bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonlinear Biot waves in porous media with application to unconsolidated granular media
Authors: Dazel Olivier , Tournat Vincent
Published: February 2010

The nonlinear propagation through porous media is investigated in the framework of Biot theory. For illustration, and considering the current interest for the determination of the elastic properties of granular media, the case of nonlinear propagation in “model” granular media (disordered packings of noncohesive elastic beads of the same size embedded in a visco-thermal fluid) is considered. The solutions of linear Biot waves are first obtained, considering the appropriate geometrical and physical parameters of the medium. Then, making use of the method of successive approximations of nonlinear acoustics, the solutions for the second harmonic Biot waves are derived by considering a quadratic nonlinearity in the solid frame constitutive law (which takes its origin from the high nonlinearity of contacts between grains). The propagation in a semi-infinite medium with velocity dispersion, frequency dependent dissipation, and nonlinearity is first analyzed. The case of a granular medium slab with rigid boundaries, often considered in experiments, is then presented. Finally, the importance of mode coupling between solid and fluid waves is evaluated, depending on the actual fluid, the bead diameter, or the applied static stress on the beads. The application of these results to other media supporting Biot waves (porous ceramics, polymer foams, etc.) is straightforward.
Unsupervised speech segmentation: An analysis of the hypothesized phone boundaries
Authors: Scharenborg Odette , Wan Vincent , Ernestus Mirjam
Published: February 2010

Despite using different algorithms, most unsupervised automatic phone segmentation methods achieve similar performance in terms of percentage correct boundary detection. Nevertheless, unsupervised segmentation algorithms are not able to perfectly reproduce manually obtained reference transcriptions. This paper investigates fundamental problems for unsupervised segmentation algorithms by comparing a phone segmentation obtained using only the acoustic information present in the signal with a reference segmentation created by human transcribers. The analyses of the output of an unsupervised speech segmentation method that uses acoustic change to hypothesize boundaries showed that acoustic change is a fairly good indicator of segment boundaries: over two-thirds of the hypothesized boundaries coincide with segment boundaries. Statistical analyses showed that the errors are related to segment duration, sequences of similar segments, and inherently dynamic phones. In order to improve unsupervised automatic speech segmentation, current one-stage bottom-up segmentation methods should be expanded into two-stage segmentation methods that are able to use a mix of bottom-up information extracted from the speech signal and automatically derived top-down information. In this way, unsupervised methods can be improved while remaining flexible and language-independent.
Ultrasound characterization of red blood cell aggregation with intervening attenuating tissue-mimicking phantoms
Authors: Franceschini Emilie , Yu François T. H. , Destrempes François , Cloutier Guy
Published: February 2010

The analysis of the ultrasonic frequency-dependent backscatter coefficient of aggregating red blood cells reveals information about blood structural properties. The difficulty in applying this technique in vivo is due to the frequency-dependent attenuation caused by intervening tissue layers that distorts the spectral content of signals backscattered by blood. An optimization method is proposed to simultaneously estimate tissue attenuation and blood structure properties, and was termed the structure factor size and attenuation estimator (SFSAE). An ultrasound scanner equipped with a wide-band 25MHz probe was used to insonify porcine blood sheared in both Couette and tubular flow devices. Since skin is one of the most attenuating tissue layers during in vivo scanning, four skin-mimicking phantoms with different attenuation coefficients were introduced between the transducer and the blood flow. The SFSAE gave estimates with relative errors below 25% for attenuations between 0.115 and 0.411dB∕MHz and kR<2.08 (k being the wave number and R the aggregate radius). The SFSAE can be useful to examine in vivo and in situ abnormal blood conditions suspected to promote pathophysiological cardiovascular consequences.
Nonlinear reflection of shock shear waves in soft elastic media
Authors: Pinton Gianmarco , Coulouvrat François , Gennisson Jean-Luc , Tanter Mickaël
Published: February 2010

For fluids, the theoretical investigation of shock wave reflection has a good agreement with experiments when the incident shock Mach number is large. But when it is small, theory predicts that Mach reflections are physically unrealistic, which contradicts experimental evidence. This von Neumann paradox is investigated for shear shock waves in soft elastic solids with theory and simulations. The nonlinear elastic wave equation is approximated by a paraxial wave equation with a cubic nonlinear term. This equation is solved numerically with finite differences and the Godunov scheme. Three reflection regimes are observed. Theory is developed for shock propagation by applying the Rankine–Hugoniot relations and entropic constraints. A characteristic parameter relating diffraction and non-linearity is introduced and its theoretical values are shown to match numerical observations. The numerical solution is then applied to von Neumann reflection, where curved reflected and Mach shocks are observed. Finally, the case of weak von Neumann reflection, where there is no reflected shock, is examined. The smooth but non-monotonic transition between these three reflection regimes, from linear Snell–Descartes to perfect grazing case, provides a solution to the acoustical von Neumann paradox for the shear wave equation. This transition is similar to the quadratic non-linearity in fluids.
Effects of a curved vocal tract with grid-generated tongue profile on low-order formants
Authors: Milenkovic Paul H. , Yaddanapudi Srikanth , Vorperian Houri K. , Kent Raymond D.
Published: February 2010

A hyperbolic grid-generation algorithm allows investigation of the effect of vocal-tract curvature on low-order formants. A smooth two-dimensional (2D) curve represents the combined lower lip, tongue, and anterior pharyngeal wall profile as displacements from the combined upper lip, palate, and posterior pharyngeal wall outline. The algorithm is able to generate tongue displacements beyond the local radius of strongly curved sections of the palate. The 2D grid, along with transverse profiles of the lip, oral-pharyngeal, and epilarynx regions, specifies a vocal conduit from which an effective area function may be determined using corrections to acoustic parameters resulting from duct curvature; the effective area function in turn determines formant frequencies through an acoustic transmission-line calculation. Results of the corrected transmission line are compared with a three-dimensional finite element model. The observed effects of the curved vocal tract on formants F1 and F2 are in order of importance, as follows: (1) reduction in midline distances owing to curvature of the palate and the bend joining the palate to the pharynx, (2) the curvature correction to areas and section lengths, and (3) adjustments to the palate-tongue distance required to produce smooth tongue shapes at large displacements from the palate.
Encapsulated contrast microbubble radial oscillation associated with postexcitation pressure peaks
Authors: Santin M. D. , King D. A. , Foiret J. , Haak A. , O’Brien W. D. , Bridal S. L.
Published: February 2010

This work combines modeling and experiment to assess encapsulated microbubble oscillations associated with broadband pressure peaks detected after microbubble excitation (postexcitation signals). Data were acquired from albumin-shelled and phospholipid-shelled microbubbles using a passive cavitation detector consisting of a confocally aligned 2.8-MHz transmitter and 13-MHz receiver. Microbubbles in weak solutions were insonified with a 5-cycle pulse at a peak rarefactional pressure of 2.0±0.2 MPa. For each microbubble type, at least 100 received signals were identified as individual-microbubble responses. The average broadband noise from signals with postexcitation response was 4.2–7.2 dB higher than from signals without postexcitation. Pressure-time responses for each microbubble type were simulated using the model by Marmottant et al. [J. Acoust. Soc. Am. 118, 3499–3505 (2005)], with insonification conditions matching the experiment. Increased broadband noise predicted for microbubbles with postexcitation response was consistent with that observed experimentally (4.0–8.9 dB). The model predicted that postexcitation signals occur only when the radial oscillation exceeds both the shell break-up threshold and twice the initial radius (free bubble inertial cavitation threshold).
Mindlin plate theory for damage detection: Imaging of flexural inhomogeneities
Authors: Rose L. R. Francis , Wang Chun H.
Published: February 2010

The scattering of plate waves by localized damage or defects that can be modeled as flexural inhomogeneities is examined within the framework of Mindlin plate theory. These inhomogeneities are characterized by variations in one or more of the four plate-theory parameters: the bending stiffness, shear stiffness, rotary inertia, and transverse inertia. It is shown that the Born approximation for the scattered field leads to a plate-theory analog of the Fourier diffraction theorem, which relates the far-field scattering amplitude to the spatial Fourier transform of the inhomogeneity variations. The application of this result is illustrated by using synthetic data derived for an idealized model of a delamination as a flexural inhomogeneity, ignoring mode coupling effects. A computationally efficient implementation of the filtered back-propagation algorithm, based on the eigensystem of the scattering operator, is employed for image reconstruction. The implications for in-situ imaging of structural damage in plate-like structures are briefly discussed, and some directions for further work are indicated.
A mesh-free approach to acoustic scattering from multiple spheres nested inside a large sphere by using diagonal translation operators
Authors: Hesford Andrew J. , Astheimer Jeffrey P. , Greengard Leslie F. , Waag Robert C.
Published: February 2010

A multiple-scattering approach is presented to compute the solution of the Helmholtz equation when a number of spherical scatterers are nested in the interior of an acoustically large enclosing sphere. The solution is represented in terms of partial-wave expansions, and a linear system of equations is derived to enforce continuity of pressure and normal particle velocity across all material interfaces. This approach yields high-order accuracy and avoids some of the difficulties encountered when using integral equations that apply to surfaces of arbitrary shape. Calculations are accelerated by using diagonal translation operators to compute the interactions between spheres when the operators are numerically stable. Numerical results are presented to demonstrate the accuracy and efficiency of the method.
Speech levels in meeting rooms and the probability of speech privacy problems
Authors: Bradley J. S. , Gover B. N.
Published: February 2010

Speech levels were measured in a large number of meetings and meeting rooms to better understand their influence on the speech privacy of closed meeting rooms. The effects of room size and number of occupants on average speech levels, for meetings with and without sound amplification, were investigated. The characteristics of the statistical variations of speech levels were determined in terms of speech levels measured over 10s intervals at locations inside, but near the periphery of the meeting rooms. A procedure for predicting the probability of speech being audible or intelligible at points outside meeting rooms is proposed. It is based on the statistics of meeting room speech levels, in combination with the sound insulation characteristics of the room and the ambient noise levels at locations outside the room.
Black-capped (Poecile atricapillus) and mountain chickadee (Poecile gambeli) contact call contains species, sex, and individual identity features
Authors: Guillette Lauren M. , Bloomfield Laurie L. , Batty Emily R. , Dawson Michael R. W. , Sturdy Christopher B.
Published: February 2010

The tseet contact call, common to both black-capped and mountain chickadees, is among the most frequently produced call of each species, but has remained little studied until now. In the current study, the authors characterized the tseet call of adult allopatric and sympatric black-capped and mountain chickadees in terms of nine acoustic features in a fashion similar to descriptive accounts of both species’ chick-a-dee calls. Summary statistics, the potential for individual coding, and classification by linear discriminant analysis were used to describe the tseet call. The authors were able to correctly classify tseet calls in terms of which group or individual produced it with high accuracy. Furthermore, several acoustic features are highly individualized, indicating that the chickadees may use these features to identify signalers as individuals or members of a particular group.
Vector intensity reconstructions in a volume surrounding a rigid spherical microphone array
Authors: Williams Earl G. , Takashima Kazuhiro
Published: February 2010

A technique is described to image the vector intensity in the near field of a spherical array of microphones flush mounted in a rigid sphere. The spatially measured pressure is decomposed into Fourier harmonics in order to reconstruct the volumetric vector intensity outside the sphere. The theory for this reconstruction is developed in this paper. The resulting intensity images are very successful at locating and quantifying unknown exterior acoustic sources, ideal for application in noise control problems in interior spaces such as automobiles and airplanes. Arrays of varying numbers of microphones and radii are considered and compared and errors are computed for both theory and experiment. It is demonstrated that this is an ill-posed problem below a cutoff frequency depending on array design, requiring Tikhonov regularization below cutoff. There is no low frequency limit on operation, although the signal-to-noise ratio is the determining factor for high-spatial resolution at low frequencies. It is shown that the upper frequency limit is set by the number of microphones in the array and is independent of noise. The accuracy of the approach is assessed by considering the exact solution for the scattering of a point source by a rigid sphere. Several field experiments are presented to demonstrate the utility of the technique. In these experiments, the partial field decomposition technique is used and holograms of multiple exterior sources are separated and their individual volumetric intensity fields imaged. In this manner, the intensity fields of two uncorrelated tube sources in an anechoic chamber are isolated from one another and separated intensity maps are obtained from over a broad frequency range. In a practical application, the vector intensity field in the interior of an automobile cabin is mapped at the fundamental of the engine vibration using the rigid sphere positioned at the driver’s head. The source regions contributing to the interior cabin noise are identified.
Monaural sound-source-direction estimation using the acoustic transfer function of a parabolic reflection board
Authors: Takashima Ryoichi , Takiguchi Tetsuya , Ariki Yasuo
Published: February 2010

This paper presents a sound-source-direction estimation method using only a single microphone with a parabolic reflection board. A simple signal-power-based method using a parabolic antenna has been proposed in the radar field. But the signal-power-based method is not effective for finding the direction of a talking person due to the varying power of the uttered speech signals. In this paper, the sound-source-direction estimation method focuses on the acoustic transfer function instead of the signal power. The use of the parabolic reflection board leads to a difference in the acoustic transfer functions of the target direction and the non-target directions, where the parabolic reflector and its associated microphone rotate together and observe the speech at each angle. The acoustic transfer function is estimated from the observed speech using the statistics of clean speech signals. Its effectiveness has been confirmed by monaural sound-source-direction estimation experiments in a room environment.
Theoretical model for the threshold onset of contrast microbubble oscillations
Authors: Doinikov Alexander A. , Bouakaz Ayache
Published: February 2010

It has been reported recently through high speed optical observations of phospholipid-coated contrast microbubbles that there is a threshold value for the acoustic pressure amplitude below which the radial oscillation of the microbubbles does not occur. In this Letter, it is suggested that this threshold behavior results from the fact that a phospholipid layer, as a physical material, has a certain value of the limiting shear stress so that its deformation does not start until this limiting value is exceeded. A theoretical model is proposed for the description of this phenomenon. The model explains the experimentally observed dependence of the threshold onset of microbubble oscillation on the initial bubble radius.
Properties of a nonlinear version of the stimulus-frequency otoacoustic emission
Authors: Walsh Kyle P. , Pasanen Edward G. , McFadden Dennis
Published: February 2010

A procedure for extracting the nonlinear component of the stimulus-frequency otoacoustic emission (SFOAE) is described. This nSFOAE measures the amount by which the cochlear response deviates from linear additivity when the input stimulus is doubled in amplitude. When a 4.0-kHz tone was presented alone, the magnitude of the nSFOAE response remained essentially constant throughout the 400-ms duration of the tone; response magnitude did increase monotonically with increasing tone level. When a wideband noise was presented alone, nSFOAE magnitude increased over the initial 100-to200-ms portion of the 400-ms duration of the noise. When the tone and the wideband noise were presented simultaneously, nSFOAE magnitude decreased momentarily, then increased substantially for about the first 100ms and then remained strong for the remainder of the presentation. Manipulations of the noise bandwidth revealed that the low-frequency components were primarily responsible for this rising, dynamic response; no rising segment was seen with bandpass or highpass noise. The rising, dynamic nSFOAE response is likely attributable to activation of the medial olivocochlear efferent system. This perstimulatory emission appears to have the potential to provide information about the earliest stages of auditory processing for stimuli commonly used in psychoacoustical tasks.
Effects of stimulus duration on amplitude modulation processing with cochlear implants
Authors: Luo Xin , Galvin John J. , Fu Qian-Jie
Published: February 2010

This study investigated temporal integration processes underlying cochlear implant (CI) users’ amplitude modulation processing. Thresholds for modulation detection (AMDTs) and modulation frequency discrimination (AMFDTs) were measured for 50-, 100-, and 200-Hz modulation frequencies with stimulus durations from 50 to 400 ms in eight adult CI users. The results showed significant interactions between modulation frequency and stimulus duration for AMDTs and AMFDTs. The data suggest that temporal integration limits CI users’ sensitivity to low temporal pitch over short durations, and that temporal integration over longer durations may not enhance CI users’ sensitivity to high temporal pitch.
A simple method to account for size effects in the transfer matrix method
Authors: Rhazi Dilal , Atalla Noureddine
Published: February 2010

The transfer matrix method based is extensively used and well-validated for predicting the transmission loss of multilayer structures. However, this method leads to poor results at low frequencies due to the infinite extent assumption it is based on. This paper presents an efficient implementation of a Rayleigh-integral based method to account for the finite size effects. The accuracy of the method is illustrated by various examples.
Modulation rate discrimination using half-wave rectified and sinusoidally amplitude modulated stimuli in cochlear-implant users
Authors: Kreft Heather A. , Oxenham Andrew J. , Nelson David A.
Published: February 2010

Detection and modulation rate discrimination were measured in cochlear-implant users for pulse-trains that were either sinusoidally amplitude modulated or were modulated with half-wave rectified sinusoids, which in acoustic hearing have been used to simulate the response to low-frequency temporal fine structure. In contrast to comparable results from acoustic hearing, modulation rate discrimination was not statistically different for the two stimulus types. The results suggest that, in contrast to binaural perception, pitch perception in cochlear-implant users does not benefit from using stimuli designed to more closely simulate the cochlear response to low-frequency pure tones.
Median-plane sound localization as a function of the number of spectral channels using a channel vocoder
Authors: Goupell Matthew J. , Majdak Piotr , Laback Bernhard
Published: February 2010

Using a vocoder, median-plane sound localization performance was measured in eight normal-hearing listeners as a function of the number of spectral channels. The channels were contiguous and logarithmically spaced in the range from 0.3to16kHz. Acutely testing vocoded stimuli showed significantly worse localization compared to noises and 100pulse∕s click trains, both of which were tested after feedback training. However, localization for the vocoded stimuli was better than chance. A second experiment was performed using two different 12-channel spacings for the vocoded stimuli, now including feedback training. One spacing was from experiment 1. The second spacing (called the speech-localization spacing) assigned more channels to the frequency range associated with speech. There was no significant difference in localization between the two spacings. However, even with training, localizing 12-channel vocoded stimuli remained worse than localizing virtual wideband noises by 4.8° in local root-mean-square error and 5.2% in quadrant error rate. Speech understanding for the speech-localization spacing was not significantly different from that for a typical spacing used by cochlear-implant users. These experiments suggest that current cochlear implants have a sufficient number of spectral channels for some vertical-plane sound localization capabilities, albeit worse than normal-hearing listeners, without loss of speech understanding.
The effect of signal duration on the underwater hearing thresholds of two harbor seals (Phoca vitulina) for single tonal signals between 0.2 and 40 kHz
Authors: Kastelein Ronald A. , Hoek Lean , Wensveen Paul J. , Terhune John M. , de Jong Christ A. F.
Published: February 2010

The underwater hearing sensitivities of two 2-year-old female harbor seals were quantified in a pool built for acoustic research by using a behavioral psycho-acoustic technique. The animals were trained only to respond when they detected an acoustic signal (“go/no-go” response). Detection thresholds were obtained for pure tone signals (frequencies: 0.2–40 kHz; durations: 0.5–5000 ms, depending on the frequency; 59 frequency-duration combinations). Detection thresholds were quantified by varying the signal amplitude by the 1-up, 1-down staircase method, and were defined as the stimulus levels, resulting in a 50% detection rate. The hearing thresholds of the two seals were similar for all frequencies except for 40 kHz, for which the thresholds differed by, on average, 3.7 dB. There was an inverse relationship between the time constant (τ), derived from an exponential model of temporal integration, and the frequency [log(τ)=2.86−0.94 log(f);τ in ms and f in kHz]. Similarly, the thresholds increased when the pulse was shorter than ∼780 cycles (independent of the frequency). For pulses shorter than the integration time, the thresholds increased by 9–16 dB per decade reduction in the duration or number of cycles in the pulse. The results of this study suggest that most published hearing thresholds ≤1 kHz for harbor seals are probably not absolute, as they were derived from signals with durations shorter than the time constants for those frequencies.
Ray-based blind deconvolution in ocean sound channels
Authors: Sabra Karim G. , Song Hee-Chun , Dowling David R.
Published: February 2010

This letter describes a ray-based blind deconvolution technique for ocean sound channels that produces broadband estimates of the source-to-array impulse response and the original source waveform from array-measured signals corrupted by (unknown) multipath propagation. The technique merely requires elementary knowledge of array geometry and sound speed at the array location. It is based on identifying a ray arrival direction to separate source waveform and acoustic-propagation phase contributions to the received signals. This technique successfully decoded underwater telecommunication sequences in the bandwidth 3–4 kHz that were broadcast 4 km in a 120-m-deep ocean sound channel without a-priori knowledge of sound channel characteristics.
Structural damage identification in plates via nonlinear structural intensity maps
Authors: Semperlotti Fabio , Conlon Stephen C.
Published: February 2010

A nonlinear structural intensity concept is presented as an approach for the identification of defects displaying nonlinear vibration behavior. The nonlinear structural dynamic response exhibited by a riveted joint with loosened fasteners connecting a stiffener with a flat panel is investigated. The excitation, generating elastic waves with dominant bending components, triggers the nonlinear contact between the plate and the stiffener inducing a dynamic response rich with nonlinear harmonics. Experimental structural intensity maps are evaluated at the super-harmonic frequencies. This technique provides an experimental approach for the characterization and two dimensional visualization of nonlinear types of defects.
The neural code for interaural time difference in human auditory cortex
Authors: Salminen Nelli H. , Tiitinen Hannu , Yrttiaho Santeri , May Patrick J. C.
Published: February 2010

A magnetoencephalography study was conducted to reveal the neural code of interaural time difference (ITD) in the human cortex. Widely used crosscorrelator models predict that the code consists of narrow receptive fields distributed to all ITDs. The present findings are, however, more in line with a neural code formed by two opponent neural populations: one tuned to the left and the other to the right hemifield. The results are consistent with models of ITD extraction in the auditory brainstem of small mammals and, therefore, suggest that similar computational principles underlie human sound source localization.
Reconstructing Past Seawater Mg/Ca and Sr/Ca from Mid-Ocean Ridge Flank Calcium Carbonate Veins
Authors: Coggon Rosalind M. , Teagle Damon A. H. , Smith-Duque Christopher E. , Alt Jeffrey C. , Cooper Matthew J.
Published: February 2010

Cations in the Veins

Major events in Earth's history, from climate change to tectonic activity, can be revealed by reconstructing past conditions of the oceans. Clues from ancient ocean chemistry can be found in the cation content of fossilized microorganisms, marine carbonates, or salt deposits from old coastal zones. As these proxies are prone to inconsistencies between samples and methodologies,

Coggon
et al.

(p.
1114
, published online 4 February; see the Perspective by

Elderfield

) estimated past seawater composition from the geochemistry of resistant carbonate veins precipitated within fresh basalts on the sea floor. The sudden rise to modern-day levels of ocean magnesium:calcium and strontium:calcium ratios occurred about 24 million years ago, and can be explained by a decrease in seafloor hydrothermal activity combined with a decrease in river discharge.
NMR Structure Determination for Larger Proteins Using Backbone-Only Data
Authors: Raman Srivatsan , Lange Oliver F. , Rossi Paolo , Tyka Michael , Wang Xu , Aramini James , Liu Gaohua , Ramelot Theresa A. , Eletsky Alexander , Szyperski Thomas , Kennedy Michael A. , Prestegard James , Montelione Gaetano T. , Baker David
Published: February 2010

Examining the Backbone

Determination of tertiary protein structures by nuclear magnetic resonance (NMR) currently relies heavily on side-chain NMR data. The assignment of side-chain atoms is challenging. In addition, proteins larger than 15 kilodaltons (kD) must be deuterated to improve resolution and this eliminates the possibility of measuring long-range interproton distance constraints. Now

Raman
et al.

(p.
1014
, published online 4 February) use backbone-only NMR data—chemical shifts, residual dipolar coupling, and backbone amide proton distances—available from highly deuterated proteins to guide conformational searching in the Rosetta structure prediction protocol. Using this new protocol, they were able to generate accurate structures for proteins of up to 25 kD.
Regulation of Alternative Splicing by Histone Modifications
Authors: Luco Reini F. , Pan Qun , Tominaga Kaoru , Blencowe Benjamin J. , Pereira-Smith Olivia M. , Misteli Tom
Published: February 2010

Histones and Alternative Splicing

Alternative splicing—the inclusion of different combinations of gene exons within a messenger RNA transcript—occurs in the majority of human genes and is regulated by basal and tissue-specific splicing factors, by transcription kinetics, and by chromatin structure.

Luco
et al.

(p.
996
, published online 4 February) analyzed the alternative splicing of the
human fibroblast growth factor receptor 2
gene in tissue culture cells and found that inclusion of exon IIIb or IIIc was modulated by the levels of histone H3 lysine 36 trimethylation (H3-K36me3) and H3-K4me3. Histone H3-K36me3 enrichment correlated with binding of the chromatin protein, MRG15. The MRG15 protein in turn recruited the polypyrimidine tract–binding protein (PTB) splicing factor, which acts to repress alternative exon inclusion, thus establishing a direct link between histone modifications and the splicing machinery.
Plumage Color Patterns of an Extinct Dinosaur
Authors: Li Quanguo , Gao Ke-Qin , Vinther Jakob , Shawkey Matthew D. , Clarke Julia A. , D’Alba Liliana , Meng Qingjin , Briggs Derek E. G. , Prum Richard O.
Published: February 2010

Dinosaur Plumage

Coloration and appearance provide important behavioral and evolutionary information in animals. However, for the most part, we do not know the coloration of fossil terrestrial animals.

Li
et al.

(p.
1369
, published online 4 February) have reconstructed the appearance of a theropod dinosaur by mapping features of its well-preserved feathers and comparing them with modern samples from birds. Feather color is partly determined by melanosome density and shape, and this information is preserved in a recently discovered fossil from China. The dinosaur was gray with white limbs and had a reddish crest and a speckled face.
Burning history, time of burning, and year effects on plant community structure and heterogeneity in Fescue Prairie
Authors: Gross D. V. , Romo J. T.
Published: February 2010

Structure, as well as spatial and temporal heterogeneity in plant species composition were studied in a Festuca hallii (Vasey) Piper – dominated Prairie in Canada for 6 years following burning before, during, or after the growing season on sites burned 1× or 3×. Structure, spatial heterogeneity, and temporal heterogeneity were never (P > 0.05) influenced by the time of burning. Diversity and richness of graminoids, perennial forbs, and shrubs fluctuated among years after burning, but were unaffected by burning history. Excepting shrubs, canopy cover of plant functional groups positively correlated with precipitation. After a single burn, spatial heterogeneity in species composition increased with years after burning, indicating plant communities were becoming patchier, whereas those burned 3× did not change predictably through time. Spatial heterogeneity in species composition between consecutive years was positively correlated, but temporal heterogeneity in species composition did not correlate with spatial heterogeneity. Burning history and precipitation appear important in controlling the plant community structure and spatial heterogeneity in species composition in Fescue Prairie.
Rhizoctonia fungi enhance the growth of the endangered orchid Cymbidium goeringii
Authors: Wu Jianrong , Ma Huancheng , Lü Mei , Han Sufen , Zhu Youyong , Jin Hui , Liang Junfeng , Liu Li , Xu Jianping
Published: February 2010

Orchids are among the most prized ornamental plants in many societies throughout the world. As a result, consumer demands have created a significant pressure on wild populations of many species, including Cymbidium goeringii Rchb. f., a rare terrestrial orchid endemic in China, Korea, and Japan. To help conserve natural populations of C. goeringii, we recently started investigating methods to cultivate these orchids. Here we fulfilled Koch’s postulates and demonstrated that fungal strains isolated from the roots of natural Cymbidium plants increased fresh mass, plant height, number of leaves, and root length of C. goeringii, and that the two fungal strains originally isolated from C. goeringii showed overall greater effects on growth than two other strains from other Cymbidium species. Internal transcribed spacer sequence analyses revealed that the four fungal strains likely represented at least two new taxonomic groups, both belonging to the family Ceratobasidiaceae of the Rhizoctonia fungi. Our study demonstrated that these fungal strains could potentially help the commercial cultivation of the increasingly rare and endangered orchid C. goeringii.
Inference of phylogenetic relationships among the subfamilies of grasses (Poaceae: Poales) using meso-scale exemplar-based sampling of the plastid genome
Authors: Saarela Jeffery M. , Graham Sean W.
Published: February 2010

To clarify phylogenetic relationships among grass (Poaceae) subfamilies and to better resolve the placement of Poaceae in Poales, we surveyed 17 plastid genes and associated noncoding regions (∼15.5 kb per taxon, about 1/10 of the plastid genome) for exemplar representatives from 10 grass subfamilies and a broad sample of related monocots. We found general concordance in relationships and support levels among gene regions and data partitions across analyses, with some exceptions in Bayesian analyses. Different phylogenetic criteria generally agreed on backbone relationships, and the support values we inferred were generally as good as or better than those in other studies that employed more taxa for fewer genes to estimate the same backbone. Within grasses, we found robust support for the monophyly of subfamily Anomochlooideae and for the Bambusoideae–Ehrhartoideae–Pooideae (BEP) clade, and moderate support for a sister-group relationship between Bambusoideae and Pooideae. Most relationships in the strongly supported Panicoideae–Aristidoideae–Chloridoideae–Micrairoideae–Arundinoideae–Danthonioideae (PACMAD) clade were not resolved consistently, probably because the current intensive sampling of genes is still insufficient to resolve short internal branches. Our data infer a well-supported clade that includes the grass family and two small families of grass-like plants, Ecdeiocoleaceae and Joinvilleaceae, but we did not satisfactorily resolve the relationships among these three families. A generally accelerated substitution rate in Poaceae plastid genomes is shared with some, but not all, lineages that are closely related to grasses in the larger clade of commelinid monocots, which may complicate inference of the sister group of the grasses in all current studies.
Seasonal variation and distribution at different soil depths of arbuscular mycorrhizal fungi spores in a tropical sclerophyllous shrubland
Authors: Cuenca Gisela , Lovera Milagros
Published: February 2010

Limited information is available for the diversity of arbuscular mycorrhizal fungi (AMF) in most tropical soils. To assess the biodiversity of AMF in a sclerophyllous shrubland ecosystem, an exhaustive collection of spores from soil collected in the Venezuelan Guayana was undertaken. Spores were collected from the first 15 cm of soil, four times throughout the year, and at four different depths during dry and wet seasons. A total of 50 AMF morphotypes were collected in the field, and 2 more were isolated from pot cultures. There was a reduction in spore density with soil depth, although richness of spores remained the same up to a depth of 45 cm. Spore density and richness based on soil cores were higher in the dry season than in the rainy season. Only 24% of the AMF morphotypes present could be identified to species level, since most of them did not fit published descriptions available. It is important to perform an exhaustive sampling of spores in the different seasons throughout the year and at different soil depths to obtain an accurate view of AMF spore diversity associated with a particular ecosystem.
Statut symbiotique et souches de rhizobia associées à l’Acacia tortilissubsp.raddiana[Acacia raddianas. s.], mimosoïdée des régions désertiques de l’Algérie
Authors: Noureddine Nazhat-Ezzaman , Amrani Saïd , Aïd Fatiha
Published: February 2010

L’ Acacia tortilis (Forsskal) Hayne subsp. raddiana (Savi) Brenan [ Acacia raddiana Savi s. s.] est la légumineuse ligneuse la plus répandue dans les régions désertiques d’Algérie. En tant qu’espèce bien adaptée, elle offre un potentiel d’intérêt pour le boisement ou le reboisement de ces régions. Sa capacité d’établir une symbiose fixatrice d’azote avec les rhizobia constitue un caractère important pour son développement et son adaptation aux conditions du milieu. Pour ces raisons, nous avons mené une étude portant sur la prévalence de la symbiose chez cette espèce et sur la caractérisation des souches de rhizobia associées. L’étude a porté sur 101 plants provenant de neuf sites naturels et de huit pépinières et nous a permis d’établir que l’A. tortilis subsp. raddiana est généralement nodulé et fixateur d’azote, malgré les conditions édaphiques défavorables qui prévalent en milieu naturel et dans les pépinières du sud du pays. La caractérisation symbiotique de 51 souches de rhizobia associées à l’A. tortilis subsp. raddiana nous a permis de montrer que celles-ci ne sont pas très spécifiques et qu’elles sont capables, pour la plupart, de former des nodules fixateurs d’azote chez les autres espèces d’acacias des régions désertiques de l’Algérie, en particulier l’ Acacia seyal Del. et l’ Acacia ehrenbergiana Hayne. Ces souches représentent donc un potentiel pour la production d’inoculants destinés à la bactérisation de l’A. tortilis subsp. raddiana, mais également des autres espèces d’acacias. L’analyse des profils de restriction du gène de l’ARN 16S des souches de rhizobia associées a permis de mettre en évidence leur grande diversité. Elles étaient représentées essentiellement par les espèces du genre Ensifer avec une prédominance de l’ Ensifer meliloti et, dans une moindre mesure, par des espèces des genres Mesorhizobium et Rhizobium , comme cela a déjà été rapporté par de nombreux auteurs dans d’autres régions d’Afrique. En plus des espèces de rhizobia reconnues comme étant capables de s’associer avec l’A. tortilis raddiana, nous avons isolé cinq souches que nous n’avons pas pu identifier, par réaction en chaîne de la polymérase – polymorphisme de la longueur du fragment de restriction du gène de l’ARN 16S, et qui pourraient constituer une nouvelle espèce génotypique.
Interspecific covariation between stomatal density and other functional leaf traits in a local flora
Authors: Loranger Jessy , Shipley Bill
Published: February 2010

Despite the importance of stomata in leaf functioning, and despite the recent interest in interspecific leaf trait covariation in functional ecology, little is known about how stomatal density relates to other leaf traits in a broad interspecific context. This is especially important because stomatal density has been widely used to deduce temporal variation in atmospheric CO2 concentrations [CO2atm] from fossilized or herbarium leaves. We therefore measured stomatal density, specific leaf area (SLA) and its components, leaf thickness, and leaf chlorophyll content in both sun and shade leaves of 169 individuals from 52 angiosperm species in southwestern Quebec. Using mixed models, we show that stomatal density decreases allometrically with increasing SLA and chlorophyll content, and increases allometrically with increasing lamina thickness. The sun–shade contrast changes the intercepts, but not the slopes, of these relationships. It is important to take into consideration these relations when correlating stomatal density with [CO2], to avoid spurious interpretations.
Ultrastructural observations of the mature megagametophyte and the fertilization in wheat (Triticum aestivum)
Authors: You Ruilin , Jensen William A.
Published: February 2010

The mature embryo sac of wheat contains an egg apparatus composed of an egg cell and two synergids at the micropylar end, a central cell with two large polar nuclei in the middle, and a mass of 20 to 30 antipodals at the chalazal end. A comparison was made of the ultrastructural features of the various cells of the embryo sac. The features included the position of the nucleus and vacuoles, the number, structure, and distribution of organelles, and the extent of the cell walls surrounding each cell. The pollen tube enters one synergid through the filiform apparatus from the micropyle. The penetration and discharge of the pollen tube causes the further degeneration of that synergid, which had already undergone changes before pollination. The second synergid does not change further in appearance following the penetration of the first by the pollen-altered tube. Half an hour after pollination at 20–25 °C, two male nuclei are seen in the cytoplasm of the egg and the central cell. At about 1 h after pollination, one sperm has made contact with the egg nucleus, while the other sperm is fusing with one of the polar nuclei.
A developmental study of the early stages in vesicular–arbuscular mycorrhiza formation
Authors: Brundrett M. C. , Piché Y. , Peterson R. L.
Published: February 2010

A new experimental procedure was developed to produce samples of leek roots containing early stages in colonization by vesicular–arbuscular mycorrhizal (VAM) fungi. This procedure involved transplanting leek seedlings into a pot culture containing an established symbiosis. Abundant colonization of seedling roots occurred in 1 week. Samples harvested at 2-day intervals after exposure to the inoculum were used to determine the time course of colonization. Contact of the root by external hyphae occurred after approximately 1 day, followed by penetration of hyphae into the root at about 2 days, arbuscule formation within 3–4 days, and vesicle formation after 4–5 days. The average distance from growing root apices at which each of the above events first occurred and the growth rate of intercellular hyphae were also estimated. Stages in root colonization were then documented using the chlorazol black E staining procedure. This transplant procedure should allow the production of abundant material at early stages in VAM development for chemical and morphological investigations as well as provide an efficient inoculation procedure.
Fungal parasites of bdelloid rotifers: Diheterospora
Authors: Barron G. L.
Published: February 2010

Descriptions and illustrations are given for 12 species of Diheterospora recovered from parasitized rotifers in Ontario. Four of these species have been previously described and eight are described for the first time.
Characteristics and origin of a new birch species, Betula murrayana, from southeastern Michigan
Authors: Barnes Burton V. , Dancik Bruce P.
Published: February 2010

A new taxon, Betula murrayana, is described from southeastern Michigan. This birch appears to be an oetoploid (2n = 112) derivative of an unreduced gamete of Purpus birch (B. × purpusii Schneid. = B. alleghaniensis Britt. × B. pumila L., 2n = 70) and a reduced gamete of yellow birch (B. alleghaniensis, 2n = 84). Betula murrayana has relatively uniform, good, large pollen grains and leaf stomata larger than its putative ancestors; this multistemmed plant has larger leaves and fruits than the hybrid.
Races chromosomiques chez Festuca rubra sensu lato (Poaceae) dans l'est du Québec
Authors: Dubé Martin , Morisset Pierre , Murdock Janouk
Published: February 2010

Twenty-eight chromosome number determinations in Festuca rubra L. s.l. from eastern Québec show the occurrence of both hexaploids (n = 21) and octoploids (n = 28). Some characters distinguish both cytotypes, but they can be modified by cultivation. All the octoploids are identified as F. diffusa Dumort., an introduced species.
Assessing sample size and variable number in multivariate data, with specific reference to cone morphology variation in a population of Picea sitchensis
Authors: Scagel Rob , El-Kassaby Y. A. , Emanuel J.
Published: February 2010

A multivariate extension of univariate sample size estimation is outlined that enables one to determine sample size for a multivariate study. The procedure is presented and illustrated by application to intraindividual and interindividual variation of cone morphology in a population of Picea sitchensis (Bong.) Carr. The method involves the stabilization of a scalar estimate of the structure of the correlation matrix (the determinant) among variables for a given sample size. The sample-specific dependency of previously described methods is avoided by random selection of several replicates in nonstructured and structured (nested) models. The procedure is best applied in pilot studies where it can aid in the characterization of multivariate data prior to analysis. Additionally, repeatability estimates for cone scale morphology are presented.
Développement du fruit de Prunus virginiana (Rosaceae)
Authors: Labrecque Michel , Barabé Denis , Vieth Joachim
Published: February 2010

The development of the fruit of Prunus virginiana L. is followed from full bloom to ripening. The maturation process, which lasts 10 weeks is characterized by three distinct stages. Two periods of rapid growth (at the beginning and the end of ripening) are separated by a stage of retarded growth. Soon after the fertilization, the mesocarp increases in thickness, owing to an enlargement of the cells of the later tissue rather than by an increase in the number of cells. By the end of the first period of growth, the endocarp begins to enlarge. In this situation, the increase of thickness is predominantly due to cell division. At the completion of its development, we observed two distinct zones in the endocarp. The inner portion is formed of 6 to 7 layers of lignified cells extending tangentially along the cavity, while the outer portion is composed of 15 to 20 isodiametric sclereids. The second stage of the development is characterized by an important delay in the growth of the pericarp. However, the cessation of the increase coincides with some important changes in the seed, while the endosperm, and almost simultaneously, the embryo rapidly expand. During the maturation of the seed, we noted that the endosperm cells enlarged, their cytoplasm became thicker, and their arrangement in the tissue appeared more regular. Throughout the third phase of the development, a new period of rapid growth is observed. In the mesocarp, the cells enlarged in the radial direction. The development of the fruit of P. virginiana L. and its vascular patterns have been analysed in comparison with those of other fruits of Prunus.