Background: Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common ori...
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Background: Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of substitutions are additionally involved in the divergence, the homology detection becomes difficult even at the DNA level. Results: We developed a novel method to infer distant homology relations of two proteins, that accounts for frameshift and point mutations that may have affected the coding sequences. We design a dynamicprogramming alignment algorithm over memory-efficient graph representations of the complete set of putative DNA sequences of each protein, with the goal of determining the two putative DNA sequences which have the best scoring alignment under a powerful scoring system designed to reflect the most probable evolutionary process. Our implementation is freely available at http://***/path/. Conclusions: Our approach allows to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples.
When Hamiltonians are nonsmooth, we define viscosity solutions of the Aronsson equation and prove that value functions of the corresponding deterministic optimal control problems are solutions if they are bilateral vi...
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When Hamiltonians are nonsmooth, we define viscosity solutions of the Aronsson equation and prove that value functions of the corresponding deterministic optimal control problems are solutions if they are bilateral viscosity solutions of the Hamilton-Jacobi-Bellman equation. We characterize such a property in several ways, in particular it follows that a value function which is an absolute minimizer is a bilateral viscosity solution of the HJB equation and these two properties are often equivalent. We also determine that bilateral solutions of HJB equations are unique among absolute minimizers with prescribed boundary conditions.
This paper explores the optimization of an ice-storage air conditioning system in consideration of both minimal life-cycle cost and efficiency of ice-storage tank. Such air-conditioning system consists primarily of ic...
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This paper explores the optimization of an ice-storage air conditioning system in consideration of both minimal life-cycle cost and efficiency of ice-storage tank. Such air-conditioning system consists primarily of ice-storage tank, screw-type chiller and auxiliary equipment. Optimization is carried Out using dynamicprogramming algorithm, where the power consumption models of the chiller and its auxiliary equipment as well as the heat transport in ice-storage tank are established based on manufacturer's data. Initial cost and operation cost are objective functions, and the performance of chiller and ice-storage tanks are constraints. Through simulation analysis using numerical program, system optimization and analysis are carried out to obtain optimum chiller and ice-storage tank capacity. Finally, results are used to probe some design guidelines regarding life-cycle cost and payback period under chiller priority and ice priority control strategies. (C) 2004 Elsevier Ltd. All rights reserved.
Saliva has great potential as a bio-fluid for point-of-use measurement of the human stress response. The purpose of this study was to evaluate the diurnal variation of salivary cortisol (CORT) and salivary amylase act...
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ISBN:
(纸本)9781845642013
Saliva has great potential as a bio-fluid for point-of-use measurement of the human stress response. The purpose of this study was to evaluate the diurnal variation of salivary cortisol (CORT) and salivary amylase activity (SAA) under the condition of a fatigued state. The subjects were I I emergency medical doctors who worked for the Department of Emergency and Critical Care Medicine in 24 h-shifts, and their diurnal variations were measured three times in one month during the 24h-shift workday. As a control experiment, 6 subjects' diurnal variations were measured during a holiday period. The saliva samples were collected 4 times in total during an examination. The mean CORT of a workday showed its lowest value of 1.07 +/- 0.55 ng/ml before sleep (24:00), and was highest at 4.76 +/- 3.16 ng/ml at the start of a daytime duty (9:00) (p < 0.01). In contrast, the mean CORT of a holiday showed its lowest value of 1.48 +/- 1.00 ng/ml in the afternoon and a highest value of 4.74 +/- 2.76 ng/ml the next morning (p < 0.05). The mean SAA of a workday showed its lowest value of 59.3 +/- 31.5 kU/l during a daytime duty (12:00- 14:00) and was highest at 112.7 +/- 90.1 kU/l at the start of night-time duty (18:00). These salivary biomarkers CORT and SAA on both workdays and holidays showed diurnal variation. In particular, the diurnal variation of CORT followed a well-defined 'bath-tub' shaped curve. A negative correlation of -0.36 was observed between the individual's CORT and SAA in workdays and of -0.62 in holidays, as determined by using the dynamic programming method. It was suggested that the fatigued state of humans is possibly reflected in the diurnal variations of CORT and SAA.
We consider a serial supply chain consisting of a supplier and a manufacturer, where production, inventory, transportation, backlogging and subcontracting decisions are integrated. A sequence of deterministic but non-...
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ISBN:
(纸本)9781424439706
We consider a serial supply chain consisting of a supplier and a manufacturer, where production, inventory, transportation, backlogging and subcontracting decisions are integrated. A sequence of deterministic but non-stationary demands of the manufacturer for single good needs to be satisfied by the supplier over a finite horizon. In each period, the supplier can produce items by himself, also can use the subcontracting option if he can not satisfy the manufacturer's need, or due to the cost consideration. Generally, manufacturer's order decisions can influence the supplier's profits straightly, and on the contrary, supplier's plan of production also can influence the cost of manufacturer. Hence, it is not appropriate to take them as one group with public benefit sometimes. We establish a bi-level programming model in which the manufacturer is the leader, the supplier is the follower and the production and subcontracting capacities are stationary. The manufacturer as the leader, first gives the decisions of ordering, aiming to reduce the cost of himself, then the follower-supplier, decides his plan of production or subcontracting according to the manufacture's order to minimize his own cost. By solving the model, we can get the relative optimal schemes satisfied by both of the manufacturer and the supplier.
A mathematical model of tumor growth therapy is considered. The total amount of a drug is bounded and fixed. The problem is to choose an optimal therapeutic strategy, i.e., to choose an amount of the drug permanently ...
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A mathematical model of tumor growth therapy is considered. The total amount of a drug is bounded and fixed. The problem is to choose an optimal therapeutic strategy, i.e., to choose an amount of the drug permanently affecting the tumor that minimizes the number of tumor cells by a given time. The problem is solved by the dynamic programming method. Exact and approximate solutions to the corresponding Hamilton-Jacobi-Bellman equation are found. An error estimate is proved. Numerical results are presented.
Regarding the current situation and problems, which exist in Modular Company's dispatch dynamicprogramming system that is widely used in open-pit truck real-time dispatching, two concepts for the completion of pr...
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Regarding the current situation and problems, which exist in Modular Company's dispatch dynamicprogramming system that is widely used in open-pit truck real-time dispatching, two concepts for the completion of production target and the current truck flow saturation were proposed, and based on which the guideline of real-time optimized open-pit truck dispatching method was dissertated. Based on the results of truck flow programming, and the system stochastic factors and the transportation distance being taken into account, the truck real-time dispatching was optimized in its entirety. This method is not only suitable for the instance of shovel-truck matched, but also applicable for that of shovel-truck mismatched. And it also can be applied to empty truck dispatching as well as heavy truck dispatching. This method being used in an open-pit mine, it has been proved that production efficiency could be increased by 8.0%~17.8%. The result shows this method has better applicability and practicability.
An exhaust duct system in semiconductor factory is designed using the dynamic programming method (DPM), which considers system pressure equilibrium and the least life-cycle cost to derive the duct size and fan capacit...
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An exhaust duct system in semiconductor factory is designed using the dynamic programming method (DPM), which considers system pressure equilibrium and the least life-cycle cost to derive the duct size and fan capacity. An example of alkaline gas exhaust system is provided to understand the characteristics of DPM and to compare with the conventional duct design methods. Since DPM contains the concept of minimizing the life-cycle cost, the design results not only guarantee each path to share the same pressure, but also bear a smaller cost than other methods. The limit on duct diameter or flow velocity is added to the computation process. As a result, all the derived outcomes satisfy the requirements on the range of duct diameter or flow velocity. The differences between the design and simulation (actual operation) results under DPM are much lower than those of other methods. Thus, an exhaust duct system that best approximates the actual operation may be designed using DPM. (C) 2003 Published by Elsevier Science Ltd.
Background: Non-coding DNA sequences comprise a very large proportion of the total genomic content of mammals, most other vertebrates, many invertebrates, and most plants. Unraveling the functional significance of non...
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Background: Non-coding DNA sequences comprise a very large proportion of the total genomic content of mammals, most other vertebrates, many invertebrates, and most plants. Unraveling the functional significance of non-coding DNA depends on how well we are able to align non-coding DNA sequences. However, the alignment of non-coding DNA sequences is more difficult than aligning protein-coding sequences. Results: Here we present an improved pair-hidden-Markov-Model (pair HMM) based method for performing global pairwise alignment of non-coding DNA sequences. The method uses an explicit model of indel length frequency distribution which can be specified, and allows any time reversible model of nucleotide substitution. The method uses a deterministic global optimiser to find the alignment with the highest posterior probability. We test MCALIGN2 in simulations, and compare it to a previous Monte Carlo based method (MCALIGN), to the pair HMM method of Knudsen and Miyamoto, and to a heuristic method (AVID) that performed very well in a previous simulation study. We show that the pair HMM methods have excellent performance for all combinations of parameter values we have considered. MCALIGN2 is up to ten times faster than MCALIGN. MCALIGN2 is more accurate in resolving indels given an accurate explicit model than heuristic methods, but is computationally slower. Conclusion: MCALIGN2 produces better quality alignments by explicitly using biological knowledge about the indel length distribution and time reversible models of nucleotide substitution. As a result, it can outperform other available sequence alignment methods for the cases we have considered to align non-coding DNA sequences.
This paper presents scheduling models for dispatching vehicles to accomplish a sequence of container jobs at the container terminal, in which the starting times as well as the order of vehicles for carrying out these ...
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This paper presents scheduling models for dispatching vehicles to accomplish a sequence of container jobs at the container terminal, in which the starting times as well as the order of vehicles for carrying out these jobs need to be determined. To deal with this scheduling problem, three mixed 0 - 1 integer programming models, Model I, Model II and Model III are provided. We present interesting techniques to reformulate the two mixed integer programming models, Model I and Model II, as pure 0-1 integer programming problems with simple constraint sets and present a lower bound for the optimal value of Model I. Model III is a complicated mixed integer programming model because it involves a set of non-smooth constraints, but it can be proved that its solutions may be obtained by the so-called greedy algorithm. We present numerical results showing that Model III is the best among these three models and the greedy algorithm is capable of solving large scale problems.
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