bluuebunny/crossref_metadata_2025_split huggingface dataset:
Persistent Replication of Human Immunodeficiency Virus Type 1 despite Treatment of Pulmonary Tuberculosis in Dually Infected Subjects
Authors: Kizza Harriet Mayanja , Rodriguez Benigno , Quinones-Mateu Miguel , Mirza Muneer , Aung Htin , Yen-Lieberman Belinda , Starkey Colleen , Horter Libby , Peters Pierre , Baseke Joy , Johnson John L. , Toossi Zahra 
Published: November 2005

ABSTRACTTuberculosis (TB) is the most common life-threatening infection in human immunodeficiency virus (HIV)-infected persons and frequently occurs before the onset of severe immunodeficiency. Development of TB is associated with increased HIV type 1 (HIV-1) viral load, a fall in CD4 lymphocyte counts, and increased mortality. The aim of this study was to examine how treatment of pulmonary TB affected HIV-1 activity in HIV-1/TB-coinfected subjects with CD4 cell counts of >100 cells/μl. HIV-1/TB-coinfected subjects were recruited in Kampala, Uganda, and were monitored over time. Based upon a significant (0.5 log10copies/ml) decrease in viral load by the end of treatment, two patient groups could be distinguished. Responders (n= 17) had more rapid resolution of anemia and pulmonary lesions on chest radiography during TB treatment. This group had a significant increase in viral load to levels not different from those at baseline 6 months after completion of TB treatment. HIV-1 viral load in nonresponders (n= 10) with TB treatment increased and at the 6 month follow-up was significantly higher than that at the time of diagnosis of TB. Compared to baseline levels, serum markers of macrophage activation including soluble CD14 decreased significantly by the end of TB treatment in responders but not in nonresponders. These data further define the impact of pulmonary TB on HIV-1 disease. HIV-1 replication during dual HIV-1/TB infection is not amenable to virologic control by treatment of TB alone. Concurrent institution of highly active antiretroviral treatment needs to be evaluated in patients dually infected with pulmonary TB and HIV-1.
Immunological Markers of the R4 Protein of
Streptococcus agalactiae
Authors: Maeland Johan A. , Bevanger Lars , Lyng Randi Valsoe 
Published: November 2005

ABSTRACT

This study focuses on immunological markers of R4, an important
Streptococcus
group B (GBS) protein. The results obtained by using rabbit antisera and purified proteins for antigens in enzyme-linked immunosorbent assay-based experiments provided evidence that R4 possesses two antigenic determinants. One of the determinants is shared with the alpha-like protein 3 (Alp3) of GBS, was named R4/Alp3 common, and was expressed by GBS, which possessed the Alp3-encoding gene
alp3
or the R4-encoding gene
rib
. The other antigenic determinant was detected only in
rib
-positive GBS organisms and was named R4 specific. This determinant probably is an immunological marker unique to the R4 protein. Neither of the antigenic R4 determinants showed serological cross-reactivity with the GBS proteins Cα, Cβ, and R3 or with alpha-like protein 2. Of 60 clinical serotype III GBS strains, 56 (93%) isolates possessed the
rib
gene and 50 (89%) of the
rib
-positive isolates expressed levels of R4 detectable by antibody-based tests, consistent with R4 expression failure or low-level expression in ∼10% of
rib
-positive GBS.
alp3
was not detected in type III GBS but was possessed by six of eight type V strains and six of six type VIII strains. All
alp3
-positive strains were recognized by the R4/Alp3 common antibodies, but none of them were recognized by the R4-specific antibodies. NCTC 9828, a reference strain for R3 and R4, expressed the determinant R4/Alp3 common but not R4 specific. A monoclonal R4 antibody, previously considered to be R4 specific and used in GBS serotyping, targeted R4/Alp3 common and is thus not R4 specific. The results show that failure to discriminate between R4 specific and R4/Alp3 common by antisera designed for GBS serotyping can result in the false identification of Alp3 as R4 or vice versa, whereas anti-R4 antibodies targeting only the determinant R4 specific will detect only R4. Both R4 and Alp3 need further evaluation with respect to the immunobiological function of each distinct antigenic determinant, for instance, with regard to their potential as GBS vaccine components.
Selected RD1 Peptides for Active Tuberculosis Diagnosis: Comparison of a Gamma Interferon Whole-Blood Enzyme-Linked Immunosorbent Assay and an Enzyme-Linked Immunospot Assay
Authors: Goletti Delia , Vincenti Donatella , Carrara Stefania , Butera Ornella , Bizzoni Federica , Bernardini Giuliana , Amicosante Massimo , Girardi Enrico 
Published: November 2005

ABSTRACT

We recently set up a gamma interferon (IFN-γ) enzyme-linked immunospot assay (ELISPOT), using selected early secreted antigenic target 6 (ESAT-6) peptides, that appears specific for active tuberculosis (A-TB). However, ELISPOT is difficult to automate. Thus, the objective of this study was to determine if the same selected peptides may be used in a technique more suitable for routine work in clinical laboratories, such as whole-blood enzyme-linked immunosorbent assay (WBE). For this purpose, 27 patients with A-TB and 41 control patients were enrolled. Our WBE, using the already described selected peptides from ESAT-6 plus three new ones from culture filtrate protein 10, was performed, and data were compared with those obtained by ELISPOT. Using our selected peptides, IFN-γ production, evaluated by both WBE and ELISPOT, was significantly higher in patients with A-TB than in controls (
P
< 0.0001). Statistical analysis showed a good correlation between the results obtained by WBE and ELISPOT (
r
= 0.80,
P
< 0.001). To substantiate our data, we compared our WBE results with those obtained by QuantiFERON-TB Gold, a whole-blood assay based on region of difference 1 (RD1) overlapping peptides approved for TB infection diagnosis. We observed a slightly higher sensitivity with QuantiFERON-TB Gold than with our WBE (89% versus 81%); however, our test provided a better specificity result (90% versus 68%). In conclusion, results obtained by WBE based on selected RD1 peptides significantly correlate with those generated by ELISPOT. Moreover, our assay appears more specific for A-TB diagnosis than QuantiFERON-TB Gold, and thus it may represent a complementary tool for A-TB diagnosis for routine use in clinical laboratories.
Serological Responses in Patients with Severe Acute Respiratory Syndrome Coronavirus Infection and Cross-Reactivity with Human Coronaviruses 229E, OC43, and NL63
Authors: Chan K. H. , Cheng V. C. C. , Woo P. C. Y. , Lau S. K. P. , Poon L. L. M. , Guan Y. , Seto W. H. , Yuen K. Y. , Peiris J. S. M. 
Published: November 2005

ABSTRACT

The serological response profile of severe acute respiratory syndrome (SARS) coronavirus (CoV) infection was defined by neutralization tests and subclass-specific immunofluorescent (IF) tests using serial sera from 20 patients. SARS CoV total immunoglobulin (Ig) (IgG, IgA, and IgM [IgGAM]) was the first antibody to be detectable. There was no difference in time to seroconversion between the patients who survived (
n
= 14) and those who died (
n
= 6). Although SARS CoV IgM was still detectable by IF tests with 8 of 11 patients at 7 months postinfection, the geometric mean titers dropped from 282 at 1 month postinfection to 19 at 7 months (
P
= 0.001). In contrast, neutralizing antibody and SARS CoV IgGAM and IgG antibody titers remained stable over this period. The SARS CoV antibody response was sometimes associated with an increase in preexisting IF IgG antibody titers for human coronaviruses OC43, 229E, and NL63. There was no change in IF IgG titer for virus capsid antigen from the herpesvirus that was used as an unrelated control, Epstein-Barr virus. In contrast, patients who had OC43 infections, and probably also 229E infections, without prior exposure to SARS CoV had increases of antibodies specific for the infecting virus but not for SARS CoV. There is a need for awareness of cross-reactive antibody responses between coronaviruses when interpreting IF serology.
Comparison of Galactomannan Detection, PCR-Enzyme-Linked Immunosorbent Assay, and Real-Time PCR for Diagnosis of Invasive Aspergillosis in a Neutropenic Rat Model and Effect of Caspofungin Acetate
Authors: Scotter Jennifer M. , Chambers Stephen T. 
Published: November 2005

ABSTRACT

The performance of different in vitro diagnostic tests for the diagnosis of invasive aspergillosis (IA) was investigated in a transiently neutropenic rat model. Rats were immunosuppressed with cyclophosphamide and then inoculated intravenously with 1.5 × 10
4
CFU
Aspergillus fumigatus
spores. Animals were then either treated with caspofungin acetate, 1 mg/kg/day for 7 days, or not treated. PCR-enzyme-linked immunosorbent assay (ELISA), real-time PCR, and galactomannan (GM) detection were performed on postmortem blood samples, along with culture of liver, lung, and kidney homogenate. Caspofungin-treated animals showed a decrease in residual tissue burden of
A. fumigatus
from organ homogenate compared to untreated animals (
P
< 0.002). PCR-ELISA returned positive results for 11/17 animals treated with antifungal agents and for 10/17 untreated animals. Galactomannan was positive in 8/17 caspofungin-treated animals and 4/17 untreated animals. Real-time PCR was positive in 2/17 treated and 3/17 untreated animals. This study demonstrates that PCR-ELISA is a more sensitive test than either GM detection (
P
= 0.052) or real-time PCR (
P
< 0.01) for diagnosis of IA but that any of the three tests may return false-negative results in cases of histologically proven disease. Galactomannan indices from animals treated with antifungal agents showed a trend (
P
= 0.1) towards higher levels than those of untreated animals, but no effect was observed with PCR-ELISA indices (
P
= 0.29). GM detection, as previously described, may be enhanced by the administration of caspofungin, but PCR-ELISA appears not to be affected in the same way. We conclude that PCR-ELISA is a more sensitive and reliable method for laboratory diagnosis of IA.
Isolation and Characterization of the Promoter and Partial Enhancer Region of the Porcine Inter-α-Trypsin Inhibitor Heavy Chain 4 Gene
Authors: Harraghy Niamh , Mitchell Timothy J. 
Published: November 2005

ABSTRACT
A porcine genomic library was screened for clones containing the promoter of the major acute-phase protein in pigs, inter-α-trypsin heavy chain 4 (ITIH4). Following isolation of the promoter, a functional analysis was performed with Hep3B cells. The promoter was induced by interleukin-6 (IL-6) but not by IL-1β. However, IL-1β was shown to inhibit the IL-6-induced activation of the porcine ITIH4 promoter.
Immunogenicity of Fowlpox Virus Expressing the Avian Influenza Virus H5 Gene (TROVAC AIV-H5) in Cats
Authors: Karaca Kemal , Swayne David E. , Grosenbaugh Deborah , Bublot Michel , Robles Amy , Spackman Erica , Nordgren Robert 
Published: November 2005

ABSTRACT
Vaccination of cats with fowlpox virus expressing the avian influenza (AI) virus H5 hemagglutinin gene (TROVAC AI) resulted in detectable hemagglutination inhibition (HI) antibody responses to the homologous A/Turkey/Ireland/1378/83 (H5N8) (A/tky/Ire/83) AI virus antigen. The HI antibody responses to heterologous A/Chicken/Indonesia/7/03 (H5N1) (A/ck/Indonesia/03) AI virus antigen were also detected in all vaccinated cats, but only after booster vaccinations. The vaccine described in this study and other poxvirus-vectored vaccines may be of value for the prophylaxis of AI virus-associated morbidity and mortality in mammals.
Detection ofBabesia canis rossi,B. canis vogeli, andHepatozoon canisin Dogs in a Village of Eastern Sudan by Using a Screening PCR and Sequencing Methodologies
Authors: Oyamada Maremichi , Davoust Bernard , Boni Mickaël , Dereure Jacques , Bucheton Bruno , Hammad Awad , Itamoto Kazuhito , Okuda Masaru , Inokuma Hisashi 
Published: November 2005

ABSTRACTBabesiaandHepatozooninfections of dogs in a village of eastern Sudan were analyzed by using a single PCR and sequencing. Among 78 dogs, 5 were infected withBabesia canis rossiand 2 others were infected withB. canis vogeli. Thirty-three dogs were positive forHepatozoon. Hepatozoon caniswas detected by sequence analysis.
FORMAL METHOD FOR AUTOMATED TRANSFORMATION OF LOTOS SPECIFICATIONS TO ESTELLE SPECIFICATIONS
Authors: EL-GENDY HAZEM , EL-KADHI NABIL 
Published: November 2005

ISO and IEC have jointly developed two Formal Description Techniques (FDTs) for specifying distributed real time systems such as computer/telecommunications protocols. These are Lotos and Estelle. In this paper, a formal method for automated transformation of a Lotos specification to an Estelle specification is presented. The method is applicable to various Lotos specification styles and to various communications protocols of ISO OSI layers. Our method has applications in conformance testing of such systems and building common semantic model for the various FDTs. In this paper, we develop an algorithm for constructing a 'Data Oriented'-Restricted Behavior Tree T that represent both the control flow aspects and the data flow aspects of the system. Then, we develop an algorithm for constructing the Estelle specifications from T. A minimization rule is also developed to optimize the size of the Estelle specification by reducing both the number of states and the number of transitions.
Model driven development with Ada
Authors: Lapping Andy 
Published: November 2005

System and software development has become an increasingly complex science. With so many emerging devices, processors, systems specification languages, software implementation languages, and tools for all of these, there needs to be a common denominator in the development process that brings focus back on the application. Model-Driven Development (MDD) based on the UML has emerged as the preferred approach by a growing number of systems engineers and software developers for addressing this growing complexity. The UML has proven to be the standard visual representation language capable of providing both systems and software teams with a coherent set of interchangeable artefacts that fully describe an application with rich enough specification to be able to design and implement it in Ada.
This paper examines the pros and cons of a Model Based Approach, the problems that might be encountered and some possible solutions.
The CAP project - an interim evaluation
Authors: Needham R. M. 
Published: November 2005

The CAP project has included the design and construction of a computer with an unusual and very detailed structure of memory protection, and subsequently the development of an operating system which fully exploits the protection facilities. The present paper passes the work in review and draws conclusions about good and bad aspects of the system. The basic architecture of the CAP machine is described in [1] and a largely prospective description of the protection system is given in [2].
The project was started as an experiment in hardware memory protection. A computer was to be designed in which operating system development was easy, in which ruggedness was produced by a much more fine-grained network of firewalls than was (or is) usual, and in which the full range of protection facilities was available to the writers of subsystems. Simplicity of mechanism was a very important goal, although some emphasis was placed on flexibility of protection policy.
Measurements of sharing in Multics
Authors: Montgomery Warren A. 
Published: November 2005

There are many good arguments for implementing information systems as distributed systems. These arguments depend on the extent to which interactions between machines in the distributed implementation can be minimized. Sharing among users of a computer utility is a type of interaction that may be difficult to provide in a distributed system.
This paper defines a number of parameters that can be used to characterize such sharing. This paper reports measurements that were made on the M.I.T. Multics system in order to obtain estimates of the values of these parameters for that system. These estimates are upper bounds on the amount of sharing and show that although Multics was designed to provide active sharing among its users, very little sharing actually takes place. Most of the sharing that does take place is sharing of system programs, such as the compilers and editors.
Design and verification of secure systems
Authors: Rushby J. M. 
Published: November 2005

This paper reviews some of the difficulties that arise in the verification of kernelized secure systems and suggests new techniques for their resolution.
It is proposed that secure systems should be conceived as distributed systems in which security is achieved partly through the physical separation of its individual components and partly through the mediation of trusted functions performed within some of those components. The purpose of a security kernel is simply to allow such a 'distributed' system to actually run within a single processor; policy enforcement is not the concern of a security kernel.
This approach decouples verification of components which perform trusted functions from verification of the security kernel. This latter task may be accomplished by a new verification technique called 'proof of separability' which explicitly addresses the security relevant aspects of interrupt handling and other issues ignored by present methods.
A comparison of two network-based file servers
Authors: Mitchell James G. , Dion Jeremy 
Published: November 2005

This paper compares two working file servers in terms of their design goals, implementation issues, performance, and service experience. One server, the Xerox Distributed File System (XDFS) [10], was built at the Xerox Palo Alto Research Center; the other, the Cambridge File Server (CFS) [2, 3, 4], was built at the Cambridge University Computer Laboratory.
Both file servers support concurrent random access to files over a network, and each offers an atomic transaction mechanism covering modifications to files.
A reliable object-oriented data repository for a distributed computer system
Authors: Svobodova Liba 
Published: November 2005

The repository described in this paper is a component of a distributed data storage system for a network of many autonomous machines that might run diverse applications. The repository is a server machine that provides very large, very reliable long-term storage for both private and shared data objects. The repository can handle both very small and very large data objects, and it supports atomic update of groups of objects that might be distributed over several repositories. Each object is represented as a history of its states; in the actual implementation, an object is a list of immutable versions.
The core of the repository is stable append-only storage called Version Storage (VS). VS contains the histories of all data objects in the repository as well as all information needed for crash recovery. To maintain the current versions of objects online, a copying scheme was adopted that resembles techniques of real-time garbage collection. VS can be implemented with optical disks.
Sequencing computation steps in a network
Authors: Herbert A. J. , Needham R. M. 
Published: November 2005

It is sometimes necessary in the course of a distributed computation to arrange that a certain set of operations is carried out in the correct order and the correct number of times (typically once). If several sets of operations are performed on different machines on the network there is no obvious mechanism for enforcing such ordering constraints in a fully distributed way. This lack basically stems from the difficulty of preventing copying and repetition of messages by machines and from the impossibility of constraining externally the actions of machines in response to messages that come into their hands.
This paper presents a possible method for ensuring the integrity of sequences of operations on different machines. The technique may be thought of as a means of enabling machines to ensure that requests made of them are valid and timely, not as means of centralized control of services.
Performing remote operations efficiently on a local computer network
Authors: Spector Alfred Z. 
Published: November 2005

This paper discusses communication among computers connected by a very high speed local network and focuses on ways to support distributed programs that require efficient interprocessor communication. It is motivated by the availability of increasingly high speed local networks and inefficiencies in existing communication subsystems.
Mechanisms such as remote procedure calls, monitor calls, and message passing primitives are bases for interprocessor communication at high levels (i.e., within a programming language). At lower levels, interprocessor communication occurs via the transmission of data over some communication medium. On a local network, this basic communication mechanism is the transmission of packets.
This paper is concerned with an intermediate communication layer for high speed local networks. To provide overall efficiency, this layer should provide communication primitives that (1) are a good basis on which to implement high level primitives and (2) are specialized enough to be implemented efficiently; for example, in a combination of microcode and hardware.

To analyze communication primitives for this intermediate layer, we present a communication model called the
remote reference/remote operation
model in which a taxonomy of communication primitives is defined. We illustrate the model by describing an implementation of simple communication primitives on Xerox Alto computers interconnected with a 3 megabit Ethernet.
A study of file sizes and functional lifetimes
Authors: Satyanarayanan M. 
Published: November 2005

The performance of a file system depends strongly on the characteristics of the files stored in it. This paper discusses the collection, analysis and interpretation of data pertaining to files in the computing environment of the Computer Science Department at Carnegie-Mellon University (CMU-CSD). The information gathered from this work will be used in a variety of ways:1. As a data point in the body of information available on file systems.2. As input to a simulation or analytic model of a file system for a local network, being designed and imlemented at CMU-CSD [1].3. As the basis of implementation decisions and parameters for the file system just mentioned.4. As a step toward understanding how a user community creates, maintains and uses files.