bluuebunny/crossref_metadata_2025 huggingface dataset:
An Approach for 3D Visualization of Discrete Event Simulation
Authors: Zhong Yongmin , Shirinzadeh Bijan
Published: July 2008

This paper presents a new approach to create 3D visualization from discrete simulation results. This approach connects discrete event simulation directly to 3D animation with its novel methods of analyzing and converting discrete simulation results into animation events to trigger 3D animation. In addition, it constructs a 3D animation framework for the visualization of discrete simulation results. This framework supports the reuse of both the existing 3D animation objects and behavior components, and allows the rapid development of new 3D animation objects by users with no special knowledge in computer graphics but average computer skills. This approach has been implemented with the software component technology, and successfully applied in industry. Results from its practice in an electronics assembly factory are also provided in the paper to demonstrate the performance of this new approach.
Representing Functionality to Support Reuse: Conceptual and Supporting Functions
Authors: Bohm Matt R. , Stone Robert B.
Published: July 2008

In order to accurately produce computer generated design tools, methods of incorporating non-conventional functional representations of artifacts need to be incorporated and standardized. Without formalized representations of artifact attributes such as manufacturing, feature specific and form specific details, comprehensive design models and tools cannot be generated. This paper describes a user-need driven approach of addressing shortcomings in product representations by comparing standard hand generated design tools to computer-generated tools. By pinpointing discrepancies between the two sets of models, additional artifact functional representations are identified and defined. The additional functional representations, dubbed as supporting functions, are then used to complete the existing artifact functional representations. As a test for the newly found supporting functions, their representations are cataloged along side standard functional representations within a design repository. The results are computer-generated design tools that identically match their human-generated counterparts.
Survey and Investigation of Hand Motion Processing Technologies for Compliance With Shape Conceptualization
Authors: Varga Edit , Horva´th Imre , Rusa´k Zolta´n , de Smit Bram , Broek Han
Published: July 2008

An evergreen topic of human-computer interaction research is multi-modality. It has been considered important for the user interface of future computer aided conceptual design systems and what is hoped is that integration of, for instance, voice control, hand gesture/motion processing, and physical object scanning can increase both the semantic level and the efficiency of the interaction. In the area of computer mediated shape conceptualization, especially human hand motion detection and processing can play an important role. The authors’ research focuses on the study of the opportunities offered by hand motion processing in shape conceptualization. As a first step they have studied the state of the art and analyzed the technologies applicable to hand motion processing. This paper reports on the findings. The various technologies have been sorted in four categories: direct incomplete, direct complete, indirect incomplete and indirect complete detection. First, the principles supporting this categorization are explained in Section 2. The next four sections of the paper investigate the hand motion detection and processing technologies. Section 7 discusses the characteristics and operational parameters from the aspect of using hand motion for shape input in conceptual design. Our conclusion is that the currently known technologies do not absolutely support processing of a language of hand motions that is under development for creative shape conceptualization. Therefore, the hand motion language needs to be redesigned and adapted to the best technology.
A New Algorithm of Minimum Irregular Closure Retrieving
Authors: Zeng Yi , Zhang Yi , Cheng Gang , Lv Pan-Lang , Yu Jing-Hu , Qi Ji-Yang , Chen Hong , Qiu Yu-Min
Published: July 2008

In a set of new developed integrated expert numerical control system of CAD/CAM, to satisfy the special request for the intellectual process on the figures in CAD section, we designed an algorithm to retrieve minimum irregular closures from DXF and DWG files automatically. A new kind of data structure identifying angle-wing-edge-structure is established. By applying special linearizing operation to this kind of data structure, we can describe all elements of graph. Then the new algorithm for yielding all minimum closures and the maximum outer contour is showed. An example is provided to elaborate this procedure. The time complexity of the algorithm is O(n2) so that it can improve the intelligence of CAD system. Having been used by our customers, it is proved that this method works very well. In addition, it is also easy for us to apply it to computational geometry, pattern recognition, path analysis, curve generating, and so on.
Direct Manipulation of Feature Models in Web-Based Collaborative Design
Authors: Bidarra Rafael , van Bunnik Andre´ , Bronsvoort Willem F.
Published: July 2008

Providing advanced 3D interactive facilities to users of a client-server collaborative modeling system presents a great challenge when thin clients are involved, mainly due to their lack of both a full-fledged CAD model and adequate modeling and solving functionalities. This paper presents a new approach that provides a convenient representation of feature model data suitable for direct manipulation of feature models at such clients. In particular, feature handles are proposed to support interactive feature editing. This approach combines all advantages of a thin client approach with the sort of 3D direct manipulation facilities usually only found in powerful standalone CAD systems.
A Visualization-Based Approach to Engineering Kinematics Using Cognitive Models
Authors: Sathyanarayana Dileep , Krishnamurty Sundar
Published: July 2008

Visualization and spatial reasoning are integral to developing an understanding of contemporary sciences. They form the basis for understanding a wide variety of topics across science, mathematics and engineering, including molecular structures, topologies, motion and forces, and manufacturing processes. Within engineering, it can be argued that challenging and time consuming topics such as kinematics can be better taught by faculty, and hence better understood and appreciated by students, by advancing our understanding of human visualization and spatial reasoning and using this knowledge to develop computer-based visualization instruction in ways that maximize their effectiveness. The achievement of such a goal will require importing proven extant theories from other fields such as psychology, education, engineering and computer science. This paper presents the results of one such effort for teaching engineering kinematics. The motivation for this work can be found in cognitive science literature, where motion comprehension has been identified and studied as a mental task. Accordingly, a major task in doing this work involved the study of cognitive models of motion comprehension, and identifying key stages present in them. Mapping such key stages in motion comprehension on to kinematics domain, this paper presents the framework for the visual comprehension based pedagogical approach to kinematics. A web-based gear-trains tutor has been developed to demonstrate this concept. Results from the tests on a controlled population of engineering students are presented and the efficacy of a visual comprehension based approach as an instructional tool is discussed.
Coping With Unintended Behavior of Users and Products: Ontological Modelling of Product Functionality and Use
Authors: van der Vegte Wilfred , Kitamura Yoshinobu , Koji Yusuke , Mizoguchi Riichiro
Published: July 2008

The function-behavior representation language FBRL was originally devised for modeling and knowledge management of intended product behavior. This paper explores its potential for application to other-than-intended behavior in a product-use context by introducing consideration of the user and the environment. We found that slightly adapted building blocks from as-is FBRL can be applied to behavior that is unintended and/or not performed by the product. To support anticipation of unintended behavior in design, special attention has to be paid to the knowledge that connects product functions, user actions and environment behavior. We distinguish typical and atypical forms of unintended use. Some forms of typical unintended use can be directly derived from the intended use. Yet, most forms of unintended use require additional knowledge, e.g., from user observations. To include such knowledge, subsequent effort has to be put into its systematization. In this paper, an ontological scheme is presented for models of the product, the user and the environment and related use processes. We present an example and discuss how supporting tools can help designers to deal with unintended use. In the example case, a modeling schema for unintended behaviors of products is extended towards unintended behaviors of users.
Review of Product Information Retrieval: Representation and Indexing
Authors: Li Zhanjun , Liu Min , Ramani Karthik
Published: July 2008

Engineers spend a significant amount of time searching for the right product information during the design and manufacturing process. A large amount as well as various types of product information have been generated and are available within the engineering databases. But representing and indexing the products effectively and retrieving them efficiently, remains a challenge. The purpose of this survey is to document the current state of research and development. We then identify avenues for exploration and provide a comparison of the advantages, disadvantages, and limitations among the various techniques. This survey concludes by suggesting possible future research directions.
Requirements Modeling for System Engineering Using SysML, the Systems Modeling Language
Authors: Balmelli Laurent , Moore Alan
Published: July 2008

In this paper we present the model supporting the Requirement diagram in the emerging standard SysML, the System Modeling Language. SysML is the extension to System Engineering of the Unified Modeling Language (UML) proposed by the SysML and recently accepted as a answer to the Request for Proposal from the Object Modeling Group (OMG). We explain the rationale behind the construct of the model and give several examples to illustrate its features.
Collaboration Support System Based on Visualization of Communication Processes
Authors: Kobayashi Masakazu , Yoshimura Masataka , Nishiwaki Shinji , Izui Kazuhiro
Published: July 2008

This paper focuses on the creative side of collaboration and constructs a support system that enhances designers’ creativity during collaborative design projects. In order to support creative group activity during such endeavors, the support system proposed here enables design team members to visualize the interactive communication processes during creative group activity from two viewpoints, one global, and the other local. In the global view of communication flow, the transition of topics and relationships between topics are visualized, whereas in the local view, the details of each communication process can be visualized. Both these types of visualization have two inherent merits. The first is to help designers clearly understand the flow of interactive communication processes and enable them to effectively balance two concurrent actions: their individual creative thinking, and their intercommunication with fellow design team members. The second merit stems from sharing the process of exploring new ideas. Generally, the discovery and initial germination of new ideas is done alone, via individual cogitation, and the sharing of individual explorative processes and areas of exploration is often difficult. However, the visualization procedure proposed in this paper can represent such processes and areas at a useful level of detail, so that team members can cooperatively explore new ideas as a group and derive synergistic benefits. Thus, the two merits of the proposed system can lead to more effective and efficient creative group activity.
Mg/Al Ordering in Layered Double Hydroxides Revealed by Multinuclear NMR Spectroscopy
Authors: Sideris Paul J. , Nielsen Ulla Gro , Gan Zhehong , Grey Clare P.
Published: July 2008

The anion-exchange ability of layered double hydroxides (LDHs) has been exploited to create materials for use in catalysis, drug delivery, and environmental remediation. The specific cation arrangements in the hydroxide layers of hydrotalcite-like LDHs, of general formula Mg
2+

1–
x

Al
3+

x

OH
2
(Anion
n–

x
/
n

)·
y
H
2
O, have, however, remained elusive, and their elucidation could enhance the functional optimization of these materials. We applied rapid (60 kilohertz) magic angle spinning (MAS) to obtain high-resolution hydrogen-1 nuclear magnetic resonance (
1
H NMR) spectra and characterize the magnesium and aluminum distribution. These data, in combination with
1
H-
27
Al double-resonance and
25
Mg triple-quantum MAS NMR data, show that the cations are fully ordered for magnesium:aluminum ratios of 2:1 and that at lower aluminum content, a nonrandom distribution of cations persists, with no Al
3+
-Al
3+
close contacts. The application of rapid MAS NMR methods to investigate proton distributions in a wide range of materials is readily envisaged.
Bloodstream Infections Caused by Extended-Spectrum-β-Lactamase- Producing
Escherichia coli
: Risk Factors for Inadequate Initial Antimicrobial Therapy
Authors: Tumbarello Mario , Sali Michela , Trecarichi Enrico Maria , Leone Fiammetta , Rossi Marianna , Fiori Barbara , De Pascale Gennaro , D'Inzeo Tiziana , Sanguinetti Maurizio , Fadda Giovanni , Cauda Roberto , Spanu Teresa
Published: July 2008

Extended-spectrum-β-lactamase (ESBL)-producing strains of
Escherichia coli
are a significant cause of bloodstream infections (BSI) in hospitalized and nonhospitalized patients. We previously showed that delaying effective antimicrobial therapy in BSI caused by ESBL producers significantly increases mortality. The aim of this retrospective 7-year analysis was to identify risk factors for inadequate initial antimicrobial therapy (IIAT) (i.e., empirical treatment based on a drug to which the isolate had displayed in vitro resistance) for inpatients with BSI caused by ESBL-producing
E. coli
. Of the 129 patients considered, 56 (43.4%) received IIAT for 48 to 120 h (mean, 72 h). Independent risk factors for IIAT include an unknown BSI source (odds ratios [OR], 4.86; 95% confidence interval [CI], 1.98 to 11.91;
P
= 0.001), isolate coresistance to ≥3 antimicrobials (OR, 3.73; 95% CI, 1.58 to 8.83;
P
= 0.003), hospitalization during the 12 months preceding BSI onset (OR, 3.33; 95% CI, 1.42 to 7.79;
P
= 0.005), and antimicrobial therapy during the 3 months preceding BSI onset (OR, 2.65; 95% CI, 1.11 to 6.29;
P
= 0.02). IIAT was the strongest risk factor for 21-day mortality and significantly increased the length of hospitalization after BSI onset. Our results underscore the need for a systematic approach to the management of patients with serious infections by ESBL-producing
E. coli
. Such an approach should be based on sound, updated knowledge of local infectious-disease epidemiology, detailed analysis of the patient's history with emphasis on recent contact with the health care system, and aggressive attempts to identify the infectious focus that has given rise to the BSI.
Mutations in the
fks1
Gene in
Candida albicans
,
C. tropicalis
, and
C. krusei
Correlate with Elevated Caspofungin MICs Uncovered in AM3 Medium Using the Method of the European Committee on Antibiotic Susceptibility Testing
Authors: Desnos-Ollivier Marie , Bretagne Stéphane , Raoux Dorothée , Hoinard Damien , Dromer Françoise , Dannaoui Eric
Published: July 2008

Mutations in two specific regions of the Fks1 subunit of 1,3-β-
d
-glucan synthase are known to confer decreased caspofungin susceptibility on
Candida
spp. Clinical isolates of
Candida
spp. (404
Candida albicans
, 62
C. tropicalis
, and 21
C. krusei
isolates) sent to the French National Reference Center were prospectively screened for susceptibility to caspofungin in vitro by the broth microdilution reference method of the Antifungal Susceptibility Testing Subcommittee of the European Committee on Antibiotic Susceptibility Testing (AFST-EUCAST). Twenty-eight isolates (25
C. albicans
, 2
C. tropicalis
, and 1
C. krusei
isolate) for which the caspofungin MIC was above the MIC that inhibited 90% of the isolates of the corresponding species (MIC
90
) were subjected to molecular analysis in order to identify mutations in the
fks1
gene. Substitutions in the deduced protein sequence of Fks1 were found for 8 isolates, and 20 isolates had the wild-type sequence. Among the six
C. albicans
isolates harboring mutations, six patterns were observed involving amino acid changes at positions 641, 645, 649, and 1358. For
C. tropicalis
, one isolate showed an L644W mutation, and for one
C. krusei
isolate, two mutations, L658W and L701M, were found. Two media, RPMI medium and AM3, were tested for their abilities to distinguish between isolates with wild-type Fks1 and those with mutant Fks1. In RPMI medium, caspofungin MICs ranged from 0.25 to 2 μg/ml for wild-type isolates and from 1 to 8 μg/ml for mutant isolates. A sharper difference was observed in AM3: all wild-type isolates were inhibited by 0.25 μg/ml of caspofungin, while caspofungin MICs for all mutant isolates were ≥0.5 μg/ml. These data demonstrate that clinical isolates of
C. albicans
,
C. tropicalis
, and
C. krusei
with decreased susceptibility to caspofungin in vitro have diverse mutations in the
fks1
gene and that AM3 is potentially a better medium than RPMI for distinguishing between mutant and wild-type isolates using the AFST-EUCAST method.
Relationship between Vancomycin MIC and Failure among Patients with Methicillin-Resistant
Staphylococcus aureus
Bacteremia Treated with Vancomycin
Authors: Lodise T. P. , Graves J. , Evans A. , Graffunder E. , Helmecke M. , Lomaestro B. M. , Stellrecht K.
Published: July 2008

There is growing concern that vancomycin has diminished activity for methicillin-resistant
Staphylococcus aureus
(MRSA) infections, with vancomycin MICs at the high end of the CLSI susceptibility range. Despite this growing concern, there are limited clinical data to support this notion. To better elucidate this, a retrospective cohort study was conducted among patients with MRSA bloodstream infections who were treated with vancomycin between January 2005 and May 2007. The inclusion criteria were as follows: at least 18 years old, nonneutropenic, with an MRSA culture that met the CDC criteria for bloodstream infection, had received vancomycin therapy within 48 h of the index blood culture, and survived >24 h after vancomycin administration. Failure was defined as 30-day mortality, bacteremia ≥10 days on vancomycin therapy, or a recurrence of MRSA bacteremia within 60 days of vancomycin discontinuation. Classification and regression tree (CART) analysis identified the vancomycin MIC breakpoint associated with an increased probability of failure. During the study period, 92 patients met the inclusion criteria. The vancomycin MIC breakpoint derived by CART analysis was ≥1.5 mg/liter. The 66 patients with vancomycin MICs of ≥1.5 mg/liter had a 2.4-fold increase in failure compared to patients with MICs of ≤1.0 mg/liter (36.4% and 15.4%, respectively;
P
= 0.049). In the Poisson regression, a vancomycin MIC of ≥1.5 mg/liter was independently associated with failure (adjusted risk ratio, 2.6; 95% confidence interval, 1.3 to 5.4;
P
= 0.01). These data strongly suggest that patients with MRSA bloodstream infections with vancomycin MICs of ≥1.5 mg/liter respond poorly to vancomycin. Alternative anti-MRSA therapies should be considered for these patients.
Association of Fluconazole Pharmacodynamics with Mortality in Patients with Candidemia
Authors: Baddley John W. , Patel Mukesh , Bhavnani Sujata M. , Moser Stephen A. , Andes David R.
Published: July 2008

Recent studies of nonneutropenic patients with candidemia or candidiasis suggest that fluconazole pharmacodynamic parameters correlate with clinical outcomes; however, additional data of correlation to mortality in patients with candidemia would be valuable. We assessed the impact of MICs for
Candida
, fluconazole pharmacodynamics, and patient characteristics on all-cause mortality with use of a prospective cohort of 96 hospitalized patients with candidemia. Among 84 patients for whom
Candida
isolates were available for testing, the most frequent
Candida
species isolated were
Candida albicans
(44%), followed by
Candida parapsilosis
(20.2%), and
Candida glabrata
(20.2%). Fluconazole resistance (MIC of ≥64 μg/ml) was present in 7 (8.3%) to 10 (11.9%) of 84 isolates, depending on the MIC endpoint determination method (50% or 80% inhibition read at 24 or 48 h). Overall mortality occurred in 27 (28.1%) of 96 patients, and nonsurvivors were more likely to have fluconazole-resistant isolates (25% versus 6.7%;
P
= 0.02). Multivariable analysis demonstrated an association between fluconazole resistance and mortality, but it did not reach statistical significance (odds ratio, 5.3; 95% confidence interval, 0.8 to 33.4;
P
= 0.08). By pharmacodynamic analysis, a fluconazole area under the concentration-time curve/MIC of <11.5 or MIC of ≥64 was associated with increased patient mortality (
P
≤ 0.09). These data support previous findings of an antifungal exposure-response relationship to mortality in patients with candidemia. In addition, similar MICs were obtained using a 24- or 48-h MIC endpoint determination, thus providing the opportunity to assess earlier the impact of isolate susceptibility on therapy.
Role of Plasma Proteins in Pharmacokinetics of Micafungin, an Antifungal Antibiotic, in Analbuminemic Rats
Authors: Abe Fumie , Ueyama Jun , Kawasumi Noriyo , Nadai Masayuki , Hayashi Tamon , Kato Miki , Ohnishi Masafumi , Saito Hiroko , Takeyama Naoshi , Hasegawa Takaaki
Published: July 2008

There were no significant differences in the pharmacokinetics of micafungin and expression of hepatic multidrug resistance-associated protein 2 (ABCC2/Mrp2) between analbuminemic and Sprague-Dawley rats. Micafungin bound strongly to high-density lipoprotein (HDL) and moderately to gamma globulin. These results suggest that HDL and gamma globulin contribute to the pharmacokinetics of micafungin.
Combinations of Cyclophilin Inhibitor NIM811 with Hepatitis C Virus NS3-4A Protease or NS5B Polymerase Inhibitors Enhance Antiviral Activity and Suppress the Emergence of Resistance
Authors: Mathy Joanna E. , Ma Sue , Compton Teresa , Lin Kai
Published: July 2008

Chronic hepatitis C virus (HCV) infection remains a major global health burden while current interferon-based therapy is suboptimal. Efforts to develop more effective antiviral agents mainly focus on two viral targets: NS3-4A protease and NS5B polymerase. However, resistant mutants against these viral specific inhibitors emerge quickly both in vitro and in patients, particularly in the case of monotherapy. An alternative and complementary strategy is to target host factors such as cyclophilins that are also essential for viral replication. Future HCV therapies will most likely be combinations of multiple drugs of different mechanisms to maximize antiviral activity and to suppress the emergence of resistance. Here, the effects of combining a host cyclophilin inhibitor NIM811 with other viral specific inhibitors were investigated in vitro using HCV replicon. All of the combinations led to more pronounced antiviral effects than any single agent, with no significant increase of cytotoxicity. Moreover, the combination of NIM811 with a nucleoside (NM107) or a non-nucleoside (thiophene-2-carboxylic acid) polymerase inhibitor was synergistic, while the combination with a protease inhibitor (BILN2061) was additive. Resistant clones were selected in vitro with these inhibitors. Interestingly, it was much more difficult to develop resistance against NIM811 than viral specific inhibitors. No cross-resistance was observed among these inhibitors. Most notably, NIM811 was highly effective in blocking the emergence of resistance when used in combination with viral protease or polymerase inhibitors. Taken together, these results illustrate the significant advantages of combining inhibitors targeting both viral and host factors as key components of future HCV therapies.
Complete Sequence of p07-406, a 24,179-Base-Pair Plasmid Harboring theblaVIM-7Metallo-β-Lactamase Gene in aPseudomonas aeruginosaIsolate from the United States
Authors: Li Hongyang , Toleman Mark A. , Bennett Peter M. , Jones Ronald N. , Walsh Timothy R.
Published: July 2008

An outbreak involving aPseudomonas aeruginosastrain that was resistant to all tested antimicrobials except polymyxin B occurred in a hospital in Houston, TX. Previous studies on this strain showed that it possesses a novel mobile metallo-β-lactamase (MBL) gene, designatedblaVIM-7, located on a plasmid (p07-406). Here, we report the complete sequence, annotation, and functional characterization of this plasmid. p07-406 is 24,179 bp in length, and 29 open reading frames were identified related to known or putatively recognized proteins. Analysis of this plasmid showed it to be comprised of four distinct regions: (i) a region of 5,200 bp having a Tn501-like mercuric resistance (mer) transposon upstream of the replication region; (ii) a Tn3-like transposon carrying a truncated integron with ablaVIM-7gene and an insertion sequence inserted at the other end of this transposon; (iii) a region of four genes, upstream of the Tn3-like transposon, possessing very high similarity to plasmid pXcB fromXanthomonas campestrispv.citricommonly associated with plants; (iv) a backbone sequence similar to the backbone structure of the IncP group plasmid Rms149, pB10, and R751. This is the first plasmid to be sequenced carrying an MBL gene and highlights the amelioration of DNA segments from disparate origins, most noticeably from plant pathogens.
Effects of Subinhibitory Concentrations of Antibiotics on SOS and DNA Repair Gene Expression in
Staphylococcus aureus
Authors: Mesak Lili Rosana , Miao Vivian , Davies Julian
Published: July 2008

Reporter clones of
Staphylococcus aureus
with different SOS response- and DNA repair-associated promoter-
lux
gene fusion constructs were constructed to study the effects of sub-MICs of antibiotics on the transcription of the SOS and methyl mismatch repair (MMR) genes. Fluoroquinolones (FQs) upmodulated both the SOS and the MMR genes. The patterns of antibiotic-induced transcriptional modulation were altered in FQ-resistant mutants.
Correlation of Antimicrobial Resistance with β-Lactamases, the OmpA-Like Porin, and Efflux Pumps in Clinical Isolates of
Acinetobacter baumannii
Endemic to New York City
Authors: Bratu Simona , Landman David , Martin Don Antonio , Georgescu Claudiu , Quale John
Published: July 2008

Acinetobacter baumannii
strains resistant to all β-lactams, aminoglycosides, and fluoroquinolones have emerged in many medical centers. Potential mechanisms contributing to antimicrobial resistance were investigated in 40 clinical isolates endemic to New York City. The isolates were examined for the presence of various β-lactamases, aminoglycoside-modifying enzymes, and mutations in
gyrA
and
parC
. Expression of the genes encoding the β-lactamase AmpC, the efflux systems AdeABC and AbeM, and the OmpA-like porin was also examined by real-time reverse transcription-PCR. No VIM, IMP, KPC, OXA-23-type, OXA-24-type, or OXA-58 β-lactamases were detected, although several isolates had acquired
bla
SHV-5
. Most cephalosporin-resistant isolates had increased levels of expression of
ampC
and/or had acquired
bla
SHV-5
; however, isolates without these features still had reduced susceptibility to cefepime that was mediated by the AdeABC efflux system. Although most isolates with IS
Aba1
upstream of the
bla
OXA-51
-like carbapenemase gene were resistant to meropenem, several remained susceptible to imipenem. The presence of aminoglycoside-modifying enzymes and gyrase mutations accounted for aminoglycoside and fluoroquinolone resistance, respectively. The increased expression of
adeABC
was not an important contributor to aminoglycoside or fluoroquinolone resistance but did correlate with reduced susceptibility to tigecycline. The expression of
abeM
and
ompA
and phenotypic changes in OmpA did not correlate with antimicrobial resistance.
A. baumannii
has become a well-equipped nosocomial pathogen; defining the relative contribution of these and other mechanisms of antimicrobial resistance will require further investigation.
Inhibition of Malaria Parasite Development by a Cyclic Peptide That Targets the Vital Parasite Protein SERA5
Authors: Fairlie W. Douglas , Spurck Tim P. , McCoubrie Joanne E. , Gilson Paul R. , Miller Susanne K. , McFadden Geoffrey I. , Malby Robyn , Crabb Brendan S. , Hodder Anthony N.
Published: July 2008

The serine repeat antigen (SERA) proteins of the malaria parasitesPlasmodiumspp. contain a putative enzyme domain similar to that of papain family cysteine proteases. InPlasmodium falciparumparasites, more than half of the SERA family proteins, including the most abundantly expressed form, SERA5, have a cysteine-to-serine substitution within the putative catalytic triad of the active site. Although SERA5 is required for blood-stage parasite survival, the occurrence of a noncanonical catalytic triad casts doubt on the importance of the enzyme domain in this function. We used phage display to identify a small (14-residue) disulfide-bonded cyclic peptide (SBP1) that targets the enzyme domain of SERA5. Biochemical characterization of the interaction shows that it is dependent on the conformation of both the peptide and protein. Addition of this peptide to parasite cultures compromised development of late-stage parasites compared to that of control parasites or those incubated with equivalent amounts of the carboxymethylated peptide. This effect was similar in two different strains ofP. falciparumas well as in a transgenic strain where the gene encoding the related serine-type parasitophorous vacuole protein SERA4 was deleted. In compromised parasites, the SBP1 peptide crosses both the erythrocyte and parasitophorous vacuole membranes and accumulates within the parasitophorous vacuole. In addition, both SBP1 and SERA5 were identified in the parasite cytosol, indicating that the plasma membrane of the parasite was compromised as a result of SBP1 treatment. These data implicate an important role for SERA5 in the regulation of the intraerythrocytic development of late-stage parasites and as a target for drug development.
Inactivation of
ibeA
and
ibeT
Results in Decreased Expression of Type 1 Fimbriae in Extraintestinal Pathogenic
Escherichia coli
Strain BEN2908
Authors: Cortes Mélanie A. M. , Gibon Julien , Chanteloup Nathalie K. , Moulin-Schouleur Maryvonne , Gilot Philippe , Germon Pierre
Published: July 2008

IbeA in extraintestinal pathogenic
Escherichia coli
(ExPEC) strains was previously described for its role in invasion. Here we investigated the role of IbeA and IbeT, encoded by a gene located downstream of
ibeA
, in the adhesion of the avian ExPEC strain BEN2908 to human brain microvascular endothelial cells (HBMEC). The Δ
ibeA
mutant was less adhesive to HBMEC than the wild-type strain BEN2908 was. Because strain BEN2908 also expresses type 1 fimbriae, we measured the adhesion specifically due to IbeA by comparing the adhesive properties of a Δ
fim
derivative of strain BEN2908 to those of a double Δ
fim
Δ
ibeA
mutant. No differences were observed, indicating that the reduction of adhesion in BEN2908 Δ
ibeA
could be due to a decrease in type 1 fimbria expression. We indeed showed that the decreased adhesion of BEN2908 Δ
ibeA
was correlated with a decrease in type 1 fimbria expression. Accordingly, more bacteria had a
fim
promoter orientated in the off position in a culture of BEN2908 Δ
ibeA
than in a culture of BEN2908. Expression of
fimB
and
fimE
, two genes encoding recombinases participating in controlling the orientation of the
fim
promoter, was decreased in BEN2908 Δ
ibeA
. A reduction of type 1 fimbria expression due to a preferential orientation of the
fim
promoter in the off position was also seen in an
ibeT
mutant of strain BEN2908. We finally suggest a role for IbeA and IbeT in modulating the expression of type 1 fimbriae through an as yet unknown mechanism.
Fine Antigenic Specificity and Cooperative Bactericidal Activity of Monoclonal Antibodies Directed at the Meningococcal Vaccine Candidate Factor H-Binding Protein
Authors: Beernink Peter T. , Welsch Jo Anne , Bar-Lev Michal , Koeberling Oliver , Comanducci Maurizio , Granoff Dan M.
Published: July 2008

No broadly protective vaccine is available for the prevention of group B meningococcal disease. One promising candidate is factor H-binding protein (fHbp), which is present in all strains but often sparsely expressed. We prepared seven murine immunoglobulin G monoclonal antibodies (MAbs) against fHbp from antigenic variant group 2 (v.2) or v.3 (∼40% of group B strains). Although none of the MAbs individually elicited bactericidal activity with human complement, all had activity in different combinations. We used MAb reactivity with strains expressing fHbp polymorphisms and site-specific mutagenesis to identify residues that are important for epitopes recognized by six of the v.2 or v.3 MAbs and by two v.1 MAbs that were previously characterized. Residues affecting v.2 or v.3 epitopes resided between amino acids 174 and 216, which formed an eight-stranded beta-barrel in the C domain, while residues affecting the v.1 epitopes included amino acids 121 and 122 of the B domain. Pairs of MAbs were bactericidal when their respective epitopes involved residues separated by 16 to 20 Å and when at least one of the MAbs inhibited the binding of fH, a downregulatory complement protein. In contrast, there was no cooperative bactericidal activity when the distance between residues was ≥27 Å or ≤14 Å, which correlated with the inhibition of the binding of one MAb by the other MAb. Thus, a model for anti-fH MAb bactericidal activity against strains expressing low levels of fHbp requires the binding of two MAbs directed at nonoverlapping epitopes, which activates the classical complement pathway as well as inhibits fH binding. The latter increases the susceptibility of the organism to complement-mediated bacteriolysis.
Phenotypic Switching inCryptococcus neoformansContributes to Virulence by Changing the Immunological Host Response
Authors: Guerrero Abraham , Fries Bettina C.
Published: July 2008

Cryptococcus neoformansis an encapsulated opportunistic organism that can undergo phenotypic switching. In this process, the parent smooth colony (SM) switches to a more virulent mucoid colony (MC) variant. The host responses mounted against the SM and MC variants differ, and lower tissue interleukin 10 (IL-10) levels are consistently observed in lungs of MC-infected C57BL/6 and BALB/c mice. This suggested different roles of this cytokine in SM and MC infections. The objective of this study was to compare survival rates and characterize the host responses of SM- and MC-infected IL-10-depleted (IL-10−/−) mice, which exhibit a Th1-polarized immune response and are considered resistant hosts. As expected, SM-infected IL-10−/−mice survived longer than wild-type mice, whereas MC-infected IL-10−/−mice did not exhibit a survival benefit. Consistent with this observation, we demonstrated marked differences in the inflammatory responses of SM- and MC-infected IL-10−/−and wild-type mice. This included a more Th1-polarized inflammatory response with enhanced recruitment of macrophages and natural killer and CD8 cells in MC- than in SM-infected IL-10−/−and wild-type mice. In contrast, both SM-infected IL-10−/−and wild-type mice exhibited higher recruitment of CD4 cells, consistent with enhanced survival and differences in recruitment and Th1/Th2 polarization. Lung tissue levels of IL-21, IL-6, IL-4, transforming growth factor beta, IL-12, and gamma interferon were higher in MC-infected IL-10−/−and wild-type mice than in SM-infected mice, whereas tumor necrosis factor alpha levels were higher in SM-infected IL-10−/−mice. In conclusion, the MC variant elicits an excessive inflammatory response in a Th1-polarized host environment, and therefore, the outcome is negatively affected by the absence of IL-10.
Pmp-Like Proteins Pls1 and Pls2 Are Secreted into the Lumen of the
Chlamydia trachomatis
Inclusion
Authors: Jorgensen Ine , Valdivia Raphael H.
Published: July 2008

The obligate intracellular pathogen
Chlamydia trachomatis
secretes effector proteins across the membrane of the pathogen-containing vacuole (inclusion) to modulate host cellular functions. In an immunological screen for secreted chlamydial proteins, we identified CT049 and CT050 as potential inclusion membrane-associated proteins. These acidic, nonglobular proteins are paralogously related to the passenger domain of the polymorphic membrane protein PmpC and, like other Pmp proteins, are highly polymorphic among
C. trachomatis
ocular and urogenital strains. We generated antibodies to these Pmp-like secreted (Pls) proteins and determined by immunofluorescence microscopy that Pls1 (CT049) and Pls2 (CT050) localized to globular structures within the inclusion lumen and at the inclusion membrane. Fractionation of membranes and cytoplasmic components from infected cells by differential and density gradient centrifugation further indicated that Pls1 and Pls2 associated with membranes distinct from the bulk of bacterial and inclusion membranes. The accumulation of Pls1 and, to a lesser extent, Pls2 in the inclusion lumen was insensitive to the type III secretion inhibitor C1, suggesting that this translocation system is not essential for Pls protein secretion. In contrast, Pls secretion and stability were sensitive to low levels of β-lactam antibiotics, suggesting that a functional cell wall is required for Pls secretion from the bacterial cell. Finally, we tested the requirement for these proteins in
Chlamydia
infection by microinjecting anti-Pls1 and anti-Pls2 antibodies into infected cells. Coinjection of anti-Pls1 and -Pls2 antibodies partially inhibited expansion of the inclusion. Because Pls proteins lack classical
sec
-dependent secretion signals, we propose that Pls proteins are secreted into the inclusion lumen by a novel mechanism to regulate events important for chlamydial replication and inclusion expansion.
AMycobacterium tuberculosisRpf Double-Knockout Strain Exhibits Profound Defects in Reactivation from Chronic Tuberculosis and Innate Immunity Phenotypes
Authors: Russell-Goldman Eleanor , Xu Jiayong , Wang Xiaobing , Chan John , Tufariello JoAnn M.
Published: July 2008

Resuscitation-promoting factors (Rpfs), apparent peptidoglycan hydrolases, have been implicated in the reactivation of dormant bacteria. We previously demonstrated that deletion ofrpfBimpaired reactivation ofMycobacterium tuberculosisin a mouse model. BecauseM. tuberculosisencodes five Rpf paralogues, redundant functions among the family members might obscurerpfsingle-knockout phenotypes. A series ofrpfdouble knockouts were therefore generated. One double mutant, ΔrpfAB, exhibited several striking phenotypes. Consistent with the proposed cell wall-modifying function of Rpfs, ΔrpfABexhibited an altered colony morphology. Although ΔrpfABgrew comparably to the parental strain in axenic culture, in vivo it exhibited deficiency in reactivation induced in C57BL/6 mice by the administration of nitric oxide synthase inhibitor (aminoguanidine) or by CD4+T-cell depletion. Notably, the reactivation deficiency of ΔrpfABwas more severe than that of ΔrpfBin aminoguanidine-treated mice. A similar deficiency was observed in ΔrpfABreactivation from a drug-induced apparently sterile state in infected NOS2−/−mice upon cessation of antimycobacterial therapy. Secondly, ΔrpfABshowed a persistence defect not seen with the ΔrpfBor ΔrpfAsingle mutants. Interestingly, ΔrpfABexhibited impaired growth in primary mouse macrophages and induced higher levels of the proinflammatory cytokines tumor necrosis factor alpha and interleukin 6. Simultaneous reintroduction ofrpfAandrpfBinto the double-knockout strain complemented the colony morphology and macrophage cytokine secretion phenotypes. Phenotypes related to cell wall composition and macrophage responses suggest thatM. tuberculosisRpfs may influence the outcome of reactivation, in part, by modulating innate immune responses to the bacterium.
Evaluation of a New Etest Vancomycin-Teicoplanin Strip for Detection of Glycopeptide-Intermediate
Staphylococcus aureus
(GISA), in Particular, Heterogeneous GISA
Authors: Yusof Anne , Engelhardt Anette , Karlsson Åsa , Bylund Lina , Vidh Pamela , Mills Karen , Wootton Mandy , Walsh Timothy R.
Published: July 2008

Glycopeptide-intermediate
Staphylococcus aureus
(GISA) and, in particular, heterogeneous GISA (hGISA) are difficult to detect by standard MIC methods, and thus, an accurate detection method for clinical practice and surveillances is needed. Two prototype Etest strips designed for hGISA/GISA resistance detection (GRD) were evaluated using a worldwide collection of hGISA/GISA strains covering the five major clonal lineages. A total of 150 strains comprising 15 GISA and 60 hGISA strains (defined by population analysis profiles-area under the curve [PAP-AUC]), 70 glycopeptide-susceptible
S. aureus
(GSSA) strains, and 5
S. aureus
ATCC reference strains were tested. For standardized Etest vancomycin (VA) MIC testing, the modified Etest macromethod with VA and teicoplanin (TP) strips tested with a heavier inoculum using brain heart infusion agar (BHI) and two glycopeptide screening agar plates (6 μg/ml VA/BHI and 5 μg/ml Mueller-Hinton agar [MHA]) were tested in parallel with the two new Etest GRD strips: a VA 32 (0.5-μg/ml)-TP 32 (0.5-μg/ml) double-sided gradient (E-VA/TP) with one prototype overlaid with a nutrient (E-VA/TP+S) to enhance the growth of hGISA. The Etest GRD strips were tested with a standard 0.5-McFarland standard inoculum using MHA and MHA plus 5% blood (MHB) and were read at 18 to 24 and 48 h. The interpretive MIC cutoffs used for the new Etest GRD strips at 24 and 48 h were as follows: for GISA, TP or VA, ≥8, and a standard VA MIC of ≥6; for hGISA, TP or VA, ≥8, and a standard VA MIC of ≤4. The results on MHB at 48 h showed that E-VA/TP+S had high specificity (94%) and sensitivity (95%) in comparison to PAP-AUC and was able to detect all GISA (
n
= 15) and 98% of hGISA (
n
= 60) strains. In contrast, the glycopeptide screening plates performed poorly for hGISA. The new Etest GRD strip (E-VA/TP+S), utilizing standard media and inocula, is a simple and acceptable tool for detection of hGISA/GISA for clinical and epidemiologic purposes.
Molecular Defects Caused by Temperature-Sensitive Mutations in Semliki Forest Virus nsP1
Authors: Lulla Valeria , Sawicki Dorothea L. , Sawicki Stanley G. , Lulla Aleksei , Merits Andres , Ahola Tero
Published: July 2008

Alphavirus replicase protein nsP1 has multiple functions during viral RNA synthesis. It catalyzes methyltransferase and guanylyltransferase activities needed in viral mRNA capping, attaches the viral replication complex to cytoplasmic membranes, and is required for minus-strand RNA synthesis. Two temperature-sensitive (
ts
) mutations in Semliki Forest virus (SFV) were previously identified within nsP1:
ts
10 (E529D) and
ts
14 (D119N). Recombinant viruses containing these individual mutations reproduced the features of the original
ts
strains. We now find that the capping-associated enzymatic activities of recombinant nsP1, containing
ts
10 or
ts
14 lesions, were not
ts
. The mutant proteins and polyproteins also were membrane bound, mutant nsP1 interacted normally with the other nonstructural proteins, and there was no major defect in nonstructural polyprotein processing in the mutants, although
ts
14 surprisingly displayed slightly retarded processing. The two mutant viruses were specifically defective in minus-strand RNA synthesis at the restrictive temperature. Integrating data from SFV and Sindbis virus, we discuss the domain structure of nsP1 and the relative positioning of and interactions between the replicase proteins. nsP1 is suggested to contain a specific subdomain involved in minus-strand synthesis and interaction with the polymerase nsP4 and the protease nsP2.
Comprehensive Characterization of Extracellular Herpes Simplex Virus Type 1 Virions
Authors: Loret Sandra , Guay Ginette , Lippé Roger
Published: July 2008

The herpes simplex virus type 1 (HSV-1) genome is contained in a capsid wrapped by a complex tegument layer and an external envelope. The poorly defined tegument plays a critical role throughout the viral life cycle, including delivery of capsids to the nucleus, viral gene expression, capsid egress, and acquisition of the viral envelope. Current data suggest tegumentation is a dynamic and sequential process that starts in the nucleus and continues in the cytoplasm. Over two dozen proteins are assumed to be or are known to ultimately be added to virions as tegument, but its precise composition is currently unknown. Moreover, a comprehensive analysis of all proteins found in HSV-1 virions is still lacking. To better understand the implication of the tegument and host proteins incorporated into the virions, highly purified mature extracellular viruses were analyzed by mass spectrometry. The method proved accurate (95%) and sensitive and hinted at 8 different viral capsid proteins, 13 viral glycoproteins, and 23 potential viral teguments. Interestingly, four novel virion components were identified (U
L
7, U
L
23, U
L
50, and U
L
55), and two teguments were confirmed (ICP0 and ICP4). In contrast, U
L
4, U
L
24, the U
L
31/U
L
34 complex, and the viral U
L
15/U
L
28/U
L
33 terminase were undetected, as was most of the viral replication machinery, with the notable exception of U
L
23. Surprisingly, the viral glycoproteins gJ, gK, gN, and U
L
43 were absent. Analyses of virions produced by two unrelated cell lines suggest their protein compositions are largely cell type independent. Finally, but not least, up to 49 distinct host proteins were identified in the virions.
NEURAL ADAPTIVE CONTROL FOR VIBRATION SUPPRESSION IN COMPOSITE FIN-TIP OF AIRCRAFT
Authors: SURESH S. , KANNAN N. , SUNDARARAJAN N. , SARATCHANDRAN P.
Published: July 2008

In this paper, we present a neural adaptive control scheme for active vibration suppression of a composite aircraft fin tip. The mathematical model of a composite aircraft fin tip is derived using the finite element approach. The finite element model is updated experimentally to reflect the natural frequencies and mode shapes very accurately. Piezo-electric actuators and sensors are placed at optimal locations such that the vibration suppression is a maximum. Model-reference direct adaptive neural network control scheme is proposed to force the vibration level within the minimum acceptable limit. In this scheme, Gaussian neural network with linear filters is used to approximate the inverse dynamics of the system and the parameters of the neural controller are estimated using Lyapunov based update law. In order to reduce the computational burden, which is critical for real-time applications, the number of hidden neurons is also estimated in the proposed scheme. The global asymptotic stability of the overall system is ensured using the principles of Lyapunov approach. Simulation studies are carried-out using sinusoidal force functions of varying frequency. Experimental results show that the proposed neural adaptive control scheme is capable of providing significant vibration suppression in the multiple bending modes of interest. The performance of the proposed scheme is better than the H∞ control scheme.