bluuebunny/crossref_metadata_2025_split huggingface dataset:
Longitudinal Study of Intestinal
Entamoeba histolytica
Infections in Asymptomatic Adult Carriers
Authors: Blessmann Joerg , Ali Ibne Karim M. , Ton Nu Phuong A. , Dinh Binh T. , Ngo Viet Tram Q. , Le Van An , Clark C. Graham , Tannich Egbert 
Published: October 2003

ABSTRACT

To gain insight into the dynamics of intestinal
Entamoeba histolytica
infection, a longitudinal study was performed over an observation period of 15 months with a group of 383 randomly selected adult individuals (mean age, 38.5 years) living in an area of amebiasis endemicity in central Vietnam. Ameba infection was diagnosed by using species-specific PCR and DNA extracted directly from fecal samples. The results indicated an
E. histolytica
prevalence of 11.2% and an annual new infection rate of 4.1% in the study population. Follow-up of the 43 individuals who were
E. histolytica
positive at enrollment suggested a regular exponential decline in infection of about 3% per month and a mean half-life of infection of more than 15 months. However, the reinfection rate for this group of participants was 2.7 times higher than that predicted for the study population as a whole. Both the reappearance of the parasite after successful treatment of
E. histolytica
infection and changes in “genetic fingerprints” of parasites during the course of infection revealed an annual new infection rate of about 11.5%. Thus, the mean half-life of
E. histolytica
infection was calculated to be 12.9 months (95% confidence interval, 10.2 to 15.6 months). Notably, none of the participants developed symptoms compatible with invasive intestinal amebiasis, and only one of the subjects developed an amebic liver abscess during the observation period.
Species Diversity and Polymorphism in theExophiala spiniferaClade Containing Opportunistic Black Yeast-Like Fungi
Authors: de Hoog G. S. , Vicente V. , Caligiorne R. B. , Kantarcioglu S. , Tintelnot K. , Gerrits van den Ende A. H. G. , Haase G. 
Published: October 2003

ABSTRACTA monophyletic group of black yeast-like fungi containing opportunistic pathogens aroundExophiala spiniferais analyzed using sequences of the small-subunit (SSU) and internal transcribed spacer (ITS) domains of ribosomal DNA. The group contains yeast-like and annellidic species (anamorph genusExophiala) in addition to sympodial taxa (anamorph generaRamichloridiumandRhinocladiella). The new speciesExophiala oligosperma,Ramichloridium basitonum, andRhinocladiella similisare introduced and compared with their morphologically similar counterparts at larger phylogenetic distances outside theE. spiniferaclade.Exophiala jeanselmeiis redefined. New combinations are proposed inExophiala:Exophiala exophialaeforPhaeococcomyces exophialaeandExophiala heteromorphaforE. jeanselmeivar.heteromorpha.
Optimization of Real-Time PCR Assay for Rapid and Sensitive Detection of Eubacterial 16S Ribosomal DNA in Platelet Concentrates
Authors: Mohammadi Tamimount , Reesink Henk W. , Vandenbroucke-Grauls Christina M. J. E. , Savelkoul Paul H. M. 
Published: October 2003

ABSTRACT

A real-time PCR assay was developed for rapid detection of eubacterial 16S ribosomal DNA in platelet concentrates. The sensitivity of this assay can be hampered by contaminating DNA in the PCR reagents. Digestion of the PCR reagents with
Sau
3AI prior to PCR amplification was effective in eliminating this contaminating DNA without affecting the sensitivity of the assay.
National Department of Defense Surveillance Data for Antibiotic Resistance and
emm
Gene Types of Clinical Group A Streptococcal Isolates from Eight Basic Training Military Sites
Authors: Barrozo Christopher P. , Russell Kevin L. , Smith Tyler C. , Hawksworth Anthony W. , Ryan Margaret A. K. , Gray Gregory C. 
Published: October 2003

ABSTRACT

Antibiotic resistance and
emm
gene types were examined from 692 Group A streptococci isolates from eight United States military basic training sites between 1998 and 2001. Macrolide resistance was associated with geographic sites and
emm
type. These data are useful for vaccine development initiatives and antimicrobial treatment considerations.
Real-Time PCR Assay Targets the 23S-5S Spacer for Direct Detection and Differentiation of
Legionella
spp. and
Legionella pneumophila
Authors: Herpers Bjorn L. , de Jongh Bartelt M. , van der Zwaluw Kim , van Hannen Erik J. 
Published: October 2003

ABSTRACT

A real-time PCR for the ABI Prism 7000 system targeting the 23S-5S spacer of
Legionella
spp. was developed. Simultaneous detection and differentiation of
Legionella
spp. and
Legionella pneumophila
within 90 min and without post-PCR melting-curve analysis was achieved using two TaqMan probes. In sputum samples from 23 controls and 17 patients with legionellosis, defined by positive culture, urinary antigen testing, or seroconversion, 94% sensitivity and 100% specificity were observed.
Investigation of
Staphylococcus aureus
Isolates Identified as Erythromycin Intermediate by the Vitek-1 System: Comparison with Results Obtained with the Vitek-2 and Phoenix Systems
Authors: Tang Patrick , Low Donald E. , Atkinson Sandra , Pike Karen , Ashi-Sulaiman Aisha , Simor Andrew , Richardson Susan , Willey Barbara M. 
Published: October 2003

ABSTRACT

We identified 69
Staphylococcus aureus
isolates that were erythromycin intermediate as reported by the Vitek-1 system using the GPS-105 card. Of the 57 strains that were available for further testing, all were erythromycin resistant by broth microdilution and the Phoenix system, while the Vitek-2 system identified 55 of 57 strains (96%) as erythromycin resistant. The majority of isolates (54 of 57 [95%]) exhibited the inducible MLS (macrolide-lincosamide-streptogramin family) phenotype, as shown by the double-disk test. We recommend that all
S. aureus
strains determined as erythromycin intermediate by the Vitek-1 system be interpreted as resistant to erythromycin.
Improved PCR for Detection of the Highly Leukotoxic JP2 Clone of
Actinobacillus actinomycetemcomitans
in Subgingival Plaque Samples
Authors: Poulsen Knud , Ennibi Oum-Keltoum , Haubek Dorte 
Published: October 2003

ABSTRACT

The JP2 clone of
Actinobacillus actinomycetemcomitans
is associated with early-onset periodontitis in certain ethnic populations of African origin. Here, we describe and evaluate a set of primers for PCR to assay for the presence of
A. actinomycetemcomitans
and to discriminate between JP2-like strains and other genotypes in subgingival plaque samples.
Subtyping of
Salmonella enterica
Serovar Typhimurium Outbreak Strains Isolated from Humans and Animals in Iceland
Authors: Gudmundsdottir Sigrun , Hardardottir Hjordis , Gunnarsson Eggert 
Published: October 2003

ABSTRACT

A total of 75
Salmonella enterica
serovar Typhimurium strains of various (mainly human and animal) origins were typed by pulsed-field gel electrophoresis (PFGE) and phage typing. These strains were collected during an outbreak in Iceland in 1999 and 2000. The typing revealed that 84% of the strains belonged to the same PFGE and phage type (PT), namely, PFGE type 1Aa and PT 1.
Dissemination of Extended-Spectrum β-Lactamase-Producing
Enterobacteriaceae
in Pediatric Intensive Care Units
Authors: Wu Tsu-Lan , Chia Ju-Hsin , Su Lin-Hui , Kuo An-Jing , Chu Chishih , Chiu Cheng-Hsun 
Published: October 2003

ABSTRACT

To study the growing trend of extended-spectrum β-lactamase (ESBL)-producing
Enterobacteriaceae
in pediatric intensive care units (PICUs), 88 nonrepetitive ESBL-producing isolates were prospectively collected and analyzed by molecular methods during a 16-month period. The emergence and dissemination of ESBL-producing
Enterobacteriaceae
in PICUs are the consequence of the clonal dissemination of a few epidemic strains along with the horizontal transmission of resistance gene-carrying plasmids among bacterial organisms.
Detection of Differences in the Nucleotide and Amino Acid Sequences of Diphtheria Toxin fromCorynebacterium diphtheriaeandCorynebacterium ulceransCausing Extrapharyngeal Infections
Authors: Sing Andreas , Hogardt Michael , Bierschenk Suse , Heesemann Jürgen 
Published: October 2003

ABSTRACTWhileCorynebacterium ulceranscan mimic classical diphtheria, extrapharyngeal infections are extremely rare. Sequencing of the diphtheria toxin (DT)-encodingtoxgene of twoC. ulceransisolates from extrapharyngeal infections revealed differences fromC. diphtheriaeDT sequences, mainly in the translocation and receptor-binding domains.C. ulceranssupernatants were much less potent than supernatant fromC. diphtheriae. AC. ulceransDT-specific PCR is described below.
Evaluation of the TRUGENE
HCV 5
′
NC
Genotyping Kit with the New GeneLibrarian Module 3.1.2 for Genotyping of Hepatitis C Virus from Clinical Specimens
Authors: Germer Jeffrey J. , Majewski David W. , Rosser Michael , Thompson Amber , Mitchell P. Shawn , Smith Thomas F. , Elagin Slava , Yao Joseph D.C. 
Published: October 2003

ABSTRACT

The TRUGENE
HCV 5′NC
genotyping kit (GeneLibrarian modules 3.1.1 and 3.1.2) and VERSANT HCV genotyping assay were compared by using 96 hepatitis C virus (HCV) RNA-positive patient specimens, including HCV genotypes 1, 2, 3, 4, 5, 6, and 10. The TRUGENE
HCV 5
′
NC
genotyping kit (GeneLibrarian module 3.1.2) yielded the most accurate genotyping results.
Molecular Analysis of Group A Streptococcal Isolates Associated with Scarlet Fever in Southern Taiwan between 1993 and 2002
Authors: Yan Jing-Jou , Liu Ching-Chuan , Ko Wen-Chien , Hsu Shui-Yuan , Wu Hsiu-Mei , Lin Yee-Shin , Lin Ming T. , Chuang Woei-Jer , Wu Jiunn-Jong 
Published: October 2003

ABSTRACTCollected between 1993 and 2002 at a Taiwanese university hospital, 77 group A streptococcus isolates associated with scarlet fever were grouped byemmtyping and pulsed-field gel electrophoresis. The predominance of anemm1clone before 1996 and the presence of genetically diverseemm1andemm4strains thereafter were found.
Detection of
Yersinia pestis
in Sputum by Real-Time PCR
Authors: Loïez Caroline , Herwegh Stéphanie , Wallet Frédéric , Armand Sylvie , Guinet Françoise , Courcol René J. 
Published: October 2003

ABSTRACT

A 5′ nuclease PCR assay for detection of the
Yersinia pestis
plasminogen activator (
pla
) gene in human respiratory specimens with simulated
Y. pestis
infection was developed. An internal positive control was added to the reaction mixture in order to detect the presence of PCR inhibitors that are often found in biological samples. The assay was 100% specific for
Y. pestis
. In the absence of inhibitors, a sensitivity of 10
2
CFU/ml of respiratory fluid was obtained. When inhibitors were present, detection of
Y. pestis
DNA required a longer sample treatment time and an initial concentration of bacteria of at least 10
4
CFU/ml. The test's total turnaround time was less than 5 h. The assay described here is well suited to the rapid diagnosis of pneumonic plague, the form of plague most likely to result from a bioterrorist attack.
Surveillance for Respiratory Syncytial Virus in Infants Hospitalized for Acute Lower Respiratory Infection in Chile (1989 to 2000)
Authors: Avendaño Luis F. , Palomino María Angélica , Larrañaga Carmen 
Published: October 2003

ABSTRACT
Hospitalized infants (4,618) were studied for lower respiratory infections from 1989 through 2000 by routine immunofluorescence assay and viral isolation. The hospitalization rate for respiratory syncytial virus (RSV) averaged 2% per year. The fatality rate was 0.1%. Monthly RSV detection varied from 14 to 88%, and epidemics lasted 3.5 to 6 months. From 1994 high-early versus low-late epidemic patterns alternately were observed, the first influenced by a group B strain.
Bipolaris spiciferaCauses Fungus Balls of the Sinuses and Triggers Polypoid Chronic Rhinosinusitis in an Immunocompetent Patient
Authors: Buzina Walter , Braun Hannes , Schimpl Kerstin , Stammberger Heinz 
Published: October 2003

ABSTRACTWe report the rare case of a 19-year-old immunocompetent male suffering both from fungus balls of the sinuses and from chronic rhinosinusitis with massive polyposis. Endoscopic sinus surgery revealed grayish brown necrotic masses embedded in viscous eosinophilic mucus. Inoculated onto petri dishes, these masses as well as the mucus grew a dark pigmented fungus, which was identified asBipolaris spicifera.
Persistent Multiple Pulmonary Nodules in a Nonimmunocompromised Woman after Varicella-Related Myelitis Treated with Acyclovir
Authors: Schvoerer Evelyne , Frechin Valéry , Warter André , Gasser Bernard , Jouin Hervé , Gut Jean-Pierre , Stoll-Keller Françoise 
Published: October 2003

ABSTRACT
Persistent multiple pulmonary nodules were observed on the chest X ray of a nonimmunocompromised woman 6 months after she was treated with acyclovir for a varicella-related myelitis without respiratory symptoms. Early antiviral therapy given for varicella infections might decrease the intensity of clinical symptoms without actually preventing the occurrence of varicella-zoster virus-related lesions such as the persistent pulmonary nodules reported here.
The Lattice Molecular Automaton(LMA): A Simulation System for Constructive Molecular Dynamics
Authors: Mayer Bernd , Rasmussen Steen 
Published: October 2003

Molecular self-assembly is frequently encountered in biochemical systems generating higher order structures with well-defined functionalities. However, the driving forces underlying these processes are not well understood. The Lattice Molecular Automaton (LMA) is a deterministic computational tool suitable for simulation of self-organization processes in large scale, molecular systems. This paper introduces the basic computational concepts needed to formulate molecular dynamics and self-assembly in a discrete field, cellular automaton environment: Molecular objects are encoded as data structures on a 2D triangular lattice. Propagating force particles together with kinetic and potential energy terms define simulation objects that specify molecular dynamics and force field properties. As an example, the simulation of polymer dynamics in an aqueous environment is shown. In this paper we focus on the mathematical and algorithmic formulation of a variety of intra- and intermolecular interactions. Thermodynamical characteristics together with a variety of other physico-chemical properties of the LMA are discussed in detail in Ref. 1.
Computational Power of Quantum Machines, Quantum Grammars and Feasible Computation
Authors: Krishnamurthy E. V. 
Published: October 2003

This paper studies the computational power of quantum computers to explore as to whether they can recognize properties which are in nondeterministic polynomial-time class (NP) and beyond. To study the computational power, we use the Feynman's path integral (FPI) formulation of quantum mechanics. From a computational point of view the Feynman's path integral computes a quantum dynamical analogue of the k-ary relation computed by an Alternating Turing machine (ATM) using AND-OR Parallelism. Hence, if we can find a suitable mapping function between an instance of a mathematical problem and the corresponding interference problem, using suitable potential functions for which FPI can be integrated exactly, the computational power of a quantum computer can be bounded to that of an alternating Turing machine that can solve problems in NP (e.g, factorization problem) and in polynomial space. Unfortunately, FPI is exactly integrable only for a few problems (e.g., the harmonic oscillator) involving quadratic potentials; otherwise, they may be only approximately computable or noncomputable. This means we cannot in general solve all quantum dynamical problems exactly except for those special cases of quadratic potentials, e.g., harmonic oscillator. Since there is a one to one correspondence between the quantum mechanical problems that can be analytically solved and the path integrals that can be exactly evaluated, we can say that the noncomputability of FPI implies quantum unsolvability. This is the analogue of classical unsolvability. The Feynman's path graph can be considered as a semantic parse graph for the quantum mechanical sentence. It provides a semantic valuation function of the terminal sentence based on probability amplitudes to disambiguate a given quantum description and obtain an interpretation in a linear time. In Feynman's path integral, the kernels are partially ordered over time (different alternate paths acting concurrently at the same time) and multiplied. The semantic valuation is computable only if the FPI is computable. Thus both the expressive power and complexity aspects quantum computing are mirrored by the exact and efficient integrability of FPI.
Symbolic Computation of Turbulence and Energy Dissipation in the Taylor Vortex Model
Authors: Fateman Richard J. 
Published: October 2003

Using a classic example proposed by G. I. Taylor, we reconsider through the use of computer algebra, the mathematical analysis of a fundamental process in turbulent flow, namely: How do large scale eddies evolve into smaller scale ones to the point where they are effectively absorbed by viscosity? The explicit symbolic series solution of this problem, even for cleverly chosen special cases, requires daunting algebra, and so numerical methods have become quite popular. Yet an algebraic approach can provide substantial insight, especially if it can be pursued with modest human effort. The specific example we use dates to 1937 when Taylor and Green8 first published a method for explicitly computing successive approximations to formulas describing the three-dimensional evolution over time of what is now called a Taylor–Green vortex. With the aid of a computer algebra system, we have duplicated Taylor and Green's efforts and obtained more detailed time-series results. We have extended their approximation of the energy dissipation from order 5 in time to order 14, including the variation with viscosity. Rather than attempting additional interpretation of results for fluid flow (for which, see papers by Brachet et al.,2,3 we examine the promise of computer algebra in pursuing such problems in fluid mechanics.
Competitive Dynamic Multiprocessor Allocation for Parallel Applications
Authors: Brecht Timothy , Deng Xiaotie , Gu Nian 
Published: October 2003

We study dynamic multiprocessor allocation policies for parallel jobs, which allow the preemption and reallocation of processors to take place at any time. The objective is to minimize the completion time of the last job to finish executing (the makespan). We characterize a parallel job using two parameter. The job's parallelism, Pi, which is the number of tasks being executed in parallel by a job, and its execution time, li, when Pi processors are allocated to the job. The only information available to the scheduler is the parallelism of jobs. The job execution time is not known to the scheduler until the job's execution is completed. We apply the approach of competitive analysis to compare preemptive scheduling policies, and are interested in determining which policy achieves the best competitive ratio (i.e., is within the smallest constant factor of optimal). We devise an optimal competitive scheduling policy for scheduling two parallel jobs on P processors. Then, we apply the method to schedule N parallel jobs on P processors. Finally we extend our work to incorporate jobs for which the number of parallel tasks changes during execution (i.e., jobs with multiple phases of parallelism).
A Routing Strategy for Object-Oriented Applications in Massively Parallel Architectures
Authors: Boari Maurelio , Corradi Antonioo , Stefanelli Cesare , Leonardi Letizia 
Published: October 2003

Parallel object-oriented environments have a high degree of dynamicity and need specialised support to achieve efficiency of execution. Static strategies are not suitable for these environments: any prediction before execution can only roughly estimate the real behaviour. In object-oriented environments, the decision to create/destroy objects is usually taken at run-time and object allocation can change during the execution. The requirement of dynamicity should be considered in the design of every component of the support. The routing system, for instance, must ensure delivery even in case of object dynamic allocation/reallocation. The paper argues that routing algorithms for parallel object-oriented environments in massively parallel architectures should be both adaptive and efficient. We adopted a routing strategy designed to be effective in case of objects dynamically created/destroyed and capable of moving during the execution. Our adaptive strategy does not assume any knowlegde of both object allocation and system topology configuration.
Optimal and Near–Optimal Solutions for Hard Compilation Problems
Authors: Kremer Ulrich 
Published: October 2003

An optimizing compiler typically uses multiple program representations at different levels of program and performance abstractions in order to be able to perform transformations that – at least in the majority of cases – will lead to an overall improvement in program performance. The complexities of the program and performance abstractions used to formulate compiler optimization problems have to match the complexities of the high–level programming model and of the underlying target system. Scalable parallel systems typically have multi–level memory hierarchies and able to exploit coarse–grain and fine–grain parallelism. Most likely, future systems will have even deeper memory hierarchies and more granularities of parallelism. As a result, future compiler optimizations will have to use more and more complex, multi–level computation and performance models in order to keep up with the complexities of their future target systems. Most of the optimization problems encountered in highly optimizing compilers are already NP–hard, and there is little hope that most newly encountered optimization formulations will not be at least NP–hard as well. To face this "complexity crisis", new methods are needed to evaluate the benefits of a compiler optimization formulation. A crucial step in this evaluation process is to compute the optimal solution of the formulation. Using ad–hoc methods to compute optimal solutions to NP–complete problems may be prohibitively expensive. Recent improvements in mixed integer and 0–1 integer programming suggest that this technology may provide the key to efficient, optimal and near–optimal solutions to NP–complete compiler optimization problems. In fact, early results indicate that integer programming formulations may be efficient enough to be included in not only evaluation prototypes, but in production programming environments or even production compilers. This paper discusses the potential benefits of integer programming as a tool to deal with NP–complete compiler optimization formulations in compilers and programming environments.
Compile-Time Cache Performance Prediction and Its Application to Tiling
Authors: Kaplow Wesley K. , Szymanski Boleslaw K. 
Published: October 2003

Tiling has been used by parallelizing compilers to define fine-grain parallel tasks and to optimize cache performance. In this paper we present a novel compile-time technique, called miss-driven cache simulation, for determining loop tile sizes that achieve the highest cache hit-rate. The widening disparity between a processor's peak instruction rate and main memory access time in modern computer systems makes this kind of optimization increasingly important for overall program efficiency. Our simulation technique generates only those references of a loop nest that may generate a cache memory miss and processes them on an architecturally accurate cache model at compile-time. Processing only a small portion of the memory reference trace of a program yields simulation speeds in the millions of memory references per second on workstations, with statistics of misses per reference and inter-reference interference counts gathered at the same time. These simulation speeds and statistics allow for the accurate analysis of the impact of cache optimizations at compile-time. We discuss the results of applying this method to guide loop tiling for such commonly used computational kernels as matrix multiplication and Jacobi iteration for various cache parameters.