bluuebunny/crossref_metadata_2025 huggingface dataset:
Micromachined reconfigurable microphone array for wind tunnel testing.
Authors: Krause Joshua S. , Bright Alfram V. , Moeller Mark J. , Gallman Judith M. , White Robert D.
Published: July 2011

A surface micromachined, front-vented, 64 channel (8×8), capacitively sensed microphone array-on-a-chip devices for aeroacoustic testing is described. The arrays are fabricated using the MEMSCAP PolyMUMPs polysilicon surface micromachining process, with a Parylene-C passivation layer. The devices are packaged with low profile interconnects, presenting a maximum of 100 μm of surface topology. The array electronics allow the microphone outputs to be redirected to one of two channels, allowing dynamic reconfiguration of the effective transducer shape in software. Measured microphone sensitivity is 0.15 mV/Pa for an individual microphone and 8.7 mV/Pa for the entire array, in close agreement with model predictions. The microphones and electronics operate over the 200–40 000 Hz band. The dynamic range extends from 60 dB SPL in a 1 Hz band to greater than 150 dB SPL. Element variability is ±0.05 mV/Pa in sensitivity with an array yield of 95%. Off-chip electronics provide 80 dB off isolation. Preliminary wind tunnel testing at flow rates of up to 23 m/s indicates that the devices continue to operate in flow without damage, and can be successfully reconfigured on the fly. Analysis of measured boundary layer pressure spectra at six flow rates from 5 to 23 m/s is underway.
Direct algebraic localization of a proximate source from instantaneous or short-time Fourier transform measurements on circular array.
Authors: Ando Shigeru
Published: July 2011

The purpose of this study is to obtain an inversion formula of direction and distance of a proximate source from sound pressure distribution on a circular array. The approach will be important both in theoretical aspects and in practical usage for providing rapid initial estimates in more general multi-source conditions. Our approach is based on the weighted integral method (WIM) [IEEE Trans. SP 57, (2009), Inverse Problems 26, 015011 (2010)] for signal/source parameter estimation. The WIM is composed of two steps: (1) describing the problem with a partial differential equation (PDE) and a measurement scheme in a finite region and (2) integrating the PDE on the measurement region with appropriate weight functions to obtain equations for solving the parameters. The integration by parts eliminates the differential-of-field terms in the PDE. The weight functions are chosen so that the differentials generated instead by the integration have simpler forms and also the integral boundary terms at edges of the region will vanish successfully. We begin with the location-constraint PDE [ASA/ASJ meeting (2006)] and obtain exact formulas, an instantaneous one including time-differentials and an STFT-based one with frequency decomposition, for a proximate source. We show several experimental results using 16-element circular microphone array.
Digital beamsteering system using acoustic transducer array.
Authors: Lee Chong Hyun , Bae Jinho , Paeng Dong-Guk , Lee Jaeil , Kim Seongil
Published: July 2011

Acoustic signal processing can be applied to sonar, acoustic communications and multimedia applications. Especially transmitting acoustic signal to the desired direction has many applications in military and industry. In this paper, we present digital beamsteering algorithm using parametric array transducers. To generate the desired beampattern, the proposed algorithm utilizes the complex weight instead of time delay. With this complex operation, many algorithms including constant beamwidth algorithm and linear constrained beamforming algorithms can be applied to make versatile transmitting beampatterns. To verify the generated beampattern, we build acoustic beamsteering system by using commercial transducers and LABVIEW software and hardware. The system includes GUI software, which allows user to change many parameters such as number of sensors, complex weight of each sensor, type of transmit data, etc. The GUI can also be easily modified and extended to accommodate the characteristics of transducers. With the laboratory experiments, we verified the performance of the algorithm and system. The proposed algorithm and system can be used to build many application systems such as multimedia, acoustic communications, and sonar system. [Work supported by Grant No. UD100014DD.]
Synchronizing data for tracking moving targets with passive acoustic arrays.
Authors: Goldman Geoffrey
Published: July 2011

To accurately track targets moving at high speed with passive acoustic arrays, the propagation delay time needs to be accounted for in the signal processing algorithms. The data from each array need to be synchronized to a common reference time relative to the acoustic signal generated at the target. One approach is to synchronize the data at each array by simply delaying it, then estimates of the direction of arrival (DOA) and possibly the time of arrival (TOA) can be performed. Alternatively, non-synchronized estimates of the DOA and TOA, calculated relative to a common sample time at the sensors, can be synchronized by interpolation based upon the estimated propagation delay time. For a kinematic target model with constant acceleration, the propagation delay time from the target to the acoustic array can be determined by solving a fourth-order polynomial equation. For many scenarios, the propagation delay time can be accurately estimated by performing a second-order or third-order Machaurin series approximation. The target kinematics can be estimated using standard algorithms that initially assume no propagation delays in the data. As the delays are incorporated into the estimates of DOA and TOA, the results will improve.
Exploiting towed array maneuvers for online maximum likelihood field directionality estimation.
Authors: Rogers Jeffrey S. , Krolik Jeffrey L.
Published: July 2011

Passive estimation of the time-varying field directionality using a towed acoustic array remains a central problem in passive sonar. Typically, array processing algorithms are designed around the assumption of a linear array and fail to take advantage of the dynamics associated with a towed array. Performance of such systems can often be complicated by left-right ambiguities associated with the array as well as poor resolution near endfire directions. In this paper, the dynamics of the towed array are exploited allowing for left-right disambiguation as well as improved endfire resolution. A new method for online spatial spectrum estimation is presented. The maximum likelihood (ML) of the time-varying field is solved for using a single expectation maximization step after each received data snapshot. A multi-source, dynamic simulation is used to illustrate the proposed algorithm’s ability to suppress ambiguous towed-array backlobes and resolve closely spaced interferers near endfire which pose challenges for conventional beamforming approaches, especially during array maneuvers. Simulation results suggest the online ML method offers improved M-of-N detection performance over that of conventional beamforming. [This work was supported by ONR.]
Hermetic array processing for underwater echo-ranging systems.
Authors: Woodsum Harvey C.
Published: July 2011

Hermetic array processing provides enhanced beam width resolution, as well as correspondingly greater gain against ambient noise and reverberation, without the requirement of data-adaptive processing. The technique derives from the discrete hermetic (spectral) transform, and has been applied to an underwater echo-ranging system deployed in an underwater security system. Theoretical and empirical results are also described, and the impact on sonar system performance is presented. A description of practical implementation issues and a comparison to traditional adaptive beamforming are shown.
Polyvinylidene fluoride membrane hydrophone low-frequency response to medical shockwaves.
Authors: Bailey Michael R. , Maxwell Adam D. , Pishchalnikov Yuri A. , Sapozhnikov Oleg A.
Published: July 2011

Lithotripsy shockwaves are particularly difficult to measure because of their wide signal bandwidth and large pressures. A polyvinylidene fluoride (PVDF) membrane hydrophone and preamplifier were built and tested. A broad-focus electromagnetic lithotripter was used to calibrate the PVDF hydrophone. A fiber optic probe hydrophone (FOPH) with known impulse response was used as a measurement standard for secondary calibration. A low-frequency circuit model for the PVDF membrane electrodes in an infinite conductive medium was developed. The model response was compared with signals recorded by the FOPH and PVDF hydrophone at different levels of water conductivity ranging from 1 to 1300 μS/cm. Measured waveforms were distorted by high-pass filtering effects of the water conductivity. The model results showed good agreement with the measured waveforms and provided a correction for the system. When the input impedance was altered appropriately or the hydrophone was submerged in a nonconductive fluid, the PVDF and FOPH waveforms appeared nearly identical. The PVDF hydrophone is capable of measuring lithotripsy shockwaves accurately when the low-frequency response is properly taken into account. [Work supported by NIH DK43881, NIH EB007643, and NSBRI through NASA NCC 9-58.]
A cross-linguistic study of intonation: English learners’ production of Mandarin intonation.
Authors: Zhang Yanhong , Yuan Jiahong
Published: July 2011

Learners of non-tonal languages have to learn to manipulate complicated F0 patterns arising from the interaction between lexical tones and sentential intonation. This study examines how native English speakers deal with the effect of lexical tones in producing Mandarin intonation. Considering the boundary tone is indicative of statement-question contrasts, this study compares tonal features of sentential final syllable carrying four lexical tones in different intonations by native Mandarin and native English speakers. Acoustic analyzes indicated that both English and Mandarin speakers produced higher F0 of the boundary tone in question than in statement regardless of the lexical tones, but no difference in duration and intensity between statement-question contrasts was found. Pitch values in English speakers’ utterances were generally lower than that of Mandarin speakers. Perceptual test showed that the accuracy rate of statements across four lexical tones for English and Mandarin speakers were close to each other, but English speakers’ question utterances were poorly perceived in comparison to Mandarin speakers’ utterances, suggesting that English speakers had difficulty in producing Mandarin question sentences, especially when the final syllable carries tone 1 or tone 4. English speakers’ poor performance on question intonation was attributed to the influence of their native prosodic system.
Vowel laxing in Indonesian as a test case for interaction of morphological and syllabic structure.
Authors: McCloy Daniel R.
Published: July 2011

Lax (also known as, centralized) vowel allophones are attested in Indonesian for non-low vowels in closed syllables [e.g., Sneddon (1996)]. In consonant-final stems with vowel-initial suffixes (ke+apik+an), phonological theory (the maximal onset principle) predicts the stem-final consonant to syllabify with the suffix (ke.a.pi.kan) and the preceding vowel to manifest as unreduced. This study compares speaker-normalized formant values for such vowels against formant values for vowels in stem-final open syllables with obstruent-initial affixes (men+jadi+kan) and vowels in monomorphemic contexts (tikam). Word-final open and closed syllables (jadi, cerdik) are included as reference points in the vowel space. Male and female L1 speakers of standard Indonesian are recorded reading three randomizations of the word list. Data collection is ongoing, but preliminary results suggest that for front (unround) vowels in stem-final closed syllables with vowel-initial affixes (ke+apik+an), the formant values fall between the values for prototypical lax and non-lax Indonesian vowels; no clear pattern has yet emerged for back (round) vowels. Findings suggest that morphological structure (i.e., whether a segment “belongs” to stem or affix) may constrain syllabification or cause deviations from preferred syllable structures.
Grouping and the verbal transformation effect: The influence of formant transitions.
Authors: Stachurski Marcin , Summers Robert J. , Roberts Brian
Published: July 2011

Listening to a recorded word repeated many times produces verbal transformations (VTs) to different forms; this effect may be due in part to perceptual re-grouping of the speech sounds. Six CVC words producing strong formant transitions between the initial consonant and vowel (e.g., “short”) were recorded and monotonized at F0=130 Hz; each word was paired with another producing weak formant transitions (e.g., “fort”). Each set of six words was used to derive another in which the CV transitions were edited out and replaced with samples selected from the neighboring steady-state portions. For each word pair, the amount of splicing applied to the weak-transition stimulus (30–70 ms) was matched to that required for its strong-transition counterpart, and the VTs obtained for 3-min sequences of the edited and unedited versions were compared. Listeners reported more VT forms in the spliced than in the unedited case for the strong-transition words, but not for those with weak transitions. Hence, the effect is not an artifact of splicing, but arises from the removal of the strong transitions. This finding supports earlier studies suggesting that formant transitions play an important role in binding disparate speech segments together into a single auditory stream. [Work supported by EPSRC.]
Finite cylinder mode identification in scattering using finite elements, Fourier decomposition, and background subtraction.
Authors: Thiessen David B. , Marston Timothy M. , Marston Philip L.
Published: July 2011

Finite elements are widely used for calculating the acoustic scattering by objects for which a partial wave series solution is not available. When interpreting the results of such calculations for the purpose of developing signal processing methods, it can be helpful to identify the elastic modes of the object excited by the incident sound. One approach to this is examined here for a finite metallic circular cylinder. Since the object is rotationally symmetric it is convenient to use a Fourier basis to speed up the calculations [Zampolli et al., J. Acoust. Soc. Am. 122, 1472–1485 (2007)]. This also has the advantage of using the scattering amplitude associated with a given Fourier index to extract mode information. It is also helpful to subtract from the computed complex amplitude the corresponding scattering by a rigid or nearly rigid object having the same size and shape as the cylinder. For some situations this can be compared with quantitative ray theory and experimental results using reversible synthetic aperture sonar processing. [Work supported by ONR.]
Acoustic-trawl surveys to assess walleye pollock in Alaska: challenges faced and progress made.
Authors: Wilson Christopher D.
Published: July 2011

Large-scale acoustic-trawl surveys have been regularly conducted for over 3 decades by researchers at the NOAA, Alaska Fisheries Science Center (AFSC) to assess walleye pollock (Theragra chalcogramma) in Alaska. Research within the AFSC acoustics program (MACE) has addressed several of the challenges associated with both the acoustics and trawling aspects of these surveys. Acoustic issues include species classification of the acoustic data, fish avoidance to survey vessels, and in situ target strength measurements. Large trawls typically form an integral part of acoustic surveys to confirm the species identity of backscatter and to collect other biological information needed to convert the echo integral into numbers and weight of animals per unit area. MACE staff have also made significant progress in evaluating the selectivity of the large midwater trawls used during their acoustic surveys as well as in developing other direct sampling tools to help interpret the acoustic backscatter data. This presentation will highlight these and other recent advanced technologies and methods that are being developed and used by the MACE program to improve acoustic-trawl surveys in Alaska and elsewhere.
Assessing rockfish abundance in complex habitats using acoustics and cameras.
Authors: Jones Darin T. , Weber Thomas C. , Rooper Christopher N. , Butler John L. , Wilson Christopher D. , De Robertis Alex
Published: July 2011

Many species of rockfishes (Sebastes spp.) are difficult to assess using trawl surveys due to their propensity to aggregate near the seafloor in rocky high relief areas. A feasibility study was conducted during October 2009 in such an area south of Kodiak Island, AK, to evaluate the use of standard fisheries acoustic survey methods in conjunction with stereo-video cameras for estimating the distribution and abundance of dusky and northern rockfishes. Uniformly spaced parallel transects were repeatedly surveyed using single beam echosounders over several days. A multibeam echosounder was used to characterize the seafloor as trawlable or untrawlable and these designations were corroborated by camera. Rockfish abundance was estimated using a combination of acoustic and camera measurements. At least 80% of the rockfish detections were observed in untrawlable habitat areas, and within 2.0 m of the seafloor. Over half of the rockfish seen by the camera were within the acoustic dead zone. Repeat passes exhibited high precision and there was no significant difference in fish abundance or height off bottom between night and day. Future work is planned during summer 2011 to evaluate the feasibility of using these methods in broader areas and for other rockfishes in the Gulf of Alaska.
Accounting for uncertainty in acoustic estimates.
Authors: Sullivan Patrick , Rudstam Lars
Published: July 2011

The process of converting raw acoustic signals into estimates of fish abundance can be noisy and complicated. Is the method we use to calculate mean abundances the best that is statistically achievable? If we are to put effort into increasing sample size or refining estimates, where should we focus our attention? Once we understand the uncertainty associated with a given step in the conversion process, how do we include that uncertainty in characterizing the final estimates? In this paper, we develop a mechanism that is part Monte Carlo and part Bayesian to address known sources of uncertainty in the acoustic assessment process. Estimation steps are followed sequentially from Sv to abundance and the variances are carried along through each step. The structure of the analysis facilitates examination of the effects of the various parts of the analysis on the quality of the final outputs. Acoustic scientists can use this approach to help prioritize their own research and assessment designs.
Exploratory measurements using a broadband, split beam echo sounder system.
Authors: Ona Egil , Andersen Lars N. , Solli Haakon , Macaulay Gavin , Calise Lucio , Patel Ruben , Korneliussen Rolf , Knutsen Tor
Published: July 2011

A prototype broadband echo sounder has been used for measuring zooplankton and fish in a new collaborative project between the Institute of Marine Research and Kongsberg Maritime-Simrad. The prototype system used is a Simrad broadband system which includes a transceiver operating from 10–500 kHz. We have mainly used the transceiver together with four separate Simrad ESXX-7CD standard pressure resistant transducers, the ES70-7CD, ES120-7CD, ES200-7CD, and ES333-7CD, covering the band from 50 to 450 kHz. The research has so far concentrated on data output formats, calibration methods, and measurements from single targets in ex situ and in situ situations. Examples of recorded reflected spectra for selected calibration and biological targets will be shown and the potential for improved aquatic ecosystem assessment discussed.
Metrics to characterize vertical distributions of pelagic fauna in large acoustic datasets.
Authors: Urmy Samuel S. , Horne John K.
Published: July 2011

Active acoustics are a valuable addition to ocean observatories, allowing the detection of animals throughout the water column with high temporal and spatial resolution. The resulting datasets are large and can be difficult to describe and visualize in their entirety. We assembled a suite of metrics to parsimoniously characterize the vertical distribution of animal densities, including measures of abundance, density, location, dispersion, occupancy, evenness, and aggregation. We also developed and tested an unsupervised algorithm for detecting and counting backscatter layers within an echogram, using a gradient-based classification. These metrics were used to analyze data from the Deep Echo Integrating Marine Observatory System (DEIMOS), a 38 kHz upward-looking acoustic package deployed at the MARS observatory node in Monterey Bay, CA. The metrics successfully captured biological dynamics across multiple time scales, including seasonal, diel, and tidal variability, in addition to episodic events such as transient aggregations. All metric series showed significant positive autocorrelations at lags less than 26 days and as long as 103 days. Their frequency spectra were power-law distributed with exponents between −0.84 and −1.73. This approach could be expanded to two or three dimensions, providing an effective means to quantify the temporal variability of any spatial density distribution.
Comment on “Activation of β-Catenin in Dendritic Cells Regulates Immunity Versus Tolerance in the Intestine”
Authors: Murphy Kenneth M.
Published: July 2011

Manicassamy
et al
. (Reports, 13 August 2010, p. 849) deleted β-catenin in intestinal immune cells using a CD11c-driven Cre recombinase, which decreased anti-inflammatory mediators and increased inflammatory bowel disease. However, the deletion of β-catenin in macrophages remains a caveat to their interpretation that Wnt signaling programs dendritic cells into a tolerogenic state. Development of strains expressing Cre in a more finely lineage-restricted pattern may help resolve this issue.
Synaptic Pruning by Microglia Is Necessary for Normal Brain Development
Authors: Paolicelli Rosa C. , Bolasco Giulia , Pagani Francesca , Maggi Laura , Scianni Maria , Panzanelli Patrizia , Giustetto Maurizio , Ferreira Tiago Alves , Guiducci Eva , Dumas Laura , Ragozzino Davide , Gross Cornelius T.
Published: July 2011

A good brain needs a good vacuum cleaner.
Redesigning Flood Insurance
Authors: Michel-Kerjan Erwann , Kunreuther Howard
Published: July 2011

Improved knowledge from a range of disciplines will be needed to price the much-needed financial products appropriately.
Atmospheric Carbon Injection Linked to End-Triassic Mass Extinction
Authors: Ruhl Micha , Bonis Nina R. , Reichart Gert-Jan , Damsté Jaap S. Sinninghe , Kürschner Wolfram M.
Published: July 2011

The end-Triassic mass extinction coincided with a massive release of carbon to the atmosphere and rapid climate change.
Supramolecular Archimedean Cages Assembled with 72 Hydrogen Bonds
Authors: Liu Yuzhou , Hu Chunhua , Comotti Angiolina , Ward Michael D.
Published: July 2011

Crystalline cages held together by hydrogen bonds can trap a wide range of molecules based on their size.
Experimental and Theoretical Differential Cross Sections for a Four-Atom Reaction: HD + OH → H
2
O + D
Authors: Xiao Chunlei , Xu Xin , Liu Shu , Wang Tao , Dong Wenrui , Yang Tiangang , Sun Zhigang , Dai Dongxu , Xu Xin , Zhang Dong H. , Yang Xueming
Published: July 2011

A theoretical analysis of a four-atom reaction has a level of detail and accuracy previously restricted to three-atom systems.
Start of the Wilson Cycle at 3 Ga Shown by Diamonds from Subcontinental Mantle
Authors: Shirey Steven B. , Richardson Stephen H.
Published: July 2011

Mineral inclusions in diamonds reveal that the modern pattern of continent movements began around 3 billion years ago.
Revealing a Parasite's Invasive Trick
Authors: Baum Jake , Cowman Alan F.
Published: July 2011

A study of an important parasite reveals the core structure of the apicomplexan moving junction.
Breakthroughs for Development
Authors: Shah Rajiv
Published: July 2011

There are many ways to describe the goal of international development, but one is to think of it as changing a situation in which billions of people have access to the benefits of science and technology while billions do not. Throughout history, some of the greatest successes in development have come from extending the reach of scientific and technological breakthroughs to those who lacked access. We must continue to harness the ingenuity of the world's top researchers and scientific leaders to achieve development goals.
Complexity Surrounds HIV Prevention Advances
Authors: Cohen Jon
Published: July 2011

Two trials have showed, for the first time, that giving relatively safe and inexpensive antiretroviral pills each day to uninfected people dramatically reduced the risk of heterosexual transmission of HIV.
One Sick Mummy Gets a Double Diagnosis
Authors: Pringle Heather
Published: July 2011

Researchers found an amazingly high infection intensity of whipworm in a 200-year-old adult mummy from Piraino, Italy, according to a poster presented at the meeting.
Adeno-Associated Virus Antibody Profiles in Newborns, Children, and Adolescents
Authors: Calcedo Roberto , Morizono Hiroki , Wang Lili , McCarter Robert , He Jianping , Jones David , Batshaw Mark L. , Wilson James M.
Published: July 2011

Neutralizing antibodies (NAb) to an adeno-associated virus (AAV) vector due to previous natural infection with wild-type AAV can significantly limit gene transfer. NAb titers to AAV serotype 2 (AAV2) and AAV8 in human subjects (0 to 18 years) were studied. NAb prevalence is moderate at birth, decreases markedly from 7 to 11 months, and then progressively increases through childhood and adolescence.
Isolation of Potentially Useful Antigens from Cyathostomin Third-Stage Larvae by Using a Fast Protein Liquid Chromatography One-Step Method
Authors: Paz-Silva A. , Francisco R. , Rodríguez I. , Francisco I. , Cazapal-Monteiro C. F. , Arias M. S. , Suárez J. L. , Sánchez-Andrade R.
Published: July 2011

Three major protein complexes (51, 29, and 15 kDa, named P1 to P3, respectively) were resolved by gel filtration of the excretory/secretory antigens collected from a mixture of horse cyathostomin third-stage larvae (L3s). The potential application for the detection of infected horses was assessed with an enzyme-linked immunosorbent assay (ELISA) by the comparison of the serological and copromicroscopical results. The value of the area under the receiver operating characteristic (ROC) curve was higher than 0.9 when the three peaks were used. Elevated values (>90%) for the sensitivity, specificity, and the positive-likelihood ratio were also observed for all the antigen complexes. A significant increment in the IgG antibody levels 4 weeks prior to the observation of eggs in the feces of weanlings naturally infected was recorded. Our results indicate that the evaluation of chemotherapy is possible by using immunoenzymatic probes and fast protein liquid chromatography (FPLC)-purified antigens. Data collected in the present investigation indicate that FPLC isolation offers a very helpful one-step method for collecting antigens with diagnostic potential to be employed in immunoenzymatic probes.
Comparison of a Commercially Available Repetitive-Element PCR System (DiversiLab) with PCR Ribotyping for Typing of Clostridium difficile Strains
Authors: Eckert C. , Van Broeck J. , Spigaglia P. , Burghoffer B. , Delmée M. , Mastrantonio P. , Barbut F.
Published: July 2011

This study compared a repetitive-element PCR (rep-PCR) method (DiversiLab system) to PCR ribotyping. The discriminatory power of rep-PCR was 0.997. Among the PCR ribotype 027 isolates tested, different rep types could be distinguished. rep-PCR showed a higher discriminatory power than PCR ribotyping. Nevertheless, this method requires technical skill, and visual interpretation of rep-PCR fingerprint patterns may be difficult.
Recurrent Intravascular-Catheter-Related Bacteremia Caused by Delftia acidovorans in a Hemodialysis Patient
Authors: Chotikanatis Kobkul , Bäcker Martin , Rosas-Garcia Gabriela , Hammerschlag Margaret R.
Published: July 2011

We report the first case of recurrent intravascular-catheter-related bacteremia in a pediatric hemodialysis patient caused by
Delftia acidovorans
, previously called
Comamonas acidovorans
or
Pseudomonas acidovorans
. The patient had a history of multiple infections of central vascular catheters with other organisms, requiring courses of antibiotics and catheter replacements. Previously reported cases of
D. acidovorans
infections are reviewed. The isolate appeared to become resistant to cephalosporins after antibiotic treatment, but resistance could not be confirmed with additional testing.
In vitro
susceptibility testing for cephalosporins is not reliable for this organism.
First Reported Case of Catheter-Related Fungemia Due to Candida mengyuniae
Authors: Alcoba-Florez J. , Laich F. , Pérez-Roth E. , Ode-Febles J. , Méndez-Álvarez S.
Published: July 2011

We report a case of intravenous catheter-associated fungemia caused by the recently described species
Candida mengyuniae
, a yeast not previously associated with human disease. The infection occurred in an 89-year-old woman with pancreatic adenocarcinoma. Yeast isolates recovered from a catheter and blood were identified as
C. mengyuniae
by sequencing of the 18S, 5.8S internal transcribed spacer, and D1/D2 26S ribosomal DNA domains.
Multiplex 5′ Nuclease-Quantitative PCR for Diagnosis of Relapsing Fever in a Large Tanzanian Cohort
Authors: Reller Megan E. , Clemens Emily G. , Schachterle Steve E. , Mtove George A. , Sullivan David J. , Dumler J. Stephen
Published: July 2011

Relapsing fever (RF) is caused by tick- and louse-borne
Borrelia
spp., is characterized by recurrent fever, and is often misdiagnosed as malaria. Because of submicroscopic bacteremia, microscopy can be insensitive between febrile bouts. We designed a multiplex quantitative PCR (qPCR) assay to distinguish RF
Borrelia
from
Plasmodium falciparum
and
P. vivax
. The assay specifically (100%) amplified pathogenic RF
Borrelia
(1 copy/reaction). We then tested blood from participants within a Tanzanian cohort assessed at scheduled intervals and with fever. Among 8,617 blood samples from 2,057 participants surveyed routinely, 7 (0.08%) samples and 7 (0.3%) participants had RF DNA (median, 4.4 × 10
3
copies/ml). Of 382 samples from 310 febrile persons, 15 (3.9%) samples from 13 (4.2%) participants had RF DNA (median, 7.9 × 10
2
copies/ml). Five (1.3%) samples from 4 (1.3%) participants were found to harbor
Borrelia
by microscopy. We conclude that multiplex qPCR holds promise for improved clinical diagnosis and epidemiologic assessment of RF.
Improved Detection of Respiratory Viruses in Pediatric Outpatients with Acute Respiratory Illness by Real-Time PCR Using Nasopharyngeal Flocked Swabs
Authors: Munywoki Patrick Kiio , Hamid Fauzat , Mutunga Martin , Welch Steve , Cane Patricia , Nokes D. James
Published: July 2011

Detection of respiratory viruses by real-time multiplexed PCR (M-PCR) and of respiratory syncytial virus (RSV) by M-PCR and immunofluorescence (IF) was evaluated using specimens collected by nasopharyngeal flocked swabbing (NFS) and nasal washes (NW). In children with mild respiratory illness, NFS collection was superior to NW collection for detection of viruses by M-PCR (sensitivity, 89.6% versus 79.2%;
P
= 0.0043). NFS collection was noninferior to NW collection in the detection of RSV by IF.
Reversible Inhibition of Murine Cytomegalovirus Replication by Gamma Interferon (IFN-γ) in Primary Macrophages Involves a Primed Type I IFN-Signaling Subnetwork for Full Establishment of an Immediate-Early Antiviral State
Authors: Kropp Kai A. , Robertson Kevin A. , Sing Garwin , Rodriguez-Martin Sara , Blanc Mathieu , Lacaze Paul , Hassim Muhamad F. B. Noor , Khondoker Mizanur R. , Busche Andreas , Dickinson Paul , Forster Thorsten , Strobl Birgit , Mueller Mathias , Jonjic Stipan , Angulo Ana , Ghazal Peter
Published: July 2011

Activated macrophages play a central role in controlling inflammatory responses to infection and are tightly regulated to rapidly mount responses to infectious challenge. Type I interferon (alpha/beta interferon [IFN-α/β]) and type II interferon (IFN-γ) play a crucial role in activating macrophages and subsequently restricting viral infections. Both types of IFNs signal through related but distinct signaling pathways, inducing a vast number of interferon-stimulated genes that are overlapping but distinguishable. The exact mechanism by which IFNs, particularly IFN-γ, inhibit DNA viruses such as cytomegalovirus (CMV) is still not fully understood. Here, we investigate the antiviral state developed in macrophages upon reversible inhibition of murine CMV by IFN-γ. On the basis of molecular profiling of the reversible inhibition, we identify a significant contribution of a restricted type I IFN subnetwork linked with IFN-γ activation. Genetic knockout of the type I-signaling pathway, in the context of IFN-γ stimulation, revealed an essential requirement for a primed type I-signaling process in developing a full refractory state in macrophages. A minimal transient induction of IFN-β upon macrophage activation with IFN-γ is also detectable. In dose and kinetic viral replication inhibition experiments with IFN-γ, the establishment of an antiviral effect is demonstrated to occur within the first hours of infection. We show that the inhibitory mechanisms at these very early times involve a blockade of the viral major immediate-early promoter activity. Altogether our results show that a primed type I IFN subnetwork contributes to an immediate-early antiviral state induced by type II IFN activation of macrophages, with a potential further amplification loop contributed by transient induction of IFN-β.
Pathogenic Old World Hantaviruses Infect Renal Glomerular and Tubular Cells and Induce Disassembling of Cell-to-Cell Contacts
Authors: Krautkrämer Ellen , Grouls Stephan , Stein Nadine , Reiser Jochen , Zeier Martin
Published: July 2011

Viral hemorrhagic fevers are characterized by enhanced permeability. One of the most affected target organs of hantavirus-induced hemorrhagic fever with renal syndrome is the kidney, and an infection often results in acute renal failure. To study the underlying cellular effects leading to kidney dysfunction, we infected human renal cell types
in vitro
that are critical for the barrier functions of the kidney, and we examined kidney biopsy specimens obtained from hantavirus-infected patients. We analyzed the infection and pathogenic effects in tubular epithelial and glomerular endothelial renal cells and in podocytes. Both epithelial and endothelial cells and podocytes were susceptible to hantavirus infection
in vitro
. The infection disturbed the structure and integrity of cell-to-cell contacts, as demonstrated by redistribution and reduction of the tight junction protein ZO-1 and the decrease in the transepithelial resistance in infected epithelial monolayers. An analysis of renal biopsy specimens from hantavirus-infected patients revealed that the expression and the localization of the tight junction protein ZO-1 were altered compared to renal biopsy specimens from noninfected individuals. Both tubular and glomerular cells were affected by the infection. Furthermore, the decrease in glomerular ZO-1 correlates with disease severity induced by glomerular dysfunction. The finding that different renal cell types are susceptible to hantaviral infection and the fact that infection results in the breakdown of cell-to-cell contacts provide useful insights in hantaviral pathogenesis.
Anti-Severe Acute Respiratory Syndrome Coronavirus Spike Antibodies Trigger Infection of Human Immune Cells via a pH- and Cysteine Protease-Independent FcγR Pathway
Authors: Jaume Martial , Yip Ming S. , Cheung Chung Y. , Leung Hiu L. , Li Ping H. , Kien Francois , Dutry Isabelle , Callendret Benoît , Escriou Nicolas , Altmeyer Ralf , Nal Beatrice , Daëron Marc , Bruzzone Roberto , Peiris J. S. Malik
Published: July 2011

Public health measures successfully contained outbreaks of the severe acute respiratory syndrome coronavirus (SARS-CoV) infection. However, the precursor of the SARS-CoV remains in its natural bat reservoir, and reemergence of a human-adapted SARS-like coronavirus remains a plausible public health concern. Vaccination is a major strategy for containing resurgence of SARS in humans, and a number of vaccine candidates have been tested in experimental animal models. We previously reported that antibody elicited by a SARS-CoV vaccine candidate based on recombinant full-length Spike-protein trimers potentiated infection of human B cell lines despite elicitingin vivoa neutralizing and protective immune response in rodents. These observations prompted us to investigate the mechanisms underlying antibody-dependent enhancement (ADE) of SARS-CoV infectionin vitro. We demonstrate here that anti-Spike immune serum, while inhibiting viral entry in a permissive cell line, potentiated infection of immune cells by SARS-CoV Spike-pseudotyped lentiviral particles, as well as replication-competent SARS coronavirus. Antibody-mediated infection was dependent on Fcγ receptor II but did not use the endosomal/lysosomal pathway utilized by angiotensin I converting enzyme 2 (ACE2), the accepted receptor for SARS-CoV. This suggests that ADE of SARS-CoV utilizes a novel cell entry mechanism into immune cells. Different SARS vaccine candidates elicit sera that differ in their capacity to induce ADE in immune cells despite their comparable potency to neutralize infection in ACE2-bearing cells. Our results suggest a novel mechanism by which SARS-CoV can enter target cells and illustrate the potential pitfalls associated with immunization against it. These findings should prompt further investigations into SARS pathogenesis.
Gamma Interferon Controls Mouse Polyomavirus InfectionIn Vivo
Authors: Wilson Jarad J. , Lin Eugene , Pack Christopher D. , Frost Elizabeth L. , Hadley Annette , Swimm Alyson I. , Wang Jun , Dong Ying , Breeden Cynthia P. , Kalman Daniel , Newell Kenneth A. , Lukacher Aron E.
Published: July 2011

Human polyomaviruses are associated with substantial morbidity in immunocompromised patients, including those with HIV/AIDS, recipients of bone marrow and kidney transplants, and individuals receiving immunomodulatory agents for autoimmune and inflammatory diseases. No effective antipolyomavirus agents are currently available, and no host determinants have been identified to predict susceptibility to polyomavirus-associated diseases. Using the mouse polyomavirus (MPyV) infection model, we recently demonstrated that perforin-granzyme exocytosis, tumor necrosis factor alpha (TNF-α), and Fas did not contribute to control of infection or virus-induced tumors. Gamma interferon (IFN-γ) was recently shown to inhibit replication by human BK polyomavirus in primary cultures of renal tubular epithelial cells. In this study, we provide evidence that IFN-γ is an important component of the host defense against MPyV infection and tumorigenesis. In immortalized and primary cells, IFN-γ reduces expression of MPyV proteins and impairs viral replication. Mice deficient for the IFN-γ receptor (IFN-γR−/−) maintain higher viral loads during MPyV infection and are susceptible to MPyV-induced tumors; this increased viral load is not associated with a defective MPyV-specific CD8+T cell response. Using an acute MPyV infection kidney transplant model, we further show that IFN-γR−/−donor kidneys harbor higher MPyV levels than donor kidneys from wild-type mice. Finally, administration of IFN-γ to persistently infected mice significantly reduces MPyV levels in multiple organs, including the kidney, a major reservoir for persistent mouse and human polyomavirus infections. These findings demonstrate that IFN-γ is an antiviral effector molecule for MPyV infection.
Hepatitis B Virus Genotype C Isolates with Wild-Type Core Promoter Sequence Replicate Less Efficiently than Genotype B Isolates but Possess Higher Virion Secretion Capacity
Authors: Qin Yanli , Tang Xiaoli , Garcia Tamako , Hussain Munira , Zhang Jiming , Lok Anna , Wands Jack , Li Jisu , Tong Shuping
Published: July 2011

Infection by hepatitis B virus (HBV) genotype C is associated with a prolonged viremic phase, delayed hepatitis B e antigen (HBeAg) seroconversion, and an increased incidence of liver cirrhosis and hepatocellular carcinoma compared with genotype B infection. Genotype C is also associated with the more frequent emergence of core promoter mutations, which increase genome replication and are independently associated with poor clinical outcomes. We amplified full-length HBV genomes from serum samples from Chinese and U. S. patients with chronic HBV infection and transfected circularized genome pools or dimeric constructs of individual clones into Huh7 cells. The two genotypes could be differentiated by Western blot analysis due to the reactivities of M and L proteins toward a monoclonal pre-S2 antibody and slightly different S-protein mobilities. Great variability in replication capacity was observed for both genotypes. The A1762T/G1764A core promoter mutations were prevalent in genotype C isolates and correlated with increased replication capacity, while the A1752G/T mutation frequently found in genotype B isolates correlated with a low replication capacity. Importantly, most genotype C isolates with wild-type core promoter sequence replicated less efficiently than the corresponding genotype B isolates due to less efficient transcription of the 3.5-kb RNA. However, genotype C isolates often displayed more efficient virion secretion. We propose that the low intracellular levels of viral DNA and core protein of wild-type genotype C delay immune clearance and trigger the subsequent emergence of A1762T/G1764A core promoter mutations to upregulate replication; efficient virion secretion compensates for the low replication capacity to ensure the establishment of persistent infection by genotype C.
Immediate-Early Protein ME53 Forms Foci and Colocalizes with GP64 and the Major Capsid Protein VP39 at the Cell Membranes of Autographa californica Multiple Nucleopolyhedrovirus-Infected Cells
Authors: de Jong Jondavid , Theilmann David A. , Arif Basil M. , Krell Peter J.
Published: July 2011

me53
is an immediate-early/late gene found in all lepidopteran baculoviruses sequenced to date. Deletion of
me53
results in a greater-than-1,000-fold reduction in budded-virus production in tissue culture (J. de Jong, B. M. Arif, D. A. Theilmann, and P. J. Krell, J. Virol. 83:7440-7448, 2009). We investigated the localization of ME53 using an ME53 construct fused to green fluorescent protein (GFP). ME53:GFP adopted a primarily cytoplasmic distribution at early times postinfection and a primarily nuclear distribution at late times postinfection. Additionally, at late times ME53:GFP formed distinct foci at the cell periphery. These foci colocalized with the major envelope fusion protein GP64 and frequently with VP39 capsid protein, suggesting that these cell membrane regions may represent viral budding sites. Deletion of
vp39
did not influence the distribution of ME53:GFP; however, deletion of
gp64
abolished ME53:GFP foci at the cell periphery, implying an association between ME53 and GP64. Despite the association of ME53 and GP64, ME53 fractionated with the nucleocapsid only after budded-virus fractionation. Together these findings suggest that ME53 may be providing a scaffold that bridges the viral envelope and nucleocapsid.
Emerging Theme: Cellular PDZ Proteins as Common Targets of Pathogenic Viruses
Authors: Javier Ronald T. , Rice Andrew P.
Published: July 2011

More than a decade ago, three viral oncoproteins, adenovirus type 9 E4-ORF1, human T-lymphotropic virus type 1 Tax, and high-risk human papillomavirus E6, were found to encode a related carboxyl-terminal PDZ domain-binding motif (PBM) that mediates interactions with a select group of cellular PDZ proteins. Recent studies have shown that many other viruses also encode PBM-containing proteins that bind to cellular PDZ proteins. Interestingly, these recently recognized viruses include not only some with oncogenic potential (hepatitis B virus, rhesus papillomavirus, cottontail rabbit papillomavirus) but also many without this potential (influenza virus, Dengue virus, tick-borne encephalitis virus, rabies virus, severe acute respiratory syndrome coronavirus, human immunodeficiency virus). Examination of the cellular PDZ proteins that are targets of viral PBMs reveals that the viral proteins often interact with the same or similar types of PDZ proteins, most notably Dlg1 and other members of the membrane-associated guanylate kinase protein family, as well as Scribble. In addition, cellular PDZ protein targets of viral PBMs commonly control tight junction formation, cell polarity establishment, and apoptosis. These findings reveal a new theme in virology wherein many different virus families encode proteins that bind and perturb the function of cellular PDZ proteins. The inhibition or perturbation of the function of cellular PDZ proteins appears to be a widely used strategy for viruses to enhance their replication, disseminate in the host, and transmit to new hosts.
Synthesis of 7-substituted 3-β-D-ribofuranosyl-3H-imidazo[2,1-i]purines
Authors: Karskela Tuomas , Klika Karel D. , Lönnberg Harri
Published: July 2011

A method for the synthesis of 7-substituted 3-β-D-ribofuranosyl-3H-imidazo[2,1-i]purines has been devised whereby compounds were prepared in a few steps from a common intermediate, 3-(2′,3′-O-isopropylidene-β-D-ribofuranosyl)-3H-imidazo[2,1-i]purine-7-carbaldehyde, obtained from the reaction of 2′,3′-O-isopropylideneadenosine with bromomalonaldehyde. The formyl group of the carbaldehyde was subsequently reductively aminated and the resulting secondary amines were then further derivatized either by acylation, lactamization or reductive alkylation.
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry and database for identification of Legionella species 1This study was presented in part at the 110th American Society for Microbiology Annual Meeting, 23–27 May 2010, San Diego, California.
Authors: He Ying , Chang Tsung C. , Li Haijing , Shi Gongyi , Tang Yi-Wei
Published: July 2011

More than 20 species of Legionella have been identified in relation to human infections. Rapid detection and identification of Legionella isolates is clinically useful to differentiate between infection and contamination and to determine treatment regimens. We explored the use of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) Biotyper system (Bruker Daltonik GmbH, Bremen, Germany) for the identification of Legionella species. The MALDI MS spectra were generated and compared with the Biotyper database, which includes 25 Legionella strains covering 22 species and four Legionella pneumophila serogroups. A total of 83 blind-coded Legionella strains, consisting of 54 reference and 29 clinical strains, were analyzed in the study. Overall, the Biotyper system correctly identified 51 (61.4%) of all strains and isolates to the species level. For species included in the Biotyper database, the method identified 51 (86.4%) strains out of 59 Legionella strains to the correct species level, including 24 (100%) L. pneumophila and 27 (77.1%) non-L. pneumophila strains. The remaining 24 Legionella strains, belonging to species not covered by the Biotyper database, were either identified to the Legionella genus level or had no reliable identification. The Biotyper system produces constant and reproducible MALDI MS spectra for Legionella strains and can be used for rapid and accurate Legionella identification. More Legionella strains, especially the non-L. pneumophila strains, need to be included in the current Biotyper database to cover varieties of Legionella species and to increase identification accuracy.