Importance of estimating matrix quality for modeling species distribution in complex tropical landscapes: a test with Atlantic forest small mammals

Information to guide decision making is especially urgent in human dominated landscapes in the tropics, where urban and agricultural frontiers are still expanding in an unplanned manner. Nevertheless, most studies that have investigated the influence of landscape structure on species distribution have not considered the heterogeneity of altered habitats of the matrix, which is usually high in human dominated landscapes. Using the distribution of small mammals in forest remnants and in the four main altered habitats in an Atlantic forest landscape, we investigated 1) how explanatory power of models describing species distribution in forest remnants varies between landscape structure variables that do or do not incorporate matrix quality and 2) the importance of spatial scale for analyzing the influence of landscape structure. We used standardized sampling in remnants and altered habitats to generate two indices of habitat quality, corresponding to the abundance and to the occurrence of small mammals. For each remnant, we calculated habitat quantity and connectivity in different spatial scales, considering or not the quality of surrounding habitats. The incorporation of matrix quality increased model explanatory power across all spatial scales for half the species that occurred in the matrix, but only when taking into account the distance between habitat patches (connectivity). These connectivity models were also less affected by spatial scale than habitat quantity models. The few consistent responses to the variation in spatial scales indicate that despite their small size, small mammals perceive landscape features at large spatial scales. Matrix quality index corresponding to species occurrence presented a better or similar performance compared to that of species abundance. Results indicate the importance of the matrix for the dynamics of fragmented landscapes and suggest that relatively simple indices can improve our understanding of species distribution, and could be applied in modeling, monitoring and managing complex tropical landscapes.

Human Stem Cell Cultures from Cleft Lip/Palate Patients Show Enrichment of Transcripts Involved in Extracellular Matrix Modeling By Comparison to Controls

Nonsyndromic cleft lip and palate (NSCL/P) is a complex disease resulting from failure of fusion of facial primordia, a complex developmental process that includes the epithelial-mesenchymal transition (EMT). Detection of differential gene transcription between NSCL/P patients and control individuals offers an interesting alternative for investigating pathways involved in disease manifestation. Here we compared the transcriptome of 6 dental pulp stem cell (DPSC) cultures from NSCL/P patients and 6 controls. Eighty-seven differentially expressed genes (DEGs) were identified. The most significant putative gene network comprised 13 out of 87 DEGs of which 8 encode extracellular proteins: ACAN, COL4A1, COL4A2, GDF15, IGF2, MMP1, MMP3 and PDGFa. Through clustering analyses we also observed that MMP3, ACAN, COL4A1 and COL4A2 exhibit co-regulated expression. Interestingly, it is known that MMP3 cleavages a wide range of extracellular proteins, including the collagens IV, V, IX, X, proteoglycans, fibronectin and laminin. It is also capable of activating other MMPs. Moreover, MMP3 had previously been associated with NSCL/P. The same general pattern was observed in a further sample, confirming involvement of synchronized gene expression patterns which differed between NSCL/P patients and controls. These results show the robustness of our methodology for the detection of differentially expressed genes using the RankProd method. In conclusion, DPSCs from NSCL/P patients exhibit gene expression signatures involving genes associated with mechanisms of extracellular matrix modeling and palate EMT processes which differ from those observed in controls. This comparative approach should lead to a more rapid identification of gene networks predisposing to this complex malformation syndrome than conventional gene mapping technologies.

Matrix metalloproteinases, TIMPs and growth factors regulating ameloblastoma behaviour

Aims: Ameloblastoma is an odontogenic neoplasm with local invasiveness and recurrence. We have previously suggested that growth factors and matrix metalloproteinases (MMPs) influence ameloblastoma invasiveness(1). The aim was to study expression of MMPs, tissue inhibitor of metalloproteinases (TIMPs) and growth factors in ameloblastoma. Methods and results: Thirteen cases of solid/multicystic ameloblastoma were examined. As a control, calcifying cystic odontogenic tumour (CCOT), a non-invasive odontogenic neoplasm with ameloblastomatous epithelium was also studied. Immunohistochemistry detected MMPs, TIMPs and growth factors in ameloblastoma and CCOT. The labelling index (LI) of MMP-9 and TIMP-2 was significantly higher in ameloblastoma compared with CCOT. The LI of epidermal growth factor (EGF), transforming growth factor (TGF)-alpha and epidermal growth factor receptor (EGFR) was also increased in ameloblastoma. This neoplasm showed greater expression of MMPs, TIMPs and growth factors compared with CCOT. We then analysed these molecules in ameloblastoma cells and stroma. Ameloblastoma cells exhibited increased LI of MMP-1, -2 and EGFR. We found a positive correlation between EGF and TIMP-1, and between TGF-alpha and TIMP-2. It is known that signals generated by growth factors are transduced by the ERK pathway. Ameloblastoma stroma exhibited the phosphorylated (activated) form of ERK. Conclusions: These results suggest an interplay involving growth factors MMPs and TIMPs that may contribute to ameloblastoma behaviour. Signals generated by this molecular network would be transduced by ERK 1/2 pathway.

Maternal diabetes affects specific extracellular matrix components during placentation

During embryo implantation, invasive trophoblast cells mediate embryo invasion into the decidualized stroma, forming a rich network of lacunae that connect the embryonic tissues to the maternal blood vessels. Placentation is probably guided by the composition and organization of the endometrial extracellular matrix. Certain pathological conditions that occur during pregnancy, including diabetes, have been linked to abnormal placental morphology and consequent fetal morbidity. We used immunoperoxidase techniques to identify members of the collagen, proteoglycan and glycoprotein families in the various compartments of the rat placenta and to determine whether experimentally induced diabetes affects placental morphology and alters the distribution of these molecules during pregnancy. Single injections of alloxan (40 mg kg(-1) i.v.) were used to induce diabetes on day 2 of pregnancy in Wistar rats. Placentas were collected on days 14, 17, and 20. Type I and III collagen, as well as the proteoglycans decorin and biglycan, were found to be distributed throughout the placentas of control and diabetic rats. In both groups, laminin expression decreased at the end of pregnancy. In contrast, fibronectin was detected in the labyrinth region of diabetic rats at all gestational stages studied, whereas it was detected only at term pregnancy in the placentas of control rats. These results show for the first time that some extracellular matrix molecules are modulated during placental development. However, as diabetic rats presented increased fibronectin deposition exclusively in the labyrinth region, we speculate that diabetes alters the microenvironment at the maternal-fetal interface, leading to developmental abnormalities in the offspring.

The ""decarbonization"" of the world`s energy matrix

Decarbonizing the world`s energy matrix is the strategy being implemented by most countries to reduce CO(2) emissions and thus contribute to achieve the ultimate objectives of the Climate Convention. The evolution of the carbon intensity (I(c)=CO(2)/GDP) in the period 1990-2007 was encouraging but not sufficient to reduce the growth of carbon emission. As a result of COP-15 in Copenhagen these countries (and regions) made pledges that could lead to more reduction: for the United States a 17% reduction in CO(2) emissions by 2020 below the level of 2005: for the European Union a 20% reduction in CO(2) emissions by 2020 below the 1990 level: for China a 40-45% reduction in the carbon intensity and for India a 20-25% reduction in carbon intensity by 2020. We analyzed the consequences of such pledges and concluded that the expected yearly rate of decrease of the carbon intensity follows basically the ""business as usual"" trend in the period 1990-2007 and will, in all likelihood, be insufficient to reduce carbon emissions up to 2020. (C) 2010 Elsevier Ltd. All rights reserved.

A Time Efficient Optical Model for GATE Simulation of a LYSO Scintillation Matrix Used in PET Applications

A time efficient optical model is proposed for GATE simulation of a LYSO scintillation matrix coupled to a photomultiplier. The purpose is to avoid the excessively long computation time when activating the optical processes in GATE. The usefulness of the model is demonstrated by comparing the simulated and experimental energy spectra obtained with the dual planar head equipment for dosimetry with a positron emission tomograph ( DoPET). The procedure to apply the model is divided in two steps. Firstly, a simplified simulation of a single crystal element of DoPET is used to fit an analytic function that models the optical attenuation inside the crystal. In a second step, the model is employed to calculate the influence of this attenuation in the energy registered by the tomograph. The use of the proposed optical model is around three orders of magnitude faster than a GATE simulation with optical processes enabled. A good agreement was found between the experimental and simulated data using the optical model. The results indicate that optical interactions inside the crystal elements play an important role on the energy resolution and induce a considerable degradation of the spectra information acquired by DoPET. Finally, the same approach employed by the proposed optical model could be useful to simulate a scintillation matrix coupled to a photomultiplier using single or dual readout scheme.

On S-matrix factorization of the Landau-Lifshitz model

We consider the three-particle scattering S-matrix for the Landau-Lifshitz model by directly computing the set of the Feynman diagrams up to the second order. We show, following the analogous computations for the non-linear Schrdinger model [1, 2], that the three-particle S-matrix is factorizable in the first non-trivial order.

Perturbation treatment of symmetry breaking within random matrix theory

We discuss the applicability, within the random matrix theory, of perturbative treatment of symmetry breaking to the experimental data on the flip symmetry breaking in quartz crystal. We found that the values of the parameter that measures this breaking are different for the spacing distribution as compared to those for the spectral rigidity. We consider both two-fold and three-fold symmetries. The latter was found to account better for the spectral rigidity than the former. Both cases, however, underestimate the experimental spectral rigidity at large L. This discrepancy can be resolved if an appropriate number of eigenfrequencies is considered to be missing in the sample. Our findings are relevant for symmetry violation studies in general. (C) 2008 Elsevier B.V. All rights reserved.

Hyperfine and magnetic properties of Fe-Cu clusters and Fe precipitates embedded in a Cu matrix

Using the first-principles real-space linear muffin-tin orbital method within the atomic sphere approximation (RS-LMTO-ASA) we study hyperfine and local magnetic properties of substituted pure Fe and Fe-Cu clusters in an fcc Cu matrix. Spin and orbital contributions to magnetic moments, hyperfine fields and the Mossbauer isomer shifts at the Fe sites in Fe precipitates and Fe-Cu alloy clusters of sizes up to 60 Fe atoms embedded in the Cu matrix are calculated and the influence of the local environment on these properties is discussed.

Magnetic and optical characterization of Mn-doped PbS nanocrystals supported in oxide glass matrix

The evidence of successful growth of Mn-doped PbS (Pb(1-x)Mn(x)S) nanocrystals (NCs) in SiO(2)-Na(2)CO(3)-Al(2)O(3)-PbO(2)-B(2)O(3) template, using the fusion method, is reported on in this study. The as-grown Pb(1-x)Mn(x)S NC is characterized using optical absorption, electron paramagnetic resonance, and atomic force microscopy. The data are discussed in terms of two distinct scenarios, namely a core-doped and a shell-doped nanostructure. (C) 2008 Elsevier B.V. All rights reserved.

Using phospholipid Langmuir and Langmuir-Blodgett films as matrix for urease immobilization

The immobilization of enzymes in organized two-dimensional matrices is a key requirement for many biotechnological applications. In this paper, we used the Langmuir-Blodgett (LB) technique to obtain controlled architectures of urease immobilized in solid supports, whose physicochemical properties were investigated in detail. Urease molecules were adsorbed at the air-water interface and incorporated into Langmuir monolayers of the phospholipid dipalmitoyl phosphatidyl glycerol (DPPG). Incorporation of urease made DPPG monolayers more flexible and caused the reduction of the equilibrium and dynamic elasticity of the film. Urease and DPPG-urease mixed monolayers could be transferred onto solid substrates, forming LB films. A close packing arrangement of urease was obtained, especially in the mixed LB films, which was inferred with nanogravimetry and electrochemistry measurements. From the blocking effect of the LB films deposited onto indium tin oxide (ITO) substrates, the electrochemical properties of the LB films pointed to a charge transport controlled by the lipid architecture. (c) 2007 Elsevier Inc. All rights reserved.

Thin films prepared from tungstate glass matrix

Vitreous samples containing high concentrations of WO3 (above 40% M) have been used as a target to prepare thin films. Such films were deposited using the electron beam evaporation method onto soda-lime glass substrates. These films were characterized by X-ray diffraction (XRD), perfilometry, X-ray energy dispersion spectroscopy (EDS), M-Lines and UV-vis absorption spectroscopy. In this work, experimental parameters were established to obtain stable thin films showing a chemical composition close to the glass precursor composition and with a high concentration of WO3. These amorphous thin films of about 4 mu m in thickness exhibit a deep blue coloration but they can be bleached by thermal treatment near the glass transition temperature. Such bleached films show several guided modes in the visible region and have a high refractive index. Controlled crystallization was realized and thus it was possible to obtain WO3 microcrystals in the amorphous phase. (C) 2007 Elsevier B.V. All rights reserved.

Influence of pH on the incorporation and growth of Pb(2)CrO(5) crystallites in silica matrix

Pb(2)CrO(5) nanoparticles were embedded in an amorphous SiO(2) matrix by the sol-gel process. The pH and heat treatment effects were evaluated in terms of structural, microstructural and optical properties from Pb(2)CrO(5)/SiO(2) compounds. X-ray diffraction (XRD), high resolution transmission electron microscopy (HR-TEM), energy dispersive spectroscopy (EDS), and diffuse reflectance techniques were employed. Kubelka-Munk theory was used to calculate diffuse reflectance spectra that were compared to the experimental results. Finally, colorimetric coordinates of the Pb(2)CrO(5)/SiO(2) compounds were shown and discussed. In general, an acid pH initially dissolves Pb(2)CrO(5) nanoparticles and following heat treatment at 600 A degrees C crystallized into PbCrO(4) composition with grain size around 6 nm in SiO(2) matrix. No Pb(2)CrO(5) solubilization was observed for basic pH. These nanoparticles were incorporated in silica matrix showing a variety of color ranging from yellow to orange.

On the generalized eigenvalue method for energies and matrix elements in lattice field theory

We discuss the generalized eigenvalue problem for computing energies and matrix elements in lattice gauge theory, including effective theories such as HQET. It is analyzed how the extracted effective energies and matrix elements converge when the time separations are made large. This suggests a particularly efficient application of the method for which we can prove that corrections vanish asymptotically as exp(-(E(N+1) - E(n))t). The gap E(N+1) - E(n) can be made large by increasing the number N of interpolating fields in the correlation matrix. We also show how excited state matrix elements can be extracted such that contaminations from all other states disappear exponentially in time. As a demonstration we present numerical results for the extraction of ground state and excited B-meson masses and decay constants in static approximation and to order 1/m(b) in HQET.

Matrix Representation of the Stationary Measure for the Multispecies TASEP

In this work we construct the stationary measure of the N species totally asymmetric simple exclusion process in a matrix product formulation. We make the connection between the matrix product formulation and the queueing theory picture of Ferrari and Martin. In particular, in the standard representation, the matrices act on the space of queue lengths. For N > 2 the matrices in fact become tensor products of elements of quadratic algebras. This enables us to give a purely algebraic proof of the stationary measure which we present for N=3.