bluuebunny/crossref_metadata_2025 huggingface dataset:
Incorporating evolutionary principles into environmental management and policy
Authors: Lankau Richard , Jørgensen Peter Søgaard , Harris David J. , Sih Andrew
Published: February 2011

As policymakers and managers work to mitigate the effects of rapid anthropogenic environmental changes, they need to consider organisms’ responses. In light of recent evidence that evolution can be quite rapid, this now includes evolutionary responses. Evolutionary principles have a long history in conservation biology, and the necessary next step for the field is to consider ways in which conservation policy makers and managers can proactively manipulate evolutionary processes to achieve their goals. In this review, we aim to illustrate the potential conservation benefits of an increased understanding of evolutionary history and prescriptive manipulation of three basic evolutionary factors: selection, variation, and gene flow. For each, we review and propose ways that policy makers and managers can use evolutionary thinking to preserve threatened species, combat pest species, or reduce undesirable evolutionary changes. Such evolution‐based management has potential to be a highly efficient and consistent way to create greater ecological resilience to widespread, rapid, and multifaceted environmental change.
Newly rare or newly common: evolutionary feedbacks through changes in population density and relative species abundance, and their management implications
Authors: Lankau Richard A. , Strauss Sharon Y.
Published: February 2011

Environmental management typically seeks to increase or maintain the population sizes of desirable species and to decrease population sizes of undesirable pests, pathogens, or invaders. With changes in population size come long‐recognized changes in ecological processes that act in a density‐dependent fashion. While the ecological effects of density dependence have been well studied, the evolutionary effects of changes in population size, via changes in ecological interactions with community members, are underappreciated. Here, we provide examples of changing selective pressures on, or evolution in, species as a result of changes in either density of conspecifics or changes in the frequency of heterospecific versus conspecific interactions. We also discuss the management implications of such evolutionary responses in species that have experienced rapid increases or decreases in density caused by human actions.
Consequences of immunopathology for pathogen virulence evolution and public health: malaria as a case study
Authors: Long Gráinne H. , Graham Andrea L.
Published: February 2011

Evolutionary theories explaining virulence—the fitness damage incurred by infected hosts—often focus on parasite strategies for within‐host exploitation. However, much virulence can be caused by the host’s own immune response: for example, pro‐inflammatory cytokines, although essential for killing malaria parasites, also damage host tissue. Here we argue that immune‐mediated virulence, or ‘immunopathology,’ may affect malaria virulence evolution and should be considered in the design of medical interventions. Our argument is based on the ability of immunopathology to disrupt positive virulence‐transmission relationships assumed under the trade‐off theory of virulence evolution. During rodent malaria infections, experimental reduction of inflammation using reagents approved for field use decreases virulence but increases parasite transmission potential. Importantly, rodent malaria parasites exhibit genetic diversity in the propensity to induce inflammation and invest in transmission‐stage parasites in the presence of pro‐inflammatory cytokines. If immunopathology positively correlates with malaria parasite density, theory suggests it could select for relatively low malaria virulence. Medical interventions which decrease immunopathology may therefore inadvertently select for increased malaria virulence. The fitness consequences to parasites of variations in immunopathology must be better understood in order to predict trajectories of parasite virulence evolution in heterogeneous host populations and in response to medical interventions.
Evolution in agriculture: the application of evolutionary approaches to the management of biotic interactions in agro‐ecosystems
Authors: Thrall Peter H. , Oakeshott John G. , Fitt Gary , Southerton Simon , Burdon Jeremy J. , Sheppard Andy , Russell Robyn J. , Zalucki Myron , Heino Mikko , Ford Denison R.
Published: February 2011

Anthropogenic impacts increasingly drive ecological and evolutionary processes at many spatio‐temporal scales, demanding greater capacity to predict and manage their consequences. This is particularly true for agro‐ecosystems, which not only comprise a significant proportion of land use, but which also involve conflicting imperatives to expand or intensify production while simultaneously reducing environmental impacts. These imperatives reinforce the likelihood of further major changes in agriculture over the next 30–40 years. Key transformations include genetic technologies as well as changes in land use. The use of evolutionary principles is not new in agriculture (e.g. crop breeding, domestication of animals, management of selection for pest resistance), but given land‐use trends and other transformative processes in production landscapes, ecological and evolutionary research in agro‐ecosystems must consider such issues in a broader systems context. Here, we focus on biotic interactions involving pests and pathogens as exemplars of situations where integration of agronomic, ecological and evolutionary perspectives has practical value. Although their presence in agro‐ecosystems may be new, many traits involved in these associations evolved in natural settings. We advocate the use of predictive frameworks based on evolutionary models as pre‐emptive management tools and identify some specific research opportunities to facilitate this. We conclude with a brief discussion of multidisciplinary approaches in applied evolutionary problems.
Access to Long‐Term Care: The True Cause of Hospital Congestion?
Authors: Patrick Jonathan
Published: February 2011

Much attention has been paid to lengthy wait times in emergency departments (EDs) and much research has sought to improve ED performance. However, ED congestion is often caused by the inability to move patients into the wards while the wards in turn are often congested primarily due to patients waiting for a bed in a long‐term care (LTC) facility. The scheduling of clients to LTC is a complex problem that is compounded by the variety of LTC beds (different facilities and room accommodations), the presence of client choice and the competing demands of the hospital and community populations. We present a Markov decision process (MDP) model that determines the required access in order for the census of patients waiting for LTC in the hospitals to remain below a given threshold. We further present a simulation model that incorporates both hospital and community demand for LTC in order to predict the impact of implementing the policy derived from the MDP on the community client wait times and to aid in capacity planning for the future. We test the MDP policy vs. current practice as well as against a number of other proposed policy changes.
Nanotechnology applications in medicine and dentistry
Authors: Gupta Jyoti
Published: February 2011

Nanotechnology, or nanoscience, refers to the research and development of an applied science at the atomic, molecular, or macromolecular levels (i.e. molecular engineering, manufacturing). The prefix “nano” is defined as a unit of measurement in which the characteristic dimension is one billionth of a unit. Although the nanoscale is small in size, its potential is vast. As nanotechnology expands in other fields, clinicians, scientists, and manufacturers are working to discover the uses and advances in biomedical sciences. Applications of nanotechnology in medical and dental fields have only approached the horizon with opportunities and possibilities for the future that can only be limited by our imagination. This paper provides an early glimpse of nanotechnology applications in medicine and dentistry to illustrate their potentially far‐reaching impacts on clinical practice. It also narrates the safety issues concerning nanotechnology applications.
Changes in the oral cavity might reflect psychological disorders in some patients
Authors: Abetz Lanny M. , Savage Neil W. , Kenardy Justin
Published: February 2011

Aim:  The treatment of oral dysesthesias, such as burning mouth syndrome, can be challenging. Patient acceptance of the role of psychological etiological factors might be improved if there are clinical signs that patients could confirm themselves, which could be used as reinforcement of clinical discussions. Published associations between psychological disorder and various oral signs and symptoms are not suited to this purpose, as they are ambiguous in origin and implication. Others, used clinically in this situation, are not supported by published literature. Therefore, the purpose of this study was to determine if a demonstrable relationship could be established between psychological profile and the appearance and function of the oral cavity.

Methods:  Seventy‐nine participants underwent an oral examination and completed a Depression Anxiety Stress Scale‐21 questionnaire. Correlations were calculated between clinical variables and the raw Depression Anxiety Stress Scale scores. Univariate analyses determined variables with significant differences between a high‐risk and normal group, and multiple logistic regression models were calculated for these.

Results:  Various oral signs and symptoms were found to correlate with depression, anxiety, and/or stress, with some predictive of psychological disturbance.

Conclusions:  These signs and symptoms might be used to reinforce the psychological aspects of an oral dysesthesia.
Numerical Investigation of Stall Flutter
Authors: Ekaterinaris J. A. , Platzer M. F.
Published: February 2011

Unsteady, separated, high Reynolds number flow over an airfoil undergoing oscillatory motion is investigated numerically. The compressible form of the Reynolds-averaged governing equations is solved using a high-order, upwind biased numerical scheme. The turbulent flow region is computed using a one-equation turbulence model. The computed results show that the key to the accurate prediction of the unsteady loads at stall flutter conditions is the modeling of the transitional flow region at the leading edge. A simplified criterion for the transition onset is used. The transitional flow region is computed with a modified form of the turbulence model. The computed solution, where the transitional flow region is included, shows that the small laminar/transitional separation bubble forming during the pitch-up motion has a decisive effect on the near-wall flow and the development of the unsteady loads. Detailed comparisons of computed fully turbulent and transitional flow solutions with experimental data are presented.
Radial Mixing in an Axial Turbine
Authors: Dring R. P.
Published: February 2011

The objective of this work was to examine radial mixing in an axial turbine from a number of different perspectives. These include: (1) its impact on the spanwise distributions of the force on the airfoils and the change in the fluid momentum as it passed between them, (2) the mixing coefficient distribution based on measured secondary flow velocities, and (3) comparisons of measured and calculated profile redistribution for an axisymmetric inlet profile and for profiles generated by introducing hot and cold streaks upstream of the turbine. It was seen that a simple diffusive transport model could give a good prediction of most of the measured results.
Unsteady Boundary Layers on a Flat Plate Disturbed by Periodic Wakes: Part I—Measurement of Wake-Affected Heat Transfer and Wake-Induced Transition Model
Authors: Funazaki K.
Published: February 2011

Measurements of wake-affected heat transfer distributions on a flat plate are made by use of a wake generator that consists of a rotating disk and several types of circular cylinder. The main purpose of this study is to construct a wake-induced transition model in terms of an intermittency factor, considering the evolution of the wake-induced turbulent region, a so-called turbulent patch in a distance–time diagram. A comparison between the proposed transition model and the measured heat transfer data reveals that the transition model yields good agreement with the measured data of all test conditions in this study.
The Influence of Blade Wakes on the Performance of Interturbine Diffusers
Authors: Dominy R. G. , Kirkham D. A.
Published: February 2011

Interturbine diffusers provide continuity between HP and LP turbines while diffusing the flow upstream of the LP turbine. Increasing the mean turbine diameter offers the potential advantage of reducing the flow factor in the following stages, leading to increased efficiency. The flows associated with these interturbine diffusers differ from those in simple annular diffusers both as a consequence of their high-curvature S-shaped geometry and of the presence of wakes created by the upstream turbine. It is shown that even the simplest two-dimensional wakes result in significantly modified flows through such ducts. These introduce strong secondary flows demonstrating that fully three-dimensional, viscous analysis methods are essential for correct performance modeling.
Direct Outer Ring Cooling of a High Speed Jet Engine Mainshaft Ball Bearing: Experimental Investigation Results
Authors: Gloeckner Peter , Dullenkopf Klaus , Flouros Michael
Published: February 2011

Operating conditions in high speed mainshaft ball bearings applied in new aircraft propulsion systems require enhanced bearing designs and materials. Rotational speeds, loads, demands on higher thrust capability, and reliability have increased continuously over the last years. A consequence of these increasing operating conditions are increased bearing temperatures. A state of the art jet engine high speed ball bearing has been modified with an oil channel in the outer diameter of the bearing. This oil channel provides direct cooling of the outer ring. Rig testing under typical flight conditions has been performed to investigate the cooling efficiency of the outer ring oil channel. In this paper, the experimental results including bearing temperature distribution, power dissipation, and bearing oil pumping and the impact on oil mass and parasitic power loss reduction are presented.
Experiments on Elastic Polyether Polyurethane Foams Under Multiaxial Loading: Mechanical Response and Strain Fields
Authors: Dai Xiangyu , Sabuwala Tapan , Gioia Gustavo
Published: February 2011

We study experimentally the mechanical response of elastic polyether polyurethane (EPP) foams up to large strains over the range of commercially available densities and for a variety of loading conditions. To this end, we subject the foams in a set of EPP foams to five different tests, namely, compression along the rise direction, compression along a transverse direction, tension along the rise direction, simple shear combined with compression along the rise direction, and hydrostatic pressure combined with compression along the rise direction. The set of EPP foams consists of foams of five apparent densities ranging from 50.3 kg/m3 to 221 kg/m3. For each test and foam density, we report the mechanical response in the form of a stress-strain curve or a force-displacement curve. For some tests and foam densities, we use a digital image correlation method to measure the strain field on the surface of the foam. In a discussion of our experimental results, we put emphasis on the relation between the stress-strain or force-displacement curve recorded in a test and the attendant strain fields.
Characteristics of Turbulent Three-Dimensional Wall Jets
Authors: Agelin-Chaab M. , Tachie M. F.
Published: February 2011

Three-dimensional turbulent wall jet was investigated using a particle image velocimetry technique. Three Reynolds numbers based on the jet exit velocity and diameter of 5000, 10,000, and 20,000 were studied. Profiles of the mean velocities, turbulence intensities, and Reynolds shear stresses as well as two-point velocity correlations and proper orthogonal decomposition analyses were used to document the salient features of the wall jets. The decay and spread rates are independent of Reynolds numbers in the self-similar region. The estimated values of 1.15, 0.054, and 0.255 for the decay rate, wall-normal spread rate, and lateral spread rate, respectively, are within the range of values reported in the literature. The two-point correlation analysis showed that the inclination of the streamwise velocity correlation contours in the inner layer is 11±3 deg in the wall region, which is similar to those of canonical turbulent boundary layers. The results from the proper orthogonal decomposition indicate that low-order modes contribute more to the turbulence statistics in the self-similar region than in the developing region. The Reynolds shear stresses are the biggest benefactors of the low-order mode contribution while the wall-normal turbulence intensities are the least.
The Refined Theory of One-Dimensional Quasi-Crystals in Thick Plate Structures
Authors: Gao Yang , Ricoeur Andreas
Published: February 2011

For one-dimensional quasi-crystals, the refined theory of thick plates is explicitly established from the general solution of quasi-crystals and the Luré method without employing ad hoc stress or deformation assumptions. For a homogeneous plate, the exact equations and solutions are derived, which consist of three parts: the biharmonic part, the shear part, and the transcendental part. For a nonhomogeneous plate, the exact governing differential equations and solutions under pure normal loadings and pure shear loadings, respectively, are obtained directly from the refined plate theory. In an illustrative example, explicit expressions of analytical solutions are obtained for torsion of a rectangular quasi-crystal plate.
Low-Cost Kit of Plastic Modular Adaptors for External Transtibial Prostheses
Authors: Torrealba Rafael R. , Müller-Karger Carmen M.
Published: February 2011

There is a very large need for prosthetic components in developing countries, where such devices are imported and prohibitively expensive. This work explores the possibility of developing and manufacturing prosthetic components locally in Venezuela while preserving high quality and function. We aimed at developing a kit of plastic modular adaptors for external transtibial prostheses. The project covers design, stress analyses, and function assessment of the components. Design criteria were established from the state-of-the-art of prosthetic adaptors in commercial models and international patents. The resulting kit comprises four adaptors of simple design. Their response was studied with stress analysis, using the finite element method, applying static loads for different instants of gait during the stance phase. The simulation of the adaptors shows that the stresses presented for a person weighing up to 980 N (100 kg) do not reach the yield strength of nylon 6.6. Then, five kits of adaptors were manufactured with this thermoplastic material using conventional metal-working machines. The resulting components are lighter and cheaper than equivalent imported metallic ones. The kits were adapted to four patients and assessed via gait analysis and questionnaire. A very good function is observed, with neither significant difference in most of spatiotemporal gait parameters compared to normal values (p<0.05) nor significant asymmetries between prosthetic and sound sides. From the questionnaire, stiffness, maneuverability, and comfort ability of the manufactured kits was found high by all the patients. A 3 months adaptation period was also completed by the patients prior to performing the gait analyses. This period is considered a first field trial of the adaptors; however, these results will be complemented in the future, as the kits were not tested to structural fatigue.
Advanced Deconvolution Technique for Analyzing Multirate Well Test Data
Authors: Cheng Yueming , Lee W. John , McVay Duane A.
Published: February 2011

Deconvolution allows the test analyst to estimate the constant-rate transient pressure response of a reservoir-well system, and assists us in system identification and parameter estimation. Unfortunately, deconvolution amplifies the noise contained in data. Often, we cannot identify the reservoir system from deconvolved results owing to solution instability caused by noise in measured data. We previously presented a deconvolution technique based on the fast Fourier transform that we applied to a single buildup or drawdown period. In this paper, we extend our previous work and apply the deconvolution technique based on the fast Fourier transform to arbitrarily changing rate profiles such as multirate tests. The deconvolution results, which represent a constant-rate pressure drawdown response spanning the entire duration of the test, can provide helpful insight into the correct reservoir description. We have improved our original deconvolution method in number of ways, particularly with the introduction of an iterative algorithm that produces stable deconvolution results. We demonstrate application of our deconvolution method to analysis of synthetic and field examples, including both flow and shut-in periods. Our deconvolution method can efficiently reproduce the characteristic responses of the reservoir-well system and increase our confidence in parameter estimates.
An elementary exposition of the Efimov effect
Authors: Bhaduri Rajat K. , Chatterjee Arindam , van Zyl Brandon P.
Published: February 2011

Two particles that are just shy of binding may develop an infinite number of shallow bound states when a third particle is added. This counterintuitive effect was first predicted by Efimov for identical bosons interacting with a short-range pairwise potential. The Efimov effect persists for nonidentical particles if at least two of the three bonds are almost bound. The Efimov effect has recently been verified experimentally using ultracold atoms. We explain the origin of this effect using elementary quantum mechanics and summarize the experimental evidence for it.
The Crystal Structure of the Signal Recognition Particle in Complex with Its Receptor
Authors: Ataide Sandro F. , Schmitz Nikolaus , Shen Kuang , Ke Ailong , Shan Shu-ou , Doudna Jennifer A. , Ban Nenad
Published: February 2011

Guanine triphosphate controls changes in the signal recognition particle that facilitate transfer of the signal sequence to the translocon.
Deflating the Genomic Bubble
Authors: Evans James P. , Meslin Eric M. , Marteau Theresa M. , Caulfield Timothy
Published: February 2011

Unrealistic expectations and uncritical translation of genetic discoveries may undermine other promising approaches to preventing disease and improving health.
Spin Selectivity in Electron Transmission Through Self-Assembled Monolayers of Double-Stranded DNA
Authors: Göhler B. , Hamelbeck V. , Markus T. Z. , Kettner M. , Hanne G. F. , Vager Z. , Naaman R. , Zacharias H.
Published: February 2011

Photoelectrons emitted from a DNA-covered gold surface can have an unbalanced spin population of up to 60%.
Facing Up to Vexing Choices
Conservation Science
Balancing the Needs of People and Nature

by Peter Kareiva and Michelle Marvier

Roberts, Greenwood Village, CO, 2011. 573 pp. $90, £50, €60. ISBN 9781936221066.
Authors: Fanshawe John
Published: February 2011

The authors place stewardship of both human welfare and biodiversity at the center of the challenges facing researchers interested in sustainability and conservation.
The Genomic Foundation Is Shifting
Authors: Mattick John S.
Published: February 2011

The most important outcome of the human genome project has been to expose the fallacy that most genetic information is expressed as proteins.
High-Priced Recruiting of Talent Abroad Raises Hackles
Authors: Xin Hao
Published: February 2011

The Chinese government will soon announce a new initiative to lure up to 10 winners of prestigious international science prizes to China each year by offering what may be the heftiest reward ever paid to individual researchers.
Science in Ivins Case Not Ironclad, NRC Says
Authors: Bhattacharjee Yudhijit
Published: February 2011

The scientific evidence behind the U.S. government's implication of U.S. Army researcher Bruce Ivins as the perpetrator of the 2001 anthrax letter attacks is not as strong as claimed by the FBI, according to a long-awaited review by the National Research Council released this week.
Can This DNA Sleuth Help Catch Criminals?
Authors: Enserink Martin
Published: February 2011

Forensic geneticist Manfred Kayser is exploring whether DNA found at a crime scene can predict what a suspect looks like.
NASA Weighs Asteroids: Cheaper Than Moon, But Still Not Easy
Authors: Kerr Richard A.
Published: February 2011

Budgetary realities are driving U.S. astronauts away from the moon toward near-Earth asteroids, but the new goal on the way to Mars should prove uniquely challenging.
Europe's Eager Reformer Takes on Framework Funding Goliath
Authors: Vogel Gretchen
Published: February 2011

An outsider to the scientific community, the E.U.'s new research commissioner promises to cut red tape, champion basic research, and fight to save ITER
A Celebration of the Genome, Part III
Authors: Jasny Barbara R. , Zahn Laura M.
Published: February 2011

The tenth anniversary of the first publications of the human genome sequence provides an opportunity for a set of diverse thinkers to reflect on what the achievement has meant for themselves and their communities, as well as future directions.
Development and Evaluation of a Latex Agglutination Test for the Serodiagnosis of Paracoccidioidomycosis
Authors: Silveira-Gomes Fabíola , Sarmento Dayse Nogueira , Pinto Thifany Mendes , Pimentel Rosiane Ferreira , Nepomuceno Lívia Barreto , Espírito Santo Elaine Patrícia T. , Mesquita-da-Costa Maurimélia , Camargo Zoilo Pires , Marques-da-Silva Silvia Helena
Published: February 2011

Paracoccidioidomycosis (PCM) is the most prevalent systemic mycosis in Latin America. It is caused by the dimorphic fungusParacoccidioides brasiliensis. The immunodiffusion (ID) test is one of the most widely used techniques for PCM serologic diagnosis due to the simplicity and low costs of its execution. However, it requires trained and qualified people to execute it. The purpose of this study was to evaluate a latex particle agglutination (LA) test for the detection of anti-P. brasiliensisantibodies by using pooled crude exoantigens from the fungus. Fifty-one serum samples obtained from patients with PCM were tested. Positivity was observed in 84% (43/51) of these patients, and the agglutination patterns varied from small clumps with a cloudy background to large clumps with a clear background. The antibody titer reactivity ranged from 1:2 to 1:64. Cross-reactivity was observed in sera from patients with aspergillosis, histoplasmosis, and nonfungal disease. Serum samples obtained from healthy donors were not reactive. The sensitivity and specificity of the LA test were 84% and 81%, respectively. When comparing the LA test with the double-immunodiffusion test, we found an agreement of 92%. Further work is needed to improve the performance of the LA assay before it can be proposed as a reliable diagnostic tool, mainly in laboratories with little infrastructure.
Increased Cell-Mediated Immune Responses in Patients with Recurrent Herpes Simplex Virus Type 2 Meningitis
Authors: Franzen-Röhl Elisabeth , Schepis Danika , Lagrelius Maria , Franck Kristina , Jones Petra , Liljeqvist Jan-Åke , Bergström Tomas , Aurelius Elisabeth , Kärre Klas , Berg Louise , Gaines Hans
Published: February 2011

The clinical picture of herpes simplex virus type 2 (HSV-2) infection includes genital blisters and less frequently meningitis, and some individuals suffer from recurrent episodes of these manifestations. We hypothesized that adaptive and/or innate immune functional deficiencies may be a major contributing factor in susceptibility to recurrent HSV-2 meningitis. Ten patients with recurrent HSV-2 meningitis were studied during clinical remission. For comparison, 10 patients with recurrent genital HSV infections as well as 21 HSV-seropositive and 19 HSV-seronegative healthy blood donors were included. HSV-specific T cell blasting and cytokine secretion were evaluated in whole blood cultures. HSV-2-induced NK cell gamma interferon production, dendritic cell Toll-like receptor (TLR) expression, and TLR agonist-induced alpha interferon secretion were analyzed. Patients with recurrent HSV-2 meningitis had elevated T cell blasting and Th1 and Th2 cytokine production in response to HSV antigens compared to those of patients with recurrent genital infections. A somewhat increased NK cell response, increased dendritic cell expression of TLR3 and -9, and increased TLR-induced alpha interferon responses were also noted. Contrary to our expectation, recurrent HSV-2 meningitis patients have increased HSV-specific adaptive and innate immune responses, raising the possibility of immune-mediated pathology in the development of recurrent HSV2 meningitis.
Modulation of Plasmid DNA Vaccine Antigen Clearance by Caspase 12 RNA Interference Potentiates Vaccination
Authors: Geiben-Lynn Ralf , Frimpong-Boateng Kwesi , Letvin Norman L.
Published: February 2011

The magnitude of the immune responses elicited by plasmid DNA vaccines might be limited, in part, by the duration of vaccine antigen expressionin vivo. To explore strategies for improving plasmid DNA vaccine efficacy, we studied the apoptotic process in myocytes of mice vaccinated intramuscularly. We found that after vaccination, the proapoptotic protein caspase 12 (Casp12) was upregulated in myocytes coincident with the loss of vaccine antigen expression. To harness this observation to improve plasmid DNA vaccine efficacy, we used RNA interference technology, coadministering plasmid DNA expressing a short hairpin RNA (shRNA) of Casp12 with plasmid DNA vaccine constructs. This treatment with shRNA Casp12, administered twice within the first 10 days following vaccine administration, increased antigen expression 7-fold, the antigen-specific CD8+T cell immune response 6-fold, and antigen-specific antibody production 5-fold. This study demonstrates the critical role for Casp12 in plasmid DNA vaccine-induced immune responses and shows that increased antigen expression mediated by down-modulation of Casp12 can be used to potentiate vaccine efficacy.
Rapid Genotyping of Human Papillomavirus by Post-PCR Array-Based Hybridization Techniques
Authors: Pierik Anke , Zwanenburg Chris , Moerland Elna , Broer Dirk , Stapert Henk , van den Brule Adriaan J. C.
Published: February 2011

Kinetic hybridization measurements on a microarray are expected to become a valuable tool for genotyping applications. A method has been developed that enables kinetic hybridization measurements of PCR products on a low-density microarray. This is accomplished by pumping a solution containing PCR products up and down through a porous microarray substrate. After every pumping cycle, the fluorescently labeled PCR products hybridized to capture probes immobilized on the solid surface of the porous microarray substrate are measured. By this method, both binding curves and high-resolution melting curves are obtained instead of the single endpoint hybridization intensities as with commonly used post-PCR array-based hybridization techniques. We used 20 subtypes of the human papillomavirus (HPV) as a model system to test our detection method and blindly analyzed 216 clinical samples. We compared our microarray flowthrough method with a reference method, PCR followed by a
r
everse
l
ine
b
lot (RLB). Real-time hybridization measurements followed by high-resolution melting curves of low concentrations of fluorescently labeled HPV targets on a microarray were successfully carried out without any additional chemical signal amplification. The results of our new method were in good agreement (93%, with a kappa coefficient of κ = 0.88 [95% CI, 0.81 to 0.94]) with the RLB results. All discrepant samples were analyzed by a third method, enzyme immunoassay (EIA). Furthermore, in a number of cases, we were able to identify false-positive samples by making use of the information contained in the kinetic binding and melting curves. This clearly demonstrates the added value of the use of kinetic measurements and high-resolution melting curves, especially for highly homologous targets.
Clinical and Laboratory Characteristics of Invasive Infections Due to Methicillin-Resistant Staphylococcus aureus Isolates Demonstrating a Vancomycin MIC of 2 Micrograms per Milliliter: Lack of Effect of Heteroresistant Vancomycin-Intermediate S. aureus Phenotype
Authors: Satola S. W. , Lessa F. C. , Ray S. M. , Bulens S. N. , Lynfield R. , Schaffner W. , Dumyati G. , Nadle J. , Patel J. B. ,   for the Active Bacterial Core surveillance (ABCs) MRSA Investigators
Published: February 2011

We describe clinical and laboratory characteristics of invasive methicillin-resistant
Staphylococcus aureus
(MRSA) infections with vancomycin MICs of 2 μg/ml and compare heteroresistant-intermediate
S. aureus
(hVISA) to non-hVISA. Health care-associated community-onset infections were the most common and resulted in frequent complications and relapses. hVISA-infected patients were more likely to have been hospitalized in the year prior to MRSA culture.
Development and Validation of a Multiplex PCR for Detection of Scedosporium spp. in Respiratory Tract Specimens from Patients with Cystic Fibrosis
Authors: Harun Azian , Blyth Christopher C. , Gilgado Felix , Middleton Peter , Chen Sharon C.-A. , Meyer Wieland
Published: February 2011

The emergence of
Scedosporium
infections in diverse groups of individuals, which are often treatment refractory, warrants timely and accurate laboratory diagnosis. Species- or group-specific primers based on internal transcribed spacer (ITS) sequence polymorphisms were designed for
Scedosporium aurantiacum
,
Scedosporium dehoogii
,
Scedosporium prolificans
,
Pseudallescheria boydii
species complex (former clade 5)
/Pseudallescheria apiosperma
(formerly classified as
S. apiospermum
sensu lato) and
Pseudallescheria minutispora
. Primers for
S. aurantiacum
,
S. prolificans
, and
P. boydii
species complex/
P. apiosperma
were incorporated into a multiplex PCR assay for the detection and identification of the three major clinically important
Scedosporium
species and validated using sputum specimens collected from patients seen at a major Australian cystic fibrosis clinic. The multiplex PCR assay showed 100% specificity in identifying the three major clinically relevant
Scedosporium
species from pure culture. When evaluated using DNA extracts from sputa, sensitivity and specificity of the multiplex PCR assay were 62.1% and 97.2%, respectively. This highly species-specific multiplex PCR assay offers a rapid and simple method of detection of the most clinically important
Scedosporium
species in respiratory tract specimens.
First Cases of Microsporidiosis in Transplant Recipients in Spain and Review of the Literature
Authors: Galván A. L. , Martín Sánchez A. M. , Pérez Valentín M. A. , Henriques-Gil N. , Izquierdo F. , Fenoy S. , del Aguila C.
Published: February 2011

Microsporidia are currently considered emerging pathogens responsible for life-threatening infections in organ transplant recipients. Here, we describe the first cases of intestinal microsporidiosis by
Enterocytozoon bieneusi
genotype D in two non-HIV-infected renal transplant recipients from Spain. Previously reported cases of microsporidiosis in organ transplant recipients have also been reviewed, highlighting the necessity of considering organ transplant recipients a risk group for microsporidiosis. A systematic search for these parasites is recommended in cases of persistent diarrhea and in the differential diagnosis of other syndromes, such as chronic fever of unknown etiology.
Evaluation of the Abbott RealTi
m
e CT/NG Assay in Comparison to the Roche Cobas Amplicor CT/NG Assay
Authors: Cheng Annie , Qian Qinfang , Kirby James E.
Published: February 2011

Several commercial methods exist for the molecular detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
in clinical samples. Here we evaluated the performance characteristics of the newly FDA-cleared Abbott RealTi
m
e CT/NG assay (where “CT” stands for
Chlamydia trachomatis
and “NG” stands for
Neisseria gonorrhoeae
) that uses the automated
m
2000 molecular platform. Results were compared to those of the Roche Cobas Amplicor CT/NG assay. A total of 926 cervical swab, 45 female urine, 6 male urethral swab, and 407 male urine specimens from 1,384 patients were examined. After resolving all Roche
N. gonorrhoeae
-positive results with two additional real-time PCR assays, we found that the agreement between the assays was excellent. For urine samples, there was 99.6% positive agreement and 97.7% negative agreement for
C. trachomatis
, and for male urine samples, there was 100% positive agreement and 99.7% negative agreement for
N. gonorrhoeae
. For cervical swab samples, there was 98.8% positive agreement and 98.5% negative agreement for
C. trachomatis
, and there was 96.6% positive agreement and 99.8% negative agreement for
N. gonorrhoeae
. In limiting dilution analyses, we found that the Abbot assay was more sensitive than the Roche assay for both
C. trachomatis
and
N. gonorrhoeae
. In addition, there appeared to be an enhanced ability of the Abbott assay to detect dual infections, especially in the presence of large amounts of
N. gonorrhoeae
and small amounts of
C. trachomatis
organisms. In summary, we conclude that the Abbott RealTi
m
e CT/NG assay is an accurate and automated new addition to the available testing options for
C. trachomatis
and
N. gonorrhoeae
.
Evaluation of a DNA Microarray (Check-MDR CT102) for Rapid Detection of TEM, SHV, and CTX-M Extended-Spectrum β-Lactamases and of KPC, OXA-48, VIM, IMP, and NDM-1 Carbapenemases
Authors: Naas Thierry , Cuzon Gaelle , Bogaerts Pierre , Glupczynski Youri , Nordmann Patrice
Published: February 2011

The Check-MDR CT102 microarray, aimed at identifying bacteria producing extended-spectrum β-lactamase (ESBL) (SHV, TEM, and CTX-M) and carbapenemase (KPC, OXA-48, VIM, IMP, and NDM-1), was evaluated on a total of 144 Gram-negative strains expressing various β-lactamases. The sensitivity and specificity were 100% for most tested genes, suggesting that this assay allows accurate identification of common ESBL and carbapenemase producers from bacterial cultures.
Impact of Amino Acid Mutations in PB2, PB1-F2, and NS1 on the Replication and Pathogenicity of Pandemic (H1N1) 2009 Influenza Viruses
Authors: Ozawa Makoto , Basnet Sarmila , Burley Lisa M. , Neumann Gabriele , Hatta Masato , Kawaoka Yoshihiro
Published: February 2011

Here, we assessed the effects of PB1-F2 and NS1 mutations known to increase the pathogenicity of influenza viruses on the replication and pathogenicity in mice of pandemic (H1N1) 2009 influenza viruses. We also characterized viruses possessing a PB1-F2 mutation that was recently identified in pandemic (H1N1) 2009 influenza virus isolates, with and without simultaneous mutations in PB2 and NS1. Our results suggest that some NS1 mutations and the newly identified PB1-F2 mutation have the potential to increase the replication and/or pathogenicity of pandemic (H1N1) 2009 influenza viruses.
Severe Restriction of Xenotropic Murine Leukemia Virus-Related Virus Replication and Spread in Cultured Human Peripheral Blood Mononuclear Cells
Authors: Chaipan Chawaree , Dilley Kari A. , Paprotka Tobias , Delviks-Frankenberry Krista A. , Venkatachari Narasimhan J. , Hu Wei-Shau , Pathak Vinay K.
Published: February 2011

Xenotropic murine leukemia virus-related virus (XMRV) is a gammaretrovirus recently isolated from human prostate cancer and peripheral blood mononuclear cells (PBMCs) of patients with chronic fatigue syndrome (CFS). We and others have shown that host restriction factors APOBEC3G (A3G) and APOBEC3F (A3F), which are expressed in human PBMCs, inhibit XMRV in transient-transfection assays involving a single cycle of viral replication. However, the recovery of infectious XMRV from human PBMCs suggested that XMRV can replicate in these cells despite the expression of APOBEC3 proteins. To determine whether XMRV can replicate and spread in cultured PBMCs even though it can be inhibited by A3G/A3F, we infected phytohemagglutinin-activated human PBMCs and A3G/A3F-positive and -negative cell lines (CEM and CEM-SS, respectively) with different amounts of XMRV and monitored virus production by using quantitative real-time PCR. We found that XMRV efficiently replicated in CEM-SS cells and viral production increased by >4,000-fold, but there was only a modest increase in viral production from CEM cells (<14-fold) and a decrease in activated PBMCs, indicating little or no replication and spread of XMRV. However, infectious XMRV could be recovered from the infected PBMCs by cocultivation with a canine indicator cell line, and we observed hypermutation of XMRV genomes in PBMCs. Thus, PBMCs can potentially act as a source of infectious XMRV for spread to cells that express low levels of host restriction factors. Overall, these results suggest that hypermutation of XMRV in human PBMCs constitutes one of the blocks to replication and spread of XMRV. Furthermore, hypermutation of XMRV proviruses at GG dinucleotides may be a useful and reliable indicator of human PBMC infection.
Herpes Simplex Virus 2 MicroRNA miR-H6 Is a Novel Latency-Associated Transcript-Associated MicroRNA, but Reduction of Its Expression Does Not Influence the Establishment of Viral Latency or the Recurrence Phenotype
Authors: Tang Shuang , Bertke Andrea S. , Patel Amita , Margolis Todd P. , Krause Philip R.
Published: February 2011

The herpes simplex virus 2 (HSV-2) viral microRNA (miRNA) designated miR-H6 is located upstream of the latency-associated transcript (LAT) promoter region on the strand opposite the LAT. Deletion of the LAT promoter and part of LAT exon 1 abolished HSV-2 miR-H6 expression in acutely and latently infected guinea pig dorsal root ganglia (DRG), suggesting that this region is needed both for the expression of LAT-encoded miRNAs and for miR-H6 expression
in vivo
. Relative to cells infected with a viral rescuant, miR-H6 expression was significantly reduced in cells infected with a mutant HSV-2 virus, NotPolyA, with an insertion of a simian virus (SV40) polyadenylation signal sequence between the LAT promoter and miR-H6 sequences. In addition, expression of miR-H6, but not LAT or viral DNA, was significantly reduced in both mouse trigeminal ganglia (TG) and guinea pig DRG latently infected with the NotPolyA mutant. Guinea pigs infected with NotPolyA experienced reduced neurological complications of acute infection relative to those infected with the rescuant, but the recurrence phenotype of the NotPolyA mutant was similar to those of its rescuant and wild-type HSV-2, indicating that reduction of miR-H6 expression is not by itself able to alter the establishment of latency for the wild-type virus or the recurrence phenotype. Furthermore, the mutation in NotPolyA did not affect the propensity of wild-type HSV-2 to establish latency in neurons positive for subtype marker KH10. In contrast to published reports regarding its HSV-1 homolog, HSV-2 miR-H6 did not affect ICP4 expression in transfected or infected cells. We hypothesize that viral miRNAs associated with LAT expression are likely to work collectively, contributing to the phenotype attributed to the LAT.
Regulation of Foamy Virus Protease Activity by Viral RNA: a Novel and Unique Mechanism among Retroviruses
Authors: Hartl Maximilian J. , Bodem Jochen , Jochheim Fabian , Rethwilm Axel , Rösch Paul , Wöhrl Birgitta M.
Published: February 2011

Foamy viruses (FVs) synthesize the Pol precursor protein from a specific transcript. Thus, in contrast to what was found for orthoretroviruses, e.g., human immunodeficiency virus, no Gag-Pol precursor protein is synthesized. Foamy viral Pol consists of a protease (PR) domain, a reverse transcriptase domain, and an integrase domain and is processed into a mature protease-reverse transcriptase (PR-RT) fusion protein and the integrase. Protease activity has to be strictly regulated in order to avoid premature Gag and Pol processing before virus assembly. We have demonstrated recently that FV protease is an inactive monomer with a very weak dimerization tendency and postulated protease activation through dimerization. Here, we identify a specific protease-activating RNA motif (PARM) located in the
pol
region of viral RNA which stimulates PR activity
in vitro
and
in vivo
, revealing a novel and unique mechanism of retroviral protease activation. This mechanism is strikingly different to that of orthoretroviruses, where the protease can be activated even in the absence of viral RNA during the assembly of virus-like particles. Although it has been shown that the integrase domain is important for Pol uptake, activation of the foamy virus protease is integrase independent. We show that at least two foamy virus PR-RT molecules bind to the PARM and only RNAs containing the PARM result in significant activation of the protease. DNA harboring the PARM is not capable of protease activation. Structure determination of the PARM by selective 2′ hydroxyl acylation analyzed by primer extension (SHAPE) revealed a distinct RNA folding, important for protease activation and thus virus maturation.
Recombinant Adenovirus Serotype 26 (Ad26) and Ad35 Vaccine Vectors Bypass Immunity to Ad5 and Protect Nonhuman Primates against Ebolavirus Challenge
Authors: Geisbert Thomas W. , Bailey Michael , Hensley Lisa , Asiedu Clement , Geisbert Joan , Stanley Daphne , Honko Anna , Johnson Joshua , Mulangu Sabue , Pau Maria Grazia , Custers Jerome , Vellinga Jort , Hendriks Jenny , Jahrling Peter , Roederer Mario , Goudsmit Jaap , Koup Richard , Sullivan Nancy J.
Published: February 2011

The use of adenoviruses (Ad) as vaccine vectors against a variety of pathogens has demonstrated their capacity to elicit strong antibody and cell-mediated immune responses. Adenovirus serotype C vectors, such as Ad serotype 5 (Ad5), expressing Ebolavirus (EBOV) glycoprotein (GP), protect completely after a single inoculation at a dose of 10
10
viral particles. However, the clinical application of a vaccine based on Ad5 vectors may be hampered, since impairment of Ad5 vaccine efficacy has been demonstrated for humans and nonhuman primates with high levels of preexisting immunity to the vector. Ad26 and Ad35 segregate genetically from Ad5 and exhibit lower seroprevalence in humans, making them attractive vaccine vector alternatives. In the series of studies presented, we show that Ad26 and Ad35 vectors generate robust antigen-specific cell-mediated and humoral immune responses against EBOV GP and that Ad5 immune status does not affect the generation of GP-specific immune responses by these vaccines. We demonstrate partial protection against EBOV by a single-shot Ad26 vaccine and complete protection when this vaccine is boosted by Ad35 1 month later. Increases in efficacy are paralleled by substantial increases in T- and B-cell responses to EBOV GP. These results suggest that Ad26 and Ad35 vectors warrant further development as candidate vaccines for EBOV.