ALBERT

Description: The paper introduces a technique that decomposes the dynamics of a nonlinear system about an equilibrium into low-order components, which then can be used to reconstruct the full dynamics. This is a nonlinear analogue of linear modal analysis. The dynamics is decomposed using Invariant Spectral Foliation (ISF), which is defined as the smoothest invariant foliation about an equilibrium and hence unique under general conditions. The conjugate dynamics of an ISF can be used as a reduced order model. An ISF can be fitted to vibration data without carrying out a model identification first. The theory is illustrated on a analytic example and on free-vibration data of a clamped-clamped beam.

Description: The stick–slip model of a Girling brake is composed of nonlinear and coupled differential equations that reproduce the friction occurring in this mechanical system. The brake is equivalent to a body sliding on a belt. The problem is very interesting since the possible solutions, which are very sensitive to the parameters of the system, show a chaotic behaviour. In this contribution, the model, which is designed following network method rules, is explained in detail and runs on standard electrical circuit simulation software to provide the displacement and the velocity of the sliding body and the phase planes. In comparison with other models, the considered system does not include dampers to get a more unstable behaviour. Furthermore, a suitable selection of parameters is implemented to reduce the computational time.

Description: The drivers in actual traffic differ in the aggressiveness in driving behaviors, which will finally be reflected in the interaction between vehicles and fluctuations in flows. In this paper, we try to study the effect of driving aggressiveness on the traffic stability by proposing an extended microscopic car-following model, in which the optimal velocity is reconstructed to divide the drivers in traffic system into two groups according to driving aggressiveness of each individual. The stability condition of the proposed model is derived to explore its ability against a small perturbation by use of the linear stability theory. We obtain the neutral stability lines for different percentages of drivers with a higher driving aggressiveness, finding that the traffic flow trends to stable with the increase in the percentage for higher driving aggressiveness drivers when the average headway is less than a critical value or greater than another critical value, but when the average headway falls into the intermediate range between the two critical values, the traffic flow becomes more and more unstable with increase in the percentage of drivers with a higher driving aggressiveness. Finally, numerical simulations are conducted to verify these theoretical results and examine how the percentage of vehicles driven by higher driving aggressiveness drivers affects the traffic flux of the vehicle system.

Description: This paper investigates adaptive synchronization of stochastic time-varying delay dynamical networks with complex-variable systems. By using the complex inequality, stochastic analysis theory and two kinds of random disturbances, several sufficient conditions to ensure adaptive synchronization for stochastic time-varying delay networks with complex-variable systems. To illustrate the effectiveness of the synchronization conditions derived in this paper, numerical examples are provided finally.

Description: This paper presents the unified cooperative strategies for the salvo attack of multiple missiles on the basis of the traditional proportional navigation (PN) algorithm. The cooperative guidance laws are developed in a quite simple formulation consisting of a PN component for target capture and a coordination component for simultaneous arrival. The centralized coordination algorithms have better performance when the global information of time-to-go can be obtained by each missile, whereas the decentralized coordination algorithms come into effect when the group member is only able to collect information from its neighbors. The cooperative strategies can achieve a simultaneous attack against both stationary and maneuvering targets. Numerical simulations are used to demonstrate that the proposed approaches are feasible and flexible for the salvo attack of multiple missiles. The capturability analyses of the cooperative guidance laws are also performed by discussing the selection of gain parameters.

Description: In this work we complete the integrability conditions (i.e., conditions for the existence of a local analytic first integral) for a family of a resonant saddle perturbed with homogeneous quintic nonlinearities studied in a previous work. In order to obtain the necessary conditions we use modular arithmetic computations.

Description: The chaotic behavior of the secondary asteroid in a system of binary asteroids due to the asphericity and orbital eccentricity is investigated analytically and numerically. The binary asteroids are modeled with a sphere–ellipsoid model, in which the secondary asteroid is ellipsoid. The first-order resonance is studied for different values of asphericity and eccentricity of the secondary asteroid. The results of the Chirikov method are verified by Poincare section which show good agreement between analytical and numerical methods. It is also shown that asphericity and eccentricity affect the size of resonance regions such that beyond the threshold value, the resonance overlapping occurs and widespread chaos is visible.

Description: An efficient and secure three-party authenticated key agreement protocol is proposed to enable two users to establish a common secret key for exchanging confidential and authenticated information with the help of a trusted server. The proposed protocol only employs extended chaotic maps and hash operations, i.e., it does not require a server public key, symmetric cryptosystems, time-consuming modular exponential computations, or time-consuming modular exponential computations and scalar multiplications on elliptic curve. A round-efficient version of the proposed protocol is also implemented by rearranging and sending the messages in parallel. The session security of the proposed protocol is based on the Chebyshev chaotic map-based Diffie–Hellman assumption. Compared to related chaotic map-based approaches, the proposed protocol not only requires lower computational cost, but also has fewer transmissions.

Description: In this paper, a novel adaptive neural network control approach is presented for a class of uncertain discrete-time nonlinear strict-feedback systems with input saturation. By combining single neural network approximation and minimal learning parameter technique, the proposed approach is able to eliminate the complexity growing problem and alleviate the explosion of learning parameters. An auxiliary design system is incorporated into the control scheme to overcome the problem of input saturation constraints. Following this approach, the designed controller contains only one actual control law and one adaptive law, the numbers of input variables and weights of neural network updated online are decreased drastically, and the number of parameter updated online for whole system is reduced to only one. Compared with the existing methods, the adaptive mechanism with much simpler controller structure and minimal learning parameterization is achieved; therefore, the computational burden is lighter. It is shown via Lyapunov theory that all signals in the closed-loop system are uniformly ultimately bounded. Finally, simulation results via two examples are employed to illustrate the effectiveness and merits of the proposed scheme.

Description: This paper investigates the problem of global coordinated tracking of a multi-agent system with input additive uncertainties and disturbances via bounded control inputs. Scheduled low-and-high gain feedback-based distributed coordinated tracking protocols are developed. It is shown that, under the assumptions that each agent is asymptotically null controllable with bounded controls and the network is connected, global coordinated tracking of the multi-agent system can be achieved. We finally show some numerical simulations to verify and illustrate the theoretical results.

Description: In this paper, a four-neuron delayed system with inertial terms is considered. By studying the distribution of the eigenvalues of the associated characteristic equation, we derive the critical values where double Hopf bifurcation occurs. Then by employing the perturbation-incremental scheme for the system, bifurcation diagrams are obtained. Furthermore, we carry out bifurcation analysis showing that there exist a stable fixed point, two stable periodic solutions, co-existence of a pair of stable periodic solutions and quasi-periodic motion in the neighborhood of the double Hopf critical point. We also find some interesting phenomena that the dynamical period switching occurs in some delayed regions. Finally, some numerical simulations are performed to support the theoretical analysis.

Description: Analytical spatiotemporal soliton solutions of the coupled nonlinear Schrödinger equation are derived in the (3  \(+\)  1)-dimensional inhomogeneous \(\mathcal {PT}\) -symmetric nonlinear couplers by means of the Hirota bilinear method. Based on these analytical solutions, we construct abundant spatiotemporal soliton structures and discuss the expansion and compression behaviors of spatiotemporal soliton structures in a periodic modulation system.

Description: In this paper we develop a systematic and self-consistent procedure based on a set of compatibility conditions for identifying all maximal (eight parameter) and non-maximal (one and two parameter) symmetry groups associated with the mixed quadratic-linear Liénard-type equation, \(\ddot{x} + f(x){\dot{x}}^{2} + g(x)\dot{x}+h(x)= 0\) , where \(f(x),\,g(x)\) and h ( x ) are arbitrary functions of x . With the help of this procedure we show that a symmetry function b ( t ) is zero for non-maximal cases, whereas it is not so for the maximal case. On the basis of this result the symmetry analysis gets divided into two cases, (i) the maximal symmetry group \((b\ne 0)\) and (ii) non-maximal symmetry groups \((b=0)\) . We then identify the most general form of the mixed quadratic linear Liénard-type equation in each of these cases. In the case of eight-parameter symmetry group, the identified general equation becomes linearizable. In the case of non-maximal symmetry groups the identified equations are all integrable. The integrability of all the equations is proved either by providing the general solution or by constructing time-independent Hamiltonians.

Description: This paper reveals the dynamical behaviors of a coupled network consisting of four neural sub-networks and multiple two-way couplings of neurons between the individual sub-networks. Different types of time delays are introduced into the internal connections within the individual sub-networks and the couplings between the sub-networks. Stability switches of the network equilibrium and Hopf bifurcation are analyzed by discussing the associated characteristic equation. The conditions for the existence of different patterns of oscillations are discussed. By using the Lyapunov’s second method, the global stability of the network equilibrium is studied. Numerical simulations are performed to validate the theoretical results, and rich dynamical behaviors are observed, such as synchronous oscillations, multiple stability switches between the rest state and oscillations, phase-locked oscillations, asynchronous oscillations, and the coexistence of different patterns of bifurcated oscillations.

Description: A significant impediment to the deployment of vibration-based energy harvesting devices has been the limitation of most low-frequency transducers, usually in the form of unimorph or bimorph cantilever beam, to extract energy from a very narrow bandwidth around the transducer’s fundamental frequency. In such devices, a slight deviation from the fundamental frequency causes a significant reduction in the level of harvested power by several orders of magnitudes. Additionally, most of the current research efforts on the design of piezoelectric energy harvesters have had limited success in achieving low resonance frequency. To overcome these challenges, we introduce an enhanced broadband low-frequency piezomagnetoelastic energy harvester. This harvester consists of a partially covered piezoelectric cantilever beam with a fixed magnet mass at the top of the magnet tip mass. A nonlinear distributed-parameter model based on Euler–Bernoulli beam theory and Galerkin discretization is developed. This electromechanical model is validated with previous experimental measurements for a specific value of the spacing distance between the two magnets. A parametric study is performed to determine the effects of the spacing distance between the two magnets on the static position of the harvester, natural frequency, and level of the harvested power. It is demonstrated that a decrease between the two attractive magnets results in a decrease in the natural frequency of the harvester with a strong softening behavior which gives the opportunity to harvest energy at broadband low-frequency range. The results also show that the presence and importance of the softening behavior depends on the electrical load resistance. In conclusion, the results show that depending on the available low excitation frequency, an enhanced piezoelectric energy harvester can be tuned and optimized by changing the spacing distance between the two tip magnets.

Description: In this paper, we are interested to justified two typical hypotheses that appear in the convergence analysis, \(|\lambda |\le 2\) and \(z_0\) sufficient close to \(z^*\) . In order to proof these ideas, the dynamics of a damped two-step Newton-type method for solving nonlinear equations and systems is presented. We present the parameter space for values of the damping factor in the complex plane, focusing our attention in such values for which the fixed points related to the roots are attracting. Moreover, we study the stability of the strange fixed points, showing that there exists attracting cycles and chaotical behavior for some choices of the damping factor.

Description: We consider memelements (memristors and memductors) with special periodic responses (mixed-mode oscillations) and 2D one-period loops yielding constant parameters describing the memelements as single units or components of oscillating circuits. One of the parameters is the action parameter having the dimensions of energy   \(\times \)   time and the SI unit Joule   \(\times \)   second . The remaining loops and parameters correspond to energy of magnetic and electric fields, power and rms current and voltage values. Special mixed one-period loops are also analyzed with pairs of signals associated with two different components of the circuits. The areas enclosed by various loops result in special equations which can be derived from the underlying ODE model of the circuits. The action of a memelement is equivalent to the time integral of the Lagrangian \(L(w,w')\) , where w is the internal state variable of a memelement. The analysis of memristive circuits and their parameters is considered in the framework of mixed-mode oscillations. Also, the unit of action for memelements is proposed to be called Chua ( \(=\) Joule \(\,\times \)   second ) to honor L.O. Chua for his work on memristors and memristive circuits.

Description: In this paper, the binary Bell polynomials are employed to find the bilinear form, bilinear Bäcklund transformation and Lax pair for the (3+1)-dimensional BKP equation. Based on Hirota’s bilinear form and three-wave method, multi-soliton solutions are presented. Furthermore, a new bilinear Bäcklund transformation is constructed via applying a gauge transformation to the Bäcklund transformation in bilinear form.

Description: In this paper, a \((2 + 1)\) -dimensional generalized shallow water wave equation is investigated through bilinear Hirota method. Interestingly, the breather-type and lump-type soliton solutions are obtained. Furthermore, dynamic properties of the soliton waves are revealed by means of the asymptotic analysis. Based on Hirota bilinear method and Riemann theta function, we succeed in constructing quasi-periodic wave solutions with a generalized form. We also display the asymptotic properties of these quasi-periodic wave solutions and point out the relation between the quasi-periodic wave solutions and the soliton solutions.

Description: In this paper, the classical problem and the inverse problem of generalized synchronization for different dimensional chaotic dynamical systems in discrete time are investigated. The generalized synchronization results have been derived using active control method and Lyapunov stability theory. Numerical simulations are performed to verify the effectiveness of the proposed schemes.

Description: Under investigation in this paper is a generalized \((2+1)\) -dimensional Korteweg–de Vries equation, which could describe many nonlinear phenomena in plasma physics. By virtue of the Bell’s polynomials, a straightforward way is presented to succinctly construct its bilinear form, bilinear Bäcklund transformation and Lax pairs. Once the Lax pairs obtained, the important infinite conservation laws of the equation are directly found. Moreover, based on the bilinear formalism, we construct the Riemann theta function periodic wave solutions and soliton solutions. Finally, the relationships between the periodic wave solutions and soliton solutions are strictly established, and the asymptotic behavior of the periodic waves is also presented with detailed proof.

Description: In the present paper, we study regular and chaotic dynamics from planar oscillations of a dumbbell satellite under the influence of the gravity field generated by an oblate body, considering the effect of the zonal harmonic parameter \(J_{2}\) . We theoretically show the existence of chaotic oscillations provided that the eccentricity becomes arbitrarily small, and the parameter \(J_{2}\) is of the same order of magnitude as the eccentricity. This is carried out by applying the so-called Melnikov method. Finally, for arbitrarily chosen values for the parameters involved in such a problem, we study the transition from regular to chaotic oscillations for a dumbbell satellite via the analysis of chaotic maps and Poincaré surfaces of section, respectively.

Description: We obtain some results on transitivity for cyclically permuted direct product maps, that is, maps of the form \(F\left( x_{1},x_{2},\ldots ,x_{n}\right) =\left( f_{\sigma (1)}\left( x_{\sigma (1)}\right) ,f_{\sigma (2)}\left( x_{\sigma (2)}\right) ,\ldots ,f_{\sigma (n)}\left( x_{\sigma (n)}\right) \right) \) , defined from the Cartesian product \(I^n\) onto itself, where \(I=[0,1]\) , \(\sigma \) is a cyclic permutation of \(\{1,2,\ldots ,n\}\) \((n\ge 2)\) and each map \(f_{\sigma (j)}:I\rightarrow I\) is continuous, \(j\in \{1,\ldots ,n\}\) . In particular, we prove that for \(n\ge 3\) the transitivity of F is equivalent to the total transitivity, and if \(n=2\) , we give a splitting result for transitive maps. Moreover, we extend well-known properties of transitivity from interval maps to cyclically permuted direct product maps. To do it, we use the strong link between F and the compositions \(\varphi _j=f_{\sigma (j)}\circ \ldots \circ f_{\sigma ^n(j)},\, j\in \{1,\ldots ,n\}.\)

Description: In this paper, targeted energy transfer from a nonlinear continuous system to a nonlinear energy sink (NES) is investigated. For this purpose, the equation of a nonlinear beam with simply supported ends, on which the NES is attached, is derived using Rayleigh–Ritz method and the Lagrange equation. Then, parameters of the NES are optimized by both sensitivity analysis and particle swarm optimization (PSO) method. Analysis of the energy transfer between the nonlinear beam and the NES is presented, using the complexification-averaging method, too. Attaching an NES to a nonlinear continuous system and using the PSO method to obtain the optimized parameters of the NES is a new development, presented in this work. Also, here, more than one mode of the beam has been considered for analysis of energy transfer between the NES and different modes of the primary system.

Description: In this work we present a pseudo-random Bit Generator via unidimensional multi-modal discrete dynamical systems called k -modal maps. These multi-modal maps are based on the logistic map and are useful to yield pseudo-random sequences with longer period, i.e., in order to attend the problem of periodicity. In addition the pseudo-random sequences generated via multi-modal maps are evaluated with the statistical suite of test from NIST and satisfactory results are obtained when they are used as key stream. Furthermore, we show the impact of using these sequences in a stream cipher resulting in a better encryption quality correlated with the number of modals of the chaotic map. Finally, a statistical security analysis applied to cipher images is given. The proposed algorithm to encrypt is able to resist the chosen-plaintext attack and differential attack because the same set of encryption keys generates a different cipher image every time it is used.

Description: In this paper, we numerically study the effect of ion channel noise on the synchronization of delayed Newman–Watts network of stochastic Hodgkin–Huxley neurons. It is found that time delay can induce synchronization transitions only when channel noise intensity is intermediate, and the synchronization transitions become most obvious when channel noise intensity is optimal. As channel noise intensity is varied, the neurons can also exhibit synchronization transitions, and the phenomenon is enhanced when time delay is tuned at around time delays that can induce synchronization transitions. Moreover, this phenomenon becomes most obvious when the value of coupling strength or the value of network randomness is optimal. These results show that channel noise has a subtle regulation effect on the synchronization of the neuronal network. These findings may find potential implications for the normal and pathological functions in the brain and the information processing and transmission in neural systems.

Description: Using the tool of Turing instability for partial differential equations, we investigate the spatiotemporal distributions for solutions of a predator–prey-type reaction–diffusion model with spatiotemporal delay. The linear stability conditions of Turing instability, which induce bifurcation patterns in this model, are obtained. Moreover, according to these conditions, we numerically calculate the bifurcation diagrams by using time delay and the predator rate as parameters. The effects of two parameters in the different bifurcation diagrams are also demonstrated through numerical computations and lead to some spatiotemporal patterns of this model, which enrich the pattern formation of predator–prey models.

Description: A new two-lane traffic lattice hydrodynamic model is proposed with the consideration of the global average-and-optimal flux difference effect based on the local relative flux two-lane lattice model. First, the influence of the global average-and-optimal flux difference on the stability of traffic flow is investigated through linear stability theory. The results reveal that the unstable region will be shrunk by taking the global average-and-optimal flux difference effect into account. Additionally, by using the reductive perturbation method, the mKdV equation near the critical point is derived and traffic jam transition can be described by its kink–antikink soliton solution. The good agreement between the numerical simulations and the analytical results shows that traffic congestion can be suppressed efficiently by considering the global average-and-optimal flux difference and the local relative flux effects in two-lane traffic system and the local relative flux is more important than the global average-and-optimal flux difference in stabilizing traffic flow.

Description: Under investigation in this paper is a \((2+1)\) -dimensional Korteweg–de Vries-type equation, which can describe the propagation of nonlinear waves such as the shallow-water waves, surface and internal waves. By virtue of the Bell polynomials, symbolic computation and auxiliary independent variable, the bilinear forms, Bäcklund transformations and soliton solutions are obtained. Solitonic propagation and elastic collisions between/among the two- and three-solitons are discussed analytically and graphically. It can be seen that, after each collision, solitonic shapes and amplitudes keep invariant except for some phase shifts, and the smaller-amplitude soliton moves faster and overtakes the larger.

Description: Based on the optimal velocity model, a new continuum model considering traffic jerk effect is presented in this paper. Then, the critical condition for the steady traffic flow is deduced. Near the neutral stability line, nonlinear analysis is taken to derive the KdV-Burgers equation for describing the density wave, and one of the solutions is given. Numerical simulation is carried out to study the influence about the traffic jerk effect.

Description: The nonlinear dynamical behavior of the hysteretic rheological device proposed in Carboni et al. (J Eng Mech 2014 ) is investigated. The device can provide nonlinear hysteretic forces to a one-degree-of-freedom (one-dof) mass through suitable assemblies of NiTiNOL and steel wire ropes subject to tension–flexure cycles. The simultaneous occurrence of interwire friction, phase transformations and geometric nonlinearities is the key feature of the obtained material behavior. Frequency-response curves (FRCs) of the system subject to base excitation are obtained numerically via a continuation procedure together with stability analysis and experimentally by carrying out shaking table tests, respectively. The phenomenological identification of the material behaviors through force–displacement cycles, reported in Carboni et al. (J Eng Mech 2014 ), is employed for the computation of the FRCs and the equivalent damping ratios as function of the displacement amplitude. The different restoring forces give rise to whole new families of nonlinear hysteretic oscillators governed by softening, hardening and softening–hardening behaviors depending on the oscillation amplitude.

Description: The modeling of the piezoelectric actuator is very important for the fast and accurate nano-positioning control. However, the complex creep, vibration and hysteresis dynamics make the modeling very difficult. Because there are often model uncertainties in the first-principle model, the model identification from the experimental data is very necessary. Most identification approaches only consider partial dynamics of the creep, vibration and hysteresis. Though they can be combined together after they are individually identified from different experiments, it is difficult to design the completely decoupled experiment. In this study, an incremental Hammerstein-like modeling approach is proposed to identify the creep, vibration and hysteresis dynamics from one experiment. The model is called nonlinear–linear–linear-Hammerstein-like model, where one dynamic nonlinear system is used to model the hysteresis and two dynamic linear systems are used to model the creep and vibration. The creep and vibration are assumed to be decoupled, and there is a known upper bound on the order of the creep model. A two-stage incremental modeling approach is proposed to reduce the modeling complexity, where the slow dynamics of the hysteresis and creep are estimated first and then the residual of this model is used to estimate the fast dynamics of the vibration. In each stage, the model structure and order are determined by a locally regularized orthogonal least-squares-based model term selection algorithm and the parameters are estimated using a regularized least-squares method. The effectiveness of the proposed modeling approach is verified by the simulations and experiments on typical piezoelectric actuators.

Description: This paper investigates the problem of harvesting energy from transverse base vibration by a laminated piezoelectric beam. The beam is fixed at one end and subjected to a compressive load at the other end. The electromechanical model is set up, and the corresponding equations are derived by extended Hamilton principle. The simulation is carried out, and the results are obtained. The response under harmonic excitation exhibits that the system experiences period-doubling bifurcation and chaos as frequency varies, and the buckled state can generate more power compared to the unbuckled one. Coherence resonance is proved and can be observed when the system is subjected to Gauss white noise excitation, which can be used to optimize the efficiency of energy harvesting.

Description: In this paper, we present a new scheme for the secured transmission of discrete information based on hyperchaotic discrete dynamics. The system is a modified-Henon hyperchaotic discrete-time oscillator considered as transmitter and a delayed step-by-step observer used as receiver. The transmitter parameters play the role of secret keys of the transmission scheme. To increase the robustness of the secure data transmission against known plain-text attacks, the message to be sent is encrypted by additional secret keys and inserted by inclusion method in the chaotic discrete-time system dynamics. By this way, the parameters used as secret keys cannot be identified with usual techniques. Simulation results are presented to highlight the performances of the proposed method. One of the main contributions of this paper is to demonstrate the feasibility of discrete realization of a chaotic observer-based secured transmission scheme. Indeed, experimental implementation results using Arduino Uno board validate the proposed approach, since it exhibits good performances of throughput and cost in terms of resources used.

Description: This paper is concerned with the problem of complex function projective synchronization for uncertain networked chaotic complex systems. Based on Lyapunov stability, an adaptive control method is proposed for complex modified projective synchronization, which guarantees that the general drive-response networked chaotic complex systems are synchronized up to a complex scaling function matrix. Moreover, a complex fuzzy logic-based observer is designed to compensate for the model uncertainties and the external disturbances that exist in response networks, without prior information about uncertain factors. Numerical simulations are presented to demonstrate the effectiveness of the proposed method.

Description: We investigate the spatiotemporal behaviour of a network where the local dynamics at the nodes (sites) is governed by piecewise linear maps. The local maps we consider exhibit the interesting and potentially useful property of robust chaos. We study the coupled system of such maps with varying fraction of random non-local connections, where the random links may be static, or may change over time. While this system is always unsynchronized under regular connections, synchronized chaos emerges when some of the links are rewired randomly. Further, increasing the frequency of link changes and fraction of random links significantly enhances the range of synchronization. Additionally, dynamic random links are also found to suppress unbounded dynamics in parameter regimes where blow-ups occurred under regular coupling.

Description: Chaotic delay systems are abundant in nature and play a significant role in engineering applications and in describing global behaviors of physical systems. This work presents novel first-order chaotic delay systems with the simplest nonlinearities. The exponential, absolute value, and hyperbolic and signum functions, which arise in many systems like electronic circuits, are utilized to generate chaotic delay systems. The practical realization of chaotic delay systems is carried out with all-pass filters and diode-based electronic circuits. Bifurcation diagrams using numerical simulations and experimental results are provided to verify the existence and feasibility of the novel chaotic delay systems. It is expected that the novel chaotic delay systems and the novel electronic implementation circuits will contribute to some practical applications and modeling of physical systems or events in different fields.

Description: Based on the state-dependent Riccati equation (SDRE) technique, in this paper, a suboptimal pinning control scheme is proposed to synchronize linearly coupled complex networks. The Lyapunov direct method is used to analyze the stability of the closed-loop control system, where it leads to a LMI criterion for pinning synchronization. It is shown that the time interval for synchronization of the proposed SDRE controllers is faster comparing with the results in the latest literatures. It is also shown that the minimum required coupling weights for the network synchronization in a finite desired time is decreased when some specified nodes in the network are pinned with the SDRE controllers. Based on the proposed criterion for pinned nodes selection, the network performances for different topological structures are investigated and the results are compared. The results indicate that the coupling weights for network synchronization in finite desired time in random Erdos Reiny networks are minimum when the pinned nodes are selected based on the minimum matching theorem. In small-world and scale-free networks, the minimum required coupling weight for network synchronization in finite desired time decreases when the highest degree nodes are pinned.

Description: In recent years, digital image processing has become commonplace with growing powerful and available image editing software. People without any professional technique can also manipulate and forge digital images easily. One of the most popular manners of digital image forgeries is the copy–move image forgery. Extensive researches in detecting copy–move forgery have made a deal of achievements, but most presented methods based on these researches have been only focus on some simple composite forgeries and not able to detect different types of post-processed forgeries. In this paper, we aim to deal with the post-processed forgery operations and scenarios, mainly geometric distortion. We introduce analytical Fourier–Mellin transform (AFMT) and focus on its discretization. We propose discrete analytical Fourier–Mellin transform (DAFMT). We also pay attention to high performance of DAFMT in detecting the copy–move image forgeries. Due to the AFMT described in polar coordinate, so we need to convert coordinate system from polar to Cartesian coordinates. To be computed conveniently, we define an auxiliary disk template to accomplish this conversion. We devote to the use of our proposed DAFMT in detection of image forgeries. A great deal of researches and experiments show that the proposed DAFMT can effectively resist translation, rotation, scaling, and added Gaussian noise operations. Compared with other relevant up-to-date methods, experiments also prove that DAFMT has made a progress in detecting and identifying the forgery images which are suffered from geometric distortion operations.

Description: The problem of controlling synchrony in bistable networks, which possess coherent and incoherent attractors in a certain range of parameters, is considered. Along with the known Kuramoto-type models, we introduce the bistable networks consisting of all-to-all coupled noisy FitzHugh-Nagumo neurons as well as chaotic Rulkov neurons. We suggest two different algorithms to switch the bistable networks from the stable coherent state to the stable incoherent state. One of them is an act-and-wait control method, which utilizes the mean field measurements and homogeneous time delayed feedback perturbations with the periodically switched on and off feedback gain. We show that this algorithm is efficient for the globally coupled populations. Another algorithm is based on the multisite coordinated reset stimulation. The algorithm is nonfeedback, but it uses inhomogeneous perturbations and is efficient even for the networks with a complex scale-free topology. In addition to the numerical analysis of finite-size networks, the analytical results for the Kuramoto-type models in the thermodynamic limit are presented.

Description: Considering topography conditions, economic factors and driving safety, in real traffic, a road may be built as curved road. Traffic flow on curved road is different from the one on straight road. And it is worth to investigate the influencing mechanism of traffic flow on curved road. In order to investigate traffic flow on curved road analytically, in this paper, an extended one-dimensional lattice hydrodynamic model for traffic flow on curved road is proposed. The stability condition is obtained by the use of linear stability analysis. It is shown that the stability of traffic flow varies with the radian, friction coefficient and curvature radius of curved road. The Burgers, Korteweg–de Vries and modified Korteweg–de Vries equations are derived to describe the nonlinear density waves in the stable, metastable and unstable regions, respectively. The simulations are given to verify the analytical results. The results, which obtained from the theoretical analysis and numerical simulations, show that traffic flow may be affected by the angle going into curved road, the increment of angle, friction coefficient and curvature radius of curved road. And the maximal theoretical flux and velocity of traffic flow are influenced by the above factors as well.

Description: This paper focuses on the adaptive modified hybrid function projective synchronization with complex function transformation matrix (CMHFPS) for different dimensional chaotic (hyperchaotic) systems with complex variables and unknown complex parameters. The chaotic systems are considerably different from those in the existing closely related literature. Moreover, the transformation matrix in this type of chaos synchronization is not a square matrix, and its elements are complex functions. In particular, by constructing appropriate Lyapunov functions dependent on complex variables, the adaptive controllers are designed to synchronize different dimensional complex chaos (hyperchaos) with complex parameters in the sense of CMHFPS, and the complex update laws for estimating unknown complex parameters of complex chaotic systems are also given. Finally, two examples are presented to illustrate the effectiveness and feasibility of the theoretical results.

Description: In this paper, an experimental verification of the vibro-impact capsule model proposed by Liu et al. in (Int. J. Mech. Sci, 66:2–11; 2013a , Int. J. Mech. Sci, 72:39–54; 2013b , Int. J. Non-Linear Mech., 70, 30–46; 2015 ) is presented. The capsule dynamics is investigated experimentally by varying the stiffness of the support spring, and the frequency and the amplitude of excitation. The novel design of the experimental set-up is discussed, and comparisons between the experiments and numerical simulations are presented showing a good agreement. The conducted bifurcation analysis indicates that the behaviour of the system is mainly periodic and that a fine tuning of the control parameters can significantly improve the performance of the system. The main findings provide a better insight into the vibro-impact systems subject to nonlinear friction, and the experimental rig can be used to predict the dynamic behaviour of these systems.

Description: Nucleobase modifications dramatically alter nucleic acid structure and thermodynamics. 2-thiouridine (s 2 U) is a modified nucleobase found in tRNAs and known to stabilize U:A base pairs and destabilize U:G wobble pairs. The recently reported crystal structures of s 2 U-containing RNA duplexes do not entirely explain the mechanisms responsible for the stabilizing effect of s 2 U or whether this effect is entropic or enthalpic in origin. We present here thermodynamic evaluations of duplex formation using ITC and UV thermal denaturation with RNA duplexes containing internal s 2 U:A and s 2 U:U pairs and their native counterparts. These results indicate that s 2 U stabilizes both duplexes. The stabilizing effect is entropic in origin and likely results from the s 2 U-induced preorganization of the single-stranded RNA prior to hybridization. The same preorganizing effect is likely responsible for structurally resolving the s 2 U:U pair-containing duplex into a single conformation with a well-defined H-bond geometry. We also evaluate the effect of s 2 U on single strand conformation using UV- and CD-monitored thermal denaturation and on nucleoside conformation using 1 H NMR spectroscopy, MD and umbrella sampling. These results provide insights into the effects that nucleobase modification has on RNA structure and thermodynamics and inform efforts toward improving both ribozyme-catalyzed and nonenzymatic RNA copying.

Description: DNA interstrand crosslinks (ICLs) are the primary mechanism for the cytotoxic activity of many clinical anticancer drugs, and numerous strategies for forming ICLs have been developed. One such method is using crosslink-forming oligonucleotides (CFOs). In this study, we designed a 4-amino-6-oxo-2-vinylpyrimidine (AOVP) derivative with an acyclic spacer to react selectively with guanine. The AOVP CFO exhibited selective crosslinking reactivity with guanine and thymine in DNA, and with guanine in RNA. These crosslinking reactions with guanine were accelerated in the presence of CoCl 2 , NiCl 2 , ZnCl 2 and MnCl 2 . In addition, we demonstrated that the AOVP CFO was reactive toward 8-oxoguanine opposite AOVP in the duplex DNA. The structural analysis of each guanine and 8-oxoguanine adduct in the duplex DNA was investigated by high-resolution NMR. The results suggested that AOVP reacts at the N2 amine in guanine and at the N1 or N2 amines in 8-oxoguanine in the duplex DNA. This study demonstrated the first direct determination of the adduct structure in duplex DNA without enzyme digestion.

Description: The sequencing of the full transcriptome (RNA-seq) has become the preferred choice for the measurement of genome-wide gene expression. Despite its widespread use, challenges remain in RNA-seq data analysis. One often-overlooked aspect is normalization. Despite the fact that a variety of factors or ‘batch effects’ can contribute unwanted variation to the data, commonly used RNA-seq normalization methods only correct for sequencing depth. The study of gene expression is particularly problematic when it is influenced simultaneously by a variety of biological factors in addition to the one of interest. Using examples from experimental neuroscience, we show that batch effects can dominate the signal of interest; and that the choice of normalization method affects the power and reproducibility of the results. While commonly used global normalization methods are not able to adequately normalize the data, more recently developed RNA-seq normalization can. We focus on one particular method, RUVSeq and show that it is able to increase power and biological insight of the results. Finally, we provide a tutorial outlining the implementation of RUVSeq normalization that is applicable to a broad range of studies as well as meta-analysis of publicly available data.

Description: Many antiproliferative G-quadruplexes (G4s) arise from the folding of GT-rich strands. Among these, the Thrombin Binding Aptamer (TBA), as a rare example, adopts a monomolecular well-defined G4 structure. Nevertheless, the potential anticancer properties of TBA are severely hampered by its anticoagulant action and, consequently, no related studies have appeared so far in the literature. We wish to report here that suitable chemical modifications in the TBA sequence can preserve its antiproliferative over anticoagulant activity. Particularly, we replaced one residue of the TT or TGT loops with a dibenzyl linker to develop seven new quadruplex-forming TBA based sequences (TBA-bs), which were studied for their structural (CD, CD melting, 1D NMR) and biological (fibrinogen, PT and MTT assays) properties. The three-dimensional structures of the TBA-bs modified at T13 (TBA-bs13) or T12 (TBA-bs12), the former endowed with selective antiproliferative activity, and the latter acting as potently as TBA in both coagulation and MTT assays, were further studied by 2D NMR restrained molecular mechanics. The comparative structural analyses indicated that neither the stability, nor the topology of the G4s, but the different localization of the two benzene rings of the linker was responsible for the loss of the antithrombin activity for TBA-bs13.

Description: A structural and functional classification of H/ACA and H/ACA-like motifs is obtained from the analysis of the H/ACA guide RNAs which have been identified previously in the genomes of Euryarchaea (Pyrococcus) and Crenarchaea (Pyrobaculum). A unified structure/function model is proposed based on the common structural determinants shared by H/ACA and H/ACA-like motifs in both Euryarchaea and Crenarchaea. Using a computational approach, structural and energetic rules for the guide:target RNA-RNA interactions are derived from structural and functional data on the H/ACA RNP particles. H/ACA(-like) motifs found in Pyrococcus are evaluated through the classification and their biological relevance is discussed. Extra-ribosomal targets found in both Pyrococcus and Pyrobaculum might support the hypothesis of a gene regulation mediated by H/ACA(-like) guide RNAs in archaea.

Description: Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events.

Description: Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST—the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST. Specifically, our experiments conducted on a 12-core server show that HS-BLASTN can be 22 times faster than MegaBLAST and exhibits better parallel performance than MegaBLAST. HS-BLASTN is written in C++ and the related source code is available at https://github.com/chenying2016/queries under the GPLv3 license.

Description: Due to their high affinity and specificity, aptamers have been widely used as effective inhibitors in clinical applications. However, the ability to activate protein function through aptamer-protein interaction has not been well-elucidated. To investigate their potential as target-specific agonists, we used SELEX to generate aptamers to the insulin receptor (IR) and identified an agonistic aptamer named IR-A48 that specifically binds to IR, but not to IGF-1 receptor. Despite its capacity to stimulate IR autophosphorylation, similar to insulin, we found that IR-A48 not only binds to an allosteric site distinct from the insulin binding site, but also preferentially induces Y1150 phosphorylation in the IR kinase domain. Moreover, Y1150-biased phosphorylation induced by IR-A48 selectively activates specific signaling pathways downstream of IR. In contrast to insulin-mediated activation of IR, IR-A48 binding has little effect on the MAPK pathway and proliferation of cancer cells. Instead, AKT S473 phosphorylation is highly stimulated by IR-A48, resulting in increased glucose uptake both in vitro and in vivo . Here, we present IR-A48 as a biased agonist able to selectively induce the metabolic activity of IR through allosteric binding. Furthermore, our study also suggests that aptamers can be a promising tool for developing artificial biased agonists to targeted receptors.

Description: Ten eleven translocation (Tet) family-mediated DNA oxidation on 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) represents a novel epigenetic modification that regulates dynamic gene expression during embryonic stem cells (ESCs) differentiation. Through the role of Tet on 5hmC regulation in stem cell development is relatively defined, how the Tet family is regulated and impacts on ESCs lineage development remains elusive. In this study, we show non-coding RNA regulation on Tet family may contribute to epigenetic regulation during ESCs differentiation, which is suggested by microRNA-29b (miR-29b) binding sites on the Tet1 3' untranslated region (3' UTR). We demonstrate miR-29b increases sharply after embyoid body (EB) formation, which causes Tet1 repression and reduction of cellular 5hmC level during ESCs differentiation. Importantly, we show this miR-29b/Tet1 regulatory axis promotes the mesendoderm lineage formation both in vitro and in vivo by inducing the Nodal signaling pathway and repressing the key target of the active demethylation pathway, Tdg. Taken together, our findings underscore the contribution of small non-coding RNA mediated regulation on DNA demethylation dynamics and the differential expressions of key mesendoderm regulators during ESCs lineage specification. MiR-29b could potentially be applied to enrich production of mesoderm and endoderm derivatives and be further differentiated into desired organ-specific cells.

Description: The emergence of multidrug-resistant pathogens will make current antibiotics ineffective. For linezolid, a member of the novel oxazolidinone class of antibiotics, 10 nucleotide mutations in the ribosome have been described conferring resistance. Hypotheses for how these mutations affect antibiotics binding have been derived based on comparative crystallographic studies. However, a detailed description at the atomistic level of how remote mutations exert long-distance effects has remained elusive. Here, we show that the G2032A-C2499A double mutation, located 〉 10 Å away from the antibiotic, confers linezolid resistance by a complex set of effects that percolate to the binding site. By molecular dynamics simulations and free energy calculations, we identify U2504 and C2452 as spearheads among binding site nucleotides that exert the most immediate effect on linezolid binding. Structural reorganizations within the ribosomal subunit due to the mutations are likely associated with mutually compensating changes in the effective energy. Furthermore, we suggest two main routes of information transfer from the mutation sites to U2504 and C2452. Between these, we observe cross-talk, which suggests that synergistic effects observed for the two mutations arise in an indirect manner. These results should be relevant for the development of oxazolidinone derivatives that are active against linezolid-resistant strains.

Description: Genes from yeast to mammals are frequently subject to non-coding transcription of their antisense strand; however the genome-wide role for antisense transcription remains elusive. As transcription influences chromatin structure, we took a genome-wide approach to assess which chromatin features are associated with nascent antisense transcription, and contrast these with features associated with nascent sense transcription. We describe a distinct chromatin architecture at the promoter and gene body specifically associated with antisense transcription, marked by reduced H2B ubiquitination, H3K36 and H3K79 trimethylation and increased levels of H3 acetylation, chromatin remodelling enzymes, histone chaperones and histone turnover. The difference in sense transcription between genes with high or low levels of antisense transcription is slight; thus the antisense transcription-associated chromatin state is not simply analogous to a repressed state. Using mutants in which the level of antisense transcription is reduced at GAL1 , or altered genome-wide, we show that non-coding transcription is associated with high H3 acetylation and H3 levels across the gene, while reducing H3K36me3. Set1 is required for these antisense transcription-associated chromatin changes in the gene body. We propose that nascent antisense and sense transcription have fundamentally distinct relationships with chromatin, and that both should be considered canonical features of eukaryotic genes.

Description: Clonal populations accumulate mutations over time, resulting in different haplotypes. Deep sequencing of such a population in principle provides information to reconstruct these haplotypes and the frequency at which the haplotypes occur. However, this reconstruction is technically not trivial, especially not in clonal systems with a relatively low mutation frequency. The low number of segregating sites in those systems adds ambiguity to the haplotype phasing and thus obviates the reconstruction of genome-wide haplotypes based on sequence overlap information. Therefore, we present EVORhA, a haplotype reconstruction method that complements phasing information in the non-empty read overlap with the frequency estimations of inferred local haplotypes. As was shown with simulated data, as soon as read lengths and/or mutation rates become restrictive for state-of-the-art methods, the use of this additional frequency information allows EVORhA to still reliably reconstruct genome-wide haplotypes. On real data, we show the applicability of the method in reconstructing the population composition of evolved bacterial populations and in decomposing mixed bacterial infections from clinical samples.

Description: Upon stable cell line generation, chromosomal integration site of the vector DNA has a major impact on transgene expression. Here we apply an active gene environment, rather than specified genetic elements, in expression vectors used for random integration. We generated a set of Bacterial Artificial Chromosome (BAC) vectors with different open chromatin regions, promoters and gene regulatory elements and tested their impact on recombinant protein expression in CHO cells. We identified the Rosa26 BAC as the most efficient vector backbone showing a nine-fold increase in both polyclonal and clonal production of the human IgG-Fc. Clonal protein production was directly proportional to integrated vector copy numbers and remained stable during 10 weeks without selection pressure. Finally, we demonstrated the advantages of BAC-based vectors by producing two additional proteins, HIV-1 glycoprotein CN54gp140 and HIV-1 neutralizing PG9 antibody, in bioreactors and shake flasks reaching a production yield of 1 g/l.

Description: Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data ( 3DBG ), and a 3D genome browser to visualize and explore 3D genome structures ( 3DGB ). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/ .

Description: Due to their relatively low-cost per sample and broad, gene-centric coverage of CpGs across the human genome, Illumina's 450k arrays are widely used in large scale differential methylation studies. However, by their very nature, large studies are particularly susceptible to the effects of unwanted variation. The effects of unwanted variation have been extensively documented in gene expression array studies and numerous methods have been developed to mitigate these effects. However, there has been much less research focused on the appropriate methodology to use for accounting for unwanted variation in methylation array studies. Here we present a novel 2-stage approach using RUV-inverse in a differential methylation analysis of 450k data and show that it outperforms existing methods.

Description: Telomerase is a reverse transcriptase that maintains telomeres on the ends of chromosomes, allowing rapidly dividing cells to proliferate while avoiding senescence and apoptosis. Understanding telomerase gene expression and splicing at the single cell level could yield insights into the roles of telomerase during normal cell growth as well as cancer development. Here we use droplet-based single cell culture followed by single cell or colony transcript abundance analysis to investigate the relationship between cell growth and transcript abundance of the telomerase genes encoding the RNA component (hTR) and protein component (hTERT) as well as hTERT splicing. Jurkat and K562 cells were examined under normal cell culture conditions and during exposure to curcumin, a natural compound with anti-carcinogenic and telomerase activity-reducing properties. Individual cells predominantly express single hTERT splice variants, with the α+/β– variant exhibiting significant transcript abundance bimodality that is sustained through cell division. Sub-lethal curcumin exposure results in reduced bimodality of all hTERT splice variants and significant upregulation of alpha splicing, suggesting a possible role in cellular stress response. The single cell culture and transcript abundance analysis method presented here provides the tools necessary for multiparameter single cell analysis which will be critical for understanding phenotypes of heterogeneous cell populations, disease cell populations and their drug response.

Description: Based on the stability theory of fractional-order systems, using the fractional-order Lyapunov direct method, in this paper, the Mittag–Leffler stability for fractional-order Lorenz and fractional-order Lorenz-family system is investigated, respectively. We propose the definition of the Mittag–Leffler stability; some sufficient conditions for the Mittag–Leffler stability are obtained by selecting properly the parameters and the initial values of system. Finally, numerical simulations are performed to verify the theoretical analysis.

Description: In this paper, cluster synchronization on multiple sub-networks of complex networks with nonidentical nodes, stochastic disturbances and time-varying delays is investigated. Based on the leader–follower model, an improved network structure model for realizing the cluster synchronization on multiple sub-networks of complex networks is presented. In this improved network model, the complex networks are divided into multiple pairs of matching sub-networks, each of which consists of a leaders’ sub-network and a followers’ sub-network, such that the dynamics of the nodes belonging to the same pair of matching sub-networks are identical, while the ones belonging to different pairs of unmatched sub-networks are nonidentical. Furthermore, the nodes in a sub-network may be inevitably influenced by some stochastic disturbances and time-varying delays. In this new setting, the aim is to design some suitable pinning controllers on the chosen nodes of each followers’ sub-network, such that the proposed method for realizing the cluster synchronization has good immunity to the influence of these stochastic factors. By using the Lyapunov stability theory and stochastic differential equation theory, some cluster synchronization criteria, and a pinning scheme that the nodes with very large or low degrees are good candidates for applying pinning controllers, are established such that all the nodes in each sub-network are exponentially synchronized to the average state of their matching leaders. Then, the attack and robustness of the pinning scheme are discussed. Finally, some simulation examples are presented to verify the theoretical analysis.

Description: This paper introduces a new segmentation technique to segment incomplete nutrient-deficient crop images by imputing missing pixels. Usually, each image contains pixels holding information about intensity, but sometimes image can miss some pixels (that is, the pixel without an appropriate intensity value). An image with missing pixels is called an incomplete image. Intuitionistic fuzzy clustering algorithm is a useful tool for clustering images, but it is not directly applicable for incomplete images. For example, segmentation of nutrient deficiency portions in the presence of missing pixels leads to error in segmentation. Crop images with nutrient deficiency might have missing pixels due to inherent defects in imaging equipment or due to environmental conditions. In this paper, nutrient deficiency in crop images is segmented after imputation of missing pixels based on intuitionistic fuzzy C-means color clustering algorithm. Experiments are performed on various incomplete crop images. Through the derived results and evaluated comparisons with other methods, namely K-means, fuzzy K-means, principal component analysis, regularized expectation maximization and fuzzy C-means algorithms, it has been proven that the proposed method performs well.

Description: Theoretical analysis of a suspended nano-mechanical membrane subject to an optical driving field in an optomechanical cavity is presented, which is confirmed through numerical simulations. In the presence of an optical field between its mirrors, the high-finesse optomechanical resonator acts as an oscillator driven by a radiation pressure force. The periodic nature of the radiation pressure force makes the nano-mechanical membrane in the optomechanical system as a kicked harmonic oscillator. Mathematically the physical system displays a stochastic web map that helps to understand several properties of the kicked membrane in classical phase space. We find that our web map is area preserving and displays quasiperiodic symmetrical structures in phase space which we express as q -fold symmetry. It is shown that under appropriate control of certain parameters, namely the frequency ratio and the kicking strength, the dynamics of kicked membrane exhibits chaotic dynamics. We provide the stability analysis by means of Lyapunov exponent and survival probability.

Description: We study the coupled nonlinear Schrödinger equation in the (2+1)-dimensional inhomogeneous \(\mathcal {PT}\) -symmetric nonlinear couplers and obtain \(\mathcal {PT}\) -symmetric and \(\mathcal {PT}\) -antisymmetric vortex soliton solutions. The dynamical behaviors of the completely localized structures (vortex solitons) are analytically and numerically investigated in a diffraction decreasing system with exponential profile. Numerical results indicate that one vortex soliton with different topological charges can stably propagate a long distance. The space between two humps and the modulation depth of vortex solitons add when the topological charge increases. However, the change tendency of the amplitude and width of vortex solitons is same with the increase in topological charge.

Description: The detection of shaft cracks within operating rotors is an old subject of scientific research. Several signal- and model-based approaches are developed. Here two approaches used for crack detection in rotating machinery, model-based and signal-based approaches, are compared. Strength and weak points are discussed and compared for the two approaches using two representative applicable methods, in order to achieve a comparative overview of these two available techniques. The PI-observer-based method is considered, as modern model-based technique, to give indication about possibilities and limitations of such kind of methods. A novel signal-based approach is introduced, based on SVM and wavelets as an example for a modern machine learning technique. The concepts of severity estimation and service life prediction are investigated in the proposed approach. Furthermore, a brief comparative discussion is presented in the contribution, including ideas for combination of the introduced approaches, in order to achieve more comprehensive and more robust monitoring system applied to the detection of shaft cracks in rotating machines.

Description: This paper proposes a novel approach to study the problem of master–slave synchronization for chaotic delayed Lur’e systems with sampled-data feedback control. Specifically, first, it is assumed that the sampling intervals are randomly variable but bounded. By getting the utmost out of the usable information on the actual sampling pattern and the nonlinear part condition, a newly augmented Lyapunov–Krasovskii functional is constructed via a more general delay-partition approach. Second, in order to obtain less conservative synchronization criteria, a novel integral inequality is developed by the mean of the new adjustable parameters. Third, a longer sampling period is achieved by using a double integral form of Wirtinger-based integral inequality. Finally, three numerical examples with simulations of Chua’s circuit are given to demonstrate the effectiveness and merits of the proposed methods.

Description: In this article, new and general exact traveling wave solutions including soliton-like solutions, triangular-type solutions, single and combined nondegenerate Jacobi elliptic wave function-like solutions, doubly periodic-like solutions are obtained for integrable (2+1)-dimensional Maccari system. This system is frequently introduced to define the motion of the isolated waves, localized in a very small part of space, in many fields such as quantum field theory, hydrodynamics, in plasma physics to describe the behavior of the sonic Langmuir solitons, and also in nonlinear optics. Based on the generalized elliptic equation, an algebraic method is used to construct a series of exact solutions. Being concise and straightforward, the calculations demonstrate the effectiveness and convenience of the method for solving other nonlinear partial differential equations.

Description: A new kind of vibration isolation and mitigation device with high damping is designed and fabricated for reducing dynamic responses of a platform under the excitation with wide frequency range. Tests are carried out to consider the influence of the frequency and amplitude of excitation on the properties of the device. The dynamic model of the platform incorporating with the vibration isolation and mitigation devices is established, and dynamic responses of the mitigated platform are calculated under different excitations. It can be shown from comparison between responses of the mitigated and unmitigated structures in time domain and frequency domain that the devices can significantly reduce dynamic responses of the platform.

Description: The nonlinear longitudinal wave equation, describing the propagation of optical solitons in magneto-electro-elastic circular rod, is investigated analytically. Two integration tools that are traveling wave hypothesis and G \(^{\prime }\) /G expansion scheme are recruited to extract explicit soliton solutions. The existence conditions are derived.

Description: We derive variable separation solutions of the ( \(1+1\) )-dimensional KdV-type model by means of the modified tan h -function method with three different ansätz. Superficially speaking, the positive and negative power-symmetric ansatz seems to be better than the positive-power ansatz and radical sign combined ansatz because the positive and negative power-symmetric ansatz can construct the most forms of variable separation solutions. Actually, we find that various “different” solutions obtained by the modified tanh-function method are not independent, and many of the so-called new solutions are equivalent to one another. Moreover, in the two- or multi-component system, if we construct localized coherent structures for a special component based on variable separation solutions, we must note the structure constructed by the other component for the same equation in order to avoid the appearance of some divergent and un-physical structures. We hope that these results above contribute to the analysis on exact solutions and the construction of localized structures for other nonlinear models.

Description: This work presents an analytical study of dynamic behaviors of solitons in the electrical transmission line. The nonlinear dynamical model that is the modified Zakharov–Kuznetsov equation with an external force is investigated. Via the Riccati equation mapping scheme, explicit twenty seven traveling wave solutions, which include periodic solutions, rational wave solution, soliton solutions as well as soliton-like solutions, are constructed for the first time.

Description: Here, we present a simple, modular and efficient strategy that allows the 3'-terminal labeling of DNA, regardless of whether it has been chemically or enzymatically synthesized or isolated from natural sources. We first incorporate a range of modified nucleotides at the 3'-terminus, using terminal deoxynucleotidyl transferase. In the second step, we convert the incorporated nucleotides, using either of four highly efficient click chemistry-type reactions, namely copper-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, Staudinger ligation or Diels-Alder reaction with inverse electron demand. Moreover, we create internal modifications, making use of either ligation or primer extension, after the nucleotidyl transferase step, prior to the click reaction. We further study the influence of linker variants on the reactivity of azides in different click reactions. We find that different click reactions exhibit distinct substrate preferences, a fact that is often overlooked, but should be considered when labeling oligonucleotides or other biomolecules with click chemistry. Finally, our findings allowed us to extend our previously published RNA labeling strategy to the use of a different copper-free click chemistry, namely the Staudinger ligation.

Description: Despite the increasing knowledge about DNA methylation, the understanding of human epigenome evolution is in its infancy. Using whole genome bisulfite sequencing we identified hundreds of differentially methylated regions (DMRs) in humans compared to non-human primates and estimated that ~25% of these regions were detectable throughout several human tissues. Human DMRs were enriched for specific histone modifications and the majority were located distal to transcription start sites, highlighting the importance of regions outside the direct regulatory context. We also found a significant excess of endogenous retrovirus elements in human-specific hypomethylated. We reported for the first time a close interplay between inter-species genetic and epigenetic variation in regions of incomplete lineage sorting, transcription factor binding sites and human differentially hypermethylated regions. Specifically, we observed an excess of human-specific substitutions in transcription factor binding sites located within human DMRs, suggesting that alteration of regulatory motifs underlies some human-specific methylation patterns. We also found that the acquisition of DNA hypermethylation in the human lineage is frequently coupled with a rapid evolution at nucleotide level in the neighborhood of these CpG sites. Taken together, our results reveal new insights into the mechanistic basis of human-specific DNA methylation patterns and the interpretation of inter-species non-coding variation.

Description: The product of the Plasmodium falciparum genes clag3.1 and clag3.2 plays a fundamental role in malaria parasite biology by determining solute transport into infected erythrocytes. Expression of the two clag3 genes is mutually exclusive, such that a single parasite expresses only one of the two genes at a time. Here we investigated the properties and mechanisms of clag3 mutual exclusion using transgenic parasite lines with extra copies of clag3 promoters located either in stable episomes or integrated in the parasite genome. We found that the additional clag3 promoters in these transgenic lines are silenced by default, but under strong selective pressure parasites with more than one clag3 promoter simultaneously active are observed, demonstrating that clag3 mutual exclusion is strongly favored but it is not strict. We show that silencing of clag3 genes is associated with the repressive histone mark H3K9me3 even in parasites with unusual clag3 expression patterns, and we provide direct evidence for heterochromatin spreading in P. falciparum . We also found that expression of a neighbor ncRNA correlates with clag3.1 expression. Altogether, our results reveal a scenario where fitness costs and non-deterministic molecular processes that favor mutual exclusion shape the expression patterns of this important gene family.

Description: MicroRNAs are a class of small regulatory RNAs that are generated from primary miRNA (pri-miRNA) transcripts with a stem-loop structure. Accuracy of the processing of pri-miRNA into mature miRNA in plants can be enhanced by SERRATE (SE) and HYPONASTIC LEAVES 1 (HYL1). HYL1 activity is regulated by the FIERY2 (FRY2)/RNA polymerase II C-terminal domain phosphatase-like 1 (CPL1). Here, we discover that HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5) and two serine/arginine-rich splicing factors RS40 and RS41, previously shown to be involved in pre-mRNA splicing, affect the biogenesis of a subset of miRNA. These proteins are required for correct miRNA strand selection and the maintenance of miRNA levels. FRY2 dephosphorylates HOS5 whose phosphorylation status affects its subnuclear localization. HOS5 and the RS proteins bind both intronless and intron-containing pri-miRNAs. Importantly, all of these splicing-related factors directly interact with both HYL1 and SE in nuclear splicing speckles. Our results indicate that these splicing factors are directly involved in the biogenesis of a group of miRNA.

Description: AlgR is a key transcriptional regulator required for the expression of multiple virulence factors, including type IV pili and alginate in Pseudomonas aeruginosa . However, the regulon and molecular regulatory mechanism of AlgR have yet to be fully elucidated. Here, among 157 loci that were identified by a ChIP-seq assay, we characterized a gene, mucR , which encodes an enzyme that synthesizes the intracellular second messenger cyclic diguanylate (c-di-GMP). A algR strain produced lesser biofilm than did the wild-type strain, which is consistent with a phenotype controlled by c-di-GMP. AlgR positively regulates mucR via direct binding to its promoter. A algR mucR double mutant produced lesser biofilm than did the single algR mutant, demonstrating that c-di-GMP is a positive regulator of biofilm formation. AlgR controls the levels of c-di-GMP synthesis via direct regulation of mucR . In addition, the cognate sensor of AlgR, FimS/AlgZ, also plays an important role in P. aeruginosa virulence. Taken together, this study provides new insights into the AlgR regulon and reveals the involvement of c-di-GMP in the mechanism underlying AlgR regulation.

Description: Phosphorylation of the C-terminal domain of the largest subunit of RNA polymerase II (Pol II), especially Ser2 and Ser5 residues, plays important roles in transcription and mRNA processing, including 5' end capping, splicing and 3' end processing. These phosphorylation events stimulate mRNA processing, however, it is not clear whether splicing activity affects the phosphorylation status of Pol II. In this study, we found that splicing inhibition by potent splicing inhibitors spliceostatin A (SSA) and pladienolide B or by antisense oligos against snRNAs decreased phospho-Ser2 level, but had little or no effects on phospho-Ser5 level. In contrast, transcription and translation inhibitors did not decrease phospho-Ser2 level, therefore inhibition of not all the gene expression processes cause the decrease of phospho-Ser2. SSA treatment caused early dissociation of Pol II and decrease in phospho-Ser2 level of chromatin-bound Pol II, suggesting that splicing inhibition causes downregulation of phospho-Ser2 through at least these two mechanisms.

Description: Facioscapulohumeral dystrophy (FSHD) is an epi/genetic satellite disease associated with at least two satellite sequences in 4q35: (i) D4Z4 macrosatellite and (ii) β-satellite repeats (BSR), a prevalent part of the 4qA allele. Most of the recent FSHD studies have been focused on a DUX4 transcript inside D4Z4 and its tandem contraction in FSHD patients. However, the D4Z4-contraction alone is not pathological, which would also require the 4qA allele. Since little is known about BSR, we investigated the 4qA BSR functional role in the transcriptional control of the FSHD region 4q35. We have shown that an individual BSR possesses enhancer activity leading to activation of the Adenine Nucleotide Translocator 1 gene ( ANT1 ), a major FSHD candidate gene. We have identified ZNF555, a previously uncharacterized protein, as a putative transcriptional factor highly expressed in human primary myoblasts that interacts with the BSR enhancer site and impacts the ANT1 promoter activity in FSHD myoblasts. The discovery of the functional role of the 4qA allele and ZNF555 in the transcriptional control of ANT1 advances our understanding of FSHD pathogenesis and provides potential therapeutic targets.

Description: The roles of translesion synthesis (TLS) DNA polymerases in bypassing the C8–2'-deoxyguanosine adduct (dG-C8-IQ) formed by 2-amino-3-methylimidazo[4,5- f ]quinoline (IQ), a highly mutagenic and carcinogenic heterocyclic amine found in cooked meats, were investigated. Three plasmid vectors containing the dG-C8-IQ adduct at the G 1 -, G 2 - or G 3 -positions of the Nar I site (5'-G 1 G 2 CG 3 CC-3') were replicated in HEK293T cells. Fifty percent of the progeny from the G 3 construct were mutants, largely G-〉T, compared to 18% and 24% from the G 1 and G 2 constructs, respectively. Mutation frequency (MF) of dG-C8-IQ was reduced by 38–67% upon siRNA knockdown of pol , whereas it was increased by 10–24% in pol knockdown cells. When pol and pol were simultaneously knocked down, MF of the G 1 and G 3 constructs was reduced from 18% and 50%, respectively, to 〈3%, whereas it was reduced from 24% to 〈1% in the G 2 construct. In vitro TLS using yeast pol showed that it can extend G 3 *:A pair more efficiently than G 3 *:C pair, but it is inefficient at nucleotide incorporation opposite dG-C8-IQ. We conclude that pol and pol cooperatively carry out the majority of the error-prone TLS of dG-C8-IQ, whereas pol is involved primarily in its error-free bypass.

Description: The MRE11/RAD50/NBS1 (MRN) complex plays a central role as a sensor of DNA double strand breaks (DSB) and is responsible for the efficient activation of ataxia-telangiectasia mutated (ATM) kinase. Once activated ATM in turn phosphorylates RAD50 and NBS1, important for cell cycle control, DNA repair and cell survival. We report here that MRE11 is also phosphorylated by ATM at S676 and S678 in response to agents that induce DNA DSB, is dependent on the presence of NBS1, and does not affect the association of members of the complex or ATM activation. A phosphosite mutant (MRE11S676AS678A) cell line showed decreased cell survival and increased chromosomal aberrations after radiation exposure indicating a defect in DNA repair. Use of GFP-based DNA repair reporter substrates in MRE11S676AS678A cells revealed a defect in homology directed repair (HDR) but single strand annealing was not affected. More detailed investigation revealed that MRE11S676AS678A cells resected DNA ends to a greater extent at sites undergoing HDR. Furthermore, while ATM-dependent phosphorylation of Kap1 and SMC1 was normal in MRE11S676AS678A cells, there was no phosphorylation of Exonuclease 1 consistent with the defect in HDR. These results describe a novel role for ATM-dependent phosphorylation of MRE11 in limiting the extent of resection mediated through Exonuclease 1.

Description: To gain a wider view of the pathways that regulate mitochondrial function, we combined the effect of heat stress on respiratory capacity with the discovery potential of a genome-wide screen in Saccharomyces cerevisiae . We identified 105 new genes whose deletion impairs respiratory growth at 37°C by interfering with processes such as transcriptional regulation, ubiquitination and cytosolic tRNA wobble uridine modification via 5-methoxycarbonylmethyl-2-thiouridine formation. The latter process, specifically required for efficient decoding of AA-ending codons under stress conditions, was covered by multiple genes belonging to the Elongator (e.g. ELP3 ) and urmylation (e.g., NCS6 ) pathways. ELP3 or NCS6 deletants had impaired mitochondrial protein synthesis. Their respiratory deficiency was selectively rescued by overexpression of tRNA Lys UUU as well by overexpression of genes ( BCK1 and HFM1 ) with a strong bias for the AAA codon read by this tRNA. These data extend the mitochondrial regulome, demonstrate that heat stress can impair respiration by disturbing cytoplasmic translation of proteins critically involved in mitochondrial function and document, for the first time, the involvement in such process of the Elongator and urmylation pathways. Given the conservation of these pathways, the present findings may pave the way to a better understanding of the human mitochondrial regulome in health and disease.

Description: Recent studies strongly suggest that in bacterial cells the order of genes along the chromosomal origin-to-terminus axis is determinative for regulation of the growth phase-dependent gene expression. The prediction from this observation is that positional displacement of pleiotropic genes will affect the genetic regulation and hence, the cellular phenotype. To test this prediction we inserted the origin-proximal dusB-fis operon encoding the global regulator FIS in the vicinity of replication terminus on both arms of the Escherichia coli chromosome. We found that the lower fis gene dosage in the strains with terminus-proximal dusB-fis operons was compensated by increased fis expression such that the intracellular concentration of FIS was homeostatically adjusted. Nevertheless, despite unchanged FIS levels the positional displacement of dusB-fis impaired the competitive growth fitness of cells and altered the state of the overarching network regulating DNA topology, as well as the cellular response to environmental stress, hazardous substances and antibiotics. Our finding that the chromosomal repositioning of a regulatory gene can determine the cellular phenotype unveils an important yet unexplored facet of the genetic control mechanisms and paves the way for novel approaches to manipulate bacterial physiology.

Description: In bacteria and archaea, short fragments of foreign DNA are integrated into Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) loci, providing a molecular memory of previous encounters with foreign genetic elements. In Escherichia coli , short CRISPR-derived RNAs are incorporated into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Recent structures of Cascade capture snapshots of this seahorse-shaped RNA-guided surveillance complex before and after binding to a DNA target. Here we determine a 3.2 Å x-ray crystal structure of Cascade in a new crystal form that provides insight into the mechanism of double-stranded DNA binding. Molecular dynamic simulations performed using available structures reveal functional roles for residues in the tail, backbone and belly subunits of Cascade that are critical for binding double-stranded DNA. Structural comparisons are used to make functional predictions and these predictions are tested in vivo and in vitro . Collectively, the results in this study reveal underlying mechanisms involved in target-induced conformational changes and highlight residues important in DNA binding and protospacer adjacent motif recognition.

Description: DNA damage, arising from endogenous metabolism or exposure to environmental agents, may perturb the transmission of genetic information by blocking DNA replication and/or inducing mutations, which contribute to the development of cancer and likely other human diseases. Hydroxyl radical attack on the C1', C3' and C4' of 2-deoxyribose can give rise to epimeric 2-deoxyribose lesions, for which the in vivo occurrence and biological consequences remain largely unexplored. Through independent chemical syntheses of all three epimeric lesions of 2'-deoxyguanosine (dG) and liquid chromatography-tandem mass spectrometry analysis, we demonstrated unambiguously the presence of substantial levels of the α-anomer of dG (α-dG) in calf thymus DNA and in DNA isolated from mouse pancreatic tissues. We further assessed quantitatively the impact of all four α-dN lesions on DNA replication in Escherichia coli by employing a shuttle-vector method. We found that, without SOS induction, all α-dN lesions except α-dA strongly blocked DNA replication and, while replication across α-dA was error-free, replicative bypass of α-dC and α-dG yielded mainly C-〉A and G-〉A mutations. In addition, SOS induction could lead to markedly elevated bypass efficiencies for the four α-dN lesions, abolished the G-〉A mutation for α-dG, pronouncedly reduced the C-〉A mutation for α-dC and triggered T-〉A mutation for α-dT. The preferential misincorporation of dTMP opposite the α-dNs could be attributed to the unique base-pairing properties of the nucleobases elicited by the inversion of the configuration of the N -glycosidic linkage. Our results also revealed that Pol V played a major role in bypassing α-dC, α-dG and α-dT in vivo . The abundance of α-dG in mammalian tissue and the impact of the α-dNs on DNA replication demonstrate for the first time the biological significance of this family of DNA lesions.

Description: We have examined the three-dimensional organization of the yeast genome during quiescence by a chromosome capture technique as a means of understanding how genome organization changes during development. For exponentially growing cells we observe high levels of inter-centromeric interaction but otherwise a predominance of intrachromosomal interactions over interchromosomal interactions, consistent with aggregation of centromeres at the spindle pole body and compartmentalization of individual chromosomes within the nucleoplasm. Three major changes occur in the organization of the quiescent cell genome. First, intrachromosomal associations increase at longer distances in quiescence as compared to growing cells. This suggests that chromosomes undergo condensation in quiescence, which we confirmed by microscopy by measurement of the intrachromosomal distances between two sites on one chromosome. This compaction in quiescence requires the condensin complex. Second, inter-centromeric interactions decrease, consistent with prior data indicating that centromeres disperse along an array of microtubules during quiescence. Third, inter-telomeric interactions significantly increase in quiescence, an observation also confirmed by direct measurement. Thus, survival during quiescence is associated with substantial topological reorganization of the genome.

Description: Cross-talk between competitive endogenous RNAs (ceRNAs) through shared miRNAs represents a novel layer of gene regulation that plays important roles in the physiology and development of cancers. However, a global view of their system-level properties across various types of cancers is still unknown. Here, we constructed the mRNA related ceRNA–ceRNA interaction landscape across 20 cancer types by systematically analyzing molecular profiles of 5203 tumors and miRNA regulations. Our study highlights the conserved features shared by pan-cancer and higher similarity within similar origin cell type. Moreover, a core ceRNA network was identified. Function analysis identified a common theme of cancer hallmarks, however they exhibit phenotype-specific connectivity patterns. Besides, we found a marked rewiring in the ceRNA program between various cancers, and further revealed conserved and rewired network ceRNA hubs in each cancer, which were tensely competitive interactions to constitute conserved and cancer-specific modules. By providing mechanistic linkage between known cancer miRNAs, their mediated ceRNA–ceRNA interactions, and the associations with known cancer hallmarks, the inferred cancer ceRNA–ceRNA interaction landscape will serve as a powerful public resource for further biological discoveries of tumorigenesis.

Description: Replicative helicases are essential ATPases that unwind DNA to initiate chromosomal replication. While bacterial replicative DnaB helicases are hexameric, Helicobacter pylori DnaB ( Hp DnaB) was found to form double hexamers, similar to some archaeal and eukaryotic replicative helicases. Here we present a structural and functional analysis of Hp DnaB protein during primosome formation. The crystal structure of the Hp DnaB at 6.7 Å resolution reveals a dodecameric organization consisting of two hexamers assembled via their N-terminal rings in a stack-twisted mode. Using fluorescence anisotropy we show that Hp DnaB dodecamer interacts with single-stranded DNA in the presence of ATP but has a low DNA unwinding activity. Multi-angle light scattering and small angle X-ray scattering demonstrate that interaction with the DnaG primase helicase-binding domain dissociates the helicase dodecamer into single ringed primosomes. Functional assays on the proteins and associated complexes indicate that these single ringed primosomes are the most active form of the helicase for ATP hydrolysis, DNA binding and unwinding. These findings shed light onto an activation mechanism of Hp DnaB by the primase that might be relevant in other bacteria and possibly other organisms exploiting dodecameric helicases for DNA replication.