A reliable measure of similarity based on dependency for short time series: an application to gene expression networks

Background: Microarray techniques have become an important tool to the investigation of genetic relationships and the assignment of different phenotypes. Since microarrays are still very expensive, most of the experiments are performed with small samples. This paper introduces a method to quantify dependency between data series composed of few sample points. The method is used to construct gene co-expression subnetworks of highly significant edges. Results: The results shown here are for an adapted subset of a Saccharomyces cerevisiae gene expression data set with low temporal resolution and poor statistics. The method reveals common transcription factors with a high confidence level and allows the construction of subnetworks with high biological relevance that reveals characteristic features of the processes driving the organism adaptations to specific environmental conditions. Conclusion: Our method allows a reliable and sophisticated analysis of microarray data even under severe constraints. The utilization of systems biology improves the biologists ability to elucidate the mechanisms underlying celular processes and to formulate new hypotheses.

Zn uptake, physiological response and stress attenuation in mycorrhizal jack bean growing in soil with increasing Zn concentrations

The influence of arbuscular mycorrhizal fungi (AMF) inoculation on Canavalia ensiformis growth. nutrient and Zn uptake, and on some physiological parameters in response to increasing soil Zn concentrations was studied. Treatments were applied in seven replicates in a 2 x 4 factorial design, consisting of the inoculation or not with the AMF Glomus etunicatum, and the addition of Zn to soil at the concentrations of 0, 100, 300 and 900 mg kg(-1). AMF inoculation enhanced the accumulation of Zn in tissues and promoted biomass yields and root nodulation. Mycorrhizal plants exhibited relative tolerance to Zn up to 300 mg kg(-1) without exhibiting visual symptoms of toxicity, in contrast to non-mycorrhizal plants which exhibited a significant growth reduction at the same soil Zn concentration. The highest concentration of Zn added to soil was highly toxic to the plants. Leaves of plants grown in high Zn concentration exhibited a Zn-induced proline accumulation and also an increase in soluble amino acid contents; however proline contents were lower in mycorrhizal jack beans. Plants in association or not with the AMF exhibited marked differences in the foliar soluble amino acid profile and composition in response to Zn addition to soil. In general, Zn induced oxidative stress which could be verified by increased lipid peroxidation rates and changes in catalase, ascorbate peroxidase, glutathione reductase and superoxide dismutase activities. In summary, G. etunicatum was able to maintain an efficient symbiosis with jack bean plants in moderately contaminated Zn-soils, improving plant performance under those conditions, which is likely to be due to a combination of physiological and nutritional changes caused by the intimate relation between fungus and plant. The enhanced Zn uptake by AMF inoculated jack bean plants might be of interest for phytoremediation purposes. (C) 2009 Elsevier Ltd. All rights reserved.

Characterization of fungal soil communities by F-RISA and arbuscular mycorrhizal fungi from Araucaria angustifolia forest soils after replanting and wildfire disturbances

The Fungal Ribosomal Intergenic Spacer Analysis (F-RISA) was used to characterize soil fungal communities from three ecosystems of Araucaria angustifolia from Brazil: a native forest and two replanted forest ecosystems, one of them with a past history of wildfire. The arbuscular mycorrhizal fungi (AMF) infection was evaluated in Araucaria roots of 18-month-old axenic plants previously inoculated with soils collected from those areas in a greenhouse experiment. The principal component analysis of F-RISA profiles showed different soil fungal community between the three studied areas. Sixty three percent of F-RISA fragments amplified in the soil and the substrate samples presented lengths between 500 and 700 bp. The number of Operational Taxonomic Units (OTUs) was 34 for soil and 38 for substrate, however, more fragments were detected in soil (214) than in substrate (163). An in silico F-RISA analysis to compare our data with ITS1-5.8S-ITS2 sequences from NCBI database showed the presence of Ascomycota, Basidiomycota and Glomeromycota among the soil and substrate fungal communities. AMF infection was higher in plants inoculated with soil from the native forest and the replanted forest with wildfire, both presenting similar chemical characteristics but with different disturbance levels. These results indicate that soil chemical composition may influence the soil fungal community structures rather than the anthropogenic or fire disturbances.

Dosage-dependent shift in the spore community of arbuscular mycorrhizal fungi following application of tannery sludge

The controlled disposal of tannery sludge in agricultural soils is a viable alternative for recycling such waste; however, the impact of this practice on the arbuscular mycorrhizal fungi (AMF) communities is not well understood. We studied the effects of low-chromium tannery sludge amendment in soils on AMF spore density, species richness and diversity, and root colonization levels. Sludge was applied at four doses to an agricultural field in Rolandia, Parana state, Brazil. The sludge was left undisturbed on the soil surface and then the area was harrowed and planted with corn. The soil was sampled at four intervals and corn roots once within a year (2007/2008). AMF spore density was low (1 to 49 spores per 50 cm(3) of soil) and decreased as doses of tannery sludge increased. AMF root colonization was high (64%) and unaffected by tannery sludge. Eighteen AMF species belonging to six genera (Acaulospora, Glomus, Gigaspora, Scutellospora, Paraglomus, and Ambispora) were recorded. At the sludge doses of 9.0 and 22.6 Mg ha(-1), we observed a decrease in AMF species richness and diversity, and changes in their relative frequencies. Hierarchical grouping analysis showed that adding tannery waste to the soil altered AMF spore community in relation to the control, modifying the mycorrhizal status of soil and selectively favoring the sporulation of certain species.

Climatic simulations of the eastern Andes low-level jet and its dependency on convective parameterizations

The South American low level jet (SALLJ) of the Eastern Andes is investigated with Regional Climate Model version 3 (RegCM3) simulations during the 2002-2003 austral summer using two convective parameterizations (Grell and Emanuel). The simulated SALLJ is compared with the special observations of SALLJEX (SALLJ Experiment). Both the Grell and Emanuel schemes adequately simulate the low level flow over South America. However, there are some intensity differences. Due to the larger (smaller) convective activity, the Emanuel (Grell) scheme simulates more intense (weaker) low level wind than analysis in the tropics and subtropics. The objectives criteria of Sugahara (SJ) and Bonner (BJ) were used for LLJ identification. When applied to the observations, both criteria suggest a larger frequency of the SALLJ in Santa Cruz, followed by Mariscal, Trinidad and Asuncin. In Mariscal and Asuncin, the diurnal cycle indicates that SJ occurs mainly at 12 UTCs (morning), while the BJ criterion presents the SALLJ as more homogenously distributed. The concentration into two of the four-times-a-day observations does not allow conclusions about the diurnal cycle in Santa Cruz and Trinidad. The simulated wind profiles result in a lower than observed frequency of SALLJ using both the SJ and BJ criteria, with fewer events obtained with the BJ. Due to the stronger simulated winds, the Emanuel scheme produces an equal or greater relative frequency of SALLJ than the Grell scheme. However, the Grell scheme using the SJ criterion simulates the SALLJ diurnal cycle closer to the observed one. Although some discrepancies between observed and simulated mean vertical profiles of the horizontal wind are noted, there is large agreement between the composites of the vertical structure of the SALLJ, especially when the SJ criterion is used with the Grell scheme. On an intraseasonal scale, a larger southward displacement of SALLJ in February and December when compared with January has been noted. The Grell and Emanuel schemes simulated this observed oscillation in the low-level flow. However, the spatial pattern and intensity of rainfall and circulation anomalies simulated by the Grell scheme are closer to the analyses than those obtained with the Emanuel scheme.

Consumo alimentar e ecologia de populações ribeirinhas em dois ecossistemas amazônicos: um estudo comparativo

OBJETIVO: Este artigo analisa e compara os dados de consumo alimentar de duas populações ribeirinhas da Amazônia vivendo em ecossistemas contrastantes de floresta tropical: a várzea estacional e a floresta de terra firme. MÉTODOS: Foi estudado o consumo alimentar de 11 unidades domésticas na várzea (Ilha de Ituqui, Município de Santarém) e 17 na terra firme (Floresta Nacional de Caxiuanã, Municípios de Melgaço e Portel). O método utilizado foi o recordatório de 24 horas. As análises estatísticas foram executadas com o auxílio do programa Statistical Package for Social Sciences 12.0. RESULTADOS: Em ambos os ecossistemas, os resultados confirmam a centralidade do pescado e da mandioca na dieta local. Porém, a contribuição de outros itens alimentares secundários, tais como o açaí (em Caxiuanã) e o leite in natura (em Ituqui), também foi significante. Além disso, o açúcar revelou ser uma fonte de energia confiável para enfrentar as flutuações sazonais dos recursos naturais. Parece haver ainda uma maior contribuição energética dos peixes para a dieta de Ituqui, provavelmente em função da maior produtividade dos rios e lagos da várzea em relação à terra firme. Por fim, Ituqui revelou uma maior dependência de itens alimentares comprados, enquanto Caxiuanã mostrou estar ainda bastante vinculada à agricultura e às redes locais de troca. CONCLUSÃO: Além dos resultados confirmarem a importância do pescado e da mandioca, também mostraram que produtos industrializados, como o açúcar, têm um papel importante nas dietas, podendo apontar para tendências no consumo alimentar relacionadas com a atual transição nutricional e com a erosão, em diferentes níveis, dos sistemas de subsistência locais.

Radiocarbon geochronology of the sediments of the São Paulo Bight (southern Brazilian upper margin)

The aim of this work was to generate an inventory of the data on radiocarbon datings obtained from sediments of the São Paulo Bight (southern Brazilian upper margin) and to analyze the data in terms of Late Quaternary sedimentary processes and sedimentation rates. A total of 238 radiocarbon datings from materials collected using differents ampling procedures was considered for this work. The sedimentation rates varied from less than 2 to 68 cm.kyr-1. The highest sedimentation rate values were found in a low-energy (ría type) coastal system as well as in the upwelling zones of Santa Catarina and Cabo Frio. The lowest rates were found on the outer shelf and upper slopes. Our results confirm the strong dependency of the shelf currents, with an emphasis to the terrigenous input from the Río de La Plata outflow which is transported via the Brazilian Coastal Current, as well as of the coupled Brazil Current - Intermediate Western Boundary Current (BC-IWBC) dynamics on the sedimentary processes. At least three indicators ofthe paleo sea level were found at 12200 yr BP (conventional radiocarbon age) (103 meters below sea level - mbsl),8300-8800 cal yr BP (13 mbsl) and 7700-8100 cal yr BP (6 mbsl).

Morphological features and vascularization study of caprine cyclic corpus luteum

Corpus luteum is a temporary endocrine gland that regulates either the estrous cycle and pregnancy. It presents extreme dependency on the adequate blood supply. This work aims to evaluate goat corpus luteum (CL) vascular density (VD) over the estrous cycle. For that purpose, 20 females were submitted to estrus synchronization/ovulation treatment using a medroxyprogesterone intra-vaginal sponge as well as intramuscular (IM) application of cloprostenol and equine chorionic gonadotrophine (eCG). After sponge removal, estrus was identified at about 72hs. Once treatment was over, female goats were then subdivided into 4 groups (n=5 each) and slaughtered on days 2, 12, 16 and 22 after ovulation (p.o). Ovaries were collected, withdrawn and weighted. CL and ovaries had size and area recorded. Blood samples were collected and the plasma progesterone (P4) was measured through RIA commercial kits. The VD was 24.42±6.66, 36.26±5.61, 8.59±2.2 and 3.97±1.12 vessels/mm² for days 2, 12, 16 and 22 p.o, respectively. Progesterone plasma concentrations were 0.49±0.08, 2.63±0.66, 0.61±0.14 and 0.22±0.04ng/ml for days 2, 12, 16 e 22 p.o, respectively. Studied parameters were affected by the estrous cycle phase. Values greater than 12 p.o were observed. In the present work we observed that ovulation occurred predominantly in the right ovary (70% of the animals), which in turn presented bigger measures than the contra lateral one. There is a meaningful relationship between the weight and size of the ovary and these of CL (r=0.87, r=0.70, respectively, p<0.05). It is possible to conclude that morphology of goat's ovaries and plasma progesterone concentration changed according to estrous cycle stages. We propose these parameters can be used as indicators of CL functional activity.

Recovery and upgrading bovine rumen protein by extrusion: effect of lipid content on protein disulphide cross-linking, solubility and molecular weight

Bovine rumen protein with two levels of residual lipids (1.9 per cent or 3.8 per cent) was subjected to thermoplastic extrusion under different temperatures and moisture contents. Protein solubility in different buffers, disulphide cross-linking and molecular weight distribution were determined on the extrudates. After extrusion, samples with 1.9 per cent residual lipids content had a higher concentration of protein insoluble by undetermined forces, irrespective of feed moisture and processing temperature used. Lipid content of 3.8 per cent in the feed material resulted in more protein participating in the extrudate network through non-covalent interactions (hydrophobic and electrostatic) and disulphide bonds. A small dependency of the extrusion process on moisture and temperature and a marked dependency on lipid content, especially phospholipid, was observed, Electrophoresis under non-reducing conditions showed that protein extrusion with low feed moisture promoted high molecular breakdown inside the barrel, probably due to intense shear force, and further protein aggregation at the die end

A simple procedure for reliability assessment of thin composite plates against buckling

In some circumstances ice floes may be modeled as beams. In general this modeling supposes constant thickness, which contradicts field observations. Action of currents, wind and the sequence of contacts, causes thickness to vary. Here this effect is taken into consideration on the modeling of the behavior of ice hitting inclined walls of offshore platforms. For this purpose, the boundary value problem is first equated. The set of equations so obtained is then transformed into a system of equations, that is then solved numerically. For this sake an implicit solution is developed, using a shooting method, with the accompanying Jacobian. In-plane coupling and the dependency of the boundary terms on deformation, make the problem non-linear and the development particular. Deformation and internal resultants are then computed for harmonic forms of beam profile. Forms of giving some additional generality to the problem are discussed.

Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview

Background: DAPfinder and DAPview are novel BRB-ArrayTools plug-ins to construct gene coexpression networks and identify significant differences in pairwise gene-gene coexpression between two phenotypes. Results: Each significant difference in gene-gene association represents a Differentially Associated Pair (DAP). Our tools include several choices of filtering methods, gene-gene association metrics, statistical testing methods and multiple comparison adjustments. Network results are easily displayed in Cytoscape. Analyses of glioma experiments and microarray simulations demonstrate the utility of these tools. Conclusions: DAPfinder is a new friendly-user tool for reconstruction and comparison of biological networks.

Notes on Acaulospora bireticulata Rothwell & Trappe and first record of Acaulospora koskei Blask. from Brazil)

(Notes on Acaulospora bireticulata Rothwell & Trappe and first record of Acaulospora koskei Blask. from Brazil). Our knowledge of species distribution in arbuscular mycorrhizal fungi (AMF) is still limited and morphological variations found in isolates of one species may provide additional insight for understanding the characters used in the taxonomy of this group. The aims of this work were to expand biogeographical data regarding Acaulospora koskei Blaszk. and Acaulospora bireticulata Rothwell & Trappe, both found in an Araucaria Forest in Sao Paulo state, Brazil, as well as to compare the descriptions of these species with those of other similar AMF.

A numerical model for the description of the nonlinear behaviour of multi-leaf masonry walls

A nonlinear finite element model was developed to simulate the nonlinear response of three-leaf masonry specimens, which were subjected to laboratory tests with the aim of investigating the mechanical behaviour of multiple-leaf stone masonry walls up to failure. The specimens consisted of two external leaves made of stone bricks and mortar joints, and an internal leaf in mortar and stone aggregate. Different loading conditions, typologies of the collar joints, and stone types were taken into account. The constitutive law implemented in the model is characterized by a damage tensor, which allows the damage-induced anisotropy accompanying the cracking process to be described. To follow the post-peak behaviour of the specimens with sufficient accuracy it was necessary to make the damage model non-local, to avoid mesh-dependency effects related to the strain-softening behaviour of the material. Comparisons between the predicted and measured failure loads are quite satisfactory in most of the studied cases. (c) 2007 Elsevier Ltd. All rights reserved.

Influence of physical and geometrical parameters on three-dimensional load transfer mechanism at tunnel face

Three-dimensional discretizations used in numerical analyses of tunnel construction normally include excavation step lengths much shorter than tunnel cross-section dimensions. Simulations have usually worked around this problem by using excavation steps that are much larger than the actual physical steps used in a real tunnel excavation. In contrast, the analyses performed in this study were based on finely discretized meshes capable of reproducing the excavation lengths actually used in tunnels, and the results obtained for internal forces are up to 100% greater than those found in other analyses available in the literature. Whereas most reports conclude that internal forces depend on support delay length alone, this study shows that geometric path dependency (reflected by excavation round length) is very strong, even considering linear elasticity. Moreover, many other solutions found in the literature have also neglected the importance of the relative stiffness between the ground mass and support structure, probably owing to the relatively coarse meshes used in these studies. The analyses presented here show that relative stiffness may account for internal force discrepancies in the order of 60%. A dimensionless expression that takes all these parameters into account is presented as a good approximation for the load transfer mechanism at the tunnel face.

Impact of plastic deformation on magnetoacoustic properties of Fe-2%Si alloy

The paper presents the results of a complementary study including magnetic hysteresis loops B(H), magnetic Barkhausen noise (MBN) and magnetoacoustic emission (MAE) signals measurements for plastically deformed Fe-2%Si samples. The investigated samples had been plastically deformed with plastic strain level (epsilon(p)) up to 8%. The properties of B(H) loops are quantified using the coercivity H(C) and maximum differential permeability mu(rmax) as parameters. The MBN and MAE voltage signals were analysed by means of rms-like voltage (Ub and Ua, respectively) envelopes, plotted as a function of applied field strength. Integrals of the Ub and Ua voltages over half of a period of magnetization were then calculated. It has been found that He and integrals of Ub increase, while mu(rmax) decreases monotonically with increasing epsilon(p). The MAE (Ua) peak voltage at first decreases, then peaks at epsilon(p) approximate to 1.5% and finally decreases again. The integral of the Ua voltage at first increases for low epsilon(p) and then decreases for epsilon(p) > 1.5%. All those various dependence types suggest the possibility of detection of various stages of microstructure change. The above-mentioned results are discussed qualitatively in the paper. Some modelling of the discussed dependency is also presented. (C) 2008 Elsevier Ltd. All rights reserved.