bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterizing noise and perceived work environment in a neurological intensive care unit
Authors: Ryherd Erica E. , Waye Kerstin Persson , Ljungkvist Linda
Published: February 2008

The hospital sound environment is complex. Alarms, medical equipment, activities, and ventilation generate noise that may present occupational problems as well as hinder recovery among patients. In this study, sound measurements and occupant evaluations were conducted in a neurological intensive care unit. Staff completed questionnaires regarding psychological and physiological reactions to the sound environment. A-weighted equivalent, minimum, and maximum (LAeq,LAFMin,LAFMax) and C-weighted peak (LCPeak) sound pressure levels were measured over five days at patient and staff locations. Acoustical descriptors that may be explored further were investigated, including level distributions, restorative periods, and spectral content. Measurements near the patients showed average LAeq values of 53–58dB. The mean length of restorative periods (LAeq below 50dB for more than 5min) was 9 and 13min for day and night, respectively. Ninety percent of the time, the LAFMax levels exceeded 50dB and LCPeak exceeded 70dB. Dosimeters worn by the staff revealed higher noise levels. Personnel perceived the noise as contributing to stress symptoms. Compared to the majority of previous studies, this study provides a more thorough description of intensive care noise and aids in understanding how the sound environment may be disruptive to occupants.
Vibrational modes of free nanoparticles: From atomic to continuum scales
Authors: Ramirez Fernando , Heyliger Paul R. , Rappé Anthony K. , Leisure Robert G.
Published: February 2008

Vibration analysis of free standing silicon nanoparticles, with sizes ranging from 0.732 to 4.223nm, are calculated using two different methods: molecular mechanics and classical continuum elasticity. Three different geometries are studied: cubes, spheres, and tetrahedrons. Continuum mechanics methods provide good estimates of the lowest natural frequency of particles having at least 836 (R>1.5nm) and 800 (R>1.28nm) atoms for cube- and tetrahedron-shaped nanostructures, respectively. Equations for vibrational frequencies of smaller particles as a function of size are proposed. The vibrational modes obtained from both methods were practically the same for the sphere- and tetrahedron-shaped particles with a large number of atoms. However, for the cube geometry only the shape of the modes corresponding to the lowest couple of frequencies occur in the same order. In general, vibrational modes shapes obtained using both methods are the same although the order in which they appear may be shifted.
Perceptual learning of spectrally degraded speech and environmental sounds
Authors: Loebach Jeremy L. , Pisoni David B.
Published: February 2008

Adaptation to the acoustic world following cochlear implantation does not typically include formal training or extensive audiological rehabilitation. Can cochlear implant (CI) users benefit from formal training, and if so, what type of training is best? This study used a pre-/posttest design to evaluate the efficacy of training and generalization of perceptual learning in normal hearing subjects listening to CI simulations (eight-channel sinewave vocoder). Five groups of subjects were trained on words (simple/complex), sentences (meaningful/anomalous), or environmental sounds, and then were tested using an open-set identification task. Subjects were trained on only one set of materials but were tested on all stimuli. All groups showed significant improvement due to training, which successfully generalized to some, but not all stimulus materials. For easier tasks, all types of training generalized equally well. For more difficult tasks, training specificity was observed. Training on speech did not generalize to the recognition of environmental sounds; however, explicit training on environmental sounds successfully generalized to speech. These data demonstrate that the perceptual learning of degraded speech is highly context dependent and the type of training and the specific stimulus materials that a subject experiences during perceptual learning has a substantial impact on generalization to new materials.
Prediction of the sound field above a patchwork of absorbing materials
Authors: Lanoye R. , Vermeir G. , Lauriks W. , Sgard F. , Desmet W.
Published: February 2008

The aim of this paper is to investigate the acoustic performance of sound absorbing materials through a numerical wave based prediction technique. The final goal of this work is to get insight into the acoustic behavior of a combination of sound absorbing patches. In order to address a wide frequency range, a model based on the Trefftz approach is adopted. In this approach, the dynamic field variables are expressed in terms of global wave function expansions that satisfy the governing dynamic equations exactly. Therefore, approximation errors are associated only with the boundary conditions of the considered problem. This results in a computationally efficient technique. The main advantage of this method is the fact that the sound absorbing patches do not have to be locally reacting. In this article, the wave based method is described and experimentally validated for the case of normal incidence sound absorption identification in a standing wave tube. Afterwards, the method is applied to simulate some interesting setups of absorbing materials.
Across-site patterns of modulation detection in listeners with cochlear implants
Authors: Pfingst Bryan E. , Burkholder-Juhasz Rose A. , Xu Li , Thompson Catherine S.
Published: February 2008

In modern cochlear implants, much of the information required for recognition of important sounds is conveyed by temporal modulation of the charge per phase in interleaved trains of electrical pulses. In this study, modulation detection thresholds (MDTs) were used to assess listeners’ abilities to detect sinusoidal modulation of charge per phase at each available stimulation site in their 22-electrode implants. Fourteen subjects were tested. MDTs were found to be highly variable across stimulation sites in most listeners. The across-site patterns of MDTs differed considerably from subject to subject. The subject-specific patterns of across-site variability of MDTs suggest that peripheral site-specific characteristics, such as electrode placement and the number and condition of surviving neurons, play a primary role in determining modulation sensitivity. Across-site patterns of detection thresholds (T levels), maximum comfortable loudness levels (C levels) and dynamic ranges (DRs) were not consistently correlated with across-site patterns of MDTs within subjects, indicating that the mechanisms underlying across-site variation in these measures differed from those underlying across-site variation in MDTs. MDTs sampled from multiple sites in a listener’s electrode array might be useful for diagnosing across-subject differences in speech recognition with cochlear implants and for guiding strategies to improve the individual’s perception.
Numerical evaluation of tree canopy shape near noise barriers to improve downwind shielding
Authors: Van Renterghem T. , Botteldooren D.
Published: February 2008

The screen-induced refraction of sound by wind results in a reduced noise shielding for downwind receivers. Placing a row of trees behind a highway noise barrier modifies the wind field, and this was proven to be an important curing measure in previous studies. In this paper, the wind field modification by the canopy of trees near noise barriers is numerically predicted by using common quantitative tree properties. A realistic range of pressure resistance coefficients are modeled, for two wind speed profiles. As canopy shape influences vertical gradients in the horizontal component of the wind velocity, three typical shapes are simulated. A triangular crown shape, where the pressure resistance coefficient is at maximum at the bottom of the canopy and decreases linearly toward the top, is the most interesting configuration. A canopy with uniform aerodynamic properties with height behaves similarly at low wind speeds. The third crown shape that was modeled is the ellipse form, which has a worse performance than the first two types, but still gives a significant improvement compared to barriers without trees. With increasing wind speed, the optimum pressure resistance coefficient increases. Coniferous trees are more suited than deciduous trees to increase the downwind noise barrier efficiency.
Performance analysis of direct-sequence spread-spectrum underwater acoustic communications with low signal-to-noise-ratio input signals
Authors: Yang T. C. , Yang Wen-Bin
Published: February 2008

Direct-sequence spread-spectrum signals collected from the TREX04 experiment are analyzed to determine the bit-error-rate (BER) as a function of the input signal-to-noise ratio (SNR) for a single receiver. A total of 1160 packets of data are generated by adding ambient noise data collected at sea to the signal data (in postprocessing) to create signals with different input-SNR, some as low as −15dB. Two methods are analyzed in detail, both using a time-updated channel impulse-response estimate as a (matched) filter to mitigate the multipath-induced interferences. The first method requires an independent estimate of the time-varying channel impulse-response function; the second method uses the channel impulse-response estimated from the previous symbol as the matched filter. The first method yields an average BER <10−2 for input-SNR as low as −12dB and the second method yields a similar performance for input-SNR as low as −8dB. The measured BERs are modeled using the measured signal amplitude fluctuation statistics and processing gain obtained by de-spreading the received signal with the transmitted code sequence. Performance losses caused by imprecise symbol synchronization at low input-SNR, uncertainty in channel estimation, and signal fading are quantitatively modeled and compared with data.
Measurements of inner and outer streaming vortices in a standing waveguide using laser doppler velocimetry
Authors: Moreau Solenn , Bailliet Hélène , Valière Jean-Christophe
Published: February 2008

Measurements of the axial streaming velocity are performed by means of laser doppler velocimetry in an experimental apparatus consisting of a waveguide having loudspeakers at each end for high intensity sound levels. Streaming is characterized by an appropriate Reynolds number ReNL, the case ReNL⪡1 corresponding to the so-called slow streaming and the case ReNL⩾1 being referred to as fast streaming. The variation of axial streaming velocity with respect to the transverse coordinate is compared to the available slow streaming theory. Streaming fluid flow is measured both in the core region and in the near wall region. Streaming velocity in the center of the guide agrees reasonably well with the slow streaming theory for small ReNL but deviates significantly from such predictions for ReNL>20 and its evolution for further increasing ReNL is discussed. Then streaming behavior in the near wall region is particularly studied. For ReNL<70, two vortices are present across the guide section as predicted by slow streaming theory. Then it appears that, when the Reynolds number is increased, two other vortices become visible in the near wall region. Different stages for the generation and evolution of these inner streaming vortices are presented.
Stop consonant voicing and intraoral pressure contours in women and children
Authors: Koenig Laura L. , Lucero Jorge C.
Published: February 2008

Previous authors have established that stop consonant voicing is more limited in young children than adults, and have ascribed this to immature vocal-tract pressure management. Physical development relevant to speech aerodynamics continues into adolescence, suggesting that consonant voicing development may also persist into the school-age years. This study explored the relationship between stop consonant voicing and intraoral pressure contours in women, 5year olds, and 10year olds. Productions of intervocalic /p b/ were recorded from eight speakers at each age. Measures were made of stop consonant voicing and δ, a measure designed to characterize the time course of intraoral pressure increase in stops, following Müller and Brown [Speech and Language: Advances in Basic Research and Practice, edited by N. Lass (Academic, Madison, 1980), Vol. 4, pp. 318–389]. Age effects for stop consonant voicing and δ were not statistically significant, but correlations between δ and stop voicing were less often significant and sometimes reversed in the children, providing some evidence of immature aerodynamic control. The current data, as well as those of Müller and Brown, also show that the δ measure may yield some paradoxical values, indicating that more work is needed on methods of assessing time-varying characteristics of intraoral pressure.
Acoustical determination of the parameters governing thermal dissipation in porous media
Authors: Olny Xavier , Panneton Raymond
Published: February 2008

In this paper, the question of the acoustical determination of macroscopic thermal parameters used to describe heat exchanges in rigid open-cell porous media subjected to acoustical excitations is addressed. The proposed method is based on the measurement of the dynamic bulk modulus of the material, and analytical inverse solutions derived from different semiphenomenological models governing the thermal dissipation of acoustic waves in the material. Three models are considered: (1) Champoux–Allard model [J. Appl. Phys. 20, 1975–1979 (1991)] requiring knowledge of the porosity and thermal characteristic length, (2) Lafarge et al. model [J. Acoust. Soc. Am. 102, 1995–2006 (1997)] using the same parameters and the thermal permeability, and (3) Wilson model [J. Acoust. Soc. Am. 94, 1136–1145 (1993)] that requires two adjusted parameters. Except for the porosity that is obtained from direct measurement, all the other thermal parameters are derived from the analytical inversion of the models. The method is applied to three porous materials—a foam, a glass wool, and a rock wool—with very different thermal properties. It is shown that the method can be used to assess the validity of the descriptive models for a given material.
Robustness and constraints of ambient noise inversion
Authors: Arvelo Juan I.
Published: February 2008

One of the most dominant sources of error in the estimation of sonar performance in shallow water is the geoacoustic description of the sea floor. As reviewed in this paper, various investigators have studied the possible use of ambient noise to infer some key parameters such as the critical angle, geoacoustic properties, or bottom loss. A simple measurement approach to infer the bottom loss from ambient noise measurement on a vertical line array (VLA) is very attractive from environmental and operational perspectives. This paper presents a sensitivity study conducted with simulations and measurements that demonstrates mitigating factors to maximize the accuracy of estimated bottom loss. This paper quantifies the robustness and operational constraints of this measurement approach using an ambient noise model that accounts for wind, shipping, and thermal noise. Also demonstrated are the effects of unaccounted water absorption, array tilt, nearby ship interference, flow noise, calibration error, and array deformation on sonar performance estimation. VLA measurements collected during the Asian Seas International Acoustics Experiment in May-June 2001 were also processed to validate the approach via comparisons with measured bottom loss and transmission loss.
An echolocation visualization and interface system for dolphin research
Authors: Amundin Mats , Starkhammar Josefin , Evander Mikael , Almqvist Monica , Lindström Kjell , Persson Hans W.
Published: February 2008

The present study describes the development and testing of a tool for dolphin research. This tool was able to visualize the dolphin echolocation signals as well as function as an acoustically operated “touch screen.” The system consisted of a matrix of hydrophones attached to a semitransparent screen, which was lowered in front of an underwater acrylic panel in a dolphin pool. When a dolphin aimed its sonar beam at the screen, the hydrophones measured the received sound pressure levels. These hydrophone signals were then transferred to a computer where they were translated into a video image that corresponds to the dynamic sound pressure variations in the sonar beam and the location of the beam axis. There was a continuous projection of the image back onto the hydrophone matrix screen, giving the dolphin an immediate visual feedback to its sonar output. The system offers a whole new experimental methodology in dolphin research and since it is software-based, many different kinds of scientific questions can be addressed. The results were promising and motivate further development of the system and studies of sonar and cognitive abilities of dolphins.
Multifrequency ultrasound radiation force excitation and motion detection of harmonically vibrating scatterers
Authors: Urban Matthew W.
Published: February 2008

Elasticity imaging is a medical imaging modality that creates images based on the mechanical response of tissue. In some techniques, ultrasound radiation force has been used to deform tissue and ultrasonic or other techniques detect the tissue displacement. The focus of this dissertation was development of methods utilizing multiple ultrasound frequencies simultaneously to produce multifrequency harmonic radiation force and development of harmonic motion detection techniques adapted for vibrometry with simultaneous radiation force excitation. Beamforming for multifrequency radiation force was developed analytically, numerically, and experimentally. Sample applications in the fields of vibrometry and vibro-acoustic breast imaging are shown. Numerical models for harmonic motion detection of a vibrating reflective target and a vibrating scattering medium were developed. Parametric analyses were performed to extensively analyze the error in the vibration amplitude and phase measurements. An experimental method using multifrequency radiation force and harmonic motion detection with a single transducer is described and experimental results for a reflective target and scattering medium are shown. This work produced techniques for excitation and measurement of small amplitude harmonic motion for performing vibro-acoustography and vibrometry in a multiplexed manner. Models of vibration responses were developed to further understanding of current and future applications in vibro-acoustography and vibrometry.
Real-Time PCR Assays for Quantification and Differentiation of
Vibrio vulnificus
Strains in Oysters and Water
Authors: Gordon Katrina V. , Vickery Michael C. , DePaola Angelo , Staley Christopher , Harwood Valerie J.
Published: February 2008

Vibrio vulnificus
is an autochthonous estuarine bacterium and a pathogen that is frequently transmitted via raw shellfish. Septicemia can occur within 24 h; however, isolation and confirmation from water and oysters require days. Real-time PCR assays were developed to detect and differentiate two 16S rRNA variants, types A and B, which were previously associated with environmental sources and clinical fatalities, respectively. Both assays could detect 10
2
to 10
3
V. vulnificus
total cells in seeded estuarine water and in oyster homogenates. PCR assays on 11 reference
V. vulnificus
strains and 22 nontarget species gave expected results (type A or B for
V. vulnificus
and negative for nontarget species). The relationship between cell number and cycle threshold for the assays was linear (
R
2
= >0.93). The type A/B ratio of Florida clinical isolates was compared to that of isolates from oysters harvested in Florida waters. This ratio was 19:17 in clinical isolates and 5:8 (
n
= 26) in oysters harvested from restricted sites with poor water quality but was 10:1 (
n
= 22) in oysters from permitted sites with good water quality. A substantial percentage of isolates from oysters (19.4%) were type AB (both primer sets amplified), but no isolates from overlying waters were type AB. The real-time PCR assays were sensitive, specific, and quantitative in water samples and could also differentiate the strains in oysters without requiring isolation of
V. vulnificus
and may therefore be useful for rapid detection of the pathogen in shellfish and water, as well as further investigation of its population dynamics.
Rapid Growth of Planktonic
Vibrio cholerae
Non-O1/Non-O139 Strains in a Large Alkaline Lake in Austria: Dependence on Temperature and Dissolved Organic Carbon Quality
Authors: Kirschner Alexander K. T. , Schlesinger Jane , Farnleitner Andreas H. , Hornek Romana , Süß Beate , Golda Beate , Herzig Alois , Reitner Bettina
Published: February 2008

Vibrio cholerae
non-O1/non-O139 strains have caused several cases of ear, wound, and blood infections, including one lethal case of septicemia in Austria, during recent years. All of these cases had a history of local recreational activities in the large eastern Austrian lake Neusiedler See. Thus, a monitoring program was started to investigate the prevalence of
V. cholerae
strains in the lake over several years. Genetic analyses of isolated strains revealed the presence of a variety of pathogenic genes, but in no case did we detect the cholera toxin gene or the toxin-coregulated pilus gene, both of which are prerequisites for the pathogen to be able to cause cholera. In addition, experiments were performed to elucidate the preferred ecological niche of this pathogen. As size filtration experiments indicated and laboratory microcosms showed, endemic
V. cholerae
could rapidly grow in a free-living state in natural lake water at growth rates similar to those of the bulk natural bacterial population. Temperature and the quality of dissolved organic carbon had a highly significant influence on
V. cholerae
growth. Specific growth rates, growth yield, and enzyme activity decreased markedly with increasing concentrations of high-molecular-weight substances, indicating that the humic substances originating from the extensive reed belt in the lake can inhibit
V. cholerae
growth.
In Situ-Synthesized Virulence and Marker Gene Biochip for Detection of Bacterial Pathogens in Water
Authors: Miller Sarah M. , Tourlousse Dieter M. , Stedtfeld Robert D. , Baushke Samuel W. , Herzog Amanda B. , Wick Lukas M. , Rouillard Jean Marie , Gulari Erdogan , Tiedje James M. , Hashsham Syed A.
Published: February 2008

Pathogen detection tools with high reliability are needed for various applications, including food and water safety and clinical diagnostics. In this study, we designed and validated an in situ-synthesized biochip for detection of 12 microbial pathogens, including a suite of pathogens relevant to water safety. To enhance the reliability of presence/absence calls, probes were designed for multiple virulence and marker genes (VMGs) of each pathogen, and each VMG was targeted by an average of 17 probes. Hybridization of the biochip with amplicon mixtures demonstrated that 95% of the initially designed probes behaved as predicted in terms of positive/negative signals. The probes were further validated using DNA obtained from three different types of water samples and spiked with pathogen genomic DNA at decreasing relative abundance. Excellent specificity for making presence/absence calls was observed by using a cutoff of 0.5 for the positive fraction (i.e., the fraction of probes yielding a positive signal for a given VMG). A split multiplex PCR design for simultaneous amplification of the VMGs resulted in a detection limit of between 0.1 and 0.01% relative abundance, depending on the type of pathogen and the VMG. Thermodynamic analysis of the hybridization patterns obtained with DNA from the different water samples demonstrated that probes with a hybridization Gibbs free energy of approximately −19.3 kcal/mol provided the best trade-off between sensitivity and specificity. The developed biochip may be used to detect the described bacterial pathogens in water samples when parallel and specific detection is required.
Role of Migratory Birds in Introduction and Range Expansion of
Ixodes scapularis
Ticks and of
Borrelia burgdorferi
and
Anaplasma phagocytophilum
in Canada
Authors: Ogden N. H. , Lindsay L. R. , Hanincová K. , Barker I. K. , Bigras-Poulin M. , Charron D. F. , Heagy A. , Francis C. M. , O'Callaghan C. J. , Schwartz I. , Thompson R. A.
Published: February 2008

During the spring in 2005 and 2006, 39,095 northward-migrating land birds were captured at 12 bird observatories in eastern Canada to investigate the role of migratory birds in northward range expansion of Lyme borreliosis, human granulocytic anaplasmosis, and their tick vector,
Ixodes scapularis
. The prevalence of birds carrying
I. scapularis
ticks (mostly nymphs) was 0.35% (95% confidence interval [CI] = 0.30 to 0.42), but a nested study by experienced observers suggested a more realistic infestation prevalence of 2.2% (95% CI = 1.18 to 3.73). The mean infestation intensity was 1.66 per bird. Overall, 15.4% of
I. scapularis
nymphs (95% CI = 10.7 to 20.9) were PCR positive for
Borrelia burgdorferi
, but only 8% (95% CI = 3.8 to 15.1) were positive when excluding nymphs collected at Long Point, Ontario, where
B. burgdorferi
is endemic. A wide range of
ospC
and
rrs
-
rrl
intergenic spacer alleles of
B. burgdorferi
were identified in infected ticks, including those associated with disseminated Lyme disease and alleles that are rare in the northeastern United States. Overall, 0.4% (95% CI = 0.03 to 0.41) of
I. scapularis
nymphs were PCR positive for
Anaplasma phagocytophilum
. We estimate that migratory birds disperse 50 million to 175 million
I. scapularis
ticks across Canada each spring, implicating migratory birds as possibly significant in
I. scapularis
range expansion in Canada. However, infrequent larvae and the low infection prevalence in ticks carried by the birds raise questions as to how
B. burgdorferi
and
A. phagocytophilum
become endemic in any tick populations established by bird-transported ticks.
Discovery of the Autonomously Replicating Plasmid pMF1 from
Myxococcus fulvus
and Development of a Gene Cloning System in
Myxococcus xanthus
Authors: Zhao Jing-yi , Zhong Li , Shen Mei-juan , Xia Zhi-jie , Cheng Qiu-xiang , Sun Xia , Zhao Guo-ping , Li Yue-zhong , Qin Zhong-jun
Published: February 2008

Myxobacteria are very important due to their unique characteristics, such as multicellular social behavior and the production of diverse and novel bioactive secondary metabolites. However, the lack of autonomously replicating plasmids has hindered genetic manipulation of myxobacteria for decades. To determine whether indigenous plasmids are present, we screened about 150 myxobacterial strains, and a circular plasmid designated pMF1 was isolated from
Myxococcus fulvus
124B02. Sequence analysis showed that this plasmid was 18,634 bp long and had a G+C content of 68.7%. Twenty-three open reading frames were found in the plasmid, and 14 of them were not homologous to any known sequence. Plasmids containing the gene designated pMF1.14, which encodes a large unknown protein, were shown to transform
Myxococcus xanthus
DZ1 and DK1622 at high frequencies (∼10
5
CFU/μg DNA), suggesting that the locus is responsible for the autonomous replication of pMF1. Shuttle vectors were constructed for both
M. xanthus
and
Escherichia coli
. The
pilA
gene, which is essential for pilus formation and social motility in
M. xanthus
, was cloned into the shuttle vectors and introduced into the
pilA
-deficient mutant DK10410. The transformants subsequently exhibited the ability to form pili and social motility. Autonomously replicating plasmid pMF1 provides a new tool for genetic manipulation in
Myxococcus.
Enhanced Heterologous Production of Desosaminyl Macrolides and Their Hydroxylated Derivatives by Overexpression of the
pikD
Regulatory Gene in
Streptomyces venezuelae
Authors: Jung Won Seok , Jeong Soon Jeong , Park Sung Ryeol , Choi Cha Yong , Park Byoung Chul , Park Je Won , Yoon Yeo Joon
Published: February 2008

To elevate the production level of heterologous polyketide in
Streptomyces venezuelae
, an additional copy of the positive regulatory gene
pikD
was introduced into the pikromycin (Pik) polyketide synthase (PKS) deletion mutant of
S. venezuelae
ATCC 15439 expressing tylosin PKS genes. The resulting mutant strain showed enhanced production of both tylactone (TL) and desosaminyl tylactone (DesTL) of 2.7- and 17.1-fold, respectively. The notable increase in DesTL production strongly suggested that PikD upregulates the expression of the desosamine (
des
) biosynthetic gene cluster. In addition, two hydroxylated forms of DesTL were newly detected from the extract of this mutant. These hydroxylated forms presumably resulted from a PikD-dependent increase in expression of the
pikC
gene that encodes P450 hydroxylase. Gene expression analysis by reverse transcriptase PCR and bioconversion experiments of 10-deoxymethynolide, narbonolide, and TL into the corresponding desosaminyl macrolides indicated that PikD is a positive regulator of the
des
and
pikC
genes, as well as the Pik PKS genes. These results demonstrate the role of PikD as a pathway-specific positive regulator of the entire Pik biosynthetic pathway and its usefulness in the development of a host-vector system for efficient heterologous production of desosaminyl macrolides and novel hydroxylated compounds.
Characterization and Application of a Glucose-Repressible Promoter in
Francisella tularensis
Authors: Horzempa Joseph , Tarwacki Deanna M. , Carlson Paul E. , Robinson Cory M. , Nau Gerard J.
Published: February 2008

Francisella tularensis
, the causative agent of tularemia, is a category A biodefense agent. The examination of gene function in this organism is limited due to the lack of available controllable promoters. Here, we identify a promoter element of
F. tularensis
LVS that is repressed by glucose (termed the
Francisella g
lucose-
r
epressible
p
romoter, or FGRp), allowing the management of downstream gene expression. In bacteria cultured in medium lacking glucose, this promoter induced the expression of a red fluorescent protein allele,
tdtomato
. FGRp activity was used to produce antisense RNA of
iglC
, an important virulence factor, which severely reduced IglC protein levels. Cultivation in glucose-containing medium restored IglC levels, indicating the usefulness of this promoter for controlling both exogenous and chromosomal gene expression. Moreover, FGRp was shown to be active during the infection of human macrophages by using the fluorescence reporter. In this environment, the FGRp-mediated expression of antisense
iglC
by
F. tularensis
LVS resulted in reduced bacterial fitness, demonstrating the applicability of this promoter. An analysis of the genomic sequence indicated that this promoter region controls a gene, FTL_0580, encoding a hypothetical protein. A deletion analysis determined the critical sites essential for FGRp activity to be located within a 44-bp region. This is the first report of a conditional promoter and the use of antisense constructs in
F. tularensis
, valuable genetic tools for studying gene function both in vitro and in vivo.
A Ferroxidase Encoded by
FOX1
Contributes to Iron Assimilation under Conditions of Poor Iron Nutrition in
Chlamydomonas
Authors: Chen Jen-Chih , Hsieh Scott I. , Kropat Janette , Merchant Sabeeha S.
Published: February 2008

When the abundance of the
FOX1
gene product is reduced,
Chlamydomonas
cells grow poorly in iron-deficient medium, but not in iron-replete medium, suggesting that FOX1-dependent iron uptake is a high-affinity pathway. Alternative pathways for iron assimilation, such as those involving ZIP family transporters IRT1 and IRT2, may be operational.
“
Candidatus
Cloacamonas Acidaminovorans”: Genome Sequence Reconstruction Provides a First Glimpse of a New Bacterial Division
Authors: Pelletier Eric , Kreimeyer Annett , Bocs Stéphanie , Rouy Zoé , Gyapay Gábor , Chouari Rakia , Rivière Delphine , Ganesan Akila , Daegelen Patrick , Sghir Abdelghani , Cohen Georges N. , Médigue Claudine , Weissenbach Jean , Le Paslier Denis
Published: February 2008

Many microorganisms live in anaerobic environments. Most of these microorganisms have not yet been cultivated. Here, we present, from a metagenomic analysis of an anaerobic digester of a municipal wastewater treatment plant, a reconstruction of the complete genome of a bacterium belonging to the WWE1 candidate division. In silico proteome analysis indicated that this bacterium might derive most of its carbon and energy from the fermentation of amino acids, and hence, it was provisionally classified as “
Candidatus
Cloacamonas acidaminovorans.” “
Candidatus
Cloacamonas acidaminovorans” is probably a syntrophic bacterium that is present in many anaerobic digesters. This report highlights how environmental sequence data might provide genomic and functional information about a new bacterial clade whose members are involved in anaerobic digestion.
Control of Acetic Acid Fermentation by Quorum Sensing via
N
-Acylhomoserine Lactones in
Gluconacetobacter intermedius
Authors: Iida Aya , Ohnishi Yasuo , Horinouchi Sueharu
Published: February 2008

A number of gram-negative bacteria regulate gene expression in a cell density-dependent manner by quorum sensing via
N
-acylhomoserine lactones (AHLs).
Gluconacetobacter intermedius
NCI1051, a gram-negative acetic acid bacterium, produces three different AHLs,
N
-decanoyl-
l
-homoserine lactone,
N
-dodecanoyl-
l
-homoserine lactone, and an
N
-dodecanoyl-
l
-homoserine lactone with a single unsaturated bond in its acyl chain, as determined by liquid chromatography-tandem mass spectrometry. Two genes encoding an AHL synthase and a cognate regulator were cloned from strain NCI1051 and designated
ginI
and
ginR
, respectively. Disruption of
ginI
or
ginR
abolished AHL production, indicating that NCI1051 contains a single set of quorum-sensing genes. Transcriptional analysis showed that
ginI
is activated by GinR, which is consistent with the finding that there is an inverted repeat whose nucleotide sequence is similar to the sequence bound by members of the LuxR family at position −45 with respect to the transcriptional start site of
ginI
. A single gene, designated
ginA
, located just downstream of
ginI
is transcribed by read-through from the GinR-inducible
ginI
promoter. A
ginA
mutant, as well as the
ginI
and
ginR
mutants, grew more rapidly in medium containing 2% (vol/vol) ethanol and accumulated acetic acid at a higher rate with a greater final yield than parental strain NCI1051. In addition, these mutants produced larger amounts of gluconic acid than the parental strain. These data demonstrate that the GinI/GinR quorum-sensing system in
G. intermedius
controls the expression of
ginA
, which in turn represses oxidative fermentation, including acetic acid and gluconic acid fermentation.
Anthrose Biosynthetic Operon of
Bacillus anthracis
Authors: Dong Shengli , McPherson Sylvia A. , Tan Li , Chesnokova Olga N. , Turnbough Charles L. , Pritchard David G.
Published: February 2008

The exosporium of
Bacillus anthracis
spores consists of a basal layer and an external hair-like nap. The nap is composed primarily of the glycoprotein BclA, which contains a collagen-like region with multiple copies of a pentasaccharide side chain. This oligosaccharide possesses an unusual terminal sugar called anthrose, followed by three rhamnose residues and a protein-bound
N
-acetylgalactosamine. Based on the structure of anthrose, we proposed an enzymatic pathway for its biosynthesis. Examination of the
B. anthracis
genome revealed six contiguous genes that could encode the predicted anthrose biosynthetic enzymes. These genes are transcribed in the same direction and appear to form two operons. We introduced mutations into the
B. anthracis
chromosome that either delete the promoter of the putative upstream, four-gene operon or delete selected genes in both putative operons. Spores produced by strains carrying mutations in the upstream operon completely lacked or contained much less anthrose, indicating that this operon is required for anthrose biosynthesis. In contrast, inactivation of the downstream, two-gene operon did not alter anthrose content. Additional experiments confirmed the organization of the anthrose operon and indicated that it is transcribed from a σ
E
-specific promoter. Finally, we demonstrated that anthrose biosynthesis is not restricted to
B. anthracis
as previously suggested.
TOWARDS AUTOMATIC TESTING OF IMAGING SOFTWARE BY MEANS OF RANDOM AND METAMORPHIC TESTING
Authors: GUDERLEI RALPH , MAYER JOHANNES
Published: February 2008

Testing of imaging software is a challenging task, which is usually done manually. For this purpose, well-known test images are generally used whose expected output can be specified in advance or the actual result is visually inspected by the tester. In the present paper, an approach is described that allows to test imaging software fully automatically. Several random models are proposed for test data generation. Metamorphic relations are presented that can be used to generate follow-up test cases and evaluate the result. The models for test data generation and the oracle solutions are compared using mutation analysis. The presented approach is quite generally applicable in the field of imaging software.
A TRANSLATOR OF SOFTWARE ARCHITECTURE DESIGN FROM SAM TO JAVA
Authors: FU YUJIAN , DONG ZHIJIANG , HE XUDONG
Published: February 2008

A software architecture design has many benefits including aiding comprehension, supporting early analysis, and providing guidance for subsequent development activities. An additional major benefit is if a partial prototype implementation can be automatically generated from a given software architecture design. However, in the past decade less progress was made on automatically realizing software architecture designs. In this paper, we present a translator for automatically generating an implementation from a software architectural description. The implementation not only captures the functionality of the given architecture description, but also contains additional monitoring code for ensuring desirable behavior properties through runtime verification. Our method takes a software description written in SAM, a software architecture model integrating dual formal methods Petri nets and temporal logic, and generates ArchJava/Java/AspectJ code. More specifically, the structure of a SAM architecture description produces ArchJava code, the behavior models of components/connectors represented in Petri nets lead to plain Java code, and the property specifications defined in temporal logic generate AspectJ code; the above code segments are then integrated into Java code. An experimental result is provided.
ON FAVOURABLE CONDITIONS FOR ADAPTIVE RANDOM TESTING
Authors: CHEN TSONG YUEH , KUO FEI-CHING , ZHOU ZHI QUAN
Published: February 2008

Recently, adaptive random testing (ART) has been developed to enhance the fault-detection effectiveness of random testing (RT). It has been known in general that the fault-detection effectiveness of ART depends on the distribution of failure-causing inputs, yet this understanding is in coarse terms without precise details. In this paper, we conduct an in-depth investigation into the factors related to the distribution of failure-causing inputs that have an impact on the fault-detection effectiveness of ART. This paper gives a comprehensive analysis of the favourable conditions for ART. Our study contributes to the knowledge of ART and provides useful information for testers to decide when it is more cost-effective to use ART.
TWO SOLUTIONS OF THE BAHRI–CORON PROBLEM IN PUNCTURED DOMAINS VIA THE FIXED POINT TRANSFER
Authors: CLAPP MÓNICA , WETH TOBIAS
Published: February 2008

We consider the problem [Formula: see text] where Ω is a bounded smooth domain in ℝN, N ≥ 3, and [Formula: see text] is the critical Sobolev exponent. We assume that Ω is annular shaped, i.e. there are constants R2 > R1 > 0 such that {x ∈ ℝN : R1 < |x| < R2} ⊂ Ω and {x ∈ ℝN : |x| < R1}\Ω ≠ ∅. Coron [7] showed that there is one positive solution to this problem if R2/R1 is large enough. We establish the existence of at least two pairs of nontrivial solutions in this case. The proof combines a deformation argument on the Nehari manifold with cohomological information derived from Dold's fixed point transfer. To deal with the lack of compactness, an energy estimate recently proved by one of the authors is used.
VERTEX OPERATOR ALGEBRAS AND THE VERLINDE CONJECTURE
Authors: HUANG YI-ZHI
Published: February 2008

We prove the Verlinde conjecture in the following general form: Let V be a simple vertex operator algebra satisfying the following conditions: (i) V(n)= 0 for n < 0, V(0)= ℂ1 and V′ is isomorphic to V as a V-module. (ii) Every ℕ-gradable weak V-module is completely reducible. (iii) V is C2-cofinite. (In the presence of Condition (i), Conditions (ii) and (iii) are equivalent to a single condition, namely, that every weak V-module is completely reducible.) Then the matrices formed by the fusion rules among the irreducible V-modules are diagonalized by the matrix given by the action of the modular transformation τ ↦ -1/τ on the space of characters of irreducible V-modules. Using this result, we obtain the Verlinde formula for the fusion rules. We also prove that the matrix associated to the modular transformation τ ↦ -1/τ is symmetric.
SCHEME FOR QUANTUM CLONING OF AN UNKNOWN N-PARTICLE ENTANGLED STATE WITH ASSISTANCE
Authors: MA PENG-CHENG , ZHAN YOU-BANG
Published: February 2008

In this paper, we present a scheme which can realize quantum cloning of an unknown N-particle entangled state and its orthogonal complement state with assistance offered by a state preparer. The first stage of the scheme requires usual teleportation via N non-maximally entangled particle pairs as quantum channel. In the second stage of the scheme, with the assistance (through a N-particle projective measurement) of the preparer, the perfect copies and complement copies of an unknown N-particle entangled state can be obtained.
SIMULTANEOUS QUANTUM STATE TELEPORTATION VIA THE LOCKED ENTANGLEMENT CHANNEL
Authors: WANG MEIYU , YAN FENGLI , GAO TING , LI YOUCHENG
Published: February 2008

We present a simultaneous quantum state teleportation scheme, in which receivers cannot recover their quantum state separately. When they want to recover their respective quantum state, they must perform an unlocking operator together.
Nanobiotechnology and Cell Biology: Micro- and Nanofabricated Surfaces to Investigate Receptor-Mediated Signaling
Authors: Torres Alexis J. , Wu Min , Holowka David , Baird Barbara
Published: February 2008

Advances in microfabrication and nanofabrication are opening new opportunities to investigate complicated questions of cell biology in ways not before possible. In particular, the spatial regulation of cellular processes can be examined by engineering the chemical and physical environment to which the cell responds. Lithographic methods and selective chemical modification schemes can provide biocompatible surfaces that control cellular interactions on the micron and submicron scales on which cells are organized. Combined with fluorescence microscopy and other approaches of cell biology, a widely expanded toolbox is becoming available. This review illustrates the potential of these integrated engineering tools, with an emphasis on patterned surfaces, for investigating fundamental mechanisms of receptor-mediated signaling in cells. We highlight progress made with immune cells and in particular with the IgE receptor system, which has been valuable for developing technology to gain new information about spatial regulation in signaling events.
Decreased NO signaling leads to enhanced vasoconstrictor responsiveness in skeletal muscle arterioles of the ZDF rat prior to overt diabetes and hypertension
Authors: Lesniewski Lisa A. , Donato Anthony J. , Behnke Bradley J. , Woodman Christopher R. , Laughlin M. Harold , Ray Chester A. , Delp Michael D.
Published: February 2008

Approximately 40% of patients with type 2 diabetes present with concurrent hypertension at the time of diabetes diagnosis. Increases in peripheral vascular resistance and correspondingly enhanced vasoconstrictor capacity could have profound implications for the development of hypertension and the progression of insulin resistance to overt diabetes. The purpose of this study was to determine whether skeletal muscle arteriolar vasoconstrictor dysfunction precedes or occurs concurrently with the onset of diabetes and hypertension. Male Zucker diabetic fatty (ZDF) rats were studied at 7, 13, and 20 wk of age to represent prediabetic and short-term and long-term diabetic states, respectively. Conscious mean arterial pressure (MAP), fasted plasma insulin and glucose, vasoconstrictor responses, and passive mechanical properties of isolated skeletal muscle arterioles were measured in prediabetic, diabetic, and age-matched control rats. Elevated MAP was manifest in short-term diabetes (control 117 ± 1, diabetic 135 ± 3 mmHg) and persisted with long-term diabetes (control 113 ± 2, diabetic 135 ± 3 mmHg). This higher MAP was preceded by augmented arteriolar vasoconstrictor responses to norepinephrine and endothelin-1 and followed by diminished β-adrenergic vasodilation and enhanced myogenic constriction in long-term diabetes. Furthermore, we demonstrate that diminished nitric oxide (NO) signaling underlies the increases in vasoconstrictor responsiveness in arterioles from prediabetic and diabetic rats. Arteriolar stiffness was not different between control and prediabetic or diabetic rats at any time point studied. Collectively, these results indicate that increases in vasoconstrictor responsiveness resulting from diminished NO signaling in skeletal muscle arterioles precede the development of diabetes and hypertension in ZDF rats.
Key role of α1β1-integrin in the activation of PI3-kinase-Akt by flow (shear stress) in resistance arteries
Authors: Loufrani Laurent , Retailleau Kevin , Bocquet Arnaud , Dumont Odile , Danker Kerstin , Louis Huguette , Lacolley Patrick , Henrion Daniel
Published: February 2008

Resistance arteries are the site of the earliest manifestations of many cardiovascular and metabolic diseases. Flow (shear stress) is the main physiological stimulus for the endothelium through the activation of vasodilatory pathways generating flow-mediated dilation (FMD). The role of FMD in local blood flow control and angiogenesis is well established, and alterations in FMD are early markers of cardiovascular disorders. α1-Integrin, which has a role in angiogenesis, could be involved in FMD. FMD was studied in mesenteric resistance arteries (MRA) isolated in arteriographs. The role of α1-integrins in FMD was tested with selective antibodies and mice lacking the gene encoding for α1-integrins. Both anti-α1blocking antibodies and genetic deficiency in α1-integrin in mice (α1−/−) inhibited FMD without affecting receptor-mediated (acetylcholine) endothelium-dependent dilation or endothelium-independent dilation (sodium nitroprusside). Similarly, vasoconstrictor tone (myogenic tone and phenylephrine-induced contraction) was not affected. In MRA phosphorylated Akt and phosphatidylinositol 3-kinase (PI3-kinase) were significantly lower in α1−/−mice than in α1+/+mice, although total Akt and endothelial nitric oxide synthase (eNOS) were not affected. Pharmacological blockade of PI3-kinase-Akt pathway with LY-294002 inhibited FMD. This inhibitory effect of LY-294002 was significantly lower in α1−/−mice than in α1+/+mice. Thus α1-integrin has a key role in flow (shear stress)-dependent vasodilation in resistance arteries by transmitting the signal to eNOS through activation of PI3-kinase and Akt. Because of the central role of flow (shear stress) activation of the endothelium in vascular disorders, this finding opens new perspectives in the pathophysiology of the microcirculation and provides new therapeutic targets.