Syntactic vs. Semantic Locality: How Good Is a Cheap Approximation?

Extracting a subset of a given OWL ontology that captures all the ontology's knowledge about a specified set of terms is a well-understood task. This task can be based, for instance, on locality-based modules (LBMs). These come in two flavours, syntactic and semantic, and a syntactic LBM is known to contain the corresponding semantic LBM. For syntactic LBMs, polynomial extraction algorithms are known, implemented in the OWL API, and being used. In contrast, extracting semantic LBMs involves reasoning, which is intractable for OWL 2 DL, and these algorithms had not been implemented yet for expressive ontology languages. We present the first implementation of semantic LBMs and report on experiments that compare them with syntactic LBMs extracted from real-life ontologies. Our study reveals whether semantic LBMs are worth the additional extraction effort, compared with syntactic LBMs

Neutrino helicity asymmetries in leptogenesis

It is pointed out that the heavy singlet neutrinos characteristic of leptogenesis develop asymmetries in the abundances of the two helicity states as a result of the same mechanism that generates asymmetries in the standard lepton sector. Neutrinos and standard leptons interchange asymmetries in collisions with each other. It is shown that an appropriate quantum number, B-L', combining baryon, lepton and neutrino asymmetries, is not violated as fast as the standard B-L. This suppresses the washout effects relevant for the derivation of the final baryon asymmetry. One presents detailed calculations for the period of neutrino thermal production in the framework of the singlet seesaw mechanism.Comment: 11 pages, 1 figure, revtex, matches PRD versio

Tibet in World War II

The author explores the causes and manifestations of Tibetan neutrality in World War II, based on reference materials, diplomatic documents and correspondence, program documents, memoirs, journalism. Evidence is given that Tibet, which was an autonomous state (with the status of political autonomy) under the suzerainty of China (according to the Simla Convention of 1914), aspired to independence. Lhasa aimed at the international recognition of the sovereign status of Tibet and its separation from China. It was revealed that the adoption of strict neutrality by Tibet in 1941 was due to the fact that the anti-Chinese abbot of the Taktra monastery Agvan Sungra took the post of regent under the young Dalai Lama. It is noted that the position of strict neutrality of Tibet was contrary to the Simla Convention of 1914, according to which Tibet recognized China’s suzerainty over itself. It is shown that Tibet’s refusal to let US and British Empire military supplies to China through India was a serious help to Japan, since in 1942 the Japanese army captured Burma, and Tibet became the only military supply route for China. It has been proven that Tibetan neutrality significantly limited the possibilities of China, the British Empire and the United States in the war against Japan

Assembling nanostructures from DNA using a composite nanotweezers with a shape memory effect

The article demonstrates a technique for fabricating a structure with the inclusion of suspended DNA threads and manipulating them using composite nanotweezers with shape memory effect. This technique could be suitable for stretching of nanothin DNA-like conductive threads and for measuring their electrical conductivity, including the I-V characteristic directly in the electron microscope chamber, where the nanotweezers provide a two-sided clamping of the DNA tip, giving a stable nanocontact to the DNA bundle. Such contact, as a part of 1D nanostructure, is more reliable during manipulations with nanothreads than traditional measurements when a nanothread is touched by a thin needle, for example, in a scanning tunnel microscope.Comment: To be presented on IEEE 3M-NANO 201

Synthesis of novel poly(dG)-poly(dG)-poly(dC) triplex structure by Klenow exo− fragment of DNA polymerase I

The extension of the G-strand of long (700 bp) poly(dG)-poly(dC) by the Klenow exo− fragment of DNA polymerase I yields a complete triplex structure of the H-DNA type. High-performance liquid chromatography analysis demonstrates that the length of the G-strand is doubled during the polymerase synthesis. Fluorescence resonance energy transfer analysis shows that the 5′ ends of the G- and the C-strands, labeled with fluorescein and TAMRA, respectively, are positioned close to each other in the product of the synthesis. Atomic force microscopy morphology imaging shows that the synthesized structures lack single-stranded fragments and have approximately the same length as the parent 700 bp poly(dG)-poly(dC). CD spectrum of the polymer has a large negative peak at 278 nm, which is characteristic of the poly(dG)-poly(dG)-poly(dC) triplex. The polymer is resistant to DNase and interacts much more weakly with ethidium bromide as compared with the double-stranded DN

Synthesis of novel poly(dG)–poly(dG)–poly(dC) triplex structure by Klenow exo(−) fragment of DNA polymerase I

The extension of the G-strand of long (700 bp) poly(dG)–poly(dC) by the Klenow exo(−) fragment of DNA polymerase I yields a complete triplex structure of the H-DNA type. High-performance liquid chromatography analysis demonstrates that the length of the G-strand is doubled during the polymerase synthesis. Fluorescence resonance energy transfer analysis shows that the 5′ ends of the G- and the C-strands, labeled with fluorescein and TAMRA, respectively, are positioned close to each other in the product of the synthesis. Atomic force microscopy morphology imaging shows that the synthesized structures lack single-stranded fragments and have approximately the same length as the parent 700 bp poly(dG)–poly(dC). CD spectrum of the polymer has a large negative peak at 278 nm, which is characteristic of the poly(dG)–poly(dG)–poly(dC) triplex. The polymer is resistant to DNase and interacts much more weakly with ethidium bromide as compared with the double-stranded DNA

C-A test of DNA force fields

The DNA duplex may be locally strongly bent in complexes with proteins, for example, with polymerases or in a nucleosome. At such bends, the DNA helix is locally in the non-canonical forms A (with a narrow major groove and a large amount of north sugars) or C (with a narrow minor groove and a large share of BII phosphates). To model the formation of such complexes by molecular dynamics methods, the force field is required to reproduce these conformational transitions for a naked DNA. We analyzed the available experimental data on the B-C and B-A transitions under the conditions easily implemented in modeling: in an aqueous NaCl solution. We selected six DNA duplexes which conformations at different salt concentrations are known reliably enough. At low salt concentrations, poly(GC) and poly(A) are in the B-form, classical and slightly shifted to the A-form, respectively. The duplexes ATAT and GGTATACC have a strong and salt concentration dependent bias toward the A-form. The polymers poly(AC) and poly(G) take the C- and A-forms, respectively, at high salt concentrations. The reproduction of the behavior of these oligomers can serve as a test for the balance of interactions between the base stacking and the conformational flexibility of the sugar-phosphate backbone in a DNA force field. We tested the AMBER bsc1 and CHARMM36 force fields and their hybrids, and we failed to reproduce the experiment. In all the force fields, the salt concentration dependence is very weak. The known B-philicity of the AMBER force field proved to result from the B-philicity of its excessively strong base stacking. In the CHARMM force field, the B-form is a result of a fragile balance between the A-philic base stacking (especially for G:C pairs) and the C-philic backbone. Finally, we analyzed some recent simulations of the LacI-, SOX-4-, and Sac7d-DNA complex formation in the framework of the AMBER force field.Comment: 14 pages, 4 figures plus one TOC picture, 5 table

Nanosilver in Biomedicine: Advantages and Restrictions

Nanosilver (in a range 1–100 nm) binds with thyol-, amino- and carboxy-groups of aminoacid residues of proteins and nucleic acids, thus providing inactivation of pathogenic multidrug-resistant microorganisms. Besides antibacterial, antiviral, antifungal and anti-cancer properties Ag-based nanomaterials possess anti-inflammatory, anti-angiogenesis and antiplatelet features. Drug efficacy depends on their stability, toxicity and host immune response. Citrate coated Ag nanoparticles (NPs) remain stable colloid solutions in deionized water but not in the presence of ions due to replacement of Ag+ by electrolyte ions, potential formation of insoluble AgCl, subsequent catalyzed oxidative corrosion of Ag and further dissolution of surface layer of Ag2O. Protein shells protect core of AgNPs from oxidation, dissolution, aggregation and provide specific interactions with ligands. These nanoconjugates can be used for immunoassays and diagnostics but the sensitivity threshold does not exceed 10 pg Cytotoxicity of AgNPs conjugated with proteins is associated with the rate of intracellular Ag+ release, a ‘Trojan horse’ effect, and exceeds one of Ag+ because of endocytosis uptake of NPs but not ions. Relatively toxic nanosilver causes immunosuppression of the majority of cytokines with a few exceptions (IL-1β, G-CSF, MCP-1) whereas AgNO3 additionally activate TNFα and IL8 gene expression

Experimental investigation and modeling through using the solution-diffusion concept of pervaporation dehydration of ethanol and isopropanol by ceramic membranes HybSi

© 2016Results of experimental investigation of pervaporation dehydration of ethanol and isopropanol by HybSi membranes at concentrations of organic component in the feed in the range from ~50 to ~99 wt%, feed temperatures 60, 70 and 80 °C and permeate pressures 5 and 20 mm Hg are presented. The experimental data demonstrate a nonmonotonic dependence of separation factor on water concentration in the feed with maximum value of separation factor reached at water concentration in the feed of several percent for both ethanol dehydration and isopropanol dehydration. Values of both total permeate flux and separation factor for the isopropanol dehydration case are higher than for the ethanol dehydration case. Results of the experimental investigation are compared with similar results of other researchers obtained for pervaporation dehydration of ethanol and isopropanol by membranes coated with a selective layer made of silica-based and zeolite-based materials. Based on the “solution-diffusion” concept, a mathematical model is developed for the pervaporation process, which includes three parameters, two of which are permeability coefficients for pure components and the third parameter defines “active pores fraction”. Use of the model can lead to essential reduction of the number of pervaporation experiments needed for designing a pervaporation pilot plant as well as assist in determining optimum operating conditions of the pervaporation process. Results of calculations carried out with use of the proposed model are compared versus results of experimental investigation of pervaporation dehydration of ethanol and isopropanol by HybSi membranes, pervaporation dehydration of glycerin by HybSi membranes (of other researchers) and pervaporation dehydration of ethanol by NaA zeolite-based membranes (of other researchers). Results of calculations agree reasonably well with all considered experimental data. Additionally, the model allows determining the optimum thickness of the selective layer of HybSi membranes