PerFSeeB: Designing Long High-weight Single Spaced Seeds for Full Sensitivity Alignment with a Given Number of Mismatches

Background: Technical progress in computational hardware allows researchers to use new approaches for sequence alignment problems. A standard procedure is usually based on pre-aligning of short subsequences followed by proper comparison of neighbouring parts. For this purpose index files are created that store all subsequences (or numbers associated with them) and their positions within a reference sequence. Index files designed on subsequences of 32–64 symbols for a human reference genome can now be easily stored without any compression even on a budget computer. The main goal now is to choose a combination of symbols (a spaced seed) that will tolerate various mismatches between reference and given sequences. An ideal spaced seed should allow us to find all such positions (full sensitivity). By increasing the seed’s weight by one we usually reduce the number of candidate positions fourfold. At the same time longer seeds also reduce the number of signatures to be checked. Results: Several algorithms to assist seed generation are presented. The first one allows us to find all permitted spaced seeds iteratively. The results obtained with the algorithm show specific patterns of the seeds of the highest weight. Among the best seeds, there are periodic seeds with a simple relation between the period of a seed, its length and the length of a read. The second algorithm generates blocks for periodic seeds. A list of blocks is found for blocks of up to 50 symbols and up to 9 mismatches. The third algorithm uses those lists to find spaced seeds for reads of an arbitrary length. Conclusions: Lists of long high-weight spaced seeds are found and available in Supplementary Materials. The seeds are best in terms of weights compared to seeds from other papers and can usually be applied to shorter reads. Codes for all algorithms are available at https://github.com/vtman/PerFSeeB.

FUNDAMENTALS OF FOLK PROVERBS FORMED ON THE BASIS OF THE LEXICAL-SPIRITUAL GROUP OF INSECTS

This article reveals the basics of Uzbek folk paremas formed on the basis of the lexical-spiritual group of "Insects''. According to it, the Uzbek folk parems, formed on the basis of the lexical-spiritual group of "Insects'', are mostly formed by the appearance, biological characteristics, color and lifestyle of insects. It was noted that in the Uzbek folk paremas formed on the basis of insect names, paremas formed on the basis of harmful insect names are more common. The reason for this is that there are more harmful species of insects than beneficial ones, and another reason is the idea that bad people are quick to notice, indifferent to everything, indifferent to everything that does no good to those around them, rather than good people who benefit society. The Uzbek folk parems formed on the basis of the names of "Insects" are substantiated by the fact that they appear in the semaphores as a positive character-defining, moderate-character-defining, negative-character-determining factor. In Uzbek folk paremas, it is said that the names of insects serve as a means of providing imagery to express people's appearance, behavior, character, speech, just to name a few, and building a proper comparison, analogy, transfer of meaning.

Framework for the Comparison and Selection of Schemes for Multi-Factor Authentication

Authentication is the process of verifying a user’s identity for them to access a system’s resources. An authentication factor is a piece of information used for this authentication. Three well-known groups of authentication factors exist: knowledge-based (what you know), possession-based (what you have) and inherence-based (what you are). Authentication schemes belonging to distinct authentication factors can be combined in a multi-factor manner to increase security. Although multiple multi-factor proposals are seen in literature, the absence of a method that allows a proper comparison and selection of these authentication methods, based on an application’s security requirements, can be observed. Existing frameworks for the analysis of authentication methods have been identified through the realization of a systematic literature review, but most of these focus on specific contexts and do not provide a generic enough solution. Due to the above, this research focuses on the creation of a recommendation framework that guides in the comparison and selection of single and multi-factor authentication schemes, considering both the application’s requirements and its context. This has been attained not only through the knowledge found in literature, but the experience from industry experts has been compiled as well through the collaboration with a multinational software development company. Consequently, the knowledge found in literature has been obtained from a systematic literature review, whereas the experience from industry experts was obtained through a survey and interviews. The framework proposal has been generated based on the above and has been validated through an expert panel and a case study methodology in collaboration with the partnered software development company. A tool prototype has been constructed as well. The result is a recommendation framework for the comparison and selection of authentication methods that can support this decision process in multiple contexts.

Efficacy of EDTA and HEDP Chelators in the Removal of Mature Biofilm of Enterococcus faecalis by PUI and XPF File Activation

Background: Biofilm removal from the root canal during endodontic treatment is necessary to prevent further complications. Irrigation is essential to success. Several irrigants have been proposed without a proper comparison. The aim of the study is to compare the antibacterial capacity of different activated irrigants using passive ultrasonic activation (PUI) or XP-Endo finisher (XPF). Methods: A total of 100 instrumented teeth were incubated in an Eppendorf tube containing 0.5 McFarland of Enterococcus faecalis and incubated for 2 weeks at 37 °C. Roots were divided into 5 groups (n = 20) according to the irrigant type: ethylenediaminetetraacetic acid (EDTA) (17%), ethydronic acid (HEDP) (9%) mixed with 5.25% sodium hypochlorite (NaOCl), EDTA (17%) mixed with 5.25% NaOCl, PBS, and a control group. Each group was divided into two subgroups (n = 10): PUI and XPF. Results: As compared to the untreated control group, the irrigators included in the study had a significant effect in bacteria reduction. The obtained results show HEDP to be the most effective irrigant, since no bacteria were recovered after treatment of this group, followed by EDTA mixed with NaOCl and, finally, the EDTA-irrigated group. Conclusions: HEDP is the best irrigating agent in combination with XPF or PUI file activation to eliminate bacteria in our experimental model.

Comparative studies of dual bronchodilation in COPD

Dual bronchodilation therapy is becoming the cornerstone for the treatment of COPD because the clinical benefits of LABA/LAMA fixed-dose combinations (FDCs) are now extensively established. Therefore, it not surprising that a number of LAMA/LABA combinations in a single inhaler have now been approved for clinical use as treatments for patients with COPD. Regrettably, very few head-to-head studies between all of the available LABA/LAMA FDCs have been carried out. This makes choosing the most appropriate FDC difficult. Comparative effectiveness research that also uses conventional meta-analyses to compare different care strategies can help generate useful information. A bidimensional comparative analysis across LAMA/LABA FDCs has suggested constant superiority for tiotropium/olodaterol. However, considering that there is not an equivalent amount of evidence on efficacy outcomes for all LAMA/LABA FDCs, a proper comparison between the different LAMA/LABA FDCs cannot be made yet, and the information available is still rather inconsistent.

Computational Drug Repurposing: Classification of the Research Opportunities and Challenges

Background: : Drug repurposing has grown significantly in recent years. Research and innovation in drug repurposing are extremely popular due to its practical and explicit advantages. However, its adoption into practice is slow because researchers and industries have to face various challenges. Objective:: As this field, there is a lack of a comprehensive platform for systematic identification for removing development limitations. This paper deals with a comprehensive classification of challenges in drug repurposing. Methods: Initially, a classification of various existing repurposing models is propounded. Next, the benefits of drug repurposing are summarized. Further, a categorization for computational drug repurposing shortcomings is presented. Finally, the methods are evaluated based on their strength to addressing the drawbacks. Results:: This work can offer a desirable platform for comparing the computational repurposing methods by measuring the methods in light of these challenges. Conclusion:: A proper comparison could prepare guidance for a genuine understanding of methods. Accordingly, this comprehension of the methods will help researchers eliminate the barriers thereby developing and improving methods. Furthermore, in this study, we conclude why despite all the benefits of drug repurposing, it is not being done anymore.

Comparison of FPGA and Microcontroller Implementations of an Innovative Method for Error Magnitude Evaluation in Reed–Solomon Codes

Reed–Solomon (RS) codes are one of the most used solutions for error correction logic in data communications. RS decoders are composed of several blocks: among them, many efforts have been made to optimize the error magnitude evaluation module. This paper aims to assess the performance of an innovative algorithm introduced in the literature by Lu et al. under different systems configurations and hardware platforms. Several configurations of the encoded message chosen between those typically used in different applications have been designed to be run on an FPGA (field programmable gate array) device and an MCU (microcontroller unit). The performances have been evaluated in terms of resource usage and output delay for the FPGA and in terms of code execution time for the MCU. As a benchmark in the analysis, the well-established Forney’s method is exploited: it has been implemented in the same configurations and on the same hardware platforms for a proper comparison. The results show that the theoretical finding are fully confirmed only in the MCU implementation, while on FPGA, the choice of one method with respect to the other depends on the optimization feature (i.e., time or area) that has been decided as a preference in the specific application.

A Size-Dependent Coupled Symplectic and Finite Element Method for Steady-State Forced Vibration of Built-Up Nanobeam Systems

A novel size-dependent coupled symplectic and finite element method (FEM) is proposed to study the steady-state forced vibration of built-up nanobeam system resting on elastic foundations. The overall system is modeled as a combination of nonlocal Timoshenko beams. A new analytical subsystem modeling with formulation and another numerical subsystem modeling are developed and discussed. In the analytical subsystem model, the uniform nanobeams are modeled and solved by a new approach based on a series of analytical symplectic eigensolutions. The numerical subsystem model applies a nonlocal FEM to solve nonuniform nanobeams. Analytical and numerical solutions are presented, and a proper comparison between the two approaches is established. Comprehensive and accurate numerical result is subsequently presented to illustrate the accuracy and reliability of the coupled method. The new results established are expected to have reference values for future studies.

Methods for Asssessing Energy Efficiency of Grain Dryers

The article presents an algorithm for calculating selected energy assessment indexes for grain driers. Particular attention was paid to the conversion of the equations obtained for the operating conditions of the drying process into equations allowing the calculation of indexes for the standard drying conditions. The indexes obtained allow a proper comparison of dryers operating in varied atmospheric conditions, as well as humidity and temperature of the dried material.

BetaScan2: Standardized statistics to detect balancing selection utilizing substitution data:

The recently reported statistic β detects balanced haplotypes without the need for genomic data from an outgroup species. Here we present an extension to the method that incorporates between-species substitution data into the β statistic framework. We show that this approach outperforms existing summary statistics in simulations. We also present the variance of β with and without substitution data, allowing calculation of a standardized score. Besides providing a measure of significance, this enables a proper comparison of β values across varying underlying parameters, a feature lacking from some related methods.