bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of Bacterial Diversity during Antibiotic Treatment of Intubated Patients Colonized with
Pseudomonas aeruginosa
Authors: Flanagan J. L. , Brodie E. L. , Weng L. , Lynch S. V. , Garcia O. , Brown R. , Hugenholtz P. , DeSantis T. Z. , Andersen G. L. , Wiener-Kronish J. P. , Bristow J. 
Published: April 2007

ABSTRACT

Management of airway infections caused by
Pseudomonas aeruginosa
is a serious clinical challenge, but little is known about the microbial ecology of airway infections in intubated patients. We analyzed bacterial diversity in endotracheal aspirates obtained from intubated patients colonized by
P. aeruginosa
by using 16S rRNA clone libraries and microarrays (PhyloChip) to determine changes in bacterial community compositions during antibiotic treatment. Bacterial 16S rRNA genes were absent from aspirates obtained from patients briefly intubated for elective surgery but were detected by PCR in samples from all patients intubated for longer periods. Sequencing of 16S rRNA clone libraries demonstrated the presence of many orally, nasally, and gastrointestinally associated bacteria, including known pathogens, in the lungs of patients colonized with
P. aeruginosa
. PhyloChip analysis detected the same organisms and many additional bacterial groups present at low abundance that were not detected in clone libraries. For each patient, both culture-independent methods showed that bacterial diversity decreased following the administration of antibiotics, and communities became dominated by a pulmonary pathogen.
P. aeruginosa
became the dominant species in six of seven patients studied, despite treatment of five of these six with antibiotics to which it was sensitive in vitro. Our data demonstrate that the loss of bacterial diversity under antibiotic selection is highly associated with the development of pneumonia in ventilated patients colonized with
P. aeruginosa.
Interestingly, PhyloChip analysis demonstrated reciprocal changes in abundance between
P. aeruginosa
and the class
Bacilli
, suggesting that these groups may compete for a similar ecological niche and suggesting possible mechanisms through which the loss of microbial diversity may directly contribute to pathogen selection and persistence.
Evaluation of Real-Time PCR Laboratory-Developed Tests Using Analyte-Specific Reagents for Cytomegalovirus Quantification
Authors: Caliendo Angela M. , Ingersoll Jessica , Fox-Canale Andrea M. , Pargman Sabine , Bythwood Tameka , Hayden Mary K. , Bremer James W. , Lurain Nell S. 
Published: April 2007

ABSTRACT

Viral load testing for cytomegalovirus (CMV) has become the standard for the diagnosis of infection and monitoring of therapy at many transplant centers. However, no viral load test has been approved by the FDA. Therefore, many laboratories rely on laboratory-developed assays. This study evaluated the performance characteristics of two real-time PCR tests developed using the
artus
CMV analyte-specific reagents (ASRs). One version is distributed by Abbott Molecular and the other by QIAGEN. For plasma specimens, the Abbott test had a limit of detection of 2.3 log
10
copies/ml and a linear range up to at least 6.0 log
10
copies/ml. Comparison of plasma viral loads using the Abbott test and the Roche Amplicor Monitor test showed a mean difference of −0.012 log
10
copies/ml. In addition, the Abbott test viral loads correlated with the Digene Hybrid Capture assay ratios. Viral loads obtained from plasma specimens tested by the Abbott and QIAGEN tests were in very close agreement (mean difference, 0.144 log
10
copies/ml). When the QIAGEN test was evaluated with the QIAGEN, MagNA Pure, and easyMAG extraction methods, the viral loads for all three methods were within 0.370 log
10
copies/ml. Thus, there is good agreement between viral loads obtained by the different tests using the same extraction method or by the same test using different extraction methods. The availability of real-time PCR ASRs provides additional reagents that can be used for CMV viral load testing.
The Cytomegalovirus-Specific CD4+T-Cell Response Expands with Age and Markedly Alters the CD4+T-Cell Repertoire
Authors: Pourgheysari Batoul , Khan Naeem , Best Donna , Bruton Rachel , Nayak Laxman , Moss Paul A. H. 
Published: April 2007

ABSTRACTImmune function in the elderly is associated with a number of phenotypic and functional abnormalities, and this phenomenon of immune senescence is associated with increased susceptibility to infection. The immune response to pathogens frequently declines with age, but the CD8+T-cell response to cytomegalovirus (CMV) is unusual, as it demonstrates a significant expansion over time. Here we have documented the CD4+T-cell immune response to CMV in healthy donors of different ages. The magnitude of the CMV-specific CD4+T-cell immune response increases from a mean of 2.2% of the CD4+T-cell pool in donors below 50 years of age to 4.7% in donors aged over 65 years. In addition, CMV-specific CD4+T cells in elderly donors demonstrate decreased production of interleukin-2 and less dependence on costimulation. CMV seropositivity is associated with marked changes in the phenotype of the overall CD4+T-cell repertoire in healthy aged donors, including an increase in CD57+expression and a decrease in CD28 and CD27 expression, a phenotypic profile characteristic of immune senescence. This memory inflation of CMV-specific CD4+T cells contributes to evidence that CMV infection may be damaging to immune function in elderly individuals.
Characterization of Protein-Protein Interactions Critical for Poliovirus Replication: Analysis of 3AB and VPg Binding to the RNA-Dependent RNA Polymerase
Authors: Strauss Daniel M. , Wuttke Deborah S. 
Published: April 2007

ABSTRACT
Two critical interactions within the poliovirus RNA replication complex are those of the RNA-dependent RNA polymerase 3D with the viral proteins 3AB and VPg. 3AB is a membrane-binding protein responsible for the localization of the polymerase to the membranous vesicles at which replication occurs. VPg (a peptide comprising the 3B region of 3AB) is the 22-residue soluble product of 3AB cleavage and serves as the protein primer for RNA replication. The detailed interactions of these proteins with the RNA-dependent RNA polymerase 3D were analyzed to elucidate the precise roles of 3AB and VPg in the viral RNA replication complex. Using a membrane-based pull-down assay, we have identified a binding “hot-spot” spanning residues 100 to 104 in the 3B (VPg) region of 3AB which plays a critical role in mediating the interaction of 3AB with the polymerase. Isothermal titration calorimetry shows that the interaction of VPg with 3D is enthalpically driven, with a dissociation constant of 11 μM. Mutational analyses of VPg indicate that a subset of the residues important for 3AB-3D binding are also important for VPg-3D binding. Two residues in particular, P14 and R17, were shown to be absolutely critical for the binding interaction. This work provides the direct characterization of two binding interactions critical for the replication of this important class of viruses and identifies a conserved polymerase binding sequence responsible for targeting the polymerase.
Direct Comparison of Antigen Production and Induction of Apoptosis by Canarypox Virus- and Modified Vaccinia Virus Ankara-Human Immunodeficiency Virus Vaccine Vectors
Authors: Zhang Xiugen , Cassis-Ghavami Farah , Eller Mike , Currier Jeff , Slike Bonnie M. , Chen Xuemin , Tartaglia James , Marovich Mary , Spearman Paul 
Published: April 2007

ABSTRACT

Recombinant poxvirus vectors are undergoing intensive evaluation as vaccine candidates for a variety of infectious pathogens. Avipoxviruses, such as canarypox virus, are replication deficient in mammalian cells by virtue of a poorly understood species-specific restriction. Highly attenuated vaccinia virus strains such as modified vaccinia virus Ankara (MVA) are similarly unable to complete replication in most mammalian cells but have an abortive-late phenotype, in that the block to replication occurs post-virus-specific DNA replication. In this study, an identical expression cassette for human immunodeficiency virus
gag
,
pro
, and
env
coding sequences was placed in canarypox virus and MVA vector backbones in order to directly compare vector-borne expression and to analyze differences in vector-host cell interactions. Antigen production by recombinant MVA was shown to be greater than that from recombinant canarypox virus in the mammalian cell lines and in the primary human cells tested. This observation was primarily due to a longer duration of antigen production in recombinant MVA-infected cells. Apoptosis induction was found to be more profound with the empty canarypox virus vector than with MVA. Remarkably, however, the inclusion of a
gag/pro/env
expression cassette altered the kinetics of apoptosis induction in recombinant MVA-infected cells to levels equal to those found in canarypox virus-infected cells. Antigen production by MVA was noted to be greater in human dendritic cells and resulted in enhanced T-cell stimulation in an in vitro antigen presentation assay. These results reveal differences in poxvirus vector-host cell interactions that should be relevant to their use as immunization vehicles.
Productive Varicella-Zoster Virus Infection of Cultured Intact Human Ganglia
Authors: Gowrishankar Kavitha , Slobedman Barry , Cunningham Anthony L. , Miranda-Saksena Monica , Boadle Ross A. , Abendroth Allison 
Published: April 2007

ABSTRACT
Varicella-zoster virus (VZV) is a species-specific herpesvirus which infects sensory ganglia. We have developed a model of infection of human intact explant dorsal root ganglia (DRG). Following exposure of DRG to VZV, viral antigens were detected in neurons and nonneuronal cells. Enveloped virions were visualized by transmission electron microscopy in neurons and nonneuronal cells and within the extracellular space. Moreover, rather than remaining highly cell associated during infection of cultured cells, such as fibroblasts, cell-free VZV was released from infected DRG. This model enables VZV infection of ganglionic cells to be studied in the context of intact DRG.
Clinical epidemiological study of employees exposed to surfactant blend containing perfluorononanoic acid
Authors: Mundt Diane J , Mundt Kenneth A , Luippold Rose S , Schmidt Michael D , Farr Craig H 
Published: April 2007

Introduction:An epidemiological study was conducted of a perfluorononanoic acid (PFNA) surfactant blend, to investigate whether clinical differences were apparent between employees who were potentially exposed to the surfactant and those who were not exposed. The surfactant blend, which is related to other previously studied perfluorinated materials, is used in the production of some high-performance polymers.Methods:All 630 individuals employed at a polymer production facility using PFNA (CAS No 72968-38-8) at any time between 1 January 1989 and 1 July 2003 were included in the cohort. Plausibly related laboratory test results were abstracted from annual medical examination records, including liver enzyme function and blood lipids. Detailed work histories, available for all employees, provided the basis for determining exposure category. Thirty two clinical parameters were evaluated by exposure level at five points in time, determined to reflect changes in possible exposure intensity, as well as greatest number of records available. Annual cross-sectional analyses and longitudinal analyses that accounted for multiple measurements per person were conducted separately for men and women, by exposure groups.Results:Differences by exposure group for all laboratory measures, adjusted for age and body mass index, were small and not clinically significant. Although some statistically significant pair-wise differences were observed, these observations were not consistent between men and women, or over the five analysis windows. For the seven outcome variables (liver enzymes and blood lipids) examined in separate longitudinal models, no significant increase or decrease was observed by unit increase in cumulative exposure intensity score.Conclusion:This is the first epidemiological study investigating the possible health effects in humans associated with exposure to PFNA blend. Based on laboratory measures assessed over more than a decade, no adverse clinical effects were detected from occupational exposure to PFNA blend.
Uses of CONFER at Wayne State University (abstract only)
Authors: McCord Alan 
Published: April 2007

CONFER is used by a variety of organizations which have no
direct contact with any MTS site (the CONFER host computer system).
In many cases, the main contact of the CONFER user is with the
third party vendor or consultant who is supporting the networking
effort. Several problems arise when the third party relationship is
not broadened to include the institutional consulting and
documentation efforts. Such problems include:1. Overload on the
time of the third-party consultant.2. Production of custom
documentation which parallels the institutional documentation.3.
User perceptions that they are not "ready" for institutional
documentation.4. Development of abbreviated cognitive maps of the
system and its user network.5. Users exchange superstitious views
of how the system works.While it is not yet clear that the
absorption of third-party, mediated networks will solve such
problems, it is an obvious first step to a solution.

MTS Help Facility

A version of CONFER is tentatively planned for use as the
principal Help Facility at WSU. A subset of CONFER capabilities
will be employed to decrease demands on the system.
Features of the Help Facility will include agenda string
searches, execution of computer assisted instruction lessons from
within tbe CONFERence, a "suggestion box" facility, and user
modelling features intended to decrease user frustration and
maximize efficiency. Existing help files will be called from the
Help Facility to increase the redundancy of available help to the
user.
The agenda used will be multi-dimensional, allowing the user to
search for help within subject areas, type of information and skill
level. For example, the user would be able to view all items which
serve as tutorials on statistical packages with the CONFER command:
AGENDA TUTORIALS+STATISTICS. Similarly, the user will be able to
search item descriptors or text for character strings, such as
using WHICH "SPSS" to locate all items dealing with SPSS.
Requests for help will be sent directly to various CSC
departments, and responded to either via CONFER or telephone. User
suggestions and requests will be screened on a continuing basis by
CSC staff, and changes to the information contained in each item
will be made as a result of these suggestions. Materials developed
by users will be solicited for inclusion in the Help Facility.
A comparison of two recent approaches to machine parameterization for mathematical software
Authors: Smith Brian T. 
Published: April 2007

Recently, there have been published two different proposals for expressing the dependence of numerical software on the environment. One proposal, which is essentially described in two papers [1,2]** characterizes the dependence of the software on the machine architecture essentially in terms of the representation of floating point entities in the machine. The second, more recent proposal, described in [3] characterizes the dependence of the software on the environment in terms of models both the floating point numbers and of the behavior of the arithmetic unit of the machine.
The purpose of this paper is to expose and clarify the differences and similarities between these two approaches. It is the author's opinion that the two approaches interpreted in their strictest sense serve two distinct purposes. When each is interpreted imprecisely, their roles overlap.
In order that the comparisons briefly discussed below are fully understood, we need to briefly summarize the separate approaches. Since our interest here is in the parameterization of the numerical aspects of the environment, the non-numerical parameters discussed in [1] and the considerations of implementation discussed in [2,3] will not be considered here.
A transportable system for management and exchange of programs and other text
Authors: Snyder W. V. 
Published: April 2007

Computer software is usually exchanged between different computer facilities via punched cards or magnetic tape. For up to about 1000 images, cards are cheaper and probably easier to deal with than tape. The primary problem with cards is the variety of punch codes. Frequently, one also has the minor nuisance of repunching cards damaged in transit. For larger amounts of data, tape is cheaper, but there are so many tape formats in use that the recipient frequently has trouble reading a tape, even if the format is simple and well defined. Occasionally, one has the problem of parity errors, which make a tape essentially worthless. When test data, modules in several languages, computer output or documentation are included, the lack of organization in the material can cause a substantial amount of unnecessary human labor.
This paper presents a system for exchanging information on tape, that allows information about the data to be included with the data. The system is designed for portability, but requires a few simple machine dependent modules. These modules are available for a variety of machines, and a bootstrapping procedure is provided. The system allows content selected reading of the tape, and a simple text editing facility is provided. Although the system recognizes 30 commands, information may be extracted from the tape by using as few as three commands. In addition to its use for information exchange, we expect the system to find use in maintaining large libraries of text.
The Clustered AGgregation (CAG) technique leveraging spatial and temporal correlations in wireless sensor networks
Authors: Yoon Sunhee , Shahabi Cyrus 
Published: April 2007

Sensed data in Wireless Sensor Networks (WSN) reflect the spatial and temporal correlations of physical attributes existing intrinsically in the environment. In this article, we present the Clustered AGgregation (CAG) algorithm that forms clusters of nodes sensing similar values within a given threshold (spatial correlation), and these clusters remain unchanged as long as the sensor values stay within a threshold over time (temporal correlation). With CAG, only one sensor reading per cluster is transmitted whereas with Tiny AGgregation (TAG) all the nodes in the network transmit the sensor readings. Thus, CAG provides energy efficient and approximate aggregation results with small and often negligible and bounded error.
In this article we extend our initial work in CAG in five directions: First, we investigate the effectiveness of CAG that exploits the temporal as well as spatial correlations using both the measured and modeled data. Second, we design CAG for two modes of operation (interactive and streaming) to enable CAG to be used in different environments and for different purposes. Interactive mode provides mechanisms for one-shot queries, whereas the streaming mode provides those for continuous queries. Third, we propose a fixed range clustering method, which makes the performance of our system independent of the magnitude of the sensor readings and the network topology. Fourth, using mica2 motes, we perform a large-scale measurement of real environmental data (temperature and light, both indoor and outdoor) and the wireless radio reliability, which were used for both analytical modeling and simulation experiments. Fifth, we model the spatially correlated data using the properties of our real world measurements.
Our experimental results show that when we compute the average of sensor readings in the network using the CAG interactive mode with the user-provided error threshold of, 20%, we can save 68.25% of transmissions over TAG with only 2.46% inaccuracy in the result. The streaming mode of CAG can save even more transmissions (up to 70.24% in our experiments) over TAG, when data shows high spatial and temporal correlations. We expect these results to hold in reality, because we used the mica2 radio profile and empirical datasets for our simulation study. CAG is the first system that leverages spatial and temporal correlations to improve energy efficiency of in-network aggregation. This study analytically and empirically validates CAG's effectiveness.
A feedback-controlled interface for treadmill locomotion in virtual environments
Authors: Lichtenstein Lee , Barabas James , Woods Russell L. , Peli Eli 
Published: April 2007

Virtual environments (VEs) allow safe, repeatable, and controlled evaluations of obstacle avoidance and navigation performance of people with visual impairments using visual aids. Proper simulation of mobility in a VE requires an interface, which allows subjects to set their walking pace. Using conventional treadmills, the subject can change their walking speed by pushing the tread with their feet, while leveraging handrails or ropes (self-propelled mode). We developed a feedback-controlled locomotion interface that allows the VE workstation to control the speed of the treadmill, based on the position of the user. The position and speed information is also used to implement automated safety measures, so that the treadmill can be halted in case of erratic behavior.
We compared the feedback-controlled to the self-propelled mode by using speed-matching tasks (follow a moving object or match the speed of an independently moving scene) to measure the efficacy of each mode in maintaining constant subject position, subject control of the treadmill, and subject pulse rates. In addition, we measured the perception of speed in the VE on each mode.
The feedback-controlled mode required less physical exertion than self-propelled. The average position of subjects on the feedback-controlled treadmill was always within a centimeter of the desired position. There was a smaller standard deviation in subject position when using the self-propelled mode than when using the feedback-controlled mode, but the difference averaged less than 6 cm across all subjects walking at a constant speed. Although all subjects underestimated the speed of an independently moving scene at higher speeds, their estimates were more accurate when using the feedback-controlled treadmill than the self-propelled.
Analysis of the SPV secure routing protocol
Authors: Raghavan Barath , Panjwani Saurabh , Mityagin Anton 
Published: April 2007

We analyze a secure routing protocol, Secure Path Vector (SPV), proposed in SIGCOMM 2004. SPV aims to provide authenticity for route announcements in the Border Gateway Protocol (BGP) using an efficient alternative to ordinary digital signatures, called constant-time signatures. Today, SPV is often considered the best cryptographic defense for BGP.
We find subtle flaws in the design of SPV which lead to attacks that can be mounted by 60% of Autonomous Systems in the Internet. In addition, we study several of SPV's design decisions and assumptions and highlight the requirements for security of routing protocols. In light of our analysis, we reexamine the need for constant-time signatures and find that certain standard digital signature schemes can provide the same level of efficiency for route authenticity.