ageing animals and retrieving information about diet and nutrition. The distribution of trace elements in great ape and fossil hominin cementum has not been studied previously. Synchrotron X-ray fluorescence (SXRF) enables rapid scanning of large tissue areas with high resolution of elemental distributions. First, we used SXRF to map calcium, phosphorus, strontium and zinc distributions in great ape dentine and cementum...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29321270/phenotypes-can-be-robust-and-evolvable-if-mutations-have-non-local-effects-on-sequence-constraints
#11
Marcel Weiß, Sebastian E Ahnert
The mapping between biological genotypes and phenotypes plays an important role in evolution, and understanding the properties of this mapping is crucial to determine the outcome of evolutionary processes. One of the most striking properties observed in several genotype-phenotype (GP) maps is the positive correlation between the robustness and evolvability of phenotypes. This implies that a phenotype can be strongly robust against mutations and at the same time evolvable to a diverse range of alternative phenotypes...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29321269/adding-levels-of-complexity-enhances-robustness-and-evolvability-in-a-multilevel-genotype-phenotype-map
#12
Pablo Catalán, Andreas Wagner, Susanna Manrubia, José A Cuesta
Robustness and evolvability are the main properties that account for the stability and accessibility of phenotypes. They have been studied in a number of computational genotype-phenotype maps. In this paper, we study a metabolic genotype-phenotype map defined in toyLIFE, a multilevel computational model that represents a simplified cellular biology. toyLIFE includes several levels of phenotypic expression, from proteins to regulatory networks to metabolism. Our results show that toyLIFE shares many similarities with other seemingly unrelated computational genotype-phenotype maps...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29321268/computational-techniques-for-ecg-analysis-and-interpretation-in-light-of-their-contribution-to-medical-advances
#13
REVIEW
Aurore Lyon, Ana Mincholé, Juan Pablo Martínez, Pablo Laguna, Blanca Rodriguez
Widely developed for clinical screening, electrocardiogram (ECG) recordings capture the cardiac electrical activity from the body surface. ECG analysis can therefore be a crucial first step to help diagnose, understand and predict cardiovascular disorders responsible for 30% of deaths worldwide. Computational techniques, and more specifically machine learning techniques and computational modelling are powerful tools for classification, clustering and simulation, and they have recently been applied to address the analysis of medical data, especially ECG data...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29321267/extreme-call-amplitude-from-near-field-acoustic-wave-coupling-in-the-stridulating-water-insect-micronecta-scholtzi-micronectinae
#14
Andrew Reid, David J W Hardie, David Mackie, Joseph C Jackson, James F C Windmill
Underwater acoustic transducers, particularly at low frequencies, are beset by problems of scale and inefficiency due to the large wavelengths of sound in water. In insect mating calls, a high call volume is usually desirable, increasing the range of signal transmission and providing a form of advertisement of the signaller's quality to a potential mate; however, the strength of the call is constrained by body size and by the need to avoid predators who may be listening in. Male crickets and water boatmen avoid some of the limitations of body size by exploiting resonant structures, which produce sharply tuned species-specific songs, but call frequency and volume remain linked to body size...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29321266/optimization-based-synthesis-of-stochastic-biocircuits-with-statistical-specifications
#15
Yuta Sakurai, Yutaka Hori
Model-guided design has become a standard approach to engineering biomolecular circuits in synthetic biology. However, the stochastic nature of biomolecular reactions is often overlooked in the design process. As a result, cell-cell heterogeneity causes unexpected deviation of biocircuit behaviours from model predictions and requires additional iterations of design-build-test cycles. To enhance the design process of stochastic biocircuits, this paper presents a computational framework to systematically specify the level of intrinsic noise using well-defined metrics of statistics and design highly heterogeneous biocircuits based on the specifications...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29321265/contribution-of-low-temperature-single-molecule-techniques-to-structural-issues-of-pigment-protein-complexes-from-photosynthetic-purple-bacteria
#16
REVIEW
Alexander Löhner, Richard Cogdell, Jürgen Köhler
As the electronic energies of the chromophores in a pigment-protein complex are imposed by the geometrical structure of the protein, this allows the spectral information obtained to be compared with predictions derived from structural models. Thereby, the single-molecule approach is particularly suited for the elucidation of specific, distinctive spectral features that are key for a particular model structure, and that would not be observable in ensemble-averaged spectra due to the heterogeneity of the biological objects...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29298959/lumbar-model-generator-a-tool-for-the-automated-generation-of-a-parametric-scalable-model-of-the-lumbar-spine
#17
C E Lavecchia, D M Espino, K M Moerman, K M Tse, D Robinson, P V S Lee, D E T Shepherd
Low back pain is a major cause of disability and requires the development of new devices to treat pathologies and improve prognosis following surgery. Understanding the effects of new devices on the biomechanics of the spine is crucial in the development of new effective and functional devices. The aim of this study was to develop a preliminary parametric, scalable and anatomically accurate finite-element model of the lumbar spine allowing for the evaluation of the performance of spinal devices. The principal anatomical surfaces of the lumbar spine were first identified, and then accurately fitted from a previous model supplied by S14 Implants (Bordeaux, France)...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29298958/langevin-dynamics-encapsulate-the-microscopic-and-emergent-macroscopic-properties-of-midge-swarms
#18
A M Reynolds
In contrast to bird flocks, fish schools and animal herds, midge swarms maintain cohesion but do not possess global order. High-speed imaging techniques are now revealing that these swarms have surprising properties. Here, I show that simple models found on the Langevin equation are consistent with this wealth of recent observations. The models predict correctly that large accelerations, exceeding 10 g, will be common and they predict correctly the coexistence of core condensed phases surrounded by dilute vapour phases...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29298957/optimizing-targeted-vaccination-across-cyber-physical-networks-an-empirically-based-mathematical-simulation-study
#19
Enys Mones, Arkadiusz Stopczynski, Alex 'Sandy' Pentland, Nathaniel Hupert, Sune Lehmann
Targeted vaccination, whether to minimize the forward transmission of infectious diseases or their clinical impact, is one of the 'holy grails' of modern infectious disease outbreak response, yet it is difficult to achieve in practice due to the challenge of identifying optimal targets in real time. If interruption of disease transmission is the goal, targeting requires knowledge of underlying person-to-person contact networks. Digital communication networks may reflect not only virtual but also physical interactions that could result in disease transmission, but the precise overlap between these cyber and physical networks has never been empirically explored in real-life settings...
January 2018: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29298956/inversion-of-friction-anisotropy-in-a-bio-inspired-asymmetrically-structured-surface
#20
Halvor T Tramsen, Stanislav N Gorb, Hao Zhang, Poramate Manoonpong, Zhendong Dai, Lars Heepe
Friction anisotropy is an important property of many surfaces that usually facilitate the generation of motion in a preferred direction. Such surfaces are very common in biological systems and have been the templates for various bio-inspired materials with similar tribological properties. So far friction anisotropy is considered to be the result of an asymmetric arrangement of surface nano- and microstructures. However, here we show by using bio-inspired sawtooth-structured surfaces that the anisotropic friction properties are not only controlled by an asymmetric surface topography, but also by the ratio of the sample-substrate stiffness, the aspect ratio of surface structures, and by the substrate roughness...
January 2018: Journal of the Royal Society, Interface
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