bluuebunny/crossref_metadata_2025 huggingface dataset:
On the sound field of a resilient disk in free space
Authors: Mellow Tim
Published: April 2008

Radiation characteristics are calculated for a circular planar sound source in free space with a uniform surface pressure distribution, which can be regarded as a freely suspended membrane with zero mass and stiffness. This idealized dipole source is shown to have closed form solutions for its far-field pressure response and radiation admittance. The latter is found to have a simple mathematical relationship with the radiation impedance of a rigid piston in an infinite baffle. Also, a single expansion is derived for the near-field pressure field, which degenerates to a closed form solution on the axis of symmetry. From the normal gradient of the surface pressure, the surface velocity is calculated. The near-field expression is then generalized to an arbitrary surface pressure distribution. It is shown how this can be used as a simplified solution for a rigid disk in free space or a more realistic sound source such as pre-tensioned membrane in free space with non-zero mass and a clamped rim.
Measurement of vocal-tract influence during saxophone performance
Authors: Scavone Gary P. , Lefebvre Antoine , da Silva Andrey R.
Published: April 2008

This paper presents experimental results that quantify the range of influence of vocal tract manipulations used in saxophone performance. The experiments utilized a measurement system that provides a relative comparison of the upstream windway and downstream air column impedances under normal playing conditions, allowing researchers and players to investigate the effect of vocal-tract manipulations in real time. Playing experiments explored vocal-tract influence over the full range of the saxophone, as well as when performing special effects such as pitch bending, multiphonics, and “bugling.” The results show that, under certain conditions, players can create an upstream windway resonance that is strong enough to override the downstream system in controlling reed vibrations. This can occur when the downstream air column provides only weak support of a given note or effect, especially for notes with fundamental frequencies an octave below the air column cutoff frequency and higher. Vocal-tract influence is clearly demonstrated when pitch bending notes high in the traditional range of the alto saxophone and when playing in the saxophone’s extended register. Subtle timbre variations via tongue position changes are possible for most notes in the saxophone’s traditional range and can affect spectral content from at least 800–2000Hz.
Localization of multiple acoustic sources with small arrays using a coherence test
Authors: Mohan Satish , Lockwood Michael E. , Kramer Michael L. , Jones Douglas L.
Published: April 2008

Direction finding of more sources than sensors is appealing in situations with small sensor arrays. Potential applications include surveillance, teleconferencing, and auditory scene analysis for hearing aids. A new technique for time-frequency-sparse sources, such as speech and vehicle sounds, uses a coherence test to identify low-rank time-frequency bins. These low-rank bins are processed in one of two ways: (1) narrowband spatial spectrum estimation at each bin followed by summation of directional spectra across time and frequency or (2) clustering low-rank covariance matrices, averaging covariance matrices within clusters, and narrowband spatial spectrum estimation of each cluster. Experimental results with omnidirectional microphones and colocated directional microphones demonstrate the algorithm’s ability to localize 3–5 simultaneous speech sources over 4s with 2–3 microphones to less than 1 degree of error, and the ability to localize simultaneously two moving military vehicles and small arms gunfire.
Orthotropic material properties of the gerbil basilar membrane
Authors: Liu Shuangqin , White Robert D.
Published: April 2008

In this paper, two sets of experimental results to extract the two effective elastic moduli, the effective shear modulus, and the effective Poisson’s ratio for the gerbil cochlear partition are analyzed. In order to accomplish this, a geometrically nonlinear composite orthotropic plate model is employed. The model is used to predict both out-of-plane and in-plane motion of the partition under a static finite area distributed load. This loading condition models the small, but finite size, probe tips used in experiments. Both in-plane and out-of-plane motion are needed for comparison with recent experimental results. It is shown that the spatial decay rate (the space constant) for the in-plane deflection is different than for the out-of-plane deflection, which has a significant effect on the derived partition properties. The size of the probe tip is shown to have little influence on the results. Results are presented for two types of boundary conditions. Orthotropy ratios determined from the experimental data are found to vary with longitudinal position and choice of boundary conditions. Orthotropy ratios (the ratio of the two elastic moduli) are in the range of 65 close to the base to 10 in the upper middle turn of the cochlea.
An acoustical array combining microphones and piezoelectric devices
Authors: Matsumoto Mitsuharu , Hashimoto Shuji
Published: April 2008

This paper describes an acoustical array combining microphones and piezoelectric devices. Conventional microphone arrays have been widely utilized to realize noise reduction, sound separation and direction of arrival estimation system. However, when a conventional microphone array is mounted on a real system, such as a machine, vehicle or robot, the microphones are set extremely close to the system’s actual body. In such cases, the noise from the system itself, such as motors, gears, and engines, namely internal noise, often becomes a troublesome problem. It is difficult to reduce internal noise utilizing a conventional microphone array because internal noise sources are extremely close to the microphones. As internal noise is not always stationary, statistically independent or sparse, most useful blind source separation approaches, such as independent component analysis and the sparseness approach, cannot be employed. Our aim is to reduce internal noise utilizing microphones and piezoelectric devices attached to the internal noise source. In this paper, a general description of the acoustical array is formulated and the characteristic features of microphones and piezoelectric devices in an acoustical array are given. An acoustical array combining microphones and piezoelectric devices is also described with some experimental results.
A comparison of statistically optimized near field acoustic holography using single layer pressure-velocity measurements and using double layer pressure measurements
Authors: Jacobsen Finn , Chen Xinyi , Jaud Virginie
Published: April 2008

Statistically optimized near field acoustic holography (SONAH) is usually based on the assumption that all sources are on one side of the measurement plane whereas the other side is source free. An extension of the SONAH procedure based on measurement with an array of pressure-velocity probes has recently been suggested. An alternative method uses a double layer array of pressure transducers. Both methods make it possible to distinguish between sources on the two sides of the array and thus suppress the influence of extraneous noise and reflections coming from the “wrong” side. This letter compares the two methods.
Effects of in-the-ear microphone directionality on sound direction identification
Authors: Chung King , Neuman Arlene C. , Higgins Michael
Published: April 2008

As advanced signal processing algorithms have been proposed to enhance hearing protective device (HPD) performance, it is important to determine how directional microphones might affect the localization ability of users and whether they might cause safety hazards. The effect of in-the-ear microphone directivity was assessed by measuring sound source identification of speech in the horizontal plane. Recordings of speech in quiet and in noise were made with Knowles Electronic Manikin for Acoustic Research wearing bilateral in-the-ear hearing aids with microphones having adjustable directivity (omnidirectional, cardioid, hypercardioid, supercardioid). Signals were generated from 16 locations in a circular array. Sound direction identification performance of eight normal hearing listeners and eight hearing-impaired listeners revealed that directional microphones did not degrade localization performance and actually reduced the front–back and lateral localization errors made when listening through omnidirectional microphones. The summed rms speech level for the signals entering the two ears appear to serve as a cue for making front–back discriminations when using directional microphones in the experimental setting. The results of this study show that the use of matched directional microphones when worn bilaterally do not have a negative effect on the ability to localize speech in the horizontal plane and may thus be useful in HPD design.
Tissue mimicking materials for dental ultrasound
Authors: Singh Rahul S. , Culjat Martin O. , Grundfest Warren S. , Brown Elliott R. , White Shane N.
Published: April 2008

While acoustic tissue mimicking materials have been explored for a variety of soft and hard biological tissues, no dental hard tissue mimicking materials have been characterized. Tooth phantoms are necessary to better understand acoustic phenomenology within the tooth environment and to accelerate the advancement of dental ultrasound imaging systems. In this study, soda lime glass and dental composite were explored as surrogates for human enamel and dentin, respectively, in terms of compressional velocity, attenuation, and acoustic impedance. The results suggest that a tooth phantom consisting of glass and composite can effectively mimic the acoustic behavior of a natural human tooth.
Interpretations on principal components analysis of head-related impulse responses in the median plane
Authors: Hwang Sungmok , Park Youngjin
Published: April 2008

A principal components analysis of the median-plane head-related impulse responses (HRIRs) in the CIPIC HRTF database reveals that the individual HRIRs can be reconstructed by a linear combination of 12 principal components (PCs) within 5% of error in the least-squares sense. The PCs include the intersubject and interelevation variations in the median-plane HRIRs. Each PC provides sound cues for the front–back discrimination and/or the vertical perception. There exist common systematic elevation dependencies in the weights of lower-numbered PCs which contribute to the pinna/head diffractions, whereas the elevation dependencies in the weights of higher-numbered PCs are different from subject to subject.
Tactile enhancement of auditory and visual speech perception in untrained perceivers
Authors: Gick Bryan , Jóhannsdóttir Kristín M. , Gibraiel Diana , Mühlbauer Jeff
Published: April 2008

A single pool of untrained subjects was tested for interactions across two bimodal perception conditions: audio-tactile, in which subjects heard and felt speech, and visual-tactile, in which subjects saw and felt speech. Identifications of English obstruent consonants were compared in bimodal and no-tactile baseline conditions. Results indicate that tactile information enhances speech perception by about 10 percent, regardless of which other mode (auditory or visual) is active. However, within-subject analysis indicates that individual subjects who benefit more from tactile information in one cross-modal condition tend to benefit less from tactile information in the other.
Bending wavelet for flexural impulse response
Authors: Büssow Richard
Published: April 2008

The work addresses the definition of a wavelet that is adapted to analyze a flexural impulse response of a beam or plate that can be modeled with the Euler–Bernoulli bending theory. The wavelet gives the opportunity to directly analyze the dispersion characteristics of a pulse. The aim is to localize a source or to measure material parameters. An overview of the mathematical properties of the wavelet is presented. An algorithm for the optimal extraction of the dispersion characteristics with the use of genetic algorithms is outlined. The application of the wavelet is shown in an example and experiment.
Temporary hearing loss influences post-stimulus time histogram and single neuron action potential estimates from human compound action potentials
Authors: Lichtenhan Jeffery T. , Chertoff Mark E.
Published: April 2008

An analytic compound action potential (CAP) obtained by convolving functional representations of the post-stimulus time histogram summed across auditory nerve neurons [P(t)] and a single neuron action potential [U(t)] was fit to human CAPs. The analytic CAP fit to pre- and postnoise-induced temporary hearing threshold shift (TTS) estimated in vivo P(t) and U(t) and the number of neurons contributing to the CAPs (N). The width of P(t) decreased with increasing signal level and was wider at the lowest signal level following noise exposure. P(t) latency decreased with increasing signal level and was shorter at all signal levels following noise exposure. The damping and oscillatory frequency of U(t) increased with signal level. For subjects with large amounts of TTS, U(t) had greater damping than before noise exposure particularly at low signal levels. Additionally, U(t) oscillation was lower in frequency at all click intensities following noise exposure. N increased with signal level and was smaller after noise exposure at the lowest signal level. Collectively these findings indicate that neurons contributing to the CAP during TTS are fewer in number, shorter in latency, and poorer in synchrony than before noise exposure. Moreover, estimates of single neuron action potentials may decay more rapidly and have a lower oscillatory frequency during TTS.
Cortical sensitivity to periodicity of speech sounds
Authors: Yrttiaho Santeri , Tiitinen Hannu , May Patrick J. C. , Leino Sakari , Alku Paavo
Published: April 2008

Previous non-invasive brain research has reported auditory cortical sensitivity to periodicity as reflected by larger and more anterior responses to periodic than to aperiodic vowels. The current study investigated whether there is a lower fundamental frequency (F0) limit for this effect. Auditory evoked fields (AEFs) elicited by natural-sounding 400ms periodic and aperiodic vowel stimuli were measured with magnetoencephalography. Vowel F0 ranged from normal male speech (113Hz) to exceptionally low values (9Hz). Both the auditory N1m and sustained fields were larger in amplitude for periodic than for aperiodic vowels. The AEF sources for periodic vowels were also anterior to those for the aperiodic vowels. Importantly, the AEF amplitudes and locations were unaffected by the F0 decrement of the periodic vowels. However, the N1m latency increased monotonically as F0 was decreased down to 19Hz, below which this trend broke down. Also, a cascade of transient N1m-like responses was observed in the lowest F0 condition. Thus, the auditory system seems capable of extracting the periodicity even from very low F0 vowels. The behavior of the N1m latency and the emergence of a response cascade at very low F0 values may reflect the lower limit of pitch perception.
Segregation of Axial Motor and Sensory Pathways via Heterotypic Trans-Axonal Signaling
Authors: Gallarda Benjamin W. , Bonanomi Dario , Müller Daniel , Brown Arthur , Alaynick William A. , Andrews Shane E. , Lemke Greg , Pfaff Samuel L. , Marquardt Till
Published: April 2008

Execution of motor behaviors relies on circuitries effectively integrating immediate sensory feedback to efferent pathways controlling muscle activity. It remains unclear how, during neuromuscular circuit assembly, sensory and motor projections become incorporated into tightly coordinated, yet functionally separate pathways. We report that, within axial nerves, establishment of discrete afferent and efferent pathways depends on coordinate signaling between coextending sensory and motor projections. These heterotypic axon-axon interactions require motor axonal EphA3/EphA4 receptor tyrosine kinases activated by cognate sensory axonal ephrin-A ligands. Genetic elimination of trans-axonal ephrin-A → EphA signaling in mice triggers drastic motor-sensory miswiring, culminating in functional efferents within proximal afferent pathways. Effective assembly of a key circuit underlying motor behaviors thus critically depends on trans-axonal signaling interactions resolving motor and sensory projections into discrete pathways.
Leiomodin Is an Actin Filament Nucleator in Muscle Cells
Authors: Chereau David , Boczkowska Malgorzata , Skwarek-Maruszewska Aneta , Fujiwara Ikuko , Hayes David B. , Rebowski Grzegorz , Lappalainen Pekka , Pollard Thomas D. , Dominguez Roberto
Published: April 2008

Initiation of actin polymerization in cells requires nucleation factors. Here we describe an actin-binding protein, leiomodin, that acted as a strong filament nucleator in muscle cells. Leiomodin shared two actin-binding sites with the filament pointed end–capping protein tropomodulin: a flexible N-terminal region and a leucine-rich repeat domain. Leiomodin also contained a C-terminal extension of 150 residues. The smallest fragment with strong nucleation activity included the leucine-rich repeat and C-terminal extension. The N-terminal region enhanced the nucleation activity threefold and recruited tropomyosin, which weakly stimulated nucleation and mediated localization of leiomodin to the middle of muscle sarcomeres. Knocking down leiomodin severely compromised sarcomere assembly in cultured muscle cells, which suggests a role for leiomodin in the nucleation of tropomyosin-decorated filaments in muscles.
Posaconazole against
Candida glabrata
Isolates with Various Susceptibilities to Fluconazole
Authors: Spreghini Elisabetta , Maida Carmelo Massimo , Tomassetti Serena , Orlando Fiorenza , Giannini Daniele , Milici Maria Eleonora , Scalise Giorgio , Barchiesi Francesco
Published: April 2008

We investigated the in vitro activities of posaconazole (POS), fluconazole (FLC), amphotericin B (AMB), and caspofungin (CAS) against four clinical isolates of
Candida glabrata
with various susceptibilities to FLC (FLC MICs ranging from 1.0 to >64 μg/ml). POS MICs ranged from ≤0.03 to 0.5 μg/ml; AMB MICs ranged from 0.25 to 2.0 μg/ml, while CAS MICs ranged from 0.03 to 0.25 μg/ml. When FLC MICs increased, so did POS MICs, although we did not observe any isolate with a POS MIC greater than 0.5 μg/ml. Time-kill experiments showed that POS, FLC, and CAS were fungistatic against all isolates, while AMB at eight times the MIC was fungicidal against three out of four isolates of
C. glabrata
tested. Then, we investigated the activity of POS in an experimental model of disseminated candidiasis using three different isolates of
C. glabrata
: one susceptible to FLC (S; FLC MICs ranging from 1.0 to 4.0 μg/ml; POS MIC of ≤0.03 μg/ml), one susceptible in a dose-dependent manner (SDD; FLC MICs ranging from 32 to 64 μg/ml; POS MICs ranging from 0.125 to 0.25 μg/ml), and another one resistant to FLC (R; FLC MIC of >64 μg/ml; POS MIC of 0.5 μg/ml). FLC significantly reduced the kidney burden of mice infected with the S strain (
P
= 0.0070) but not of those infected with the S-DD and R strains. POS was significantly effective against all three isolates at reducing the kidney fungal burden with respect to the controls (
P
ranging from 0.0003 to 0.029). In conclusion, our data suggest that POS may be a useful option in the management of systemic infections caused by
C. glabrata
. Additionally, the new triazole may be a therapeutic option in those cases where an FLC-resistant isolate is found to retain a relatively low POS MIC.
Population Pharmacokinetics of Rifampin in Pulmonary Tuberculosis Patients, Including a Semimechanistic Model To Describe Variable Absorption
Authors: Wilkins Justin J. , Savic Radojka M. , Karlsson Mats O. , Langdon Grant , McIlleron Helen , Pillai Goonaseelan , Smith Peter J. , Simonsson Ulrika S. H.
Published: April 2008

This article describes the population pharmacokinetics of rifampin in South African pulmonary tuberculosis patients. Three datasets containing 2,913 rifampin plasma concentration-time data points, collected from 261 South African pulmonary tuberculosis patients aged 18 to 72 years and weighing 28.5 to 85.5 kg and receiving regular daily treatment that included administration of rifampin (450 to 600 mg) for at least 10 days, were pooled. A compartmental pharmacokinetic model was developed using nonlinear mixed-effects modeling. Variability in the shape of the absorption curve was described using a flexible transit compartment model, in which a delay in the onset of absorption and a gradually changing absorption rate were modeled as the passage of drug through a chain of hypothetical compartments, ultimately reaching the absorption compartment. A previously described implementation was extended to allow its application to multiple-dosing data. The typical population estimate of oral clearance was 19.2 liters·h
−1
, while the volume of distribution was estimated to be 53.2 liters. Interindividual variability was estimated to be 52.8% for clearance and 43.4% for volume of distribution. Interoccasional variability was estimated for CL/F (22.5%) and mean transit time during absorption (67.9%). The use of single-drug formulations was found to increase both the mean transit time (by 104%) and clearance (by 23.6%) relative to fixed-dose-combination use. A strong correlation between clearance and volume of distribution suggested substantial variability in bioavailability, which could have clinical implications, given the dependence of treatment effectiveness on exposure. The final model successfully described rifampin pharmacokinetics in the population studied and is suitable for simulation in this context.
Multivalent Presentation of Antihantavirus Peptides on Nanoparticles Enhances Infection Blockade
Authors: Hall Pamela R. , Hjelle Brian , Brown David C. , Ye Chunyan , Bondu-Hawkins Virginie , Kilpatrick Kathleen A. , Larson Richard S.
Published: April 2008

Viral entry into susceptible host cells typically results from multivalent interactions between viral surface proteins and host entry receptors. In the case of Sin Nombre virus (SNV), a New World hantavirus that causes hantavirus cardiopulmonary syndrome, infection involves the interaction between viral membrane surface glycoproteins and the human integrin αvβ3. Currently, there are no therapeutic agents available which specifically target SNV. To address this problem, we used phage display selection of cyclic nonapeptides to identify peptides that bound SNV and specifically prevented SNV infection in vitro. We synthesized cyclic nonapeptides based on peptide sequences of phage demonstrating the strongest inhibition of infection, and in all cases, the isolated peptides were less effective at blocking infection (9.0% to 27.6% inhibition) than were the same peptides presented by phage (74.0% to 82.6% inhibition). Since peptides presented by the phage were pentavalent, we determined whether the identified peptides would show greater inhibition if presented in a multivalent format. We used carboxyl linkages to conjugate selected cyclic peptides to multivalent nanoparticles and tested infection inhibition. Two of the peptides, CLVRNLAWC and CQATTARNC, showed inhibition that was improved over that of the free format when presented on nanoparticles at a 4:1 nanoparticle-to-virus ratio (9.0% to 32.5% and 27.6% to 37.6%, respectively), with CQATTARNC inhibition surpassing 50% when nanoparticles were used at a 20:1 ratio versus virus. These data illustrate that multivalent inhibitors may disrupt polyvalent protein-protein interactions, such as those utilized for viral infection of host cells, and may represent a useful therapeutic approach.
Enhancement of Diagnostic Efficiency by a Gamma Interferon Release Assay for Pulmonary Tuberculosis
Authors: Kanunfre Kelly Aparecida , Leite Olavo Henrique Munhoz , Lopes Max Igor , Litvoc Marcelo , Ferreira Antonio Walter
Published: April 2008

This study was designed to examine the use of the QuantiFERON-TB Gold assay as an aid in the diagnosis of active pulmonary tuberculosis (TB) in Brazilian patients. Using the receiver operating characteristic curve, the cutoff was adjusted to ≥0.20 IU/ml. The sensitivity increased to 86%, with 100% specificity. All TB patients with negative sputum smear microscopy and negative culture results were positive using this test.
The Innate Immune Response toSalmonella entericaSerovar Typhimurium by Macrophages Is Dependent on TREM2-DAP12
Authors: Charles Julia F. , Humphrey Mary Beth , Zhao Xiaodan , Quarles Ellen , Nakamura Mary C. , Aderem Alan , Seaman William E. , Smith Kelly D.
Published: April 2008

Macrophage recognition ofSalmonella entericaserovar Typhimurium leads to a cascade of signaling events, including the activation of Src family and Syk kinases and the production of reactive oxygen species (ROS), which are critical for host innate defense during early stages of bacterial infection. ROS production depends on the NADPH oxidase, but little is known about the innate immune receptors and proximal adapters that regulateSalmonella-induced ROS. Herein, we demonstrate that serovar Typhimurium induces ROS through a pathway that requires both triggering receptor expressed on myeloid cells 2 (TREM2) and DAP12. This pathway is highly analogous to the pathways utilized by Fc receptors and integrins to regulate ROS production. Oral infection of mice with serovar Typhimurium demonstrates that the DAP12-dependent pathway regulates cecal colonization during early stages ofSalmonellainfection. Thus, DAP12 is an important regulator ofSalmonella-induced ROS production in macrophages, and TREM2 is essential for linking DAP12 to the innate response to serovar Typhimurium.
Streptococcus pneumoniae
Surface Protein PcpA Elicits Protection against Lung Infection and Fatal Sepsis
Authors: Glover David T. , Hollingshead Susan K. , Briles David E.
Published: April 2008

Previous studies have suggested that pneumococcal choline binding protein A (PcpA) is important for the full virulence of
Streptococcus pneumoniae
, and its amino acid sequence suggests that it may play a role in cellular adherence. PcpA is under the control of a manganese-dependent regulator and is only expressed at low manganese concentrations, similar to those found in the blood and lungs. PcpA expression is repressed under high manganese concentrations, similar to those found in secretions. In this study, we have demonstrated that PcpA elicits statistically significant protection in murine models of pneumonia and sepsis. In the model of pneumonia with each of four challenge strains, statistically fewer
S. pneumoniae
cells were recovered from the lungs of mice immunized with PcpA and alum versus mice immunized with alum only. The immunizations reduced the median CFU by 4- to 400-fold (average of 28-fold). In the model of sepsis using strain TIGR4, PcpA expression resulted in shorter times to become moribund and subcutaneous immunization with PcpA increased survival times of mice infected with wild-type PcpA-expressing pneumococci.
RespiratoryFrancisella tularensisLive Vaccine Strain Infection Induces Th17 Cells and Prostaglandin E2, Which Inhibits Generation of Gamma Interferon-Positive T Cells
Authors: Woolard Matthew D. , Hensley Lucinda L. , Kawula Thomas H. , Frelinger Jeffrey A.
Published: April 2008

Two key routes ofFrancisella tularensisinfection are through the skin and airway. We wished to understand how the route of inoculation influenced the primary acute adaptive immune response. We show that an intranasal inoculation of theF. tularensislive vaccine strain (LVS) with a 1,000-fold-smaller dose than an intradermal dose results in similar growth kinetics and peak bacterial burdens. In spite of similar bacterial burdens, we demonstrate a difference in the quality, magnitude, and kinetics of the primary acute T-cell response depending on the route of inoculation. Further, we show that prostaglandin E2secretion in the lung is responsible for the difference in the gamma interferon (IFN-γ) response. Intradermal inoculation led to a large number of IFN-γ+T cells 7 days after infection in both the spleen and the lung. In contrast, intranasal inoculation induced a lower number of IFN-γ+T cells in the spleen and lung but an increased number of Th17 cells in the lung. Intranasal infection also led to a significant increase of prostaglandin E2(PGE2) in the bronchoalveolar lavage fluid. Inhibition of PGE2production with indomethacin treatment resulted in increased numbers of IFN-γ+T cells and decreased bacteremia in the lungs of intranasally inoculated mice. This research illuminates critical differences in acute adaptive immune responses between inhalational and dermal infection withF. tularensisLVS mediated by the innate immune system and PGE2.
Expression of the
Mycobacterium tuberculosis acr
-Coregulated Genes from the DevR (DosR) Regulon Is Controlled by Multiple Levels of Regulation
Authors: Vasudeva-Rao Hema M. , McDonough Kathleen A.
Published: April 2008

Little is known about how
Mycobacterium tuberculosis
regulates gene expression in response to its host environment, despite its importance as a pathogen. We previously characterized 10

a

cr
-
c
oregulated
g
enes (ACGs), all of which belong to the DevR (DosR) “dormancy” regulon, and identified one to three copies of a conserved 18-bp palindromic DNA motif in the promoter of each ACG family member. In the present study, we used base substitution analyses to assess the importance of individual motif copies and to identify additional regulatory sequences in five ACG promoters. Regulation of
acr
,
acg
, Rv2623,
narK2
, and Rv1738 was examined by using single-copy
M. tuberculosis
promoter-
lacZ
reporter constructs in
Mycobacterium bovis
BCG under conditions of ambient air versus hypoxia, each in shaking versus standing shallow culture conditions. We found that regulation of these ACG promoters is more heterogeneous than expected and is controlled at multiple levels. In addition to the positive regulation previously associated with DevR (DosR) and the 18-bp ACG motif, we identified negative regulation associated with sequences in the 5′ untranslated regions of
acg
and Rv2623 and positive regulation associated with far upstream regulatory regions of
narK2
and Rv1738. The importance of individual ACG motifs varied among the promoters examined, and Rv1738 was exceptional in that its ACG motif copies were associated with negative, rather than positive, regulation under some conditions. Further understanding of this important regulon requires the identification of additional regulators that compete and/or collaborate with DevR (DosR) to regulate its individual gene members.
Genetic Differentiation of
Escherichia coli
O157:H7 Clades Associated with Human Disease by Real-Time PCR
Authors: Riordan James T. , Viswanath Sandeep B. , Manning Shannon D. , Whittam Thomas S.
Published: April 2008

The rapid and accurate identification of
Escherichia coli
O157:H7 strains is central to reducing the impact of outbreaks. A real-time PCR-based approach to differentiating major outbreak lineages of O157 with novel single-nucleotide polymorphisms is described. The utility of this method is in detection of hypervirulent strains in cases of clinical disease.
Cleavage of Group 1 Coronavirus Spike Proteins: How Furin Cleavage Is Traded Off against Heparan Sulfate Binding upon Cell Culture Adaptation
Authors: de Haan C. A. M. , Haijema B. J. , Schellen P. , Schreur P. Wichgers , te Lintelo E. , Vennema H. , Rottier P. J. M.
Published: April 2008

A longstanding enigmatic feature of the group 1 coronaviruses is the uncleaved phenotype of their spike protein, an exceptional property among class I fusion proteins. Here, however, we show that some group 1 coronavirus spike proteins carry a furin enzyme recognition motif and can actually be cleaved, as demonstrated for a feline coronavirus. Interestingly, this feature can be lost during cell culture adaptation by a single mutation in the cleavage motif; this, however, preserves a heparan sulfate binding motif and renders infection by the virus heparan sulfate dependent. We identified a similar cell culture adaptation for the human coronavirus OC43.
Functions of the ORF9-to-ORF12 Gene Cluster in Varicella-Zoster Virus Replication and in the Pathogenesis of Skin Infection
Authors: Che Xibing , Reichelt Mike , Sommer Marvin H. , Rajamani Jaya , Zerboni Leigh , Arvin Ann M.
Published: April 2008

The gene cluster composed of varicella-zoster virus (VZV) open reading frame 9 (ORF9) to ORF12 encodes four putative tegument proteins and is highly conserved in most alphaherpesviruses. In these experiments, the genes within this cluster were deleted from the VZV parent Oka (POKA) individually or in combination, and the consequences for VZV replication were evaluated with cultured cells in vitro and with human skin xenografts in SCID mice in vivo. As has been reported for ORF10, ORF11 and ORF12 were dispensable for VZV replication in melanoma and human embryonic fibroblast cells. In contrast, deletion of ORF9 was incompatible with the recovery of infectious virus. ORF9 localized to the virion tegument and formed complexes with glycoprotein E, which is an essential protein, in VZV-infected cells. Recombinants lacking ORF10 and ORF11 (POKAΔ10/11), ORF11 and ORF12 (POKAΔ11/12), or ORF10, ORF11 and ORF12 (POKAΔ10/11/12) were viable in cultured cells. Their growth kinetics did not differ from those of POKA, and nucleocapsid formation and virion assembly were not disrupted. In addition, these deletion mutants showed no differences compared to POKA in infectivity levels for primary human tonsil T cells. Deletion of ORF12 had no effect on skin infection, whereas replication of POKAΔ11, POKAΔ10/11, and POKAΔ11/12 was severely reduced, and no virus was recovered from skin xenografts inoculated with POKAΔ10/11/12. These results indicate that with the exception of ORF9, the individual genes within the ORF9-to-ORF12 gene cluster are dispensable and can be deleted simultaneously without any apparent effect on VZV replication in vitro but that the ORF10-to-ORF12 cluster is essential for VZV virulence in skin in vivo.
Poliovirus 2A
Pro
Increases Viral mRNA and Polysome Stability Coordinately in Time with Cleavage of eIF4G
Authors: Kempf Brian J. , Barton David J.
Published: April 2008

Poliovirus (PV) 2A protease (2A
Pro
) cleaves eukaryotic initiation factors 4GI and 4GII (eIF4GI and eIF4GII) within virus-infected cells, effectively halting cap-dependent mRNA translation. PV mRNA, which does not possess a 5′ cap, is translated via cap-independent mechanisms within viral protease-modified messenger ribonucleoprotein (mRNP) complexes. In this study, we determined that 2A
Pro
activity was required for viral polysome formation and stability. 2A
Pro
cleaved eIF4GI and eIF4GII as PV polysomes assembled. A 2A
Cys109Ser
(2A
Pro
with a Cys109Ser mutation) protease active site mutation that prevented cleavage of eIF4G coordinately inhibited the de novo formation of viral polysomes, the stability of viral polysomes, and the stability of PV mRNA within polysomes. 2A
Cys109Ser
-associated defects in PV mRNA and polysome stability correlated with defects in PV mRNA translation. 3C
Pro
activity was not required for viral polysome formation or stability. 2A
Pro
-mediated cleavage of eIF4G along with poly(rC) binding protein binding to the 5′ terminus of uncapped PV mRNA appear to be concerted mechanisms that allow PV mRNA to form mRNP complexes that evade cellular mRNA degradation machinery.
Self-Assembly of Heteroarm Star Copolymers Studied by Lattice Monte Carlo Simulation
Authors: Havránková Jitka , Limpouchová Zuzana , Procházka Karel
Published: April 2008

Results of lattice Monte Carlo simulations on the self-assembly of heteroarm star copolymers in strongly selective solvents (athermal for A arms and considerably bad for B arms) are presented. The arms are modeled as the self-avoiding walks on a simple cubic lattice tethered to the point. A modified simulation algorithm and an improved recognition criterion of associated structures developed in our previous study are used. The paper is a continuation of our systematic study of heteroarm star copolymers and focuses on the effect of the ratio of numbers of soluble to insoluble arms and the distribution of A and B segments in short or long arms on the self-assembly. It confirms the predictable effect of the soluble-to-insoluble arm number ratio on the association behavior. Nevertheless, the comparison of results for different architectures with the same numbers of soluble and insoluble segments, but different lengths of soluble and insoluble arms shows a strong effect of the distribution of A and B segments in different arms.
Influence of Hatchery Smolt Releases on Adult Salmon Production and its Variability
Authors: McCarl B. A. , Rettig R. B.
Published: April 2008

Regression studies of salmon stock-recruitment relations require a priori assumptions concerning the nature of stock variability as influenced by smolt populations. Such assumptions can lead to biased estimates of the relationships of smolts to the production of adult salmon. This paper utilizes a statistical method which allows the data to determine the interrelationship of smolts and adult production mean and variability without imposing a priori restrictions on the form of such. The estimation process yields two estimated relationships — one explaining the effect of hatchery releases on expected adult production and another explaining the effects of the hatchery releases on the standard deviation of adult production. Application of this model suggests that the standard deviation of adult production increases with the square of the number of seaward migrants both for Hokkaido chum salmon (Oncorhynchus keta) and for Oregon coho salmon (O. kisutch) and that incorrect inferences may have been obtained about density dependence by other authors because of the imposed a priori assumptions and/or data adequacy.
Periphyton Biomass and Species Composition in a Coastal Rainforest Stream in British Columbia: Effects of Environmental Changes Caused by Logging
Authors: Shortreed Ken S. , Stockner John G.
Published: April 2008

Periphyton biomass, species composition, and accumulation rates on Plexiglas substrates were determined in a 6-yr study from 1974 to 1979 in Carnation Creek, Vancouver Island, B.C. During the first 2 yr of the study, the watershed was unlogged. Clearcut logging during the remainder of the study resulted in increases in light intensity of over 100% at some sites, slight increases in stream temperature (2–3 °C in summer) and increases in some dissolved ion concentrations. Phosphorus concentrations were similar throughout the study. Diatoms were the most common class of algae, and Achnanthes minutissima and Synedra rumpens were the most common diatoms. Filamentous chlorophytes (predominantly Mougeotia sp. with some Draparnaldia sp., Spirogyra sp., and Zygnema sp.) occurred sporadically throughout the study but were more common after logging, primarily as a result of increased light intensity. Although highest recorded periphyton biomass and accumulation rates occurred after logging, post-logging values were generally similar to those recorded prior to logging. We attributed this to the lack of increase in phosphorus concentrations after logging.
Population and Trophic Dynamics of Pacific hake (Merluccius productus)
Authors: Francis Robert C.
Published: April 2008

This paper explores the population and trophic dynamics of the coastal stock of Pacific hake (Merluccius productus). In particular, the biological mechanisms of growth, mortality (natural and fishing), migration, and bioenergetics are quantified in such a way that both fishery and trophic dynamics can be explored. The central focus of the analysis is an age-structured computer simulation model. Both uniform and seasonal relationships of weight on age are derived and provide markedly different estimates of trophic demands. Variable age-specific natural mortality yields cohort analysis estimates of stock biomass which correspond more closely to survey estimates than estimates based on constant natural mortality. Bioenergetic simulations indicate that both production of and consumption by hake may be considerably lower than for other similar gadoid species. The ratio of total annual production (growth and recruitment) to biomass is estimated to be 0.35 and the average annual daily consumption is estimated to be 0.4% BWD.
Sea Urchin (Strongylocentrotus droebachiensis) Aggregating Behavior Investigated by a Subtidal Multifactorial Experiment
Authors: Bernstein B. B. , Schroeter S. C. , Mann K. H.
Published: April 2008

We performed a multilevel factorial field experiment to identify the effects of five factors on sea urchins' (Strongylocentrotus droebachiensis) aggregating behavior. The factors were (1) source of urchins (kelpbed or barrens), (2) density of urchins (high or low), (3) location of treatment (kelpbed or barrens), (4) the presence and type of invertebrate predators (crabs or lobsters), and (5) season (summer or winter). These manipulative experiments were performed in flexible, resilient cages designed to withstand the severe wave surge in Nova Scotia's shallow subtidal environment. Interactions identified by ANOVA among the various factors showed that urchins aggregate more at high (20∙m−2) than at low (4∙m−2) density. The presence of lobsters in the kelpbed, and of crabs in the barrens, triggered the formation of even larger aggregations. These aggregations remain in the open even in the presence of predators. We argue that this behavioral mechanism (a defensive aggregation response to lobsters in the kelpbed) is the trigger that precipitates widespread destructive urchin grazing and the transformation of kelpbeds to barrens. Lobsters thus play two opposite roles. At low urchin density lobsters keep urchins in hiding and thereby contribute to kelpbed persistence. At higher urchin density, lobsters trigger the formation of large, exposed urchin aggregations that graze destructively on kelp. Urchin responses to predators are probably mediated by a combination of conditioning and sensitivity to biochemical cues. The large-scale change in community structure, from kelpbed to barrens, can thus be understood in terms of the adaptive behavioral responses of individual organisms. We review the roles of other predators in this system and show that they have varying effects on the intensity of urchin grazing, depending on urchin density, season, and habitat type.
Contaminant Accumulation and Physiological Response in Rainbow Trout (Salmo gairdneri) Reared on Naturally Contaminated Diets
Authors: Hilton J. W. , Hodson P. V. , Braun H. E. , Leatherland J. L. , Slinger S. J.
Published: April 2008

Juvenile rainbow trout were reared for 24 wk on practical-type diets formulated with fish meals derived from coho salmon (Oncorhynchus kisutch) taken from Lake Michigan, Lake Ontario, and the Pacific Ocean. Levels of contaminants (DDT, chlordane, dieldrin, mirex, and PCBs) increased 10-fold from control and Pacific Ocean salmon-based diets to Lake Ontario salmon-based diets. Rainbow trout accumulated contaminants in direct proportion to dietary levels. However, there were no significant differences in the final body weights, feed to gain ratios, or mortality rates of the trout reared on the different test diets. No signs of abnormal behavior or any indication of histopathological abnormalities were observed in any of the fish. There were no signs of thyroid hyperplasia or any significant decline in serum T3 or T4 levels with increasing dietary contaminant levels. Therefore, rainbow trout do not appear to have been affected by the uptake and accumulation of contaminants. However, the trout did not appear to regulate their body burden of contaminants; this ultimately could prove to be toxic and may adversely affect the ability of these fish to reproduce and survive. The final concentrations of mirex and PCBs in the Lake Ontario-fed fish exceeded the allowed limits to protect human health; therefore, fish meals produced from Lake Ontario salmon are unsuitable as a source of feed for aquaculture of rainbow trout intended for human consumption.
Geothermal Effects on Stream Benthos: Separate Influences of Thermal and Chemical Components on Periphyton and Macroinvertebrates
Authors: Lamberti Gary A. , Resh Vincent H.
Published: April 2008

Stream microcosms were used in situ to evaluate the separate effects of the thermal and chemical components of geothermal fluids from natural hot springs (which simulate accidental releases from geothermal energy developments) on benthic microorganisms and macroinvertebrates of Big Sulphur Creek, a third-order stream at The Geysers, Sonoma Co., California, USA. The thermal component of geothermal fluids had greater influence than the chemical component in determining benthic community features in Big Sulphur Creek. A natural input of geothermal fluids to Big Sulphur Creek, which elevated both temperature (by 7.5°) and chemical levels (e.g. boron by 10 times, NO3-N by 4 times, PO4-P by 2 times), increased benthic chlorophyll a by 40 times, bacterial numbers by 10 times, and macroinvertebrate density by 2 times. The stream microcosms showed that heating of nongeothermal water by 8° (i.e. thermal exposure alone) similarly increased chlorophyll a by 40 times and bacterial numbers by 2 times, but macroinvertebrate density declined by one fourth. Cooling of geothermal water by 14.5° (i.e. chemical exposure alone) reduced algal productivity but increased macroinvertebrate density by 70 times. Naturally occurring geochemical concentrations apparently can be tolerated by many aquatic organisms in Big Sulphur Creek, but changes in water temperature significantly alter benthic community structure.
Experimental study of reinforced masonry walls subjected to combined axial load and out-of-plane bendingThis article is one of a selection of papers published in this Special Issue on Masonry.
Authors: Liu Y. , Hu K.
Published: April 2008

Twelve reinforced masonry wall specimens with nominal dimensions of 2400 mm × 800 mm × 150 mm were tested under eccentric compressive loading with varying eccentricity to thickness ratios, e/t, and end eccentricity ratios, e1/e2. Pinned-pinned support conditions resulted in a slenderness ratio of 17.1 for all specimens. Test results showed that the variation of ultimate load, Pu, and effective modulus of rigidity values, EIeff, at failure depended on the type of failure mode, which was influenced by e/t and e1/e2ratios and their interaction. Comparing ultimate loads obtained by test against those calculated using the EIeffvalues from the Canadian standard CSA S304.1-04 and against the ones calculated using the EIeffvalues proposed herein indicates that, while the moment magnifier method used in the current Canadian design standard to account for secondary effects is effective, the standard underestimates EIeffvalues, especially in regions where compression-controlled failure tends to predominate and, thus, leads to a conservative design. However, the use of proposed EIeffvalues in combination with the moment magnifier method provides estimations of ultimate loads in reasonably good agreement with test results.
Shake table tests on the out-of-plane response of unreinforced masonry wallsThis article is one of a selection of papers published in this Special Issue on Masonry.
Authors: Meisl C. S. , Elwood K. J. , Ventura C. E.
Published: April 2008

Given sufficient anchorage to the diaphragms, out-of-plane walls in unreinforced masonry (URM) buildings have been shown to crack above midheight and then rock as two rigid bodies. This study investigates the sensitivity of the rocking response to the type of ground motion and the quality of the wall construction. Shake table tests were conducted on four full-scale multi-wythe walls, all with a height to thickness (h/t) ratio of 12 but of varying construction quality and subjected to three different ground motions. All walls experienced cracking at less than one half of the 2005 National Building Code of Canada (NBCC) level for Vancouver, but exhibited a stable rocking behaviour without collapse beyond a ground motion 1.5 times the 2005 NBCC level.