bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of the stress orientation distribution function using pulsed neutron sources
Authors: Wang Y. D. , Wang X.-L. , Stoica A. D. , Richardson J. W. , Lin Peng R.
Published: January 2003

The stress orientation distribution function (SODF) was recently introduced as a mean-field representation to describe the grain-orientation dependence of intergranular stress. Pulsed neutron sources are ideally suited for the determination of the SODF since multiple reflections can be measured simultaneously with comparable precision. A method is developed for constructing the SODF from strain pole figures measured with a pulsed neutron source and demonstrated with cold-rolled interstitial-free steel. The experimental results are compared with those measured with a reactor-based constant-wavelength diffractometer. It is shown that access to a large number of reflections on a pulsed neutron source improves the precision of the experimental SODF and facilitatesin situstudies of the evolution of the intergranular stress during deformation and annealing.
New method for determining hexagonal direction indices and their relationship to crystallographic directions
Authors: Hofmann D. C. , Lubarda V. A.
Published: January 2003

A new method for determining the hexagonal direction indices is introduced, which is more practical than other commonly used methods. The relationship between the crystallographic directions and hexagonal direction indices for face-centered cubic crystals is derived. Different sets of hexagonal indices for equivalent crystallographic directions are discussed.
Energy-dispersive X-ray diffraction on thin films and its application to superconducting samples
Authors: Rossi Albertini V. , Paci B. , Meloni S. , Caminiti R. , Bencivenni L.
Published: January 2003

Energy-dispersive X-ray diffraction is applied to investigate double-layer PBCO/YBCO thin films deposited by laser ablation. The merits of this technique for the structural study of films are discussed. It is shown that the rocking curves of the Bragg reflections of a film along thecdirection can be simultaneously collected, allowing the accurate evaluation of its angular spread. A systematic displacement of the rocking curves of the film with respect to those of the substrate was found, revealing a slight divergence of the growth direction from the normal to the substrate surface.
Numerical computation of critical properties and atomic basins from three-dimensional grid electron densities
Authors: Katan C. , Rabiller P. , Lecomte C. , Guezo M. , Oison V. , Souhassou M.
Published: January 2003

InteGriTyis a software package that performs topological analysis following the AIM (atoms in molecules) approach on electron densities given on three-dimensional grids. Tricubic interpolation is used to obtain the density, its gradient and the Hessian matrix at any required position. Critical points and integrated atomic properties have been derived from theoretical densities calculated for the compounds NaCl and TTF–2,5Cl2BQ (tetrathiafulvalene–2,5-dichlorobenzoquinone), thus covering the different kinds of chemical bonds: ionic, covalent, hydrogen bonds and other intermolecular contacts.
Improved measures of quality for the atomic pair distribution function
Authors: Peterson Peter F. , Božin Emil S. , Proffen Thomas , Billinge Simon J. L.
Published: January 2003

The introduction of neutron spallation-source instruments, such as the General Materials Diffractometer (GEM) at ISIS, allows measurement of pair distribution function (PDF) data at significantly higher rates than previously possible. As a result of the increased rate, a single experiment can produce over a hundred individual runs. Manual processing of all these data using traditional methods becomes inconvenient and inefficient. This article presents quality criteria that help produce automated direct Fourier transformed PDFs of quality similar to hand-processed data, and compares optimization methods.
Preliminary tests on the use of an acoustic levitator for liquid X-ray diffraction experiments
Authors: Cerenius Yngve , Oskarsson Åke , Santesson Sabina , Nilsson Staffan , Kloo Lars
Published: January 2003

Some preliminary tests at the crystallography beamline I711 at the MAX II synchrotron in Lund, Sweden, have shown that it is possible to use acoustical levitation to keep a droplet of liquid and solid (powder) samples in an X-ray beam for a sufficient time for collection of the X-ray diffraction pattern.
A simple and rapid method for mounting protein crystals at room temperature
Authors: Mac Sweeney Aengus , D'Arcy Allan
Published: January 2003

Cryocooling of protein crystals for X-ray data collection has now become a routine method in the majority of biostructural laboratories. The improvement of facilities at synchrotron sources and their increased use has made it essential to have properly frozen crystals for optimal data collection. Although in general crystals can be cooled without significant damage, there are often cases in which crystals with slight disorder or twinning problems suffer considerably during the freezing process. In other cases, poor or mosaic diffraction may be blamed on the cryoprotectant or cooling protocol. Many crystals may be wasted in searching for the best freezing conditions when the intrinsic quality of the crystals is poor. In principle, the collection of room-temperature diffraction data would provide a reference that would allow the detection of crystal damage caused by addition of cryoprotectant or by cryocooling. In practice, however, many investigators are reluctant to do this, one reason being that capillary mounting of crystals is a tedious method, especially for those who are new to crystallography. Here a simplified method for mounting crystals at room temperature is reported, which requires little expertise and no expensive equipment.
Real-space interpretation of spin-echo small-angle neutron scattering
Authors: Krouglov Timofei , de Schepper Ignatz M. , Bouwman Wim G. , Rekveldt M. Theo
Published: January 2003

Spin-echo small-angle neutron scattering (SESANS) is a novel real-space scattering technique. SESANS measures a correlation-like functionG(Z), the meaning of which was unknown until now. Here a direct real-space interpretation ofG(Z) through the particle scattering density and pair correlation function is given. One-dimensional and two-dimensional SESANS are compared. The case of non-interacting particles is considered in detail with an explicit geometrical interpretation. General methods for the calculation of structural parameters, such as the total scattering length and the radius of gyration, are developed. Analytical expressions ofG(Z) for non-interacting solid spheres, hollow spheres and Gaussian coils are derived. The case of solid spheres is compared with experimental data.
“Hardwiring” an organization’s service performance
Authors: Schlesinger Leonard A.
Published: January 2003

Explains the term “hardwiring” a term used in computer hardware and software development as being related to “hotwiring” when an automobile’s ignition wire is put into direct contact with the power source to the starter, bypassing the ignition key. States that hardwiring is what leaders in industry are doing at several levels to link the success of their employees closely with that of their customers so that gains achieved in the past can provide assumptions for the future. Concludes that the impact of such action engineers lasting change and gains in value for an organization.
Determining and assessing the determinants of e‐service operations
Authors: Surjadjaja Heston , Ghosh Sid , Antony Jiju
Published: January 2003

The rapid growth of the Internet has provided tremendous opportunities for service companies to offer quality services. The prime drivers and motivations for offering such services through the Net are to reduce transaction costs and to provide efficient and effective service to customers. But what are the determinants essential for building a successful electronic service (e‐service) operation? This paper addresses this specific issue by isolating the essential determinants from the available literature, and assessing them individually to obtain better insights and understanding. This could help companies to design and develop robust foundations on which to build successful e‐service operations. The boundaries between e‐service, e‐business and e‐commerce are blurred and sometimes confusing. This paper aims to clarify some of these ambiguities.
Business process re‐engineering in Malaysian banks and finance companies
Authors: Wei Khong Kok , Richardson Stanley
Published: January 2003

Business process re‐engineering (BPR) is a management technique that radically rethinks and redesigns business processes to achieve dramatic improvements in business performance such as customer service and quality. The acceptance of BPR has been reinforced by the implementation of re‐engineering initiatives in many Malaysian banking institutions and the Central Bank of Malaysia, Bank Negara, is in favour of these initiatives. Nevertheless the effectiveness of BPR in this context has hitherto not been investigated. The aim of this paper is to investigate the effectiveness of the critical success factors (CSFs) of BPR implementation process in the Malaysian banks and finance companies. Several hypotheses were tested concerning the relationships between the CSFs of the BPR implementation process and the performance of the enterprise, i.e. customer service performance and business performance. With the assistance of Institut Bank‐bank Malaysia (IBBM), 103 questionnaires were completed and analysed.
A frequency tunable half‐wave resonator using a MEMS variable capacitor
Authors: Bell Patrick , Hoivik Nils , Bright Victor , Popovic Zoya
Published: January 2003

A frequency tunable half‐wave resonator at 3 GHz is presented with a microelectromechanical systems (MEMS) variable capacitor as the tuning element. The capacitor is fabricated using the multi‐user MEMS process (MUMPs) technology provided by JDS/Cronos, and transferred to an alumina substrate by an in‐house developed flip‐chip process. This capacitor is electrostatically actuated. The resultingC‐Vresponse is linear with a slope of 0.05 pF/V for a wide range of actuation voltages. The MEMS device has a capacitance ratio of 3:1 for 0‐70 V bias, with aQ‐factor of 140 measured at 1 GHz. A half‐wave tunable microstrip resonator with bias lines is designed to include this MEMS device, which exhibits linear tuning over 180 MHz (6 percent) centered around 3 GHz with a constant 3 dB bandwidth of 160 MHz over the entire tuning range. The power consumption of the MEMS device was measured to be negligible.
Materials characterization of the effect of mechanical bending on area array package interconnects
Authors: Rooney Daniel T. , Todd Castello N. , Cibulsky Mike , Abbott Doug , Xie Dongji
Published: January 2003

The mechanical integrity of solder joint interconnects in PWB assemblies with micro ‐ BGA, chip scale, and LGA packages are being questioned as the size and pitch decrease. Three‐point cyclic bend testing provides a useful tool for characterizing the expected mechanical cycling fatigue reliability of PWB assemblies. Cyclic bend testing is useful for characterizing bending issues in electronic assemblies such as repetitive keypad actuation in cell phone products. This paper presents the results of three‐point bend testing of PWB assemblies with fine pitch packages. The methodology of materials analyses of the metallurgy of solder interconnects following mechanical bending and thermal cycle testing is described.
Mechanically fixed and thermally insulated micromechanical structures for GaAs heterostructure based MEMS devices
Authors: Lalinsky´ T. , Haščík Sˇ. , Mozolová Ž. , Burian E. , Krnáč M. , Tomáška M. , Škriniarová J. , Drzˇík M. , Kosticˇ I. , Matay L.
Published: January 2003

A new micromachining technology of mechanically fixed and thermally insulated cantilevers, bridges and islands was developed to be used for design of GaAs heterostructure based microelectromechanical systems (MEMS) devices. Based on the micromachining technology, two different MEMS devices were designed and analyzed. The first one was micromechanical thermal converter (MTC) and the second one was a micromechanical coplanar waveguide (MCPW). The basic electro‐thermal as well as microwave properties of the MEMS devices designed are investigated. The results obtained are also supported by simulation. The advantages of the fixed micromechanical structures in the field of design of new MEMS devices are discussed.
Advanced thick film system for AlN substrates
Authors: Wang Y.L. , Carroll A.F. , Smith J.D. , Cho Y. , Bacher R.J. , Anderson D.K. , Crumpton J.C. , Needes C.R.S.
Published: January 2003

Substrates with high thermal conductivity continue to be in great demand for their ability to enable smaller and denser high power circuits. BeO has been used for this purpose for many years with thick film materials. However, due to health and environmental concerns with BeO, many manufacturers feel compelled to switch to alternative substrates. This paper will discuss a thick film system consisting of conductors, dielectric, and resistors developed specifically for use with the most likely alternative, AlN substrates. This system will soon find broad use in applications such as power resistors for telecom, optoelectronic submounts, and high‐power automotive applications.
A reinterpretation of the dimerization interface of the N‐terminal Domains of STATs
Authors: Chen Xiaomin , Bhandari Rashna , Vinkemeier Uwe , van den Akker Focco , Darnell James E. , Kuriyan John
Published: January 2003

The crystal structures of the N‐terminal domain (N‐domain) and the core region of the STAT family of transcription factors have been determined previously. STATs can form cooperative higher order structures (tetramers or higher oligomers) while bound to DNA. The crystal packing in the STAT4 N‐domain crystal structure, determined at 1.5 Å resolution, suggests two alternate organizations of the N‐domain dimer. We now present the results of site directed mutagenesis of residues predicted to be involved at each dimer interface. Our results indicate that the dimer interface suggested earlier as being physiologically relevant is, in fact, unlikely to be so. Given the alternative model for the N‐domain dimer, the ability of the N‐domain to mediate interactions of two STAT dimers on DNA remains unchanged.
Directing the mode of nitrite binding to a copper‐containing nitrite reductase from Alcaligenes faecalis S‐6: Characterization of an active site isoleucine
Authors: Boulanger Martin J. , Murphy Michael E.P.
Published: January 2003

Unlike the heme cd1‐based nitrite reductase enzymes, the molecular mechanism of copper‐containing nitrite reductases remains controversial. A key source of controversy is the productive binding mode of nitrite in the active site. To identify and characterize the molecular determinants associated with nitrite binding, we applied a combinatorial mutagenesis approach to generate a small library of six variants at position 257 in nitrite reductase from Alcaligenes faecalis S‐6. The activities of these six variants span nearly two orders of magnitude with one variant, I257V, the only observed natural substitution for Ile257, showing greater activity than the native enzyme. High‐resolution (> 1.8 Å) nitrite‐soaked crystal structures of these variants display different modes of nitrite binding that correlate well with the altered activities. These studies identify for the first time that the highly conserved Ile257 in the native enzyme is a key molecular determinant in directing a catalytically competent mode of nitrite binding in the active site. The O‐coordinate bidentate binding mode of nitrite observed in native and mutant forms with high activity supports a catalytic model distinct from the heme cd1 NiRs.

(The atomic coordinates for I257V[NO2−], I257L[NO2−], I257A[NO2−], I257T[NO2−], I257M[NO2−] and I257G[NO2−] AfNiR have been deposited in the Protein Data Bank [PDB identification codes are listed in Table 2].)
Protein conformational changes studied by diffusion NMR spectroscopy: Application to helix‐loop‐helix calcium binding proteins
Authors: Weljie Aalim M. , Yamniuk Aaron P. , Yoshino Hidenori , Izumi Yoshinobu , Vogel Hans J.
Published: January 2003

Pulsed‐field gradient (PFG) diffusion NMR spectroscopy studies were conducted with several helix‐loop‐helix regulatory Ca2+‐binding proteins to characterize the conformational changes associated with Ca2+‐saturation and/or binding targets. The calmodulin (CaM) system was used as a basis for evaluation, with similar hydrodynamic radii (Rh) obtained for apo‐ and Ca2+‐CaM, consistent with previously reported Rh data. In addition, conformational changes associated with CaM binding to target peptides from myosin light chain kinase (MLCK), phosphodiesterase (PDE), and simian immunodeficiency virus (SIV) were accurately determined compared with small‐angle X‐ray scattering results. Both sets of data demonstrate the well‐established collapse of the extended Ca2+‐CaM molecule into a globular complex upon peptide binding. The Rh of CaM complexes with target peptides from CaM‐dependent protein kinase I (CaMKI) and an N‐terminal portion of the SIV peptide (SIV‐N), as well as the anticancer drug cisplatin were also determined. The CaMKI complex demonstrates a collapse analogous to that observed for MLCK, PDE, and SIV, while the SIV‐N shows only a partial collapse. Interestingly, the covalent CaM–cisplatin complex shows a near complete collapse, not expected from previous studies. The method was extended to related calcium binding proteins to show that the Rh of calcium and integrin binding protein (CIB), calbrain, and the calcium‐binding region from soybean calcium‐dependent protein kinase (CDPK) decrease on Ca2+‐binding to various extents. Heteronuclear NMR spectroscopy suggests that for CIB and calbrain this is likely because of shifting the equilibrium from unfolded to folded conformations, with calbrain forming a dimer structure. These results demonstrate the utility of PFG‐diffusion NMR to rapidly and accurately screen for molecular size changes on protein–ligand and protein–protein interactions for this class of proteins.
Computational design of a water‐soluble analog of phospholamban
Authors: Slovic Avram M. , Summa Christopher M. , Lear James D. , DeGrado William F.
Published: January 2003

Membrane proteins and water‐soluble proteins share a similar core. This similarity suggests that it should be possible to water‐solubilize membrane proteins by mutating only their lipid‐exposed residues. We have developed computational tools to design water‐soluble variants of helical membrane proteins, using the pentameric phospholamban (PLB) as our test case. To water‐solublize PLB, the membrane‐exposed positions were changed to polar or charged amino acids, while the putative core was left unaltered. We generated water‐soluble phospholamban (WSPLB), and compared its properties to its predecessor PLB. In aqueous solution, WSPLB mimics all of the reported properties of PLB including oligomerization state, helical structure, and stabilization upon phosphorylation. We also characterized the truncated mutant WSPLB (21–52) comprising only the former transmembrane segment of PLB. This peptide shows a decreased specificity for forming a pentameric oligomerization state.
Crystal structure of a trimeric form of dephosphocoenzyme A kinase from Escherichia coli
Authors: O'Toole Nicholas , Barbosa João A.R.G. , Li Yunge , Hung Li‐Wei , Matte Allan , Cygler Miroslaw
Published: January 2003

Coenzyme A (CoA) is an essential cofactor used in a wide variety of biochemical pathways. The final step in the biosynthesis of CoA is catalyzed by dephosphocoenzyme A kinase (DPCK, E.C. 2.7.1.24). Here we report the crystal structure of DPCK from Escherichia coli at 1.8 Å resolution. This enzyme forms a tightly packed trimer in its crystal state, in contrast to its observed monomeric structure in solution and to the monomeric, homologous DPCK structure from Haemophilus influenzae. We have confirmed the existence of the trimeric form of the enzyme in solution using gel filtration chromatography measurements. Dephospho‐CoA kinase is structurally similar to many nucleoside kinases and other P‐loop‐containing nucleotide triphosphate hydrolases, despite having negligible sequence similarity to these enzymes. Each monomer consists of five parallel β‐strands flanked by α‐helices, with an ATP‐binding site formed by a P‐loop motif. Orthologs of the E. coli DPCK sequence exist in a wide range of organisms, including humans. Multiple alignment of orthologous DPCK sequences reveals a set of highly conserved residues in the vicinity of the nucleotide/CoA binding site.
Trapping of peptide‐based surrogates in an artificially created channel of cytochrome c peroxidase
Authors: Hays Anna‐Maria A. , Gray Harry B. , Goodin David B.
Published: January 2003

As recently described, the deliberate removal of the proposed electron transfer pathway from cytochrome c peroxidase resulted in the formation of an extended ligand‐binding channel. The engineered channel formed a template for the removed peptide segment, suggesting that synthetic surrogates might be introduced to replace the native electron transfer pathway. This approach could be united with the recent development of sensitizer‐linked substrates to initiate and study electron transfer, allowing access to unresolved issues about redox mechanism of the enzyme. Here, we present the design, synthesis, and screening of a peptide library containing natural and unnatural amino acids to identify the structural determinants for binding this channel mutant. Only one peptide, (benzimidazole‐propionic acid)‐Gly‐Ala‐Ala, appeared to interact, and gave evidence for both reversible and kinetically trapped binding, suggesting multiple conformations for the channel protein. Notably, this peptide was the most analogous to the removed electron transfer sequence, supporting the use of a cavity‐template strategy for design of specific sensitizer‐linked substrates as replacements for the native electron transfer pathway.
Structural variation and inhibitor binding in polypeptide deformylase from four different bacterial species
Authors: Smith Kathrine J. , Petit Chantal M. , Aubart Kelly , Smyth Martin , McManus Edward , Jones Jo , Fosberry Andrew , Lewis Ceri , Lonetto Michael , Christensen Siegfried B.
Published: January 2003

Polypeptide deformylase (PDF) catalyzes the deformylation of polypeptide chains in bacteria. It is essential for bacterial cell viability and is a potential antibacterial drug target. Here, we report the crystal structures of polypeptide deformylase from four different species of bacteria: Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, and Escherichia coli. Comparison of these four structures reveals significant overall differences between the two Gram‐negative species (E. coli and H. influenzae) and the two Gram‐positive species (S. pneumoniae and S. aureus). Despite these differences and low overall sequence identity, the S1′ pocket of PDF is well conserved among the four enzymes studied. We also describe the binding of nonpeptidic inhibitor molecules SB‐485345, SB‐543668, and SB‐505684 to both S. pneumoniae and E. coli PDF. Comparison of these structures shows similar binding interactions with both Gram‐negative and Gram‐positive species. Understanding the similarities and subtle differences in active site structure between species will help to design broad‐spectrum polypeptide deformylase inhibitor molecules.
Vibrio cholerae cytolysin is composed of an α‐hemolysin‐like core
Authors: Olson Rich , Gouaux Eric
Published: January 2003

The enteric pathogen Vibrio cholerae secretes a water‐soluble 80‐kD cytolysin, Vibrio cholerae cytolysin (VCC) that assembles into pentameric channels following proteolytic activation by exogenous proteases. Until now, VCC has been placed in a unique class of pore‐forming toxins, distinct from paradigms such as Staphyloccal α‐hemolysin. However, as reported here, amino acid sequence analysis and three‐dimensional structure modeling indicate that the core component of the VCC toxin is related in sequence and structure to a family of hemolysins from Staphylococcus aureus that include leukocidin F and α‐hemolysin. Furthermore, our analysis has identified the channel‐forming region of VCC and a potential lipid head‐group binding site, and suggests a conserved mechanism of assembly and lysis. An additional domain in the VCC toxin is related to plant lectins, conferring additional target cell specificity to the toxin.
Expression, solubilization, and biochemical characterization of the tight junction transmembrane protein claudin‐4
Authors: Mitic Laura L. , Unger Vinzenz M. , Anderson James Melvin
Published: January 2003

The tight junction tetraspan protein claudin‐4 creates a charge‐selective pore in the paracellular pathway across epithelia. The structure of the pore is unknown, but is presumed to result from transcellular adhesive contacts between claudin's extracellular loops. Here we report the expression of claudin‐4 by baculovirus infection of Sf9 cells and describe the biochemical analysis suggesting it has a hexameric quaternary configuration. We show the detergent perfluoro‐octanoic acid is able to maintain oligomeric claudin species. Sucrose velocity centrifugation and laser light scattering are also used to investigate the oligomeric state of claudin‐4. In contrast to proteins of similar topology, such as gap junction family connexins, the oligomeric state of claudins appears more dynamic. These data suggest the structural organization of claudins in tight junction pores is unique.
Structural composition of βI‐ and βII‐proteins
Authors: Sreerama Narasimha , Woody Robert W.
Published: January 2003

Circular dichroism spectra of proteins are sensitive to protein secondary structure. The CD spectra of α‐rich proteins are similar to those of model α‐helices, but β‐rich proteins exhibit CD spectra that are reminiscent of CD spectra of either model β‐sheets or unordered polypeptides. The existence of these two types of CD spectra for β‐rich proteins form the basis for their classification as βI‐ and βII‐proteins. Although the conformation of β‐sheets is largely responsible for the CD spectra of βI‐proteins, the source of βII‐protein CD, which resembles that of unordered polypeptides, is not completely understood. The CD spectra of unordered polypeptides are similar to that of the poly(Pro)II helix, and the poly(Pro)II‐type (P2) structure forms a significant fraction of the unordered conformation in globular proteins. We have compared the β‐sheet and P2 structure contents in β‐rich proteins to understand the origin of βII‐protein CD. We find that βII‐proteins have a ratio of P2 to β‐sheet content greater than 0.4, whereas for βI‐proteins this ratio is less than 0.4. The β‐sheet content in βI‐proteins is generally higher than that in βII‐proteins. The origin of two classes of CD spectra for β‐rich proteins appears to lie in their relative β‐sheet and P2 structure contents.
Influence of Extracellular Bactericidal Agents on Bacteria within Macrophages
Authors: Hamrick Terri S. , Diaz Adam H. , Havell Edward A. , Horton John R. , Orndorff Paul E.
Published: January 2003

We employed gentamicin-sensitive and -resistant derivatives of
Escherichia coli
in a macrophage phagocytosis assay that compared λ bacteriophage and gentamicin as extracellular bactericidal agents. Colony counts and direct microscopic examination of phagocytized
E. coli
supported the conclusion that gentamicin entered macrophages, even at low concentrations, and contributed to their bactericidal activity. Also, two
E. coli
strains differing in the ability to express the adhesin of type 1 pili (FimH) were distinguishably different in intracellular survival when λ was used as the extracellular killing agent but were indistinguishable when gentamicin was employed.
Molecular and Phenotypic Analysis of the CS54 Island ofSalmonella entericaSerotype Typhimurium: Identification of Intestinal Colonization and Persistence Determinants
Authors: Kingsley Robert A. , Humphries Andrea D. , Weening Eric H. , de Zoete Marcel R. , Winter Sebastian , Papaconstantinopoulou Anastasia , Dougan Gordon , Bäumler Andreas J.
Published: January 2003

TheshdAgene is carried on a 25-kb genetic island at centisome 54 (CS54 island) of theSalmonella entericaserotype Typhimurium chromosome. In addition toshdA, the CS54 island ofSalmonellaserotype Typhimurium strain LT2 contains four open reading frames designatedratA,ratB,sivI, andsivH. DNA hybridization analysis revealed that the CS54 island is comprised of two regions with distinct phylogenetic distribution within the genusSalmonella. Homologues ofshdAandratBwere detected only in serotypes ofSalmonella entericasubsp. I. In contrast, sequences hybridizing withratA,sivI, andsivHwere present inS. entericasubsp. II andS. bongoriin addition toS. entericasubsp. I. Deletion of theratAandsivIgenes did not alter the ability ofSalmonellaserotype Typhimurium to colonize the organs of mice. Insertional inactivation of thesivHgene resulted in defective colonization of the Peyer's patches of the terminal ileum but normal colonization of the cecum, mesenteric lymph nodes, and spleen. Deletion of theshdAgene resulted in decreased colonization of the cecum and Peyer's patches of the terminal ileum and colonization to a lesser degree in the mesenteric lymph nodes and spleen 5 days post-oral inoculation of mice. A strain containing a deletion in theratBgene exhibited a defect for the colonization of the cecum but not of the Peyer's patches, mesenteric lymph nodes, and spleen. TheshdAandratBdeletion strains exhibited a shedding defect in mice, whereas thesivHdeletion strain was shed at numbers similar to the wild type. These data suggest that colonization of the murine cecum is required for efficient fecal shedding in mice.
Availability of Complement Bound toStaphylococcus aureusTo Interact with Membrane Complement Receptors Influences Efficiency of Phagocytosis
Authors: Cunnion K. M. , Zhang H.-M. , Frank M. M.
Published: January 2003

Complement-mediated opsonization of encapsulatedStaphylococcus aureus(CP+) of the predominant capsule types, 5 and 8, remains poorly understood. Our previous work showed that complement is important for mouse survival of CP+ type 5 bacteremia and that the type 5 capsule inhibits the binding of opsonic C3 fragments to the organism. The importance of complement-mediated opsonization of CP+ was tested by neutrophil phagocytosis assays. Complement-mediated opsonization of CP+ increased phagocytosis by 57% compared to opsonization in complement-inhibited serum. Agar-grown CP+, enhancing capsule expression, was phagocytosed only one-tenth as well as the capsule-negative organisms (CP−), supporting the belief that staphylococcal polysaccharide capsules impair phagocytosis. Despite relatively poor phagocytosis of CP+ compared to CP−, complement activation increased the phagocytosis of CP+ by 103%. Thus, complement in normal human serum may have an important role in opsonizing CP+, even when capsule expression is strong. The ability of bound C3 fragments to interact with complement receptor 1 (CD35) on the membrane of human erythrocytes was tested in an immune adherence assay.S. aureuscapsule was able to mask C3 fragments on the organism from binding to complement receptor 1. The inhibition of C3 binding to CP+ and the masking of deposited C3 fragments caused by the presence of capsule was associated with markedly decreased phagocytosis. The addition of anti-capsule antibodies to normal human serum was found to markedly improve the recognition of deposited C3 fragments by complement receptor 1 even when the absolute number of C3 molecules bound toS. aureuswas not increased.
Oral Treponemes and Their Outer Membrane Extracts Activate Human Gingival Epithelial Cells through Toll-Like Receptor 2
Authors: Asai Yasuyuki , Jinno Takayoshi , Ogawa Tomohiko
Published: January 2003

Oral treponemes are considered to be important in the development and progression of periodontal diseases. We investigated the mechanisms of recognition and activation of human gingival epithelial cells (HGEC) with the oral treponemesTreponema denticola,Treponema vincentii, andTreponema mediumand their outer membrane extracts (OMEs).T. vincentiiandT. mediumbut notT. denticolaproduced interleukin 8 (IL-8) in an HGEC culture. Further, all three treponemes induced IL-8 mRNA expression and NF-κB activation in HGEC. Among them,T. denticolaespecially exhibited trypsin- and chymotrypsin-like protease activities, and the addition of chymostatin, a chymotrypsin protease inhibitor, resulted in detectable IL-8 production by HGEC cultured withT. denticola. Additionally, IL-8 mRNA expression in HGEC cultured with the three treponemes and their OMEs was definitely inhibited by the mouse anti-human Toll-like receptor 2 (TLR2) monoclonal antibody TL2.1. These findings suggest that oral treponemes and their OMEs activate HGEC through TLR2.
Heterogeneity of Mycolactones Produced by Clinical Isolates of
Mycobacterium ulcerans
: Implications for Virulence
Authors: Mve-Obiang Armand , Lee Richard E. , Portaels Françoise , Small P. L. C.
Published: January 2003

Mycobacterium ulcerans
is the causative agent of Buruli ulcer, a severe necrotizing skin disease endemic in tropical countries. Clinical evidence suggests that
M. ulcerans
isolates from Asia, Mexico, and Australia may be less virulent than isolates from Africa. In vivo studies suggest that mycolactone, a polyketide-derived macrolide toxin, plays a major role in the tissue destruction and immune suppression which occur in cases of Buruli ulcer. Mycolactones were extracted from 34 isolates of
M. ulcerans
representing strains from Africa, Malaysia, Asia, Australia, and Mexico. Thin-layer chromatography, mass spectroscopic analysis, and cytopathic assays of partially purified mycolactones from these isolates revealed that
M. ulcerans
produces a heterogeneous mixture of mycolactone variants. Mycolactone A/B, the most biologically active mycolactone species, was identified by mass spectroscopy as [M
+
Na]
+
at
m/z
765.5 in all cytotoxic isolates except for those from Mexico. Mycolactone C [M+Na]
+
at
m/z
726.3 was the dominant mycolactone species in eight Australian isolates, and mycolactone D [M+Na]
+
m/z
781.2 was characteristic of two Asian strains. Mycolactone species are conserved within specific geographic areas, suggesting that there may be a correlation between mycolactone profile and virulence. In addition, the core lactone, [M+Na]
+
m/z
447.4, was identified as a minor species, supporting the hypothesis that mycolactones are synthesized by two polyketide synthases. A cytopathic assay of the core lactone showed that this molecule is sufficient for cytotoxicity, although it is much less potent than the complete mycolactone.
Use of a Promoter Trap System in
Bacillus anthracis
and
Bacillus subtilis
for the Development of Recombinant Protective Antigen-Based Vaccines
Authors: Gat O. , Inbar I. , Aloni-Grinstein R. , Zahavy E. , Kronman C. , Mendelson I. , Cohen S. , Velan B. , Shafferman A.
Published: January 2003

We have recently reported
Bacillus anthracis
attenuated live vaccine strains efficiently expressing recombinant protective antigen (rPA) and have shown a direct correlation between the level of rPA secreted by these cells and efficacy (S. Cohen, I. Mendelson, Z. Altboum, D. Kobiler, E. Elhanany, T. Bino, M. Leitner, I. Inbar, H. Rosenberg, Y. Gozes, R. Barak, M. Fisher, C. Kronman, B. Velan, and A. Shafferman, Infect. Immun.
68:
4549-4558, 2000). To isolate more potent
Bacillus
promoters for a further increase in the production of rPA, we developed a promoter trap system based on various
gfp
reporter genes adapted for use in both
Bacillus subtilis
and
B. anthracis
backgrounds. Accordingly, a
B. anthracis
library of 6,000 clones harboring plasmids with chromosomal
B. anthracis
DNA fragments inserted upstream from
gfpuv
was constructed. Based on fluorescence intensity, 57 clones carrying potentially strong promoters were identified, some of which were DNA sequenced. The most potent
B. anthracis
promoter identified (P
ntr
; 271 bp) was 500 times more potent than the native
pagA
promoter and 70 times more potent than the α-amylase promoter (P
amy
). This very potent promoter was tested along with the other promoters (which are three, six, and eight times more potent than P
amy
) for the ability to drive expression of rPA in either
B. subtilis
or
B. anthracis
. The number of cell-associated pre-PA molecules in
B. anthracis
was found to correlate well with the strength of the promoter. However, there appeared to be an upper limit to the amount of mature PA secreted into the medium, which did not exceed that driven by P
amy
. Furthermore, the rPA constructs fused to the very potent promoters proved to be deleterious to the bacterial hosts and consequently led to genetic instability of the PA expression plasmid. Immunization with attenuated
B. anthracis
expressing rPA under the control of promoters more potent than P
amy
was less efficient in eliciting anti-PA antibodies than that attained with P
amy
. The results are consistent with the notion that overexpression of PA leads to severe secretion stress and have practical implications for the design of second-generation rPA-based vaccines.
Application of a
Saccharomyces cerevisiae
Model To Study Requirements for Trafficking of
Yersinia pestis
YopM in Eucaryotic Cells
Authors: Skrzypek Elżbieta , Myers-Morales Tanya , Whiteheart Sidney W. , Straley Susan C.
Published: January 2003

YopM is a leucine-rich repeat (LRR) virulence protein that is delivered into host cells when any of the three human-pathogenic species of
Yersinia
binds to mammalian cells. It exhibits heterogeneity of size and sequence among the yersiniae, but the functional consequences of this variability are not yet known.
Yersinia pestis
YopM was previously shown to accumulate in the nuclei of infected HeLa cells by a mechanism that requires vesicular trafficking. In this study, we characterized the trafficking of
Y. pestis
YopM in a
Saccharomyces cerevisiae
model previously found to support nuclear localization of YopM from an enteropathogenic
Yersinia
strain (C. F. Lesser and S. I. Miller, EMBO J. 20:1840-1849, 2001).
Y. pestis
YopM was N-terminally fused to the yeast enhanced green fluorescent protein (yEGFP) and inducibly expressed in the cytoplasm. yEGFP-YopM localized to the yeast nucleus, showing that this property is conserved for YopMs so far tested and that infection and the presence of other Yops are not required for its trafficking. When expressed in
S. cerevisiae
that is temperature sensitive for vesicular transport, YopM failed to accumulate in the nucleus at the nonpermissive temperature but did accumulate when the permissive temperature was restored. This shows that vesicular trafficking also is required in yeast for normal localization of YopM. YopM consists of a 71-residue leader sequence, 15 LRRs, and a 32-residue tail. Deletion analysis revealed that the leader sequence or tail is alone insufficient to direct YopM to the nucleus, showing that the LRR structure is required. Both the N-terminal and C-terminal halves of YopM localized to the nucleus, indicating the possible presence of two nuclear localization signals (NLSs) in YopM or domains in YopM where an NLS-containing protein might bind; this fits with the presence of two highly conserved regions among
Yersinia
YopMs. yEGFP-YopM lacking LRRs 4 to 7 or 7 to 10 accumulated in the nucleus in yeast, and YopM lacking these LRRs concentrated normally in the HeLa cell nucleus after delivery by
Yersinia
infection, showing that these LRRs are not essential for YopM trafficking in eucaryotic cells. However, because
Y. pestis
carrying either of these YopMs is strongly compromised in virulence in mice, these findings revealed that LRRs 4 to 10 map a region of YopM or support a conformation of YopM that is necessary for a pathogenic effect.
DNA Alkylation Damage as a Sensor of Nitrosative Stress in
Mycobacterium tuberculosis
Authors: Durbach Steven I. , Springer Burkhard , Machowski Edith E. , North Robert J. , Papavinasasundaram K. G. , Colston M. Jo , Böttger Erik C. , Mizrahi Valerie
Published: January 2003

One of the cellular consequences of nitrosative stress is alkylation damage to DNA. To assess whether nitrosative stress is registered on the genome of
Mycobacterium tuberculosis
, mutants lacking an alkylation damage repair and reversal operon were constructed. Although hypersensitive to the genotoxic effects of
N
-methyl-
N
′-nitro-
N
-nitrosoguanidine in vitro, the mutants displayed no phenotype in vivo, suggesting that permeation of nitrosative stress to the level of cytotoxic DNA damage is restricted.
ON WLS-CHEBYSHEV FIR DIGITAL FILTERS
Authors: DINIZ PAULO S. R. , NETTO SERGIO L.
Published: January 2003

A new numerical approach for designing FIR digital filters is proposed. The method is able to compromise maximum stopband attenuation and minimum stopband energy requirements. The approach is based on the weighted-least-squares (WLS) method using, at each iteration, a different weight function, which is made constant within a given frequency interval. In that manner, digital filters with partially equiripple and partially WLS-like stopbands are efficiently obtained. Generality of the method makes it suitable for the design of linear- and arbitrary-phase FIR filters.
A NEW CALL ADMISSION CONTROL METHOD BASED ON THE ESTIMATION OF THE LOST CELL
Authors: PAP LÁSZlÓ , IMRE SÁNDOR
Published: January 2003

Due to the capability to serve a large number and various types of user traffic, ATM (Asynchronous Transfer Mode) networks are going to be the leading role in telecommunications in the immediate future. To guarantee high quality communications for a lot of customers and efficient use of network resources, the ATM network management has to contain appropriate Call Admission Control (CAC) algorithms. Choosing suitable network and user models, the CAC problem can be traced back to statistical inequalities. This paper introduces a CAC technique based on the Mean Value of the Lost Cells (MVLC) instead of using Cell Loss Probability that follows Gaussian approach. Two methods are presented which are able to estimate efficiently the MVLC. These methods are based on special transformation of the Chernoff bound.
FASTER SIMILARITY SEARCH FOR MULTIMEDIA DATA VIA QUERY TRANSFORMATIONS
Authors: LANG CHRISTIAN A. , SINGH AMBUJ K.
Published: January 2003

The performance of nearest neighbor (NN) queries degrades noticeably with increasing dimensionality of the data due to reduced selectivity of high-dimensional data and an increased number of seek operations during NN-query execution. If the NN-radii would be known in advance, the disk accesses could be reordered such that seek operations are minimized. We therefore propose a new way of estimating the NN-radius based on the fractal dimensionality and sampling. It is applicable to any page-based index structure. We show that the estimation error is considerably lower than for previous approaches. In the second part of the paper, we present two applications of this technique. We show how the radius estimations can be used to transform k-NN queries into at most two range queries, and how it can be used to reduce the number of page reads during all-NN queries. In both cases, we observe significant speedups over traditional techniques for synthetic and real-world data.
VIEWS OR POINTS OF VIEW ON IMAGES
Authors: ORIA VINCENT , TAMER ÖZSU M.
Published: January 2003

Images like other multimedia data need to be described as it is difficult to grasp their semantics from the raw data. With the emergence of standards like MPEG-7, multimedia data will be increasingly produced together with some semantic descriptors. But a description of a multimedia data is just an interpretation, a point of view on the data and different interpretations can exist for the same multimedia data. In this paper we explore the use of view techniques to define and manage different points of view on images. Views have been widely used in relational database management systems to extend modeling capabilities, and to provide logical data independence. Since our image model is defined on an object-oriented model, we will first propose a powerful object-oriented mechanism based on the distinction between class and type. The object view is used in the image view definition. The image view mechanism exploits the separation of the physical representation in an image of a real world object from the real object itself to allow different interpretations of an image region. Finally we will discuss the implementation of the image view mechanisms on the existing object models.
CONTENT-BASED IMAGE RETRIEVAL WITH RELEVANCE FEEDBACK USING ADAPTIVE PROCESSING OF TREE-STRUCTURE IMAGE REPRESENTATION
Authors: WANG ZHIYONG , CHI ZHERU , FENG DAGAN , TSOI AH CHUNG
Published: January 2003

Content-based image retrieval has become an essential technique in multimedia data management. However, due to the difficulties and complications involved in the various image processing tasks, a robust semantic representation of image content is still very difficult (if not impossible) to achieve. In this paper, we propose a novel content-based image retrieval approach with relevance feedback using adaptive processing of tree-structure image representation. In our approach, each image is first represented with a quad-tree, which is segmentation free. Then a neural network model with the Back-Propagation Through Structure (BPTS) learning algorithm is employed to learn the tree-structure representation of the image content. This approach that integrates image representation and similarity measure in a single framework is applied to the relevance feedback of the content-based image retrieval. In our approach, an initial ranking of the database images is first carried out based on the similarity between the query image and each of the database images according to global features. The user is then asked to categorize the top retrieved images into similar and dissimilar groups. Finally, the BPTS neural network model is used to learn the user's intention for a better retrieval result. This process continues until satisfactory retrieval results are achieved. In the refining process, a fine similarity grading scheme can also be adopted to improve the retrieval performance. Simulations on texture images and scenery pictures have demonstrated promising results which compare favorably with the other relevance feedback methods tested.