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An efficient alignment algorithm for masked sequences
Kim, Jin Wook,Park, Kunsoo Elsevier 2007 Theoretical computer science Vol.370 No.1
<P><B>Abstract</B></P><P>We consider the alignment problem where sequences may have masked regions. The bases in masked regions are either unspecified or unknown, and they will be denoted by N. We present an efficient algorithm that finds an optimal local alignment by skipping such masked regions of sequences. Our algorithm works for both the affine gap penalty model and the linear gap penalty model. The time complexity of our algorithm is O((n−T)(m−S)+vm+wn) time, where n and m are the lengths of given sequences A and B, T and S are the numbers of base N in A and B, and v and w are the numbers of masked regions in A and B, respectively.</P>
ON GENERALIZED VECTOR QUASI-VARIATIONAL TYPE INEQUALITIES
Cho, Y.J.,Salahuddin, Salahuddin,Ahmad, M.K. The Youngnam Mathematical Society 2010 East Asian mathematical journal Vol.26 No.1
In this paper, we consider and study a new class of generalized vector quasi-variational type inequalities and obtain some existence theorems for both under compact and noncompact assumptions in topological vector spaces without using monotonicity. For the noncompact case, we use the concept of escaping sequences.
ON GENERALIZED VECTOR QUASI-VARIATIONAL TYPE INEQUALITIES
Y. J. Cho,M. K. Ahmad,Salahuddin 영남수학회 2010 East Asian mathematical journal Vol.26 No.1
In this paper, we consider and study a new class of generalized vector quasi-variational type inequalities and obtain some existence theorems for both under compact and noncompact assumptions in topological vector spaces without using monotonicity. For the noncompact case, we use the concept of escaping sequences.
Kim, Y.-K.,Park, H.-W.,Yang, J.-S.,Oh, S.-Y.,Chang, Y.-S.,Shin, E.-S.,Lee, J.-E.,Kim, S.,Gho, Y. S.,Cho, S.-H.,Min, K.-U.,Kim, Y.-Y. Blackwell Scientific Publications 2007 Clinical and experimental allergy Vol.37 No.4
<P>Summary</P><P>Background</P><P>The hyper-sensitivity reaction of IgE, with its high-affinity receptors (FcϵRI), is central to the phenomenon of atopic diseases.</P><P>Objective</P><P>To evaluate the genetic effects of non-synonymous single-nucleotide polymorphisms (SNPs) of FcϵRI on intermediate phenotypes of asthma, i.e. atopy and airway hyper-responsiveness (AHR), in the Korean general population.</P><P>Subjects and methods</P><P>Atopy and AHR were evaluated in a cohort of 2055 subjects, aged 10–18 years, using skin prick tests (SPTs) for common aeroallergens and total serum IgE and methacholine bronchial provocation tests. All FcϵRI-α, FcϵRI-β, and FcϵRI-γ gene exons of 24 healthy subjects were sequenced to locate informative non-synonymous SNPs (minor allele frequency >2%). Informative SNPs were then scored, using the high-throughput single base extension method. Relative risk (RR) was determined by multiple logistic regression analysis, after adjusting for confounding factors. The functional relevance of non-synonymous SNPs was analysed using the sorting intolerant from tolerant (SIFT) program.</P><P>Results</P><P>The SNP search found only one informative non-synonymous SNP in FcϵRI-β: E237G (minor allele frequency=0.21). The positive rate of AHR was lower among subjects with the 237<SUP>*</SUP>E allele than among those with 237<SUP>*</SUP>G [RR (95% confidence interval)=0.41 (0.19–0.89); <I>P</I>=0.01]. However, the E237G substitution was not associated with either a positive SPT response or total serum IgE levels. Sequence evolution analysis predicted that the E237G variation is an intolerant amino acid substitution, with functional importance.</P><P>Conclusion</P><P>In the Korean general population, AHR is significantly associated with the E237G polymorphism of FcϵRI-β, which results in an intolerant amino acid substitution.</P>
Poly Buragohain,Peng Lin,Ankit Garg,Sreedeep S,David Hui 대한토목학회 2019 KSCE JOURNAL OF CIVIL ENGINEERING Vol.23 No.12
Inorganic macro cations (Na+, K+ and Ca+) co-exist in agricultural and municipal landfill sites. The retention behavior of these ions in different soils and combinations (binary and ternary system) has not been fully understood by previous studies. This study seeks to probe into the retention behavior of macro cations (Na+, K+, Ca+2) in six different soils under multiple combinations of ions solution. The retention of common ions was quantified by using Freundlich and Langmuir isotherms. Na+ (single) pollutant-soil interaction was desorbed in most of the soils. The retention of K+ and Ca+2 was much greater than that of Na+. There is no definite trend for retention of Na+ in the presence of K+. For all soils, the retention results of K+ in the presence of Na+ decreased. Affinity for K+ was greater than that for Ca+2 in most of the soils. This study also demonstrated the affinity sequence of the ion retention for each soil and the percentage reduction of ions in competition with respect to single ions. Anomalous trends of the isotherm parameter fitting suggested the limitation of the mathematical models in predicting the experimental data. These results can be helpful in improving accuracy of fate prediction of pollutant fate and thus, design of waste containment facilities for various wastes that contains inorganic ions.
김지만,박종옥,신영희,Kim, Ji-Man,Park, Jong-Ok,Shin, Young-Hee 대한약학회 2008 약학회지 Vol.52 No.1
Alismatis Rhizoma has been used as diuretics and antiphlogistics in the Chinese oriental medicine. A trypsin inhibitor was isolated from Alismatis Rhizoma using DEAE ion exchange column, trypsin affinity column, and FPLC chromatography, and its activity and characteristics were studied. The purifed Alismatis Rhizoma trypsin inhibitor (ARTI) was estimated to be about 22 kDa. The sequence determination on N-terminal amino acid residues and 84 amino acid residues has been completed, yet no homology has been found with trypsin inhibitors reported at NCBI. ARTI did not show inhibitory activities on chymotrypsin and elastase, however it exhibited a significant inhibitory activity on bovine trypsin, and formed a complex with rat liver 10-formyltetrahydrofolate dehydrogenase.
N과 X를 포함하는 DNA 서열을 위한 효율적인 지역정렬 알고리즘
김진욱(Jin Wook Kim) 한국정보과학회 2010 정보과학회 컴퓨팅의 실제 논문지 Vol.16 No.3
지역정렬(local alignment) 알고리즘은 주어진 두 서열에서 서로 유사한 부분 문자열을 찾아내는 알고리즘이다. DNA 서열은 A, C, G, T 외에 N과 X도 가질 수 있는데, N과 X는 DNA로부터 염기배열 정보를 뽑아낼 때 실험적인 이유로 혹은 다른 이유로 일부 배열 정보를 잃어버린 경우에 사용된다. 본 논문에서는 A, C, G, T 이외에 N과 X를 모두 갖는 DNA 서열의 affine gap penalty metric에 대한 지역정렬을 찾는 효율적인 알고리즘을 제시한다. 이는 N만 처리할 수 있는 Kim-Park 알고리즘을 N과 X를 모두 처리할 수 있도록 성공적으로 확장한 결과이며, 더불어 새로운 문자가 추가되더라도 바로 적용이 가능한 일반화된 결과이다. A local alignment algorithm finds a substring pair of given two strings where two substrings of the pair are similar to each other. A DNA sequence can consist of not only A, C, G, and T but also N and X where N and X are used when the original bases lose their information for various reasons. In this paper, we present an efficient local alignment algorithm for two DNA sequences including N and X using the affine gap penalty metric. Our algorithm is an extended version of the Kim-Park algorithm and can be extended in case of including other characters which have similar properties to N and X.
Democracy and the Human Development Sequence
Jairo Acuñ,a–,Alfaro 연세대학교 빈곤문제국제개발연구원 2012 Journal of Poverty Alleviation and International D Vol.3 No.2
This paper provides a parsimonious empirical test of the relationship between democracy and HD, using time-series cross-sectional data on 164 countries from 1972 to 2002. The paper specifies a similar partial model to those found in the global comparative literature on democracy and development in an effort to replicate earlier findings and advance the proposition that there are strong reciprocal connections between HD and democratization that form two chains which reinforce one another cumulatively over time. The statistical analysis aims to show that the causal relationship forms two chains that run in both directions. This gives rise to virtuous and vicious circles, with good or bad performance on human development and democracy reinforcing each other. Cross-country partial regressions show a significant relationship in both directions. Yet evidence over time has strong sequential implications, and where a choice is necessary, democracy should be given sequencing priority over HD and economic growth, respectively. The discussion is relevant in lieu of ongoing debates about post 2015 Millennium Development Goals in regards to governance and democratization.