Optimal Dynamic Allocation of Conservation Funding Among Priority Regions

The optimal allocation of conservation resources between biodiverse conservation regions has generally been calculated using stochastic dynamic programming, or using myopic heuristics. These solutions are hard to interpret and may not be optimal. To overcome these two limitations, this paper approaches the optimal conservation resource allocation problem using optimal control theory. A solution using Pontryagin’s maximum principle provides novel insight into the general properties of efficient conservation resource allocation strategies, and allows more extensive testing of the performance of myopic heuristics. We confirmed that a proposed heuristic (minimize short-term loss) yields near-optimal results in complex allocation situations, and found that a qualitative allocation feature observed in previous analyses (bang-bang allocation) is a general property of the optimal allocation strategy.     

Fast, optimal alignment of three sequences using linear gap costs

Alignment algorithms can be used to infer a relationship between sequences when the true relationship is unknown. Simple alignment algorithms use a cost function that gives a fixed cost to each possible point mutation-mismatch, deletion, insertion. These algorithms tend to find optimal alignments that have many small gaps. It is more biologically plausible to have fewer longer gaps rather than many small gaps in an alignment. To address this issue, linear gap cost algorithms are in common use for aligning biological sequence data. More reliable inferences are obtained by aligning more than two sequences at a time. The obvious dynamic programming algorithm for optimally aligning k sequences of length n runs in O(n(k)) time. This is impractical if k>/=3 and n is of any reasonable length. Thus, for this problem there are many heuristics for aligning k sequences, however, they are not guaranteed to find an optimal alignment. In this paper, we present a new algorithm guaranteed to find the optimal alignment for three sequences using linear gap costs. This gives the same results as the dynamic programming algorithm for three sequences, but typically does so much more quickly. It is particularly fast when the (three-way) edit distance is small. Our algorithm uses a speed-up technique based on Ukkonen's greedy algorithm (Ukkonen, 1983) which he presented for two sequences and simple costs.     

Simulated annealing with different vessel assignment strategies for the continuous berth allocation problem

The berth allocation problem is an optimization problem concerning seaside operations at container terminals. This study investigates the dynamic and continuous berth allocation problem (BAP), whose objective is to minimize the total weighted service time and the deviation cost from vessels’ preferred position. The problem is formulated as a mixed integer programming model. Due to that the BAP is NP-hard, two efficient and effective simulated annealing (SA) algorithms are proposed to locate vessels along the quay. The first SA assigns vessels to available positions along the quay from the left to the right, while the second assigns vessels from both sides. Both small and large-scale instances in the literature are tested to evaluate the effectiveness of the proposed SA algorithms using the optimization software Gurobi and heuristic algorithms from the literature. The results indicate that the proposed SAs can provide optimal solutions in small-scale instances and updates the best solutions in large-scale instances. The improvement over other comparing heuristics is statistically significant.     

Robust optimization for resource-constrained project scheduling with uncertain activity durations

The purpose of this paper is to propose models for project scheduling when there is considerable uncertainty in the activity durations, to the extent that the decision maker cannot with confidence associate probabilities with the possible outcomes of a decision. Our modeling techniques stem from robust discrete optimization, which is a theoretical framework that enables the decision maker to produce solutions that will have a reasonably good objective value under any likely input data scenario. We develop and implement a scenario-relaxation algorithm and a scenario-relaxation-based heuristic. The first algorithm produces optimal solutions but requires excessive running times even for medium-sized instances; the second algorithm produces high-quality solutions for medium-sized instances and outperforms two benchmark heuristics.     

Heuristics for the FMS-loading and part-type-selection problems

In this article, we study the FMS-loading and part-type-selection problems, in which each part is processed by a series of operations. Two heuristic methods are presented for the objectives of balancing workloads and meeting due dates. These heuristics perform a specific evaluation of the objective function at each iteration. The goal of Heuristic#1 is to achieve workload balance. The additional goal of Heuristic#2 is to reduce the number of late part types. The loading and part-type selection must satisfy a tooling constraint. Computational results are encouraging and indicate significant improvement over the existing methods.     

Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function

Gap penalty is an important component of the scoring scheme that is needed when searching for homologous proteins and for accurate alignment of protein sequences. Most homology search and sequence alignment algorithms employ a heuristic ‘affine gap penalty’ scheme q + r × n, in which q is the penalty for opening a gap, r the penalty for extending it and n the gap length. In order to devise a more rational scoring scheme, we examined the pattern of gaps that occur in a database of structurally aligned protein domain pairs. We find that the logarithm of the frequency of gaps varies linearly with the length of the gap, but with a break at a gap of length 3, and is well approximated by two linear regression lines with R² values of 1.0 and 0.99. The bilinear behavior is retained when gaps are categorized by secondary structures of the two residues flanking the gap. Similar results were obtained when another, totally independent, structurally aligned protein pair database was used. These results suggest a modification of the affine gap penalty function.     

Sequential Decision Rules for Managing Nematodes with Crop Rotations

A dynamic model of nematode populations under a crop rotation that includes both host and nonhost crops is developed and used to conceptualize the problem of economic control. The steady state of the dynamic system is used to devise an approximately optimal decision policy, which is then applied to cyst nematode (Heterodera schachtii) control in a rotation of sugarbeet with nonhost crops. Long-run economic returns from this approximately optimal decision rule are compared with results from solution of the exact dynamic optimization model. The simple decision rule based on the steady state provides long-run average returns that are similar to the fully optimal solution. For sugarbeet and H. schachtii, the simplified rule can be calculated by maximizing a relatively simple algebraic expression with respect to the number of years in the sequence of nonhost crops. Maximization is easy because only integers are of interest and the number of years in nonhost crops is typically small. Solution of this problem indirectly yields an approximation to the optimal dynamic economic threshold density of nematodes in the soil. The decision rule requires knowledge of annual nematode population change under host and nonhost crops, and the relationship between crop yield and nematode population density.     

塔里木荒漠河岸林干扰状况与林隙特征

对塔里木河中游荒漠河岸林林隙基本特征和干扰状况进行了研究。结果表明：形成的林隙形状近似于椭圆形,椭圆长短轴比率在扩展林隙(EG)和冠空隙(CG)有所不同,平均分别为1.52和2.31;林隙密度约为62.5个?hm-2, EG和CG在塔里木荒漠河岸林景观中的面积比例分别为69.52%和29.03%,干扰频率分别为1.45%?a-1和0.61%?a-1,林隙干扰返回间隔期约为164a。林隙大小结构表现出以小林隙为主的偏正态分布,EG大小40—200m2,CG大小0—80m2。林隙形成速率为1.30个?hm-2a-1,20—30a前形成的林隙最多。林隙形成方式由树木折干 枯立形成的最为普遍,占形成木总数95.73%。林隙大多由2—5株形成木形成, 而由4株形成木创造的林隙最多,平均每个林隙拥有形成木4.1株。林隙形成木主要为森林建群种,林隙形成木分布最多的径级在5—25cm,高度在4—8m,每株形成木所能形成的EG面积为27.12m2, CG面积为11.32m2。边缘木的径级结构呈正态分布,而高度结构呈偏左的正态分布,平均每个林隙拥有8.375株边缘木,林隙边缘木平均胸径比形成木平均胸径高73.1%,表明荒漠河岸林林隙干扰十分频繁,地下水位的持续下降是林隙形成的驱动力。     

On the Relationship Between Formal and Heuristic Components in Problem Solving

The field of heuristic computer programming, which in the past decade has undergone extensive development, has come up against the difficulty of formalizing problem- solving methods peculiar to human beings. From this difficulty has arisen the problem of the relationship between heuristics (methods of heuristic search) and algorithms. In characterizing existing heuristic programs, their formulators have noted that there exists no sharp boundary between heuristics and algorithms (10). Differences that are recognized in this area result merely from the scope of the class of problems for which a program is constructed and the attendant features of the programs, such as the criteria of choice of attributes, systematization, selectivity, etc., rather than from the fundamental structure of heuristics and algorithms or their form of expression (10).     

Heuristic and optimal solutions for set-covering problems in conservation biology

Area-selection methods have recently gained prominence in conservation biology. A typical problem is to identify the minimum number of areas required to represent all species over some geographic region. Iterative heuristic methods have been developed by conservation scientists to solve these problems, although the solutions cannot be guaranteed to be optimal. Although optimal solutions can often be found, heuristics continue to be popular as they are perceived to be faster and more transparent as they are intuitively easy to understand. We used distributional data for 1921 bird species, 939 mammal species, 405 snake species, and 617 amphibian species compiled at the Zoological Museum, Univ. of Copenhagen for all 1° cells of mainland sub-Saharan Africa to compare the quality of the solutions found using two heuristic methods (simple-greedy algorithm and a progressive-rarity algorithm) with optimal solutions. We found that the heuristic methods considered here often provide solutions as good as optimal solutions. Even in those cases where the optimal solutions were better the difference was relatively small, with the heuristics providing solutions requiring a 2–10% increase in area selected compared with the optimal solution, which importantly, represented an increase of <1% of the total area. Our study also suggests that the heuristic algorithms performed least well for datasets with few single cell endemics and taxa that tend to have larger range sizes. Despite the good quality of solutions using heuristics there was no time penalty associated with finding optimal solutions for the problems considered here, suggesting that the major obstacle to their use is making optimal methods accessible to conservation biologists. We encourage conservation biologists to work with operations researchers and so gain the benefit of their expertise and experience in solving these kinds of problems.     

Gap dynamics and regeneration strategies in <Emphasis Type="Italic">Juniperus-Laurus</Emphasis> forests of the Azores Islands

We asked the following questions regarding gap dynamics and regeneration strategies in Juniperus-Laurus forests: How important are gaps for the maintenance of tree diversity? What are the regeneration strategies of the tree species? Thirty canopy openings were randomly selected in the forest and in each the expanded gap area was delimited. Inside expanded gaps the distinction was made between gap and transition zone. In the 30 expanded gaps a plot, enclosing the gap and transition zone, was placed. In order to evaluate the differences in regeneration and size structure of tree species between forest and expanded gaps, 30 control plots were also delimited in the forest, near each expanded gap. In the 60 plots the number of seedlings, saplings, basal sprouts and adults of tree species were registered. Canopy height and width of adult individuals were also measured. The areas of the 30 gaps and expanded gaps were measured and the gap-maker identified. Juniperus-Laurus forests have a gap dynamic associated with small scale disturbances that cause the death, on average, of two trees, mainly of Juniperus brevifolia. Gap and expanded gap average dimensions are 8 and 25 m², respectively. Gaps are of major importance for the maintenance of tree diversity since they are fundamental for the regeneration of all species, with the exception of Ilex azorica. Three types of regeneration behaviour and five regeneration strategies were identified: (1) Juniperus brevifolia and Erica azorica are pioneer species that regenerate in gaps from seedlings recruited after gap formation. However, Juniperus brevifolia is a pioneer persistent species capable of maintaining it self in the forest due to a high longevity and biomass; (2) Laurus azorica and Frangula azorica are primary species that regenerate in gaps from seedlings or saplings recruited before gap formation but Laurus azorica is able to maintain it self in the forest through asexual regeneration thus being considered a primary persistent species; (3) Ilex azorica is a mature species that regenerates in the forest.     

小兴安岭阔叶红松混交林林隙特征

对小兴安岭阔叶红松混交林林隙基本特征进行了研究。结果表明:林隙的线状密度为31.78个/km,冠空隙和扩展林隙所占的面积比例分别为15.71%和30.78%;冠空隙的年干扰频率为0.46%,干扰轮回期约为434.8a。冠空隙的大小变化在42.12—372.52m2之间,平均为153.37m2;扩展林隙的大小变化在98.65m2—633.10m2之间,平均为300.44m2。冠空隙和扩展林隙面积分布格局均符合Weibull分布。林隙形成方式主要为干基折断,占总形成木总数的35.29%,其次为掘根风倒,占28.43%。平均每个林隙的形成木为4.98株,由红松、白桦、枫桦、冷杉形成,径级在20—30 cm之间,高度在15—30 m之间。冠空隙的直径与高度比值的相对频率的分布呈单峰型曲线,当比值为0.30—0.45时,出现峰值;而扩展林隙的直径与高度比值的相对频率的分布呈双峰型曲线,当比值分别为0.75—0.90和1.05—1.15时,出现峰值。林隙边缘木胸径级的多度分布和高度级多度分布符合Weibull分布,但不符合正态分布。约13.41%的边缘木未出现偏冠现象,偏冠率在0.5—0.7之间的边缘木占70.49%。     

Control of an Assembly System with Processing Time and Subassembly-Type Uncertainty

We address the problem of controlling an assembly system in which the processing times as well as the types of subassemblies are stochastic. The quality (or performance) of the final part depends on the characteristics of the subassemblies to be assembled, which are not constant. Furthermore, the processing time of a subassembly is random. We analyze the trade-off between the increase in the potential value of parts gained by delaying the assembly operation and the inventory costs caused by this delay. We also consider the effects of processing time uncertainty. Our problem is motivated by the assembly of passive and active plates in flat panel display manufacturing. We formulate the optimal control problem as a Markov decision process. However, the optimal policy is very complex, and we therefore develop simple heuristic policies. We report the results of a simulation study that tests the performance of our heuristics. The computational results indicate that the heuristics are effective for a wide variety of cases.     

RALBA: a computation-aware load balancing scheduler for cloud computing

Cloud computing serves as a platform for remote users to utilize the heterogeneous resources in data-centers to compute High-Performance Computing jobs. The physical resources are virtualized in Cloud to entertain user services employing Virtual Machines (VMs). Job scheduling is deemed as a quintessential part of Cloud and efficient utilization of VMs by Cloud Service Providers demands an optimal job scheduling heuristic. An ideal scheduling heuristic should be efficient, fair, and starvation-free to produce a reduced makespan with improved resource utilization. However, static heuristics often lead to inefficient and poor resource utilization in the Cloud. An idle and underutilized host machine in Cloud still consumes up to 70% of the energy required by an active machine (Ray, in Indian J Comput Sci Eng 1(4):333–339, 2012). Consequently, it demands a load-balanced distribution of workload to achieve optimal resource utilization in Cloud. Existing Cloud scheduling heuristics such as Min–Min, Max–Min, and Sufferage distribute workloads among VMs based on minimum job completion time that ultimately causes a load imbalance. In this paper, a novel Resource-Aware Load Balancing Algorithm (RALBA) is presented to ensure a balanced distribution of workload based on computation capabilities of VMs. The RABLA framework comprises of two phases: (1) scheduling based on computing capabilities of VMs, and (2) the VM with earliest finish time is selected for jobs mapping. The outcomes of the RALBA have revealed that it provides substantial improvement against traditional heuristics regarding makespan, resource utilization, and throughput.     

An Omega(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem

The gene-duplication problem is to infer a species supertree from gene trees that are confounded by complex histories of gene duplications. This problem is NP-hard and thus requires efficient and effective heuristics. Existing heuristics perform a stepwise search of the tree space, where each step is guided by an exact solution to an instance of a local search problem. We improve on the time complexity of the local search problem by a factor of n2= log n, where n is the size of the resulting species supertree. Typically, several thousand instances of the local search problem are solved throughout a stepwise heuristic search. Hence, our improvement makes the gene-duplication problem much more tractable for large-scale phylogenetic analyses.     

Hyperspectral remote detection of niche partitioning among canopy trees driven by blowdown gap disturbances in the Central Amazon

Advanced recruitment and neutral processes play important roles in determining tree species composition in tropical forest canopy gaps, with few gaps experiencing clear secondary successional processes. However, most studies are limited to the relatively limited spatial scales provided by forest inventory plots, and investigations over the entire range of gap size are needed to better understand how ecological processes vary with tree mortality events. This study employed a landscape approach to test the hypothesis that tree species composition and forest structural attributes differ between large blowdown gaps and relatively undisturbed primary forest. Spectral mixture analysis on hyperspectral satellite imagery was employed to direct field sampling to widely distributed sites, and blowdown plots were compared with undisturbed primary forest plots. Tree species composition and forest structural attributes differed markedly between gap and non-gap sites, providing evidence of niche partitioning in response to disturbance across the region. Large gaps were dominated by classic Neotropical pioneer genera such as Cecropia and Vismia, and average tree size was significantly smaller. Mean wood density of trees recovering in large gaps (0.55 g cm⁻³) was significantly lower than in primary forest plots (0.71 g cm⁻³), a difference similar to that found when comparing less dynamic (i.e., tree recruitment, growth, and mortality) Central Amazon forests with more dynamic Western Amazon forests. Based on results, we hypothesize that the importance of neutral processes weaken, and niche processes strengthen, in determining community assembly along a gradient in gap size and tree mortality intensity. Over evolutionary time scales, pervasive dispersal among colonizers could result in the loss of tree diversity in the pioneer guild through competitive exclusion. Results also underscore the importance of considering disturbance processes across the landscape when addressing forest carbon balance.     

长白山红松阔叶林林冠空隙特征的研究

将林冠空隙干扰作为红松阔叶林动态维持的重要因素,对长白山红松阔叶林林 冠空隙的形成方式、出现频度、分布格局、结构及林冠空隙内形成本的数量、年龄分布、种 群特征等进行了系统分析．结果表明．长白山阔叶红松林多数林冠空隙由双形成本形成, 每个林冠空隙拥有的形成木为２．４４株;林冠空隙形成的速率为０．９２个ｈｍ２·ａ－１,林冠空 隙干扰的间隔期（周转期）为７５１ａ;扩展林冠空隙面积大多在１００～６００ ｍ２之间,其中以 ４００～５００ ｍ２所占比例最大．冠空隙在５０～３５０ ｍ２之间,其中以２００～２５０ ｍ２所占比例最 大;每个形成本所形成的扩展林冠空隙平均面积为 １４１ ８２ ｍ２,形成的冠空隙面积平均为 ６７．６３ ｍ２．     

A reliable simulator for dynamic flux balance analysis

Dynamic flux balance analysis (DFBA) provides a platform for detailed design, control and optimization of biochemical process technologies. It is a promising modeling framework that combines genome‐scale metabolic network analysis with dynamic simulation of the extracellular environment. Dynamic flux balance analysis assumes that the intracellular species concentrations are in equilibrium with the extracellular environment. The resulting underdetermined stoichiometric model is solved under the assumption of a biochemical objective such as growth rate maximization. The model of the metabolism is coupled with the dynamic mass balance equations of the extracellular environment via expressions for the rates of substrate uptake and product excretion, which imposes additional constraints on the linear program (LP) defined by growth rate maximization of the metabolism. The linear program is embedded into the dynamic model of the bioreactor, and together with the additional constraints this provides an accurate model of the substrate consumption, product secretion, and biomass production during operation. A DFBA model consists of a system of ordinary differential equations for which the evaluation of the right‐hand side requires not only function evaluations, but also the solution of one or more linear programs. The numerical tool presented here accurately and efficiently simulates large‐scale dynamic flux balance models. The main advantages that this approach has over existing implementation are that the integration scheme has a variable step size, that the linear program only has to be solved when qualitative changes in the optimal flux distribution of the metabolic network occur, and that it can reliably simulate behavior near the boundary of the domain where the model is defined. This is illustrated through large‐scale examples taken from the literature. Biotechnol. Bioeng. 2013; 110: 792–802. © 2012 Wiley Periodicals, Inc.     

Radar Tracking and Motion-Sensitive Cameras on Flowers Reveal the Development of Pollinator Multi-Destination Routes over Large Spatial Scales

Central place foragers, such as pollinating bees, typically develop circuits (traplines) to visit multiple foraging sites in a manner that minimizes overall travel distance. Despite being taxonomically widespread, these routing behaviours remain poorly understood due to the difficulty of tracking the foraging history of animals in the wild. Here we examine how bumblebees (Bombus terrestris) develop and optimise traplines over large spatial scales by setting up an array of five artificial flowers arranged in a regular pentagon (50 m side length) and fitted with motion-sensitive video cameras to determine the sequence of visitation. Stable traplines that linked together all the flowers in an optimal sequence were typically established after a bee made 26 foraging bouts, during which time only about 20 of the 120 possible routes were tried. Radar tracking of selected flights revealed a dramatic decrease by 80% (ca. 1500 m) of the total travel distance between the first and the last foraging bout. When a flower was removed and replaced by a more distant one, bees engaged in localised search flights, a strategy that can facilitate the discovery of a new flower and its integration into a novel optimal trapline. Based on these observations, we developed and tested an iterative improvement heuristic to capture how bees could learn and refine their routes each time a shorter route is found. Our findings suggest that complex dynamic routing problems can be solved by small-brained animals using simple learning heuristics, without the need for a cognitive map.     

Seed predation patterns favor the regeneration of dominant species in forest gaps compared with the understory in an oak-pine mixed forest

Recent studies have demonstrated the higher likelihood of regeneration in forest gaps compared with the understory for the dominant species in pine-oak mixed forest. Here, we tested whether rodent seed predation or dispersal was beneficial for gap regeneration. We tracked the seed predation and dispersal of Quercus aliena var. acuteserrata and Pinus armandii using coded plastic tags in the forest understory close to gaps. Our results demonstrated that the proportions of initial buried seeds of both species were significantly more abundant in the forest understory compared with gaps. After seed caching, however, significantly lower proportions of the seeds of both species survived in the forest understory compared with gaps during the 30-day observation period. The final survival proportions of the seeds cached in the forest understory were lower than those cached in the gaps the next spring, which indicated that small rodents rarely retrieved scatter-hoarded seeds from forest gaps. Our findings suggest that rodent seed predation patterns contribute to the regeneration of the dominant species in gaps compared with the understory in a pine-oak mixed forest. In the study area, reforestation usually involves planting seedlings but direct sowing in forest gaps may be an alternative means of accelerating forest recovery and successional processes.