MHCWeb: Converting a WWW database into a knowledge-based collaborative environment

The World Wide Web (WWW) is useful for distributing scientific data. Most existing web data resources organize their information either in structured flat files or relational databases with basic retrieval capabilities. For databases with one or a few simple relations, these approaches are successful, but they can be cumbersome when there is a data model involving multiple relations between complex data. We believe that knowledge-based resources offer a solution in these cases. Knowledge bases have explicit declarations of the concepts in the domain, along with the relations between them. They are usually organized hierarchically, and provide a global data model with a controlled vocabulary, We have created the OWEB architecture for building online scientific data resources using knowledge bases. OWEB provides a shell for structuring data, providing secure and shared access, and creating computational modules for processing and displaying data. In this paper, we describe the translation of the online immunological database MHCPEP into an OWEB system called MHCWeb. This effort involved building a conceptual model for the data, creating a controlled terminology for the legal values for different types of data, and then translating the original data into the new structure. The 0 WEB environment allows for flexible access to the data by both users and computer programs.

Analytical solution to the zero-inertia problem for surge flow phenomena in nonprismatic channels

Surge flow phenomena. e.g.. as a consequence of a dam failure or a flash flood, represent free boundary problems. ne extending computational domain together with the discontinuities involved renders their numerical solution a cumbersome procedure. This contribution proposes an analytical solution to the problem, It is based on the slightly modified zero-inertia (ZI) differential equations for nonprismatic channels and uses exclusively physical parameters. Employing the concept of a momentum-representative cross section of the moving water body together with a specific relationship for describing the cross sectional geometry leads, after considerable mathematical calculus. to the analytical solution. The hydrodynamic analytical model is free of numerical troubles, easy to run, computationally efficient. and fully satisfies the law of volume conservation. In a first test series, the hydrodynamic analytical ZI model compares very favorably with a full hydrodynamic numerical model in respect to published results of surge flow simulations in different types of prismatic channels. In order to extend these considerations to natural rivers, the accuracy of the analytical model in describing an irregular cross section is investigated and tested successfully. A sensitivity and error analysis reveals the important impact of the hydraulic radius on the velocity of the surge, and this underlines the importance of an adequate description of the topography, The new approach is finally applied to simulate a surge propagating down the irregularly shaped Isar Valley in the Bavarian Alps after a hypothetical dam failure. The straightforward and fully stable computation of the flood hydrograph along the Isar Valley clearly reflects the impact of the strongly varying topographic characteristics on the How phenomenon. Apart from treating surge flow phenomena as a whole, the analytical solution also offers a rigorous alternative to both (a) the approximate Whitham solution, for generating initial values, and (b) the rough volume balance techniques used to model the wave tip in numerical surge flow computations.

Prediction of promiscuous peptides that bind HLA class I molecules

Promiscuous T-cell epitopes make ideal targets for vaccine development. We report here a computational system, multipred, for the prediction of peptide binding to the HLA-A2 supertype. It combines a novel representation of peptide/MHC interactions with a hidden Markov model as the prediction algorithm. multipred is both sensitive and specific, and demonstrates high accuracy of peptide-binding predictions for HLA-A*0201, *0204, and *0205 alleles, good accuracy for *0206 allele, and marginal accuracy for *0203 allele. multipred replaces earlier requirements for individual prediction models for each HLA allelic variant and simplifies computational aspects of peptide-binding prediction. Preliminary testing indicates that multipred can predict peptide binding to HLA-A2 supertype molecules with high accuracy, including those allelic variants for which no experimental binding data are currently available.

A director theory for visco-elastic folding instabilities in multilayered rock

A model for finely layered visco-elastic rock proposed by us in previous papers is revisited and generalized to include couple stresses. We begin with an outline of the governing equations for the standard continuum case and apply a computational simulation scheme suitable for problems involving very large deformations. We then consider buckling instabilities in a finite, rectangular domain. Embedded within this domain, parallel to the longer dimension we consider a stiff, layered beam under compression. We analyse folding up to 40% shortening. The standard continuum solution becomes unstable for extreme values of the shear/normal viscosity ratio. The instability is a consequence of the neglect of the bending stiffness/viscosity in the standard continuum model. We suggest considering these effects within the framework of a couple stress theory. Couple stress theories involve second order spatial derivatives of the velocities/displacements in the virtual work principle. To avoid C-1 continuity in the finite element formulation we introduce the spin of the cross sections of the individual layers as an independent variable and enforce equality to the spin of the unit normal vector to the layers (-the director of the layer system-) by means of a penalty method. We illustrate the convergence of the penalty method by means of numerical solutions of simple shears of an infinite layer for increasing values of the penalty parameter. For the shear problem we present solutions assuming that the internal layering is oriented orthogonal to the surfaces of the shear layer initially. For high values of the ratio of the normal-to the shear viscosity the deformation concentrates in thin bands around to the layer surfaces. The effect of couple stresses on the evolution of folds in layered structures is also investigated. (C) 2002 Elsevier Science Ltd. All rights reserved.

Finite element modelling of reactive fluids mixing and mineralization in pore-fluid saturated hydrothermal/sedimentary basins

We present the finite element simulations of reactive mineral carrying fluids mixing and mineralization in pore-fluid saturated hydrothermal/sedimentary basins. In particular we explore the mixing of reactive sulfide and sulfate fluids and the relevant patterns of mineralization for Load, zinc and iron minerals in the regime of temperature-gradient-driven convective flow. Since the mineralization and ore body formation may last quite a long period of time in a hydrothermal basin, it is commonly assumed that, in the geochemistry, the solutions of minerals are in an equilibrium state or near an equilibrium state. Therefore, the mineralization rate of a particular kind of mineral can be expressed as the product of the pore-fluid velocity and the equilibrium concentration of this particular kind of mineral Using the present mineralization rate of a mineral, the potential of the modern mineralization theory is illustrated by means of finite element studies related to reactive mineral-carrying fluids mixing problems in materially homogeneous and inhomogeneous porous rock basins.

Large amplitude folding in finely layered viscoelastic rock structures

We analyze folding phenomena in finely layered viscoelastic rock. Fine is meant in the sense that the thickness of each layer is considerably smaller than characteristic structural dimensions. For this purpose we derive constitutive relations and apply a computational simulation scheme (a finite-element based particle advection scheme; see MORESI et al., 2001) suitable for problems involving very large deformations of layered viscous and viscoelastic rocks. An algorithm for the time integration of the governing equations as well as details of the finite-element implementation is also given. We then consider buckling instabilities in a finite, rectangular domain. Embedded within this domain, parallel to the longer dimension we consider a stiff, layered plate. The domain is compressed along the layer axis by prescribing velocities along the sides. First, for the viscous limit we consider the response to a series of harmonic perturbations of the director orientation. The Fourier spectra of the initial folding velocity are compared for different viscosity ratios. Turning to the nonlinear regime we analyze viscoelastic folding histories up to 40% shortening. The effect of layering manifests itself in that appreciable buckling instabilities are obtained at much lower viscosity ratios (1:10) as is required for the buckling of isotropic plates (1:500). The wavelength induced by the initial harmonic perturbation of the director orientation seems to be persistent. In the section of the parameter space considered here elasticity seems to delay or inhibit the occurrence of a second, larger wavelength. Finally, in a linear instability analysis we undertake a brief excursion into the potential role of couple stresses on the folding process. The linear instability analysis also provides insight into the expected modes of deformation at the onset of instability, and the different regimes of behavior one might expect to observe.

Effects of hot intrusions on pore-fluid flow and heat transfer in fluid-saturated rocks

We use the finite element method to solve coupled problems between pore-fluid flow and heat transfer in fluid-saturated porous rocks. In particular, we investigate the effects of both the hot pluton intrusion and topographically driven horizontal flow on the distributions of the pore-flow velocity and temperature in large-scale hydrothermal systems. Since general mineralization patterns are strongly dependent on distributions of both the pore-fluid velocity and temperature fields, the modern mineralization theory has been used to predict the general mineralization patterns in several realistic hydrothermal systems. The related numerical results have demonstrated that: (1) The existence of a hot intrusion can cause an increase in the maximum value of the pore-fluid velocity in the hydrothermal system. (2) The permeability of an intruded pluton is one of the sensitive parameters to control the pore-fluid flow, heat transfer and ore body formation in hydrothermal systems. (3) The maximum value of the pore-fluid velocity increases when the bottom temperature of the hydrothermal system is increased. (4) The topographically driven flow has significant effects on the pore-fluid flow, temperature distribution and precipitation pattern of minerals in hydrothermal systems. (5) The size of the computational domain may have some effects on the pore-fluid flow and heat transfer, indicating that the size of a hydrothermal system may affect the pore-fluid flow and heat transfer within the system. (C) 2003 Elsevier Science B.V. All rights reserved.

Prediction of carbon monoxide in fires by conditional moment closure

Carbon monoxide is the chief killer in fires. Dangerous levels of CO can occur when reacting combustion gases are quenched by heat transfer, or by mixing of the fire plume in a cooled under- or overventilated upper layer. In this paper, carbon monoxide predictions for enclosure fires are modeled by the conditional moment closure (CMC) method and are compared with laboratory data. The modeled fire situation is a buoyant, turbulent, diffusion flame burning under a hood. The fire plume entrains fresh air, and the postflame gases are cooled considerably under the hood by conduction and radiation, emulating conditions which occur in enclosure fires and lead to the freezing of CO burnout. Predictions of CO in the cooled layer are presented in the context of a complete computational fluid dynamics solution of velocity, temperature, and major species concentrations. A range of underhood equivalence ratios, from rich to lean, are investigated. The CMC method predicts CO in very good agreement with data. In particular, CMC is able to correctly predict CO concentrations in lean cooled gases, showing its capability in conditions where reaction rates change considerably.

Anisotropic convection model for the earth's mantle

The paper presents a theory for modeling flow in anisotropic, viscous rock. This theory has originally been developed for the simulation of large deformation processes including the folding and kinking of multi-layered visco-elastic rock (Muhlhaus et al. [1,2]). The orientation of slip planes in the context of crystallographic slip is determined by the normal vector - the director - of these surfaces. The model is applied to simulate anisotropic mantle convection. We compare the evolution of flow patterns, Nusselt number and director orientations for isotropic and anisotropic rheologies. In the simulations we utilize two different finite element methodologies: The Lagrangian Integration Point Method Moresi et al [8] and an Eulerian formulation, which we implemented into the finite element based pde solver Fastflo (www.cmis.csiro.au/Fastflo/). The reason for utilizing two different finite element codes was firstly to study the influence of an anisotropic power law rheology which currently is not implemented into the Lagrangian Integration point scheme [8] and secondly to study the numerical performance of Eulerian (Fastflo)- and Lagrangian integration schemes [8]. It turned out that whereas in the Lagrangian method the Nusselt number vs time plot reached only a quasi steady state where the Nusselt number oscillates around a steady state value the Eulerian scheme reaches exact steady states and produces a high degree of alignment (director orientation locally orthogonal to velocity vector almost everywhere in the computational domain). In the simulations emergent anisotropy was strongest in terms of modulus contrast in the up and down-welling plumes. Mechanisms for anisotropic material behavior in the mantle dynamics context are discussed by Christensen [3]. The dominant mineral phases in the mantle generally do not exhibit strong elastic anisotropy but they still may be oriented by the convective flow. Thus viscous anisotropy (the main focus of this paper) may or may not correlate with elastic or seismic anisotropy.

A comparative study of similarity measures for manufacturing cell formation

We introduced a spectral clustering algorithm based on the bipartite graph model for the Manufacturing Cell Formation problem in [Oliveira S, Ribeiro JFF, Seok SC. A spectral clustering algorithm for manufacturing cell formation. Computers and Industrial Engineering. 2007 [submitted for publication]]. It constructs two similarity matrices; one for parts and one for machines. The algorithm executes a spectral clustering algorithm on each separately to find families of parts and cells of machines. The similarity measure in the approach utilized limited information between parts and between machines. This paper reviews several well-known similarity measures which have been used for Group Technology. Computational clustering results are compared by various performance measures. (C) 2008 The Society of Manufacturing Engineers. Published by Elsevier Ltd. All rights reserved.

A spectral clustering algorithm for manufacturing cell formation

A graph clustering algorithm constructs groups of closely related parts and machines separately. After they are matched for the least intercell moves, a refining process runs on the initial cell formation to decrease the number of intercell moves. A simple modification of this main approach can deal with some practical constraints, such as the popular constraint of bounding the maximum number of machines in a cell. Our approach makes a big improvement in the computational time. More importantly, improvement is seen in the number of intercell moves when the computational results were compared with best known solutions from the literature. (C) 2009 Elsevier Ltd. All rights reserved.

Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system

Background: A major goal in the post-genomic era is to identify and characterise disease susceptibility genes and to apply this knowledge to disease prevention and treatment. Rodents and humans have remarkably similar genomes and share closely related biochemical, physiological and pathological pathways. In this work we utilised the latest information on the mouse transcriptome as revealed by the RIKEN FANTOM2 project to identify novel human disease-related candidate genes. We define a new term patholog to mean a homolog of a human disease-related gene encoding a product ( transcript, anti-sense or protein) potentially relevant to disease. Rather than just focus on Mendelian inheritance, we applied the analysis to all potential pathologs regardless of their inheritance pattern. Results: Bioinformatic analysis and human curation of 60,770 RIKEN full-length mouse cDNA clones produced 2,578 sequences that showed similarity ( 70 - 85% identity) to known human-disease genes. Using a newly developed biological information extraction and annotation tool ( FACTS) in parallel with human expert analysis of 17,051 MEDLINE scientific abstracts we identified 182 novel potential pathologs. Of these, 36 were identified by computational tools only, 49 by human expert analysis only and 97 by both methods. These pathologs were related to neoplastic ( 53%), hereditary ( 24%), immunological ( 5%), cardio-vascular (4%), or other (14%), disorders. Conclusions: Large scale genome projects continue to produce a vast amount of data with potential application to the study of human disease. For this potential to be realised we need intelligent strategies for data categorisation and the ability to link sequence data with relevant literature. This paper demonstrates the power of combining human expert annotation with FACTS, a newly developed bioinformatics tool, to identify novel pathologs from within large-scale mouse transcript datasets.

Modelling the Distribution of Ischaemic Stroke-Specific Survival Time Using an EM-based Mixture Approach with Random Effects Adjustment

A two-component survival mixture model is proposed to analyse a set of ischaemic stroke-specific mortality data. The survival experience of stroke patients after index stroke may be described by a subpopulation of patients in the acute condition and another subpopulation of patients in the chronic phase. To adjust for the inherent correlation of observations due to random hospital effects, a mixture model of two survival functions with random effects is formulated. Assuming a Weibull hazard in both components, an EM algorithm is developed for the estimation of fixed effect parameters and variance components. A simulation study is conducted to assess the performance of the two-component survival mixture model estimators. Simulation results confirm the applicability of the proposed model in a small sample setting. Copyright (C) 2004 John Wiley Sons, Ltd.

Evaluation of the enthalpy of formation, proton affinity, and gas-phase basicity of gamma-butyrolactone and 2-pyrrolidinone by isodesmic reactions

The knowledge of thermochemical parameters such as the enthalpy of formation, gas-phase basicity, and proton affinity may be the key to understanding molecular reactivity. The obtention of these thermochemical parameters by theoretical chemical models may be advantageous when experimental measurements are difficult to accomplish. The development of ab initio composite models represents a major advance in the obtention of these thermochemical parameters,. but these methods do not always lead to accurate values. Aiming at achieving a comparison between the ab initio models and the hybrid models based on the density functional theory (DFT), we have studied gamma-butyrolactone and 2-pyrrolidinone with a goal of obtaining high-quality thermochemical parameters using the composite chemical models G2, G2MP2, MP2, G3, CBS-Q, CBS-4, and CBS-QB3; the DFT methods B3LYP, B3P86, PW91PW91, mPW1PW, and B98; and the basis sets 6-31G(d), 6-31+G(d), 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p), 6-311G(d), 6-311+G(d), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p), aug-cc-pVDZ, and aug-cc-pVTZ. Values obtained for the enthalpies of formation, proton affinity, and gas-phase basicity of the two target molecules were compared to the experimental data reported in the literature. The best results were achieved with the use of DFT models, and the B3LYP method led to the most accurate data.

Drinfield twists and alegebraic Bethe ansatz of the supersymmetric t-J model

We construct the Drinfeld twists (factorizing F-matrices) for the supersymmetric t-J model. Working in the basis provided by the F-matrix (i.e. the so-called F-basis), we obtain completely symmetric representations of the monodromy matrix and the pseudo-particle creation operators of the model. These enable us to resolve the hierarchy of the nested Bethe vectors for the gl(2\1) invariant t-J model.