Switch Region for Pathogenic Structural Change in Conformational Disease and Its Prediction

Many diseases are believed to be related to abnormal protein folding. In the first step of such pathogenic structural changes, misfolding occurs in regions important for the stability of the native structure. This destabilizes the normal protein conformation, while exposing the previously hidden aggregation-prone regions, leading to subsequent errors in the folding pathway. Sites involved in this first stage can be deemed switch regions of the protein, and can represent perfect binding targets for drugs to block the abnormal folding pathway and prevent pathogenic conformational changes. In this study, a prediction algorithm for the switch regions responsible for the start of pathogenic structural changes is introduced. With an accuracy of 94%, this algorithm can successfully find short segments covering sites significant in triggering conformational diseases (CDs) and is the first that can predict switch regions for various CDs. To illustrate its effectiveness in dealing with urgent public health problems, the reason of the increased pathogenicity of H5N1 influenza virus is analyzed; the mechanisms of the pandemic swine-origin 2009 A(H1N1) influenza virus in overcoming species barriers and in infecting large number of potential patients are also suggested. It is shown that the algorithm is a potential tool useful in the study of the pathology of CDs because: (1) it can identify the origin of pathogenic structural conversion with high sensitivity and specificity, and (2) it provides an ideal target for clinical treatment.

Numerical investigation on a transition prediction model

A new transition prediction model is introduced, which couples the intermittency effect into the turbulence transport equations and takes the characteristics of fluid transition into consideration to mimic the exact process of transition. Test cases include a two-dimensional incompressible plate and a two-dimensional NACA0012 airfoil. Performance of this transition model for incompressible flows is studied, with numerical results consistent to experimental data. The requirement of grid resolution for this transition model is also studied.

The evolution of intermediate castration virulence and ant coexistence in a spatially structured environment

Theory suggests that spatial structuring should select for intermediate levels of virulence in parasites, but empirical tests are rare and have never been conducted with castration (sterilizing) parasites. To test this theory in a natural landscape, we co

Configural processing of different topologically structured figures: an ERP Study

According to Chen's theory, topological differences are perceived faster than feature differences in early visual perception. We hypothesized that topological perception is caused by the sensitivity in discriminating figures with and without "holes". An E

Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

Prediction and elucidation of the population dynamics of Microcystis spp. in Lake Dianchi (China) by means of artificial neural networks

Lake Dianchi is a shallow and turbid lake, located in Southwest China. Since 1985, Lake Dianchi has experienced severe cyanabacterial blooms (dominated by Microcystis spp.). In extreme cases, the algal cell densities have exceeded three billion cells per liter. To predict and elucidate the population dynamics ofMicrocystis spp. in Lake Dianchi, a neural network based model was developed. The correlation coefficient (R 2) between the predicted algal concentrations by the model and the observed values was 0.911. Sensitivity analysis was performed to clarify the algal dynamics to the changes of environmental factors. The results of a sensitivity analysis of the neural network model suggested that small increases in pH could cause significantly reduced algal abundance. Further investigations on raw data showed that the response of Microcystis spp. concentration to pH increase was dependent on algal biomass and pH level. When Microcystis spp. population and pH were moderate or low, the response of Microcystis spp. population would be more likely to be positive in Lake Dianchi; contrarily, Microcystis spp. population in Lake Dianchi would be more likely to show negative response to pH increase when Microcystis spp. population and pH were high. The paper concluded that the extremely high concentration of algal population and high pH could explain the distinctive response of Microcystis spp. population to +1 SD (standard deviation) pH increase in Lake Dianchi. And the paper also elucidated the algal dynamics to changes of other environmental factors. One SD increase of water temperature (WT) had strongest positive relationship with Microcystis spp. biomass. Chemical oxygen demand (COD) and total phosphorus (TP) had strong positive effect on Microcystis spp. abundance while total nitrogen (TN), biological oxygen demand in five days (BOD5), and dissolved oxygen had only weak relationship with Microcystis spp. concentration. And transparency (Tr) had moderate positive relationship with Microcystis spp. concentration.

Prediction of the retentions of polybrominated dibenzo-p-dioxins (PBDDs) by using the retentions of polychlorinated dibenzo-p-dioxins (PCDDs)

The retention equations ln k' = A + B/T of 49 polychlorinated dibenzo-p-dioxins (PCDDs) and 4 polybrominated dibenzo-p-dioxins (PBDDs) in gas chromatography (GC) have been investigated to evaluate the properties of regression coefficients A and B. The quantitative relationships between A and B values of PCDDs and those of PBDDs are found. The regression equations derived have correlation coefficients greater than 0.997. The A, B values of any PBDD can be predicted by using the A, B values of the PCDD according to these relationships. Using these predicted A and B values, the retention times of all PBDDs can be predicted at any temperature program. It is very useful to identify the peak position of any PBDD because at present there are only a few standards of PBDDs available. (C) 2000 Elsevier Science Ltd. All rights reserved.

First-principles prediction of the magnetism of 3d transition-metal-doped Rocksalt MgO

Using first-principles band structure methods, we have systematically studied the electronic structures, magnetic stabilities, and half-metal properties of 3d transition-metal (TM) doped Rocksalt MgO compounds TMMg3O4 (TM = V, Cr, Mn, Fe, Co, and Ni). The calculations reveal that only CrMg3O4 has a ferromagnetic stability among the six compounds, which is explained by double-exchange mechanism. The magnetic stability is affected by the doping concentration of TM if the top valance band is composed of partially occupied t(2g) states. In addition, CrMg3O4 is a half-metallic ferromagnet. The origins of half-metallic and ferromagnetic properties are explored. The Curie temperature (T-c) of CrMg3O4 is 182 K. And it is hard for CrMg3O4 to deform due to the large bulk modulus and shear modulus, so it is a promising spintronic material. Our calculations provide the first available information on the magnetic properties of 3d TM-doped MgO.

Prediction and suppression of strong dispersive coupling in microracetrack channel drop filters

For a four-port microracetrack channel drop filter, unexpected transmission characteristics due to strong dispersive coupling are demonstrated by the light tunneling between the input-output waveguides and the resonator, where a large dropping transmission at off-resonance wavelengths is observed by finite-difference time-domain simulation. It causes a severe decline of the extinction ratio and finesse. An appropriate decrease of the coupling strength is found to suppress the dispersive coupling and greately increase the extinction ratio and finesse, a decreased coupling strength can be realized by the application of an asymmetrical coupling waveguide structure. In addition, the profile of the coupling dispersion in the transmission spectra can be predicted based on a coupled mode theory analysis of an equivalent system consisting of two coupling straight waveguides. The effects of structure parameters on the transmission spectra obtained by this method agree well with the numerical results. It is useful to avoid the strong dispersive coupling region in the filter design. (c) 2007 Optical Society of America.

Fabrication of Nano-structured VOx Film by Low Temperature Ion Beam Sputtering and Reductive Annealing

VOx thin films have been fabricated by low temperature ion beam sputtering and post reductive annealing process. Semiconductor-metal phase transition is observed for the film annealed at 400 degrees C for 2 hours. The film also shows a polycrystal structure with grain size from 50nm to 150nm. The VOx thin films fabricated by this process have a TCR up to -2.7% at room temperature. Our results indicate a promising fabrication method of the nano-structured VOx film with relatively high TCR and semiconductor-metal phase transition.

Low Temperature Deposited Nano-structured Vanadium Oxide Thin Films for Uncooled Infrared Detectors

A novel process of room temperature ion beam sputtering deposition of vanadium oxide films and low temperature post annealing for uncooled infrared detectors was proposed in this work. VOx thin films with relatively low square resistance (70 K Omega / square) and large temperature coefficient of resistance (more than 3%/K) at room temperature were fabricated using this low temperature process which was very compatible with the process of uncooled infrared detectors based on micromachined technology. Furthermore, chemical composition and film surface have been characterized using X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM) respectively. The results showed that the main composition of the processed thin films was V2O5 and the thin films were in the process of crystallization.

An Accurate and Fast Behavioral Model for PLL Frequency Synthesizer Phase Noise/Spurs Prediction

This paper presents a behavior model for PLL Frequency Synthesizer. All the noise sources are modeled with noise voltages or currents in time-domain. An accurate VCO noise model is introduced, including both thermal noise and 1/f noise. The behavioral model can be co-simulated with transistor level circuits with fast speed and provides more accurate phase noise and spurs prediction. Comparison shows that simulation results match very well with measurement results.

Comparing the Performance of Biomimetic Pattern Recognition with W8 and SVM on Prediction of Horizontal Gene Transfers in Bacteria Genomes

National Natural Science Foundation of China 60753001

Enhanced photocatalytic activity of TiO2 nano-structured thin film with a silver hierarchical configuration

TiO2 sol-gels with various Ag/TiO2 molar ratios from 0 to 0.9% were used to fabricate silver-modified nano-structured TiO2 thin films using a layer-by-layer dip-coating (LLDC) technique. This technique allows obtaining TiO2 nano-structured thin films with a silver hierarchical configuration. The coating of pure TiO2 sol-gel and Ag-modified sol-gel was marked as T and A, respectively. According to the coating order and the nature of the TiO2 sol-gel, four types of the TiO2 thin films were constructed, and marked as AT (bottom layer was Ag modified, surface layer was pure TiO,), TA (bottom layer was pure TiO,, surface layer was Ag modified), TT (pure TiO, thin film) and AA (TiO, thin film was uniformly Ag modified). These thin films were characterized by means of linear sweep voltammetry (LSV), X-ray diffraction (XRD), scanning electron microscopy (SEM), electrochemical impedance spectroscopy and transient photocurrent (I-ph). LSV confirmed the existence of Ago state in the TiO, thin film. SEM and XRD experiments indicated that the sizes of the TiO,, nanoparticles of the resulting films were in the order of TT > AT > TA > AA, suggesting the gradient Ag distribution in the films. The SEM and XRD results also confirmed that Ag had an inhibition effect on the size growth of anatase nanoparticles. Photocatalytic activities of the resulting thin films were also evaluated in the photocatalytic degradation process of methyl orange. The preliminary results demonstrated the sequence of the photocatalytic activity of the resulting films was AT > TA > AA > TT. This suggested that the silver hierarchical configuration can be used to improve the photocatalytic activity of TiO2 thin film.