Adaptive Quantile Estimation and its Application in Analysis of Biological Signals

Quantiles and their estimations are the basis for solving numerous problems of statistics. The paper presents adaptive recursive estimation methods for this statistical parameter. Its specifical properties are investigated and the possibilities of applications in computer assisted analysis of biological signals are demonstrated even satisfying real time requirements.     

Firefly luciferase: Purification and immobilization

The state of the art of firefly luciferase research is reviewed with special emphasis on its purification and immobilization. The notion of bioluminescence and its role in APT monitoring is described. The need to purify luciferase and the advantages of immobilization are discussed. An insight into the existing methods of luciferase purification and immobilization is given. The scope of the bioluminescent assay is underlined.     

自适应蚁群算法在DNA中的应用

主要讨论了自适应蚁群算法在DNA序列比对中的应用,主要的过程是：首先,我们设一个计分函数和一个得分策略,在任意给出一对DNA序列,建立一个序列比对矩阵．现由4只蚂蚁从左上角向右下角移动,并且最终到达右下角,那么这4只蚂蚁随意走出4条路径,根据4条路径得出4对等长的比对,再依照计分函数分别计算出4条路径的比对得分,再由1．3式进一步验证4条路径的平均得分值,取其中得分最高（即最优路径）路径;进行第二次信息素增量的调整,方法是根据蚂蚁所走过的方向和该方向上得分比例计算出来的,信息素的变化量利用矩阵来存储,那么下一次蚂蚁所选的路径就要根据以前在各条路径上的信息素浓度总和的大小选择移动方向,最终经过有限次迭代,蚂蚁就会找到一条最优路径,也就是一条与原来DNA最相似的DNA链．     

An Evolutionary Firefly Algorithm for the Estimation of Nonlinear Biological Model Parameters

The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test.     

Firefly luminescence: a historical perspective and recent developments.

Significant advances have occurred regarding our knowledge of firefly luciferase mechanisms. Although most of this progress was an outcome of molecular biology and structural studies, important achievements have also occurred on its fundamental chemistry. Those developments are here summarized and presented in a historical perspective.     

Adaptive Barebones Salp Swarm Algorithm with Quasi-oppositional Learning for Medical Diagnosis Systems:A Comprehensive Analysis

The Salp Swarm Algorithm(SSA)may have trouble in dropping into stagnation as a kind of swarm intelligence method.This paper developed an adaptive barebones salp...     

萤火虫的发光行为及其功能起源

发光生物因其活体能自发荧光而倍受关注,萤火虫(鞘翅目:萤科)是被研究最多的发光生物,因为成虫发光在其性选择以及求偶交配中起着重要作用.由于萤火虫的发光是一个消耗能量(ATP),的化学反应过程,因而其发光在成虫之外的虫态也具有重要意义.本文就萤火虫成虫和幼虫的发光行为、功能意义进行了综述,并结合萤火虫的饲养观察对其卵和蛹的发光行为进行了描述,探讨了卵和蛹的形态阶段发光的生物学功能以及生物荧光的起源进化.这将有助于理解萤火虫及其它生物自发荧光的本质和起源进化过程.     

Properties of the Proximate Parameter Tuning Regularization Algorithm

An important aspect of systems biology research is the so-called “reverse engineering” of cellular metabolic dynamics from measured input-output data. This allows researchers to estimate and validate both the pathway’s structure as well as the kinetic constants. In this paper, the recently published ‘Proximate Parameter Tuning’ (PPT) method for the identification of biochemical networks is analysed. In particular, it is shown that the described PPT algorithm is essentially equivalent to a sequential linear programming implementation of a constrained optimization problem. The corresponding objective function consists of two parts, the first emphasises the data fitting where a residual 1-norm is used, and the second emphasises the proximity of the calculated parameters to the specified nominal values, using an ∞-norm. The optimality properties of PPT algorithm solution as well as its geometric interpretation are analyzed. The concept of optimal parameter locus is applied for the exploration of the entire family of optimal solutions. An efficient implementation of the parameter locus is also developed. Parallels are drawn with 1-norm parameter deviation regularization which attempt to fit the data with a minimal number of parameters. Finally, a small example is used to illustrate all of these properties.     

Firefly bioluminescence: a mechanistic approach of luciferase catalyzed reactions

Luciferase is a general term for enzymes catalyzing visible light emission by living organisms (bioluminescence). The studies carried out with Photinus pyralis (firefly) luciferase allowed the discovery of the reaction leading to light production. It can be regarded as a two-step process: the first corresponds to the reaction of luciferase's substrate, luciferin (LH(2)), with ATP-Mg(2+) generating inorganic pyrophosphate and an intermediate luciferyl-adenylate (LH(2)-AMP); the second is the oxidation and decarboxylation of LH(2)-AMP to oxyluciferin, the light emitter, producing CO(2), AMP, and photons of yellow-green light (550- 570 nm). In a dark reaction LH(2)-AMP is oxidized to dehydroluciferyl-adenylate (L-AMP). Luciferase also shows acyl-coenzyme A synthetase activity, which leads to the formation of dehydroluciferyl-coenzyme A (L-CoA), luciferyl-coenzyme A (LH(2)-CoA), and fatty acyl-CoAs. Moreover luciferase catalyzes the synthesis of dinucleoside polyphosphates from nucleosides with at least a 3'-phosphate chain plus an intact terminal pyrophosphate moiety. The LH(2) stereospecificity is a particular feature of the bioluminescent reaction where each isomer, D-LH(2) or L-LH(2), has a specific function. Practical applications of the luciferase system, either in its native form or with engineered proteins, encloses the analytical assay of metabolites like ATP and molecular biology studies with luc as a reporter gene, including the most recent and increasing field of bioimaging.     

Discriminant Analysis and its Application to Medical Data

Discriminant procedures are often used to classify data based on observed characteristics of the response variables. This paper discusses the validation techniques in the use of discriminant function approach. Numerical example is used to illustrate its application.     

中国萤火虫云南窗萤荧光素酶cDNA的克隆表达和序列分析

从一种来自中国日行性萤火虫(云南窗萤)发光器官mRNA中克隆、测序并表达了有功能的荧光素酶.云南窗萤荧光素酶的cDNA序列有1647个碱基,编码548个氨基酸残基.从推测得到的氨基酸序列的比对分析得出:云南窗萤的荧光素酶与来自Lampyris noctiluca,L.turkestanicus和Nyctophila cf.caucasica三种萤火虫的荧光素酶有97.8%的序列一致性.从推测得出的氨基酸序列进行系统发育分析,其结果表明:云南窗萤和Lampyris Nyctophila聚在一起,与同属的发光强夜行性的萤火虫不形成的单系.云南窗萤荧光素酶在大肠杆菌中表达的条带大约70kDa,并且在有荧光素存在时发出黄绿色荧光.对荧光素酶的结构模拟和分析表明,云南窗萤荧光素酶基因的氨基端和羧基端结构域之间的裂沟处存在这5个多肽环,这正是从其他荧光素酶推测得到的催化荧光反应时的底物结合位点.云南窗萤和窗萤属的其他3种萤火虫的荧光素酶卡目比,有13个不同氨基酸位点,位于模拟分子结构的表面.对于这些多肽环、不刚氨基酸残基和晶体结构的进一步研究有利于解释日行和夜行性萤火虫荧光素酶的差异.     

A Brief Review: The Z-curve Theory and its Application in Genome Analysis

In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.     

Firefly Courtship: Behavioral and Morphological Predictors of Male Mating Success in Photinus greeni

Differences in male mating success can generate selection on male morphological traits and courtship behaviors involved in male–male competition or female mate choice. In Photinus fireflies (Coleoptera: Lampyridae), courtship is based on bioluminescent flash signals produced by both sexes. We conducted field observations of Photinus greeni fireflies engaged in competitive courtships, in which females are able to simultaneously assess several males, to identify male morphological traits and courtship behaviors that might predict male mating success. Male morphological traits did not differ between males that successfully mated compared with unsuccessful males (dialoging males that did not mate). However, courtship behavioral interactions differed: successful males tended to have higher flash pattern rates (number of flash patterns per minute), and their courtship flashes were more likely to be answered by females. We also examined how the risk of predation by Photuris fireflies altered courtship behavior of their Photinus prey. When predatory Photuris fireflies were present, P. greeni females were less likely to mate, and showed decreased flash responses to most males. However, P. greeni males that did successfully mate in spite of Photuris presence were males that maintained high flash pattern rates that elicited female responses. These results suggest that both female mate choice and Photuris predation exert strong selective pressures on the evolution of courtship signals in Photinus fireflies.     

Experimental Evaluation of a Braille-Reading-Inspired Finger Motion Adaptive Algorithm

Braille reading is a complex process involving intricate finger-motion patterns and finger-rubbing actions across Braille letters for the stimulation of appropriate nerves. Although Braille reading is performed by smoothly moving the finger from left-to-right, research shows that even fluent reading requires right-to-left movements of the finger, known as “reversal”. Reversals are crucial as they not only enhance stimulation of nerves for correctly reading the letters, but they also show one to re-read the letters that were missed in the first pass. Moreover, it is known that reversals can be performed as often as in every sentence and can start at any location in a sentence. Here, we report experimental results on the feasibility of an algorithm that can render a machine to automatically adapt to reversal gestures of one’s finger. Through Braille-reading-analogous tasks, the algorithm is tested with thirty sighted subjects that volunteered in the study. We find that the finger motion adaptive algorithm (FMAA) is useful in achieving cooperation between human finger and the machine. In the presence of FMAA, subjects’ performance metrics associated with the tasks have significantly improved as supported by statistical analysis. In light of these encouraging results, preliminary experiments are carried out with five blind subjects with the aim to put the algorithm to test. Results obtained from carefully designed experiments showed that subjects’ Braille reading accuracy in the presence of FMAA was more favorable then when FMAA was turned off. Utilization of FMAA in future generation Braille reading devices thus holds strong promise.