Identification and resolution of conflicts during ontological integration using rules

Abstract: Integration of ontologies of information sources and consumers is an important phase in achieving web‐based interoperability. The present work describes an approach for identifying certain semantic conflicts while integrating ontologies of heterogeneous information sources. This paper is focused on the identification of homonymy and synonymy between elements in ontologies. In the present work the concepts of homonymy and synonymy are synonymous to naming conflicts and entity identifier conflicts, respectively, and partial synonymy is synonymous to schema isomorphism conflicts. The concept of the mask of interoperability is introduced for the identification of synonymy. The mask of interoperability is expressed in a declarative way as a set of rules, which can then be used for resolution of conflicts during integration of ontologies. As proof of concept, ontologies are implemented using the XML‐based ontology language Ontology Web Language (OWL), and the rules are implemented using the emerging rule language Semantic Web Rule Language (SWRL). This representation in OWL and SWRL allows the ontology to be executable, flexibly extendable and platform‐independent. The OWL facts and SWRL rules are used by the Jess and Bossam reasoning engine to identify semantic homonymy and synonymy.     

Adsorption–desorption noise in plasmonic chemical/biological sensors for multiple analyte environment

We investigated intrinsic noise in plasmonic sensors caused by adsorption and desorption of gaseous analytes on the sensor surface. We analyzed a general situation when there is a larger number of different analyte species. We applied our model to calculate various analyte mixtures, including some environmental pollutants, toxic and dangerous substances. The spectral density of mean square refractive index fluctuations follows a dependence similar to that of generation-recombination noise in photodetectors, flat at lower frequencies and sharply decreasing at higher. Some of the calculated noise levels are well within the detection range of conventional surface plasmon resonance sensors. An AD noise peak is observed in temperature dependence of mean square refractive index fluctuations, thus sensor operating temperature may be optimized to obtain larger signal to noise ratio. A significant property of AD noise is its rise with the decreasing plasmon sensor area, which means that it will be even more pronounced in modern nanoplasmonic devices. Our consideration is valid both for conventional surface plasmon resonance devices and for general nanoplasmonic devices.     

Oxidation of methane in a wide range of pressures and effect of inert gases

The analysis of methane oxidation in a wide range of pressures (0.05–10 atm) demonstrates that the efficiency of CH₃ radicals recombination is of great importance for high selectivity of C₂ hydrocarbons formation. The relative efficiency of different “colliders” assisting the stabilization of exited C₂H*₆ molecules increases in the series: solid surface> Ar> He. The increase of the overall reaction rate upon increasing pressure of the inert gases in the case of catalysts having a higher surface area and more developed pore structure is likely due to the contribution of the surface-induced chain reaction in the volume of pores.     

CTLA-4 Expression Is a Promising Biomarker of Idiopathic Pulmonary Arterial Hypertension and Allows Differentiation of the Type of Pulmonary Hypertension

Pulmonary arterial hypertension (PAH) is an increasingly frequently diagnosed disease, the molecular mechanisms of which have not been thoroughly investigated. The aim of our study was to investigate subpopulations of lymphocytes to better understand their role in the molecular pathomechanisms of various types of PAH and to find a suitable biomarker that could be useful in the differential diagnosis of PAH. Using flow cytometry, we measured the frequencies of lymphocyte subpopulations CD4+CTLA-4+, CD8+ CTLA-4+ and CD19+ CTLA-4+ in patients with different types of PAH, namely pulmonary arterial hypertension associated with congenital heart disease (CHD-PAH), pulmonary arterial hypertension associated with connective tissue disorders (CTD-PAH), chronic thromboembolic pulmonary hypertension (CTEPH) and idiopathic pulmonary arterial hypertension (iPAH), and in an age- and sex-matched control group in relation to selected clinical parameters. Patients in the iPAH group had the significantly highest percentage of CD4+CTLA-4+ T lymphocytes among all PAH groups, as compared to those in the control group (p < 0.001), patients with CTEPH (p < 0.001), CTD-PAH (p < 0.001) and CHD-PAH (p < 0.01). In iPAH patients, the percentages of CD4+CTLA-4+ T cells correlated strongly positively with the severity of heart failure New York Heart Association (NYHA) Functional Classification (r = 0.7077, p < 0.001). Moreover, the percentage of B CD19+CTLA-4+ cells strongly positively correlated with the concentration of NT-proBNP (r = 0.8498, p < 0.001). We have shown that statistically significantly higher percentages of CD4+CTLA-4+ (p ≤ 0.01) and CD8+ CTLA-4+ (p ≤ 0.001) T cells, measured at the time of iPAH diagnosis, were found in patients who died within 5 years of the diagnosis, which allows us to consider both of the above lymphocyte subpopulations as a negative prognostic/predictive factor in iPAH. CTLA-4 may be a promising biomarker of noninvasive detection of iPAH, but its role in planning the treatment strategy of PAH remains unclear. Further studies on T and B lymphocyte subsets are needed in different types of PAH to ascertain the relationships that exist between them and the disease.     

CHID1 Is a Novel Prognostic Marker of Non-Small Cell Lung Cancer

There is an urgent need for identification of new prognostic markers and therapeutic targets for non-small cell lung cancer (NSCLC). In this study, we evaluated immune cells markers in 100 NSCLC specimens. Immunohistochemical analysis revealed no prognostic value for the markers studied, except CD163 and CD206. At the same time, macrophage markers iNOS and CHID1 were found to be expressed in tumor cells and associated with prognosis. We showed that high iNOS expression is a marker of favorable prognosis for squamous cell lung carcinoma (SCC), and NSCLC in general. Similarly, high CHID1 expression is a marker of good prognosis in adenocarcinoma and in NSCLC in general. Analysis of prognostic significance of a high CHID1/iNOS expression combination showed favorable prognosis with 20 months overall survival of patients from the low CHID1/iNOS expression group. For the first time, we demonstrated that CHID1 can be expressed by NSCLC cells and its high expression is a marker of good prognosis for adenocarcinoma and NSCLC in general. At the same time, high expression of iNOS in tumor cells is a marker of good prognosis in SCC. When used in combination, CHID1 and iNOS show a very good prognostic capacity for NSCLC. We suggest that in the case of lung cancer, tumor-associated macrophages are likely ineffective as a therapeutic target. At the same time, macrophage markers expressed by tumor cells may be considered as targets for anti-tumor therapy or, as in the case of CHID1, as potential anti-tumor agents.     

Pre-Senescence Induction in Hepatoma Cells Favors Hepatitis C Virus Replication and Can Be Used in Exploring Antiviral Potential of Histone Deacetylase Inhibitors

Recent evidence suggests that fibrotic liver injury in patients with chronic hepatitis C correlates with cellular senescence in damaged liver tissue. However, it is still unclear how senescence can affect replication of the hepatitis C virus (HCV). In this work, we report that an inhibitor of cyclin-dependent kinases 4/6, palbociclib, not only induced in hepatoma cells a pre-senescent cellular phenotype, including G1 arrest in the cell cycle, but also accelerated viral replicon multiplication. Importantly, suppression of HCV replication by direct acting antivirals (DAAs) was barely affected by pre-senescence induction, and vice versa, the antiviral activities of host-targeting agents (HTAs), such as inhibitors of human histone deacetylases (HDACi), produced a wide range of reactions—from a dramatic reduction to a noticeable increase. It is very likely that under conditions of the G1 arrest in the cell cycle, HDACi exhibit their actual antiviral potency, since their inherent anticancer activity that complicates the interpretation of test results is minimized.     

Difluoromethylornithine (DFMO), an Inhibitor of Polyamine Biosynthesis,and Antioxidant N-Acetylcysteine Potentiate Immune Response in Mice to the Recombinant Hepatitis C Virus NS5B Protein

Hepatitis C virus (HCV) is one of the main triggers of chronic liver disease. Despite tremendous progress in the HCV field, there is still no vaccine against this virus. Potential vaccines can be based on its recombinant proteins. To increase the humoral and, especially, cellular immune response to them, more effective adjuvants are needed. Here, we evaluated a panel of compounds as potential adjuvants using the HCV NS5B protein as an immunogen. These compounds included inhibitors of polyamine biosynthesis and urea cycle, the mTOR pathway, antioxidants, and cellular receptors. A pronounced stimulation of cell proliferation and interferon-γ (IFN-γ) secretion in response to concanavalin A was shown for antioxidant N-acetylcysteine (NAC), polyamine biosynthesis inhibitor 2-difluoromethylornithine (DFMO), and TLR9 agonist CpG ODN 1826 (CpG). Their usage during the immunization of mice with the recombinant NS5B protein significantly increased antibody titers, enhanced lymphocyte proliferation and IFN-γ production. NAC and CpG decreased relative Treg numbers; CpG increased the number of myeloid-derived suppressor cells (MDSCs), whereas neither NAC nor DFMO affected MDSC counts. NAC and DFMO suppressed NO and interleukin 10 (IL-10) production by splenocytes, while DFMO increased the levels of IL-12. This is the first evidence of immunomodulatory activity of NAC and DFMO during prophylactic immunization against infectious diseases.     

Monitoring the curing processes of epoxy oligomers with partially substituted polyethoxymetallosiloxanes by IR spectroscopy and thermomechanical analysis

In this work, the curing of «ED-20» epoxy resin with partially siloxy-substituted aluminum, iron, and zirconium siloxanes that we obtained previously was studied. The initial content of a metallosiloxane in the compositions was 5–50 wt% with respect to the resin. In all the cases, thermal curing was used to obtain a series of samples in the form of solid homogeneous materials. The fact of the epoxy ring opening in the resin was confirmed by IR spectroscopy. The catalytic properties of the metal atom in a metallosiloxane were found to affect the curing process. The samples demonstrate rather a high resistance to thermooxidative destruction, and in most cases, their glass transition temperatures are lower than those obtained upon standard curing of «ED-20» resin with triethylenetetramine. Partially siloxy-substituted metalloalkoxysiloxanes can be efficient agents for curing and formation of a hybrid material based on epoxy resins.     

Large-scale parallel arrays of silicon nanowires via block copolymer directed self-assembly

Extending the resolution and spatial proximity of lithographic patterning below critical dimensions of 20 nm remains a key challenge with very-large-scale integration, especially if the persistent scaling of silicon electronic devices is sustained. One approach, which relies upon the directed self-assembly of block copolymers by chemical-epitaxy, is capable of achieving high density 1?:?1 patterning with critical dimensions approaching 5 nm. Herein, we outline an integration-favourable strategy for fabricating high areal density arrays of aligned silicon nanowires by directed self-assembly of a PS-b-PMMA block copolymer nanopatterns with a L(0) (pitch) of 42 nm, on chemically pre-patterned surfaces. Parallel arrays (5 × 10(6) wires per cm) of uni-directional and isolated silicon nanowires on insulator substrates with critical dimension ranging from 15 to 19 nm were fabricated by using precision plasma etch processes; with each stage monitored by electron microscopy. This step-by-step approach provides detailed information on interfacial oxide formation at the device silicon layer, the polystyrene profile during plasma etching, final critical dimension uniformity and line edge roughness variation nanowire during processing. The resulting silicon-nanowire array devices exhibit Schottky-type behaviour and a clear field-effect. The measured values for resistivity and specific contact resistance were ((2.6 ± 1.2) × 10(5)Ωcm) and ((240 ± 80) Ωcm(2)) respectively. These values are typical for intrinsic (un-doped) silicon when contacted by high work function metal albeit counterintuitive as the resistivity of the starting wafer (～10 Ωcm) is 4 orders of magnitude lower. In essence, the nanowires are so small and consist of so few atoms, that statistically, at the original doping level each nanowire contains less than a single dopant atom and consequently exhibits the electrical behaviour of the un-doped host material. Moreover this indicates that the processing successfully avoided unintentional doping. Therefore our approach permits tuning of the device steps to contact the nanowires functionality through careful selection of the initial bulk starting material and/or by means of post processing steps e.g. thermal annealing of metal contacts to produce high performance devices. We envision that such a controllable process, combined with the precision patterning of the aligned block copolymer nanopatterns, could prolong the scaling of nanoelectronics and potentially enable the fabrication of dense, parallel arrays of multi-gate field effect transistors.     

Influence of residual solvent on physical and chemical properties of amorphous glassy polymer films

One of the most important areas of current research is the study of the influence of the prehistory of samples of amorphous glassy polymers on their physical and chemical properties. The study of structural changes by high temperature IR spectroscopy compared with of quantum chemical calculations allows for an understanding of the mechanism and nature of such processes. The changes in the structure of the polymer chain depending on the type of solvent used in the formation of the films are demonstrated using the examples of several different classes of polymers. In turn, the impact of such changes in the structure on the physical and chemical properties of the polymer films is demonstrated. © 2013 Society of Chemical Industry