Reconnection current sheet structure in a turbulent medium

In the presence of turbulence, magnetic field lines lose their dynamical identity and particles entrained on field lines diffuse through space at a rate determined by the amplitude of the turbulence. In previous work (Lazarian and Vishniac, 1999; Kowal et al., 2009; Eyink et al., 2011) we showed that this leads to reconnection speeds which are independent of resistivity. In particular, in Kowal et al. (2009) we showed that numerical simulations were consistent with the predictions of this model. Here we examine the structure of the current sheet in simulations of turbulent reconnection. Laminar flows consistent with the Sweet-Parker reconnection model produce very thin and well ordered currents sheets. On the other hand, the simulations of Kowal et al. (2009) show a strongly disordered state even for relatively low levels of turbulence. Comparing data cubes with and without reconnection, we find that large scale field reversals are the cumulative effect of many individual eddies, each of which has magnetic properties which are not very different from turbulent eddies in a homogeneous background. This implies that the properties of stationary and homogeneous MHD turbulence are a reasonable guide to understanding turbulence during large scale magnetic reconnection events. In addition, dissipation and high energy particle acceleration during reconnection events take place over a macroscopic volume, rather than being confined to a narrow zone whose properties depend on microscopic transport coefficients.

The Ecological Basis for Biogeographic Classification: an Example in Orchid Bees (Apidae: Euglossini)

Biogeography has been difficult to apply as a methodological approach because organismic biology is incomplete at levels where the process of formulating comparisons and analogies is complex. The study of insect biogeography became necessary because insects possess numerous evolutionary traits and play an important role as pollinators. Among insects, the euglossine bees, or orchid bees, attract interest because the study of their biology allows us to explain important steps in the evolution of social behavior and many other adaptive tradeoffs. We analyzed the distribution of morphological characteristics in Colombian orchid bees from an ecological perspective. The aim of this study was to observe the distribution of these attributes on a regional basis. Data corresponding to Colombian euglossine species were ordered with a correspondence analysis and with subsequent hierarchical clustering. Later, and based on community proprieties, we compared the resulting hierarchical model with the collection localities to seek to identify a biogeographic classification pattern. From this analysis, we derived a model that classifies the territory of Colombia into 11 biogeographic units or natural clusters. Ecological assumptions in concordance with the derived classification levels suggest that species characteristics associated with flight performance, nectar uptake, and social behavior are the factors that served to produce the current geographical structure.

A two-layer approximation to the Brazil Current-Intermediate Western Boundary Current System between 20 degrees S and 28 degrees S

It has been shown that the vertical structure of the Brazil Current (BC)-Intermediate Western Boundary Current (IWBC) System is dominated by the first baroclinic mode at 22 degrees S-23 degrees S. In this work, we employed the Miami Isopycnic Coordinate Ocean Model to investigate whether the rich mesoscale activity of this current system, between 20 degrees S and 28 degrees S, is reproduced by a two-layer approximation of its vertical structure. The model results showed cyclonic and anticyclonic meanders propagating southwestward along the current axis, resembling the dynamical pattern of Rossby waves superposed on a mean flow. Analysis of the upper layer zonal velocity component, using a space-time diagram, revealed a dominant wavelength of about 450 km and phase velocity of about 0.20 ms(-1) southwestward. The results also showed that the eddy-like structures slowly grew in amplitude as they moved downstream. Despite the simplified design of the numerical experiments conducted here, these results compared favorably with observations and seem to indicate that weakly unstable long baroclinic waves are responsible for most of the variability observed in the BC-IWBC system. (C) 2009 Elsevier Ltd. All rights reserved.

Is the meander growth in the Brazil Current system off Southeast Brazil due to baroclinic instability?

Temporally-growing frontal meandering and occasional eddy-shedding is observed in the Brazil Current (BC) as it flows adjacent to the Brazilian Coast. No study of the dynamics of this phenomenon has been conducted to date in the region between 22 degrees S and 25 degrees S. Within this latitude range, the flow over the intermediate continental slope is marked by a current inversion at a depth that is associated with the Intermediate Western Boundary Current (IWBC). A time series analysis of 10-current-meter mooring data was used to describe a mean vertical profile for the BC-IWBC jet and a typical meander vertical structure. The latter was obtained by an empirical orthogonal function (EOF) analysis that showed a single mode explaining 82% of the total variance. This mode structure decayed sharply with depth, revealing that the meandering is much more vigorous within the BC domain than it is in the IWBC region. As the spectral analysis of the mode amplitude time series revealed no significant periods, we searched for dominant wavelengths. This search was done via a spatial EOF analysis on 51 thermal front patterns derived from digitized AVHRR images. Four modes were statistically significant at the 95% confidence level. Modes 3 and 4, which together explained 18% of the total variance, are associated with 266 and 338-km vorticity waves, respectively. With this new information derived from the data, the [Johns, W.E., 1988. One-dimensional baroclinically unstable waves on the Gulf Stream potential vorticity gradient near Cape Hatteras. Dyn. Atmos. Oceans 11, 323-350] one-dimensional quasi-geostrophic model was applied to the interpolated mean BC-IWBC jet. The results indicated that the BC system is indeed baroclinically unstable and that the wavelengths depicted in the thermal front analysis are associated with the most unstable waves produced by the model. Growth rates were about 0.06 (0.05) days(-1) for the 266-km (338-km) wave. Moreover, phase speeds for these waves were low compared to the surface BC velocity and may account for remarks in the literature about growing standing or stationary meanders off southeast Brazil. The theoretical vertical structure modes associated with these waves resembled very closely to the one obtained for the current-meter mooring EOF analysis. We interpret this agreement as a confirmation that baroclinic instability is an important mechanism in meander growth in the BC system. (C) 2008 Elsevier B.V. All rights reserved.

Insights into the morphology of the Serra da Cangalha impact structure from geophysical modeling

Forward modeling is commonly applied to gravity field data of impact structures to determine the main gravity anomaly sources. In this context, we have developed 2.5-D gravity models of the Serra da Cangalha impact structure for the purpose of investigating geological bodies/structures underneath the crater. Interpretation of the models was supported by ground magnetic data acquired along profiles, as well as by high resolution aeromagnetic data. Ground magnetic data reveal the presence of short-wavelength anomalies probably related to shallow magnetic sources that could have been emplaced during the cratering process. Aeromagnetic data show that the basement underneath the crater occurs at an average depth of about 1.9 km, whereas in the region beneath the central uplift it is raised to 0.51 km below the current surface. These depths are also supported by 2.5-D gravity models showing a gentle relief for the basement beneath the central uplift area. Geophysical data were used to provide further constraints for numeral modeling of crater formation that provided important information on the structural modification that affected the rocks underneath the crater, as well as on shock-induced modifications of target rocks. The results showed that the morphology is consistent with the current observations of the crater and that Serra da Cangalha was formed by a meteorite of approximately 1.4 km diameter striking at 12 km s-1.

Echinococcus granulosus Antigen B Structure: Subunit Composition and Oligomeric States

Background: Antigen B (AgB) is the major protein secreted by the Echinococcus granulosus metacestode and is involved in key host-parasite interactions during infection. The full comprehension of AgB functions depends on the elucidation of several structural aspects that remain unknown, such as its subunit composition and oligomeric states. Methodology/Principal Findings: The subunit composition of E. granulosus AgB oligomers from individual bovine and human cysts was assessed by mass spectrometry associated with electrophoretic analysis. AgB8/1, AgB8/2, AgB8/3 and AgB8/4 subunits were identified in all samples analyzed, and an AgB8/2 variant (AgB8/2v8) was found in one bovine sample. The exponentially modified protein abundance index (emPAI) was used to estimate the relative abundance of the AgB subunits, revealing that AgB8/1 subunit was relatively overrepresented in all samples. The abundance of AgB8/3 subunit varied between bovine and human cysts. The oligomeric states formed by E. granulosus AgB and recombinant subunits available, rAgB8/1, rAgB8/2 and rAgB8/3, were characterized by native PAGE, light scattering and microscopy. Recombinant subunits showed markedly distinct oligomerization behaviors, forming oligomers with a maximum size relation of rAgB8/3 >rAgB8/2>rAgB8/1. Moreover, the oligomeric states formed by rAgB8/3 subunit were more similar to those observed for AgB purified from hydatid fluid. Pressure-induced dissociation experiments demonstrated that the molecular assemblies formed by the more aggregative subunits, rAgB8/2 and rAgB8/3, also display higher structural stability. Conclusions/Significance: For the first time, AgB subunit composition was analyzed in samples from single hydatid cysts, revealing qualitative and quantitative differences between samples. We showed that AgB oligomers are formed by different subunits, which have distinct abundances and oligomerization properties. Overall, our findings have significantly contributed to increase the current knowledge on AgB expression and structure, highlighting issues that may help to understand the parasite adaptive response during chronic infection.

Light emission and current rectification in a molecular device: Experiment and theory

We have investigated optical and transport properties of the molecular structure 2,3,4,5-tetraphenyl-1-phenylethynyl-cyclopenta-2,4-dienol experimentally and theoretically. The optical spectrum was calculated using Hartree-Fock-intermediate neglect of differential overlap-configuration interaction model. The experimental photoluminescence spectrum showed a peak around 470nm which was very well described by the modeling. Electronic transport measurements showed a diode-like effect with a strong current rectification. A phenomenological microscopic model based on non-equilibrium Green's function technique was proposed and a very good description electronic transport was obtained. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4767457]

A novel XML document structure comparison framework based-on sub-tree commonalities and label semantics

XML similarity evaluation has become a central issue in the database and information communities, its applications ranging over document clustering, version control, data integration and ranked retrieval. Various algorithms for comparing hierarchically structured data, XML documents in particular, have been proposed in the literature. Most of them make use of techniques for finding the edit distance between tree structures, XML documents being commonly modeled as Ordered Labeled Trees. Yet, a thorough investigation of current approaches led us to identify several similarity aspects, i.e., sub-tree related structural and semantic similarities, which are not sufficiently addressed while comparing XML documents. In this paper, we provide an integrated and fine-grained comparison framework to deal with both structural and semantic similarities in XML documents (detecting the occurrences and repetitions of structurally and semantically similar sub-trees), and to allow the end-user to adjust the comparison process according to her requirements. Our framework consists of four main modules for (i) discovering the structural commonalities between sub-trees, (ii) identifying sub-tree semantic resemblances, (iii) computing tree-based edit operations costs, and (iv) computing tree edit distance. Experimental results demonstrate higher comparison accuracy with respect to alternative methods, while timing experiments reflect the impact of semantic similarity on overall system performance.

Phospholipase D2:A Pivotal Player Modulating RBL-2H3 Mast Cell Structure

The current study examined the role of PLD2 in the maintenance of mast cell structure. Phospholipase D (PLD) catalyzes hydrolysis of phosphatidylcholine to produce choline and phosphatidic acid (PA). PLD has two isoforms, PLD1 and PLD2, which vary in expression and localization depending on the cell type. The mast cell line RBL-2H3 was transfected to overexpress catalytically active (PLD2CA) and inactive (PLD2CI) forms of PLD2. The results of this study show that PLD2CI cells have a distinct star-shaped morphology, whereas PLD2CA and RBL-2H3 cells are spindle shaped. In PLD2CI cells, the Golgi complex was also disorganized with dilated cisternae, and more Golgi-associated vesicles were present as compared with the PLD2CA and RBL-2H3 cells. Treatment with exogenous PA led to the restoration of the wild-type Golgi complex phenotype in PLD2CI cells. Conversely, treatment of RBL-2H3 and PLD2CA cells with 1% 1-Butanol led to a disruption of the Golgi complex. The distribution of acidic compartments, including secretory granules and lysosomes, was also modified in PLD2CI cells, where they concentrated in the perinuclear region. These results suggest that the PA produced by PLD2 plays an important role in regulating cell morphology in mast cells. (J Histochem Cytochem 60:386-396, 2012)

Structure- and Ligand-Based Structure-Activity Relationships for a Series of Inhibitors of Aldolase

Aldolase has emerged as a promising molecular target for the treatment of human African trypanosomiasis. Over the last years, due to the increasing number of patients infected with Trypanosoma brucei, there is an urgent need for new drugs to treat this neglected disease. In the present study, two-dimensional fragment-based quantitative-structure activity relationship (QSAR) models were generated for a series of inhibitors of aldolase. Through the application of leave-one-out and leave-many-out cross-validation procedures, significant correlation coefficients were obtained (r(2) = 0.98 and q(2) = 0.77) as an indication of the statistical internal and external consistency of the models. The best model was employed to predict pK(i) values for a series of test set compounds, and the predicted values were in good agreement with the experimental results, showing the power of the model for untested compounds. Moreover, structure-based molecular modeling studies were performed to investigate the binding mode of the inhibitors in the active site of the parasitic target enzyme. The structural and QSAR results provided useful molecular information for the design of new aldolase inhibitors within this structural class.

The Role of Dyslipidemia on Ocular Surface, Lacrimal and Meibomian Gland Structure and Function

Purpose: Dyslipidemia is characterized by high lipid blood levels that are risk factors for cardiovascular diseases, which are leading causes of death. However, it is unclear whether dyslipidemia is a cause of the dry eye syndrome (DES). Therefore we determined in transgenic mice models of dyslipidemia, whether there is an association with DES development. Methods: Dyslipidemic models included male and female adult mice overexpressing apolipoprotein CIII (Apo CIII), LDL receptor knockout (LDLR-KO) and ApoE knockout (ApoE-KO). They were compared with age-and gender-matched C57BL/6 mice. Ocular health was evaluated based on corneal slit lamp assessment, phenol red thread test (PRT) and impression cytology. Blood lipid profiles and histology of meibomian and lacrimal glands were also evaluated. Effects of high-fat diet and aging were observed in LDLR-KO and ApoCIII strains, respectively. Results: Body weight and lacrimal gland weight were significantly higher in male mice compared to females of the same strain (P < 0.05). Body weight was significantly lower in LDLRKO mice receiving high lipid diet compared to their controls (P = 0.0043). ApoE-KO were hypercholesterolemic and ApoCIII hypertriglyceridemic while LDLR-KO showed increases in both parameters. The PRT test was lower in male LDLR-KO mice with high-fat diet than control mice with standard diet (P = 0.0273). Aging did not affect lacrimal structural or functional parameters of ApoCIII strain. Conclusions: DES development is not solely dependent on dyslipidemia in relevant mice models promoting this condition. On the other hand, lacrimal gland structure and function are differentially impacted by lipid profile changes in male and female mice. This dissociation suggests that other factors beside dyslipidemia impact on tear film dysfunction and DES development.