Piecewise smooth systems near a co-dimension 2 discontinuity manifold: can one say what should happen?

We consider a piecewise smooth system in the neighborhood of a co-dimension 2 discontinuity manifold $\Sigma$. Within the class of Filippov solutions, if $\Sigma$ is attractive, one should expect solution trajectories to slide on $\Sigma$. It is well known, however, that the classical Filippov convexification methodology is ambiguous on $\Sigma$. The situation is further complicated by the possibility that, regardless of how sliding on $\Sigma$ is taking place, during sliding motion a trajectory encounters so-called generic first order exit points, where $\Sigma$ ceases to be attractive. In this work, we attempt to understand what behavior one should expect of a solution trajectory near $\Sigma$ when $\Sigma$ is attractive, what to expect when $\Sigma$ ceases to be attractive (at least, at generic exit points), and finally we also contrast and compare the behavior of some regularizations proposed in the literature. Through analysis and experiments we will confirm some known facts, and provide some important insight: (i) when $\Sigma$ is attractive, a solution trajectory indeed does remain near $\Sigma$, viz. sliding on $\Sigma$ is an appropriate idealization (of course, in general, one cannot predict which sliding vector field should be selected); (ii) when $\Sigma$ loses attractivity (at first order exit conditions), a typical solution trajectory leaves a neighborhood of $\Sigma$; (iii) there is no obvious way to regularize the system so that the regularized trajectory will remain near $\Sigma$ as long as $\Sigma$ is attractive, and so that it will be leaving (a neighborhood of) $\Sigma$ when $\Sigma$ looses attractivity. We reach the above conclusions by considering exclusively the given piecewise smooth system, without superimposing any assumption on what kind of dynamics near $\Sigma$ (or sliding motion on $\Sigma$) should have been taking place.Comment: 19 figure

Apoptosis- and survival-related gene mRNA profile in peripheral blood leukocytes in children with acute EBV infectious mononucleosis

Acute EBV-associated mononucleosis develops mainly in children and in patients with functionally impaired immune system. Consequently, it may result in developing secondary immunodeficiency, neoplasms as well as diverse alterations in cell-mediated immune reaction. Despite extensively examining molecular mechanisms of EBV infection, it is also necessary seek for new molecular and genetic factors underlying pathogenesis of EBV-mediated mononucleosis and EBV-associated malignant cell transformation is necessary, which might be used in clinical practice to monitor clinical score as well as predictive parameters for EBV-associated complications such as immunocompromised conditions and neoplasms. Here, we proposed to use our splicing sensitive DNA microarrays to perform a comprehensive semi-quantitative mRNA expression analysis for major apoptosis- and survival-related signaling components in peripheral blood leukocytes collected from children with acute EBV infectious mononucleosis as well as during recovery period. Using such DNA microchips allowed to assess both total (denoted by Σ) and separate transcript expression resulting from alternative splicing. It was shown that the balance of mRNA levels in acute phase of EBV-infectious mononucleosis was shifted towards upregulated expression of anti-apoptotic factors and components of of NF-κB-linked pro-survival signaling able to profoundly augment apoptosis resistance. Moreover, some EBV-associated changes (BIM/BCL2L11-Σ, PUMA/ BBC3-NM_001127241, BID-Σ, CASP3-Σ, NFKB1-Σ, RELA-Σ) were in agreement with the data published before. In addition, we also found previously unknown changes in level of EBV-associated coding and noncoding transcripts (DCR1/ TNFRSF10C-NM_003841, DR5/TNFRSF10B-NR_027140, CASP6 beta/CASP6-NM_032992, CASP7-NM_033338). Analyzing their properties allowed to suggest that they play an important role in the pathogenesis of EBV-associated mononucleosis. However, at asymptomatic recovery stage, level of some mRNA expression was kept altered compared to healthy volunteers (DCR2/TNFRSF10D-NM_003840, CASP8-Σ, CASP3-Σ, BIM/BCL2L11-Σ, BCL2-NM_000633, MCL1-Σ, BCL-W/BCL2L2-Σ, BCL-XL/BCL2L1-NM_138578, BIRC2-NM_001166, XIAP-NM_001167, TRAF2-NM_021138, MAP3K14-Σ, NFKB1-Σ), which may point at postponed EBV-associated molecular consequences. On one hand, such changes may be due to long-lasting anti-EBV immune response, whereas, on the other hand, they might be influenced by EBV-associated factors facilitating virus persistence. Overall, we identified the molecular features predisposing to chronic course of EBV-infection. The data obtained further expand our understanding about the molecular pathogenetic mechanisms for EBV infectious mononucleosis

Expression analysis of apoptotic and survival genes in blood leukocytes of children with various forms of HHV-6 infection

Despite that human herpes virus type 6 (HHV-6) is extremely spread worldwide, molecular mechanisms of behind HHV-6 infection pathogenesis remain largely unexplored. No molecular markers were found linked to unfavorable course of HHV-6 infection which could allow to ease up selecting proper therapy and preventing development of complications. The aim of the study was to analyze expression of apoptosis and survival-related genes in blood leukocytes from 7–17-year-old children upon various forms of HHV-6 infection. The analysis was carried out by using DNA microarrays developed by us allowing to assess changes in expression level both of individual mRNAs and total gene set (-Σ). It was shown that during the acute phase of HHV-6 infection mRNA level was shifted toward pro-apoptotic factors. In the convalescence phase, most altered mRNA levels returned to normal. We have identified a set of mRNAs and genes whose expression level was significantly changed in acute disease phase. According to available data, these factors play an important role in regulation of studied signaling pathways. In order to search for HHV-6-associated factors, which markedly affect disease pattern of severe herpesvirus mixed infection, we analyzed significant changes of mRNA and genes expression levels in patients with severe HHV-6+EBV+CMV mixed infection and EBV+CMV mixed infection of moderate severity compared with healthy donors. The levels of 5 mRNAs (FAF1-NM_007051, DAPK2-NM_014326, CASP8AP2-NM_001137667, CASP8-NM_033356, BTK-NM_001287345) and 3 genes (FAS-Σ, Puma/BBC3-Σ, ITCH-Σ) were significantly increased in severe mixed infection comorbid with HHV-6 (EBV+CMV+HHV-6) but without HHV-6 (EBV+CMV) compared with healthy donors. Most of detected factors belong to Fas-mediated apoptosis pathway, and may be considered as candidate prognostic development factors of severe herpes virus infection involving HHV-6. This study profoundly extends existing understanding on molecular pathogenesis of HHV-6 infection involving apoptosis and pro-survival signaling pathways. Marked changes of mRNA and gene levels most likely contributed to the pathogenesis of HHV-6 as well as severe HHV-6+EBV+CMV mixed infection

Application of Spectroscopy Methods for Indication and Identification of Pathogenic Biological Agents

The review presents data on application of UV, IR and optical spectroscopy methods for non-specific indication of pathogenic biological agents, and IR Fourier spectroscopy, and Raman spectroscopy - for their identification. Considered are advantages, disadvantages and prospects of different spectroscopy methods application for monitoring of the environment for the presence of pathogenic biological agents

Application of MALDI Mass-Spectrometry for Diagnostics of Particularly Dangerous Infectious Diseases: Current State of Affairs and Prospects

Mass spectrometry is a modern physical-chemical analytical method that provides for qualitative and quantitative assessment of the substance composition. It is based on pre-ionization of the atoms and molecules included into it. One of the advanced methods of ionization, due to which mass-spectrometry investigation of macromolecules has become a frequent practice, is matrix-assisted laser desorption/ionization (MALDI). The essence of it is the pulsed laser irradiation of the matter under study, mixed with the matrix. The review discusses current data on MALDI mass-spectrometry application for the performance of species-specific and genus-specific identification of microorganisms at the premises of diagnostic laboratories. Considered are the basic advantages of MALDI-TOF identification as compared to bacteriologic, immunologic, and molecular-genetic methods of assessment. Allocated is the mass-spectrometry position in the system of laboratory diagnostics of infectious diseases, including particularly dangerous ones, in the territory of the Russian Federation

Non-Specific Indication of Microorganisms in Environmental Samples

The review presents an analysis of modern methods and instruments for performing nonspecific detection of pathogenic biological agents in environmental objects. Discussed are technological characteristics of application of these methods for the detection of biological substances of protein nature in samples. The spectrum of means for non-specific PBA detection includes home-produced and foreign field devices based on protein contamination indication using various colorimetry variants. Technologies for remote and direct monitoring of environment for the presence of aerosols of biological nature are represented by hybrid lidar systems (biolidars) and biodetectors. For PBA nucleic acids tracing, the complexes based on DNA molecule binding with fluorophore with further fluorescence detection are described. Given are the examples of chemiluminescent analysis application in the developed automatic impurity detectors, as well as systems using bioluminescence. Based on the literature data analysis, put forward is a possible algorithm for indication of pathogenic biological agents when carrying out monitoring of the environment in zones of possible emergency situation occurrence and mass events holding

MALDI-TOF Mass-Spectrometry Analysis of Plague Agent Strains

Objective of the study was to demonstrate practicability of data base creation, containing reference mass-spectra of agents of particularly dangerous infections, using MALDI-TOF mass-spectrometry, by the example of plague agent strains. Materials and methods. MALDI-TOF mass-spectrometry was deployed for the obtainment of mass-spectra of ribosomal proteins from the microorganisms under investigation with the help of mass-spectrometers - Microflex LT. Results and conclusions. Carried out was comparative analysis of the obtained mass-spectra of 10 Y. pestis strains and reference spectra of Y. tuberculosis , contained in commercial data base of MALDI Biotyper 3.1 (Bruker Daltonics, Germany). Developed data base was validated in the process of identification of plague microbe strains, isolated in the territory of natural plague foci of the Russian Federation. That data base provided for correct identification of Y. pestis strains up to a species

Methodological basics for differential detection of EBV1/EBV2 and HHV6A/HHV6B

Among a whole variety of EBV- and HHV6-linked diseases only infectious mononucleosis is subject to official statistical reporting in Russia that substantially complicates objective assessment of etiological structure, incidence rate, characteristics of developing epidemic process. Currently, the data on the genetic EBV heterogeneity, even at the level of the main types (EBV1 and EBV2), as well as HHV6A and HHV6B, prevalence and clinical importance are mainly limited to foreign research publications. Few publications assessing this issue are available in Russian scientific papers. At the same time, examining circulation of virus genetic types (variants) and use of such data in implementing epidemiological surveillance after some other infections have been commonly practiced. One of the key issues is the level of developed laboratory support for molecular genetic monitoring. The goal of the study was to improve methodological basics for differential detection of HHV6A/B and the major EBV types. There were used samples of peripheral blood leukocytes collected from children aged 1–15 years with acute (n = 50) and asymptomatic infectious mononucleosis (n = 29). The detection and quantification of EBV and HHV6 DNA was performed by using real-time PCR. For differential determination of EBV1/EBV2 and HHV6A/HHV6B, an optimized one-round PCR with electrophoretic agarose gel detection amplification products was used. The data from our own study showed that frequency of detected EBV and HHV6 DNA in acute infectious mononucleosis patients comprised 74 and 72% compared to control group reaching 35 and 74%, respectively. It was found that among the examined children of Nizhny Novgorod Region, EBV1 and HHV6B prevailed in the viral population that agrees with existing insights about their geographical distribution in the adjacent territories. EBV2 was found in a single sample only in the control group. HHV6A was not detected in any of the groups. The methodological approach optimized in this study allows to separately detect HHV6A/HHV6B and the main EBV types according to a unified laboratory protocol, whereas combining it with additional stage of DNA enrichment increases the diagnostic sensitivity of PCR analysis, minimizes proportion of discordant and false negative results. Such an integrated approach can be applied for diagnostic, epidemiological and research purposes

Novel long-chain neurotoxins from Bungarus candidus distinguish the two binding sites in muscle-type nicotinic acetylcholine receptors

αδ-Bungarotoxins, a novel group of long-chain α-neurotoxins, manifest different affinity to two agonist/competitive antagonist binding sites of muscle-type nicotinic acetylcholine receptors (nAChRs), being more active at the interface of α–δ subunits. Three isoforms (αδ-BgTx-1–3) were identified in Malayan Krait (Bungarus candidus) from Thailand by genomic DNA analysis; two of them (αδ-BgTx-1 and 2) were isolated from its venom. The toxins comprise 73 amino acid residues and 5 disulfide bridges, being homologous to α-bungarotoxin (α-BgTx), a classical blocker of muscle-type and neuronal α7, α8, and α9α10 nAChRs. The toxicity of αδ-BgTx-1 (LD50 = 0.17–0.28 µg/g mouse, i.p. injection) is essentially as high as that of α-BgTx. In the chick biventer cervicis nerve–muscle preparation, αδ-BgTx-1 completely abolished acetylcholine response, but in contrast with the block by α-BgTx, acetylcholine response was fully reversible by washing. αδ-BgTxs, similar to α-BgTx, bind with high affinity to α7 and muscle-type nAChRs. However, the major difference of αδ-BgTxs from α-BgTx and other naturally occurring α-neurotoxins is that αδ-BgTxs discriminate the two binding sites in the Torpedo californica and mouse muscle nAChRs showing up to two orders of magnitude higher affinity for the α–δ site as compared with α–ε or α–γ binding site interfaces. Molecular modeling and analysis of the literature provided possible explanations for these differences in binding mode; one of the probable reasons being the lower content of positively charged residues in αδ-BgTxs. Thus, αδ-BgTxs are new tools for studies on nAChRs