• Title/Summary/Keyword: Combinatorial optimization

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Generation of single stranded DNA with selective affinity to bovine spermatozoa

  • Vinod, Sivadasan Pathiyil;Vignesh, Rajamani;Priyanka, Mani;Tirumurugaan, Krishnaswamy Gopalan;Sivaselvam, Salem Nagalingam;Raj, Gopal Dhinakar
    • Animal Bioscience
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    • v.34 no.10
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    • pp.1579-1589
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    • 2021
  • Objective: This study was conducted to generate single stranded DNA oligonucleotides with selective affinity to bovine spermatozoa, assess its binding potential and explore its potential utility in trapping spermatozoa from suspensions. Methods: A combinatorial library of 94 mer long oligonucleotide was used for systematic evolution of ligands by exponential enrichment (SELEX) with bovine spermatozoa. The amplicons from sixth and seventh rounds of SELEX were sequenced, and the reads were clustered employing cluster database at high identity with tolerance (CD-HIT) and FASTAptamer. The enriched nucleotides were predicted for secondary structures by Mfold, motifs by Multiple Em for Motif Elicitation and 5' labelled with biotin/6-FAM to determine the binding potential and binding pattern. Results: We generated 14.1 and 17.7 million reads from sixth and seventh rounds of SELEX respectively to bovine spermatozoa. The CD-HIT clustered 78,098 and 21,196 reads in the top ten clusters and FASTAptamer identified 2,195 and 4,405 unique sequences in the top three clusters from the sixth and seventh rounds, respectively. The identified oligonucleotides formed secondary structures with delta G values between -1.17 to -26.18 kcal/mol indicating varied stability. Confocal imaging with the oligonucleotides from the seventh round revealed different patterns of binding to bovine spermatozoa (fluorescence of the whole head, spot of fluorescence in head and mid- piece and tail). Use of a 5'-biotin tagged oligonucleotide from the sixth round at 100 pmol with 4×106 spermatozoa could trap almost 80% from the suspension. Conclusion: The binding patterns and ability of the identified oligonucleotides confirms successful optimization of the SELEX process and generation of aptamers to bovine spermatozoa. These oligonucleotides provide a quick approach for selective capture of spermatozoa from complex samples. Future SELEX rounds with X- or Y- enriched sperm suspension will be used to generate oligonucleotides that bind to spermatozoa of a specific sex type.

Multi-objective Genetic Algorithm for Variable Selection in Linear Regression Model and Application (선형회귀모델의 변수선택을 위한 다중목적 유전 알고리즘과 응용)

  • Kim, Dong-Il;Park, Cheong-Sool;Baek, Jun-Geol;Kim, Sung-Shick
    • Journal of the Korea Society for Simulation
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    • v.18 no.4
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    • pp.137-148
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    • 2009
  • The purpose of this study is to implement variable selection algorithm which helps construct a reliable linear regression model. If we use all candidate variables to construct a linear regression model, the significance of the model will be decreased and it will cause 'Curse of Dimensionality'. And if the number of data is less than the number of variables (dimension), we cannot construct the regression model. Due to these problems, we consider the variable selection problem as a combinatorial optimization problem, and apply GA (Genetic Algorithm) to the problem. Typical measures of estimating statistical significance are $R^2$, F-value of regression model, t-value of regression coefficients, and standard error of estimates. We design GA to solve multi-objective functions, because statistical significance of model is not to be estimated by a single measure. We perform experiments using simulation data, designed to consider various kinds of situations. As a result, it shows better performance than LARS (Least Angle Regression) which is an algorithm to solve variable selection problems. We modify algorithm to solve portfolio selection problem which construct portfolio by selecting stocks. We conclude that the algorithm is able to solve real problems.

Memory Organization for a Fuzzy Controller.

  • Jee, K.D.S.;Poluzzi, R.;Russo, B.
    • Proceedings of the Korean Institute of Intelligent Systems Conference
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    • 1993.06a
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    • pp.1041-1043
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    • 1993
  • Fuzzy logic based Control Theory has gained much interest in the industrial world, thanks to its ability to formalize and solve in a very natural way many problems that are very difficult to quantify at an analytical level. This paper shows a solution for treating membership function inside hardware circuits. The proposed hardware structure optimizes the memoried size by using particular form of the vectorial representation. The process of memorizing fuzzy sets, i.e. their membership function, has always been one of the more problematic issues for the hardware implementation, due to the quite large memory space that is needed. To simplify such an implementation, it is commonly [1,2,8,9,10,11] used to limit the membership functions either to those having triangular or trapezoidal shape, or pre-definite shape. These kinds of functions are able to cover a large spectrum of applications with a limited usage of memory, since they can be memorized by specifying very few parameters ( ight, base, critical points, etc.). This however results in a loss of computational power due to computation on the medium points. A solution to this problem is obtained by discretizing the universe of discourse U, i.e. by fixing a finite number of points and memorizing the value of the membership functions on such points [3,10,14,15]. Such a solution provides a satisfying computational speed, a very high precision of definitions and gives the users the opportunity to choose membership functions of any shape. However, a significant memory waste can as well be registered. It is indeed possible that for each of the given fuzzy sets many elements of the universe of discourse have a membership value equal to zero. It has also been noticed that almost in all cases common points among fuzzy sets, i.e. points with non null membership values are very few. More specifically, in many applications, for each element u of U, there exists at most three fuzzy sets for which the membership value is ot null [3,5,6,7,12,13]. Our proposal is based on such hypotheses. Moreover, we use a technique that even though it does not restrict the shapes of membership functions, it reduces strongly the computational time for the membership values and optimizes the function memorization. In figure 1 it is represented a term set whose characteristics are common for fuzzy controllers and to which we will refer in the following. The above term set has a universe of discourse with 128 elements (so to have a good resolution), 8 fuzzy sets that describe the term set, 32 levels of discretization for the membership values. Clearly, the number of bits necessary for the given specifications are 5 for 32 truth levels, 3 for 8 membership functions and 7 for 128 levels of resolution. The memory depth is given by the dimension of the universe of the discourse (128 in our case) and it will be represented by the memory rows. The length of a world of memory is defined by: Length = nem (dm(m)+dm(fm) Where: fm is the maximum number of non null values in every element of the universe of the discourse, dm(m) is the dimension of the values of the membership function m, dm(fm) is the dimension of the word to represent the index of the highest membership function. In our case then Length=24. The memory dimension is therefore 128*24 bits. If we had chosen to memorize all values of the membership functions we would have needed to memorize on each memory row the membership value of each element. Fuzzy sets word dimension is 8*5 bits. Therefore, the dimension of the memory would have been 128*40 bits. Coherently with our hypothesis, in fig. 1 each element of universe of the discourse has a non null membership value on at most three fuzzy sets. Focusing on the elements 32,64,96 of the universe of discourse, they will be memorized as follows: The computation of the rule weights is done by comparing those bits that represent the index of the membership function, with the word of the program memor . The output bus of the Program Memory (μCOD), is given as input a comparator (Combinatory Net). If the index is equal to the bus value then one of the non null weight derives from the rule and it is produced as output, otherwise the output is zero (fig. 2). It is clear, that the memory dimension of the antecedent is in this way reduced since only non null values are memorized. Moreover, the time performance of the system is equivalent to the performance of a system using vectorial memorization of all weights. The dimensioning of the word is influenced by some parameters of the input variable. The most important parameter is the maximum number membership functions (nfm) having a non null value in each element of the universe of discourse. From our study in the field of fuzzy system, we see that typically nfm 3 and there are at most 16 membership function. At any rate, such a value can be increased up to the physical dimensional limit of the antecedent memory. A less important role n the optimization process of the word dimension is played by the number of membership functions defined for each linguistic term. The table below shows the request word dimension as a function of such parameters and compares our proposed method with the method of vectorial memorization[10]. Summing up, the characteristics of our method are: Users are not restricted to membership functions with specific shapes. The number of the fuzzy sets and the resolution of the vertical axis have a very small influence in increasing memory space. Weight computations are done by combinatorial network and therefore the time performance of the system is equivalent to the one of the vectorial method. The number of non null membership values on any element of the universe of discourse is limited. Such a constraint is usually non very restrictive since many controllers obtain a good precision with only three non null weights. The method here briefly described has been adopted by our group in the design of an optimized version of the coprocessor described in [10].

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