LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis

Background DNA methylation is commonly measured using bisulfite sequencing (BS-seq). The quality of a BS-seq library is measured by its bisulfite conversion efficiency. Libraries with low conversion rates are typically excluded from analysis resulting in reduced coverage and increased costs. Results We have developed a probabilistic method and software, LuxRep, that implements a general linear model and simultaneously accounts for technical replicates (libraries from the same biological sample) from different bisulfite-converted DNA libraries. Using simulations and actual DNA methylation data, we show that including technical replicates with low bisulfite conversion rates generates more accurate estimates of methylation levels and differentially methylated sites. Moreover, using variational inference speeds up computation time necessary for whole genome analysis. Conclusions In this work we show that taking into account technical replicates (i.e. libraries) of BS-seq data of varying bisulfite conversion rates, with their corresponding experimental parameters, improves methylation level estimation and differential methylation detection.

Software tool for evaluation of reliability and survivability of complex technical system based on logical-probabilistic methodology

The paper presents solutions for estimation and analysis of complex system (CS) reliability and survivability indicators based on the logical-probabilistic approach. Modified logical-probabilistic method and software tool for evaluating the reliability and survivability of onboard equipment (OE) of small satellites were developed (SS). The correctness of the suggested method and software tool was shown by computational experiments on some systems of CS SS similar to Belarusian SS, and later compared with the “Arbitr” software complex results.

Optimization of standard arrival procedures at Sheremetyevo airport using rnav path terminators

Holding patterns are established at international airports to make the arriving traffic flow smooth and efficient. One of the main aims of holding patterns is to extend the aircraft arrival route, which allows ATC units to arrange the sequence on the arrival routes more effectively. The article considers the current methods and offers new ideas to improve the efficiency of the inbound traffic flow management using Paths and Terminators concept with HA holding patterns for standard arrival routes at Sheremetyevo Airport. As the main idea for optimizing air traffic management on this stage and reducing the workload on the controller, it is proposed to create extra routes in addition to the existing ones which include holding patterns, that will be used when needed to ensure a well-ordered traffic. The probabilistic method is used to calculate the maximum capacity of existing and proposed arrival routes with holding patterns. The proposed options for restructuring the airspace of the Moscow Terminal Control Area with preserving waypoints of starting standard arrival routes are presented.

The Importance of Risk Factors, Methods of Their Calculation and Evaluation, Prognosis in Medicine (Literature Review; Examples of Their Use in Own Clinical Practice) – Second Notice

Introduction. Despite the latest advances in modern medicine, the direct etiological factors of many diseases remain unknown or it is impossible to determine the significance of each of them in their occurrence, so the theory of risk factors is extremely relevant for both theoretical and practical medicine. There are also often situations in which it is necessary to determine the optimal tactics of patient care, because preventive, curative and rehabilitation activities of the doctor require timely prediction of the occurrence probability, further course of the pathological process, its complications, recurrences under the influence of certain environmental factors, threatening and terminal stages, side effects of drugs. Therefore, the need for a practical solution to these problems has become the basis for the theory of risk factors and prognosis methods. The aim of the study. Describe the importance of risk factors and methods of their calculation and evaluation, prognosis in medicine, using literature sources, provide specific examples of their use in own clinical practice. Materials and methods. Content analysis, method of system and comparative analysis, bibliosemantic method of studying the current scientific researches concerning studying of the importance of risk factors and a technique of their calculation and estimation, prognosis in medicine were used. Sources were searched in scientometric databases: PubMed, Medline, Springer, Google Scholar, Research Gate by keywords: risk factors, one-way analysis, multi-factor analysis. 54 literary sources in English and Ukrainian, which highlight the importance of risk factors and methods of their calculation and evaluation, prognosis in medicine were selected and analyzed, we describe the results of their use in our own clinical practice. Results. The concept of risk, as the probability of an adverse event or outcome, is most often used in analytical studies, which are planned to identify the causes and their prevalence of certain conditions. "Risk" cannot be measured directly by the results of information evaluation in one person, but is calculated on the basis of selective observation of a group of persons who are under the influence (exposed group) of a certain factor. Risk factors are potentially pathogenic factors, in contact with which a person may develop a disease. A full analysis of pathological processes, assessment of risk factors and actual risks are impossible without prognosis, as well as multivariate analysis, which is often based on the probabilistic method of A. Wald or the survival curves construction. In practical health care, cases of medical and social research and in clinical studies, it is often necessary to identify the trends (predict) in changes of a certain condition. Conclusions. Determining the risk factors, calculating the actual risks and prognosis play an important role in medicine, because in the doctor's practice there are daily situations that need to determine the optimal tactics taking into account trends, course, severity and results of treatment, therefore, their definition/calculation must be clear and understandable. Depending on the case, the doctor can use the analysis of the score for certain factors, create risk groups, develop a monitoring plan etc. As a result, it becomes possible to create a plan of preventive measures and timely correction of treatment. Keywords: risk, relative risk, absolute risk, chance, forecast.

Potential Human Exposure to Mercury (Hg) in a Chlor-Alkali Plant Impacted Zone: Risk Characterization Using Updated Site Assessment Data

Industrial activities have resulted in severe environmental contamination that may expose rural and urban populations to unacceptable health risks. For example, chlor-alkali plants (CAPs) have historically contributed mercury (Hg) contamination in different environmental compartments. One such site (a burden from the Soviet Union) is located in an industrial complex in Pavlodar, Kazakhstan. Earlier studies showed the CAP operating in the second half of the twentieth century caused elevated Hg levels in soil, water, air, and biota. However, follow-up studies with thorough risk characterization are missing. The present study aims to provide a detailed risk characterization based on the data from a recent site assessment around the former CAP. The ⅀HI (hazard index) ranged from 9.30 × 10−4 to 0.125 (deterministic method) and from 5.19 × 10−4 to 2.54 × 10−2 (probabilistic method). The results indicate acceptable excess human health risks from exposure to Hg contamination in the region, i.e., exposure to other Hg sources not considered. Air inhalation and soil ingestion pathways contributed to the highest ⅀HI values (up to 99.9% and 92.0%, respectively). The residential exposure scenario (among four) presented the greatest human health risks, with ⅀HI values ranging from 1.23 × 10−2 to 0.125. Although the local urban and rural population is exposed to acceptable risks coming from exposure to Hg-contaminated environmental media, an assessment of contamination directly on the former CAP site on the industrial complex could not be performed due to access prohibition. Furthermore, the risks from ingesting contaminated fish were not covered as methyl-Hg was not targeted. An additional assessment may be needed for the scenarios of exposure of workers on the industrial complex and of the local population consuming fish from contaminated Lake Balkyldak. Studies on the fate and transport of Hg in the contaminated ecosystem are also recommended considering Hg methylation and subsequent bioaccumulation in the food chain.

DANGERS ARISING FROM APPLICATION OF THE PROBABILISTIC METHOD (AS INCLUDED IN SOLAS 2009 Ch.II-1) TO MEASURING LEVEL OF SAFETY OF CARGO SHIPS

From application of a probability based methods to evaluating safety of ships arise certain dangers of hazardous conditions omissions and results misinterpretations. In this paper a few areas in which these dangers occur are identified and described. The purpose of this work was to highlight these areas and suggest a way forward for developing methods for evaluation of safety of ships that would address these identified dangers. In this work the Author focuses on mathematical analysis of selected equations provided in the currently used method as included in SOLAS 2009 Convention. The following factors were selected for evaluation: pi – probability of a selected damage occurring, si – probability of surviving a selected damage, A – Attained Subdivision Index and R – Required Subdivision Index. From the performed analysis the conclusions are drawn that there are numerous areas where application of the investigated method may lead to dangers to maintaining controllable level of ship safety.

A Meeting Point of Probability, Graphs, and Algorithms: The Lovász Local Lemma and Related Results—A Survey

A classic and fundamental result, known as the Lovász Local Lemma, is a gem in the probabilistic method of combinatorics. At a high level, its core message can be described by the claim that weakly dependent events behave similarly to independent ones. A fascinating feature of this result is that even though it is a purely probabilistic statement, it provides a valuable and versatile tool for proving completely deterministic theorems. The Lovász Local Lemma has found many applications; despite being originally published in 1973, it still attracts active novel research. In this survey paper, we review various forms of the Lemma, as well as some related results and applications.

The calculation of required fire resistance limits for engineering structures of technological pipe racks at oil and gas processing plants on the basis of an evaluation of the time needed for personnel evacuation and rescue in case of fire

Introduction. GOST R 12.3.047-2012 standard offers a methodology for determination of required fire resistance limits of engineering structures. This methodology is based on a comparison of values of the fire resistance limit and the equivalent fire duration. However, in practice incidents occur when, in absence of regulatory fire resistance requirements, a facility owner, who has relaxed the fire resistance requirements prescribed by GOST R 12.3.047–2012, is ready to accept its potential loss in fire for economic reasons. In this case, one can apply the probability of safe evacuation and rescue to compare distributions of fire resistance limits, on the one hand, and evacuation and rescue time, on the other hand.A methodology for the identification of required fire resistance limits. The probabilistic method for the identification of required fire resistance limits, published in work [1], was tested in this study. This method differs from the one specified in GOST R 12.3.047-2012. The method is based on a comparison of distributions of such random values, as the estimated time of evacuation or rescue in case of fire at a production facility and fire resistance limits for engineering structures.Calculations of required fire resistance limits. This article presents a case of application of the proposed method to the rescue of people using the results of full-scale experiments, involving a real pipe rack at a gas processing plant [2].Conclusions. The required fire resistance limits for pipe rack structures of a gas processing plant were identified. The calculations took account of the time needed to evacuate and rescue the personnel, as well as the pre-set reliability of structures, given that the personnel evacuation and rescue time in case of fire is identified in an experiment.