Shower approach in the simulation of ion scattering from solids

An efficient approach for the simulation of ion scattering from solids is proposed. For every encountered atom, we take multiple samples of its thermal displacements among those which result in scattering with high probability to finally reach the detector. As a result, the detector is illuminated by intensive "showers", where each event of detection must be weighted according to the actual probability of the atom displacement. The computational cost of such simulation is orders of magnitude lower than in the direct approach and a comprehensive analysis of multiple and plural scattering effects becomes possible. We use the new method for two purposes. First, the accuracy of the approximate approaches, developed mainly for ion-beam structural analysis, is verified. Second, the possibility to reproduce a wide class of experimental conditions is used to analyze some basic features of ion-solid collisions: the role of double violent collisions in low-energy ion scattering; the origin of the "surface peak" in scattering from amorphous samples; the low-energy tail in the energy spectra of scattered medium-energy ions due to plural scattering; the degradation of blocking patterns in 2D angular distributions with increasing depth of scattering. As an example of simulation for ions of MeV energies, we verify the time-reversibility for channeling/blocking of 1 MeV protons in a W crystal. The possibilities of analysis that our approach offers may be very useful for various applications in particular for structural analysis with atomic resolution.Comment: 16 pages, 9 figures. Finally published version; large parts reformulated, Fig. 9 and references adde

Stop-words in keyphrase extraction problem

Keyword extraction problem is one of the most significant tasks in information retrieval. High-quality keyword extraction sufficiently influences the progress in the following subtasks of information retrieval: classification and clustering, data mining, knowledge extraction and representation, etc. The research environment has specified a layout for keyphrase extraction. However, some of the possible decisions remain uninvolved in the paradigm. In the paper the authors observe the scope of interdisciplinary methods applicable to automatic stop list feeding. The chosen method belongs to the class of experiential models. The research procedure based on this method allows to improve the quality of keyphrase extraction on the stage of candidate keyphrase building. Several ways to automatic feeding of the stop lists are proposed in the paper as well. One of them is based on provisions of lexical statistics and the results of its application to the discussed task point out the non-gaussian nature of text corpora. The second way based on usage of the Inspec train collection to the feeding of stop lists improves the quality considerably

Determination of EGFR gene somatic mutations in tissues and plasma of patients with non-small cell lung cancer

© 2017, Pleiades Publishing, Ltd. Activating mutations in the EGFR gene influence cell proliferation, angiogenesis, and increases metastatic ability of non-small cell lung cancer (NSCLC) cells; they have a significant impact on the choice of medical therapy of NSCLC. The use of targeted therapy with tyrosine kinase inhibitors requires performance of appropriate genetic tests in NSCLC patients. The aim of this study was to develop a real-time PCRbased diagnostic test-system for rapid and cost-effective analysis of EGFR mutations in paraffin blocks and plasma and to perform comparative estimation of diagnostic characteristics features of real-time wild type blocking PCR and digital PCR. The study included 156 patients with different degrees of lung adenocarcinoma differentiation. A simple and efficient real-time PCR-based method for detection of L858R activating mutation and del19 deletion in the EGFR gene in DNA isolated from paraffin blocks or blood has been developed. The test system for EGFR mutations has been validated using 411 samples of paraffin blocks. The proposed system demonstrated high efficiency for DNA testing from paraffin blocks: a concordance with results of testing by means a Therascreen® EGFR RGQ PCR Kit (Qiagen, Germany) was 100%. Applicability of this test system has been also demonstrated for detection of mutations in plasma

Determination of EGFR gene somatic mutations in tissues and plasma of patients with advanced non-small cell lung cancer

The presence of activating mutations in the EGFR gene influences cell proliferation, angiogenesis, and increases metastatic ability; it has a significant impact on the choice of medical therapy of non-small cell lung cancer (NSCLC). The use of targeted therapy with tyrosine kinase inhibitors requires performance of appropriate genetic tests. The aim of this study was to design a real-time PCR-based diagnostic kit for fast and cheap of EGFR mutations testing in paraffin blocks and plasma, and kit validation using samples from patients with NSCLC, and also comparative estimation of diagnostic features of real-time PCR with wild type blocking and digital PCR for mutation testing in blood plasma. The study included 156 patients with various types of adenocarcinoma differentiation. It was designed a simple and efficient real-time PCR-based method of detecting L858R activating mutation and del19 deletion in the EGFR gene for DNA isolated from paraffin blocks. Kit for EGFR mutations was validated using 411 samples of paraffin blocks. The proposed system showed high efficiency for DNA testing from paraffin blocks: a concordance with results of testing with therascreen® EGFR RGQ PCR Kit ("Qiagen", Germany) was 100%. It has been shown the possibility of using this test system for the detection of mutations in plasma

The ethnic-specific spectrum of germline nucleotide variants in DNA damage response and repair genes in hereditary breast and ovarian cancer patients of Tatar descent

© 2018 Frontiers Media S.A. All Rights Reserved. The Russian population consists of more than 100 ethnic groups, presenting a unique opportunity for the identification of hereditary pathogenic mutations. To gain insight into the landscape of heredity pathogenic variants, we employed targeted next-generation sequencing to analyze the germline mutation load in the DNA damage response and repair genes of hereditary breast and ovary cancer syndrome (HBOCS) patients of Tatar ethnicity, which represents ∼4% of the total Russian population. Several pathogenic mutations were identified in DNA double-strand break repair genes, and the spectrum of these markers in Tatar patients varied from that previously reported for patients of Slavic ancestry. The CDK12 gene encodes cyclin-dependent kinase 12, the key transcriptional regulator of the genes involved in DNA damage response and repair. CDK12 analysis in a cohort of HBOCS patients of Tatar decent identified a c.1047-2A>G nucleotide variant in the CDK12 gene in 8 of the 106 cases (7.6%). The c.1047-2A>G nucleotide variant was identified in 1 of the 93 (1.1%) HBOCS patients with mixed or unknown ethnicity and in 1 of the 238 (0.42%) healthy control patients of mixed ethnicity (Tatars and non-Tatars) (p = 0.0066, OR = 11.18, CI 95% = 1.53-492.95, Tatar and non-Tatar patients vs. healthy controls). In a group of mixed ethnicity patients from Tatarstan, with sporadic breast and/or ovarian cancer, this nucleotide variant was detected in 2 out of 93 (2.2%) cases. In a cohort of participants of Slavic descent from Moscow, comprising of 95 HBOCS patients, 80 patients with sporadic breast and/or ovarian cancer, and 372 healthy controls, this nucleotide variant was absent. Our study demonstrates a strong predisposition for the CDK12 c.1047-2A>G nucleotide variant in HBOCS in patients of Tatar ethnicity and identifies CDK12 as a novel gene involved in HBOCS susceptibility

Anticorrosive effects and antimicrobial properties of alkyldimethyl(hydroxyalkyl)ammonium bromides

Quaternary ammonium compounds containing the hydroxyalkyl moiety in the head group have been synthesized. These compounds exhibit a micelle-forming ability, high anticorrosive activity, and antimicrobial action. The compounds of the formula R(CH3)2N+(CH2CH 2CH2OH)Br- with R = C14H 29-C18H37 are characterized by a protective effect higher than 90-99% at 10 mg/l with respect to hydrogen sulfide corrosion, inhibiting properties against carbon dioxide corrosion (84-98% at 10-25 mg/l), and bactericidal action on sulfate-reducing bacteria (10-50 mg/l). © 2011 Pleiades Publishing, Ltd

A novel MECA3 region in human 3p21.3 harboring putative tumor suppressor genes and oncogenes

Aim of this article is to perform the detailed analysis of 3p (especially 3p21 region) to discover novel potential oncogenes and/or tumor suppressors