Spectroscopic Microwave Dielectric Model of Moist Soils

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PHOG: a database of supergenomes built from proteome complements

BACKGROUND: Orthologs and paralogs are widely used terms in modern comparative genomics. Existing procedures for resolving orthologous/paralogous relationships are often based on manual revision of clusters of orthologous groups and/or lack any rigorous evolutionary base. DESCRIPTION: We developed a completely automated procedure that creates clusters of orthologous groups at each node of the taxonomy tree (PHOGs – Phylogenetic Orthologous Groups). As a result of this procedure, a tree of orthologous groups was obtained. Each cluster is a "supergene" and it is represented by an "ancestral" sequence obtained from the multiple alignment of orthologous and paralogous genes. The procedure has been applied to the taxonomy tree of organisms from all three domains of life. Protein complements from 50 bacterial, archaeal and eukaryotic species were used to create PHOGs at all tree nodes. 51367 PHOGs were obtained at the root node. CONCLUSION: The PHOG database demonstrates that it is possible to automatically process any number of sequenced genomes and to reconstruct orthologous and paralogous relationships between genomes using a rigorous evolutionary approach. This database can become a very useful tool in various areas of comparative genomics

Structural health monitoring of rotating blades on helicopters

The paper discusses the structural health monitoring of rotating blades on helicopters (RBH) based on the application of Modal Analysis. The study discussed in this paper includes the experimental validation of state-of-the-art techniques for the on-line measurement of dynamic signals of helicopter rotating units, optimization of the sensor type for rotating unit measurement, analysis of the practical applicability of modal analysis techniques for condition-based monitoring of rotating structures and estimation of the efficiency of the experimental system for the identification of practical damages of blades. The research was conducted using helicopter blade models operating within an experimental test bench. The capabilities of diagnostic technique application to main rotor gears and bearings are also presented. Conclusions are made about the successful analysis of the operational modal analysis technique applicability for the structural health monitoring of a rotating blade, and its effectiveness for damage identification. Two strategies of the RBH repair – with a continuously condition-based monitoring with the proposed technology and one without such monitoring, were discussed. The Markov chain reliability models for each strategy were analyzed and the reliability improvement factor for the proposed monitoring technology in comparison with a traditional one was evaluated. It is shown that the reliability improvement factor is more effective for the proposed method as compared to the traditional one

Effectiveness of application of modal analysis for the monitoring of stressed or operated structures

This paper presents a brief summary of the research results of the application of experimental and operational modal analysis (EMA and OMA) effectiveness for the assessment of the change in the condition of operating structures by modifying their dynamic characteristics. Special focus is given to the topicality of the operational modal analysis for the definition of the dynamic features of the structures (frequencies, modes and deformation) under near-natural conditions. The research was conducted using two operating laboratory models, when the first one imitated a part of a fuel/gas pipeline and the second – a helicopter blade. The results of finite-element model simulation, identification of natural mode and the influence of the two types of virtual defects on the changes in the dynamic properties are provided. The work describes the results of experimental research of the dynamic behaviour of the pipe model, using the methods of OMA and comparing them with the modelling results. The research results demonstrate how the modification of the condition of the large-scaled models impacts pipe and blade models when the defects of local and global nature are introduced

Transplanckian bremsstrahlung and black hole production

Classical gravitational bremsstrahlung in particle collisions at transplanckian energies is studied in ${\mathcal M}_4\times {\mathcal T}^d$. The radiation efficiency $\epsilon\equiv E_{\rm rad}/E_{\rm initial}$ is computed in terms of the Schwarzschild radius $r_S(\sqrt{s})$, the impact parameter $b$ and the Lorentz factor $\gamma_{\rm cm}$ and found to be $\epsilon=C_d (r_S/b)^{3d+3} \gamma_{\rm cm}^{2d+1}$, larger than previous estimates by many powers of $\gamma_{\rm cm}\gg 1$. The result is reliable for impact parameters in the overlap of $r_S\lambda_C$, with $b_c$ marking (for $d\neq 0$) the loss of the notion of classical trajectories and $\lambda_C\equiv \hbar/mc$ the Compton length of the scattered particles. The condition on $s$ and $m$ for extreme radiation damping and (presumably) no black hole production is also derived.Comment: 4 pages, revtex 4. The discussion section is changed to better clarify the region of validity of our calculation. The physical conclusions and the abstract are modified accordingly. A few more references added. We just added the preprint number CCTP-2010-1

Classical ultra-relativistic scattering in ADD

The classical differential cross-section is calculated for high-energy small-angle gravitational scattering in the factorizable model with toroidal extra dimensions. The three main features of the classical computation are: (a) It involves summation over the infinite Kaluza-Klein towers but, contrary to the Born amplitude, it is finite with no need of an ultraviolet cutoff. (b) It is shown to correspond to the non-perturbative saddle-point approximation of the eikonal amplitude, obtained by the summation of an infinite number of ladder graphs of the quantum theory. (c) In the absence of extra dimensions it reproduces all previously known results.Comment: 12 pages, minor change

Luminescent coordination polymers based on Ca²⁺ and octahedral cluster anions [{M₆Clⁱ₈}Clᵃ₆}²⁻ (M = Mo, W) : synthesis and thermal stability studies

Luminescent coordination polymers (CPs) based of inexpensive stable precursors are attractive materials for applications. Here we report the synthesis and evaluation of the stability and photophysical characteristics of the first examples of phosphorescent CPs based on octahedral molybdenum and tungsten cluster anions. Specifically 1D CP trans-[{Ca(OPPh₃)₄}{{M₆Clⁱ₈}Clᵃ₆}]∞ (M = Mo, W) can be obtained either directly at increased temperature or via intermediate phases [cis-Ca(OPPh₃)₄(H₂O)₂][{M₆Clⁱ₈}Clᵃ₆]∙2CH₃CN that are stable at room-temperature, but convert to the titled CP at temperatures above 100 °C

Cellular internalisation, bioimaging and dark and photodynamic cytotoxicity of silica nanoparticles doped by {Mo₆I₈}⁴⁺ metal clusters

Silica nanoparticles (SNPs) doped by hexanuclear molybdenum cluster complexes [{Mo₆X₈}L₆]n (X = Cl, Br, or I; L = various inorganic or organic ligands) have been recently suggested as materials with a high potential for biomedical applications due to both the outstanding photoluminescent properties and the ability to efficiently generate singlet oxygen upon photoirradiation. However, no studies were undertaken so far to prove this concept. Therefore, here we examined the potential of photoluminescent SNPs doped by {Mo₆I₈}⁴⁺ for such applications as bioimaging and photodynamic therapy using human epidermoid larynx carcinoma (Hep-2) cell line as a model. Our results demonstrated both: (i) significant luminescence from cells with internalised molybdenum cluster doped SNPs combined with the low cytotoxicity of particles in the darkness and (ii) significant cytotoxicity of the particles upon photoirradiation. Thus, this research provides strong experimental evidence for high potential of molybdenum cluster doped materials in such biomedical applications as optical bioimaging, biolabeling and photodynamic therapy

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies

<p>Abstract</p> <p>Background</p> <p>Recent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins, that is, prediction of exact specificity to a ligand or, more broadly, to a binding partner of any kind.</p> <p>Results</p> <p>We present a method, SDPclust, for identification of protein functional subfamilies coupled with prediction of specificity-determining positions (SDPs). SDPclust predicts specificity in a phylogeny-independent stochastic manner, which allows for the correct identification of the specificity for proteins that are separated on a phylogenetic tree, but still bind the same ligand. SDPclust is implemented as a Web-server <url>http://bioinf.fbb.msu.ru/SDPfoxWeb/</url> and a stand-alone Java application available from the website.</p> <p>Conclusions</p> <p>SDPclust performs a simultaneous identification of specificity determinants and specificity groups in a statistically robust and phylogeny-independent manner.</p

RegTransBase—a database of regulatory sequences and interactions in a wide range of prokaryotic genomes

RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several databases describing interactions between regulatory proteins and their binding sites are already being maintained, they either focus mostly on the model organisms Escherichia coli and Bacillus subtilis or are entirely computationally derived. RegTransBase describes a large number of regulatory interactions reported in many organisms and contains the following types of experimental data: the activation or repression of transcription by an identified direct regulator, determining the transcriptional regulatory function of a protein (or RNA) directly binding to DNA (RNA), mapping or prediction of a binding site for a regulatory protein and characterization of regulatory mutations. Currently, RegTransBase content is derived from about 3000 relevant articles describing over 7000 experiments in relation to 128 microbes. It contains data on the regulation of about 7500 genes and evidence for 6500 interactions with 650 regulators. RegTransBase also contains manually created position weight matrices (PWM) that can be used to identify candidate regulatory sites in over 60 species. RegTransBase is available at