bluuebunny/crossref_metadata_2025 huggingface dataset:
Monte Carlo Simulation of Particle-Cracking Damage Evolution in Metal Matrix Composites
Authors: Liu H. T. , Sun L. Z. , Wu H. C.
Published: June 2005

In the modeling of microstructural damage mechanisms of composites, damage evolution plays an important role and has significant effects on the overall nonlinear behavior of composites. In this study, a microstructural Monte Carlo simulation method is proposed to predict the volume fraction evolution of damaged particles due to particle-cracking for metal matrix composites with randomly distributed spheroidal particles. The performance function is constructed using a stress-based damage criterion. A micromechanics-based elastoplastic and damage model is applied to compute the local stress field and to estimate the overall nonlinear response of the composites with particle-cracking damage mechanism. The factors that affect the damage evolution are investigated and the effects of particle shape and damage strength on damage evolution are discussed in detail. Simulation results are compared with experiments and good agreement is obtained.
Acoustic characteristics of an electrodynamic planar digital loudspeaker using noise shaping technology
Authors: Hayama Atsushi , Furihata Kenji , Asano David K. , Yanagisawa Takesaburo
Published: June 2005

The present study extends our previous work [Furihata et al., J. Acoust. Soc. Am. 114, 174–184 (2003)] by investigating our electrodynamic planar loudspeaker when driven by a 12 bit digital signal with noise shaping. Changing the structure of the loudspeaker can lead to improvement, but in this paper improvements that can be made using signal processing are investigated. Results show that the digital loudspeaker demonstrated good linearity over its 84 dB dynamic range from 40 Hz to 10 kHz. This shows that a 12 bit digital loudspeaker which is equivalent to a 16 bit one is possible.
The vibro-acoustic response and analysis of a full-scale aircraft fuselage section for interior noise reduction
Authors: Herdic Peter C. , Houston Brian H. , Marcus Martin H. , Williams Earl G. , Baz Amr M.
Published: June 2005

The surface and interior response of a Cessna Citation fuselage section under three different forcing functions (10–1000 Hz) is evaluated through spatially dense scanning measurements. Spatial Fourier analysis reveals that a point force applied to the stiffener grid provides a rich wavenumber response over a broad frequency range. The surface motion data show global structural modes (≲150 Hz), superposition of global and local intrapanel responses (∼150–450 Hz), and intrapanel motion alone (≳450 Hz). Some evidence of Bloch wave motion is observed, revealing classical stop/pass bands associated with stiffener periodicity. The interior response (≲150 Hz) is dominated by global structural modes that force the interior cavity. Local intrapanel responses (≳150 Hz) of the fuselage provide a broadband volume velocity source that strongly excites a high density of interior modes. Mode coupling between the structural response and the interior modes appears to be negligible due to a lack of frequency proximity and mismatches in the spatial distribution. A high degree-of-freedom finite element model of the fuselage section was developed as a predictive tool. The calculated response is in good agreement with the experimental result, yielding a general model development methodology for accurate prediction of structures with moderate to high complexity.
Modeling Rayleigh and Stoneley waves and other interface and boundary effects with the parabolic equation
Authors: Jerzak Wayne , Siegmann William L. , Collins Michael D.
Published: June 2005

An improved approach for handling boundaries, interfaces, and continuous depth dependence with the elastic parabolic equation is derived and benchmarked. The approach is applied to model the propagation of Rayleigh and Stoneley waves. Depending on the choice of dependent variables, the operator in the elastic wave equation may not factor or the treatment of interfaces may be difficult. These problems are resolved by using a formulation in terms of the vertical displacement and the range derivative of the horizontal displacement. These quantities are continuous across horizontal interfaces, which permits the use of Galerkin’s method to discretize in depth. This implementation extends the capability of the elastic parabolic equation to handle arbitrary depth dependence and should lead to improvements for range-dependent problems.
Fine structure spectrography and its application in speech
Authors: Dajani Hilmi R. , Wong Willy , Kunov Hans
Published: June 2005

A filterbank-based algorithm for time-varying spectral analysis is proposed. The algorithm, which is an enhanced realization of the conventional spectrogram, consists of hundreds or thousands of highly overlapping wideband filter/detector stages, followed by a peak detector that probes the filter/detector outputs at very short time intervals. Analysis with synthetic modulated signals illustrates how the proposed method demodulates these signals. The resulting spectrogram-like display, referred to as a “fine structure spectrogram,” shows the fine structure of the modulations in substantially higher detail than is possible with conventional spectrograms. Error evaluation is performed as a function of various parameters of a single- and two-component synthetic modulated signal, and of parameters of the analysis system. In speech, the fine structure spectrogram can detect small frequency and amplitude modulations in the formants. It also appears to identify additional significant time-frequency components in speech that are not detected by other methods, making it potentially useful in speech processing applications.
Beamforming with air-coupled surface waves around a sphere and circular cylinder (L)
Authors: Daigle Gilles A. , Stinson Michael R. , Ryan James G.
Published: June 2005

Beamforming using a microphone array mounted on the surface of a rigid or impedance sphere and cylinder is discussed. The introduction of a structure into the space occupied by or immediately adjacent to the array gives the array an effectively larger aperture and the possibility of enhanced performance. Additional improvements can be obtained through the introduction of a surface that permits air-coupled surface waves to propagate. Since surface waves travel at a speed less than the speed of sound in free space, the aperture of the array can be effectively further increased.
Fluctuations in diffuse field–field correlations and the emergence of the Green’s function in open systems
Authors: Weaver Richard L. , Lobkis Oleg I.
Published: June 2005

Recent intense interest in diffuse field correlation functions, with applications to passive imaging in underwater acoustics and seismology, has raised questions about the degree with which a retrieved waveform can be expected to conform to the Green’s function, and in particular the degree with which a ray arrival may be discerned. On considering a simple scalar wave model consisting of fields with distributed random sources, the difffuse field-field correlation function R is defined as a sum of correlation integrals, one for each of the many distinct distributed sources. It is then shown that this ensemble of fields has a correlation function with expectation 〈R〉 equal to the Green’s function. This model also lends itself to calculations of the variance of R, and thus to estimates of the degree to which an R calculated using finite amounts of data will conform to the Green’s function. The model predicts that such conformation is strongest at low frequencies. Ray arrivals are detectable if sufficient data have been collected, but the amount of data needed scales in three dimensions with the square of the source–receiver separation, and the square of the frequency. Applications to seismology are discussed.
Equal sensation curves for whole-body vibration expressed as a function of driving force
Authors: Mansfield Neil J. , Maeda Setsuo
Published: June 2005

Previous studies have shown that the seated human is most sensitive to whole-body vertical vibration at about 5 Hz. Similarly, the body shows an apparent mass resonance at about 5 Hz. Considering these similarities between the biomechanical and subjective responses, it was hypothesized that, at low frequencies, subjective ratings of whole-body vibration might be directly proportional to the driving force. Twelve male subjects participated in a laboratory experiment where subjects sat on a rigid seat mounted on a shaker. The magnitude of a test stimulus was adjusted such that the subjective intensity could be matched to a reference stimulus, using a modified Bruceton test protocol. The sinusoidal reference stimulus was 8-Hz vibration with a magnitude of 0.5 m/s2 rms (or 0.25 m/s2 rms for the 1-Hz test); the sinusoidal test stimuli had frequencies of 1, 2, 4, 16, and 32 Hz. Equal sensation contours in terms of seat acceleration showed data similar to those in the literature. Equal sensation contours in terms of force showed a nominally linear response at 1, 2, and 4 Hz, but an increasing sensitivity at higher frequencies. This is in agreement with a model derived from published subjective and objective fitted data.
Forced responses of solid axially polarized piezoelectric ceramic finite cylinders with internal losses
Authors: Ebenezer D. D. , Ravichandran K. , Ramesh R. , Padmanabhan Chandramouli
Published: June 2005

A method is presented to determine the forced responses of piezoelectric cylinders using weighted sums of only certain exact solutions to the equations of motion and the Gauss electrostatic conditions. One infinite set of solutions is chosen such that each field variable is expressed in terms of Bessel functions that form a complete set in the radial direction. Another infinite set of solutions is chosen such that each field variable is expressed in terms of trigonometric functions that form a complete set in the axial direction. Another solution is used to account for the electric field that can exist even when there is no vibration. The weights are determined by using the orthogonal properties of the functions and are used to satisfy specified, arbitrary, axisymmetric boundary conditions on all the surfaces. Special cases including simultaneous mechanical and electrical excitation of cylinders are presented. All numerical results are in excellent agreement with those obtained using the finite element software ATILA. For example, the five lowest frequencies at which the conductance and susceptance of a stress-free cylinder, of length 10 mm and radius 5 mm, reach a local maximum or minimum differ by less than 0.01% from those computed using ATILA.
The influence of finite cavities on the sound insulation of double-plate structures
Authors: Brunskog Jonas
Published: June 2005

Lightweight walls are often designed as frameworks of studs with plates on each side—a double-plate structure. The studs constitute boundaries for the cavities, thereby both affecting the sound transmission directly by short-circuiting the plates, and indirectly by disturbing the sound field between the plates. The paper presents a deterministic prediction model for airborne sound insulation including both effects of the studs. A spatial transform technique is used, taking advantage of the periodicity. The acoustic field inside the cavities is expanded by means of cosine-series. The transmission coefficient (angle-dependent and diffuse) and transmission loss are studied. Numerical examples are presented and comparisons with measurement are performed. The result indicates that a reasonably good agreement between theory and measurement can be achieved.
An autocorrelation model with place dependence to account for the effect of harmonic number on fundamental frequency discrimination
Authors: Bernstein Joshua G. W. , Oxenham Andrew J.
Published: June 2005

Fundamental frequency (f0) difference limens (DLs) were measured as a function of f0 for sine- and random-phase harmonic complexes, bandpass filtered with 3-dB cutoff frequencies of 2.5 and 3.5 kHz (low region) or 5 and 7 kHz (high region), and presented at an average 15 dB sensation level (approximately 48 dB SPL) per component in a wideband background noise. Fundamental frequencies ranged from 50 to 300 Hz and 100 to 600 Hz in the low and high spectral regions, respectively. In each spectral region, f0 DLs improved dramatically with increasing f0 as approximately the tenth harmonic appeared in the passband. Generally, f0 DLs for complexes with similar harmonic numbers were similar in the two spectral regions. The dependence of f0 discrimination on harmonic number presents a significant challenge to autocorrelation (AC) models of pitch, in which predictions generally depend more on spectral region than harmonic number. A modification involving a “lag window”is proposed and tested, restricting the AC representation to a limited range of lags relative to each channel’s characteristic frequency. This modified unitary pitch model was able to account for the dependence of f0 DLs on harmonic number, although this correct behavior was not based on peripheral harmonic resolvability.
A novel method for estimating the focal size of two confocal high-intensity focused ultrasound transducers
Authors: Chen Wen-Shiang , Ma Ping-Mo , Liu Hao-Li , Yeh Chih-Kuang , Chen Min-Shin , Chang Chein-Wei
Published: June 2005

Estimating the focal size and position of a high-intensity focused ultrasound (HIFU) transducer remains a challenge since traditional methods, such as hydrophone scanning or schlieren imaging, cannot tolerate high pressures, are directional, or provide low resolution. The difficulties increase when dealing with the complex beam pattern of a multielement HIFU transducer array, e.g., two transducers facing each other. In the present study we show a novel approach to the visualization of the HIFU focus by using shockwave-generated bubbles and a diagnostic B-mode scanner. Bubbles were generated and pushed by shock waves toward the HIFU beam, and were trapped in its pressure valleys. These trapped bubbles moved along the pressure valleys and thereby delineated the shape and size of the HIFU beam. The main and sidelobes of 1.1- and 3.5 MHz HIFU beams were clearly visible, and could be measured with a millimeter resolution. The combined foci could also be visualized by observing the generation of sustained inertial cavitation and enhanced scattering. The results of this study further demonstrate the possibility of reducing the inertial cavitation threshold by the local introduction of shock wave-generated bubbles, which might be useful when bubble generation and cavitation-related bioeffects are intended within a small region in vivo.
Background noise cancellation for improved acoustic detection of manatee vocalizations
Authors: Yan Zheng , Niezrecki Christopher , Beusse Diedrich O.
Published: June 2005

The West Indian manatee (Trichechus manatus latirostris) has become endangered partly because of an increase in the number of collisions with boats. A device to alert boaters of the presence of manatees, so that a collision can be avoided, is desired. A practical implementation of the technology is dependent on the hydrophone spacing and range of detection. These parameters are primarily dependent on the manatee vocalization strength, the decay of the signal’s strength with distance, and the background noise levels. An efficient method to extend the detection range by using background noise cancellation is proposed in this paper. An adaptive line enhancer (ALE) that can detect and track narrow band signals buried in broadband noise is implemented to cancel the background noise. The results indicate that the ALE algorithm can efficiently extract the manatee calls from the background noise. The improved signal-to-noise ratio of the signal can be used to extend the range of detection of manatee vocalizations and reduce the false alarm and missing detection rate in their natural habitat.
Effects of exposure to seismic airgun use on hearing of three fish species
Authors: Popper Arthur N. , Smith Michael E. , Cott Peter A. , Hanna Bruce W. , MacGillivray Alexander O. , Austin Melanie E. , Mann David A.
Published: June 2005

Seismic airguns produce considerable amounts of acoustic energy that have the potential to affect marine life. This study investigates the effects of exposure to a 730 in.3 airgun array on hearing of three fish species in the Mackenzie River Delta, the northern pike (Esox lucius), broad whitefish (Coregonus nasus), and lake chub (Couesius plumbeus). Fish were placed in cages in the 1.9 m of water and exposed to five or 20 airgun shots, while controls were placed in the same cage but without airgun exposure. Hearing in both exposed and control fish were then tested using the auditory brainstem response (ABR). Threshold shifts were found for exposed fish as compared to controls in the northern pike and lake chub, with recovery within 24 hours of exposure, while there was no threshold shift in the broad whitefish. It is concluded that these three species are not likely to be substantially impacted by exposure to an airgun array used in a river seismic survey. Care must be taken, however, in extrapolation to other species and to fishes exposed to airguns in deeper water or where the animals are exposed to a larger number of airgun shots over a longer period of time.
Thermodynamic cycles executed in a looped-tube thermoacoustic engine (L)
Authors: Ueda Yuki , Biwa Tetsushi , Mizutani Uichiro , Yazaki Taichi
Published: June 2005

A looped-tube thermoacoustic engine is composed of only a stack of plates, across which a steep temperature gradient is furnished. In spite of the absence of any mechanical parts like pistons and valves, the energy conversion from heat flow into acoustic power flow is performed in the stack. The thermoacoustically induced acoustic field was observed through the simultaneous measurements of pressure and velocity of the working gas, and the thermodynamic cycle executed in the stack was studied. The experimental results show that the acoustic field is tuned without any external forces so as to realize the efficient thermodynamic cycles as possible.
Invariance of evoked-potential echo-responses to target strength and distance in an echolocating false killer whale
Authors: Supin Alexander Ya. , Nachtigall Paul E. , Au Whitlow W. L. , Breese Marlee
Published: June 2005

Brain auditory evoked potentials (AEPs) were recorded in a false killer whale Pseudorca crassidens trained to accept suction-cup EEG electrodes and to detect targets by echolocation. AEP collection was triggered by echolocation pulses transmitted by the animal. The target strength varied from −22 to −40 dB; the distance varied from 1.5 to 6 m. All the records contained two AEP sets: the first one of a constant latency (transmission-related AEP) and a second one with a delay proportional to the distance (echo-related AEP). The amplitude of echo-related AEPs was almost independent of both target strength and distance, though combined variation of these two parameters resulted in echo intensity variation within a range of 42 dB. The amplitude of transmission-related AEPs was independent of distance but dependent on target strength: the less the target strength, the higher the amplitude. Recording of transmitted pulses has not shown their intensity dependence on target strength. It is supposed that the constancy of echo-related AEP results from variation of hearing sensitivity depending on the target strength and release of echo-related responses from masking by transmitted pulses depending on the distance.
Vascular sounds as an indicator of hemodialysis access patency
Authors: Mansy Hansen , Hoxie Silas , Patel Nilesh , Sandler Richard
Published: June 2005

Background: Vascular access for renal dialysis is a lifeline for about 200000 individuals in North America. Stethoscope auscultation of vascular sounds has some utility in the assessment of access patency, yet may be highly skill dependent. The objective of this study is to identify acoustic parameters that are related to changes in vascular access patency. Methods: Fifteen patients participated in the study. Their vascular sounds were recorded before and after angiography, which was accompanied by angioplasty in most patients. The sounds were acquired using two electronic stethoscopes and then digitized and analyzed on a personal computer. Results: Vessel stenosis changes were found to be associated with changes in acoustic amplitude and/or spectral energy distribution. Certain acoustic parameters correlated well (correlation coefficient=0.98, p less than 0.0001) with the change in the degree of stenosis, suggesting that stenosis severity may be predictable from these parameters. Parameters also appeared to be sensitive to modest diameter changes (greater than 20%), (p less than 0.005, Wilcoxon rank sum test). Conclusions: Computerized analysis of vascular sounds may have utility in vessel patency surveillance. Further testing using longitudinal studies may be warranted. [Work supported by NIH/NIDDK DK 59685.]
Mechanism of Divergent Growth Factor Effects in Mesenchymal Stem Cell Differentiation
Authors: Kratchmarova Irina , Blagoev Blagoy , Haack-Sorensen Mandana , Kassem Moustapha , Mann Matthias
Published: June 2005

Closely related signals often lead to very different cellular outcomes. We found that the differentiation of human mesenchymal stem cells into bone-forming cells is stimulated by epidermal growth factor (EGF) but not platelet-derived growth factor (PDGF). We used mass spectrometry–based proteomics to comprehensively compare proteins that were tyrosine phosphorylated in response to EGF and PDGF and their associated partners. More than 90% of these signaling proteins were used by both ligands, whereas the phosphatidylinositol 3-kinase (PI3K) pathway was exclusively activated by PDGF, implicating it as a possible control point. Indeed, chemical inhibition of PI3K in PDGF-stimulated cells removed the differential effect of the two growth factors, bestowing full differentiation effect onto PDGF. Thus, quantitative proteomics can directly compare entire signaling networks and discover critical differences capable of changing cell fate.
Structure of the Ultrathin Aluminum Oxide Film on NiAl(110)
Authors: Kresse Georg , Schmid Michael , Napetschnig Evelyn , Shishkin Maxim , Köhler Lukas , Varga Peter
Published: June 2005

The well-ordered aluminum oxide film formed by oxidation of the NiAl(110) surface is the most intensely studied metal surface oxide, but its structure was previously unknown. We determined the structure by extensive ab initio modeling and scanning tunneling microscopy experiments. Because the topmost aluminum atoms are pyramidally and tetrahedrally coordinated, the surface is different from all Al
2
O
3
bulk phases. The film is a wide-gap insulator, although the overall stoichiometry of the film is not Al
2
O
3
but Al
10
O
13
. We propose that the same building blocks can be found on the surfaces of bulk oxides, such as the reduced corundum (0001) surface.
Epigenetic Transgenerational Actions of Endocrine Disruptors and Male Fertility
Authors: Anway Matthew D. , Cupp Andrea S. , Uzumcu Mehmet , Skinner Michael K.
Published: June 2005

Transgenerational effects of environmental toxins require either a chromosomal or epigenetic alteration in the germ line. Transient exposure of a gestating female rat during the period of gonadal sex determination to the endocrine disruptors vinclozolin (an antiandrogenic compound) or methoxychlor (an estrogenic compound) induced an adult phenotype in the F
1
generation of decreased spermatogenic capacity (cell number and viability) and increased incidence of male infertility. These effects were transferred through the male germ line to nearly all males of all subsequent generations examined (that is, F
1
to F
4
). The effects on reproduction correlate with altered DNA methylation patterns in the germ line. The ability of an environmental factor (for example, endocrine disruptor) to reprogram the germ line and to promote a transgenerational disease state has significant implications for evolutionary biology and disease etiology.
Allosteric Mechanisms of Signal Transduction
Authors: Changeux Jean-Pierre , Edelstein Stuart J.
Published: June 2005

Forty years ago, a simple model of allosteric mechanisms (indirect interactions between distinct sites), used initially to explain feedback-inhibited enzymes, was presented by Monod, Wyman, and Changeux. We review the MWC theory and its applications for the understanding of signal transduction in biology, and also identify remaining issues that deserve theoretical and experimental substantiation.
Accelerated Intestinal Epithelial Cell Turnover: A New Mechanism of Parasite Expulsion
Authors: Cliffe Laura J. , Humphreys Neil E , Lane Thomas E. , Potten Chris S. , Booth Cath , Grencis Richard K.
Published: June 2005

The functional integrity of the intestinal epithelial barrier forms a major defense against invading pathogens, including gastrointestinal-dwelling nematodes, which are ubiquitous in their distribution worldwide. Here, we show that an increase in the rate of epithelial cell turnover in the large intestine acts like an “epithelial escalator” to expel
Trichuris
and that the rate of epithelial cell movement is under immune control by the cytokine interleukin-13 and the chemokine CXCL10. This host protective mechanism against intestinal pathogens has implications for our wider understanding of the multifunctional role played by intestinal epithelium in mucosal defense.
Professional Antigen-Presentation Function by Human γδ T Cells
Authors: Brandes Marlène , Willimann Katharina , Moser Bernhard
Published: June 2005

Human γδ T cells are considered to play a vital role in protective immunity through cytokine secretion and cytotoxic activity. We report that cells expressing the Vγ2Vδ2
+
–T cell receptor (Vδ2
+
T cells) also display principal characteristics of professional antigen-presenting cells such as dendritic cells. Thus, when activated, these cells efficiently processed and displayed antigens and provided co-stimulatory signals sufficient for strong induction of naïve αβ T cell proliferation and differentiation. We suggest that, upon microbial activation, Vδ2
+
T cells participate in the induction of adaptive immune responses and that these cells may be a useful tool in vaccine development and immunotherapy.
Feeling the Beat: Movement Influences Infant Rhythm Perception
Authors: Phillips-Silver Jessica , Trainor Laurel J.
Published: June 2005

We hear the melody in music, but we feel the beat. We demonstrate that the perception of musical rhythm is a multisensory experience in infancy. In particular, movement of the body, by bouncing on every second versus every third beat of an ambiguous auditory rhythm pattern, influences whether that auditory rhythm pattern is encoded in duple form (a march) or in triple form (a waltz). Visual information is not necessary for the effect, indicating that it likely reflects a strong, early-developing interaction between auditory and vestibular information in the human nervous system.
Directed Assembly of Block Copolymer Blends into Nonregular Device-Oriented Structures
Authors: Stoykovich Mark P. , Müller Marcus , Kim Sang Ouk , Solak Harun H. , Edwards Erik W. , de Pablo Juan J. , Nealey Paul F.
Published: June 2005

Self-assembly is an effective strategy for the creation of periodic structures at the nanoscale. However, because microelectronic devices use free-form design principles, the insertion point of self-assembling materials into existing nanomanufacturing processes is unclear. We directed ternary blends of diblock copolymers and homopolymers that naturally form periodic arrays to assemble into nonregular device-oriented structures on chemically nanopatterned substrates. Redistribution of homopolymer facilitates the defect-free assembly in locations where the domain dimensions deviate substantially from those formed in the bulk. The ability to pattern nonregular structures using self-assembling materials creates new opportunities for nanoscale manufacturing.
The First Chemical Enrichment in the Universe and the Formation of Hyper Metal-Poor Stars
Authors: Iwamoto Nobuyuki , Umeda Hideyuki , Tominaga Nozomu , Nomoto Ken'ichi , Maeda Keiichi
Published: June 2005

The recent discovery of a hyper–metal-poor (HMP) star, with a metallicity Fe/H smaller than 1/100,000 of the solar ratio, together with one earlier HMP star, has raised a challenging question whether these HMP stars are the actual first-generation, low-mass stars of the universe. We argue that these HMP stars are second-generation stars formed from gases that were chemically enriched by the first-generation supernovae. The key to this solution is the very unusual abundance patterns of these HMP stars and the similarities and differences between them. We can reproduce these abundance features with core-collapse “faint” supernova models that include extensive matter mixing and fallback during explosions.
Diverse Roots Even Only in the West
Authors: Lloyd Geoffrey
Published: June 2005

Ancient Medicine
.
By Vivian Nutton
. Routledge, London. 2004. 500 pp. $115, £65. ISBN 0-415-08611-6. Sciences of Antiquity.

In this detailed survey of the course of Western medicine from early Greece to the late Roman Empire, the author uses both archaeological and written records to explore such topics as the training and practices of doctors, the diseases they attempted to treat, their social circumstances, and the connections between medicine and religion.
It's a Wrap
Authors: Sternberg Esther M.
Published: June 2005

Mummy
. The Inside Story. At the British Museum, London, through 14 August 2005.
www.thebritishmuseum.ac.uk/mummy

Mummy
. The Inside Story.
By John H. Taylor
. British Museum Press, London, 2004. 48 pp. Paper, £5.99. ISBN 0-7141-1962-8. Abrams, New York. Paper, $14.95, C$22.50. ISBN 0-8109-9181-0.

The film uses CT-scan data to present a virtual unwrapping of the 3000-year-old mummy of Nesperennub, priest of Karnak.
Genetic Diversity and Antibiotic Resistance Patterns in aCampylobacterPopulation Isolated from Poultry Farms in Switzerland
Authors: Wittwer M. , Keller J. , Wassenaar T. M. , Stephan R. , Howald D. , Regula G. , Bissig-Choisat B.
Published: June 2005

The diversity and genetic interrelation ofCampylobacter jejuniandC. coliisolated from Swiss poultry were assessed by three independent typing methods. Samples were derived prior to slaughter from 100 randomly selected flocks (five birds per flock) raised on three different farm types. The observed flock prevalence was 54% in total, with 50% for conventional and 69% for free-range farms. Birds held on farms with a confined roaming area had the lowest prevalence of 37%.Campylobacterisolates were characterized by amplified fragment length polymorphism (AFLP), restriction fragment length polymorphism offlaAPCR fragments (flaA-RFLP), and disk diffusion testing for eight antimicrobial agents that are commonly used in veterinary or human medicine in Switzerland. Analysis of the genotypic results indicates that theCampylobacterpopulation in Swiss poultry is genetically highly diverse. Nevertheless, occasionally, isolates with identical or nearly identical characteristics were isolated from different farms or farm types in different locations. Genetic typing by AFLP andflaA-RFLP was found to be complementary. The majority of isolates (67%) were susceptible to all tested antibiotics; however, single, double, and triple resistances were observed in 7%, 23%, and 2% of the strains, respectively. There was no correlation between genotype and antibiotic resistance. Surprisingly, sulfonamide resistance was frequently found together with streptomycin resistance. Our findings illustrate the results of common genetic exchange in the studied bacterial population.
Erosion and Subsequent Transport State of
Escherichia coli
from Cowpats
Authors: Muirhead Richard William , Collins Robert Peter , Bremer Philip James
Published: June 2005

Processes by which fecal bacteria enter overland flow and their transportation state to surface waters are poorly understood, making the effectiveness of measures designed to intercept this pathway, such as vegetated buffer strips, difficult to predict. Freshly made and aged (up to 30 days) cowpats were exposed to simulated rainfall, and samples of the cowpat material and runoff were collected.
Escherichia coli
in the runoff samples were separated into attached (to particles) and unattached fractions, and the unattached fraction was analyzed to determine if the cells were clumped. Within cowpats,
E. coli
grew for 6 to 14 days, rather than following a typical logarithmic die-off curve.
E. coli
numbers in the runoff correlated with numbers inside the cowpat. Most of the
E. coli
organisms eroded from the cowpats were transported as single cells, and only a small percentage (about 8%) attached to particles. The erosion of
E. coli
from cowpats and the state in which the cells were transported did not vary with time within a single rainfall event or over time as the cowpats aged and dried out. These findings indicate that cowpats can remain a significant source of
E. coli
in overland flow for more than 30 days. As well, most of the
E. coli
organisms eroded from cowpats will occur as readily transportable single cells.
Identification of a Gene Cluster for the Formation of Extracellular Polysaccharide Precursors in the Chemolithoautotroph
Acidithiobacillus ferrooxidans
Authors: Barreto Marlen , Jedlicki Eugenia , Holmes David S.
Published: June 2005

A cluster of five genes, proposed to be involved in the formation of extracellular polysaccharide (EPS) precursors via the Leloir pathway, have been identified in the acidophilic autotroph
Acidithiobacillus ferrooxidans
. The order of the genes is
luxA-galE-galK-pgm-galM
, encoding a LuxA-like protein, UDP-glucose 4-epimerase, galactokinase, phosphoglucomutase, and galactose mutarotase, respectively. The
gal
cluster forms a single transcriptional unit and is therefore an operon. Two other putative genes of the Leloir pathway,
galU
, potentially encoding UDP-glucose pyrophosphorylase, and a gene designated
galT-like
, which may encode a galactose-1-phosphate uridylyltransferase-like activity, were found unlinked in the genome. Using semiquantitative reverse transcription-PCR, the genes of the
gal
operon were shown to be expressed more during growth in iron medium than in growth in sulfur medium. The functions of
galE
,
pgm
,
galU
, and the
galT-like
gene were validated by complementation of
Escherichia coli
mutants and by in vitro enzyme assays. The data suggest that
A. ferrooxidans
is capable of synthesizing the EPS precursors UDP-glucose and UDP-galactose. In addition, genes
rfbA
, -
B
, -
C
, and -
D
were identified in the genome of
A. ferrooxidans
, suggesting that it can also synthesize the EPS precursor dTDP-rhamnose. Since EPSs constitute the major bulk of biofilms, this study may provide an initial model for the metabolic pathways involved in biofilm formation in
A. ferrooxidans
and aid in understanding the role of biofilms in mineral leaching and the formation of acid mine drainage.
High-Frequency Conjugation System Facilitates Biofilm Formation and pAMβ1 Transmission by
Lactococcus lactis
Authors: Luo Hongliang , Wan Kai , Wang Hua H.
Published: June 2005

The importance of conjugation as a mechanism to spread biofilm determinants among microbial populations was illustrated with the gram-positive bacterium
Lactococcus lactis
. Conjugation triggered the enhanced expression of the clumping protein CluA, which is a main biofilm attribute in lactococci. Clumping transconjugants further transmitted the biofilm-forming elements among the lactococcal population at a much higher frequency than the parental nonclumping donor. This cell-clumping-associated high-frequency conjugation system also appeared to serve as an internal enhancer facilitating the dissemination of the broad-host-range drug resistance gene-encoding plasmid pAMβ1 within
L. lactis
, at frequencies more than 10,000 times higher than those for the nonclumping parental donor strain. The implications of this finding for antibiotic resistance gene dissemination are discussed.
Starvation Response ofSaccharomyces cerevisiaeGrown in Anaerobic Nitrogen- or Carbon-Limited Chemostat Cultures
Authors: Thomsson Elisabeth , Gustafsson Lena , Larsson Christer
Published: June 2005

Anaerobic starvation conditions are frequent in industrial fermentation and can affect the performance of the cells. In this study, the anaerobic carbon or nitrogen starvation response ofSaccharomyces cerevisiaewas investigated for cells grown in anaerobic carbon or nitrogen-limited chemostat cultures at a dilution rate of 0.1 h−1at pH 3.25 or 5. Lactic or benzoic acid was present in the growth medium at different concentrations, resulting in 16 different growth conditions. At steady state, cells were harvested and then starved for either carbon or nitrogen for 24 h under anaerobic conditions. We measured fermentative capacity, glucose uptake capacity, intracellular ATP content, and reserve carbohydrates and found that the carbon, but not the nitrogen, starvation response was dependent upon the previous growth conditions. All cells subjected to nitrogen starvation retained a large portion of their initial fermentative capacity, independently of previous growth conditions. However, nitrogen-limited cells that were starved for carbon lost almost all their fermentative capacity, while carbon-limited cells managed to preserve a larger portion of their fermentative capacity during carbon starvation. There was a positive correlation between the amount of glycogen before carbon starvation and the fermentative capacity and ATP content of the cells after carbon starvation. Fermentative capacity and glucose uptake capacity were not correlated under any of the conditions tested. Thus, the successful adaptation to sudden carbon starvation requires energy and, under anaerobic conditions, fermentable endogenous resources. In an industrial setting, carbon starvation in anaerobic fermentations should be avoided to maintain a productive yeast population.
sacB
–5-Fluoroorotic Acid–
pyrE
-Based Bidirectional Selection for Integration of Unmarked Alleles into the Chromosome of
Rhodobacter capsulatus
Authors: Yano Takahiro , Sanders Carsten , Catalano John , Daldal Fevzi
Published: June 2005

The gram-negative, purple nonsulfur, facultative photosynthetic bacterium
Rhodobacter capsulatus
is a widely used model organism and has well-developed molecular genetics. In particular, interposon mutagenesis using selectable gene cartridges is frequently employed for construction of a variety of chromosomal knockout mutants. However, as the gene cartridges are often derived from antibiotic resistance-conferring genes, their numbers are limited, which restricts the construction of multiple knockout mutants. In this report,
sacB
—5-fluoroorotic acid (5FOA)—
pyrE
-based bidirectional selection that facilitates construction of unmarked chromosomal knockout mutations is described. The
R. capsulatus pyrE
gene encoding orotate phosphoribosyl transferase, a key enzyme of the de novo pyrimidine nucleotide biosynthesis pathway, was used as an interposon in a genetic background that is auxotrophic for uracil (Ura
−
) and hence resistant to 5FOA (5FOA
r
). Although Ura
+
selection readily yielded chromosomal allele replacements via homologous recombination, selection for 5FOA
r
to replace
pyrE
with unmarked alleles was inefficient. To improve the latter step, 5FOA
r
selection was combined with sucrose tolerance selection using a suicide plasmid carrying the
Bacillus subtilis sacB
gene encoding levansucrase that induces lethality upon exposure to 5% (wt/vol) sucrose in the growth medium. Sucrose-tolerant, 5FOA
r
colonies that were obtained carried chromosomal unmarked mutant alleles of the target gene via double crossovers between the resident
pyrE-
marked and incoming unmarked alleles. The effectiveness of this double selection was proven by seeking insertion and deletion alleles of
helC
involved in
R. capsulatus
cytochrome
c
biogenesis, which illustrated the usefulness of this system as a genetic means for facile construction of
R. capsulatus
unmarked chromosomal mutants.
Persistence and Differential Survival of Fecal Indicator Bacteria in Subtropical Waters and Sediments
Authors: Anderson Kimberly L. , Whitlock John E. , Harwood Valerie J.
Published: June 2005

Fecal coliforms and enterococci are indicator organisms used worldwide to monitor water quality. These bacteria are used in microbial source tracking (MST) studies, which attempt to assess the contribution of various host species to fecal pollution in water. Ideally, all strains of a given indicator organism (IO) would experience equal persistence (maintenance of culturable populations) in water; however, some strains may have comparatively extended persistence outside the host, while others may persist very poorly in environmental waters. Assessment of the relative contribution of host species to fecal pollution would be confounded by differential persistence of strains. Here, freshwater and saltwater mesocosms, including sediments, were inoculated with dog feces, sewage, or contaminated soil and were incubated under conditions that included natural stressors such as microbial predators, radiation, and temperature fluctuations. Persistence of IOs was measured by decay rates (change in culturable counts over time). Decay rates were influenced by IO, inoculum, water type, sediment versus water column location, and
Escherichia coli
strain. Fecal coliform decay rates were significantly lower than those of enterococci in freshwater but were not significantly different in saltwater. IO persistence according to mesocosm treatment followed the trend: contaminated soil > wastewater > dog feces.
E. coli
ribotyping demonstrated that certain strains were more persistent than others in freshwater mesocosms, and the distribution of ribotypes sampled from mesocosm waters was dissimilar from the distribution in fecal material. These results have implications for the accuracy of MST methods, modeling of microbial populations in water, and efficacy of regulatory standards for protection of water quality.
Rapid Differentiation and In Situ Detection of 16 Sourdough
Lactobacillus
Species by Multiplex PCR
Authors: Settanni Luca , van Sinderen Douwe , Rossi Jone , Corsetti Aldo
Published: June 2005

A two-step multiplex PCR-based method was designed for the rapid detection of 16 species of lactobacilli known to be commonly present in sourdough. The first step of multiplex PCR was developed with a mixture of group-specific primers, while the second step included three multiplex PCR assays with a mixture of species-specific primers. Primers were derived from sequences that specify the 16S rRNA, the 16S-23S rRNA intergenic spacer region, and part of the 23S rRNA gene. The primer pairs designed were shown to exclusively amplify the targeted
rrn
operon fragment of the corresponding species. Due to the reliability of simultaneously identifying
Lactobacillus plantarum
,
Lactobacillus pentosus
, and
Lactobacillus paraplantarum
, a previously described multiplex PCR method employing
recA
gene-derived primers was included in the multiplex PCR system. The combination of a newly developed, quick bacterial DNA extraction method from sourdough and this multiplex PCR assay allows the rapid in situ detection of several sourdough-associated lactobacilli, including the recently described species
Lactobacillus rossii
, and thus represents a very useful alternative to culture-based methodologies.
An Ergot Alkaloid Biosynthesis Gene and Clustered Hypothetical Genes from
Aspergillus fumigatus
Authors: Coyle Christine M. , Panaccione Daniel G.
Published: June 2005

The ergot alkaloids are a family of indole-derived mycotoxins with a variety of significant biological activities.
Aspergillus fumigatus
, a common airborne fungus and opportunistic human pathogen, and several fungi in the relatively distant taxon
Clavicipitaceae
(clavicipitaceous fungi) produce different sets of ergot alkaloids. The ergot alkaloids of these divergent fungi share a four-member ergoline ring but differ in the number, type, and position of the side chains. Several genes required for ergot alkaloid production are known in the clavicipitaceous fungi, and these genes are clustered in the genome of the ergot fungus
Claviceps purpurea
. We investigated whether the ergot alkaloids of
A. fumigatus
have a common biosynthetic and genetic origin with those of the clavicipitaceous fungi. A homolog of
dmaW
, the gene controlling the determinant step in the ergot alkaloid pathway of clavicipitaceous fungi, was identified in the
A. fumigatus
genome. Knockout of
dmaW
eliminated all known ergot alkaloids from
A. fumigatus
, and complementation of the mutation restored ergot alkaloid production. Clustered with
dmaW
in the
A. fumigatus
genome are sequences corresponding to five genes previously proposed to encode steps in the ergot alkaloid pathway of
C. purpurea
, as well as additional sequences whose deduced protein products are consistent with their involvement in the ergot alkaloid pathway. The corresponding genes have similarities in their nucleotide sequences, but the orientations and positions within the cluster of several of these genes differ. The data indicate that the ergot alkaloid biosynthetic capabilities in
A. fumigatus
and the clavicipitaceous fungi had a common origin.
Host Distributions of Uncultivated Fecal
Bacteroidales
Bacteria Reveal Genetic Markers for Fecal Source Identification
Authors: Dick Linda K. , Bernhard Anne E. , Brodeur Timothy J. , Santo Domingo Jorge W. , Simpson Joyce M. , Walters Sarah P. , Field Katharine G.
Published: June 2005

The purpose of this study was to examine host distribution patterns among fecal bacteria in the order
Bacteroidales
, with the goal of using endemic sequences as markers for fecal source identification in aquatic environments. We analyzed
Bacteroidales
16S rRNA gene sequences from the feces of eight hosts: human, bovine, pig, horse, dog, cat, gull, and elk. Recovered sequences did not match database sequences, indicating high levels of uncultivated diversity. The analysis revealed both endemic and cosmopolitan distributions among the eight hosts. Ruminant, pig, and horse sequences tended to form host- or host group-specific clusters in a phylogenetic tree, while human, dog, cat, and gull sequences clustered together almost exclusively. Many of the human, dog, cat, and gull sequences fell within a large branch containing cultivated species from the genus
Bacteroides
. Most of the cultivated
Bacteroides
species had very close matches with multiple hosts and thus may not be useful targets for fecal source identification. A large branch containing cultivated members of the genus
Prevotella
included cloned sequences that were not closely related to cultivated
Prevotella
species. Most ruminant sequences formed clusters separate from the branches containing
Bacteroides
and
Prevotella
species. Host-specific sequences were identified for pigs and horses and were used to design PCR primers to identify pig and horse sources of fecal pollution in water. The primers successfully amplified fecal DNAs from their target hosts and did not amplify fecal DNAs from other species. Fecal bacteria endemic to the host species may result from evolution in different types of digestive systems.