bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Novel Approach in the Direct Kinematics of Stewart Platform Mechanisms with Planar Platforms
Authors: Akçali İ. D. , Mutlu H. 
Published: December 2005

Abstract
In handling the kinematic analysis of two rigid bodies connected to each other by six legs through the use of six double spherical joints, methods have been implemented both in the formulation and solution phases of the problem. A three-dimensional problem has been viewed, in fact, as a multitude of two-dimensional works on several planes, the intersections of which yield relationships allowing transition between adjacent planes. Thus formulation is purely based on the geometric structure consisting of eight planes of interest, ending in the three fundamental equations involving three angles between the base and side triangular planes. In solving the resulting three equations, an efficient strategy has been established to come up with 16 solution sets effectively. Extensions of the theory have been shown to include the analyses of other Stewart platform models. Efficiency and effectiveness of the approach has been verified on numerical examples.
Estimation
of Time-Varying Inlet Temperature and Heat Flux in Turbulent Circular Pipe
Flow
Authors: Chen Cha’o-Kuang , Wu Li-Wen , Yang Yue-Tzu 
Published: December 2005

Abstract
This study addresses the conjugate heat transfer problem of hydrodynamically developed turbulent flow in a circular pipe. An inverse method is used to estimate the time-varying inlet temperature and the outer-wall heat flux simultaneously on the basis of temperature measurements taken at two different locations within the pipe flow. The present approach rearranges the matrix forms of the governing differential equations and then applies a whole domain estimation with the function specification method and the linear least-squares-error method to determine the two boundary conditions of the pipe flow. The dimensionless temperature data obtained from the direct problem are used to simulate the temperature measurements. The influence of temperature measurement errors upon the precision of the estimated results is investigated. The proposed method provides several advantages compared to traditional methods: (1) it yields a solution within a single computational iteration, (2) no prior information is required regarding the functional form of the quantities of interest, (3) no initial guesses of the unknown parameter values are required, and (4) the inverse problem can be solved in a linear domain. This study also considers the influence of the location of the temperature measurement sensors upon the accuracy of the calculated results. The numerical results confirm that the proposed method provides an efficient, robust, and accurate means of estimating the inlet temperature and outer-wall heat flux simultaneously in turbulent pipe flow.
Laminar Flow and Heat Transfer in the Entrance Region of Trapezoidal
Channels With Constant Wall Temperature
Authors: Renksizbulut Metin , Niazmand Hamid 
Published: December 2005

Abstract
Simultaneously developing three-dimensional laminar flow and heat transfer in the entrance region of trapezoidal channels have been investigated using numerical methods in the Reynolds number range from 10 to 1000. The principal and secondary velocity fields, the temperature field, and all associated heat and momentum exchange parameters have been examined. The present results for the fully developed flow region of the channels compare well with the available literature. In the entrance region, it is observed that the axial velocity profiles develop overshoots near the walls and particularly at the channel corners. It is shown that boundary-layer type of approximations, which lead to Reynolds-number-independent Poiseuille and Nusselt numbers, can be used for Reynolds numbers over 50 and after a few hydraulic diameters from the channel inlet. It is also shown that hydrodynamic entrance lengths calculated with methods based on fully developed flow data are grossly in error. New correlations are proposed for the entrance length, and for the friction and heat transfer coefficients.
Active Thermal Control
of Distributed Parameter Systems Excited at Multiple
Frequencies
Authors: Richter Christoph
C. , Lienhard John
        H. 
Published: December 2005

Abstract
In testing packaged high-power integrated circuits, active thermal control is useful in providing die-level temperature stability. A time-varying heat load is applied to the surface of the package to compensate for the time-varying test power sequence applied to the die. An earlier study determined the proper control heat load for a single-frequency sinusoidal variation in die power subject to a finite allowed temperature variation on the die. Actual test power sequences contain many frequencies at various phase angles, each contributing to the temperature variation of the die. In the present study, we develop a method of controlling multiple frequency test sequences subject to a finite temperature tolerance. It is shown that the total control power may be minimized assigning temperature tolerances to the highest frequencies in the test power sequence.
Phage Library Screening for the Rapid Identification and In Vivo Testing of Candidate Genes for a DNA Vaccine against
Mycoplasma mycoides
subsp.
mycoides
Small Colony Biotype
Authors: March John B. , Jepson Catherine D. , Clark Jason R. , Totsika Makrina , Calcutt Michael J. 
Published: December 2005

ABSTRACT

A new strategy for rapidly selecting and testing genetic vaccines has been developed, in which a whole genome library is cloned into a bacteriophage λ ZAP Express vector which contains both prokaryotic (P
lac
) and eukaryotic (P
CMV
) promoters upstream of the insertion site. The phage library is plated on
Escherichia coli
cells, immunoblotted, and probed with hyperimmune and/or convalescent-phase antiserum to rapidly identify vaccine candidates. These are then plaque purified and grown as liquid lysates, and whole bacteriophage particles are then used directly to immunize the host, following which P
CMV
-driven expression of the candidate vaccine gene occurs. In the example given here, a semirandom genome library of the bovine pathogen
Mycoplasma mycoides
subsp.
mycoides
small colony (SC) biotype was cloned into λ ZAP Express, and two strongly immunodominant clones, λ-A8 and λ-B1, were identified and subsequently tested for vaccine potential against
M. mycoides
subsp.
mycoides
SC biotype-induced mycoplasmemia. Sequencing and immunoblotting indicated that clone λ-A8 expressed an isopropyl-β-
d
-thiogalactopyranoside (IPTG)-inducible
M. mycoides
subsp.
mycoides
SC biotype protein with a 28-kDa apparent molecular mass, identified as a previously uncharacterized putative lipoprotein (MSC_0397). Clone λ-B1 contained several full-length genes from the
M. mycoides
subsp.
mycoides
SC biotype pyruvate dehydrogenase region, and two IPTG-independent polypeptides, of 29 kDa and 57 kDa, were identified on immunoblots. Following vaccination, significant anti-
M. mycoides
subsp.
mycoides
SC biotype responses were observed in mice vaccinated with clones λ-A8 and λ-B1. A significant stimulation index was observed following incubation of splenocytes from mice vaccinated with clone λ-A8 with whole live
M. mycoides
subsp.
mycoides
SC biotype cells, indicating cellular proliferation. After challenge, mice vaccinated with clone λ-A8 also exhibited a reduced level of mycoplasmemia compared to controls, suggesting that the MSC_0397 lipoprotein has a protective effect in the mouse model when delivered as a bacteriophage DNA vaccine. Bacteriophage-mediated immunoscreening using an appropriate vector system offers a rapid and simple technique for the identification and immediate testing of putative candidate vaccines from a variety of pathogens.
Interaction with CagF Is Required for Translocation of CagA into the Host via theHelicobacter pyloriType IV Secretion System
Authors: Couturier Marc Roger , Tasca Elizabetta , Montecucco Cesare , Stein Markus 
Published: December 2005

ABSTRACTDevelopment of severe gastric diseases is strongly associated with those strains ofHelicobacter pylorithat contain thecagpathogenicity island (PAI) inserted into the chromosome. ThecagPAI encodes a type IV secretion system that translocates the major disease-associated virulence protein, CagA, into the host epithelial cell. CagA then affects host signaling pathways, leading to cell elongations and inflammation. Since the precise mechanism by which the CagA toxin is translocated by the type IV secretion system remained elusive, we used fusion proteins and immunoprecipitation studies to identify CagA-interacting secretion components. Here we demonstrate that CagA, in addition to other yet-unidentified proteins, interacts with CagF, presumably at the inner bacterial membrane. This interaction is required for CagA translocation, since an isogenic nonpolarcagFmutant was translocation deficient. Our results suggest that CagF may be a protein with unique chaperone-like function that is involved in the early steps of CagA recognition and delivery into the type IV secretion channel.
Identification ofBorrelia burgdorferiOuter Surface Proteins
Authors: Brooks Chad S. , Vuppala Santosh R. , Jett Amy M. , Akins Darrin R. 
Published: December 2005

ABSTRACTSeveralBorrelia burgdorferiouter surface proteins have been identified over the past decade that are up-regulated by temperature- and/or mammalian host-specific signals as this spirochete is transmitted from ticks to mammals. Given the potential role(s) that these differentially up-regulated proteins may play inB. burgdorferitransmission and Lyme disease pathogenesis, much attention has recently been placed on identifying additional borrelial outer surface proteins. To identify uncharacterizedB. burgdorferiouter surface proteins, we previously performed a comprehensive gene expression profiling analysis of temperature-shifted and mammalian host-adaptedB. burgdorferi. The combined microarray analyses revealed that many genes encoding known and putative outer surface proteins are down-regulated in mammalian host-adaptedB. burgdorferi. At the same time, however, several different genes encoding putative outer surface proteins were found to be up-regulated during the transmission and infection process. Among the putative outer surface proteins identified, biochemical and surface localization analyses confirmed that seven (Bb0405, Bb0689, BbA36, BbA64, BbA66, BbA69, and BbI42) are localized to the surface ofB. burgdorferi. Furthermore, enzyme-linked immunosorbent assay analysis using serum from tick-infested baboons indicated that all seven outer surface proteins identified are immunogenic and that antibodies are generated against all seven during a natural infection. Specific antibodies generated against all seven of these surface proteins were found to be bactericidal againstB. burgdorferi, indicating that these newly identified outer surface proteins are prime candidates for analysis as second-generation Lyme disease vaccinogens.
Characterization, Distribution, and Expression of Novel Genes among Eight Clinical Isolates of
Streptococcuspneumoniae
Authors: Shen Kai , Gladitz John , Antalis Patricia , Dice Bethany , Janto Benjamin , Keefe Randy , Hayes Jay , Ahmed Azad , Dopico Richard , Ehrlich Nathan , Jocz Jennifer , Kropp Laura , Yu Shujun , Nistico Laura , Greenberg David P. , Barbadora Karen , Preston Robert A. , Post J. Christopher , Ehrlich Garth D. , Hu Fen Z. 
Published: December 2005

ABSTRACT

Eight
low-passage-number
Streptococcus pneumoniae
clinical isolates,
each of a different serotype and a different multilocus sequence type,
were obtained from pediatric participants in a pneumococcal vaccine
trial. Comparative genomic analyses were performed with these strains
and two
S. pneumoniae
reference strains. Individual genomic
libraries were constructed for each of the eight clinical isolates,
with an average insert size of ∼1 kb. A total of 73,728 clones
were picked for arraying, providing more than four times genomic
coverage per strain. A subset of 4,793 clones were sequenced, for which
homology searches revealed that 750 (15.6%) of the sequences were
unique with respect to the TIGR4 reference genome and 263 (5.5%) clones
were unrelated to any available streptococcal sequence. Hypothetical
translations of the open reading frames identified within these novel
sequences showed homologies to a variety of proteins, including
bacterial virulence factors not previously identified in
S.
pneumoniae
. The distribution and expression patterns of 58 of
these novel sequences among the eight clinical isolates were analyzed
by PCR- and reverse transcriptase PCR-based analyses, respectively.
These unique sequences were nonuniformly distributed among the eight
isolates, and transcription of these genes in planktonic cultures was
detected in 81% (172/212) of their genic occurrences. All 58 novel
sequences were transcribed in one or more of the clinical strains,
suggesting that they all correspond to functional genes. Sixty-five
percent (38/58) of these sequences were found in 50% or less of the
clinical strains, indicating a significant degree of genomic plasticity
among natural
isolates.
Involvement of
potD
in
Streptococcus pneumoniae
Polyamine Transport and Pathogenesis
Authors: Ware D. , Jiang Y. , Lin W. , Swiatlo E. 
Published: December 2005

ABSTRACT

Polyamines such as putrescine, spermidine, and cadaverine are small, polycationic molecules that are required for optimal growth in all cells. The intracellular concentrations of these molecules are maintained by de novo synthesis and transport pathways. The human pathogen
Streptococcus pneumoniae
possesses a putative
po
lyamine
t
ransporter (
pot
) operon that consists of the four
pot
-specific genes
potABCD
. The studies presented here examined the involvement of
potD
in polyamine transport and in pneumococcal pathogenesis. A
potD
-deficient mutant was created in the mouse-virulent serotype 3 strain WU2 by insertion duplication mutagenesis. The growth of the WU2Δ
potD
mutant was identical to that of the wild-type strain WU2 in vitro in rich media. However, WU2Δ
potD
possessed severely delayed growth compared to wild-type WU2 in the presence of the polyamine biosynthesis inhibitors DFMO (α-dimethyl-fluroornitithine) and MGBG [methylgloxal-
bis
(guanyl hydrazone)]. The mutant strain also showed a significant attenuation in virulence within murine models of systemic and pulmonary infection regardless of the inoculation route or location. These data suggest that
potD
is involved in pneumococcal polyamine transport and is important for pathogenesis within various infection models.
Transcriptional Activation of the
Staphylococcus aureus putP
Gene by Low-Proline-High Osmotic Conditions and during Infection of Murine and Human Tissues
Authors: Schwan William R. , Lehmann Lynn , McCormick James 
Published: December 2005

ABSTRACT

Staphylococcus aureus
can grow virtually anywhere in the human body but needs to import proline through low- and high-affinity proline transporters to survive. This study examined the regulation of the
S. aureus putP
gene, which encodes a high-affinity proline permease.
putP
::
lacZ
and
putP
::
lux
transcriptional fusions were constructed and integrated into the genomes of several
S. aureus
strains. Enzyme activity was measured after growth in media with various osmolyte concentrations. As osmolarity rose,
putP
expression increased, with a plateau at 2 M for NaCl in strain LL3-1. Proline concentrations as low as 17.4 μM activated expression of the
putP
gene. The
putP
::
lux
fusion was also integrated into the genomes of
S. aureus
strains that were either SigB inactive (LL3-1, 8325-4, and SH1003) or SigB active (Newman and SH1000). SigB inactive strains showed increased
putP
gene expression as NaCl concentrations rose, whereas SigB active strains displayed a dramatic decrease in
putP
expression, suggesting that the alternative sigma factor B plays a negative role in
putP
regulation. Mice inoculated with
S. aureus
strains containing the
putP
::
lux
fusion exhibited up to a 715-fold increase in
putP
expression, although levels in the various murine organs differed. Moreover, urine from human patients infected with
S. aureus
showed elevated
putP
levels by use of a PCR procedure, whereas blood and some abscess material had no significant increase. Thus,
putP
is transcriptionally activated by a low-proline and high osmotic environment both in growth media and in murine or human clinical specimens.
Fibronectin Binding Protein BBK32 of the Lyme Disease Spirochete Promotes Bacterial Attachment to Glycosaminoglycans
Authors: Fischer Joshua R. , LeBlanc Kimberly T. , Leong John M. 
Published: December 2005

ABSTRACT

Borrelia burgdorferi
, the agent of Lyme disease, causes a multisystemic illness that can affect the skin, heart, joints, and nervous system and is capable of attachment to diverse cell types. Among the host components recognized by this spirochete are fibronectin and glycosaminoglycans (GAGs). Three surface-localized GAG-binding bacterial ligands, Bgp, DbpA, and DbpB, have been previously identified, but recent studies suggested that at least one additional GAG-binding ligand is expressed on the spirochetal surface when the spirochete is adapted to the mammalian host environment. BBK32 is a surface lipoprotein that is produced during infection and that has been shown to bind to fibronectin. In this study, we show that, when BBK32 was produced from a shuttle vector in an otherwise nonadherent high-passage
B. burgdorferi
strain, the protein localized on the bacterial surface and conferred attachment to fibronectin and to mammalian cell monolayers. In addition, the high-passage strain producing BBK32 bound to purified preparations of the GAGs dermatan sulfate and heparin, as well as to these GAGs on the surfaces of cultured mammalian cells. Recombinant BBK32 recognized purified heparin, indicating that the bacterial attachment to GAGs was due to direct binding by BBK32. This GAG-binding activity of BBK32 is apparently independent of fibronectin recognition, because exogenous heparin had no effect on BBK32-mediated bacterial binding to fibronectin.
Platelets Potentiate Brain Endothelial Alterations Induced byPlasmodium falciparum
Authors: Wassmer Samuel C. , Combes Valéry , Candal Francisco J. , Juhan-Vague Irène , Grau Georges E. 
Published: December 2005

ABSTRACTBrain lesions of cerebral malaria (CM) are characterized by a sequestration ofPlasmodium falciparum-parasitized red blood cells (PRBC) and platelets within brain microvessels, as well as by blood-brain barrier (BBB) disruption. In the present study, we evaluated the possibility that PRBC and platelets induce functional alterations in brain endothelium. In a human brain endothelial cell line, named HBEC-5i, exhibiting most of the features demanded for a pathophysiological study of BBB, tumor necrosis factor (TNF) or lymphotoxin α (LT-α) reduced transendothelial electrical resistance (TEER), enhanced the permeability to 70-kDa dextran, and increased the release of microparticles, a recently described indicator of disease severity in CM patients. In vitro cocultures showed that platelets or PRBC can have a direct cytotoxic effect on activated, but not on resting, HBEC-5i cells. Platelet binding was required, as platelet supernatant had no effect. Furthermore, platelets potentiated the cytotoxicity of PRBC for TNF- or LT-α-activated HBEC-5i cells when they were added prior to these cells on the endothelial monolayers. This effect was not observed when platelets were added after PRBC. Both permeability and TEER were strongly affected, and the apoptosis rate of HBEC-5i cells was dramatically increased. These findings provide insights into the mechanisms by which platelets can be deleterious to the brain endothelium during CM.
Inhibition of Chlamydiae by Primary Alcohols Correlates with the Strain-Specific Complement of Plasticity Zone Phospholipase D Genes
Authors: Nelson David E. , Crane Deborah D. , Taylor Lacey D. , Dorward David W. , Goheen Morgan M. , Caldwell Harlan D. 
Published: December 2005

ABSTRACT

Members of the genus
Chlamydia
are obligate intracellular pathogens that have a unique biphasic developmental cycle and interactions with host cells. Many genes that dictate host infection tropism and, putatively, pathogenic manifestations of disease are clustered in a hypervariable region of the genome termed the plasticity zone (PZ). Comparative genomics studies have determined that an uncharacterized family of PZ genes encoding orthologs of eukaryotic and prokaryotic members of the phospholipase D (PLD) enzyme family varies among chlamydiae. Here, we show that the PZ PLD (pzPLD) of
Chlamydia trachomatis
are transcribed during both normal and persistent infection and that the corresponding PLD proteins are predominately localized in reticulate bodies on the inner leaflet of the inclusion membrane. Further, we show that strains of chlamydiae encoding the pzPLD, but not a strain lacking these genes, are inhibited by primary alcohols, potent PLD inhibitors, during growth in HeLa 229 cells. This inhibitory effect is amplified approximately 5,000-fold during recovery from persistent infection. These findings suggest that the chlamydial pzPLD may be important, strain-specific, pathogenesis factors in vivo.
Role of Intimin-Tir Interactions and the Tir-Cytoskeleton Coupling Protein in the Colonization of Calves and Lambs by
Escherichia coli
O157:H7
Authors: Vlisidou Isabella , Dziva Francis , La Ragione Roberto M. , Best Angus , Garmendia Junkal , Hawes Pippa , Monaghan Paul , Cawthraw Shaun A. , Frankel Gad , Woodward Martin J. , Stevens Mark P. 
Published: December 2005

ABSTRACT

Intimin facilitates intestinal colonization by enterohemorrhagic
Escherichia coli
O157:H7; however, the importance of intimin binding to its translocated receptor (Tir) as opposed to cellular coreceptors is unknown. The intimin-Tir interaction is needed for optimal actin assembly under adherent bacteria in vitro, a process which requires the Tir-cytoskeleton coupling protein (TccP/EspF
U
) in
E. coli
O157:H7. Here we report that
E. coli
O157:H7
tir
mutants are at least as attenuated as isogenic
eae
mutants in calves and lambs, implying that the role of intimin in the colonization of reservoir hosts can be explained largely by its binding to Tir. Mutation of
tccP
uncoupled actin assembly from the intimin-Tir-mediated adherence of
E. coli
O157:H7 in vitro but did not impair intestinal colonization in calves and lambs, implying that pedestal formation may not be necessary for persistence. However, an
E. coli
O157:H7
tccP
mutant induced typical attaching and effacing lesions in a bovine ligated ileal loop model of infection, suggesting that TccP-independent mechanisms of actin assembly may operate in vivo.
A σ
28
-Regulated Nonflagella Gene Contributes to Virulence of
Campylobacter jejuni
81-176
Authors: Goon Scarlett , Ewing Cheryl P. , Lorenzo Maria , Pattarini Dawn , Majam Gary , Guerry Patricia 
Published: December 2005

ABSTRACT

A
Campylobacter jejuni
81-176 mutant in Cj0977 was fully motile but reduced >3 logs compared to the parent in invasion of intestinal epithelial cells in vitro. The mutant was also attenuated in a ferret diarrheal disease model. Expression of Cj0977 protein was dependent on a minimal flagella structure.