Using Ideas of Kolmogorov Complexity for Studying Biological Texts

Kolmogorov complexity furnishes many useful tools for studying different natural processes that can be expressed using sequences of symbols from a finite alphabet (texts), such as genetic texts, literary and music texts, animal communications, etc. Although Kolmogorov complexity is not algorithmically computable, in a certain sense it can be estimated by means of data compressors. Here we suggest a method of analysis of sequences based on ideas of Kolmogorov complexity and mathematical statistics, and apply this method to biological (ethological) ??texts.?? A distinction of the suggested method from other approaches to the analysis of sequential data by means of Kolmogorov complexity is that it belongs to the framework of mathematical statistics, more specifically, that of hypothesis testing. This makes it a promising candidate for being included in the toolbox of standard biological methods of analysis of different natural texts, from DNA sequences to animal behavioural patterns (ethological ??texts??). Two examples of analysis of ethological texts are considered in this paper. Theses examples show that the proposed method is a useful tool for distinguishing between stereotyped and flexible behaviours, which is important for behavioural and evolutionary studies.     

Trifluoromethylation of [60]- and [70]Fullerene in the Ionization Chamber of a Mass Spectrometer

Abstract

Both [60]- and [70]fullerene react with either the Scherer radical (perfluorodiisopropylethylmethyl, C₉F₁₉), a mixture of branched perfluorononenes (C₉F₁₈, the product of hexafluoropropene trimerization), or β-fluorosulphatotetrafluoroethyldiheptafluoroisopropylmethyl radical (C₉F₁₈OSO₂F) in the ionization chamber of a mass spectrometer to give the positive parent ions of trifluoromethylation products, the reaction being accompanied by hydrogen addition. The reaction occurs at least partly on the walls of the ionization chamber, by a radical mechanism employing CF₃ radicals formed from the radical reactants both thermally and under electron impact; only the latter route occurs with the perfluorononenes.     

An updated version of BoltzWann: A code for the evaluation of thermoelectric and electronic transport properties with a maximally-localized Wannier functions basis

BoltzWann is a code to evaluate thermoelectric and electronic transport properties of extended systems with a maximally-localized Wannier function basis set. The semiclassical Boltzmann transport equations for the homogeneous infinite system are solved in the constant relaxation-time approximation and band energies and band derivatives are obtained via Wannier interpolations. Thanks to the exponential localization of the Wannier functions obtained, very high accuracy in the Brillouin zone integrals can be achieved with very moderate computational costs. Moreover, the analytical expression for the band derivatives in the Wannier basis resolves any issues that may occur when evaluating derivatives near band crossings. We present here an updated version of the BoltzWann code, which is now fully integrated within Wannier90 version 2.0, with minor bug fixes and the possibility to study also two-dimensional systems.     

Focusing of Novosibirsk Free Electron Laser (NovoFEL) radiation into paraxial segment

Abstract

We demonstrate results of studies of a silicon binary diffractive optical element (DOE) focusing a terahertz laser Gaussian beam into a paraxial segment. The characteristics of the DOE were examined on a Novosibirsk Free Electron Laser beam of 141-μm wavelength.     

Guidelines and recommendations for indoor use of fuel cells and hydrogen systems

Hydrogen energy applications often require that systems are used indoors (e.g., industrial trucks for materials handling in a warehouse facility, fuel cells located in a room, or hydrogen stored and distributed from a gas cabinet). It may also be necessary or desirable to locate some hydrogen system components/equipment inside indoor or outdoor enclosures for security or safety reasons, to isolate them from the end-user and the public, or from weather conditions.Using of hydrogen in confined environments requires detailed assessments of hazards and associated risks, including potential risk prevention and mitigation features. The release of hydrogen can potentially lead to the accumulation of hydrogen and the formation of a flammable hydrogen-air mixture, or can result in jet-fires. Within Hyindoor European Project, carried out for the EU Fuel Cells and Hydrogen Joint Undertaking safety design guidelines and engineering tools have been developed to prevent and mitigate hazardous consequences of hydrogen release in confined environments. Three main areas are considered: Hydrogen release conditions and accumulation, vented deflagrations, jet fires and including under-ventilated flame regimes (e.g., extinguishment or oscillating flames and steady burns). Potential RCS recommendations are also identified.     

Model reference adaptive control of state delayed system with actuator failures

This paper develops adaptive state feedback control schemes for a class of linear systems with state delay in the presence of unknown actuator failures. The main contributions of this paper are the development of two controller parametrizations which attempt to anticipate the future states, the introduction of an appropriate Lyapunov–Krasovskii type functional to design the new class of adaptation algorithms, and a stability proof.     

Cell-Based Optimization of Covalent Reversible Ketoamide Inhibitors Bridging the Unprimed to the Primed Site of the Proteasome β5 Subunit

The ubiquitin-proteasome system (UPS) is an established therapeutic target for approved drugs to treat selected hematologic malignancies. While drug discovery targeting the UPS focuses on irreversibly binding epoxyketones and slowly-reversibly binding boronates, optimization of novel covalent-reversibly binding warheads remains largely unattended. We previously reported α-ketoamides to be a promising reversible lead motif, yet the cytotoxic activity required further optimization. This work focuses on the lead optimization of phenoxy-substituted α-ketoamides combining the structure-activity relationships from the primed and the non-primed site of the proteasome β5 subunit. Our optimization strategy is accompanied by molecular modeling, suggesting occupation of P1′ by a 3-phenoxy group to increase β5 inhibition and cytotoxic activity in leukemia cell lines. Key compounds were further profiled for time-dependent inhibition of cellular substrate conversion. Furthermore, the α-ketoamide lead structure 27 does not affect escape response behavior in Danio rerio embryos, in contrast to bortezomib, which suggests increased target specificity.     

A Comprehensive Review of Genetically Engineered Mouse Models for Prader-Willi Syndrome Research

Prader-Willi syndrome (PWS) is a neurogenetic multifactorial disorder caused by the deletion or inactivation of paternally imprinted genes on human chromosome 15q11-q13. The affected homologous locus is on mouse chromosome 7C. The positional conservation and organization of genes including the imprinting pattern between mice and men implies similar physiological functions of this locus. Therefore, considerable efforts to recreate the pathogenesis of PWS have been accomplished in mouse models. We provide a summary of different mouse models that were generated for the analysis of PWS and discuss their impact on our current understanding of corresponding genes, their putative functions and the pathogenesis of PWS. Murine models of PWS unveiled the contribution of each affected gene to this multi-facetted disease, and also enabled the establishment of the minimal critical genomic region (PWScr) responsible for core symptoms, highlighting the importance of non-protein coding genes in the PWS locus. Although the underlying disease-causing mechanisms of PWS remain widely unresolved and existing mouse models do not fully capture the entire spectrum of the human PWS disorder, continuous improvements of genetically engineered mouse models have proven to be very powerful and valuable tools in PWS research.