bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of the Hybrid Capture 2 and cobas 4800 Tests for Detection of High-Risk Human Papillomavirus in Specimens Collected in PreservCyt Medium
Authors: Wong Anita A. , Fuller Jeff , Pabbaraju Kanti , Wong Sallene , Zahariadis George 
Published: November 2011

ABSTRACT

Clinical cervical cytology specimens (
n
= 466) collected in PreservCyt (Hologic Inc.) were used to evaluate the agreement between Hybrid Capture 2 (hc2; Qiagen) and cobas 4800 (c4800; Roche Molecular Diagnostics) for the detection of high-risk human papillomavirus (HR HPV) genotype infections. The agreement between the two assays was 93.8% (kappa = 0.87; 95% confidence interval, 0.828 to 0.918), with 186 and 251 concordant positive and negative results, respectively. All 186 concordant positives were confirmed using the Linear Array (LA; Roche Molecular Diagnostics) genotyping test. Of the 29 samples with discordant results (6.2%), 18 were hc2 positive and LA verified 17 as positive for HR HPV. Eleven discordant specimens were c4800 positive, and LA confirmed 5 as positive for HR HPV. As of October 2009, practice guidelines in Alberta, Canada, recommend reflex HPV testing for women over 30 years old with atypical squamous cells of undetermined significance (ASCUS) and for women over 50 years old with low-grade squamous intraepithelial lesions (LSIL) to help prioritize those who should undergo further evaluation. In this study, agreement between hc2 and c4800 results for samples from women over 30 years old with ASCUS cytology was 92.3% (
n
= 13), while no samples from women over 50 years old with LSIL cytology were identified for analysis.
Direct MALDI-TOF Mass Spectrometry Assay of Blood Culture Broths for Rapid Identification of Candida Species Causing Bloodstream Infections: an Observational Study in Two Large Microbiology Laboratories
Authors: Spanu Teresa , Posteraro Brunella , Fiori Barbara , D'Inzeo Tiziana , Campoli Serena , Ruggeri Alberto , Tumbarello Mario , Canu Giulia , Trecarichi Enrico Maria , Parisi Gabriella , Tronci Mirella , Sanguinetti Maurizio , Fadda Giovanni 
Published: November 2011

ABSTRACT

We evaluated the reliability of the Bruker Daltonik's MALDI Biotyper system in species-level identification of yeasts directly from blood culture bottles. Identification results were concordant with those of the conventional culture-based method for 95.9% of
Candida albicans
(187/195) and 86.5% of non-
albicans Candida
species (128/148). Results were available in 30 min (median), suggesting that this approach is a reliable, time-saving tool for routine identification of
Candida
species causing bloodstream infection.
Cooperation between Viral Interferon Regulatory Factor 4 and RTA To Activate a Subset of Kaposi's Sarcoma-Associated Herpesvirus Lytic Promoters
Authors: Xi Xiangmei , Persson Linda M. , O'Brien Michael W. , Mohr Ian , Wilson Angus C. 
Published: November 2011

ABSTRACT
The four Kaposi's sarcoma-associated herpesvirus (KSHV)-encoded interferon (IFN) regulatory factor homologues (vIRF1 to vIRF4) are used to counter innate immune defenses and suppress p53. The vIRF genes are arranged in tandem but differ in function and expression. In KSHV-infected effusion lymphoma lines, K10.5/vIRF3 and K11/vIRF2 mRNAs are readily detected during latency, whereas K9/vIRF1 and K10/vIRF4 mRNAs are upregulated during reactivation. Here we show that the K10/vIRF4 promoter responds to the lytic switch protein RTA in KSHV-infected cells but is essentially unresponsive in uninfected cells. Coexpression of RTA with vIRF4 is sufficient to restore regulation, a property not shared by other vIRFs. The K9/vIRF1 promoter behaves similarly, and production of infectious virus is enhanced by the presence of vIRF4. Synergy requires the DNA-binding domain (DBD) and C-terminal IRF homology regions of vIRF4. Mutations of arginine residues within the putative DNA recognition helix of vIRF4 or the invariant cysteines of the adjacent CxxC motif abolish cooperation with RTA, in the latter case by preventing self-association. The oligomerization and transactivation functions of RTA are also essential for synergy. The K10/vIRF4 promoter contains two transcription start sites (TSSs), and a 105-bp fragment containing the proximal promoter is responsive to vIRF4/RTA. Binding of a cellular factor(s) to this fragment is altered when both viral proteins are present, suggesting a possible mechanism for transcriptional synergy. Reliance on coregulators encoded by either the host or viral genome provides an elegant strategy for expanding the regulatory potential of a master regulator, such as RTA.
Distinct Domains in ORF52 Tegument Protein Mediate Essential Functions in Murine Gammaherpesvirus 68 Virion Tegumentation and Secondary Envelopment
Authors: Wang Lili , Guo Haitao , Reyes Nichole , Lee Shaoying , Bortz Eric , Guo Fengli , Sun Ren , Tong Liang , Deng Hongyu 
Published: November 2011

ABSTRACT
Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus are etiologically associated with several types of human malignancies. However, as these two human gammaherpesviruses do not replicate efficiently in cultured cells, the morphogenesis of gammaherpesvirus virions is poorly understood. Murine gammaherpesvirus 68 (MHV-68) provides a tractable model to define common, conserved features of gammaherpesvirus biology. ORF52 of MHV-68 is conserved among gammaherpesviruses. We have previously shown that this tegument protein is essential for the envelopment and egress of viral particles and solved the crystal structure of ORF52 dimers. To more closely examine its role in virion maturation, we performed immunoelectron microscopy of MHV-68-infected cells and found that ORF52 localized to both mature, extracellular virions and immature viral particles in the cytoplasm. ORF52 consists of three α-helices followed by one β-strand. To understand the structural requirements for ORF52 function, we constructed mutants of ORF52 and examined their ability to complement an ORF52-null MHV-68 virus. Mutations in conserved residues in the N-terminal α1-helix and C terminus, or deletion of the α2-helix, resulted in a loss-of-function phenotype. Furthermore, the α1-helix was crucial for the predominantly punctate cytoplasmic localization of ORF52, while the α2-helix was a key domain for ORF52 dimerization. Immunoprecipitation experiments demonstrated that ORF52 interacts with another MHV-68 tegument protein, ORF42; however, a single point mutation in R95 in the C terminus of ORF52 led to the loss of this interaction. Moreover, the homologues of MHV-68 ORF52 in Kaposi's sarcoma-associated herpesvirus and Epstein-Barr virus complement the defect in ORF52-null MHV-68 and interact with MHV-68 ORF52. Taken together, these data uncover the relationship between the α-helical structure and the molecular basis for ORF52 function. This is the first structure-based functional domain mapping study for an essential gammaherpesvirus tegument protein.
High-Resolution Analysis of Intrahost Genetic Diversity in Dengue Virus Serotype 1 Infection Identifies Mixed Infections
Authors: Thai Khoa T. D. , Henn Matthew R. , Zody Michael C. , Tricou Vianney , Nguyet Nguyen Minh , Charlebois Patrick , Lennon Niall J. , Green Lisa , de Vries Peter J. , Hien Tran Tinh , Farrar Jeremy , van Doorn H. Rogier , de Jong Menno D. , Birren Bruce W. , Holmes Edward C. , Simmons Cameron P. 
Published: November 2011

ABSTRACT

Little is known about the rate at which genetic variation is generated within intrahost populations of dengue virus (DENV) and what implications this diversity has for dengue pathogenesis, disease severity, and host immunity. Previous studies of intrahost DENV variation have used a low frequency of sampling and/or experimental methods that do not fully account for errors generated through amplification and sequencing of viral RNAs. We investigated the extent and pattern of genetic diversity in sequence data in domain III (DIII) of the envelope (E) gene in serial plasma samples (
n
= 49) taken from 17 patients infected with DENV type 1 (DENV-1), totaling some 8,458 clones. Statistically rigorous approaches were employed to account for artifactual variants resulting from amplification and sequencing, which we suggest have played a major role in previous studies of intrahost genetic variation. Accordingly, nucleotide sequence diversities of viral populations were very low, with conservative estimates of the average levels of genetic diversity ranging from 0 to 0.0013. Despite such sequence conservation, we observed clear evidence for mixed infection, with the presence of multiple phylogenetically distinct lineages present within the same host, while the presence of stop codon mutations in some samples suggests the action of complementation. In contrast to some previous studies we observed no relationship between the extent and pattern of DENV-1 genetic diversity and disease severity, immune status, or level of viremia.
Monoclonal Antibody-Based Antigenic Mapping of Norovirus GII.4-2002
Authors: Lindesmith Lisa C. , Debbink Kari , Swanstrom Jesica , Vinjé Jan , Costantini Verónica , Baric Ralph S. , Donaldson Eric F. 
Published: November 2011

ABSTRACT
Noroviruses are the primary cause of epidemic gastroenteritis in humans, and GII.4 strains cause ∼80% of the overall disease burden. Surrogate neutralization assays using sera and mouse monoclonal antibodies (MAbs) suggest that antigenic variation maintains GII.4 persistence in the face of herd immunity, as the emergence of new pandemic strains is accompanied by newly evolved neutralization epitopes. To potentially identify specific blockade epitopes that are likely neutralizing and evolving between pandemic strains, mice were hyperimmunized with GII.4-2002 virus-like particles (VLPs) and the resulting MAbs were characterized by biochemical and immunologic assays. All of the MAbs but one recognized GII.4 VLPs representing strains circulating from 1987 to 2009. One MAb weakly recognized GII.4-1987 and -1997 while strongly interacting with 2002 VLPs. This antibody was highly selective and effective at blocking only GII.4-2002-ligand binding. Using bioinformatic analyses, we predicted an evolving GII.4 surface epitope composed of amino acids 407, 412, and 413 and subsequently built mutant VLPs to test the impact of the epitope on MAb binding and blockade potential. Replacement of the 2002 epitope with the epitopes found in 1987 or 2006 strains either reduced or ablated enzyme immunoassay recognition by the GII.4-2002-specific blockade MAb. These data identify a novel, evolving blockade epitope that may be associated with protective immunity, providing further support for the hypotheses that GII.4 norovirus evolution results in antigenic variation that allows the virus to escape from protective herd immunity, resulting in new epidemic strains.
Reassortment and Mutation of the Avian Influenza Virus Polymerase PA Subunit Overcome Species Barriers
Authors: Mehle Andrew , Dugan Vivien G. , Taubenberger Jeffery K. , Doudna Jennifer A. 
Published: November 2011

ABSTRACT

The emergence of new pandemic influenza A viruses requires overcoming barriers to cross-species transmission as viruses move from animal reservoirs into humans. This complicated process is driven by both individual gene mutations and genome reassortments. The viral polymerase complex, composed of the proteins PB1, PB2, and PA, is a major factor controlling host adaptation, and reassortment events involving polymerase gene segments occurred with past pandemic viruses. Here we investigate the ability of polymerase reassortment to restore the activity of an avian influenza virus polymerase that is normally impaired in human cells. Our data show that the substitution of human-origin PA subunits into an avian influenza virus polymerase alleviates restriction in human cells and increases polymerase activity
in vitro
. Reassortants with 2009 pandemic H1N1 PA proteins were the most active. Mutational analyses demonstrated that the majority of the enhancing activity in human PA results from a threonine-to-serine change at residue 552. Reassortant viruses with avian polymerases and human PA subunits, or simply the T552S mutation, displayed faster replication kinetics in culture and increased pathogenicity in mice compared to those containing a wholly avian polymerase complex. Thus, the acquisition of a human PA subunit, or the signature T552S mutation, is a potential mechanism to overcome the species-specific restriction of avian polymerases and increase virus replication. Our data suggest that the human, avian, swine, and 2009 H1N1-like viruses that are currently cocirculating in pig populations set the stage for PA reassortments with the potential to generate novel viruses that could possess expanded tropism and enhanced pathogenicity.
Mucosal and Peripheral Lin
−
HLA-DR
+
CD11c/123
−
CD13
+
CD14
−
Mononuclear Cells Are Preferentially Infected during Acute Simian Immunodeficiency Virus Infection
Authors: Moore Andrew C. , Bixler Sandra L. , Lewis Mark G. , Verthelyi Daniela , Mattapallil Joseph J. 
Published: November 2011

ABSTRACT

Massive infection of memory CD4 T cells is a hallmark of early simian immunodeficiency virus (SIV) infection, with viral infection peaking at day 10 postinfection (p.i.), when a majority of memory CD4 T cells in mucosal and peripheral tissues are infected. It is not clear if mononuclear cells from the monocyte and macrophage lineages are similarly infected during this early phase of explosive HIV and SIV infections. Here we show that, at day 10 p.i., Lin
−
HLA-DR
+
CD11c/123
−
CD13
+
CD14
−
macrophages in the jejunal mucosa were infected, albeit at lower levels than CD4 memory T cells. Interestingly, Lin
−
HLA-DR
+
CD11c/123
−
CD13
+
CD14
−
macrophages in peripheral blood, like their mucosal counterparts, were preferentially infected compared to Lin
−
HLA-DR
+
CD11c/123
−
CD13
+
CD14
+
monocytes, suggesting that differentiated macrophages were selectively infected by SIV. CD13
+
CD14
−
macrophages expressed low levels of CD4 compared to CD4 T cells but expressed similar levels of CCR5 as lymphocytes. Interestingly, CD13
+
CD14
−
macrophages expressed Apobec3G at lower levels than CD13
+
CD14
+
monocytes, suggesting that intracellular restriction may contribute to the differential infection of mononuclear subsets. Taken together, our results suggest that CD13
+
CD14
−
macrophages in mucosal and peripheral tissues are preferentially infected very early during the course of SIV infection.
HIV-1 Clinical Isolates Resistant to CCR5 Antagonists Exhibit Delayed Entry Kinetics That Are Corrected in the Presence of Drug
Authors: Putcharoen Opass , Lee Sun Hee , Henrich Timothy J. , Hu Zixin , Vanichanan Jakapat , Coakley Eoin , Greaves Wayne , Gulick Roy M. , Kuritzkes Daniel R. , Tsibris Athe M. N. 
Published: November 2011

ABSTRACT

HIV CCR5 antagonists select for
env
gene mutations that enable virus entry via drug-bound coreceptor. To investigate the mechanisms responsible for viral adaptation to drug-bound coreceptor-mediated entry, we studied viral isolates from three participants who developed CCR5 antagonist resistance during treatment with vicriviroc (VCV), an investigational small-molecule CCR5 antagonist. VCV-sensitive and -resistant viruses were isolated from one HIV subtype C- and two subtype B-infected participants; VCV-resistant isolates had mutations in the V3 loop of gp120 and were cross-resistant to TAK-779, an investigational antagonist, and maraviroc (MVC). All three resistant isolates contained a 306P mutation but had variable mutations elsewhere in the V3 stem. We used a virus-cell β-lactamase (BlaM) fusion assay to determine the entry kinetics of recombinant viruses that incorporated full-length VCV-sensitive and -resistant envelopes. VCV-resistant isolates exhibited delayed entry rates in the absence of drug, relative to pretherapy VCV-sensitive isolates. The addition of drug corrected these delays. These findings were generalizable across target cell types with a range of CD4 and CCR5 surface densities and were observed when either population-derived or clonal envelopes were used to construct recombinant viruses. V3 loop mutations alone were sufficient to restore virus entry in the presence of drug, and the accumulation of V3 mutations during VCV therapy led to progressively higher rates of viral entry. We propose that the restoration of pre-CCR5 antagonist therapy HIV entry kinetics drives the selection of V3 loop mutations and may represent a common mechanism that underlies the emergence of CCR5 antagonist resistance.
Identification of New Viral Genes and Transcript Isoforms during Epstein-Barr Virus Reactivation using RNA-Seq
Authors: Concha Monica , Wang Xia , Cao Subing , Baddoo Melody , Fewell Claire , Lin Zhen , Hulme William , Hedges Dale , McBride Jane , Flemington Erik K. 
Published: November 2011

ABSTRACT
Using an enhanced RNA-Seq pipeline to analyze Epstein-Barr virus (EBV) transcriptomes, we investigated viral and cellular gene expression in the Akata cell line following B-cell-receptor-mediated reactivation. Robust induction of EBV gene expression was observed, with most viral genes induced >200-fold and with EBV transcripts accounting for 7% of all mapped reads within the cell. After induction, hundreds of candidate splicing events were detected using the junction mapper TopHat, including a novel nonproductive splicing event at the gp350/gp220 locus and several alternative splicing events at the LMP2 locus. A more detailed analysis of lytic LMP2 transcripts showed an overall lack of the prototypical type III latency splicing events. Analysis of nuclear versus cytoplasmic RNA-Seq data showed that the lytic forms of LMP2, EBNA-2, EBNA-LP, and EBNA-3A, -3B, and -3C have higher nuclear-to-cytoplasmic accumulation ratios than most lytic genes, including classic late genes. These data raise the possibility that at least some lytic transcripts derived from these latency gene loci may have unique, noncoding nuclear functions during reactivation. Our analysis also identified two previously unknown genes, BCLT1 and BCRT2, that map to the BamHI C-region of the EBV genome. Pathway analysis of cellular gene expression changes following B-cell receptor activation identified an inflammatory response as the top predicted function and ILK and TREM1 as the top predicted canonical pathways.
Mica-controlled anisotropy within mid-to-upper crustal mylonites: an EBSD study of mica fabrics in the Alpine Fault Zone, New Zealand
Authors: Dempsey Edward D. , Prior Dave J. , Mariani Elisabetta , Toy Virginia G. , Tatham Daniel J. 
Published: November 2011

Abstract
The lattice preferred orientation (LPO) of both muscovite and biotite were measured by electron backscatter diffraction (EBSD) and these data, together with the LPOs of the other main constituent minerals, were used to produce models of the seismic velocity anisotropy of the Alpine Fault Zone. Numerical experiments examine the effects of varying modal percentages of mica within the fault rocks. These models suggest that when the mica modal proportions approach 20% in quartzofeldspathic mylonites the intrinsic seismic anisotropy of the studied fault zone is dominated by mica, with the direction of the fastest P and S wave velocities strongly dependent on the mica LPOs. The LPOs show that micas produce three distinct patterns within mylonitic fault zones: C-fabric, S-fabric and a composite S–C fabric. The asymmetry of the LPOs can be used as kinematic indicators for the deformation within mylonites. Kinematic data from the micas matches the kinematic interpretation of quartz LPOs and field data. The modelling of velocities and velocity anisotropies from sample LPOs is consistent with geophysical data from the crust under the Southern Alps. The Alpine Fault mylonites and parallel Alpine schists have intrinsic P-wave velocity anisotropies of 12% and S-wave anisotropies of 10%.
Phase I, Dose-Escalation Trial of the Oral Cyclin-Dependent Kinase 4/6 Inhibitor PD 0332991, Administered Using a 21-Day Schedule in Patients with Advanced Cancer
Authors: Flaherty Keith T. , LoRusso Patricia M. , DeMichele Angela , Abramson Vandana G. , Courtney Rachel , Randolph Sophia S. , Shaik M. Naveed , Wilner Keith D. , O'Dwyer Peter J. , Schwartz Gary K. 
Published: November 2011

Abstract
Purpose: To identify the dose-limiting toxicity (DLT) and maximum tolerated dose (MTD) of the first-in-class, oral CDK4/6 inhibitor PD 0332991 administered once daily for 21 of 28 days (3/1 schedule) in patients with retinoblastoma protein (Rb)-positive advanced solid tumors and to describe pharmacokinetic–pharmacodynamic relationships relative to drug effects.
Experimental Design: This open-label phase I study (NCT00141297) enrolled patients who received PD 0332991 orally in six dose-escalation cohorts in a standard 3 + 3 design.
Results: Forty-one patients were enrolled. DLTs were observed in five patients (12%) overall; at the 75, 125, and 150 mg once daily dose levels. The MTD and recommended phase II dose of PD 0332991 was 125 mg once daily. Neutropenia was the only dose-limiting effect. After cycle 1, grade 3 neutropenia, anemia, and leukopenia occurred in five (12%), three (7%), and one (2%) patient(s), respectively. The most common non-hematologic adverse events included fatigue, nausea, and diarrhea. Thirty-seven patients were evaluable for tumor response; 10 (27%) had stable disease for ≥4 cycles of whom six derived prolonged benefit (≥10 cycles). PD 0332991 was slowly absorbed (median Tmax, 5.5 hours), and slowly eliminated (mean half-life was 25.9 hours) with a large volume of distribution (mean, 2,793 L). The area under the concentration–time curve increased linearly with dose. Using an Emax model, neutropenia was shown to be proportional to exposure.
Conclusions: PD 0332991 warrants phase II testing at 125 mg once daily, at which dose neutropenia was the sole significant toxicity. Clin Cancer Res; 18(2); 568–76. ©2011 AACR.