Speciation as an active force in promoting genetic evolution

There is a growing appreciation among evolutionary biologists that the rate and tempo of molecular evolution might often be altered at or near the time of speciation, i.e. that speciation is in some way a special time for genes. Molecular phylogenies frequently reveal increased rates of genetic evolution associated with speciation and other lines of investigation suggest that various types of abrupt genomic disruption can play an important role in promoting speciation via reproductive isolation. These phenomena are in conflict with the gradual view of molecular evolution that is implicit in much of our thinking about speciation and in the tools of modern biology. This raises the prospect of studying the molecular evolutionary consequences of speciation per se and studying the footprint of speciation as an active force in promoting genetic divergence. Here we discuss the reasons to believe that speciation can play such a role and elaborate on possible mechanisms for accelerated rates of evolution following speciation. We provide an example of how it is possible detect whether accelerated bursts of evolution occur in neutral and/or adaptive regions of genes and discuss the implications of rapid episodes of change for conventional models of molecular evolution. Speciation might often owe more to ephemeral and essentially arbitrary events that cause reproductive isolation than to the gradual and regular tug of natural selection that draws a species into a new niche.

Surface based hypothesis verification in intensity images using geometric and appearance data

In this paper we discuss current work concerning Appearance-based and CAD-based vision; two opposing vision strategies. CAD-based vision is geometry based, reliant on having complete object centred models. Appearance-based vision builds view dependent models from training images. Existing CAD-based vision systems that work with intensity images have all used one and zero dimensional features, for example lines, arcs, points and corners. We describe a system we have developed for combining these two strategies. Geometric models are extracted from a commercial CAD library of industry standard parts. Surface appearance characteristics are then learnt automatically by observing actual object instances. This information is combined with geometric information and is used in hypothesis evaluation. This augmented description improves the systems robustness to texture, specularities and other artifacts which are hard to model with geometry alone, whilst maintaining the advantages of a geometric description.

Learning enhanced 3D models for vehicle tracking

This paper presents an enhanced hypothesis verification strategy for 3D object recognition. A new learning methodology is presented which integrates the traditional dichotomic object-centred and appearance-based representations in computer vision giving improved hypothesis verification under iconic matching. The "appearance" of a 3D object is learnt using an eigenspace representation obtained as it is tracked through a scene. The feature representation implicitly models the background and the objects observed enabling the segmentation of the objects from the background. The method is shown to enhance model-based tracking, particularly in the presence of clutter and occlusion, and to provide a basis for identification. The unified approach is discussed in the context of the traffic surveillance domain. The approach is demonstrated on real-world image sequences and compared to previous (edge-based) iconic evaluation techniques.

Visual surveillance using deformable models of vehicles

This paper presents recent developments to a vision-based traffic surveillance system which relies extensively on the use of geometrical and scene context. Firstly, a highly parametrised 3-D model is reported, able to adopt the shape of a wide variety of different classes of vehicle (e.g. cars, vans, buses etc.), and its subsequent specialisation to a generic car class which accounts for commonly encountered types of car (including saloon, batchback and estate cars). Sample data collected from video images, by means of an interactive tool, have been subjected to principal component analysis (PCA) to define a deformable model having 6 degrees of freedom. Secondly, a new pose refinement technique using “active” models is described, able to recover both the pose of a rigid object, and the structure of a deformable model; an assessment of its performance is examined in comparison with previously reported “passive” model-based techniques in the context of traffic surveillance. The new method is more stable, and requires fewer iterations, especially when the number of free parameters increases, but shows somewhat poorer convergence. Typical applications for this work include robot surveillance and navigation tasks.

The impact of uncertainty in satellite data on the assessment of flood inundation models

The performance of flood inundation models is often assessed using satellite observed data; however these data have inherent uncertainty. In this study we assess the impact of this uncertainty when calibrating a flood inundation model (LISFLOOD-FP) for a flood event in December 2006 on the River Dee, North Wales, UK. The flood extent is delineated from an ERS-2 SAR image of the event using an active contour model (snake), and water levels at the flood margin calculated through intersection of the shoreline vector with LiDAR topographic data. Gauged water levels are used to create a reference water surface slope for comparison with the satellite-derived water levels. Residuals between the satellite observed data points and those from the reference line are spatially clustered into groups of similar values. We show that model calibration achieved using pattern matching of observed and predicted flood extent is negatively influenced by this spatial dependency in the data. By contrast, model calibration using water elevations produces realistic calibrated optimum friction parameters even when spatial dependency is present. To test the impact of removing spatial dependency a new method of evaluating flood inundation model performance is developed by using multiple random subsamples of the water surface elevation data points. By testing for spatial dependency using Moran’s I, multiple subsamples of water elevations that have no significant spatial dependency are selected. The model is then calibrated against these data and the results averaged. This gives a near identical result to calibration using spatially dependent data, but has the advantage of being a statistically robust assessment of model performance in which we can have more confidence. Moreover, by using the variations found in the subsamples of the observed data it is possible to assess the effects of observational uncertainty on the assessment of flooding risk.

A high-resolution near-infrared extraterrestrial solar spectrum derived from ground-based Fourier transform spectrometer measurements

A detailed spectrally-resolved extraterrestrial solar spectrum (ESS) is important for line-by-line radiative transfer modeling in the near-infrared (near-IR). Very few observationally-based high-resolution ESS are available in this spectral region. Consequently the theoretically-calculated ESS by Kurucz has been widely adopted. We present the CAVIAR (Continuum Absorption at Visible and Infrared Wavelengths and its Atmospheric Relevance) ESS which is derived using the Langley technique applied to calibrated observations using a ground-based high-resolution Fourier transform spectrometer (FTS) in atmospheric windows from 2000–10000 cm-1 (1–5 μm). There is good agreement between the strengths and positions of solar lines between the CAVIAR and the satellite-based ACE-FTS (Atmospheric Chemistry Experiment-FTS) ESS, in the spectral region where they overlap, and good agreement with other ground-based FTS measurements in two near-IR windows. However there are significant differences in the structure between the CAVIAR ESS and spectra from semi-empirical models. In addition, we found a difference of up to 8 % in the absolute (and hence the wavelength-integrated) irradiance between the CAVIAR ESS and that of Thuillier et al., which was based on measurements from the Atmospheric Laboratory for Applications and Science satellite and other sources. In many spectral regions, this difference is significant, as the coverage factor k = 2 (or 95 % confidence limit) uncertainties in the two sets of observations do not overlap. Since the total solar irradiance is relatively well constrained, if the CAVIAR ESS is correct, then this would indicate an integrated “loss” of solar irradiance of about 30 W m-2 in the near-IR that would have to be compensated by an increase at other wavelengths.

Transition from suppressed to active convection modulated by a weak-temperature gradient derived large-scale circulation

Numerical simulations are performed to assess the influence of the large-scale circulation on the transition from suppressed to active convection. As a model tool, we used a coupled-column model. It consists of two cloud-resolving models which are fully coupled via a large-scale circulation which is derived from the requirement that the instantaneous domain-mean potential temperature profiles of the two columns remain close to each other. This is known as the weak-temperature gradient approach. The simulations of the transition are initialized from coupled-column simulations over non-uniform surface forcing and the transition is forced within the dry column by changing the local and/or remote surface forcings to uniform surface forcing across the columns. As the strength of the circulation is reduced to zero, moisture is recharged into the dry column and a transition to active convection occurs once the column is sufficiently moistened to sustain deep convection. Direct effects of changing surface forcing occur over the first few days only. Afterward, it is the evolution of the large-scale circulation which systematically modulates the transition. Its contributions are approximately equally divided between the heating and moistening effects. A transition time is defined to summarize the evolution from suppressed to active convection. It is the time when the rain rate within the dry column is halfway to the mean value obtained at equilibrium over uniform surface forcing. The transition time is around twice as long for a transition that is forced remotely compared to a transition that is forced locally. Simulations in which both local and remote surface forcings are changed produce intermediate transition times.

Can retired galaxies mimic active galaxies? Clues from the Sloan Digital Sky Survey

The classification of galaxies as star forming or active is generally done in the ([O III]/H beta, [N II]/H alpha) plane. The Sloan Digital Sky Survey (SDSS) has revealed that, in this plane, the distribution of galaxies looks like the two wings of a seagull. Galaxies in the right wing are referred to as Seyfert/LINERs, leading to the idea that non-stellar activity in galaxies is a very common phenomenon. Here, we argue that a large fraction of the systems in the right wing could actually be galaxies which stopped forming stars. The ionization in these `retired` galaxies would be produced by hot post-asymptotic giant branch stars and white dwarfs. Our argumentation is based on a stellar population analysis of the galaxies via our STARLIGHT code and on photoionization models using the Lyman continuum radiation predicted for this population. The proportion of LINER galaxies that can be explained in such a way is, however, uncertain. We further show how observational selection effects account for the shape of the right wing. Our study suggests that nuclear activity may not be as common as thought. If retired galaxies do explain a large part of the seagull`s right wing, some of the work concerning nuclear activity in galaxies, as inferred from SDSS data, will have to be revised.

In Vitro Activity of the Antifungal Plant Defensin RsAFP2 against Candida Isolates and Its In Vivo Efficacy in Prophylactic Murine Models of Candidiasis

We show that RsAFP2, a plant defensin that interacts with fungal glucosylceramides, is active against Candida albicans, inhibits to a lesser extent other Candida species, and is nontoxic to mammalian cells. Moreover, glucosylceramide levels in Candida species correlate with RsAFP2 sensitivity. We found RsAFP2 prophylactically effective against murine candidiasis.

Soluble one-dimensional particle conservation models with infinitely many absorbing states

Particle conservation lattice-gas models with infinitely many absorbing states are studied on a one-dimensional lattice. As one increases the particle density, they exhibit a phase transition from an absorbing to an active phase. The models are solved exactly by the use of the transfer matrix technique from which the critical behavior was obtained. We have found that the exponent related to the order parameter, the density of active sites, is 1 for all studied models except one of them with exponent 2.

Comparative study of liponucleosides in Langmuir monolayers as cell membrane models

Liponucleosides may assist the anchoring of nucleic acid nitrogen bases into biological membranes for tailored nanobiotechnological applications. To this end precise knowledge about the biophysical and chemical details at the membrane surface is required. In this paper, we used Langmuir monolayers as simplified cell membrane models and studied the insertion of five lipidated nucleosides. These molecules varied in the type of the covalently attached lipid group, the nucleobase, and the number of hydrophobic moieties attached to the nucleoside. All five lipidated nucleosides were found to be surface-active and capable of forming stable monolayers. They could also be incorporated into dipalmitoylphosphatidylcholine (DPPC) monolayers, four of which induced expansion in the surface pressure isotherm and a decrease in the surface compression modulus of DPPC. In contrast, one nucleoside possessing three alkyl chain modifications formed very condensed monolayers and induced film condensation and an increase in the compression modulus for the DPPC monolayer, thus reflecting the importance of the ability of the nucleoside molecules to be arranged in a closely packed manner. The implications of these results lie on the possibility of tuning nucleic acid pairing by modifying structural characteristics of the liponucleosides. (C) 2010 Elsevier B.V. All rights reserved.

Generalized partition function zeros of 1D spin models and their critical behavior at edge singularities

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

HOW TO EFFICIEN TLY INCORPORATE FACTS DEVICES IN OPTIMAL ACTIVE POWER FLOW MODEL

This paper presents for the first time how to easily incorporate facts devices in an optimal active power flow model such that an efficient interior-point method may be applied. The optimal active power flow model is based on a network flow approach instead of the traditional nodal formulation that allows the use of an efficiently predictor-corrector interior point method speed up by sparsity exploitation. The mathematical equivalence between the network flow and the nodal models is addressed, as well as the computational advantages of the former considering the solution by interior point methods. The adequacy of the network flow model for representing facts devices is presented and illustrated on a small 5-bus system. The model was implemented using Matlab and its performance was evaluated with the 3,397-bus and 4,075-branch Brazilian power system which show the robustness and efficiency of the formulation proposed. The numerical results also indicate an efficient tool for optimal active power flow that is suitable for incorporating facts devices.

Estudo cinético da degradação térmica e catalítica de petróleo pesado usando Al-MCM-41

The mesoporous nanostructured materials have been studied for application in the oil industry, in particular Al-MCM-41, due to the surface area around 800 to 1.000 m2 g-1 and, pore diameters ranging from 2 to 10 nm, suitable for catalysis to large molecules such as heavy oil. The MCM-41 has been synthesized by hydrothermal method, on which aluminum was added, in the ratio Si/Al equal to 50, to increase the generation of active acid sites in the nanotubes. The catalyst was characterized by X-ray diffraction (XRD), surface area by the BET method and, the average pore volume BJH method using the N2 adsorption, absorption spectroscopy in the infrared Fourier Transform (FT-IR) and determination of surface acidity with application of a probe molecule - n-butylamine. The catalyst showed well-defined structural properties and consistent with the literature. The overall objective was to test the Al-MCM-41 as catalyst and thermogravimetric perform tests, using two samples of heavy oil with API º equal to 14.0 and 18.5. Assays were performed using a temperature range of 30-900 ° C and heating ratios (β) ranging from 5, 10 and 20 °C min-1.The aim was to verify the thermogravimetric profiles of these oils when subjected to the action of the catalyst Al- MCM-41. Therefore, the percentage ranged catalyst applied 1, 3, 5, 10 and 20 wt%, and from the TG data were applied two different kinetic models: Ozawa-Flynn-Wall (OFW) and Kissinger-Akahrira-Sunose (KAS).The apparent activation energies found for both models had similar values and were lower for the second event of mass loss known as cracking zone, indicating a more effective performance of Al-MCM-41 in that area. Furthermore, there was a more pronounced reduction in the value of activation energy for between 10 and 20% by weight of the oil-catalyst mixture. It was concluded that the Al-MCM-41 catalyst has applicability in heavy oils to reduce the apparent activation energy of a catalyst-oil system, and the best result with 20% by weight of Al-MCM-41

pH-cycling models for in vitro evaluation of the efficacy of fluoridated dentifrices for caries control: strengths and limitations

Despite a plethora of in situ studies and clinical trials evaluating the efficacy of fluoridated dentifrices on caries control, in vitro pH cycling models are still broadly used because they mimic the dynamics of mineral loss and gain involved in caries formation. This paper critically reviews the current literature on existing pH-cycling models for the in vitro evaluation of the efficacy of fluoridated dentifrices for caries control, focusing on their strengths and limitations. A search was undertaken in the MEDLINE electronic journal database using the keywords "pH-cycling", "demineralization", "remineralization", "in vitro", "fluoride", "dentifrice". The primary outcome was the decrease of demineralization or the increase of remineralization as measured by different methods (e. g.: transverse microradiography) or tooth fluoride uptake. Inclusion of studies, data extraction and quality assessment were undertaken independently and in duplicate by two members of the review team. Disagreements were solved by discussion and consensus or by a third party. One hundred and sixteen studies were included, of which 42 addressed specifically the comparison of dentifrices using different pH-cycling models. The other studies included meta-analysis or reviews, data about the effect of different fluoride sources on de-remineralization, different methods for analysis de-remineralization and chemical variables and characteristics of dental hard tissues that might have influence on de-remineralization processes. Generally, the studies presented ability to detect known results established by clinical trials, to demonstrate dose-related responses in the fluoride content of the dentifrices, and to provide repeatability and reproducibility between tests. In order to accomplish these features satisfactorily, it is mandatory to take into account the type of substrate and baseline artificial lesion, as well as the adequate response variables and statistical approaches to be used. This critical review of literature showed that the currently available pH-cycling models are appropriate to detect dose-response and pH-response of fluoride dentifrices, and to evaluate the impact of new active principles on the effect of fluoridated dentifrices, as well as their association with other anti-caries treatments.