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FMEA is a very popular and effective analysis. The main advantage is the arrangemnet of expert groups, which define risks, their effects and organize corrective and preventive actions. But such analysis also has some disadvantage, first of all it is the uncertainties, the other one is the need to choose the corrective event among those that have been suggested. Besides, a typical model for assessing the risks of potential failures of the coating applied by the method of gas-thermal plasma spraying on the blades of a gas turbine of a gas turbine engine has been developed. The model is based on the Design Failure Mode and Effect Analysis. The structural and functional analysis of the coating design was carried out. The failures resulting from the failure of the coating to perform the function are determined. The potential causes and consequences of failures have been identified. An assessment of the risks of failures was carried out and the priority of actions for their elimination was established. Measures to improve the quality of the coating applied by the method of gas-thermal plasma spraying are described.

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses., Nature Methods, 19 (8), ISSN:1548-7105, ISSN:1548-7091

Although most existing genome assemblers are based on de Bruijn graphs, the construction of these graphs for large genomes and large k-mer sizes has remained elusive. This algorithmic challenge has become particularly pressing with the emergence of long, high-fidelity (HiFi) reads that have been recently used to generate a semi-manual telomere-to-telomere assembly of the human genome. To enable automated assemblies of long, HiFi reads, we present the La Jolla Assembler (LJA), a fast algorithm using the Bloom filter, sparse de Bruijn graphs and disjointig generation. LJA reduces the error rate in HiFi reads by three orders of magnitude, constructs the de Bruijn graph for large genomes and large k-mer sizes and transforms it into a multiplex de Bruijn graph with varying k-mer sizes. Compared to state-of-the-art assemblers, our algorithm not only achieves five-fold fewer misassemblies but also generates more contiguous assemblies. We demonstrate the utility of LJA via the automated assembly of a human genome that completely assembled six chromosomes.

Although plasmids are important for bacterial survival and adaptation, plasmid detection and assembly from genomic, let alone metagenomic, samples remain challenging. The recently developed plasmidSPAdes assembler addressed some of these challenges in the case of isolate genomes but stopped short of detecting plasmids in metagenomic assemblies, an untapped source of yet to be discovered plasmids. We present the metaplasmidSPAdes tool for plasmid assembly in metagenomic data sets that reduced the false positive rate of plasmid detection compared with the state-of-the-art approaches. We assembled plasmids in diverse data sets and have shown that thousands of plasmids remained below the radar in already completed genomic and metagenomic studies. Our analysis revealed the extreme variability of plasmids and has led to the discovery of many novel plasmids (including many plasmids carrying antibiotic-resistance genes) without significant similarities to currently known ones.

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the community-driven initiative for the Critical Assessment of Metagenome Interpretation (CAMI). In its second challenge, CAMI engaged the community to assess their methods on realistic and complex metagenomic datasets with long and short reads, created from ∼1,700 novel and known microbial genomes, as well as ∼600 novel plasmids and viruses. Altogether 5,002 results by 76 program versions were analyzed, representing a 22x increase in results.Substantial improvements were seen in metagenome assembly, some due to using long-read data. The presence of related strains still was challenging for assembly and genome binning, as was assembly quality for the latter. Taxon profilers demonstrated a marked maturation, with taxon profilers and binners excelling at higher bacterial taxonomic ranks, but underperforming for viruses and archaea. Assessment of clinical pathogen detection techniques revealed a need to improve reproducibility. Analysis of program runtimes and memory usage identified highly efficient programs, including some top performers with other metrics. The CAMI II results identify current challenges, but also guide researchers in selecting methods for specific analyses.

Although most existing genome assemblers are based on the de Bruijn graphs, it remains unclear how to construct these graphs for large genomes and largek-mer sizes. This algorithmic challenge has become particularly important with the emergence of long high-fidelity (HiFi) reads that were recently utilized to generate a semi-manual telomere-to-telomere assembly of the human genome and to get a glimpse into biomedically important regions that evaded all previous attempts to sequence them. To enable automated assemblies of long and accurate reads, we developed a fast LJA algorithm that reduces the error rate in these reads by three orders of magnitude (making them nearly error-free) and constructs the de Bruijn graph for large genomes and largek-mer sizes. Since the de Bruijn graph constructed for a fixedk-mer size is typically either too tangled or too fragmented, LJA uses a new concept of a multiplex de Bruijn graph with varyingk-mer sizes. We demonstrate that LJA improves on the state-of-the-art assemblers with respect to both accuracy and contiguity and enables automated telomere-to-telomere assemblies of entire human chromosomes.

CrAssphage is the most abundant virus identified in the human gut virome and the founding member of a large group of bacteriophages that infect bacteria of the phylum Bacteroidetes and have been discovered by metagenomics of both animal-associated and environmental habitats. By analysis of circular contigs from human gut microbiomes, we identified nearly 600 genomes of crAss-like phages. Phylogenetic analysis of conserved genes demonstrates the monophyly of crAss-like phages, which can be expected to become a new order of viruses, and of 5 distinct branches, likely, families within that order. Two of these putative families have not been identified previously. The phages in one of these groups have large genomes (145-192 kilobases) and contain an unprecedented high density of self-splicing introns and inteins. Many crAss-like phages encode suppressor tRNAs that enable readthrough of UGA or UAG stop-codons, mostly, in late phage genes, which could represent a distinct anti-defense strategy. Another putative anti-defense mechanism that might target an unknown defense system in Bacteroidetes inhibiting phage DNA replication involves multiple switches of the phage DNA polymerase type between A and B families. Thus, comparative genomic analysis of the expanded assemblage of crAss-like phages reveals several unusual features of genome architecture and expression as well as phage biology that were not apparent from the previous crAssphage analyses.

SPAdes-St. Petersburg genome Assembler-was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single-cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole-genome sequencing and metagenomic datasets. In addition, we present guidelines for understanding results with use cases for each pipeline, and several additional support protocols that help in using SPAdes properly. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Assembling isolate bacterial datasets Basic Protocol 2: Assembling metagenomic datasets Basic Protocol 3: Assembling sets of putative plasmids Basic Protocol 4: Assembling transcriptomes Basic Protocol 5: Assembling putative biosynthetic gene clusters Support Protocol 1: Installing SPAdes Support Protocol 2: Providing input via command line Support Protocol 3: Providing input data via YAML format Support Protocol 4: Restarting previous run Support Protocol 5: Determining strand-specificity of RNA-seq data.

Risk is an integral part of the activities of any organization. The automotive industry is influenced by many factors that can contribute to a decrease in the financial performance of enterprises in a given industry. At the same time, the performance of enterprises in the automotive industry is significantly affected by market risks; the main ones are currency and interest risks. This article highlights the main methods and tools for managing market risks in the automotive industry. The analysis of market risks was carried out on the example of representatives of this industry (PJSC KAMAZ, PJSC SOLLERS, PJSC AVTOVAZ), the main methods of market risk management that are used by Russian enterprises of the automotive industry are outlined. The paper proposes an algorithm for minimizing market risks at the enterprises of the automotive industry through hedging, hedging mechanism with the help of exchange derivatives is also described. In conclusion, measures have been developed to improve the market risk management system in the automotive industry.

The article is devoted to the use of a computational statistical experiment using the Monte Carlo method when assessing the stability of the technical characteristics of an automobile generating installation in mass production. The algorithm calculates the stability of the performance of a batch of generators selected at random. The Monte-Carlo method consists in the multiple calculation of parameters according to a certain formalized scheme, which is the mathematical description of this process. The process under study is to determine the effect of technological errors in the manufacture of dimensional parameters, subject to certain statistical laws of distribution, on the electromagnetic characteristics of the generator

Background The possibility of generating large RNA-sequencing datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the organisms with finished and well-annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing, and paralogous genes. Results Herein we describe the novel transcriptome assembler rnaSPAdes, which has been developed on top of the SPAdes genome assembler and explores computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-sequencing datasets, and briefly highlight strong and weak points of different assemblers. Conclusions Based on the performed comparison between different assembly methods, we infer that it is not possible to detect the absolute leader according to all quality metrics and all used datasets. However, rnaSPAdes typically outperforms other assemblers by such important property as the number of assembled genes and isoforms, and at the same time has higher accuracy statistics on average comparing to the closest competitors.

Motivation The emergence of high-throughput sequencing technologies revolutionized genomics in early 2000s. The next revolution came with the era of long-read sequencing. These technological advances along with novel computational approaches became the next step towards the automatic pipelines capable to assemble nearly complete mammalian-size genomes. Results In this manuscript, we demonstrate performance of the state-of-the-art genome assembly software on six eukaryotic datasets sequenced using different technologies. To evaluate the results, we developed QUAST-LG—a tool that compares large genomic de novo assemblies against reference sequences and computes relevant quality metrics. Since genomes generally cannot be reconstructed completely due to complex repeat patterns and low coverage regions, we introduce a concept of upper bound assembly for a given genome and set of reads, and compute theoretical limits on assembly correctness and completeness. Using QUAST-LG, we show how close the assemblies are to the theoretical optimum, and how far this optimum is from the finished reference. Availability and implementation http://cab.spbu.ru/software/quast-lg Supplementary information Supplementary data are available at Bioinformatics online.

The article considers different methods of creation of a company's organizational model based on the principles of teal organizations. The basis of the management system of each company is its organizational model, in accordance such model managerial policy, management principles, rules and procedures are formed in the organizations. Depending on the selected organizational model, the organization has a certain set of distinctive features that affect the appearance of strengths and weaknesses, as well as system limitations. A company with a more developed organizational structure, as a rule has a higher flexibility in the management and implementation of stakeholder requirements, higher productivity and efficiency compared to organization with less developed organizational structure. In accordance with the theory of spectral dynamics exists an evolutionary development of organizational structures. Any organization that has a particular organizational structure needs to improve to move to the next level of development. Teal organization — is the highest level of organizational evolution, achieving which a company ensures stable development. These principles are reviewed on the example of the engineering company RusConsultProject.

Car manufacturing is a complicated task: a manufacturer accomplishes a large amount of work for collecting and managing the information about a competitive position of a particular car model in order to satisfy a customer. However, solving technical problem of database support does not allow providing conformity of information to a real competitive position of a car model. The present paper suggests a monitoring system of information conformity, which can help achieve a required level of information accuracy.

Recent advances in single-cell genomics provide an alternative to largely gene-centric metagenomics studies, enabling whole-genome sequencing of uncultivated bacteria. However, single-cell assembly projects are challenging due to (i) the highly nonuniform read coverage and (ii) a greatly elevated number of chimeric reads and read pairs. While recently developed single-cell assemblers have addressed the former challenge, methods for assembling highly chimeric reads remain poorly explored. We present algorithms for identifying chimeric edges and resolving complex bulges in de Bruijn graphs, which significantly improve single-cell assemblies. We further describe applications of the single-cell assembler SPAdes to a new approach for capturing and sequencing "microbial dark matter" that forms small pools of randomly selected single cells (called a mini-metagenome) and further sequences all genomes from the mini-metagenome at once. On single-cell bacterial datasets, SPAdes improves on the recently developed E+V-SC and IDBA-UD assemblers specifically designed for single-cell sequencing. For standard (cultivated monostrain) datasets, SPAdes also improves on A5, ABySS, CLC, EULER-SR, Ray, SOAPdenovo, and Velvet. Thus, recently developed single-cell assemblers not only enable single-cell sequencing, but also improve on conventional assemblers on their own turf. SPAdes is available for free online download under a GPLv2 license.

One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been improved algorithms for utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.

In article approaches to an assessment of stability of functioning of a production system of machine-building enterprise are considered, criteria of an assessment of stability of functioning of a production system are defined and mechanisms of ensuring its stability are given