Discovering promising regions to help global numerical optimization algorithms

We have developed an algorithm using a Design of Experiments technique for reduction of search-space in global optimization problems. Our approach is called Domain Optimization Algorithm. This approach can efficiently eliminate search-space regions with low probability of containing a global optimum. The Domain Optimization Algorithm approach is based on eliminating non-promising search-space regions, which are identifyed using simple models (linear) fitted to the data. Then, we run a global optimization algorithm starting its population inside the promising region. The proposed approach with this heuristic criterion of population initialization has shown relevant results for tests using hard benchmark functions.

Genetic Contribution for Non-Syndromic Cleft Lip With or Without Cleft Palate (NS CL/P) in Different Regions of Brazil and Implications for Association Studies

Non-syndromic cleft lip with or without cleft palate (NS CL/P) is a complex disease in which heritability estimates vary widely depending on the population studied. To evaluate the importance of genetic contribution to NS CL/P in the Brazilian population, we conducted a study with 1,042 families from five different locations (Santarem, Fortaleza, Barbalha, Maceio, and Rio de Janeiro). We also evaluated the role of consanguinity and ethnic background. The proportion of familial cases varied significantly across locations, with the highest values found in Santarem (44%) and the lowest in Maceio (23%). Heritability estimates showed a higher genetic contribution to NS CL/P in Barbalha (85%), followed by Santarem (71%), Rio de Janeiro (70%), Fortaleza (64%), and Maceio (45%). Ancestry was not correlated with the occurrence of NS CL/P or with the variability in heritability. Only in Rio de Janeiro was the coefficient of inbreeding significantly larger in NS CL/P families than in the local population. Recurrence risk for the total sample was approximately 1.5-1.6%, varying according to the location studied (0.6-0.7% in Maceio to 2.2-2.8% in Barbalha). Our findings show that the degree of genetic contribution to NS CL/P varies according to the geographic region studied, and this difference cannot be attributed to consanguinity or ancestry. These findings suggest that Barbalha is a promising region for genetic studies. The data presented here will be useful in interpreting results from molecular analyses and show that care must be taken when pooling samples from different populations for association studies. (C) 2011 Wiley-Liss, Inc.

Fission-track dating of South American natural glasses: an overview

Although many glass-bearing horizons can be found in South American volcanic complexes or sedimentary series, only a relatively few tephra and obsidian-bearing volcanic fields have been studied using the fission-track (FT) dating method. Among them, the volcanics located in the Sierra de Guamani (east of Quito, Ecuador) were studied by several authors. Based upon their ages, obsidians group into three clusters: (1) very young obsidians, similar to 0.2Ma old, (2) intermediate-age obsidians, similar to 0.4- similar to 0.8 Ma old, and (3) older obsidians, similar to 1.4- similar to 1.6 Ma old. The FT method is also an efficient alternative technique for identification of the sources of prehistoric obsidian artefacts. Provenance studies carried out in South America have shown that the Sierra de Guamani obsidian occurrences were important sources of raw material for toot making during pre-Columbian times. Glasses originated from these sources were identified in sites distributed over relatively wide areas of Ecuador and Colombia.Only a few systematic studies on obsidians in other sectors were carried out. Nevertheless, very singular glasses have been recognised in South America, such as Macusanite (Peru) and obsidian Quiron (Argentina), which are being proposed as additional reference materials for FT dating. Analyses of tephra beds interstratified with sedimentary deposits revealed the performance of FT dating in tephrochronological studies. A remarkable example is the famous deposit outcropping at Farola Monte Hermoso, near Bahia Blanca (Buenos Aires Province), described for the first time by the middle of the 19th century by Charles Darwin.Considering the large number of volcanic glasses that were recognised in volcanic complexes and in sedimentary series, South America is a very promising region for the application of FT dating. The examples given above show that this technique may yield important results in different disciplinary fields. (c) 2005 Elsevier Ltd. All rights reserved.

Investigating Smart Sampling as a population initialization method for Differential Evolution in continuous problems

Recently, researches have shown that the performance of metaheuristics can be affected by population initialization. Opposition-based Differential Evolution (ODE), Quasi-Oppositional Differential Evolution (QODE), and Uniform-Quasi-Opposition Differential Evolution (UQODE) are three state-of-the-art methods that improve the performance of the Differential Evolution algorithm based on population initialization and different search strategies. In a different approach to achieve similar results, this paper presents a technique to discover promising regions in a continuous search-space of an optimization problem. Using machine-learning techniques, the algorithm named Smart Sampling (SS) finds regions with high possibility of containing a global optimum. Next, a metaheuristic can be initialized inside each region to find that optimum. SS and DE were combined (originating the SSDE algorithm) to evaluate our approach, and experiments were conducted in the same set of benchmark functions used by ODE, QODE and UQODE authors. Results have shown that the total number of function evaluations required by DE to reach the global optimum can be significantly reduced and that the success rate improves if SS is employed first. Such results are also in consonance with results from the literature, stating the importance of an adequate starting population. Moreover, SS presents better efficacy to find initial populations of superior quality when compared to the other three algorithms that employ oppositional learning. Finally and most important, the SS performance in finding promising regions is independent of the employed metaheuristic with which SS is combined, making SS suitable to improve the performance of a large variety of optimization techniques. (C) 2012 Elsevier Inc. All rights reserved.

Fermentation medium and oxygen transfer conditions that maximize the xylose conversion to ethanol by Pichia stipitis

The xylose conversion to ethanol by Pichia stipitis was studied. In a first step, the necessity of supplementing the fermentation medium with urea. MgSO(4) x 7H(2)O, and/or yeast extract was evaluated through a 2(3) full factorial design. The simultaneous addition of these three nutritional sources to the fermentation medium, in concentrations of 2.3, 1.0, and 3.0 g/l, respectively, showed to be important to improve the ethanol production in detriment of the substrate conversion to cell. In a second stage, fermentation assays performed in a bioreactor under different K(L)a (volumetric oxygen transfer coefficient) conditions made possible understanding the influence of the oxygen transfer on yeast performance, as well as to define the most suitable range of values for an efficient ethanol production. The most promising region to perform this bioconversion process was found to be between 2.3 and 4.9 h(-1), since it promoted the highest ethanol production results with practically exhaustion of the xylose from the medium. These findings contribute for the development of an economical and efficient technology for large scale production of second generation ethanol. (C) 2011 Elsevier Ltd. All rights reserved.

Feasibility assessment of sugarcane expansion in southwest Goiás, Brazil based on the GIS technology.

The current study approaches the sugarcane culture expansion in Southwestern Goiás, especially in Mineiros, Quirinópolis and Rio Verde counties, which represent different times and responses to this process. The current logistics structure and future prospects for sugarcane and its derivatives transportation are studied at national level with emphasis to the aforementioned micro-region. Maps showing land use and land cover in three different years were generated from Landsat TM-5 satellite images and they were used to analyze the dynamics of changes in land use and in land cover. The region is marked by strong and rapid growth in the agricultural sector and its sugar-energy industry has been expanding in recent years, although with different aspects among its counties. Since it is a promising region in this sector, due to the favorable soil and weather conditions to the crop, the region requires more investment and planning in logistics to ensure production flow and to make it stronger within domestic and foreign markets.

Earthen plasters based on illitic soils from Barrocal region of Algarve: contributions for building performance and sustainability

Clayish earth-based mortars can be considered eco-efficient products for indoor plastering since they can contribute to improve important aspects of building performance and sustainability. Apart from being products with low embodied energy when compared to other types of mortars used for interior plastering, mainly due to the use raw clay as natural binder, earth-based plasters may give a significant contribution for health and comfort of inhabitants. Due to high hygroscopicity of clay minerals, earth-based mortars present a high adsorption and desorption capacity, particularly when compared to other type of mortars for interior plastering. This capacity allows earth-based plasters to act as a moisture buffer, balancing the relative humidity of the indoor environment and, simultaneously, acting as a passive removal material, improving air quality. Therefore, earth-based plasters may also passively promote the energy efficiency of buildings, since they may contribute to decreasing the needs of mechanical ventilation and air conditioning. This study is part of an ongoing research regarding earth-based plasters and focuses on mortars specifically formulated with soils extracted from Portuguese ‘Barrocal’ region, in Algarve sedimentary basin. This region presents high potential for interior plastering due to regional geomorphology, that promote the occurrence of illitic soils characterized by a high adsorption capacity and low expansibility. More specifically, this study aims to assess how clayish earth and sand ratio of mortars formulation can influence the physical and mechanical properties of plasters. For this assessment four mortars were formulated with different volumetric proportions of clayish earth and siliceous sand. The results from the physical and mechanical characterization confirmed the significantly low linear shrinkage of all the four mortars, as well as their extraordinary adsorption-desorption capacity. These results presented a positive correlation with mortars´ clayish earth content and are consistent with the mineralogical analysis, that confirmed illite as the prevalent clay mineral in the clayish earth used for this study. Regarding mechanical resistance, although the promising results of the adhesion test, the flexural and compressive strength results suggest that the mechanical resistance of these mortars should be slightly improved. Considering the present results the mortars mechanical resistance improvement may be achieved through the formulation of mortars with higher clayish earth content, or alternatively, through the addition of natural fibers to mortars formulation, very common in this type of mortars. Both those options will be investigated in future research.

Avaliação do padrão de metilação da DMR (Differentially Methylated Region) dos gnes IGF2 e H19 em carcinomas uroteliais

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Precolumbian land use and settlement pattern in the Santarém region, lower Amazon

Uma das áreas mais promissoras para o estudo das sociedades pré-colombianas complexas na bacia do rio Amazonas é a área do baixo curso dos rios Tapajós, Trombetas e Nhamundá. Há relatos escritos sobre os Konduri e os Tapajós, apresentando informações sobre a sua organização social regional, padrões de comércio, a abundância de alimentos, e o mundo material. Assim, evidências arqueológicas – sítios imensos, solos antrópicos, e belos artefatos – podem ser contrastadas com a informação escrita. Estes ricos depósitos culturais estão desaparecendo a um ritmo alarmante, à medida em que os centros urbanos crescem e se expande a agricultura na região. Apesar desta situação, pouca pesquisa arqueológica tem sido realizada na área, especialmente quando se trata de investigar os antigos padrões de assentamento e redes de trocas. Nos últimos anos, temos realizado pesquisas na bacia do baixo rio Tapajós. O registro arqueológico indica que a cerâmica mostrando forte semelhança estilística forte com a encontrada no grande sítio central está espalhada por pelo menos 90 quilômetros ao sul da presente cidade de Santarém. Este artigo apresenta os resultados de uma pesquisa regional realizada nas proximidades de Santarém, no planalto de Belterra e Alter do Chão, oferecendo uma análise preliminar do sistema de assentamentos na região.

Stable water isotopes of precipitation and firn cores from the northern Antarctic Peninsula region as a proxy for climate reconstruction

In order to investigate the climate variability in the northern Antarctic Peninsula region, this paper focuses on the relationship between stable isotope content of precipitation and firn, and main meteorological variables (air temperature, relative humidity, sea surface temperature, and sea ice extent). Between 2008 and 2010, we collected precipitation samples and retrieved firn cores from several key sites in this region. We conclude that the deuterium excess oscillation represents a robust indicator of the meteorological variability on a seasonal to sub-seasonal scale. Low absolute deuterium excess values and the synchronous variation of both deuterium excess and air temperature imply that the evaporation of moisture occurs in the adjacent Southern Ocean. The delta O-18-air temperature relationship is complicated and significant only at a (multi)seasonal scale. Backward trajectory calculations show that air-parcels arriving at the region during precipitation events predominantly originate at the South Pacific Ocean and Bellingshausen Sea. These investigations will be used as a calibration for ongoing and future research in the area, suggesting that appropriate locations for future ice core research are located above 600 m a.s.l. We selected the Plateau Laclavere, Antarctic Peninsula as the most promising site for a deeper drilling campaign.

New evidence for involvement of the entorhinal region in schizophrenia: a combined MRI volumetric and DTI study

Postmortem examinations and magnetic resonance imaging (MRI) studies suggest involvement of the entorhinal cortex (EC) in schizophrenic psychoses. However, the extent and nature of the possible pathogenetical process underlying the observed alterations of this limbic key region for processing of multimodal sensory information remains unclear. Three-dimensional high-resolution MRI volumetry and evaluation of the regional diffusional anisotropy based on diffusion tensor imaging (DTI) were performed on the EC of 15 paranoid schizophrenic patients and 15 closely matched control subjects. In schizophrenic patients, EC volumes showed a slight, but not significant, decrease. However, the anisotropy values, expressed as inter-voxel coherences (COH), were found to be significantly decreased by 17.9% (right side) and 12.5% (left side), respectively, in schizophrenics. Reduction of entorhinal diffusional anisotropy can be hypothesized to be functionally related to disturbances in the perforant path, the principal efferent EC fiber tract supplying the limbic system with neuronal input from multimodal association centers. Combinations of different MRI modalities are a promising approach for the detection and characterization of subtle brain tissue alterations.

Evaluation of promising technologies for soil salinity amelioration in Timpaki (Crete): A participatory approach

Soil salinity management can be complex, expensive, and time demanding, especially in arid and semi-arid regions. Besides taking no action, possible management strategies include amelioration and adaptation measures. Here we apply the World Overview of Conservation Approaches and Technologies (WOCAT) framework for the systematic analysis and evaluation and selection of soil salinisation amelioration technologies in close collaboration with stakeholders. The participatory approach is applied in the RECARE (Preventing and Remediating degradation of soils in Europe through Land Care) project case study of Timpaki, a semiarid region in south-central Crete (Greece) where the main land use is horticulture in greenhouses irrigated by groundwater. Excessive groundwater abstractions have resulted in a drop of the groundwater level in the coastal part of the aquifer, thus leading to seawater intrusion and in turn to soil salinisation. The documented technologies are evaluated for their impacts on ecosystem services, cost, and input requirements using a participatory approach and field evaluations. Results show that technologies which promote maintaining existing crop types while enhancing productivity and decreasing soil salinity are preferred by the stakeholders. The evaluation concludes that rainwater harvesting is the optimal solution for direct soil salinity mitigation, as it addresses a wider range of ecosystem and human well-being benefits. Nevertheless, this merit is offset by poor financial motivation making agronomic measures more attractive to users.

Heat flow values in the Sea of Okhotsk region

Tectonic structure and anomalous distributions of geophysical fields of the Sea of Okhotsk region are considered; the lack of reliable data on age of the lithosphere beneath basins of various origin in the Sea of Okhotsk is noted. Model calculations based on geological and geophysical data yielded 65 Ma (Cretaceous-Paleocene boundary) age for the Central Okhotsk rise underlain by the continental lithosphere. This estimate agrees with the age (the end of Cretaceous) derived from seismostratigraphic data. A comparative analysis of theoretical and measured heat flows in the Akademii Nauk Rise, underlain by the thinned continental crust, is performed. The analysis points to a higher (by 20%) value of the measured thermal background of the rise, which is consistent with high negative gradient of gravity anomalies in this area. Calculations yielded 36 Ma (Early Oligocene) age and lithosphere thickness of 50 km for the South Okhotsk depression, whose seafloor was formed by processes of back-arc spreading. The estimated age of the depression is supported by kinematic data on the region; the calculated thickness of the lithosphere coincides with the value estimated from data of magnetotelluric sounding here. This indicates that formation time (36 Ma) of the South Okhotsk depression was estimated correctly. Numerical modeling performed for determination of the basement age of rifting basins in the Sea of Okhotsk gave the following estimates: 18 Ma (Early Miocene) for the Deryugin Basin, 12 Ma (Middle Miocene) for the TINRO Basin, and 23 Ma (Late Oligocene) for the West Kamchatka Trough. These estimates agree with formation time (Oligocene-Quaternary) of the sedimentary cover in rifting basins of the Sea of Okhotsk derived from geological and geophysical data. Model temperature estimates are obtained for lithologic and stratigraphic boundaries of the sedimentary cover in the Deryugin and TINRO Basins and the West Kamchatka Trough; the temperature analysis indicates that the latter two structures are promising for oil and hydrocarbon gas generation; the West Kamchatka Trough possesses better reservoir properties compared to the TINRO and Deryugin Basins. The latter is promising for generation of hydrocarbon gas. Paleogeodynamic reconstructions of the Sea of Okhotsk region evolution are obtained for times of 90, 66, and 36 Ma on the base of kinematic, geomagnetic, structural, tectonic, geothermal, and other geological and geophysical data.

Deep observation of the NGC1275 region with MAGIC: search of diffuse gamma-ray emission from cosmic rays in the Perseus cluster

Clusters of galaxies are expected to be reservoirs of cosmic rays (CRs) that should produce diffuse γ-ray emission due to their hadronic interactions with the intra-cluster medium. The nearby Perseus cool-core cluster, identified as the most promising target to search for such an emission, has been observed with the MAGIC telescopes at very-high energies (VHE, E ≥ 100 GeV) for a total of 253 hr from 2009 to 2014. The active nuclei of NGC 1275, the central dominant galaxy of the cluster, and IC 310, lying at about 0.6º from the centre, have been detected as point-like VHE γ-ray emitters during the first phase of this campaign. We report an updated measurement of the NGC 1275 spectrum, which is described well by a power law with a photon index Γ = 3.6 ± 0.2_(stat) ± 0.2_(syst) between 90 GeV and 1200 GeV. We do not detect any diffuse γ-ray emission from the cluster and so set stringent constraints on its CR population. To bracket the uncertainties over the CR spatial and spectral distributions, we adopt different spatial templates and power-law spectral indexes α. For α = 2.2, the CR-to-thermal pressure within the cluster virial radius is constrained to be ≤ 1 − 2%, except if CRs can propagate out of the cluster core, generating a flatter radial distribution and releasing the CR-to-thermal pressure constraint to ≤ 20%. Assuming that the observed radio mini-halo of Perseus is generated by secondary electrons from CR hadronic interactions, we can derive lower limits on the central magnetic field, B_(0), that depend on the CR distribution. For α = 2.2, B_(0) ≥ 5 − 8 µG, which is below the ∼25 µG inferred from Faraday rotation measurements, whereas for α ≤ 2.1, the hadronic interpretation of the diffuse radio emission contrasts with our γ-ray flux upper limits independently of the magnetic field strength.

Identification and characterization of a liver stage-specific promoter region of the malaria parasite Plasmodium.

During the blood meal of a Plasmodium-infected mosquito, 10 to 100 parasites are inoculated into the skin and a proportion of these migrate via the bloodstream to the liver where they infect hepatocytes. The Plasmodium liver stage, despite its clinical silence, represents a highly promising target for antimalarial drug and vaccine approaches. Successfully invaded parasites undergo a massive proliferation in hepatocytes, producing thousands of merozoites that are transported into a blood vessel to infect red blood cells. To successfully develop from the liver stage into infective merozoites, a tight regulation of gene expression is needed. Although this is a very interesting aspect in the biology of Plasmodium, little is known about gene regulation in Plasmodium parasites in general and in the liver stage in particular. We have functionally analyzed a novel promoter region of the rodent parasite Plasmodium berghei that is exclusively active during the liver stage of the parasite. To prove stage-specific activity of the promoter, GFP and luciferase reporter assays have been successfully established, allowing both qualitative and accurate quantitative analysis. To further characterize the promoter region, the transcription start site was mapped by rapid amplification of cDNA ends (5'-RACE). Using promoter truncation experiments and site-directed mutagenesis within potential transcription factor binding sites, we suggest that the minimal promoter contains more than one binding site for the recently identified parasite-specific ApiAP2 transcription factors. The identification of a liver stage-specific promoter in P. berghei confirms that the parasite is able to tightly regulate gene expression during its life cycle. The identified promoter region might now be used to study the biology of the Plasmodium liver stage, which has thus far proven problematic on a molecular level. Stage-specific expression of dominant-negative mutant proteins and overexpression of proteins normally active in other life cycle stages will help to understand the function of the proteins investigated.