bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Performance of the Automated NucliSENS easyMAG and EasyQ Systems versus the Roche AmpliPrep-AMPLICOR Combination for High-Throughput Monitoring of Human Immunodeficiency Virus Load
Authors: Stevens W. , Horsfield P. , Scott L. E. 
Published: February 2007

ABSTRACT

This study presents the data of an evaluation of the automated Nuclisens easyMAG and EasyQ systems versus the Roche AmpliPrep-AMPLICOR combination for testing of high-volume human immunodeficiency virus (HIV) load. This represents a follow-up of a previous study investigating the performance of the real-time Nuclisens assay using the semiautomated NucliSENS miniMAG extraction procedure. Three hundred eighteen patient samples were analyzed using both methods. The easyMAG-EasyQ HIV type 1 system has a higher sensitivity and broader dynamic range than the Cobas AmpliPrep-AMPLICOR system when the standard Roche assay is used alone, 25 to 3,000,000 IU/ml versus 400 to 750,000 HIV RNA copies/ml, respectively. There was significant correlation between the assays (0.93;
P
< 0.0001), with good accuracy (percent similarity mean μ = 96%), good precision (percent similarity standard deviation = 4.97%), and overall good agreement with a low percent similarity coefficient of variation of 5.17 to 6.11%. Bland-Altman analysis revealed that the AMPLICOR assay generated higher values than the EasyQ combination, with 95% of results within clinically acceptable limits. The throughput of samples was greatly improved using the easyMAG-EasyQ system, allowing 144 samples to be processed within 6 h. The potential for contamination has been dramatically reduced using the automated extraction system. Additional negative controls have been added to the kit to monitor for contamination based on the South African experience. This assay thus presents a real option for monitoring HIV load assays in high-volume testing environments.
Evaluation of Microscopic Observation Drug Susceptibility Assay for Detection of Multidrug-Resistant
Mycobacterium tuberculosis
Authors: Shiferaw Girum , Woldeamanuel Yimtubezinash , Gebeyehu Mekdes , Girmachew Feven , Demessie Daniel , Lemma Eshetu 
Published: January 2007

ABSTRACT

Early detection of multidrug-resistant
Mycobacterium tuberculosis
(MDR-TB) is of primary importance for both patient management and infection control. Optimal methods for identifying drug-resistant
Mycobacterium tuberculosis
in a timely and affordable way in resource-limited settings are not yet available. This study prospectively evaluated a low-technology but rapid drug susceptibility testing method, the microscopic observation drug susceptibility assay (MODS), in the concurrent detection of
M. tuberculosis
and its susceptibilities to isoniazid and rifampin (two drugs defining multidrug-resistant
M. tuberculosis
) directly from sputum specimens. Sputum samples were collected from 262 smear-positive TB patients in Addis Ababa, Ethiopia. To undertake MODS, 100 μl of decontaminated samples was inoculated into a 24-well plate containing 1 ml of 7H9 broth with and without appropriate drugs. The assay uses an inverted-light microscope to detect characteristic mycobacterial growth in liquid culture. Of 262 smear-positive patients, MODS detected 254 (96.9%) and culture in Löwenstein-Jensen medium detected 247 (94.3%) (
P
= 0.016). For the 247 cultures, the sensitivity, specificity, and accuracy of MODS for detecting MDR-TB were 92.0, 99.5, and 98.8%, respectively, using the method of proportion as a reference (concordance, 98.8%; kappa value, 0.932). Results for MODS were obtained in a median time of 9 days. MODS is an optimal alternative method for identifying MDR-TB in a timely and affordable way in resource-limited settings.
Molecular Identification of Unusual Pathogenic Yeast Isolates by Large Ribosomal Subunit Gene Sequencing: 2 Years of Experience at the United Kingdom Mycology Reference Laboratory
Authors: Linton Christopher J. , Borman Andrew M. , Cheung Grace , Holmes Ann D. , Szekely Adrien , Palmer Michael D. , Bridge Paul D. , Campbell Colin K. , Johnson Elizabeth M. 
Published: January 2007

ABSTRACT

Rapid identification of yeast isolates from clinical samples is particularly important given their innately variable antifungal susceptibility profiles. We present here an analysis of the utility of PCR amplification and sequence analysis of the hypervariable D1/D2 region of the 26S rRNA gene for the identification of yeast species submitted to the United Kingdom Mycology Reference Laboratory over a 2-year period. A total of 3,033 clinical isolates were received from 2004 to 2006 encompassing 50 different yeast species. While more than 90% of the isolates, corresponding to the most common
Candida
species, could be identified by using the AUXACOLOR2 yeast identification kit, 153 isolates (5%), comprised of 47 species, could not be identified by using this system and were subjected to molecular identification via 26S rRNA gene sequencing. These isolates included some common species that exhibited atypical biochemical and phenotypic profiles and also many rarer yeast species that are infrequently encountered in the clinical setting. All 47 species requiring molecular identification were unambiguously identified on the basis of D1/D2 sequences, and the molecular identities correlated well with the observed biochemical profiles of the various organisms. Together, our data underscore the utility of molecular techniques as a reference adjunct to conventional methods of yeast identification. Further, we show that PCR amplification and sequencing of the D1/D2 region reliably identifies more than 45 species of clinically significant yeasts and can also potentially identify new pathogenic yeast species.
Testing the Interaction between NOD-2 Status and Serological Response toMycobacterium paratuberculosisin Cases of Inflammatory Bowel Disease
Authors: Bernstein Charles N. , Wang Ming-Hsi , Sargent Michael , Brant Steven R. , Collins Michael T. 
Published: January 2007

ABSTRACTIn a population-based case-control study we have previously shown that 14% of healthy Manitobans carry one or two mutations in the NOD-2 locus, a gene highly associated with Crohn's disease (CD). The NOD-2 protein is the receptor responsible for recognition of bacterial peptidoglycans, and it is plausible that NOD-2 is involved in the recognition of mycobacteria. Thirty-seven percent of Manitobans with CD had ≥1 NOD-2 mutation, leading to a threefold increased risk of CD for single-mutant carriers and a 30-fold increased risk for double-mutant carriers. In the same population groups, we assessed the seroprevalence forMycobacterium paratuberculosisand found it to be 35%, with no differences between CD, ulcerative colitis (UC), and controls. Because of high rates of CD and UC in Manitoba, we assessed whether there was an interaction between carrying a NOD-2 mutation andM. paratuberculosisseropositivity. An enzyme-linked immunosorbent assay for serum antibodies toM. paratuberculosisin cattle was adapted for human use. DNA was purified from whole blood. Subjects were genotyped for three NOD-2 variants, G908R, Cins1007fs, and R702W. Multivariate logistic regression analysis showed that NOD-2 gene mutations significantly associated with CD, butM. paratuberculosisserology did not. Furthermore, there was no interaction between NOD-2 mutation status andM. paratuberculosisserology status. For those with the NOD-2 mutation, the likelihood of CD subjects having positiveM. paratuberculosisserology was similar to that of controls (odds ratio, 1.31; 95% confidence interval, 0.55-3.11). No interaction could be proven for UC or by combining CD and UC compared to controls. In conclusion, we could not find an interaction between the NOD-2 genotype andM. paratuberculosisserology in relationship to CD or UC.
International Quality Assurance Study for Characterization ofStreptococcus pyogenes
Authors: Neal Shona , Beall Bernard , Ekelund Kim , Henriques-Normark Birgitta , Jasir Aftab , Johnson Dwight , Kaplan Edward , Lovgren Marguerite , Reinert Ralf Rene ,   Members of the Strep-EURO Study Group and International Streptococcus Reference Laboratories, Efstratiou Androulla 
Published: February 2007

ABSTRACTSurveillance of group A streptococcal (GAS) infections was undertaken as a major component of the European Commission-funded project on severe GAS disease in Europe (strep-EURO). One aim of strep-EURO was to improve the quality of GAS characterization by standardization of methods. An external quality assurance study (EQA) was therefore carried out to evaluate current global performance. Eleven strep-EURO and seven other streptococcal reference centers received a panel of 20 coded GAS isolates for typing. Conventional phenotypic typing (based on cell surface T and M protein antigens and opacity factor [OF] production) and molecular methods (emmgene typing) were used either as single or combined approaches to GAS typing. T typing was performed by 16 centers; 12 centers found one or more of the 20 strains nontypeable (typeability, 89%), and 11 centers reported at least one incorrect result (concordance, 93%). The 10 centers that tested for OF production achieved 96% concordance. Limited availability of antisera resulted in poor typeability values from the four centers that performed phenotypic M typing (41%), three of which also performed anti-OF typing (typeability, 63%); however, concordance was high for both M (100%) and anti-OF (94%) typing. In contrast, the 15 centers that performedemmgene sequencing achieved excellent typeability (97%) and concordance (98%), although comparison of the performance between centers yielded typeability rates from 65 to 100% and concordance values from 83 to 100%. With the rapid expansion and use of molecular genotypic methods to characterize GAS, continuation of EQA is essential in order to achieve international standardization and comparison of type distributions.
Impact of V2 Mutations on Escape from a Potent Neutralizing Anti-V3 Monoclonal Antibody during In Vitro Selection of a Primary Human Immunodeficiency Virus Type 1 Isolate
Authors: Shibata Junji , Yoshimura Kazuhisa , Honda Akiko , Koito Atsushi , Murakami Toshio , Matsushita Shuzo 
Published: January 2007

ABSTRACTKD-247, a humanized monoclonal antibody to an epitope of gp120-V3 tip, has potent cross-neutralizing activity against subtype B primary human immunodeficiency virus type 1 (HIV-1) isolates. To assess how KD-247 escape mutants can be generated, we induced escape variants by exposing bulked primary R5 virus, MOKW, to increasing concentrations of KD-247 in vitro. In the presence of relatively low concentrations of KD-247, viruses with two amino acid mutations (R166K/D167N) in V2 expanded, and under high KD-247 pressure, a V3 tip substitution (P313L) emerged in addition to the V2 mutations. However, a virus with a V2 175P mutation dominated during passaging in the absence of KD-247. Using domain swapping analysis, we demonstrated that the V2 mutations and the P313L mutation in V3 contribute to partial and complete resistance phenotypes against KD-247, respectively. To identify the V2 mutation responsible for the resistance to KD-247, we constructed pseudoviruses with single or double amino acid mutations in V2 and measured their sensitivity to neutralization. Interestingly, the neutralization phenotypes were switched, so that amino acid residue 175 (Pro or Leu) located in the center of V2 was exchanged, indicating that the amino acid at position 175 has a crucial role, dramatically changing the Env oligomeric state on the membrane surface and affecting the neutralization phenotype against not only anti-V3 antibody but also recombinant soluble CD4. These data suggested that HIV-1 can escape from anti-V3 antibody attack by changing the conformation of the functional envelope oligomer by acquiring mutations in the V2 region in environments with relatively low antibody concentrations.
Downregulation of CD4 by Human Immunodeficiency Virus Type 1 Nef Is Dependent on Clathrin and Involves Direct Interaction of Nef with the AP2 Clathrin Adaptor
Authors: Chaudhuri Rittik , Lindwasser O. Wolf , Smith William J. , Hurley James H. , Bonifacino Juan S. 
Published: February 2007

ABSTRACT

Nef, an accessory protein of human and simian immunodeficiency viruses, is a critical determinant of pathogenesis that promotes the progression from infection to AIDS. The pathogenic effects of Nef are in large part dependent on its ability to downregulate the macrophage and T-cell coreceptor, CD4. It has been proposed that Nef induces downregulation by linking the cytosolic tail of CD4 to components of the host-cell protein trafficking machinery. To identify these components, we developed a novel Nef-CD4 downregulation system in
Drosophila melanogaster
S2 cells. We found that human immunodeficiency virus type 1 (HIV-1) Nef downregulates human CD4 in S2 cells and that this process is subject to the same sequence requirements as in human cells. An RNA interference screen targeting protein trafficking genes in S2 cells revealed a requirement for clathrin and the clathrin-associated, plasma membrane-localized AP2 complex in the downregulation of CD4. The requirement for AP2 was confirmed in the human cell line HeLa. We also used a yeast three-hybrid system and glutathione
S
-transferase pull-down analyses to demonstrate a robust, direct interaction between HIV-1 Nef and AP2. This interaction requires a dileucine motif in Nef that is also essential for downregulation of CD4. Together, these results support a model in which HIV-1 Nef downregulates CD4 by promoting its accelerated endocytosis by a clathrin/AP2 pathway.
Understanding frailty
Authors: Lally Frank , Crome Peter 
Published: February 2007

Abstract
The term “frailty” is used loosely to describe a range of conditions in older people, including general debility and cognitive impairment. There is no clear consensus on the definition of frailty; however, it is proposed that frailty comprises a collection of biomedical factors which influences an individual's physiological state in a way that reduces his or her capacity to withstand environmental stresses. Only a subset of older people are at risk of becoming frail; these are vulnerable, prone to dependency and have reduced life expectancy. These health outcomes contribute to an increased demand for medical and social care, and are associated with increased economic costs. As demographic trends indicate a rise in the older population, this healthcare burden will increase. This review aims to encapsulate the current debate surrounding the concept of frailty, with emphasis on proposed definitions of frailty which may be relevant to its identification in the clinical setting.
Early Detection and Rapid Isolation of Leukemia-Reactive Donor T Cells for Adoptive Transfer Using the IFN-γ Secretion Assay
Authors: Jedema Inge , Meij Pauline , Steeneveld Esther , Hoogendoorn Mels , Nijmeijer Bart A. , van de Meent Marian , van Luxemburg-Heijs Simone A.P. , Willemze Roel , Falkenburg J.H. Frederik 
Published: January 2007

Abstract
Purpose: The poor immunogenicity of most leukemias and the lack of specificity of the donor T cells limit the in vivo effectiveness of conventional donor lymphocyte infusions in many patients suffering from persistent or recurrent leukemia after allogeneic stem cell transplantation. These limitations may be overcome by the adoptive transfer of in vitro generated leukemia-reactive T cells. Although the potential clinical efficacy of this approach has been shown previously, lack of reproducibility of the procedure and the inability to show persistence and survival of the transferred T cells hampered further clinical application. The purpose of this study was to develop a new, broadly applicable strategy for the efficient generation and isolation of leukemia-reactive T cells with a better probability to survive and expand in vivo.
Experimental Design: Myeloid and B-cell leukemias were modified into professional immunogenic antigen-presenting cells, and used to stimulate HLA-matched donor T cells. After two stimulations, responding donor T cells were isolated based on their secretion of IFN-γ and tested for their capacity to recognize and kill the primary leukemia.
Results: Using one universal stimulation and isolation protocol for various forms of leukemia, T-cell populations containing high frequencies of leukemia-reactive T cells could reproducibly be generated and early isolated under mild stimulatory conditions. Isolated T cells still had high proliferative potential and their reactivity seemed to be restricted to cells of the patient's hematopoiesis.
Conclusion: We here show a new robust procedure for the generation and isolation of leukemia-reactive T cells for adoptive transfer.
Biological Aspects and Binding Strategies of Vascular Endothelial Growth Factor in Renal Cell Carcinoma
Authors: Rini Brian I. , Rathmell W.Kimryn 
Published: January 2007

AbstractVascular endothelial growth factor (VEGF) is a key mediator in the pathogenesis of renal cell carcinoma (RCC). VEGF is up-regulated in clear cell RCC as a result of loss of the von Hippel-Lindau tumor suppressor gene and subsequent activation of the hypoxia response pathway. VEGF expression drives the migration and proliferation of endothelial cells to support the extensive angiogenesis in RCC. Strategies have been developed to bind and neutralize VEGF and have been investigated in RCC with promising results. Bevacizumab, a VEGF ligand-binding antibody, has shown prolonged time-to-progression versus placebo in treatment-refractory RCC patients and is being investigated currently in multiple RCC settings. VEGF-Trap is also a VEGF binding molecule with ongoing investigation in RCC.
A novel three-dimensional model to quantify metastatic melanoma invasion
Authors: Ghajar Cyrus M. , Suresh Vinod , Peyton Shelly R. , Raub Christopher B. , Meyskens Frank L. , George Steven C. , Putnam Andrew J. 
Published: February 2007

Abstract
Although attempts to develop any viable chemotherapeutic approaches to combat metastatic cancers have largely failed, potential genetic targets to halt metastatic progression continue to be identified. As drugs are developed to address these targets, there is a need for high-throughput systems that accurately reproduce in vivo microenvironments to gauge their efficacy. Accordingly, we have developed a three-dimensional in vitro culture system representative of the environment present upon secondary metastasis to quantitatively measure tumor cell invasion in this setting three-dimensionally. Culturing melanomas of different metastatic capacities within the system showed that each cell type invades the matrix in a manner commensurate to its known metastatic potential in vivo. Moreover, the developed quantitative schemes were put to use to characterize the effect of microenvironmental influences (i.e., matrix components, interstitial cell presence) on planar and vertical melanoma invasion. We propose this novel, quantitative system as a useful tool to assess the effects of pharmacologic and/or microenvironmental influences on tumor cell invasion at a metastatic site. [Mol Cancer Ther 2007;6(2):552–61]
CD44 Regulates Vascular Gene Expression in a Proatherogenic Environment
Authors: Zhao Liang , A. Hall Jason , Levenkova Natasha , Lee Eric , Middleton Melissa K. , Zukas Alicia M. , Rader Daniel J. , Rux John J. , Puré Ellen 
Published: February 2007

Objective—To identify early changes in vascular gene expression mediated by CD44 that promote atherosclerotic disease in apolipoprotein E (apoE)–deficient (apoE−/−) mice.Methods and Results—We demonstrate that CD44 is upregulated and functionally activated in aortic arch in the atherogenic environment of apoE−/− mice relative to wild-type (C57BL/6) controls. Moreover, CD44 activation even in apoE−/− mice is selective to lesion-prone regions because neither the thoracic aorta from apoE−/− mice nor the aortic arch of C57BL/6 mice exhibited upregulation of CD44 compared with thoracic aorta of CD57BL/6 mice. Consistent with these observations, gene expression profiling using cDNA microarrays and quantitative polymerase chain reaction revealed that ≈155 of 19 200 genes analyzed were differentially regulated in the aortic arch, but not in the thoracic aorta, in apoE−/− CD44−/− mice compared with apoE−/− CD44+/+ mice. However, these genes were not regulated by CD44 in the context of a C57BL/6 background, illustrating the selective impact of CD44 on gene expression in a proatherogenic environment. The patterns of differential gene expression implicate CD44 in focal adhesion formation, extracellular matrix deposition, and angiogenesis, processes critical to atherosclerosis.Conclusions—CD44 is an early mediator of atherogenesis by virtue of its ability to regulate vascular gene expression in response to a proatherogenic environment.
Direct Estimation of the Reynolds Stress Vertical Structure in the Nearshore
Authors: Feddersen Falk , Williams A. J. 
Published: January 2007

Abstract
Measurements of the vertical Reynolds stress components in the wave-dominated nearshore are required to diagnose momentum and turbulence dynamics. Removing wave bias from Reynolds stress estimates is critical to a successful diagnosis. Here two existing Reynolds stress estimation methods (those of Trowbridge, and Shaw and Trowbridge) for wave-dominated environments and an extended method (FW) that is a combination of the two are tested with a vertical array of three current meters deployed in 3.2-m water depth off an ocean beach. During the 175-h-long experiment the instruments were seaward of the surfzone and the alongshore current was wind driven. Intercomparison of Reynolds stress methods reveals that the Trowbridge method is wave bias dominated. Tests of the integrated cospectra are used to reject bad Reynolds stress estimates, and the Shaw and Trowbridge estimates are rejected more often than FW estimates. With the FW method, wave bias remains apparent in the cross-shore component of the Reynolds stress. However, the alongshore component of Reynolds stress measured at the three current meters are related to each other with a vertically uniform first EOF containing 73% of the variance, indicating the presence of a constant stress layer. This is the first time the vertical structure of Reynolds stress has been measured in a wave-dominated environment. The Reynolds stress is, albeit weakly, related to the wind stress and a parameterized bottom stress. Using derived wave bias and bottom stress parameterizations, the effect of wave bias on Reynolds stress estimates is shown to be weaker for more typical surfzone conditions (with both stronger waves and currents than those observed here).
Turbulence Anisotropy Determined by Wind Profiler Radar and Its Correlation with Rain Events in Montreal, Canada
Authors: Hocking Anna , Hocking Wayne K. 
Published: January 2007

Abstract
Turbulence inhomogeneities at 3-m scales can be either isotropic or anisotropic, and the degree of anisotropy can be measured with VHF wind profiler radars. Studies over a period of two years in Montreal, Quebec, Canada, have shown that for this site during nonwinter months, the occurrence of isotropic turbulence at 3-m scales serves as a useful diagnostic for the occurrence of rainfall. Turbulent eddies are expected to be most isotropic when wind shears are weak and the atmosphere is either unstable or close to instability. The measurements show that when the turbulence is most isotropic, rainfall is very common. Furthermore, the development of quasi-isotropic turbulence usually occurs before the onset of precipitation. Lead times are typically of the order of 1 to 6 h. Correlation coefficients between the occurrence of strong isotropy and the development of rain generally exceed 0.6, and can be as high as 0.7. Further studies will be required to determine whether this phenomenon is specific to the Montreal area, or can be applied to other locations as well.