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Journal of the Royal Society, Interface

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https://www.readbyqxmd.com/read/28904005/the-coefficient-of-determination-r-2-and-intra-class-correlation-coefficient-from-generalized-linear-mixed-effects-models-revisited-and-expanded
#1
Shinichi Nakagawa, Paul C D Johnson, Holger Schielzeth
The coefficient of determination R(2) quantifies the proportion of variance explained by a statistical model and is an important summary statistic of biological interest. However, estimating R(2) for generalized linear mixed models (GLMMs) remains challenging. We have previously introduced a version of R(2) that we called [Formula: see text] for Poisson and binomial GLMMs, but not for other distributional families. Similarly, we earlier discussed how to estimate intra-class correlation coefficients (ICCs) using Poisson and binomial GLMMs...
September 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28878033/a-light-dependent-magnetoreception-mechanism-insensitive-to-light-intensity-and-polarization
#2
Susannah Worster, Henrik Mouritsen, P J Hore
Billions of migratory birds navigate thousands of kilometres every year aided by a magnetic compass sense, the biophysical mechanism of which is unclear. One leading hypothesis is that absorption of light by specialized photoreceptors in the retina produces short-lived chemical intermediates known as radical pairs whose chemistry is sensitive to tiny magnetic interactions. A potentially serious but largely ignored obstacle to this theory is how directional information derived from the Earth's magnetic field can be separated from the much stronger variations in the intensity and polarization of the incident light...
September 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28878032/effect-of-aspirin-on-tumour-cell-colony-formation-and-evolution
#3
Dominik Wodarz, Ajay Goel, C Richard Boland, Natalia L Komarova
Aspirin is known to reduce the risk of colorectal cancer (CRC) incidence, but the underlying mechanisms are not fully understood. In a previous study, we quantified the in vitro growth kinetics of different CRC tumour cell lines treated with varying doses of aspirin, measuring the rate of cell division and cell death. Here, we use these measured parameters to calculate the chances of successful clonal expansion and to determine the evolutionary potential of the tumour cell lines in the presence and absence of aspirin...
September 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28878031/collective-memory-in-primate-conflict-implied-by-temporal-scaling-collapse
#4
Edward D Lee, Bryan C Daniels, David C Krakauer, Jessica C Flack
In biological systems, prolonged conflict is costly, whereas contained conflict permits strategic innovation and refinement. Causes of variation in conflict size and duration are not well understood. We use a well-studied primate society model system to study how conflicts grow. We find conflict duration is a 'first to fight' growth process that scales superlinearly, with the number of possible pairwise interactions. This is in contrast with a 'first to fail' process that characterizes peaceful durations. Rescaling conflict distributions reveals a universal curve, showing that the typical time scale of correlated interactions exceeds nearly all individual fights...
September 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28855389/correction-of-an-equilibrium-for-phenotypic-variance-in-fluctuating-environments-owing-to-epigenetics
#5
Oana Carja, Marcus W Feldman
No abstract text is available yet for this article.
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28855388/using-stochastic-epidemiological-models-to-evaluate-conservation-strategies-for-endangered-amphibians
#6
Brian Drawert, Marc Griesemer, Linda R Petzold, Cheryl J Briggs
Recent outbreaks of chytridiomycosis, the disease of amphibians caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), have contributed to population declines of numerous amphibian species worldwide. The devastating impacts of this disease have led researchers to attempt drastic conservation measures to prevent further extinctions and loss of biodiversity. The conservation measures can be labour-intensive or expensive, and in many cases have been unsuccessful. We developed a mathematical model of Bd outbreaks that includes the effects of demographic stochasticity and within-host fungal load dynamics...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28855387/a-biophysical-approach-to-daunorubicin-interaction-with-model-membranes-relevance-for-the-drug-s-biological-activity
#7
Ana Catarina Alves, Daniela Ribeiro, Miguel Horta, José L F C Lima, Cláudia Nunes, Salette Reis
Daunorubicin is extensively used in chemotherapy for diverse types of cancer. Over the years, evidence has suggested that the mechanisms by which daunorubicin causes cytotoxic effects are also associated with interactions at the membrane level. The aim of the present work was to study the interplay between daunorubicin and mimetic membrane models composed of different ratios of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), sphingomyelin (SM) and cholesterol (Chol). Several biophysical parameters were assessed using liposomes as mimetic model membranes...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28855386/human-movement-cooperation-and-the-effectiveness-of-coordinated-vector-control-strategies
#8
Chris M Stone, Samantha R Schwab, Dina M Fonseca, Nina H Fefferman
Vector-borne disease transmission is often typified by highly focal transmission and influenced by movement of hosts and vectors across different scales. The ecological and environmental conditions (including those created by humans through vector control programmes) that result in metapopulation dynamics remain poorly understood. The development of control strategies that would most effectively limit outbreaks given such dynamics is particularly urgent given the recent epidemics of dengue, chikungunya and Zika viruses...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28855385/finite-cell-size-effects-on-protein-variability-in-turing-patterned-tissues
#9
Javier Buceta
Herein we present a framework to characterize different sources of protein expression variability in Turing patterned tissues. In this context, we introduce the concept of granular noise to account for the unavoidable fluctuations due to finite cell-size effects and show that the nearest-neighbours autocorrelation function provides the means to measure it. To test our findings, we perform in silico experiments of growing tissues driven by a generic activator-inhibitor dynamics. Our results show that the relative importance of different sources of noise depends on the ratio between the characteristic size of cells and that of the pattern domains and on the ratio between the pattern amplitude and the effective intensity of the biochemical fluctuations...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28835544/optimization-of-fermentation-conditions-for-the-production-of-curcumin-by-engineered-escherichia-coli
#10
Márcia R Couto, Joana L Rodrigues, Lígia R Rodrigues
Curcumin is a plant secondary metabolite with outstanding therapeutic effects. Therefore, there is a great interest in developing new strategies to produce this high-value compound in a cheaper and environmentally friendly way. Curcumin heterologous production in Escherichia coli using artificial biosynthetic pathways was previously demonstrated using synthetic biology approaches. However, the culturing conditions to produce this compound were not optimized and so far only a two-step fermentation process involving the exchange of culture medium allowed high concentrations of curcumin to be obtained, which limits its production at an industrial scale...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28835543/zonation-of-hepatic-fat-accumulation-insights-from-mathematical-modelling-of-nutrient-gradients-and-fatty-acid-uptake
#11
Jana Schleicher, Uta Dahmen, Reinhard Guthke, Stefan Schuster
Intrinsic of non-alcoholic fatty liver diseases is an aberrant accumulation of triglycerides (steatosis), which occurs inhomogeneously within lobules. To improve our understanding of the mechanisms involved in this zonation patterning, we developed a mathematical multicompartment model of hepatic fatty acid metabolism accompanied by blood flow simulations. A model analysis determines the influence of the uptake process of fatty acids, the porto-central gradient of plasma fatty acid concentration, and the oxygen supply via blood on the zonation of triglyceride accumulation...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28835542/host-population-structure-and-treatment-frequency-maintain-balancing-selection-on-drug-resistance
#12
Sarah Cobey, Edward B Baskerville, Caroline Colijn, William Hanage, Christophe Fraser, Marc Lipsitch
It is a truism that antimicrobial drugs select for resistance, but explaining pathogen- and population-specific variation in patterns of resistance remains an open problem. Like other common commensals, Streptococcus pneumoniae has demonstrated persistent coexistence of drug-sensitive and drug-resistant strains. Theoretically, this outcome is unlikely. We modelled the dynamics of competing strains of S. pneumoniae to investigate the impact of transmission dynamics and treatment-induced selective pressures on the probability of stable coexistence...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28835541/modelling-variability-in-cardiac-electrophysiology-a-moment-matching-approach
#13
Eliott Tixier, Damiano Lombardi, Blanca Rodriguez, Jean-Frédéric Gerbeau
The variability observed in action potential (AP) cardiomyocyte measurements is the consequence of many different sources of randomness. Often ignored, this variability may be studied to gain insight into the cell ionic properties. In this paper, we focus on the study of ionic channel conductances and describe a methodology to estimate their probability density function (PDF) from AP recordings. The method relies on the matching of observable statistical moments and on the maximum entropy principle. We present four case studies using synthetic and sets of experimental AP measurements from human and canine cardiomyocytes...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28835540/size-and-dielectric-properties-of-skeletal-stem-cells-change-critically-after-enrichment-and-expansion-from-human-bone-marrow-consequences-for-microfluidic-cell-sorting
#14
Miguel Xavier, María C de Andrés, Daniel Spencer, Richard O C Oreffo, Hywel Morgan
The capacity of bone and cartilage to regenerate can be attributed to skeletal stem cells (SSCs) that reside within the bone marrow (BM). Given SSCs are rare and lack specific surface markers, antibody-based sorting has failed to deliver the cell purity required for clinical translation. Microfluidics offers new methods of isolating cells based on biophysical features including, but not limited to, size, electrical properties and stiffness. Here we report the characterization of the dielectric properties of unexpanded SSCs using single-cell microfluidic impedance cytometry (MIC)...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28794163/very-weak-oscillating-magnetic-field-disrupts-the-magnetic-compass-of-songbird-migrants
#15
Alexander Pakhomov, Julia Bojarinova, Roman Cherbunin, Raisa Chetverikova, Philipp S Grigoryev, Kirill Kavokin, Dmitry Kobylkov, Regina Lubkovskaja, Nikita Chernetsov
Previously, it has been shown that long-distance migrants, garden warblers (Sylvia borin), were disoriented in the presence of narrow-band oscillating magnetic field (1.403 MHz OMF, 190 nT) during autumn migration. This agrees with the data of previous experiments with European robins (Erithacus rubecula). In this study, we report the results of experiments with garden warblers tested under a 1.403 MHz OMF with various amplitudes (∼0.4, 1, ∼2.4, 7 and 20 nT). We found that the ability of garden warblers to orient in round arenas using the magnetic compass could be disrupted by a very weak oscillating field, such as an approximate 2...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28794162/the-relative-compliance-of-energy-storing-tendons-may-be-due-to-the-helical-fibril-arrangement-of-their-fascicles
#16
Tom Shearer, Chavaunne T Thorpe, Hazel R C Screen
A nonlinear elastic microstructural model is used to investigate the relationship between structure and function in energy-storing and positional tendons. The model is used to fit mechanical tension test data from the equine common digital extensor tendon (CDET) and superficial digital flexor tendon (SDFT), which are used as archetypes of positional and energy-storing tendons, respectively. The fibril crimp and fascicle helix angles of the two tendon types are used as fitting parameters in the mathematical model to predict their values...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28794161/how-pigeons-couple-three-dimensional-elbow-and-wrist-motion-to-morph-their-wings
#17
Amanda K Stowers, Laura Y Matloff, David Lentink
Birds change the shape and area of their wings to an exceptional degree, surpassing insects, bats and aircraft in their ability to morph their wings for a variety of tasks. This morphing is governed by a musculoskeletal system, which couples elbow and wrist motion. Since the discovery of this effect in 1839, the planar 'drawing parallels' mechanism has been used to explain the coupling. Remarkably, this mechanism has never been corroborated from quantitative motion data. Therefore, we measured how the wing skeleton of a pigeon (Columba livia) moves during morphing...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28768883/structural-coloured-feathers-of-mallards-act-by-simple-multilayer-photonics
#18
Doekele G Stavenga, Casper J van der Kooi, Bodo D Wilts
The blue colours of the speculum of the mallard (Anas platyrhynchos), both male and female, and the green head feathers of the male arise from light interacting with stacks of melanosomes residing in the feather barbules. Here, we show that the iridescent colours can be quantitatively explained with an optical multilayer model by using a position-dependent effective refractive index, which results from the varying ratio of melanin and keratin. Reflectance spectra obtained by multilayer modelling and three-dimensional finite-difference time-domain calculations were virtually identical...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28768882/connexin-membrane-materials-as-potent-inhibitors-of-breast-cancer-cell-migration
#19
Silvia Ferrati, Avinash K Gadok, Ashlee D Brunaugh, Chi Zhao, Lara A Heersema, Hugh D C Smyth, Jeanne C Stachowiak
Gap junction (GJ) channels facilitate cell-cell communication through the exchange of chemical and mechanical signals, ensuring proper tissue development and homeostasis. The complex, disease stage-dependent role of connexins in breast cancer progression has been extensively studied over the past two decades. In the early stages of breast cancer, substantial evidence supports the role of GJ channels, formed by connexins at the interfaces between neighbouring cells, as suppressors of cell migration and proliferation...
August 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28768881/hydrodynamic-advantages-of-swimming-by-salp-chains
#20
Kelly R Sutherland, Daniel Weihs
Salps are marine invertebrates comprising multiple jet-propelled swimming units during a colonial life-cycle stage. Using theory, we show that asynchronous swimming with multiple pulsed jets yields substantial hydrodynamic benefit due to the production of steady swimming velocities, which limit drag. Laboratory comparisons of swimming kinematics of aggregate salps (Salpa fusiformis and Weelia cylindrica) using high-speed video supported that asynchronous swimming by aggregates results in a smoother velocity profile and showed that this smoother velocity profile is the result of uncoordinated, asynchronous swimming by individual zooids...
August 2017: Journal of the Royal Society, Interface
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