bluuebunny/crossref_metadata_2025 huggingface dataset:
Use of Pressurized Differential Scanning Calorimetry (PDSC) to Evaluate Effectiveness of Additives in Vegetable Oil Lubricants
Authors: Cheenkachorn Kraipat , Lloyd Wallis A. , Perez Joseph M.
Published: February 2009

Use of renewable resources to replace petroleum base stocks in lubricants is attractive. Research on additives enhanced by current advances in genetic and chemical modifications has resulted in improved oxidative stability of vegetable oils. Like most oxidation processes, the oxidative degradation of vegetable oils is complex. The auto-oxidation free radical mechanisms and hydroperoxide theories of oxidation have been well studied. Factors that influence the degradation of oils include temperature, surface reactivity, rates of formation of radicals, chemical composition factors such as olefin and aromatic content and additive effectiveness. This uses pressurized differential scanning calorimetry to evaluate the oxidative stability of four biodegradable fluids with and without additives. The oleic acid content of the four fluids ranged from 83 to 23 percent. Reaction kinetics are used to explain observed differences in phase transformation and polymerization reactions. Additive selection to obtain maximum effectiveness in the base stocks is reported.
Investigation of the Applicability of SODAR for Wind Resource Measurements in Complex and Inhomogeneous Terrain
Authors: Rogers Anthony L. , Manwell James F. , Grills George G.
Published: February 2009

Increasingly, SODAR (Sonic Detection And Ranging) systems are being used for wind measurements as an alternative to tower-mounted anemometry. SODARs uses acoustic signals to resolve u, v, and w wind velocity components at multiple heights. The accuracy of SODAR measurements are affected by underestimation of wind speeds due to volume sampling, spurious signals from ambient noise or reflected SODAR signals, the effects of precipitation on estimates of vertical wind speeds and, sometimes, sampling of different volumes for each velocity component. Typically missing or ambiguous data increases with height. This paper evaluates the applicability of SODAR for wind resource measurements in complex and inhomogeneous terrain. The evaluation is based on data collected at three Massachusetts sites: Mt. Tom, Thompson Island and Northfield Mountain. The terrain at Mt. Tom and at Northfield Mountain is complex. Thompson Island data are compared to nearby anemometry and the usefulness of the SODAR for evaluating wind shear in offshore sites is considered. SODAR data from Northfield Mountain, collected next to a tower with standard anemometry and at a nearby site, are compared to the anemometry data. Additional operational issues related to the use of SODAR for wind resource measurements are discussed.
Analysis of Blunt Trailing Edge Airfoils
Authors: Standish K. J. , van Dam C. P.
Published: February 2009

The adoption of blunt trailing edge airfoils for the inner regions of large wind turbine blades has been proposed. Blunt trailing edge airfoils would not only provide increased structural volume, but have also been found to improve the lift characteristics of airfoils and therefore allow for section shapes with a greater maximum thickness. Limited experimental data makes it difficult for wind turbine designers to consider and conduct tradeoff studies using these section shapes. This lack of experimental data precipitated the present analysis of blunt trailing edge airfoils using computational fluid dynamics. Several computational techniques are applied including a viscous/inviscid interaction method and several Reynolds-averaged Navier-Stokes methods.
New Fatigue Data for Wind Turbine Blade Materials
Authors: Mandell John F. , Samborsky Daniel D. , Wang Lei , Wahl Neil K.
Published: February 2009

This paper reports on recent fatigue data of interest to the wind turbine industry in several areas: (a) very high cycle S-N data; (b) refined Goodman Diagram; (c) effects of fiber waviness; and (d) large tow carbon fibers. Tensile fatigue results from a specialized high frequency small strand testing facility have been carried out to 1010 cycles in some cases, beyond the expected cycle range for turbines. While the data cannot be used directly in design due to the specialized test specimen, the data trends help to clarify the proper models for extrapolating from standard coupons to higher cycles. The results for various fiber and matrix systems also provide insight into basic failure mechanisms. For spectrum loading predictions, a more detailed Goodman Diagram has been developed with additional R-values (R is the ratio of minimum to maximum stress in a cycle). The data of greatest interest were obtained for tensile fatigue with low cyclic amplitudes, close to R = 1.0, to clarify the shape of the diagram as the cyclic amplitude approaches zero. These data may significantly shorten lifetime predictions compared with traditional Goodman Diagram constructions based on more limited data. The effects of material/process induced flaws on properties continues to be a major concern, particularly with large tow carbon fabrics. The results of a study of fiber waviness effects on compressive strength show significant strength reductions for severe waviness which can be introduced in resin infusion processes. The final section presents new fatigue results for large tow carbon/fiberglass hybrid composites. Epoxy resin laminates show marginally higher compressive strength and fatigue resistance with carbon fibers. Improved compressive static and fatigue performance is found with stitched fabrics as compared with woven fabrics.
Modeling of Blades as Equivalent Beams for Aeroelastic Analysis
Authors: Malcolm David J. , Laird Daniel L.
Published: February 2009

A procedure has been developed and tested to derive a set of one-dimensional beam properties that will duplicate the behavior of a full three-dimensional finite element model of a wind turbine blade. This allows the full features of a detailed model to be transferred to an aeroelastic code for dynamic simulation of the complete wind turbine. The process uses the NuMAD interface to generate an ANSYS® finite element model to which a set of six unit loads are applied at the tip. The displacement results are used in a series of MATLAB routines to extract the stiffness matrices of the desired beam elements. Tests have been carried out on a number of blades and the stiffness matrices incorporated into ADAMS® models of the blades and complete wind turbines.
Low-frequency components in harbor porpoise (Phocoena phocoena) clicks: communication signal, by-products, or artifacts?
Authors: Hansen M. , Wahlberg M. , Madsen P. T.
Published: February 2009

Underwater sound signals for biosonar and communication normally have different source properties to serve the purposes of generating efficient acoustic backscatter from small objects or conveying information to conspecifics. Harbor porpoises (Phocoena phocoena) are nonwhistling toothed whales that produce directional, narrowband, high-frequency (HF) echolocation clicks. This study tests the hypothesis that their 130kHz HF clicks also contain a low-frequency (LF) component more suited for communication. Clicks from three captive porpoises were analyzed to quantify the LF and HF source properties. The LF component is 59 (S.E.M=1.45dB)dB lower than the HF component recorded on axis, and even at extreme off-axis angles of up to 135°, the HF component is 9dB higher than the LF component. Consequently, the active space of the HF component will always be larger than that of the LF component. It is concluded that the LF component is a by-product of the sound generator rather than a dedicated pulse produced to serve communication purposes. It is demonstrated that distortion and clipping in analog tape recorders can explain some of the prominent LF components reported in earlier studies, emphasizing the risk of erroneous classification of sound types based on recording artifacts.
Lateralization of Huggins pitch
Authors: Zhang Peter Xinya , Hartmann William M.
Published: February 2009

The Huggins pitch is a sensation of pitch generated from a broadband noise having a narrowband boundary region where the interaural phase difference varies rapidly as a function of frequency. Models of binaural hearing predict that the pitch image should be well lateralized. A direct psychophysical experimental method was used to estimate the lateral positions of Huggins pitch images with two different forms of phase boundaries, linear phase and stepped phase. A third experiment measured the lateral positions of sine tones with controlled interaural phase differences. The results showed that the lateralization of Huggins pitch stimuli was similar to that of the corresponding sine tones and that the lateralizations of the two forms of Huggins pitch phase boundaries were even more similar to one another. Both Huggins pitches and sine tones revealed strong laterality compression (exponent≈0.5). Ambiguous stimuli, with an interaural phase difference of 180°, were consistently lateralized on one side or the other according to individual asymmetries—an effect called “earedness.” An appendix to this article develops a new first-order lateralization model, the salient phase density model, which combines attributes of previous models of dichotic pitch lateralization.
Nonlinear modulation of Lamb modes by clapping delamination
Authors: Shkerdin G. , Glorieux C.
Published: February 2009

The nonlinear interaction between a high frequency probing Lamb wave and a bilayer containing a tangential delamination at the interlayer interface, whose contact conditions are dynamically changing due to a high amplitude Lamb wave with a long wavelength, is modeled in a quasistationary approach. The impact of the evolution of the contact condition on the mode conversion coefficients that describe the interaction of the probing wave with the delamination region leads to spectral enrichment due to cross-modulation spectral components between the probing wave and the modulating wave. The dynamical behavior of the normal displacement at the externally accessible surfaces is investigated for two different types of incident probing wave, both for an absorbing and a nonabsorbing bilayer structure, for variations in the contact quality modulation and as a function of defect size. The results can serve as a parametric guide for experimentalists considering the use of nonlinear harmonic generation of Lamb waves as a tool for nondestructive testing of bilayers, such as rubber-steel composites, in storage tanks and pipelines.
Speed of sound in bubble-free ice
Authors: Vogt Christian , Laihem Karim , Wiebusch Christopher
Published: February 2009

The speed of sound in a large volume of bubble-free ice was measured with high accuracy using a linear array of six piezoceramic lead zirconium titanate (PZT) receivers. This array was deployed in an ∼3 m3 water tank, which was cooled down to −20 °C. The freezing process was performed inside a cooling container. Bubble-free ice was obtained using a freeze control unit, which filters and degases the water during the freezing process. A dedicated geometry was used to position PZT receivers and an emitter such that systematic errors were minimized. With this setup the longitudinal and the transverse components of the speed of sound were measured at temperatures between 17 and 0 °C in water and between 0 and −20 °C in ice with an uncertainty of ∼0.3%.
Modified variance ratio for objective detection of transient evoked potentials in bottlenose dolphins (Tursiops truncatus)
Authors: Finneran James J.
Published: February 2009

Evoked potential studies have often relied on one or more human observers to visually assess the averaged waveforms and decide if a response is present. Although simple and easy to implement, response detection strategies based on human observers are inherently subjective and depend on the observers’ experience and biases. To avoid these shortcomings, some recent marine animal studies utilizing auditory steady-state responses have applied frequency-domain, statistically based objective detection methods; however, statistically based objective methods have not yet been applied to marine animal tests involving transient evoked responses, which are normally analyzed in the time domain. The present study applied a modified version of the variance ratio FSP to determine the presence or absence of evoked responses in two bottlenose dolphins (Tursiops truncatus) stimulated with tone pips. The appropriate degrees of freedom for the statistical tests were empirically determined in four dolphins. The modified variance ratio was found to be a useful tool and to provide an objective statistical approach for the detection of transient evoked potentials.
Role of masker predictability in the cocktail party problem
Authors: Jones Gary L. , Litovsky Ruth Y.
Published: February 2009

In studies of the cocktail party problem, the number and locations of maskers are typically fixed throughout a block of trials, which leaves out uncertainty that exists in real-world environments. The current experiments examined whether there is (1) improved speech intelligibility and (2) increased spatial release from masking (SRM), as predictability of the number/locations of speech maskers is increased. In the first experiment, subjects identified a target word presented at a fixed level in the presence of 0, 1, or 2 maskers as predictability of the masker configuration ranged from 10% to 80%. The second experiment examined speech reception thresholds and SRM as (a) predictability of the masker configuration is increased from 20% to 80% and/or (b) the complexity of the listening environment is decreased. In the third experiment, predictability of the masker configuration was increased from 20% up to 100% while minimizing the onset delay between maskers and the target. All experiments showed no effect of predictability of the masker configuration on speech intelligibility or SRM. These results suggest that knowing the number and location(s) of maskers may not necessarily contribute significantly to solving the cocktail party problem, at least not when the location of the target is known.
The role of temporal-masking patterns in the determination of subjective duration and loudness for ramped and damped sounds
Authors: Ries Dennis T. , Schlauch Robert S. , DiGiovanni Jeffrey J.
Published: February 2009

The association between temporal-masking patterns, duration, and loudness for broadband noises with ramped and damped envelopes was examined. Duration and loudness matches between the ramped and damped sounds differed significantly. Listeners perceived the ramped stimuli to be longer and louder than the damped stimuli, but the outcome was biased by the stimulus context. Next, temporal-masking patterns were measured for ramped- and damped-broadband noises using three (0.5, 1.5, and 4.0kHz) 10ms probe tones presented individually at various temporal delays. Predictions of subjective duration derived from masking results underpredicted the matching results. Loudness estimates derived from models that assume persistence of neural activity after stimulus offset [Glasberg B. R., and Moore, B. C. J. (2002). “A model of loudness applicable to time-varying sounds,” J. Audio. Eng. Soc. 50, 331–341; Chalupper, J., and Fastl, H. (2002) “Dynamic loudness model (DLM) for normal and hearing-impaired listeners,” Acust. Acta Acust. 88, 378–386] were greater for ramped sounds than for damped sounds and were close to the average results obtained via the matching task. Differences in simultaneous-masked thresholds for these stimuli could not account for the loudness-matching results. Decay suppression of the later occurring portion of the damped stimulus may account for the differences in perception due to the stimulus context; however, a parsimonious implementation of this process that accounts for both subjective duration and loudness judgments remains unclear.
Comparing the optimal signal conditions for recording cubic and quadratic distortion product otoacoustic emissions
Authors: Bian Lin , Chen Shixiong
Published: February 2009

Odd- and even-order distortion products (DPs), evoked by two primary tones (f1,f2,f1<f2), represent different aspects of cochlear nonlinearity. The cubic and quadratic difference tones (CDT 2f1−f2 and QDT f2−f1) are prominent representatives of the odd and even DPs. Distortion product otoacoustic emissions (DPOAEs) were measured within a primary level (L1,L2) space over a wide range of f2∕f1 ratios to compare the optimal signal conditions for these DPs. For CDT, the primary level difference decreased as L1 increased with a rate proportional to the f2∕f1 ratio. Moreover, the optimal ratio increased with L1. A set of two formulas is proposed to describe the optimal signal conditions. However, for a given level of a primary, increasing the other tone level could maximize the QDT amplitude. The frequency ratio at the maximal QDT was about 1.3 and quite constant across different primary levels. A notch was found in the QDT amplitude at the f2∕f1 ratio of about 1.22–1.25. These opposite behaviors suggest that the optimal recording conditions are different for CDT and QDT due to the different aspects in the cochlear nonlinearity. Optimizing the DPOAE recordings could improve the reliability in clinical or research practices.
Diffusion regime for high-frequency vibrations of randomly heterogeneous structures
Authors: Savin Éric
Published: February 2009

The evolution of the high-frequency vibrational energy density of slender heterogeneous structures such as Timoshenko beams or thick shells is depicted by transport equations or radiative transfer equations (RTEs) in the presence of random heterogeneities. A diffusive regime arises when their correlation lengths are comparable to the wavelength, among other possible situations, and waves are multiply scattered. The purpose of this paper is to expound how diffusion approximations of the RTEs for elastic structures can be derived and to discuss the relevance of the vibrational conductivity analogy invoked in the structural acoustics literature. Its main contribution is the consideration of a heterogeneous background medium with varying parameters and the effects of polarization of elastic waves. The paper also outlines some of the remarkable features of the diffusive regime: depolarization of waves, energy equipartition, and asymptotic Fick’s law.
Vibroacoustic behavior of clamp mounted double-panel partition with enclosure air cavity
Authors: Xin F. X. , Lu T. J. , Chen C. Q.
Published: February 2009

A theoretical study on the vibroacoustic performance of a rectangular double-panel partition clamp mounted in an infinite acoustic rigid baffle is presented. With the clamped boundary condition taken into account by the method of modal function, a double Fourier series solution to the dynamic response of the structure is obtained by employing the weighted residual method (i.e., the Galerkin method). The double series solution can be considered as the exact solution of the problem, as the structural and acoustic-structural coupling effects are fully accounted for and the solution converges numerically. The accuracy of the theoretical predictions is checked against existing experimental data, with good agreement achieved. The influence of several key parameters on the sound isolation capability of the double-panel configuration is then systematically studied, including panel dimensions, thickness of air cavity, elevation angle, and azimuth angle of incidence sound. The present method is suitable for double-panel systems of finite or infinite extent and is applicable for both low- and high-frequency ranges. With these merits, the proposed method compares favorably with a number of other approaches, e.g., finite element method, boundary element method, and statistical energy analysis method.
Structural acoustics model of the violin radiativity profile
Authors: Bissinger George
Published: February 2009

Violin radiativity profiles are dominated by the Helmholtz-like A0 cavity mode (∼280Hz), first corpus bending modes B1− and B1+ (∼500Hz), and BH and bridge-filter peaks (∼2.4kHz and ∼3.5kHz, respectively), with falloff above ∼4kHz. The B1 modes—dependent on two low-lying free-plate modes—are proposed to excite A0 via coupling to B1-driven in-phase f-hole volume flows. VIOCADEAS data show that A0 radiativity increases primarily as A0-B1− frequency difference decreases, consistent with Meinel’s 1937 experiment for too-thick/too-thin plate thicknesses, plus sound post removal and violin octet baritone results. The vibration→acoustic energy filter, FRAD, computed from shape-material-independent radiation and total damping, peaks at the critical frequency fcrit, estimated from a free-plate mode by analogy to flat-plate bending. Experimentally, fcrit decreased as this plate mode (and B1+) frequency increased. Simulations show that increasing plate thicknesses lowers fcrit, reduces FRAD, and moves the spectral balance toward lower frequencies. Incorporating string→corpus filters (including bridge versus bridge-island impedances) provides a model for overall violin radiativity. This model—with B1 and A0-B1 couplings, and fcrit (computed from a free-plate mode important to B1) strongly affecting the lowest and highest parts of the radiativity profile—substantiates prior empirical B1—sound quality linkages.
Visualizations of sound energy across coupled rooms using a diffusion equation model
Authors: Jing Yun , Xiang Ning
Published: February 2009

Visualizations, based on a diffusion equation model, are presented for both steady-state and transient sound energy. For steady-state sound-pressure level distributions, animations created by scanning from the primary room to the secondary room reveal discontinuous transitions of sound energy caused by a location change from the wall area to the aperture area. Animations of time-dependent energy flow directions visualize the energy flows across coupled spaces. This study also reveals a “reversal” characteristic of energy flow directions which seems to be dependent on the size and location of the aperture.
Videokymographic analysis of irregular vocal fold vibration in laryngeal paralysis.
Authors: Kimura Miwako , Tayama Niro , Chan Roger W.
Published: February 2009

Despite recent advances in high-speed digital imaging methods, laryngeal stroboscopic imaging is still commonly used for the clinical diagnosis and assessment of voice disorders. Yet standard videostroboscopy, designed for the examination of periodic or near-periodic vibration, is unable to provide detailed information on irregular vocal fold vibratory patterns. This study examined the vocal fold vibratory patterns of two patients with unilateral vocal fold paralysis with high-speed digital kymographic imaging. Laryngeal vibration was examined before and after the medialization procedure of arytenoid adduction, and relevant features were extracted from the videokymographic images. Results demonstrated two distinct vibratory frequencies for the contralateral vocal folds in both subjects prior to the procedure (269 Hz vs 361 Hz, and 114 Hz vs 154 Hz), but a single vibratory frequency following medialization (361, and 154 Hz). The restoration of vibratory symmetry after arytenoid adduction indicated that this procedure could significantly improve the synchronization and entrainment between asymmetric vocal folds, in parallel with improvements in glottal competence.
Evidence for Ecological Speciation and Its Alternative
Authors: Schluter Dolph
Published: February 2009

Natural selection commonly drives the origin of species, as Darwin initially claimed. Mechanisms of speciation by selection fall into two broad categories: ecological and mutation-order. Under ecological speciation, divergence is driven by divergent natural selection between environments, whereas under mutation-order speciation, divergence occurs when different mutations arise and are fixed in separate populations adapting to similar selection pressures. Tests of parallel evolution of reproductive isolation, trait-based assortative mating, and reproductive isolation by active selection have demonstrated that ecological speciation is a common means by which new species arise. Evidence for mutation-order speciation by natural selection is more limited and has been best documented by instances of reproductive isolation resulting from intragenomic conflict. However, we still have not identified all aspects of selection, and identifying the underlying genes for reproductive isolation remains challenging.
Queen Ants Make Distinctive Sounds That Are Mimicked by a Butterfly Social Parasite
Authors: Barbero Francesca , Thomas Jeremy A , Bonelli Simona , Balletto Emilio , Schönrogge Karsten
Published: February 2009

Ants dominate terrestrial ecosystems through living in complex societies whose organization is maintained via sophisticated communication systems. The role of acoustics in information exchange may be underestimated. We show that
Myrmica schencki
queens generate distinctive sounds that elicit increased benevolent responses from workers, reinforcing their supreme social status. Although fiercely defended by workers, ant societies are infiltrated by specialist insects that exploit their resources. Sounds produced by pupae and larvae of the parasitic butterfly
Maculinea rebeli
mimic those of queen ants more closely than those of workers, enabling them to achieve high status within ant societies. We conclude that acoustical mimicry provides another route for infiltration for ∼10,000 species of social parasites that cheat ant societies.
Signature of the End-Cretaceous Mass Extinction in the Modern Biota
Authors: Krug Andrew Z. , Jablonski David , Valentine James W.
Published: February 2009

The long-term effects of mass extinctions on spatial and evolutionary dynamics have been poorly studied. Here we show that the evolutionary consequences of the end-Cretaceous [Cretaceous/Paleogene (K/Pg)] mass extinction persist in present-day biogeography. The geologic ages of genera of living marine bivalves show a significant break from a smooth exponential distribution, corresponding to the K/Pg boundary. The break reflects a permanent increase in origination rates, intermediate between the Mesozoic rate and the post-extinction recovery pulse. This global rate shift is most clearly seen today in tropical bioprovinces and weakens toward the poles. Coupled with the modern geographic distributions of taxa originating before and after the K/Pg boundary, this spatial pattern indicates that tropical origination rates after the K/Pg event have left a permanent mark on the taxonomic and biogeographic structure of the modern biota, despite the complex Cenozoic history of marine environments.
Molecular and Evolutionary History of Melanism in North American Gray Wolves
Authors: Anderson Tovi M. , vonHoldt Bridgett M. , Candille Sophie I. , Musiani Marco , Greco Claudia , Stahler Daniel R. , Smith Douglas W. , Padhukasahasram Badri , Randi Ettore , Leonard Jennifer A. , Bustamante Carlos D. , Ostrander Elaine A. , Tang Hua , Wayne Robert K. , Barsh Gregory S.
Published: February 2009

Morphological diversity within closely related species is an essential aspect of evolution and adaptation. Mutations in the
Melanocortin 1 receptor
(
Mc1r
) gene contribute to pigmentary diversity in natural populations of fish, birds, and many mammals. However, melanism in the gray wolf,
Canis lupus
, is caused by a different melanocortin pathway component, the
K
locus, that encodes a beta-defensin protein that acts as an alternative ligand for Mc1r. We show that the melanistic
K
locus mutation in North American wolves derives from past hybridization with domestic dogs, has risen to high frequency in forested habitats, and exhibits a molecular signature of positive selection. The same mutation also causes melanism in the coyote,
Canis latrans
, and in Italian gray wolves, and hence our results demonstrate how traits selected in domesticated species can influence the morphological diversity of their wild relatives.
Comment on "Human-Specific Gain of Function in a Developmental Enhancer"
Authors: Duret Laurent , Galtier Nicolas
Published: February 2009

Prabhakar
et al
. (Reports, 5 September 2008, p. 1346) argued that the conserved noncoding sequence
HACNS1
has undergone positive selection and contributed to human adaptation. However, the pattern of substitution in
HACNS1
is more consistent with the neutral process of biased gene conversion (BGC). The reported human-specific gain of function is likely due to the accumulation of deleterious mutations driven by BGC, not positive selection.
Changes in Cortical Dopamine D1 Receptor Binding Associated with Cognitive Training
Authors: McNab Fiona , Varrone Andrea , Farde Lars , Jucaite Aurelija , Bystritsky Paulina , Forssberg Hans , Klingberg Torkel
Published: February 2009

Working memory is a key function for human cognition, dependent on adequate dopamine neurotransmission. Here we show that the training of working memory, which improves working memory capacity, is associated with changes in the density of cortical dopamine D1 receptors. Fourteen hours of training over 5 weeks was associated with changes in both prefrontal and parietal D1 binding potential. This plasticity of the dopamine D1 receptor system demonstrates a reciprocal interplay between mental activity and brain biochemistry in vivo.
Dynamic Order-Disorder in Atomistic Models of Structural Glass Formers
Authors: Hedges Lester O. , Jack Robert L. , Garrahan Juan P. , Chandler David
Published: February 2009

The glass transition is the freezing of a liquid into a solid state without evident structural order. Although glassy materials are well characterized experimentally, the existence of a phase transition into the glass state remains controversial. Here, we present numerical evidence for the existence of a novel first-order dynamical phase transition in atomistic models of structural glass formers. In contrast to equilibrium phase transitions, which occur in configuration space, this transition occurs in trajectory space, and it is controlled by variables that drive the system out of equilibrium. Coexistence is established between an ergodic phase with finite relaxation time and a nonergodic phase of immobile molecular configurations. Thus, we connect the glass transition to a true phase transition, offering the possibility of a unified picture of glassy phenomena.
Sequential Sympatric Speciation Across Trophic Levels
Authors: Forbes Andrew A. , Powell Thomas H.Q. , Stelinski Lukasz L. , Smith James J. , Feder Jeffrey L.
Published: February 2009

A major cause for biodiversity may be biodiversity itself. As new species form, they may create new niches for others to exploit, potentially catalyzing a chain reaction of speciation events across trophic levels. We tested for such sequential radiation in the
Rhagoletis pomonella
(Diptera: Tephritidae) complex, a model for sympatric speciation via host plant shifting. We report that the parasitic wasp
Diachasma alloeum
(Hymenoptera: Braconidae) has formed new incipient species as a result of specializing on diversifying fly hosts, including the recently derived apple-infesting race of
R. pomonella
. Furthermore, we show that traits that differentially adapt
R. pomonella
flies to their host plants have also quickly evolved and serve as ecological barriers to reproduction, isolating the wasps. Speciation therefore cascades as the effects of new niche construction move across trophic levels.
Two Thresholds, Three Male Forms Result in Facultative Male Trimorphism in Beetles
Authors: Rowland J. Mark , Emlen Douglas J.
Published: February 2009

Male animals of many species deploy conditional reproductive strategies that contain distinct alternative phenotypes. Such facultatively expressed male tactics are assumed to be due to a single developmental threshold mechanism switching between the expression of two alternative phenotypes. However, we discovered a clade of dung beetles that commonly expresses two threshold mechanisms, resulting in three alternative phenotypes (male trimorphism). Once recognized, we found trimorphism in other beetle families that involves different types of male weapons. Evidence that insects assumed to be dimorphic can express three facultative male forms suggests that we need to adjust how we think about animal mating systems and the evolution of conditional strategies.
Transcription Analysis of Genes Encoding Homologues of Reductive Dehalogenases in “
Dehalococcoides
” sp. Strain CBDB1 by Using Terminal Restriction Fragment Length Polymorphism and Quantitative PCR
Authors: Wagner Anke , Adrian Lorenz , Kleinsteuber Sabine , Andreesen Jan R. , Lechner Ute
Published: February 2009

The transcription of reductive dehalogenase homologous (
rdh
) genes of “
Dehalococcoides
” sp. strain CBDB1 was investigated during the growth and reductive dechlorination of 1,2,3- and 1,2,4-trichlorobenzene (TCB). A method was developed to monitor the expression of all 32
rdhA
genes present in the genome based on reverse transcription-PCR amplification with 13 degenerate primer pairs and terminal restriction fragment length polymorphism (t-RFLP) analysis. With this approach, the upregulation of the transcription of 29
rdhA
genes was indicated in response to 1,2,3- and 1,2,4-TCB added after a substrate depletion period of 72 h. The transcription of the remaining three
rdhA
genes additionally was detected using specific primers. While most
rdhA
genes were upregulated similarly in cultures after induction with 1,2,3-TCB or 1,2,4-TCB, three
rdhA
genes responded differentially to 1,2,3- and 1,2,4-TCB, as revealed by the comparison of t-RFLP profiles. The enhanced transcription of cbdbA1453 and cbdbA187 was observed in the presence of 1,2,3-TCB, while the transcription of cbdbA1624 was strongly induced by 1,2,4-TCB. Comparison of t-RFLP profiles obtained from cDNA and genomic DNA indicated a particularly high induction of the transcription of
cbrA
(=cbdbA84) by both TCBs. As indicated by reverse transcription-quantitative PCR, the transcription of these plus two other
rdhA
genes (cbdbA1588 and cbdbA1618) increased within 48 to 72 h by one or two orders of magnitude. Subsequently, transcript levels slowly decreased and approached initial transcript levels several days after complete dehalogenation. Finally,
cbrA
was transcribed to a level of 22 transcripts per
cbrA
gene, suggesting that
cbrA
mRNA could be an appropriate biomarker for the investigation of the natural dechlorination potential at chlorobenzene-contaminated sites.
Inactivation of Bacterial Pathogens following Exposure to Light from a 405-Nanometer Light-Emitting Diode Array
Authors: Maclean Michelle , MacGregor Scott J. , Anderson John G. , Woolsey Gerry
Published: February 2009

This study demonstrates the susceptibility of a variety of medically important bacteria to inactivation by 405-nm light from an array of light-emitting diodes (LEDs), without the application of exogenous photosensitizer molecules. Selected bacterial pathogens, all commonly associated with hospital-acquired infections, were exposed to the 405-nm LED array, and the results show that both gram-positive and gram-negative species were successfully inactivated, with the general trend showing gram-positive species to be more susceptible than gram-negative bacteria. Detailed investigation of the bactericidal effect of the blue-light treatment on
Staphylococcus aureus
suspensions, for a range of different population densities, demonstrated that 405-nm LED array illumination can cause complete inactivation at high population densities: inactivation levels corresponding to a 9-log
10
reduction were achieved. The results, which show the inactivation of a wide range of medically important bacteria including methicillin-resistant
Staphylococcus aureus
, demonstrate that, with further development, narrow-spectrum 405-nm visible-light illumination from an LED source has the potential to provide a novel decontamination method with a wide range of potential applications.
Detection of
Campylobacter
Bacteria in Air Samples for Continuous Real-Time Monitoring of
Campylobacter
Colonization in Broiler Flocks
Authors: Olsen Katja N. , Lund Marianne , Skov Julia , Christensen Laurids S. , Hoorfar Jeffrey
Published: February 2009

Improved monitoring tools are important for the control of
Campylobacter
bacteria in broiler production. In this study, we compare the sensitivities of detection of
Campylobacter
by PCR with feces, dust, and air samples during the lifetimes of broilers in two poultry houses and conclude that the sensitivity of detection of
Campylobacter
in air is comparable to that in other sample materials. Profiling of airborne particles in six poultry houses revealed that the aerodynamic conditions were dependent on the age of the chickens and very comparable among different poultry houses, with low proportions of particles in the 0.5- to 2-μm-diameter range and high proportions in the 2- to 5-μm-diameter range.
Campylobacter
could also be detected by PCR in air samples collected at the hanging stage during the slaughter process but not at the other stages tested at the slaughterhouse. The exploitation of airborne dust in poultry houses as a sample material for the detection of
Campylobacter
and other pathogens provides an intriguing possibility, in conjunction with new detection technologies, for allowing continuous or semicontinuous monitoring of colonization status.
Prediction of a Required Log Reduction with Probability for
Enterobacter sakazakii
during High-Pressure Processing, Using a Survival/Death Interface Model
Authors: Koseki Shige , Matsubara Maki , Yamamoto Kazutaka
Published: February 2009

A probabilistic model for predicting
Enterobacter sakazakii
inactivation in trypticase soy broth (TSB) and infant formula (IF) by high-pressure processing was developed. The modeling procedure is based on a previous model (S. Koseki and K. Yamamoto, Int. J. Food Microbiol. 116:136-143, 2007) that describes the probability of death of bacteria. The model developed in this study consists of a total of 300 combinations of pressure (400, 450, 500, 550, or 600 MPa), pressure-holding time (1, 3, 5, 10, or 20 min), temperature (25 or 40°C), inoculum level (3, 5, or 7 log
10
CFU/ml), and medium (TSB or IF), with each combination tested in triplicate. For each replicate response of
E. sakazakii
, survival and death were scored with values of 0 and 1, respectively. Data were fitted to a logistic regression model in which the medium was treated as a dummy variable. The model predicted that the required pressure-holding times at 500 MPa for a 5-log reduction in IF with 90% achievement probability were 26.3 and 7.9 min at 25 and 40°C, respectively. The probabilities of achieving 5-log reductions in TSB and IF by treatment with 400 MPa at 25°C for 10 min were 92 and 3%, respectively. The model enabled the identification of a minimum processing condition for a required log reduction, regardless of the underlying inactivation kinetics pattern. Simultaneously, the probability of an inactivation effect under the predicted processing condition was also provided by taking into account the environmental factors mentioned above.
Three Genomes from the PhylumAcidobacteriaProvide Insight into the Lifestyles of These Microorganisms in Soils
Authors: Ward Naomi L. , Challacombe Jean F. , Janssen Peter H. , Henrissat Bernard , Coutinho Pedro M. , Wu Martin , Xie Gary , Haft Daniel H. , Sait Michelle , Badger Jonathan , Barabote Ravi D. , Bradley Brent , Brettin Thomas S. , Brinkac Lauren M. , Bruce David , Creasy Todd , Daugherty Sean C. , Davidsen Tanja M. , DeBoy Robert T. , Detter J. Chris , Dodson Robert J. , Durkin A. Scott , Ganapathy Anuradha , Gwinn-Giglio Michelle , Han Cliff S. , Khouri Hoda , Kiss Hajnalka , Kothari Sagar P. , Madupu Ramana , Nelson Karen E. , Nelson William C. , Paulsen Ian , Penn Kevin , Ren Qinghu , Rosovitz M. J. , Selengut Jeremy D. , Shrivastava Susmita , Sullivan Steven A. , Tapia Roxanne , Thompson L. Sue , Watkins Kisha L. , Yang Qi , Yu Chunhui , Zafar Nikhat , Zhou Liwei , Kuske Cheryl R.
Published: February 2009

The complete genomes of three strains from the phylumAcidobacteriawere compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of theProteobacteria, theCyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator superfamily transporters and high-affinity ABC transporters for sugars, suggesting that they are best suited to low-nutrient conditions. They appear capable of nitrate and nitrite reduction but not N2fixation or denitrification. The genomes contained numerous genes that encode siderophore receptors, but no evidence of siderophore production was found, suggesting that they may obtain iron via interaction with other microorganisms. The presence of cellulose synthesis genes and a large class of novel high-molecular-weight excreted proteins suggests potential traits for desiccation resistance, biofilm formation, and/or contribution to soil structure. Polyketide synthase and macrolide glycosylation genes suggest the production of novel antimicrobial compounds. Genes that encode a variety of novel proteins were also identified. The abundance of acidobacteria in soils worldwide and the breadth of potential carbon use by the sequenced strains suggest significant and previously unrecognized contributions to the terrestrial carbon cycle. Combining our genomic evidence with available culture traits, we postulate that cells of these isolates are long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions, and are well equipped to tolerate fluctuations in soil hydration.
Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities
Authors: Ramette Alban
Published: February 2009

Molecular fingerprinting techniques offer great promise for analyzing changes in microbial community structure, especially when dealing with large number of samples. However, a serious limitation has been the lack of quantification offered by such techniques since the relative abundances of the identified operational taxonomic units (OTUs) in the original samples are not measured. A quantitative fingerprinting approach designated “qfingerprinting” is proposed here. This method involves serial dilutions of the sample of interest and further systematic fingerprinting of all dilution series. Using the ultimate dilutions for which OTU are still PCR amplifiable and taking into account peak size inaccuracy and peak reproducibility, the relative abundance of each OTU is then simultaneously determined over a scale spanning several orders of magnitude. The approach was illustrated by using a quantitative version of automated ribosomal intergenic spacer analysis (ARISA), here called qARISA. After validating the concept with a synthetic mixture of known DNA targets, qfingerprinting was applied to well-studied marine sediment samples to examine specific changes in OTU abundance associated with sediment depth. The new strategy represents a major advance for the detailed quantitative description of specific OTUs within complex communities. Further ecological applications of the new strategy are also proposed.
Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities
Authors: Baker Brett J. , Tyson Gene W. , Goosherst Lindsey , Banfield Jillian F.
Published: February 2009

Microscopic eukaryotes are known to have important ecosystem functions, but their diversity in most environments remains vastly unexplored. Here we analyzed an 18S rRNA gene library from a subsurface iron- and sulfur-oxidizing microbial community growing in highly acidic (pH < 0.9) runoff within the Richmond Mine at Iron Mountain (northern California). Phylogenetic analysis revealed that the majority (68%) of the sequences belonged to fungi. Protists falling into the deeply branching lineage named the acidophilic protist clade (APC) and the class
Heterolobosea
were also present. The APC group represents kingdom-level novelty, with <76% sequence similarity to 18S rRNA gene sequences of organisms from other environments. Fluorescently labeled oligonucleotide rRNA probes were designed to target each of these groups in biofilm samples, enabling abundance and morphological characterization. Results revealed that the populations vary significantly with the habitat and no group is ubiquitous. Surprisingly, many of the eukaryotic lineages (with the exception of the APC) are closely related to neutrophiles, suggesting that they recently adapted to this extreme environment. Molecular analyses presented here confirm that the number of eukaryotic species associated with the acid mine drainage (AMD) communities is low. This finding is consistent with previous results showing a limited diversity of archaea, bacteria, and viruses in AMD environments and suggests that the environmental pressures and interplay between the members of these communities limit species diversity at all trophic levels.
Prevalence and Characterization of Salmonellae in Commercial Ground Beef in the United States
Authors: Bosilevac Joseph M. , Guerini Michael N. , Kalchayanand Norasak , Koohmaraie Mohammad
Published: February 2009

Commercially produced ground beef samples (
n
= 4,136) were collected from seven regions of the United States over a 24-month period (July 2005 to June 2007) and analyzed for the presence of
Salmonella enterica
by using methods that concurrently provided total prevalence and enumerable levels. The overall prevalence of
Salmonella
strains was 4.2%. Enumeration showed that 94.2% were present at levels below 2 CFU/g. Regional monthly prevalences of
Salmonella
strains varied from 1.8% to 6.5% but were not statistically different (
P
> 0.05). All
Salmonella
isolates were serotyped and their antibiotic susceptibilities determined and analyzed by pulsed-field gel electrophoresis (PFGE). The most common serotypes identified were
Salmonella enterica
serotypes Montevideo, Anatum, Muenster, and Mbandaka, with these accounting for one-half of the isolates obtained. The prevalence of multidrug-resistant (MDR)
Salmonella
was determined to be 0.6%. The most common MDR serotypes were
Salmonella enterica
serotypes Dublin, Reading, and Typhimurium. MDR strains had resistance to between 2 and 10 antibiotics. There were no regional differences in prevalence of MDR
Salmonella
. PFGE analysis revealed that indistinguishable XbaI and AvrII restriction digest patterns (RDPs) could be observed in isolates of the same serotype found in different regions and months of sampling. The RDPs of 19
Salmonella
strains were compared to RDPs in the PulseNet USA database. Thirteen were indistinguishable from existing patterns, and the number of records for each ranged from 1 to 478. These data show that
Salmonella
prevalence in commercial ground beef is low and suggest that attempts to identify sources contributing to
Salmonella
in ground beef by serotype, antibiogram, and PFGE cannot be made without additional documented evidence.