Typology of Regions and Cities of Russia by Causes of Death

U Rusiji je evidentan problem visoke stope smrtnosti u usporedbi sa zemljama sa sličnim životnim standardom. To se posebno uočava na regionalnoj razini gdje su razlike u smrtnosti i strukturi smrtnosti ogromne. Regije Rusije nalaze se u različitim fazama epidemiološke tranzicije. To se izražava u razlikama u njihovoj stopi smrtnosti i razlikama u strukturi uzroka smrti. Regije i najveći gradovi zemlje ponekad se radikalno razilaze, što uvelike komplicira istraživanje. Ovaj rad predstavlja tipologiju regija i velikih gradova Ruske Federacije prema glavnim klasama uzroka smrti u 2015. godini i njihove kartografske prikaze. Prostorne se značajke smrtnosti prema glavnim uzrocima smrti određuju odvojeno za muškarce i žene. Procjena je izvršena klasifikacijom prema demografskim pokazateljima (uzroci smrtnosti: neke zarazne i parazitske bolesti; tumori; bolesti krvožilnog sustava; bolesti dišnog sustava; bolesti probavnog sustava; vanjski uzroci smrti). Skup podataka obuhvaćao je 250 teritorijalnih jedinica: 85 regija (uključujući gradove od saveznog značaja) i 165 velikih gradova s populacijom većom o 100 000. Na temelju primarne statistike izračunane su standardizirane stope smrtnosti. Klasifikacija je provedena prema algoritmu koji je razvio jedan od autora. Prikazana nam klasifikacija omogućuje isticanje specifičnih karakteristika pojedinih skupina regija i analizu s većim stupnjem točnosti.The problem of the high mortality rate, in comparison with countries with similar living standards, is extremely urgent in Russia. It is especially noticeable at the regional level, where differences in mortality and its structure are enormous. The regions of Russia are at different stages of epidemiological transition. This is expressed in differences in their mortality rates and differences in the structure of causes of death. The regions and largest cities of the country are sometimes diverge radically, which greatly complicates research. This paper presents a typology of regions and large cities of the Russian Federation according to the main classes of causes of death in 2015 and its cartography. The spatial features of mortality according to the main causes of death are determined separately for men and women. The assessment was carried out using classification by demographic indicators (causes of mortality: some infectious and parasitic diseases; tumours; diseases of the circulatory system; respiratory diseases; diseases of the digestive system; external causes of death). The dataset included 250 territorial units: 85 regions (including cities of federal significance) and 165 large cities with populations of over 100,000. Based on the primary statistics, standardised mortality rates were calculated. The classification was carried out according to an algorithm developed by one of the authors. The classification presented allows us to highlight the specific characteristics of individual groups of regions and analyse them with a greater degree of accuracy

Epizootic Situation on Anaplasmosis of Small Ruminants in the Irkutsk Region

Anaplasmosis of ruminants is a group of natural focal infections caused by bacteria from the genus Anaplasma of the Anaplasmataceae family. The main etiological agent of anaplasmosis in sheep, goats, and wild ruminants is Anaplasma ovis, which parasitizes in the erythrocytes of these animals. The purpose of this study was the finding and identification of Anaplasma spp. in the blood of small ruminants using genetic methods and obtaining data on the distribution of anaplasmosis in the Irkutsk region. 20 goat blood samples, 611 sheep blood samples and 209 Dermacentor nuttalli ticks from 12 districts of the Irkutsk region were examined for the presence of Anaplasma spp. Only one type of anaplasma, A. ovis, was found among the genotyped samples. A. ovis was found in the blood of sheep and goats in all of the studied districts of the Irkutsk region. The proportion of sheep blood samples containing anaplasma DNA varied from 30 % to 85 %, in goats – from 10 % to 100 % in different districts, and averaged 57.8 % in sheep and 55,0 % in goats. Frequency of infection of D. nuttalli ticks with A. ovis was 5.7 %. The nucleotide sequences of the samples detected in the blood of small ruminants on the territory of the Irkutsk region differed from each other by a single nucleotide substitution and were identical to the sequences of the type strain Haibei, as well as the sequences of A. ovis previously found in the blood of sheep from Mongolia, deer from China, and Dermacentor niveus and Dermacentor nuttalli ticks from China. These sequences were also identical to the sequences previously found in the blood of sheep from Altai and in Dermacentor nuttalli ticks from Tuva, which indicates the wide distribution of these A. ovis genovariants in Siberia and the probable role of D. nuttalli as a carrier of the agent of anaplasmosis of small ruminants in the Irkutsk region

Genetic heterogeneity of <i>Rickettsia helvetica</i> population

Background. To date, the genetic variability of Rickettsia helvetica has not been sufficiently studied.The aim. To study the prevalence and genetic variability of R. helvetica in Ixodes spp. collected in Western Siberia and the Russian Far East.Materials and methods. Ixodes  spp. collected from rodents in the Omsk province, Western Siberia (n = 280) and collected by flagging on Putyatin and Russky Islands in Primorsky Krai, Russian Far East (n = 482) were analyzed for the presence of Rickettsia spp. All positive samples were genotyped for the gltA gene fragment. For a number of R. helvetica samples, fragments of the 16S rRNA, ompA, ompB, sca4, htrA, and groEL genes and 23S–5S intergenic spacer were additionally sequenced.Results. Four Rickettsia species (R. helvetica, “Candidatus Rickettsia tarasevichiae”, “Candidatus Rickettsia uralica”, and “Candidatus Rickettsia mendelii”) were found. Of them, R. helvetica was identified in 72.2 % of Ixodes apronophorus and 18.8 % of  Ixodes trianguliceps from the Omsk province and in single Ixodes persulcatus from the Omsk province and Putyatin Island. This is the first finding of Rickettsia spp. in I. apronophorus. All known R. helvetica sequences from this study and the GenBank database belonged to four well supported monopheletic groups forming genetic lineages I–IV. Lineage I included European isolates from Ixodes ricinus, Western Siberian isolates from I. persulcatus, and some sequences from I. apronophorus. All R. helvetica sequences from I. trianguliceps from the Omsk province and I. persulcatus from  the  Komi Republic and one sequence from I.  apronophorus were assigned to  lineage  II. Most sequences from I.  apronophorus formed lineage  III; all known R. helvetica sequences from I. persulcatus from the Far East formed genetic lineage IV.Conclusion. The genetic heterogeneity of R. helvetica population was first demonstrated. Known isolates of R. helvetica are reliably assigned to four genetic lineages, but not in all cases the association of different lineages with a specific tick species or specific territory was observed

Detection of Babesia and Anaplasmataceae bacteria in small mammals from Irkutsk and Novosibirsk regions

Tissue samples from 228 small mammals captured from 2013 to 2015 in four districts of Irkutsk region and in one district of Novosibirsk region were examined for the presence of Anaplasmataceae bacteria and Babesia parasites by nested PCR method with subsequent sequencing of positive samples. In Ekhirit-Bulagatskiy District of Irkutsk region, Babesia microti DNA was found in 10.9 % of small mammals, Anaplasma phagocytophilum DNA - in 7.3 %, and Ehrlichia muris DNA - in 1.8 %. Infected mammals were not found in the other three examined districts of Irkutsk region. In Novosibirsk region, B. microti DNA was found in 8.9 % of small rodents, A. phagocytophilum DNA - in 8.9 % of small mammals, and Candidatus Neoehrlichia mikurensis DNA - in 8.9 % of small mammals. The identified infection agents corresponded to microorganism species and genetic variants previously found in Ixodes persulcatus ticks but not in ticks of other species

Highly sensitive feature detection for high resolution LC/MS

<p>Abstract</p> <p>Background</p> <p>Liquid chromatography coupled to mass spectrometry (LC/MS) is an important analytical technology for e.g. metabolomics experiments. Determining the boundaries, centres and intensities of the two-dimensional signals in the LC/MS raw data is called feature detection. For the subsequent analysis of complex samples such as plant extracts, which may contain hundreds of compounds, corresponding to thousands of features – a reliable feature detection is mandatory.</p> <p>Results</p> <p>We developed a new feature detection algorithm <it>centWave </it>for high-resolution LC/MS data sets, which collects regions of interest (partial mass traces) in the raw-data, and applies continuous wavelet transformation and optionally Gauss-fitting in the chromatographic domain. We evaluated our feature detection algorithm on dilution series and mixtures of seed and leaf extracts, and estimated recall, precision and F-score of seed and leaf specific features in two experiments of different complexity.</p> <p>Conclusion</p> <p>The new feature detection algorithm meets the requirements of current metabolomics experiments. <it>centWave </it>can detect close-by and partially overlapping features and has the highest overall recall and precision values compared to the other algorithms, <it>matchedFilter </it>(the original algorithm of <it>XCMS</it>) and the centroidPicker from <it>MZmine</it>. The <it>centWave </it>algorithm was integrated into the Bioconductor R-package <it>XCMS </it>and is available from <url>http://www.bioconductor.org/</url></p

Genetic and biochemical characterization of staphylococci occurring in Novosibirsk, Russia

Staphylococci are capable of penetrating many human tissues and organs, causing superficial and deep purulent infections, respiratory and urinary tract infections, food poisoning and intoxication. Last years, coagulase­negative staphylococci were the cause of infection in many cases. Infectious agents, namely Staphylococcus epidermidis, Staphylococcus haemolyticus, and Staphylococcus hominis, were detected more often as nosocomial infections. A particular danger of these infections is a high virulence and  pathogenicity of bacterial strains and their resistance to various anti ­ biotics. Methicillin­resistant staphylococci are especially difficult to treat. The correct identification of staphylococci and their sensitivity to antibiotics are important for clinical diagnosis and appointment of adequate drug therapy. Rapid and accurate identification of Staphylococcus species and detection of their sensitivity to antibiotics is quite important. The aim of this study was to study staphylococci isolated in Novosibirsk from human, animal and environmental samples. A collection of 100 staphylococcus strains was analyzed. Staphylococcus species were identified by sequencing the 16S rRNA gene. Eleven staphylococcus species were identified. Among the strains obtained from hospitalized patients, Staphylococcus aure us dominated (79.1 %), Staphylococcus  epidermidis amounted to about 12.5 %. However, S. aureus and S. epi dermidis strains were isolated in an approximately equal proportion from community­associated samples. Identification of coagulase positive strains was performed using a standard biochemical method and by real­time PCR of the coa gene. 100 % coincidence between the presence of the gene and coagulase activity for S. aureus strains was recorded, which suggests that detection of the coa gene can be used as a correct method for S. aure us identification. A high coincidence rate (99 %) was reveal ed between the phenotypic resistance to oxacillin and the presence of the staphylococcal mecA gene. The study of staphylococci for the presence of the mecA gene can be considered as an alternative to the phenotypical method for identification of methicillin­resistant strains of staphylococci

Identification of metabolic pathways influenced by the G-protein coupled receptors GprB and GprD in Aspergillus nidulans

Heterotrimeric G-protein-mediated signaling pathways play a pivotal role in transmembrane signaling in eukaryotes. Our main aim was to identify signaling pathways regulated by A. nidulans GprB and GprD G-protein coupled receptors (GPCRs). When these two null mutant strains were compared to the wild-type strain, the DeltagprB mutant showed an increased protein kinase A (PKA) activity while growing in glucose 1% and during starvation. In contrast, the DeltagprD has a much lower PKA activity upon starvation. Transcriptomics and (1)H NMR-based metabolomics were performed on two single null mutants grown on glucose. We noted modulation in the expression of 11 secondary metabolism gene clusters when the DeltagprB and DeltagprD mutant strains were grown in 1% glucose. Several members of the sterigmatocystin-aflatoxin gene cluster presented down-regulation in both mutant strains. The genes of the NR-PKS monodictyphenone biosynthesis cluster had overall increased mRNA accumulation in DeltagprB, while in the DeltagprD mutant strain the genes had decreased mRNA accumulation. Principal component analysis of the metabolomic data demonstrated that there was a significant metabolite shift in the DeltagprD strain. The (1)H NMR analysis revealed significant expression of essential amino acids with elevated levels in the DeltagprD strain, compared to the wild-type and DeltagprB strains. With the results, we demonstrated the differential expression of a variety of genes related mainly to secondary metabolism, sexual development, stress signaling, and amino acid metabolism. We propose that the absence of GPCRs triggered stress responses at the genetic level. The data suggested an intimate relationship among different G-protein coupled receptors, fine-tune regulation of secondary and amino acid metabolisms, and fungal development