bluuebunny/crossref_metadata_2025 huggingface dataset:
Crystal structure of an enhancer of rudimentary homolog (ERH) at 2.1 Å resolution
Authors: Arai Ryoichi , Kukimoto‐Niino Mutsuko , Uda‐Tochio Hiroko , Morita Satoshi , Uchikubo‐Kamo Tomomi , Akasaka Ryogo , Etou Yuuka , Hayashizaki Yoshihide , Kigawa Takanori , Terada Takaho , Shirouzu Mikako , Yokoyama Shigeyuki
Published: June 2005

The enhancer of rudimentary gene, e(r), of Drosophila melanogaster encodes an enhancer of rudimentary (ER) protein with functions implicated in pyrimidine biosynthesis and the cell cycle. The ER homolog (ERH) is highly conserved among vertebrates, invertebrates, and plants. Xenopus laevis ERH was reported to be a transcriptional repressor. Here we report the 2.1 Å crystal structure of murine ERH (Protein Data Bank ID 1WZ7), determined by the multiwavelength anomalous dispersion (MAD) method. The monomeric structure of ERH comprises a single domain consisting of three α‐helices and four β‐strands, which is a novel fold. In the crystal structure, ERH assumes a dimeric structure, through interactions between the β‐sheet regions. The formation of an ERH dimer is consistent with the results of analytical ultracentrifugation. The residues at the core region and at the dimer interface are highly conserved, suggesting the conservation of the dimer formation as well as the monomer fold. The long flexible loop (44∼53) is also significantly conserved, suggesting that this loop region may be important for the functions of ERH. In addition, the putative phosphorylation sites are located at the start of the β2‐strand (Thr18) and at the start of the α1‐helix (Ser24), implying that the phosphorylation might cause some structural changes.
A Novel Methodology for Thermal Analysis of a Composite System Consisting of a Porous Medium and an Adjacent Fluid Layer
Authors: Min Jung Yim , Kim Sung Jin
Published: June 2005

An innovative methodology is presented for the purpose of analyzing fluid flow and heat transfer in a porous–fluid composite system, where the porous medium is assumed to have a periodic structure, i.e., solid and fluid phases repeat themselves in a regular pattern. With the present method, analytical solutions for the velocity and temperature distributions are obtained when the distributions in the adjacent fluid layer are allowed to vary in the directions both parallel and perpendicular to the interface between the porous medium and the adjacent fluid layer. The analytical solutions are validated by comparing them with the corresponding numerical solutions for the case of the ideal composite channel, and with existing experimental data. The present analytical solutions have a distinctive advantage in that they do not involve any unknown coefficients resulting from the previous interfacial conditions. Moreover, by comparing interfacial conditions derived from the present study with the stress- and flux-jump conditions developed by previous investigators, the unknown coefficients included in the stress- and flux-jump conditions are analytically determined and are shown to depend on the porosity, the Darcy number and the pore diameter.
The Effect of Support Grid Design on Azimuthal Variation in Heat Transfer Coefficient for Rod Bundles
Authors: Holloway Mary V. , Conover Timothy A. , McClusky Heather L. , Beasley Donald E. , Conner Michael E.
Published: June 2005

Support grids are an integral part of nuclear reactor fuel bundle design. Features, such as split-vane pairs, are located on the downstream edge of support grids to enhance heat transfer and delay departure from nucleate boiling in the fuel bundle. The complex flow fields created by these features cause spatially varying heat transfer conditions on the surfaces of the rods. Azimuthal variations in heat transfer for three specific support grid designs, a standard grid, split-vane pair grid, and disc grid, are measured in the present study using a heated, thin film sensor. Normalized values of the azimuthal variations in Nusselt number are presented for the support grid designs at axial locations ranging from 2.2 to 36.7 Dh. Two Reynolds numbers, Re=28,000 and Re=42,000 are tested. The peak-to-peak azimuthal variation in normalized Nusselt number is largest just downstream of the support grids and decreases to a minimum value by the end of the grid span. A comparison of the azimuthal heat transfer characteristics between the support grids indicates distinctive results for each type of support grid design tested. The split-vane pair grid exhibits the largest peak-to-peak variation in azimuthal heat transfer of +30% to −15% just downstream of the grid at 2.2 Dh. The disc grid has the most uniform azimuthal heat transfer distribution with a peak-to-peak value of ±4% for all axial locations tested.
Three-Dimensional Characterization of a Pure Thermal Plume
Authors: Pham Minh Vuong , Plourde Fre´de´ric , Kim Son Doan
Published: June 2005

Pure thermal plumes have been investigated by two-dimensional (2D) and three-dimensional (3D) particle imaging velocimetry (PIV) techniques. While classical plume features have been checked out, time-dependent analysis allows one to clearly detect contraction and expulsion phases which are mainly driven by turbulent structure behavior. Balance of momentum equation demonstrates the link between stronger structures and expulsion-contraction motion mainly dominated by plume engulfment during contraction phases. A ratio of 3 between entrained mass flow rate during contraction and expulsion phases has been estimated. A new method, never previously applied to pure thermal plume, allows one to accurately characterize entrainment mechanism and for the first time, the latter renders it possible to estimate the entrainment coefficient all along the plume height, even close to the heating source. Moreover, entrainment coefficient is found to be 20% higher with direct method as opposed to the classical differential one widely used in the literature. Such a huge gap is found to be due to the fluctuating density and velocity part. Even through it markedly contributes to an enhanced entrainment mechanism, the role of fluctuation was generally overlooked in the previous works devoted to entrainment coefficient estimate.
Forced and Free Flow in a Vertical Annular Duct Under Nonaxisymmetric Conditions
Authors: Barletta A. , Lazzari S.
Published: June 2005

The combined forced and free flow in a vertical annular duct is studied under the hypothesis of steady-state parallel laminar flow. The Boussinesq approximation is invoked and the viscous dissipation is considered as negligible. The thermal boundary conditions are such that axial symmetry does not occur and temperature does not change in the axial direction. The dimensionless local balance equations are solved analytically by means of the Fourier series expansion method. The analytical expressions of the dimensionless temperature field, of the dimensionless velocity field, and of the Fanning friction factor are obtained.
Thermal Resistance of Nanowire-Plane Interfaces
Authors: Bahadur V. , Xu J. , Liu Y. , Fisher T. S.
Published: June 2005

This paper employs continuum principles combined with van der Waals theory to estimate the thermal contact resistance between nanowires and planar substrates. This resistance is modeled using elastic deformation theory and thermal resistance relations. The contact force between a nanowire and substrate is obtained through a calculation of the van der Waals interaction energy between the two. The model estimates numerical values of constriction and gap resistances for several nanowire-substrate combinations with water and air as the surrounding media. The total interface resistance is almost equal to the gap resistance when the surrounding medium has a high thermal conductivity. For a low-conductivity medium, the interface resistance is dominated by the constriction resistance, which itself depends significantly on nanowire and substrate conductivities. A trend observed in all calculations is that the interface resistance increases with smaller nanowires, showing that interface resistance will be a significant parameter in the design and performance of nanoelectronic devices.
Mold Accessibility via Gauss Map Analysis
Authors: Elber Gershon , Chen Xianming , Cohen Elaine
Published: June 2005

In manufacturing processes like injection molding or die casting, a two-piece mold is required to be separable, that is, be able to have both pieces of the mold removed in opposite directions while interfering neither with the mold nor with each other. The fundamental problem is to find a viewing (i.e., separating) direction, from which a valid partition line (i.e., the contact curves of the two mold pieces) exists. While previous research work on this problem exists for polyhedral models, verifying and finding such a partition line for general freeform shapes, represented by NURBS surfaces, is still an open question. This paper shows that such a valid partition exists for a compact surface of genus g, if and only if there is a viewing direction from which the silhouette consists of exactly g+1 nonsingular disjoint loops. Hence, the two-piece mold separability problem is essentially reduced to the topological analysis of silhouettes. In addition, we deal with removing almost vertical surface regions from the mold so that the form can more easily be extracted from the mold. It follows that the aspect graph, which gives all topologically distinct silhouettes, allows one to determine the existence of a valid partition as well as to find such a partition when it exists. In this paper, we present an aspect graph computation technique for compact free-form objects represented as NURBS surfaces. All the vision event curves (parabolic curves, flecnodal curves, and bitangency curves) relevant to mold separability are computed by symbolic techniques based on the NURBS representation, combined with numerical processing. An image dilation technique is then used for robust aspect graph cell decomposition on the sphere of viewing directions. Thus, an exact solution to the two-piece mold separability problem is given for such models.
Fitting and Manipulating Freeform Shapes Using Templates
Authors: Song Y. , Vergeest J. S. M. , Bronsvoort W. F.
Published: June 2005

Finding effective and efficient tools for complex freeform shape modification continues to be a challenging problem in computer graphics and computer-aided design. Although current approaches give reasonable results, their computation time and complexity often prevent their further development in more complex cases, especially in reusing an existing design. In this paper, for a better control of existing freeform shapes, deformable freeform feature templates are introduced. By the advantage of a small number of intrinsic parameters, a given freeform shape can be quickly approximated by one of the deformable templates. The deformable templates are further developed to track and match complex freeform shapes, resulting in extendable templates. With mappings, the original shape and the approximated template are associated. Thus, further shape manipulations can be conducted effectively using high-level intrinsic shape parameters. Experiments were carried out to verify the proposed algorithms. It is also described how the matching and manipulating techniques can be applied in computer graphics and computer-aided design applications.
Trivariate Simplex Splines for Inhomogeneous Solid Modeling in Engineering Design
Authors: Hua Jing , He Ying , Qin Hong
Published: June 2005

This paper presents a new inhomogeneous solid modeling paradigm for engineering design. The proposed paradigm can represent, model, and render multidimensional physical attributes across any volumetric objects of complicated geometry and topology. A modeled object is formulated with a trivariate simplex spline defined over a tetrahedral decomposition of its three-dimensional domain. Heterogeneous material attributes associated with solid geometry can be easily modeled and edited by manipulating the control vectors and∕or associated knots of trivariate simplex splines. We also develop a feature-sensitive fitting algorithm that can reconstruct a compact, continuous trivariate simplex spline from measured, structured, or unstructured volumetric grids of real-world inhomogeneous objects. In addition, we propose a fast direct rendering algorithm for interactive data analysis and visualization of the simplex spline volumes. Our experiments demonstrate that the proposed paradigm augments the current engineering design techniques with new and unique advantages.
Fast Continuous Collision Detection for Articulated Models
Authors: Redon Stephane , Lin Ming C. , Manocha Dinesh , Kim Young J.
Published: June 2005

We present a novel algorithm to perform continuous collision detection for articulated models. Given two discrete configurations of the links of an articulated model, we use an “arbitrary in-between motion” to interpolate its motion between two successive time steps and check the resulting trajectory for collisions. Our approach uses a three-stage pipeline: (1) dynamic bounding-volume hierarchy (D-BVH) culling based on interval arithmetic; (2) culling refinement using the swept volume of line swept spheres (LSS’) and graphics hardware accelerated queries; (3) exact contact computation using OBB trees and continuous collision detection between triangular primitives. The overall algorithm computes the time of collision and contact locations, and prevents any interpenetration between the articulated model and the environment. We have implemented the algorithm and tested its performance on a 2.4GHz Pentium PC with 1Gbyte of RAM and a NVIDIA GeForce FX 5800 graphics card. In practice, our algorithm is able to perform accurate and continuous collision detection between articulated models and modestly complex environments at nearly interactive rates.
Verification of Scanned Engineering Parts with CAD Models Based on Discrete Curvature Estimation
Authors: Lipshitz B. , Fischer A.
Published: June 2005

The manufacturing industry constantly needs to verify machined objects against their original CAD models. Given a prototype design, an engineer should be able to determine whether the part was manufactured well; that is, whether it fits the CAD model exactly. However, derivative computations are unstable for real data, and the estimated curvature is thus very sensitive to noise. Moreover, in many cases, spatial fitting of corresponding points is not sufficient. The current work utilizes the curvature properties to inspect manufactured parts that have been reconstructed from noisy and densely sampled data.
Contouring Medial Surface of Thin-Plate Structures Using Local Marching Cubes
Authors: Fujimori Tomoyuki , Suzuki Hiromasa , Kobayashi Yohei , Kase Kiwamu
Published: June 2005

This paper describes a new algorithm for contouring a medial surface from CT (computed tomography) data of a thin-plate structure. Thin-plate structures are common in mechanical structures, such as car body shells. When designing thin-plate structures in CAD (computer-aided design) and CAE (computer-aided engineering) systems, their shapes are usually represented as surface models associated with their thickness values. In this research, we are aiming at extracting medial surface models of thin-plate structures from their CT data for use in CAD and CAE systems. Commonly used isosurfacing methods, such as marching cubes, are not applicable to contour the medial surface. Therefore, we first extract medial cells (cubes comprising eight neighboring voxels) from the CT data using a skeletonization method to apply the marching cubes algorithm for extracting the medial surface. It is not, however, guaranteed that the marching cubes algorithm can contour those medial cells (in short, not “marching cubeable”). In this study, therefore we developed cell operations that correct topological connectivity to guarantee such marching cubeability. We then use this method to assign virtual signs to the voxels to apply the marching cubes algorithm to generate triangular meshes of a medial surface and map the thicknesses of thin-plate structures to the triangle meshes as textures. A prototype system was developed to verify some experimental results.
Liquid-Crystal Thermography: Illumination Spectral Effects. Part
1—Experiments
Authors: Anderson M. R. , Baughn J. W.
Published: June 2005

Experiments have been performed to examine the spectral effects of the illumination source on the hue-temperature characteristics of thermochromic liquid crystals (TLCs) used in a liquid-crystal thermography system. Five illumination sources were compared in this study. It was found that “full spectrum” sources, which have a relatively uniform radiant intensity across the visible spectrum, tend to have the lowest temperature uncertainties and the broadest useful ranges, which are desirable calibration attributes. Radiation in the infrared, which leads to (usually undesirable) heating of a test surface, and in the ultraviolet, which can damage TLCs, are discussed for the various light sources. Experimental observations of the effect that UV damage has on liquid crystal calibrations are also provided. The use of a new method called background subtraction and the use of white balancing are investigated as methods of improving the calibration characteristics of TLCs. The uncertainty in temperature associated with different illumination sources and both background subtraction and white balancing is determined and discussed. It is shown that these methods can reduce the uncertainty in some cases.
Condensation From Pure Steam and Steam–Air Mixtures on Integral-Fin Tubes in a Bank
Authors: Briggs Adrian , Sabaratnam Sritharan
Published: June 2005

Data are reported for condensation of steam with and without the presence of air on three rows of integral-fin tubes situated in a bank of plain tubes. The data cover a wide range of vapor velocities and air concentrations. Unlike previously reported data for plain tubes using the same test bank and apparatus, the heat-transfer coefficients for the finned tubes were largely unaffected by vapor velocity. When compared to a plain tube of fin-tip diameter and at the same vapor side temperature difference, heat-transfer enhancement ratios between 3.7 and 4.9 were found for the finned tubes compared to a plain tube in quiescent vapor conditions, while values between 1.9 and 3.9 were found when compared to a plain tube at the same vapor velocity. When compared to the plain tubes, the heat transfer to the finned tubes was much more susceptible to the presence of noncondensing gas (air) in the vapor, with enhancement ratios falling as low as 1.5 compared to the plain tubes when even small concentrations of air were present.
An Effective Unit Cell Approach to Compute the Thermal Conductivity of Composites With Cylindrical Particles
Authors: Ganapathy Deepak , Singh Kulwinder , Phelan Patrick E. , Prasher Ravi
Published: June 2005

This paper introduces a novel method, combining effective medium theory and the finite differences method, to model the effective thermal conductivity of cylindrical-particle-laden composite materials. Typically the curvature effects of cylindrical or spherical particles are ignored while calculating the thermal conductivity of composites containing such particles through numerical techniques, such that the particles are modeled as cuboids or cubes. An alternative approach to mesh the particles into small volumes is just about impossible, as it leads to highly intensive computations to get accurate results. On the other hand, effective medium theory takes the effect of curvature into account, but cannot be used at high volume fractions because it does not take into account the effects of percolation. In this paper, a novel model is proposed where the cylindrical particles are still treated as squares (cuboids), but to capture the effect of curvature, an effective conductivity is assigned to the particles by using the effective medium approach. The authors call this the effective unit cell approach. Results from this model for different volume fractions, on average, have been found to lie within ±5% of experimental thermal conductivity data.
Thermochromic Liquid Crystal Thermography: Illumination Spectral Effects. Part 2: Theory
Authors: Anderson M. R. , Baughn J. W.
Published: June 2005

A theoretical model of a Thermochromic Liquid Crystal (TLC) imaging system was developed to aid in understanding the results of experiments on spectral effects and to investigate the various factors affecting the hue-temperature calibration of TLC’s. The factors in the model include the spectral distribution of the illumination source and UV filter, surface reflection of both the TLC and background, and the sensing device (camera) spectral characteristics and gain settings. It was found that typical hue-temperature calibration curves could not be entirely explained by a TLC reflectivity model with either a monochromatic spike or a narrow bandwidth reflectivity, which is often assumed. Experimental results could be explained, however, by a model that reflects over a relatively large band of wavelengths. The spectral characteristics of the five illumination sources (those for which experiments were performed) were considered. Background reflection, which commonly accounts for 30%–50% of the reflected light, was found to significantly attenuate the hue-temperature calibration curves toward the background hue value. The effect of the illumination source on the hue-temperature calibration curves is demonstrated and several experimentally observed phenomena are explained by the results of the theoretical calculations, specifically the spectral reflective properties of the liquid crystals and the transmissivity of the R, G, and B filters in the image capture camera.
Heat flux determination from measured heating rates using thermographic phosphors
Authors: Walker D. G.
Published: June 2005

A new method for measuring the heating rate (defined as the time rate of change of temperature) and estimating heat flux from the heating rate is proposed. The example problem involves analytic heat conduction in a one-dimensional slab, where the measurement location of temperature or heating rate coincides with the location of the estimated heat flux. The new method involves the solution to a Volterra equation of the second kind, which is inherently more stable than Volterra equations of the first kind. The solution for heat flux from a measured temperature is generally a first kind Volterra equation. Estimates from the new approach are compared to estimates from measured temperatures. The heating rate measurements are accomplished by leveraging the temperature dependent decay rate of thermographic phosphors (TGP). Results indicate that the new data-reduction method is far more stable than the usual minimization of temperature residuals, which results in errors that are 1.5–12 times larger than those of the new approach. Furthermore, noise in TGP measurements was found to give an uncertainty of 4% in the heating rate measurement, which is comparable to the noise introduced in the test case data. Results of the simulations and the level of noise in TGP measurements suggest that this novel approach to heat flux determination is viable.
Preliminary Evaluation of Whole-Blood Gamma Interferon Release for Clinical Assessment of Cellular Immunity in Patients with Active Coccidioidomycosis
Authors: Ampel Neil M. , Nelson Daniel K. , Chavez Suzette , Naus Kathryn A. , Herman Amanda B. , Li Lijin , Simmons Keira A. , Pappagianis Demosthenes
Published: June 2005

Assessment of the cellular immune response in coccidioidomycosis has epidemiologic and prognostic importance. Measurement of delayed-type hypersensitivity to skin testing has been used in the past to determine cellular immunity in coccidioidomycosis. However, no skin tests are currently available in the United States. Assay of gamma interferon (IFN-γ) release in whole blood in response to incubation with antigen has been used to assess cellular immunity in tuberculosis. We used a similar assay using the coccidioidal antigen preparation T27K to measure the in vitro cellular immune responses among a cohort of 69 subjects with active coccidioidomycosis. IFN-γ release was bimodal, with concentrations above and below 5 IU/ml. Using multivariate logistic regression, underlying disease and disseminated or chronic pulmonary coccidioidomycosis was significantly associated with the release of IFN-γ at a concentration of <5 IU/ml (
P
= 0.02 or 0.05, respectively). In addition, the release IFN-γ concentration was <5 IU/ml in all subjects with a clinical severity score of ≥6 (
P
= 0.02). The release IFN-γ concentration correlated with expression of CD69 on T lymphocytes in an in vitro assay using T27K as the antigen (Spearman's rho = 0.59;
P
< 0.01). These results suggest that the IFN-γ release assay with T27K as the antigen may be a useful clinical test for assessing cellular immunity in patients with active coccidioidomycosis.
Inhibitory Receptors CD85j, LAIR-1, and CD152 Down-Regulate Immunoglobulin and Cytokine Production by Human B Lymphocytes
Authors: Merlo Andrea , Tenca Claudya , Fais Franco , Battini Lorenzo , Ciccone Ermanno , Grossi Carlo E. , Saverino Daniele
Published: June 2005

Class switching consists in the substitution of the heavy-chain constant region of immunoglobulin M (IgM) with that of IgG, IgA, or IgE. This enables antibodies to acquire new effector functions that are crucial to combat invading pathogens. Class switching usually requires engagement of CD40 on B cells by CD40 ligand (CD40L) on antigen-activated CD4+T cells and the production of cytokines. The process must be regulated tightly because abnormal IgG and IgA production favors the onset of autoimmunity, whereas increased switching to IgE leads to atopy. These inflammatory disorders can be triggered or exacerbated by costimulatory signals. Although thoroughly investigated on T cells, the roles of the inhibitory receptors CD85j, LAIR-1, and CD152 on B-cell functions have not been fully elucidated. In this study we show that cross-linking of the B-cell inhibitory receptors by specific monoclonal antibodies inhibits IgG and IgE production, reduces the percentage of IgG- and IgE-expressing B cells, and down-regulates interleukin 8 (IL-8), IL-10, and tumor necrosis factor alpha production. These effects were demonstrated using different B-cell stimulatory pathways (recall antigens, CD40L-transfected cells plus IL-4, and lipopolysaccharide plus IL-4). It thus appears that CD85j, LAIR-1, and CD152 play a central role for the control of IL-4-driven isotype switching.
Protective Antigen and Toxin Neutralization Antibody Patterns in Anthrax Vaccinees Undergoing Serial Plasmapheresis
Authors: Pittman Phillip R. , Leitman Susan F. , Oro Julio G. Barrera , Norris Sarah L. , Marano Nina M. , Ranadive Manmohan V. , Sink Bonnie S. , McKee Kelly T.
Published: June 2005

Recipients of licensed anthrax vaccine (AVA; Biothrax) could serve as a source of hyperimmune plasma and immunoglobulin for therapy and prophylaxis. We measured serum antibodies during serial weekly to biweekly plasmapheresis in 38 individuals previously vaccinated with 4 to 27 doses of AVA. Immunoglobulin G (IgG) to protective antigen (PA) and toxin neutralization assay (TNA) antibody levels were highly correlated (r= 0.86930 andP< 0.0001 for anti-PA concentration versus TNA concentration). Significant decreases in antibody titer and concentration were observed over time when compared for the number of days from the last AVA injection (P< 0.0001 for both anti-PA and TNA concentration) and for the number of days from the first plasmapheresis (P= 0.0007 for anti-PA concentration andP= 0.0025 for TNA concentration). The rate of the decrease in total IgG concentration (half-life [t1/2] = 198.90 days after first plasmapheresis) was significantly less than the decrease in anti-PA IgG (t1/2= 63.53 days) (P< 0.0001), indicating that the reduction in anti-PA IgG was more likely due to natural decay than plasmapheresis. The time since the last injection and the time after initial plasmapheresis are important elements in considering an optimal schedule for collecting anthrax hyperimmune plasma. Good correlation between IgG to PA and TNA antibodies suggests that the anti-PA enzyme-linked immunosorbent assay can be used as a high-throughput screen for functional immune reactivity in donor plasma units.
Effects of Absorption with Pneumococcal Type 22F Polysaccharide on Maternal, Cord Blood, and Infant Immunoglobulin G Antipneumococcal Polysaccharide Antibodies
Authors: Inostroza J. , Villanueva S. , Mason K. , Leiva L. E. , Sorensen R. U.
Published: June 2005

The aim of this study was to evaluate the effect of absorption with pneumococcal type 22F polysaccharide on antipneumococcal antibody titers in unimmunized Chilean pregnant women and on antibodies in their offspring at birth and 3, 6, and 12 months of age. Sera from 10 healthy pregnant women and from their offspring at birth and at 3, 6, and 12 months of age were studied. Immunoglobulin G antibodies against serotypes 1, 3, 4, 5, 6B, 9V, 14, 18, 19F, and 23F were measured by a standardized enzyme-linked immunosorbent assay method. All sera were absorbed with polysaccharide C, and aliquots of each serum were absorbed with polysaccharide 22F. Individual results were expressed in μg/ml based on the standard serum pool 89-SF. Absorption with polysaccharide 22F reduced antibody concentrations in all samples and to all 10 serotypes studied. Reduction was highest in maternal sera and in cord blood, but it was also present at 3, 6, and 12 months of age. The percent reduction ranged from 24% for serotype 14 to 50% for serotype 1 in maternal samples and from 20% for serotype 18C to 49% for serotype 4 in cord blood samples. The percentages of transplacental transmission were similar for nonabsorbed and absorbed maternal fetal pairs. Absorption with serotype 22F had a significant impact on antipneumococcal antibody concentrations in unimmunized pregnant women and in their offspring. Our results suggest that absorption with 22F polysaccharide needs to be performed in studies of transplacental transmission of antipneumococcal antibodies.
Borreliacidal OspC Antibodies Specific for a Highly Conserved Epitope Are Immunodominant in Human Lyme Disease and Do Not Occur in Mice or Hamsters
Authors: Lovrich Steven D. , Jobe Dean A. , Schell Ronald F. , Callister Steven M.
Published: June 2005

Humans produce highly specific borreliacidal antibodies against outer surface protein C (OspC) shortly after infection with
Borrelia burgdorferi
sensu stricto. We previously demonstrated the epitope recognized by immunoglobulin M (IgM) and IgG OspC borreliacidal antibodies was located within the 50 amino acids nearest the carboxy (C) terminus. In this study, we show the immunodominant epitope is located in the highly conserved region within the seven C-terminal amino acids. Six early Lyme disease sera that contained borreliacidal activity and IgM and/or IgG OspC antibodies were chosen randomly and adsorbed with truncated OspC containing the 16 or 7 amino acids nearest the C terminus. Adsorptions with each truncated protein abrogated the borreliacidal activity completely. In addition, only small concentrations of OspC antibodies remained detectable by enzyme-linked immunosorbent assay and Western blotting. Moreover, borreliacidal OspC antibodies were not induced in laboratory mice or hamsters despite heavy infections with
B. burgdorferi
spirochetes. These findings confirm that borreliacidal antibodies comprise the majority of the IgM and IgG OspC antibody response in human Lyme disease and that the epitope is located in the highly conserved C terminus. In addition, rodent animal models appear to be inappropriate subjects for assessing the effectiveness of the epitope for serodiagnosis or as a human Lyme disease vaccine.
Demonstration of Components of Antigen 85 Complex in Cerebrospinal Fluid of Tuberculous Meningitis Patients
Authors: Kashyap Rajpal S. , Dobos Karen M. , Belisle John T. , Purohit Hemant J. , Chandak Nitin H. , Taori Girdhar M. , Daginawala Hatim F.
Published: June 2005

Tuberculous meningitis (TBM) is the most common form of chronic infection of the central nervous system. Despite the magnitude of the problem, the general diagnostic outlook is discouraging. Specifically, there is no generally accepted early confirmative diagnosis protocol available for TBM. Various
Mycobacterium tuberculosis
antigens are now recognized as potential markers for diagnosis of TBM. However, their presence remains questionable, and many of these antigens are reported in the blood but not in the cerebrospinal fluid (CSF). This study identifies a specific protein marker in CSF which will be useful in early diagnosis of TBM. We have demonstrated the presence of a 30-kDa protein band in CSF of 100% (
n
= 5) of confirmed and 90% (
n
= 138) of suspected TBM patients out of 153 TBM patients. The 30-kDa band was excised from the gel, destained extensively, and digested with trypsin. The resulting peptides were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Partially purified proteins from CSF samples of TBM were analyzed by two-dimensional polyacrylamide gel electrophoresis and Western blotting. Immunoblotting and enzyme-linked immunosorbent assay (ELISA) were performed to confirm the presence of proteins in the 30-kDa protein band. The antigen 85 (Ag 85) complex was detected in CSF of TBM patients by indirect ELISA using antibodies against Ag 85 complex. The results of this study showed the 30-kDa protein band contained MTB proteins Rv3804c (Ag85A) and Rv1886c (Ag 85B), both members of the Ag85 complex. This was also confirmed by using immunotechniques such as indirect ELISA and the dot immunobinding assay. Detection of Ag85 complex was observed in CSF of 89% (71 out of 80) of suspected TBM patients that were 30-kDa protein positive. The observed 30-kDa protein in the CSF is comprised of the MTB Ag85 complex. This protein was earlier reported to be present in the blood of patients with extra-central nervous system tuberculosis. Therefore, this finding suggests that this protein can be used as a molecular marker for any type of tuberculous infection. It also provides a more sensitive immunoassay option for the early and confirmatory diagnosis of TBM.
Evaluation of PCR-Based Assay for Diagnosis of Spotted Fever Group Rickettsiosis in Human Serum Samples
Authors: Choi Yeon-Joo , Lee Seung-Hyun , Park Kyung-Hee , Koh Young-Sang , Lee Keun-Hwa , Baik Hyung-Suk , Choi Myung-Sik , Kim Ik-Sang , Jang Won-Jong
Published: June 2005

A nested PCR assay was developed for the detection of spotted fever group (SFG) rickettsiae in serum samples. The assay was based on specific primers derived from the rickettsial outer membrane protein B gene (
rompB
) of
Rickettsia conorii
. An SFG rickettsia-specific signal is obtained from
R. akari
,
R. japonica
,
R. sibirica
, and
R. conorii
. Other bacterial species tested did not generate any signal, attesting to the specificity of the assay. As few as seven copies of the
rompB
gene of
R. conorii
could be detected in 200 μl of serum sample. The assay was evaluated with a panel of sera obtained from patients with acute-phase febrile disease tested by immunofluorescent antibody assay (IFA). The SFG rickettsia-specific DNA fragment was detected in 71 out of 100 sera, which were proven to have immunoglobulin M antibodies against SFG rickettsial antigen by IFA. The results were further confirmed by restriction fragment length polymorphism and sequencing analysis of the DNA fragments. The results indicated that this PCR assay is suitable for the diagnosis of spotted fever group rickettsiosis in Korea.
Antibody Response to
Actinomyces
Antigen and Dental Caries Experience: Implications for Caries Susceptibility
Authors: Levine Martin , Owen Willis L. , Avery Kevin T.
Published: June 2005

Fluoridated dentifrices reduce dental caries in subjects who perform effective oral hygiene.
Actinomyces naeslundii
increases in teeth-adherent microbial biofilms (plaques) in these subjects, and a well-characterized serum immunoglobulin G (IgG) antibody response (
Actinomyces
antibody [A-Ab]) is also increased. Other studies suggest that a serum IgG antibody response to streptococcal
d
-alanyl poly(glycerophosphate) (S-Ab) may indicate caries experience associated strongly with gingival health and exposure to fluoridated water. The aim of this study was to investigate relationships between A-Ab response, oral hygiene, S-Ab response, and caries experience. Measurements were made of A-Ab and S-Ab concentrations, caries experience (number of decayed, missing, and filled teeth [DMFT], number of teeth surfaces [DMFS], and number of decayed teeth needing treated [DT]), exposure to fluoridated water (Flu), mean clinical pocket depth (PD; in millimeters), and extent of plaque (PL) and gingival bleeding on probing (BOP). A-Ab concentration, the dependent variable in a multiple regression analysis, increased with S-Ab concentration and decreased with PL and DMFT adjusted for Flu (
R
2
= 0.51,
P
< 0.002). Residual associations with age, DMFS, DT, and BOP were not significant. In addition, an elevated A-Ab response, defined from immunoprecipitation and immunoassay measurements, indicated a significant, 30% reduction in DMFT after adjustment for significant age and Flu covariance (analysis of variance with covariance F statistic = 10.6,
P
< 0.003; S-Ab response and interactions not significant). Thus, an elevated A-Ab response indicates less caries in subjects performing effective oral hygiene using fluoridated dentifrices. Conversely, a low A-Ab response is suggestive of decreased
A. naeslundii
binding to saliva-coated apatite and greater caries experience, as reported by others.
Antibody Responses to Recombinant Protein Fragments of the Major Outer Membrane Protein and Polymorphic Outer Membrane Protein POMP90 inChlamydophila abortus-Infected Pregnant Sheep
Authors: Livingstone Morag , Entrican Gary , Wattegedera Sean , Buxton David , McKendrick Iain J. , Longbottom David
Published: June 2005

Chlamydophila abortusis one of the major causes of infectious abortion in pregnant sheep (enzootic abortion of ewes or EAE) worldwide. Organisms shed in infected placentas and uterine discharges at lambing time are the main sources of environmental contamination, responsible for transmission to susceptible animals and possible human contacts. In the present study, a recently developed test, based on a recombinant fragment of the polymorphic outer membrane protein POMP90 (rOMP90-4 indirect enzyme-linked immunosorbent assay [iELISA]) and one based on the variable segment 2 (VS2) region of the major outer membrane protein (MOMP) (MOMP VS2 iELISA) were compared using sera fromC. abortus-infected ewes at different stages throughout pregnancy. The rOMP90 iELISA detected antibody much earlier in pregnancy than the MOMP iELISA, which, like the complement fixation test, detected antibody only at the time of abortion or lambing. No anti-MOMP antibody response could be detected in three of seven experimentally infected ewes. Furthermore, the rOMP90 iELISA detected antibody in an animal that seroconverted during the course of the study, which the MOMP iELISA failed to detect. Overall, the results show that the rOMP90-4 iELISA is considerably more sensitive than the MOMP VS2 iELISA for identifying animals infected withC. abortus. Earlier detection of infection will allow appropriate control measures to be taken to reduce environmental contamination, thus limiting the spread of infection, financial losses, and the possible risks of zoonotic transmission to humans.
Several Recombinant Capsid Proteins of Equine Rhinitis A Virus Show Potential as Diagnostic Antigens
Authors: Li Fan , Stevenson Rachel A. , Crabb Brendan S. , Studdert Michael J. , Hartley Carol A.
Published: June 2005

Equine rhinitis A virus
(ERAV) is a significant pathogen of horses and is also closely related to
Foot-and-mouth disease virus
(FMDV). Despite these facts, knowledge of the prevalence and importance of ERAV infections remains limited, largely due to the absence of a simple, robust diagnostic assay. In this study, we compared the antigenicities of recombinant full-length and fragmented ERAV capsid proteins expressed in
Escherichia coli
by using sera from experimentally infected and naturally exposed horses. We found that, from the range of antigens tested, recombinant proteins encompassing the C-terminal region of VP1, full-length VP2, and the N-terminal region of VP2 reacted specifically with antibodies present in sera from each of the five experimentally infected horses examined. Antibodies to epitopes on VP2 (both native and recombinant forms) persisted longer postinfection (>105 days) than antibodies specific for epitopes on other fragments. Our data also suggest that B-cell epitopes within the C terminus of VP1 and N terminus of VP2 contribute to a large proportion of the total reactivity of recombinant VP1 and VP2, respectively. Importantly, the reactivity of these VP1 and VP2 recombinant proteins in enzyme-linked immunosorbent assays (ELISAs) correlated well with the results from a range of native antigen-based serological assays using sera from 12 field horses. This study provides promising candidates for development of a diagnostic ERAV ELISA.
Opsonization Effects onMycobacterium aviumsubsp.paratuberculosis-Macrophage Interactions
Authors: Hostetter J. , Kagan R. , Steadham E.
Published: June 2005

High antibody titers in ruminants infected withMycobacterium aviumsubsp.paratuberculosiscorrelates with disease progression. Effects of humoral responses during mycobacterial infection are not completely understood. This study suggests that activation status may be an important factor in determining macrophage ability to limit proliferation of opsonizedM. aviumsubsp.paratuberculosis.
Surface Envelope Glycoprotein Is B-Lymphocyte Immunodominant in Sheep Naturally Infected with Ovine Progressive Pneumonia Virus
Authors: Herrmann Lynn M. , McGuire Travis C. , Hötzel Isidro , Lewis Gregory S. , Knowles Donald P.
Published: June 2005

The B-lymphocyte-immunodominant antigen involved in naturally ovine progressive pneumonia virus (OPPV)-infected mature sheep remains unknown. Therefore, the amount of antibody in sera from 10 naturally OPPV-infected sheep was evaluated by immunoprecipitation (IP) of the major viral proteins in [
35
S]methionine/cysteine-labeled OPPV (whole virus) lysate. Using an excess of OPPV proteins in whole-virus lysate, 8 out of 10 sheep had the highest serum antibody IP endpoint titers to the gp135 surface envelope glycoprotein (SU). Also, 2 out of 10 sheep had equivalent serum antibody IP endpoint titers to the transmembrane glycoprotein oligomer (TM90) and SU. Since these data indicate that SU is the immunodominant protein in most mature sheep persistently infected with OPPV, SU-specific diagnostic serological assays can be utilized for OPPV diagnosis.
CELLULAR AUTOMATON SIMULATION OF THE ESCAPING PEDESTRIAN FLOW IN CORRIDOR
Authors: QIU BING , TAN HUILI , ZHANG CHAOYING , KONG LINGJIANG , LIU MUREN
Published: June 2005

A multi-speed cellular automaton is used to simulate the escaping pedestrian flow in a corridor under the open boundary condition. Keeping the total number of people fixed, and pedestrians moving in different speeds, we studied the evolution of pedestrian flow by varying the parameters of system size. The relationships between parameters of system size and the transition time are discussed in this paper. It is found that the transition time tc closely depends on the width (W) of corridor and the maximum speed V max of people, it scales as tc∝W-0.80±0.06, and [Formula: see text], in which α increases with the width of doors. However, the width of doors and the strength of drift have little influence on the transition time.
ACCELERATING CONVERGENCE OF MOLECULAR DYNAMICS-BASED STRUCTURAL RELAXATION
Authors: CHRISTENSEN A.
Published: June 2005

We describe strategies to accelerate the terminal stage of molecular dynamics (MD)-based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve efficiency. We also discuss the implementation aspects. Secondly, we explore the final state refinement acceleration by a combination with the conjugate gradient technique, where the key ingredient is an implicit corrector step. Finally, we test the feasibility of passive Hessian matrix accumulation from an MD trajectory, as another route for final phase acceleration. Our suggestions may be implemented within most MD quench implementations with a few, straightforward lines of code, thus maintaining the appealing simplicity of the MD quench algorithms. In this paper, we also bridge the conceptual gap between the MD quench algorithms inspired from physics and the mathematically rooted line search algorithms.
ON THE CONSENSUS THRESHOLD FOR THE OPINION DYNAMICS OF KRAUSE–HEGSELMANN
Authors: FORTUNATO SANTO
Published: June 2005

In the consensus model of Krause–Hegselmann, opinions are real numbers between 0 and 1, and two agents are compatible if the difference of their opinions is smaller than the confidence bound parameter ∊. A randomly chosen agent takes the average of the opinions of all neighboring agents which are compatible with it. We propose a conjecture, based on numerical evidence, on the value of the consensus threshold ∊cof this model. We claim that ∊ccan take only two possible values, depending on the behavior of the average degree d of the graph representing the social relationships, when the population N approaches infinity: if d diverges when N→∞, ∊cequals the consensus threshold ∊i~0.2 on the complete graph; if instead d stays finite when N→∞, ∊c=1/2 as for the model of Deffuant et al.
A STUDY ON THE RANDOMNESS OF THE DIGITS OF π
Authors: TU SHU-JU , FISCHBACH EPHRAIM
Published: June 2005

We apply a newly-developed computational method, Geometric Random Inner Products (GRIP), to quantify the randomness of number sequences obtained from the decimal digits of π. Several members from the GRIP family of tests are used, and the results from π are compared to those calculated from other random number generators. These include a recent hardware generator based on an actual physical process, turbulent electroconvection. We find that the decimal digits of π are in fact good candidates for random number generators and can be used for practical scientific and engineering computations.
REACTION DYNAMICS OF Nin (n =19 and 20) WITH D2: DEPENDENCE ON CLUSTER SIZE, TEMPERATURE AND INITIAL ROVIBRATIONAL STATES OF THE MOLECULE
Authors: BÖYÜKATA MUSTAFA , GÜVENÇ ZİYA B. , ÖZÇELİK SULEYMAN , DURMUŞ PERİHAN , JELLINEK JULIUS
Published: June 2005

The Ni n (n =19, 20) + D 2 (v, j) collision systems have been studied to investigate the dependence of cluster reactivity on the cluster temperature and the initial rovibrational states of the molecule using quasiclassical molecular dynamics simulations. The clusters are described by an embedded atom potential, whereas the interaction between the molecule and the cluster is modeled by a LEPS (London–Eyring–Polani–Sato) potential energy function. Reaction (dissociative adsorption) cross-sections are computed as functions of the collision energy for different initial rovibrational states of the molecule and for different temperatures of the clusters. Rovibrational, temperature and size-dependent rate constants are also presented, and the results are compared with earlier studies. Initial vibrational excitation of the molecule increases the reaction cross-section more efficiently than the initial rotational excitation. The reaction cross-sections strongly depend on the collision energies below 0.1 eV .