bluuebunny/crossref_metadata_2025_split huggingface dataset:
In Vitro Cell-Mediated Immune Responses of Human Immunodeficiency Virus-Infected and -Uninfected Individuals to Whole Cytomegalovirus Antigens and Their Subunits
Authors: Weinberg A. , Spritzler J. , Nokta M. , Schrier R. , Landay A. , Brown D. , Pollard R. 
Published: June 2008

ABSTRACT

The aim of this study was to optimize the ability to detect cytomegalovirus (CMV)-specfic cell-mediated immunity (CMI) in human immunodeficiency virus (HIV)-infected individuals by comparing different assays (the lymphocyte proliferation assay [LPA] and assays for gamma interferon [IFN-γ] and interleukin-2 [IL-2] production) and CMV antigenic preparations. Thresholds discriminating positive from negative CMI results were developed with specimens from 36 CMV-seropositive and 21 CMV-seronegative healthy individuals. The analysis showed that the CMI elicited by any of the four CMV whole lysates tested in this study tended to be more robust and sensitive than the responses to the subunit antigens gB and pp65. LPA and inducible IFN-γ but not IL-2 were highly sensitive measures of CMV-specific CMI in HIV-infected and -uninfected individuals. The ability to detect CMV-specific LPA or IFN-γ responses in HIV-infected individuals significantly increased with higher CD4 cell numbers. Nevertheless, the proportion of HIV-infected subjects with CD4 counts of ≥500 cells/μl who had a detectable CMV-specific CMI remained significantly lower than that of healthy adults. The ability to detect CMV-specific CMI in HIV-infected individuals decreased with higher levels of HIV replication, with discriminative thresholds of 10
3
to 10
4
HIV RNA copies/ml of plasma, for LPA or inducible IFN-γ production elicited by different antigens. The LPA responses obtained with CMV whole lysate and phytohemagglutinin were significantly correlated in HIV-infected subjects but not uninfected controls, indicating a novel characteristic of the CMI defect caused by HIV. The intrasubject variabilities of the CMV-specific CMI were similar in HIV-infected and -uninfected individuals. These data show that LPA and the inducible IFN-γ production elicited by CMV whole lysates may be used to assess modifications of the immune competency of HIV-infected individuals.
Randomized Clinical Trial Assessing the Safety and Immunogenicity of Oral Microencapsulated Enterotoxigenic
Escherichia coli
Surface Antigen 6 with or without Heat-Labile Enterotoxin with Mutation R192G
Authors: Lapa Joyce A. , Sincock Stephanie A. , Ananthakrishnan Madhumita , Porter Chad K. , Cassels Frederick J. , Brinkley Carl , Hall Eric R. , van Hamont John , Gramling Joseph D. , Carpenter Colleen M. , Baqar S. , Tribble David R. 
Published: June 2008

ABSTRACT

An oral, microencapsulated anti-colonization factor 6 antigen (meCS6) vaccine, with or without heat-labile enterotoxin with mutation R192G (LT
R192G
) (mucosal adjuvant), against enterotoxigenic
Escherichia coli
(ETEC) was evaluated for regimen and adjuvant effects on safety and immunogenicity. Sixty subjects were enrolled into a three-dose, 2-week interval or four-dose, 2-day interval regimen. Each regimen was randomized into two equal groups of meCS6 alone (1 mg) or meCS6 with adjuvant (2 μg of LT
R192G
). The vaccine was well tolerated and no serious adverse events were reported. Serologic response to CS6 was low in all regimens (0 to 27%). CS6-immunogloublin A (IgA) antibody-secreting cell (ASC) responses ranged from 36 to 86%, with the highest level in the three-dose adjuvanted regimen; however, the magnitude was low. As expected, serologic and ASC LT responses were limited to adjuvanted regimens, with the exception of fecal IgA, which appeared to be nonspecific to LT administration. Further modifications to the delivery strategy and CS6 and adjuvant dose optimization will be needed before conducting further clinical trials with this epidemiologically important class of ETEC.
Sensitive and Broadly Reactive Reverse Transcription-PCR Assays To Detect Novel Paramyxoviruses
Authors: Tong Suxiang , Chern Shur-Wern Wang , Li Yan , Pallansch Mark A. , Anderson Larry J. 
Published: June 2008

ABSTRACT

We have developed a set of reverse transcription-PCR assays for the detection and identification of known and novel paramyxoviruses in clinical specimens. Primers were designed from the conserved motifs of the polymerase
pol
gene sequences to detect members of the
Paramyxovirinae
or
Pneumovirinae
subfamily or groups of genera within the
Paramyxovirinae
subfamily. The consensus-degenerate hybrid oligonucleotide primer design and seminested or nested PCR assay design were used to enhance the breadth of reactivity and sensitivity of the respective assays. Using expressed RNA and 10-fold dilution series of virus-infected tissue culture isolates from different members of the family or genera, these assays were able to detect on average between 100 and 500 copies of template RNA. The assays were specific to the respective group of genera or subfamily viruses. This set of primers enhances our ability to look for novel viruses in outbreaks and diseases of unknown etiology.
Cord Formation in a Clinical Isolate of
Mycobacterium marinum
Authors: Staropoli John F. , Branda John A. 
Published: June 2008

ABSTRACT

Cord formation is a characteristic property of the cultured
Mycobacterium tuberculosis
complex species. We describe a case of
Mycobacterium marinum
demonstrating robust cord formation. Nontuberculous mycobacteria can form true cords in broth culture but do so rarely, despite the fact that many species contain the cell wall glycolipid that mediates cord formation.
Evaluation and Validation of a PulseNet Standardized Pulsed-Field Gel Electrophoresis Protocol for Subtyping
Vibrio parahaemolyticus
: an International Multicenter Collaborative Study
Authors: Kam Kai Man , Luey Cindy K. Y. , Parsons Michele B. , Cooper Kara L. F. , Nair G. B. , Alam M. , Islam M. Atiqul , Cheung Danny T. L. , Chu Y. W. , Ramamurthy T. , Pazhani G. P. , Bhattacharya S. K. , Watanabe H. , Terajima J. , Arakawa E. , Ratchtrachenchai O.-A. , Huttayananont S. , Ribot Efrain M. , Gerner-Smidt Peter , Swaminathan Bala 
Published: June 2008

ABSTRACT

The pandemic spread of
Vibrio parahaemolyticus
is an international public health issue. Because of the outbreak potential of the organism, it is critical to establish an internationally recognized molecular subtyping protocol for
V. parahaemolyticus
that is both rapid and robust as a means to monitor its further spread and to guide control measures in combination with epidemiologic data. Here we describe the results of a multicenter, multicountry validation of a new PulseNet International standardized
V. parahaemolyticus
pulsed-field gel electrophoresis (PFGE) protocol. The results are from a composite analysis of 36 well-characterized
V. parahaemolyticus
isolates from six participating laboratories, and the isolates represent predominant serotypes and various genotypes isolated from different geographic regions and time periods. The discriminatory power is very high, as 34 out of 36 sporadic
V. parahaemolyticus
strains tested fell into 34 distinguishable PFGE groups when the data obtained with two restriction enzymes (SfiI and NotI) were combined. PFGE was further able to cluster members of known pandemic serogroups. The study also identified quality measures which may affect the performance of the protocol. Nonadherence to the recommended procedure may lead to high background in the PFGE gel patterns, partial digestion, and poor fragment resolution. When these quality measures were implemented, the PulseNet
V. parahaemolyticus
protocol was found to be both robust and reproducible among the collaborating laboratories.
Multicenter Evaluation of the New Vitek 2
Neisseria
-
Haemophilus
Identification Card
Authors: Rennie Robert P. , Brosnikoff Cheryl , Shokoples Sandy , Reller L. Barth , Mirrett Stanley , Janda William , Ristow Kathy , Krilcich Ann 
Published: June 2008

ABSTRACT

The new
Neisseria-Haemophilus
identification (NH) card for Vitek 2 was compared with 16S rRNA gene sequencing (16S) as the reference method for accurate identification of
Neisseria
spp.,
Haemophilus
spp., and other fastidious gram-negative bacteria. Testing was performed on the Vitek 2 XL system with modified software at three clinical trial laboratories. Reproducibility was determined with nine ATCC quality control strains tested 20 times over a minimum of 10 days at all three sites. A challenge set of 30 strains with known identifications and 371 recent fresh and frozen clinical isolates were also tested. Expected positive and negative biochemical reactions were also evaluated for substrate reproducibility. All microorganisms were tested on the NH card, and all clinical and stock isolates were saved for 16S testing. All reproducibility tests yielded expected results within a 95% confidence interval. For challenge microorganisms, there was 98% overall correct identification, including 8% low discrimination, 2% incorrect identification, and 0% unidentified. For clinical strains, there was 96.5% overall correct identification, including 10.2% low discrimination, 2.7% incorrect identification, and 0.8% unidentified. The 2.7% (10/371) of clinical isolates that gave an incorrect identification consisted of 7 isolates correct to genus and 3 strains incorrect to genus. There were an additional 27 strains (primarily
Neisseria
species) for which the 16S identification result was different from the NH card result. These were all unclaimed species by the system. The new NH card met all performance criteria within a 95% confidence interval compared to identification of clinical isolates by 16S.
Correlation of MIC with Outcome for
Candida
Species Tested against Caspofungin, Anidulafungin, and Micafungin: Analysis and Proposal for Interpretive MIC Breakpoints
Authors: Pfaller M. A. , Diekema D. J. , Ostrosky-Zeichner L. , Rex J. H. , Alexander B. D. , Andes D. , Brown S. D. , Chaturvedi V. , Ghannoum M. A. , Knapp C. C. , Sheehan D. J. , Walsh T. J. 
Published: June 2008

ABSTRACT

The CLSI Antifungal Subcommittee followed the M23-A2 “blueprint” to develop interpretive MIC breakpoints for anidulafungin, caspofungin, and micafungin against
Candida
species. MICs of ≤2 μg/ml for all three echinocandins encompass 98.8 to 100% of all clinical isolates of
Candida
spp. without bisecting any species group and represent a concentration that is easily maintained throughout the dosing period. Data from phase III clinical trials demonstrate that the standard dosing regimens for each of these agents may be used to treat infections due to
Candida
spp. for which MICs are as high as 2 μg/ml. An MIC predictive of resistance to these agents cannot be defined based on the data from clinical trials due to the paucity of isolates for which MICs exceed 2 μg/ml. The clinical data set included only three isolates from patients treated with an echinocandin (caspofungin) for which the MICs were >2 μg/ml (two
C. parapsilosis
isolates at 4 μg/ml and one
C. rugosa
isolate at 8 μg/ml). Based on these data, the CLSI subcommittee has decided to recommend a “susceptible only” breakpoint MIC of ≤2 μg/ml due to the lack of echinocandin resistance in the population of
Candida
isolates thus far. Isolates for which MICs exceed 2 μg/ml should be designated “nonsusceptible” (NS). For strains yielding results suggestive of an NS category, the organism identification and antimicrobial-susceptibility test results should be confirmed. Subsequently, the isolates should be submitted to a reference laboratory that will confirm the results by using a CLSI reference dilution method.
European Emergence of Ciprofloxacin-Resistant
Escherichia coli
Clonal Groups O25:H4-ST 131 and O15:K52:H1 Causing Community-Acquired Uncomplicated Cystitis
Authors: Cagnacci Simone , Gualco Laura , Debbia Eugenio , Schito Gian Carlo , Marchese Anna 
Published: June 2008

ABSTRACT

A total of 148
E. coli
strains displaying reduced susceptibility to ciprofloxacin (MIC ≥ 2 μg/ml) and causing uncomplicated urinary tract infections in eight European countries during 2003 to 2006 were studied. Their phylogenetic groups, biochemical profiles, and antibiotic susceptibilities were determined. Determination of the O:H serotype, pulsed-field gel electrophoresis (PFGE), randomly amplified polymorphic DNA (RAPD) PCR, and multilocus sequence typing provided additional discrimination. The majority (82.4%) of the microorganisms (122/148) carried resistance to two or more additional drugs, with the pattern ciprofloxacin-trimethoprim-sufamethoxazole-tetracycline-ampicillin being the most represented (73 strains out of 148; 49.3%). Extended-spectrum beta-lactamase production was detected in 12/148 strains (8.1%), with CTX-M-15 being the most-common enzyme. Six strains out of the whole collection studied (4.0%) contained a
qnrB
-like gene. Overall, 55 different PFGE or RAPD PCR profiles could be distinguished, indicating a substantial heterogeneity. However, about one-third (51/148) of the strains belonged to two clonal groups: O15:K52:H1 (phylogenetic group B2, lactose-nonfermenting variant, ciprofloxacin MIC of 16 μg/ml) and O25:H4 sequence type 131 (ST-131) (phylogenetic group D, ciprofloxacin MIC of ≥32 μg/ml). With the exception of Poland, strains of these two groups were isolated in samples from all participating countries but more frequently in samples from Spain and Italy. In some representative strains of the two main clonal groups, alterations in GyrA and ParC were the basic mechanism of fluoroquinolone resistance. In some members of the O25:H4 ST-131 group, displaying a ciprofloxacin MIC of >32 μg/ml, additional OmpF loss or pump efflux overexpression was found. In the Mediterranean area, strains belonging to these two clonal groups played a major role in determining the high rate of fluoroquinolone-resistant
E. coli
strains observed in the community.
Single-Step PCR Using (GACA)
4
Primer: Utility for Rapid Identification of Dermatophyte Species and Strains
Authors: Shehata Atef S. , Mukherjee Pranab K. , Aboulatta Hassan N. , El Akhras Atef I. , Abbadi Said H. , Ghannoum Mahmoud A. 
Published: June 2008

ABSTRACT

Dermatophytes are fungi that belong to three genera:
Epidermophyton, Microsporum
, and
Trichophyton
. Identification of dermatophyte species is essential for appropriate diagnosis and treatment of dermatophytosis. Routine identification depends on macroscopic and microscopic morphology, which is time-consuming and does not identify dermatophyte strains. In this study, two PCR-based methods were compared for their abilities to identify 21 dermatophyte isolates obtained from Egyptian patients to the species and strain levels. The first method employed a two-step method: PCR amplification, using ITS1 and ITS4 as primers, followed by restriction enzyme digestion using the endonuclease MvaI. The second method employed a one-step approach employing the repetitive oligonucleotide (GACA)
4
as a primer. Dermatophyte strains were also identified using a conventional culture method. Our results showed that the conventional culture method identified four species:
Microsporum canis, Trichophyton mentagrophytes, Trichophyton rubrum
, and
Trichophyton violaceum
. Moreover, both PCR methods agreed with the diagnosis made using the conventional approach. Furthermore, ITS1/ITS4-based PCR provided no strain differentiation, while (GACA)
4
-based PCR identified different varieties among the
T. mentagrophytes
isolates. Taken together, our results suggest that (GACA)
4
-based PCR has utility as a simple and rapid method for identification of dermatophyte species as well as utility for differentiation of
T. mentagrophytes
variants.
Human Papillomavirus Genotype Specificity of Hybrid Capture 2
Authors: Castle Philip E. , Solomon Diane , Wheeler Cosette M. , Gravitt Patti E. , Wacholder Sholom , Schiffman Mark 
Published: June 2008

ABSTRACT
Hybrid Capture 2 (hc2), a clinical test for carcinogenic human papillomavirus (HPV) DNA, has proven to be a sensitive but only modestly specific predictor of cervical precancer and cancer risk. Some of its nonspecificity for clinical end points can be ascribed to cross-reactivity with noncarcinogenic HPV genotypes. However, the reference genotyping tests that have been used for these comparisons are also imperfect. We therefore sought to describe further the HPV genotype specificity of hc2 by comparing the hc2 results to paired results from two related PGMY09/11 L1 primer-based HPV genotyping assays: Linear Array (LA) and its prototype predecessor, the line blot assay (LBA). LA and LBA results were considered separately and combined (detection by either assay or both assays) for 37 individual HPV genotypes and HPV risk group categories (carcinogenic HPV > noncarcinogenic HPV > negative). Baseline specimens from 3,179 of 3,488 (91.5%) women referred to ALTS (a clinical trial to evaluate the management strategies for women with atypical squamous cells of undetermined significance [ASCUS] or low-grade squamous intraepithelial lesions) because of an ASCUS Papanicolaou smear were tested by all three assays. Among single-genotype infections with genotypes targeted by hc2 as detected by either PCR assay, HPV genotype 35 (HPV35) (86.4%), HPV56 (84.2%), and HPV58 (76.9%) were the most likely to test positive by hc2. Among single-genotype infections with genotypes not targeted by hc2 as detected by either assay, HPV82 (80.0%), HPV66 (60.0%) (recently classified as carcinogenic), HPV70 (59.1%), and HPV67 (56.3%) were the most likely to test positive by hc2. Among women who tested negative for carcinogenic HPV by both PCR tests and were positive for noncarcinogenic HPV by either test, 28% of women were hc2 positive. Conversely, 7.8% of all hc2-positive results in this population were due to cross-reactivity of hc2 with untargeted, noncarcinogenic HPV genotypes. In conclusion, hc2 cross-reacts with certain untargeted, noncarcinogenic HPV genotypes that are phylogenetically related to the targeted genotypes, but the degree of cross-reactivity may be less than previously reported.
Purulent Pericarditis with Greenish Pericardial Effusion Caused by
Shewanella algae
Authors: Tan Che-Kim , Lai Chih-Cheng , Kuar Wei-Khie , Hsueh Po-Ren 
Published: June 2008

ABSTRACT

We report the first case of purulent pericarditis with greenish pericardial effusion caused by
Shewanella algae
in a patient with gastric and gallbladder cancer. This case expands the reported spectrum of infection caused by
S. algae
and raises the possibility that
S. algae
is a causative pathogen for purulent pericarditis.
Autofluorescence of Mycobacteria as a Tool for Detection of
Mycobacterium tuberculosis
Authors: Patiño Sol , Alamo Lorenzo , Cimino Mena , Casart Yveth , Bartoli Fulvia , García María J. , Salazar Leiria 
Published: June 2008

ABSTRACT

The diagnosis of tuberculosis in developing countries still relies on direct sputum examination by light microscopy, a method that is easy to perform and that is widely applied. However, because of its poor sensitivity and requirement for significant labor and training, light microscopy examination detects the bacilli in only 45 to 60% of all people whose specimens are culture positive for
Mycobacterium tuberculosis
. Therefore, new diagnostic methods that would enable the detection of the undiagnosed infected population and allow the early commencement of antituberculosis treatment are needed. In this work, the potential use of mycobacterial cyan autofluorescence for the detection of
Mycobacterium tuberculosis
was explored. The tubercle bacilli were easily visualized as brilliant fluorescent bacilli by microscopy and were easily tracked ex vivo during macrophage infection. Assays with seeded sputum and a 96-well microplate reader fluorimeter indicated that <10
6
bacilli ml
−1
of sputum could be detected. Moreover, the use of microplates allowed the examination of only 200 μl of sputum per sample without a loss of sensitivity. Treatment with heat or decontaminating chemical agents did not interfere with the autofluorescence assay; on the contrary, they improved the level of bacterial detection. Autofluorescence for the detection of bacilli is rapid and easy to perform compared to other methodologies and can be performed with minimal training, making this method suitable for implementation in developing countries.
CD4 Binding Affinity Determines Human Immunodeficiency Virus Type 1-Induced Alpha Interferon Production in Plasmacytoid Dendritic Cells
Authors: Haupt Sabrina , Donhauser Norbert , Chaipan Chawaree , Schuster Philipp , Puffer Bridget , Daniels Rod S. , Greenough Thomas C. , Kirchhoff Frank , Schmidt Barbara 
Published: June 2008

ABSTRACTPlasmacytoid dendritic cells (PDC) are major producers of type I interferons (IFN) in response to human immunodeficiency virus type 1 (HIV-1) infection. To better define the underlying mechanisms, we studied the magnitude of alpha IFN (IFN-α) induction by recombinant viruses containing changes in the Env protein that impair or disrupt CD4 binding or expressing primaryenvalleles with differential coreceptor tropism. We found that the CD4 binding affinity but not the viral coreceptor usage is critical for the attachment of autofluorescing HIV-1 to PDC and for subsequent IFN-α induction. Our results illustrate the importance of the gp120-CD4 interaction in determining HIV-1-induced immune stimulation via IFN-α production.
Magnitude and Quality of Vaccine-Elicited T-Cell Responses in the Control of Immunodeficiency Virus Replication in Rhesus Monkeys
Authors: Sun Yue , Santra Sampa , Schmitz Jörn E. , Roederer Mario , Letvin Norman L. 
Published: June 2008

ABSTRACT

While a diversity of immunogens that elicit qualitatively different cellular immune responses are being assessed in clinical human immunodeficiency virus vaccine trials, the consequences of those varied responses for viral control remain poorly understood. In the present study, we evaluated the induction of virus-specific T-cell responses in rhesus monkeys using a series of diverse vaccine vectors. We assessed both the magnitude and the functional profile of the virus-specific CD8
+
T cells by measuring gamma interferon, interleukin-2, and tumor necrosis factor alpha production. We found that the different vectors generated virus-specific T-cell responses of different magnitudes and with different functional profiles. Heterologous prime-boost vaccine regimens induced particularly high-frequency virus-specific T-cell responses with polyfunctional repertoires. Yet, immediately after a pathogenic simian-human immunodeficiency virus (SHIV) challenge, no significant differences were observed between these cohorts of vaccinated monkeys in the magnitudes or the functional profiles of their virus-specific CD8
+
T cells. This finding suggests that the high viral load shapes the functional repertoire of the cellular immune response during primary infection. Nevertheless, in all vaccination regimens, higher frequency and more polyfunctional vaccine-elicited virus-specific CD8
+
T-cell responses were associated with better viral control after SHIV challenge. These observations highlight the contributions of both the quality and the magnitude of vaccine-elicited cellular immune responses in the control of immunodeficiency virus replication.