Quantitative determination of optical transmission through subwavelength slit arrays in Ag films: Role of surface wave interference and local coupling between adjacent slits

Measurement of the transmitted intensity from a coherent monomode light source through a series of subwavelength slit arrays in Ag films, with varying array pitch and number of slits, demonstrates enhancement (suppression) by factors of as much as 6 (9) when normalized to the transmission efficiency of an isolated slit. Pronounced minima in the transmitted intensity are observed at array pitches corresponding to lambda(SPP), 2 lambda(SPP), and 3 lambda(SPP), where lambda(SPP) is the wavelength of the surface plasmon polariton (SPP). The position of these minima arises from destructive interference between incident propagating waves and pi-phase-shifted SPP waves. Increasing the number of slits to four or more does not increase appreciably the per-slit transmission intensity. A simple interference model fits well the measured transmitted intensity profile.

Transition-metal 13-atom clusters assessed with solid and surface-biased functionals

First-principles density-functional theory studies have reported open structures based on the formation of double simple-cubic (DSC) arrangements for Ru(13), Rh(13), Os(13), and Ir(13), which can be considered an unexpected result as those elements crystallize in compact bulk structures such as the face-centered cubic and hexagonal close-packed lattices. In this work, we investigated with the projected augmented wave method the dependence of the lowest-energy structure on the local and semilocal exchange-correlation (xc) energy functionals employed in density-functional theory. We found that the local-density approximation (LDA) and generalized-gradient formulations with different treatment of the electronic inhomogeneities (PBE, PBEsol, and AM05) confirm the DSC configuration as the lowest-energy structure for the studied TM(13) clusters. A good agreement in the relative total energies are obtained even for structures with small energy differences, e. g., 0.10 eV. The employed xc functionals yield the same total magnetic moment for a given structure, i.e., the differences in the bond lengths do not affect the moments, which can be attributed to the atomic character of those clusters. Thus, at least for those systems, the differences among the LDA, PBE, PBEsol, and AM05 functionals are not large enough to yield qualitatively different results. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3577999]

Regional scale analysis of landform configuration with base-level (isobase) maps

Base-level maps (or ""isobase maps"", as originally defined by Filosofov, 1960), express a relationship between valley order and topography. The base-level map can be seen as a ""simplified"" version of the original topographic surface, from which the ""noise"" of the low-order stream erosion was removed. This method is able to identify areas with possible tectonic influence even within lithologically uniform domains. Base-level maps have been recently applied in semi-detail scale (e.g., 1:50 000 or larger) morphotectonic analysis. In this paper, we present an evaluation of the method's applicability in regional-scale analysis (e.g., 1:250 000 or smaller). A test area was selected in northern Brazil, at the lower course of the Araguaia and Tocantins rivers. The drainage network extracted from SRTM30_PLUS DEMs with spatial resolution of approximately 900 m was visually compared with available topographic maps and considered to be compatible with a 1:1,000 000 scale. Regarding the interpretation of regional-scale morphostructures, the map constructed with 2nd and 3rd-order valleys was considered to present the best results. Some of the interpreted base-level anomalies correspond to important shear zones and geological contacts present in the 1:5 000 000 Geological Map of South America. Others have no correspondence with mapped Precambrian structures and are considered to represent younger, probably neotectonic, features. A strong E-W orientation of the base-level lines over the inflexion of the Araguaia and Tocantins rivers, suggest a major drainage capture. A N-S topographic swath profile over the Tocantins and Araguaia rivers reveals a topographic pattern which, allied with seismic data showing a roughly N-S direction of extension in the area, lead us to interpret this lineament as an E-W, southward-dipping normal fault. There is also a good visual correspondence between the base-level lineaments and geophysical anomalies. A NW-SE lineament in the southeast of the study area partially corresponds to the northern border of the Mosquito lava field, of Jurassic age, and a NW-SE lineament traced in the northeastern sector of the study area can be interpreted as the Picos-Santa Ines lineament, identifiable in geophysical maps but with little expression in hypsometric or topographic maps.

Gene Expression Complex Networks: Synthesis, Identification, and Analysis

Thanks to recent advances in molecular biology, allied to an ever increasing amount of experimental data, the functional state of thousands of genes can now be extracted simultaneously by using methods such as cDNA microarrays and RNA-Seq. Particularly important related investigations are the modeling and identification of gene regulatory networks from expression data sets. Such a knowledge is fundamental for many applications, such as disease treatment, therapeutic intervention strategies and drugs design, as well as for planning high-throughput new experiments. Methods have been developed for gene networks modeling and identification from expression profiles. However, an important open problem regards how to validate such approaches and its results. This work presents an objective approach for validation of gene network modeling and identification which comprises the following three main aspects: (1) Artificial Gene Networks (AGNs) model generation through theoretical models of complex networks, which is used to simulate temporal expression data; (2) a computational method for gene network identification from the simulated data, which is founded on a feature selection approach where a target gene is fixed and the expression profile is observed for all other genes in order to identify a relevant subset of predictors; and (3) validation of the identified AGN-based network through comparison with the original network. The proposed framework allows several types of AGNs to be generated and used in order to simulate temporal expression data. The results of the network identification method can then be compared to the original network in order to estimate its properties and accuracy. Some of the most important theoretical models of complex networks have been assessed: the uniformly-random Erdos-Renyi (ER), the small-world Watts-Strogatz (WS), the scale-free Barabasi-Albert (BA), and geographical networks (GG). The experimental results indicate that the inference method was sensitive to average degree k variation, decreasing its network recovery rate with the increase of k. The signal size was important for the inference method to get better accuracy in the network identification rate, presenting very good results with small expression profiles. However, the adopted inference method was not sensible to recognize distinct structures of interaction among genes, presenting a similar behavior when applied to different network topologies. In summary, the proposed framework, though simple, was adequate for the validation of the inferred networks by identifying some properties of the evaluated method, which can be extended to other inference methods.

Role of the gp85/Trans-Sialidases in Trypanosoma cruzi Tissue Tropism: Preferential Binding of a Conserved Peptide Motif to the Vasculature In Vivo

Background: Transmitted by blood-sucking insects, the unicellular parasite Trypanosoma cruzi is the causative agent of Chagas' disease, a malady manifested in a variety of symptoms from heart disease to digestive and urinary tract dysfunctions. The reasons for such organ preference have been a matter of great interest in the field, particularly because the parasite can invade nearly every cell line and it can be found in most tissues following an infection. Among the molecular factors that contribute to virulence is a large multigene family of proteins known as gp85/trans-sialidase, which participates in cell attachment and invasion. But whether these proteins also contribute to tissue homing had not yet been investigated. Here, a combination of endothelial cell immortalization and phage display techniques has been used to investigate the role of gp85/trans-sialidase in binding to the vasculature. Methods: Bacteriophage expressing an important peptide motif (denominated FLY) common to all gp85/trans-sialidase proteins was used as a surrogate to investigate the interaction of this motif with the endothelium compartment. For that purpose phage particles were incubated with endothelial cells obtained from different organs or injected into mice intravenously and the number of phage particles bound to cells or tissues was determined. Binding of phages to intermediate filament proteins has also been studied. Findings and Conclusions: Our data indicate that FLY interacts with the endothelium in an organ-dependent manner with significantly higher avidity for the heart vasculature. Phage display results also show that FLY interaction with intermediate filament proteins is not limited to cytokeratin 18 (CK18), which may explain the wide variety of cells infected by the parasite. This is the first time that members of the intermediate filaments in general, constituted by a large group of ubiquitously expressed proteins, have been implicated in T. cruzi cell invasion and tissue homing.

Identification of protein-coding and non-coding RNA expression profiles in CD34(+) and in stromal cells in refractory anemia with ringed sideroblasts

Background: Myelodysplastic syndromes (MDS) are a group of clonal hematological disorders characterized by ineffective hematopoiesis with morphological evidence of marrow cell dysplasia resulting in peripheral blood cytopenia. Microarray technology has permitted a refined high-throughput mapping of the transcriptional activity in the human genome. Non-coding RNAs (ncRNAs) transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression, and in the regulation of exon-skipping and intron retention. Characterization of ncRNAs in progenitor cells and stromal cells of MDS patients could be strategic for understanding gene expression regulation in this disease. Methods: In this study, gene expression profiles of CD34(+) cells of 4 patients with MDS of refractory anemia with ringed sideroblasts (RARS) subgroup and stromal cells of 3 patients with MDS-RARS were compared with healthy individuals using 44 k combined intron-exon oligoarrays, which included probes for exons of protein-coding genes, and for non-coding RNAs transcribed from intronic regions in either the sense or antisense strands. Real-time RT-PCR was performed to confirm the expression levels of selected transcripts. Results: In CD34(+) cells of MDS-RARS patients, 216 genes were significantly differentially expressed (q-value <= 0.01) in comparison to healthy individuals, of which 65 (30%) were non-coding transcripts. In stromal cells of MDS-RARS, 12 genes were significantly differentially expressed (q-value <= 0.05) in comparison to healthy individuals, of which 3 (25%) were non-coding transcripts. Conclusions: These results demonstrated, for the first time, the differential ncRNA expression profile between MDS-RARS and healthy individuals, in CD34(+) cells and stromal cells, suggesting that ncRNAs may play an important role during the development of myelodysplastic syndromes.

Cross-Talk Between Mitochondria and NADPH Oxidase: Effects of Mild Mitochondrial Dysfunction on Angiotensin II-Mediated Increase in Nox Isoform Expression and Activity in Vascular Smooth Muscle Cells

Mitochondria and NADPH oxidase activation are concomitantly involved in pathogenesis of many vascular diseases. However, possible cross-talk between those ROS-generating systems is unclear. We induced mild mitochondrial dysfunction due to mitochondrial DNA damage after 24 h incubation of rabbit aortic smooth muscle (VSMC) with 250 ng/mL ethidium bromide (EtBr). VSMC remained viable and had 29% less oxygen consumption, 16% greater baseline hydrogen peroxide, and unchanged glutathione levels. Serum-stimulated proliferation was unaltered at 24 h. Although PCR amplification of several mtDNA sequences was preserved, D-Loop mtDNA region showed distinct amplification of shorter products after EtBr. Such evidence for DNA damage was further enhanced after angiotensin-II (AngII) incubation. Remarkably, the normally observed increase in VSMC membrane fraction NADPH oxidase activity after AngII was completely abrogated after EtBr, together with failure to upregulate Nox1 mRNA expression. Conversely, basal Nox4 mRNA expression increased 1.6-fold, while being unresponsive to AngII. Similar loss in AngII redox response occurred after 24 h antimycin-A incubation. Enhanced Nox4 expression was unassociated with endoplasmic reticulum stress markers. Protein disulfide isomerase, an NADPH oxidase regulator, exhibited increased expression and inverted pattern of migration to membrane fraction after EtBr. These results unravel functionally relevant cross-talk between mitochondria and NADPH oxidase, which markedly affects redox responses to AngII. Antioxid Redox Signal 11, 1265-1278.

Schistosoma mansoni Tegument Protein Sm29 Is Able to Induce a Th1-Type of Immune Response and Protection against Parasite Infection

Background: Schistosomiasis continues to be a significant public health problem. This disease affects 200 million people worldwide and almost 800 million people are at risk of acquiring the infection. Although vaccine development against this disease has experienced more failures than successes, encouraging results have recently been obtained using membrane-spanning protein antigens from the tegument of Schistosoma mansoni. Our group recently identified Sm29, another antigen that is present at the adult worm tegument surface. In this study, we investigated murine cellular immune responses to recombinant (r) Sm29 and tested this protein as a vaccine candidate. Methods and Findings: We first show that Sm29 is located on the surface of adult worms and lung-stage schistosomula through confocal microscopy. Next, immunization of mice with rSm29 engendered 51%, 60% and 50% reduction in adult worm burdens, in intestinal eggs and in liver granuloma counts, respectively (p<0.05). Protective immunity in mice was associated with high titers of specific anti-Sm29 IgG1 and IgG2a and elevated production of IFN-gamma, TNF-alpha and IL-12, a typical Th1 response. Gene expression analysis of worms recovered from rSm29 vaccinated mice relative to worms from control mice revealed a significant (q<0.01) down-regulation of 495 genes and up-regulation of only 22 genes. Among down-regulated genes, many of them encode surface antigens and proteins associated with immune signals, suggesting that under immune attack schistosomes reduce the expression of critical surface proteins. Conclusion: This study demonstrates that Sm29 surface protein is a new vaccine candidate against schistosomiasis and suggests that Sm29 vaccination associated with other protective critical surface antigens is the next logical strategy for improving protection.

Surface effects in the magnetic properties of crystalline 3 nm ferrite nanoparticles chemically synthesized

We have systematically studied the magnetic properties of ferrite nanoparticles with 3, 7, and 11 nm of diameter with very narrow grain size distributions. Samples were prepared by the thermal decomposition of Fe (acac)(3) in the presence of surfactants giving nanoparticles covered by oleic acid. High resolution transmission electron microscopy (HRTEM) images and XRD diffraction patterns confirms that all samples are composed by crystalline nanoparticles with the spinel structure expected for the iron ferrite. ac and dc magnetization measurements, as well in-field Mossbauer spectroscopy, indicate that the magnetic properties of nanoparticles with 11 and 7 nm are close to those expected for a monodomain, presenting large M(S) (close to the magnetite bulk). Despite the crystalline structure observed in HRTEM images, the nanoparticles with 3 nm are composed by a magnetically ordered region (core) and a surface region that presents a different magnetic order and it contains about 66% of Fe atoms. The high saturation and irreversibility fields in the M(H) loops of the particles with 3 nm together with the misalignment at 120 kOe in the in-field Mossbauer spectrum of surface component indicate a high surface anisotropy for the surface atoms, which is not observed for the core. For T < 10 K, we observe an increase in the susceptibility and of the magnetization for former sample, indicating that surface moments tend to align with applied field increasing the magnetic core size. (C) 2010 American Institute of Physics. [doi:10.1063/1.3514585]

Full-dimensional analytical ab initio potential energy surface of the ground state of HOI

Extensive ab initio calculations using a complete active space second-order perturbation theory wavefunction, including scalar and spin-orbit relativistic effects with a quadruple-zeta quality basis set were used to construct an analytical potential energy surface (PES) of the ground state of the [H, O, I] system. A total of 5344 points were fit to a three-dimensional function of the internuclear distances, with a global root-mean-square error of 1.26 kcal mol(-1). The resulting PES describes accurately the main features of this system: the HOI and HIO isomers, the transition state between them, and all dissociation asymptotes. After a small adjustment, using a scaling factor on the internal coordinates of HOI, the frequencies calculated in this work agree with the experimental data available within 10 cm(-1). (C) 2011 American Institute of Physics. [doi: 10.1063/1.3615545]

High performance gold nanorods and silver nanocubes in surface-enhanced Raman spectroscopy of pesticides

The behavior of Au nanorods and Ag nanocubes as analytical sensors was evaluated for three different classes of herbicides. The use of such anisotropic nanoparticles in surface-enhanced Raman scattering (SERS) experiments allows the one to obtain the spectrum of crystal violet dye in the single molecule regime, as well as the pesticides dichlorophenoxyacetic acid (2,4-D), trichlorfon and ametryn. Such metallic substrates show high SERS performance at low analyte concentrations making them adequate for use as analytical sensors. Density functional theory (DFT) calculations of the geometries and vibrational wavenumbers of the adsorbates in the presence of silver or gold atoms were used to elucidate the nature of adsorbate-nanostructure bonding in each case and support the enhancement patterns observed in each SERS spectrum.

Chromic materials for responsive surface-enhanced resonance Raman scattering systems: a nanometric pH sensor

The use of chromic materials for responsive surface-enhanced resonance Raman scattering (SERRS) based nanosensors is reported. The potential of nano-chromic SERRS is demonstrated with the use of the halochrome methyl yellow to fabricate an ultrasensitive pH optical sensor. Some of the challenges of the incorporation of chromic materials with metal nanostructures are addressed through the use of computational calculations and a comparison to measured SERRS and surface-enhanced Raman scattering (SERS) spectra is presented. A strong correlation between the measured SERRS and the medium's proton concentration is demonstrated for the pH range 2-6. The high sensitivity achieved by the use of resonance Raman conditions is shown through responsive SERRS measurements from only femtolitres of volume and with the concentration of the reporting molecules approaching the single molecule regime.

Surface structure effects on the electrochemical oxidation of ethanol on platinum single crystal electrodes

Ethanol oxidation has been studied on Pt(111), Pt(100) and Pt(110) electrodes in order to investigate the effect of the surface structure and adsorbing anions using electrochemical and FTIR techniques. The results indicate that the surface structure and anion adsorption affect significantly the reactivity of the electrode. Thus, the main product of the oxidation of ethanol on the Pt(111) electrode is acetic acid, and acetaldehyde is formed as secondary product. Moreover, the amount of CO formed is very small, and probably associated with the defects present on the electrode surface. For that reason, the amount of CO(2) is also small. This electrode has the highest catalytic activity for the formation of acetic acid in perchloric acid. However, the formation of acetic acid is inhibited by the presence of specifically adsorbed anions, such as (bi) sulfate or acetate, which is the result of the formation of acetic acid. On the other hand, CO is readily formed at low potentials on the Pt(100) electrode, blocking completely the surface. Between 0.65 and 0.80 V, the CO layer is oxidized and the production of acetaldehyde and acetic acid is detected. The Pt(110) electrode displays the highest catalytic activity for the splitting of the C-C bond. Reactions giving rise to CO formation, from either ethanol or acetaldehyde, occur at high rate at any potential. On the other hand, the oxidation of acetaldehyde to acetic acid has probably the lower reaction rate of the three basal planes.

Reconstruction of core and surface nanoparticles: The example of Pt(55) and Au(55)

Cuboctahedron (CUB) and icosahedron (ICO) model structures are widely used in the study of transition-metal (TM) nanoparticles (NPs), however, it might not provide a reliable description for small TM NPs such as the Pt(55) and Au(55) systems in gas phase. In this work, we combined density-functional theory calculations with atomic configurations generated by the basin hopping Monte Carlo algorithm within the empirical Sutton-Chen embedded atom potential. We identified alternative lower energy configurations compared with the ICO and CUB model structures, e. g., our lowest energy structures are 5.22 eV (Pt(55)) and 2.01 eV (Au(55)) lower than ICO. The energy gain is obtained by the Pt and Au diffusion from the ICO core region to the NP surface, which is driven by surface compression (only 12 atoms) on the ICO core region. Therefore, in the lowest energy configurations, the core size reduces from 13 atoms (ICO, CUB) to about 9 atoms while the NP surface increases from 42 atoms (ICO, CUB) to about 46 atoms. The present mechanism can provide an improved atom-level understanding of small TM NPs reconstructions.

Nanogravimetric and voltammetric studies of a Pt-Rh alloy surface and its behavior for methanol oxidation

This paper describes the preparation of a Pt-Rh alloy surface electrodeposited on Pt electrodes and its electrocatalytic characterization for methanol oxidation. The X-ray photoelectronic spectroscopy ( XPS) results demonstrate that the surface composition is approximately 24 at-% Rh and 76 % Pt. The cyclic voltammetry (CV) and electrochemical quartz crystal (EQCN) results for the alloy were associated, for platinum, to the well known profile in acidic medium. For Rh, on the alloy, the generation of rhodium hydroxide species (Rh(OH)(3) and RhO(OH)(3)) was measured. During the successive oxidation-reduction cycles the mass returns to its original value, indicating the reversibility of the processes. It was not observed rhodium dissolution during the cycling. The 76/24 at % Pt-Rh alloy presented singular electrocatalytic activity for methanol electrooxidation, which started at more negative potentials compared to pure Pt (70 mV). During the sweep towards more negative potentials, there is only weak CO re-adsorption on both Rh and Pt-Rh alloy surfaces, which can be explained by considering the interaction energy between Rh and CO.