Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns

Nucleosomes are basic units of DNA packing in eukaryotes. Their structure is well conserved from yeast to human and consists of the histone octamer core and 147 bp DNA wrapped around it. Nucleosomes are bound to a majority of the eukaryotic genomic DNA, including its regulatory regions. Hence, they also play a major role in gene regulation. For the latter, their precise positioning on DNA is essential. In the present paper, we describe Galaxy dnpatterntools—software package for nucleosome DNA sequence analysis and mapping. This software will be useful for computational biologists practitioners to conduct more profound studies of gene regulatory mechanisms.     

Enlightening darkness to diffraction limit and beyond: comparison and optimization of different polarizations for dark spot generation

We compare generation of a dark spot using focusing of beams with azimuthal polarizion, radial polarization with a vortex, and a circular polarization with either a first or second order vortex. By optimization of the amplitude-phase pupil, it is ascertained that azimuthal polarization is the most suitable one to obtain the diffraction bounded dark spot per se whose scalar approximation limit has FWHM=0.29λ. Consequently, for dark spot generation, this polarization plays the role of the radial polarization in creation of the diffraction-limited bright spot. Using azimuthal polarization, it is shown that an amplitude-phase filter allows generation of a subdiffractive dark spot in a prescribed finite area.     

Microsatellite Instability in Russian Patients with Colorectal Cancer

The aim of this study was to determine the characteristics of Russian patients with microsatellite instability (MSI) tumors. MSI in the tumor was determined in 514 patients with colon cancer using PCR and subsequent fragment analysis for five markers (NR21, NR24, BAT25, BAT26, and NR27). In the presence of microsatellite instability, the mismatch repair (MMR) system genes were examined using the NGS and MLPA methods to establish the diagnosis of Lynch syndrome. The overall frequency of MSI tumors was 15%: at stage I—19% (9/48), at stage II—21% (44/213), at stage III—16% (26/160), and at stage IV—2% (2/93). Patients with MSI tumors differed in the age of diagnosis, tumor localization, time of cancer recurrence, and stage of the disease. The overall and disease-free survival of patients whose tumors had MSI status was higher than that of patients with microsatellite-stable status, p = 0.04 and p = 0.02, respectively. Analysis of overall and disease-free survival of patients with Lynch syndrome and patients with sporadic colon cancer, but with MSI status, did not reveal significant differences, p = 0.52 and p = 0.24, respectively. The age of patients with Lynch syndrome was significantly younger than that of patients with sporadic colon cancer whose tumors had MSI status (p < 0.001).     

A Preparative Method for the Isolation of Calponin from Molluscan Catch Muscle

We describe the development of a preparative method to isolate molluscan catch muscle, calponin. This method is based on the ability of calponin to interact with actin in a temperature-dependent manner. After extracting thin filaments, as previously described, the extract was ultracentrifuged at 2 °C. While other surface proteins of thin filaments co-precipitated with actin, calponin, along with some minor contaminants, remained in the supernatant. Calponin was purified through cation-exchange chromatography. The yield of pure protein was four-fold higher than that achieved through high-temperature extraction. To evaluate functionally isolated proteins, we determined the effect of calponin on Mg²⁺-ATPase activity of hybrid and non-hybrid actomyosin. The degree of ATPase inhibition was consistent with previously published data but strongly dependent on the environmental conditions and source of actin and myosin used. Furthermore, at low concentrations, calponin could induce the ATPase activity of hybrid actomyosin. This result was consistent with data indicating that calponin can modulate actin conformation to increase the relative content of “switched on” actin monomers in thin filaments. We assume that calponin obtained by the isolation method proposed herein is a fully functional protein that can both inhibit and induce the ATPase activity.     

The quest for a Quantum Neural Network

With the overwhelming success in the field of quantum information in the last decades, the ‘quest’ for a Quantum Neural Network (QNN) model began in order to combine quantum computing with the striking properties of neural computing. This article presents a systematic approach to QNN research, which so far consists of a conglomeration of ideas and proposals. Concentrating on Hopfield-type networks and the task of associative memory, it outlines the challenge of combining the nonlinear, dissipative dynamics of neural computing and the linear, unitary dynamics of quantum computing. It establishes requirements for a meaningful QNN and reviews existing literature against these requirements. It is found that none of the proposals for a potential QNN model fully exploits both the advantages of quantum physics and computing in neural networks. An outlook on possible ways forward is given, emphasizing the idea of Open Quantum Neural Networks based on dissipative quantum computing.     

Microstructure and luminescence properties of the high pressure high temperature sintered AlN–TiN ceramics

Composite ceramics of titanium nitride grains incorporated in an aluminium nitride matrix have been synthesized by high pressure high temperature treatment of a mechanical mixture of AlN–TiN (3 mol % TiN) powders. The microstructure of the samples analysed by means of electron beam microanalysis and Raman spectroscopy shows that the formation of cubic AlN in the composite begins near titanium nitride grains. The areas of mixed chemical composition, which can be assigned to the formation of the solid solutions Al_1?xTi_xN, have been observed at the phase interfaces. The luminescence properties of AlN–TiN ceramics have been considered focusing on the choice of high pressure and high temperature treatment conditions. Three main components at 2.0 eV, 2.4 eV and 3.1 eV are revealed in the cathodoluminescence spectra analysed quantitatively. The observed emission originates from the radiative transitions with participation of valence band states, oxygen-vacancy centres (V_Al–O_N), nitrogen vacancies V_N, and shallow donors which form a complex system of energy levels in the bandgap of the wurtzite-type AlN.     

Parallel time scales and two-dimensional manufacturer and individual customer warranties

We deal with a system whose failures depend on several parallel effects, such as the time in use L and the mileage H. Manufacturer warranties are typically described by a two-dimensional region in the (L, H)-plane. A proper determination of the warranty limits must be based on a two-dimensional distribution of time to failure on this plane. The aim of this paper is to demonstrate the possibility of designing individual warranties for a “nontypical” customer who has a very low or very high usage rate b = H/L, and to show a simple way to calculate warranty limits by minimizing the lifetime coefficient of variation. The latter is carried out by introducing the “best” combined time scale in the form K = (1-ε)L+εH which provides the minimal lifetime coefficient of variation.     

BER Performance of Finite in Time Optimal FTN Signals for the Viterbi Algorithm

In this article, we consider the faster than Nyquist (FTN) technology in aspects of the application of the Viterbi algorithm (VA). Finite in time optimal FTN signals are used to provide a symbol rate higher than the “Nyquist barrier” without any encoding. These signals are obtained as the solutions of the corresponding optimization problem. Optimal signals are characterized by intersymbol interference (ISI). This fact leads to significant bit error rate (BER) performance degradation for “classical” forms of signals. However, ISI can be controlled by the restriction of the optimization problem. So we can use optimal signals in conditions of increased duration and an increased symbol rate without significant energy losses. The additional symbol rate increase leads to the increase of the reception algorithm complexity. We consider the application of VA for optimal FTN signals reception. The application of VA for receiving optimal FTN signals with increased duration provides close to the potential performance of BER, while the symbol rate is twice above the Nyquist limit.     

Optimal traffic control synthesis for an isolated intersection

A continuous dynamical model of a simplified controlled isolated intersection is derived in order to find and analyze an optimal control policy to minimize total delay. An analytical solution of the optimal control problem with constrained signal light control is presented. The optimal synthesis is found for the four principal control constraint cases. Previous results from the 1960s and 70s are discussed.