Robust parameter settings of evolutionary algorithms for the optimisation of agricultural systems models

Numerical optimisation methods are being more commonly applied to agricultural systems models, to identify the most profitable management strategies. The available optimisation algorithms are reviewed and compared, with literature and our studies identifying evolutionary algorithms (including genetic algorithms) as superior in this regard to simulated annealing, tabu search, hill-climbing, and direct-search methods. Results of a complex beef property optimisation, using a real-value genetic algorithm, are presented. The relative contributions of the range of operational options and parameters of this method are discussed, and general recommendations listed to assist practitioners applying evolutionary algorithms to the solution of agricultural systems. (C) 2001 Elsevier Science Ltd. All rights reserved.

Granulocyte-colony-stimulating factor (G-CSF)-primed allogeneic bone marrow: significantly less graft-versus-host disease and comparable engraftment to G-CSF-mobilized peripheral blood stem cells

Prospective studies have shown rapid engraftment using granulocyte-colony-stimulating factor-mobilized peripheral blood stem cells (G-PBSCs) for allogeneic transplantation, though the risks for graft-versus-host disease (GVHD) may be increased. It was hypothesized that the use of G-CSF to prime bone marrow (GBM) would allow rapid engraftment without increased risk for GVHD compared with G-PBSC. Patients were randomized to receive G-BM or G-PBSCs for allogeneic stem cell transplantation. The study was designed (beta < .8) to detect a difference in the incidence of chronic GVHD of 33% ( < .05). The plan was to recruit 100 patients and to conduct an interim analysis when the 6-month follow-up point was reached for the first 50 patients. Fifty-seven consecutive patients were recruited (G-BM, n = 28; G-PBSC, n = 29). Patients in the G-PBSC group received 3-fold more CD34(+) and 9-fold more CD3(+) cells. Median times to neutrophil (G-BM, 16 days; G-PBSC, 14 days; P < .1) and platelet engraftment (G-BM, 14 days; G-PBSC, 12 days; P < .1) were similar. The use of G-PBSC was associated with steroid refractory acute GVHD (G-BM, 0%; G-PBSC, 32%; P < .001), chronic GVHD (G-BM, 22%; G-PBSC, 80%; P < .02), and prolonged requirement for immunosuppressive therapy (G-BM, 173 days; G-PBSC, 680 days; P < .009). Survival was similar for the 2 groups. Compared with G-PBSC the use of G-BM resulted in comparable engraftment, reduced severity of acute GVHD, and less subsequent chronic GVHD. (Blood. 2001;98:3186-3191) (C) 2001 by The American Society of Hematology.

Colony-stimulating factor-1 suppresses responses to CpG DNA and expression of toll-like receptor 9 but enhances responses to lipopolysaccharide in murine macrophages

During bacterial infections, the balance between resolution of infection and development of sepsis is dependent upon the macrophage response to bacterial products. We show that priming of murine bone marrow-derived macrophages (BMMs) with CSF-1 differentially regulates the response to two such stimuli, LPS and immunostimulatory (CpG) DNA. CSF-1 pretreatment enhanced IL-6, IL-12, and TNF-alpha production in response to LPS but suppressed the same response to CpG DNA. CSF-1 also regulated cytokine gene expression in response to CpG DNA and LPS; CpG DNA-induced IL-12 p40, IL-12 p35, and TNF-alpha mRNAs were all suppressed by CSF-1 pretreatment. CSF-1 pretreatment enhanced LPS-induced IL-12 p40 mRNA but not TNF-alpha and IL-12 p35 mRNAs, suggesting that part of the priming effect is posttranscriptional. CSF-1 pretreatment also suppressed CpG DNA-induced nuclear translocation of NF-kappaB and phosphorylation of the mitogen-activated protein kinases p38 and extracellular signal-related kinases-1/2 in BMMs, indicating that early events in CpG DNA signaling were regulated by CSF-1. Expression of Toll-like receptor (TLR)9, which is necessary for responses to CpG DNA, was markedly suppressed by CSF-1 in both BMMs and thioglycolate-elicited peritoneal macrophages. CSF-1 also down-regulated expression of TLR1, TLR2, and TLR6, but not the LPS receptor, TLR4, or TLR5. Hence, CSF-1 may regulate host responses to pathogens through modulation of TLR expression. Furthermore, these results suggest that CSF-1 and CSF-1R antagonists may enhance the efficacy of CpG DNA in vivo.

Using siting algorithms in the design of marine reserve networks

Using benthic habitat data from the Florida Keys (USA), we demonstrate how siting algorithms can help identify potential networks of marine reserves that comprehensively represent target habitat types. We applied a flexible optimization tool-simulated annealing-to represent a fixed proportion of different marine habitat types within a geographic area. We investigated the relative influence of spatial information, planning-unit size, detail of habitat classification, and magnitude of the overall conservation goal on the resulting network scenarios. With this method, we were able to identify many adequate reserve systems that met the conservation goals, e.g., representing at least 20% of each conservation target (i.e., habitat type) while fulfilling the overall aim of minimizing the system area and perimeter. One of the most useful types of information provided by this siting algorithm comes from an irreplaceability analysis, which is a count of the number of, times unique planning units were included in reserve system scenarios. This analysis indicated that many different combinations of sites produced networks that met the conservation goals. While individual 1-km(2) areas were fairly interchangeable, the irreplaceability analysis highlighted larger areas within the planning region that were chosen consistently to meet the goals incorporated into the algorithm. Additionally, we found that reserve systems designed with a high degree of spatial clustering tended to have considerably less perimeter and larger overall areas in reserve-a configuration that may be preferable particularly for sociopolitical reasons. This exercise illustrates the value of using the simulated annealing algorithm to help site marine reserves: the approach makes efficient use of;available resources, can be used interactively by conservation decision makers, and offers biologically suitable alternative networks from which an effective system of marine reserves can be crafted.

Growth hormone receptor and insulin-like growth factor-I immunoreactivity in osteoclast-like cells during tooth eruption in the toothless (Osteopetrotic) rat following treatment with colony-stimulating factor-1

In the toothless (tl/tl) osteopetrotic rat, teeth form but fail to erupt. Treatment of tl/tl rats with colony-stimulating factor-1 (CSF-1) activates bone resorption by osteoclasts, permits tooth eruption, and up-regulates the immunoreactivity of bone marrow mononuclear cells to growth hormone receptor (GHr) and insulin-like growth factor (IGF)-I. This study examined the distribution of tartrate-resistant acid phosphatase (TRAP) and immunoreactivity for GHr and IGF-I in osteoclast-like cells located on the alveolar bone margin, adjacent to the lower first molar crown, in 14-day-old normal and tl/tl rats, following treatment with CSF-1. Osteoclast-like cells demonstrated a positive reaction for TRAP, GHr, and IGF-I in all groups. However, in tl/tl tissue, osteoclast-like cells were generally negative for GHr. There was no significant difference in the total number of TRAP, GHr, and IGF-I-positive osteoclast-like cells on the adjacent bone margin in normal, normal treated with CSF-1, and tl/tl rats. CSF-1 treatment of the tl/tl rat significantly increased the total number of osteoclast-like cells, which were positive for TRAP (p < 0.001), GHr (p < 0.05) and IGF-I (P < 0.01).

Fast, scalable master equation solution algorithms. IV. Lanczos iteration with diffusion approximation preconditioned iterative inversion

In this paper we propose a second linearly scalable method for solving large master equations arising in the context of gas-phase reactive systems. The new method is based on the well-known shift-invert Lanczos iteration using the GMRES iteration preconditioned using the diffusion approximation to the master equation to provide the inverse of the master equation matrix. In this way we avoid the cubic scaling of traditional master equation solution methods while maintaining the speed of a partial spectral decomposition. The method is tested using a master equation modeling the formation of propargyl from the reaction of singlet methylene with acetylene, proceeding through long-lived isomerizing intermediates. (C) 2003 American Institute of Physics.

Fast, scalable master equation solution algorithms. III. Direct time propagation accelerated by a diffusion approximation preconditioned iterative solver

In this paper we propose a novel fast and linearly scalable method for solving master equations arising in the context of gas-phase reactive systems, based on an existent stiff ordinary differential equation integrator. The required solution of a linear system involving the Jacobian matrix is achieved using the GMRES iteration preconditioned using the diffusion approximation to the master equation. In this way we avoid the cubic scaling of traditional master equation solution methods and maintain the low temperature robustness of numerical integration. The method is tested using a master equation modelling the formation of propargyl from the reaction of singlet methylene with acetylene, proceeding through long lived isomerizing intermediates. (C) 2003 American Institute of Physics.

Knowledge-based system on optimum design of liquid retaining structures with genetic algorithms

This paper delineates the development of a prototype hybrid knowledge-based system for the optimum design of liquid retaining structures by coupling the blackboard architecture, an expert system shell VISUAL RULE STUDIO and genetic algorithm (GA). Through custom-built interactive graphical user interfaces under a user-friendly environment, the user is directed throughout the design process, which includes preliminary design, load specification, model generation, finite element analysis, code compliance checking, and member sizing optimization. For structural optimization, GA is applied to the minimum cost design of structural systems with discrete reinforced concrete sections. The design of a typical example of the liquid retaining structure is illustrated. The results demonstrate extraordinarily converging speed as near-optimal solutions are acquired after merely exploration of a small portion of the search space. This system can act as a consultant to assist novice designers in the design of liquid retaining structures.

Ant colony search algorithm for the optimal power flow problem

To maintain a power system within operation limits, a level ahead planning it is necessary to apply competitive techniques to solve the optimal power flow (OPF). OPF is a non-linear and a large combinatorial problem. The Ant Colony Search (ACS) optimization algorithm is inspired by the organized natural movement of real ants and has been successfully applied to different large combinatorial optimization problems. This paper presents an implementation of Ant Colony optimization to solve the OPF in an economic dispatch context. The proposed methodology has been developed to be used for maintenance and repairing planning with 48 to 24 hours antecipation. The main advantage of this method is its low execution time that allows the use of OPF when a large set of scenarios has to be analyzed. The paper includes a case study using the IEEE 30 bus network. The results are compared with other well-known methodologies presented in the literature.

Ant colony system based approach to single machine scheduling problems: weighted tardiness scheduling problem

The paper introduces an approach to solve the problem of generating a sequence of jobs that minimizes the total weighted tardiness for a set of jobs to be processed in a single machine. An Ant Colony System based algorithm is validated with benchmark problems available in the OR library. The obtained results were compared with the best available results and were found to be nearer to the optimal. The obtained computational results allowed concluding on their efficiency and effectiveness.

Swarm intelligence for scheduling: a review

Swarm Intelligence generally refers to a problem-solving ability that emerges from the interaction of simple information-processing units. The concept of Swarm suggests multiplicity, distribution, stochasticity, randomness, and messiness. The concept of Intelligence suggests that problem-solving approach is successful considering learning, creativity, cognition capabilities. This paper introduces some of the theoretical foundations, the biological motivation and fundamental aspects of swarm intelligence based optimization techniques such Particle Swarm Optimization (PSO), Ant Colony Optimization (ACO) and Artificial Bees Colony (ABC) algorithms for scheduling optimization.

Comparison of different breast planning techniques and algorithms for radiation therapy treatment

This work aims at investigating the impact of treating breast cancer using different radiation therapy (RT) techniques – forwardly-planned intensity-modulated, f-IMRT, inversely-planned IMRT and dynamic conformal arc (DCART) RT – and their effects on the whole-breast irradiation and in the undesirable irradiation of the surrounding healthy tissues. Two algorithms of iPlan BrainLAB treatment planning system were compared: Pencil Beam Convolution (PBC) and commercial Monte Carlo (iMC). Seven left-sided breast patients submitted to breast-conserving surgery were enrolled in the study. For each patient, four RT techniques – f-IMRT, IMRT using 2-fields and 5-fields (IMRT2 and IMRT5, respectively) and DCART – were applied. The dose distributions in the planned target volume (PTV) and the dose to the organs at risk (OAR) were compared analyzing dose–volume histograms; further statistical analysis was performed using IBM SPSS v20 software. For PBC, all techniques provided adequate coverage of the PTV. However, statistically significant dose differences were observed between the techniques, in the PTV, OAR and also in the pattern of dose distribution spreading into normal tissues. IMRT5 and DCART spread low doses into greater volumes of normal tissue, right breast, right lung and heart than tangential techniques. However, IMRT5 plans improved distributions for the PTV, exhibiting better conformity and homogeneity in target and reduced high dose percentages in ipsilateral OAR. DCART did not present advantages over any of the techniques investigated. Differences were also found comparing the calculation algorithms: PBC estimated higher doses for the PTV, ipsilateral lung and heart than the iMC algorithm predicted.