bluuebunny/crossref_metadata_2025 huggingface dataset:
The P Domain of Norovirus Capsid Protein Forms Dimer and Binds to Histo-Blood Group Antigen Receptors
Authors: Tan Ming , Hegde Rashmi S. , Jiang Xi
Published: May 2004

Noroviruses (NVs) are the most important pathogen of epidemic nonbacterial gastroenteritis. The recent finding that NVs recognize human histo-blood group antigens (HBGAs) as receptors provided a new approach to study the pathogenesis of NVs. Using computational and site-directed mutagenesis approaches, our investigators previously identified a plausible binding pocket in the P domain of the NV capsids. In this study, we further characterize the role of the P domain in the interaction with human HBGA receptors using three NV strains representing three binding patterns. Our results show that the isolated P domain, although it did not form virus-like particles (VLPs), formed dimers, and the dimers bound HBGAs with the same patterns as those of the intact viral capsids. In contrast, the S domain, which formed small, thin-layer VLPs, did not bind A, B, or H HBGAs. A chimera containing the S domain of VA387 and the P domain of MOH revealed a binding pattern of the P donor strain (MOH). Deletion experiments revealed that an intact P domain is necessary for receptor binding. The P domain dimers are stable over a broad range of pH (2 to 11) or under strong denaturing conditions. Taken together, our results suggest that the P domain of NV contains essential elements for strain-specific binding to receptors. Further study of the P domain will provide useful information about the virus-receptor interaction. The high yield and easy production of the recombinant P protein in the
Escherichia coli
expression system will provide a simple approach to this goal.
A Novel
cis
-Acting Element Facilitates Minus-Strand DNA Synthesis during Reverse Transcription of the Hepatitis B Virus Genome
Authors: Shin Myeong-Kyun , Lee Jehan , Ryu Wang-Shick
Published: May 2004

Hepadnaviruses replicate through reverse transcription of an RNA pregenome, resulting in a relaxed circular DNA genome. The first 3 or 4 nucleotides (nt) of minus-strand DNA are synthesized by the use of a bulge in a stem-loop structure near the 5′ end of the pregenome as a template. This primer is then transferred to a complementary UUCA motif, termed an acceptor, within DR1* near the 3′ end of the viral pregenome via 4-nt homology, and it resumes minus-strand DNA synthesis: this process is termed minus-strand transfer or primer translocation. Aside from the sequence identity of the donor and acceptor, little is known about the sequence elements contributing to minus-strand transfer. Here we report a novel
cis
-acting element, termed the β5 region (28 nt in length), located 20 nt upstream of DR1*, that facilitates minus-strand DNA synthesis. The deletion or inversion of the sequence including the β5 region diminished minus-strand DNA synthesis initiated at DR1*. Furthermore, the insertion of the β5 region into its own position in a mutant in which the sequences including the β5 region were replaced restored minus-strand DNA synthesis at DR1*. We speculate that the β5 region facilitates minus-strand transfer, possibly by bringing the acceptor site in proximity to the donor site via base pairing or by interacting with protein factors involved in this process.
Clades of Adeno-Associated Viruses Are Widely Disseminated in Human Tissues
Authors: Gao Guangping , Vandenberghe Luk H. , Alvira Mauricio R. , Lu You , Calcedo Roberto , Zhou Xiangyang , Wilson James M.
Published: May 2004

The potential for usingAdeno-associated virus(AAV) as a vector for human gene therapy has stimulated interest in theDependovirusgenus. Serologic data suggest that AAV infections are prevalent in humans, although analyses of viruses and viral sequences from clinical samples are extremely limited. Molecular techniques were used in this study to successfully detect endogenous AAV sequences in 18% of all human tissues screened, with the liver and bone marrow being the most predominant sites. Sequence characterization of rescued AAV DNAs indicated a diverse array of molecular forms which segregate into clades whose members share functional and serologic similarities. One of the most predominant human clades is a hybrid of two previously described AAV serotypes, while another clade was found in humans and several species of nonhuman primates, suggesting a cross-species transmission of this virus. These data provide important information regarding the biology of parvoviruses in humans and their use as gene therapy vectors.
High Beta-Chemokine Expression Levels in Lymphoid Tissues of Simian/Human Immunodeficiency Virus 89.6-Vaccinated Rhesus Macaques Are Associated with Uncontrolled Replication of Simian Immunodeficiency Virus Challenge Inoculum
Authors: LaFranco-Scheuch Lisa , Abel Kristina , Makori Norbert , Rothaeusler Kristina , Miller Christopher J.
Published: May 2004

Viral suppression by noncytolytic CD8+T cells, in addition to that by classic antiviral CD8+cytotoxic T lymphocytes, has been described for human immunodeficiency virus and simian immunodeficiency virus (SIV) infections. However, the role of soluble effector molecules, especially beta-chemokines, in antiviral immunity is still controversial. In an attenuated vaccine model, approximately 60% of animals immunized with simian/human immunodeficiency virus (SHIV) 89.6 and then challenged intravaginally with SIVmac239 controlled viral replication (viral RNA level in plasma, <104copies/ml) and were considered protected (K. Abel, L. Compton, T. Rourke, D. Montefiori, D. Lu, K. Rothaeusler, L. Fritts, K. Bost, and C. J. Miller, J. Virol.77:3099-3118, 2003). To determine the in vivo importance of beta-chemokine secretion and CD8+-T-cell proliferation in the control of viral replication in this vaccine model, we examined the relationship between viral RNA levels in the axillary and genital lymph nodes of vaccinated, protected (n= 20) and vaccinated, unprotected (n= 11) monkeys by measuring beta-chemokine mRNA levels and protein expression, the frequency of CD8+T cells expressing beta-chemokines, and the extent of CD8+-T-cell proliferation. Tissues from uninfected (n= 3) and unvaccinated, SIVmac239-infected (n= 9) monkeys served as controls. Axillary and genital lymph nodes from unvaccinated and vaccinated, unprotected monkeys had significantly higher beta-chemokine mRNA expression levels and increased numbers of beta-chemokine-positive cells than did vaccinated, protected animals. Furthermore, the lymph nodes of vaccinated, unprotected monkeys had significantly higher numbers of beta-chemokine+CD8+T cells than did vaccinated, protected monkeys. Lymph nodes from vaccinated, unprotected animals also had significantly more CD8+-T-cell proliferation and marked lymph node hyperplasia than the lymph nodes of vaccinated, protected monkeys. Thus, higher levels of virus replication were associated with increased beta-chemokine secretion and there is no evidence that beta-chemokines contributed to the SHIV89.6-mediated control of viral replication after intravaginal challenge with SIVmac239.
Activation of Stat3 Transcription Factor by
Herpesvirus Saimiri
STP-A Oncoprotein
Authors: Chung Young-Hwa , Cho Nam-hyuk , Garcia Maria Ines , Lee Sun-Hwa , Feng Pinghui , Jung Jae U.
Published: May 2004

The saimiri transforming protein (STP) oncogene of
Herpesvirus saimiri
subgroup A strain 11 (STP-A11) is not required for viral replication but is required for lymphoid cell immortalization in culture and lymphoma induction in primates. We previously showed that STP-A11 interacts with cellular Src kinase through its SH2 binding motif and that this interaction elicits Src signal transduction. Here we demonstrate that STP-A11 interacts with signal transducer and activator of transcription 3 (Stat3) independently of Src association and that the amino-terminal short proline-rich motif of STP-A11 and the central linker region of Stat3 are necessary for their interaction. STP-A11 formed a triple complex with Src kinase and Stat3 where Src kinase phosphorylated Stat3, resulting in the nuclear localization and transcriptional activation of Stat3. Consequently, the constitutively active Stat3 induced by STP-A11 elicited cellular signal transduction, which ultimately induced cell survival and proliferation upon serum deprivation. Furthermore, this activity was strongly correlated with the induction of Fos, cyclin D1, and Bcl-XL expression. These results demonstrate that STP-A11 independently targets two important cellular signaling molecules, Src and Stat3, and that these proteins cooperate efficiently to induce STP-A11-mediated transformation.
Membrane Association of Greasy Grouper Nervous Necrosis Virus Protein A and Characterization of Its Mitochondrial Localization Targeting Signal
Authors: Guo Yan Xiang , Chan Shzu-Wei , Kwang Jimmy
Published: May 2004

Localization of RNA replication to intracellular membranes is a universal feature of positive-strand RNA viruses. The betanodavirus greasy grouper (
Epinephelus tauvina
) nervous necrosis virus (GGNNV) is a positive-RNA virus with one of the smallest genomes among RNA viruses replicating in fish cells. To understand the localization of GGNNV replication complexes, we generated polyclonal antisera against protein A, the GGNNV RNA-dependent RNA polymerase. Protein A was detected at 5 h postinfection in infected sea bass cells. Biochemical fractionation experiments revealed that GGNNV protein A sedimented with intracellular membranes upon treatment with an alkaline pH and a high salt concentration, indicating that GGNNV protein A is tightly associated with intracellular membranes in infected cells. Confocal immunofluorescence microscopy and bromo-UTP incorporation studies identified mitochondria as the intracellular site of protein A localization and viral RNA synthesis. In addition, protein A fused with green fluorescent protein (GFP) was detected in the mitochondria in transfected cells and was demonstrated to be tightly associated with intracellular membranes by biochemical fractionation analysis and membrane flotation assays, indicating that protein A alone was sufficient for mitochondrial localization in the absence of RNA replication, nonstructural protein B, or capsid proteins. Three sequence analysis programs showed two regions of hydrophobic amino acid residues, amino acids 153 to 173 and 229 to 249, to be transmembrane domains (TMD) that might contain a membrane association domain. Membrane fraction analysis showed that the major domain is N-terminal amino acids 215 to 255, containing the predicted TMD from amino acids 229 to 249. Using GFP as the reporter by systematically introducing deletions of these two regions in the constructs, we further confirmed that the N-terminal amino acids 215 to 255 of protein A function as a mitochondrial targeting signal.
Development of a Novel Helper-Dependent Adenovirus-Epstein-Barr Virus Hybrid System for the Stable Transformation of Mammalian Cells
Authors: Dorigo Oliver , Gil Jose S. , Gallaher Sean D. , Tan Brenton T. , Castro Maria G. , Lowenstein Pedro R. , Calos Michele P. , Berk Arnold J.
Published: May 2004

Epstein-Barr virus (EBV) episomes are stably maintained in permissive proliferating cell lines due to EBV nuclear antigen 1 (EBNA-1) protein-mediated replication and segregation. Previous studies showed the ability of EBV episomes to confer long-term transgene expression and correct genetic defects in deficient cells. To achieve quantitative delivery of EBV episomes in vitro and in vivo, we developed a binary helper-dependent adenovirus (HDA)-EBV hybrid system that consists of one HDA vector for the expression of Cre recombinase and a second HDA vector that contains all of the sequences for the EBV episome flanked by
loxP
sites. Upon coinfection of cells, Cre expressed from the first vector recombined
loxP
sites on the second vector. The resulting circular EBV episomes expressed a transgene and contained the EBV-derived family of repeats, an EBNA-1 expression cassette, and 19 kb of human DNA that functions as a replication origin in mammalian cells. This HDA-EBV hybrid system transformed 40% of cultured cells. Transgene expression in proliferating cells was observed for over 20 weeks under conditions that selected for the expression of the transgene. In the absence of selection, EBV episomes were lost at a rate of 8 to 10% per cell division. Successful delivery of EBV episomes in vivo was demonstrated in the liver of transgenic mice expressing Cre from the albumin promoter. This novel gene transfer system has the potential to confer long-term episomal transgene expression and therefore to correct genetic defects with reduced vector-related toxicity and without insertional mutagenesis.
Murine Gammaherpesvirus 68 Open Reading Frame 31 Is Required for Viral Replication
Authors: Jia Qingmei , Wu Ting-Ting , Liao Hsiang-I , Chernishof Vasili , Sun Ren
Published: May 2004

Murine gammaherpesvirus 68 (MHV-68) is genetically related to the human gammaherpesviruses, Kaposi's sarcoma-associated herpesvirus (KSHV/HHV-8) and Epstein-Barr virus (EBV). It has been proposed as a model for gammaherpesvirus infection and pathogenesis. Open reading frame 31 (ORF31) is conserved among the
Beta
- and
Gammaherpesvirinae
subfamily, and there is no known mammalian homologue of this protein. The function of MHV-68 ORF31 and its viral homologues has not yet been determined. We described here a primary characterization of this protein and its requirement for lytic replication. The native MHV-68 ORF31 was detected at peak levels by 24 h postinfection, and the FLAG-tagged and green fluorescent protein fusion ORF31 were localized in the cytoplasm and nucleus in a diffuse pattern. Two independent experimental approaches were then utilized to demonstrate that ORF31 was required for lytic replication. First, small interfering RNA generated against ORF31 expression blocked protein expression and virus production in transfected cells. Then, two-independent bacterial artificial chromosome-derived ORF31-null MHV-68 mutants (31STOP) were generated and found to be defective in virus production in fibroblast cells. This defect can be rescued in
trans
by MHV-68 ORF31 and importantly by its KSHV homologue. A repair virus of 31STOP was also generated by homologous recombination in fibroblast cells. Finally, we showed that the defect in ORF31 blocked late lytic protein expression. Our results demonstrate that MHV-68 ORF31 is required for viral lytic replication, and its function is conserved in its KSHV homologue.
Late Assembly Motifs of Human T-Cell Leukemia Virus Type 1 and Their Relative Roles in Particle Release
Authors: Heidecker Gisela , Lloyd Patricia A. , Fox Kristi , Nagashima Kunio , Derse David
Published: May 2004

Three late assembly domain consensus motifs, namely PTAP, PPPY, and LYPXL, have been identified in different retroviruses. They have been shown to interact with the cellular proteins TSG101, Nedd4, and AP2 or AIP, respectively. Human T-cell leukemia virus type 1 (HTLV-1) has a PPPY and a PTAP motif, separated by two amino acids, located at the end of MA, but only the PPPY motif is conserved in the deltaretrovirus group. Like other retroviral peptides carrying the late motif, MA is mono- or di-ubiquitinated. A mutational analysis showed that 90% of PPPY mutant particles were retained in the cell compared to 15% for the wild-type virus. Mutations of the PTAP motif resulted in a 20% decrease in particle release. In single-cycle infectivity assays, the infectious titers of late motif mutants correlated with the amounts of released virus, as determined by an enzyme-linked immunosorbent assay. We observed binding of MA to the WW domains of the Nedd4 family member WWP1 but not to the amino-terminal ubiquitin E2 variant domain of TSG101 in mammalian two-hybrid analyses. The binding to WWP1 was eliminated when the PPPY motif was mutated. However, MA showed binding to TSG101 in the yeast two-hybrid system that was dependent on an intact PTAP motif. A dominant-negative (DN) mutant of WWP1 could inhibit budding of the intact HTLV-1 virus. In contrast, DN TSG101 only affected the release of virus-like particles encoded by Gag expression plasmids. Electron and fluorescent microscopy showed that Gag accumulates in large patches in the membranes of cells expressing viruses with PPPY mutations. Very few tethered immature particles could be detected in these samples, suggesting that budding is impaired at an earlier step than in other retroviruses.
Herpesvirus Protease Inhibition by Dimer Disruption
Authors: Shimba Nobuhisa , Nomura Anson M. , Marnett Alan B. , Craik Charles S.
Published: May 2004

Kaposi's sarcoma-associated herpesvirus (KSHV), like all herpesviruses, encodes a protease (KSHV Pr), which is necessary for the viral lytic cycle. Herpesvirus proteases function as obligate dimers; however, each monomer has an intact, complete active site which does not interact directly with the other monomer across the dimer interface. Protein grafting of an interfacial KSHV Pr α-helix onto a small stable protein, avian pancreatic polypeptide, generated a helical 30-amino-acid peptide designed to disrupt the dimerization of KSHV Pr. The chimeric peptide was optimized through protein modeling of the KSHV Pr-peptide complex. Circular dichroism analysis and gel filtration chromatography revealed that the rationally designed peptide adopts a helical conformation and is capable of disrupting KSHV Pr dimerization, respectively. Additionally, the optimized peptide inhibits KSHV Pr activity by 50% at a ∼200-fold molar excess of peptide to KSHV Pr, and the dissociation constant was estimated to be 300 μM. Mutagenesis of the interfacial residue M197 to a leucine resulted in an inhibitory concentration which was twofold higher for KSHV Pr M197L than for KSHV Pr, in agreement with the model that the dimer interface is involved in peptide binding. These results indicate that the dimer interface, as well as the active sites, of herpesvirus proteases is a viable target for inhibiting enzyme activity.
Partitioning mycorrhizal influence on water relations of Phaseolus vulgaris into soil and plant components
Authors: Augé Robert M , Sylvia David M , Park Soon , Buttery Brian R , Saxton Arnold M , Moore Jennifer L , Cho Keunho
Published: May 2004

There is growing appreciation of arbuscular mycorrhizal effects on soil properties and their potential consequences on plant behavior. We examined the possibility that mycorrhizal soil may directly influence plant water relations. Using wild-type and noncolonizing bean mutants planted into soils previously produced using mycorrhizal or nonmycorrhizal sorghum plants, we partitioned mycorrhizal influence on stomatal conductance and drought resistance into soil and root components, testing whether effects of mycorrhizal fungi occurred mostly via mycorrhization of roots, mycorrhization of soil, or both. The mutation itself had no effect on any water relations parameter. Colonization by Gigaspora margarita Gerdemann & Trappe and Glomus intraradices Schenck & Smith had appreciable effects on leaf water potential at the lethal point and on osmotic adjustment, relative to nonmycorrhizal plants of comparable size. Mycorrhizal effects on drought resistance were attributable to an effect on the plant itself rather than to an effect of mycorrhizal soil. Mycorrhizal effects on stomatal conductance were attributable to mycorrhization of both roots and soil, as well as to mycorrhization of roots alone. Surprisingly, merely growing in a mycorrhizal soil resulted in promotion of stomatal conductance of nonmycorrhizal plants in both amply watered and droughted plants. Mycorrhizal effects on droughted plants did not appear to be related to altered soil water retention properties, as Gigaspora margarita and Glomus intraradices altered the soil's moisture characteristic curve only slightly.Key words: arbuscular mycorrhizal symbiosis, bean, drought, Gigaspora margarita, Glomus intraradices, stomatal conductance.
Studies in the Alismataceae. XII. Floral organogenesis in Damasonium alisma and Baldellia ranunculoides, and comparisons with Butomus umbellatus
Authors: Charlton W A
Published: May 2004

Floral organogenesis of Damasonium alisma Mill. occurs at first in an alternating trimerous pattern typical of Alismataceae, with the formation of three sepals, then three bulges, corresponding to the CA (common perianthandroecium) primordia described in some other Alismataceae, alternating with the sepals. A petal is initiated on each bulge, and a pair of stamens is initiated either on or close to it. Three carpels are initiated in positions alternating with the petals and stamen pairs, and three further carpels then arise above and between the first three. At maturity and in fruit the carpels lie in a whorled arrangement. Floral development in Baldellia ranunculoides (L.) Parl. is identical up to the initiation of the six stamens. After this, six carpel primordia are formed alternating with the stamens, and further carpel primordia arise alternating with those previously formed. In Butomus, up to the initiation of the first six stamens, the general plan of development resembles that of the two Alismataceae. Three further whorls of organs arise in alternation: a whorl of three stamens arises over the stamen pairs followed by two whorls each of three carpel primordia. It is argued that the trimerous appearance of the whorl of sepals (or outer perianth in Butomus) arises de novo and represents a genuine expression of trimery. However, most of the subsequent features of development in these flowers can be seen as arising from phyllotactic mechanisms that cause new primordia to arise between and above pre-existing ones. Consequently the appearance of trimerous or hexamerous whorls above the first whorl of perianth does not represent a fundamental feature of development. The nature of variations in the positional relationships of inner perianth, stamen, and carpel primordia in various Alismataceae and Butomus strengthen the case that there is a significant developmental association between inner perianth members and associated pairs of stamens, which may be connected with the evolution of the flowers from pseudanthial structures.Key words: Baldellia, Butomus, Damasonium, Alismatidae, flower, organogenesis.
Regioselectivity in SNH reactions of some 3-nitro-1,5-naphthyridines with chloromethyl phenyl sulfone
Authors: Grzegożek Maria , Szpakiewicz Barbara
Published: May 2004

3-Nitro-1,5-naphthyridine and its 2-substituted derivatives react with the carbanion of chloromethyl phenyl sulfone to give hydrogen-substitution products at position 4 in high yield. The intermediacy of 4-(phenylsulfonyl)chloromethyl σ adducts of 2-R-3-nitro-1,5-naphthyridines (R = H, D, Cl, OC2H5, NHCH3, OH) was established by1H NMR spectroscopy. A convenient synthesis of 2-N-methylamino-3-nitro-1,5-naphthyridine is reported. Key words: 3-nitro-1,5-naphthyridines, anionic (phenylsulfonyl)chloromethyl σ adducts, vicarious nucleophilic substitution.
Preparation of 4-anilino-6-aryl-2H-pyran-2-ones from trilithiated acetoacetanilides and aromatic esters
Authors: Downs Jennifer R , Grant Sally P , Townsend Jessica D , Schady Deborah A , Pastine Stefan J , Embree Mildred C , Metz Clyde R , Pennington William T , Bailey Walsch Rosa D , Beam Charles F
Published: May 2004

Acetoacetanilide and 4′-chloroacetoacetanilide were trilithiated with excess lithium diisopropylamide and condensed with several aromatic esters, followed by neutralization, separate acid cyclization, and rearrangements. After C-acylation of trilithiated acetoacetanilides and cyclization to 4H-pyran-4-ones, these compounds underwent multistep rearrangements to 4-anilino-6-aryl-2H-pyran-2-ones.Key words: pyranones, trianions, Claisen-type condensations, rearrangements.
PRICING OF THE AMERICAN PUT UNDER LÉVY PROCESSES
Authors: Levendorskiǐ S. Z.
Published: May 2004

We consider the American put with finite time horizon T, assuming that, under an EMM chosen by the market, the stock returns follow a regular Lévy process of exponential type. We formulate the free boundary value problem for the price of the American put, and develop the non-Gaussian analog of the method of lines and Carr's randomization method used in the Gaussian option pricing theory. The result is the (discretized) early exercise boundary and prices of the American put for all strikes and maturities from 0 to T. In the case of exponential jump-diffusion processes, a simple efficient pricing scheme is constructed. We show that for many classes of Lévy processes, the early exercise boundary is separated from the strike price by a non-vanishing margin on the interval [0, T), and that as the riskless rate vanishes, the optimal exercise price goes to zero uniformly over the interval [0, T), which is in the stark contrast with the Gaussian case.
AN AVERAGE LINEAR TIME ALGORITHM FOR WEB USAGE MINING
Authors: BORGES JOSÉ , LEVENE MARK
Published: May 2004

In this paper, we study the complexity of a data mining algorithm for extracting patterns from user web navigation data that was proposed in previous work.3 The user web navigation sessions are inferred from log data and modeled as a Markov chain. The chain's higher probability trails correspond to the preferred trails on the web site. The algorithm implements a depth-first search that scans the Markov chain for the high probability trails. We show that the average behaviour of the algorithm is linear time in the number of web pages accessed.
STUDY ON SIMILARITY AND SIMILARITY REASONING
Authors: HE BIN
Published: May 2004

Based on extension models of a new science called Extenics, this paper presents formalized study on similarity and similarity reasoning. The concepts of δ-similarity and δ-similar extension elements are introduced firstly, and then the substitution principles of similarity for solving incompatible problems are set up, showing that similarity substitution is an effective way to solve incompatible problems in the practical world. In addition, the quantitative calculation of similarity is discussed. Finally, three basic rules for similarity reasoning are developed as well.
A NEGOTIATION FRAMEWORK FOR ORGANIZATIONAL INFORMATION SYSTEMS
Authors: ZAROUR NACEREDDINE , BOUFAIDA MAHMOUD , SEINTURIER LIONEL
Published: May 2004

In the last few years there has been a growing need for organizations to build cooperative information systems. These organizations and their processes that manipulate vast quantities of information are based on heterogeneous, distributed and autonomous data sources. However, without appropriated techniques of negotiation, any execution of organizational information systems would yield to disjoining and error-prone behavior, while requiring excessive effort to build and maintain. In this paper, we present a flexible negotiation framework, which is based on social constraints and conversation plans. The infrastructure of this framework may well fit the negotiation needs of organizational information systems in a highly dynamic and unpredictable environment. This framework has been implemented as a negotiation service in our cooperative application environment. Some examples are given from manufacturing applications.
cWINNOWER ALGORITHM FOR FINDING FUZZY DNA MOTIFS
Authors: LIANG S. , SAMANTA M. P. , BIEGEL B. A.
Published: May 2004

The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich in proteinbinding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. The algorithm finds such motifs if a clique consisting of a suffciently large number of mutated copies of the motif (i.e., the signals) is present in the DNA sequence. The cWINNOWER algorithm substantially improves the sensitivity of the winnower method of Pevzner and Sze by imposing a consensus constraint, enabling it to detect much weaker signals. We studied the minimum detectable clique size qc as a function of sequence length N for random sequences. We found that qc increases linearly with N for a fast version of the algorithm based on counting threemember sub-cliques. Imposing consensus constraints reduces qc by a factor of three in this case, which makes the algorithm dramatically more sensitive. Our most sensitive algorithm, which counts four-member sub-cliques, needs a minimum of only 13 signals to detect motifs in a sequence of length N=12,000 for (l,d)=(15,4).
INDEX-BASED SIMILARITY SEARCH FOR PROTEIN STRUCTURE DATABASES
Authors: ÇAMOĞLU ORHAN , KAHVECI TAMER , SINGH AMBUJ K.
Published: May 2004

We propose new methods for finding similarities in protein structure databases. These methods extract feature vectors on triplets of SSEs (Secondary Structure Elements) of proteins. The feature vectors are then indexed using a multidimensional index structure. Our first technique considers the problem of finding proteins similar to a given query protein in a protein dataset. It quickly finds promising proteins using the index structure. These proteins are then aligned to the query protein using a popular pairwise alignment tool such as VAST. We also develop a novel statistical model to estimate the goodness of a match using the SSEs. Our second technique considers the problem of joining two protein datasets to find an all-to-all similarity. Experimental results show that our techniques improve the pruning time of VAST 3 to 3.5 times, while keeping the sensitivity similar. Our technique can also be incorporated with DALI and CE to improve their running times by a factor of 2 and 2.7 respectively. The software is available online at .
AN EMPIRICAL STUDY OF THE UNIVERSAL CHEMICAL KEY ALGORITHM FOR ASSIGNING UNIQUE KEYS TO CHEMICAL COMPOUNDS
Authors: GROSSMAN ROBERT , KASTURI PAVAN , HAMELBERG DONALD , LIU BING
Published: May 2004

In this paper, we introduce an algorithm that assigns an essentially unique key called the Universal Chemical Key (UCK) to molecular structures. The molecular structures are represented as labeled graphs whose nodes abstract atoms and whose edges abstract bonds. The algorithm was tested on 236,917 compounds obtained from the National Cancer Institute (NCI) database of chemical compounds. On this database, the UCK algorithm assigned unique keys for chemicals with distinct molecular structures.
Inferable Centers, Centering Transitions, and the Notion of Coherence
Authors: Fais Laurel
Published: May 2004

A centering analysis of the corpus of Japanese e-mail that is examined in this article relies heavily on the inclusion of inferable centers. However, utilizing this type of center results in a high level of indeterminacy in labeling transitions and thus in characterizing the coherence of the corpus. The difficulty lies in the requirement of identity of discourse entities in the definitions of transition states. Lexical cohesion is proposed as a well-defined notion to replace the intuitions captured by the use of inferable centers. Two new transitions, based on lexical relatedness instead of identity, supplement the standard definitions and more adequately characterize coherence in this corpus. Implications and extensions of the proposal are discussed.
Learning Domain Ontologies from Document Warehouses and Dedicated Web Sites
Authors: Navigli Roberto , Velardi Paola
Published: May 2004

We present a method and a tool, OntoLearn, aimed at the extraction of domain ontologies from Web sites, and more generally from documents shared among the members of virtual organizations. OntoLearn first extracts a domain terminology from available documents. Then, complex domain terms are semantically interpreted and arranged in a hierarchical fashion. Finally, a general-purpose ontology, WordNet, is trimmed and enriched with the detected domain concepts. The major novel aspect of this approach is semantic interpretation, that is, the association of a complex concept with a complex term. This involves finding the appropriate WordNet concept for each word of a terminological string and the appropriate conceptual relations that hold among the concept components. Semantic interpretation is based on a new word sense disambiguation algorithm, called structural semantic interconnections.
Flow around a Complex Building: Comparisons between Experiments and a Reynolds-Averaged Navier–Stokes Approach
Authors: Calhoun Ronald , Gouveia Frank , Shinn Joseph , Chan Stevens , Stevens Dave , Lee Robert , Leone John
Published: May 2004

An experiment investigating flow around a single complex building was performed in 2000. Sonic anemometers were placed around the building, and two-dimensional wind velocities were recorded. An energy-budget and wind-measuring station was located upstream to provide stability and inflow conditions. In general, the sonic anemometers were located in a horizontal plane around the building at a height of 2.6 m above the ground. However, at the upwind wind station, two levels of the wind were measured. The resulting database can be sampled to produce mean wind fields associated with specific wind directions such as 210°, 225°, and 240°. The data are available generally and should be useful for testing computational fluid dynamical models for flow around a building. An in-house Reynolds-averaged Navier–Stokes approach was used to compare with the mean wind fields for the predominant wind directions. The numerical model assumed neutral flow and included effects from a complex array of trees in the vicinity of the building. Two kinds of comparisons are presented: 1) direct experimental versus modeled vector comparisons and 2) a numerical metric approach that focuses on wind magnitude and direction errors. The numerical evaluation generally corroborates the vector-to-vector inspection, showing reasonable agreement for the mean wind fields around the building. However, regions with special challenges for the model were identified. In particular, recirculation regions were especially difficult for the model to capture correctly. In the 240° case, there is a tendency for the model to exaggerate the turning effect in the wind caused by the effect of the building. Two different kinds of simulations were performed: 1) predictive calculations with a reasonable but not high-fidelity representation of the building's architectural complexity and 2) postexperiment calculations in which a large number of architectural features were well represented. Although qualitative evidence from inspection of the angles of the vectors in key areas such as around the southeast corner of the building indicated an improvement from the higher-fidelity representation of the building, the general numerical evaluation indicated little difference in the quality of the two solutions.
The Impact of Doppler Lidar Wind Observations on a Single-Level Meteorological Analysis
Authors: Riishøjgaard L. P. , Atlas R. , Emmitt G. D.
Published: May 2004

Through the use of observation operators, modern data assimilation systems have the capability to ingest observations of quantities that are not themselves model variables but are mathematically related to those variables. An example of this is the so-called line-of-sight (LOS) winds that a spaceborne Doppler wind lidar (DWL) instrument would provide. The model or data assimilation system ideally would need information about both components of the horizontal wind vectors, whereas the observations in this case would provide only the projection of the wind vector onto a given direction. The estimated or analyzed value is then calculated essentially as a weighted average of the observation itself and the model-simulated value of the observed quantity. To assess the expected impact of a DWL, it is important to examine the extent to which a meteorological analysis can be constrained by the LOS winds. The answer to this question depends on the fundamental character of the atmospheric flow fields that are analyzed, but, just as important, it also depends on the real and assumed error covariance characteristics of these fields. A single-level wind analysis system designed to explore these issues has been built at the NASA Data Assimilation Office. In this system, simulated wind observations can be evaluated in terms of their impact on the analysis quality under various assumptions about their spatial distribution and error characteristics and about the error covariance of the background fields. The basic design of the system and experimental results obtained with it are presented. The experiments were designed to illustrate how such a system may be used in the instrument concept definition phase.
The Australian Air Quality Forecasting System. Part II: Case Study of a Sydney 7-Day Photochemical Smog Event
Authors: Hess G. D. , Tory K. J. , Cope M. E. , Lee S. , Puri K. , Manins P. C. , Young M.
Published: May 2004

The performance of the Australian Air Quality Forecasting System (AAQFS) is examined by means of a case study of a 7-day photochemical smog event in the Sydney region. This was the worst smog event for the 2000/ 01 oxidant season, and, because of its prolonged nature, it provided the opportunity to demonstrate the ability of AAQFS to forecast situations involving recirculation of precursors and remnant ozone, fumigation, and complex meteorological dynamics. The forecasting system was able to successfully predict high values of ozone, although at times the peak concentrations for the inland stations were underestimated. The dynamics for the Sydney region require a sensitive balance between the synoptic and mesoscale flows. Often high concentrations of ozone were advected inland by the sea breeze. On two occasions the system forecast a synoptic flow that was too strong, which blocked the inland advancement of the sea breeze. The peak ozone forecasts were underpredicted at the inland stations on those occasions. An examination of possible factors causing forecast errors has indicated that the AAQFS is more sensitive to errors in the meteorological conditions, rather than in the emissions or chemical mechanism in the Sydney region.
Quartic moveout coefficient for a dipping azimuthally anisotropic layer
Authors: Pech Andrés , Tsvankin Ilya
Published: May 2004

Interpretation and inversion of azimuthally varying nonhyperbolic reflection moveout requires accounting for both velocity anisotropy and subsurface structure. Here, our previously derived exact expression for the quartic moveout coefficient A4is applied to P‐wave reflections from a dipping interface overlaid by a medium of orthorhombic symmetry.

The weak‐anisotropy approximaton for the coefficient A4in a homogeneous orthorhombic layer is controlled by the anellipticity parameters η(1), η(2), and η(3), which are responsible for time processing of P‐wave data. If the dip plane of the reflector coincides with the vertical symmetry plane [x1, x3], A4on the dip line is proportional to the in‐plane anellipticity parameter η(2)and always changes sign for a dip of 30○. The quartic coefficient on the strike line is a function of all three η–parameters, but for mild dips it is mostly governed by η(1)—the parameter defined in the incidence plane [x2, x3]. Whereas the magnitude of the dip line A4typically becomes small for dips exceeding 45○, the nonhyperbolic moveout on the strike line may remain significant even for subvertical reflectors. The character of the azimuthal variation of A4depends on reflector dip and is quite sensitive to the signs and relative magnitudes of η(1), η(2), and η(3). The analytic results and numerical modeling show that the azimuthal pattern of the quartic coefficient can contain multiple lobes, with one or two azimuths of vanishing A4between the dip and strike directions.

The strong influence of the anellipticity parameters on the azimuthally varying coefficient A4suggests that nonhyperbolic moveout recorded in wide‐azimuth surveys can help to constrain the anisotropic velocity field. Since for typical orthorhombic models that describe naturally fractured reservoirs the parameters η(1,2,3)are closely related to the fracture density and infill, the results of azimuthal nonhyperbolic moveout analysis can also be used in reservoir characterization.
Migration velocity analysis in factorized VTI media
Authors: Sarkar Debashish , Tsvankin Ilya
Published: May 2004

One of the main challenges in anisotropic velocity analysis and imaging is simultaneous estimation of velocity gradients and anisotropic parameters from reflection data. Approximating the subsurface by a factorized VTI (transversely isotropic with a vertical symmetry axis) medium provides a convenient way of building vertically and laterally heterogeneous anisotropic models for prestack depthmigration.

The algorithm for P‐wave migration velocity analysis (MVA) introduced here is designed for models composed of factorized VTI layers or blocks with constant vertical and lateral gradients in the vertical velocity VP0. The anisotropic MVA method is implemented as an iterative two‐step procedure that includes prestack depth migration (imaging step) followed by an update of the medium parameters (velocity‐analysis step). The residual moveout of the migrated events, which is minimized during the parameter updates, is described by a nonhyperbolic equation whose coefficients are determined by 2D semblance scanning.

For piecewise‐factorized VTI media without significant dips in the overburden, the residual moveout of P‐wave events in image gathers is governed by four effective quantities in each block: (1) the normal‐moveout velocity Vnmoat a certain point within the block, (2) the vertical velocity gradient kz, (3) the combination kx[Formula: see text] of the lateral velocity gradient kxand the anisotropic parameter δ, and (4) the anellipticity parameter η. We show that all four parameters can be estimated from the residual moveout for at least two reflectors within a block sufficiently separated in depth. Inversion for the parameter η also requires using either long‐spread data (with the maximum offset‐to‐depth ratio no less than two) from horizontal interfaces or reflections from dipping interfaces.

To find the depth scale of the section and build a model for prestack depth migration using the MVA results, the vertical velocity VP0needs to be specified for at least a single point in each block. When no borehole information about VP0is available, a well‐focused image can often be obtained by assuming that the vertical‐velocity field is continuous across layer boundaries. A synthetic test for a three‐layer model with a syncline structure confirms the accuracy of our MVA algorithm in estimating the interval parameters Vnmo, kz, kx, and η and illustrates the influence of errors in the vertical velocity on the image quality.
Nonlinear and dispersive acoustic wave propagation
Authors: Hokstad Ketil
Published: May 2004

Because of cracks and poor consolidation, rocks may have large third‐and fourth‐order nonlinear elastic moduli. Even though strains are small, nonlinear effects may be important in acoustic wave transmission experiments. A nonlinear and dispersive extension of Hooke's law is proposed. Combined with Newton's law, this gives a nonlinear and dispersive acoustic wave equation. For some combinations of nonlinear and dispersive parameters, the wave equation can be reduced to the Korteweg‐deVries equation, such that analytical solutions can be obtained. Finite‐difference simulations with an initial Ricker wavelet show that the nonlinear terms in the wave equation steepen the wavefront and higher harmonics in the frequency spectrum. When dispersion is included, a nonlinear stress–strain relation with hysteresis is observed.
Volume Change Measurement of Soil Specimen in Triaxial Test
Authors: Leong EC , Agus SS , Rahardjo H
Published: May 2004

Measuring the volume change of a soil specimen during a test has become a standard routine in laboratory testing. Accurate volume change measurement does not depend solely on the resolution of the measurement devices used but also on other factors such as the measurement method, cell pressure, temperature fluctuations, system creep, and system compliance. This paper examines volume change measurement inferred from the volume of the confining water in a triaxial cell. In particular, the effects of stiffness of the pressure cell and temperature fluctuations on the accuracy of the volume change measurements are investigated. A method to correct for temperature effects on the volume of water in a triaxial pressure cell for providing a more reliable measurement of the volume change of a soil specimen is suggested. The suggested method can also be applied in triaxial apparatuses using double cells.
Determination of the Soil Water Characteristic Curve of Highly Compressible Materials: Case Study of Pulp and Paper By-Product
Authors: Cabral AR , Planchet L , Marinho FA , Lefebvre G
Published: May 2004

A technique was developed for the determination of various points of the soil-water characteristic curve (SWCC)—including the air entry value (AEV)—of compressible materials from one single test. The testing setup, which employs the axis-translation technique, is presented and the testing methodology, explained. With the proposed methodology, it is possible to determine the volume of the sample at various stages of the desaturation process, thus making it possible to determine the degree of saturation and volumetric water content for each level of suction applied. The results of some tests performed on deinking residues (DR), a fibrous and highly compressible industrial by-product used in geoenvironmental works, are presented and discussed. It is shown that if volume changes that samples undergo during desaturation are not considered, the volumetric water content and degree of saturation of the sample is underestimated at all suction values. One important consequence is that lower hydraulic conductivities are obtained from mathematical models based on the SWCC.
Frequency Domain Determination of G Using Bender Elements
Authors: Greening PD , Nash DFT
Published: May 2004

Methods for determination of shear wave velocity (vs) with bender elements using frequency domain techniques are reviewed. An enhanced method is proposed, which is quicker and provides more information than existing techniques. The method can be implemented using a spectrum analyzer—a common piece of hardware.

The validity of the method is demonstrated by means of a series of bench top tests on a reconstituted clay sample. The results are compared both with existing frequency domain practice and with established time-domain techniques.

The results reveal that the system comprising benders elements and soil sample is dispersive. The relationship between velocity and frequency is established in detail for several propagation paths through the sample, allowing some insight to be gained into the factors influencing the dispersion characteristics.
A Physical Model for Sloping Capillary Barriers
Authors: Tami D , Rahardjo H , Leong E-C , Fredlund DG
Published: May 2004

A physical capillary barrier model has been developed to study the mechanism and the effectiveness of a capillary barrier for slope stabilization purposes. A sloping two-layer capillary barrier model consisting of a relatively fine soil layer over a relatively coarse soil layer was constructed inside a specially designed apparatus. Simulated rainfalls of different intensities and durations representative of tropical climatic conditions were applied through a rainfall simulator. Various instruments consisting of tensiometers for pore-water pressure measurement, time domain reflectometry (TDR) for water content measurement, magnetic flow meter and electronic weight balances for water balance measurements were used in the experiment. The results obtained from various types of instrumentation were in good agreement. The experimental results show that the performance of the capillary barrier under the influence of a high precipitation rate is primarily governed by the storage capacity of the relatively fine soil of the capillary barrier.
Transition Toughness Modeling of Steels Since RKR
Authors: Kirk MT , Natishan MAE , Wagenhofer M
Published: May 2004

In this paper we trace the development of transition fracture toughness models from the landmark paper of Ritchie, Knott, and Rice in 1973 up through the current day. While such models have become considerably more sophisticated since 1973, none have achieved the goal of blindly predicting fracture toughness data. In this paper we suggest one possible way to obtain such a predictive model.