Generic systolic array for genetic algorithms

The authors present a systolic design for a simple GA mechanism which provides high throughput and unidirectional pipelining by exploiting the inherent parallelism in the genetic operators. The design computes in O(N+G) time steps using O(N2) cells where N is the population size and G is the chromosome length. The area of the device is independent of the chromosome length and so can be easily scaled by replicating the arrays or by employing fine-grain migration. The array is generic in the sense that it does not rely on the fitness function and can be used as an accelerator for any GA application using uniform crossover between pairs of chromosomes. The design can also be used in hybrid systems as an add-on to complement existing designs and methods for fitness function acceleration and island-style population management

The curious case of the camelthorn: competition, coexistence and nest-site limitation in a multispecies mutualism

Myrmecophyte plants house ants in domatia in exchange for protection from herbivores. Ant-myrmecophyte mutualisms exhibit two general patterns due to competition between ants for plant occupancy: i) domatia nest-sites are a limiting resource and ii) each individual plant hosts one ant species at a time. However, individual camelthorn trees (Vachellia erioloba) typically host two to four ant species simultaneously, often coexisting in adjacent domatia on the same branch. Such fine-grain spatial coexistence brings into question the conventional wisdom on ant-myrmecophyte mutualisms. Camelthorn ants appear not to be nest-site limited, despite low abundance of suitable domatia, and have random distributions of nest-sites within and across trees. These patterns suggest a lack of competition between ants for domatia and contrast strongly with other ant-myrmecophyte systems. Comparison of this unusual case with others suggests that spatial scale is crucial to coexistence or competitive exclusion involving multiple ant species. Furthermore, coexistence may be facilitated when co-occurring ant species diverge strongly on at least one niche axis. Our conclusions provide recommendations for future ant-myrmecophyte research, particularly in utilising multispecies systems to further our understanding of mutualism biology.

Tectonic implications of a paleomagnetic study of the Sarmiento Ophiolitic Complex, southern Chile

A paleomagnetic study was carried out on the Late Jurassic Sarmiento Ophiolitic Complex (SOC) exposed in the Magallanes fold and thrust belt in the southern Patagonian Andes (southern Chile). This complex, mainly consisting of a thick succession of pillow-lavas, sheeted dikes and gabbros, is a seafloor remnant of the Late Jurassic to Early Cretaceous Rocas Verdes basin that developed along the south-western margin of South America. Stepwise thermal and alternating field demagnetization permitted the isolation of a post-folding characteristic remanence, apparently carried by fine grain (SD?) magnetite, both in the pillow-lavas and dikes. The mean ""in situ"" direction for the SOC is Dec: 286.9 degrees, Inc: -58.5 degrees, alpha-95: 6.9 degrees, N: 11 (sites). Rock magnetic properties, petrography and whole-rock K-Ar ages in the same rocks are interpreted as evidence of correlation between remanence acquisition and a greenschist facies metamorphic overprint that must have occurred during latest stages or after closure and tectonic inversion of the basin in the Late Cretaceous. The mean remanence direction is anomalous relative to the expected Late Cretaceous direction from stable South America. Particularly, a declination anomaly over 50 degrees is suggestively similar to paleomagnetically interpreted counter clockwise rotations found in thrust slices of the Jurassic El Quemado Fm. located over 100 km north of the study area in Argentina. Nevertheless, a significant ccw rotation of the whole SOC is difficult to reconcile with geologic evidence and paleogeographic models that suggest a narrow back-arc basin sub-parallel to the continental margin. A rigid-body 30 degrees westward tilting of the SOC block around a horizontal axis trending NNW, is considered a much simpler explanation, being consistent with geologic evidence. This may have occurred as a consequence of inverse reactivation of old normal faults, which limit both the SOC exposures and the Cordillera Sarmiento to the East. The age of tilting is unknown but it must postdate remanence acquisition in the Late Cretaceous. Two major orogenic events of the southern Patagonian Andes, in the Eocene (ca. 42 Ma) and Middle Miocene (ca. 12 Ma), respectively, could have caused the proposed tilting. (C) 2008 Elsevier B.V. All rights reserved.

Caracterização de compósitos Nb-20%cu obtidos por moagem de alta energia e sinterizados por fase líquida

In this work, was studied the formation of a composite of the refractory metal niobium with copper, through the process of high-energy milling and liquid phase sintering. The HEM can be used to synthesize composite powders with high homogeneity and fine size particle distribution. It may also produce the solid solubility in immiscible systems such as Nb-Cu, or extend the solubility of systems with limited solubility. Therefore, in the immiscible system Cu-Nb, the high-energy milling was successfully used to obtain the composite powder particles. Initially, the formation of composite particles during the HEM and the effect of preparation technique on the microstructure of the material was evaluated. Four loads of Nb and Cu powders containing 20%wt Cu were synthesized by MAE in a planetary type ball mill under different periods of grinding. The influence of grinding time on the metal particles is evaluated during the process by the withdrawal of samples at intermediate times of milling. After compaction under different forces, the samples were sintered in a vacuum furnace. The liquid phase sintering of these samples prepared by HEM produced a homogeneous and fine grained. The composite particles forming the sintered samples are the addition of a hard phase (Nb) with a high melting point, and a ductile phase (Cu) with low melting point and high thermal and electrical conductivities. Based on these properties, the Nb-Cu system is a potential material for many applications, such as electrical contacts, welding electrodes, coils for generating high magnetic fields, heat sinks and microwave absorbers, which are coupled to electronic devices. The characterization techniques used in this study, were laser granulometry, used to evaluate the homogeneity and particle size, and the X-ray diffraction, in the phase identification and to analyze the crystalline structure of the powders during milling. The morphology and dispersion of the phases in the composite powder particles, as well the microstructures of the sintered samples, were observed by scanning electron microscopy (SEM). Subsequently, the sintered samples are evaluated for density and densification. And finally, they were characterized by techniques of measuring the electrical conductivity and microhardness, whose properties are analyzed as a function of the parameters for obtaining the composite

Sistema de alimentação de livre escolha com milho em grão ou moído e concentrado proteico para frangos de corte

O experimento teve como objetivo avaliar os sistemas de alimentação convencional ou de livre escolha, utilizando 6 dietas a base de milho em grão ou moído e concentrado protéico sobre o desempenho de frangos de corte do l° ao 45° dia de idade. O delineamento experimental foi inteiramente casualizado em esquema fatorial 6x2 (6 tratamentos e 2 sexos), com 3 repetições de 30 aves. Os tratamentos foram: T1-Milho moído + Concentrado do 1° ao 45° dia, fornecidos misturados; T2-Milho moído + Concentrado do 1° ao 45° dia, fornecidos separados em 2 comedouros; T3- Milho moído + Concentrado, fornecidos misturados, do l° ao 14° dia e do 15° ao 45° dia, milho em grão + concentrado, fornecidos misturados; T4 Milho moído + Concentrado, fornecidos misturados, do 1° ao 14° dia e do 15° ao 45° dia, milho em grão + concentrado, fornecidos separados; T5 - Milho moído + Concentrado, fornecidos misturados do 1° ao 21° dia e do 22° ao 45° dia, milho em grão + concentrado, fornecidos misturados; T6- Milho moído + Concentrado, fornecidos separados, do l ° ao 21° dia e do 22° ao 45° dia, milho em grão + concentrado, fornecidos misturados. Pêlos resultados e condições que realizou-se o presente trabalho conclui-se que: o milho em grão pode ser fornecido a frangos de corte misturado ao concentrado a partir do 15° dia de idade; o milho moído não proporcionou bons resultados de desempenho no programa de alimentação de livre escolha: as aves alimentadas com milho em grão apresentaram maior peso de moela, bem como acumularam mais gordura na carcaça; autilização de milho em grão fornecido junto ao concentrado, embora tenha proporcionado desempenho ligeiramente inferior à ração convencional, pode ser considerado satisfarório, sendo uma alternativa para pequenos produtores avícolas.

Correlação entre propriedades petrográficas e comportamento tecnológico e de alterabilidade das rochas ornamentais silicáticas Diamante Negro (BA), Ocre Itabira e Banco Galaxy (ES)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Produção e caracterização física e mecânica de compósito plástico-madeira

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Interactive quadrangulation with reeb atlases and connectivity textures

Creating high-quality quad meshes from triangulated surfaces is a highly nontrivial task that necessitates consideration of various application specific metrics of quality. In our work, we follow the premise that automatic reconstruction techniques may not generate outputs meeting all the subjective quality expectations of the user. Instead, we put the user at the center of the process by providing a flexible, interactive approach to quadrangulation design. By combining scalar field topology and combinatorial connectivity techniques, we present a new framework, following a coarse to fine design philosophy, which allows for explicit control of the subjective quality criteria on the output quad mesh, at interactive rates. Our quadrangulation framework uses the new notion of Reeb atlas editing, to define with a small amount of interactions a coarse quadrangulation of the model, capturing the main features of the shape, with user prescribed extraordinary vertices and alignment. Fine grain tuning is easily achieved with the notion of connectivity texturing, which allows for additional extraordinary vertices specification and explicit feature alignment, to capture the high-frequency geometries. Experiments demonstrate the interactivity and flexibility of our approach, as well as its ability to generate quad meshes of arbitrary resolution with high-quality statistics, while meeting the user's own subjective requirements.

Computational methods for the analysis of protein structure and function

The vast majority of known proteins have not yet been experimentally characterized and little is known about their function. The design and implementation of computational tools can provide insight into the function of proteins based on their sequence, their structure, their evolutionary history and their association with other proteins. Knowledge of the three-dimensional (3D) structure of a protein can lead to a deep understanding of its mode of action and interaction, but currently the structures of <1% of sequences have been experimentally solved. For this reason, it became urgent to develop new methods that are able to computationally extract relevant information from protein sequence and structure. The starting point of my work has been the study of the properties of contacts between protein residues, since they constrain protein folding and characterize different protein structures. Prediction of residue contacts in proteins is an interesting problem whose solution may be useful in protein folding recognition and de novo design. The prediction of these contacts requires the study of the protein inter-residue distances related to the specific type of amino acid pair that are encoded in the so-called contact map. An interesting new way of analyzing those structures came out when network studies were introduced, with pivotal papers demonstrating that protein contact networks also exhibit small-world behavior. In order to highlight constraints for the prediction of protein contact maps and for applications in the field of protein structure prediction and/or reconstruction from experimentally determined contact maps, I studied to which extent the characteristic path length and clustering coefficient of the protein contacts network are values that reveal characteristic features of protein contact maps. Provided that residue contacts are known for a protein sequence, the major features of its 3D structure could be deduced by combining this knowledge with correctly predicted motifs of secondary structure. In the second part of my work I focused on a particular protein structural motif, the coiled-coil, known to mediate a variety of fundamental biological interactions. Coiled-coils are found in a variety of structural forms and in a wide range of proteins including, for example, small units such as leucine zippers that drive the dimerization of many transcription factors or more complex structures such as the family of viral proteins responsible for virus-host membrane fusion. The coiled-coil structural motif is estimated to account for 5-10% of the protein sequences in the various genomes. Given their biological importance, in my work I introduced a Hidden Markov Model (HMM) that exploits the evolutionary information derived from multiple sequence alignments, to predict coiled-coil regions and to discriminate coiled-coil sequences. The results indicate that the new HMM outperforms all the existing programs and can be adopted for the coiled-coil prediction and for large-scale genome annotation. Genome annotation is a key issue in modern computational biology, being the starting point towards the understanding of the complex processes involved in biological networks. The rapid growth in the number of protein sequences and structures available poses new fundamental problems that still deserve an interpretation. Nevertheless, these data are at the basis of the design of new strategies for tackling problems such as the prediction of protein structure and function. Experimental determination of the functions of all these proteins would be a hugely time-consuming and costly task and, in most instances, has not been carried out. As an example, currently, approximately only 20% of annotated proteins in the Homo sapiens genome have been experimentally characterized. A commonly adopted procedure for annotating protein sequences relies on the "inheritance through homology" based on the notion that similar sequences share similar functions and structures. This procedure consists in the assignment of sequences to a specific group of functionally related sequences which had been grouped through clustering techniques. The clustering procedure is based on suitable similarity rules, since predicting protein structure and function from sequence largely depends on the value of sequence identity. However, additional levels of complexity are due to multi-domain proteins, to proteins that share common domains but that do not necessarily share the same function, to the finding that different combinations of shared domains can lead to different biological roles. In the last part of this study I developed and validate a system that contributes to sequence annotation by taking advantage of a validated transfer through inheritance procedure of the molecular functions and of the structural templates. After a cross-genome comparison with the BLAST program, clusters were built on the basis of two stringent constraints on sequence identity and coverage of the alignment. The adopted measure explicity answers to the problem of multi-domain proteins annotation and allows a fine grain division of the whole set of proteomes used, that ensures cluster homogeneity in terms of sequence length. A high level of coverage of structure templates on the length of protein sequences within clusters ensures that multi-domain proteins when present can be templates for sequences of similar length. This annotation procedure includes the possibility of reliably transferring statistically validated functions and structures to sequences considering information available in the present data bases of molecular functions and structures.

Ontologies and Methods for Interoperability of Engineering Analysis Models (EAMS) in an E-Design Environment

ABSTRACT ONTOLOGIES AND METHODS FOR INTEROPERABILITY OF ENGINEERING ANALYSIS MODELS (EAMS) IN AN E-DESIGN ENVIRONMENT SEPTEMBER 2007 NEELIMA KANURI, B.S., BIRLA INSTITUTE OF TECHNOLOGY AND SCIENCES PILANI INDIA M.S., UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Ian Grosse Interoperability is the ability of two or more systems to exchange and reuse information efficiently. This thesis presents new techniques for interoperating engineering tools using ontologies as the basis for representing, visualizing, reasoning about, and securely exchanging abstract engineering knowledge between software systems. The specific engineering domain that is the primary focus of this report is the modeling knowledge associated with the development of engineering analysis models (EAMs). This abstract modeling knowledge has been used to support integration of analysis and optimization tools in iSIGHT FD , a commercial engineering environment. ANSYS , a commercial FEA tool, has been wrapped as an analysis service available inside of iSIGHT-FD. Engineering analysis modeling (EAM) ontology has been developed and instantiated to form a knowledge base for representing analysis modeling knowledge. The instances of the knowledge base are the analysis models of real world applications. To illustrate how abstract modeling knowledge can be exploited for useful purposes, a cantilever I-Beam design optimization problem has been used as a test bed proof-of-concept application. Two distinct finite element models of the I-beam are available to analyze a given beam design- a beam-element finite element model with potentially lower accuracy but significantly reduced computational costs and a high fidelity, high cost, shell-element finite element model. The goal is to obtain an optimized I-beam design at minimum computational expense. An intelligent KB tool was developed and implemented in FiPER . This tool reasons about the modeling knowledge to intelligently shift between the beam and the shell element models during an optimization process to select the best analysis model for a given optimization design state. In addition to improved interoperability and design optimization, methods are developed and presented that demonstrate the ability to operate on ontological knowledge bases to perform important engineering tasks. One such method is the automatic technical report generation method which converts the modeling knowledge associated with an analysis model to a flat technical report. The second method is a secure knowledge sharing method which allocates permissions to portions of knowledge to control knowledge access and sharing. Both the methods acting together enable recipient specific fine grain controlled knowledge viewing and sharing in an engineering workflow integration environment, such as iSIGHT-FD. These methods together play a very efficient role in reducing the large scale inefficiencies existing in current product design and development cycles due to poor knowledge sharing and reuse between people and software engineering tools. This work is a significant advance in both understanding and application of integration of knowledge in a distributed engineering design framework.

Diet Roughage Ingredients for Newly Weaned Calves

Several commodity feeds that are high in fiber are available that may substitute for corn cobs in a complete starting ration. This study was designed to evaluate the use of soyhulls and sunflower meal as substitutes for corncobs as a roughage source for newly weaned calves. One-hundred-and-fifty calves from the ISU Rhodes Research Farm were weaned, weighed, sorted by sex, and stratified by weight to eight pens. Two pens of each sex were assigned to one of two diet treatments. Calves fed the corncob diet consumed two pounds more feed dry matter, gained 1.5 pounds more per day, and were more efficient the first 14 days on feed. The soyhull diet was quite fine in particle size, and some feed particle separation occurred in the bunk. Some compensatory performance may have occurred with the soyhull diet the second 14 days on feed, although no statistical differences existed. This suggests that palatability, feed presentation, and bunk characteristics are important considerations in selecting roughage sources for complete starting diets for newly weaned calves.

Highly accurate evaluation of GPS synchronization for TDOA localization

Clock synchronization is critical for the operation of a distributed wireless network system. In this paper we investigate on a method able to evaluate in real time the synchronization offset between devices down to nanoseconds (as needed for positioning). The method is inspired by signal processing algorithms and relies on fine-grain time information obtained during the reconstruction of the signal at the receiver. Applying the method to a GPS-synchronized system show that GPS-based synchronization has high accuracy potential but still suffers from short-term clock drift, which limits the achievable localization error.

Methodology for GPS Synchronization Evaluation with High Accuracy

Clock synchronization in the order of nanoseconds is one of the critical factors for time-based localization. Currently used time synchronization methods are developed for the more relaxed needs of network operation. Their usability for positioning should be carefully evaluated. In this paper, we are particularly interested in GPS-based time synchronization. To judge its usability for localization we need a method that can evaluate the achieved time synchronization with nanosecond accuracy. Our method to evaluate the synchronization accuracy is inspired by signal processing algorithms and relies on fine grain time information. The method is able to calculate the clock offset and skew between devices with nanosecond accuracy in real time. It was implemented using software defined radio technology. We demonstrate that GPS-based synchronization suffers from remaining clock offset in the range of a few hundred of nanoseconds but the clock skew is negligible. Finally, we determine a corresponding lower bound on the expected positioning error.

Sedimentary facies, clay mineralogy and geochemistry of the Paleogene sediments of ODP Site 105-647

Claystones immediately overlying the early Eocene age ocean-floor basalt, cored at Ocean Drilling Program (ODP) Site 647, underwent hydrothermal and thermal alterations originating from the basalt, which resulted in changes in both the mineralogical and chemical composition of the sediments. Chlorites and higher magnesium and iron concentrations were found in the lowermost sediment sequence. Upcore, changes in the bulk chemical composition of the sediments become smaller, when compensated for variations in the carbonate content originating from biogenic and authigenic components. Chlorite disappears upcore, but still only part of the swelling clay minerals have survived the thermal influence. Thirty meters above the basalt, the clay mineralogy and chemical composition become uniform throughout the Paleogene section. Iron-rich smectites (i.e., nontronitic types), totally dominate the clay mineral assemblage. Biogenic components, responsible for the dominant part of the calcite and cristobalite contents, vary in amount in the upper part, and so do the authigenic carbonate and sulfide contents. Detrital components, such as kaolinite, illite, quartz, and feldspars, make up a very small proportion of the sediment record. The nontronitic smectites are believed to be authigenic, formed by a supply of iron from the continuous formation of ocean-floor basalt in the ridge area that reacted with the detrital and biogenic silicates and alumina silicates.

Environmental magnetism, geochemical measurements and colour reflectance of two sediment cores: GeoB4905-4 off Cameroon and GeoB4906-3 off Gabon

We combine environmental magnetism, geochemical measurements and colour reflectance to study two late Quaternary sediment cores: GeoB 4905-4 at 2° 30 N off Cameroon and GeoB 4906-3 at 0° 44 N off Gabon. This area is suitable for investigating precipitation changes over Central and West Africa because of its potential to record input of aeolian and fluvial sediments. Three magnetozones representing low and high degree of alteration of the primary rock magnetic signals were identified. The magnetic signature is dominated by fine-grained magnetite, while residual haematite prevails in the reduced intervals, showing increase in concentration and fine grain size at wet intervals. Our records also show millennial-scale changes in climate during the last glacial and interglacial cycles. At the northern location, the past 5.5 ka are marked by high-frequency oscillations of Ti and colour reflectance, which suggests aeolian input and hence aridity. The southern location remains under the influence of the Intertropical Convergence Zone and thus did not register aeolian signals. The millennial-scale climatic signals indicate that drier and/or colder conditions persisted during the late Holocene and are synchronous with the 900 a climatic cycles observed in Northern Hemisphere ice core records.