Continuum electrostatic approach for evaluating positions and interactions of proteins in a bilayer membrane

Orientations of proteins in the membranes are crucial to their function and stability. Unfortunately the exact positions of these proteins in the lipid bilayer are mostly undetermined. Here, the spatial orientation of membrane proteins within the lipid membrane was evaluated using a Poisson–Boltzmann solvent continuum approach to calculate the electrostatic free energy of the protein solvation at various orientations in an implicit bilayer. The solvation energy was obtained by computing the difference in electrostatic energies of the protein in water and in lipid/water environments, treating each as an implicit solvent model. The optimal position of transmembrane proteins (TMP) in a lipid bilayer is identified by the minimum in the “downhill” pathway of the solvation energy landscape. The energy landscape pattern was considerably conserved in various TMP classes. Evaluation of the position of 1060 membrane proteins from the orientations of proteins in membranes (OPM) database revealed that most of the polytopic and β-barrel proteins were in good agreement with those of the OPM database. The study provides a useful scheme for estimating the membrane solvation energy made by lipid-exposed amino acids in membrane proteins. In addition, our results tested with the bacterial potassium channel model demonstrated the potential usefulness of the approach in assessing the quality of membrane protein models. The present approach should be applicable for constructing transmembrane proteins–lipid configuration suitable for membrane protein simulations and will have utility for the structural modeling of membrane proteins.     

Molecular interaction networks in the analyses of sequence variation and proteomics data

Protein–protein interaction networks are typically generated in standard cell lines or model organisms as it is prohibitively difficult to record large interaction datasets from specific tissues or disease models at a reasonable pace. Although the interaction data are of high confidence, they thus do not reflect in vivo relationships as such. A wealth of physiologically relevant protein information, obtained under different conditions and from different systems, is available including information on genetic variation, protein levels, and PTMs. However, these data are difficult to assess comprehensively because the relationships between the entities remain elusive from the measurements. Here, we exemplarily highlight recent studies that gained deeper insight from genetic variation, protein, and PTM measurements using interaction information pointing toward the importance and potential of interaction networks for the interpretation of sequencing and proteomics data.     

Signal-adaptive discrete evolutionary transform as a sparse time–frequency representation

Discrete evolutionary transform (DET) has usually been applied to signals in a blind-way without using any parameters to characterize the signal. For this reason, it is not optimal and needs improvement by using some information about the signal. In this paper, we propose an improvement for the discrete evolutionary transform in order to obtain a sparse representation and redefine the generalized time-bandwidth product optimal short-time Fourier transform as a special case of it. In case of linear FM-type signals, the optimized kernel function of the transform is determined according to signal parameters including the instantaneous frequency. The performance of the adaptive-DET is illustrated on three distinct cases. In case of multi-component LFM signals, when the concentration of the proposed distribution is compared to the ordinary sinusoidal-DET, the improvement is computed as 28% in terms of the ratio of norms. Furthermore we define a new and a general class of distribution functions named as the short-time generalized discrete Fourier transform (ST-GDFT) which is a larger set of signal representations including the adaptive-DET.     

Adaptive detection of range-spread targets without secondary data in multichannel autoregressive process

Adaptive detection of range-spread targets without secondary data is addressed in a multichannel autoregressive Gaussian disturbance with unknown space–time covariance matrix, by utilizing the Rao test. The proposed Rao test without secondary data is theoretically proved to be asymptotically (large-sample in the number of temporal observations) constant false alarm rate with respect to unknown space–time covariance matrix, thanks to an asymptotic equivalence between the Rao test and the generalized likelihood ratio test. Moreover, the performance loss due to no secondary data can be remedied by appropriately increasing the temporal dimension. The performance assessment conducted by Monte Carlo simulation, also in comparison with the existing detector without secondary data, confirms the effectiveness of the proposed detectors.     

An impulse control approach to dike height optimization

This paper determines the optimal timing of dike heightenings as well as the corresponding optimal dike heightenings to protect against floods. To derive the optimal policy, we design an algorithm based on the Impulse Control Maximum Principle. In this way, this paper presents one of the first real-life applications of the Impulse Control Maximum Principle developed by Blaquière. We show that the proposed impulse control (IC) approach performs better than dynamic programming with respect to computational time. This is caused by the fact that IC does not need discretization in time.     

Particle filters and occlusion handling for rigid 2D–3D pose tracking

In this paper, we address the problem of 2D–3D pose estimation. Specifically, we propose an approach to jointly track a rigid object in a 2D image sequence and to estimate its pose (position and orientation) in 3D space. We revisit a joint 2D segmentation/3D pose estimation technique, and then extend the framework by incorporating a particle filter to robustly track the object in a challenging environment, and by developing an occlusion detection and handling scheme to continuously track the object in the presence of occlusions. In particular, we focus on partial occlusions that prevent the tracker from extracting an exact region properties of the object, which plays a pivotal role for region-based tracking methods in maintaining the track. To this end, a dynamical choice of how to invoke the objective functional is performed online based on the degree of dependencies between predictions and measurements of the system in accordance with the degree of occlusion and the variation of the object’s pose. This scheme provides the robustness to deal with occlusions of an obstacle with different statistical properties from that of the object of interest. Experimental results demonstrate the practical applicability and robustness of the proposed method in several challenging scenarios.     

An efficient and secure approach for a cloud collaborative editing

The demand for cloud-based collaborative editing service is rising along with the tremendously increased popularity in cloud computing. In the cloud-based collaborative editing environment, the data are stored in the cloud and able to be accessed from everywhere through every compatible device with the Internet. The information is shared with every accredited user in a group. In other words, multiple authorized users of the group are able to work on the same document and edit the document collaboratively and synchronously online. Meanwhile, during the whole collaborative editing process, the encryption technique is eventually applied to protect and secure the data. The encryption for the collaborative editing, however, could require much time to operate. To elevate the efficiency of the encryption, this study first analyzes the text editing in the collaborative service and presents a framework of the Red–Black tree, named as rbTree-Doc. The rbTree-Doc can reduce the amount of data to be encrypted. Although the trade-off for creating the Red–Black tree introduces extra cost, the experimental results of using rbTree-Doc in text editing operations, such as insertion and removal, show improved efficiency compared with other whole-document encryption strategy. Using rbTree-Doc, the efficiency is improved by 31.04% compared to that 3DES encryption is applied and by 23.94% compared to that AES encryption is applied.     

New features of the Mott-Hubbard insulator gap of parent HTS compounds found by resonance Raman scattering and UV-excited ordinary Raman scattering

Optical absorption at the insulating gap in the parent phase of cuprate superconductors shows a broad exciton-like peak near 1.7 eV, followed by a gradual decrease in absorption persisting 1 eV above the gap. By using ultraviolet laser lines to excite Raman spectra, we have found a Raman peak 0.2 eV below the first absorption peak in insulating cuprates. The Raman peak is much narrower than the absorption peak and hasA _2g symmetry. We assign it to an exciton consisting of a hole transition from Cu to a linear combination of Cud _xy and nearest neighbor Op orbitals. We have also studied the resonance Raman profile for two-magnon Raman scattering in the same samples. We find a sharp resonance feature at about 2.7 eV, and little Raman intensity for photon energies at the 1.7 eV absorption peak. The state created at the peak must therefore be an inappropriate intermediate state for the double spin-flip Raman process.