bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental Evaluation of Numerical Continuation and Bifurcation Methods Applied to Autogyro Rotor Blade Aeromechanical Stability
Authors: Lowenberg Mark , Rezgui Djamel , Bunniss Peter
Published: July 2010

This paper presents a systematic assessment of the use of continuation and bifurcation techniques, in investigating the nonlinear periodic behaviour of rotor blades in forward autorotation. Our aim is to illustrate the potential of these tools in revealing complex blade dynamics, when used in combination (not necessarily in real time) with physical testing. We show a simple procedure to promote understanding of an existing engineering instability problem when uncertainties in the numerical modelling are present. It is proposed that continuation and bifurcation methods can play a significant role in developing numerical/experimental techniques for studying blade dynamics for both autorotating and powered rotors, which can be applied even at the preliminary design phase.
AggieNav: A Small, Well Integrated Navigation Sensor System for Small Unmanned Aerial Vehicles
Authors: Coopmans Calvin
Published: July 2010

Small UAV performance is limited by the sensors used in the navigational systems. Several solutions of various complexity and cost exist, however no ready-made solutions exist for a high-accuracy, low-cost UAV system. Presented is AggieNav: a small, integrated navigational 6 degree-of-freedom with compass and GPS sensor package designed for ideal navigation of small UAVs. System, hardware, and embedded software design for the system is detailed.
Fractional Order Proportional Derivative (FOPD) and FO[PD] Controller Design for Networked Position Servo Systems
Authors: Jin Yongshun , Chen YangQuan , Wang Chunyang , Luo Ying
Published: July 2010

This paper considers the fractional order proportional derivative (FOPD) controller and fractional order [proportional derivative] (FO[PD]) controller for networked position servo systems. The systematic design schemes of the networked position servo system with a time delay are presented. It follows from the Bode plot of the FOPD system and the FO[PD] that the given gain crossover frequency and phase margin are fulfilled. Moreover, the phase derivative w.r.t. the frequency is zero, which means that the closed-loop system is robust to gain variations at the given gain crossover frequency. However, sometimes we can not get the controller parameters to meet our robustness requirement. In this paper, we have studied on this situation and presented the requirement of the gain cross frequency, and phase margin in the designing process. For the comparison of fractional order controllers with traditional integer order controller, the integer order proportional integral differential (IOPID) was also designed by using the same proposed method. The simulation results have verified that FOPD and FO[PD] are effective for networked position servo. The simulation results also reveal that both FOPD controller and FO[PD] controller outperform IO-PID controller for this type of system.
AggieAir: An Integrated and Effective Small Multi-UAV Command, Control and Data Collection Architecture
Authors: Coopmans Calvin , Han Yiding
Published: July 2010

Small UAV performance depends on an effective and efficient command system architecture. Based on an existing UAV system called Paparazzi, AggieAir is a full flight system capable of handling single or multiple UAVs with single or multiple payloads per airframe. System-level block diagrams are presented and specific details about implementation and results are provided.
Immune System-Inspired Dynamic Multi-Robot Coordination
Authors: Khan Muhammad Tahir , de Silva Clarence
Published: July 2010

This paper investigates multi-robot coordination for the deployment of autonomous mobile robots in order to carry out a specific task. A key to utilizing of the full potential of cooperative multi-robot systems is effective and efficient multi-robot coordination. The paper presents a novel method of multi-robot coordination based on an Artificial Immune System. The developed approach relies on Jern’s Immune Network Theory, which concerns how an antibody stimulates or suppresses another antibody and recognizes non-self antigens. In the present work, the robots are analogous to antibodies and the robotic task is analogous to an antigen in a biological immune system. Furthermore, stimulation and suppression in an immune system correspond to communication among robots. The artificial immune system will select the appropriate number of antibodies autonomously to eliminate the antigens. The developed method of multirobot coordination is verified by computer simulation.
Mathematical Morphology in Multi-Dexel Representation
Authors: Zhao Wei , Qian Xiaoping
Published: July 2010

Mathematical morphology provides a set-theoretic approach for spatial structure analysis and is particularly useful for describing the spatial relationship between a tool under motion and the part surface. However, its usage in three-dimension has so far been limited in part due to its computational complexity. This paper presents a multi-dexel based computer implementation of morphology operations. Three dimensional objects (tools and parts) are represented as collections of dexels (depth elements) in multiple directions. Morphology operations such as dilation and erosion are then converted to a series of 1D set operations in each direction. We show that our definition of multi-dexel is formal and our implementation is complete. We present our implementation results on three morphological applications: AFM image simulation, noise removal in 3D mesh, and NC path generation.
Programmable Multispectral Imager Development as Light Weight Payload for Low Cost Fixed Wing Unmanned Aerial Vehicles
Authors: Han Yiding , Jensen Austin , Dou Huifang
Published: July 2010

In this paper, we have developed a light-weight and cost-efficient multispectral imager payload for low cost fixed wing UAVs (Unmanned Aerial Vehicles) that need no runway for takeoff and landing. The imager is band-reconfigurable, covering both visual (RGB) and near infrared (NIR) spectrum. The number of the RGB and NIR sensors is scalable, depending on the demands of specific applications. The UAV on-board microcomputer programs and controls the imager system, synchronizing each camera individually to capture airborne imagery. It also bridges the payload to the UAV system by sending and receiving message packages. The airborne imagery is time-stamped with the corresponding local and geodetic coordinates data measured by the onboard IMU (Inertia Measurement Unit) and GPS (Global Positioning System) module. Subsequently, the imagery will be orthorectified with the recorded geo-referencing data. The application of such imager system includes multispectral remote sensing, ground mapping, target recognition, etc. In this paper, we will outline the technologies, demonstrate our experimental results from actual UAV flight missions, and compare the results with our previous imager system.
Object Pose Estimation for Multi-Robot Cooperative Object Transportation
Authors: Siriwardana Pallege Gamini Dilupa , Khan Muhammad Tahir , de Silva Clarence W.
Published: July 2010

Object recognition and pose estimation are essential for an object transportation system with mobile robots. This paper investigates an approach for pose (position and orientation) estimation of an ordinary object using a laser range finder mounted on the mobile robot. First the CCD camera of the robot finds and identifies an object to be transported in the work environment. On locating a color blob marked on the object, the robot adjusts its pose to move the color blob into the center of the camera frame. Finally a laser range finder is activated to compute the distance and the angle between the laser source and the object. The information acquired in this manner is utilized by the robot to determine a proper pushing location on the object to be transported to goal location. The developed methodology is verified by a series of physical experiments. In the experiments, the object is placed at different positions and orientations and the developed scheme is executed in order to establish its robustness.
Ontology-Driven Integration of CAD/CAE Applications: Strategies and Comparisons
Authors: Zhu Lijuan , Jayaram Uma , Jayaram Sankar , Kim OkJoon
Published: July 2010

In this paper we present a detailed exploration of ontology-driven approaches and strategies for integrating product data between CAD/CAE applications. We structure the ontology model into three layers: General Domain Ontology, Domain Specific Ontology, and Application Specific Ontology. In particular, Application Specific Ontologies are built for PRO/E, CATIA, and a virtual assembly design tool called VADE. This allows the integration processes to be demonstrated for a) two applications in the common domain of product design, and b) two applications in different domains, one in the product design domain and the other in an assembly simulation domain. In addition, these ontology-driven strategies are compared with two other approaches. The first study focuses on the knowledge modeling aspect and compares the ontology approach with a standard modeling language, UML. The second study focuses on data integration and translation aspect and compares the ontology-driven approach with a traditional one. It is concluded that an ontology-driven approach is superior for solving heterogeneous data problems involving multiple applications by managing data on semantic level.
Pre-Run-Time Scheduling of Asynchronous and Periodic Processes With Offsets, Release Times, Deadlines, Precedence and Exclusion Relations
Authors: Xu Jia
Published: July 2010

Utilizing non-zero offsets when scheduling real-time periodic processes significantly increases the chances of satisfying all the timing constraints in a real-time system. In this paper, a method that enables the utilization of non-zero offsets in the pre-run-time scheduling of asynchronous and periodic processes with release times, deadlines, precedence and exclusion relations on either a uniprocessor or on a multiprocessor in real-time embedded systems is presented. This paper also identifies for the first time, the set of general conditions that a periodic process newpi with release time rnewpi, computation time cnewpi, deadline dnewpi, period prdnewpi, permitted range of offset onewpi, must satisfy, in order to satisfy the timing constraints of any given asynchronous process ai with computation time cai, deadline dai, minimum time between two consecutive requests minai, and earliest time that asynchronous process ai can make a request for execution lai. A method based on these general conditions for converting asynchronous processes with earliest request times into new periodic processes with offset constraints is also introduced.
Shape Design Using 1/F Fluctuation Characteristics
Authors: Maekawa Katsuhiro
Published: July 2010

An attempt has been made to develop a method of introducing 1/f fluctuation characteristics into aesthetic objects. First, topographic features of various tea bowls are measured using laser metrology, and their wave patterns are analyzed by the FFT and characterized by using power spectrums. The quantification of an affective factor involved on the outer surface of the tea bowls shows that the handmade tea bowls have an inclination close to −1 on the spatial frequency-power spectrum diagram, which means that it has 1/f fluctuation characteristics. A mass-produced one, on the other hand, tends to have an inclination of near −2, which gives us a monotonous or dull impression. Next, the 1/f fluctuation property is applied to shape design, in which the surface of a tea bowl is created using the measured texture. Rapid prototyping technology is employed to substantiate the model, and it has been confirmed that the accuracy of duplicates is satisfactory. Finally, a mathematical model with 1/f fluctuation characteristics is illustrated to mimic a real handmade tea bowl by using the proposed method.
Stable Inversion Using the Assumed-Modes Rayleigh-Ritz Approximation for Tip Tracking of an Elastic Beam
Authors: Mandali Priyanka , Sun Qiao
Published: July 2010

Inversion control has been very successful in the control of nonlinear dynamical systems. However, when applied to flexible manipulators, inverse dynamics through direct integration in temporal space causes unbounded controller command. For nearly three decades, researchers have exhausted all possible solutions. Still, a perfect solution does not exist that would yield a perfect tip tracking. It has been suggested that seeking an inverse dynamics solution for a given tip trajectory is an ill-posed problem. It has also been suggested that increasing model accuracy by including more terms in a truncated beam model worsens the controller’s ability of stability. In this paper, we seek to understand the nature of the inverse dynamics instability. We use one assumed mode to approximate the beam deflection in a single link manipulator. The mode shape is chosen to ensure a boundedness of the inverse dynamics solution. Such solution is then applied in an inversion controller. Numerical simulations and experiments have both been conducted to show its performance.
Distributed-Parameters Base Modeling and Vibration Analysis of Microcantilevers Used in Atomic Force Microscopy
Authors: Abouelsoud A. A. , Abdo Ahmed J.
Published: July 2010

Friction-induced self-sustained oscillation result in a very robust limit cycle that characterizes stick-slip motion. This motion should be avoided because it creates unwanted noise, diminishes accuracy, and increases wear. The stick-slip motion produced by a mass-spring-damper on a moving belt is analyzed using Lyapunov second method, which is based on constructing a positive definite function and checking the condition for which its time derivative is negative semi-definite. From this condition an estimate of the amplitude of the velocity of the limit cycle of the stick-slip motion is obtained. This estimate is found to be the zero of a certain function derived from the Coulomb friction model. An estimate of the amplitude of the displacement is also found. It is shown that the simulation results of the amplitude and the estimated amplitude are in a good match.
On Adaptivity in Coarse Grain Molecular Dynamics
Authors: Bhalerao Kishor D. , Anderson Kurt S. , Laederach Alain
Published: July 2010

Coarse grain molecular models have gained increasing importance in recent years to understand the macroscopic behavior of large molecular chains such as RNA which are fundamental to many biological processes. In such models, the chemical bonds are considered to be of fixed length and constituent molecules are approximated as rigid or flexible bodies connected via kinematic joints. It has already been demonstrated that the coarse grain models are capable of capturing the global conformational behavior of molecular systems. However, there is no formal way to guide the model coarsening process. One way to enhance the simulation speed and accuracy is to make the system adaptive and allow it to efficiently change the structure and model as the simulation progresses. This paper discusses the challenges in building an adaptive system and proposes certain parameters which could be used to introduce adaptivity in coarse grain molecular dynamics.
Experimental Impact of a Pendulum With the Sand
Authors: Lee Seunghun , Marghitu Dan B.
Published: July 2010

In this paper, a compound pendulum impacting a granular media is studied and the influences of initial impact velocity and impact angle are examined. The resistance forces are studied as the sum of a dynamic frictional force (velocity dependent) and a static resistance force (depth dependent). The penetrating angle is increasing with initial impact velocity as expected. However, the stopping time is decreasing with initial impact velocity for all initial impact angles in our system.
MEMS Gyroscopes Susceptibility to High Frequency Acoustic Noise
Authors: Roth Grant , Flowers George T. , Dean Robert
Published: July 2010

MEMS gyroscopes are becoming more prevalent in inexpensive inertial measurement units used in a variety of harsh environments. It has been shown in previous studies that high power high frequency acoustic noise can have a detrimental effect on these devices. This study examines the threshold of the sound power levels required at these high frequencies to generate detrimental effects on the output of MEMS gyroscopes. This study provides basic background work for further research into mitigation techniques for higher powered high frequency acoustic noise.
Shared Social Responsibility: A Field Experiment in Pay-What-You-Want Pricing and Charitable Giving
Authors: Gneezy Ayelet , Gneezy Uri , Nelson Leif D. , Brown Amber
Published: July 2010

The Greater Good

Zero-sum games (if I win, then you lose) offer an easily grasped heuristic for all sorts of social interactions, especially those that involve money. For instance, companies may offer to contribute some portion of their revenues to charitable causes as an inducement to customers, but it is generally assumed that these pass-throughs directly diminish the corporate bottom line.

Gneezy
et al.

(p.
325
; see the Perspective by

DellaVigna

) have designed a framework that encourages both customers and companies to contribute toward social goods, and, in field tests, this design increased charitable contributions as well as corporate revenues.
Chemoattraction to Dimethylsulfoniopropionate Throughout the Marine Microbial Food Web
Authors: Seymour Justin R. , Simó Rafel , Ahmed Tanvir , Stocker Roman
Published: July 2010

Sulfur Signal Dinner

Phytoplankton produces large amounts of the compound dimethylsulfoniopropionate (DMSP), which can be transformed into the gas dimethylsulfide and emitted into the atmosphere in sufficient quantities to affect cloud formation. The functional role of DMSP is somewhat unclear, but it is degraded by marine bacteria as a source of reduced carbon and sulfur. It also acts as a foraging cue for a variety of aquatic animals ranging from copepods to marine mammals. Now,

Seymour
et al.

(p.
342
) have developed a microfluidic device to observe the behavior of motile microorganisms in response to pulses of DMSP. Contrary to accepted thought, these compounds appear primarily to play a defensive role—for most motile organisms, they are strongly attractive and act as an important infochemical throughout the marine food web.
Hedgehog Signaling Regulates Segment Formation in the Annelid
Platynereis
Authors: Dray Nicolas , Tessmar-Raible Kristin , Le Gouar Martine , Vibert Laura , Christodoulou Foteini , Schipany Katharina , Guillou Aurélien , Zantke Juliane , Snyman Heidi , Béhague Julien , Vervoort Michel , Arendt Detlev , Balavoine Guillaume
Published: July 2010

Hedgehog and Segmentation

Segmentation is a key characteristic of body plan organization in some of the largest animal groups, including annelids, arthropods, and vertebrates, but its evolutionary origins remain debated. In arthropod embryos, the Hedgehog signaling pathway plays a crucial role in the axial patterning of developing segments.

Dray
et al.

(p.
339
) analyzed the function of this conserved pathway in the annelid worm
Platynereis
by using specific small molecule inhibitors and found a similar role for Hedgehog signaling in shaping segments in this animal. Thus, Hedgehog was involved in segment formation in the last common ancestor of the protostome animals, earlier in metazoan evolution than previously assumed.
The Ongoing Mystery of Sea-Floor Methane
Authors: Alperin Marc , Hoehler Tori
Published: July 2010

Our understanding of a major methane sink is based on studies of quiescent sediments and dynamic seeps. But do the same processes operate in both environments?
Chromosome Size Differences May Affect Meiosis and Genome Size
Authors: Wang John , Chen Pei-Jiun , Wang George J. , Keller Laurent
Published: July 2010

Deletions and insertions affect chromosome segregation in the worm
Caenorhabditis elegans
.
Meniscus-Confined Three-Dimensional Electrodeposition for Direct Writing of Wire Bonds
Authors: Hu Jie , Yu Min-Feng
Published: July 2010

Wired

Just as there are difficulties in making integrated circuits smaller and faster, barriers are also being reached in the fabrication of wires that connect chips to the motherboard.
Hu and Yu
(p.
313
) describe the directed electrodeposition and bonding of copper and platinum wires via a meniscus delivered from a micropipette containing a deposition solution. Wires could be deposited on a range of substrates and were significantly smaller than those obtained using existing techniques. This approach may be useful for device packaging and might offer new approaches for constructing tailored nanoscale structures.
Hiding in Plain Sight
Authors: Rosenberg Miriam I. , Desplan Claude
Published: July 2010

Small peptides encoded by a so-called long noncoding RNA play an active role in regulating gene expression.
Belief, Reason, and Insight
The Price of Altruism
George Price and the Search for the Origins of Kindness

by Oren Harman

Norton, New York, 2010. 461 pp. $27.95, C$35. ISBN 9780393067781. Bodley Head, London. £20. ISBN 9781847920621.
Authors: Frank Steven A.
Published: July 2010

Harmon weaves together the story of George Price's tormented life, his profound contributions to evolutionary theory, and sketches of others whose work also increased our understanding of game theory, group selection, and altruism.
Consumers Who Care
Authors: DellaVigna Stefano
Published: July 2010

Can consumers and businesses benefit from socially responsible pricing?
Sickle Cell Disease at 100 Years
Authors: Orkin Stuart H. , Higgs Douglas R.
Published: July 2010

Effective strategies to treat sickle cell disease could involve manipulating the type of hemoglobin produced in patients.
U.S. Panel Weighs Guidelines for Synthetic Biology
Authors: Kaiser Jocelyn
Published: July 2010

Last week, the United States began the highest review to date—in the president's bioethics commission—of problems that could come out of the young field of synthetic biology. The commission will take a "deep dive" into the subject before coming back with advice by the end of this year, said the panel's co-chair.
Scientists Eulogize Center—And Prepare for Stiff Competition
Authors: Finkel Elizabeth
Published: July 2010

The Australian government has omitted the Australian Stem Cell Centre from its 2011 budget, which will force ASCC to close next June. The move will hamper Australia's ability to compete in a hot research field, some scientists claim.
How a Little Fish Keeps Overfished Ecosystem Productive
Authors: Pennisi Elizabeth
Published: July 2010

Off the coast of southwest Africa, researchers have discovered that a small fish called the bearded goby feasts on jellyfish, and in doing so, helps to sustain seabirds, mammals, and larger fish in that ecosystem. In this week's issue of
Science
, they describe this fish's unusual lifestyle, which includes hiding out on the muddy sea floor in water toxic to other fish.
A Song of Science
Authors: Mervis Jeffrey
Published: July 2010

Thomas Nassif, a former science teacher who's now finishing his Ph.D. in behavioral neuroscience, uses a story about migrating birds to help elementary school teachers improve their content knowledge.
When Lightning Strikes
Authors: Mervis Jeffrey
Published: July 2010

Lessons about lightning, composting, and how to build battery-powered cars were among the activities at an event organized for National Lab Day, an ongoing, computer-based, nationwide effort to link teachers with local science professionals.
National Lab Day: Image Gallery
Authors: Mervis Jeffrey
Published: July 2010

A
slide show
captures some National Lab Day activities at Theodore Roosevelt High School and Bell Multicultural High School.
Confronting Anatomy's Nazi Past
Authors: Pringle Heather
Published: July 2010

Studies are uncovering a symbiosis between the Nazi regime, which needed to dispose of executed prisoners, and anatomical institutes, which sought bodies for study.
Immunogenicity Associated with the Routine Use of an Influenza A H1N1 Vaccine in Health Care Personnel in Guangzhou, China
Authors: Di Biao , Xu Xinhong , Li Tiegang , Lu Enjie , Wu Jibin , Liu Yanhui , Chen Yiyun , Pickerill Sam , Wang Ming
Published: July 2010

We present immunogenicity data on the routine vaccination of 103 health care personnel during the 2009 H1N1 national vaccination campaign. The seroprotection rate (percentage of samples with hemagglutination inhibition titers of ≥1:40) was 83.2% at 30 days postvaccination, lower than those obtained in previously published controlled trials. Low baseline antibody levels and an increase in seroprotection in a negative-control cohort suggest that the virus remains prevalent.
Use of Dense Granule Antigen GRA6 in an Immunoglobulin G Avidity Test To Exclude AcuteToxoplasma gondiiInfection during Pregnancy
Authors: Elyasi Hossein , Babaie Jalal , Fricker-Hidalgo Hélène , Brenier-Pinchart Marie-Pierre , Zare Mehrak , Sadeghiani Ghazaleh , Assmar Mehdi , Pelloux Hervé , Golkar Majid
Published: July 2010

The usefulness of a specific immunoglobulin G (IgG) avidity enzyme-linked immunosorbent assay (ELISA) based on recombinant GRA6 antigen for distinguishing between acute and chronicToxoplasmainfection was investigated. Two sets of serum samples obtained from pregnant women with acute, chronic, or noToxoplasmainfection collected in France and Iran were used. Among the French subjects, 19 of 20 (95%) women who experienced seroconversion during the past 4 months before sampling displayed low-avidity IgG antibodies against GRA6, while all 17 (100%) women with chronic infection had high-avidity antibodies. When the Euroimmun IgG avidity ELISA was used, 15 of 19 (78.9%) recently infected women had low-avidity antibodies, and 20 of 22 (90.9%) women with chronic infection displayed high-avidity antibodies. The results suggested better performance of the GRA6 avidity ELISA than the Euroimmun avidity ELISA for exclusion of a recent infection occurring less than 4 months previously. Similarly, all 35 Iranian women with acuteToxoplasmainfection had low-avidity antibodies against GRA6, whereas all 34 women with chronic infection displayed IgG antibodies of high avidity, indicating the value of GRA6 avidity testing for ruling out a recent infection. Avidity tests based on lysed whole-cellToxoplasma gondiiantigen are currently used to exclude recently acquired infections; however, the use of recombinant antigen(s) might improve the diagnostic performance of avidity tests and facilitate the development of more standardized assays.
Comparison of Immunologic Assays for Detecting Immune Responses in HIV Immunotherapeutic Studies: AIDS Clinical Trials Group Trial A5181
Authors: Macatangay Bernard J. C. , Zheng Lu , Rinaldo Charles R. , Landay Alan L. , Pollard Richard B. , Pahwa Savita , Lederman Michael M. , Bucy R. Pat
Published: July 2010

This study was designed to evaluate which of several T-cell-specific, immune response assays are the most relevant in measuring the key characteristics of an effective immune response to HIV-1. Using 5 HIV-1 antigens as stimulants, we assessed lymphocyte proliferation, supernatant gamma interferon (IFN-γ) cytokine production (CP), single-cell IFN-γ production by enzyme-linked immunospot (ELISPOT) assay, with and without Epstein-Barr virus-transformed B-lymphoblastoid cell lines (B-LCLs), and intracellular cytokine production (ICC) for IFN-γ and interleukin 2 (IL-2) by flow cytometry. We used these to compare specimens from HIV-1-infected subjects who were virally suppressed with a stable antiretroviral therapy (ART) regimen (group A) with specimens from subjects not on ART but with HIV-1 viremia of <3,000 copies/ml (group B). The lymphocyte proliferation assay (LPA) did not significantly differentiate between the two groups. Using fresh peripheral blood mononuclear cells (PBMCs), the CP and ELISPOT assays for IFN-γ detected the greatest differences between the two groups, specific for three of the five HIV-1 antigens, whereas significant differences were seen only in response to one antigen when cryopreserved cells were used. The strongest correlations were seen between the CP and ELISPOT assays. The ELISPOT B-LCL assay showed a cell concentration-dependent increase in IFN-γ production compared to that shown by the standard ELISPOT assay but did not differentiate between the groups. In the ICC assay, greater numbers of IFN-γ-producing T cells were seen in group B, and little or no detectable IL-2 production was seen in both groups. These studies highlight complexities of immunologic monitoring of T-cell responses in multisite clinical trials in HIV infection and outline considerations for optimizing these efforts.
Infection during Infancy and Long Incubation Period of Leprosy Suggested in a Case of a Chimpanzee Used for Medical Research
Authors: Suzuki Koichi , Udono Toshifumi , Fujisawa Michiko , Tanigawa Kazunari , Idani Gen'ichi , Ishii Norihisa
Published: July 2010

The length of the incubation period of leprosy following
Mycobacterium leprae
infection has never been conclusively determined, owing to the lack of a method to demonstrate the presence of an asymptomatic infection. We report a rare case of leprosy in a chimpanzee in which a 30-year incubation period was strongly suggested by single nucleotide polymorphism (SNP) analysis.
Evaluation of Pulsed-Field Gel Electrophoresis Profiles for Identification of
Salmonella
Serotypes
Authors: Zou Wen , Lin Wei-Jiun , Foley Steven L. , Chen Chun-Houh , Nayak Rajesh , Chen James J.
Published: July 2010

Pulsed-field gel electrophoresis (PFGE) is a standard typing method for isolates from
Salmonella
outbreaks and epidemiological investigations. Eight hundred sixty-six
Salmonella enterica
isolates from eight serotypes, including Heidelberg (
n
= 323), Javiana (
n
= 200), Typhimurium (
n
= 163), Newport (
n
= 93), Enteritidis (
n
= 45), Dublin (
n
= 25), Pullorum (
n
= 9), and Choleraesuis (
n
= 8), were subjected to PFGE, and their profiles were analyzed by random forest classification and compared to conventional hierarchical cluster analysis to determine potential predictive relationships between PFGE banding patterns and particular serotypes. Cluster analysis displayed only the underlying similarities and relationships of the isolates from the eight serotypes. However, for serotype prediction of a nonserotyped
Salmonella
isolate from its PFGE pattern, random forest classification provided better accuracy than conventional cluster analysis. Discriminatory DNA band class markers were identified for distinguishing
Salmonella
serotype Heidelberg, Javiana, Typhimurium, and Newport isolates.
Rapid Identification of Bacterial Pathogens in Positive Blood Culture Bottles by Use of a Broad-Based PCR Assay Coupled with High-Resolution Melt Analysis
Authors: Won Helen , Rothman Richard , Ramachandran Padmini , Hsieh Yu-Hsiang , Kecojevic Aleksandar , Carroll Karen C. , Aird Deborah , Gaydos Charlotte , Yang Samuel
Published: July 2010

We evaluated a broad-based PCR assay coupled with high-resolution melt analysis for rapid bacterial identification in patients with bacterial sepsis. With a reference library of 60 clinically relevant bacterial species, 52 positive blood culture samples were tested. Our assay identified 46/52 samples at the species level, with 100% concordance to culture findings.
Comparative Evaluation of the Vitek 2 Yeast Susceptibility Test and CLSI Broth Microdilution Reference Method for Testing Antifungal Susceptibility of Invasive Fungal Isolates in Italy: the GISIA3 Study
Authors: Borghi Elisa , Iatta Roberta , Sciota Rita , Biassoni Caterina , Cuna Teresa , Montagna Maria Teresa , Morace Giulia
Published: July 2010

The newly available AST-YS01 Vitek 2 cards were evaluated, and the results were compared with those obtained by the CLSI M27-A2 microdilution reference method. Clinical fungal isolates, including 614 isolates of
Candida
spp., 10
Cryptococcus neoformans
isolates, 1
Geotrichum capitatum
isolate, and 2 quality control strains, were tested for their susceptibilities to amphotericin B, fluconazole, and voriconazole using both methods. The majority of fungal isolates were susceptible to all antifungal agents tested: the MIC
90
values determined by the Vitek 2 and CLSI methods were 0.5 and 1 μg/ml, respectively, for amphotericin B; 8 and 16 μg/ml, respectively, for fluconazole; and <0.12 and 0.25 μg/ml, respectively, for voriconazole. Overall there was excellent categorical agreement (CA) between the methods (99.5% for amphotericin B, 92% for fluconazole, 98.2% for voriconazole), but discrepancies were observed within species. The CAs for fluconazole were low for
Candida glabrata
and
Candida krusei
when the results of the CLSI method at 48 h were considered. Moreover, the fully automated commercial system did not detect the susceptibility of
Cryptococcus neoformans
to voriconazole. The Vitek 2 system can be considered a valid support for antifungal susceptibility testing of fungi, but testing of susceptibility to agents not included in the system (e.g., echinocandins and posaconazole) should be performed with other methods.
Characterization of RD-114 Virus Isolated from a Commercial Canine Vaccine Manufactured Using CRFK Cells
Authors: Yoshikawa Rokusuke , Sato Eiji , Igarashi Tatsuhiko , Miyazawa Takayuki
Published: July 2010

Recently, we found that several commercial pet vaccines were contaminated with an infectious endogenous retrovirus, RD-114-related virus. Here, we determined the entire nucleotide sequences of RD-114-related viruses isolated from CRFK cells and a vaccine manufactured using CRFK cells. These RD-114-related viruses were nearly identical to the authentic RD-114 virus.
Recognition of Potentially Novel Human Disease-Associated Pathogens by Implementation of Systematic 16S rRNA Gene Sequencing in the Diagnostic Laboratory
Authors: Keller Peter M. , Rampini Silvana K. , Büchler Andrea C. , Eich Gerhard , Wanner Roger M. , Speck Roberto F. , Böttger Erik C. , Bloemberg Guido V.
Published: July 2010

Clinical isolates that are difficult to identify by conventional means form a valuable source of novel human pathogens. We report on a 5-year study based on systematic 16S rRNA gene sequence analysis. We found 60 previously unknown 16S rRNA sequences corresponding to potentially novel bacterial taxa. For 30 of 60 isolates, clinical relevance was evaluated; 18 of the 30 isolates analyzed were considered to be associated with human disease.
Comparison of
Leishmania
OligoC-TesT PCR with Conventional and Real-Time PCR for Diagnosis of Canine
Leishmania
Infection
Authors: Carson Connor , Quinnell Rupert J. , Holden Jennifer , Garcez Lourdes M. , Deborggraeve Stijn , Courtenay Orin
Published: July 2010

There is a need for standardization and simplification of the existing methods for molecular detection of
Leishmania infantum
in the canine reservoir host. The commercially available OligoC-TesT kit incorporates standardized PCR reagents with rapid oligochromatographic dipstick detection of PCR products and is highly sensitive for use in humans but not yet independently validated for use in dogs. Here we compare the sensitivity of OligoC-TesT with those of nested kinetoplast DNA (kDNA) PCR, nested internal transcribed spacer 1 (ITS-1) PCR, and a PCR-hybridization protocol, using longitudinal naturally infected canine bone marrow samples whose parasite burdens were measured by real-time quantitative PCR (qPCR). The sensitivity of OligoC-TesT for infected dogs was 70% (95% confidence interval [CI], 63 to 78%), similar to that of kDNA PCR (72%; 95% CI, 65 to 80%;
P
= 0.69) but significantly greater than those of PCR-hybridization (61%; 95% CI, 53 to 69%;
P =
0.007) and ITS-1 nested PCR (54%; 95% CI, 45 to 62%;
P
< 0.001); real-time qPCR had the highest sensitivity (91%; 95% CI, 85 to 95%;
P
< 0.001). OligoC-TesT sensitivity was greater for polysymptomatic and oligosymptomatic dogs than for asymptomatic dogs (93%, 74%, and 61%, respectively;
P
= 0.005), a trend also observed for the other qualitative PCR methods tested (
P
≤ 0.05). Test positivity increased with increasing parasite burdens, as measured by real-time qPCR: OligoC-TesT and kDNA PCR detected 100% and 99% of positive samples when parasite burdens exceeded 74 and 49 parasites/ml, respectively. OligoC-TesT has high sensitivity for detection of canine
Leishmania
infections; its ease of operation and ease of interpretation are further advantages for veterinary diagnostic laboratories and for large-scale survey work in developing countries.
Genetic Determinants of Mouse Hepatitis Virus Strain 1 Pneumovirulence
Authors: Leibowitz Julian L. , Srinivasa Rajiv , Williamson Shawn T. , Chua Ming Ming , Liu Mingfeng , Wu Samantha , Kang Hyojeung , Ma Xue-Zhong , Zhang Jianhua , Shalev Itay , Smith Robert , Phillips Melville J. , Levy Gary A. , Weiss Susan R.
Published: July 2010

We report here investigation into the genetic basis of mouse hepatitis virus strain 1 (MHV-1) pneumovirulence. Sequencing of the 3′ one-third of the MHV-1 genome demonstrated that the genetic organization of MHV-1 was similar to that of other strains of MHV. The hemagglutinin esterase (HE) protein was truncated, and reverse transcription-PCR (RT-PCR) studies confirmed previous work that suggested that the MHV-1 HE is a pseudogene. Targeted recombination was used to select chimeric viruses containing either the MHV-1 S gene or genes encoding all of the MHV-1 structural proteins, on an MHV-A59 background. Challenge studies in mice demonstrated that expression of the MHV-1 S gene within the MHV-A59 background (rA59/SMHV-1) increased the pneumovirulence of MHV-A59, and mice infected with this recombinant virus developed pulmonary lesions that were similar to those observed with MHV-1, although rA59/SMHV-1was significantly less virulent. Chimeras containing all of the MHV-1 structural genes on an MHV-A59 background were able to reproduce the severe acute respiratory syndrome (SARS)-like pathology observed with MHV-1 and reproducibly increased pneumovirulence relative to rA59/SMHV-1, but were still much less virulent than MHV-1. These data suggest that important determinants of pneumopathogenicity are contained within the 3′ one-third of the MHV-1 genome, but additional important virulence factors must be encoded in the genome upstream of the S gene. The severity of the pulmonary lesions observed correlates better with elevated levels of inflammatory cytokines than with viral replication in the lungs, suggesting that pulmonary disease has an important immunological component.
Structure and Capsid Association of the Herpesvirus Large Tegument Protein UL36
Authors: Newcomb William W. , Brown Jay C.
Published: July 2010

The tegument of all herpesviruses contains a high-molecular-weight protein homologous to herpes simplex virus (HSV) UL36. This large (3,164 amino acids), essential, and multifunctional polypeptide is located on the capsid surface and present at 100 to 150 copies per virion. We have been testing the idea that UL36 is important for the structural organization of the tegument. UL36 is proposed to bind directly to the capsid with other tegument proteins bound indirectly by way of UL36. Here we report the results of studies carried out with HSV type 1-derived structures containing the capsid but lacking a membrane and depleted of all tegument proteins except UL36 and a second high-molecular-weight protein, UL37. Electron microscopic analysis demonstrated that, compared to capsids lacking a tegument, these capsids (called T36 capsids) had tufts of protein located at the vertices. Projecting from the tufts were thin, variably curved strands with lengths (15 to 70 nm) in some cases sufficient to extend across the entire thickness of the tegument (∼50 nm). Strands were sensitive to removal from the capsid by brief sonication, which also removed UL36 and UL37. The findings are interpreted to indicate that UL36 and UL37 are the components of the tufts and of the thin strands that extend from them. The strand lengths support the view that they could serve as organizing features for the tegument, as they have the potential to reach all parts of the tegument. The variably curved structure of the strands suggests they may be flexible, a property that could contribute to the deformable nature of the tegument.
Assessing the Viral Fitness of Oseltamivir-Resistant Influenza Viruses in Ferrets, Using a Competitive-Mixtures Model
Authors: Hurt Aeron C. , Nor'e Siti Sarah , McCaw James M. , Fryer Helen R. , Mosse Jennifer , McLean Angela R. , Barr Ian G.
Published: July 2010

To determine the relative fitness of oseltamivir-resistant strains compared to susceptible wild-type viruses, we combined mathematical modeling and statistical techniques with a novel
in vivo
“competitive-mixtures” experimental model. Ferrets were coinfected with either pure populations (100% susceptible wild-type or 100% oseltamivir-resistant mutant virus) or mixed populations of wild-type and oseltamivir-resistant influenza viruses (80%:20%, 50%:50%, and 20%:80%) at equivalent infectivity titers, and the changes in the relative proportions of those two viruses were monitored over the course of the infection during within-host and over host-to-host transmission events in a ferret contact model. Coinfection of ferrets with mixtures of an oseltamivir-resistant R292K mutant A(H3N2) virus and a R292 oseltamivir-susceptible wild-type virus demonstrated that the R292K mutant virus was rapidly outgrown by the R292 wild-type virus in artificially infected donor ferrets and did not transmit to any of the recipient ferrets. The competitive-mixtures model was also used to investigate the fitness of the seasonal A(H1N1) oseltamivir-resistant H274Y mutant and showed that within infected ferrets the H274Y mutant virus was marginally outgrown by the wild-type strain but demonstrated equivalent transmissibility between ferrets. This novel
in vivo
experimental method and accompanying mathematical analysis provide greater insight into the relative fitness, both within the host and between hosts, of two different influenza virus strains compared to more traditional methods that infect ferrets with only pure populations of viruses. Our statistical inferences are essential for the development of the next generation of mathematical models of the emergence and spread of oseltamivir-resistant influenza in human populations.
The Transmission Efficiency of
Tomato Yellow Leaf Curl Virus
by the Whitefly
Bemisia tabaci
Is Correlated with the Presence of a Specific Symbiotic Bacterium Species
Authors: Gottlieb Yuval , Zchori-Fein Einat , Mozes-Daube Netta , Kontsedalov Svetlana , Skaljac Marisa , Brumin Marina , Sobol Iris , Czosnek Henryk , Vavre Fabrice , Fleury Frédéric , Ghanim Murad
Published: July 2010

Tomato yellow leaf curl virus
(TYLCV) (
Geminiviridae
:
Begomovirus
) is exclusively vectored by the whitefly
Bemisia tabaci
(Gennadius) (Hemiptera: Aleyrodidae). TYLCV transmission depends upon a 63-kDa GroEL protein produced by the vector's endosymbiotic bacteria.
B. tabaci
is a species complex comprising several genetically distinct biotypes that show different secondary-symbiont fauna. In Israel, the B biotype harbors
Hamiltonella
, and the Q biotype harbors
Wolbachia
and
Arsenophonus.
Both biotypes harbor
Rickettsia
and
Portiera
(the obligatory primary symbionts). The aim of this study was to determine which
B. tabaci
symbionts are involved in TYLCV transmission using
B. tabaci
populations collected in Israel. Virus transmission assays by
B. tabaci
showed that the B biotype efficiently transmits the virus, while the Q biotype scarcely transmits it. Yeast two-hybrid and protein pulldown assays showed that while the GroEL protein produced by
Hamiltonella
interacts with TYLCV coat protein, GroEL produced by
Rickettsia
and
Portiera
does not. To assess the role of
Wolbachia
and
Arsenophonus
GroEL proteins (GroELs), we used an immune capture PCR (IC-PCR) assay, employing
in vivo
- and
in vitro
-synthesized GroEL proteins from all symbionts and whitefly artificial feeding through membranes. Interaction between GroEL and TYLCV was found to occur in the B biotype, but not in the Q biotype. This assay further showed that release of virions protected by GroEL occurs adjacent to the primary salivary glands. Taken together, the GroEL protein produced by
Hamiltonella
(present in the B biotype, but absent in the Q biotype) facilitates TYLCV transmission. The other symbionts from both biotypes do not seem to be involved in transmission of this virus.
Epstein-Barr Virus LF2 Protein Regulates Viral Replication by Altering Rta Subcellular Localization
Authors: Heilmann Andreas M. F. , Calderwood Michael A. , Johannsen Eric
Published: July 2010

The switch from Epstein-Barr virus (EBV) latent infection to lytic replication is governed by two viral transactivators, Zta and Rta. We previously reported that the EBV protein LF2 binds Rta, inhibits Rta promoter activation, and blocks EBV replication in cells. In addition, LF2 induces SUMO2/3 modification of Rta. We now show that this modification occurs at four lysines within the Rta activation domain (426, 446, 517, and 530) and that sumoylation of Rta is not essential for its repression. Coexpression studies demonstrated that Rta is sequestered to the extranuclear cytoskeleton in the presence of LF2. We mapped the LF2 binding site to Rta amino acids (aa) 476 to 519 and showed that LF2 binding is critical for Rta relocalization and repression. The core of this binding site, Rta aa 500 to 526, confers LF2-mediated relocalization and repression onto the artificial transcription factor GAL4-VP16. Mutational analysis of LF2 provided further evidence that Rta redistribution is essential for repression. Rta localization changes during replication of the LF2-positive P3HR1 genome, but not during replication of the LF2-negative B95-8 genome. BLRF2 protein expression was decreased and delayed in P3HR1 cells compared with B95-8 cells, consistent with reduced Rta activity. By contrast, BMRF1 expression, regulated primarily by Zta, did not differ significantly between the two cell lines. Our results support a model in which LF2 regulates EBV replication by binding to Rta and redistributing it out of the nucleus.
Different Rotavirus Strains Enter MA104 Cells through Different Endocytic Pathways: the Role of Clathrin-Mediated Endocytosis
Authors: Gutiérrez Michelle , Isa Pavel , Sánchez-San Martin Claudia , Pérez-Vargas Jimena , Espinosa Rafaela , Arias Carlos F. , López Susana
Published: July 2010

Rotaviruses, the single most important agents of acute severe gastroenteritis in children, are nonenveloped viruses formed by a three-layered capsid that encloses a genome formed by 11 segments of double-stranded RNA. The mechanism of entry of these viruses into the host cell is not well understood. The best-studied strain, RRV, which is sensitive to neuraminidase (NA) treatment of the cells, uses integrins α2β1 and αvβ3 and the heat shock protein hsc70 as receptors and enters MA104 cells through a non-clathrin-, non-caveolin-mediated pathway that depends on a functional dynamin and on the presence of cholesterol on the cell surface. In this work, using a combination of pharmacological, biochemical, and genetic approaches, we compared the entry characteristics of four rotavirus strains known to have different receptor requirements. We chose four rotavirus strains that represent all phenotypic combinations of NA resistance or sensitivity and integrin dependence or independence. We found that even though all the strains share their requirements for hsc70, dynamin, and cholesterol, three of them differ from the simian strain RRV in the endocytic pathway used. The human strain Wa, porcine strain TFR-41, and bovine strain UK seem to enter the cell through clathrin-mediated endocytosis, since treatments that inhibit this pathway block their infectivity; consistent with this entry route, these strains were sensitive to changes in the endosomal pH. The inhibition of other endocytic mechanisms, such as macropinocytosis or caveola-mediated uptake, had no effect on the internalization of the rotavirus strains tested here.