bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Topiramate on Kainate‐ and Domoate‐Activated [14C]Guanidinium Ion Flux Through GluR6 Channels in Transfected BHK Cells Using Cytostar‐T Scintillating Microplates
Authors: Smith L. , Price‐Jones M. , Hughes K. , Egebjerg J. , Poulsen F. , Wiberg F.C. , Shank R. P.
Published: August 2005

Purpose: This study was undertaken to test the hypothesis that topiramate (TPM) exerts a negative modulatory effect on some types of α‐amino‐3‐hydroxy‐5‐methyl‐isoxazole‐4‐proprionic acid (AMPA)/kainate receptors by binding to the site at which protein kinase A (PKA) phosphory‐lates the receptor‐channel complex.

Methods: The effect of TPM on kainate‐ or domoate‐induced [14C]guanidinium ion flux through iGluR6 channels expressed in baby hamster kidney (BHK) cells was evaluated. Because the hypothesis predicts that TPM will bind only in the dephos‐phorylated state, a variety of experimental conditions were used to either promote or impede the phosphorylation of the receptor‐channel complex. These included the use of dibutyryl cyclic adenosine monophosphate (cAMP) and forskolin to activate PKA, H‐9 and H‐89 to inhibit PKA, and okadaic acid to inhibit protein phosphatases.

Results: Kainate (1 μM) induced a gradual accumulation of [14C]guanidinium into the cells that plateaued ∼30 min after initiation of the reaction, whereas domoate (0·1 μM) caused a rapid accumulation into the cells that peaked within 5 min; thereafter, the amount of [14C]guanidinium in the cells declined gradually. Topiramate, at 0·1 and 100 μM, did not significantly affect the [14C]guanidinium accumulation under any of the experimental conditions used.

Conclusions: The results of this study are not consistent with the hypothesis tested. However, the results must be interpreted cautiously because iGluR6 receptors expressed in the BHK cells and the functional state of proteins that regulate AMPA/receptors (e.g., PSD‐95) may not be sufficiently similar to the receptors and functional state in neurons to serve as a true test of the hypothesis.
Clinical Pharmacology of Topiramate: A Review
Authors: Garnett William R.
Published: August 2005

Clinical success with an antiepileptic drug (AED) depends primarily on its efficacy and tolerability. Clinicians also need to have a basic understanding of an AED's pharma‐cokinetic characteristics, particularly those affecting the potential for drug interactions such as hepatic enzyme inhibition or induction and protein‐binding displacement. Successful treatment may be complicated by pharmacokinetic characteristics such as a short half‐life, nonlinear kinetics, and active metabolites. Pharmacokinetic characteristics that make a drug easy to use may affect patient adherence. In general, newer AEDs such as topiramate (TPM) are simpler to use than traditional AEDs because they have more favorable pharmacokinetic characteristics and fewer drug interactions.
Periodontal treatment of two siblings with juvenile hyaline fibromatosis
Authors: Hakki Sema S. , Ataoglu Tamer , Avunduk Mustafa C. , Erdemli Esra , Gunhan Omer , Rahman Nazneen
Published: August 2005

Background and Aim: Juvenile hyaline fibromatosis (JHF) is an autosomal recessive disease that presents with multiple subcutaneous nodular tumours, gingival fibromatosis, flexion contractures of the joint and hyaline material accumulation in extracellular area. Recently, the causative gene for JHF, capillary morphogenesis protein 2 (CMG2) was identified. In this case report, periodontal status, treatment and follow‐up together with histopathologic evaluation of gingival tissue specimens and mutation screening of two JHF cases are presented.

Case Reports: A 10‐year‐old female (case 1) and her 3‐year‐old brother (case 2) were first examined in our department with a complaint of gingival hyperplasia in 1991. Symptoms of the disease were detected in two of four siblings in the family. Several gingivectomy operations were carried out over 11 years with hygiene motivation and initial phase therapy. After the last gingivectomy operation in 2002, the patients were reviewed frequently.

Results and Conclusions: Although there was linear marginal gingival inflammation, no remarkable enlargement was noted at last appointment. Histopathological findings showed increased amounts of subepithelial nodular connective tissue, thinned epithelial mucosa, separated inter‐cellular bridges and decreased numbers of connective tissue cells in gingival tissue samples. Electron microscopic examinations supported the histopathological findings. Mutation screening of CMG2 demonstrated that the siblings were homozygous for a pathogenic missense mutation, V386F. Our clinical findings demonstrate that gingivectomy is useful and frequent periodontal visits are important for maintaining oral hygiene and decreasing growth rate of gingiva in JHF.
Multidimensional Assessment Using the Adolescent Pediatric Pain Tool: A Case Report
Authors: Crandall Margie , Savedra Marilyn
Published: August 2005

PURPOSE.  Children's and adolescents’ pain experiences are complex and multidimensional. Therefore, assessing a single dimension of pain intensity is in many instances inadequate. The purpose of this case report is to illustrate the benefits of using a multidimensional pain tool to assess vaso‐occlusive pain in children and adolescents with sickle cell disease.

CONCLUSIONS.  The adolescent pediatric pain tool (APPT) provides a valid multidimensional pain assessment that facilitates individual pain assessments that optimize children's and adolescents’ pain relief interventions and outcomes.

PRACTICE IMPLICATIONS.  The APPT is particularly valuable when clinicians encounter children and adolescents experiencing complex, difficult to manage pain.
ELECTROLYZED WATER AND ITS CORROSIVENESS ON VARIOUS SURFACE MATERIALS COMMONLY FOUND IN FOOD PROCESSING FACILITIES
Authors: AYEBAH BEATRICE , HUNG YEN‐CON
Published: August 2005

ASTM A‐36 medium carbon steel, 110 copper, 3003‐H14 aluminum, polyvinylchloride (PVC) type 1 and 304 stainless steel coupons were immersed in electrolyzed (EO) water, chlorine water, modified EO water and deionized water for a period of 8 days, and the properties of these types of water, weights and surface roughness of the coupons were monitored. EO water significantly increased (P < 0.05) the surface roughness of carbon steel, aluminum and copper with time; however, chlorine water, modified EO water and deionized water produced minimal changes on these materials. Regardless of the treatment water used, the surface roughness of stainless steel and PVC essentially remained the same. Carbon steel, copper, aluminum and stainless steel had a fair, good, good and outstanding corrosion resistance in EO water, respectively. Chlorine and modified EO water had a much less corrosive effect than EO water on all the materials tested.
LIMPNESS OF FRIED POTATO SLABS DURING POST‐FRYING PERIOD
Authors: MIRANDA MISAEL L. , AGUILERA JOSÉ MIGUEL , BERIESTAIN CAROLINA I.
Published: August 2005

The rupture stress (RS) of fried potato slices (1.60 mm thick) and of the crust of fried potato slabs (FPS) having lengths of 60 mm and sides of 8, 10 and 12 mm, was determined during the post‐frying period by a puncture test. The RS of fried potato slices decreased as water activity increased from 0.22 to 0.85. The RS of FPS diminished in the first 5–6 min when exposed to ambient conditions and remained almost constant thereafter. A novel videotape technique and image analysis were used to follow deflection of FPS in the post‐frying period. An apparent modulus based on the composite structure of FPS and calculated from beam mechanics decreased with time in a trend similar to that of the textural parameters. We concluded that changes in physical properties of the crust because of moisture accumulation are the major causes of loss of texture (limpness) in FPS during the post‐frying period.
An Investigation on Manufacturing of the Straight Bevel Gear Using End Mill by CNC Milling Machine
Authors: O¨zel Cihan , I˙nan Ali , O¨zler Latif
Published: August 2005

Accurate manufacturing of bevel gears is an important problem for small workshops because the module milling cutters used for manufacturing are not accurate enough for the task. In this study, manufacturing of straight bevel gears is investigated by using end mills in CNC milling with a vertical machining center. By using this method, use of auxiliary apparatus, special cutters (such as the circular cutter, the rack cutter, etc.), and special machine tools are not required. For the study, first the straight bevel gear was modeled by Tredgold’s approach and manufacturing equations of the straight bevel gear were obtained. For the straight bevel gear manufacturing, a macro program was prepared and used. Afterward, the straight bevel gear was manufactured by using this program in a CNC milling machine, the Dyna 2900 machine. The results of the measurement data for a single tooth on the gear manufactured and the theoretical values are presented and discussed.
Automated Type Synthesis of Planar Mechanisms Using Numeric Optimization With Genetic Algorithms
Authors: Liu Yi , McPhee John
Published: August 2005

This paper presents a novel method for the automated type synthesis of planar mechanisms and multibody systems. The method explicitly includes topology as a design variable in an optimization framework based on a genetic algorithm (GA). Each binary string genome of the GA represents the concatenation of the upper-right triangular portion of the link adjacency matrix of a mechanism. Different topologies can be explored by the GA by applying genetic operators to the genomes. The evolutionary process is not dependent on the results obtained from enumeration. Two examples of topology-based optimization show the applicability of this method to mechanism type synthesis problems. This method is distinct from others in the literature in that it represents the first fully automated algorithm for solving a general type synthesis problem with the help of a numeric optimizer.
Conceptual Design and Dimensional Synthesis of a Reconfigurable Hybrid Robot
Authors: Li Meng , Huang Tian , Zhang Dawei , Zhao Xueman , Hu S. Jack , Chetwynd Derek G.
Published: August 2005

This paper deals with the conceptual design of a novel four-degree-of-freedom (dof) modularized robot which is composed of a 2-dof parallel mechanism plus a 2-dof rotating head attached to the moving platform. Patented with the name Bicept, the robot is the two-dimensional version of the Tricept robot and is designed as a reconfigurable module that can readily be integrated with 1-dof feed mechanism or a fixed base in order to form a set of reconfigurable robots with parallel-serial architecture. The dimensional synthesis of the 2-dof parallel mechanism as a component of the Bicept robot is also carried out by solving a one-dimensional nonlinear equation associated with the strut-length constraint. The dimensional parameters corresponding to various width-height ratios of the work space are obtained via examples.
Thermal Stress Analysis for Rapid Thermal Process With Convective Cooling
Authors: Hung Shih-Yu , Chao Ching-Kong
Published: August 2005

A fast temperature ramp of rapid thermal processing (RTP) with convective cooling used to shorten the cooling time for the wafer is presented in this paper. Based on thermal and stress analyses, the behavior of the highly coupled physics in RTP, such as radiative heat transfer, transient flow, and thermal stress is studied in detail. From simulation results of the flow field, a large recirculation cell between the wafer edge and the chamber wall is predicted and the effect of buoyancy on the behavior of the flow field is examined. Since the buoyancy-induced recirculation aggregates thermal nonuniformity due to edge effect, a guard ring is then suggested to be placed at the edge of the wafer to reduce the heat loss from the wafer edge and reflect the radiative energy back into the wafer during the cooling process. Furthermore, a large inlet gas mass flow rate is found to suppress the recirculation and shorten the cooling time. However, a fast convective cooling rate would result in a significant temperature difference between center and edge of the wafer, thus causing material failure due to an increase of thermal stresses.
Experimental Analysis of the Near Wake from a Ducted Thruster at True and Near Bollard Pull Conditions Using Stereo Particle Image Velocimetry (SPIV)
Authors: El Lababidy S. , Bose N. , Liu P. , Walker D. , Di Felice F.
Published: August 2005

Thrusters working at low advance coefficients are employed in a wide range of offshore and marine applications on Floating, Production, Storage, and Offloading (FPSO) systems; shuttle tankers; tug boats; and mobile offshore units. Therefore, an understanding of the flow around the thrusters is of great practical interest. Despite this interest, there is lack of knowledge in the description of the hydrodynamic characteristics of a ducted thruster’s wake at bollard pull and low advance coefficient values. This work was aimed at providing detailed data about the hydrodynamic characteristics of a Dynamic Positioning (DP) thruster near wake flow at different low advance coefficient values. Wake measurements were made during cavitation tunnel tests carried out on a ducted propeller model at the Italian Ship Model Basin (INSEAN), Rome, Italy. Through these experiments, the DP thruster near wake velocity components at different downstream axial planes, up to 1.5 diameters downstream, were obtained using a Stereoscopic Particle Image Velocimetry (SPIV) system. These experiments were carried out at different advance coefficient (J) values [bollard pull (J=0), J=0.4 and J=0.45].
Modeling and Sensitivity Analysis of Laser Tracking Systems by Skew-Ray Tracing Method
Authors: Lin Psang Dain , Lu Chia-Hung
Published: August 2005

Laser tracking systems, such as the Leica LTD 500, are used for precision position measurement of large or distant objects, for example, the alignment of aircraft wings or bridge girders during assembly. A laser tracker’s performance is theoretically better than other common metrology equipment, such as coordinate measuring machines (CMMs). It is desirable that a flexible laser tracking system replaces the standard CMM, but measurement accuracy is highly dependent on the accuracy of its rotating mirror mechanism and its link dimension variance during tracker manufacture and assembly. Therefore this study presents a skew-ray tracing method for modeling and sensitivity analysis of laser tracking systems. First, the geometric relations of position-detector and interferometer readings are derived in terms of the laser tracker’s parameters using skew-ray tracing method. Effects of corner-cube alignment errors on sensor readings are also investigated theoretically, and it is found that misalignment of the corner-cube causes errors in path length and, therefore, misestimation of distance. Effects of mirror mechanism dimension errors are also investigated by sensitivity analysis. This study will be of use to theoretical and practical studies involving the modeling, design, and use of laser tracking systems and similar devices.
3′,5′-Cyclic Diguanylic Acid Reduces the Virulence of Biofilm-Forming
Staphylococcus aureus
Strains in a Mouse Model of Mastitis Infection
Authors: Brouillette Eric , Hyodo Mamoru , Hayakawa Yoshihiro , Karaolis David K. R. , Malouin François
Published: July 2005

The cyclic dinucleotide 3′,5′-cyclic diguanylic acid (c-di-GMP) is a naturally occurring small molecule that regulates important signaling systems in bacteria. We have recently shown that c-di-GMP inhibits
Staphylococcus aureus
biofilm formation in vitro and its adherence to HeLa cells. We now report that c-di-GMP treatment has an antimicrobial and antipathogenic activity in vivo and reduces, in a dose-dependent manner, bacterial colonization by biofilm-forming
S. aureus
strains in a mouse model of mastitis infection. Intramammary injections of 5 and 50 nmol of c-di-GMP decreased colonization (bacterial CFU per gram of gland) by 0.79 (
P
> 0.05) and 1.44 (
P
< 0.01) logs, respectively, whereas 200-nmol doses allowed clearance of the bacteria below the detection limit with a reduction of more than 4 logs (
P
< 0.001) compared to the untreated control groups. These results indicate that cyclic dinucleotides potentially represent an attractive and novel drug platform which could be used alone or in combination with other agents or drugs in the prevention, treatment, or control of infection.
Role of the AcrAB-TolC Efflux Pump in Determining Susceptibility of
Haemophilus influenzae
to the Novel Peptide Deformylase Inhibitor LBM415
Authors: Dean Charles R. , Narayan Shubha , Daigle Denis M. , Dzink-Fox JoAnn L. , Puyang Xiaoling , Bracken Kathryn R. , Dean Karl E. , Weidmann Beat , Yuan Zhengyu , Jain Rakesh , Ryder Neil S.
Published: July 2005

Haemophilus influenzae
isolates vary widely in their susceptibilities to the peptide deformylase inhibitor LBM415 (MIC range, 0.06 to 32 μg/ml); however, on average, they are less susceptible than gram-positive organisms, such as
Staphylococcus aureus
and
Streptococcus pneumoniae
. Insertional inactivation of the
H. influenzae acrB
or
tolC
gene in strain NB65044 (Rd strain KW20) increased susceptibility to LBM415, confirming a role for the AcrAB-TolC pump in determining resistance. Consistent with this, sequencing of a PCR fragment generated with primers flanking the
acrRA
region from an LBM415-hypersusceptible
H. influenzae
clinical isolate revealed a genetic deletion of
acrA
. Inactivation of
acrB
or
tolC
in several clinical isolates with atypically reduced susceptibility to LBM415 (MIC of 16 μg/ml or greater) significantly increased susceptibility, confirming that the pump is also a determinant of decreased susceptibility in these clinical isolates. Examination of
acrR
, encoding the putative repressor of pump gene expression, from several of these strains revealed mutations introducing frameshifts, stop codons, and amino acid changes relative to the published sequence, suggesting that loss of pump repression leads to decreased susceptibility. Supporting this, NB65044
acrR
mutants selected by exposure to LBM415 at 8 μg/ml had susceptibilities to LBM415 and other pump substrates comparable to the least sensitive clinical isolates and showed increased expression of pump genes.
Correspondence of In Vitro and In Vivo Fluconazole Dose-Response Curves for
Cryptococcus neoformans
Authors: Larsen Robert A. , Bauer Madeline , Thomas Ann M. , Sanchez Alejandro , Citron Diane , Rathbun Meri , Harrison Thomas S.
Published: July 2005

We conducted in vitro experiments to evaluate the susceptibility of a clinical isolate of
Cryptococcus neoformans
to a wide range of concentrations of fluconazole. In vitro susceptibility was tested using broth macrodilution methods modified to provide a numeric count of viable organisms. The association between the quantitative in vitro response and fluconazole drug concentrations was estimated using local nonparametric regression. Regression analysis was used to assess the correspondence between the in vitro fluconazole concentration-response curve and the murine dose-response curve observed in our previously reported murine model. The regression model was then used to predict the murine response. There was a strong correspondence between in vitro measures of response to fluconazole alone and the previously reported biologic effects seen in the mouse. In vitro antifungal drug susceptibility testing can reliably predict the murine response to fluconazole.
Bactericidal and Morphological Effects of NE-2001, a Novel Synthetic Agent Directed against
Helicobacter pylori
Authors: Dai Guofei , Cheng Ni , Dong Lei , Muramatsu Mutsumi , Xiao Shudong , Wang Ming-Wei , Zhu De-Xu
Published: July 2005

The antibacterial activities of NE-2001 were tested against 24 clinical isolates of
Helicobacter pylori
and compared with those of amoxicillin, clarithromycin, metronidazole, and furazolidone. The MIC
50
and MIC
90
of this synthetic compound on the isolates were 8 and 16 μg/ml, respectively. This action was highly selective against
Helicobacter pylori
; there was a >4-fold difference between the concentration of NE-2001 required to inhibit the growth of
Helicobacter pylori
and that required to inhibit the growth of common aerobic and anaerobic bacteria. Exposure of
Helicobacter pylori
(ATCC43504) to NE-2001 at the MIC (4 μg/ml), or at a greater concentration, resulted in an extensive loss of viability. The phenomenon was also observed at pH levels between 3.0 and 7.0. When two clinical
Helicobacter pylori
strains were successively cultured at subinhibitory concentrations of NE-2001, no significant changes in the bactericidal effects were found. The morphological alterations of
Helicobacter pylori
cells (ATCC43504), exposed to NE-2001 at various concentrations for 6 h, were observed using transmission electron microcopy. The bacterium displayed features such as swelling, vacuole-like structures in the cytoplasm, and cell destruction following exposure to NE-2001. The efficacy of NE-2001 was maintained when evaluated in eight clinical isolates resistant to metronidazole and five isolates resistant to both metronidazole and clarithromycin (MIC ranging between 4 and 16 μg/ml). The above-described results suggest that NE-2001 may have the potential to be developed as a candidate agent for the treatment of
Helicobacter pylori
infection.
Effect of Antibiotic Treatment on Growth of and Toxin Production by
Clostridium difficile
in the Cecal Contents of Mice
Authors: Pultz Nicole J. , Donskey Curtis J.
Published: July 2005

In mice, subcutaneous administration of antibiotics that disrupt the anaerobic microflora (i.e., clindamycin, piperacillin-tazobactam, and ceftriaxone) facilitated in vitro growth of and toxin production by
Clostridium difficile
in cecal contents, whereas antibiotics that cause minimal disruption of the anaerobic microflora (i.e., levofloxacin, cefepime, and aztreonam) did not.
Effect of Various Antibacterial Preparations on the Pathogenic Oral Flora in Elderly Patients Fed via Nasogastric Tube
Authors: Leibovitz Arthur , Carmeli Yehuda , Segal Refael
Published: July 2005

Oropharyngeal colonization by pathogenic gram-negative bacilli (GNB) and
Staphylococcus aureus
is associated with aspiration pneumonia. Decolonization in high-risk populations may be important. We prospectively evaluated six antiseptic compounds in nasogastric tube-fed frail elderly patients; only polymixine reduced oropharyngeal colonization with GNB. None had an effect on
S. aureus
colonization.
Prevalence of Resistance Mechanisms against Macrolides and Lincosamides in Methicillin-Resistant Coagulase-Negative Staphylococci in the Czech Republic and Occurrence of an Undefined Mechanism of Resistance to Lincosamides
Authors: Novotna Gabriela , Adamkova Václava , Janata Jiri , Melter Oto , Spizek Jaroslav
Published: July 2005

High occurrence of the non-macrolide-lincosamide-streptogramin B resistance genes
msrA
(53%) and
linA
/
linA
′ (30%) was found among 98 methicillin-resistant coagulase-negative staphylococci additionally resistant to macrolides and/or lincosamides. The gene
msrA
predominated in
Staphylococcus haemolyticus
(43 of 62 isolates). In
Staphylococcus epidermidis
, it was present in 7 of 27 isolates. A novel mechanism of resistance to lincosamides appears to be present in 10 genetically related isolates of
S. haemolyticus
in the absence of
ermA
,
ermC
,
msrA
, and
linA
/
linA
′.
Coordinated Replication and Sequestration of
oriC
and
dnaA
Are Required for Maintaining Controlled Once-per-Cell-Cycle Initiation in
Escherichia coli
Authors: Riber Leise , Løbner-Olesen Anders
Published: August 2005

Escherichia coli
cells were constructed in which the
dnaA
gene was moved to a location opposite
oriC
on the circular chromosome. In these cells the
dnaA
gene was replicated with significant delay relative to the origin. Consequently, the period where the newly replicated and hemimethylated
oriC
was sequestered no longer coincided with the period where the
dnaA
gene promoter was sequestered. DnaA protein synthesis was therefore expected to continue during origin sequestration. Despite a normal length of the sequestration period in such cells, they had increased origin content and also displayed asynchrony of initiation. This indicated that reinitiation occasionally occurred at some origins within the same cell cycle. The extra initiations took place in spite of a reduction in total DnaA protein concentration to about half of the wild-type level. We propose that this more efficient utilization of DnaA protein results from an increased availability at the end of the origin sequestration period. Therefore, coordinated sequestration of
oriC
and
dnaA
is required for maintaining controlled once-per-cell-cycle initiation.
Molecular Characterization of a Widespread, Pathogenic, and Antibiotic Resistance-Receptive
Enterococcus faecalis
Lineage and Dissemination of Its Putative Pathogenicity Island
Authors: Nallapareddy Sreedhar R. , Wenxiang Huang , Weinstock George M. , Murray Barbara E.
Published: August 2005

Enterococcus faecalis
, a common cause of endocarditis and known for its capacity to transfer antibiotic resistance to other pathogens, has recently emerged as an important, multidrug-resistant nosocomial pathogen. However, knowledge of its lineages and the potential of particular clones of this species to disseminate and cause disease is limited. Using a nine-gene multilocus sequence typing (MLST) scheme, we identified an evolving and widespread clonal complex of
E. faecalis
that has caused outbreaks and life-threatening infections. Moreover, this unusual clonal complex was found to contain isolates of unexpected relatedness, including the first known U.S. vancomycin-resistant enterococcus (
E. faecalis
strain V583), the first known penicillinase-producing (Bla
+
)
E. faecalis
isolate, and the previously described widespread clone of penicillinase producers, a trait found in <0.1% of
E. faecalis
isolates. All members of this clonal cluster (designated as BVE for Bla
+
Van
r
endocarditis) were found to contain a previously described putative pathogenicity island (PAI). Further analysis of this PAI demonstrated its dissemination worldwide, albeit with considerable variability, confirmed its association with clinical isolates, and found a common insertion site in different clonal lineages. PAI deletions, MLST, and the uncommon resistances were used to predict the evolution of the BVE clonal cluster. The finding of a virulent and highly successful clonal complex of
E. faecalis
with different members resistant to the primary therapies of choice, ampicillin and vancomycin, has important implications for the evolution of virulence and successful lineages and for public health monitoring and control.
The
Escherichia coli
CpxA-CpxR Envelope Stress Response System Regulates Expression of the Porins OmpF and OmpC
Authors: Batchelor Eric , Walthers Don , Kenney Linda J. , Goulian Mark
Published: August 2005

We performed transposon mutagenesis of a two-color fluorescent reporter strain to identify new regulators of the porin genes
ompF
and
ompC
in
Escherichia coli
. Screening of colonies by fluorescence microscopy revealed numerous mutants that exhibited interesting patterns of porin expression. One mutant harbored an insertion in the gene encoding the histidine kinase CpxA, the sensor for a two-component signaling system that responds to envelope stress. The
cpxA
mutant exhibited increased transcription of
ompC
and a very strong decrease in transcription of
ompF
under conditions in which acetyl phosphate levels were high. Subsequent genetic analysis revealed that this phenotype is dependent on phosphorylation of the response regulator CpxR and that activation of CpxA in wild-type cells results in similar regulation of porin expression. Using DNase I footprinting, we demonstrated that CpxR binds upstream of both the
ompF
and
ompC
promoters. It thus appears that two distinct two-component systems, CpxA-CpxR and EnvZ-OmpR, converge at the porin promoters. Within the context of envelope stress, outer membrane beta-barrel proteins have generally been associated with the sigma E pathway. However, at least for the classical porins OmpF and OmpC, our results show that the Cpx envelope stress response system plays a role in regulating their expression.
Carboxyl-Terminal Protease RegulatesBrucella suisMorphology in Culture and Persistence in Macrophages and Mice
Authors: Bandara Aloka B. , Sriranganathan Nammalwar , Schurig Gerhardt G. , Boyle Stephen M.
Published: August 2005

The putative carboxyl-terminal processing protease (CtpA) ofBrucella suis1330 is a member of a novel family of endoproteases involved in the maturation of proteins destined for the cell envelope. TheB. suisCtpA protein shared up to 77% homology with CtpA proteins of other bacteria. A CtpA-deficientBrucellastrain (1330ΔctpA), generated by allelic exchange, produced smaller colonies on enriched agar plates and exhibited a 50% decrease in growth rate in enriched liquid medium and no growth in salt-free enriched medium compared to the wild-type strain 1330 or thectpA-complemented strain 1330ΔctpA[pBBctpA]. Electron microscopy revealed that in contrast to the native coccobacillus shape of wild-type strain 1330, strain 1330ΔctpApossessed a spherical shape, an increased cell diameter, and cell membranes partially dissociated from the cell envelope. In the J774 mouse macrophage cell line, 24 h after infection, the CFU of the strain 1330ΔctpAdeclined by approximately 3 log10CFU relative to wild-type strain 1330. Nine weeks after intraperitoneal inoculation of BALB/c mice, strain 1330ΔctpAhad cleared from spleens but strain 1330 was still present. These observations suggest that the CtpA activity is necessary for the intracellular survival ofB. suis. Relative to the saline-injected mice, strain 1330ΔctpA-vaccinated mice exhibited 4 to 5 log10CFU of protection against challenge with virulentB. abortusstrain 2308 orB. suisstrain 1330 but no protection againstB. melitensisstrain 16 M. This is the first report correlating a CtpA deficiency with cell morphology and attenuation ofB. suis.
Analysis of the Role of RsbV, RsbW, and RsbY in Regulating σ
B
Activity in
Bacillus cereus
Authors: van Schaik Willem , Tempelaars Marcel H. , Zwietering Marcel H. , de Vos Willem M. , Abee Tjakko
Published: August 2005

The alternative sigma factor σ
B
is an important regulator of the stress response of
Bacillus cereus
. Here, the role of the regulatory proteins RsbV, RsbW, and RsbY in regulating σ
B
activity in
B. cereus
is analyzed. Functional characterization of RsbV and RsbW showed that they act as an anti-sigma factor antagonist and an anti-sigma factor, respectively. RsbW can also act as a kinase on RsbV. These data are in line with earlier functional characterizations of RsbV and RsbW homologs in
B. subtilis
. The
rsbY
gene is unique to
B. cereus
and its closest relatives and is predicted to encode a protein with an N-terminal CheY domain and a C-terminal PP2C domain. In an
rsbY
deletion mutant, the σ
B
response upon stress exposure was almost completely abolished, but the response could be restored by complementation with full-length
rsbY
. Expression analysis showed that
rsbY
is transcribed from both a σ
A
-dependent promoter and a σ
B
-dependent promoter. The central role of RsbY in regulating the activity of σ
B
indicates that in
B. cereus
, the σ
B
activation pathway is markedly different from that in other gram-positive bacteria.
TOPOLOGICAL QUIVERS
Authors: MUHLY PAUL S. , TOMFORDE MARK
Published: August 2005

Topological quivers are generalizations of directed graphs in which the sets of vertices and edges are locally compact Hausdorff spaces. Associated to such a topological quiver [Formula: see text] is a C*-correspondence, and from this correspondence one may construct a Cuntz–Pimsner algebra [Formula: see text]. In this paper we develop the general theory of topological quiver C*-algebras and show how certain C*-algebras found in the literature may be viewed from this general perspective. In particular, we show that C*-algebras of topological quivers generalize the well-studied class of graph C*-algebras and in analogy with that theory much of the operator algebra structure of [Formula: see text] can be determined from [Formula: see text]. We also show that many fundamental results from the theory of graph C*-algebras have natural analogues in the context of topological quivers (often with more involved proofs). These include the gauge-invariant uniqueness theorem, the Cuntz–Krieger uniqueness theorem, descriptions of the ideal structure, and conditions for simplicity.
ACCELERATION OF DIFFUSION IN SUBCRITICALLY TILTED PERIODIC POTENTIALS
Authors: AGUDOV NIKOLAY , SAFONOV ALEXEY
Published: July 2005

We study the enhancement of effective diffusion coefficient of an overdamped Brownian particle in tilted periodical potential profile. For analysis we use the model piece-wise linear potential, where independent variation of the potential profile parameters (such as height and width of potential barriers, width of potential wells and period of potential profile) is possible. This approach allows to investigate the influence of potential profile shape on the conditions for the diffusion acceleration, maximal value of the diffusion coefficient, values of noise intensity and the tilt for which the maximum occurs. For the large barriers and subcritical tilt the results are generalized for arbitrary shape of potential profile.
An empirical study of industrial requirements engineering process assessment and improvement
Authors: Sommerville Ian , Ransom Jane
Published: August 2005

This article describes an empirical study in industry of requirements engineering process maturity assessment and improvement. Our aims were to evaluate a requirements engineering process maturity model and to assess if improvements in requirements engineering process maturity lead to business improvements. We first briefly describe the process maturity model that we used and modifications to this model to accommodate process improvement. We present initial maturity assessment results for nine companies, describe how process improvements were selected and present data on how RE process maturity changed after these improvements were introduced. We discuss how business benefits were assessed and the difficulties of relating process maturity improvements to these business benefits. All companies reported business benefits and satisfaction with their participation in the study. Our conclusions are that the RE process maturity model is useful in supporting maturity assessment and in identifying process improvements and there is some evidence to suggest that process improvement leads to business benefits. However, whether these business benefits were a consequence of the changes to the RE process or whether these benefits resulted from side-effects of the study such as greater self-awareness of business processes remains an open question.
Kode Vicious Unleashed
Authors: Neville-Neil George
Published: August 2005

Dear KV, My officemate writes methods that are 1,000 lines long and claims they are easier to understand than if they were broken down into a smaller set of methods. How can we convince him his code is a maintenance nightmare?
Do consumers understand the role of privacy seals in e-commerce?
Authors: Moores Trevor
Published: August 2005

E-Commerce sales in the U.S. totaled $56.0 billion in 2003, an increase of 26.4% over the 2002 total of $44.3 billion [7]. This increase was achieved at a time when the U.S. economy teetered in and out of recession. While e-commerce sales are expected to grow rapidly, Jupiter Research speculates that privacy concerns will cause billions in lost sales for Internet-related businesses [2]. Although all commercial and business transactions require an element of trust, the amount of data required to complete an online B2C transaction and the potential for fraud has continually raised privacy concerns [1, 9].
Delivering real-world ubiquitous location systems
Authors: Borriello Gaetano , Chalmers Matthew , LaMarca Anthony , Nixon Paddy
Published: August 2005

To be widely adopted, location-aware computing must be as effortless, familiar, and rewarding as searching the Web. There are many challenges to this quest, but recent progress has demonstrated accurate location estimation using available wireless networking.
Sensate media
Authors: Paradiso Joseph A.
Published: August 2005

The ability to blend diverse sensors in close proximity promises to usher in a new generation of electronic skins that hold the potential for revolutionary applications.
Kode Vicious Reloaded
Authors: Neville-Neil George
Published: August 2005

The program should be a small project, but every time I start specifying the objects and methods it seems to grow to a huge size, both in the number of lines and the size of the final program.
Expected, sensed, and desired
Authors: Benford Steve , Schnädelbach Holger , Koleva Boriana , Anastasi Rob , Greenhalgh Chris , Rodden Tom , Green Jonathan , Ghali Ahmed , Pridmore Tony , Gaver Bill , Boucher Andy , Walker Brendan , Pennington Sarah , Schmidt Albrecht , Gellersen Hans , Steed Anthony
Published: August 2005

Movements of interfaces can be analyzed in terms of whether they are expected, sensed, and desired. Expected movements are those that users naturally perform; sensed are those that can be measured by a computer; and desired movements are those that are required by a given application. We show how a systematic comparison of expected, sensed, and desired movements, especially with regard to how they do not precisely overlap, can reveal potential problems with an interface and also inspire new features. We describe how this approach has been applied to the design of three interfaces: pointing flashlights at walls and posters in order to play sounds; the Augurscope II, a mobile augmented reality interface for outdoors; and the Drift Table, an item of furniture that uses load sensing to control the display of aerial photographs. We propose that this approach can help to build a bridge between the analytic and inspirational approaches to design and can help designers meet the challenges raised by a diversification of sensing technologies and interface forms, increased mobility, and an emerging focus on technologies for everyday life.
Concise descriptions of subsets of structured sets
Authors: Pu Ken Q. , Mendelzon Alberto O.
Published: August 2005

We study the problem of economical representation of subsets of structured sets, which are sets equipped with a set cover or a family of preorders. Given a structured set
U
, and a language L whose expressions define subsets of
U
, the problem of minimum description length in L (L-MDL) is: “given a subset
V
of
U
, find a shortest string in L that defines
V
.” Depending on the structure and the language, the MDL-problem is in general intractable. We study the complexity of the MDL-problem for various structures and show that certain specializations are tractable. The families of focus are hierarchy, linear order, and their multidimensional extensions; these are found in the context of statistical and OLAP databases. In the case of general OLAP databases, data organization is a mixture of multidimensionality, hierarchy, and ordering, which can also be viewed naturally as a cover-structured ordered set. Efficient algorithms are provided for the MDL-problem for hierarchical and linearly ordered structures, and we prove that the multidimensional extensions are NP-complete. Finally, we illustrate the application of the theory to summarization of large result sets and (multi) query optimization for ROLAP queries.
CCured: type-safe retrofitting of legacy software
Authors: Necula George C. , Condit Jeremy , Harren Matthew , McPeak Scott , Weimer Westley
Published: August 2005

This article describes CCured, a program transformation system that adds type safety guarantees to existing C programs. CCured attempts to verify statically that memory errors cannot occur, and it inserts run-time checks where static verification is insufficient.CCured extends C's type system by separating pointer types according to their usage, and it uses a surprisingly simple type inference algorithm that is able to infer the appropriate pointer kinds for existing C programs. CCured uses physical subtyping to recognize and verify a large number of type casts at compile time. Additional type casts are verified using run-time type information. CCured uses two instrumentation schemes, one that is optimized for performance and one in which metadata is stored in a separate data structure whose shape mirrors that of the original user data. This latter scheme allows instrumented programs to invoke external functions directly on the program's data without the use of a wrapper function.We have used CCured on real-world security-critical network daemons to produce instrumented versions without memory-safety vulnerabilities, and we have found several bugs in these programs. The instrumented code is efficient enough to be used in day-to-day operations.
Establishing and maintaining long-term human-computer relationships
Authors: Bickmore Timothy W. , Picard Rosalind W.
Published: August 2005

This research investigates the meaning of “human-computer relationship” and presents techniques for constructing, maintaining, and evaluating such relationships, based on research in social psychology, sociolinguistics, communication and other social sciences. Contexts in which relationships are particularly important are described, together with specific benefits (like trust) and task outcomes (like improved learning) known to be associated with relationship quality. We especially consider the problem of designing for long-term interaction, and define
relational agents
as computational artifacts designed to establish and maintain long-term social-emotional relationships with their users. We construct the first such agent, and evaluate it in a controlled experiment with 101 users who were asked to interact daily with an exercise adoption system for a month. Compared to an equivalent task-oriented agent without any deliberate social-emotional or relationship-building skills, the relational agent was respected more, liked more, and trusted more, even after four weeks of interaction. Additionally, users expressed a significantly greater desire to continue working with the relational agent after the termination of the study. We conclude by discussing future directions for this research together with ethical and other ramifications of this work for HCI designers.
The language of privacy
Authors: Boyle Michael , Greenberg Saul
Published: August 2005

Video media spaces are an excellent crucible for the study of privacy. Their design affords opportunities for misuse, prompts ethical questions, and engenders grave concerns from both users and nonusers. Despite considerable discussion of the privacy problems uncovered in prior work, questions remain as to how to design a privacy-preserving video media space and how to evaluate its effect on privacy. The problem is more deeply rooted than this, however. Privacy is an enormous concept from which a large vocabulary of terms emerges. Disambiguating the meanings of and relationships between these terms facilitates understanding of the link between privacy and design. In this article, we draw from resources in environmental psychology and computer-supported cooperative work (CSCW) to build a broadly and deeply rooted vocabulary for privacy. We relate the vocabulary back to the real and hard problem of designing privacy-preserving video media spaces. In doing so, we facilitate analysis of the privacy-design relationship.
Instant messaging and the future of language
Authors: Baron Naomi S.
Published: August 2005

The writing style commonly used in IMing, texting, and other forms of computer-mediated communication need not spell the end of normative language.
Understanding the interactivity between television and mobile commerce
Authors: Davis Robert , Yung David
Published: August 2005

Changing audience dynamics from passivity to active participation.
Tight upper bounds on the number of candidate patterns
Authors: Geerts Floris , Goethals Bart , Bussche Jan Van Den
Published: August 2005

In the context of mining for frequent patterns using the standard levelwise algorithm, the following question arises: given the current level and the current set of frequent patterns, what is the maximal number of candidate patterns that can be generated on the next level? We answer this question by providing tight upper bounds, derived from a combinatorial result from the sixties by Kruskal and Katona. Our result is useful to secure existing algorithms from a combinatorial explosion of the number of candidate patterns.
Relational languages for metadata integration
Authors: Wyss Catharine M. , Robertson Edward L.
Published: August 2005

In this article, we develop a relational algebra for metadata integration,
Federated Interoperable Relational Algebra
(FIRA). FIRA has many desirable properties such as compositionality, closure, a deterministic semantics, a modest complexity, support for nested queries, a subalgebra equivalent to canonical Relational Algebra (RA), and robustness under certain classes of schema evolution. Beyond this, FIRA queries are capable of producing fully dynamic output schemas, where the number of relations and/or the number of columns in relations of the output varies dynamically with the input instance. Among existing query languages for relational metadata integration, only FIRA provides generalized dynamic output schemas, where the values in any (fixed) number of input columns can determine output schemas.Further contributions of this article include development of an extended relational model for metadata integration, the
Federated Relational Data Model
, which is strictly downward compatible with the relational model. Additionally, we define the notion of
Transformational Completeness
for relational query languages and postulate FIRA as a canonical transformationally complete language. We also give a declarative, SQL-like query language that is equivalent to FIRA, called
Federated Interoperable Structured Query Language
(FISQL).While our main contributions are conceptual, the federated model, FISQL/FIRA, and the notion of transformational completeness nevertheless have important applications to data integration and OLAP. In addition to summarizing these applications, we illustrate the use of FIRA to optimize FISQL queries using rule-based transformations that directly parallel their canonical relational counterparts. We conclude the article with an extended discussion of related work as well as an indication of current and future work on FISQL/FIRA.
What’s on Your Hard Drive?
Authors: Maurer Jim
Published: August 2005

Echoing a recent editor’s note, it’s fun to imagine a future where software development is abstracted to the point where we just say, “Hey, Deep Thought, build me this call-center application. Marvin, here, will get you the specs,” and voila, the software is designed, developed, tested, and deployed. Until then, however, we’re stuck using these darn development tools. Being of human derivation (and therefore imperfect), they are perfect targets for our frustration—and praise.