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Orienteering problem (OP) is a routing problem, where the aim is to generate a path through set of nodes, which would maximize total score and would not exceed the budget. In this paper, we present an extension of classic OP—Orienteering Problem with Functional Profits (OPFP), where the score of a specific point depends on its characteristics, position in the route, and other points in the route. For solving OPFP, we developed an open-source framework for solving orienteering problems, which utilizes four core components of OP in its modular architecture. Fully-written in Go programming language our framework can be extended for solving different types of tasks with different algorithms; this was demonstrated by implementation of two popular algorithms for OP solving—Ant Colony Optimization and Recursive Greedy Algorithm. Computational efficiency of the framework was shown through solving four well-known OP types: classic Orienteering Problem (OP), Orienteering Problem with Compulsory Vertices (OPCV), Orienteering Problem with Time Windows (OPTW), and Time Dependent Orienteering Problem (TDOP) along with OPFP. Experiments were conducted on a large multi-source dataset for Saint Petersburg, Russia, containing data from Instagram, TripAdvisor, Foursquare and official touristic website. Our framework is able to construct touristic paths for different OP types within few seconds using dataset with thousands of points of interest. [ABSTRACT FROM AUTHOR]

We here describe the first fossil remains of a green lizard of the Lacerta group from the late Miocene (MN 13) of the Solnechnodolsk locality in southern European Russia. This region of Europe is crucial for our understanding of the paleobiogeography and evolution of these middle-sized lizards. Although this clade has a broad geographical distribution across the continent today, its presence in the fossil record has only rarely been reported. In contrast to that, the material described here is abundant, consists of a premaxilla, maxillae, frontals, parietals, jugals, quadrate, pterygoids, dentaries and vertebrae. The comparison of these elements to all extant green lizard species shows that these fossils are indistinguishable from Lacerta trilineata. Thus, they form the first potential evidence of the occurrence of this species in the Miocene. This may be also used as a potential calibration point for further studies. Together with other lizard fossils, Solnechnodolsk shows an interesting combination of survivors and the dawn of modern species. This locality provides important evidence for the transition of an archaic Miocene world to the modern diversity of lizards in Europe. In addition, this article represents a contribution to the knowledge of the comparative osteological anatomy of the selected cranial elements in lacertids. This study gives special emphasis to the green lizards, but new data are also presented for related taxa, e.g., Timon lepidus, Podarcis muralis or Zootoca vivipara. Although the green lizards include several cryptic species for which determination based on isolated osteological material would be expected to be difficult, our comparisons show several important morphological differences, although a high degree of variability is present. [ABSTRACT FROM AUTHOR]

The goal of this work was to study the phenotypic susceptibility and resistance determinants of N. gonorrhoeae isolates to beta-lactam antimicrobials (benzylpenicillin and ceftriaxone). A total of 522 clinical isolates collected in Russia in 2015–2017 were analysed for susceptibility using the agar dilution method. DNA loci involved in antimicrobial resistance were identified using DNA microarray analysis and sequencing. Resistance to benzylpenicillin remained high, with 7.7% of isolates resistant (MICpen > 1 mg/L) and 47.5% of isolates showing intermediate susceptibility (MICpen = 0.12–1 mg/L). The most frequent resistance determinant (72.4% isolates) was the Asp345 insertion in penA, both as a single mutation and in combination with other mutations, particularly with the substitution Leu421Pro in ponA (39.0%). Mutations affecting the influx and efflux of drugs were also found, including amino acid substitutions in PorB (26.8% isolates) and delA in the promoter region of mtrR (22.8%). The accumulation of mutations in chromosomal genes (penA, pon, porA, and mtrR) led to a stepwise increase in MICpen to values characteristic of intermediate resistance. The presence of blaTEM plasmids was found in 25 isolates (4.8%), resulting in a strong increase in resistance to penicillin (MICpen > 16 mg/L) compared with the chromosomal mutations; 23 plasmids were of the African type with TEM-1 beta-lactamase, and two plasmids were of the Toronto/Rio type with TEM-135 beta-lactamase. Only three isolates were found with reduced susceptibility to ceftriaxone, with MICcef = 0.12–0.25 mg/L. Sequencing of penA did not reveal mutations associated with resistance to third-generation cephalosporins, and the gene structure was non-mosaic. The majority of isolates (21 of 25) carrying the blaTEM plasmid also contained the conjugative plasmid with tetM (resistance to tetracyclines), consistent with previously reported data that the presence of the conjugative plasmid facilitates the transfer of other plasmids associated with antimicrobial resistance. [ABSTRACT FROM AUTHOR]

Tick-borne encephalitis virus (TBEV) is the most important tick-transmitted pathogen. It belongs to the Flaviviridae family and causes severe human neuroinfections. In this study, protective efficacy of the chimeric antibody chFVN145 was examined in mice infected with strains belonging to the Far-Eastern, European, and Siberian subtypes of TBEV, and the antibody showed clear therapeutic efficacy when it was administered once one, two, or three days after infection. The efficacy was independent of the TBEV strain used to infect the mice; however, the survival rate of the mice was dependent on the dose of TBEV and of the antibody. No enhancement of TBEV infection was observed when the mice were treated with non-protective doses of chFVN145. Using a panel of recombinant fragments of the TBEV glycoprotein E, the neutralizing epitope for chFVN145 was localized in domain III of the TBEV glycoprotein E, in a region between amino acid residues 301 and 359. In addition, three potential sites responsible for binding with chFVN145 were determined using peptide phage display libraries, and 3D modeling demonstrated that the sites do not contact the fusion loop and, hence, their binding with chFVN145 does not result in increased attachment of TBEV to target cells. [ABSTRACT FROM AUTHOR]

Background: Eastern European countries have some of the highest rates of cardiovascular disease (CVD) mortality, much of which cannot be adequately accounted for by conventional CVD risk factors. Psychosocial and socioeconomic factors may affect risk of CVD, but relatively few studies on this issue have been undertaken in Eastern Europe. We investigated whether various psychosocial factors are associated with CVD mortality independently from each other and whether they can help explain differences in CVD mortality between Eastern European populations.Methods: Participants were from the Health, Alcohol and Psychological factors in Eastern Europe (HAPIEE) cohort study in Russia, Poland and the Czech Republic, including a total of 20,867 men and women aged 43-74 years and free of CVD at baseline examination during 2002-2005. Participants were followed-up for CVD mortality after linkage to national mortality registries for a median of 7.2 years.Results: During the follow-up, 556 participants died from CVD. After mutual adjustment, six psychosocial and socioeconomic factors were associated with increased risk of CVD death: unemployment, low material amenities, depression, being single, infrequent contacts with friends or relatives. The hazard ratios [HRs] for these six factors ranged between 1.26 [95% confidence interval 1.14-1.40] and 1.81 [95% confidence interval 1.24-2.64], fully adjusted for each other, and conventional cardiovascular risk factors. Population-attributable fractions ranged from 8% [4%-13%] to 22% [11%-31%] for each factor, when measured on average across the three cohorts. However, the prevalence of psychosocial and socioeconomic risk factors and their HRs were similar between the three countries. Altogether, these factors could not explain why participants from Russia had higher CVD mortality when compared to participants from Poland/Czech Republic. Limitations of this study include measurement error that could lead to residual confounding; and the possibilities for reverse causation and/or unmeasured confounding from observational studies to lead to associations that are not causal in nature.Conclusions: Six psychosocial and socioeconomic factors were associated with cardiovascular mortality, independent of each other. Differences in mortality between cohorts from Russia versus Poland or Check Republic remained unexplained. [ABSTRACT FROM AUTHOR]

The influenza epidemic in 2015–2016 in Russia is characterized by a sharp increase of influenza cases (beginning from the second week of 2016) with increased fatalities. Influenza was confirmed in 20 fatal cases registered among children (0–10 years), in 5 cases among pregnant women, and in 173 cases among elderly people (60 years and older). Two hundred and ninety nine people died from influenza were patients with some chronic problems. The overwhelming majority among the deceased (more than 98%) were not vaccinated against influenza. We isolated 109 influenza A(H1N1)pdm09 and one A(H3N2) virus strains from 501 autopsy material samples. The antigenic features of the strains were similar to the vaccine strains. A phylogenic analysis of hemagglutinin revealed that influenza A(H1N1)pdm09 virus strains belonged to 6B genetic group that had two main dominant subgroups during the 2015–2016 season. In Russia strains of the first group predominated. We registered an increased proportion of strains with D222G mutation in receptor-binding site. A herd immunity analysis carried out immediately prior to the epidemic showed that 34.4% blood sera samples collected in different regions of Russia were positive to A/California/07/09(H1N1)pdm09. We came to a conclusion that public awareness enhancement is necessary to reduce unreasonable refusals of vaccination. [ABSTRACT FROM AUTHOR]

ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has been a common threat, with large USA300 epidemics in the United States. The global geographical structure of ST8/SCCmecIV has not yet been fully elucidated. We herein determined the complete circular genome sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome was inverted relative to USA300. Two IS256, oppositely oriented, at IS256-enriched hot spots were implicated with the one-megabase genomic inversion (MbIN) and vSaβ split. The behavior of IS256 was flexible: its insertion site (att) sequences on the genome and junction sequences of extrachromosomal circular DNA were all divergent, albeit with fixed sizes. A similar multi-IS256 system was detected, even in prevalent ST239 healthcare-associated MRSA in Russia, suggesting IS256’s strong transmission potential and advantage in evolution. Regarding epidemiology, all ST8/SCCmecIVc strains from European, Siberian, and Far Eastern Russia, examined had MbIN, and geographical expansion accompanied divergent spa types and resistance to fluoroquinolones, chloramphenicol, and often rifampicin. Russia ST8/SCCmecIVc has been associated with life-threatening infections such as pneumonia and sepsis in both community and hospital settings. Regarding virulence, the OC8 genome carried a series of toxin and immune evasion genes, a truncated giant surface protein gene, and IS256 insertion adjacent to a pan-regulatory gene. These results suggest that unique single ST8/spa1(t008)/SCCmecIVc CA-MRSA (clade, Russia ST8-IVc) emerged in Russia, and this was followed by large geographical expansion, with MbIN as an epidemiological marker, and fluoroquinolone resistance, multiple virulence factors, and possibly a multi-IS256 system as selective advantages. [ABSTRACT FROM AUTHOR]

Pathogenic variants in the GJB2 gene, encoding connexin 26, are known to be a major cause of hearing impairment (HI). More than 300 allelic variants have been identified in the GJB2 gene. Spectrum and allelic frequencies of the GJB2 gene vary significantly among different ethnic groups worldwide. Until now, the spectrum and frequency of the pathogenic variants in exon 1, exon 2 and the flanking intronic regions of the GJB2 gene have not been described thoroughly in the Sakha Republic (Yakutia), which is located in a subarctic region in Russia. The complete sequencing of the non-coding and coding regions of the GJB2 gene was performed in 393 patients with HI (Yakuts—296, Russians—51, mixed and other ethnicities—46) and in 187 normal hearing individuals of Yakut (n = 107) and Russian (n = 80) populations. In the total sample (n = 580), we revealed 12 allelic variants of the GJB2 gene, 8 of which were recessive pathogenic variants. Ten genotypes with biallelic recessive pathogenic variants in the GJB2 gene (in a homozygous or a compound heterozygous state) were found in 192 out of 393 patients (48.85%). We found that the most frequent GJB2 pathogenic variant in the Yakut patients was c.-23+1G>A (51.82%) and that the second most frequent was c.109G>A (2.37%), followed by c.35delG (1.64%). Pathogenic variants с.35delG (22.34%), c.-23+1G>A (5.31%), and c.313_326del14 (2.12%) were found to be the most frequent among the Russian patients. The carrier frequencies of the c.-23+1G>A and с.109G>A pathogenic variants in the Yakut control group were 10.20% and 2.80%, respectively. The carrier frequencies of с.35delG and c.101T>C were identical (2.5%) in the Russian control group. We found that the contribution of the GJB2 gene pathogenic variants in HI in the population of the Sakha Republic (48.85%) was the highest among all of the previously studied regions of Asia. We suggest that extensive accumulation of the c.-23+1G>A pathogenic variant in the indigenous Yakut population (92.20% of all mutant chromosomes in patients) and an extremely high (10.20%) carrier frequency in the control group may indicate a possible selective advantage for the c.-23+1G>A carriers living in subarctic climate. [ABSTRACT FROM AUTHOR]

Lethal infections with canine distemper virus (CDV) have recently been diagnosed in Amur tigers (Panthera tigris altaica), but long-term implications for the population are unknown. This study evaluates the potential impact of CDV on a key tiger population in Sikhote-Alin Biosphere Zapovednik (SABZ), and assesses how CDV might influence the extinction potential of other tiger populations of varying sizes. An individual-based stochastic, SIRD (susceptible-infected-recovered/dead) model was used to simulate infection through predation of infected domestic dogs, and/or wild carnivores, and direct tiger-to-tiger transmission. CDV prevalence and effective contact based on published and observed data was used to define plausible low- and high-risk infection scenarios. CDV infection increased the 50-year extinction probability of tigers in SABZ by 6.3% to 55.8% compared to a control population, depending on risk scenario. The most significant factors influencing model outcome were virus prevalence in the reservoir population(s) and its effective contact rate with tigers. Adjustment of the mortality rate had a proportional impact, while inclusion of epizootic infection waves had negligible additional impact. Small populations were found to be disproportionately vulnerable to extinction through CDV infection. The 50-year extinction risk in populations consisting of 25 individuals was 1.65 times greater when CDV was present than that of control populations. The effects of density dependence do not protect an endangered population from the impacts of a multi-host pathogen, such as CDV, where they coexist with an abundant reservoir presenting a persistent threat. Awareness of CDV is a critical component of a successful tiger conservation management policy. [ABSTRACT FROM AUTHOR]