bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of Bilateral Bronchoalveolar Lavage for Diagnosis of Ventilator-Associated Pneumonia
Authors: Zaccard Colleen R. , Schell Ronald F. , Spiegel Carol A. 
Published: July 2009

ABSTRACT
Ventilator-associated pneumonia (VAP) is a common nosocomial infection causing significant morbidity and mortality. The goal of this study was to determine the efficacy of bilateral versus unilateral bronchoalveolar lavage (BAL) for the detection of the causative bacterial agents of VAP. We retrospectively studied the quantitative bacterial cultures of 399 BAL sample pairs collected from 287 mechanically ventilated patients over a 5-year period at a U.S. tertiary-care teaching hospital. Trauma was the underlying illness in 69% of patients. No evidence of bacterial infection was found in 226 BAL pairs (56.6%). Among 173 positive BAL sample pairs, significant bacterial counts were detected exclusively in 6.4% of left-lung and 12.1% of right-lung samples. In contrast, 81.5% of positive sample pairs had significant bacterial counts in both lungs. All bacteria recovered at significant concentrations from bilateral samples would have been detected in a unilateral right-lung sample in 89% of positive sample pairs. Unilateral sampling would have failed to recover one or more significant isolates in 11% of positive pairs had only the right lung been sampled and in 16.7% had only the left lung been sampled. Our study shows that preferential sampling of the right lung improves the diagnostic efficacy of unilateral BAL for the detection of the etiologic agents of VAP. If bilateral sampling is performed, our results also indicate that pooling left- and right-lung samples for a single quantitative culture is comparable to processing samples individually.
Evaluation of the Cavidi ExaVir Load Assay (Version 3) for Plasma Human Immunodeficiency Virus Type 1 Load Monitoring
Authors: Greengrass Vicki L. , Plate Megan M. , Steele Pauline M. , Denholm Justin T. , Cherry Catherine L. , Morris Lisa M. , Hearps Anna , Crowe Suzanne M. 
Published: July 2009

ABSTRACT

We evaluated the new low-cost ExaVir Load (version 3) reverse transcriptase viral load assay against the Roche Cobas Amplicor assay. Results for samples tested using the reverse transcriptase assay correlated well with those obtained with the Roche assay (
r
= 0.85;
n
= 202). The version 3 reverse transcriptase assay shows improved sensitivity compared to the previous version.
Airway Infection with a Novel
Cupriavidus
Species in Persons with Cystic Fibrosis
Authors: Kalka-Moll Wiltrud Maria , LiPuma John J. , Accurso Frank J. , Plum Georg , van Koningsbruggen Silke , Vandamme Peter 
Published: July 2009

ABSTRACT

We describe the recovery and identification of a bacterium that represents a new species of the genus
Cupriavidus
from cultures of respiratory tract specimens from two patients with cystic fibrosis (CF). The elucidation of the role of this species in CF lung disease will require an evaluation of a greater number of cases.
Report of Neonatal Meningitis Due to
Salmonella enterica
Serotype Agona and Review of Breast Milk-Associated Neonatal
Salmonella
Infections
Authors: Cooke Fiona J. , Ginwalla Sara , Hampton Michael D. , Wain John , Ross-Russell Robert , Lever Andrew , Farrington Mark 
Published: July 2009

ABSTRACT

We present the first documented case of
Salmonella enterica
serotype Agona meningitis in a 6-day-old baby.
S. enterica
serotype Agona was isolated concurrently from infant cerebrospinal fluid and parental fecal samples, and
Salmonella
was isolated from breast milk. The role of breast milk in transmission of
Salmonella enterica
is discussed.
Assessment of Flocked Swabs for Use in Identification of Streptococcal Pharyngitis
Authors: Goldfarb David M. , Slinger Robert , Tam Ron K. , Barrowman Nicholas , Chan Francis 
Published: July 2009

ABSTRACT
We compared the performance of flocked swabs to that of traditional swabs for culture of beta-hemolytic streptococci in children with pharyngitis. Sensitivity was higher for flocked swabs, but this did not reach statistical significance. We conclude that flocked swabs can be used in place of traditional swabs for diagnosis of streptococcal pharyngitis.
Prevalence and Management of Invalid GeneXpert Enterovirus Results Obtained with Cerebrospinal Fluid Samples: a 2-Year Study
Authors: Sefers Susan E. , Raymer Anna K. , Kilby Jessica T. , Persing David H. , Tang Yi-Wei 
Published: July 2009

ABSTRACTA total of 525 cerebrospinal fluid (CSF) samples submitted during the 2007 and 2008 enteroviral seasons were included in a study to determine the prevalence of and potential risk factors for invalid Cepheid GeneXpert enterovirus assay (GXEA) results, as well as possible solutions for the problem. The invalid GXEA results were reported for 43 (8.2%) specimens and correlated with increased visibility of red blood cells (P< 0.0001) but not with CSF xanthochromia and clotting. Invalid GXEA result rates were markedly diminished by 82.1% and 96.0% and test sensitivities were minimally decreased by 1.7% and 3.6% when these specimens were tested at a 1:5 dilution and after a freeze-thaw cycle, respectively.
Selective Expression of Human Immunodeficiency Virus Nef in Specific Immune Cell Populations of Transgenic Mice Is Associated with Distinct AIDS-Like Phenotypes
Authors: Hanna Zaher , Priceputu Elena , Chrobak Pavel , Hu Chunyan , Dugas Véronique , Goupil Mathieu , Marquis Miriam , de Repentigny Louis , Jolicoeur Paul 
Published: July 2009

ABSTRACTWe previously reported that CD4C/human immunodeficiency virus (HIV)Neftransgenic (Tg) mice, expressing Nef in CD4+T cells and cells of the macrophage/dendritic cell (DC) lineage, develop a severe AIDS-like disease, characterized by depletion of CD4+T cells, as well as lung, heart, and kidney diseases. In order to determine the contribution of distinct populations of hematopoietic cells to the development of this AIDS-like disease, five additional Tg strains expressing Nef through restricted cell-specific regulatory elements were generated. These Tg strains express Nef in CD4+T cells, DCs, and macrophages (CD4E/HIVNef); in CD4+T cells and DCs (mCD4/HIVNefand CD4F/HIVNef); in macrophages and DCs (CD68/HIVNef); or mainly in DCs (CD11c/HIVNef). None of these Tg strains developed significant lung and kidney diseases, suggesting the existence of as-yet-unidentified Nef-expressing cell subset(s) that are responsible for inducing organ disease in CD4C/HIVNefTg mice. Mice from all five strains developed persistent oral carriage ofCandida albicans, suggesting an impaired immune function. Only strains expressing Nef in CD4+T cells showed CD4+T-cell depletion, activation, and apoptosis. These results demonstrate that expression of Nef in CD4+T cells is the primary determinant of their depletion. Therefore, the pattern of Nef expression in specific cell population(s) largely determines the nature of the resulting pathological changes.
Novel Translation Products from Simian Immunodeficiency Virus SIVmac239 Env-Encoding mRNA Contain both Rev and Cryptic T-Cell Epitopes
Authors: Maness Nicholas J. , Sacha Jonah B. , Piaskowski Shari M. , Weisgrau Kimberly L. , Rakasz Eva G. , May Gemma E. , Buechler Matthew B. , Walsh Andrew D. , Wilson Nancy A. , Watkins David I. 
Published: July 2009

ABSTRACTUnderstanding the correlates of immune protection against human immunodeficiency virus and simian immunodeficiency virus (SIV) will require defining the entire cellular immune response against the viruses. Here, we define two novel translation products from the SIVenvmRNA that are targeted by the T-cell response in SIV-infected rhesus macaques. The shorter product is a subset of the larger product, which contains both the first exon of the Rev protein and a translated portion of therevintron. Our data suggest that the translation of viral alternate reading frames may be an important source of T-cell epitopes, including epitopes normally derived from functional proteins.
Upregulation of Interleukin 7 Receptor Alpha and Programmed Death 1 Marks an Epitope-Specific CD8+T-Cell Response That Disappears following Primary Epstein-Barr Virus Infection
Authors: Sauce Delphine , Larsen Martin , Abbott Rachel J. M. , Hislop Andrew D. , Leese Alison M. , Khan Naeem , Papagno Laura , Freeman Gordon J. , Rickinson Alan B. 
Published: July 2009

ABSTRACTIn immunocompetent individuals, the stability of the herpesvirus-host balance limits opportunities to study the disappearance of a virus-specific CD8+T-cell response. However, we noticed that in HLA-A*0201-positive infectious mononucleosis (IM) patients undergoing primary Epstein-Barr virus (EBV) infection, the initial CD8 response targets three EBV lytic antigen-derived epitopes, YVLDHLIVV (YVL), GLCTLVAML (GLC), and TLDYKPLSV (TLD), but only the YVL and GLC reactivities persist long-term; the TLD response disappears within 10 to 27 months. While present, TLD-specific cells remained largely indistinguishable from YVL and GLC reactivities in many phenotypic and functional respects but showed unique temporal changes in two markers of T-cell fate, interleukin 7 receptor alpha (IL-7Rα; CD127) and programmed death 1 (PD-1). Thus, following the antigen-driven downregulation of IL-7Rα seen on all populations in acute IM, in every case, the TLD-specific population recovered expression unusually quickly post-IM. As well, in four of six patients studied, TLD-specific cells showed very strong PD-1 upregulation in the last blood sample obtained before the cells’ disappearance. Our data suggest that the disappearance of this individual epitope reactivity from an otherwise stable EBV-specific response (i) reflects a selective loss of cognate antigen restimulation (rather than of IL-7-dependent signals) and (ii) is immediately preceded, and perhaps mediated, by PD-1 upregulation to unprecedented levels.
RNA-Based Regulation of Transcription and Translation of Aureusvirus Subgenomic mRNA1
Authors: Xu Wei , White K. Andrew 
Published: July 2009

ABSTRACT

Cucumber leaf spot virus
(CLSV) is an aureusvirus (family
Tombusviridae
) that has a positive-sense RNA genome encoding five proteins. During infections, CLSV transcribes two subgenomic (sg) mRNAs and the larger of the two, sg mRNA1, encodes coat protein. Here, the viral RNA sequences and structures that regulate transcription and translation of CLSV sg mRNA1 were investigated. A medium-range RNA-RNA interaction in the CLSV genome, spanning 148 nucleotides, was found to be required for the efficient transcription of sg mRNA1. Further analysis indicated that the structure formed by this interaction acted as an attenuation signal required for transcription of sg mRNA1 via a premature termination mechanism. Translation of coat protein from sg mRNA1 was determined to be facilitated by a 5′-terminal stem-loop structure in the message that resembled a tRNA anticodon stem-loop. The results from mutational analysis indicated that the 5′-terminal stem-loop mediated efficient base pairing with a 3′-cap-independent translational enhancer at the 3′ end of the message, leading to efficient translation of coat protein from sg mRNA1. Comparison of the regulatory RNA structures for sg mRNA1 of CLSV to those used by the closely related tombusviruses and certain cellular RNAs revealed interesting differences and similarities that provide evolutionary and mechanistic insights into RNA-based regulatory strategies.
Genetic Inactivation of Poliovirus Infectivity by Increasing the Frequencies of CpG and UpA Dinucleotides within and across Synonymous Capsid Region Codons
Authors: Burns Cara C. , Campagnoli Ray , Shaw Jing , Vincent Annelet , Jorba Jaume , Kew Olen 
Published: July 2009

ABSTRACT
Replicative fitness of poliovirus can be modulated systematically by replacement of preferred capsid region codons with synonymous unpreferred codons. To determine the key genetic contributors to fitness reduction, we introduced different sets of synonymous codons into the capsid coding region of an infectious clone derived from the type 2 prototype strain MEF-1. Replicative fitness in HeLa cells, measured by plaque areas and virus yields in single-step growth experiments, decreased sharply with increased frequencies of the dinucleotides CpG (suppressed in higher eukaryotes and most RNA viruses) and UpA (suppressed nearly universally). Replacement of MEF-1 capsid codons with the corresponding codons from another type 2 prototype strain (Lansing), a randomization of MEF-1 synonymous codons, increased the %G+C without increasing CpG, and reductions in the effective number of codons used had much smaller individual effects on fitness. Poliovirus fitness was reduced to the threshold of viability when CpG and UpA dinucleotides were saturated within and across synonymous codons of a capsid region interval representing only ∼9% of the total genome. Codon replacements were associated with moderate decreases in total virion production but large decreases in the specific infectivities of intact poliovirions and viral RNAs. Replication of codon replacement viruses, but not MEF-1, was temperature sensitive at 39.5°C. Synthesis and processing of viral intracellular proteins were largely unaltered in most codon replacement constructs. Replacement of natural codons with synonymous codons with increased frequencies of CpG and UpA dinucleotides may offer a general approach to the development of attenuated vaccines with well-defined antigenicities and very high genetic stabilities.
Derivation and Characterization of a Simian Immunodeficiency Virus SIVmac239 Variant with Tropism for CXCR4
Authors: Del Prete Gregory Q. , Haggarty Beth , Leslie George J. , Jordan Andrea P. O. , Romano Josephine , Wang Nathaniel , Wang Jianbin , Holmes Michael C. , Montefiori David C. , Hoxie James A. 
Published: July 2009

ABSTRACT

Like human immunodeficiency virus type 1 (HIV-1), most simian immunodeficiency virus (SIV) strains use CCR5 to establish infection. However, while HIV-1 can acquire the ability to use CXCR4, SIVs that utilize CXCR4 have rarely been reported. To explore possible barriers against SIV coreceptor switching, we derived an R5X4 variant, termed 239-ST1, from the R5 clone SIVmac239 by serially passaging virus in CD4
+
CXCR4
+
CCR5
−
SupT1 cells. A 239-ST1
env
clone, designated 239-ST1.2-32, used CXCR4 and CCR5 in cell-cell fusion and reporter virus infection assays and conferred the ability for rapid, cytopathic infection of SupT1 cells to SIVmac239. Viral replication was inhibitable by the CXCR4-specific antagonist AMD3100, and replication was abrogated in a novel CXCR4
−
SupT1 line. Surprisingly, parental SIVmac239 exhibited low-level replication in SupT1 cells that was not observed in CXCR4
−
SupT1 cells. Only two mutations in the 239-ST1.2-32 Env, K47E in the C1 domain and L328W in the V3 loop, were required for CXCR4 use in cell-cell fusion assays, although two other V3 changes, N316K and I324M, improved CXCR4 use in infection assays. An Env cytoplasmic tail truncation, acquired during propagation of 239-ST1 in SupT1 cells, was not required. Compared with SIVmac239, 239-ST1.2-32 was more sensitive to neutralization by five of seven serum and plasma samples from SIVmac239-infected rhesus macaques and was approximately 50-fold more sensitive to soluble CD4. Thus, SIVmac239 can acquire the ability to use CXCR4 with high efficiency, but the changes required for this phenotype may be distinct from those for HIV-1 CXCR4 use. This finding, along with the increased neutralization sensitivity of this CXCR4-using SIV, suggests a mechanism that could select strongly against this phenotype in vivo.
Identification of Ongoing Human Immunodeficiency Virus Type 1 (HIV-1) Replication in Residual Viremia during Recombinant HIV-1 Poxvirus Immunizations in Patients with Clinically Undetectable Viral Loads on Durable Suppressive Highly Active Antiretroviral Therapy
Authors: Shiu Carlum , Cunningham Coleen K. , Greenough Thomas , Muresan Petronella , Sanchez-Merino Victor , Carey Vincent , Jackson J. Brooks , Ziemniak Carrie , Fox Lawrence , Belzer Marvin , Ray Stuart C. , Luzuriaga Katherine , Persaud Deborah 
Published: July 2009

ABSTRACTIn most human immunodeficiency virus type 1 (HIV-1)-infected individuals who achieve viral loads of <50 copies/ml during highly active antiretroviral therapy (HAART), low levels of plasma virus remain detectable for years by ultrasensitive methods. The relative contributions of ongoing virus replication and virus production from HIV-1 reservoirs to persistent low-level viremia during HAART remain controversial. HIV-1 vaccination of HAART-treated individuals provides a model for examining low-level viremia, as immunizations may facilitate virus replication and sequence evolution. In a phase 1 trial of modified vaccinia virus Ankara/fowlpox virus-based HIV-1 vaccines in 20 HIV-infected young adults receiving HAART, we assessed the prevalence of low-level viremia and sequence evolution, using ultrasensitive viral load (<6.5 copies/ml) and genotyping (five-copy sensitivity) assays. Viral evolution, consisting of new drug resistance mutations and novel amino acid changes within a relevant HLA-restricted allele (e.g., methionine, isoleucine, glutamine, or arginine for leucine at position 205 of RT), was found in 1 and 3 of 20 subjects, respectively. Sequence evolution was significantly correlated with levels of viremia of between 6.5 and <50 copies/ml (P= 0.03) and was more likely to occur within epitopes presented by relevant HLA alleles (P< 0.001). These findings suggest that ongoing virus replication contributes to low-level viremia in patients on HAART and that this ongoing replication is subject to CD8+T-cell selective pressures.
Distribution of Endogenous Retroviruses in Crocodilians
Authors: Jaratlerdsiri Weerachai , Rodríguez-Zárate Clara J. , Isberg Sally R. , Damayanti Chandramaya Siska , Miles Lee G. , Chansue Nantarika , Moran Chris , Melville Lorna , Gongora Jaime 
Published: July 2009

ABSTRACT

Knowledge of endogenous retroviruses (ERVs) in crocodilians (Crocodylia) is limited, and their distribution among extant species is unclear. Here we analyzed the phylogenetic relationships of these retroelements in 20 species of crocodilians by studying the
pro-pol
gene. The results showed that crocodilian ERVs (CERVs) cluster into two major clades (CERV 1 and CERV 2). CERV 1 clustered as a sister group of the genus
Gammaretrovirus
, while CERV 2 clustered distantly with respect to all known ERVs. Interestingly, CERV 1 was found only in crocodiles (Crocodylidae). The data generated here could assist future studies aimed at identifying orthologous and paralogous ERVs among crocodilians.
Simian Varicella Virus Induces Apoptosis in Monkey Kidney Cells by the Intrinsic Pathway and Involves Downregulation of Bcl-2 Expression
Authors: Pugazhenthi Subbiah , Gilden Donald H. , Nair Sreekala , McAdoo Anne , Wellish Mary , Brazeau Elizabeth , Mahalingam Ravi 
Published: July 2009

ABSTRACT

Simian varicella virus (SVV) causes varicella in primates, becomes latent in ganglionic neurons, and reactivates to produce zoster. SVV produces a cytopathic effect in monkey kidney cells in tissue culture. To study the mechanism by which SVV-infected cells die, we examined markers of apoptosis 24 to 64 h postinfection (hpi). Western blot analysis of virus-infected cell lysates revealed a significant increase in the levels of the cleaved active form of caspase-3, accompanied by a parallel increase in caspase-3 activity at 40 to 64 hpi. Caspase-9, a marker for the intrinsic pathway, was activated significantly in SVV-infected cells at all time points, whereas trace levels of the active form of caspase-8, an extrinsic pathway marker, was detected only at 64 hpi. Bcl-2 expression at the mRNA and protein levels was decreased by 50 to 70% throughout the course of virus infection. Release of cytochrome
c
, an activator of caspase-9, from mitochondria into the cytoplasm was increased by 200% at 64 hpi. Analysis of Vero cells infected with SVV expressing green fluorescent protein (SVV-GFP) at 64 hpi revealed colocalization of the active forms of caspase-3 and caspase-9 and terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling (TUNEL) staining with GFP. A significant decrease in the
bcl-2
mRNA levels along with an abundance of mRNA specific for SVV genes 63, 40, and 21 was seen in the fraction of Vero cells that were infected with SVV-GFP. Together, these findings indicate that SVV induces apoptosis in cultured Vero cells through the intrinsic pathway in which Bcl-2 is downregulated.
Hepatitis C Virus Core Protein and Cellular Protein HAX-1 Promote 5-Fluorouracil-Mediated Hepatocyte Growth Inhibition
Authors: Banerjee Arup , Saito Kousuke , Meyer Keith , Banerjee Sutapa , Ait-Goughoulte Malika , Ray Ratna B. , Ray Ranjit 
Published: July 2009

ABSTRACTHepatitis C virus (HCV) often causes chronic infection and may lead to hepatocellular carcinoma (HCC). We have shown previously that HCV core protein has pleiotropic functions, including transcriptional regulation of a number of cellular genes, although the mechanism for gene regulation remains unclear. In this study, a mammalian two-hybrid screen identified a novel binding partner, HS1-associated protein X-1 (HAX-1), for HCV core protein from a human liver cDNA library. An association between HAX-1 and HCV core protein was further verified by confocal microscopy and coimmunoprecipitation in HepG2 cells expressing HCV core or full-length (FL) gene. Both HCV core protein and a chemotherapeutic agent for HCC, 5-flouorouracil (5-FU), are known to modulate p53. We examined here whether an association between core and HAX-1 has any functional relevance to p53 modulation in 5-FU-treated cells. For this, the role of HAX-1 on 5-FU treatment was examined in HepG2 cells expressing HCV core or FL gene using cell proliferation, p53 expression, and caspase activation analysis. Cells expressing HCV-core or FL gene were more susceptible to 5-FU-induced growth inhibition than control cells, whereas cell survival was enhanced after suppression of HAX-1 by small interfering RNA. Further, 5-FU-mediated p53 expression was reduced with concurrent HAX-1 suppression in core- or polyprotein-expressing cells compared to control HepG2 cells, and caspase-2 and -7 activities were diminished. On the other hand, HCV core protein did not play a detectable role in 5-FU-mediated caspase-7 activation in the absence of functional p53 in Hep3B or Huh-7 cells. These observations underscore an association between HCV core and HAX-1, which promotes 5-FU mediated p53-dependent caspase-7 activation and hepatocyte growth inhibition.