Showing papers by "Technical University of Denmark published in 1997"

Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.

Abstract: We have developed a new method for the identification of signal peptides and their cleavage sites based on neural networks trained on separate sets of prokaryotic and eukaryotic sequence. The method performs significantly better than previous prediction schemes and can easily be applied on genome-wide data sets. Discrimination between cleaved signal peptides and uncleaved N-terminal signal-anchor sequences is also possible, though with lower precision. Predictions can be made on a publicly available WWW server.

On the Design of Compliant Mechanisms Using Topology Optimization

Abstract: This paper presents a method for optimal design of compliant mechanism topologies. The method is based on continuum-type topology optimization techniques and finds the optimal compliant mechanism topology within a given design domain and a given position and direction of input and output forces. By constraining the allowed displacement at the input port, it is possible to control the maximum stress level in the compliant mechanism. The ability of the design method to find a mechanism with complex output behavior is demonstrated by several examples. Some of the optimal mechanism topologies have been manufactured, both in macroscale (hand-size) made in Nylon, and in microscale (<.5mm)) made of micromachined glass.

Surface electronic structure and reactivity of transition and noble metals

Abstract: We present self-consistent density functional calculations using the LMTO-ASA method of the variations in the surface electronic structure for pseudomorfic overlayers and impurities of Fe, Co, Ni, Cu, Ru, Rh, Pd, Ag, Ir, Pt, and Au on the other metals. Knowledge of these variations is of importance in understanding trends in the reactivity of metal surfaces. A simple model is presented which gives a description of the overall trends in the self-consistently calculated results.

A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.

Abstract: We have developed a new method for the identification of signal peptides and their cleavage sites based on neural networks trained on separate sets of prokaryotic and eukaryotic sequences. The method performs significantly better than previous prediction schemes, and can easily be applied to genome-wide data sets. Discrimination between cleaved signal peptides and uncleaved N-terminal signal-anchor sequences is also possible, though with lower precision. Predictions can be made on a publicly available WWW server: .

Comparison of annual maximum series and partial duration series methods for modeling extreme hydrologic events: 1. At-site modeling

Abstract: Two different models for analyzing extreme hydrologic events, based on, respectively, partial duration series (PDS) and annual maximum series (AMS), are compared. The PDS model assumes a generalized Pareto distribution for modeling threshold exceedances corresponding to a generalized extreme value distribution for annual maxima. The performance of the two models in terms of the uncertainty of the T-year event estimator is evaluated in the cases of estimation with, respectively, the maximum likelihood (ML) method, the method of moments (MOM), and the method of probability weighted moments (PWM). In the case of ML estimation, the PDS model provides the most efficient T-year event estimator. In the cases of MOM and PWM estimation, the PDS model is generally preferable for negative shape parameters, whereas the AMS model yields the most efficient estimator for positive shape parameters. A comparison of the considered methods reveals that in general, one should use the PDS model with MOM estimation for negative shape parameters, the PDS model with exponentially distributed exceedances if the shape parameter is close to zero, the AMS model with MOM estimation for moderately positive shape parameters, and the PDS model with ML estimation for large positive shape parameters. Since heavy-tailed distributions, corresponding to negative shape parameters, are far the most common in hydrology, the PDS model generally is to be preferred for at-site quantile estimation.

Microprestress-Solidification Theory for Concrete Creep. I: Aging and Drying Effects

Abstract: A new physical theory and constitutive model for the effects of long-term aging and drying on concrete creep are proposed. The previously proposed solidification theory, in which the aging is explained and modeled by the volume growth (into the pores of hardened portland cement paste) of a nonaging viscoelastic constituent (cement gel), cannot explain long-term aging because the volume growth of the hydration products is too short-lived. The paper presents an improvement of the solidification theory in which the viscosity of the flow term of the compliance function is a function of a tensile microprestress carried by the bonds and bridges crossing the micropores (gel pores) in the hardened cement gel. The microprestress is generated by the disjoining pressure of the hindered adsorbed water in the micropores and by very large and highly localized volume changes caused by hydration or drying. The long-term creep, deviatoric as well as volumetric, is assumed to originate from viscous shear slips between the opposite walls of the micropores in which the bonds or bridges that cross the micropores and transmit the microprestress break and reform. The long-term aging exhibited by the flow term in the creep model is caused by relaxation of the tensile microprestress transverse to the slip plane. The Pickett effect (drying creep) is caused by changes of the microprestress balancing the changes in the disjoining pressure, which in turn are engendered by changes of the relative humidity in the capillary pores. Numerical implementation, application and comparison with test data is relegated to a companion paper that follows in this issue.

Phase diagrams for surface alloys

Abstract: We discuss surface alloy phases and their stability based on surface phase diagrams constructed from the surface energy as a function of the surface composition. We show that in the simplest cases of pseudomorphic overlayers there are four generic classes of systems, characterized by the sign of the heat of segregation from the bulk and the sign of the excess interactions between the atoms in the surface (the surface mixing energy). We also consider the more complicated cases with ordered surface phases, nonpseudomorphic overlayers, second layer segregation, and multilayers. The discussion is based on density-functional calculations using the coherent-potential approximation and on effective-medium theory. We give self-consistent density-functional results for the segregation energy and surface mixing energy for all combinations of the transition and noble metals. Finally we discuss in detail the cases Ag/Cu(100), Pt/Cu(111), Ag/Pt(111), Co/Cu(111), Fe/Cu(111), and Pd/Cu(110) in connection with available experimental results.

Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae

Abstract: A stoichiometric model describing the anaerobic metabolism of Saccharomyces cerevisiae during growth on a defined medium was derived. The model was used to calculate intracellular fluxes based on measurements of the uptake of substrates from the medium, the secretion of products from the cells, and of the rate of biomass formation. Furthermore, measurements of the biomass composition and of the activity of key enzymes were used in the calculations. The stoichiometric network consists of 37 pathway reactions involving 43 compounds of which 13 were measured (acetate, CO2, ethanol, glucose, glycerol, NH+ 4, pyruvate, succinate, carbohydrates, DNA, lipids, proteins and RNA). The model was used to calculate the production rates of malate and fumarate and the ethanol measurement was used to validate the model. All rate measurements were performed on glucose-limited continuous cultures in a high-performance bioreactor. Carbon balances closed within 98%. The calculations comprised flux distributions at specific growth rates of 0.10 and 0.30 h-1. The fluxes through reactions located around important branch points of the metabolism were compared, i.e. the split between the pentose phosphate and the Embden-Meyerhoff-Parnas pathways. Also the model was used to show the probable existence of a redox shunt across the inner mitochondrial membrane consisting of the reactions catalysed by the mitochondrial and the cytosolic alcohol dehydrogenase. Finally it was concluded that cytosolic isocitrate dehydrogenase is probably not present during growth on glucose. The importance of basing the flux analysis on accurate measurements was demonstrated through a sensitivity analysis. It was found that the accuracy of the measurements of CO2, ethanol, glucose, glycerol and protein was critical for the correct calculation of the flux distribution.

The Interpolation Attack on Block Ciphers

Abstract: In this paper we introduce a new method of attacks on block ciphers, the interpolation attack. This new method is useful for attacking ciphers using simple algebraic functions (in particular quadratic functions) as S-boxes. Also, ciphers of low non-linear order are vulnerable to attacks based on higher order differentials. Recently, Knudsen and Nyberg presented a 6-round prototype cipher which is provably secure against ordinary differential cryptanalysis. We show how to attack the cipher by using higher order differentials and a variant of the cipher by the interpolation attack. It is possible to successfully cryptanalyse up to 32 rounds of the variant using about 232 chosen plaintexts with a running time less than 264. Using higher order differentials, a new design concept for block ciphers by Kiefer is also shown to be insecure. Rijmen et al presented a design strategy for block ciphers and the cipher SHARK. We show that there exist ciphers constructed according to this design strategy which can be broken faster than claimed. In particular, we cryptanalyse 5 rounds of a variant of SHARK, which deviates only slightly from the proposed SHARK.

Neural Network Prediction of Translation Initiation Sites in Eukaryotes: Perspectives for EST and Genome Analysis

Abstract: Translation in eukaryotes does not always start at the first AUG in an mRNA, implying that context information also plays a role. This makes prediction of translation initiation sites a non-trivial task, especially when analysing EST and genome data where the entire mature mRNA sequence is not known. In this paper, we employ artificial neural networks to predict which AUG triplet in an mRNA sequence is the start codon. The trained networks correctly classified 88 % of Arabidopsis and 85 % of vertebrate AUG triplets. We find that our trained neural networks use a combination of local start eodon context and global sequence information. Furthermore, analysis of false predictions shows that AUGs in frame with the actual start codon are more frequently selected than out-of-frame AUGs, suggesting that our networks use reading frame detection. A number of conflicts between neural network predictions and database annotations are analysed in detail, leading to identification of possible database errors.

Dynamics of an Interacting Particle System: Evidence of Critical Slowing Down

Abstract: The dynamics of a magnetic particle system consisting of ultrafine Fe-C particles of monodisperse nature has been investigated in a large time window, ${10}^{\ensuremath{-}9}--{10}^{4}\mathrm{s}$, using M\"ossbauer spectroscopy, ac susceptibility, and zero field cooled magnetic relaxation measurements. By studying two samples from the same dilution series, with concentrations of 5 and $6\ifmmode\times\else\texttimes\fi{}{10}^{\ensuremath{-}3}\mathrm{vol}%$, respectively, it has been found that dipole-dipole interaction increases the characteristic relaxation time of the particle system at all temperatures investigated. The results for the most concentrated particle assembly are indicative of collective magnetic dynamics and critical slowing down at a finite temperature, ${T}_{g}\ensuremath{\approx}40\mathrm{K}$. Close to and below the transition temperature, an aging phenomenon is observed, another manifestation of collective magnetic dynamics.

Two Methods for Improving Performance of a HMM and their Application for Gene Finding

Abstract: A hidden Markov model for gene finding consists of submodels for coding regions, splice sites, introns, intergenic regions and possibly more. It is described how to estimate the model as a whole from labeled sequences instead of estimating the individual parts independently from subsequences. It is argued that the standard maximum likelihood estimation criterion is not optimal for training such a model. Instead of maximizing the probability of the DNA sequence, one should maximize the probability of the correct prediction. Such a criterion, called conditional maximum likelihood, is used for the gene finder 'HMM-gene'. A new (approximative) algorithm is described, which finds the most probable prediction summed over all paths yielding the same prediction. We show that these methods contribute significantly to the high performance of HMMgene.

Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices

Abstract: Within the last decades NMR spectroscopy has undergone tremendous development and has become a powerful analytical tool for the investigation of intracellular flux distributions in biochemical networks using (13)C-labeled substrates. Not only are the experiments much easier to conduct than experiments employing radioactive tracer elements, but NMR spectroscopy also provides additional information on the labeling pattern of the metabolites. Whereas the maximum amount of information obtainable with (14)C-labeled substrates is the fractional enrichment in the individual carbon atom positions, NMR spectroscopy can also provide information on the degree of labeling at neighboring carbon atom positions by analyzing multiplet patterns in NMR spectra or using 2-dimensional NMR spectra. It is possible to quantify the mole fractions of molecules that show a specific labeling pattern, i.e., information of the isotopomer distribution in metabolite pools can be obtained. The isotopomer distribution is the maximum amount of information that in theory can be obtained from (13)C-tracer studies. The wealth of information contained in NMR spectra frequently leads to overdetermined algebraic systems. Consequently, fluxes must be estimated by nonlinear least squares analysis, in which experimental labeling data is compared with simulated steady state isotopomer distributions. Hence, mathematical models are required to compute the steady state isotopomer distribution as a function of a given set of steady state fluxes. Because 2(n) possible labeling patterns exist in a molecule of n carbon atoms, and each pattern corresponds to a separate state in the isotopomer model, these models are inherently complex. Model complexity, so far, has restricted usage of isotopomer information to relatively small metabolic networks. A general methodology for the formulation of isotopomer models is described. The model complexity of isotopomer models is reduced to that of classical metabolic models by expressing the 2(n) isotopomer mass balances of a metabolite pool in a single matrix equation. Using this approach an isotopomer model has been implemented that describes label distribution in primary carbon metabolism, i.e., in a metabolic network including the Embden-Meyerhof-Parnas and pentose phosphate pathway, the tricarboxylic acid cycle, and selected anaplerotic reaction sequences. The model calculates the steady state label distribution in all metabolite pools as a function of the steady state fluxes and is applied to demonstrate the effect of selected anaplerotic fluxes on the labeling pattern of the pathway intermediates.

Use of Rietveld refinement for elastic macrostrain determination and for evaluation of plastic strain history from diffraction spectra

Abstract: Macrostrain variations in engineering components are frequently examined using neutron diffraction, at both reactors and pulsed sources. It is desirable to minimize the sampling volume in order to maximize the spatial resolution, although this increases the required measurement time. At reactors, macrostrain behavior is inferred from a single lattice reflection (deemed to be representative of the bulk response). At a pulsed source, a complete diffraction pattern is recorded and accordingly it is natural to fit the entire diffraction spectra using a Rietveld [J. Appl. Cryst. 2, 65 (1969)] refinement. This means that an idealized crystal structure is fit to the measured distorted crystal structure, which includes deviation of the measured lattice reflections from the ideal due to elastoplastic strain anisotropies, which are dependent on the particular lattice reflection (hkl) considered. We show that elastic macrostrains calculated from lattice parameter changes in Rietveld refinements (without accounting for hkl dependent anisotropies) are almost identical to the bulk elastic response and are comparable to the response obtained from a single lattice reflection typically used by practitioners at a steady state source. Moreover good refinements on the complete pattern are obtained with short measurement times compared to what is required for good statistics for single reflections. By incorporating a description of the elastic strain anisotropy expected in cubic materials into the Rietveld code, an empirical prediction of plastic strain history is possible. The validity of these arguments is demonstrated by analysis of a uniaxial tensile load test and a reanalysis of previously reported data taken on a deformed stainless steel ring. The plastic strain predictions compare favorably with a finite element model.

Total Volatile Organic Compounds (TVOC) in Indoor Air Quality Investigations

Abstract: The amount of volatile organic compounds (VOCs) in indoor air, usually called TVOC (total volatile organic compounds), has been measured using different definitions and techniques which yield different results. This report recommends a definition of TVOC referring to a specified range of VOCs and it proposes a method for the measurement of this TVOC entity. Within the specified range, the measured concentrations of identified VOCs (including 64 target compounds) are summed up, concentrations of non-identified compounds in toluene equivalents are added and, together with the identified VOCs, they give the TVOC value. The report reviews the TVOC concept with respect to its usefulness for exposure assessment and control and for the prediction of health or comfort effects. Although the report concludes that at present it is not possible to use TVOC as an effect predictor, it affirms the usefulness of TVOC for characterizing indoor pollution and for improving source control as required from the points of view of health, comfort, energy efficiency and sustainability.

On the definition and modelling of streamflow drought duration and deficit volume

Abstract: The threshold level approach is used to define drought characteristics, i.e. drought duration and deficit volume from time series of daily streamflow. Three different procedures for pooling dependent droughts are compared: a method based on an inter-event time and volume criterion (IC), a moving average procedure (MA), and a method based on the sequent peak algorithm (SPA). The extreme values of drought duration and deficit volume are analysed using both an annual maximum series (AMS) and a partial duration series (PDS) approach. Two Danish catchments with very different flow regimes were used in the study. The IC and MA methods provided virtually the same sample statistics of the AMS of drought duration and deficit volume for all thresholds considered. The results of the SPA method differed significantly from the other two methods for high thresholds due to the presence of multi-year droughts. For analysis of seasonal droughts the SPA method is restricted to low thresholds. The occurrence of a l...

Plant-derived vaccine protects target animals against a viral disease

Abstract: The successful expression of animal or human virus epitopes on the surface of plant viruses has recently been demonstrated. These chimeric virus particles (CVPs) could represent a cost-effective and safe alternative to conventional animal cell-based vaccines. We report the insertion of oligonucleotides coding for a short linear epitope from the VP2 capsid protein of mink enteritis virus (MEV) into an infectious cDNA clone of cowpea mosaic virus and the successful expression of the epitope on the surface of CVPs when propagated in the black-eyed bean, Vigna unguiculata. The efficacy of the CVPs was established by the demonstration that one subcutaneous injection of 1 mg of the CVPs in mink conferred protection against clinical disease and virtually abolished shedding of virus after challenge with virulent MEV, demonstrating the potential utility of plant CVPs as the basis for vaccine development. The epitope used occurs in three different virus species-MEV, canine parvovirus, and feline panleukopenia virus- and thus the same vaccine could be used in three economically important viral hosts-mink, dogs, and cats, respectively.

O-GLYCBASE Version 3.0: A revised database of O-glycosylated proteins

Abstract: O-GLYCBASE is an updated database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the SWISS-PROT database. Entries include information about species, sequence, glycosylation sites and glycan type. O-GLYCBASE is now fully cross-referenced to the SWISS-PROT, PIR, PROSITE, PDB, EMBL, HSSP, LISTA and MIM databases. Compared with version 1.0 the number of entries have increased by 34%. Revision of the O-glycan assignment was performed on 20% of the entries. Sequence logos displaying the acceptor specificity patterns for the GalNAc, mannose and GlcNAc transferases are shown. The O-GLYCBASE database is available through WWW or by anonymous FTP.

Molecular Dynamics Modeling of Clay Minerals. 1. Gibbsite, Kaolinite, Pyrophyllite, and Beidellite

Abstract: A molecular dynamics model for clays and the oxide minerals is desirable for studying the kinetics and thermodynamics of adsorption processes. To this end, a valence force field for aluminous, dioctahedral clay minerals was developed. Novel aspects of this development include the bending potential for octahedral O−Al−O angles, which uses a quartic polynomial to create a double-well potential with minima at both 90° and 180°. Also, atomic point charges were derived from comparisons of ab initio molecular electrostatic potentials with X-ray diffraction-based deformation electron densities. Isothermal−isobaric molecular dynamics simulations of quartz, gibbsite, kaolinite, and pyrophyllite were used to refine the potential energy parameters. The resultant force field reproduced all the major structural parameters of these minerals to within 1% of their experimentally determined values. Transferability of the force field to simulations of adsorption onto clay mineral surfaces was tested through simulations of ...

Micromechanical models for graded composite materials

Abstract: Elastic response of selected plane-array models of graded composite microstructures is examined under both uniform and linearly varying boundary tractions and displacements, by means of detailed finite element studies of large domains containing up to several thousand inclusions. Models consisting of piecewise homogeneous layers with equivalent elastic properties estimated by Mori-Tanaka and selfconsistent methods are also analysed under similar boundary conditions. Comparisons of the overall and local fields predicted by the discrete and homogenized models are made using a C/SiC composite system with very different Young's moduli of the phases, and relatively steep composition gradients. The conclusions reached from these comparisons suggest that in those parts of the graded microstructure which have a well-defined continuous matrix and discontinuous second phase, the overall properties and local fields are predicted by Mori-Tanaka estimates. On the other hand, the response of graded materials with a skeletal microstructure in a wide transition zone between clearly defined matrix phases is better approximated by the self-consistent estimates. Certain exceptions are noted for loading by overall transverse shear stress. The results suggest that the averaging methods originally developed for statistically homogeneous aggregates may be selectively applied, with a reasonable degree of confidence, to aggregates with composition gradients, subjected to both uniform and nonuniform overall loads.

Stability of the perforated layer (PL) phase in diblock copolymer melts

Abstract: We reexamine the stability of hexagonally modulated layer (HML) and hexagonally perforated layer (HPL) morphologies in a number of block copolymer systems of low to moderate molecular weight. Using small-angle X-ray scattering and dynamic mechanical spectroscopy, we show that these structures are long-lived nonequilibrium states which convert to the bicontinuous gyroid (G) morphology upon isothermal annealing. Comparison of phase transition kinetics across chemically distinct systems spanning a wide range of molecular weights and monomeric friction coefficients reveals a composition dependence to these dynamics. This suggests effects associated with the mobility of individual chains are of lesser importance in explaining the apparent metastability of the HML and HPL structures; instead, the composition dependence of the transition mechanism appears to dominate the observed behavior. The revised phase behavior for these materials is in excellent agreement with mean-field predictions for diblock copolymer m...

Finding the most significant common sequence and structure motifs in a set of RNA sequences

Abstract: We present a computational scheme to locally align a collection of RNA sequences using sequence and structure constraints. In addition, the method searches for the resulting alignments with the most significant common motifs, among all possible collections. The first part utilizes a simplified version of the Sankoff algorithm for simultaneous folding and alignment of RNA sequences, but maintains tractability by constructing multi-sequence alignments from pairwise comparisons. The algorithm finds the multiple alignments using a greedy approach and has similarities to both CLUSTAL and CONSENSUS, but the core algorithm assures that the pairwise alignments are optimized for both sequence and structure conservation. The choice of scoring system and the method of progressively constructing the final solution are important considerations that are discussed. Example solutions, and comparisons with other approaches, are provided. The solutions include finding consensus structures identical to published ones.

Induction of Heat Shock Proteins DnaK, GroEL, and GroES by Salt Stress in Lactococcus lactis

Abstract: The bacterium Lactococcus lactis has become a model organism in studies of growth physiology and membrane transport, as a result of its simple fermentative metabolism. It is also used as a model for studying the importance of specific genes and functions during life in excess nutrients, by comparison of prototrophic wild-type strains and auxotrophic domesticated (dairy) strains. In a study of the capacity of domesticated strains to perform directed responses toward various stress conditions, we have analyzed the heat and salt stress response in the established L. lactis subsp. cremoris laboratory strain MG1363, which was originally derived from a dairy strain. After two-dimensional separation of proteins, the DnaK, GroEL, and GroES heat shock proteins, the HrcA (Orf1) heat shock repressor, and the glycolytic enzymes pyruvate kinase, glyceral-dehyde-3-phosphate dehydrogenase, and phosphoglycerate kinase were identified by a combination of Western blotting and direct N-terminal amino acid sequencing of proteins from the gels. Of 400 to 500 visible proteins, 17 were induced more than twofold during heat stress. Two classes of heat stress proteins were identified from their temporal induction pattern. The fast-induced proteins (including DnaK) showed an abruptly increased rate of synthesis during the first 10 min, declining to intermediate levels after 15 min. GroEL and GroES, which also belong to this group, maintained a high rate of synthesis after 15 min. The class of slowly induced proteins exhibited a gradual increase in the rate of synthesis after the onset of stress. Unlike other organisms, all salt stress-induced proteins in L. lactis were also subjected to heat stress induction. DnaK, GroEL, and GroES showed similar temporal patterns of induction during salt stress, resembling the timing during heat stress although at a lower induction level. These data indicate an overlap between the heat shock and salt stress responses in L. lactis.

Design Specification and Verification

Abstract: This chapter describes high-level design techniques for developing hardware or software and combinations of the two. The chapter gives both an overview of the key concepts found in a range existing languages and tools and a specific proposal for modeling the abstract behavior of a design. The aim of such high-level design techniques is to reduce the design time or effort by shifting as many decisions and analysises as possible from low-level to high-level models.

Note on free lunches and cross-validation

Abstract: The “no-free-lunch” theorems (Wolpert & Macready, 1995) have sparked heated debate in the computational learning community. A recent communication (Zhu & Rohwer, 1996) attempts to demonstrate the inefficiency of cross-validation on a simple problem. We elaborate on this result by considering a broader class of cross-validation. When used more strictly, cross-validation can yield the expected results on simple examples.

Concentration-dependent changes of PCB patterns in fish-eating mammals: structural evidence for induction of cytochrome P450

Abstract: Data sets on CB concentrations in fish-eating mammals from five laboratories were combined to test and refine a pharmacokinetic model. Clear differences in PCB patterns were observed between species. The ability to metabolize chlorobiphenyl (CB) congeners with vicinal H-atoms only in the ortho- and meta-positions and with one ortho-chlorine substituent generally increased in the order otter < cetaceans (harbor porpoise, common dolphin) < phocid seals (harbor and grey seal), but the metabolism of congeners with vicinal H-atoms in the meta- and para-positions and with two ortho-chlorines increased in the order cetaceans < seals < otter. Both categories of congeners are probably metabolized by different families of cytochrome P450 (1A and 2B) of which levels apparently differed between the cetaceans, the pinnipeds, and the otter. Within-species CB patterns differed in a concentration-dependent manner. The induction of cytochrome P450 enzymes offers the most likely explanation for this phenomenon, but starvation could have a similar effect on occasion.