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Journal of the Royal Society, Interface

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https://www.readbyqxmd.com/read/28228544/correction-to-an-integrated-modelling-framework-for-neural-circuits-with-multiple-neuromodulators
#1
Alok Joshi, Vahab Youssofzadeh, Vinith Vemana, T M McGinnity, Girijesh Prasad, KongFatt Wong-Lin
No abstract text is available yet for this article.
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28228543/characterization-of-dependencies-between-growth-and-division-in-budding-yeast
#2
Michael B Mayhew, Edwin S Iversen, Alexander J Hartemink
Cell growth and division are processes vital to the proliferation and development of life. Coordination between these two processes has been recognized for decades in a variety of organisms. In the budding yeast Saccharomyces cerevisiae, this coordination or 'size control' appears as an inverse correlation between cell size and the rate of cell-cycle progression, routinely observed in G1 prior to cell division commitment. Beyond this point, cells are presumed to complete S/G2/M at similar rates and in a size-independent manner...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28228542/accelerated-simulation-of-evolutionary-trajectories-in-origin-fixation-models
#3
Ashley I Teufel, Claus O Wilke
We present an accelerated algorithm to forward-simulate origin-fixation models. Our algorithm requires, on average, only about two fitness evaluations per fixed mutation, whereas traditional algorithms require, per one fixed mutation, a number of fitness evaluations of the order of the effective population size, Ne Our accelerated algorithm yields the exact same steady state as the original algorithm but produces a different order of fixed mutations. By comparing several relevant evolutionary metrics, such as the distribution of fixed selection coefficients and the probability of reversion, we find that the two algorithms behave equivalently in many respects...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28228541/cell-dynamics-in-tumour-environment-after-treatments
#4
Leili Shahriyari
Most cancer treatments cause necrotic cell deaths in the tumour microenvironment. Necrotic cells send signals to immune cells to start the wound healing process in the tissue. Therefore, we assume after stopping treatments there is a wound that needs to be healed. We develop a simple computational model to investigate cell dynamics during the wound healing process after treatments. The model predicts that the involvement of high-fitness cancer cells in the wound healing leads to fast relapse, and cancer cells outside of the wound can cause a slow recurrence of the tumour...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28228540/functional-optics-of-glossy-buttercup-flowers
#5
Casper J van der Kooi, J Theo M Elzenga, Jan Dijksterhuis, Doekele G Stavenga
Buttercup (Ranunculus spp.) flowers are exceptional because they feature a distinct gloss (mirror-like reflection) in addition to their matte-yellow coloration. We investigated the optical properties of yellow petals of several Ranunculus and related species using (micro)spectrophotometry and anatomical methods. The contribution of different petal structures to the overall visual signal was quantified using a recently developed optical model. We show that the coloration of glossy buttercup flowers is due to a rare combination of structural and pigmentary coloration...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28228539/three-dimensional-printing-spiders-back-and-forth-glue-application-yields-silk-anchorages-with-high-pull-off-resistance-under-varying-loading-situations
#6
Jonas O Wolff, Marie E Herberstein
The anchorage of structures is a crucial element of construction, both for humans and animals. Spiders use adhesive plaques to attach silk threads to substrates. Both biological and artificial adhesive structures usually have an optimal loading angle, and are prone to varying loading situations. Silk anchorages, however, must cope with loading in highly variable directions. Here we show that the detachment forces of thread anchorages of orb-web spiders are highly robust against pulling in different directions...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28228538/route-choice-in-pedestrians-determinants-for-initial-choices-and-revising-decisions
#7
Weichen Liao, Armel U Kemloh Wagoum, Nikolai W F Bode
In moving pedestrian crowds, the distribution of individuals over different available routes emerges from the decisions of individuals that may be influenced by the actions of others. Understanding this phenomenon not only is important for research into collective behaviour, but also has practical applications for building safety and event management. Here, we study the mechanisms underlying pedestrian route choice, focusing on how time-independent information, such as path lengths, and time-dependent information, such as queue lengths, affect both initial decisions and subsequent changes in route choices...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28228537/morphoelasticity-in-the-development-of-brown-alga-ectocarpus-siliculosus-from-cell-rounding-to-branching
#8
Fei Jia, Martine Ben Amar, Bernard Billoud, Bénédicte Charrier
A biomechanical model is proposed for the growth of the brown alga Ectocarpus siliculosus Featuring ramified uniseriate filaments, this alga has two modes of growth: apical growth and intercalary growth with branching. Apical growth occurs upon the mitosis of a young cell at one extremity and leads to a new tip cell followed by a cylindrical cell, whereas branching mainly occurs when a cylindrical cell becomes rounded and swells, forming a spherical cell. Given the continuous interplay between cell growth and swelling, a poroelastic model combining osmotic pressure and volumetric growth is considered for the whole cell, cytoplasm and cell wall...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28202595/image-based-modelling-of-skeletal-muscle-oxygenation
#9
REVIEW
B Zeller-Plumhoff, T Roose, G F Clough, P Schneider
The supply of oxygen in sufficient quantity is vital for the correct functioning of all organs in the human body, in particular for skeletal muscle during exercise. Disease is often associated with both an inhibition of the microvascular supply capability and is thought to relate to changes in the structure of blood vessel networks. Different methods exist to investigate the influence of the microvascular structure on tissue oxygenation, varying over a range of application areas, i.e. biological in vivo and in vitro experiments, imaging and mathematical modelling...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28202594/surface-microtopography-modulates-sealing-zone-development-in-osteoclasts-cultured-on-bone
#10
Michal Shemesh, Lia Addadi, Benjamin Geiger
Bone homeostasis is continuously regulated by the coordinated action of bone-resorbing osteoclasts and bone-forming osteoblasts. Imbalance between these two cell populations leads to pathological bone diseases such as osteoporosis and osteopetrosis. Osteoclast functionality relies on the formation of sealing zone (SZ) rings that define the resorption lacuna. It is commonly assumed that the structure and dynamic properties of the SZ depend on the physical and chemical properties of the substrate. Considering the unique complex structure of native bone, elucidation of the relevant parameters affecting SZ formation and stability is challenging...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28202593/a-maugis-dugdale-cohesive-solution-for-adhesion-of-a-surface-with-a-dimple
#11
A Papangelo, M Ciavarella
We study the adhesion of a surface with a 'dimple' which shows a mechanism for a bi-stable adhesive system in surfaces with spaced patterns of depressions, leading to adhesion enhancement, high dissipation and hysteresis. Recent studies were limited mainly to the very short range of adhesion (the so-called JKR regime), while we generalize the study to a Maugis cohesive model. A 'generalized Tabor parameter', given by the ratio of theoretical strength to elastic modulus, multiplied by the ratio of dimple width to depth has been found...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28202592/extinction-pathways-and-outbreak-vulnerability-in-a-stochastic-ebola-model
#12
Garrett T Nieddu, Lora Billings, James H Kaufman, Eric Forgoston, Simone Bianco
A zoonotic disease is a disease that can be passed from animals to humans. Zoonotic viruses may adapt to a human host eventually becoming endemic in humans, but before doing so punctuated outbreaks of the zoonotic virus may be observed. The Ebola virus disease (EVD) is an example of such a disease. The animal population in which the disease agent is able to reproduce in sufficient number to be able to transmit to a susceptible human host is called a reservoir. There is little work devoted to understanding stochastic population dynamics in the presence of a reservoir, specifically the phenomena of disease extinction and reintroduction...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28202591/non-classical-phase-diagram-for-virus-bacterial-coevolution-mediated-by-clustered-regularly-interspaced-short-palindromic-repeats
#13
Pu Han, Michael W Deem
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape recognition by CRISPR...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28202590/advances-in-multicellular-spheroids-formation
#14
REVIEW
X Cui, Y Hartanto, H Zhang
Three-dimensional multicellular spheroids (MCSs) have a complex architectural structure, dynamic cell-cell/cell-matrix interactions and bio-mimicking in vivo microenvironment. As a fundamental building block for tissue reconstruction, MCSs have emerged as a powerful tool to narrow down the gap between the in vitro and in vivo model. In this review paper, we discussed the structure and biology of MCSs and detailed fabricating methods. Among these methods, the approach in microfluidics with hydrogel support for MCS formation is promising because it allows essential cell-cell/cell-matrix interactions in a confined space...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28202589/catching-ghosts-with-a-coarse-net-use-and-abuse-of-spatial-sampling-data-in-detecting-synchronization
#15
Natalia Petrovskaya, Sergei Petrovskii
Synchronization of population dynamics in different habitats is a frequently observed phenomenon. A common mathematical tool to reveal synchronization is the (cross)correlation coefficient between time courses of values of the population size of a given species where the population size is evaluated from spatial sampling data. The corresponding sampling net or grid is often coarse, i.e. it does not resolve all details of the spatial configuration, and the evaluation error-i.e. the difference between the true value of the population size and its estimated value-can be considerable...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28202588/control-and-regulation-of-pathways-via-negative-feedback
#16
REVIEW
Herbert M Sauro
The biochemical networks found in living organisms include a huge variety of control mechanisms at multiple levels of organization. While the mechanistic and molecular details of many of these control mechanisms are understood, their exact role in driving cellular behaviour is not. For example, yeast glycolysis has been studied for almost 80 years but it is only recently that we have come to understand the systemic role of the multitude of feedback and feed-forward controls that exist in this pathway. In this article, control theory is discussed as an approach to dissect the control logic of complex pathways...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28179550/the-coupon-collector-urn-model-with-unequal-probabilities-in-ecology-and-evolution
#17
REVIEW
N Zoroa, E Lesigne, M J Fernández-Sáez, P Zoroa, J Casas
The sequential sampling of populations with unequal probabilities and with replacement in a closed population is a recurrent problem in ecology and evolution. Examples range from biodiversity sampling, epidemiology to the estimation of signal repertoire in animal communication. Many of these questions can be reformulated as urn problems, often as special cases of the coupon collector problem, most simply expressed as the number of coupons that must be collected to have a complete set. We aimed to apply the coupon collector model in a comprehensive manner to one example-hosts (balls) being searched (draws) and parasitized (ball colour change) by parasitic wasps-to evaluate the influence of differences in sampling probabilities between items on collection speed...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28179549/contact-mechanics-of-the-human-finger-pad-under-compressive-loads
#18
Brygida M Dzidek, Michael J Adams, James W Andrews, Zhibing Zhang, Simon A Johnson
The coefficient of friction of most solid objects is independent of the applied normal force because of surface roughness. This behaviour is observed for a finger pad except at long contact times (greater than 10 s) against smooth impermeable surfaces such as glass when the coefficient increases with decreasing normal force by about a factor of five for the load range investigated here. This is clearly an advantage for some precision manipulation and grip tasks. Such normal force dependence is characteristic of smooth curved elastic bodies...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28179548/multi-step-excitation-energy-transfer-engineered-in-genetic-fusions-of-natural-and-synthetic-light-harvesting-proteins
#19
Joshua A Mancini, Goutham Kodali, Jianbing Jiang, Kanumuri Ramesh Reddy, Jonathan S Lindsey, Donald A Bryant, P Leslie Dutton, Christopher C Moser
Synthetic proteins designed and constructed from first principles with minimal reference to the sequence of any natural protein have proven robust and extraordinarily adaptable for engineering a range of functions. Here for the first time we describe the expression and genetic fusion of a natural photosynthetic light-harvesting subunit with a synthetic protein designed for light energy capture and multi-step transfer. We demonstrate excitation energy transfer from the bilin of the CpcA subunit (phycocyanin α subunit) of the cyanobacterial photosynthetic light-harvesting phycobilisome to synthetic four-helix-bundle proteins accommodating sites that specifically bind a variety of selected photoactive tetrapyrroles positioned to enhance energy transfer by relay...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28179547/suppression-of-epileptic-seizures-via-anderson-localization
#20
Benjamin J Zhang, Maysamreza Chamanzar, Mohammad-Reza Alam
Here we show that brain seizures can be effectively suppressed through random modulation of the brain medium. We use an established mesoscale cortical model in the form of a system of coupled stochastic partial differential equations. We show that by temporal and spatial randomization of parameters governing the firing rates of the excitatory and inhibitory neuron populations, seizure waves can be significantly suppressed. We find that the attenuation is the most effective when applied to the mean threshold potential...
February 2017: Journal of the Royal Society, Interface
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