基于质粒DNA匹配问题的分子算法

给定无向图,图的最小极大匹配问题是寻找每条边都不相邻的最大集中的最小者,这个问题是著名的NP-完全问题.1994年Adleman博士首次提出用DNA计算解决NP-完全问题,以编码的DNA序列为运算对象,通过分子生物学的运算操作解决复杂的数学难题,使得NP-完全问题的求解可能得到解决.提出了基于质粒DNA的无向图的最大匹配问题的DNA分子生物算法,通过限制性内切酶的酶切和凝胶电泳完成解的产生和最终接的分离,依据分子生物学的实验手段,算法是有效并且可行的.     

Construction of Selection Indexes with Restrictions

In this paper the problem of unistage selection with inequality constraints is formulated. If the predictor and criterion variables are all normally distributed, this problem can be written as a convex programming problem, with a linear objective function and with linear constraints and a quadratic constraint. Using the duality theory, for convex nonlinear programming it is proved, that its dual problem can be transformed into a convex minimization problem with non-negativity conditions. Good computational methods are known for solving this problem. By the help of the dual problem sufficient conditions for a solution of the original primal problem are derived and illustrated by an example of practical interest.     

“Templatic backcopying” in Guarijio abbreviated reduplication

Although a wide array of phonological properties seem to backcopy in reduplication, it is an open question whether reduplicative templates can backcopy as well. It has been argued that natural languages do not have reduplicative constructions where the base truncates to match the truncated reduplicant (McCarthy & Prince, 1994; McCarthy & Prince, 1999; Spaelti, 1997; inter alia). In Guarijio Abbreviated Reduplication (Miller, 1996), however, both copies of the reduplicative construction truncate, instantiating the pattern that has been claimed not to exist. This paper argues that the Guarijio case fills this typological gap. Although the data can be given a templatic backcopying analysis, this paper defends a Morphological Doubling Theory (MDT) analysis using cophonologies (Inkelas & Zoll, 2005). In MDT, Guarijio Abbreviated Reduplication results from the parallel imposition of a truncating cophonology in each copy of the reduplicative construction. Guarijio Abbreviated Reduplication is predicted to exist by MDT together with other documented cases of parallel phonological modification in reduplication. I am grateful to many people for helpful comments and suggestions, including Isabel Barreras Aguilar, Laura Downing, Nicholas Fleisher, Andrew Garrett, Jason Haugen, Larry Hyman, Yuni Kim, Teresa McFarland, David Mortensen, Mary Paster, Eric Raimy, and Timothy Thornes as well as the audience of the LSA 2005 Annual Meeting in Oakland. I would like to extend a special thanks to Alan Yu for his detailed comments and suggestions to latter versions of this paper. I am particularly indebted to Sharon Inkelas, for her generous advice, feedback, and numerous discussions throughout the development of this paper. I am also grateful to two anonymous reviewers for their comments and criticisms, and especially to Ingo Plag for his patience and detailed suggestions as editor. All remaining errors and omissions are mine. This study was made possible by fellowships by CONACYT (Consejo Nacional de Ciencia y Tecnología, México), the University of California Institute for Mexico and the United States (UCMEXUS) and Fulbright.     

Structuring policy problems for plastics,the environment and human health: reflections from the UK

How can we strengthen the science–policy interface for plastics, the environment and human health? In a complex policy area with multiple stakeholders, it is important to clarify the nature of the particular plastics-related issue before trying to understand how to reconcile the supply and demand for evidence in policy. This article proposes a simple problem typology to assess the fundamental characteristics of a policy issue and thus identify appropriate processes for science–policy interactions. This is illustrated with two case studies from one UK Government Department, showing how policy and science meet over the environmental problems of plastics waste in the marine environment and on land. A problem-structuring methodology helps us understand why some policy issues can be addressed through relatively linear flows of science from experts to policymakers but why others demand a more reflexive approach to brokering the knowledge between science and policy. Suggestions are given at the end of the article for practical actions that can be taken on both sides.     

The paradox of magnetobiology: Analysis and prospects for solution

The formulation, content, and corollaries of the so-called kT problem are considered. The problem points to a paradox in the biological effect of weak low-frequency magnetic fields. The conventional formulation of the problem contains implicit assumptions that prove not fully valid according to the results of analysis.     

Clusterings should not be compared by visual inspection: response to Gagné & Proulx

In Heikinheimo et al . ( Journal of Biogeography , 2007, 34 , 1053–1064) we used clustering to analyse European land mammal fauna. Gagné & Proulx criticized our choice of the Euclidean distance measure in the analysis, and advocated the use of the Hellinger distance measure, claiming that this leads to very different clustering results. The criticism fails to take into account the probabilistic nature of the methods used and the fact that in this case the similarity measures correlate strongly. Gagné & Proulx used subjective inspection as the criterion of similarity between clusterings. We show that this is insufficient and misleading. Namely, owing to the local minimum problem, two clustering runs rarely give identical results. In the case of our study, the measured similarity (using the kappa statistic) between the Euclidean- and Hellinger-based clusterings is roughly equal to the similarity between two clusterings that both use the Hellinger distance but different random initialization points.     

An efficient algorithm for DNA fragment assembly in MapReduce

Fragment assembly is one of the most important problems of sequence assembly. Algorithms for DNA fragment assembly using de Bruijn graph have been widely used. These algorithms require a large amount of memory and running time to build the de Bruijn graph. Another drawback of the conventional de Bruijn approach is the loss of information. To overcome these shortcomings, this paper proposes a parallel strategy to construct de Bruijin graph. Its main characteristic is to avoid the division of de Bruijin graph. A novel fragment assembly algorithm based on our parallel strategy is implemented in the MapReduce framework. The experimental results show that the parallel strategy can effectively improve the computational efficiency and remove the memory limitations of the assembly algorithm based on Euler superpath. This paper provides a useful attempt to the assembly of large-scale genome sequence using Cloud Computing.