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Fan Zhang, Min Wu, Chee Keong Kwoh, Jie Zheng
Extracellular signals are captured and transmitted by signaling proteins inside a cell. An important type of cellular responses to the signals is the cell fate decision, e.g., apoptosis. However, the underlying mechanisms of cell fate regulation are still unclear, thus comprehensive and detailed kinetic models are not yet available. Alternatively, data-driven models are promising to bridge signaling data with the phenotypic measurements of cell fates. The traditional linear model for data-driven modeling of signaling pathways has its limitations because it assumes that the a cell fate is proportional to the activities of signaling proteins, which is unlikely in the complex biological systems...
2016: PloS One
Mona El-Sayed, Gh Eshaq, A E ElMetwally
In our study, Mg-Al-Zn mingled oxides were prepared by the co-precipitation method. The structure, composition, morphology and thermal stability of the synthesized Mg-Al-Zn mingled oxides were analyzed by powder X-ray diffraction, Fourier transform infrared spectrometry, N2 physisorption, scanning electron microscopy, differential scanning calorimetry and thermogravimetry. Batch experiments were performed to study the adsorption behavior of cobalt(II) and nickel(II) as a function of pH, contact time, initial metal ion concentration, and adsorbent dose...
October 2016: Water Science and Technology: a Journal of the International Association on Water Pollution Research
A M S Tocts, D W Johnson, A J R Carter
Theoretical links between fluctuating asymmetry (FA) and fitness have led many to use FA as a proxy for average fitness. However, studies examining whether asymmetry actually correlates with individual fitness in wild populations are relatively rare and often use simple measures of association (e.g., correlation coefficients). Consequently, the pattern of selection on asymmetry in the wild is seldom clear. We examined selection on FA of pectoral fin morphology in two wild populations of a marine fish (the kelp perch; Brachyistius frenatus)...
October 19, 2016: Evolution; International Journal of Organic Evolution
Maurice Filo, Fadi Karameh, Mariette Awad
The cochlea is an indispensable preliminary processing stage in auditory perception that employs mechanical frequency-tuning and electrical transduction of incoming sound waves. Cochlear mechanical responses are shown to exhibit active nonlinear spatiotemporal response dynamics (e.g., otoacoustic emission). To model such phenomena, it is often necessary to incorporate cochlear fluid-membrane interactions. This results in both excessively high-order model formulations and computationally intensive solutions that limit their practical use in simulating the model and analyzing its response even for simple single-tone inputs...
October 17, 2016: Biological Cybernetics
Lubo Xu, Lei Wang
Based on the linear response theory, we propose a resonance phonon (r-ph) approach to study the renormalized phonons in a few one-dimensional nonlinear lattices. Compared with the existing anharmonic phonon (a-ph) approach, the dispersion relations derived from this approach agree with the expectations of the effective phonon (e-ph) theory much better. The application is also largely extended, i.e., it is applicable in many extreme situations, e.g., high frequency, high temperature, etc., where the existing one can hardly work...
September 2016: Physical Review. E
Chandreyee Roy, S S Manna
Properties of the fiber bundle model have been studied using equal load-sharing dynamics where each fiber obeys a nonlinear stress (s)-strain (x) characteristic function s=G(x) till its breaking threshold. In particular, four different functional forms have been studied: G(x)=e^{αx}, 1+x^{α}, x^{α}, and xe^{αx} where α is a continuously tunable parameter of the model in all cases. Analytical studies, supported by extensive numerical calculations of this model, exhibit a brittle to quasibrittle phase transition at a critical value of α_{c} only in the first two cases...
September 2016: Physical Review. E
Elizabeth Gross, Brent Davis, Kenneth L Ho, Daniel J Bates, Heather A Harrington
Researchers working with mathematical models are often confronted by the related problems of parameter estimation, model validation and model selection. These are all optimization problems, well known to be challenging due to nonlinearity, non-convexity and multiple local optima. Furthermore, the challenges are compounded when only partial data are available. Here, we consider polynomial models (e.g. mass-action chemical reaction networks at steady state) and describe a framework for their analysis based on optimization using numerical algebraic geometry...
October 2016: Journal of the Royal Society, Interface
Bonnie Alexander, Andrea L Murray, Wai Yen Loh, Lillian G Matthews, Chris Adamson, Richard Beare, Jian Chen, Claire E Kelly, Sandra Rees, Simon K Warfield, Peter J Anderson, Lex W Doyle, Alicia J Spittle, Jeanie L Y Cheong, Marc L Seal, Deanne K Thompson
Investigating neonatal brain structure and function can offer valuable insights into behaviour and cognition in healthy and clinical populations; both at term age, and longitudinally in comparison with later time points. Parcellated brain atlases for adult populations are readily available, however warping infant data to adult template space is not ideal due to morphological and tissue differences between these groups. Several parcellated neonatal atlases have been developed, although there remains strong demand for manually parcellated ground truth data with detailed cortical definition...
October 7, 2016: NeuroImage
Hao Sun, Sankha Mukherjee, Chandra Veer Singh
Two new graphene allotropes, penta-graphene and phagraphene, have been proposed recently with unique electronic properties, e.g. quasi-direct band gap, direction-dependent Dirac cones and tunable Fermi velocities. However, their mechanical properties have not been fully studied yet. In this work, we have performed extensive density functional theory calculations to evaluate the mechanical properties of these two materials and compared with graphene, graphane, and pentaheptite. Our simulations show that the ultimate tensile strength (UTS) and the strain corresponding to UTS in both penta-graphene and phagraphene are smaller than that of graphene...
September 29, 2016: Physical Chemistry Chemical Physics: PCCP
Peet Cremer, Hartmut Löwen, Andreas M Menzel
Colloidal magnetic particles embedded in an elastic polymer matrix constitute a smart material called a ferrogel. It responds to an applied external magnetic field by changes in elastic properties, which can be exploited for various applications such as dampers, vibration absorbers, or actuators. Under appropriate conditions, the stress-strain behavior of a ferrogel can display a fascinating feature: superelasticity, the capability to reversibly deform by a huge amount while barely altering the applied load...
September 29, 2016: Physical Chemistry Chemical Physics: PCCP
Juan Du, Dalong Liu, Emad S Ebbini
A nonlinear filtering approach to imaging the dynamics of microbubble ultrasound contrast agents (UCA) in microvessels is presented. The approach is based on the adaptive third-order Volterra filter (TVF), which separates the linear, quadratic, and cubic components from beamformed pulse-echo ultrasound data. The TVF captures polynomial nonlinearities utilizing the full spectral components of the echo data and not from prespecified bands, e.g. second or third harmonics. This allows for imaging using broadband pulse transmission to preserve the axial resolution and the SNR...
September 29, 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
Zhichao Fan, Yihui Zhang, Qiang Ma, Fan Zhang, Haoran Fu, Keh-Chih Hwang, Yonggang Huang
Lithographically defined interconnects with filamentary, serpentine configurations have been widely used in various forms of stretchable electronic devices, owing to the ultra-high stretchability that can be achieved and the relative simple geometry that facilitates the design and fabrication. Theoretical models of serpentine interconnects developed previously for predicting the performance of stretchability were mainly based on the theory of infinitesimal deformation. This assumption, however, does not hold for the interconnects that undergo large levels of deformations before the structural failure...
August 2016: International Journal of Solids and Structures
E P Pappas, I Seimenis, A Moutsatsos, E Georgiou, P Nomikos, P Karaiskos
This work provides characterization of system-related geometric distortions present in MRIs used in Gamma Knife (GK) stereotactic radiosurgery (SRS) treatment planning. A custom-made phantom, compatible with the Leksell stereotactic frame model G and encompassing 947 control points (CPs), was utilized. MR images were obtained with and without the frame, thus allowing discrimination of frame-induced distortions. In the absence of the frame and following compensation for field inhomogeneities, measured average CP disposition owing to gradient nonlinearities was 0...
October 7, 2016: Physics in Medicine and Biology
Nicholas J C Tyler, Pablo Gregorini, Mads C Forchhammer, Karl-Arne Stokkan, Bob E H van Oort, David G Hazlerigg
Occurrence of 24-h rhythms in species apparently lacking functional molecular clockwork indicates that strong circadian mechanisms are not essential prerequisites of robust timing, and that rhythmical patterns may arise instead as passive responses to periodically changing environmental stimuli. Thus, in a new synthesis of grazing in a ruminant (MINDY), crepuscular peaks of activity emerge from interactions between internal and external stimuli that influence motivation to feed, and the influence of the light/dark cycle is mediated through the effect of low nocturnal levels of food intake on gastric function...
October 2016: Journal of Biological Rhythms
Leonie E Burgers, Wouter P Nieuwenhuis, Hanna W van Steenbergen, Elize C Newsum, Tom W J Huizinga, Monique Reijnierse, Saskia le Cessie, Annette H M van der Helm-van Mil
OBJECTIVES: MRI sensitively detects inflammation, but the clinical relevance of MRI-detected inflammation is undetermined in early arthritis. Therefore, the aim of this cross-sectional study was to investigate the association between MRI-detected inflammation of hands and feet and functional disability in early arthritis. METHODS: Five hundred and fourteen early arthritis patients, consecutively included in the Leiden Early Arthritis Clinic, were studied. At baseline a unilateral 1...
September 15, 2016: Rheumatology
G Mamatsashvili, G Khujadze, G Chagelishvili, S Dong, J Jiménez, H Foysi
To understand the mechanism of the self-sustenance of subcritical turbulence in spectrally stable (constant) shear flows, we performed direct numerical simulations of homogeneous shear turbulence for different aspect ratios of the flow domain with subsequent analysis of the dynamical processes in spectral or Fourier space. There are no exponentially growing modes in such flows and the turbulence is energetically supported only by the linear growth of Fourier harmonics of perturbations due to the shear flow non-normality...
August 2016: Physical Review. E
Elad Shamriz, Nir Dror, Boris A Malomed
We report results of an analysis of the spontaneous symmetry breaking (SSB) in a basic (actually, simplest) model that is capable of producing the SSB phenomenology in a one-dimensional setting. It is based on the Gross-Pitaevskii-nonlinear Schrödinger equation with the cubic self-attractive term and a double-well potential built as an infinitely deep potential box split by a narrow (δ functional) barrier. The barrier's strength ɛ is the single free parameter of the scaled form of the model. It may be implemented in atomic Bose-Einstein condensates and nonlinear optics...
August 2016: Physical Review. E
E G Charalampidis, P G Kevrekidis, D J Frantzeskakis, B A Malomed
We consider a two-component, two-dimensional nonlinear Schrödinger system with unequal dispersion coefficients and self-defocusing nonlinearities, chiefly with equal strengths of the self- and cross-interactions. In this setting, a natural waveform with a nonvanishing background in one component is a vortex, which induces an effective potential well in the second component, via the nonlinear coupling of the two components. We show that the potential well may support not only the fundamental bound state, but also multiring excited radial state complexes for suitable ranges of values of the dispersion coefficient of the second component...
August 2016: Physical Review. E
Petr Pecha, Václav Šmídl
A stepwise sequential assimilation algorithm is proposed based on an optimisation approach for recursive parameter estimation and tracking of radioactive plume propagation in the early stage of a radiation accident. Predictions of the radiological situation in each time step of the plume propagation are driven by an existing short-term meteorological forecast and the assimilation procedure manipulates the model parameters to match the observations incoming concurrently from the terrain. Mathematically, the task is a typical ill-posed inverse problem of estimating the parameters of the release...
November 2016: Journal of Environmental Radioactivity
V E Demidov, M Evelt, V Bessonov, S O Demokritov, J L Prieto, M Muñoz, J Ben Youssef, V V Naletov, G de Loubens, O Klein, M Collet, P Bortolotti, V Cros, A Anane
Excitation of magnetization dynamics by pure spin currents has been recently recognized as an enabling mechanism for spintronics and magnonics, which allows implementation of spin-torque devices based on low-damping insulating magnetic materials. Here we report the first spatially-resolved study of the dynamic modes excited by pure spin current in nanometer-thick microscopic insulating Yttrium Iron Garnet disks. We show that these modes exhibit nonlinear self-broadening preventing the formation of the self-localized magnetic bullet, which plays a crucial role in the stabilization of the single-mode magnetization oscillations in all-metallic systems...
2016: Scientific Reports
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