In Silico Comparison of Low- and High-Risk Human Papillomavirus Proteins

Human papillomavirus (HPV) is an important pathogen which is classified into two, high- and low-risk groups. The proteins of high-risk and low-risk HPV types have different functions. Therefore, there is a need to develop a computational method for predicting these two groups. In the present study, the physiochemical properties of all early (E1, E2, E4, E5, E6, and E7) and late (L1 and L2) proteins in high- and low-risk HPV types have been studied. The concept of receiver operating characteristic analysis and support vector machines methods has been used for comparison of high- and low-risk HPV types. The results demonstrate that amino acid composition, physiochemical, and secondary structure of E2 protein are significantly different between these two groups. The results demonstrate that in silico properties can create useful information to predict high-risk and low-risk HPV types.     

A new nanoscale and high temperature field effect transistor: Bi level FinFET

In this paper, we propose a new Bi Level Fin Field Effect Transistor (BL-FinFET) where the fin regions consist of Bi level. The novel features of the BL-FinFET are simulated and compared with a Conventional FinFET (C-FinFET). The three-dimensional and two-carrier device simulation demonstrate that the application of Bi level to the FinFET structure results in an ideal threshold voltage roll-off, reduced DIBL, excellent behavior in voltage gain at high temperatures and the gate capacitance improvement when compared with the C-FinFET. Also, this paper illustrates the benefits of the high performance BL-FinFET device over the conventional one and expands the application of Silicon on Insulator Metal Oxide Semiconductor Field Effect Transistors (SOI MOSFETs) to high temperature.     

Differential Pulse Voltammetric Determination of 2‐Methyl‐4,6‐Dinitrophenol using Bismuth Bulk Electrode

This work reports the application of bismuth bulk electrode (BiBE) for the determination of 2‐methyl‐4,6‐dinitrophenol (MDNP) by differential pulse voltammetry (DPV) in Britton‐Robinson buffer of pH 12.0 as an optimal medium. BiBE was prepared by transferring molten bismuth into a glass tube under constant stream of nitrogen. The linear concentration dependences were measured from 1 to 10 μmol ? L^?1 and from 10 to 100 μmol ? L^?1 by using optimum accumulation potential of ?0.7 V and optimum accumulation time 30 s. Under these conditions limit of determination and limit of quantification was 0.45 and 1.5 μmol ? L^?1, respectively. The developed method was successfully applied for the analysis of tap water as a model sample.     

Rheological and transport properties of sulfonated polyacrylamide hydrogels for water shutoff in porous media

In this research, an optimal hydrogel, based on sulfonated polyacrylamide, was synthesized by statistical design of experiments using central composite method. This new hydrogel composed of sulfonated polyacrylamide (AN125VLM) and chromium triacetate as copolymer and crosslinker, respectively. The bottle and rheological tests were conducted to investigate the gelation time, thermal stability, gel strength and also ultimate elastic modulus, complex modulus, and yield stress. It was found that copolymer concentration had the main effect in both rheological and transport properties of hydrogels. The sample prepared at optimum condition, i.e. copolymer concentration of 26,340 ppm and crosslinker/copolymer ratio of 0.12, had an ultimate elastic modulus of 29.9 kPa, yield stress of 800 Pa, and complex modulus of 32 kPa. A coreflooding test through fracture was carried out to examine the optimum gel performance in a porous media. A value of 483 for the residual resistance factor ratio of water to oil confirmed the high ability of the hydrogel in reducing the relative permeability of water to oil in fractured media. Copyright © 2014 John Wiley & Sons, Ltd.     

Monitoring of potential cytotoxic and inhibitory effects of titanium dioxide using on-line and non-invasive cell-based impedance spectroscopy

Titanium dioxide (TiO₂) nanoparticles (NPs) with different sizes and structures were probed for plausible cytotoxicity using electric cell-substrate impedance sensing (ECIS), a non-invasive and on-line procedure for continuous monitoring of cytotoxicity. For insect cells (Spodoptera frugiperda Sf9), the ECIS₅₀ values, i.e., the concentration required to achieve 50% inhibition of the response, differed depending on the size and shape of the TiO₂ nanostructure. The lowest ECIS₅₀ value (158 ppm) was observed for the needle shaped rutile TiO₂ (10 nm × 40 nm, 15.5 nm nominal particle size), followed by 211 ppm for P-25 (34.1 nm, 80% anatase and 20% rutile), 302 ppm for MTI5 (5.9 nm, 99% anatase) and 417 ppm for Hombitan LW-S bulk TiO₂ (169.5 nm, 99% anatase). Exposure of TiO₂ NPs to UV light at 254 nm or 365 nm exhibited no significant effect on the ECIS₅₀ value due to the aggregation of TiO₂ NPs with diminishing photocatalytic activities. Chinese hamster lung fibroblast V79 cells, exhibited no significant cytotoxicity/inhibition up to 400 ppm with P25, MTI₅ and bulk TiO₂. However, a noticeable inhibitory effect was observed (ECIS₅₀ value of 251 ppm) with rutile TiO₂ as cell spreading on the electrode surface was prevented     

Determination of amine and aldehyde surface densities: application to the study of aged plasma treated polyethylene films

The aim of this work was to test and to compare different methods reported in the literature to quantify amine and aldehyde functions on the surface of polyethylene (PE) films treated by ammonia plasma and to specify their stability against time. A low pressure ammonia plasma reactor was used to functionalize PE films with amine groups, which could be subsequently used for further immobilization of biomolecules. In order to determine the density of amine groups on the surface of treated films, various molecule probes and spectrophotometric analytical methods have been investigated. Two methods using (i) sulfosuccinimidyl 6-[3'-(2-pyridyldithio)-propionamido] hexanoate (sulfo-LC-SPDP) and (ii) 2-iminothiolane (ITL) associated with bicinchoninic acid (BCA) have been proved to be reliable and sensitive enough to estimate the surface concentration of primary amine functions. The amount of primary amino groups on the functionalized polyethylene films was found to be between 1.2 and 1.4 molecules/nm2. In a second step, the surface concentration of glutaraldehyde (GA), which is currently used as a spacer arm before immobilization of biomolecules, has been assessed: two methods were used to determine the surface density of available aldehyde functions, after the reaction of GA with the aminated polyethylene film. The concentration of GA was found to be in the same range as primary amine concentration. The influence of aging time on the density of available amino and aldehyde groups on the surfaces were evaluated under different storage conditions. The results showed that 50% of the initial density of primary amine functions remained available after storage during 6 days of the PE samples in PBS (pH 7.6) at 4 degrees C. In the case of aldehyde groups, the same percentage of the initial density (50%) remained active after storage in air at RT over a longer period, i.e., 15 days.     

Path Boxplots: A Method for Characterizing Uncertainty in Path Ensembles on a Graph

Graphs are powerful and versatile data structures that can be used to represent a wide range of different types of information. In this article, we introduce a method to analyze and then visualize an important class of data described over a graph—namely, ensembles of paths. Analysis of such path ensembles is useful in a variety of applications, in diverse fields such as transportation, computer networks, and molecular dynamics. The proposed method generalizes the concept of band depth to an ensemble of paths on a graph, which provides a center-outward ordering on the paths. This ordering is, in turn, used to construct a generalization of the conventional boxplot or whisker plot, called a path boxplot, which applies to paths on a graph. The utility of path boxplot is demonstrated for several examples of path ensembles including paths defined over computer networks and roads. Supplementary materials for this article are available online.     

New Convenient Five‐Component One‐Pot Synthesis of 3‐Alkyl‐6‐amino‐1,4‐dihydro‐4‐{[(1,2,3‐triazol‐4‐yl)methoxy]phenyl}pyrano[2,3‐c]pyrazole‐5‐carbonitrile Derivatives

3‐Alkyl‐6‐amino‐1,4‐dihydro‐4‐{[(1,2,3‐triazol‐4‐yl)methoxy]phenyl}pyrano[2,3‐c]pyrazole‐5‐carbonitrile derivatives were synthesized through a one‐pot five‐component condensation reaction.     

Stability and bifurcations analysis of rotating shafts with base excitations

Base excitation in a rotating machinery such as turbo generators, aircraft engines, etc could occur when these systems are subjected to the base movements. This paper investigates the nonlinear behavior of a symmetrical rotating shaft under base excitation when the system is in the vicinity of the main resonance. Dynamic imbalances and harmonic base excitations are the sources of excitation in this system. The equations of motion are derived using the extended Hamilton principle and are mapped into the complex plane. The complex partial differential equation of motion is transformed to the ordinary one utilizing mode shape of the linear system. The method of multiple scales is used to solve the equation of motion. The steady state solutions and their stability are determined, and the effects of damping coefficient, base excitations, and eccentricities of shaft on the stability and bifurcations of the system are investigated. The numerical integration is performed to validate the perturbation results. It is shown that the achieved results from two over-mentioned methods are in accordance with each other.     

Nano structures of group 13-15 mixed heptamer clusters: a computational study

The structural and thermodynamic characteristics of lowest-energy structures of group 13-15 mixed heptamers in two distinct series [(HM)(k)(HM')(l)(NH)(7)] (M, M' = B, Al, Ga and k + l = 7) and [(HGa)(7)(YH)(m)(Y'H)(n)] (Y,Y' = N, P, As and m + n = 7) have been systematically investigated using the density functional approach. Our main goal is to get knowledge of the preferential bonding patterns of the first three rows of group 13-15 elements for the construction of mixed heptameric clusters. Structural parameters, thermodynamic properties of oligomerization reaction, band gaps, and dipole moments of the 18 lowest-energy structures of the studied heptamers in each series are compared to their corresponding binary parents, that is, [(HM)(7)(NH)(7)] and [(HGa)(7)(YH)(7)]. The stability of different isomer structures is discussed to reveal the competitiveness of group 13 and 15 bonding. Mixed heptamers are predicted to be thermodynamically more stable compared to a mixture of monomers. However, the favorability for the generation of mixed heptamers strongly depends on the nature of inserted metal and nonmetal pairs of group 13-15. Moreover, it is found that among all studied heptamers the smaller band gaps correspond to arsenic containing species which are close to the semiconducting regime, around 4.62-4.98 eV.