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PubMed2006

Shack-Hartmann wavefront sensing with elongated sodium laser beacons: centroiding versus matched filtering.

We describe modeling and simulation results for the Thirty Meter Telescope on the degradation of sodium laser guide star Shack-Hartmann wavefront sensor measurement accuracy that will occur due to the spatial structure and temporal variations of the mesospheric sodium layer. By using a contiguous set of lidar measurements of the sodium profile, the performance of a standard centroid and of a more refined noise-optimal matched filter spot position estimation algorithm is analyzed and compared for a nominal mean signal level equal to 1000 photodetected electrons per subaperture per integration time, as a function of subaperture to laser launch telescope distance and CCD pixel readout noise. Both algorithms are compared in terms of their rms spot position estimation error due to noise, their associated wavefront error when implemented on the Thirty Meter Telescope facility adaptive optics system, their linear dynamic range, and their bias when detuned from the current sodium profile.

Journal Article↗
PubMed1998

Detection of chromatic and luminance contrast modulation by the visual system.

The data presented in this paper examine the ability of observers to detect a modulation in the contrast of chromatic and luminance gratings as a function of the carrier contrast, duration, and spatial frequency. The nature of the signal underlying this ability is investigated by examining both the paradigm used to make the measurement and the effect of grating masks on performance in the tasks. The results show that observers' ability to discriminate amplitude modulation from an unmodulated carrier is dependent on carrier contrast but only up to approximately 5-8 times carrier-detection threshold. Discrimination is, however, independent of spatial frequency [10-1 cycles per degree (cpd) component-frequency range], carrier color, and, most surprisingly, stimulus duration (1000-30 ms). This set of experiments compliments data from previous papers and assimilates many of the conclusions drawn from this previous data. There is absolutely no evidence for the existence of a distortion product mediating performance under any of the current conditions, and the data seriously question whether the visual system might use such a signal even if it does exist under more extreme conditions than those used here. The evidence suggests that the visual system detects variations in both chromatic and luminance contrast by means of a mechanism operating locally upon the spatial structure of the carrier.

Color Perception↗
PubMed2001

Beam propagation through uniaxial anisotropic media: global changes in the spatial profile.

The propagation of electromagnetic beams through uniaxial anisotropic media is investigated. The Maxwell equations are solved in the paraxial limit in terms of the plane-wave spectrum associated with each Cartesian field component. Attention is focused on the global changes in the spatial structure of the beam, which are described by means of the second-order intensity moment formalism. In particular, the propagation law for the intensity moments through this kind of media is obtained. As a consequence it is inferred that it is possible to improve the beam-quality parameter by using these media.

Journal Article↗
PubMed2003

Topological defects in moiré fringes with spiral zone plates.

We present a study of spatial structures created by superposition of spiral zone plates used for generating optical beams with phase singularities. Moiré fringes are observed that show topological defects similar to those appearing in interference patterns of optical vortices. A brief theoretical discussion is included that supports the similarities between the two phenomena. Our results may lead to interesting applications to digital information processing by optical means.

Journal Article↗
PubMed2005

Contrast statistics for foveated visual systems: fixation selection by minimizing contrast entropy.

The human visual system combines a wide field of view with a high-resolution fovea and uses eye, head, and body movements to direct the fovea to potentially relevant locations in the visual scene. This strategy is sensible for a visual system with limited neural resources. However, for this strategy to be effective, the visual system needs sophisticated central mechanisms that efficiently exploit the varying spatial resolution of the retina. To gain insight into some of the design requirements of these central mechanisms, we have analyzed the effects of variable spatial resolution on local contrast in 300 calibrated natural images. Specifically, for each retinal eccentricity (which produces a certain effective level of blur), and for each value of local contrast observed at that eccentricity, we measured the probability distribution of the local contrast in the unblurred image. These conditional probability distributions can be regarded as posterior probability distributions for the "true" unblurred contrast, given an observed contrast at a given eccentricity. We find that these conditional probability distributions are adequately described by a few simple formulas. To explore how these statistics might be exploited by central perceptual mechanisms, we consider the task of selecting successive fixation points, where the goal on each fixation is to maximize total contrast information gained about the image (i.e., minimize total contrast uncertainty). We derive an entropy minimization algorithm and find that it performs optimally at reducing total contrast uncertainty and that it also works well at reducing the mean squared error between the original image and the image reconstructed from the multiple fixations. Our results show that measurements of local contrast alone could efficiently drive the scan paths of the eye when the goal is to gain as much information about the spatial structure of a scene as possible.

Algorithms↗
PubMed2005

All-reflective snapshot hyperspectral imager for ultraviolet and infrared applications.

Snapshot hyperspectral imaging simultaneously acquires spatial and spectral information about a scene. We report on the first, to our knowledge, all-reflective snapshot hyperspectral imager in the form of a computed tomography imaging spectrometer (CTIS). The reflective design allows for instrument simplicity for applications in the ultraviolet and infrared. To realize a CTIS in a reflective Offner configuration, a reflective two-dimensional computer-generated hologram grating is fabricated on a convex spherical substrate by direct-write electron-beam lithography. Furthermore, a reconfigurable reflective field stop is implemented with a micromirror array to provide high-contrast spatial-spectral filtering, region-of-interest selection, and spatial structure formation.

Journal Article↗
PubMed2006

A model for short alpha-neurotoxin bound to nicotinic acetylcholine receptor from Torpedo californica.

Short- and long-chain alpha-neurotoxins from snake venoms are potent blockers of nicotinic acetylcholine receptors (nAChRs). Short alpha-neurotoxins consist of 60-62 amino acid residues and include 4 disulfide bridges, whereas long alpha-neurotoxins have 66-75 residues and 5 disulfides. The spatial structure of these toxins is built by three loops, I-III "fingers," confined by four disulfide bridges; the fifth disulfide of long-chain alpha-neurotoxins is situated close to the tip of central loop II. An accurate knowledge of the mode of alpha-neurotoxin-nAChR interaction is important for rational design of new nAChR agonists and antagonists for medical purposes. Ideas on the topography of toxin-nAChR complexes were based until recently on nAChR interactions with selectively labeled alpha-neurotoxins, mutations in toxins, nAChR, or both. Recently, crystal structures have been solved for the Torpedo marmorata nAChR (4A[Unwin, 2005]) and for the acetylcholine-binding protein (AChBP) complexed with mollusk alpha-conotoxin (2.4 A[Celie et al., 2005]) or alpha-cobratoxin, long-chain alpha-neurotoxin (4 A [Bourne et al., 2005]). However, there were no angstrom-resolution models for complexes of short-chain alpha-neurotoxins. Here, we report the model of the Torpedo californica nAChR extracellular domain complexed to a short-chain alpha-neurotoxin II (NTII) from Naja oxiana cobra venom.

Animals↗
PubMed2005

Genetic addiction: selfish gene's strategy for symbiosis in the genome.

The evolution and maintenance of the phenomenon of postsegregational host killing or genetic addiction are paradoxical. In this phenomenon, a gene complex, once established in a genome, programs death of a host cell that has eliminated it. The intact form of the gene complex would survive in other members of the host population. It is controversial as to why these genetic elements are maintained, due to the lethal effects of host killing, or perhaps some other properties are beneficial to the host. We analyzed their population dynamics by analytical methods and computer simulations. Genetic addiction turned out to be advantageous to the gene complex in the presence of a competitor genetic element. The advantage is, however, limited in a population without spatial structure, such as that in a well-mixed liquid culture. In contrast, in a structured habitat, such as the surface of a solid medium, the addiction gene complex can increase in frequency, irrespective of its initial density. Our demonstration that genomes can evolve through acquisition of addiction genes has implications for the general question of how a genome can evolve as a community of potentially selfish genes.

Bacteria↗
PubMedDate not supplied

Ecology of Triatoma rubrovaria (Hemiptera, Triatominae) in wild and peridomestic environments of Uruguay.

This paper describes population structure, spatial distribution and habitat selection of wild and peridomestic populations of Triatoma rubrovaria (Blanchard, 1843). Field studies were carried out at Las Piedras and La Bolsa in the Northern Department of Artigas, Uruguay. A semicircular sampling area, divided in seven or eight triangular sectors was sequentially examined from October 1990 to November 1991. At Las Piedras (typical wild habitat) 1063 T. rubrovaria bugs were collected from 84% of the rocky outcroops ("pedregales"). Abundance varied by season peaking in October-November (spring). Throughout the year, most of the population was made up of third, fourth and fifth instar nymphs; adults were found from October to March. In the peridomestic environment of La Bolsa, however T. rubrovaria was less common and showed a more irregular instar distribution. Colonized ecotopes, were those close to houses. In both sites T. rubrovaria was mainly associated with the geckonid Homonota uruguayensis and the cockroach Blaptica dubia.

Animals↗
PubMed2006

Geographic analysis of host use, development, and habitat use of an acanthocephalan species, Leptorhynchoides thecatus.

Leptorhynchoides thecatus (Linton, 1891), an acanthocephalan parasite of freshwater fishes, varies in host use, development, and habitat use throughout North America. Spatial structure of these characteristics was examined from data extracted from the literature. Geographic patterns were inferred from point comparisons using correllograms and then tested with Moran's I statistic for global and local significance, and visually from regional means within major river drainages. Species of Micropterus Lacepède, 1802 (black basses) were common hosts in most regions, except the Lower Mississippi and South Atlantic regions where species of Lepomis Rafinesque, 1819 (sunfishes) were common hosts. Development, described as the proportions of adults relative to cystacanths (extraintestinal juveniles), decreased with latitude. Habitat use of L. thecatus showed marked geographic patterns. Leptorhynchoides thecatus occurred in the intestine of sunfishes in the South Atlantic and Lower Mississippi regions, in the ceca in fish of all species included in the study in the Missouri and Texas-Gulf regions, and both in ceca and intestines in fish of all species in northern regions. Leptorhynchoides thecatus showed geographic patterning within the variable traits across the range of the species. These patterns may be the result of ecological factors or of genetic differences that might indicate L. thecatus comprises multiple cryptic species.

Acanthocephala↗
PubMed2006

Mutualistic stability in the arbuscular mycorrhizal symbiosis: exploring hypotheses of evolutionary cooperation.

The 450-million-year-old symbiosis between the majority of land plants and arbuscular mycorrhizal fungi (AMF) is one of the most ancient, abundant, and ecologically important mutualisms on Earth. Yet, the evolutionary stability of mycorrhizal associations is still poorly understood, as it follows none of the constraints thought to stabilize cooperation in other well-known mutualisms. The capacity of both host and symbiont to simultaneously interact with several partners introduces a unique dilemma; detecting and punishing those exploiting the mutualism becomes increasingly difficult if these individuals can continue to access resources from alternative sources. Here, we explore four hypotheses to explain evolutionary cooperation in the arbuscular mycorrhizal symbiosis: (1) pseudo-vertical transmission and spatial structuring of plant and fungal populations leading to local adaptation of partners; (2) luxury resource exchange in which plants trade surplus carbon for excess fungal nutrients; (3) partner choice allowing partners to associate with better cooperators; and (4) host and symbiont sanctions which actively reward good partners and punish less cooperative ones. We propose that mycorrhizal cooperation is promoted by an exchange of surplus resources between partners and enforced through sanctions by one or both partners. These mechanisms may allow plant and fungal genotypes to discriminate against individuals employing exploitative strategies, promoting patterns of partner choice. Together these selection pressures provide a framework for understanding the stabilization of mycorrhizal cooperation over evolutionary time.

Biological Evolution↗
PubMed2006

Reproductive isolation between Pogonomyrmex rugosus and two lineages with genetic caste determination.

Hybrid speciation occurs when combination of two interspecific genomes results in individuals that are of high fitness but reproductively incompatible with the parental species. Although hybrid speciation is a relatively common source of new species in plants, it appears to be a much rarer occurrence in animal taxa. Here we report on reproductive isolation and range overlap between the rough harvester ant Pogonomyrmex rugosus and two lineages with hybrid genotypes (H 1 and H2). Both lineages obligately interbreed and produce genetically distinct queen and worker offspring, a phenomenon referred to as genetic caste determination (GCD). Diploid offspring produced by gametes of the same lineage develop only into queens, whereas diploid offspring derived from gametes of distinct lineages develop into workers. We investigated small-scale patterns of gene flow between the parent and the two H lineages by sampling along an 80-km transect between a pure P. rugosus population and a two-lineage population. Microsatellite and mitochondrial markers both indicated virtually no gene flow between the parent species and either lineage even at sites where parental and H-lineage colonies co-occurred. The geographic ranges of the parental species and the two-lineage population were essentially parapatric, with a surprisingly narrow band of overlap and evidence of spatial structuring even at microgeographic scales within the transition zone. This suggests that ecological competition with the parent species plays a significant role in determining the evolutionary persistence and current distribution of the hybrid lineages and the genetic caste system.

Animals↗
PubMedDate not supplied

Spatial variability of nitrous oxide emissions and their soil-related determining factors in an agricultural field.

To evaluate spatial variability of nitrous oxide (N2O) emissions and to elucidate their determining factors on a field-scale basis, N2O fluxes and various soil properties were evaluated in a 100- x 100-m onion (Allium cepa L.) field. Nitrous oxide fluxes were determined by a closed chamber method from the one-hundred 10- x 10-m plots. Physical (e.g., bulk density and water content), chemical (e.g., total N and pH), and biological (e.g., microbial biomass C and N) properties were determined from surface soil samples (0-0.1 m) of each plot. Geostatistical analysis was performed to examine spatial variability of both N2O fluxes and soil properties. Multivariate analysis was also conducted to elucidate relationships between soil properties and observed fluxes. Nitrous oxide fluxes were highly variable (average 331 microg N m(-2) h(-1), CV 217%) and were log-normally distributed. Log-transformed N2O fluxes had moderate spatial dependence with a range of >75 m. High N2O fluxes were observed at sites with relatively low elevation. Multivariate analysis indicated that an organic matter factor and a pH factor of the principal component analysis were the main soil-related determining factors of log-transformed N2O fluxes. By combining multivariate analysis with geostatistics, a map of predicted N2O fluxes closely matched the spatial pattern of measured fluxes. The regression equation based on the soil properties explained 56% of the spatially structured variation of the log-transformed N2O fluxes. Site-specific management to regulate organic matter content and water status of a soil could be a promising means of reducing N2O emissions from agricultural fields.

Air Pollutants↗
PubMed2006

Conformational features of the Dippu-AST 8 neuropeptide from the cockroach Diploptera punctata.

Spatial structure and conformational properties of the Dippu-AST 8 (allatostatin III) neuropeptide have been investigated by the molecular mechanics method. The conformational energy and geometrical parameters corresponding to the low-energy states of the molecule are obtained. A single backbone conformation with a very restricted set of Ser 3, Phe 4 and Leu 9 amino acids positions is observed for Dippu-AST 8 neuropeptide.

Animals↗
PubMed2004

Peptides and proteins in membranes: what can we learn via computer simulations?

Membrane and membrane-active peptides and proteins play a crucial role in numerous cell processes, such as signaling, ion conductance, fusion, and others. Many of them act as highly specific and efficient drugs or drug targets, and, therefore, attract growing interest of medicinal chemists. Because of experimental difficulties with characterization of their spatial structure and mode of membrane binding, essential attention is given now to molecular modeling techniques. During the last years an important progress has been achieved in molecular dynamics (MD) and Monte Carlo (MC) simulations of peptides and proteins with explicit and/or implicit theoretical models of membranes. The first ones allow atomic-resolution studies of peptides behavior on the membrane-water interfaces. Models with implicit consideration of membrane are of a special interest because of their computational efficiency and ability to account for principal trends in protein-lipid interactions. In this approximation, the bilayer is usually treated as continuum whose properties vary along the membrane thickness, and membrane insertion is simulated using either MC or MD methods. This review surveys recent applications of both types of lipid bilayer models in computer simulations of a wide variety of peptides and proteins with different biological activities. Theoretical background of the membrane models is considered with examples of their applications to biologically relevant problems. The emphasis of the review is made on recent MC and MD computations, on structural and/or functional information, which may be obtained via molecular modeling. The approximations and shortcomings of the models, along with their perspectives in design of new membrane active drugs, are discussed.

Animals↗
PubMed2004

The problem of amino acid complementarity and antisense peptides.

The review presents three hypotheses concerning the amino acid complementarity: 1) the Mekler-Blalock antisense hypothesis; 2) the Root-Bernstein approach based on stereochemical complementarity of amino acids and anti-amino acids coded by anticodons read in parallel with the coding DNA strand; 3) Siemion hypothesis resulting from the periodicity of the genetic code. The current state of knowledge as well as the results of the implementations of these hypotheses are compared. A special attention is given to Root-Bernstein and Siemion hypotheses, which differ in only few points of the complementarity prediction. We describe methods of investigation of peptide-antipeptide pairing, including circular dichroism, mass spectrometry, affinity chromatography and other techniques. The biological applications of complementarity principle are considered, such as search for bioeffector-bioreceptor interaction systems, the influence of peptide-antipeptide pairing on the activity of peptide hormones, and the application of antipeptides in immunochemistry. The possible role of amino acid-anti-amino acid interactions in the formation of the spatial structures of peptides, proteins and protein complexes is discussed. Such problems as the pairing preferences of protein-protein interfaces, the role of the pairing in the creation of disulfide bonds and the possible appearance of such interactions in beta-structure are also examined. The main intention of the paper is to bring the complementarity problem to the attention of the scientific community, as a possible tool in proteomics, molecular design and molecular recognition.

Amino Acid Sequence↗
PubMed2006

A Bayes regression approach to array-CGH data.

This paper develops a Bayes regression model having change points for the analysis of array-CGH data by utilizing not only the underlying spatial structure of the genomic alterations but also the observation that the noise associated with the ratio of the fluorescence intensities is bigger when the intensities get smaller. We show that this Bayes regression approach is particularly suitable for the analysis of cDNA microarray-CGH data, which are generally noisier than those using genomic clones. A simulation study and a real data analysis are included to illustrate this approach.

Bayes Theorem↗