Engineering of Janus-Like Dendrimers with Peptides Derived from Glycoproteins of Herpes Simplex Virus Type 1: Toward a Versatile and Novel Antiviral Platform

Novel antiviral nanotherapeutics, which may inactivate the virus and block it from entering host cells, represent an important challenge to face viral global health emergencies around the world. Using a combination of bioorthogonal copper-catalyzed 1,3-dipolar alkyne/azide cycloaddition (CuAAC) and photoinitiated thiol–ene coupling, monofunctional and bifunctional peptidodendrimer conjugates were obtained. The conjugates are biocompatible and demonstrate no toxicity to cells at biologically relevant concentrations. Furthermore, the orthogonal addition of multiple copies of two different antiviral peptides on the surface of a single dendrimer allowed the resulting bioconjugates to inhibit Herpes simplex virus type 1 at both the early and the late stages of the infection process. The presented work builds on further improving this attractive design to obtain a new class of therapeutics.     

Velocity‐based formulations for standard and quasi‐incompressible hypoelastic‐plastic solids

We present three velocity‐based updated Lagrangian formulations for standard and quasi‐incompressible hypoelastic‐plastic solids. Three low‐order finite elements are derived and tested for non‐linear solid mechanics problems. The so‐called V‐element is based on a standard velocity approach, while a mixed velocity–pressure formulation is used for the VP and the VPS elements. The two‐field problem is solved via a two‐step Gauss–Seidel partitioned iterative scheme. First, the momentum equations are solved in terms of velocity increments, as for the V‐element. Then, the constitutive relation for the pressure is solved using the updated velocities obtained at the previous step. For the VPS‐element, the formulation is stabilized using the finite calculus method in order to solve problems involving quasi‐incompressible materials. All the solid elements are validated by solving two‐dimensional and three‐dimensional benchmark problems in statics as in dynamics. Copyright © 2016 John Wiley & Sons, Ltd.     

NMscatt: a program for calculating inelastic scattering from large biomolecular systems using classical force-field simulations

Computational tools for normal mode analysis, which are widely used in physics and materials science problems, are designed here in a single package called NMscatt (Normal Modes & scattering) that allows arbitrarily large systems to be handled. The package allows inelastic neutron and X-ray scattering observables to be calculated, allowing comparison with experimental data produced at large scale facilities. Various simplification schemes are presented for analyzing displacement vectors, which are otherwise too complicated to understand in very large systems.

Program summary

Title of program:NMscattCatalogue identifier:ADZA_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADZA_v1_0.htmlProgram obtainable from:CPC Program Library, Queen's University of Belfast, N. IrelandLicensing provisions:noNo. of lines in distributed program, including test data, etc.:573 535No. of bytes in distributed program, including test data, etc.:4 516 496Distribution format:tar.gzProgramming language:FORTRAN 77Computer:x86 PCOperating system:GNU/Linux, UNIXRAM:Depends on the system size to be simulatedWord size:32 or 64 bitsClassification:16.3External routines:LAPACKNature of problem: Normal mode analysis, phonons calculation, derivation of incoherent and coherent inelastic scattering spectra.Solution method: Full diagonalization (producing eigen-vectors and eigen-values) of dynamical matrix which is obtained from potential energy function derivation using finite difference method.Running time: About 7 hours per one k-point evaluation in sampling all modes dispersion curves for a system containing 3550 atoms in the unit cell on AMD Athlon 64 X2 Dual Core Processor 4200+.     

Desynchronization and inhibition of Kuramoto oscillators by scalar mean-field feedback

Motivated by neuroscience applications, and in particular by the deep brain stimulation treatment for Parkinson’s disease, we have recently derived a simplified model of an interconnected neuronal population under the effect of its mean-field proportional feedback. In this paper, we rely on that model to propose conditions under which proportional mean-field feedback achieves either oscillation inhibition or desynchronization. More precisely, we show that for small natural frequencies, this scalar control signal induces an inhibition of the collective oscillation. For the closed-loop system, this situation corresponds to a fixed point which is shown to be almost globally asymptotically stable in the fictitious case of zero natural frequencies and all-to-all coupling and feedback. In the case of an odd number of oscillators, this property is shown to be robust to small natural frequencies and heterogencities in both the coupling and feedback topology. On the contrary, for large natural frequencies, we show that scalar proportional mean-field feedback is able to induce desynchronization. After having recalled a formal definition for desynchronization, we show how it can be induced in a network of originally synchronized oscillators.     

Optimization of cutting conditions during cutting by using neural networks

Optimum selection of cutting conditions importantly contribute to the increase of productivity and the reduction of costs, therefore utmost attention is paid to this problem in this contribution. In this paper, a neural network-based approach to complex optimization of cutting parameters is proposed. It describes the multi-objective technique of optimization of cutting conditions by means of the neural networks taking into consideration the technological, economic and organizational limitations. To reach higher precision of the predicted results, a neural optimization algorithm is developed and presented to ensure simple, fast and efficient optimization of all important turning parameters. The approach is suitable for fast determination of optimum cutting parameters during machining, where there is not enough time for deep analysis. To demonstrate the procedure and performance of the neural network approach, an illustrative example is discussed in detail.     

Simulation of cutting forces in ball-end milling

The paper presents a simulation system (SCP) that determines the cutting forces in the ball-end milling process. The system is based on numerical methods, computer programme, theoretical knowledge of technological processes, machining and tests performed. The system for simulation of the cutting process combines the technological data base, the analytical and experimental model and the data base SCP. The experimental model contains a collection of variables of the cutting process by means of sensors and transformation of those data into numerical values, which are a starting point for data calculation of characteristic coefficients of materials. The analytical model is used to estimate the tangential, radial and axial cutting forces, along with a material data base obtained from cutting experiments. Ball-end milling test has been conducted to verify simulation results. The simulation results, are the basis for the development of the tool-designing model and for the model of optimization of the machining process cutting parameters.     

Wild Prunus Fruit Species as a Rich Source of Bioactive Compounds

Sugars, organic acids, carotenoids, tocopherols, chlorophylls, and phenolic compounds were quantified in fruit of 4 wild growing Prunus species (wild cherry, bird cherry, blackthorn, and mahaleb cherry) using HPLC‐DAD‐MSn. In wild Prunus, the major sugars were glucose and fructose, whereas malic and citric acids dominated among organic acids. The most abundant classes of phenolic compounds in the analyzed fruit species were anthocyanins, flavonols, derivatives of cinnamic acids, and flavanols. Two major groups of anthocyanins measured in Prunus fruits were cyanidin‐3‐rutinoside and cyanidin‐3‐glucoside. Flavonols were represented by 19 derivatives of quercetin, 10 derivatives of kaempferol, and 2 derivatives of isorhamnetin. The highest total flavonol content was measured in mahaleb cherry and bird cherry, followed by blackthorn and wild cherry fruit. Total phenolic content varied from 2373 (wild cherry) to 11053 mg GAE per kg (bird cherry) and ferric reducing antioxidant power antioxidant activity from 7.26 to 31.54 mM trolox equivalents per kg fruits.     

Phytochemicals in fruits of two Prunus domestica L. plum cultivars during ripening

BACKGROUND: Plums are a rich source of nutritive and bioactive compounds. The objective was to evaluate the impact of fruit tissue (flesh and peel), ripening stage and cultivar on the composition of phytochemicals in plums (Prunus domestica L.) and to analyse the relation between total antioxidant activity (TAA) and the measured variables. RESULTS: The content of total sugars and total organic acids was higher in flesh but total phenolic content (TPC) and TAA was statistically higher in plum peel. The composition of sugars depended on fruit tissue, ripening stage and the cultivar. Ripening and fruit tissue affected the composition and concentrations of organic acids. TPC of ‘Haganta’ peel increased during ripening but there was no significant time trend for ‘Jojo’ peel and flesh of both cultivars. The composition of phenolics in peel depended on the cultivar, but in flesh on the cultivar and ripening. Ripening resulted in increased total anthocyanins and TAA in peel. TAA_peel was positively correlated with TPC_peel, total anthocyanins_peel, cyanidin 3‐glucoside_peel and peonidin 3‐rutinoside_peel in the cultivar ‘Haganta’. CONCLUSION: The composition of phytochemicals in P. domestica fruit depends on fruit tissue, ripening stage and the cultivar. Peel contributes to the TAA on average 20 times more than flesh. © 2012 Society of Chemical Industry     

Robust and objective decomposition and mapping of bifurcating vessels

Computational modeling of human arteries has been broadly employed to investigate the relationships between geometry, hemodynamics and vascular disease. Recent developments in modeling techniques have made it possible to perform such analyses on realistic geometries acquired noninvasively and, thus, have opened up the possibility to extend the investigation to populations of subjects. However, for this to be feasible, novel methods for the comparison of the data obtained from large numbers of realistic models in the presence of anatomic variability must be developed. In this paper, we present an automatic technique for the objective comparison of distributions of geometric and hemodynamic quantities over the surface of bifurcating vessels. The method is based on centerlines and consists of robustly decomposing the surface into its constituent branches and mapping each branch onto a template parametric plane. The application of the technique to realistic data demonstrates how similar results are obtained over similar geometries, allowing for proper model-to-model comparison. Thanks to the computational and differential geometry criteria adopted, the method does not depend on user-defined parameters or user interaction, it is flexible with respect to the bifurcation geometry and it is readily extendible to more complex configurations of interconnecting vessels.