bluuebunny/crossref_metadata_2025 huggingface dataset:
Morphological variation and chromosome studies in Calligonum mongolicum and C. pumilum (Polygonaceae) suggests the presence of only one species
Authors: Shi Wei , Pan Borong , Gaskin John F. , Kang Xiaoshan
Published: February 2009

Calligonum spp. are common plant species in desert areas of central Asia. Since they are drought‐resistant, salt‐tolerant and grow successfully in sand, they are useful for wind‐breaks and dune stabilization. The fruit morphology is regarded as a key taxonomic character for the genus. Morphological variation among individuals and populations of Calligonum mongolicum Turcz. and C. pumilum Losinsk. is investigated in the present paper. The chromosome number for both species is also presented and found to be the same (2n=18). By combining the overlap and variation in morphological characters, the similar variational ranges and complex relationships of fruit characters, we suggest that C. pumilum should be merged with C. mongolicum and we further discuss additions and improvements to the description of C. mongolicum in ‘Flora of China’.
Abfraction: separating fact from fiction
Authors: Michael JA , Townsend GC , Greenwood LF , Kaidonis JA
Published: February 2009

Non‐carious cervical lesions involve loss of hard tissue and, in some instances, restorative material at the cervical third of the crown and subjacent root surface, through processes unrelated to caries. These non‐carious processes may include abrasion, corrosion and possibly abfraction, acting alone or in combination. Abfraction is thought to take place when excessive cyclic, non‐axial tooth loading leads to cusp flexure and stress concentration in the vulnerable cervical region of teeth. Such stress is then believed to directly or indirectly contribute to the loss of cervical tooth substance. This article critically reviews the literature for and against the concept of abfraction.

Although there is theoretical evidence in support of abfraction, predominantly from finite element analysis studies, caution is advised when interpreting results of these studies because of their limitations. In fact, there is only a small amount of experimental evidence for abfraction. Clinical studies have shown associations between abfraction lesions, bruxism and occlusal factors, such as premature contacts and wear facets, but these investigations do not confirm causal relationships. Importantly, abfraction lesions have not been reported in pre‐contemporary populations.

It is important that oral health professionals understand that abfraction is still a theoretical concept, as it is not backed up by appropriate clinical evidence. It is recommended that destructive, irreversible treatments aimed at treating so‐called abfraction lesions, such as occlusal adjustment, be avoided.
Tate–Shafarevich groups in anticyclotomic ℤp-extensions at supersingular primes
Authors: Çiperiani Mirela
Published: February 2009

Let E/ℚ be an elliptic curve and p a prime of supersingular reduction for E. Denote by $\mathrm {K}_\infty $ the anticyclotomic ℤp-extension of an imaginary quadratic field K which satisfies the Heegner hypothesis. Assuming that p splits in K/ℚ, we prove that ${\mbox {\textcyr {Sh}}} (\mathrm {K}_\infty , \mathrm {E})_{p^\infty }$ has trivial Λ-corank and, in the process, also show that $\mathrm {H^1_{Sel}}(\mathrm {K}_\infty , \mathrm {E}_{p^\infty })$ and $\mathrm {E}(\mathrm {K}_\infty )\otimes \mathbb {Q}_p/\mathbb {Z}_p$ both have Λ-corank two.
p-units in ray class fields of real quadratic number fields
Authors: Chapdelaine Hugo
Published: February 2009

Let K be a real quadratic number field and let p be a prime number which is inert in K. We denote the completion of K at the place p by Kp. We propose a p-adic construction of special elements in Kp× and formulate the conjecture that they should be p-units lying in narrow ray class fields of K. The truth of this conjecture would entail an explicit class field theory for real quadratic number fields. This construction can be viewed as a natural generalization of a construction obtained by Darmon and Dasgupta who proposed a p-adic construction of p-units lying in narrow ring class fields of K.
A Plancherel formula for Sp2n/Spn×Spn and its application
Authors: Mao Zhengyu , Rallis Stephen
Published: February 2009

We compute the spherical functions on the symmetric space Sp2n/Spn×Spn and derive a Plancherel formula for functions on the symmetric space. As an application of the Plancherel formula, we prove an identity which amounts to the fundamental lemma of a relative trace identity between Sp2n and $\widetilde {{\rm Sp}}_n$.
An Approach for the Construction of Entropy Measure and Energy Map in Machine Fault Diagnosis
Authors: Tafreshi R. , Sassani F. , Ahmadi H. , Dumont G.
Published: February 2009

This paper presents a novel wavelet-based methodology for feature extraction and classification. To compare the performance of the proposed approach with major existing methods, a number of sets of real-world machine data acquired by mounting accelerometer sensors on the cylinder head of an engine have been extensively tested. The developed method not only bypasses the demerits of the previous techniques but also demonstrates superior performance.
A Mathematical Model for Vibration-Induced Loosening of Preloaded Threaded Fasteners
Authors: Nassar Sayed A. , Yang Xianjie
Published: February 2009

A mathematical model is proposed for studying the vibration induced loosening of threaded fasteners that are subjected to harmonic transverse excitation, which often causes slippage between the contact surfaces between engaged threads and under the bolt head. Integral equations are derived for the cyclic shear forces as well as the bearing and thread friction torque components. They depend on the ratio of the relative rotational to translational velocities. The relationship between the dynamic thread shear force and bending moment is developed. When the external transverse excitation is large enough, it causes the threaded fasteners to loosen. Numerical results show that the dynamic transverse shear forces on the underhead contact surface, and between the engaged threads, decrease the bearing, and thread friction torque components. The effect of bolt preload, bearing and thread friction coefficients, the amplitude of the harmonic transverse excitation, and the bolt underhead bending on the bolt loosening are investigated. Experimental verification of the analytical model results of the bolt twisting torque is provided.
Steady State Off-Design and Transient Behavior of a Solid Oxide Fuel Cell/Gas Turbine Hybrid Power Plant With Additional Firing of the Gas Turbine Combustor
Authors: Wächter Christian , Joos Franz
Published: February 2009

The purpose of the current work is to analyze and also to verify the operating behavior of a solid oxide fuel cell/gas turbine (GT) hybrid system in order to derive necessary requirements for an appropriate control system. The studies are carried out with a control oriented simplified dynamic model of a 25 MWe hybrid system based on a conceptual design previously presented in literature. As a specific feature additional firing of the GT combustor is investigated. First the design point is defined. Then the off-design performance is presented in terms of characteristic performance maps. Based on operating map investigations an appropriate part-load operating curve is defined with considerations given to constraints (e.g., stack temperature or surge margin), efficiency, and operational flexibility. The load range goes from 40% part-load to 105% overload. To investigate the transient behavior five open loop simulations are carried out changing different model inputs, as well as all model inputs applying a 30% load change according to the operating curve. The simulated behavior reveals that the inputs should be changed with specific care to avoid critical situations during load change.
Application of Exhaust Gas Recirculation in a DLN F-Class Combustion System for Postcombustion Carbon Capture
Authors: ElKady Ahmed M. , Evulet Andrei , Brand Anthony , Ursin Tord Peter , Lynghjem Arne
Published: February 2009

This paper describes experimental work performed at General Electric, Global Research Center to evaluate the performance and understand the risks of using dry low NOx (DLN) technologies in exhaust gas recirculation (EGR) conditions. Exhaust gas recirculation is viewed as an enabling technology for increasing the CO2 concentration of the flue gas while decreasing the volume of the postcombustion separation plant and therefore allowing a significant reduction in CO2 capture cost. A research combustor was developed for exploring the performance of nozzles operating in low O2 environment at representative pressures and temperatures. A series of experiments in a visually accessible test rig have been performed at gas turbine pressures and temperatures, in which inert gases such as N2/CO2 were used to vitiate the fresh air to the levels determined by cycle models. Moreover, the paper discusses experimental work performed using a DLN nozzle used in GE’s F-class heavy-duty gas turbines. Experimental results using a research combustor operating in a partially premixed mode include the effect of EGR on operability, efficiency, and emission performance under conditions of up to 40% EGR. Experiments performed in a fully premixed mode using a DLN single nozzle combustor revealed that further reductions in NOx could be achieved while at the same time still complying with CO emissions. While most existing studies concentrate on limitations related to the minimum oxygen concentration (MOC) at the combustor exit, we report the importance of CO2 levels in the oxidizer. This limitation is as important as the MOC, and it varies with the pressure and firing temperatures.
Robustness Analysis of Mistuned Bladed Disk Using the Upper Bound of Structured Singular Value
Authors: Yao Jianyao , Wang Jianjun , Li Qihan
Published: February 2009

This paper presents a method for the robustness analysis of the bladed disk with bounded random mistuning. The robust stability and performance are evaluated by the upper bound of the structured singular value. The robust control model of the bladed disk is established in virtue of linear fractional transformation. The influences of intentional stiffness mistuning in harmonic patterns on the robustness of the mistuned bladed disk are investigated. The numerical results indicate that the robust performance of the mistuned bladed disk could be effectively enhanced by appropriate harmonic intentional mistuning. The proposed method can help us design a bladed disk, which is insensitive to dangerous random mistuning.
Performance of the Clean Exhaust Engine Concept
Authors: Noppel F. , Lucisano D. , Singh R.
Published: February 2009

The climatic effects of air-traffic pollutants, such as carbon dioxide (CO2) and mononitrogen oxides (NOx), aerosols, contrails, and aviation induced cirrus clouds, are repeatedly stressed in assessment reports. It is therefore desired to reduce all aviation emissions simultaneously. In this paper, a novel propulsion concept, which has the potential to reduce all pollutants, is assessed regarding its performance. It is based on gas turbine technology, derived from the intercooled and recuperated engine cycle. Exhaust water condensation is facilitated inside the engine to avoid the formation of contrails. Particles and aerosols are scavenged from the exhaust gases during condensation. The condensed water is partially redirected into the combustion chamber to mitigate NOx emissions via water injection technique. Calculations suggest that this new concept allows higher thermal efficiencies than conventional designs, yielding in better fuel economy and hence reduces greenhouse gas emissions. The corresponding design parameters for bypass ratio and fan pressure ratio suggest that this concept might be well suited for propfans or remotely driven fans.
Structural Health Monitoring With Autoregressive Support Vector Machines
Authors: Bornn Luke , Farrar Charles R. , Park Gyuhae , Farinholt Kevin
Published: February 2009

The use of statistical methods for anomaly detection has become of interest to researchers in many subject areas. Structural health monitoring in particular has benefited from the versatility of statistical damage-detection techniques. We propose modeling structural vibration sensor output data using nonlinear time-series models. We demonstrate the improved performance of these models over currently used linear models. Whereas existing methods typically use a single sensor’s output for damage detection, we create a combined sensor analysis to maximize the efficiency of damage detection. From this combined analysis we may also identify the individual sensors that are most influenced by structural damage.
A New 3D Finite Element for Sandwich Beams With a Viscoelastic Core
Authors: Amichi Kamel , Atalla Noureddine
Published: February 2009

A sandwich finite element for laminated steels is presented. It is based on a discrete displacement approach and allows for both symmetrical and unsymmetrical configurations. The three-layer sandwich model is built assuming a Timoshenko hypothesis for the viscoelastic core and Euler–Bernoulli hypotheses for the elastic faces, but the latter is modified to account for the rotational influence of the transversal shearing in the core. The validity and accuracy of the presented element are assessed through comparisons with numerical results of sandwich beams and sandwich rings with a variety of geometrical and mechanical properties and various boundary conditions. The present results are also compared with analytical, finite element, and experimental solutions for various boundary conditions.
Fractional Optimal Control of Continuum Systems
Authors: Tangpong X. W. , Agrawal Om P.
Published: February 2009

This paper presents a formulation and a numerical scheme for fractional optimal control (FOC) of a class of continuum systems. The fractional derivative is defined in the Caputo sense. The performance index of a fractional optimal control problem is considered as a function of both the state and the control variables, and the dynamic constraints are expressed by a partial fractional differential equation. The scheme presented relies on reducing the equations of a continuum system into a set of equations that have no space parameter. Several strategies are pointed out for this task, and one of them is discussed in detail. The numerical scheme involves discretizing the space domain into several segments, and expressing the spatial derivatives in terms of variables at spatial node points. The calculus of variations, the Lagrange multiplier, and the formula for fractional integration by parts are used to obtain the Euler–Lagrange equations for the problem. The numerical technique presented in the work of Agrawal (2006, “A Formulation and a Numerical Scheme for Fractional Optimal Control Problems,” Proceedings of the Second IFAC Conference on Fractional Differentiations and Its Applications, FDA ‘06, Porto, Portugal) for the scalar case is extended for the vector case. In this method, the FOC equations are reduced to the Volterra type integral equations. The time domain is also discretized into a number of subintervals. For the linear case, the numerical technique results in a set of algebraic equations that can be solved using a direct or an iterative scheme. An example problem is solved for various orders of fractional derivatives and different spatial and temporal discretizations. For the problem considered, only a few space grid points are sufficient to obtain good results, and the solutions converge as the size of the time step is reduced. The formulation presented is simple and can be extended to FOC of other continuum systems.
Computational Study of the Effects of Shock Waves on Film Cooling Effectiveness
Authors: Zhang C. X.-Z. , Hassan I.
Published: February 2009

The performance of a louver cooling scheme on a transonic airfoil has been studied numerically in this paper. Film cooling holes are located near the passage throat. The Mach number at the location of the jet exit is close to unity. A comparison of film cooling effectiveness between numerical prediction and experimental data for a circular hole shows that the numerical procedures are adequate. In addition to the shock-wave effects and compressibility, curvature effect was also studied by comparing cooling effectiveness on the airfoil surface with that on a flat plate. Substantially higher cooling effectiveness for the louver cooling scheme on the airfoil was predicted at blowing ratios below 1 in comparison to other cooling configurations. At higher blowing ratios than 2 the advantages of the louver cooling scheme become less obvious. It was also found that for the same cooling configuration the cooling effectiveness on the transonic airfoil is slightly higher than that on a flat plate at moderately low blowing ratios below 1. At high blowing ratios above 2 when the oblique shock becomes detached from the leading edge of the hole exits, dramatic reduction in cooling effectiveness occurs as a result of boundary layer separation due to the strong shock waves. A coolant-blockage and shaped-wedge similarity was proposed and found to be able to qualitatively explain this phenomenon satisfactorily.
Addressing Cam Wear and Follower Jump in Single-Dwell Cam-Follower Systems With an Adjustable Modified Trapezoidal Acceleration Cam Profile
Authors: Flocker Forrest W.
Published: February 2009

Presented is a modified trapezoidal cam profile with an adjustable forward and backward acceleration. The profile is suitable for single-dwell cam and follower applications. The main benefit of the profile is that it allows cam designers to choose easily a value for the maximum forward or maximum backward acceleration to achieve design objectives. An additional benefit of the profile is that it has a continuous jerk curve. Follower acceleration is one of the primary factors affecting cam wear and follower jump, two main concerns of cam designers. Large forward acceleration against a load creates cam-follower interface forces that can cause excessive wear. Backward acceleration tends to reduce the cam-follower interface force, and if the backward acceleration is sufficiently large, separation between the cam and follower (“follower jump”) can occur. The cam profile presented in this paper gives cam designers an easy way to adjust the maximum forward or backward acceleration to prevent these problems.
Secondary Air System Component Modeling for Engine Performance Simulations
Authors: Alexiou A. , Mathioudakis K.
Published: February 2009

This paper describes the modeling of typical secondary air system elements such as rotating orifices, seals, and flow passages with heat and work transfer from the surrounding surfaces. The modeling is carried out in an object-oriented simulation environment that allows the creation of different configurations in a simple and flexible manner. This makes possible to compare the performance between different designs of individual components or complete secondary air systems as well as integrate them directly in whole engine performance models. The modeling is validated against published experimental data and computational results. An example of implementation in an engine model is also presented.
Modeling Soot Formation Using Reduced Polycyclic Aromatic Hydrocarbon Chemistry in n-Heptane Lifted Flames With Application to Low Temperature Combustion
Authors: Vishwanathan Gokul , Reitz Rolf D.
Published: February 2009

A numerical study of in-cylinder soot formation and oxidation processes in n-heptane lifted flames using various soot inception species has been conducted. In a recent study by the authors, it was found that the soot formation and growth regions in lifted flames were not adequately represented by using acetylene alone as the soot inception species. Comparisons with a conceptual model and available experimental data suggested that the location of soot formation regions could be better represented if polycyclic aromatic hydrocarbon (PAH) species were considered as alternatives to acetylene for soot formation processes. Since the local temperatures are much lower under low temperature combustion conditions, it is believed that significant soot mass contribution can be attributed to PAH rather than to acetylene. To quantify and validate the above observations, a reduced n-heptane chemistry mechanism has been extended to include PAH species up to four fused aromatic rings (pyrene). The resulting chemistry mechanism was integrated into the multidimensional computational fluid dynamics code KIVA-CHEMKIN for modeling soot formation in lifted flames in a constant volume chamber. The investigation revealed that a simpler model that only considers up to phenanthrene (three fused rings) as the soot inception species has good possibilities for better soot location predictions. The present work highlights and illustrates the various research challenges toward accurate qualitative and quantitative predictions of the soot for new low emission combustion strategies for internal combustion engines.
A Comparison of Ethanol and Butanol as Oxygenates Using a Direct-Injection, Spark-Ignition Engine
Authors: Wallner Thomas , Miers Scott A. , McConnell Steve
Published: February 2009

This study was designed to evaluate a “what if” scenario in terms of using butanol as an oxygenate in place of ethanol in an engine calibrated for gasoline operation. No changes to the stock engine calibration were performed for this study. Combustion analysis, efficiency, and emissions of pure gasoline, 10% ethanol, and 10% butanol blends in a modern direct-injection four-cylinder spark-ignition engine were analyzed. Data were taken at engine speeds of 1000 rpm up to 4000 rpm with load varying from 0 N m (idle) to 150 N m. Relatively minor differences existed between the three fuels for the combustion characteristics such as heat release rate, 50% mass fraction burned, and coefficient of variation in indicated mean effective pressure at low and medium engine loads. However at high engine loads the reduced knock resistance of the butanol blend forced the engine control unit to retard the ignition timing substantially, compared with the gasoline baseline and, even more pronounced, compared with the ethanol blend. Brake specific volumetric fuel consumption, which represented a normalized volumetric fuel flow rate, was lowest for the gasoline baseline fuel due to the higher energy density. The 10% butanol blend had a lower volumetric fuel consumption compared with the ethanol blend, as expected, based on energy density differences. The results showed little difference in regulated emissions between 10% ethanol and 10% butanol. The ethanol blend produced the highest peak specific NOx due to the high octane rating of ethanol and effective antiknock characteristics. Overall, the ability of butanol to perform equally as well as ethanol from an emissions and combustion standpoint, with a decrease in fuel consumption, initially appears promising. Further experiments are planned to explore the full operating range of the engine and the potential benefits of higher blend ratios of butanol.
Carbon Capture for Automobiles Using Internal Combustion Rankine Cycle Engines
Authors: Bilger Robert W. , Wu Zhijun
Published: February 2009

Internal combustion Rankine cycle (ICRC) power plants use oxy-fuel firing with recycled water in place of nitrogen to control combustion temperatures. High efficiency and specific power output can be achieved with this cycle, but importantly, the exhaust products are only CO2 and water vapor: The CO2 can be captured cheaply on condensation of the water vapor. Here we investigate the feasibility of using a reciprocating engine version of the ICRC cycle for automotive applications. The vehicle will carry its own supply of oxygen and store the captured CO2. On refueling with conventional gasoline, the CO2 will be off-loaded and the oxygen supply replenished. Cycle performance is investigated on the basis of fuel-oxygen-water cycle calculations. Estimates are made for the system mass, volume, and cost and compared with other power plants for vehicles. It is found that high thermal efficiencies can be obtained and that huge increases in specific power output are achievable. The overall power-plant system mass and volume will be dominated by the requirements for oxygen and CO2 storage. Even so, the performance of vehicles with ICRC power plants will be superior to those based on fuel cells and they will have much lower production costs. Operating costs arising from supply of oxygen and disposal of the CO2 are expected to be around 20 c/l of gasoline consumed and about $25/tonne of carbon controlled. Over all, ICRC engines are found to be a potentially competitive option for the powering of motor vehicles in the forthcoming carbon-controlled energy market.
Swirling Annular Flow in a Steam Separator
Authors: Kataoka Hironobu , Shinkai Yusuke , Hosokawa Shigeo , Tomiyama Akio
Published: February 2009

Effects of pick-off ring configuration on the separator performance of a downscaled model of a steam separator for a boiling water nuclear reactor are examined using various types of pick-off rings. The experiments are conducted using air and water. Pressure drops in a barrel and a diffuser and diameters and velocities of droplets at the exit of the barrel are measured using differential pressure transducers and particle Doppler anemometry, respectively. The separator performance does not depend on the shape of the pick-off ring but strongly depends on the width of the gap between the pick-off ring and the barrel wall. The pressure drop in the barrel is well evaluated using the interfacial friction factor for unstable film flows. Carry-under can be estimated using a droplet velocity distribution at the exit of the separator.
Open Access and Global Participation in Science
Authors: Evans James A. , Reimer Jacob
Published: February 2009

Previous investigations into the impact of open-access journals on subsequent citations confounded open and electronic access and failed to track availability over time. With new data, we separated these effects. We demonstrate that a journal receives a modest increase in citations when it comes online freely, but the jump is larger when it first comes online through commercial sources. This effect reverses for poor countries where free-access articles are much more likely to be cited. Together, findings suggest that free Internet access widens the circle of those who read and make use of scientists' investigations.
Disruption of Vertical Motility by Shear Triggers Formation of Thin Phytoplankton Layers
Authors: Durham William M. , Kessler John O. , Stocker Roman
Published: February 2009

Thin layers of phytoplankton are important hotspots of ecological activity that are found in the coastal ocean, meters beneath the surface, and contain cell concentrations up to two orders of magnitude above ambient concentrations. Current interpretations of their formation favor abiotic processes, yet many phytoplankton species found in these layers are motile. We demonstrated that layers formed when the vertical migration of phytoplankton was disrupted by hydrodynamic shear. This mechanism, which we call gyrotactic trapping, can be responsible for the thin layers of phytoplankton commonly observed in the ocean. These results reveal that the coupling between active microorganism motility and ambient fluid motion can shape the macroscopic features of the marine ecological landscape.
Qualification of the Hemagglutination Inhibition Assay in Support of Pandemic Influenza Vaccine Licensure
Authors: Noah Diana L. , Hill Heather , Hines David , White E. Lucile , Wolff Mark C.
Published: February 2009

Continued outbreaks of highly pathogenic avian influenza over the past decade have spurred global efforts to develop antivirals and vaccines. As part of vaccine development, standard methods are needed for determining serum antibody titers in response to vaccination. Hemagglutination inhibition (HAI) assays are appropriate for assessing the immunogenicity of pandemic influenza vaccines in support of license approval. We demonstrate that a rigorous qualification of the HAI assay for H5N1 influenza virus, evaluating for precision, intermediate precision, linearity, range, specificity, and robustness, satisfies the intent of regulatory guidance for assay validation despite the lack of availability of specific reference standard antigens and antisera.
Differences in Tuberculin Reactivity as Determined in a Veterans Administration Employee Health Screening Program
Authors: Mehta Sanjay R. , MacGruder Cathy , Looney David , Johns Scott , Smith Davey M.
Published: February 2009

In response to a difference in pricing, the San Diego Veterans Administration Medical Center changed its tuberculin preparation from Tubersol to Aplisol in the fall of 2006. Following the change, an increased number of employee skin test conversions was noted. Employee tuberculin skin test converters from 2006 were screened with the QuantiFERON Gold (QFT-G) gamma interferon release assay. Those employees who tested negative by QFT-G were asked to repeat their skin test with both Tubersol and Aplisol tuberculin preparations. Of the new purified protein derivative converters, 12 of 14 returned for repeat testing with QFT-G, and the assay was negative for 83% (10/12), positive for 8% (1/12), and indeterminate for 8% (1/12) of the individuals. Nine of the individuals who were QFT-G negative agreed to repeat skin testing with both tuberculin preparations, and 7/8 (87.5%) demonstrated reactivity with the Aplisol preparation, while 0/8 (0%) reacted to the Tubersol preparation. A change from Tubersol to Aplisol resulted in elevated tuberculin skin test conversion rates that may be due to false-positive reactions. The differences in skin test reactivity between preparations support CDC guidelines that recommend that institutions should not change tuberculin preparations, as doing so may falsely increase the number of positive reactions.
Mucosal Adjuvanticity of a
Shigella
Invasin Complex with DNA-Based Vaccines
Authors: Kaminski Robert W. , Turbyfill K. Ross , Chao C. , Ching W. M. , Oaks Edwin V.
Published: February 2009

Protection against many infectious diseases may require the induction of cell-mediated and mucosal immunity. Immunization with plasmid DNA-based vaccines has successfully induced cell-mediated immune responses in small animals but is less potent in humans. Therefore, several methods are under investigation to augment DNA vaccine immunogenicity. In the current study, a mucosal adjuvant consisting of an invasin protein-lipopolysaccharide complex (Invaplex) isolated from
Shigella
spp. was evaluated as an adjuvant for DNA-based vaccines. Coadministration of plasmid DNA encoding the
Orientia tsutsugamushi
r56Karp protein with Invaplex resulted in enhanced cellular and humoral responses in intranasally immunized mice compared to immunization with DNA without adjuvant. Mucosal immunoglobulin A, directed to plasmid-encoded antigen, was detected in lung and intestinal compartments after Invaplex-DNA immunization followed by a protein booster. Moreover, immunization with Invaplex elicited
Shigella
-specific immune responses, highlighting its potential use in a combination vaccine strategy. The capacity of Invaplex to enhance the immunogenicity of plasmid-encoded genes suggested that Invaplex promoted the uptake and expression of the delivered genes. To better understand the native biological activities of Invaplex related to its adjuvanticity, interactions between Invaplex and mammalian cells were characterized. Invaplex rapidly bound to and was internalized by nonphagocytic, eukaryotic cells in an endocytic process dependent on actin polymerization and independent of microtubule formation. Invaplex also mediated transfection with several plasmid DNA constructs, which could be inhibited with monoclonal antibodies specific for IpaB and IpaC or Invaplex-specific polyclonal sera. The cellular binding and transport capabilities of Invaplex likely contribute to the adjuvanticity and immunogenicity of Invaplex.
Prevalence of Community-Associated Methicillin-Resistant
Staphylococcus aureus
in Patients with Cystic Fibrosis
Authors: Goodrich Jennifer S. , Sutton-Shields Tameaka N. , Kerr Alan , Wedd Joel P. , Miller Melissa B. , Gilligan Peter H.
Published: February 2009

We prospectively determined the prevalence of community-associated
Staphylococcus aureus
in a large cystic fibrosis (CF) center between October 2005 and October 2007. We found that 2.7% (19/707) of the CF patients who had cultures during the study period were infected with this organism, representing 14% of the total methicillin-resistant
Staphylococcus aureus
strains (
n
= 140) recovered from the patient population during the study period.
Diagnosis of
Streptococcus pneumoniae
Infections in Adults with Bacteremia and Community-Acquired Pneumonia: Clinical Comparison of Pneumococcal PCR and Urinary Antigen Detection
Authors: Smith Michael D. , Sheppard Carmen L. , Hogan Angela , Harrison Timothy G. , Dance David A. B. , Derrington Petra , George Robert C.
Published: February 2009

The diagnosis of severe
Streptococcus pneumoniae
infection relies heavily on insensitive culture techniques. To improve the usefulness of PCR assays, we developed a dual-PCR protocol (targeted at pneumolysin and autolysin) for EDTA blood samples. This was compared to the Binax NOW
S. pneumoniae
urine antigen test in patients with bacteremic pneumococcal infections. Patients with nonbacteremic community-acquired pneumonia also were tested by these methods to determine what proportion could be confirmed as pneumococcal infections. A direct comparison was made in a group of patients who each had both tests performed. The Binax NOW
S. pneumoniae
urine antigen test was positive in 51 of 58 bacteremic pneumococcal cases (sensitivity, 88%; 95% confidence interval [CI], 77 to 95%), whereas the dual PCR was positive in 31 cases (sensitivity, 53.5%; 95% CI, 40 to 67%;
P
< 0.0001), and all of these had detectable urinary antigens. Both tests gave positive results in 2 of 51 control patients (referred to as other-organism septicemia), giving a specificity of 96% (95% CI, 86.5 to 99.5%). In 77 patients with nonbacteremic community-acquired pneumonia, urinary antigen was detected significantly more often (in 21 patients [27%]) than a positive result by the dual-PCR protocol (6 [8%]) (
P
= 0.002). The development of a dual-PCR protocol enhanced the sensitivity compared to that of the individual assays, but it is still significantly less sensitive than the Binax NOW urine antigen test, as well as being more time-consuming and expensive. Urinary antigen detection is the nonculture diagnostic method of choice for patients with possible severe pneumococcal infection.
Highly Sensitive Detection of Dengue Virus Nucleic Acid in Samples from Clinically Ill Patients
Authors: Muñoz-Jordán Jorge L. , Collins Cynthia S. , Vergne Edgardo , Santiago Gilberto A. , Petersen Lyle , Sun Wellington , Linnen Jeffrey M.
Published: February 2009

Dengue virus (DENV) is a major cause of febrile illness and hemorrhagic fever in tropical and subtropical regions. Typically, patients presenting with acute dengue disease are viremic but may not have yet developed detectable titers of antibody. Therefore, early diagnosis depends mostly on detection of viral components, such as the RNA. To define the potential use of transcription-mediated amplification (TMA) DENV RNA as a diagnostic tool, we first compared its analytic sensitivity using a routine real-time reverse transcription (RT)-PCR and found that TMA is approximately 10 to 100 times more sensitive. In addition, we tested acute-phase serum samples (<5 days post-symptom onset) submitted as part of laboratory-based surveillance in Puerto Rico and determined that among patients with serologically confirmed dengue infection, TMA detected DENV RNA in almost 80% of serum specimens that were negative by the RT-PCR test used for diagnosis and in all specimens with positive RT-PCR results. We conclude that TMA is a highly sensitive method which can detect DENV RNA in approximately 89% of clinical, acute-phase serum specimens.
Low-Density Macroarray for Rapid Detection and Identification of Crimean-Congo Hemorrhagic Fever Virus
Authors: Wölfel Roman , Paweska Janusz T. , Petersen Nadine , Grobbelaar Antoinette A. , Leman Patricia A. , Hewson Roger , Georges-Courbot Marie-Claude , Papa Anna , Heiser Volker , Panning Marcus , Günther Stephan , Drosten Christian
Published: February 2009

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne viral zoonosis which occurs throughout Africa, Eastern Europe, and Asia and results in an approximately 30% fatality rate. A reverse transcription-PCR assay including a competitive internal control was developed on the basis of the most up-to-date genome information. Biotinylated amplification products were hybridized to DNA macroarrays on the surfaces of polymer supports, and hybridization events were visualized by incubation with a streptavidin-horseradish peroxidase conjugate and the formation of a visible substrate precipitate. Optimal assay conditions for the detection of as few as 6.3 genome copies per reaction were established. Eighteen geographically and historically diverse CCHF virus strains representing all clinically relevant isolates were detected. The feasibility of the assay for clinical diagnosis was validated with acute-phase patient samples from South Africa, Iran, and Pakistan. The assay provides a specific, sensitive, and rapid method for CCHF virus detection without requiring sophisticated equipment. It has usefulness for the clinical diagnosis and surveillance of CCHF infections under limited laboratory conditions in developing countries or in field situations.
The Presence of p53 Influences the Expression of Multiple Human Cytomegalovirus Genes at Early Times Postinfection
Authors: Hannemann Holger , Rosenke Kyle , O'Dowd John M. , Fortunato Elizabeth A.
Published: February 2009

Human cytomegalovirus (HCMV) is a common cause of morbidity and mortality in immunocompromised and immunosuppressed individuals. During infection, HCMV is known to employ host transcription factors to facilitate viral gene expression. To further understand the previously observed delay in viral replication and protein expression in p53 knockout cells, we conducted microarray analyses of p53
+/+
and p53
−/−
immortalized fibroblast cell lines. At a multiplicity of infection (MOI) of 1 at 24 h postinfection (p.i.), the expression of 22 viral genes was affected by the absence of p53. Eleven of these 22 genes (group 1) were examined by real-time reverse transcriptase, or quantitative, PCR (q-PCR). Additionally, five genes previously determined to have p53 bound to their nearest p53-responsive elements (group 2) and three control genes without p53 binding sites in their upstream sequences (group 3) were also examined. At an MOI of 1, >3-fold regulation was found for five group 1 genes. The expression of group 2 and 3 genes was not changed. At an MOI of 5, all genes from group 1 and four of five genes from group 2 were found to be regulated. The expression of control genes from group 3 remained unchanged. A q-PCR time course of four genes revealed that p53 influences viral gene expression most at immediate-early and early times p.i., suggesting a mechanism for the reduced and delayed production of virions in p53
−/−
cells.
Replicon Particles of Venezuelan Equine Encephalitis Virus as a Reductionist Murine Model for Encephalitis
Authors: Schäfer Alexandra , Whitmore Alan C. , Konopka Jennifer L. , Johnston Robert E.
Published: February 2009

Venezuelan equine encephalitis virus (VEE) replicon particles (VRP) were used to model the initial phase of VEE-induced encephalitis in the mouse brain. VRP can target and infect cells as VEE, but VRP do not propagate beyond the first infected cell due to the absence of the structural genes. Direct intracranial inoculation of VRP into mice induced acute encephalitis with signs similar to the neuronal phase of wild-type VEE infection and other models of virus-induced encephalitis. Using the previously established VRP-mRNP tagging system, a new method to distinguish the host responses in infected cells from those in uninfected bystander cell populations, we detected a robust and rapid innate immune response in the central nervous system (CNS) by infected neurons and uninfected bystander cells. Moreover, this innate immune response in the CNS compromised blood-brain barrier integrity, created an inflammatory response, and directed an adaptive immune response characterized by proliferation and activation of microglia cells and infiltration of inflammatory monocytes, in addition to CD4+and CD8+T lymphocytes. Taken together, these data suggest that a naïve CNS has an intrinsic potential to induce an innate immune response that could be crucial to the outcome of the infection by determining the composition and dynamics of the adaptive immune response. Furthermore, these results establish a model for neurotropic virus infection to identify host and viral factors that contribute to invasion of the brain, the mechanism(s) whereby the adaptive immune response can clear the infection, and the role of the host innate response in these processes.
Role of Kaposi's Sarcoma-Associated Herpesvirus C-Terminal LANA Chromosome Binding in Episome Persistence
Authors: Kelley-Clarke Brenna , De Leon-Vazquez Erika , Slain Katherine , Barbera Andrew J. , Kaye Kenneth M.
Published: February 2009

Kaposi's sarcoma-associated herpesvirus (KSHV) LANA is an 1,162-amino-acid protein that tethers terminal repeat (TR) DNA to mitotic chromosomes to mediate episome persistence in dividing cells. C-terminal LANA self-associates to bind TR DNA. LANA contains independent N- and C-terminal chromosome binding regions. N-terminal LANA binds histones H2A/H2B to attach to chromosomes, and this binding is essential for episome persistence. We now investigate the role of C-terminal chromosome binding in LANA function. Alanine substitutions for LANA residues
1068
LKK
1070
and
1125
SHP
1127
severely impaired chromosome binding but did not reduce the other C-terminal LANA functions of self-association or DNA binding. The
1068
LKK
1070
and
1125
SHP
1127
substitutions did not reduce LANA's inhibition of RB1-induced growth arrest, transactivation of the CDK2 promoter, or C-terminal LANA's inhibition of p53 activation of the BAX promoter. When N-terminal LANA was wild type, the
1068
LKK
1070
and
1125
SHP
1127
substitutions also did not reduce LANA chromosome association or episome persistence. However, when N-terminal LANA binding to chromosomes was modestly diminished, the substitutions in
1068
LKK
1070
and
1125
SHP
1127
dramatically reduced both LANA chromosome association and episome persistence. These data suggest a model in which N- and C-terminal LANA cooperatively associates with chromosomes to mediate full-length LANA chromosome binding and viral persistence.
The Marburg Virus 3′ Noncoding Region Structurally and Functionally Differs from That of Ebola Virus
Authors: Enterlein Sven , Schmidt Kristina M. , Schümann Michael , Conrad Dominik , Krähling Verena , Olejnik Judith , Mühlberger Elke
Published: February 2009

We have previously shown that the first transcription start signal (TSS) of Zaire Ebola virus (ZEBOV) is involved in formation of an RNA secondary structure regulating VP30-dependent transcription activation. Interestingly, transcription of Marburg virus (MARV) minigenomes occurs independently of VP30. In this study, we analyzed the structure of the MARV 3′ noncoding region and its influence on VP30 necessity. Secondary structure formation of the TSS of the first gene was experimentally determined and showed substantial differences from the structure formed by the ZEBOV TSS. Chimeric MARV minigenomes mimicking the ZEBOV-specific RNA secondary structure were neither transcribed nor replicated. Mapping of the MARV genomic replication promoter revealed that the region homologous to the sequence involved in formation of the regulatory ZEBOV RNA structure is part of the MARV promoter. The MARV promoter is contained within the first 70 nucleotides of the genome and consists of two elements separated by a spacer region, comprising the TSS of the first gene. Mutations within the spacer abolished transcription activity and led to increased replication, indicating competitive transcription and replication initiation. The second promoter element is located within the nontranslated region of the first gene and consists of a stretch of three UN
5
hexamers. Recombinant full-length MARV clones, in which the three conserved U residues were substituted, could not be rescued, underlining the importance of the UN
5
hexamers for replication activity. Our data suggest that differences in the structure of the genomic replication promoters might account for the different transcription strategies of Marburg and Ebola viruses.
Nucleotide Sequences and Modifications That Determine RIG-I/RNA Binding and Signaling Activities
Authors: Uzri Dina , Gehrke Lee
Published: February 2009

Cytoplasmic viral RNAs with 5′ triphosphates (5′ppp) are detected by the RNA helicase RIG-I, initiating downstream signaling and alpha/beta interferon (IFN-α/β) expression that establish an antiviral state. We demonstrate here that the hepatitis C virus (HCV) 3′ untranslated region (UTR) RNA has greater activity as an immune stimulator than several flavivirus UTR RNAs. We confirmed that the HCV 3′-UTR poly(U/UC) region is the determinant for robust activation of RIG-I-mediated innate immune signaling and that its antisense sequence, poly(AG/A), is an equivalent RIG-I activator. The poly(U/UC) region of the fulminant HCV JFH-1 strain was a relatively weak activator, while the antisense JFH-1 strain poly(AG/A) RNA was very potent. Poly(U/UC) activity does not require primary nucleotide sequence adjacency to the 5′ppp, suggesting that RIG-I recognizes two independent RNA domains. Whereas poly(U) 50-nt or poly(A) 50-nt sequences were minimally active, inserting a single C or G nucleotide, respectively, into these RNAs increased IFN-β expression. Poly(U/UC) RNAs transcribed in vitro using modified uridine 2′ fluoro or pseudouridine ribonucleotides lacked signaling activity while functioning as competitive inhibitors of RIG-I binding and IFN-β expression. Nucleotide base and ribose modifications that convert activator RNAs into competitive inhibitors of RIG-I signaling may be useful as modulators of RIG-I-mediated innate immune responses and as tools to dissect the RNA binding and conformational events associated with signaling.
Replicative Capacity Differences of Thymidine Analog Resistance Mutations in Subtype B and C Human Immunodeficiency Virus Type 1
Authors: Armstrong Kimberly L. , Lee Tun-Hou , Essex M.
Published: February 2009

In order to understand the impact of zidovudine resistance and thymidine analog mutations (TAMs) on subtype C human immunodeficiency virus type 1, we created mutants in subtype C reverse transcriptase (RT). The subtype B RT was placed in a subtype C backbone to act as a control. Mutants and wild-type (WT) virus were competed in a head-to-head competition assay to determine how different clones grew in the same culture. Different viruses were distinguished by sequence tags in
nef
and a quantitative-PCR assay. The 67N and 70R accessory mutations gave an advantage over the WT in subtype C, but these mutations in subtype B had replication capacities similar to that of the WT. Of the triple mutants examined, the TAM-1 types, 41L210W215Y, were the most fit in both subtypes, but only in subtype C was the replication capacity the same as that of the WT. The TAM-2 mutants, 67N70R215F, had the slowest replication in both clones. The mixed TAM pathway mutant, 67N70R215Y, in subtype C had a significant advantage over the TAM-2 mutant, but this was not seen in subtype B. When the WT viruses were competed with each other, the subtype B RT had enhanced replication relative to subtype C. The increased capacities of the 67N and 70R mutations may indicate that there will be greater transmitted resistance and persistence in a subtype C setting than what is known for subtype B.