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PubMed2004

The future of computing--new architectures and new technologies.

All modern computers are designed using the 'von Neumann' architecture and built using silicon transistor technology. Both architecture and technology have been remarkably successful. Yet there are a range of problems for which this conventional architecture is not particularly well adapted, and new architectures are being proposed to solve these problems, in particular based on insight from nature. Transistor technology has enjoyed 50 years of continuing progress. However, the laws of physics dictate that within a relatively short time period this progress will come to an end. New technologies, based on molecular and biological sciences as well as quantum physics, are vying to replace silicon, or at least coexist with it and extend its capability. The paper describes these novel architectures and technologies, places them in the context of the kinds of problems they might help to solve, and predicts their possible manner and time of adoption. Finally it describes some key questions and research problems associated with their use.

Journal Article↗
PubMed2001

3D microvascular architecture of pre-cancerous lesions and invasive carcinomas of the colon.

Despite the significance of tumour neoangiogenesis and the extensive knowledge on the molecular basis of blood vessel formation currently no quantitative data exist on the 3D microvascular architecture in human primary tumours and their precursor lesions. This prompted us to examine the 3D vascular network of normal colon mucosa, adenomas and invasive carcinomas by means of quantitative microvascular corrosion casting. Fresh hemicolectomy specimens from 20 patients undergoing cancer or polyposis coli surgery were used for corrosion casting, factor VIII and VEGF immunostaining. In addition, immunostaining was done on colorectal tissue from 33 patients with metastatic and non-metastatic carcinomas, polyposis coli and adenomas. This first quantitative analysis of intervessel and interbranching distances, branching angles and vessel diameters in human cancer specimens revealed distinct patterns of the microvascular unit in the tumour centre and periphery. Irrespective of the tumour localization and grading all individual tumours displayed qualitatively and quantitatively the same vascular architecture. This gives further evidence for the existence of a tumour type-specific vascular architecture as recently demonstrated for experimental tumours. Metastatic tumours displayed different vascular architectures only within hot spots, in terms of smaller intervascular distances than in non-metastatic tumours. Pre-cancerous lesions have in part virtually the same vascular architecture like invasive carcinomas. Comparison of VEGF immunostaining also suggests that angiogenesis sets in long before the progress towards invasive phenotypes and that the so-called angiogenic switch is more likely a sequence of events.

Adenoma↗
PubMed2006

Theoretical studies of electron transfer through dendrimeric architecture.

We have analyzed the steady-state electron transfer rate through a bridge of dendrimeric architecture. The difference between the linear chain and the dendrimeric architecture has also been demonstrated with steady-state rate as a main observable in the coherent and incoherent regimes of interactions. It is shown that generally the rate of electron transfer in dendrimeric architecture is faster than the rate associated with their linear chain counterpart with similar kind of bonding connectivities. The rate depends upon the size of the molecule, core branching, and the nature of the coupling among the different nodes on the dendrimer molecule. Depending upon the nature of the donor and acceptor, phenomenological dephasing coefficient due to environment and the geometry of the dendrimeric architecture, the modification of electron transfer rate has been studied. In the regime of fully coherent interactions where all quantum effects are considered the rate shows a multiple inversion due to the dendrimer architecture which is neither available in the regime of incoherent interaction nor in the linear chain case in similar condition. We have discussed about the applicability of our model in metal-molecule-metal junction, photoinduced electron transfer process, and molecular conductor.

Journal Article↗
PubMed2005

Age-related changes of nuclear architecture in Caenorhabditis elegans.

Mutations in lamins cause premature aging syndromes in humans, including the Hutchinson-Gilford Progeria Syndrome (HGPS) and Atypical Werner Syndrome. It has been shown that HGPS cells in culture undergo age-dependent progressive changes in nuclear architecture. However, it is unknown whether similar changes in nuclear architecture occur during the normal aging process. We have observed that major changes of nuclear architecture accompany Caenorhabditis elegans aging. We found that the nuclear architecture in most nonneuronal cell types undergoes progressive and stochastic age-dependent alterations, such as changes of nuclear shape and loss of peripheral heterochromatin. Furthermore, we show that the rate of these alterations is influenced by the insulin/IGF-1 like signaling pathway and that reducing the level of lamin and lamin-associated LEM domain proteins leads to shortening of lifespan. Our work not only provides evidence for changes of nuclear architecture during the normal aging process of a multicellular organism, but also suggests that HGPS is likely a result of acceleration of the normal aging process. Because the nucleus is vital for many cellular functions, our studies raise the possibility that the nucleus is a prominent focal point for regulating aging.

Aging↗
PubMed2006

Neural blackboard architectures: the realization of compositionality and systematicity in neural networks.

In this paper, we will first introduce the notions of systematicity and combinatorial productivity and we will argue that these notions are essential for human cognition and probably for every agent that needs to be able to deal with novel, unexpected situations in a complex environment. Agents that use compositional representations are faced with the so-called binding problem and the question of how to create neural network architectures that can deal with it is essential for understanding higher level cognition. Moreover, an architecture that can solve this problem is likely to scale better with problem size than other neural network architectures. Then, we will discuss object-based attention. The influence of spatial attention is well known, but there is solid evidence for object-based attention as well. We will discuss experiments that demonstrate object-based attention and will discuss a model that can explain the data of these experiments very well. The model strongly suggests that this mode of attention provides a neural basis for parallel search. Next, we will show a model for binding in visual cortex. This model is based on a so-called neural blackboard architecture, where higher cortical areas act as processors, specialized for specific features of a visual stimulus, and lower visual areas act as a blackboard for communication between these processors. This implies that lower visual areas are involved in more than bottom-up visual processing, something which already was apparent from the large number of recurrent connections from higher to lower visual areas. This model identifies a specific role for these feedback connections. Finally, we will discuss the experimental evidence that exists for this architecture.

Animals↗
PubMed2007

Plant architecture: a dynamic, multilevel and comprehensive approach to plant form, structure and ontogeny.

BACKGROUND AND AIMS: The architecture of a plant depends on the nature and relative arrangement of each of its parts; it is, at any given time, the expression of an equilibrium between endogenous growth processes and exogenous constraints exerted by the environment. The aim of architectural analysis is, by means of observation and sometimes experimentation, to identify and understand these endogenous processes and to separate them from the plasticity of their expression resulting from external influences. SCOPE: Using the identification of several morphological criteria and considering the plant as a whole, from germination to death, architectural analysis is essentially a detailed, multilevel, comprehensive and dynamic approach to plant development. Despite their recent origin, architectural concepts and analysis methods provide a powerful tool for studying plant form and ontogeny. Completed by precise morphological observations and appropriated quantitative methods of analysis, recent researches in this field have greatly increased our understanding of plant structure and development and have led to the establishment of a real conceptual and methodological framework for plant form and structure analysis and representation. This paper is a summarized update of current knowledge on plant architecture and morphology; its implication and possible role in various aspects of modern plant biology is also discussed.

Body Patterning↗
PubMed2006

An initial strategy for comparing proteins at the domain architecture level.

MOTIVATION: Ideally, only proteins that exhibit highly similar domain architectures should be compared with one another as homologues or be classified into a single family. By combining three different indices, the Jaccard index, the Goodman-Kruskal gamma function and the domain duplicate index, into a single similarity measure, we propose a method for comparing proteins based on their domain architectures. RESULTS: Evaluation of the method using the eukaryotic orthologous groups of proteins (KOGs) database indicated that it allows the automatic and efficient comparison of multiple-domain proteins, which are usually refractory to classic approaches based on sequence similarity measures. As a case study, the PDZ and LRR_1 domains are used to demonstrate how proteins containing promiscuous domains can be clearly compared using our method. For the convenience of users, a web server was set up where three different query interfaces were implemented to compare different domain architectures or proteins with domain(s), and to identify the relationships among domain architectures within a given KOG from the Clusters of Orthologous Groups of Proteins database. CONCLUSION: The approach we propose is suitable for estimating the similarity of domain architectures of proteins, especially those of multidomain proteins. AVAILABILITY: http://cmb.bnu.edu.cn/pdart/.

Algorithms↗
PubMed2003

A method for describing the canopy architecture of coppice poplar with allometric relationships.

A multi-scale biometric methodology for describing the architecture of fast-growing short-rotation woody crops is used to describe 2-year-old poplar clones during the second rotation. To allow for expressions of genetic variability observed within this species (i.e., growth potential, leaf morphology, coppice and canopy structure), the method has been applied to two clones: Ghoy (Gho) (Populus deltoides Bartr. ex Marsh. x Populus nigra L.) and Trichobel (Tri) (Populus trichocarpa Torr. & A. Gray x Populus trichocarpa). The method operates at the stool level and describes the plant as a collection of components (shoots and branches) described as a collection of metameric elements, themselves defined as a collection of elementary units (internode, petiole, leaf blade). Branching and connection between the plant units (i.e., plant topology) and their spatial location, orientation, size and shape (i.e., plant geometry) describe the plant architecture. The methodology has been used to describe the plant architecture of 15 selected stools per clone over a 5-month period. On individual stools, shoots have been selected from three classes (small, medium and large) spanning the diameter distribution range. Using a multi-scale approach, empirical allometric relationships were used to parameterize elementary units of the plant, topological relationships and geometry (e.g., distribution of shoot diameters on stool, shoot attributes from shoot diameter). The empirical functions form the basis of the 3-D Coppice Poplar Canopy Architecture model (3-D CPCA), which recreates the architecture and canopy structure of fast-growing coppice crops at the plot scale. Model outputs are assessed through visual and quantitative comparisons between actual photographs of the coppice canopy and simulated images. Overall, results indicate a good predictive ability of the 3-D CPCA model.

Imaging, Three-Dimensional↗
PubMed2003

An evolutionarily structured universe of protein architecture.

Protein structural diversity encompasses a finite set of architectural designs. Embedded in these topologies are evolutionary histories that we here uncover using cladistic principles and measurements of protein-fold usage and sharing. The reconstructed phylogenies are inherently rooted and depict histories of protein and proteome diversification. Proteome phylogenies showed two monophyletic sister-groups delimiting Bacteria and Archaea, and a topology rooted in Eucarya. This suggests three dramatic evolutionary events and a common ancestor with a eukaryotic-like, gene-rich, and relatively modern organization. Conversely, a general phylogeny of protein architectures showed that structural classes of globular proteins appeared early in evolution and in defined order, the alpha/beta class being the first. Although most ancestral folds shared a common architecture of barrels or interleaved beta-sheets and alpha-helices, many were clearly derived, such as polyhedral folds in the all-alpha class and beta-sandwiches, beta-propellers, and beta-prisms in all-beta proteins. We also describe transformation pathways of architectures that are prevalently used in nature. For example, beta-barrels with increased curl and stagger were favored evolutionary outcomes in the all-beta class. Interestingly, we found cases where structural change followed the alpha-to-beta tendency uncovered in the tree of architectures. Lastly, we traced the total number of enzymatic functions associated with folds in the trees and show that there is a general link between structure and enzymatic function.

Animals↗
PubMed2003

Natural genomic design in Sinorhizobium meliloti: novel genomic architectures.

The complete nucleotide sequence of the genome of Sinorhizobium meliloti, the symbiont of alfalfa, was reported in 2001 by an international consortium of laboratories. The genome comprises a chromosome of 3.65 megabases (Mb) and two megaplasmids, pSymA and pSymB, of 1.35 Mb and 1.68 Mb, respectively. Based on the nucleotide sequence of the whole genome, we designed a pathway of consecutive rearrangements leading to novel genomic architectures. In a first step we obtained derivative strains containing two replicons; in a second step we obtained a strain containing the genetic information in one single replicon of 6.68 MB. From this last architecture we isolated revertants containing two replicons, and from these we could return to the original architecture showing the three replicons. We found that the relative frequency of excision of cointegrated replicons is higher at the site used for the cointegration than at other sites. This might conciliate two apparently opposed facts: the highly dynamic state of genomic architecture in S. meliloti and the common observation that different isolates and derived cellular clones of S. meliloti usually present the architecture of one chromosome and two distinct megaplasmids. Different aspects that must be considered to obtain full advantage of the strategy of natural genomic design are discussed.

DNA Transposable Elements↗
PubMed2006

Lidar detection of underwater objects using a neuro-SVM-based architecture.

This paper presents a neural network architecture using a support vector machine (SVM) as an inference engine (IE) for classification of light detection and ranging (Lidar) data. Lidar data gives a sequence of laser backscatter intensities obtained from laser shots generated from an airborne object at various altitudes above the earth surface. Lidar data is pre-filtered to remove high frequency noise. As the Lidar shots are taken from above the earth surface, it has some air backscatter information, which is of no importance for detecting underwater objects. Because of these, the air backscatter information is eliminated from the data and a segment of this data is subsequently selected to extract features for classification. This is then encoded using linear predictive coding (LPC) and polynomial approximation. The coefficients thus generated are used as inputs to the two branches of a parallel neural architecture. The decisions obtained from the two branches are vector multiplied and the result is fed to an SVM-based IE that presents the final inference. Two parallel neural architectures using multilayer perception (MLP) and hybrid radial basis function (HRBF) are considered in this paper. The proposed structure fits the Lidar data classification task well due to the inherent classification efficiency of neural networks and accurate decision-making capability of SVM. A Bayesian classifier and a quadratic classifier were considered for the Lidar data classification task but they failed to offer high prediction accuracy. Furthermore, a single-layered artificial neural network (ANN) classifier was also considered and it failed to offer good accuracy. The parallel ANN architecture proposed in this paper offers high prediction accuracy (98.9%) and is found to be the most suitable architecture for the proposed task of Lidar data classification.

Algorithms↗
PubMed2004

An intelligent service-based network architecture for wearable robots.

We are developing a novel robot concept called the wearable robot. Wearable robots are mobile information devices capable of supporting remote communication and intelligent interaction between networked entities. In this paper, we explore the possible functions of such a robotic network and will present a distributed network architecture based on service components. In order to support the interaction and communication between the components in the wearable robot system, we have developed an intelligent network architecture. This service-based architecture involves three major mechanisms. The first mechanism involves the use of a task coordinator service such that the execution of the services can be managed using a priority queue. The second mechanism enables the system to automatically push the required service proxy to the client intelligently based on certain system-related conditions. In the third mechanism, we allow the system to automatically deliver services based on contextual information. Using a fuzzy-logic-based decision making system, the matching service can determine whether the service should be automatically delivered utilizing the information provided by the service, client, lookup service, and context sensors. An application scenario has been implemented to demonstrate the feasibility of this distributed service-based robot architecture. The architecture is implemented as extensions to the Jini network model.

Algorithms↗
PubMed2004

A subsumptive, hierarchical, and distributed vision-based architecture for smart robotics.

We present a distributed vision-based architecture for smart robotics that is composed of multiple control loops, each with a specialized level of competence. Our architecture is subsumptive and hierarchical, in the sense that each control loop can add to the competence level of the loops below, and in the sense that the loops can present a coarse-to-fine gradation with respect to vision sensing. At the coarsest level, the processing of sensory information enables a robot to become aware of the approximate location of an object in its field of view. On the other hand, at the finest end, the processing of stereo information enables a robot to determine more precisely the position and orientation of an object in the coordinate frame of the robot. The processing in each module of the control loops is completely independent and it can be performed at its own rate. A control Arbitrator ranks the results of each loop according to certain confidence indices, which are derived solely from the sensory information. This architecture has clear advantages regarding overall performance of the system, which is not affected by the "slowest link," and regarding fault tolerance, since faults in one module does not affect the other modules. At this time we are able to demonstrate the utility of the architecture for stereoscopic visual servoing. The architecture has also been applied to mobile robot navigation and can easily be extended to tasks such as "assembly-on-the-fly."

Algorithms↗
PubMed2004

Nest architecture and genetic differentiation in a species complex of Australian stingless bees.

We investigated the taxonomic significance of nest shape and its putative role in speciation in Trigona (Heterotrigona) carbonaria and T. (H.) hockingsi, two sibling species of stingless bee species from eastern Australia. These species are primarily distinguished by their nest architecture, as in all other respects they are nearly identical. We genotyped 130 colonies from six locations in Queensland at 13 microsatellite loci together with 106 additional colonies from six other Indo-Pacific Trigona species. Whether they were present in allopatry or in sympatry, colonies that displayed the T. carbonaria or the T. hockingsi nest architecture could be unambiguously differentiated at the genetic level. However, T. hockingsi colonies were classifiable into two highly differentiated paraphyletic and geographically separate populations, one in northern and one in southern Queensland. These two populations probably belong to two distinct species, T. hockingsi and T. davenporti nov. sp. Our results suggest that nest architecture characters are relevant but not sufficient criteria to identify species in this group. Consequently, modifications of nest architecture are probably not of prime importance in the speciation process of Australian stingless bees, although nest architecture differences probably result from relatively simple mechanisms. The rare interspecific hybrid colonies detected did not display a nest with an intermediate form between T. hockingsi and T. carbonaria.

Animals↗
PubMed2000

A programmable VLSI filter architecture for application in real-time vision processing systems.

An architecture is proposed for the realization of real-time edge-extraction filtering operation in an Address-Event-Representation (AER) vision system. Furthermore, the approach is valid for any 2D filtering operation as long as the convolutional kernel F(p,q) is decomposable into an x-axis and a y-axis component, i.e. F(p,q)=H(p)V(q), for some rotated coordinate system [p,q]. If it is possible to find a coordinate system [p,q], rotated with respect to the absolute coordinate system a certain angle, for which the above decomposition is possible, then the proposed architecture is able to perform the filtering operation for any angle we would like the kernel to be rotated. This is achieved by taking advantage of the AER and manipulating the addresses in real time. The proposed architecture, however, requires one approximation: the product operation between the horizontal component H(p) and vertical component V(q) should be able to be approximated by a signed minimum operation without significant performance degradation. It is shown that for edge-extraction applications this filter does not produce performance degradation. The proposed architecture is intended to be used in a complete vision system known as the Boundary-Contour-System and Feature-Contour-System Vision Model, proposed by Grossberg and collaborators. The present paper proposes the architecture, provides a circuit implementation using MOS transistors operated in weak inversion, and shows behavioral simulation results at the system level operation and electrical simulation and experimental results at the circuit level operation of some critical subcircuits.

Computer Simulation↗
PubMed1997

Bias/variance analyses of mixtures-of-experts architectures.

This article investigates the bias and variance of mixtures-of-experts (ME) architectures. The variance of an ME architecture can be expressed as the sum of two terms: the first term is related to the variances of the expert networks that comprise the architecture and the second term is related to the expert networks' covariances. One goal of this article is to study and quantify a number of properties of ME architectures via the metrics of bias and variance. A second goal is to clarify the relationships between this class of systems and other systems that have recently been proposed. It is shown that in contrast to systems that produce unbiased experts whose estimation errors are uncorrelated, ME architectures produce biased experts whose estimates are negatively correlated.

Analysis of Variance↗
PubMed2000

Properties of growing trabecular ovine bone. Part II: architectural and mechanical properties.

We aimed to highlight the relationship between age and the architectural properties of trabecular bone, to outline the patterns in which the variations in these properties take place, and to investigate the influence of the architecture on the mechanical properties of trabecular bone in growing animals. We studied 30 lambs in three age groups and 20 sheep in two age groups. Cubes of subchondral bone were cut from the proximal tibia according to a standardised protocol. They were serially sectioned and their architectural properties were determined. Similar cubes were obtained from the identical anatomical position of the contralateral tibia and their compressive mechanical properties measured. The values obtained from the skeletally immature and mature individuals were compared. Multiple regression analyses were performed between the architectural and the mechanical properties. The bone volume fraction, the mean trabecular volume, the architectural and the mechanical anisotropy, the elastic modulus, the bone strength, the energy absorption to failure, and the elastic energy correlated positively with increasing age whereas the connectivity density, the bone surface density, the ultimate strain, the absorption of viscoelastic energy and the relative loss of energy correlated inversely. The values of all variables were significantly different in the skeletally mature and immature groups. We determined the patterns in which the variations took place. The bone volume fraction of the trabecular bone tissue was found to be the major predictor of its compressive mechanical properties. Together with the mean trabecular volume and the bone surface density, it explained 81% of the variations in the compressive elastic modulus of specimens obtained from the contralateral tibiae.

Age Factors↗
PubMed2026

Pervasive context-dependent effects in the genetic architecture of complex and quantitative traits revealed by a powerful multiparent mapping population in yeast.

The genetic dissection of complex traits remains a major challenge in basic and biomedical research, but is essential for understanding the molecular pathways that shape phenotypic variation and for developing predictive models of trait and disease susceptibility. Here, we leverage a novel multiparent mapping population of budding yeast, CYClones, comprising 9,344 haploid strains derived from eight genetically diverse founders (~270,000 SNVs, ~ 1 per 44 bp, capturing 56% of common variants and 32% of all variants with a minor allele frequency greater than 0.005 in the global population), to identify quantitative trait loci (QTL) and systematically investigate the genetic architecture of growth rates across ten environmental conditions. In total, we identified 349 QTL (ranging from 18 to 49 QTL per growth condition) that explained between 60% and 100% of narrow sense heritability across traits. The high power and resolution of CYClones revealed that growth traits exhibited distinct, condition-specific genetic architectures with extensive allelic heterogeneity, where a QTL was the result of multiple tightly linked causal variants. We also observed pleiotropy among QTL with complex, trait-dependent allele effects that are also consistent with allelic heterogeneity. Genetic complexity varied widely, with some traits showing nearly Mendelian architectures, while others were highly polygenic. Introgressed loci played a prominent role in the landscape of growth rate QTL, including a QTL localized to a 2.4 kb interval in the PCA1 cadmium transporter that explains 72% of variation in cadmium resistance and is largely driven by an introgression, and a non-additive interaction between the GAL3 regulator and introgressed GAL1/7/10 alleles, extending a previously described three-locus GAL-pathway incompatibility to a four-locus interaction. In both cadmium and galactose conditions, we show that allelic variation at a small number of loci stratifies the population into regulatory or physiological subgroups, each with distinct genetic architectures, a specific manifestation of epistasis we term allele-dependent stratification. Collectively, our results provide novel insights into the genetics of growth rates in budding yeast, the architectural features of genetic complexity, and demonstrate that CYClones is a powerful platform for revealing the molecular basis of complex trait variation.

Quantitative Trait Loci↗