bluuebunny/crossref_metadata_2025 huggingface dataset:
A Novel Approach for Collaborative Interaction With Mixed Reality in Value Engineering
Authors: Wendrich Robert E.
Published: March 2012

Design and engineering in real-world projects is often influenced by reduction of the problem definition, trade-offs during decision-making, possible loss of information and monetary issues like budget constraints or value-for-money problems. In many engineering projects various stakeholders take part in the project process on various levels of communication, engineering and decision-making. During project meetings and VE sessions between the different stakeholder’s, information and data is gathered and put down analogue and/or digitally, consequently stored in reports, minutes and other modes of representation. Results and conclusions derived from these interactions are often influenced by the user’s field of experience and expertise. Personal stakes, idiosyncrasy, expectations, preferences and interpretations of the various project parts could have implications, interfere or procrastinate non-functionality and possible rupture in the collaborative setting and process leading to diminished prospective project targets, requirements and solutions. We present a hybrid tool as a Virtual Assistant (VA) during a collaborative Value Engineering (VE) session in a real-world design and engineering case. The tool supports interaction and decision-making in conjunction with a physical workbench as focal point (-s), user-interfaces that intuit the user during processing. The hybrid environment allows the users to interact un-tethered with real-world materials, images, drawings, objects and drawing instruments. In course of the processing captures are made of the various topics or issues at stake and logged as iterative instances in a database. Real-time visualization on a monitor of the captured instances are shown and progressively listed in the on-screen user interface. During or after the session the stakeholders can go through the iterative time-listing and synthesize the instances according to i.e. topic, dominance, choice or to the degree of priority. After structuring and sorting the data sets the information can be exported to a data or video file. All stakeholders receive or have access to the data files and can track-back the complete process progression. The system and information generated affords reflection, knowledge sharing and cooperation. Redistribution of data sets to other stakeholders, management or third parties becomes more efficient and congruous. Our approach we took during this experiment was to [re]search the communication, interaction and decision-making progressions of the various stakeholders during the VE-session. We observed the behavioral aspects during the various stages of user interaction, following the decision making process and the use of the tool during the course of the session. We captured the complete session on video for analysis and evaluation of the VE process within a hybrid design environment.
Product Manufacturing Information Management in Interactive Augmented Technical Drawings
Authors: Fiorentino Michele , Uva Antonio E. , Monno Giuseppe
Published: March 2012

This work presents a novel Augmented Realty (AR) application to superimpose interactive Product Manufacturing Information (PMI) onto paper technical drawings. We augment drawings with contextual data and use a novel tangible interface to access the data in a natural way. We present an optimized PMI data visualization algorithm for CAD models in order to avoid model and annotation cluttering.. Our algorithm ranks the model faces with technical annotations according to angle, distance, occlusion and area. The number of annotations visualized on 3D model is chosen following the cognitive perception theory to avoid information overload. We also extended the navigation metaphor adding the concept of tangible model navigation and flipping using the duplex drawing. As case studies we used annotated models from ASME standards. By using PC hardware and common paper drawings, this approach can be integrated at low-cost in existing industrial processes.
Effect of the Immersion Level of a Virtual Loader Simulator on the Sense of Presence
Authors: Kuusisto Jukka , Ellman Asko , Kaapu Taina , Tiainen Tarja
Published: March 2012

In mobile machine industry, work machine simulators can be used to save time and costs in product development and training. However, investing into expensive or difficult-to-use technology should be avoided if it does not affect measurable user performance or feeling of presence. At Tampere University of Technology, a virtual loader simulator has been constructed in an three-wall walk-in virtual environment. The goal of this research was to investigate how the immersivity of the simulator affects testers’ feeling of presence. A total of 25 test users performed two test runs each with different simulator setups, and the presence level of each user was evaluated by a questionnaire after both runs. The results indicate that switching from 2D view to 3D stereoscopic display did not significantly affect the sense of presence. However, with the motion platform, the test users reported clearly higher presence ratings than without it. In addition, we examined some effects of the users’ backgrounds: Test users who had experience from driving large work machines reported lower presence ratings than those without such experience. The sense of presence for frequent computer players was higher than for non-players, but only in one simulator setup.
Aspects Regarding Modular Road Design in Virtual Reality
Authors: Vasiu Ra˘zvan-Vlad , Bris¸an Cornel
Published: March 2012

This paper discusses and presents graphical representation of roads as 3D geometric object in virtual reality and Matlab in accordance with civil road construction rules concerning aspects for macro level: vertical and horizontal road alignment and micro level: surface rugosity. In the following are presented implementation methods and the advantages for road graphical modeling in 3D with the help of virtual reality in both macro and micro level. The goal of the paper is to present a modular approach for development of a fully integrated 3D road model using virtual reality with Matlab. The computed parameters are included into VRML/X3D files which are useful for development of car driving simulators.
A Techinque Based on Muscular Activation for Interacting With Virtual Environments
Authors: Belluco Paolo , Bordegoni Monica , Cugini Umberto
Published: March 2012

Interacting with computers by using the bodily motion is one of the challenging topics in the Virtual Reality field, especially as regards the interaction with large scale virtual environments. This paper presents a device for interacting with a Virtual Reality environment that is based on the detection of the muscular activity and movements of the user by the fusion of two different signals. The idea is that through muscular activities a user is capable of moving a cursor in the virtual space, and making some actions through gestures. The device is based on an accelerometer and on electromyography, a technique that derives from the medical field and that is able to recognize the electrical activity produced by skeletal muscles during their contraction. The device consists of cheap and easy to replicate components: seven electrodes pads and a small and wearable board for the acquisition of the sEMG signals from the user’s forearm, a 3 DOF accelerometer that is positioned on the user’s wrist (used for moving the cursor in the space) and a glove worn on the forearm in which these components are inserted. The device can be easily used without tedious settings and training. In order to test the functionality, performances and usability issues of the device we have implemented an application that has been tested by a group of users. Specifically, the device has been used as natural interaction technique in an application for drawing in a large scale virtual environment. The muscular activity is acquired by the device and used by the application for controlling the dimension and color of the brush.
Unified Modeling Language to Enhance the Specification of Discrete Event Systems for Virtual Reality Applications
Authors: Radkowski Rafael , Hilus Michael
Published: March 2012

This paper presents the utilization of UML (Unified Modeling Language) state diagrams and activity diagrams in order to model a discrete control system for a virtual reality (VR) application. Discrete control systems are utilized to control the behavior of a virtual model within a VR application. The common approach is to use a graphical notation, whose graphical elements represent states and messages. However, in a technical domain the discrete event system has to integrate technical simulations and engineering models. Furthermore, it needs to be flexible. An UML-based notation facilitates both. Changes are simple by replacing states and transitions of the diagrams. Engineering models are integrated by code templates, which are derived from the UML. This UML-bases notation has been tested. In summary, utilizing UML simplifies to keep track of the behavior models of virtual objects.
Towards a Scalable ESPINA for Neuroscience Data Analysis
Authors: Morales Juan , Pen˜a Jorge G. , Ferna´ndez Jaime , Rodri´guez Angel
Published: March 2012

ESPINA is an image segmentation tool designed to analyse microscopy images in order to identify neuronal structures and to produce 3D models of these structures. This tool allows to display three-dimensional volumes using auto-stereoscopic monitors. It was initially designed for workstations, but when data volume management or its processing complexity makes unfeasible the implementation of the new tools on these computers, it is necessary to resort to computing servers that delimit response times or by means of scalable solutions and algorithmic optimizations. This paper analyses the migration of this tool from the original implementation to a scalable solution and describes the experience achieved during the development of the workstation version. The proposed alternative is a distributed version of the tool that delegate heavy-computational processes to a cluster, improving the performance of the system in a master/slave architecture.
Practical Evaluation of Maintenance Work in a Mixed Reality Environment
Authors: Stelzer Ralph , Klaus Matthias , Steger Wolfgang , Steindecker Erik , Tauscher Gregor
Published: March 2012

Virtual testing is a significant part of the product development process. It is possible to completely solve many problems through the interaction of geometric models, simulation tools, human models with the help of the appropriate software. If, in the course of testing, it is necessary to take into account subjective human perception, one may profitably use a full-size system for immersive projection (VR system). Such a system particularly makes sense in evaluating manufacturing, operating, application or maintenance. The human being interacts with a product whose physical shape does not yet exist in a virtual environment. In this case, the movements of product components are generally indirectly controlled by using a flystick, a wand or a similar input device. In reality many operations in maintenance are determined by the position and posture of the maintenance personal as well as by the mass, center of gravity and dimensions of the object to be manipulated. In a Mixed Reality Environment, it is possible to achieve a meaningful subjective ergonomic evaluation of the abovementioned operations. The paper elucidates a strategy to integrate real product components into a virtual environment. The user applies the real components or tools in the immersive full-size projection of the VR system. The VR system tracks the real object. This way, it is possible to move an invisible object model in the VR system in sync with the movements of the real object. The collision detection tool provided in the VR system is available and signalises contact of the real object with the virtual environment. The demonstrated solution is under consideration for the planning and ergonomic evaluation of service activities. The need of industry for a process that can be controlled in a safe manner is of particular concern. The solution given here is aimed at maintenance to be performed on the brake system of a light-duty truck.
User-Centered Design and Evaluation of an Interactive Visual-Haptic-Auditory Interface: A User Study on Assembly
Authors: Jia Dawei , Bhatti Asim , Nahavandi Saeid
Published: March 2012

Utilizing user-centred system design and evaluation method has become an increasingly important tool to foster better usability in the field of virtual environments (VEs). In recent years, although it is still the norm that designers and developers are concerning the technological advancement and striving for designing impressive multimodal multisensory interfaces, more and more awareness are aroused among the development team that in order to produce usable and useful interfaces, it is essential to have users in mind during design and validate a new design from users’ perspective. In this paper, we describe a user study carried out to validate a newly developed haptically enabled virtual training system. By taking consideration of the complexity of individual differences on human performance, adoption and acceptance of haptic and audio-visual I/O devices, we address how well users learn, perform, adapt to and perceive object assembly training. We also explore user experience and interaction with the system, and discuss how multisensory feedback affects user performance, perception and acceptance. At last, we discuss how to better design VEs that enhance users perception, their interaction and motor activity.
Surface functionalization of graphenelike materials by carbon monoxide atmospheric plasma treatment for improved wetting without structural degradation
Authors: Zaldivar Rafael J. , Adams Paul M. , Nokes Jim , Kim Hyun I.
Published: March 2012

Oxygen plasma treatment has been extensively used to functionalize the surface of graphenelike materials. However, functionalization is usually accompanied by degradation of the structure, which may affect mechanical and electrical performance. Atmospheric plasma treatment (APT) of HOPG was performed to compare the effect of surface modification using carbon monoxide (CO) as the active gas, in comparison to O2. Both Raman and STM demonstrated nanoscale degradation of the structure when using the O2 treatment. CO treated specimens exhibited no observable damage to the material with high levels of oxygen incorporation. Instead, a well ordered monolayer of oxygen-containing film was observed on the surface of the specimens which could accommodate high levels of surface oxygen. Changes in surface characteristics were analyzed using x-ray photoelectron spectroscopy (XPS) as a function of duration. The results indicated that the use of O2 plasma resulted in only a limited oxygen uptake (O/C = 0.11), while CO APT resulted in tailorable surface O/C ratios as high as 0.65, a result not observed even when using low-pressure radio frequency plasmas. XPS analysis and Auger spectroscopy confirmed that a tailorable level of carbonyl functional groups could be evenly distributed throughout the surface. Contact angle measurements verified the formation of a highly stable hydrophilic surface. The CO treatment was also successfully applied to other nanocarbon materials such as graphene nanoplatelets with similar results.
Enhanced green emission from UV down-converting Ce3+–Tb3+ co-activated ZnAl2O4 phosphor
Authors: Tshabalala K. G. , Nagpure I. M. , Swart H. C. , Ntwaeaborwa O. M. , Cho S.-H. , Park J.-K.
Published: March 2012

Ce3+–Tb3+ co-activated ZnAl2O4 powder phosphors were prepared by a solution combustion method using urea as a fuel. X-ray diffraction characterization showed that all the powders crystallized in the well known cubic spinel phase of ZnAl2O4. An enhanced down-converted green emission associated with the 5D4→7F5 transitions of Tb3+ ions was observed at 543 nm from the ZnAl2O4:Ce3+, Tb3+ powders with different concentrations of Ce3+ and Tb3+. It was inferred from the fluorescence decay data that the enhancement was due to energy transfer from Ce3+ to Tb3+. Further, cathodoluminescence intensity degradation of the ZnAl2O4:Ce3+, Tb3+ powder phosphors was investigated when the powders were irradiated with 2 keV electrons. X-ray photoelectron spectroscopy was used to analyze the chemical and electronic states of individual elements before and after electron irradiation. The ZnAl2O4:Ce3+, Tb3+ phosphor was evaluated to be used as a UV down-converting layer in conventional silicon photovoltaic cells or as a source of green light in field emission display technologies.
Understanding image contrast to optimize procedures for focused ion beam contact level circuit editing
Authors: Niles David W. , Kee Ronald W.
Published: March 2012

Contact level focused ion beam (FIB) circuit editing (CE) is a powerful methodology to realize full thickness back side CEs with high success rates. Tungsten contacts present themselves as dark circles surrounded by bright rings and extended halos in the ion-induced secondary electron (iSE) images from the FIB. Similarly, polysilicide gates appear as gray bars surrounded by a brighter perimeter. The iSE images are compared to electron-induced secondary electron images from a scanning electron microscope. Elemental data from energy dispersive spectroscopy and topographical data from atomic force microscopy (AFM) evince that topography rather than conductivity plays a determinant role in the contrast in the iSE images. A model emerges whereby the Ga+ ion beam erodes the dielectrics more quickly than the W contacts and polysilicide gate liners, leaving the W contacts and polysilicide gate liners with rounded sidewalls protruding from the floor of the FIB trench. The high yield of secondary electrons from the sidewalls of protruding structures dominates image formation and follows the secant law with a modified exponent. Topographical data from the AFM combined with the secant law suffice to simulate the main features of iSE images although a complete interpretation of the polysilicide gates mandates considering the conductivity of the materials as well.
Online monitoring and error detection of real‐time tumor displacement prediction accuracy using control limits on respiratory surrogate statistics
Authors: Malinowski Kathleen , McAvoy Thomas J. , George Rohini , Dieterich Sonja , D'Souza Warren D.
Published: March 2012

Purpose:

To evaluate Hotelling'sT2 statistic and the input variable squared prediction error (Q(X)) for detecting large respiratory surrogate‐based tumor displacement prediction errors without directly measuring the tumor's position.

Methods:

Tumor and external marker positions from a database of 188 Cyberknife Synchrony™ lung, liver, and pancreas treatment fractions were analyzed. The first ten measurements of tumor position in each fraction were used to create fraction‐specific models of tumor displacement using external surrogates as input; the models were used to predict tumor position from subsequent external marker measurements. A partial least squares (PLS) model with four scores was developed for each fraction to determineT2 and Q(X) confidence limits based on the first ten measurements in a fraction. The T2 and Q(X) statistics were then calculated for every set of external marker measurements. Correlations between model error and both T2 and Q(X) were determined. Receiver operating characteristic analysis was applied to evaluate sensitivities and specificities of T2, Q(X), and T2∪Q(X) for predicting real‐time tumor localization errors >3 mm over a range of T2 and Q(X) confidence limits.

Results:

Sensitivity and specificity of detecting errors >3 mm varied with confidence limit selection. At 95% sensitivity,T2∪Q(X) specificity was 15%, 2% higher than either T2 or Q(X) alone. The mean time to alarm for T2∪Q(X) at 95% sensitivity was 5.3 min but varied with a standard deviation of 8.2 min. Results did not differ significantly by tumor site.

Conclusions:

The results of this study establish the feasibility of respiratory surrogate‐based online monitoring of real‐time respiration‐induced tumor motion model accuracy for lung, liver, and pancreas tumors. TheT2 and Q(X) statistics were able to indicate whether inferential model errors exceeded 3 mm with high sensitivity. Modest improvements in specificity were achieved by combining T2 and Q(X) results.
A realistic deformable prostate phantom for multimodal imaging and needle‐insertion procedures
Authors: Hungr Nikolai , Long Jean‐Alexandre , Beix Vincent , Troccaz Jocelyne
Published: March 2012

Purpose:

Phantoms are a vital step for the preliminary validation of new image‐guided procedures. In this paper, the authors present a deformable prostate phantom for use with multimodal imaging (end‐fire or side‐fire ultrasound, CT and MRI) and more specifically for transperineal or transrectal needle‐insertion procedures. It is made of soft polyvinyl chloride (PVC) plastic and includes a prostate, a perineum, a rectum, a soft periprostatic surrounding and embedded targets for image registration and needle‐targeting. Its main particularity is its realistic deformability upon manipulation.

Methods:

After a detailed manufacturing description, the imaging and mechanical characteristics of the phantom are described and evaluated. First, the speed of sound and stress‐strain relationship of the PVC material used in the phantom are described, followed by an analysis of its storage, imaging, needle‐insertion force, and deformability characteristics.

Results:

The average speed of sound in the phantom was measured to be 1380 ± 20 m/s, while the stress‐strain relationship was found to be viscoelastic and in the range of typical prostatic tissues. The mechanical and imaging characteristics of the phantom were found to remain stable at cooler storage temperatures. The phantom had clearly distinguishable morphology in all three imaging modalities, with embedded targets that could be precisely segmented, resulting in an average US‐CT rigid registration error of 0.66 mm. The mobility of the phantom prostate upon needle insertion was between 2 and 4 mm, with rotations between 0° and 2°, about the US probe head.

Conclusion:

The phantom's characteristics compare favorably within vitro and in vivo measurements found in the literature. The authors believe that this realistic phantom could be of use to researchers studying new needle‐based prostate diagnosis and therapy techniques.
Improving the sensitivity of high‐frequency subharmonic imaging with coded excitation: A feasibility study
Authors: Shekhar Himanshu , Doyley Marvin M.
Published: March 2012

Purpose:

Subharmonic intravascular ultrasound imaging (S‐IVUS) could visualize the adventitialvasa vasorum, but the high pressure threshold required to incite subharmonic behavior in an ultrasound contrast agent will compromise sensitivity—a trait that has hampered the clinical use of S‐IVUS. The purpose of this study was to assess the feasibility of using coded‐chirp excitations to improve the sensitivity and axial resolution of S‐IVUS.

Methods:

The subharmonic response of Targestar‐pTM, a commercial microbubble ultrasound contrast agent (UCA), to coded‐chirp (5%–20% fractional bandwidth) pulses and narrowband sine‐burst (4% fractional bandwidth) pulses was assessed, first using computer simulations and then experimentally. Rectangular windowed excitation pulses with pulse durations ranging from 0.25 to 3 μs were used in all studies. All experimental studies were performed with a pair of transducers (20 MHz/10 MHz), both with diameter of 6.35 mm and focal length of 50 mm. The size distribution of the UCA was measured with a CasyTM Cell counter.

Results:

The simulation predicted a pressure threshold that was an order of magnitude higher than that determined experimentally. However, all other predictions were consistent with the experimental observations. It was predicted that: (1) exciting the agent with chirps would produce stronger subharmonic response relative to those produced by sine‐bursts; (2) increasing the fractional bandwidth of coded‐chirp excitation would increase the sensitivity of subharmonic imaging; and (3) coded‐chirp would increase axial resolution. The experimental results revealed that subharmonic‐to‐fundamental ratios obtained with chirps were 5.7 dB higher than those produced with sine‐bursts of similar duration. The axial resolution achieved with 20% fractional bandwidth chirps was approximately twice that achieved with 4% fractional bandwidth sine‐bursts.

Conclusions:

The coded‐chirp method is a suitable excitation strategy for subharmonic IVUS imaging. At the 20 MHz transmission frequency and 20% fractional bandwidth, coded‐chirp excitation appears to represent the ideal tradeoff between subharmonic strength and axial resolution.
Axial radiation force exerted by general non-diffracting beams
Authors: Zhang Likun , Marston Philip L.
Published: March 2012

The axial radiation force exerted by a general non-diffracting beam on an object of arbitrary shape in lossless medium is analyzed. The object may be on or off the beam’s axis. The analysis is based on the plane-wave representation of the beam using an azimuthal function and conical angle. The analytical expression relates the force to axial projections of the extracted and scattered momentum. Using an extended optical theorem, the extinction is related to the scattering at the forward direction of the beam’s plane wave components. The axial force is expressed using the scattering amplitude and known angular functions.
Effects of repeated production on vowel distinctiveness within nonwords
Authors: Sasisekaran Jayanthi , Munson Benjamin
Published: March 2012

In the present study acoustic distinctiveness of vowels within nonwords with repeated production was investigated. Participants were 9 males and 15 females divided into two groups. Participants repeated 6 nonwords varying in phonemic composition. The mean Euclidean distance (MED) of the vowels from each production of a nonword from the center of the F1/F2 space was calculated. The changes in MED with repeated production were analyzed using linear mixed effects regression. Results revealed an increase in MED, indicating greater vowel dispersion, for the three-syllable nonwords and a significant decrease, i.e., greater reduction, in vowel dispersion for the six-syllable nonwords. Findings support the dynamic influence of sublexical processes on phonetic realization in speech production.
Gravity Field and Internal Structure of Mercury from MESSENGER
Authors: Smith David E. , Zuber Maria T. , Phillips Roger J. , Solomon Sean C. , Hauck Steven A. , Lemoine Frank G. , Mazarico Erwan , Neumann Gregory A. , Peale Stanton J. , Margot Jean-Luc , Johnson Catherine L. , Torrence Mark H. , Perry Mark E. , Rowlands David D. , Goossens Sander , Head James W. , Taylor Anthony H.
Published: March 2012

Mercury Inside and Out

The MESSENGER spacecraft orbiting Mercury has been in a ∼12-hour eccentric, near-polar orbit since 18 March 2011 (see the Perspective by

McKinnon

).

Smith
et al.

(p.
214
, published online 21 March) present the most recent determination of Mercury's gravity field, based on radio tracking of the MESSENGER spacecraft between 18 March and 23 August 2011. The results point to an interior structure that differs from those of the other terrestrial planets: the density of the planet's solid outer shell suggests the existence of a deep reservoir of high-density material, possibly an Fe-S layer.

Zuber
et al.

(p.
217
, published online 21 March) used data obtained by the MESSENGER laser altimeter through to 24 October 2011 to build a topographic map of Mercury's northern hemisphere. The map shows less variation in elevation, compared with Mars or the Moon, and its features add to the body of evidence that Mercury has sustained geophysical activity for much of its history.
If I Had a Nickel for Every Wheeze
Authors: Zeki Amir A.
Published: March 2012

Rhinovirus infection may exacerbate asthma symptoms by inducing type III interferon lambda.
False-Negative Hepatitis B Virus (HBV) Surface Antigen in a Vaccinated Dialysis Patient with a High Level of HBV DNA in the United States
Authors: Foy Matthew C. , Thio Chloe L. , Hwang Hyon S. , Saulynas Melissa , Hamilton James P. , Fine Derek M. , Atta Mohamed G.
Published: March 2012

Screening with hepatitis B surface antigen (HBsAg) is highly recommended for at-risk individuals. Mutations in the HBsAg can result in an inability to detect the virus during routine screening. We describe a hemodialysis patient found to have high levels of hepatitis B virus (HBV) DNA and HBV antibody but negative HBsAg on two routine assays.
Detection of Human Bocaviruses 1 to 4 from Nasopharyngeal Swab Samples Collected from Patients with Respiratory Tract Infections
Authors: Koseki Naoko , Teramoto Shinobu , Kaiho Miki , Gomi-Endo Rika , Yoshioka Mikio , Takahashi Yutaka , Nakayama Tsuguyo , Sawada Hiroyuki , Konno Mutsuko , Ushijima Hiroshi , Kikuta Hideaki , Ariga Tadashi , Ishiguro Nobuhisa
Published: March 2012

Human bocaviruses (HBoV) 1, 2, 3, and 4 (HBoV1-4) were detected in 132 (15.5%), 5 (0.6%), 3 (0.4%), and 5 (0.6%) of 850 nasopharyngeal swab samples collected from children with respiratory tract infections, respectively. Out of the 145 HBoV1-4-positive samples, 62 (42.8%) were codetected with other respiratory viruses.
Molecular Detection of Rifabutin-Susceptible Mycobacterium tuberculosis
Authors: Chen Huang-Yao , Yu Ming-Chih , Huang Wei-Lun , Wu Mei-Hua , Chang Yung-Lin , Che Chien-Rai , Jou Ruwen
Published: March 2012

Rapid assays are still needed to detect rifabutin (RFB) susceptibility for proper tuberculosis treatment. To assess the use of the GenoType MTBDR
plus
assay and subsequent
rpoB
gene sequencing on detection of RFB susceptibility, we analyzed 800 multidrug-resistant
Mycobacterium tuberculosis
isolates, and 13% (104/800) were RFB susceptible. Of the 104 RFB-susceptible isolates, 71 (68.3%) isolates were rapidly identified using two molecular assays, while the remaining isolates could be determined using conventional drug-susceptibility testing according to the clinician's decision.
Detection of Amphotericin B Resistance in Candida haemulonii and Closely Related Species by Use of the Etest, Vitek-2 Yeast Susceptibility System, and CLSI and EUCAST Broth Microdilution Methods
Authors: Shin Jong Hee , Kim Mi-Na , Jang Sook Jin , Ju Min Young , Kim Soo Hyun , Shin Myung Geun , Suh Soon Pal , Ryang Dong Wook
Published: March 2012

The emerging fungal pathogens
Candida haemulonii
and
Candida pseudohaemulonii
often show high-level resistance to amphotericin B (AMB). We compared the utilities of five antifungal susceptibility testing methods, i.e., the Etest using Mueller-Hinton agar supplemented with glucose and methylene blue (Etest-MH), the Etest using RPMI agar supplemented with glucose (Etest-RPG), the Vitek-2 yeast susceptibility system, and the Clinical and Laboratory Standards Institute (CLSI) and European Committee on Antimicrobial Susceptibility Testing (EUCAST) broth microdilution methods, for the detection of AMB-resistant isolates of
C. haemulonii
and closely related species. Thirty-eight clinical isolates (8
C. haemulonii
, 10
C. pseudohaemulonii
, and 20
Candida auris
isolates) were analyzed. Of the 18
C. haemulonii
and
C. pseudohaemulonii
isolates, 18, 15, 18, 10, and 9 exhibited AMB MICs of >1 μg/ml by the Etest-MH, Etest-RPG, Vitek-2, CLSI, and EUCAST methods, respectively. All 20
C. auris
isolates showed AMB MICs of ≤1 μg/ml by all five methods. Of the methods, the Etest-MH generated the broadest distribution of AMB MICs for all 38 isolates and showed the best discrimination between the
C. haemulonii
and
C. pseudohaemulonii
isolates (4 to 32 μg/ml) and those of
C. auris
(0.125 to 0.5 μg/ml). Taking the Etest-MH as the reference method, the essential agreements (within two dilutions) for the Etest-RPG, Vitek-2, CLSI, and EUCAST methods were 84, 92, 55, and 55%, respectively; the categorical agreements were 92, 92, 79, and 76%, respectively. This study provides the first data on the efficacy of the Etest-MH and its excellent agreement with Vitek-2 for discriminating AMB-resistant from AMB-susceptible isolates of these
Candida
species.
A Multidrug-Resistant Staphylococcus epidermidis Clone (ST2) Is an Ongoing Cause of Hospital-Acquired Infection in a Western Australian Hospital
Authors: Widerström Micael , McCullough Cheryll A. , Coombs Geoffrey W. , Monsen Tor , Christiansen Keryn J.
Published: March 2012

We report the molecular epidemiology of 27 clinical multidrug-resistant
Staphylococcus epidermidis
(MDRSE) isolates collected between 2003 and 2007 in an Australian teaching hospital. The dominant genotype (sequence type 2 [ST2]) accounted for 85% of the isolates tested and was indistinguishable from an MDRSE genotype identified in European hospitals, which may indicate that highly adaptable health care-associated genotypes of
S. epidermidis
have emerged and disseminated worldwide in the health care setting.
Detection of Dengue Virus Genome in Urine by Real-Time Reverse Transcriptase PCR: a Laboratory Diagnostic Method Useful after Disappearance of the Genome in Serum
Authors: Hirayama Takanori , Mizuno Yasutaka , Takeshita Nozomi , Kotaki Akira , Tajima Shigeru , Omatsu Tsutomu , Sano Kouichi , Kurane Ichiro , Takasaki Tomohiko
Published: March 2012

The reemergence of dengue virus (DENV) infection has created a requirement for improved laboratory diagnostic procedures. In this study, DENV genome detection in urine was evaluated as a diagnostic method. The DENV genome was detected by real-time reverse transcriptase PCR (RT-PCR) in urine and serum of dengue patients. The detection rate of DENV genome in urine was 25% (2/8) on disease days 0 to 3 and 32% (7/22) on days 4 to 5. The rate was 50% or higher on days 6 to 16, 52% (11/21) on days 6 to 7, 78% (7/9) on days 8 to 9, 80% (4/5) on days 10 to 11, 50% (2/4) on days 12 to 13, and 60% (3/5) on days 14 to 16. The last positive urine sample was on day 16. The detection rates in serum were highest on days 0 to 3 and were greater than 50% on days 0 to 7. Detection rates decreased thereafter, and the last positive detection was on day 11. These results indicate that the time frames for positive detection differ between urine and serum samples, whereby detection rates of 50% or higher are evident between days 6 to 16 for urine samples and days 0 to 7 for serum samples. Nucleotide sequences of PCR products were identical between urine and serum samples. The detection of DENV genome in urine samples by real-time RT-PCR is useful to confirm DENV infection, particularly after viremia disappears.
Population Genetic Structures of Staphylococcus aureus Isolates from Cats and Dogs in Japan
Authors: Sasaki Takashi , Tsubakishita Sae , Tanaka Yoshikazu , Ohtsuka Masayuki , Hongo Isamu , Fukata Tsuneo , Kabeya Hidenori , Maruyama Soichi , Hiramatsu Keiichi
Published: March 2012

We determined the population genetic structures of feline and canine
Staphylococcus aureus
strains in Japan by multilocus sequence typing (MLST). Ecological analyses suggested that multiple feline-related
S. aureus
clones, including ST133, naturally occur as commensals and can cause endogenous infections in felines. In contrast,
S. aureus
populations do not likely include any clone that exhibits tropism in domestic dogs. Even if
S. aureus
infections occur in dogs, the pathologies are likely exogenous infections.
Automated Pangenomic Analysis in Target Selection for PCR Detection and Identification of Bacteria by Use of ssGeneFinder Webserver and Its Application to Salmonella enterica Serovar Typhi
Authors: Ho Chi-Chun , Wu Alan K. L. , Tse Cindy W. S. , Yuen Kwok-Yung , Lau Susanna K. P. , Woo Patrick C. Y.
Published: March 2012

With the advent of high-throughput DNA sequencing, more than 4,000 bacterial genomes have been sequenced and are publicly available. We report a user-friendly web platform, ssGeneFinder Webserver (http://147.8.74.24/ssGeneFinder/), which is updated weekly for the automated pangenomic selection of specific targets for direct PCR detection and the identification of clinically important bacteria without the need of gene sequencing. To apply the ssGeneFinder Webserver for identifying specific targets forSalmonella entericaserovar Typhi, we analyzed 11S. Typhi genomes, generated two specific targets, and validated them using 40S. Typhi, 110 non-TyphiSalmonellaserovars (serovar Paratyphi A,n= 4; Paratyphi B,n= 1; Typhimurium,n= 5; Enteritidis,n= 12; non-Paratyphi group A,n= 6; non-Paratyphi group B,n= 29; non-Paratyphi group C,n= 12; non-Typhi group D,n= 35; group E and others,n= 6), 115Enterobacteriaceaeisolates (Escherichia,n= 78;Shigella,n= 2;Klebsiella,n= 13;Enterobacter,n= 9; others,n= 13), and 66 human stool samples that were culture negative forS. Typhi. Both targets successfully detected all typical and atypicalS. Typhi isolates, including an H1-j flagellin gene mutant, an aflagellated mutant which reacted with 2OSalmonellaantiserum, and the Vi-negative attenuated vaccine strain Ty21a. No false positive was detected from any of the bacterial isolates and stool samples. DNA sequencing confirmed the identity of all positive amplicons. The PCR assays have detection limits as low as 100 CFU per reaction and were tested using spiked stool samples. Using a pangenomic approach, ssGeneFinder Webserver generated targets specific toS. Typhi. These and other validated targets should be applicable to the identification and direct PCR detection of bacterial pathogens from uncultured, mixed, and environmental samples.
Evaluation of Pneumonia Virus of Mice as a Possible Human Pathogen
Authors: Brock Linda G. , Karron Ruth A. , Krempl Christine D. , Collins Peter L. , Buchholz Ursula J.
Published: March 2012

Pneumonia virus of mice (PVM), a relative of human respiratory syncytial virus (RSV), causes respiratory disease in mice. There is serologic evidence suggesting widespread exposure of humans to PVM. To investigate replication in primates, African green monkeys (AGM) and rhesus macaques (
n
= 4) were inoculated with PVM by the respiratory route. Virus was shed intermittently at low levels by a subset of animals, suggesting poor permissiveness. PVM efficiently replicated in cultured human cells and inhibited the type I interferon (IFN) response in these cells. This suggests that poor replication in nonhuman primates was not due to a general nonpermissiveness of primate cells or poor control of the IFN response. Seroprevalence in humans was examined by screening sera from 30 adults and 17 young children for PVM-neutralizing activity. Sera from a single child (6%) and 40% of adults had low neutralizing activity against PVM, which could be consistent with increasing incidence of exposure following early childhood. There was no cross-reaction of human or AGM sera between RSV and PVM and no cross-protection in the mouse model. In native Western blots, human sera reacted with RSV but not PVM proteins under conditions in which AGM immune sera reacted strongly. Serum reactivity was further evaluated by flow cytometry using unfixed Vero cells infected with PVM or RSV expressing green fluorescent protein (GFP) as a measure of viral gene expression. The reactivity of human sera against RSV-infected cells correlated with GFP expression, whereas reactivity against PVM-infected cells was low and uncorrelated with GFP expression. Thus, PVM specificity was not evident. Our results indicate that the PVM-neutralizing activity of human sera is not due to RSV- or PVM-specific antibodies but may be due to low-affinity, polyreactive natural antibodies of the IgG subclass. The absence of PVM-specific antibodies and restriction in nonhuman primates makes PVM unlikely to be a human pathogen.
Molecular Genetic and Biochemical Characterization of the Vaccinia Virus I3 Protein, the Replicative Single-Stranded DNA Binding Protein
Authors: Greseth Matthew D. , Boyle Kathleen A. , Bluma Matthew S. , Unger Bethany , Wiebe Matthew S. , Soares-Martins Jamaria A. , Wickramasekera Nadi T. , Wahlberg James , Traktman Paula
Published: March 2012

Vaccinia virus, the prototypic poxvirus, efficiently and faithfully replicates its ∼200-kb DNA genome within the cytoplasm of infected cells. This intracellular localization dictates that vaccinia virus encodes most, if not all, of its own DNA replication machinery. Included in the repertoire of viral replication proteins is the I3 protein, which binds to single-stranded DNA (ssDNA) with great specificity and stability and has been presumed to be the replicative ssDNA binding protein (SSB). We substantiate here that I3 colocalizes with bromodeoxyuridine (BrdU)-labeled nascent viral genomes and that these genomes accumulate in cytoplasmic factories that are delimited by membranes derived from the endoplasmic reticulum. Moreover, we report on a structure/function analysis of I3 involving the isolation and characterization of 10 clustered charge-to-alanine mutants. These mutants were analyzed for their biochemical properties (self-interaction and DNA binding) and biological competence. Three of the mutant proteins, encoded by the I3 alleles I3-4, -5, and -7, were deficient in self-interaction and unable to support virus viability, strongly suggesting that the multimerization of I3 is biologically significant. Mutant I3-5 was also deficient in DNA binding. Additionally, we demonstrate that small interfering RNA (siRNA)-mediated depletion of I3 causes a significant decrease in the accumulation of progeny genomes and that this reduction diminishes the yield of infectious virus.
Evidence for ACE2-Utilizing Coronaviruses (CoVs) Related to Severe Acute Respiratory Syndrome CoV in Bats
Authors: Demogines Ann , Farzan Michael , Sawyer Sara L.
Published: March 2012

In 2002, severe acute respiratory syndrome (SARS)-coronavirus (CoV) appeared as a novel human virus with high similarity to bat coronaviruses. However, while SARS-CoV uses the human angiotensin-converting enzyme 2 (ACE2) receptor for cellular entry, no coronavirus isolated from bats appears to use ACE2. Here we show that signatures of recurrent positive selection in the bat
ACE2
gene map almost perfectly to known SARS-CoV interaction surfaces. Our data indicate that ACE2 utilization preceded the emergence of SARS-CoV-like viruses from bats.
Virus-Derived Gene Expression and RNA Interference Vector for Grapevine
Authors: Kurth Elizabeth G. , Peremyslov Valera V. , Prokhnevsky Alexey I. , Kasschau Kristin D. , Miller Marilyn , Carrington James C. , Dolja Valerian V.
Published: March 2012

The improvement of the agricultural and wine-making qualities of the grapevine (
Vitis vinifera
) is hampered by adherence to traditional varieties, the recalcitrance of this plant to genetic modifications, and public resistance to genetically modified organism (GMO) technologies. To address these challenges, we developed an RNA virus-based vector for the introduction of desired traits into grapevine without heritable modifications to the genome. This vector expresses recombinant proteins in the phloem tissue that is involved in sugar transport throughout the plant, from leaves to roots to berries. Furthermore, the vector provides a powerful RNA interference (RNAi) capability of regulating the expression of endogenous genes via virus-induced gene-silencing (VIGS) technology. Additional advantages of this vector include superb genetic capacity and stability, as well as the swiftness of technology implementation. The most significant applications of the viral vector include functional genomics of the grapevine and disease control via RNAi-enabled vaccination against pathogens or invertebrate pests.
Establishment and Lineage Replacement of H6 Influenza Viruses in Domestic Ducks in Southern China
Authors: Huang Kai , Zhu Huachen , Fan Xiaohui , Wang Jia , Cheung Chung-Lam , Duan Lian , Hong Wenshan , Liu Yongmei , Li Lifeng , Smith David K. , Chen Honglin , Webster Robert G. , Webby Richard J. , Peiris Malik , Guan Yi
Published: March 2012

Domestic ducks in southern China act as an important reservoir for influenza viruses and have also facilitated the establishment of multiple H6 influenza virus lineages. To understand the continuing evolution of these established lineages, 297 H6 viruses isolated from domestic ducks during 2006 and 2007 were genetically and antigenically analyzed. Phylogenetic analyses showed that group II duck H6 viruses had replaced the previously predominant group I lineage and extended their geographic distribution from coastal to inland regions. Group II H6 virus showed that the genesis and development of multiple types of deletions in the neuraminidase (NA) stalk region could occur in the influenza viruses from domestic ducks. A gradual replacement of the N2 NA subtype with N6 was observed. Significant antigenic changes occurred within group II H6 viruses so that they became antigenically distinguishable from group I and gene pool viruses. Gene exchange between group II H6 viruses and the established H5N1, H9N2, or H6N1 virus lineages in poultry in the region was very limited. These findings suggest that domestic ducks can facilitate significant genetic and antigenic changes in viruses established in this host and highlight gaps in our knowledge of influenza virus ecology and even the evolutionary behavior of this virus family in its aquatic avian reservoirs.
Murine Noroviruses Bind Glycolipid and Glycoprotein Attachment Receptors in a Strain-Dependent Manner
Authors: Taube Stefan , Perry Jeffrey W. , McGreevy Eoghan , Yetming Kristen , Perkins Cheryl , Henderson Kenneth , Wobus Christiane E.
Published: March 2012

Human norovirus infections are the most common cause of acute nonbacterial gastroenteritis in humans worldwide, and glycan binding plays an important role in the susceptibility to these infections. However, due to the lack of an efficient cell culture system or small animal model for human noroviruses, little is known about the biological role of glycan binding during infection. Murine noroviruses (MNV) are also enteric viruses that bind to cell surface glycans, but in contrast to their human counterparts, they can be grown in tissue culture and a small animal host. In this study, we determined glycan-binding specificities of the MNV strains MNV-1 and CR3
in vitro
, identified molecular determinants of glycan binding, and analyzed infection
in vivo
. We showed that unlike MNV-1, CR3 binding to murine macrophages was resistant to neuraminidase treatment and glycosphingolipid depletion. Both strains depended on N-linked glycoproteins for binding, while only MNV-1 attachment to macrophages was sensitive to O-linked glycoprotein depletion.
In vivo
, CR3 showed differences in tissue tropism compared to MNV-1 by replicating in the large intestine. Mapping of a glycan-binding site in the MNV-1 capsid by reverse genetics identified a region topologically similar to the histo-blood group antigen (HBGA)-binding sites of the human norovirus strain VA387. The recombinant virus showed distinct changes in tissue tropism compared to wild-type virus. Taken together, our data demonstrate that MNV strains evolved multiple strategies to bind different glycan receptors on the surface of murine macrophages and that glycan binding contributes to tissue tropism
in vivo
.