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At least 1,063 records · Page 59Linked to original sources
PubMed2006

GiPSi:a framework for open source/open architecture software development for organ-level surgical simulation.

This paper presents the architectural details of an evolving open source/open architecture software framework for developing organ-level surgical simulations. Our goal is to facilitate shared development of reusable models, to accommodate heterogeneous models of computation, and to provide a framework for interfacing multiple heterogeneous models. The framework provides an application programming interface for interfacing dynamic models defined over spatial domains. It is specifically designed to be independent of the specifics of the modeling methods used, and therefore facilitates seamless integration of heterogeneous models and processes. Furthermore, each model has separate geometries for visualization, simulation, and interfacing, allowing the model developer to choose the most natural geometric representation for each case. Input/output interfaces for visualization and haptics for real-time interactive applications have also been provided.

Computer Simulation↗
PubMed2004

Performance of the Alex AVX-2 MIMD architecture in learning the NetTalk database.

The process of training neural networks on parallel architectures has been used to assess the performance of so many parallel machines. In this paper, we are investigating the implementation of backpropagation (BP) on the Alex AVX-2 coarse-grained MIMD machine. A host-worker parallel implementation is carried out in order to train different networks to learn the NetTalk dictionary. First, a computational model is constructed using a single processor to complete the learning process. Also, a communication model for the host-worker topology is developed in order to compute the communication overhead in the broadcasting/gathering process. Both models are then used to predict the machine performance when p processors are used and a comparison with the actual measured performance of the parallel architecture implementation is carried out. Simulation results show that both models can be used effectively to predict the machine performance for the NetTalk problem. Finally, a comparison between the AVX-2 NetTalk implementation and the performance of other parallel platforms is presented.

Artificial Intelligence↗
PubMed2004

Classification capacity of a modular neural network implementing neurally inspired architecture and training rules.

A three-layer neural network (NN) with novel adaptive architecture has been developed. The hidden layer of the network consists of slabs of single neuron models, where neurons within a slab--but not between slabs--have the same type of activation function. The network activation functions in all three layers have adaptable parameters. The network was trained using a biologically inspired, guided-annealing learning rule on a variety of medical data. Good training/testing classification performance was obtained on all data sets tested. The performance achieved was comparable to that of SVM classifiers. It was shown that the adaptive network architecture, inspired from the modular organization often encountered in the mammalian cerebral cortex, can benefit classification performance.

Animals↗
PubMed2006

Analysis of a master-slave architecture for distributed evolutionary computations.

This paper introduces a new mathematical model of the master-slave architecture for distributed evolutionary computations (EC). This model is validated using a concrete implementation based on the Distributed BEAGLE C++ framework. Results show that contrary to (current) popular belief, master-slave architectures are able to scale well over local area networks of workstations using off-the-shelf networking equipment. The main properties of the master-slave are also compared with those of the more mainstream island-model.

Artificial Intelligence↗
PubMed2003

Unit-delay focusing architecture and integrated-circuit implementation for high-frequency ultrasound.

High-frequency ultrasound (above 10 MHz) has been used successfully in many medical applications, including eye, skin, gastrointestinal, intravascular, and Doppler flow imaging. Most of these applications use single-element transducers, thereby imposing a tradeoff between resolution and depth of field. Fabrication difficulties and the need for high-speed electronic beamformers have prevented widespread use of arrays at high frequencies. In this paper, a unit-delay focusing architecture suitable for use with high-frequency ultrasound annular arrays is described. It uses a collection of identical, active delay cells that may be simultaneously varied to accomplish focusing. Results are presented for an analog integrated circuit intended for use with a five-element, 50-MHz planar annular array. Focusing is possible over an axial range for which the ratio of maximum to minimum f-number is 2.1. Unit-delay architectures also are described for curved annular arrays and linear arrays.

Electronics↗
PubMedDate not supplied

A transparently scalable visualization architecture for exploring the universe.

Modern astronomical instruments produce enormous amounts of three-dimensional data describing the physical Universe. The currently available data sets range from the solar system to nearby stars and portions of the Milky Way Galaxy, including the interstellar medium and some extrasolar planets, and extend out to include galaxies billions of light years away. Because of its gigantic scale and the fact that it is dominated by empty space, modeling and rendering the Universe is very different from modeling and rendering ordinary three-dimensional virtual worlds at human scales. Our purpose is to introduce a comprehensive approach to an architecture solving this visualization problem that encompasses the entire Universe while seeking to be as scale-neutral as possible. One key element is the representation of model-rendering procedures using power scaled coordinates (PSC), along with various PSC-based techniques that we have devised to generalize and optimize the conventional graphics framework to the scale domains of astronomical visualization. Employing this architecture, we have developed an assortment of scale-independent modeling and rendering methods for a large variety of astronomical models, and have demonstrated scale-insensitive interactive visualizations of the physical Universe covering scales ranging from human scale to the Earth, to the solar system, to the Milky Way Galaxy, and to the entire observable Universe.

Algorithms↗
PubMed2002

Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures.

The amino acid composition and architecture of all beta-barrel membrane proteins of known three-dimensional structure have been examined to generate information that will be useful in identifying beta-barrels in genome databases. The database consists of 15 nonredundant structures, including several novel, recent structures. Known structures include monomeric, dimeric, and trimeric beta-barrels with between 8 and 22 membrane-spanning beta-strands each. For this analysis the membrane-interacting surfaces of the beta-barrels were identified with an experimentally derived, whole-residue hydrophobicity scale, and then the barrels were aligned normal to the bilayer and the position of the bilayer midplane was determined for each protein from the hydrophobicity profile. The abundance of each amino acid, relative to the genomic abundance, was calculated for the barrel exterior and interior. The architecture and diversity of known beta-barrels was also examined. For example, the distribution of rise-per-residue values perpendicular to the bilayer plane was found to be 2.7 +/- 0.25 A per residue, or about 10 +/- 1 residues across the membrane. Also, as noted by other authors, nearly every known membrane-spanning beta-barrel strand was found to have a short loop of seven residues or less connecting it to at least one adjacent strand. Using this information we have begun to generate rapid screening algorithms for the identification of beta-barrel membrane proteins in genomic databases. Application of one algorithm to the genomes of Escherichia coli and Pseudomonas aeruginosa confirms its ability to identify beta-barrels, and reveals dozens of unidentified open reading frames that potentially code for beta-barrel outer membrane proteins.

Bacterial Outer Membrane Proteins↗
PubMed2000

Using a cognitive architecture to examine what develops.

Different theories of development propose alternative mechanisms by which development occurs. Cognitive architectures can be used to examine the influence of each proposed mechanism of development while keeping all other mechanisms constant. An ACT-R computational model that matched adult behavior in solving a 21-block pyramid puzzle was created. The model was modified in three ways that corresponded to mechanisms of development proposed by developmental theories. The results showed that all the modifications (two of capacity and one of strategy choice) could approximate the behavior of 7-year-old children on the task. The strategy-choice modification provided the closest match on the two central measures of task behavior (time taken per layer, r = .99, and construction attempts per layer, r = .73). Modifying cognitive architectures is a fruitful way to compare and test potential developmental mechanisms, and can therefore help in specifying "what develops."

Adult↗
PubMed1997

Epidermal remodeling in psoriasis (II): a quantitative analysis of the epidermal architecture.

Hyperproliferative psoriatic epidermis was quantitatively analyzed using a geometric model of viable epidermis. Our model was based on hexagonally arranged cylindrical papillae, which allowed the determination of the total volume of the viable epidermis and the total area of the interface with the proliferative compartment based on several parameters, such as papillary height, papillary width, and distance between neighboring papillae. The analysis assumed that the total number of viable epidermal cells paralleled the proliferative compartment in a steady state of cell flow, so a quantitative relation could be made between both volume and interface of the viable epidermis. Multiple parameters of the psoriatic epidermal architecture were measured, and variations within psoriasis were predicted by the model. The results predicted were remarkably close to the observed values. The geometric model also indicated that psoriatic epidermis could be subdivided into two distinct types, with and without a granular layer; the latter having a shorter turnover time. This is consistent with the notion that the typical psoriatic epidermis (without the granular layer) represents the expanding hyperproliferative phase, whereas the psoriatic epidermis with a granular layer represents stationary or resolving states. The model of hexagonally arranged cylindrical papillae suggested that the architecture of the psoriatic epidermis is constructed by a simple mechanism, whereby the psoriatic angulated rete-papilla pattern was produced by a two-dimensional increase in the proliferative compartment and a three-dimensional increase in the total volume of the viable epidermis.

Epidermis↗
PubMed2005

Sleep architecture in children with idiopathic generalized epilepsy.

PURPOSE: Children with epilepsy experience sleep disturbances, behavioral and attentional problems at higher rates than their peers. However, the relation between sleep disturbances and the observed behavioral and attentional abnormalities is poorly defined. METHODS: Children with primary generalized epilepsy who were seizure free and between the ages of 5 and 18 years were matched with age- and gender-matched healthy controls and underwent two consecutive nights of nocturnal polysomnography with extended electroencephalography. Connor's Continuous Performance Test (CPT) was administered to assess daytime attentional function. Parents completed the Child Behavior Checklist (CBCL) to assess their emotional-behavioral status. Two sample t tests were used to examine group differences. Spearman correlations were used to examine the relation between sleep variables and behavior and attention variables. Multiple regression analysis was used to identify independent predictors of abnormal behavior and attention among patients. RESULTS: Eleven children with primary generalized epilepsy and eight age- and sex-matched controls participated in the study. Children with epilepsy had longer stage 1 sleep percentage (7.19 +/- 3.2 vs. 4.8 +/- 3.5; p = 0.05) and latency to rapid-eye-movement (REM) sleep (123.5 +/- 40.1 vs. 101.75 +/- 24.3; p = 0.018) compared with controls. Children with epilepsy had worse attention (CPT index, 10.94 +/- 6.55 vs. 3.42 +/- 4.04; p = 0.004) and exhibited significantly higher CBCL Total Behavior and Internalizing Behavior Problem scales. Whereas regression analysis showed no independent predictors of abnormal behavior and attention, a tendency toward association between CBCL total behavior scale and REM percentage (r= 0.55; p = 0.07), and between CPT overall index and stage 1 sleep percentage (r= 0.40; p = 0.10) was noted. CONCLUSIONS: Sleep architecture is abnormal in children with primary generalized epilepsy. Further studies are needed to determine whether abnormalities in sleep architecture contribute to poor daytime behavior and attention.

Adolescent↗
PubMed2000

The genetics of phenotypic plasticity. IX. Genetic architecture, temperature, and sex differences in Drosophila melanogaster.

We examined the genetic architecture of plasticity of thorax and wing length in response to temperature in Drosophila melanogaster. Reaction norms as a function of growth temperature were analyzed in 20 isofemale lines in a natural population collected from Grande Ferrade near Bordeaux (southern France) in two different years. We found evidence for a complex genetic architecture underlying the reaction norms and differences between males and females. Reaction norms were negative quadratics. Genetic correlations were moderately high between traits within environments. Among characteristic values, the magnitudes of genetic correlations varied among traits and sexes. We hypothesized that genetic correlations among environments would decrease as temperatures became more different. This expectation was upheld for only one trait, female thorax length. For males for both traits, the correlations were large for both very similar and very different temperatures. These correlations may constrain the evolution of the shape of the reaction norms. Whether the extent of independence implies specific regulatory genes or only a specific allelic regulation of trait genes can not be decided from our results.

Animals↗
PubMed2003

Genetic architecture of differences between populations of cowpea weevil (Callosobruchus maculatus) evolved in the same environment.

We investigated the genetic architecture underlying differentiation in fitness-related traits between two pairs of populations of the seed beetle Callosobruchus maculatus (Coleoptera: Bruchidae). These populations had geographically distant (> 2000 km) origins but evolved in a uniform laboratory environment for 120 generations. For each pair of populations (Nigeria x Yemen and Cameroon x Uganda) we estimated the means of five fitness-related characters and a measure of fitness (net reproductive rate R0) in each of the parental populations and 12 types of hybrids (two F1 and two F2 lines and eight backcrosses). Models containing up to nine composite genetic parameters were fitted to the means of the 14 lines. The patterns of line means for all traits in the Nigeria x Yemen cross and for four traits (larval survival, developmental rate, female body weight, and fecundity) in the Cameroon x Uganda cross were best explained by models including additive, dominance, and maternal effects, but excluding epistasis. We did not find any evidence for outbreeding depression for any trait. An epistatic component of divergence was detected for egg hatching success and R0 in the Cameroon x Uganda cross, but its sign was opposite to that expected under outbreeding depression, that is, additive x additive epistasis had a positive effect on the performance of F2 hybrids. All traits except fecundity showed a pattern of heterosis. A large difference of egg-hatching success between the two reciprocal F1 lines in that cross was best explained as fertilization incompatibility between Cameroon females and sperm carrying Uganda genes. The results suggest that these populations have not converged to the same life-history phenotype and genetic architecture, despite 120 generations of uniform natural selection. However, the absence of outbreeding depression implies that they did not evolve toward different adaptive peaks.

Animals↗
PubMed2004

Evolutionary potential of Chamaecrista fasciculata in relation to climate change. II. Genetic architecture of three populations reciprocally planted along an environmental gradient in the great plains.

Climate change will test the evolutionary potential of populations. Information regarding the genetic architecture within and among populations is essential for prediction of evolutionary outcomes. However, little is known about the distribution of genetic variation for relevant traits in natural populations or alteration of genetic architecture in a changing environment. In this study, pedigreed families from three populations of the annual prairie legume Chamaecrista fasciculata were reciprocally transplanted in three environments across a broad latitudinal range in the Great Plains. The underlying premise of this work is that northern populations will in the future experience climates similar to current-day climates further south. Estimates of narrow-sense heritability ranged from 0.053 to 0.481, suggesting the potential for evolutionary change is possible for most traits. In general, the northern population harbored less genetic variation and had lower heritability for traits than the southern population. This population also experienced large reductions in fitness, as measured by estimated lifetime fecundity, when raised in either the intermediate or the southern climate, whereas the difference between the intermediate and southern population was less extreme. For fecundity, the pattern of cross-environment additive genetic correlations was antagonistic to evolutionary change in four of six cases when native and nonnative sites were compared. Six additional antagonistic positive correlations were found for the rate of phenological development and leaf thickness. Overall, the data suggest that if climate changes as predicted, the northern population will face a severe evolutionary challenge in the future because of low heritabilities, cross-environment genetic correlations antagonistic to selection, and demographic instability due to lower seed production in a hotter and drier climate.

Adaptation, Physiological↗
PubMed1988

Architectural morphometry in ulcerative colitis with dysplasia.

Semi-automatic image analysis was used to assess the architectural features of normal colorectal mucosa and ulcerative colitis with and without dysplasia. Eight measured and derived morphometric variables were compared with the histological grading. The main data-set variation was due to: (1) the area of mucosa and epithelium per unit length of muscularis mucosae; (2) mean mucosal and epithelial height; and (3) the percentage epithelium and number of crypts per unit length of muscularis mucosae. Discriminant analysis using the variables mean epithelial height and mean lamina propria area per unit length of muscularis mucosae separated normals (n = 10) from high-grade dysplasia (8). The classification rule allocated low-grade dysplasia (8) to the high-grade category and 60% of regeneration cases (10) to the normal mucosa group. Scatter plots of the two discriminating variables separated normal and regenerative mucosa from dysplasia. Histological review of overlapping cases allowed redesignation of a high-grade dysplasia lesion as low grade. Architectural morphometry may be of use in assessing premalignant mucosal changes in ulcerative colitis as a guide to patient surveillance and therapy.

Colitis, Ulcerative↗
PubMed2003

The molecular machines of DNA repair: scanning force microscopy analysis of their architecture.

The application of scanning force microscope (SFM, also called atomic force microscope or AFM) imaging to study the architecture of proteins and their functional assemblies on DNA has provided new and exciting information on the mechanism of vital cellular processes. Rapid progress in molecular biology has resulted in the identification and isolation of proteins and protein complexes that function in specific DNA transactions. These proteins and protein complexes can now be analysed at the single molecule level, whereby the functional assemblies are often described as nanomachines. Understanding how they work requires understanding their structure and functional arrangement in three dimensions. The SFM is uniquely suited to provide three-dimensional structural information on biomolecules at nanometre resolution. In this review we focus on recent applications of SFM to reveal detailed information on the architecture and mechanism of action of protein machinery involved in safeguarding genome stability through DNA repair processes.

DNA↗
PubMed1992

Gender differences in sleep architecture in sleep apnoea syndrome.

This study compared sleep architecture in women and men with sleep apnoea syndrome. Women (n = 126) had longer sleep latencies, greater amounts of slow wave sleep, and fewer awakenings during the night than men (n = 181), despite no differences in age, RDI (Respiratory Disturbance Index) or oxygen saturation. In a subgroup of men and women treated with nasal CPAP, gender differences generally persisted. There was no difference in the complaint of daytime sleepiness between the groups, but the women reported more fatigue during the day than the men, as well as complaining about more sleep disturbance at night. We interpret these differences in terms of known gender differences in sleep architecture and sleep complaints.

Journal Article↗
PubMed2004

Molecular architecture of the Cryptococcus neoformans capsule.

Many microbes are surrounded by phagocytosis-inhibiting capsules. We took advantage of the large size of the polysaccharide capsule of the pathogenic yeast Cryptococcus neoformans to examine capsular architecture and the relationship between molecular architecture and the interaction of the capsule with potentially opsonic serum proteins. Our experimental design used complementary approaches in which (i) assessment of permeability to macromolecules of different Stokes radii; (ii) determination of the binding of Fab fragments of anticapsular antibodies as a measure of matrix density; (iii) capsular deconstruction by treatment with dimethyl sulphoxide; and (iv) evaluation of capsule plasticity, were used to probe the molecular structure of the capsule. The results showed that the capsule is a matrix with a variable porosity that increases with distance from the cell wall. A high density of the matrix at the capsule interior prevents penetration of large macromolecules to sites near the cell wall. In contrast, the capsular edge that is the interface with phagocytes presents capsular polysaccharide in a very low density that exhibits considerable plasticity and permeability to macromolecules. Notably, the capsule of yeast cells harvested from infected tissue showed a greater matrix density than yeast cells grown in vitro under capsule induction conditions.

Antibodies, Fungal↗
PubMed2006

Nutrient availability constrains the hydraulic architecture and water relations of savannah trees.

Leaf and whole plant-level functional traits were studied in five dominant woody savannah species from Central Brazil (Cerrado) to determine whether reduction of nutrient limitations in oligotrophic Cerrado soils affects carbon allocation, water relations and hydraulic architecture. Four treatments were used: control, N additions, P additions and N plus P additions. Fertilizers were applied twice yearly, from October 1998 to March 2004. Sixty-three months after the first nutrient addition, the total leaf area increment was significantly greater across all species in the N- and the N + P-fertilized plots than in the control and in the P-fertilized plots. Nitrogen fertilization significantly altered several components of hydraulic architecture: specific conductivity of terminal stems increased with N additions, whereas leaf-specific conductivity and wood density decreased in most cases. Average daily sap flow per individual was consistently higher with N and N + P additions compared to the control, but its relative increase was not as great as that of leaf area. Long-term additions of N and N + P caused midday PsiL to decline significantly by a mean of 0.6 MPa across all species because N-induced relative reductions in soil-to-leaf hydraulic conductance were greater than those of stomatal conductance and transpiration on a leaf area basis. Phosphorus-fertilized trees did not exhibit significant changes in midday PsiL. Analysis of xylem vulnerability curves indicated that N-fertilized trees were significantly less vulnerable to embolism than trees in control and P-fertilized plots. Thus, N-induced decreases in midday PsiL appeared to be almost entirely compensated by increases in resistance to embolism. Leaf tissue water relations characteristics also changed as a result of N-induced declines in minimum PsiL: osmotic potential at full turgor decreased and symplastic solute content on a dry matter basis increased linearly with declining midday PsiL across species and treatments. Despite being adapted to chronic nutrient limitations, Cerrado woody species apparently have the capacity to exploit increases in nutrient availability by allocating resources to maximize carbon gain and enhance growth. The cost of increased allocation to leaf area relative to water transport capacity involved increased total water loss per plant and a decrease in minimum leaf water potentials. However, the risk of increased embolism and turgor loss was relatively low as xylem vulnerability to embolism and leaf osmotic characteristics changed in parallel with changes in plant water status induced by N fertilization.

Climate↗