bluuebunny/crossref_metadata_2025 huggingface dataset:
Design of a Reconfigurable, Monolithic Compliant Mechanism for a Six-Axis Nanomanipulator
Authors: Culpepper Martin L. , Kim Soohyung
Published: April 2009

In general, compliant mechanisms are single-state devices, meaning there is a one-to-one relationship between the inputs (actuation) and outputs (mechanism motion). This is particularly troublesome in precision mechanisms which offer limited flexibility in performance characteristics for high cost. In this paper we demonstrate a method which was proposed in earlier work (2002) to make a six-axis compliant mechanism with reconfigurable performance characteristics. The mechanism was synthesized using CoMeT, a compliant mechanism design tool, and optimized via FEA simulation. Experimental results show that (1) mechanism transmission ratio can be reconfigured between negative and positive numbers (2) that dynamic mode shapes may be changed and (3) that natural frequencies may be independently reconfigured. A means to handle the competing material requirements of large range and high-bandwidth is briefly presented.
Design of a Gimbaled Compliant Mechanism Stage for Precision Motion and Dynamic Control in Z, ΘX and ΘY Directions
Authors: Szczesny Spencer E. , Winter Amos G.
Published: April 2009

Obtaining precise motion control of a compliant mechanism is often hindered by competing kinematic, mechanic and dynamic requirements. Resonances limit the control bandwidth while compliance requirements limit the mechanism’s directional stiffness. This paper investigates the improvements possible for three-axis Z, θX and θY diaphragm flexure stages through the use of a design (T-Flex) with members complaint in bending and torsion. According to analytical modeling and FEA, the T-Flex is capable of removing problematic resonant modes of vibration without significantly increasing the axial or tilt stiffness. Bench-level experimentation was conducted on various configurations of compliant mechanisms to determine their effects on the motion characteristics for precision engineering applications. The results indicate that by pairing the T-Flex with a radially stiff compliant mechanism, gimbaled motion can be achieved, providing 7.0 nm/μm lateral cross-axis (parasitic) motions. The mechanism exhibits linear axial and tilt stiffness of 0.195 N/μm and 5.37×10−6 N-m/μrad, respectively. Dynamic testing agreed with the FEA prediction of the first natural frequency to within 10%. The T-Flex coupled with the stiff radial flexure has the potential to provide a precise three-axis configuration with a fundamental resonant frequency of 600 Hz.
Web-Based Mechanism Design and Analysis
Authors: Cheng Harry H. , Trang Dung T.
Published: April 2009

We have developed a Ch Mechanism Toolkit for analysis and design of mechanisms. It was developed using Ch, an embeddable C/C++ interpreter with extensions. The Ch Mechanism Toolkit allows users to write simple programs for solving complicated planar mechanism problems. As an extension to the toolkit, a Web-based system was created for performing mechanism design and analysis through the internet. This paper will discuss the design and implementation of the Ch Mechanism Toolkit as well as its corresponding web-based system. The web-based mechanism system is especially suitable for distance learning. The web-based system for mechanism design and analysis is available on the Web at http://www.softintegration/webservices/mechanism/.
Design of HP Models of Proteins by Energy Gap Criterion Using Continuous Modeling and Optimization
Authors: Koh Sung K. , Ananthasuresh G. K.
Published: April 2009

The sequence of 20 types of amino acid residues in a heteropolymer chain of a protein is believed to be the basis for the 3-D conformation (folded structure) that a protein assumes to serve its functions. We present a deterministic optimization method to design the sequence of a simplified model of proteins for a desired conformation. A design methodology developed for the topology optimization of compliant mechanisms is adapted here by converting the discrete combinatorial problem of protein sequence design to a continuous optimization problem. It builds upon our recent work which used a minimum energy criterion on a deterministic approach to protein design using continuous models. This paper focuses on the energy gap criterion, which is argued to be one of the most important characteristics determining the stable folding of a protein chain. The concepts, methodology, and illustrative examples are presented using HP models of proteins where only two types (H: hydrophobic and P: polar) of monomers are considered instead of 20. The highlight of the method presented in this paper is the drastic reduction in computational costs.
A Framework and Design Sythesis Tool Used to Generate, Evaluate and Optimize Compliant Mechanism Concepts for Research and Education Activities
Authors: Culpepper Martin L. , Kim Soohyung
Published: April 2009

In 2002, a Microsoft-MIT iCampus effort was initiated to generate methods and tools which accelerate the process by which students and researchers acquire perspective and skill in compliant mechanism design: (1) Experience and skill: A synthesis tool, CoMeT, was developed as a means for researchers and students to gain experience and skill in working with old (education) and new (research) compliant mechanisms. The simulator is based on compliance theory and screw theory. (2) Perspective: A framework, the 5 Fs, was developed to help designers form a holistic perspective on compliant mechanisms. A “big picture” view helps them systematically identify and link the important elements of a compliant mechanism problem. This opens to door for them to properly conceptualize, model and fabricate these mechanisms. In this paper we discuss the work of early compliant mechanism/instrument designers to gain insight into how they thought about, designed and taught others about compliant mechanisms. We explain how their work has influenced the development of our framework and simulator. We then show results obtained by using the framework and simulator at MIT in: (1) Compliant mechanism research: Generation of a compliant mechanism for an R&D 100 award winning, six-axis Nanomanipulator. (2) Compliant mechanism education: Use within student projects to design two devices: A compliant x-y Nanomanipulator with 30×30 μm range and a MEMS accelerometer. Both devices are designed, fabricated and tested in a semester-long class. The paper closes with an appendix which highlights the main steps of a CoMeT study on the screw axis characteristics of a four bar compliant mechanism. The CoMeT simulator and a CoMeT User’s Guide have been made publicly available for academic use at psdam.mit.edu.
Design of a Compliant Revolute Mechanism for Accurate Dynamic Characterization of Automotive Steering Columns
Authors: Culpepper Martin L. , Szczesny Spencer
Published: April 2009

It is difficult to obtain accurate measurements of the dynamic characteristics exhibited by automotive steering columns. The difficulties are due in-part to the use of lubricated contact bearings which support the column during testing. These bearings introduce damping, hysteresis, non-linear stiffness and clearance/preloaded constraints on the column. These error sources then mask the true dynamic behavior of the column, thereby preventing a better understanding of the relationship between column design, manufacturing tolerances and column vibration. With this paper, we introduce the concept of a revolute compliant mechanism that can be used in place of contact bearings to support steering columns during dynamic tests. These mechanisms do not exhibit the non-linear damping/stiffness and non-repeatable errors found in contact bearings. As a result, they can be used to design equipment that is capable of taking test data which matches theoretical predictions to within 2%. Experimental results obtained with this equipment suggest (more study is needed to confirm this) that manufacturing errors may be responsible for up to 20–30% error in predicting vibration amplitudes of components within the column, but only 2% error in predicting steering wheel vibration amplitude. Understanding this tolerance-response relationship (via this test equipment) is a necessary first step in understanding and eliminating steering wheel nibble vibrations.
A System of Calculation and Analysis of Torsional Vibration for Turbine-Generator Shafts
Authors: Du Dongmei , Zhang Zhi , He Qing
Published: May 2009

Due to the disturbance of electric power system or other shock load, the torsional vibration of turbine-generator shafts occurs. Alternative shear stress due to torsional vibration decreases the shafts life, even results in shafts broken. It is significant to calculate and analyze natural properties and the responses of tosional vibration excited by the disturbance of electric power system in order to analyze and prevent catastrophic accident. The calculation and analysis system of torsional vibration of turbine-generator shafts is developed. With multi-mass lumped model, the model of torsional vibration of turbine-generator shafts is obtained. The system calculates the natural frequencies and the modal shapes of torsional vibration with the transfer matrix method, the response of torsional vibration of shafts with the increment transfer matrix method, such as torsional angle, angular velocity, angular acceleration, cross-section torque, and torsional stress. The response spectrum of torsional vibration can be obtained by fast Fourier transform algorithm Take an example of a 200MW turbine-generator, which is in the condition of non-all-phase operation. The responses of torsional vibration of shafts are calculated and analyzed. The bolt broken reasons of the coupling of inter-pressure rotor and low-pressure rotor and the coupling of generator and exciter are discussed. The results are identical with the data recorded in field. It is proved that the system is good precision, convenient using, friendly interfacing, and visual calculating.
The Need for Accurate Primary and Secondary Air Measurement and Control in a Pulverized Coal Fired Utility
Authors: Brandt Robert O.
Published: May 2009

Air-fuel balance is the key to clean combustion. Coal-fired public utilities are under constant pressure to meet environmental air quality standards in reducing NOx emissions. Reduction of NOx is critically dependent, on controlled combustion conditions. Accurate measurement and control of the Primary and Secondary Air is an important factor in attaining this goal. Once the Primary Air can be measured accurately, the next variable to consider in the chain is the Secondary air. The actual “Burner Zone Stoichiometry” is the sum of the two air flows to any one burner plus the fuel flow. As shown in Figure 1 below, the Primary air conveys the fuel to the burner and supplies some of the combustion air. The Secondary air provides the oxygen to complete the combustion in the “Burner Zone” to the extent the burner is designed. On a typical burner, there is more combustion air delivered to the burner by the Secondary air than the Primary air generally by a factor of 2, depending on burner design. The additional air or Secondary air completes the combustion in the “Burner Zone”, based on optimizing a set of conditions such as NOx, CO, and boiler tube flame impingement. Maintaining desired stoichiometric ratio and Primary/Secondary air ratio to minimize emissions requires accurate measurement/control of the Primary and Secondary air.
Bull Run Fossil Plant Main Steam Piping Creep Evaluation
Authors: Rosario Darryl A. , Roberts Blaine W. , Turnbow M. Scott , Azzazy Salah E.
Published: May 2009

Bull Run Unit 1, rated at 950 MW, is the first of four fossil supercritical power plants at TVA; the unit went into commercial operation in 1967. The boiler, built by Combustion Engineering (CE), has a radiant reheat twin divided furnace with tangential-fired burners for burning coal. The unit’s maximum continuous rating (MCR) is 6,400,000 lbs/hr of main steam flow, with a design temperature of 1003°F and pressure of 3840 psig. Through the end of November 2003, the unit had a total of 589 cumulative starts and 253,343 operating hours. In 1986 TVA located and repaired extensive cracking in the mixing link headers (27 of 32 saddle welds cracked) downstream of the superheater outlet headers. Visible sag was also noted at the mid-span of the mixing headers. Since that time through 2003, additional cracking of girth welds in the mixing link headers was discovered, followed by cracking in the main piping girth welds at the connections to the mixing headers and at one of the connections to the turbine. From 1988 through 2003 several elastic analyses which were performed were unable to explain the observed girth weld cracking and sagging in the piping. In October 2003, TVA contracted with Structural Integrity Associates (SI) and BW Roberts Engineering Consulting to perform elastic and creep analyses of the Bull Run main steam piping system to determine the most likely contributing factors to noticeable creep sagging and cracking problems in the mixing header link piping and main steam piping girth welds, and, to develop recommendations to mitigate additional cracking and creep/sagging. The evaluations concluded that improper hanger sizing along with longer-term hanger operational problems (non-ideal loads/travel, topped/bottomed out hangers) contributed to the observable creep sagging and girth weld cracking. The elastic and creep piping analyses performed to address these issues are described in this paper.
Adaptation Application to Engine Modelling
Authors: Iyinbor Jude
Published: May 2009

The optimisation of engine performance by predictive means can help save cost and reduce environmental pollution. This can be achieved by developing a performance model which depicts the operating conditions of a given engine. Such models can also be used for diagnostic and prognostic purposes. Creating such models requires a method that can cope with the lack of component parameters and some important measurement data. This kind of method is said to be adaptive since it predicts unknown component parameters that match available target measurement data. In this paper an industrial aeroderivative gas turbine has been modelled at design and off-design points using an adaptation approach. At design point, a sensitivity analysis has been used to evaluate the relationships between the available target performance parameters and the unknown component parameters. This ensured the proper selection of parameters for the adaptation process which led to a minimisation of the adaptation error and a comprehensive prediction of the unknown component and available target parameters. At off-design point, the adaptation process predicted component map scaling factors necessary to match available off-design point performance data.
Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur
B. canadensis
Authors: Schweitzer Mary H. , Zheng Wenxia , Organ Chris L. , Avci Recep , Suo Zhiyong , Freimark Lisa M. , Lebleu Valerie S. , Duncan Michael B. , Vander Heiden Matthew G. , Neveu John M. , Lane William S. , Cottrell John S. , Horner John R. , Cantley Lewis C. , Kalluri Raghu , Asara John M.
Published: April 2009

The Birds and the Dinosaurs

The extent to which primary tissues are preserved in ancient fossils remains controversial.

Schweitzer
et al.

(p.
626
; see the news story by
Service
) describe well-preserved tissues and primary collagen sequences from the femur of an 80-million-year-old hadrosaur. The fossil preserved structures resembling primary bone tissues and vessels. Both extracts and tissue pieces were analyzed in multiple laboratories by mass spectrometry, which revealed ancient collagen sequences that support a close relation between birds and dinosaurs.
Self-Control in Decision-Making Involves Modulation of the vmPFC Valuation System
Authors: Hare Todd A. , Camerer Colin F. , Rangel Antonio
Published: April 2009

Dieter's Dilemma

The ability to exercise self-control is central to human success and well-being. However, little is known about the neurobiological underpinnings of self-control and how or why these neural mechanisms might differ between successful and unsuccessful decision-makers.

Hare
et al.

(p.
646
) used brain imaging in a dieting population undergoing real-life decisions between a healthy or a tempting, yet nutritionally inferior, choice of food. Activity in the ventromedial prefrontal cortex correlated with the value of the stimulus, termed goal value. Importantly, this activity integrated both health and taste values in individuals who were able to exert self-control in their choices, while reflecting only taste in those unable to exert self-control.
High-Frequency Holocene Glacier Fluctuations in New Zealand Differ from the Northern Signature
Authors: Schaefer Joerg M. , Denton George H. , Kaplan Michael , Putnam Aaron , Finkel Robert C. , Barrell David J. A. , Andersen Bjorn G. , Schwartz Roseanne , Mackintosh Andrew , Chinn Trevor , Schlüchter Christian
Published: April 2009

Vive La Différence

How closely do climate changes in the Northern and Southern Hemispheres resemble each other? Much discussion has concentrated on the Holocene, the warm period of the past 11,500 years in which we now live, which represents a baseline to which contemporary climate change can be compared.

Schaefer
et al.

(p.
622
; see the Perspective by

Balco

) present a chronology of glacial movement over the last 7000 years in New Zealand, which they compare to similar records from the Northern Hemisphere. Clear differences are observed between the histories of glaciers in the opposing hemispheres, which may be owing to regional controls. Thus, neither of two popular arguments—that the hemispheres change in-phase or that they change in an anti-phased manner—appear to be correct.
A Gross-Pitaevskii Treatment for Supersolid Helium
Authors: Anderson Philip W.
Published: April 2009

Glasslike Supersolid

Recent experiments with solid helium confined to the ring of a torsional oscillator at extremely low temperatures have been interpreted in terms of an exotic supersolid phase—a crystalline solid that somehow flows like a superfluid. However, behavioral differences between samples have raised many questions (see the Perspective by

Saunders

).

Hunt
et al.

(p.
632
) present a comprehensive study of the relaxation dynamics of the torsional oscillator system as a function of time and temperature. The data provides evidence for a “supersolid glass,” where glassy behavior of crystal dislocations and superfluidity can coexist. In a separate theoretical study,
Anderson
(p.
631
) argues that supersolidity ought to be a ground state for all bose solids, but that defects in the sample may mask the supersolid signature.
Competition for Light Causes Plant Biodiversity Loss After Eutrophication
Authors: Hautier Yann , Niklaus Pascal A. , Hector Andy
Published: April 2009

Shedding Light on a Problem

Human activities—mainly the application of fertilizers to farmland—have increased the availability of nutrients in terrestrial and aquatic ecosystems. In grasslands, nutrient enrichment reduces plant species diversity, but the mechanisms underlying this loss of biodiversity remain unclear.

Hautier
et al.

(p.
636
) use an experimental manipulation, addition of supplementary light to the grassland understory, which supports the idea that competition for light is the major mechanism of plant diversity loss.
Exchange of Genetic Material Between Cells in Plant Tissue Grafts
Authors: Stegemann Sandra , Bock Ralph
Published: April 2009

Hard Graft

In plants, it is not clear whether heritable changes can be induced by tissue grafting—for example, when one plant is grafted onto a different root stock.
Stegemann and Bock
(p.
649
) now show that genetic material is transferred between plants across graft junctions. This suggests that eukaryotic cells can indeed exchange genetic information, and in this way, grafting allows genes to cross species barriers. Although the exchange is limited to the site around the graft, the finding blurs the boundary between natural gene transfer and genetic engineering techniques and suggests that natural grafting may serve as a mechanism of horizontal gene transfer during evolution.
Alexander von Humboldt and the General Physics of the Earth
Authors: Jackson Stephen T.
Published: April 2009

In the early 19th century, Alexander von Humboldt laid the foundations for today's Earth system sciences.
MESSENGER Observations of Magnetic Reconnection in Mercury’s Magnetosphere
Authors: Slavin James A. , Acuña Mario H. , Anderson Brian J. , Baker Daniel N. , Benna Mehdi , Boardsen Scott A. , Gloeckler George , Gold Robert E. , Ho George C. , Korth Haje , Krimigis Stamatios M. , McNutt Ralph L. , Raines Jim M. , Sarantos Menelaos , Schriver David , Solomon Sean C. , Trávníček Pavel , Zurbuchen Thomas H.
Published: April 2009

MESSENGER from Mercury

The spacecraft MESSENGER passed by Mercury in October 2008, in what was the second of three fly-bys before it settles into the planet's orbit in 2011. Another spacecraft visited Mercury in the mid-1970s, which mapped 45% of the planet's surface. Now, after MESSENGER, only 10% of Mercury's surface remains to be imaged up close.

Denevi
et al.

(p.
613
) use this near-global data to look at the mechanisms that shaped Mercury's crust, which likely formed by eruption of magmas of different compositions over a long period of time. Like the Moon, Mercury's surface is dotted with impact craters.

Watters
et al.

(p.
618
) describe a well-preserved impact basin, Rembrandt, which is second in size to the largest known basin, Caloris. Unlike Caloris, Rembrandt is not completely filled by material of volcanic origin, preserving clues to its formation and evolution. It displays unique patterns of tectonic deformation, some of which result from Mercury's contraction as its interior cooled over time. Mercury's exosphere and magnetosphere were also observed (see the Perspective by

Glassmeier

). Magnetic reconnection is a process whereby the interplanetary magnetic field lines join the magnetospheric field lines and transfer energy from the solar wind into the magnetosphere.

Slavin
et al.

(p.
606
) report observations of intense magnetic reconnection 10 times as intense as that of Earth.

McClintock
et al.

(p.
610
) describe simultaneous, high-resolution measurements of Mg, Ca, and Na in Mercury's exosphere, which may shed light on the processes that create and maintain the exosphere.
The Geographic Footprint of Glacier Change
Authors: Balco Greg
Published: April 2009

Glacier advances and retreats over the past 10,000 years illustrate the complexity of climate dynamics.
A Circadian Loop asSIRTs Itself
Authors: Wijnen Herman
Published: April 2009

The oscillating biosynthesis of NAD
+
constitutes a feedback loop that integrates the mammalian circadian clock with metabolism.
Avoiding Unintended Toxicity
Authors: Golde Todd E. , Kukar Thomas L.
Published: April 2009

Drugs that inhibit a distinct form of γ-secretase may be useful in treating Alzheimer's disease without causing harmful side effects.
Reducing the Risks of the Wildlife Trade
Authors: Smith Katherine F. , Behrens Michael , Schloegel Lisa M. , Marano Nina , Burgiel Stas , Daszak Peter
Published: April 2009

Importation of wildlife into the United States, most with scant identification, brings an increased threat of disease and introduction of invasive species.
Three Takes on People and Water
Authors: Jasny Barbara R. , Suter Sherman J.
Published: April 2009

Three films portray varied aspects of people's relations with freshwater, a Swiss glacier, and the Dutch coast.
Africans' Deep Genetic Roots Reveal Their Evolutionary Story
Authors: Gibbons Ann
Published: April 2009

In the largest study ever of African genetic diversity, an international team of researchers
reports online
in
Science
this week that Africans are descended from 14 ancestral populations, which often correlate with language and cultural groups.
Obama Courts a Smitten Audience at the National Academy
Authors: Mervis Jeffrey
Published: April 2009

On Monday, President Barack Obama went to the National Academy of Sciences to explain his policies on science and innovation to the nation's most prestigious scientific organization.
Study Challenges Cosmic Ray–Climate Link
Authors: Kerr Richard A.
Published: April 2009

The first comprehensive modeling of how the sun might indirectly thin cloud cover and thus warm the planet suggests that cosmic rays are not up to the task by two orders of magnitude.
IOM Panel Backs Public Disclosure Of Drug Company Payments
Authors: Kaiser Jocelyn
Published: April 2009

The best way to damp down concerns about doctors' and researchers' financial conflicts of interest is to require full disclosure, according to an expert report that adds its voice to a growing chorus.
Herschel Will Open a New Vista On Infant Stars and Galaxies …
Authors: Clery Daniel
Published: April 2009

With the biggest mirror yet flown in space, Europe's new observatory will peer through a new wavelength window at the cool regions of the universe.
…While Planck Dusts the Skies For the Fingerprints of Inflation
Authors: Cho Adrian
Published: April 2009

The newborn universe supposedly expanded faster than the speed of light. The European Space Agency's Planck satellite might prove it.
Civilization's Cost: The Decline and Fall of Human Health
Authors: Gibbons Ann
Published: April 2009

AMERICAN ASSOCIATION OF PHYSICAL ANTHROPOLOGISTS, 31 MARCH-4 APRIL 2009, CHICAGO, ILLINOIS
Of Tools and Tubers
Authors: Gibbons Ann
Published: April 2009

AMERICAN ASSOCIATION OF PHYSICAL ANTHROPOLOGISTS, 31 MARCH-4 APRIL 2009, CHICAGO, ILLINOIS
Reproductive Fate Versus Environment
Authors: Gibbons Ann
Published: April 2009

AMERICAN ASSOCIATION OF PHYSICAL ANTHROPOLOGISTS, 31 MARCH-4 APRIL 2009, CHICAGO, ILLINOIS
Antibodies to Pneumococcal Proteins PhtD, CbpA, and LytC in Filipino Pregnant Women and Their Infants in Relation to Pneumococcal Carriage
Authors: Holmlund Emma , Quiambao Beatriz , Ollgren Jukka , Jaakkola Teija , Neyt Cécile , Poolman Jan , Nohynek Hanna , Käyhty Helena
Published: April 2009

This study focuses on the immunogenicity of the following three pneumococcal vaccine candidate proteins in Filipino infants, all inducing protection in animal models: pneumococcal histidine triad protein D (PhtD), choline binding protein A (CbpA), and the lysozyme LytC. The immunoglobulin G antibody concentrations to PhtD, its putative, protective, and exposed C-terminal fragment (PhtD C), CbpA, and LytC were measured by enzyme immunoassay in 52 serum samples from pregnant women, 39 cord blood samples, and consecutive serum samples (
n
= 263) from 52 newborns between 6 weeks and 10 months of age scheduled to be taken at six time points. A nasopharyngeal swab to detect pneumococcal carriage was taken parallel to the serum samples. The antibody concentrations in the cord blood samples were similar to those in the samples from the mothers. In infant sera, the geometric mean antibody concentrations (GMCs) for all three proteins decreased until the age of 18 weeks and started to increase after that age, suggesting that the infants' own antibody production started close to the age of 4 to 5 months. The increase in GMCs by age, most clear-cut for CbpA, was associated with pneumococcal carriage. Anti-PhtD concentrations were higher than anti-PhtD C concentrations but correlated well (
r
of 0.89 at 10.5 months), suggesting that antibodies are directed to the supposedly exposed and protective C-terminal part of PhtD. Our results show that young children are able to develop an antibody response to PhtD, CbpA, and LytC and encourage the development of pneumococcal protein vaccines for this age group.
Evaluation of an Immunofiltration Assay That Detects Immunoglobulin M Antibodies against the ZEBRA Protein for the Diagnosis of Epstein-Barr Virus Infectious Mononucleosis in Immunocompetent Patients
Authors: Bravo Dayana , Muñoz-Cobo Beatriz , Costa Elisa , Clari M. Angeles , Tormo Nuria , Navarro David
Published: April 2009

The performance of an immunofiltration assay (IMFA) that detects immunoglobulin M (IgM) antibodies to the Epstein-Barr virus (EBV) ZEBRA (BamHI Z EBV replication activator) protein was evaluated for the diagnosis of EBV infectious mononucleosis (IM) in immunocompetent patients. The test panel consisted of 47 sera displaying an EBV-specific antibody profile compatible with an acute primary EBV infection from patients with clinical and biological features of EBV IM, 20 sera from healthy individuals either with a past EBV infection or who were EBV seronegative, 20 sera displaying an equivocal EBV antibody pattern (viral capsid antigen IgG positive [VCA IgG+], VCA IgM+, and EBV nuclear antigen-1 IgG+), and 15 sera obtained from patients with a mononucleosis-like syndrome owing to cytomegalovirus, human herpesvirus 6, or parvovirus B19. Overall, the sensitivity and the specificity of the assay were found to be 92.5%, and 97.3%, respectively. The sensitivity of the assay for the diagnosis of heterophile antibody-negative EBV IM was 86.2%. The IMFA is rapid, easy to perform, and, thus, suitable for point-of-care testing, and it may be used as a first-line test for the diagnosis of acute EBV IM in immunocompetent patients.
9-O-Acetylated Sialoglycoproteins Are Important Immunomodulators in Indian Visceral Leishmaniasis
Authors: Ghoshal Angana , Mukhopadhyay Sumi , Saha Bibhuti , Mandal Chitra
Published: April 2009

Overexpression of disease-associated 9-O-acetylated sialoglycoproteins (9-O-AcSGPs) on peripheral blood mononuclear cells (PBMC) of visceral leishmaniasis (VL) patients (PBMCVL) compared to their levels of expression in healthy individuals has been demonstrated using a lectin, achatinin-H, with specificity toward 9-O-acetylated sialic acid derivatives α2-6 linkage with subterminalN-acetylgalactosamine (9-O-AcSAα2-6GalNAc). The decreased presence of disease-associated 9-O-AcSGPs on different immune cells of parasitologically cured individuals after successful treatment relative to the levels in patients with active VL prior to treatment was demonstrated. However, their contributory role as immunomodulatory determinants on PBMCVLremained unexplored. Accordingly, 9-O-AcSGPs on PBMCVLwere sensitized with achatinin-H, leading to their enhanced proliferation compared to that observed with different known mitogens or parasite antigen. This lymphoproliferative response was characterized by evaluation of the TH1/TH2 response by intracellular staining and enzyme-linked immunosorbent assay for secreted cytokines, and the results were corroborated by their genetic expression. Sensitized PBMCVLevidenced a mixed TH1/TH2 cellular response with a predominance of the TH1 response, indicating the ability of 9-O-AcSGPs to modulate the host cell toward a favorable response. Interestingly, the humoral and cellular responses showed a good correlation. Further, high levels of anti-9-O-AcSGP antibodies with an order of distribution of immunoglobulin M (IgM) > IgG1 = IgG3 > IgG4 > IgG2 > IgE could be explained by a mixed TH1/TH2 response. A good correlation of enhanced 9-O-AcSGPs with both the cell-mediated (r= 0.98) and humoral (r= 0.99) response was observed. In summary, it may be concluded that sensitization of 9-O-AcSGPs on PBMCVLmay provide a basis for the modulation of the host's immune response by their controlled expression, leading to a beneficial immune response and influencing the disease pathology.
Identification of
Streptococcus agalactiae
Isolates from Various Phylogenetic Lineages by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Authors: Lartigue Marie-Frédérique , Héry-Arnaud Geneviève , Haguenoer Eve , Domelier Anne-Sophie , Schmit Pierre-Olivier , van der Mee-Marquet Nathalie , Lanotte Philippe , Mereghetti Laurent , Kostrzewa Markus , Quentin Roland
Published: April 2009

Variations in proteins related to bacterial diversity may affect species identification performed using matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry. Using this method, we identified 110
Streptococcus agalactiae
isolates characterized by serotyping and multilocus sequence typing. Serotype III and sequence type 23 strains expressed the widest variation in molecular weight of putative “species-identifying” biomarker ions. Recognition of the diversity of MALDI patterns observed in strains that represent all major intraspecies lineages assists in the constitution of an optimal reference database.
First Insight into
Mycobacterium tuberculosis
Epidemiology and Genetic Diversity in Trinidad and Tobago
Authors: Baboolal Shirematee , Millet Julie , Akpaka Patrick Eberechi , Ramoutar Dottin , Rastogi Nalin
Published: April 2009

This report is based on a 1-year recruitment of all of the culture-positive
Mycobacterium tuberculosis
cases in Trinidad and Tobago (
n
= 132). The study population was characterized by a high male-to-female sex ratio of 4 and a human immunodeficiency virus-tuberculosis (TB) coinfection rate of 30%. It mainly occurred among African descendants, who represent 37.5% of the total population but 69.7% of all TB cases (
P
< 0.001). Spoligotyping resulted in 25 different patterns and 12 clusters (2 to 74 strains per cluster), with the predominance of a highly conserved spoligotype international type clone, SIT566.
Aspergillus
Section
Fumigati
Typing by PCR-Restriction Fragment Polymorphism
Authors: Staab Janet F. , Balajee S. Arunmozhi , Marr Kieren A.
Published: April 2009

Recent studies have shown that there are multiple clinically important members of the
Aspergillus
section
Fumigati
that are difficult to distinguish on the basis of morphological features (e.g.,
Aspergillus fumigatus
,
A. lentulus
, and
Neosartorya udagawae
). Identification of these organisms may be clinically important, as some species vary in their susceptibilities to antifungal agents. In a prior study, we utilized multilocus sequence typing to describe
A. lentulus
as a species distinct from
A. fumigatus
. The sequence data show that the gene encoding β-tubulin,
benA
, has high interspecies variability at intronic regions but is conserved among isolates of the same species. These data were used to develop a PCR-restriction fragment length polymorphism (PCR-RFLP) method that rapidly and accurately distinguishes
A. fumigatus
,
A. lentulus
, and
N. udagawae
, three major species within the section
Fumigati
that have previously been implicated in disease. Digestion of the
benA
amplicon with BccI generated unique banding patterns; the results were validated by screening a collection of clinical strains and by in silico analysis of the
benA
sequences of
Aspergillus
spp. deposited in the GenBank database. PCR-RFLP of
benA
is a simple method for the identification of clinically important, similar morphotypes of
Aspergillus
spp. within the section
Fumigati
.
Resistance of
Acanthamoeba
Cysts to Disinfection in Multiple Contact Lens Solutions
Authors: Johnston Stephanie P. , Sriram Rama , Qvarnstrom Yvonne , Roy Sharon , Verani Jennifer , Yoder Jonathan , Lorick Suchita , Roberts Jacquelin , Beach Michael J. , Visvesvara Govinda
Published: April 2009

Acanthamoebae are free-living amoebae found in the environment, including soil, freshwater, brackish water, seawater, hot tubs, and Jacuzzis.
Acanthamoeba
species can cause keratitis, a painful vision-threatening infection of the cornea, and fatal granulomatous encephalitis in humans. More than 20 species of
Acanthamoeba
belonging to morphological groups I, II, and III distributed in 15 genotypes have been described. Among these,
Acanthamoeba castellanii
,
A
.
polyphaga
, and
A. hatchetti
are frequently identified as causing
Acanthamoeba
keratitis (AK). Improper contact lens care and contact with nonsterile water while wearing contact lenses are known risk factors for AK. During a recent multistate outbreak, AK was found to be associated with the use of Advanced Medical Optics Complete MoisturePlus multipurpose contact lens solution, which was hypothesized to have had insufficient anti-
Acanthamoeba
activity. As part of the investigation of that outbreak, we compared the efficacies of 11 different contact lens solutions against cysts of
A. castellanii
,
A. polyphaga
, and
A. hatchetti
(the isolates of all species were genotype T4), which were isolated in 2007 from specimens obtained during the outbreak investigation. The data, generated with
A. castellanii
,
A. polyphaga
, and
A. hatchetti
cysts, suggest that the two contact lens solutions containing hydrogen peroxide were the only solutions that showed any disinfection ability, with 0% and 66% growth, respectively, being detected with
A. castellanii
and 0% and 33% growth, respectively, being detected with
A. polyphaga
. There was no statistically significant difference in disinfection efficacy between the 11 solutions for
A. hatchetti
.
Adenovirus Microsatellite Reveals Dynamics of Transmission during a Recent Epidemic of Human Adenovirus Serotype 14 Infection
Authors: Houng Huo-Shu H. , Lott Lisa , Gong Heping , Kuschner Robert A. , Lynch Julia A. , Metzgar David
Published: April 2009

This study reveals diverse-length polymorphisms in long mononucleotide repeats (microsatellites) in several serotypes of epidemic human respiratory adenovirus. The length of one of these microsatellites, a homopolymeric thymidine [poly(T)] repeat, is measured in 68 isolates of adenovirus serotype 14. These isolates were collected during a series of sudden and sometimes fatal outbreaks among both military recruits and civilians as the virus emerged for the first time in the United States in 2006 and 2007. The results demonstrate the usefulness of adenoviral microsatellites as high-resolution molecular strain markers. The described homopolymer is hypervariable in length, varying from 12 to 17 bp in the analyzed sample set. All intermediate lengths were identified in at least one isolate. Furthermore, the specific length of the marker is stable for significant periods of time (up to 7 months) at individual sites where the virus is in consistent circulation. The microsatellite also can maintain specific length identity through site-to-site transmission events, as determined by the analysis of isolates from three advanced training sites that appeared to be subject to pathogen transfer from one of the affected recruit training installations. Public database searches revealed that the polymorphic nature of the microsatellite extends to other species B serotypes, and that other polymorphic microsatellites can be identified readily in a variety of epidemic respiratory adenovirus clades. This study shows that microsatellites are a ubiquitous source of polymorphic markers for human adenoviruses and demonstrates their use through an epidemiological analysis of isolates from a recent North American epidemic.
RNA (E6 and E7) Assays versus DNA (E6 and E7) Assays for Risk Evaluation for Women Infected with Human Papillomavirus
Authors: Cattani Paola , Siddu Alessia , D'Onghia Sara , Marchetti Simona , Santangelo Rosaria , Vellone Valerio G. , Zannoni Gian Franco , Fadda Giovanni
Published: April 2009

In the majority of cases, high-risk human papillomavirus (HR HPV) infections regress spontaneously, with only a small percentage progressing to high-grade lesions. Current screening methods are based on DNA detection. An alternative would be to monitor expression of the E6 and E7 viral oncogenes continuously expressed by malignant phenotypes. In the work reported in this paper, we compared the two methods for a group of women with high-risk HPV infections. Cervical specimens from 400 women, previously found to be HPV DNA positive, were analyzed for HPV DNA by a liquid hybridization assay and typed by multiplex PCR (for types 16, 18, 31, and 33). Identification of HR HPV E6 and E7 RNA transcripts was performed using real-time reverse transcription-PCR and nucleic acid sequence-based amplification assays. Results were compared with concurrent cytological data. HR HPVs were found in 61.2% of patients. The most common genotype was HPV type 16 (HPV-16) (47.1%), followed by HPV-18, HPV-31, and HPV-33. Nine percent of cases involved other genotypes. Among 223 HPV DNA-positive samples, only 118 were positive in the RNA test. Among HPV DNA-positive patients with normal cytology, we detected E6 and E7 RNA transcripts in two cases (18.2%). The rate of detection increased gradually with the grade of the observed lesions, rising from 20% for patients with atypical squamous cells of undetermined significance to 48.1% for women with low-grade squamous intraepithelial lesions and 86.3% for those with high-grade squamous intraepithelial lesions. These results suggest that testing for HPV E6 and E7 transcripts could be a useful tool for screening and patient management, providing more accurate predictions of risk than those obtained by DNA testing.
Novel Recombinant Virus Assay for Measuring Susceptibility of Human Immunodeficiency Virus Type 1 Group M Subtypes To Clinically Approved Drugs
Authors: Covens Kris , Dekeersmaeker Nathalie , Schrooten Yoeri , Weber Jan , Schols Dominique , Quiñones-Mateu Miguel E. , Vandamme Anne-Mieke , Van Laethem Kristel
Published: April 2009

Combination therapy can successfully suppress human immunodeficiency virus (HIV) replication in patients but selects for drug resistance, requiring subsequent resistance-guided therapeutic changes. This report describes the development and validation of a novel assay that offers a uniform method to measure susceptibility to all clinically approved HIV type 1 (HIV-1) drugs targeting reverse transcriptase (RT), protease (PR), integrase (IN), and viral entry. It is an assay in which the antiviral effect on infection within a single replication cycle is measured in triply transfected U87.CD4.CXCR4.CCR5 cells, based on homologous recombination between patient-derived amplicons and molecular proviral clones tagged with the enhanced green fluorescent protein (EGFP) reporter gene and from which certain viral genomic regions are removed. The deletions stretch from p17 codon 7 to PR codon 98 in pNL4.3-ΔgagPR-EGFP, from PR codons 1 to 99 in pNL4.3-ΔPR-EGFP, from RT codons 1 to 560 in pNL4.3-ΔRT-EGFP, from IN codons 1 to 288 in pNL4.3-ΔIN-EGFP, and from gp120 codon 34 to gp41 codon 237 in pNL4.3-Δenv-EGFP. The optimized experimental conditions enable the investigation of patient samples regardless of viral subtype or coreceptor use. The extraction and amplification success rate for a set of clinical samples belonging to a broad range of HIV-1 group M genetic forms (A-J, CRF01-03, CRF05, and CRF12-13) and displaying a viral load range of 200 to >500,000 RNA copies/ml was 97%. The drug susceptibility measurements, based on discrimination between infected and noninfected cells on a single-cell level by flow cytometry, were reproducible, with coefficients of variation for resistance ranging from 7% to 31%, and were consistent with scientific literature in terms of magnitude and specificity.
Reliability of the Vitek 2 Yeast Susceptibility Test for Detection of In Vitro Resistance to Fluconazole and Voriconazole in Clinical Isolates of
Candida albicans
and
Candida glabrata
Authors: Posteraro Brunella , Martucci Rosa , La Sorda Marilena , Fiori Barbara , Sanglard Dominique , De Carolis Elena , Florio Ada Rita , Fadda Giovanni , Sanguinetti Maurizio
Published: April 2009

The Vitek 2 yeast susceptibility test was evaluated by testing 122
Candida
isolates against fluconazole and voriconazole. Excellent categorical agreement with the CLSI broth microdilution method was observed (97.5% for both the azoles). Moreover, the Vitek 2 system was able to identify all but 2 of 59 investigated fluconazole-resistant organisms.
Rapid Molecular Characterization of
Clostridium difficile
and Assessment of Populations of
C. difficile
in Stool Specimens
Authors: Wroblewski Danielle , Hannett George E. , Bopp Dianna J. , Dumyati Ghinwa K. , Halse Tanya A. , Dumas Nellie B. , Musser Kimberlee A.
Published: April 2009

Our laboratory has developed testing methods that use real-time PCR and pyrosequencing analysis to enable the rapid identification of potential hypervirulent
Clostridium difficile
strains. We describe a real-time PCR assay that detects four
C. difficile
genes encoding toxins A (
tcdA
) and B (
tcdB
) and the binary toxin genes (
cdtA
and
cdtB
), as well as a pyrosequencing assay that detects common deletions in the
tcdC
gene in less than 4 h. A subset of historical and recent
C. difficile
isolates (
n
= 31) was also analyzed by pulsed-field gel electrophoresis to determine the circulating North American pulsed-field (NAP) types that have been isolated in New York State. Thirteen different NAP types were found among the 31 isolates tested, 13 of which were NAP type 1 strains. To further assess the best approach to utilizing our conventional and molecular methods, we studied the populations of
C. difficile
in patient stool specimens (
n
= 23). Our results indicated that 13% of individual stool specimens had heterogeneous populations of
C. difficile
when we compared the molecular characterization results for multiple bacterial isolates (
n
= 10). Direct molecular analysis of stool specimens gave results that correlated well with the results obtained with cultured stool specimens; the direct molecular analysis was rapid, informative, and less costly than the testing of multiple patient stool isolates.
X-Box Binding Protein 1 Contributes to Induction of the Kaposi's Sarcoma-Associated Herpesvirus Lytic Cycle under Hypoxic Conditions
Authors: Dalton-Griffin Lucy , Wilson Sam J. , Kellam Paul
Published: April 2009

Kaposi's sarcoma-associated herpesvirus (KSHV), like other herpesviruses, has two stages to its life cycle: latency and lytic replication. KSHV is required for development of Kaposi's sarcoma, a tumor of endothelial origin, and is associated with the B-cell tumor primary effusion lymphoma (PEL) and the plasmablastic variant of multicentric Castleman's disease, all of which are characterized by predominantly latent KSHV infection. Recently, we and others have shown that the activated form of transcription factor X-box binding protein 1 (XBP-1) is a physiological trigger of KSHV lytic reactivation in PEL. Here, we show that XBP-1s transactivates the ORF50/RTA promoter though an ACGT core containing the XBP-1 response element, an element previously identified as a weakly active hypoxia response element (HRE). Hypoxia induces the KSHV lytic cycle, and active HREs that respond to hypoxia-inducible factor 1α are present in the ORF50/RTA promoter. Hypoxia also induces active XBP-1s, and here, we show that both transcription factors contribute to the induction of RTA expression, leading to the production of infectious KSHV under hypoxic conditions.
A Shared Interface Mediates Paramyxovirus Interference with Antiviral RNA Helicases MDA5 and LGP2
Authors: Parisien Jean-Patrick , Bamming Darja , Komuro Akihiko , Ramachandran Aparna , Rodriguez Jason J. , Barber Glen , Wojahn Robert D. , Horvath Curt M.
Published: April 2009

Diverse members of the
Paramyxovirus
family of negative-strand RNA viruses effectively suppress host innate immune responses through the actions of their V proteins. The V protein mediates interference with the interferon regulatory RNA helicase MDA5 to avoid cellular antiviral responses. Analysis of the interaction interface revealed the MDA5 helicase C domain as necessary and sufficient for association with V proteins from human parainfluenza virus type 2, parainfluenza virus type 5, measles virus, mumps virus, Hendra virus, and Nipah virus. The identified ∼130-residue region is highly homologous between MDA5 and the related antiviral helicase LGP2, but not RIG-I. Results indicate that the paramyxovirus V proteins can also associate with LGP2. The V protein interaction was found to disrupt ATP hydrolysis mediated by both MDA5 and LGP2. These findings provide a potential mechanistic basis for V protein-mediated helicase interference and identify LGP2 as a second cellular RNA helicase targeted by paramyxovirus V proteins.