The investigation of dangerous geological processes resulting in land subsidence while designing the main gas pipeline in South Yakutia

The number of gas main accidents has increased recently due to dangerous geological processes in underdeveloped areas located in difficult geological conditions. The paper analyses land subsidence caused by karst and thermokarst processes in the right of way, reveals the assessment criteria for geological hazards and creates zoning schemes considering the levels of karst and thermorkarst hazards

Single and molecular ion irradiation-induced effects in GaN : experiment and cumulative MD simulations

An investigation of mechanisms of enhancement of irradiation-induced damage formation in GaN under molecular in comparison to monatomic ion bombardment is presented. Ion-implantation-induced effects in wurtzite GaN bombarded with 0.6 keV amu(-1) F, P, PF2, PF4, and Ag ions at room temperature are studied experimentally and by cumulative MD simulation in the correct irradiation conditions. In the low dose regime, damage formation is correlated with a reduction in photoluminescence decay time, whereas in the high dose regime, it is associated with the thickness of the amorphous/disordered layer formed at the sample surface. In all the cases studied, a shift to molecular ion irradiation from bombardment by its monatomic constituents enhances the damage accumulation rate. Implantation of a heavy Ag ion, having approximately the same mass as the PF4 molecule, is less effective in surface damage formation, but leads to noticeably higher damage accumulation in the bulk. The cumulative MD simulations do not reveal any significant difference in the total amount of both point defects and small defect clusters produced by light monatomic and molecular ions. On the other hand, increased production of large defect clusters by molecular PF4 ions is clearly seen in the vicinity of the surface. Ag ions produce almost the same number of small, but more large defect clusters compared to the others. These findings show that the higher probability of formation of large defect clusters is important mechanism of the enhancement of stable damage formation in GaN under molecular, as well as under heavy monatomic ion irradiation.Peer reviewe

Anti-vortex state in cross-like nanomagnets

We report on results of computer micromodelling of anti-vortex states in asymmetrical cross-like ferromagnetic nanostructures and their practical realization. The arrays of cobalt crosses with 1 mkm branches, 100 nm widths of the branches and 40 nm thicknesses were fabricated using e-beam lithography and ion etching. Each branch of the cross was tapered at one end and bulbous at the other. The stable formation of anti-vortex magnetic states in these nanostructures during magnetization reversal was demonstrated experimentally using magnetic force microscopy.Comment: 19 pages, 9 figure

Bidirectional best hit r-window gene clusters

<p>Abstract</p> <p>Background</p> <p><it>Conserved gene clusters </it>are groups of genes that are located close to one another in the genomes of several species. They tend to code for proteins that have a functional interaction. The identification of conserved gene clusters is an important step towards understanding genome evolution and predicting gene function.</p> <p>Results</p> <p>In this paper, we propose a novel pairwise gene cluster model that combines the notion of bidirectional best hits with the <it>r</it>-window model introduced in 2003 by Durand and Sankoff. The bidirectional best hit (BBH) constraint removes the need to specify the minimum number of shared genes in the <it>r</it>-window model and improves the relevance of the results. We design a subquadratic time algorithm to compute the set of BBH <it>r</it>-window gene clusters efficiently.</p> <p>Conclusion</p> <p>We apply our cluster model to the comparative analysis of <it>E. coli </it>K-12 and <it>B. subtilis </it>and perform an extensive comparison between our new model and the gene teams model developed by Bergeron <it>et al</it>. As compared to the gene teams model, our new cluster model has a slightly lower recall but a higher precision at all levels of recall when the results were ranked using statistical tests. An analysis of the most significant BBH <it>r</it>-window gene cluster show that they correspond to known operons.</p

Identification of conserved gene clusters in multiple genomes based on synteny and homology

<p>Abstract</p> <p>Background</p> <p>Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the series of works on <it>gene teams</it> and <it>homology teams.</it></p> <p>Results</p> <p>Our primary contribution is a local sliding-window SYNS (SYNtenic teamS) algorithm that refines an existing family structure into orthologous sub-families by analyzing the neighborhoods around the members of a given family with a locally sliding window. The neighborhood analysis is done by computing conserved gene clusters. We evaluate our algorithm on the existing homologous families from the Genolevures database over five genomes of the Hemyascomycete phylum.</p> <p>Conclusions</p> <p>The result is an efficient algorithm that works on multiple genomes, considers paralogous copies of genes and is able to uncover orthologous clusters even in distant genomes. Resulting orthologous clusters are comparable to those obtained by manual curation.</p

Стратегии лекарственного обеспечения пациентов с хроническим вирусным гепатитом С

The report reviews the options of drug supply for patients with chronic hepatitis C in the Russian Federation and elsewhere. The results of the Moscow regional program aimed at improving the quality of medical care in such patients are discussed. The proposed measures contribute to the reduced mortality rate in patients suffering from infections. The prospects of further improvements in the availability of antiviral medications for patients with chronic viral hepatitis C are outlined. В статье рассмотрены варианты лекарственного обеспечения пациентов с хроническим вирусным гепатитом С за рубежом и в Российской Федерации. Продемонстрирована эффективность работы целевой региональной программы, направленной на повышение качества оказания медицинской помощи жителям города Москвы, страдающим хроническим вирусным гепатитом С, снижение смертности от инфекционных заболеваний. Определен вектор дальнейшего перспективного развития для повышения доступности лекарственного обеспечения противовирусной терапии (ПВТ) для пациентов с хроническим вирусным гепатитом С.

Database resources of the National Center for Biotechnology Information

In addition to maintaining the GenBank(®) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at

Predicting protein linkages in bacteria: Which method is best depends on task

<p>Abstract</p> <p>Background</p> <p>Applications of computational methods for predicting protein functional linkages are increasing. In recent years, several bacteria-specific methods for predicting linkages have been developed. The four major genomic context methods are: Gene cluster, Gene neighbor, Rosetta Stone, and Phylogenetic profiles. These methods have been shown to be powerful tools and this paper provides guidelines for when each method is appropriate by exploring different features of each method and potential improvements offered by their combination. We also review many previous treatments of these prediction methods, use the latest available annotations, and offer a number of new observations.</p> <p>Results</p> <p>Using <it>Escherichia coli </it>K12 and <it>Bacillus subtilis</it>, linkage predictions made by each of these methods were evaluated against three benchmarks: functional categories defined by COG and KEGG, known pathways listed in EcoCyc, and known operons listed in RegulonDB. Each evaluated method had strengths and weaknesses, with no one method dominating all aspects of predictive ability studied. For functional categories, as previous studies have shown, the Rosetta Stone method was individually best at detecting linkages and predicting functions among proteins with shared KEGG categories while the Phylogenetic profile method was best for linkage detection and function prediction among proteins with common COG functions. Differences in performance under COG versus KEGG may be attributable to the presence of paralogs. Better function prediction was observed when using a weighted combination of linkages based on reliability versus using a simple unweighted union of the linkage sets. For pathway reconstruction, 99 complete metabolic pathways in <it>E. coli </it>K12 (out of the 209 known, non-trivial pathways) and 193 pathways with 50% of their proteins were covered by linkages from at least one method. Gene neighbor was most effective individually on pathway reconstruction, with 48 complete pathways reconstructed. For operon prediction, Gene cluster predicted completely 59% of the known operons in <it>E. coli </it>K12 and 88% (333/418)in <it>B. subtilis</it>. Comparing two versions of the <it>E. coli </it>K12 operon database, many of the unannotated predictions in the earlier version were updated to true predictions in the later version. Using only linkages found by both Gene Cluster and Gene Neighbor improved the precision of operon predictions. Additionally, as previous studies have shown, combining features based on intergenic region and protein function improved the specificity of operon prediction.</p> <p>Conclusion</p> <p>A common problem for computational methods is the generation of a large number of false positives that might be caused by an incomplete source of validation. By comparing two versions of a database, we demonstrated the dramatic differences on reported results. We used several benchmarks on which we have shown the comparative effectiveness of each prediction method, as well as provided guidelines as to which method is most appropriate for a given prediction task.</p

Identifying Cognate Binding Pairs among a Large Set of Paralogs: The Case of PE/PPE Proteins of Mycobacterium tuberculosis

We consider the problem of how to detect cognate pairs of proteins that bind when each belongs to a large family of paralogs. To illustrate the problem, we have undertaken a genomewide analysis of interactions of members of the PE and PPE protein families of Mycobacterium tuberculosis. Our computational method uses structural information, operon organization, and protein coevolution to infer the interaction of PE and PPE proteins. Some 289 PE/PPE complexes were predicted out of a possible 5,590 PE/PPE pairs genomewide. Thirty-five of these predicted complexes were also found to have correlated mRNA expression, providing additional evidence for these interactions. We show that our method is applicable to other protein families, by analyzing interactions of the Esx family of proteins. Our resulting set of predictions is a starting point for genomewide experimental interaction screens of the PE and PPE families, and our method may be generally useful for detecting interactions of proteins within families having many paralogs