The genetic effects of Late Quaternary climatic changes over a tropical latitudinal gradient: diversification of an Atlantic Forest passerine

The increase in biodiversity from high to low latitudes is a widely recognized biogeographical pattern. According to the latitudinal gradient hypothesis (LGH), this pattern was shaped by differential effects of Late Quaternary climatic changes across a latitudinal gradient. Here, we evaluate the effects of climatic changes across a tropical latitudinal gradient and its implications to diversification of an Atlantic Forest (AF) endemic passerine. We studied the intraspecific diversification and historical demography of Sclerurus scansor, based on mitochondrial (ND2, ND3 and cytb) and nuclear (FIB7) gene sequences. Phylogenetic analyses recovered three well-supported clades associated with distinct latitudinal zones. Coalescent-based methods were applied to estimate divergence times and changes in effective population sizes. Estimates of divergence times indicate that intraspecific diversification took place during Middle-Late Pleistocene. Distinct demographic scenarios were identified, with the southern lineage exhibiting a clear signature of demographic expansion, while the central one remained more stable. The northern lineage, contrasting with LGH predictions, exhibited a clear sign of a recent bottleneck. Our results suggest that different AF regions reacted distinctly, even in opposite ways, under the same climatic period, producing simultaneously favourable scenarios for isolation and contact among populations.

Partial spectral projected gradient method with active-set strategy for linearly constrained optimization

A method for linearly constrained optimization which modifies and generalizes recent box-constraint optimization algorithms is introduced. The new algorithm is based on a relaxed form of Spectral Projected Gradient iterations. Intercalated with these projected steps, internal iterations restricted to faces of the polytope are performed, which enhance the efficiency of the algorithm. Convergence proofs are given and numerical experiments are included and commented. Software supporting this paper is available through the Tango Project web page: http://www.ime.usp.br/similar to egbirgin/tango/.

Proximal methods for nonlinear programming: double regularization and inexact subproblems

This paper describes the first phase of a project attempting to construct an efficient general-purpose nonlinear optimizer using an augmented Lagrangian outer loop with a relative error criterion, and an inner loop employing a state-of-the art conjugate gradient solver. The outer loop can also employ double regularized proximal kernels, a fairly recent theoretical development that leads to fully smooth subproblems. We first enhance the existing theory to show that our approach is globally convergent in both the primal and dual spaces when applied to convex problems. We then present an extensive computational evaluation using the CUTE test set, showing that some aspects of our approach are promising, but some are not. These conclusions in turn lead to additional computational experiments suggesting where to next focus our theoretical and computational efforts.

Development of practical HPLC methods for the separation and determination of eggplant steroidal glycoalkaloids and their aglycones

A practical set of HPLC methods was developed for the separation and determination of the eggplant steroidal glycoalkaloids, solanine, chaconine, solasonine, solamargine, and their aglycones, solasodine and solanidine. A gradient method was initially developed, but proved to be neither robust nor practical. Three separate isocratic methods using acetonitrile and ammonium dihydrogen phosphate were developed and shown to be more repeatable, less subject to fluctuations in mobile phase composition, and less time consuming. The effect of adjusting buffer pH, column temperature, and buffer type (triethylammonium phosphate vs. ammonium dihydrogen phosphate) were evaluated. It was also discovered that, by addition of 10% methanol to the acetonitrile portion of the mobile phase, more control over the separations was possible. The use of methanol as a mobile phase entrainer greatly improved separations in some cases and its effectiveness was also dependent upon column temperature. Assessments of the method recovery, limit of detection, and limit of quantitation were made using extracts from S. melongena and S. linnaeanum.

Fish community structure along a conservation gradient in Bodoquena Plateau streams, central West of Brazil.

Aim: To investigate whether composition and structure of stream ichthyofauna vary along the conservation gradient in the Bodoquena Plateau; Methods: Standardized sampling was performed in nine stream stretches (three references, three in the pasture, and three in urban areas), each 80 m long, in April, May and June/08; Results: A quantity of 8,102 individuals representing 36 species was collected. There were no significant differences with respect to absolute species richness among stretches. Urban stretches were more similar to each other than the other two groups, both regarding species composition and abundance. A set of six species was considered an indicator of reference stretches, whereas two were of pasture stretches and four of urban stretches. Poecilia reticulata and Corydoras aeneus, occurring only in urban stretches, were unique in showing the maximum values in the indicator species analysis; Conclusions: Results indicate changes in the ichthyofauna with urbanized surrounding water courses. The presence and abundance of Poecilia reticulata and Corydoras aeneus may indicate the quality loss of these environments.

Disturbances, elevation, topography and spatial proximity drive vegetation patterns along an altitudinal gradient of a top biodiversity hotspot

The correlation between vegetation patterns (species distribution and richness) and altitudinal variation has been widely reported for tropical forests, thereby providing theoretical basis for biodiversity conservation. However, this relationship may have been oversimplified, as many other factors may influence vegetation patterns, such as disturbances, topography and geographic distance. Considering these other factors, our primary question was: is there a vegetation pattern associated with substantial altitudinal variation (10-1,093 m a.s.l.) in the Atlantic Rainforest-a top hotspot for biodiversity conservation-and, if so, what are the main factors driving this pattern? We addressed this question by sampling 11 1-ha plots, applying multivariate methods, correlations and variance partitioning. The Restinga (forest on sandbanks along the coastal plains of Brazil) and a lowland area that was selectively logged 40 years ago were floristically isolated from the other plots. The maximum species richness (>200 spp. per hectare) occurred at approximately 350 m a.s.l. (submontane forest). Gaps, multiple stemmed trees, average elevation and the standard deviation of the slope significantly affected the vegetation pattern. Spatial proximity also influenced the vegetation pattern as a structuring environmental variable or via dispersal constraints. Our results clarify, for the first time, the key variables that drive species distribution and richness across a large altitudinal range within the Atlantic Rainforest. © 2013 Springer Science+Business Media Dordrecht.

Continuity of Lyapunov functions and of energy level for generalized gradient semigroup

The global attractor of a gradient-like semigroup has a Morse decomposition. Associated to this Morse decomposition there is a Lyapunov function (differentiable along solutions)-defined on the whole phase space- which proves relevant information on the structure of the attractor. In this paper we prove the continuity of these Lyapunov functions under perturbation. On the other hand, the attractor of a gradient-like semigroup also has an energy level decomposition which is again a Morse decomposition but with a total order between any two components. We claim that, from a dynamical point of view, this is the optimal decomposition of a global attractor; that is, if we start from the finest Morse decomposition, the energy level decomposition is the coarsest Morse decomposition that still produces a Lyapunov function which gives the same information about the structure of the attractor. We also establish sufficient conditions which ensure the stability of this kind of decomposition under perturbation. In particular, if connections between different isolated invariant sets inside the attractor remain under perturbation, we show the continuity of the energy level Morse decomposition. The class of Morse-Smale systems illustrates our results.

An estimate on the fractal dimension of attractors of gradient-like dynamical systems

This paper is dedicated to estimate the fractal dimension of exponential global attractors of some generalized gradient-like semigroups in a general Banach space in terms of the maximum of the dimension of the local unstable manifolds of the isolated invariant sets, Lipschitz properties of the semigroup and the rate of exponential attraction. We also generalize this result for some special evolution processes, introducing a concept of Morse decomposition with pullback attractivity. Under suitable assumptions, if (A, A*) is an attractor-repeller pair for the attractor A of a semigroup {T(t) : t >= 0}, then the fractal dimension of A can be estimated in terms of the fractal dimension of the local unstable manifold of A*, the fractal dimension of A, the Lipschitz properties of the semigroup and the rate of the exponential attraction. The ingredients of the proof are the notion of generalized gradient-like semigroups and their regular attractors, Morse decomposition and a fine analysis of the structure of the attractors. As we said previously, we generalize this result for some evolution processes using the same basic ideas. (C) 2012 Elsevier Ltd. All rights reserved.

Electronic Properties of Water in Liquid Environment. A Sequential QM/MM Study Using the Free Energy Gradient Method

There is a continuous search for theoretical methods that are able to describe the effects of the liquid environment on molecular systems. Different methods emphasize different aspects, and the treatment of both the local and bulk properties is still a great challenge. In this work, the electronic properties of a water molecule in liquid environment is studied by performing a relaxation of the geometry and electronic distribution using the free energy gradient method. This is made using a series of steps in each of which we run a purely molecular mechanical (MM) Monte Carlo Metropolis simulation of liquid water and subsequently perform a quantum mechanical/molecular mechanical (QM/MM) calculation of the ensemble averages of the charge distribution, atomic forces, and second derivatives. The MP2/aug-cc-pV5Z level is used to describe the electronic properties of the QM water. B3LYP with specially designed basis functions are used for the magnetic properties. Very good agreement is found for the local properties of water, such as geometry, vibrational frequencies, dipole moment, dipole polarizability, chemical shift, and spin-spin coupling constants. The very good performance of the free energy method combined with a QM/MM approach along with the possible limitations are briefly discussed.

The importance of plant life form on spatial associations along a subtropical coastal dune gradient

Questions Does the spatial association between isolated adult trees and understorey plants change along a gradient of sand dunes? Does this association depend on the life form of the understorey plant? Location Coastal sand dunes, southeast Brazil. Methods We recorded the occurrence of understorey plant species in 100 paired 0.25 m2 plots under adult trees and in adjacent treeless sites along an environmental gradient from beach to inland. Occurrence probabilities were modelled as a function of the fixed variables of the presence of a neighbour, distance from the seashore and life form, and a random variable, the block (i.e. the pair of plots). Generalized linear mixed models (GLMM) were fitted in a backward step-wise procedure using Akaike's information criterion (AIC) for model selection. Results The occurrence of understorey plants was affected by the presence of an adult tree neighbour, but the effect varied with the life form of the understorey species. Positive spatial association was found between isolated adult neighbour and young trees, whereas a negative association was found for shrubs. Moreover, a neutral association was found for lianas, whereas for herbs the effect of the presence of an adult neighbour ranged from neutral to negative, depended on the subgroup considered. The strength of the negative association with forbs increased with distance from the seashore. However, for the other life forms, the associational pattern with adult trees did not change along the gradient. Conclusions For most of the understorey life forms there is no evidence that the spatial association between isolated adult trees and understorey plants changes with the distance from the seashore, as predicted by the stress gradient hypothesis, a common hypothesis in the literature about facilitation in plant communities. Furthermore, the positive spatial association between isolated adult trees and young trees identified along the entire gradient studied indicates a positive feedback that explains the transition from open vegetation to forest in subtropical coastal dune environments.

Use of passive diffusion sampling method for defining NO2 concentrations gradient in São Paulo, Brazil

Abstract Background Air pollution in São Paulo is constantly being measured by the State of Sao Paulo Environmental Agency, however there is no information on the variation between places with different traffic densities. This study was intended to identify a gradient of exposure to traffic-related air pollution within different areas in São Paulo to provide information for future epidemiological studies. Methods We measured NO2 using Palmes' diffusion tubes in 36 sites on streets chosen to be representative of different road types and traffic densities in São Paulo in two one-week periods (July and August 2000). In each study period, two tubes were installed in each site, and two additional tubes were installed in 10 control sites. Results Average NO2 concentrations were related to traffic density, observed on the spot, to number of vehicles counted, and to traffic density strata defined by the city Traffic Engineering Company (CET). Average NO2concentrations were 63μg/m3 and 49μg/m3 in the first and second periods, respectively. Dividing the sites by the observed traffic density, we found: heavy traffic (n = 17): 64μg/m3 (95% CI: 59μg/m3 – 68μg/m3); local traffic (n = 16): 48μg/m3 (95% CI: 44μg/m3 – 52μg/m3) (p < 0.001). Conclusion The differences in NO2 levels between heavy and local traffic sites are large enough to suggest the use of a more refined classification of exposure in epidemiological studies in the city. Number of vehicles counted, traffic density observed on the spot and traffic density strata defined by the CET might be used as a proxy for traffic exposure in São Paulo when more accurate measurements are not available.

Iterative regularization methods for ill-posed problems

This Ph.D thesis focuses on iterative regularization methods for regularizing linear and nonlinear ill-posed problems. Regarding linear problems, three new stopping rules for the Conjugate Gradient method applied to the normal equations are proposed and tested in many numerical simulations, including some tomographic images reconstruction problems. Regarding nonlinear problems, convergence and convergence rate results are provided for a Newton-type method with a modified version of Landweber iteration as an inner iteration in a Banach space setting.

High gradient magnetic separation (HGMS) of erythrocytes infected with plasmodium falciparum

This thesis was undertaken to explore possible applications of high gradient magnetic separation (HGMS) for the separation of RBCs infected with Plasmodium falciparum, with the dual aim of establishing a novel and superior method for isolating late-stage infected cells, and of obtaining synchronized cell cultures.rnThe presented work presents protocols for HGMS of parasitized RBCs that fulfil these aims. Late-stage parasitized cell can be isolated essentially devoid of contamination with non-infected and ring-stage infected cells. Such an easy method for a highly quantitative and qualitative purification has not yet been reported. Synchronous cultures can be obtained both following depletion of late-stage infected cells, and following isolation of the latter. The quality of synchronization cultures matches that of sorbitol lysis, the current standard method for malaria culture synchronization. An advantage of HGMS is the avoidance of osmotic stress for RBCs. The new methods further have the appeal of high reproducibility, cost-effectiveness, and simple protocol.rnIt should be possible to take the methods beyond Plasmodium infected RBCs. Most magnetic separation techniques in the sector of biomedical research employ columns with a hydrophilic polymer-coated matrix. Our procedure employs an optimized buffer system. Polymer coating becomes unnecessary and uncoated columns are available at a fraction of the cost.

Regularization methods for the solution of a nonlinear least-squares problem in tomography

In this work we study a polyenergetic and multimaterial model for the breast image reconstruction in Digital Tomosynthesis, taking into consideration the variety of the materials forming the object and the polyenergetic nature of the X-rays beam. The modelling of the problem leads to the resolution of a high-dimensional nonlinear least-squares problem that, due to its nature of inverse ill-posed problem, needs some kind of regularization. We test two main classes of methods: the Levenberg-Marquardt method (together with the Conjugate Gradient method for the computation of the descent direction) and two limited-memory BFGS-like methods (L-BFGS). We perform some experiments for different values of the regularization parameter (constant or varying at each iteration), tolerances and stop conditions. Finally, we analyse the performance of the several methods comparing relative errors, iterations number, times and the qualities of the reconstructed images.

Geophysical Analysis of Seasonal Montandon Gravel Ridge Water Table Fluctuation and Moisture Gradient Variation due to Storm Events

The purpose of this research project is to continue exploring the Montandon Long-Term Hydrologic Research Site(LTHR) by using multiple geophysical methods to obtain more accurate and precise information regarding subsurface hydrologic properties of a local gravel ridge,which are important to both the health of surrounding ecosystems and local agriculture. Through using non-invasive geophysical methods such as seismic refraction, Direct Current resistivity and ground penetrating radar (GPR) instead of invasive methods such as boreholedrilling which displace sediment and may alter water flow, data collection is less likely to bias the data itself. In addition to imaging the gravel ridge subsurface, another important researchpurpose is to observe how both water table elevation and the moisture gradient (moisture content of the unsaturated zone) change over a seasonal time period and directly after storm events. The combination of three types of data collection allows the strengths of each method combine together and provide a relatively strongly supported conclusions compared to previous research. Precipitation and geophysical data suggest that an overall increase in precipitation during the summer months causes a sharp decrease in subsurface resistivity within the unsaturated zone. GPR velocity data indicate significant immediate increase in moisture content within the shallow vadose zone (< 1m), suggesting that rain water was infiltrating into the shallow subsurface. Furthermore, the combination of resistivity and GPR results suggest that the decreased resistivity within the shallow layers is due to increased ion content within groundwater. This is unexpected as rainwater is assumed to have a DC resistivity value of 3.33*105 ohm-m. These results may suggest that ions within the sediment must beincorporated into the infiltrating water.