Knowledge-Based Task Structure Planning for an Information Gathering Agent

An effective solution to model and apply planning domain knowledge for deliberation and action in probabilistic, agent-oriented control is presented. Specifically, the addition of a task structure planning component and supporting components to an agent-oriented architecture and agent implementation is described. For agent control in risky or uncertain environments, an approach and method of goal reduction to task plan sets and schedules of action is presented. Additionally, some issues related to component-wise, situation-dependent control of a task planning agent that schedules its tasks separately from planning them are motivated and discussed.

Scalable Raid Storage Based on the Structure of Multimedia File.

In professional video production, users have to access to huge multimedia files simultaneously in an error-free environment, this restriction force the use of expensive disk architectures for video servers. Previous researches proposed different RAID systems for each specific task (ingest, editing, file, play-out, etc.). Video production companies have to acquire different servers with different RAIDs systems in order to support each task in the production workflow. The solution has multiples disadvantages, duplicated material in several RAIDs, duplicated material for different qualities, transfer and transcoding processes, etc. In this work, an architecture for video servers based on the spreading of JPEG200 data in different RAIDs is presented, each individual part of the data structure goes to a specific RAID type depending on the effect that produces the data on the overall image quality, the method provide a redundancy correlated with the data rank. The global storage can be used in all the different tasks of the production workflow saving disk space, redundant files and transfers procedures.

Comparison of Airborne Laser Scanning Methods for Estimating Forest Structure Indicators Based on Lorenz Curves

The purpose of this study was to compare a number of state-of-the-art methods in airborne laser scan- ning (ALS) remote sensing with regards to their capacity to describe tree size inequality and other indi- cators related to forest structure. The indicators chosen were based on the analysis of the Lorenz curve: Gini coefficient ( GC ), Lorenz asymmetry ( LA ), the proportions of basal area ( BALM ) and stem density ( NSLM ) stocked above the mean quadratic diameter. Each method belonged to one of these estimation strategies: (A) estimating indicators directly; (B) estimating the whole Lorenz curve; or (C) estimating a complete tree list. Across these strategies, the most popular statistical methods for area-based approach (ABA) were used: regression, random forest (RF), and nearest neighbour imputation. The latter included distance metrics based on either RF (NN–RF) or most similar neighbour (MSN). In the case of tree list esti- mation, methods based on individual tree detection (ITD) and semi-ITD, both combined with MSN impu- tation, were also studied. The most accurate method was direct estimation by best subset regression, which obtained the lowest cross-validated coefficients of variation of their root mean squared error CV(RMSE) for most indicators: GC (16.80%), LA (8.76%), BALM (8.80%) and NSLM (14.60%). Similar figures [CV(RMSE) 16.09%, 10.49%, 10.93% and 14.07%, respectively] were obtained by MSN imputation of tree lists by ABA, a method that also showed a number of additional advantages, such as better distributing the residual variance along the predictive range. In light of our results, ITD approaches may be clearly inferior to ABA with regards to describing the structural properties related to tree size inequality in for- ested areas.

Structure of Alluvial Valleys from 3-D Gravity Inversion: The Low Andarax Valley (Almería, Spain) Test Case

This paper presents a gravimetric study (based on 382 gravimetric stations in an area about 32 km2) of a nearly flat basin: the Low Andarax valley. This alluvial basin, close to its river mouth, is located in the extreme south of the province of Almería and coincides with one of the existing depressions in the Betic Cordillera. The paper presents new methodological work to adapt a published inversion approach (GROWTH method) to the case of an alluvial valley (sedimentary stratification, with density increase downward). The adjusted 3D density model reveals several features in the topography of the discontinuity layers between the calcareous basement (2,700 kg/m3) and two sedimentary layers (2,400 and 2,250 kg/m3). We interpret several low density alignments as corresponding to SE faults striking about N140?145°E. Some detected basement elevations (such as the one, previously known by boreholes, in Viator village) are apparently connected with the fault pattern. The outcomes of this work are: (1) new gravimetric data, (2) new methodological options, and (3) the resulting structural conclusions.

Liquid crystal temperature sensor based on a micrometric structure and a metallic nanometric layer

This letter presents a novel temperature sensor, which consists of an interdigitated comb electrode structure with a micrometric-scale size, nanometric metallic layer, and nematic liquid crystal (NLC) film. This sensor exploits the permittivity dependence of the NLC with temperature and principle of electrical conductivity above the percolation threshold in thin film metallic layers. The latter has been demonstrated to increase the temperature sensitivity considerably. The high impedance input reduces the power dissipation, and the high enough voltage output makes it easy to measure the output signal with high precision. The operation principle and fabrication process as well as the characterization of the temperature sensor are presented. Experimental results show that the device offers a sensitivity of 9 mV/°C and is dependent on the applied voltage. This is six times greater than the same structure without the use of a nanometric layer.

UWB Monocycle Generator based on the non-linear effects of an SOA-integrated structure

In this letter, we propose and experimentally demonstrate a novel and single structure to generate ultra-wideband (UWB) pulses by means of the cross-phase modulation present in a semiconductor optical amplifier unified structure. The key components of this system is an integrated Mach-Zehnder interferometer with two semiconductor optical amplifiers and an optical processing unit. The fusion of these two components permits the generation and customization of UWB monocycle pulses. The polarity of the output pulses is easily modified through the single selection of a specific input port. Moreover, the capacity of transmitting several data sequences is demonstrated and the potentiality to adapt the system to different modulation formats is analyzed.

A unified theory of carcinogenesis based on order–disorder transitions in DNA structure as studied in the human ovary and breast

Fourier transform-infrared/statistics models demonstrate that the malignant transformation of morphologically normal human ovarian and breast tissues involves the creation of a high degree of structural modification (disorder) in DNA, before restoration of order in distant metastases. Order–disorder transitions were revealed by methods including principal components analysis of infrared spectra in which DNA samples were represented by points in two-dimensional space. Differences between the geometric sizes of clusters of points and between their locations revealed the magnitude of the order–disorder transitions. Infrared spectra provided evidence for the types of structural changes involved. Normal ovarian DNAs formed a tight cluster comparable to that of normal human blood leukocytes. The DNAs of ovarian primary carcinomas, including those that had given rise to metastases, had a high degree of disorder, whereas the DNAs of distant metastases from ovarian carcinomas were relatively ordered. However, the spectra of the metastases were more diverse than those of normal ovarian DNAs in regions assigned to base vibrations, implying increased genetic changes. DNAs of normal female breasts were substantially disordered (e.g., compared with the human blood leukocytes) as were those of the primary carcinomas, whether or not they had metastasized. The DNAs of distant breast cancer metastases were relatively ordered. These findings evoke a unified theory of carcinogenesis in which the creation of disorder in the DNA structure is an obligatory process followed by the selection of ordered, mutated DNA forms that ultimately give rise to metastases.

Toward optimized carbohydrate-based anticancer vaccines: Epitope clustering, carrier structure, and adjuvant all influence antibody responses to Lewisy conjugates in mice

The feasibility of using carbohydrate-based vaccines for the immunotherapy of cancer is being actively explored at the present time. Although a number of clinical trials have already been conducted with glycoconjugate vaccines, the optimal design and composition of the vaccines has yet to be determined. Among the candidate antigens being examined is Lewisy (Ley), a blood group-related antigen that is overexpressed on the majority of human carcinomas. Using Ley as a model for specificity, we have examined the role of epitope clustering, carrier structure, and adjuvant on the immunogenicity of Ley conjugates in mice. A glycolipopeptide containing a cluster of three contiguous Ley-serine epitopes and the Pam3Cys immunostimulating moiety was found to be superior to a similar construct containing only one Ley-serine epitope in eliciting antitumor cell antibodies. Because only IgM antibodies were produced by this vaccine, the effect on immunogenicity of coupling the glycopeptide to keyhole limpet hemocyanin was examined; although both IgM and IgG antibodies were formed, the antibodies reacted only with the immunizing structure. Reexamination of the clustered Ley-serine Pam3Cys conjugate with the adjuvant QS-21 resulted in the identification of both IgG and IgM antibodies reacting with tumor cells, thus demonstrating the feasibility of an entirely synthetic carbohydrate-based anticancer vaccine in an animal model.

PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

As the number of protein folds is quite limited, a mode of analysis that will be increasingly common in the future, especially with the advent of structural genomics, is to survey and re-survey the finite parts list of folds from an expanding number of perspectives. We have developed a new resource, called PartsList, that lets one dynamically perform these comparative fold surveys. It is available on the web at http://bioinfo.mbb.yale.edu/partslist and http://www.partslist.org. The system is based on the existing fold classifications and functions as a form of companion annotation for them, providing ‘global views’ of many already completed fold surveys. The central idea in the system is that of comparison through ranking; PartsList will rank the approximately 420 folds based on more than 180 attributes. These include: (i) occurrence in a number of completely sequenced genomes (e.g. it will show the most common folds in the worm versus yeast); (ii) occurrence in the structure databank (e.g. most common folds in the PDB); (iii) both absolute and relative gene expression information (e.g. most changing folds in expression over the cell cycle); (iv) protein–protein interactions, based on experimental data in yeast and comprehensive PDB surveys (e.g. most interacting fold); (v) sensitivity to inserted transposons; (vi) the number of functions associated with the fold (e.g. most multi-functional folds); (vii) amino acid composition (e.g. most Cys-rich folds); (viii) protein motions (e.g. most mobile folds); and (ix) the level of similarity based on a comprehensive set of structural alignments (e.g. most structurally variable folds). The integration of whole-genome expression and protein–protein interaction data with structural information is a particularly novel feature of our system. We provide three ways of visualizing the rankings: a profiler emphasizing the progression of high and low ranks across many pre-selected attributes, a dynamic comparer for custom comparisons and a numerical rankings correlator. These allow one to directly compare very different attributes of a fold (e.g. expression level, genome occurrence and maximum motion) in the uniform numerical format of ranks. This uniform framework, in turn, highlights the way that the frequency of many of the attributes falls off with approximate power-law behavior (i.e. according to V–b, for attribute value V and constant exponent b), with a few folds having large values and most having small values.

Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes

Human rhinoviruses, the most important etiologic agents of the common cold, are messenger-active single-stranded monocistronic RNA viruses that have evolved a highly complex cascade of proteolytic processing events to control viral gene expression and replication. Most maturation cleavages within the precursor polyprotein are mediated by rhinovirus 3C protease (or its immediate precursor, 3CD), a cysteine protease with a trypsin-like polypeptide fold. High-resolution crystal structures of the enzyme from three viral serotypes have been used for the design and elaboration of 3C protease inhibitors representing different structural and chemical classes. Inhibitors having α,β-unsaturated carbonyl groups combined with peptidyl-binding elements specific for 3C protease undergo a Michael reaction mediated by nucleophilic addition of the enzyme’s catalytic Cys-147, resulting in covalent-bond formation and irreversible inactivation of the viral protease. Direct inhibition of 3C proteolytic activity in virally infected cells treated with these compounds can be inferred from dose-dependent accumulations of viral precursor polyproteins as determined by SDS/PAGE analysis of radiolabeled proteins. Cocrystal-structure-assisted optimization of 3C-protease-directed Michael acceptors has yielded molecules having extremely rapid in vitro inactivation of the viral protease, potent antiviral activity against multiple rhinovirus serotypes and low cellular toxicity. Recently, one compound in this series, AG7088, has entered clinical trials.

The crystal structure of an N-terminal two-domain fragment of vascular cell adhesion molecule 1 (VCAM-1): a cyclic peptide based on the domain 1 C-D loop can inhibit VCAM-1-alpha 4 integrin interaction.

Vascular cell adhesion molecule 1 (VCAM-1) represents a structurally and functionally distinct class of immunoglobulin superfamily molecules that bind leukocyte integrins and are involved in inflammatory and immune functions. X-ray crystallography defines the three-dimensional structure of the N-terminal two-domain fragment that participates in ligand binding. Residues in domain 1 important for ligand binding reside in the C-D loop, which projects markedly from one face of the molecule near the contact between domains 1 and 2. A cyclic peptide that mimics this loop inhibits binding of alpha 4 beta 1 integrin-bearing cells to VCAM-1. These data demonstrate how crystallographic structural information can be used to design a small molecule inhibitor of biological function.

Definition of a metal-dependent/Li(+)-inhibited phosphomonoesterase protein family based upon a conserved three-dimensional core structure.

Inositol polyphosphate 1-phosphatase, inositol monophosphate phosphatase, and fructose 1,6-bisphosphatase share a sequence motif, Asp-Pro-(Ile or Leu)-Asp-(Gly or Ser)-(Thr or Ser), that has been shown by crystallographic and mutagenesis studies to bind metal ions and participate in catalysis. We compared the six alpha-carbon coordinates of this motif from the crystal structures of these three phosphatases and found that they are superimposable with rms deviations ranging from 0.27 to 0.60 A. Remarkably, when these proteins were aligned by this motif a common core structure emerged, defined by five alpha-helices and 11 beta-strands comprising 155 residues having rms deviations ranging from 1.48 to 2.66 A. We used the superimposed structures to align the sequences within the common core, and a distant relationship was observed suggesting a common ancestor. The common core was used to align the sequences of several other proteins that share significant similarity to inositol monophosphate phosphatase, including proteins encoded by fungal qa-X and qutG, bacterial suhB and cysQ (identical to amtA), and yeast met22 (identical to hal2). Evolutionary comparison of the core sequences indicate that five distinct branches exist within this family. These proteins share metal-dependent/Li(+)-sensitive phosphomonoesterase activity, and each predicted tree branch exhibits unique substrate specificity. Thus, these proteins define an ancient structurally conserved family involved in diverse metabolic pathways including inositol signaling, gluconeogenesis, sulfate assimilation, and possibly quinone metabolism. Furthermore, we suggest that this protein family identifies candidate enzymes to account for both the therapeutic and toxic actions of Li+ as it is used in patients treated for manic depressive disease.

Interplay Between Structure, Stoichiometry, and Electron Transfer Dynamics in SILAR-based Quantum Dot-Sensitized Oxides

We quantify the rate and efficiency of picosecond electron transfer (ET) from PbS nanocrystals, grown by successive ionic layer adsorption and reaction (SILAR), into a mesoporous SnO2 support. Successive SILAR deposition steps allow for stoichiometry- and size-variation of the QDs, characterized using transmission electron microscopy. Whereas for sulfur-rich (p-type) QD surfaces substantial electron trapping at the QD surface occurs, for lead-rich (n-type) QD surfaces, the QD trapping channel is suppressed and the ET efficiency is boosted. The ET efficiency increase achieved by lead-rich QD surfaces is found to be QD-size dependent, increasing linearly with QD surface area. On the other hand, ET rates are found to be independent of both QD size and surface stoichiometry, suggesting that the donor–acceptor energetics (constituting the driving force for ET) are fixed due to Fermi level pinning at the QD/oxide interface. Implications of our results for QD-sensitized solar cell design are discussed.

A new algorithm for the detection of intercluster galaxy filaments using galaxy orientation alignments

We present a new algorithm for detecting intercluster galaxy filaments based upon the assumption that the orientations of constituent galaxies along such filaments are non-isotropic. We apply the algorithm to the 2dF Galaxy Redshift Survey catalogue and find that it readily detects many straight filaments between close cluster pairs. At large intercluster separations (> 15 h(-1) Mpc), we find that the detection efficiency falls quickly, as it also does with more complex filament morphologies. We explore the underlying assumptions and suggest that it is only in the case of close cluster pairs that we can expect galaxy orientations to be significantly correlated with filament direction.