gplas : a comprehensive tool for plasmid analysis using short-read graphs

aSummary: Plasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data are often applied to large-scale bacterial comparative genomics projects but the reconstruction of plasmids from these data is facing severe limitations, such as the inability to distinguish plasmids from each other in a bacterial genome. We developed gplas, a new approach to reliably separate plasmid contigs into discrete components using sequence composition, coverage, assembly graph information and network partitioning based on a pruned network of plasmid unitigs. Gplas facilitates the analysis of large numbers of bacterial isolates and allows a detailed analysis of plasmid epidemiology based solely on short-read sequence data.Peer reviewe

Mathematical Modeling Of Horizontal Displacement Of Above-ground Gas Pipelines

The modern geodetic equipment allows observations as soon as possible, providing high accuracy and productivity. Achieving high accuracy of measurement is impossible without taking into account external factors that create influence on an observation object. Therefore, in order to evaluate an influence of thermal displacement on the results of geodetic monitoring a mathematical model of horizontal displacement of above-ground pipelines was theoretically grounded and built. In this paper we used data of experimental studies on the existing pipelines "Soyuz" and "Urengoy - Pomary - Uzhgorod". Above-ground pipeline was considered as a dynamic system "building - environment". Based on the characteristics of dynamic systems the correlation between the factors of thermal influence and horizontal displacement of the pipeline axis was defined.Establishing patterns between input factors and output response of the object can be useful not only for geodetic control, but also for their consideration in the design of new objects. It was investigated that the greatest influence on the accuracy of geodetic observations can create dispersion of high-frequency oscillations caused by daily thermal displacement. The magnitude of displacement exceeds actual measurement error.The article presents the results of calculation of high-frequency oscillations of above-ground gas pipeline.The result made it possible to substantiate the accuracy and methodology of geodetic observations of the horizontal displacement of pipeline axes taking into account an influence of cyclical thermal displacement.Research results were recommended for use in practice for enterprises that serve the main gas pipelines and successfully tested by specialists of PJSC "Ukrtransgaz" (Kharkiv, Ukraine) during the technical state control of aerial pipeline crossing in Ukraine and also can be used to form the relevant regulations

Duration of rectal colonization with extended-spectrum beta-lactamase-producing Escherichia coli: results of an open, dynamic cohort study in Dutch nursing home residents (2013–2019)

Background: In 2016, a study in a Dutch nursing home showed prolonged colonization duration of extended-spectrum β-lactamase-producing (ESBL)-ST131 compared to ESBL-non-ST131. In this study, we assessed the duration of rectal ESBL-producing E. coli (ESBL-EC) colonization in residents in the same nursing home for an extended period of six years. We aimed to estimate the influence of a possible bias when follow up is started during an outbreak. Methods: Between 2013 and 2019, repetitive point prevalence surveys were performed by culturing rectal or faecal swabs from all residents. Kaplan–Meier survival analysis was performed to calculate the median time to clearance of ESBL-EC with a log-rank analysis to test for differences between ESBL-ST131 and ESBL-non-ST131. Results: The study showed a median time to clearance of 13.0 months (95% CI 0.0–27.9) for ESBL-ST131 compared to 11.2 months (95% CI 4.8–17.6) for ESBL-non-ST131 (p = 0.044). In the subgroup analysis of residents who were ESBL-EC positive in their first survey, the median time to clearance for ST131 was 59.7 months (95% CI 23.7–95.6) compared to 16.2 months (95% CI 2.1–30.4) for ESBL-non-ST131 (p = 0.036). In the subgroup analysis of residents who acquired ESBL-EC, the median time to clearance for ST131 was 7.2 months (95% CI 2.1–12.2) compared to 7.9 months (95% CI 0.0–18.3) for ESBL-non-ST131 (p = 0.718). The median time to clearance in the ESBL-ST131 group was significantly longer in residents who were ESBL-ST131 colonised upon entering the study than in residents who acquired ESBL-ST131 during the study (p = 0.001). Conclusion: A prolonged colonization with ESBL-ST131 was only found in the subgroup who was ESBL-EC positive upon entering the study. The prolonged duration with ESBL-ST131 in the previous study was probably biased by factors that occured during (the start of) the outbreak

Numerical method for solving multipoints elliptic-parabolic equation for dehydration process

Drying is the oldest and efficient form of preserving fruits. This research focuses on the mathematical modeling of tropical fruits dehydration using instant controlled pressure drop (Détente Instantanée Controlée or known as DIC) technique. We proposed a modification of mathematical modeling to enhance the previous modeling from Haddad et al. [10]. The mathematical modeling presents the dehydration process of DIC technique which involves parameters such as pressure, water content, time dependency, dimension of region and temperature behavior. The modification of the mathematical modeling has been done by transforming the quadratic equation to partial differential equation (PDE). The simulation of the dehydration process will be illustrated through Jacobi method based on two, three and five points forward difference schemes. The sequential algorithm is developed by using Matlab 7.6.0 (R2008a) programming. The numerical analysis of finite difference schemes in terms of number of iteration, time execution, maximum error and computational cost are compared

Mathematical modeling of genome replication

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