bluuebunny/crossref_metadata_2025 huggingface dataset:
How the effects of resonant absorption on black hole reflection spectra can mimic high-velocity outflows
Authors: Gallo L. C. , Fabian A. C.
Published: September 2011

Narrow absorption lines seen in the 2–10 keV spectra of active galaxies and Galactic black holes are normally attributed to iron in high-velocity outflows or inflows. We consider the possibility that such features could arise naturally in the accretion disc. Resonant absorption by highly ionized iron (e.g. Fe xxvi and Fe xxv) in an optically thin plasma that is located above the disc and rotating with it could reproduce narrow features in the reflection component of the spectrum as it emerges from the disc. Depending on the inclination of the disc and the exact geometry of the hot plasma (e.g. whether it blanket the disc or a ring), apparently narrow absorption features could be detected between 4 and 10 keV. Such an explanation requires no high-velocity outflow/inflow and is consistent with a reflection-based interpretation for accreting black holes systems.
Evidence for cosmic evolution in the spin of the most massive black holes
Authors: Martínez-Sansigre Alejo , Rawlings Steve
Published: September 2011

We use results from simulations of the production of magnetohydrodynamic jets around black holes to derive the cosmic spin history of the most massive black holes. We assume that the efficiency of jet production is a monotonic function of spin , as given by the simulations, and that the accretion flow geometry is similarly thick for quasars accreting close to the Eddington ratio and for low-excitation radio galaxies accreting at very small Eddington rates. We use the ratio of the comoving densities of the jet power to the radiated accretion power associated with supermassive black holes with m•≳ 108 M⊙ to estimate the cosmic history of the characteristic spin . The evolution of this ratio, which increases with decreasing z, is consistent with a picture where the z∼ 0 active galactic nuclei have typically higher spins than those at z∼ 2 (with typical values –0.95 and ∼0.0–0.25, respectively). We discuss the implications in terms of the relative importance of accretion and mergers in the growth of supermassive black holes with m•≳ 108 M⊙.
X-ray evidence for the accretion disc–outflow connection in 3C 111
Authors: Tombesi F. , Sambruna R. M. , Reeves J. N. , Reynolds C. S. , Braito V.
Published: September 2011

We present the spectral analysis of three Suzaku X-ray Imaging Spectrometer observations of 3C 111 requested to monitor the predicted variability of its ultrafast outflow on ∼7 d time-scales. We detect an ionized iron emission line in the first observation and a blueshifted absorption line in the second, when the flux is ∼30 per cent higher. The location of the material is constrained at <0.006 pc from the variability. Detailed modelling supports an identification with ionized reflection off the accretion disc at ∼20–100rg from the black hole and a highly ionized and massive ultrafast outflow with velocity ∼0.1c, respectively. The outflow is most probably accelerated by radiation pressure, but additional magnetic thrust cannot be excluded. The measured high outflow rate and mechanical energy support the claims that disc outflows may have a significant feedback role. This work provides the first direct evidence for an accretion disc–outflow connection in a radio-loud active galactic nucleus, possibly linked also to the jet activity.
Novel Naphthalimide–Benzoic Acid Conjugates as Potential Apoptosis‐Inducing Agents: Design, Synthesis, and Biological Activity
Authors: Wu Aibin , Mei Ping , Xu Yufang , Qian Xuhong
Published: September 2011

A series of novel naphthalimide derivatives with 4‐[4‐(3,3‐diphenylallyl)piperazin‐1‐yl]benzoic acid as side chain were designed and synthesized. Their antitumor activities were evaluated against a variety of cancer cell lines in vitro. Preliminary results showed that most of the derivatives had cytotoxic activity comparable with that of amonafide, with IC50 values of 10−6–10−5 m. Interestingly, compound 12e had the unique antitumor activity against MCF‐7 among the cancer cell lines tested. More importantly, flow cytometric analysis indicated that compared with amonafide, the target compounds could effectively induce G2/M arrest and progress to apoptosis in HL‐60 cells after double staining with annexin V–FITC and propidium iodide. The present work provided a novel class of naphthalimide‐based derivatives with potential apoptosis‐inducing and improved antitumor activity for further optimization.
Canine intracranial neoplasia: clinical risk factors for development of epileptic seizures
Authors: Schwartz M. , Lamb C. R. , Brodbelt D. C. , Volk H. A.
Published: September 2011

Objectives: To identify clinical risk factors for seizures in dogs with intracranial neoplasia.

Methods: A cross‐sectional retrospective study of 68 dogs with histopathologically confirmed primary or secondary intracranial neoplasia, complete clinical history and magnetic resonance imaging of the brain was conducted. Signalment and clinical history were retrieved from clinical records and magnetic resonance images of the brain were re‐evaluated. Prevalence of findings was compared between dogs with and without seizures.

Results: Forty‐two dogs had tumour‐related seizures, the remaining 26 were seizure‐free. Tumour types included meningioma (23 dogs with and 5 without seizures), glioma (9 dogs with and 6 without seizures), choroid plexus tumour (2 dogs without seizures), neuroblastoma (1 dog with seizures) and metastatic/invasive tumours including lymphoma (9 dogs with and 13 without seizures). On the basis of multi‐variable logistic regression analysis, risk factors for seizures associated with intracranial neoplasia were magnetic resonance imaging findings consistent with the presence of neoplastic tissue in frontal lobe [odds ratio (OR) 9·61; 95% confidence interval (CI) 2·59 to 35·61], marked gadolinium enhancement (OR 10·41; 95% CI 2·07 to 52·30) and magnetic resonance imaging findings of subfalcine and/or subtentorial herniation (OR 3·88; 95% CI 1·10 to 13·71).

ClinicalSignificance: Dogs with primary or secondary intracranial neoplasia are at risk of seizures, particularly those with tumours that affect the frontal lobe, enhance markedly with gadolinium, or cause subfalcine and/or subtentorial herniation.
Vascular endothelial growth factor plasma levels before and after treatment of neovascular age‐related macular degeneration with bevacizumab or ranibizumab
Authors: Carneiro Ângela M. , Costa Raquel , Falcão Manuel S. , Barthelmes Daniel , Mendonça Luis S. , Fonseca Sofia L. , Gonçalves Rita , Gonçalves Conceição , Falcão‐Reis Fernando M. , Soares Raquel
Published: September 2011

Purpose:  To evaluate the changes of vascular endothelial growth factor (VEGF) plasma levels after intravitreal injections of ranibizumab or bevacizumab in patients with exudative age‐related macular degeneration (AMD).

Methods:  Forty‐three patients with exudative AMD and 19 age‐ and sex‐matched control patients without chorioretinal diseases were studied. Nineteen patients were treated with intravitreal ranibizumab 0.5 mg, 24 with intravitreal bevacizumab 1.25 mg. Blood samples were collected just before the first injection, and 28 days after three initial consecutive injections performed in 4‐weekly intervals (loading dose). Concentration of VEGF in the plasma was measured by ELISA.

Results:  At baseline, the median VEGF concentrations in controls were 180.97 pg/ml, in the bevacizumab group 189.72 pg/ml and in the ranibizumab group 191.36 pg/ml. VEGF plasma concentrations in patients with wet AMD were comparable to controls (p = 0.225). Twenty‐eight days after the third injection, a significant reduction of 42% in the median VEGF plasma levels was found in bevacizumab‐treated patients (109.97 pg/ml; p = 0.0002) but not in ranibizumab‐treated patients (189.97 pg/ml; p = 0.198) where a reduction of 0.7% in the median value was found.

Conclusions:  Intravitreal bevacizumab significantly reduced VEGF plasma levels until 28 days after intravitreal injection in patients with exudative AMD. Ranibizumab did not achieve a significant plasma VEGF reduction at the same time‐point. These findings alert to the potential systemic safety differences between the two drugs after intravitreal administration.
TNFα suppresses IFNγ‐induced MHC class II expression on retinal pigmented epithelial cells cultures
Authors: Makhoul Maya , Bruyns Catherine , Edimo William's Elong , Relvas Lia Judice , Bazewicz Magdalena , Koch Philippe , Caspers Laure , Willermain François
Published: September 2011

Purpose:  One major consequence of retinal pigment epithelium (RPE) cell activation during autoimmune uveitis is the induction of MHC II molecules expression at their surface. IFNγ is regarded as the main cytokine involved in this induction. As TNFα plays a central role in autoimmune uveitis, we investigated its effects on IFNγ‐mediated MHC II induction on RPE cells.

Methods:  Retinal pigment epithelium cells (ARPE‐19) were stimulated with IFNγ, TNFα and the anti‐TNFα antibody infliximab. The expression of MHCII and ICAM‐1 was analysed by flow cytometry. The activation and expression of IRF‐1 and STAT‐1, two proteins involved in IFNγ‐signalling pathway, were analysed by WB. Class II transactivator (CIITA) expression was monitored by qRT‐PCR and immunoprecipitation.

Results:  TNFα inhibits IFNγ‐induced MHC II expression on ARPE cells in a dose‐dependent manner. Infliximab completely reverses the inhibitory effect of TNFα. We did not observe an inhibitory effect of TNFα on the expression of ICAM‐1 induced by IFNγ. Similarly, IFNγ‐induced STAT1 phosphorylation and IRF1 expression were not affected by TNFα. On the contrary, we found that TNFα suppresses IFNγ‐induced CIITA mRNA accumulation and protein expression.

Conclusion:  TNFα inhibits IFNγ‐induced MHC II expression in RPE cells. This inhibitory effect was reversed by infliximab and was not because of a global inhibition of IFNγ ‐mediated RPE cell activation but rather to a specific down‐regulation of CIITA expression. Those findings are consistent with the role of TNFα in the resolution of inflammation and might help to elucidate the complex development of autoimmune uveitis.
Impaired activities of cyclic adenosine monophosphate‐responsive element binding protein, protein kinase A and calcium‐independent phospholipase A2 are involved in deteriorated regeneration of cirrhotic liver after partial hepatectomy in rats
Authors: Zhao Gang , Wakabayashi Rie , Shimoda Shinya , Fukunaga Yumi , Kumagai Michiaki , Tanaka Masao , Nakano Kenji
Published: September 2011

Aims:  This study is to elucidate whether cyclic adenosine monophosphate (cAMP)‐mediated signal is involved in lower regenerative potential of cirrhotic liver.

Methods:  Hepatic cAMP concentration, activities of protein kinase A (PKA), c‐AMP responsive element binding protein (CREB) and Ca2+‐independent phospholipase A2 (iPLA2) and regeneration rate were compared between rats with thioacetamide‐induced cirrhotic and normal livers after two‐third hepatectomy.

Results:  The liver regeneration estimated by the rates of [3H]‐thymidine incorporation and staining of proliferating cell nuclear antigen was significantly lower in the cirrhotic group. CREB, PKA and iPLA2 activities, assessed by western blots and electromobility shift assay, were significantly impaired after hepatectomy in the cirrhosis group. PKA and iPLA2 silencing by siRNA transfection significantly inhibited CREB activity and cell growth in transformed hepatocytes in vitro.

Conclusions:  CREB dysfunction, mediated by PKA and iPLA2 suppression, may be involved in the deteriorated liver regeneration in the cirrhotic rats.
Calculation of Frequency Response Envelope for Dynamic Systems With Uncertain Parameters
Authors: Chen Wen-Hua
Published: September 2011

Frequency response finds a wide range of applications in many engineering sectors. When variations and uncertainties exist during the operation and lifetime of an engineering system, the calculation of frequency response for an uncertain dynamic system is required in order to assess the worst cases in terms of various criteria, for example gain and phase margins in control engineering, or peak magnitude at different modes in the finite element analysis of structures. This paper describes an analytical approach toward the identification of critical interior lines that possibly contribute to the boundary of the frequency response. It is allowed that uncertain parameters perturb transfer function coefficients in a nonlinear form. Conditions for critical interior lines contributing to the boundary of the frequency response are presented. An invariant property of these critical lines under open-loop and closed-loop configurations augmented by control systems or compensators is established, which greatly simplifies the analysis, design, and verification process when using frequency domain techniques. A procedure for computing frequency response and identifying the worst cases is then developed based on the combination of symbolic and numerical computation.
Mixed
Convection From a Convectively Heated Vertical Plate to a Fluid With Internal Heat
Generation
Authors: Makinde O. D. , Aziz A.
Published: September 2011

A numerical approach has been adopted to study steady mixed convection from the right face of a vertical plate of finite thickness. Cold fluid flowing over the right face of the plate contains a heat generation that decays exponentially with a dimensionless distance from the wall. The left face of the plate is in contact with a hot flowing fluid. The heating process on that side is characterized by a convective boundary condition that takes into account the conduction resistance of the plate as well as a possible contact resistance between the hot fluid and the left face of the plate. Using a pseudo similarity approach, the continuity, momentum, and energy equations for mixed convective flow over the right face of the plate are transformed into a set of coupled ordinary differential equations. It is found that for a true similarity solution, the convective heat transfer coefficient associated with the hot fluid must be proportional to x−1/2, and both the thermal expansion coefficient and the internal heat generation rate for the cold fluid must be proportional to x−1, where x is the upward distance along the plate. The equations give local similarity solutions. The effects of local Grashof number (defined to represent a mixed convection parameter), Prandtl number, Biot number, and the internal heat generation parameter on the velocity and temperature profiles are illustrated and interpreted in physical terms. The present results agree closely with the existing results for the special cases of the problem. This close agreement lends support to the validity of the present analysis and the accuracy of the numerical computations. The paper also contains a table in which the data for the local skin friction and local Nusselt number are provided for various combination values of the parameters that govern the momentum and energy transport in the mixed boundary layer.
Cosmetic powder suspensions in compliant, fingerprintlike contacts
Authors: Timm K. , Myant C. , Spikes H. A. , Schneider M. , Ladnorg T. , Grunze M.
Published: September 2011

Cosmetic powders are regularly employed in skin creams and cosmetic formulations to improve performance and enhance skin feel. A previous study investigated the effect of particle concentration and size on the lubricating properties of powder suspensions in smooth, compliant contacts [Timm et al., Tribol. Int. (2011)]. In this paper the tribological properties of cosmetic powder suspensions are investigated in compliant contacts having model fingerprintlike surface topography. Friction coefficients were measured for a series of powder suspensions with varying particle size and concentration in a polydimethylsiloxane (PDMS)/PDMS contact. A commercial tribometer (MTM, PCS Instruments) was employed to measure friction as a function of rubbing time (20 min), under pure sliding (50 mm/s) and low load (0.5 N) conditions. Compared to results using smooth surfaces, it was clear that surface topography has a pronounced affect on the timedependent tribological behavior of the cosmetic powder suspensions studied. A two-stage friction coefficient versus time curve was observed. By varying the particle size and concentration it was shown that the duration and magnitude of each stage can be controlled.
Histone Lysine Demethylase JARID1a Activates CLOCK-BMAL1 and Influences the Circadian Clock
Authors: DiTacchio Luciano , Le Hiep D. , Vollmers Christopher , Hatori Megumi , Witcher Michael , Secombe Julie , Panda Satchidananda
Published: September 2011

The histone lysine demethylase JARID1a has demethylase-independent function in the circadian clock.
MESSENGER Observations of Transient Bursts of Energetic Electrons in Mercury’s Magnetosphere
Authors: Ho George C. , Krimigis Stamatios M. , Gold Robert E. , Baker Daniel N. , Slavin James A. , Anderson Brian J. , Korth Haje , Starr Richard D. , Lawrence David J. , McNutt Ralph L. , Solomon Sean C.
Published: September 2011

Despite having an internal magnetic field, Mercury does not have a Van Allen–type radiation belt.
MESSENGER Observations of the Spatial Distribution of Planetary Ions Near Mercury
Authors: Zurbuchen Thomas H. , Raines Jim M. , Slavin James A. , Gershman Daniel J. , Gilbert Jason A. , Gloeckler George , Anderson Brian J. , Baker Daniel N. , Korth Haje , Krimigis Stamatios M. , Sarantos Menelaos , Schriver David , McNutt Ralph L. , Solomon Sean C.
Published: September 2011

The polar regions of Mercury are important
sources of material for its ionized exosphere.
Sensing ER Stress
Authors: Kawaguchi Shinichi , Ng Davis T. W.
Published: September 2011

Direct binding of unfolded proteins to a sensor in the endoplasmic reticulum triggers sensor oligomerization and a cellular stress response.
A New Histone Code for Clocks?
Authors: Brown Steven A.
Published: September 2011

A histone-modifying protein drives circadian clocks in an unexpected way.
From Geneva to Italy Faster Than a Speeding Photon?
Authors: Cho Adrian
Published: September 2011

Some physicists were incredulous about last week's report of subatomic particles called neutrinos traveling faster than light, but others have already developed a theoretical framework that can handle potential breaches of special relativity.
NSF Touts Family-Friendly Policies as Boon to Women
Authors: Mervis Jeffrey
Published: September 2011

This week, the National Science Foundation rolled out a set of family-friendly policies that it hopes will reduce the number of young women who jettison scientific careers because of responsibilities outside the lab.
Social Scientists Wade Into the Tweet Stream
Authors: Miller Greg
Published: September 2011

In this week's issue of
Science
, researchers report their effort to use the social media site Twitter to study the collective moods of millions of people in diverse cultures around the world in real time.
Altered Eosinophil Proteome in a Patient with Hypereosinophilia from Acute Fascioliasis
Authors: Straub Christof , Burnham Jason P. , White A. Clinton , Pazdrak Konrad , Sanchez Cesar , Watanabe Luis Carlos , Kurosky Alexander , Montes Martín
Published: September 2011

We used comparative proteomics to analyze eosinophils from a patient with hypereosinophilia due to fascioliasis. Using 2-dimensional electrophoresis and mass spectrometry, we demonstrated that the eosinophil proteome was significantly altered compared to those of healthy controls.
Use of Dried-Blood-Spot Samples and In-House Assays To Identify Antiretroviral Drug Resistance in HIV-Infected Children in Resource-Constrained Settings
Authors: Ziemniak Carrie , Mengistu Yohannes , Ruff Andrea , Chen Ya-Hui , Khaki Leila , Bedri Abubaker , Simen Birgitte B. , Palumbo Paul , Eshleman Susan H. , Persaud Deborah
Published: September 2011

Monitoring HIV drug resistance is an important component of the World Health Organization's global HIV program. HIV drug resistance testing is optimal with commercially available clinically validated test kits using plasma; however, that type of testing may not be feasible or affordable in resource-constrained settings. HIV genotyping from dried blood spots (DBS) with noncommercial (in-house) assays may facilitate the capture of HIV drug resistance outcomes in resource-constrained settings but has had varying rates of success. With in-house assays for HIV reverse transcriptase, we evaluated the yield of genotyping DBS samples collected from HIV-infected children who were enrolled in two clinical trials conducted in sub-Saharan Africa (median HIV viral load, 5.88 log10HIV RNA copies/ml; range, 4.04 to 6.99). Overall, HIV genotypes were obtained for 94 (89.5%) of 105 samples tested (95% and 84% from clinical trials #1 and #2, respectively); however, successful analysis of 15 (16.1%) of the 94 samples required repeat testing using a different set of primers on previously synthesized cDNA. The yield of genotyping was lower on the DBS that were stored suboptimally from clinical trial #2 (56% versus 88% for optimally stored). Concordance with plasma genotypes derived using a clinically validated, commercial kit-based assay (ViroSeq HIV-1 genotyping system) was also assessed in a subset of children with paired testing. For 34 samples with paired DBS and plasma genotypes, there was 100% concordance for major drug resistance mutations. DBS genotyping using in-house assays provides an alternative for antiretroviral drug resistance testing in children in resource-constrained regions but may require region-specific optimization before widespread use.
High-Resolution Melting-Curve Analysis of Ligation-Mediated Real-Time PCR for Rapid Evaluation of an Epidemiological Outbreak of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli
Authors: Woksepp Hanna , Jernberg Cecilia , Tärnberg Maria , Ryberg Anna , Brolund Alma , Nordvall Michaela , Olsson-Liljequist Barbro , Wisell Karin Tegmark , Monstein Hans-Jürg , Nilsson Lennart E. , Schön Thomas
Published: September 2011

Methods for the confirmation of nosocomial outbreaks of bacterial pathogens are complex, expensive, and time-consuming. Recently, a method based on ligation-mediated PCR (LM/PCR) using a low denaturation temperature which produces specific melting-profile patterns of DNA products has been described. Our objective was to further develop this method for real-time PCR and high-resolution melting analysis (HRM) in a single-tube system optimized in order to achieve results within 1 day. Following the optimization of LM/PCR for real-time PCR and HRM (LM/HRM), the method was applied for a nosocomial outbreak of extended-spectrum-beta-lactamase (ESBL)-producing and ST131-associated
Escherichia coli
isolates (
n
= 15) and control isolates (
n
= 29), including four previous clusters. The results from LM/HRM were compared to results from pulsed-field gel electrophoresis (PFGE), which served as the gold standard. All isolates from the nosocomial outbreak clustered by LM/HRM, which was confirmed by gel electrophoresis of the LM/PCR products and PFGE. Control isolates that clustered by LM/PCR (
n
= 4) but not by PFGE were resolved by confirmatory gel electrophoresis. We conclude that LM/HRM is a rapid method for the detection of nosocomial outbreaks of bacterial infections caused by ESBL-producing
E. coli
strains. It allows the analysis of isolates in a single-tube system within a day, and the discriminatory power is comparable to that of PFGE.
Cyclospora papionis, Cryptosporidium hominis, and Human-Pathogenic Enterocytozoon bieneusi in Captive Baboons in Kenya
Authors: Li Wei , Kiulia Nicholas M. , Mwenda Jason M. , Nyachieo Atunga , Taylor Maureen B. , Zhang Xichen , Xiao Lihua
Published: September 2011

Cyclospora papionis
,
Cryptosporidium hominis
, and
Enterocytozoon bieneusi
were detected in 42 (17.9%), 6 (2.6%), and 29 (12.3%) of 235 newly captured baboons in Kenya, respectively. Most
C. hominis
subtypes and
E. bieneusi
genotypes found have been detected in humans in the area, suggesting that cross-species transmission of cryptosporidiosis and microsporidiosis is possible.
Pandemic and Seasonal Human Influenza Virus Infections in Domestic Cats: Prevalence, Association with Respiratory Disease, and Seasonality Patterns
Authors: Ali A. , Daniels J. B. , Zhang Y. , Rodriguez-Palacios A. , Hayes-Ozello K. , Mathes L. , Lee C.-W.
Published: September 2011

Domestic cats have several features that make them ideal vehicles for interspecies transmission of influenza viruses; however, they have been largely overlooked as potential reservoirs or bridging hosts. In this study, we conducted serological surveillance to assess the prevalence of novel pandemic H1N1 as well as seasonal human influenza virus infections in domestic cats in Ohio. Four hundred serum samples collected from domestic cats (September 2009 to September 2010) were tested using a hemagglutination inhibition (HI) test. The seroprevalences of pandemic H1N1, seasonal H1N1, and H3N2 were 22.5%, 33%, and 43.5%, respectively. In addition, a significant association between clinical feline respiratory disease and influenza virus infection was documented. In this sample of cats, the prevalence of pandemic H1N1 did not follow the seasonality pattern of seasonal H1N1 or H3N2 influenza, similar to observations in humans. Pandemic H1N1 seroprevalence did not vary in relation to ambient temperature changes, while the seroprevalence of seasonal H3N2 and H1N1 influenza viruses increased with the decline of ambient temperature. Our results highlight the high prevalence of influenza virus infection in domestic cats, a seasonality pattern of influenza virus infection comparable to that in humans, and an association of infection with clinical respiratory disease.
Evaluation of the GeneXpert MTB/RIF Assay for Rapid Diagnosis of Tuberculosis and Detection of Rifampin Resistance in Pulmonary and Extrapulmonary Specimens
Authors: Zeka Arzu N. , Tasbakan Sezai , Cavusoglu Cengiz
Published: September 2011

Mycobacterium tuberculosis
remains one of the most significant causes of death from an infectious agent. The rapid diagnosis of tuberculosis and detection of rifampin (RIF) resistance are essential for early disease management. The GeneXpert MTB/RIF assay is a novel integrated diagnostic device for the diagnosis of tuberculosis and rapid detection of RIF resistance in clinical specimens. We determined the performance of the MTB/RIF assay for rapid diagnosis of tuberculosis and detection of rifampin resistance in smear-positive and smear-negative pulmonary and extrapulmonary specimens obtained from possible tuberculosis patients. Two hundred fifty-three pulmonary and 176 extrapulmonary specimens obtained from 429 patients were included in the study. One hundred ten (89 culture positive and 21 culture negative for
M. tuberculosis
) of the 429 patients were considered to have tuberculosis. In pulmonary specimens, sensitivities were 100% (27/27) and 68.6% (24/35) for smear-positive and smear-negative specimens, respectively. It had a lower sensitivity with extrapulmonary specimens: 100% for smear-positive specimens (4/4) and 47.7% for smear-negative specimens (21/44). The test accurately detected the absence of tuberculosis in all 319 patients without tuberculosis studied. The MTB/RIF assay also detected 1 RIF-resistant specimen and 88 RIF-susceptible specimens, and the results were confirmed by drug susceptibility testing. We concluded that the MTB/RIF test is a simple method, and routine staff with minimal training can use the system. The test appeared to be as sensitive as culture with smear-positive specimens but less sensitive with smear-negative pulmonary and extrapulmonary specimens that include low numbers of bacilli.
Enterobius vermicularis in a 14-Year-Old Girl's Eye
Authors: Babady N. Esther , Awender Erich , Geller Robert , Miller Terry , Scheetz Gayle , Arguello Heather , Weisenberg Scott A. , Pritt Bobbi
Published: September 2011

We report an unusual case of extraintestinal infection with adultEnterobius vermicularisworms in the nares and ocular orbit of a 14-year-old girl in Illinois. Only one other similar case has been reported in the English-language literature.
The Cellular Protein Lyric Interacts with HIV-1 Gag
Authors: Engeland Christine E. , Oberwinkler Heike , Schümann Michael , Krause Eberhard , Müller Gerd A. , Kräusslich Hans-Georg
Published: September 2011

Human immunodeficiency virus type 1 (HIV-1) Gag is the main structural protein driving assembly and release of virions from infected cells. Gag alone is capable of self-assembly
in vitro
, but host factors have been shown to play a role in efficient viral replication and particle morphogenesis within the living cell. In a series of affinity purification experiments, we identified the cellular protein Lyric to be an HIV-1 Gag-interacting protein.
Lyric
was previously described to be an HIV-inducible gene and is involved in various signaling pathways. Gag interacts with endogenous Lyric via its matrix (MA) and nucleocapsid (NC) domains. This interaction requires Gag multimerization and Lyric amino acids 101 to 289. Endogenous Lyric is incorporated into HIV-1 virions and is cleaved by the viral protease. Gag-Lyric interaction was also observed for murine leukemia virus and equine infectious anemia virus, suggesting that it represents a conserved feature among retroviruses. Expression of the Gag binding domain of Lyric increased Gag expression levels and viral infectivity, whereas expression of a Lyric mutant lacking the Gag binding site resulted in lower Gag expression and decreased viral infectivity. The results of the current study identify Lyric to be a cellular interaction partner of HIV-1 Gag and hint at a potential role in regulating infectivity. Further experiments are needed to elucidate the precise role of this interaction.
Myxoma Virus Lacking the Pyrin-Like Protein M013 Is Sensed in Human Myeloid Cells by both NLRP3 and Multiple Toll-Like Receptors, Which Independently Activate the Inflammasome and NF-κB Innate Response Pathways
Authors: Rahman Masmudur M. , McFadden Grant
Published: September 2011

The myxoma virus (MYXV)-encoded pyrin domain-containing protein M013 coregulates inflammatory responses mediated by both the inflammasome and the NF-κB pathways. Infection of human THP-1 monocytic cells with a MYXV construct deleted for the M013 gene (vMyxM013-KO), but not the parental MYXV, activates both the inflammasome and NF-κB pathways and induces a spectrum of proinflammatory cytokines and chemokines, like interleukin-1β (IL-1β), tumor necrosis factor (TNF), IL-6, and monocyte chemoattractant protein 1. Here, we report that vMyxM013-KO virus-mediated activation of inflammasomes and secretion of IL-1β are dependent on the adaptor protein ASC, caspase-1, and NLRP3 receptor. However, vMyxM013-KO virus-mediated activation of NF-κB signaling, which induces TNF secretion, was independent of ASC, caspase-1, and either the NLRP3 or AIM2 inflammasome receptors. We also report that early synthesis of pro-IL-1β in response to vMyxM013-KO infection is dependent upon the components of the inflammasome complex. Activation of the NLRP3 inflammasome and secretion of IL-1β was also dependent on the release of cathepsin B and production of reactive oxygen species (ROS). By using small interfering RNA screening, we further demonstrated that, among the RIG-I-like receptors (RLRs) and Toll-like receptors (TLRs), only TLR2, TLR6, TLR7, and TLR9 contribute to the NF-κB-dependent secretion of TNF and the inflammasome-dependent secretion of IL-1β in response to vMyxM013-KO virus infection. Additionally, we demonstrate that early triggering of the mitogen-activated protein kinase pathway by vMyxM013-KO virus infection of THP-1 cells plays a critical common upstream role in the coordinate induction of both NF-κB and inflammasome pathways. We conclude that an additional cellular sensor(s)/receptor(s) in addition to the known RLRs/TLRs plays a role in the M013 knockout virus-induced activation of NF-κB pathway signaling, but the activation of inflammasomes entirely depends on sensing by the NLRP3 receptor in response to vMyxM013-KO infection of human myeloid cells.
Creation of a Nonspreading Rift Valley Fever Virus
Authors: Kortekaas Jeroen , Oreshkova Nadia , Cobos-Jiménez Viviana , Vloet Rianka P. M. , Potgieter Christiaan A. , Moormann Rob J. M.
Published: September 2011

Rift Valley fever virus (RVFV) is a mosquito-borne zoonotic bunyavirus of the genus
Phlebovirus
and a serious human and veterinary pathogen. RVFV contains a three-segmented RNA genome, which is comprised of the large (L), medium (M), and small (S) segments. The proteins that are essential for genome replication are encoded by the L and S segments, whereas the structural glycoproteins are encoded by the M segment. We have produced BHK replicon cell lines (BHK-Rep) that maintain replicating L and S genome segments. Transfection of BHK-Rep cells with a plasmid encoding the structural glycoproteins results in the efficient production of RVFV replicon particles (RRPs). To facilitate monitoring of infection, the NSs gene was replaced with an enhanced green fluorescent protein gene. RRPs are infectious for both mammalian and insect cells but are incapable of autonomous spreading, rendering their application outside biosafety containment completely safe. We demonstrate that a single intramuscular vaccination with RRPs protects mice from a lethal dose of RVFV and show that RRPs can be used for rapid virus neutralization tests that do not require biocontainment facilities. The methods reported here will greatly facilitate vaccine and drug development as well as fundamental studies on RVFV biology. Moreover, it may be possible to develop similar systems for other members of the bunyavirus family as well.
DNA Mismatch Repair Proteins Are Required for Efficient Herpes Simplex Virus 1 Replication
Authors: Mohni Kareem N. , Mastrocola Adam S. , Bai Ping , Weller Sandra K. , Heinen Christopher D.
Published: September 2011

Herpes simplex virus 1 (HSV-1) is a double-stranded DNA virus that replicates in the nucleus of its human host cell and is known to interact with many cellular DNA repair proteins. In this study, we examined the role of cellular mismatch repair (MMR) proteins in the virus life cycle. Both MSH2 and MLH1 are required for efficient replication of HSV-1 in normal human cells and are localized to viral replication compartments. In addition, a previously reported interaction between MSH6 and ICP8 was confirmed by coimmunoprecipitation and extended to show that UL12 is also present in this complex. We also report for the first time that MLH1 associates with ND10 nuclear bodies and that like other ND10 proteins, MLH1 is recruited to the incoming genome. Knockdown of MLH1 inhibits immediate-early viral gene expression. MSH2, on the other hand, which is generally thought to play a role in mismatch repair at a step prior to that of MLH1, is not recruited to incoming genomes and appears to act at a later step in the viral life cycle. Silencing of MSH2 appears to inhibit early gene expression. Thus, both MLH1 and MSH2 are required but appear to participate in distinct events in the virus life cycle. The observation that MLH1 plays an earlier role in HSV-1 infection than does MSH2 is surprising and may indicate a novel function for MLH1 distinct from its known MSH2-dependent role in mismatch repair.
A Multifunctional Protein Encoded by Turkey Herpesvirus Suppresses RNA Silencing in Nicotiana benthamiana
Authors: Jing Xiu-li , Fan Mei-na , Jia Gang , Liu Lan-wei , Ma Lin , Zheng Cheng-chao , Zhu Xiao-ping , Liu Hong-mei , Wang Xiao-yun
Published: September 2011

Many plant and animal viruses counteract RNA silencing-mediated defense by encoding diverse RNA silencing suppressors. We characterized HVT063, a multifunctional protein encoded by turkey herpesvirus (HVT), as a silencing suppressor in coinfiltration assays with green fluorescent protein transgenic
Nicotiana benthamiana
line 16c. Our results indicated that HVT063 could strongly suppress both local and systemic RNA silencing induced by either sense RNA or double-stranded RNA (dsRNA). HVT063 could reverse local silencing, but not systemic silencing, in newly emerging leaves. The local silencing suppression activity of HVT063 was also verified using the heterologous vector PVX. Further, single alanine substitution of arginine or lysine residues of the HVT063 protein showed that each selected single amino acid contributed to the suppression activity of HVT063 and region 1 (residues 138 to 141) was more important, because three of four single amino acid mutations in this region could abolish the silencing suppressor activity of HVT063. Moreover, HVT063 seemed to induce a cell death phenotype in the infiltrated leaf region, and the HVT063 dilutions could decrease the silencing suppressor activity and alleviate the cell death phenotype. Collectively, these results suggest that HVT063 functions as a viral suppressor of RNA silencing that targets a downstream step of the dsRNA formation in the RNA silencing process. Positively charged amino acids in HVT063, such as arginine and lysine, might contribute to the suppressor activity by boosting the interaction between HVT063 and RNA, since HVT063 has been demonstrated to be an RNA binding protein.
Analysis of a Neutralizing Antibody for Human Herpesvirus 6B Reveals a Role for Glycoprotein Q1 in Viral Entry
Authors: Kawabata Akiko , Oyaizu Hiroko , Maeki Takahiro , Tang Huamin , Yamanishi Koichi , Mori Yasuko
Published: September 2011

Human herpesvirus 6 (HHV-6) is a T cell-tropic betaherpesvirus. HHV-6 can be classified into two variants, HHV-6A and HHV-6B, based on differences in their genetic, antigenic, and growth characteristics and cell tropisms. The function of HHV-6B should be analyzed more in its life cycle, as more than 90% of people have the antibodies for HHV-6B but not HHV-6A. It has been shown that the cellular receptor for HHV-6A is human CD46 and that the viral ligand for CD46 is the envelope glycoprotein complex gH/gL/gQ1/gQ2; however, the receptor-ligand pair used by HHV-6B is still unknown. In this study, to identify the glycoprotein(s) important for HHV-6B entry, we generated monoclonal antibodies (MAbs) that inhibit infection by HHV-6B. Most of these MAbs were found to recognize gQ1, indicating that HHV-6B gQ1 is critical for virus entry. Interestingly, the recognition of gQ1 by the neutralizing MAb was enhanced by coexpression with gQ2. Moreover, gQ1 deletion or point mutants that are not recognized by the MAb could nonetheless associate with gQ2, indicating that although the MAb recognized the conformational epitope of gQ1 exposed by the gQ2 interaction, this epitope was not related to the gQ2 binding domain. Our study shows that HHV-6B gQ1 is likely a ligand for the HHV-6B receptor, and the recognition site for this MAb will be a promising target for antiviral agents.
Hepatitis C Virus Nucleotide Inhibitors PSI-352938 and PSI-353661 Exhibit a Novel Mechanism of Resistance Requiring Multiple Mutations within Replicon RNA
Authors: Lam Angela M. , Espiritu Christine , Bansal Shalini , Micolochick Steuer Holly M. , Zennou Veronique , Otto Michael J. , Furman Phillip A.
Published: September 2011

PSI-352938, a cyclic phosphate nucleotide, and PSI-353661, a phosphoramidate nucleotide, are prodrugs of β-
d
-2′-deoxy-2′-α-fluoro-2′-β-
C
-methylguanosine-5′-monophosphate. Both compounds are metabolized to the same active 5′-triphosphate, PSI-352666, which serves as an alternative substrate inhibitor of the NS5B RNA-dependent RNA polymerase during HCV replication. PSI-352938 and PSI-353661 retained full activity against replicons containing the S282T substitution, which confers resistance to certain 2′-substituted nucleoside/nucleotide analogs. PSI-352666 was also similarly active against both wild-type and S282T NS5B polymerases. In order to identify mutations that confer resistance to these compounds,
in vitro
selection studies were performed using HCV replicon cells. While no resistant genotype 1a or 1b replicons could be selected, cells containing genotype 2a JFH-1 replicons cultured in the presence of PSI-352938 or PSI-353661 developed resistance to both compounds. Sequencing of the NS5B region identified a number of amino acid changes, including S15G, R222Q, C223Y/H, L320I, and V321I. Phenotypic evaluation of these mutations indicated that single amino acid changes were not sufficient to significantly reduce the activity of PSI-352938 and PSI-353661. Instead, a combination of three amino acid changes, S15G/C223H/V321I, was required to confer a high level of resistance. No cross-resistance exists between the 2′-F-2′-
C
-methylguanosine prodrugs and other classes of HCV inhibitors, including 2′-modified nucleoside/-tide analogs such as PSI-6130, PSI-7977, INX-08189, and IDX-184. Finally, we determined that in genotype 1b replicons, the C223Y/H mutation failed to support replication, and although the A15G/C223H/V321I triple mutation did confer resistance to PSI-352938 and PSI-353661, this mutant replicated at only about 10% efficiency compared to the wild type.
Molecular Determinants of Arenavirus Z Protein Homo-Oligomerization and L Polymerase Binding
Authors: Loureiro Maria Eugenia , Wilda Maximiliano , Levingston Macleod Jesica M. , D'Antuono Alejandra , Foscaldi Sabrina , Buslje Cristina Marino , Lopez Nora
Published: September 2011

The arenavirus Z is a zinc-binding RING protein that has been implicated in multiple functions during the viral life cycle. These roles of Z involve interactions with viral and cellular proteins that remain incompletely understood. In this regard, Z inhibits viral RNA transcription and replication through direct interaction with the viral L polymerase. Here, we defined the L-binding domain of Tacaribe virus (TCRV) Z protein and the structural requirements mediating Z homo-oligomerization. By using site-directed mutagenesis, coimmunoprecipitation, and functional assays, we showed that residues R37, N39, W44, L50, and Y57, located around the zinc coordination site I, play a critical role in the Z-L interaction. We also found that Z protein from either TCRV or the pathogenic Junin virus (JUNV) self-associates into oligomeric forms in mammalian cells. Importantly, mutation of the myristoylation site, the strictly conserved residue G at position 2, severely impaired the ability of both TCRV Z and JUNV Z to self-interact as well as their capacity to accumulate at the plasma membrane, strongly suggesting that Z homo-oligomerization is associated with its myristoylation and cell membrane targeting. In contrast, disruption of the RING structure or substitution of W44 or N39, which are critical for L protein recognition, did not affect Z self-binding. Overall, the data presented here indicate that homo-oligomerization is not a requirement for Z-L interaction or Z-mediated polymerase activity inhibition.
A Domain in the Herpes Simplex Virus 1 Triplex Protein VP23 Is Essential for Closure of Capsid Shells into Icosahedral Structures
Authors: Kim Hong Seok , Huang Eugene , Desai Jigisha , Sole Marieta , Pryce Erin N. , Okoye Mercy E. , Person Stanley , Desai Prashant J.
Published: September 2011

VP23 is a key component of the triplex structure. The triplex, which is unique to herpesviruses, is a complex of three proteins, two molecules of VP23 which interact with a single molecule of VP19C. This structure is important for shell accretion and stability of the protein coat. Previous studies utilized a random transposition mutagenesis approach to identify functional domains of the triplex proteins. In this study, we expand on those findings to determine the key amino acids of VP23 that are required for triplex formation. Using alanine-scanning mutagenesis, we have made mutations in 79 of 318 residues of the VP23 polypeptide. These mutations were screened for function both in the yeast two-hybrid assay for interaction with VP19C and in a genetic complementation assay for the ability to support the replication of a VP23 null mutant virus. These assays identified a number of amino acids that, when altered, abolish VP23 function. Abrogation of virus assembly by a single-amino-acid change bodes well for future development of small-molecule inhibitors of this process. In addition, a number of mutations which localized to a C-terminal region of VP23 (amino acids 205 to 241) were still able to interact with VP19C but were lethal for virus replication when introduced into the herpes simplex virus 1 (HSV-1) KOS genome. The phenotype of many of these mutant viruses was the accumulation of large open capsid shells. This is the first demonstration of capsid shell accumulation in the presence of a lethal VP23 mutation. These data thus identify a new domain of VP23 that is required for or regulates capsid shell closure during virus assembly.
Modulation of NKG2D-Mediated Cytotoxic Functions of Natural Killer Cells by Viral Protein R from HIV-1 Primary Isolates
Authors: Pham Tram N. Q. , Richard Jonathan , Gerard Francine C. A. , Power Christopher , Cohen Éric A.
Published: September 2011

HIV-1 viral protein R (Vpr) from laboratory-adapted virus strains activates the DNA damage/stress sensor ATR kinase and induces cell cycle arrest at the G
2
/M phase through a process that requires Vpr to engage the DDB1-CUL4A (VprBP/DCAF-1) E3 ligase complex. Activation of this DNA damage/stress checkpoint in G
2
by Vpr was shown to modulate NKG2D-dependent NK cell effector functions via enhancing expression of NKG2D ligands, notably ULBP2. However, it is unknown whether Vpr from HIV-1 primary isolates (groups M, N, O, and P) could modulate NKG2D-mediated cytotoxic functions of NK cells. Here, we report that Vpr from most HIV-1 primary isolates can upregulate ULBP2 expression and induce NKG2D-dependent NK cell killing. Importantly, these activities were always accompanied by an active G
2
cell cycle arrest function. Interestingly, Vpr variants from group P and a clade D isolate of group M were defective at enhancing NKG2D-mediated NK cell lysis owing to their inability to augment ULBP2 expression. However, distinct mechanisms were responsible for their failure to do so. While Vpr from group P was deficient in its ability to engage the DDB1-CUL4A (VprBP/DCAF-1) E3 ligase complex, the Vpr variant from group D was unable to properly localize to the nucleus, underlining the importance of these biological properties in Vpr function. In conclusion, the ability of Vpr from HIV-1 primary isolates to regulate NK cell effector function underscores the importance of this HIV-1 accessory protein in the modulation of the host's innate immune responses.
Efficiency of Neutralizing Antibodies Targeting the CD4-Binding Site: Influence of Conformational Masking by the V2 Loop in R5-Tropic Clade C Simian-Human Immunodeficiency Virus
Authors: Watkins Jennifer D. , Diaz-Rodriguez Juan , Siddappa Nagadenahalli B. , Corti Davide , Ruprecht Ruth M.
Published: September 2011

In R5-tropic clade C simian-human immunodeficiency viruses (SHIV-Cs), we identified a 3-asparagine (3N) deletion mutation in the V2 loop stem of gp120 as the major determinant of neutralization escape of the anti-CD4-binding site (anti-CD4-bs) neutralizing monoclonal antibody (nMAb) b12. However, the more potent anti-CD4-bs nMAbs VRC01 and VRC03 were not sensitive to this mutation. Using isogenic tier 1 or tier 2 proviruses differing only in the 3N mutation, we showed that this mutation might result in selective conformational b12 epitope masking. Therefore, human immunodeficiency virus (HIV) Env immunogens targeting the CD4-bs and designed to neutralize tier 2 viruses should take conformational masking by the V2 loop into account.