Next-generation sequencing-based bulked segregant analysis without sequencing the parental genomes

Genomic regions that control traits of interest can be rapidly identified using BSA-Seq, a technology in which next-generation sequencing (NGS) is applied to bulked segregant analysis (BSA). We recently developed the significant structural variant method for BSA-Seq data analysis that exhibits higher detection power than standard BSA-Seq analysis methods. Our original algorithm was developed to analyze BSA-Seq data in which genome sequences of one parent served as the reference sequences in genotype calling, and thus required the availability of high-quality assembled parental genome sequences. Here we modified the original script to effectively detect the genomic region-trait associations using only bulk genome sequences. We analyzed two public BSA-Seq datasets using our modified method and the standard allele frequency and G-statistic methods with and without the aid of the parental genome sequences. Our results demonstrate that the genomic region(s) associated with the trait of interest could be reliably identified via the significant structural variant method without using the parental genome sequences.

Next-generation sequencing-based bulked segregant analysis without sequencing the parental genomes

The genomic region(s) that controls a trait of interest can be rapidly identified using BSA-Seq, a technology in which next-generation se-quencing (NGS) is applied to bulked segregant analysis (BSA). We recently developed the significant structural variant method for BSA-Seq data analysis that exhibits higher detection power than standard BSA-Seq analysis methods. Our original algorithm was developed to analyze BSA-Seq data in which genome sequences of one parent served as the reference sequences in genotype calling, and thus required the availability of high-quality assembled parental genome sequences. Here we modified the original script to allow for the effective detection of the genomic region-trait associations using only bulk genome sequences. We analyzed a public BSA-Seq dataset using our modified method and the standard allele frequency and G-statistic methods with and without the aid of the parental genome sequences. Our results demonstrate that the genomic region(s) associated with the trait of interest could be reliably identified only via the significant structural variant method without using the parental genome sequences.Significance StatementBSA-Seq can be utilized to rapidly identify structural varianttrait associations, and our modified significant structural variant method allows the detection of such associations without sequencing the parental genomes, leading to further lower the sequencing cost and making BSA-Seq more accessible to the research community and more applicable to the species with a large genome.

INVITRO EVALUATION OF ANTIMICROBIAL ACTIVITY OF CLOVE BUDS( EUGINEA AROMATICA)

Bioactive compounds from Eugenia aromaticum were extracted by Soxhlet using DCM ,DCM;WATER,WATER and extracts were examined for its phytocomponents along with Clove oil. These bioactive plant compounds were screened for possible antimicrobial activities against two strains of MDR S. aureus. Antimicrobial activity of extracts using agar diffusion disc variant method. The objective of this study was to evaluate technical variants used in screening methods to determine antibacterial activity of natural products. Thus, a varied range of natural products of plant were tested against two bacterial species,m Staphylococcus aureus ATCC 25923 and klebesella pnemonia ATCC 25922, by two variants of the agar diffusion method (well and disc), two variants of the bio autographic method (direct and indirect) and by microdilution assay. We concluded that the well-variant of the diffusion method was more sensitive than the disc-variant, it was found extract 1 ie,DCM and extract 2 i.e DCM;WATER had shown best results on antimicrobial activity ,phytocvhemical screening test are done for three extractsn invitro evalvation of antimicrobial activity was performed.

A non-probabilistic time-variant method for structural reliability analysis

Time-variant reliability problems commonly occur in practical engineering due to the deterioration in material properties, external disturbance and other uncertain factors. Considering the non-probabilistic method can effectively deal with the uncertainties in reliability analysis. Based on the stress–strength interference method and interval method, a time-variant stress–strength interference interval model is established by considering the stress and strength as time-variant intervals. And then, the stress and strength intervals are converted into the normalized intervals to define the non-probabilistic time-variant reliability index [Formula: see text] according to the different relationships between the limit state function and the normalized intervals. The structural state at any time can be described by the non-probabilistic time-variant reliability index [Formula: see text]. In addition, a strength power exponential degradation model is given as an example to clearly verify the non-probabilistic time-variant method, and the analysis results are compared with the interval method, the uniform distribution stress–strength interference method and the normal distribution stress–strength interference method, which confirm that the non-probabilistic time-variant method is feasible and valid to analyze the structural time-variant reliability without the probability density functions of the parameters.

Analisis Portofolio Investasi dengan Metode Multi Objektif

In the formation of an efficient portfolio, many methods can be used. Of course with its own assumptions and advantages. In the process, reasonable investor assumptions tend to be risk averse. Investors who are risk averse are investors who, when faced with two investments with the same expected return, will choose an investment with a lower risk level. If an investor has several efficient portfolio choices, then the most optimal portfolio will be chosen. Optimal portfolio with mean-variance efficient portfolio criteria, investors only invest in risky assets. Investors do not include risk free assets in their portfolios. Mean-variance efficient portfolio is defined as a portfolio that has a minimum variance among all possible portfolio that can be formed, at the mean level of the same expected return. The mean variant method of the two constraints can be used as a basis in determining the optimal portfolio weight by minimizing the risk of portfolio return with two constraints. In this article the problem referred to is symbolized by lamda and beta. With this two-constraint method, the results obtained are more detailed so that they can describe the results of a sharper analysis for an investor.

Comparison of Horizontal Displacement from Horizontal Control Network Adjustment Result Using Observation Model and Time-Variant Methods (Case Study : Horizontal Control Network of Borobudur Temple, Epoch 2002, 2003 and 2012)

Borobudur Temple is the biggest Buddhist Temple in the world protected by UNESCO. Therefore the periodical maintenance of Borobudur temple become important, deformation study through displacement analysis can be applied for it, by conducting Geodetic observation periodically. The design for Borobudur horizontal monitoring network is a relative one, the control point and monitoring points are in the deformation area. Therefore, the effect of position changes of the control point used in the horizontal network for displacement analysis of Borobudur needs to be considered, as it affects the result for the least square adjustment of the monitoring points. Two different adjustment methods used to overcome this problem, Least square adjustment using observation model and time-variant methods. This research aims to compare the horizontal displacement analysis of Borobudur resulted from these two adjustment methods. First by giving position correction for the control point at each epoch according to its displacement in least square adjustment using observation model. The second by computing position and velocity vector directly using time-variant method. The comparation of 2D horizontal displacement vector analysis was done by using vector velocity of 2D horizontal displacement from the analysis of the two adjustment methods on the interval displacement epochs between 2002 and 2003 and between 2002 and 2012. This research showed the vector magnitude and the accuration of the displacement from the analysis resulted from the two adjustment methods was different. The resulted of least square adjustment using observation model with correction of control point showed that there was significant increase in magnitude of displacement vector of the monitoring points. Displacement analysis between 2002 and 2003 the magnitude in average were 7.97 mm and the analysis between 2002 and 2012 were 37.78 mmwith consistent displacement direction of the both interval displacement to the northwest. The Time-Variant adjustment method showed an increase in the vector velocity of 2D horizontal displacement from 0.29 mm/year to 0.32 mm/year with different displacement direction. The vector magnitude of the displacement from time variant method was smaller than observation model and the standard deviation for the horizontal displacement from time variant method was slightly bigger about 0.5 mm compared to the observation model.

The concept of estimating usable floor area of buildings based on cadastral data

Usable floor area is one of the most important spatial attributes of buildings and premises. It is used, for example, to determine the basis for their taxation. Unfortunately, the question of proper determination of usable floor area in Poland has remained problematic for many years, which is closely related to the occurrence of various definitions of usable floor area in the currently binding legal acts. Consequently, usable floor area is not a universal attribute. This means that in certain cases significant discrepancies may occur between the usable floor area of the same structure, determined for different purposes. In addition, despite attempts made to unify the principles for the performance of surveys of building structures and their parts, this requirement still can not be recognized as fully met. Therefore, there is no doubt that the problem of reliability and availability of data defining the usable floor area of buildings is becoming even more important in view of the introduction of the ‘ad valorem’ tax, which has been planned for years. For this reason, this paper proposes a universal, multi-variant method of estimating usable floor area based on geometric and descriptive data of buildings contained in the cadastre. The Authors, taking into account the applicable legal regulations, have considered the possibilities of practical implementation of individual variants of this specific method. They have carried out empirical tests of effectiveness of the proposed approach. They have also defined tasks for which this method of determining the usable floor area of buildings would be particularly useful.

En enhanced matrix-free method via double step length approach for solving systems of nonlinear equations

A variant method for solving system of nonlinear equations is presented. This method use the special form of iteration with two step length parameters, we suggest a derivative-free method without computing the Jacobian via acceleration parameter as well as inexact line search procedure. The proposed method is proven to be globally convergent under mild condition. The preliminary numerical comparison reported in this paper using a large scale benchmark test problems show that the proposed method is practically quite effective.