bluuebunny/crossref_metadata_2025 huggingface dataset:
Signal processing of impedance spectrum for speed of sound and pressure measurement in plane or radial resonators
Authors: Rosenkrantz Eric , Ferrandis Jean-Yves , Leveque Gerard
Published: May 2008

The impedance of gas contained between two plane walls is a periodic function of the frequency. The frequency interval between two resonances of the gas is equal to c/2D. Furthermore, the amplitude of the resonances is proportional to the pressure. We describe a signal processing to easily deduce the speed of sound and the pressure of the gas from the impedance spectrum. We show that the modulus of the Fourier transform of the modulus of impedance, called “Tempograph,” contains all information about the gas. In some industrial cases the container is a cylinder or a sphere which can be used as a radial resonator exited by a radial wave [1, 2]. The frequency response of such resonator at high frequencies is quasi-periodic and thus the same signal processing can be used. [1] M. F. Narbey, et al., “Determination of the composition of a gas mixture in a nuclear fuel rod by an acoustic method.” INSIGHT, 42(9), 603-605 (2000). [2] A. Olson, “Helium bottle pressure measurement by portable ultrasonic technique.” 1989, Rapport de Boeing n°AD-A208 994, http://stinet.dtic.mil/str/index.html.
The physics of wedge diffraction: A model in terms of elementary diffracted waves
Authors: Ueda Mitsuhiro
Published: May 2008

A model for wedge diffraction is constructed using the virtual discontinuity principle of diffraction [1]. In the model diffracted waves are described by the sum of two elementary diffracted waves that are calculated by integrating the potential along the half line issued from the vertex of wedge. The wedge of aperture angle π/n (n=1,2,3,...) is nondiffractive since its potential can be expressed by the sum of direct waves from the point source and its mirror images. The nondiffractive wedges are useless in the conventional analysis of diffraction since there are no diffracted waves in the potential. But in this model diffracted waves of these wedges are cancelled out in the summing process. Thus the elementary diffracted waves are existed even in these wedges and far field solution for them is obtained for the nondiffractive wedge. Due to its simple structure it can be extended to the arbitrary wedge without any modification and the far field solution of diffracted waves is derived by summing the extended elementary diffracted waves in the model and it coincides with the rigorous one literally. Thus the model is verified firmly by this simple calculation. 1. M. Ueda, JASA, 95, p.2354 (1994).
Spectral and temporal modulations essential to spoken word, gender and timbre identification
Authors: Theunissen Frédéric E. , Elliott Taffeta
Published: May 2008

Human speech and musical sounds contain complex spectral and temporal modulations. Speech intelligibility, perception of melody, and identification of source characteristics (e.g., speaker gender or musical timbre) depend on spectrotemporal modulations but can be surprisingly robust to drastic spectral and temporal degradations. We systematically explored which restricted spectral and temporal modulations are essential to the perception of complex sounds. Degraded sentences and musical sounds were obtained by a novel modulation filtering procedure performed on the sound spectrogram. Temporal modulation filtering smeared the amplitude envelope by removing changes above particular Hz. Spectral modulation filtering smeared the spectral energy across frequency bands by removing changes above particular cyc/kHz. We further complemented this low-pass filtering with more specific notch-filtering. Speech intelligibility, gender recognition and musical instrument identification were assessed in psychophysical experiments. We determined that spectral modulations below ∼3.75 cyc/kHz, and temporal modulations between 1 and 7 Hz are essential for speech comprehension. Gender identification however required the presence of higher spectral modulations. Similarly the timbre and pitch of instruments was affected differentially by notch filters in these two regions of the modulation spectrum. Our research could be used to guide the design of optimal signal processing in hearing aids and cochlear implants.
Listeners' sensitivity to talker differences in voice-onset-time: Segments versus features
Authors: Theodore Rachel M. , Miller Joanne L.
Published: May 2008

Recent findings indicate that listeners are sensitive to talker differences in phonetic properties of speech, including voice-onset-time (VOT) in word-initial voiceless stop consonants. Here we extend earlier findings from our laboratory [J. S. Allen and J. L. Miller, J. Acoust. Soc. Am. 115, 3171-3813 (2004)] by examining the level of representation underlying this sensitivity. In familiarization phases, listeners heard two talkers produce pain. Critically, word-initial VOTs were manipulated such that one talker produced short VOTs and the other talker produced long VOTs. In test phases, listeners were presented with a short-VOT and long-VOT variant of either pain or cane; in both cases, listeners were asked to select which of the two VOT variants was most representative of a given talker. Results to date indicate that which variant of pain is selected at test is in line with listeners' exposure during training (replicating earlier findings), and that this effect holds even when listeners are tested on cane, which begins with a different voiceless stop than heard during training. These results suggest that listeners are sensitive to talker differences in VOT at the level of a phonetic feature, rather than at the level of a particular phonetic segment.
A virtual auditory environment for investigating the auditory signal processing of realistic sounds
Authors: Favrot Sylvain , Buchholz Jörg M.
Published: May 2008

In the present study, a novel multichannel loudspeaker-based virtual auditory environment (VAE) is introduced. The VAE aims at providing a versatile research environment for investigating the auditory signal processing in real environments, i.e., considering multiple sound sources and room reverberation. The environment is based on the ODEON room acoustic simulation software to render the acoustical scene. ODEON outputs are processed using a combination of different order Ambisonic techniques to calculate multichannel room impulse responses (mRIR). Auralization is then obtained by the convolution of the mRIR with an acoustic signal. The derivation of the mRIRs takes into account that (i) auditory localization is most sensitive to the location of the direct sound and (ii) that auditory localization performance is rather poor for early reflections and even worse for late reverberation. Throughout the VAE development, special care was taken in order to achieve a realistic auditory percept and to avoid “artifacts” such as unnatural coloration. The performance of the VAE has been evaluated and optimized on a 29 loudspeaker setup using both objective and subjective measurement techniques.
Investigation on the restitution system influence over perceived Higher Order Ambisonics sound field: a subjective evaluation involving from first to fourth order systems
Authors: Bertet Stephanie , Daniel Jérôme , Parizet Etienne , Warusfel Olivier
Published: May 2008

Among the spatial audio reproduction techniques over loudspeakers, the Higher Order Ambisonics (HOA) approach is based on a sound field spherical harmonics decomposition. By truncating the decomposition to the Mth order, it remains a finite number of components that form the spatial HOA format. The more components are used to encode the sound field, the finer the spatial resolution is. Similarly, the size of the area where the sound field is accurately recreated is proportional to the order. For an Mth encoding order, N=2M+2 equally distributed loudspeakers are recommended for a homogeneous reproduction in the horizontal plane. Adding loudspeakers does not change the spatial resolution. However, what is the influence of the restitution system on the perceived sound field? An experiment was designed in order to compare four systems (from first to fourth order) and a reference one, using similarity ratings obtained from pairwise comparisons. Two sound scenes were used, simulating an audio conference and a scene in a kitchen at home. 25 listeners participated to the experiment. The results were analysed using the Indscal method. The perceptual space appeared to be a two dimensional one, highlighting the influence of the order and the number of loudspeakers on the reproduced scenes.
Near-field binaural synthesis, experimental progress report
Authors: Menzies-Gow Dylan
Published: May 2008

A methodology was previously presented for displaying high quality binaural images of near-field complex sources, using wave reconstruction. Multipole representations of objects are transformed to Fourier-Bessel and plane wave expansions at the listener, before conversion to binaural signals. One advantage of this approach is that does not require special HRTF information other than the planewave HRTFs, and can fully render the complex field of a near object. As a first step towards a full working system, a real-time implementation is described here for displaying a monopole source using a six degrees-of-freedom infrared head tracking device.
Observations of out of plane arrivals for long range low frequency transmission in shallow water
Authors: Deferrari Harry
Published: May 2008

Two recent experiments have used long horizontal arrays to receive broadband low frequency signals propagated over long ranges in shallow water. Both used m-sequence signals that resolve pulse arrivals in time with each arrival associated with a single acoustic mode of propagation. At moderate propagation ranges, out to 20 km, wave fronts for all modes are observed to be parallel, implying an orderly two-dimensional propagation. At a much longer range, 80 km, a number of separable arrivals are observed but not necessarily with a one-to-one correspondence with modes. The paths appear to be stable and coherent in time implying that they are true Fermat paths, but their wavefront arrival angles differ suggesting the same mode is arriving from several directions, that is, by curved (out of plane paths). The paths could result from wedge effects from gentle slopes perpendicular to the propagation path or possibly from chaotic interaction with random facets of the bottom. In any case, the ultimate limitation for horizontal spatial coherence and array resolution may be the multipath interference of bundles of out of plane arrivals.
High-frequency underwater acoustic propagation in a port using the three-dimensional method of images
Authors: Beaujean Pierre-Philippe J. , Staska Matthew D.
Published: May 2008

A computer-efficient model for underwater acoustic propagation in a shallow, three-dimensional rectangular duct closed at one end has been developed using the method of images. The duct simulates a turning basin located in a port, surrounded with concrete walls and filled with sea water. The channel bottom is composed of silt. The modeled impulse response is compared with the impulse response measured between 15 kHz and 33 kHz. Despite small sensor-position inaccuracies and an approximated duct geometry, the impulse response can be modeled with a relative echo magnitude error of 1.62 dB at worst, and a relative echo location error varying between 0% and 4% when averaged across multiple measurements and sensor locations. This is a sufficient level of accuracy for the simulation of an acoustic communication system operating in the same frequency band and in shallow waters, as time fluctuations in echo magnitude commonly reach 10 dB in this type of environment.
Modeling bottom penetration for buried target detection
Authors: Lim Raymond , Sammelmann Gary S.
Published: May 2008

Sonar detection of targets buried in underwater sediments has been found to be complicated by surface roughness. In particular, current-induced ripples can diffract energy down into sandy sediments to enhance buried target detection at shallow sonar grazing angles. To validate these effects, models encompassing the dominant propagation mechanisms as well as faithfully representing the target in the environment have been used. This paper describes our efforts to adapt transition matrix and perturbation theory models to provide realistic predictions of buried target response for spherical and cylindrical shapes. Combining these models of scattering and penetration required adopting some approximations to reduce computation time while retaining accuracy. Steps taken to verify and exercise the resulting models reveal some sensitivities that accentuate the need for accurate environmental and setup ground truth for validation of detection mechanisms. [Work supported by the Office of Naval Research and the Strategic Environmental Research and Development Program, USA.]
Elastic scattering by partially-solid-filled spherical shell on the seabed: Model-data comparison and physical understanding
Authors: Tesei Alessandra , Zampolli Mario , Canepa Gaetano
Published: May 2008

Low- to mid-frequency elastic scattering measurements were conducted in the range from 5 to 40 ka on a spherical composite shell deployed proud on a sandy seabed. The object consists of a thin-walled shell made of layers of a random-fiber material, and then filled partially with an isotropic solidified epoxy resin and partially with sea water. A scaled version of the object was measured in a water tank under free field conditions. The target responses obtained with and without interaction with the seafloor boundary were compared to simulations achieved by the NURC modeling tool Axiscat. The temporal echoes of the objects were analyzed in terms of elastic waves supported by the structure, on the basis of a ray model. The strongest elastic components come from the interior solid filler. The experimental data of the sphere on the seabed were acquired in October 2006 during the EVA'06 trial off the Island of Elba. The free field data were collected in the NURC water tank.
Robust recognition and characterization of man-made objects in shallow water using time-frequency analysis
Authors: Anderson Shaun D. , Sabra Karim G. , Zakharia Manell E. , Zampolli Mario , Schmidt Henrik , Kuperman William A.
Published: May 2008

For underwater sonar, time-frequency analysis, in particular Wigner-Ville analysis, has been shown to be a relevant tool for discriminating a man made target (shell) from a natural one of the same shape (solid) and even to estimate some target characteristics (shell thickness, shear velocity...). This processing tool takes advantage of the evolutional, time dependent aspect of the echo spectrum. The estimated time-frequency patterns can be used for detection and wideband classification of sonar echoes in order to reduce false alarms. In particular, the so-called “coincidence pattern” appearing for specific frequency range is a robust time-frequency signature of man-made shells. A time-frequency analysis will be presented to understand echo formation mechanisms using a standard spherical shell model target model. The influence of the medium parameters as well as the source-receiver configuration will be investigated in free space and then extended to the case of a shallow water waveguide. The proposed approach will be tested using target scattering data collected during Experiments for Validation of Acoustic modeling techniques (EVA) sea test on the north shore of Isola D'Elba, Italy. Application to mine-hunting sonar systems will be discussed.
Bi-static scattering from buried, elastic objects in shallow water waveguides
Authors: Schmidt Henrik , Ghosh Deep
Published: May 2008

The emerging autonomous network technology is enabling new operational paradigms for the concurrent detection, classification and localization of seabed objects by collaborating AUVs. Thus, such networks can exploit the bi-static enhancement of targets which are stealthy to conventional mono-static sonars, and the resonance properties of manmade targets. Under the GOATS and SWAMSI programs MIT in collaboration with NURC have addressed the fundamental issues associated with the development of such a new sonar concept. Through a series of joint experiements, various aspects of the interaction of elastic targets, completely or partially buried in the seabed have been investicated, including the evanescent coupling of low-frequency sound (1-10 kHz) into the seabed, the coupling with structural waves in the targets, and the 3D scattering back into the water column. The analysis is performed using a spectral virtual source scattering model with an embedded spectral Green's function generator which incorporates all multiple scattering effects between the target and the seabed. The target response is represented uniquely by an impedance matrix which may be computed separately using analytical or numerical methods, depending on the target geometry. The scattering model has been combined with the OASES code to provide a comprehensive simulation environment including all the shallow water waveguide physics.[Work Supported by ONR].
Estimates of scattering strength for buried cylindrical targets ensonified by evanescent waves
Authors: Calvo David C. , Zampolli Mario , Tesei Alessandra
Published: May 2008

It is known that low-frequency subcritical sound waves can significantly scatter from targets buried in a seabed due to the significant penetration depth of the incident evanescent wave. Past computational work on scattering by buried spherical shells has been done, for example, using a T-matrix Method [R. Lim et al., J. Acoust. Soc. Am. 93, 1762-1783 (1993)], a Virtual Source Method [I. Lucifredi and H. Schmidt., J. Acoust. Soc. Am. 120, 3566-3583 (2006)], or finite-element methods [Zampolli et al., J. Acoust. Soc. Am., in press]. In addition to high-fidelity results which are expected from the preceding numerical methods, it desirable to have approximate analytical/asymptotic predictions of multistatic scattering strength for a variety of homogeneous or layered buried targets. Focusing on buried cylinders of infinite or finite-length, we first compute scattering using an approximate method that makes use of separation of variables and neglects multiple scattering between the interface and the target. Results are compared with those generated using the Axiscat/NURC/COMSOL finite-element method. Asymptotic estimates are then presented for scattering strength for objects completely buried in the seafloor for a flat interface (Work sponsored by ONR and NURC.)
Acoustic data fusion devoted to underwater vegetation mapping
Authors: Noel Claire , Viala Christophe , Coquet Michel , Zerr Benoit , Perrot Thierry
Published: May 2008

This paper presents research tasks conducted by SEMANTIC TS, in collaboration with GESMA, aimed to develop a mapping method for underwater vegetation lying on seabed. First stage is to develop a method for detecting and characterizing vegetation on the seabed using the acoustic response from a conventional single beam echo sounder. This new method is then operated simultaneously with multibeam sonar producing micro-relief information and side scan sonar providing gray scale levels associated with bottom reflectivity. Then fusion of these three data is processed. We show efficiency of these multisensor data fusion concept to get very precise seabed vegetation mapping in a way reducing truth control (video and diving investigations). Sensors and method accuracy allow obtaining, like in biomedical field, real 3D scan pictures of seabed vegetation. This study is first applied to posidonia and cymodocea, which play a key role in Mediterranean's echosystem. Then, extension of the method is investigated to address laminaria which may significantly affect the performance of acoustic and optical sensors used for sea-mines detection and this paper presents results of data fusion mapping on an Atlantic sea area covered by luminaria, studied and well known by the CEVA.
Suppression of oceanic reverberation by subspace methods
Authors: Li Xuan , Ma Xiaochuan , Hou Chaohuan
Published: May 2008

Acoustic signal processing in shallow water environments is a challenging problem because of the presence of reverberation. Based on some models of reverberation, data from sensors array is pretreated to suppress reverberation. Considering reverberation as a sum of echoes of transmitted signal, the principal component inverse (PCI) algorithm deletes the largest singulars of data matrix, which is constructed from array data. However, estimating a threshold which is needed in PCI is difficult in practice. In this paper, two new subspace methods, Deleting Big Eigenvalues and Subspace Projection are proposed. The two novel methods, substituting automatic signal-number estimation for threshold estimation, are operated via eigendecomposition. According to a simulation which takes broadband linear modulated frequency signal as transmitted signal, these two methods show a similar performance but smaller computing quantity compared with PCI.
Response to Comment on "Absence of Cooling in New Zealand and the Adjacent Ocean During the Younger Dryas Chronozone"
Authors: Barrows Timothy T. , Lehman Scott J. , Fifield L. Keith , De Deckker Patrick
Published: May 2008

Applegate
et al
. present the results of a moraine degradation model and suggest that the age of the Waiho Loop may be 1000 years older than the age we presented, thus raising the possibility that the moraine is a Younger Dryas landform. We show that this assessment is misleading on a number of grounds.
Controlled Phase Shifts with a Single Quantum Dot
Authors: Fushman Ilya , Englund Dirk , Faraon Andrei , Stoltz Nick , Petroff Pierre , Vučković Jelena
Published: May 2008

Optical nonlinearities enable photon-photon interaction and lie at the heart of several proposals for quantum information processing, quantum nondemolition measurements of photons, and optical signal processing. To date, the largest nonlinearities have been realized with single atoms and atomic ensembles. We show that a single quantum dot coupled to a photonic crystal nanocavity can facilitate controlled phase and amplitude modulation between two modes of light at the single-photon level. At larger control powers, we observed phase shifts up to π/4 and amplitude modulation up to 50%. This was accomplished by varying the photon number in the control beam at a wavelength that was the same as that of the signal, or at a wavelength that was detuned by several quantum dot linewidths from the signal. Our results present a step toward quantum logic devices and quantum nondemolition measurements on a chip.
Climate-Driven Ecosystem Succession in the Sahara: The Past 6000 Years
Authors: Kröpelin S. , Verschuren D. , Lézine A.-M. , Eggermont H. , Cocquyt C. , Francus P. , Cazet J.-P. , Fagot M. , Rumes B. , Russell J. M. , Darius F. , Conley D. J. , Schuster M. , von Suchodoletz H. , Engstrom D. R.
Published: May 2008

Desiccation of the Sahara since the middle Holocene has eradicated all but a few natural archives recording its transition from a “green Sahara” to the present hyperarid desert. Our continuous 6000-year paleoenvironmental reconstruction from northern Chad shows progressive drying of the regional terrestrial ecosystem in response to weakening insolation forcing of the African monsoon and abrupt hydrological change in the local aquatic ecosystem controlled by site-specific thresholds. Strong reductions in tropical trees and then Sahelian grassland cover allowed large-scale dust mobilization from 4300 calendar years before the present (cal yr B.P.). Today's desert ecosystem and regional wind regime were established around 2700 cal yr B.P. This gradual rather than abrupt termination of the African Humid Period in the eastern Sahara suggests a relatively weak biogeophysical feedback on climate.
Regulation of the Cellular Heat Shock Response in
Caenorhabditis elegans
by Thermosensory Neurons
Authors: Prahlad Veena , Cornelius Tyler , Morimoto Richard I.
Published: May 2008

Temperature pervasively affects all cellular processes. In response to a rapid increase in temperature, all cells undergo a heat shock response, an ancient and highly conserved program of stress-inducible gene expression, to reestablish cellular homeostasis. In isolated cells, the heat shock response is initiated by the presence of misfolded proteins and therefore thought to be cell-autonomous. In contrast, we show that within the metazoan
Caenorhabditis elegans
, the heat shock response of somatic cells is not cell-autonomous but rather depends on the thermosensory neuron, AFD, which senses ambient temperature and regulates temperature-dependent behavior. We propose a model whereby this loss of cell autonomy serves to integrate behavioral, metabolic, and stress-related responses to establish an organismal response to environmental change.
Protesting Scientists
Authors: Wolfe Audra J.
Published: May 2008

Disrupting Science
. Social Movements, American Scientists, and the Politics of the Military, 1945-1975.
By Kelly Moore
. Princeton University Press, Princeton, NJ, 2008. 325 pp. $35, £19.95. ISBN 9780691113524. Princeton Studies in Cultural Sociology.

The author examines the postwar growth of scientists' activism against the bonds that linked U.S. science to the military and governmental power.
Development of a Novel Efficient Fluorescence-Based Plaque Reduction Microneutralization Assay for Measles Virus Immunity
Authors: Haralambieva Iana H. , Ovsyannikova Inna G. , Vierkant Robert A. , Poland Gregory A.
Published: May 2008

The measurement of functional measles virus-specific neutralizing antibodies is of considerable interest for vaccine-related research. In this study, we developed and standardized a simple, rapid, highly sensitive, and reproducible fluorescence-based plaque reduction microneutralization (PRMN) assay with visual and automated readout, using a recombinant measles virus engineered to express enhanced green fluorescent protein. The assay is performed in micro format, requires less time to complete (2 versus 4 to 7 days), and is less labor-intensive and less costly than the classical plaque reduction neutralization (PRN) test, widely accepted as the “gold standard” in measles serology. Two available WHO international anti-measles virus standards and one in-house reference serum were used to develop and standardize the new assay. The mean PRMN values from repeated assays were found to be similar to those reported in the literature or assigned to the WHO standards by the classical PRN assay. For validation, we used three groups of low, moderate, and high measles virus vaccine responders’ sera with moderate values of correlation in antibody levels (mIU/ml) between PRMN and the Dade Behring immunoglobulin G enzyme immunoassay (EIA). The PRMN assay was more sensitive at low antibody levels and more informative in terms of protection than this commercial EIA. In conclusion, we have developed and validated a sensitive and high-throughput measles virus-specific PRMN that can be readily used in large population-based measles studies.
False-Positive Results by the Platelia
Aspergillus
Galactomannan Antigen Test for Patients Treated with Amoxicillin-Clavulanate
Authors: Zandijk E. , Mewis A. , Magerman K. , Cartuyvels R.
Published: May 2008

The
Aspergillus
galactomannan test is a valuable tool in the diagnosis of invasive aspergillosis. We hereby report a high rate of false-positive results by the Platelia
Aspergillus
galactomannan antigen test (Bio-Rad Laboratories) for patients treated with amoxicillin-clavulanate.
Eight Years of Experience with Molecular Identification of Human Enteroviruses
Authors: Blomqvist Soile , Paananen Anja , Savolainen-Kopra Carita , Hovi Tapani , Roivainen Merja
Published: May 2008

We have successfully typed 1,121 human enterovirus (HEV) isolates during the last 8 years by adapting partial VP1 sequencing to routine identification of HEV isolated from diverse clinical and environmental specimens. The isolates include 48 of the 59 traditional nonpoliovirus HEV serotypes and members of 8 newly discovered types, which would have remained untypeable by neutralization using the conventional cross-sectional pools of antisera.
Comparison of the NucliSens easyMAG and Qiagen BioRobot 9604 Nucleic Acid Extraction Systems for Detection of RNA and DNA Respiratory Viruses in Nasopharyngeal Aspirate Samples
Authors: Chan Kwok Hung , Yam Wing Cheong , Pang Chiu Mei , Chan Kit Man , Lam Siu Yan , Lo Kam Fai , Poon Leo L. M. , Peiris J. S. Malik
Published: May 2008

The NucliSens easyMAG and BioRot 9604 automated nucleic acid extraction systems were evaluated and compared with the manual QIAamp (Qiagen) extraction method for their abilities to extract nucleic acid from nasopharyngeal aspirate samples for the detection of RNA and DNA respiratory viruses. The nucleic acids recovered by all three methods gave comparable sensitivities in PCR tests, and the three methods gave comparable viral loads. There was no evidence of residual PCR inhibitors and no evidence of PCR cross-contamination.
Clinical Evaluation of the Sensititre YeastOne Colorimetric Antifungal Panel for Antifungal Susceptibility Testing of the Echinocandins Anidulafungin, Caspofungin, and Micafungin
Authors: Pfaller M. A. , Chaturvedi V. , Diekema D. J. , Ghannoum M. A. , Holliday N. M. , Killian S. B. , Knapp C. C. , Messer S. A. , Miskov A. , Ramani R.
Published: May 2008

A commercially prepared, dried colorimetric microdilution panel (Sensititre YeastOne Trek Diagnostic Systems, Cleveland, OH) was compared in three different laboratories with the Clinical and Laboratory Standards Institute (CLSI) reference microdilution method by testing 2 quality control strains, 25 reproducibility strains, and 404 isolates of
Candida
spp. against anidulafungin, caspofungin, and micafungin. Reference MIC endpoints and YeastOne colorimetric endpoints were read after 24 h of incubation. YeastOne endpoints were determined to be the lowest concentration at which the color in the well changed from red (positive, indicating growth) to blue (negative, indicating no growth). Excellent essential agreement (within 2 dilutions) between the reference and colorimetric MICs was observed. Overall agreement was 100% for all three agents. Categorical agreement ranged from 99.3% (anidulafungin) to 100% (caspofungin, micafungin) and interlaboratory reproducibility was 99%. The YeastOne colorimetric method appears to be comparable to the CLSI reference method for testing the susceptibility of
Candida
spp. to the echinocandins anidulafungin, caspofungin, and micafungin.
Phylogenetic Backgrounds and Virulence Profiles of Atypical Enteropathogenic
Escherichia coli
Strains from a Case-Control Study Using Multilocus Sequence Typing and DNA Microarray Analysis
Authors: Afset Jan Egil , Anderssen Endre , Bruant Guillaume , Harel Josée , Wieler Lothar , Bergh Kåre
Published: May 2008

Atypical enteropathogenetic
Escherichia coli
(EPEC) strains are frequently detected in children with diarrhea but are also a common finding in healthy children. The aim of this study was to compare the phylogenetic ancestry and virulence characteristics of atypical (
eae
positive,
stx
and
bfpA
negative) EPEC strains from Norwegian children with (
n
= 37) or without (
n
= 19) diarrhea and to search for an association between phylogenetic ancestry and diarrhea. The strains were classified in phylogenetic groups by phylogenetic marker genes and in sequence types (STs) by multilocus sequence typing. Phylogenetic ancestry was compared to virulence characteristics based on DNA microarray analysis. Serotyping and pulsed-field gel electrophoresis (PFGE) were also performed. All four phylogenetic groups, 26 different STs, and 20 different clonal groups were represented among the 56 atypical EPEC strains. The strains were separated into three clusters by overall virulence gene profile; one large cluster with A, B1, and D strains and two clusters with group B2 strains. There was considerable heterogeneity in the PFGE profiles and serotypes, and almost half of the strains were O nontypeable. The
efa1
/
lifA
gene, previously shown to be statistically linked with diarrhea in this strain collection (J. E. Afset et al., J. Clin. Microbiol. 44:3703-3711, 2006), was present in 8 of 26 STs. The two phylogenetic groups B1 and D were weakly associated with diarrhea (
P
= 0.06 and
P
= 0.09, respectively). In contrast, group B2 was isolated most frequently from healthy controls (
P
= 0.05). In conclusion, the atypical EPEC strains were heterogeneous both phylogenetically and by virulence profile. Phylogenetic ancestry was less useful as a predictor of diarrhea than were specific virulence genes.
The feasibility of a home-based moderate-intensity physical activity intervention in obese children and adolescents
Authors: Conwell Louise S , Trost Stewart G , Spence Luke , Brown Wendy J , Batch Jennifer A
Published: May 2008

Objectives

To explore the feasibility of conducting a 10-week home-based physical activity (PA) programme and evaluate the changes in insulin sensitivity (SI) commensurate with the programme in obese young people.

Design

Open-labelled intervention.

Setting

Home-based intervention with clinical assessments at a tertiary paediatric hospital.

Subjects

18 obese (body mass index (BMI)>International Obesity Task Force age and sex-specific cut-offs) children and adolescents (8–18 years, 11 girls/7 boys) were recruited. 15 participants (nine girls/six boys, mean±SE age 11.8±0.6 years, BMI-SD scores (BMI-SDS) 3.5±0.1, six prepubertal/nine pubertal) completed the intervention.

Intervention

The programme comprised biweekly home visits over 10 weeks with personalised plans implemented aiming to increase moderate-intensity PA. Pedometers and PA diaries were used as self-monitoring tools. The goals were to (1) teach participants behavioural skills related to adopting and maintaining an active lifestyle and (2) increase daily participation in PA.

Outcome measures

Mean steps/day were assessed. SIassessed by the frequently sampled intravenous glucose tolerance test and other components of the insulin resistance syndrome were measured.

Results

Mean steps/day increased significantly from 10 363±927 (baseline) to 13 013±1131 (week 10) (p<0.05). SIwas also significantly increased, despite no change in BMI-SDS, and remained so after an additional 10-week follow-up.

Conclusions

The results suggest that such a home-based PA programme is feasible. SIimproved without changes in BMI-SDS. More rigorous evaluations of such programmes are warranted.
Cardiovascular fitness modifies the associations between physical activity and abdominal adiposity in children and adolescents: the European Youth Heart Study
Authors: Ortega F B , Ruiz J R , Hurtig-Wennlöf A , Vicente-Rodríguez G , Rizzo N S , Castillo M J , Sjöström M
Published: May 2008

Objective

To examine the associations between physical activity (PA) and abdominal adiposity, as measured by waist circumference, in children and adolescents, and to test whether cardiovascular fitness (CVF) modifies these associations.

Methods

PA components were measured by accelerometry in 1075 individuals aged 9 or 15 years old. CVF was measured by a maximal cycling test. Self-reported maternal educational level, body mass index, children's birth weight and television viewing were used as confounders.

Results

Linear regression did not show any association between the PA variables and waist circumference, after controlling for sex, age and height. When stratifying by CVF level (low/high), time spent at vigorous PA was inversely associated with waist circumference (p≤0.05) in the low CVF group. Unexpectedly, in the high CVF group, the PA variables were positively associated with waist circumference (p≤0.05). In both groups, the results were unchanged after controlling for the confounders. CVF was inversely associated with waist circumference, after controlling for all PA variables (p≤0.01) and confounders (p≤0.01).

Conclusion

CVF is inversely associated with abdominal adiposity and seems to modify the associations between PA and abdominal adiposity. In low-fit children and adolescents, time spent in vigorous PA seems to be the key component linked to abdominal adiposity. This finding should be considered in further development of lifestyle intervention strategies. The results found in the high-fit group need to be confirmed.
Genetic and biochemical characterization of novel low molecular weight glutenin subunits in wheat (Triticum aestivumL.)
Authors: Sreeramulu Guttapadu , Singh Nagendra K.
Published: May 2008

Two novel low molecular weight subunits of glutenin with relative molecular mass (Mrvalues) of 30 and 32 kDa were isolated from the seeds of hexaploid wheat and characterized at genetic and biochemical levels. Among 115 Indian bread wheat cultivars analysed, 40 had a narrow doublet of the new protein bands, 69 had a wide doublet, 3 had only the faster moving band of the doublet, and the remaining 3 cultivars had only the slower moving band. These subunits could be seen in the alkylated glutenin preparations only and the genes for the faster (designated Glu-D4) and slower (designated Glu-D5) moving protein bands of the doublet were located on chromosomes 1D and 7D, respectively. Amino acid composition of the two new subunits was quite different from those of the other well-characterized gluten proteins, as the new subunits have lower amounts of proline and relatively higher amounts of glycine, aspartic acid – asparagine, cysteine, and lysine. Polyclonal antibodies raised against these polypeptides cross-reacted strongly with the major low molecular weight subunits of wheat glutenin (Glu-3 subunits), but did not cross-react with the high molecular weight glutenin subunits or monomeric gliadins. Furthermore, preliminary results on the N-terminal amino acid sequences of the new subunits show homology with the major low molecular weight glutenin subunits, suggesting an evolutionary link between the two.Key words: Triticum aestivum, glutenin subunits, gene location, immunoblotting.
Identification of introgressed segments conferring disease resistance in a tetrageneric hybrid of Triticum, Secale, Thinopyrum, and Avena
Authors: Tang Shunxue , Zhuang Jiajun , Wen Yuxiang , Ai Shanjiang Abydylla , Li Hongjie , Xu Jia
Published: May 2008

Using genomic in situ hybridization to chromosomes, we identified introgressed segments in a tetrageneric hybrid of Triticum, Avena, Thinopyrum, and Secale, which conferred high resistance to leaf rust, stem rust, stripe rust, powdery mildew, and root rot to wheat. The disease-resistance traits of the hybrid originated from three wild related genera of Triticum, namely Avena, Thinopyrum, and Secale. The new breeding system that combined traditional wide hybridization with anther culture was efficient and rapid in creating wheat germplasms resistant to major diseases.Key words: Triticum aestivum, Avena fatua, Thinopyrum intermedium, Secale cereale, wide hybridization, anther culture, genomic in situ hybridization, GISH.
Genetic diversity in North American ginseng (Panax quinquefolius L.) grown in Ontario detected by RAPD analysis
Authors: Bai Dapeng , Brandle J. , Reeleder R.
Published: May 2008

Genetic diversity within North American ginseng (Panax quinquefolius L.) grown in Ontario was investigated at the DNA level using the randomly amplified polymorphic DNA (RAPD) method via the polymerase chain reaction (PCR). A total of 420 random decamers were initially screened against DNA from four ginseng plants and 78.8% of them generated RAPD fragments. Thirty-six of the decamers that generated highly repeatable polymorphic RAPD markers were selected for further RAPD analysis of the ginseng population. With these primers, 352 discernible DNA fragments were produced from DNA of 48 ginseng plants, corresponding to an average of 9.8 fragments per primer, of which over 45% were polymorphic. The similarity coefficients among the DNA of ginseng plants analyzed were low, ranging from 0.149 to 0.605 with a mean of 0.412, indicating that a high degree of genetic diversity exists in the ginseng population. Lower levels of genetic diversity were detected among 3-year-old ginseng plants selected on the basis of greater plant height than among the plants randomly selected from the same subpopulation or over the whole population, suggesting that genetic factors at least partly contribute to morphological variation within the ginseng population and that visual selection can be effective in identifying the genetic differences. The significance of a high degree of genetic variation in the ginseng population on its potential for improvement by breeding is also discussed.Key words: Panax quinquefolius, ginseng, RAPD, genetic diversity.
Variations in the heat-induced protein pattern of severalDrosophila montiumsubgroup species (Diptera: Drosophilidae)
Authors: Konstantopoulou Irene , Drosopoulou Elena , Scouras Zacharias G.
Published: May 2008

After temperature elevation, the newly synthesized polypeptides from several Drosophila montium subgroup species, of the melanogaster species group, were analyzed in denaturing acrylamide gels. The pattern obtained is characteristic of the heat shock response already documented for many other Drosophila species, although the relative electrophoretic mobility of the "small" heat shock proteins exhibits a species-specific pattern. Based on the above pattern, the montium species are placed in three distinct groups. The present data is consistent with that previously used to propose a northeast to southwest evolutionary mode of expansion for the montium subgroup species.Key words: heat shock proteins, Drosophila montium subgroup species, evolution.
A rapid procedure for the isolation of C0t-1 DNA from plants
Authors: Zwick Michael S. , Hanson Robert E. , Islam-Faridi M. Nurul , Stelly David M. , Wing Rod A. , Price H. James , McKnight Thomas D.
Published: May 2008

In situ hybridization (ISH) for the detection of single- or low-copy sequences, particularly large DNA fragments cloned into YAC or BAC vectors, generally requires the suppression or "blocking" of highly-repetitive DNAs. C0t-1 DNA is enriched for repetitive DNA elements, high or moderate in copy number, and can therefore be used more effectively than total genomic DNA to prehybridize and competitively hybridize repetitive elements that would otherwise cause nonspecific hybridization. C0t-1 DNAs from several mammalian species are commercially available, however, none is currently available for plants to the best of our knowledge. We have developed a simple 1-day procedure to generate C0t-1 DNA without the use of specialized equipment.Key words: C0t-1 DNA, in situ hybridization, BACs, plants.
TheChironomus(Camptochironomus)tentansgenome contains two non-LTR retrotransposons
Authors: Blinov A. G. , Sobanov Y. V. , Scherbik S. V. , Aimanova K. G.
Published: May 2008

A cDNA library from salivary gland cells of Chironomus tentans was screened with a probe containing the NLRCth1 non-LTR (long terminal repeat) retrotransposon from Chironomus thummi. Several positive clones were obtained and one of them, p62, was characterized by in situ hybridization and sequencing. The sequencing analysis showed that this clone contained a 4607 bp nucleotide sequence of a new transposable element that hybridized in situ to more than 100 sites over all four C. tentans chromosomes. The detailed analysis of this sequence revealed the presence of the 3′-end of open reading frame 1 (ORF1), a complete ORF2, and a 1.3-kb 3′-end untranslated region (UTR). The new element has been designated NLRCt2 (non-LTR retrotransposon 2 from C. tentans). A comparison of the nucleotide sequences of NLRCth1 and NLRCt2 showed 30% similarity in the region of ORF1 and 70% similarity in the region of ORF2. Based on the results of Southern blot analysis, two transposable elements have been found in the C. tentans genome, one of which is identical to NLRCth1 from C. thummi. This may be explained by horizontal transmission. The second element, NLRCt2, has been found in two different forms in the C. tentans genome. These can be distinguished by the presence of the 1.3-kb 3′-end UTR in one of the forms. Since the cDNA clone investigated was isolated from a tissue-specific cDNA library, the data showed that NRLCt2 is expressed in somatic cells.Key words: Chironomus, non-LTR retrotransposon, in situ hybridization, reverse transcriptase, horizontal transmission.
Reduced recombination and distorted segregation in aSolanum tuberosum(2x) ×S.spegazzinii(2x) hybrid
Authors: Kreike C. M. , Stiekema W. J.
Published: May 2008

In this paper we describe the reduced recombination and distorted segregation in an interspecific hybrid between Solanum tuberosum and Solanum spegazzinii. To study these phenomena, a cross was made between a (di)haploid S. tuberosum, used as a female parent, and a diploid wild potato species, S. spegazzinii, used as a male parent. Next, a backcross (BC) population was made with F1genotype 38 that was backcrossed to S. tuberosum. In the backcross, S. tuberosum was used as the male parent. RFLP linkage maps were made using the F1and the BC populations, yielding linkage maps of the interspecific hybrid, S. spegazzinii, and S. tuberosum from which male and female linkage maps could be constructed. The computer program JOINMAP was used to construct and combine the separate linkage maps. Subsequently, the separate linkage maps were compared with each other, and reduced recombination was observed in the linkage maps of the male S. tuberosum and the interspecific hybrid. The reason for this reduced recombination is discussed. Another common feature in linkage maps is the observation of distorted segregation. The distorted segregation of alleles from the interspecific hybrid was studied in more detail in the BC population. Most of the distortion was probably caused by gamete selection, but for 3 loci, on chromosomes 2, 3, and 4, we found evidence for the presence of a strong selection force acting at the zygote level against homozygous genotypes.Key words: RFLP linkage map, potato, interspecific hybrid, zygote selection.
Identification of an RFLP interval containingPch2on chromosome 7AL in wheat
Authors: Peña Robert C. de la , Murray Timothy D. , Jones Stephen S.
Published: May 2008

The gene Pch2 in 'Cappelle Desprez' is one of two genes found in hexaploid wheat known to confer resistance to eyespot disease. This study was conducted to develop an RFLP linkage map of the distal portion of wheat chromosome 7AL, and to locate and identify markers closely associated with Pch2 for use in marker-assisted selection. Ten loci in addition to Pch2 were mapped on chromosome 7AL, using segregation data from 102 homozygous chromosome 7A recombinant substitution lines derived from 'Chinese Spring' × 'Chinese Spring' ('Cappelle Desprez' 7A). The Pch2 locus was bracketed by two RFLP markers, one 11.0 cM distal to Xcdo347 and the other 18.8 cM proximal to Xwg380. The position of Pch2 on chromosome 7AL is similar to that of Pch1 on chromosome 7DL, suggesting that these resistance genes are homoeoloci. Although no single marker was closely linked to Pch2, simultaneous selection of the flanking RFLP markers Xcdo347 and Xwg380 could be used for selecting Pch2, since double recombination occurred in only 3% of the recombinant population. The use of the flanking RFLP markers to select for Pch2, in combination with previously identified Pch1-linked markers, would facilitate the development of cultivars carrying two genes for resistance to eyespot.Key words: Triticum aestivum, Pseudocercosporella herpotrichoides, recombinant substitution line.