Parameter estimation for the distribution of single cell lag times.

In Quantitative Microbial Risk Assessment, it is vital to understand how lag times of individual cells are distributed over a bacterial population. Such identified distributions can be used to predict the time by which, in a growth-supporting environment, a few pathogenic cells can multiply to a poisoning concentration level. We model the lag time of a single cell, inoculated into a new environment, by the delay of the growth function characterizing the generated subpopulation. We introduce an easy-to-implement procedure, based on the method of moments, to estimate the parameters of the distribution of single cell lag times. The advantage of the method is especially apparent for cases where the initial number of cells is small and random, and the culture is detectable only in the exponential growth phase.

ILS-ESP An efficient, simple, and parameter-free algorithm for solving the permutation flow-shop problem

From a managerial point of view, the more effcient, simple, and parameter-free (ESP) an algorithm is, the more likely it will be used in practice for solving real-life problems. Following this principle, an ESP algorithm for solving the Permutation Flowshop Sequencing Problem (PFSP) is proposed in this article. Using an Iterated Local Search (ILS) framework, the so-called ILS-ESP algorithm is able to compete in performance with other well-known ILS-based approaches, which are considered among the most effcient algorithms for the PFSP. However, while other similar approaches still employ several parameters that can affect their performance if not properly chosen, our algorithm does not require any particular fine-tuning process since it uses basic "common sense" rules for the local search, perturbation, and acceptance criterion stages of the ILS metaheuristic. Our approach defines a new operator for the ILS perturbation process, a new acceptance criterion based on extremely simple and transparent rules, and a biased randomization process of the initial solution to randomly generate different alternative initial solutions of similar quality -which is attained by applying a biased randomization to a classical PFSP heuristic. This diversification of the initial solution aims at avoiding poorly designed starting points and, thus, allows the methodology to take advantage of current trends in parallel and distributed computing. A set of extensive tests, based on literature benchmarks, has been carried out in order to validate our algorithm and compare it against other approaches. These tests show that our parameter-free algorithm is able to compete with state-of-the-art metaheuristics for the PFSP. Also, the experiments show that, when using parallel computing, it is possible to improve the top ILS-based metaheuristic by just incorporating to it our biased randomization process with a high-quality pseudo-random number generator.

Probabilistic maximal covering location-allocation models with constrained waiting time or queue length for congested systems

When dealing with the design of service networks, such as healthand EMS services, banking or distributed ticket selling services, thelocation of service centers has a strong influence on the congestion ateach of them, and consequently, on the quality of service. In this paper,several models are presented to consider service congestion. The firstmodel addresses the issue of the location of the least number of single--servercenters such that all the population is served within a standard distance,and nobody stands in line for a time longer than a given time--limit, or withmore than a predetermined number of other clients. We then formulateseveral maximal coverage models, with one or more servers per service center.A new heuristic is developed to solve the models and tested in a 30--nodesnetwork.

Diversity of Odonata (Insecta) in lotic systems from Serra da Bodoquena, Mato Grosso do Sul State, Brazil

Diversity of Odonata (Insecta) in lotic systems from Serra da Bodoquena, Mato Grosso do Sul State, Brazil. A systematic survey was carried out in four lotic systems from Serra da Bodoquena, the largest natural forests of the State, from August 2007 to November 2008. 548 specimens belonging to 33 species, distributed in 5 families were sampled. Libellulidae was dominant, with 13 species, followed by Gomphidae, Coenagrionidae, Protoneuridae and Calopterygidae.

Vacancy-driven ordering in a two-dimensional binary alloy

Domain growth in a system with nonconserved order parameter is studied. We simulate the usual Ising model for binary alloys with concentration 0.5 on a two-dimensional square lattice by Monte Carlo techniques. Measurements of the energy, jump-acceptance ratio, and order parameters are performed. Dynamics based on the diffusion of a single vacancy in the system gives a growth law faster than the usual Allen-Cahn law. Allowing vacancy jumps to next-nearest-neighbor sites is essential to prevent vacancy trapping in the ordered regions. By measuring local order parameters we show that the vacancy prefers to be in the disordered regions (domain boundaries). This naturally concentrates the atomic jumps in the domain boundaries, accelerating the growth compared with the usual exchange mechanism that causes jumps to be homogeneously distributed on the lattice.

Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils

The study of the ecology of soil microbial communities at relevant spatial scales is primordial in the wide Amazon region due to the current land use changes. In this study, the diversity of the Archaea domain (community structure) and ammonia-oxidizing Archaea (richness and community composition) were investigated using molecular biology-based techniques in different land-use systems in western Amazonia, Brazil. Soil samples were collected in two periods with high precipitation (March 2008 and January 2009) from Inceptisols under primary tropical rainforest, secondary forest (5-20 year old), agricultural systems of indigenous people and cattle pasture. Denaturing gradient gel electrophoresis of polymerase chain reaction-amplified DNA (PCR-DGGE) using the 16S rRNA gene as a biomarker showed that archaeal community structures in crops and pasture soils are different from those in primary forest soil, which is more similar to the community structure in secondary forest soil. Sequence analysis of excised DGGE bands indicated the presence of crenarchaeal and euryarchaeal organisms. Based on clone library analysis of the gene coding the subunit of the enzyme ammonia monooxygenase (amoA) of Archaea (306 sequences), the Shannon-Wiener function and Simpson's index showed a greater ammonia-oxidizing archaeal diversity in primary forest soils (H' = 2.1486; D = 0.1366), followed by a lower diversity in soils under pasture (H' = 1.9629; D = 0.1715), crops (H' = 1.4613; D = 0.3309) and secondary forest (H' = 0.8633; D = 0.5405). All cloned inserts were similar to the Crenarchaeota amoA gene clones (identity > 95 %) previously found in soils and sediments and distributed primarily in three major phylogenetic clusters. The findings indicate that agricultural systems of indigenous people and cattle pasture affect the archaeal community structure and diversity of ammonia-oxidizing Archaea in western Amazon soils.

Suppression of scroll wave turbulence by noise

Rotating scroll waves are dynamical spatiotemporal structures characteristic of three-dimensional active media. It is well known that, under low excitability conditions, scroll waves develop an intrinsically unstable dynamical regime that leads to a highly disorganized pattern of wave propagation. Such a ¿turbulent¿ state bears some resemblance to fibrillation states in cardiac tissue. We show here that this unstable regime can be controlled by using a spatially distributed random forcing superimposed on a control parameter of the system. Our results are obtained from numerical simulations but an explicit analytical argument that rationalizes our observations is also presented.

Soil water erosion under different cultivation systems and different fertilization rates and forms over 10 years

The action of rain and surface runoff together are the active agents of water erosion, and further influences are the soil type, terrain, soil cover, soil management, and conservation practices. Soil water erosion is low in the no-tillage management system, being influenced by the amount and form of lime and fertilizer application to the soil, among other factors. The aim was to evaluate the effect of the form of liming, the quantity and management of fertilizer application on the soil and water losses by erosion under natural rainfall. The study was carried out between 2003 and 2013 on a Humic Dystrupept soil, with the following treatments: T1 - cultivation with liming and corrective fertilizer incorporated into the soil in the first year, and with 100 % annual maintenance fertilization of P and K; T2 - surface liming and corrective fertilization distributed over five years, and with 75 % annual maintenance fertilization of P and K; T3 - surface liming and corrective fertilization distributed over three years, and with 50 % annual maintenance fertilization of P and K; T4 - surface liming and corrective fertilization distributed over two years, and with 25 % annual maintenance fertilization of P and K; T5 - fallow soil, without liming or fertilization. In the rotation the crops black oat (Avena strigosa ), soybean (Glycine max ), common vetch (Vicia sativa ), maize (Zea mays ), fodder radish (Raphanus sativus ), and black beans (Phaseolus vulgaris ). The split application of lime and mineral fertilizer to the soil surface in a no-tillage system over three and five years, results in better control of soil losses than when split in two years. The increase in the amount of fertilizer applied to the soil surface under no-tillage cultivation increases phytomass production and reduces soil loss by water erosion. Water losses in treatments under no-tillage cultivation were low in all crop cycles, with a similar behavior as soil losses.

Suppression of scroll wave turbulence by noise

Rotating scroll waves are dynamical spatiotemporal structures characteristic of three-dimensional active media. It is well known that, under low excitability conditions, scroll waves develop an intrinsically unstable dynamical regime that leads to a highly disorganized pattern of wave propagation. Such a ¿turbulent¿ state bears some resemblance to fibrillation states in cardiac tissue. We show here that this unstable regime can be controlled by using a spatially distributed random forcing superimposed on a control parameter of the system. Our results are obtained from numerical simulations but an explicit analytical argument that rationalizes our observations is also presented.

Using spatially distributed parameters and multi-response objective functions to solve parameterization of complex applications of semi-distributed hydrological models

Application of semi-distributed hydrological models to large, heterogeneous watersheds deals with several problems. On one hand, the spatial and temporal variability in catchment features should be adequately represented in the model parameterization, while maintaining the model complexity in an acceptable level to take advantage of state-of-the-art calibration techniques. On the other hand, model complexity enhances uncertainty in adjusted model parameter values, therefore increasing uncertainty in the water routing across the watershed. This is critical for water quality applications, where not only streamflow, but also a reliable estimation of the surface versus subsurface contributions to the runoff is needed. In this study, we show how a regularized inversion procedure combined with a multiobjective function calibration strategy successfully solves the parameterization of a complex application of a water quality-oriented hydrological model. The final value of several optimized parameters showed significant and consistentdifferences across geological and landscape features. Although the number of optimized parameters was significantly increased by the spatial and temporal discretization of adjustable parameters, the uncertainty in water routing results remained at reasonable values. In addition, a stepwise numerical analysis showed that the effects on calibration performance due to inclusion of different data types in the objective function could be inextricably linked. Thus caution should be taken when adding or removing data from an aggregated objective function.

Criteria for hitting probabilities with applications to systems of stochastic wave equations

We develop several results on hitting probabilities of random fields which highlight the role of the dimension of the parameter space. This yields upper and lower bounds in terms of Hausdorff measure and Bessel-Riesz capacity, respectively. We apply these results to a system of stochastic wave equations in spatial dimension k >- 1 driven by a d-dimensional spatially homogeneous additive Gaussian noise that is white in time and colored in space.

Survival of pathogens on soybean debris under no-tillage and conventional tillage systems

A study was conducted in the subtropical area of Southern Brazil to determine the survival of pathogens in soybean residues under conventional and no-tillage cultivation systems from March to September of 1998 and 1999. The pathogens most frequently isolated were Colletotrichum truncatum, Phomopsis spp., Cercospora kikuchii, Fusarium spp., Macrophomina phaseolina, and Rhizoctonia solani. Other fungi isolated were Myrothecium roridum, Penicillium sp., Chaetomium sp., Epicoccum sp., Corynespora cassiicola and Trichoderma sp. The percent of survival of each pathogen varied according to the month and the year. Survival of C. truncatum, Phomopsis spp. and C. kikuchii were significantly reduced (p<0.05) from the first to the last evaluation either on buried debris or maintained on the soil surface. On the other hand, M. phaseolina and Fusarium spp. were either not affected or favored by burying the debris. The frequency of recovery of Fusarium spp. increased specially in debris kept under the soil. The loss of biomass, measured by debris weight along the period of this study, showed a reduction of 44.4% in the conventional system and 34.9% in the no-tillage system in 1998, when rain was better distributed. In 1999, the reduction was 48.2% and 39.0% for the conventional and no-tillage system, respectively.

Soil macrofauna under integrated crop-livestock systems in a Brazilian Cerrado Ferralsol

The objective of this work was to assess the effects of integrated crop-livestock systems, associated with two tillage and two fertilization regimes, on the abundance and diversity of the soil macrofauna. Four different management systems were studied: continuous pasture (mixed grass); continuous crop; two crop-livestock rotations (crop/pasture and pasture/crop); and native Cerrado as a control. Macrofauna was sampled using a modified Tropical Soil Biology and Fertility method, and all individuals were counted and identified at the morphospecies level for each plot. A total of 194 morphospecies were found, distributed among 30 groups, and the most representative in decreasing order of density were: Isoptera, Coleoptera larvae, Formicidae, Oligochaeta, Coleoptera adult, Diplopoda, Hemiptera, Diptera larvae, Arachnida, Chilopoda, Lepidoptera, Gasteropoda, Blattodea and Orthoptera. Soil management systems and tillage regimes affected the structure of soil macrofauna, and integrated crop-livestock systems, associated with no-tillage, especially with grass/legume species associations, had more favorable conditions for the development of "soil engineers" compared with continuous pasture or arable crops. Soil macrofauna density and diversity, assessed at morphospecies level, are effective data to measure the impact of land use in Cerrado soils.