bluuebunny/crossref_metadata_2025 huggingface dataset:
Regularization using Monte Carlo simulation to make optimal beamformers robust to system perturbations
Authors: Bai Mingsian R. , Chen Ching-Cheng
Published: May 2014

Design of optimal beamformers that withstand system perturbations such as channel mismatch, sensor position error, and pointing error has been a key issue in real-world applications of arrays. This paper aims to characterize the array performance in relation to the random perturbations from a statistical perspective. In the synthesis stage, directivity index and front-to-back ratio are employed as the performance measures for beamformer optimization. Filter coefficients of the arrays are determined using the least-squares and convex optimization approaches using the preceding performance measures. Next, Monte Carlo sampling are conducted to simulate the stochastic system perturbations following either uniform distribution or normal distribution. Statistics including the sample mean, maximum, minimum, and the maximum likelihood (ML) of the preceding performance measures are calculated. Three regularization criteria based on max-mean, max-min, and max-ML of performance measures are proposed for choosing regularization parameters used in beamformer optimization. The max-mean criterion was found most useful to determine either a simple constant or a frequency-dependent regularization parameter. To validate the proposed methods, experiments of beam patterns and automatic speech recognition test were conducted for directional and diffuse noise suppression problems, where optimal beamformers designed with the regularization parameter selected by the preceding procedures were utilized.
Measurement and simulation of acoustic radiation force on a planar reflector
Authors: Hong Z. Y. , Zhai W. , Yan N. , Wei B.
Published: May 2014

The accurate calculation of the acoustic radiation force is important for ultrasonic application techniques. Usually, the acoustic radiation force can be divided into the near-field and the far-field force according to the ratio of the emitter-reflector distance to the wavelength. In this study, appropriate theories and methods are explored to simulate the far-field and the near-field acoustic radiation force exerted on a planar reflector. The comparison between simulation and experiment indicates that the far-field force is not sensitive to the boundary shape and size while the near-field force is highly sensitive to the boundary size. Only the acoustic model with the minimized boundary size could yield the near-field force consistent with the experiment. Further calculations reveal that the far-field force first increases and then decreases with the rise of the reflector radius, and that the near-field force fluctuates with the acoustic frequency, especially when the emitter-reflector distance is very small. The near-field repulsive force can be changed into the attractive force when the acoustic frequency is lowered.
One-way approximation for the simulation of weak shock wave propagation in atmospheric flows
Authors: Gallin Louis-Jonardan , Rénier Mathieu , Gaudard Éric , Farges Thomas , Marchiano Régis , Coulouvrat François
Published: May 2014

A numerical scheme is developed to simulate the propagation of weak acoustic shock waves in the atmosphere with no absorption. It generalizes the method previously developed for a heterogeneous medium [Dagrau, Rénier, Marchiano, and Coulouvrat, J. Acoust. Soc. Am. 130, 20–32 (2011)] to the case of a moving medium. It is based on an approximate scalar wave equation for potential, rewritten in a moving time frame, and separated into three parts: (i) the linear wave equation in a homogeneous and quiescent medium, (ii) the effects of atmospheric winds and of density and speed of sound heterogeneities, and (iii) nonlinearities. Each effect is then solved separately by an adapted method: angular spectrum for the wave equation, finite differences for the flow and heterogeneity corrections, and analytical method in time domain for nonlinearities. To keep a one-way formulation, only forward propagating waves are kept in the angular spectrum part, while a wide-angle parabolic approximation is performed on the correction terms. The numerical process is validated in the case of guided modal propagation with a shear flow. It is then applied to the case of blast wave propagation within a boundary layer flow over a flat and rigid ground.
Interpulse interval discrimination within and across channels: Comparison of monopolar and tripolar mode of stimulation
Authors: Fielden Claire A. , Kluk Karolina , McKay Colette M.
Published: May 2014

Perception of temporal patterns is crucial to speech understanding and music perception in normal hearing, and is fundamental in the design and implementation of processing strategies for cochlear implants. Two experiments described here investigated the effect of stimulation mode (monopolar versus tripolar) on interpulse interval discrimination using single-electrode stimulation (experiment 1) and dual-electrode stimulation (experiment 2). Experiment 1 required participants to discriminate stimuli containing different interpulse intervals and experiment 2 required listeners to discriminate between two dual-electrode stimuli that had the same temporal pattern on each electrode, but differed in inter-electrode timing. The hypotheses were that (i) stimulation mode would affect the ability to distinguish interpulse interval patterns on a single electrode and (ii) the electrode separation range in which subjects were sensitive to inter-electrode timing would be more restricted in tripolar than in monopolar stimulation. Results in nine cochlear implant users showed that mode did not have a significant mean effect on either the ability to discriminate interpulse intervals in single-electrode stimulation or the range of electrode separation in dual-electrode stimulation in which participants were sensitive to inter-electrode timing. In conclusion, tripolar stimulation did not show any advantage in delivering temporal information within or across channels in this group.
Modal radiation patterns of baffled circular plates and membranes
Authors: Lehrmann Christiansen Thomas , Hansen Ole , Vilain Thomsen Erik , Arendt Jensen Jørgen
Published: May 2014

The far field velocity potential and radiation pattern of baffled circular plates and membranes are found analytically using the full set of modal velocity profiles derived from the corresponding equation of motion. The derivation is valid for a plate or membrane subjected to an external excitation force, which is used as a sound receiver in any medium or as a sound transmitter in a gaseous medium. A general, concise expression is given for the radiation pattern of any mode of the membrane and the plate with arbitrary boundary conditions. Specific solutions are given for the four special cases of a plate with clamped, simply supported, and free edge boundary conditions as well as for the membrane. For all non-axisymmetric modes, the velocity potential along the axis of the radiator is found to be strictly zero. In the long wavelength limit, the radiation pattern of all axisymmetric modes approaches that of a monopole, while the non-axisymmetric modes exhibit multipole behavior. Numerical results are also given, demonstrating the implications of having non-axisymmetric excitation using both a point excitation with varying eccentricity and a homogeneous excitation acting on half of the circular radiator.
Long-term, global-scale statistics of sound propagation
Authors: Cheinet Sylvain
Published: May 2014

The near-surface sound levels emitted due to a point source show a large variability caused by sound propagation through changing meteorological conditions. To assess this variability, this study uses a numerical model of sound propagation which accounts for ground reflection, atmospheric refraction, and turbulence effects. The atmospheric inputs to the model—including turbulence—are calculated from Numerical Weather Prediction data. The method is used to investigate the relative sound levels at a range of 1.5 km from a 40 Hz sound source. The outstanding diversity of sound propagation conditions is illustrated over the globe. Over the long term, the sound propagation climates at selected sites are found to be modulated by the dominant wind regimes, the seasonal and diurnal cycles. The explored sensitivities stress the need for a careful assessment of sound scattering by turbulence and absorption by the surface.
The perceived clarity of children's speech varies as a function of their default articulation rate
Authors: Redford Melissa A.
Published: May 2014

The current study investigated whether variation in children's default articulation rate might reflect individual differences in the development of articulatory timing control, which predicts a positive correlation between rate and perceived clarity (motor skills hypothesis), or whether such variation is better attributed to speech external factors, which predicts that faster rates result in poorer target attainment (undershoot hypothesis). Two different speech samples were obtained from 54 typically developing children (5;2 – 7;11). Six utterances were extracted from each sample and measured for articulation rate and segmental duration. Fourteen adult listeners rated the utterances for clarity (enunciation). Acoustic correlates of perceived clarity, pitch, and vowel quality were also measured. The findings were that age-dependent and individual differences in children's default articulation rates were due to segmental articulation and not to suprasegmental changes. The rating data indicated that utterances produced at faster rates were perceived as more clearly articulated than those produced at slower rates, regardless of a child's age. Vowel quality measures predicted perceived clarity independently of articulation rate. Overall, the results support the motor skills hypothesis: Faster default articulation rates emerge from better articulatory timing control.
Understanding the mechanisms underlying voluntary responses to pitch-shifted auditory feedback
Authors: Patel Sona , Nishimura Cristina , Lodhavia Anjli , Korzyukov Oleg , Parkinson Amy , Robin Donald A. , Larson Charles R.
Published: May 2014

Previous research has shown that vocal errors can be simulated using a pitch perturbation technique. Two types of responses are observed when subjects are asked to ignore changes in pitch during a steady vowel production, a compensatory response countering the direction of the perceived change in pitch and a following response in the same direction as the pitch perturbation. The present study investigated the nature of these responses by asking subjects to volitionally change their voice fundamental frequency either in the opposite direction (“opposing” group) or the same direction (“following” group) as the pitch shifts (±100 cents, 1000 ms) presented during the speaker's production of an /a/ vowel. Results showed that voluntary responses that followed the stimulus directions had significantly shorter latencies (150 ms) than opposing responses (360 ms). In addition, prior to the slower voluntary opposing responses, there were short latency involuntary responses that followed the stimulus direction. These following responses may involve mechanisms of imitation or vocal shadowing of acoustical stimuli when subjects are predisposed to respond to a change in frequency of a sound. The slower opposing responses may represent a control strategy that requires monitoring and correcting for errors between the feedback signal and the intended vocal goal.
ACOUSTICAL STANDARDS NEWS
Authors: Blaeser Susan B. , Schomer Paul D.
Published: May 2014

American National Standards (ANSI Standards) developed by Accredited Standards Committees S1, S2, S3, S3/SC 1, and S12 in the areas of acoustics, mechanical vibration and shock, bioacoustics, animal bioacoustics, and noise, respectively, are published by the Acoustical Society of America (ASA). In addition to these standards, ASA publishes catalogs of Acoustical Standards, both National and International. To receive copies of the latest Standards catalogs, please contact Susan B. Blaeser.

Comments are welcomed on all material in Acoustical Standards News.

This Acoustical Standards News section in JASA, as well as the National and International catalogs of Acoustical Standards, and other information on the Standards Program of the Acoustical Society of America, are available via the ASA home page: http://acousticalsociety.org.
Vowel discrimination by hearing infants as a function of number of spectral channels
Authors: Warner-Czyz Andrea D. , Houston Derek M. , Hynan Linda S.
Published: May 2014

Reduced spectral resolution negatively impacts speech perception, particularly perception of vowels and consonant place. This study assessed impact of number of spectral channels on vowel discrimination by 6-month-old infants with normal hearing by comparing three listening conditions: Unprocessed speech, 32 channels, and 16 channels. Auditory stimuli (/ti/ and /ta/) were spectrally reduced using a noiseband vocoder and presented to infants with normal hearing via visual habituation. Results supported a significant effect of number of channels on vowel discrimination by 6-month-old infants. No differences emerged between unprocessed and 32-channel conditions in which infants looked longer during novel stimulus trials (i.e., discrimination). The 16-channel condition yielded a significantly different pattern: Infants demonstrated no significant difference in looking time to familiar vs novel stimulus trials, suggesting infants cannot discriminate /ti/ and /ta/ with only 16 channels. Results support effects of spectral resolution on vowel discrimination. Relative to published reports, young infants need more spectral detail than older children and adults to perceive spectrally degraded speech. Results have implications for development of perception by infants with hearing loss who receive auditory prostheses.
Measurement and analysis of radiated sound from a low speed fan with a large tip gap
Authors: Bilka M. J. , Anthoine J. , Schram C.
Published: May 2014

The wake flow field and radiated sound from a low speed axial fan is studied experimentally. The fan geometry uses controlled diffusion blades and is designed with a low aspect ratio (0.9). The fan is installed with a large tip gap, approximately 10% of the blade span. The radiated sound field is analyzed using a known trailing edge noise formulation. First, the model is compared to an experiment of a single airfoil in a wind tunnel to assess the predictive capabilities. Second, measurements of the fan are made at two different blade loading conditions. Hot wire measurements are made in the near wake of the fan to assess the extent of the tip leakage flow for each condition. The radiated sound fields are compared with the trailing edge noise theory. Use is made of the wake measurements as an input to a surface pressure model. When the fan is operated with the optimal blade loading, the influence of the tip leakage flow is found to be of secondary acoustic impact. When the fan is operated at a high loading condition for the blades, a more significant leakage flow develops and is found to be responsible for the dominant radiated sound.
Comparison of multimicrophone probe design and processing methods in measuring acoustic intensity
Authors: Wiederhold Curtis P. , Gee Kent L. , Blotter Jonathan D. , Sommerfeldt Scott D. , Giraud Jarom H.
Published: May 2014

Three multimicrophone probe arrangements used to measure acoustic intensity are the four-microphone regular tetrahedral, the four-microphone orthogonal, and the six-microphone designs. Finite-sum and finite-difference processing methods can be used with such probes to estimate pressure and particle velocity, respectively. A numerical analysis is performed to investigate the bias inherent in each combination of probe design and processing method. Probes consisting of matched point sensor microphones both embedded and not embedded on the surface of a rigid sphere are considered. Results are given for plane wave fields in terms of root-mean-square average bias and maximum bias as a function of angle of incidence. An experimental verification of the analysis model is described. Of the combinations considered and under the stated conditions, the orthogonal probe using the origin microphone for the pressure estimate is shown to have the lowest amount of intensity magnitude bias. Lowest intensity direction bias comes from the six-microphone probe using an average of the 15 intensity components calculated using all microphone pairs. Also discussed are how multimicrophone probes can advantageously use correction factors calculated from a numerical analysis and how the results of such an analysis depend on the chosen definition of the dimensionless frequency.
Subspace array processing using spatial time-frequency distributions: Applications for denoising structural echoes of elastic targets
Authors: Sabra Karim G. , Anderson Shaun D.
Published: May 2014

Structural echoes of underwater elastic targets, used for detection and classification purposes, can be highly localized in the time-frequency domain and can be aspect-dependent. Hence such structural echoes recorded along a distributed (synthetic) aperture, e.g., using a moving receiver platform, would not meet the stationarity and multiple snapshots requirements of common subspace array processing methods used for denoising array data based on their estimated covariance matrix. To address this issue, this article introduces a subspace array processing method based on the space-time-frequency distribution (STFD) of single-snapshots of non-stationary signals. This STFD is obtained by computing Cohen's class time-frequency distributions between all pairwise combination of the recorded signals along an arbitrary aperture array. This STFD is interpreted as a generalized array covariance matrix which automatically accounts for the inherent coherence across the time-frequency plane of the received nonstationary echoes emanating from the same target. Hence, identifying the signal's subspace from the eigenstructure of this STFD provides a means for denoising these non-stationary structural echoes by spreading the clutter and noise power in the time-frequency domain; as demonstrated here numerically and experimentally using the structural echoes of a thin steel spherical shell measured along a synthetic aperture.
Thin broadband noise absorption through acoustic reactance control by electro-mechanical coupling without sensor
Authors: Zhang Yumin , Chan Yum-Ji , Huang Lixi
Published: May 2014

Broadband noise with profound low-frequency profile is prevalent and difficult to be controlled mechanically. This study demonstrates effective broadband sound absorption by reducing the mechanical reactance of a loudspeaker using a shunt circuit through electro-mechanical coupling, which induces reactance with different signs from that of loudspeaker. An RLC shunt circuit is connected to the moving coil to provide an electrically induced mechanical impedance which counters the cavity stiffness at low frequencies and reduces the system inertia above the resonance frequency. A sound absorption coefficient well above 0.5 is demonstrated across frequencies between 150 and 1200 Hz. The performance of the proposed device is superior to existing passive absorbers of the same depth (60 mm), which has lower frequency limits of around 300 Hz. A passive noise absorber is further proposed by paralleling a micro-perforated panel with shunted loudspeaker which shows potentials in absorbing band-limit impulse noise.
Harmonic generation with a dual frequency pulse
Authors: Keravnou Christina P. , Averkiou Michalakis A.
Published: May 2014

Nonlinear imaging was implemented in commercial ultrasound systems over the last 15 years offering major advantages in many clinical applications. In this work, pulsing schemes coupled with a dual frequency pulse are presented. The pulsing schemes considered were pulse inversion, power modulation, and power modulated pulse inversion. The pulse contains a fundamental frequency f and a specified amount of its second harmonic 2f. The advantages and limitations of this method were evaluated with both acoustic measurements of harmonic generation and theoretical simulations based on the KZK equation. The use of two frequencies in a pulse results in the generation of the sum and difference frequency components in addition to the other harmonic components. While with single frequency pulses, only power modulation and power modulated pulse inversion contained odd harmonic components, with the dual frequency pulse, pulse inversion now also contains odd harmonic components.
A 2.5-dimensional method for the prediction of structure-borne low-frequency noise from concrete rail transit bridges
Authors: Li Qi , Song Xiaodong , Wu Dingjun
Published: May 2014

Predicting structure-borne noise from bridges subjected to moving trains using the three-dimensional (3D) boundary element method (BEM) is a time consuming process. This paper presents a two-and-a-half dimensional (2.5D) BEM-based procedure for simulating bridge-borne low-frequency noise with higher efficiency, yet no loss of accuracy. The two-dimensional (2D) BEM of a bridge with a constant cross section along the track direction is adopted to calculate the spatial modal acoustic transfer vectors (MATVs) of the bridge using the space-wave number transforms of its 3D modal shapes. The MATVs calculated using the 2.5D method are then validated by those computed using the 3D BEM. The bridge-borne noise is finally obtained through the MATVs and modal coordinate responses of the bridge, considering time-varying vehicle-track-bridge dynamic interaction. The presented procedure is applied to predict the sound pressure radiating from a U-shaped concrete bridge, and the computed results are compared with those obtained from field tests on Shanghai rail transit line 8. The numerical results match well with the measured results in both time and frequency domains at near-field points. Nevertheless, the computed results are smaller than the measured ones for far-field points, mainly due to the sound radiation from adjacent spans neglected in the current model.
Predicting the decay time of solid body electric guitar tones
Authors: Paté Arthur , Le Carrou Jean-Loïc , Fabre Benoît
Published: May 2014

Although it can be transformed by various electronic devices, the sound of the solid body electric guitar originates from, and is strongly linked with, the string vibration. The coupling of the string with the guitar alters its vibration and can lead to decay time inhomogeneities. This paper implements and justifies a framework for the study of decay times of electric guitar tones. Two damping mechanisms are theoretically and experimentally identified: the string intrinsic damping and the damping due to mechanical coupling with the neck of the guitar. The electromagnetic pickup is shown to not provide any additional damping to the string. The pickup is also shown to be far more sensitive to the out-of-plane polarization of the string. Finally, an accurate prediction of the decay time of electric guitar tones is made possible, whose only requirements are the knowledge of the isolated string dampings and the out-of-plane conductance at the neck of the guitar. This prediction can be of great help for instrument makers and manufacturers.
Sporadic Isolation of Sabin-Like Polioviruses and High-Level Detection of Non-Polio Enteroviruses during Sewage Surveillance in Seven Italian Cities, after Several Years of Inactivated Poliovirus Vaccination
Authors: Battistone A. , Buttinelli G. , Fiore S. , Amato C. , Bonomo P. , Patti A. M. , Vulcano A. , Barbi M. , Binda S. , Pellegrinelli L. , Tanzi M. L. , Affanni P. , Castiglia P. , Germinario C. , Mercurio P. , Cicala A. , Triassi M. , Pennino F. , Fiore L.
Published: May 2014

Sewage surveillance in seven Italian cities between 2005 and 2008, after the introduction of inactivated poliovirus vaccination (IPV) in 2002, showed rare polioviruses, none that were wild-type or circulating vaccine-derived poliovirus (cVDPV), and many other enteroviruses among 1,392 samples analyzed. Two of five polioviruses (PV) detected were Sabin-like PV2 and three PV3, based on enzyme-linked immunosorbent assay (ELISA) and PCR results. Neurovirulence-related mutations were found in the 5′ noncoding region (5′NCR) of all strains and, for a PV2, also in VP1 region 143 (Ile > Thr). Intertypic recombination in the 3D region was detected in a second PV2 (Sabin 2/Sabin 1) and a PV3 (Sabin 3/Sabin 2). The low mutation rate in VP1 for all PVs suggests limited interhuman virus passages, consistent with efficient polio immunization in Italy. Nonetheless, these findings highlight the risk of wild or Sabin poliovirus reintroduction from abroad. Non-polio enteroviruses (NPEVs) were detected, 448 of which were coxsackievirus B (CVB) and 294 of which were echoviruses (Echo). Fifty-six NPEVs failing serological typing were characterized by sequencing the VP1 region (nucleotides [nt] 2628 to 2976). A total of 448 CVB and 294 Echo strains were identified; among those strains, CVB2, CVB5, and Echo 11 predominated. Environmental CVB5 and CVB2 strains from this study showed high sequence identity with GenBank global strains. The high similarity between environmental NPEVs and clinical strains from the same areas of Italy and the same periods indicates that environmental strains reflect the viruses circulating in the population and highlights the potential risk of inefficient wastewater treatments. This study confirmed that sewage surveillance can be more sensitive than acute flaccid paralysis (AFP) surveillance in monitoring silent poliovirus circulation in the population as well as the suitability of molecular approaches to enterovirus typing.
Modulation of Endogenous Indole-3-Acetic Acid Biosynthesis in Bacteroids within Medicago sativa Nodules
Authors: Bianco C. , Senatore B. , Arbucci S. , Pieraccini G. , Defez R.
Published: May 2014

To evaluate the dose-response effects of endogenous indole-3-acetic acid (IAA) on
Medicago
plant growth and dry weight production, we increased the synthesis of IAA in both free-living and symbiosis-stage rhizobial bacteroids during
Rhizobium
-legume symbiosis. For this purpose, site-directed mutagenesis was applied to modify an 85-bp promoter sequence, driving the expression of
iaaM
and
tms2
genes for IAA biosynthesis. A positive correlation was found between the higher expression of IAA biosynthetic genes in free-living bacteria and the increased production of IAA under both free-living and symbiotic conditions. Plants nodulated by RD65 and RD66 strains, synthetizing the highest IAA concentration, showed a significant (up to 73%) increase in the shoot fresh weight and upregulation of nitrogenase gene,
nifH
, compared to plants nodulated by the wild-type strain. When these plants were analyzed by confocal microscopy, using an anti-IAA antibody, the strongest signal was observed in bacteroids of
Medicago sativa
RD66 (
Ms
-RD66) plants, even when they were located in the senescent nodule zone. We show here a simple system to modulate endogenous IAA biosynthesis in bacteria nodulating legumes suitable to investigate which is the maximum level of IAA biosynthesis, resulting in the maximal increase of plant growth.
Purine Biosynthesis, Biofilm Formation, and Persistence of an Insect-Microbe Gut Symbiosis
Authors: Kim Jiyeun Kate , Kwon Jeong Yun , Kim Soo Kyoung , Han Sang Heum , Won Yeo Jin , Lee Joon Hee , Kim Chan-Hee , Fukatsu Takema , Lee Bok Luel
Published: May 2014

The
Riptortus-Burkholderia
symbiotic system is an experimental model system for studying the molecular mechanisms of an insect-microbe gut symbiosis. When the symbiotic midgut of
Riptortus pedestris
was investigated by light and transmission electron microscopy, the lumens of the midgut crypts that harbor colonizing
Burkholderia
symbionts were occupied by an extracellular matrix consisting of polysaccharides. This observation prompted us to search for symbiont genes involved in the induction of biofilm formation and to examine whether the biofilms are necessary for the symbiont to establish a successful symbiotic association with the host. To answer these questions, we focused on
purN
and
purT
, which independently catalyze the same step of bacterial purine biosynthesis. When we disrupted
purN
and
purT
in the
Burkholderia
symbiont, the Δ
purN
and Δ
purT
mutants grew normally, and only the Δ
purT
mutant failed to form biofilms. Notably, the Δ
purT
mutant exhibited a significantly lower level of cyclic-di-GMP (c-di-GMP) than the wild type and the Δ
purN
mutant, suggesting involvement of the secondary messenger c-di-GMP in the defect of biofilm formation in the Δ
purT
mutant, which might operate via impaired purine biosynthesis. The host insects infected with the Δ
purT
mutant exhibited a lower infection density, slower growth, and lighter body weight than the host insects infected with the wild type and the Δ
purN
mutant. These results show that the function of
purT
of the gut symbiont is important for the persistence of the insect gut symbiont, suggesting the intricate biological relevance of purine biosynthesis, biofilm formation, and symbiosis.
Murein Lytic Enzyme TgaA of Bifidobacterium bifidum MIMBb75 Modulates Dendritic Cell Maturation through Its Cysteine- and Histidine-Dependent Amidohydrolase/Peptidase (CHAP) Amidase Domain
Authors: Guglielmetti Simone , Zanoni Ivan , Balzaretti Silvia , Miriani Matteo , Taverniti Valentina , De Noni Ivano , Presti Ilaria , Stuknyte Milda , Scarafoni Alessio , Arioli Stefania , Iametti Stefania , Bonomi Francesco , Mora Diego , Karp Matti , Granucci Francesca
Published: May 2014

Bifidobacteria are Gram-positive inhabitants of the human gastrointestinal tract that have evolved close interaction with their host and especially with the host's immune system. The molecular mechanisms underlying such interactions, however, are largely unidentified. In this study, we investigated the immunomodulatory potential of
Bifidobacterium bifidum
MIMBb75, a bacterium of human intestinal origin commercially used as a probiotic. Particularly, we focused our attention on TgaA, a protein expressed on the outer surface of MIMBb75's cells and homologous to other known bacterial immunoactive proteins. TgaA is a peptidoglycan lytic enzyme containing two active domains: lytic murein transglycosylase (LT) and cysteine- and histidine-dependent amidohydrolase/peptidase (CHAP). We ran immunological experiments stimulating dendritic cells (DCs) with the
B. bifidum
MIMBb75 and TgaA, with the result that both the bacterium and the protein activated DCs and triggered interleukin-2 (IL-2) production. In addition, we observed that the heterologous expression of TgaA in
Bifidobacterium longum
transferred to the bacterium the ability to induce IL-2. Subsequently, immunological experiments performed using two purified recombinant proteins corresponding to the single domains LT and CHAP demonstrated that the CHAP domain is the immune-reactive region of TgaA. Finally, we also showed that TgaA-dependent activation of DCs requires the protein CD14, marginally involves TRIF, and is independent of Toll-like receptor 4 (TLR4) and MyD88. In conclusion, our study suggests that the bacterial CHAP domain is a novel microbe-associated molecular pattern actively participating in the cross talk mechanisms between bifidobacteria and the host's immune system.
Going Wireless: Fe(III) Oxide Reduction without Pili by Geobacter sulfurreducens Strain JS-1
Authors: Smith Jessica A. , Tremblay Pier-Luc , Shrestha Pravin Malla , Snoeyenbos-West Oona L. , Franks Ashley E. , Nevin Kelly P. , Lovley Derek R.
Published: May 2014

Previous studies have suggested that the conductive pili of
Geobacter sulfurreducens
are essential for extracellular electron transfer to Fe(III) oxides and for optimal long-range electron transport through current-producing biofilms. The KN400 strain of
G. sulfurreducens
reduces poorly crystalline Fe(III) oxide more rapidly than the more extensively studied DL-1 strain. Deletion of the gene encoding PilA, the structural pilin protein, in strain KN400 inhibited Fe(III) oxide reduction. However, low rates of Fe(III) reduction were detected after extended incubation (>30 days) in the presence of Fe(III) oxide. After seven consecutive transfers, the PilA-deficient strain adapted to reduce Fe(III) oxide as fast as the wild type. Microarray, whole-genome resequencing, proteomic, and gene deletion studies indicated that this adaptation was associated with the production of larger amounts of the
c
-type cytochrome PgcA, which was released into the culture medium. It is proposed that the extracellular cytochrome acts as an electron shuttle, promoting electron transfer from the outer cell surface to Fe(III) oxides. The adapted PilA-deficient strain competed well with the wild-type strain when both were grown together on Fe(III) oxide. However, when 50% of the culture medium was replaced with fresh medium every 3 days, the wild-type strain outcompeted the adapted strain. A possible explanation for this is that the necessity to produce additional PgcA, to replace the PgcA being continually removed, put the adapted strain at a competitive disadvantage, similar to the apparent selection against electron shuttle-producing Fe(III) reducers in many anaerobic soils and sediments. Despite increased extracellular cytochrome production, the adapted PilA-deficient strain produced low levels of current, consistent with the concept that long-range electron transport through
G. sulfurreducens
biofilms is more effective via pili.
Wipes Coated with a Singlet-Oxygen-Producing Photosensitizer Are Effective against Human Influenza Virus but Not against Norovirus
Authors: Verhaelen Katharina , Bouwknegt Martijn , Rutjes Saskia , de Roda Husman Ana Maria , Duizer Erwin
Published: May 2014

Transmission of enteric and respiratory viruses, including human norovirus (hNoV) and human influenza virus, may involve surfaces. In food preparation and health care settings, surfaces are cleaned with wipes; however, wiping may not efficiently reduce contamination or may even spread viruses, increasing a potential public health risk. The virucidal properties of wipes with a singlet-oxygen-generating immobilized photosensitizer (IPS) coating were compared to those of similar but uncoated wipes (non-IPS) and of commonly used viscose wipes. Wipes were spiked with hNoV GI.4 and GII.4, murine norovirus 1 (MNV-1), human adenovirus type 5 (hAdV-5), and influenza virus H1N1 to study viral persistence. We also determined residual and transferred virus proportions on steel carriers after successively wiping a contaminated and an uncontaminated steel carrier. On IPS wipes only, influenza viruses were promptly inactivated with a 5-log
10
reduction.
D
values of infectious MNV-1 and hAdV-5 were 8.7 and 7.0 h on IPS wipes, 11.6 and 9.3 h on non-IPS wipes, and 10.2 and 8.2 h on viscose wipes, respectively. Independently of the type of wipe, dry cleaning removed, or drastically reduced, initial spot contamination of hNoV on surfaces. All wipes transferred hNoV to an uncontaminated carrier; however, the risk of continued transmission by reuse of wipes after 6 and 24 h was limited for all viruses. We conclude that cleaning wet spots with dry wipes efficiently reduced spot contamination on surfaces but that cross-contamination with noroviruses by wiping may result in an increased public health risk at high initial virus loads. For influenza virus, IPS wipes present an efficient one-step procedure for cleaning and disinfecting contaminated surfaces.
Host Responses to the Pathogen Mycobacterium avium subsp. paratuberculosis and Beneficial Microbes Exhibit Host Sex Specificity
Authors: Karunasena Enusha , McMahon K. Wyatt , Chang David , Brashears Mindy M.
Published: May 2014

Differences between microbial pathogenesis in male and female hosts are well characterized in disease conditions connected to sexual transmission. However, limited biological insight is available on variances attributed to sex specificity in host-microbe interactions, and it is most often a minimized variable outside these transmission events. In this work, we studied two gut microbes—a pathogen,Mycobacterium aviumsubsp.paratuberculosis, and a probiotic,Lactobacillus animalisNP-51—and the interaction between each agent and the male and female gastrointestinal systems. This trial was conducted in BALB/c mice (n= 5 per experimental group and per sex at a given time point), with analysis at four time points over 180 days. Host responses toM. aviumsubsp.paratuberculosisandL. animaliswere sensitive to sex. Cytokines that were significantly different (P≤ 0.05) between the sexes included interleukin-1α/β (IL-1α/β), IL-17, IL-6, IL-10, IL-12, and gamma interferon (IFN-γ) and were dependent on experimental conditions. However, granulocyte-macrophage colony-stimulating factor (GM-CSF), vascular endothelial growth factor (VEGF), and IL-13/23 showed no sex specificity. A metabolomics study indicated a 0.5- to 2.0-fold (log2scale) increase in short-chain fatty acids (butyrate and acetate) in males and greater increases ino-phosphocholine or histidine from female colon tissues; variances distinct to each sex were observed with age or long-term probiotic consumption. Two genera,StaphylococcusandRoseburia, were consistently overrepresented in females compared to males; other species were specific to one sex but fluctuated depending on experimental conditions. The differences observed suggest that male and female gut tissues and microbiota respond to newly introduced microorganisms differently and that gut-associated microorganisms with host immune system responses and metabolic activity are supported by biology distinct to the host sex.
A Large Nonconserved Region of the Tethering Protein Leashin Is Involved in Regulating the Position, Movement, and Function of Woronin Bodies in Aspergillus oryzae
Authors: Han Pei , Jin Feng Jie , Maruyama Jun-ichi , Kitamoto Katsuhiko
Published: May 2014

The Woronin body is a Pezizomycotina-specific organelle that is typically tethered to the septum, but upon hyphal wounding, it plugs the septal pore to prevent excessive cytoplasmic loss. Leashin (LAH) is a large Woronin body tethering protein that contains highly conserved N- and C-terminal regions and a long (∼2,500-amino-acid) nonconserved middle region. As the involvement of the nonconserved region in Woronin body function has not been investigated, here, we functionally characterized individual regions of the LAH protein of
Aspergillus oryzae
(AoLAH). In an
Aolah
disruptant, no Woronin bodies were tethered to the septum, and hyphae had a reduced ability to prevent excessive cytoplasmic loss upon hyphal wounding. Localization analysis revealed that the N-terminal region of AoLAH associated with Woronin bodies dependently on AoWSC, which is homologous to
Neurospora crassa
WSC (Woronin body sorting complex), and that the C-terminal region was localized to the septum. Elastic movement of Woronin bodies was observed when visualized with an AoLAH N-terminal-region–enhanced green fluorescent protein (EGFP) fusion protein. An N- and C-terminal fusion construct lacking the nonconserved middle region of AoLAH was sufficient for the tethering of Woronin bodies to the septum. However, Woronin bodies were located closer to the septum and exhibited impaired elastic movement. Moreover, expression of middle-region-deleted AoLAH in the
Aolah
disruptant did not restore the ability to prevent excessive cytoplasmic loss. These findings indicate that the nonconserved middle region of AoLAH has functional importance for regulating the position, movement, and function of Woronin bodies.
Identification and Characterization of Glycoproteins on the Spore Surface of Clostridium difficile
Authors: Strong Philippa C. R. , Fulton Kelly M. , Aubry Annie , Foote Simon , Twine Susan M. , Logan Susan M.
Published: May 2014

In this study, we identify a major spore surface protein, BclA, and provide evidence that this protein is glycosylated. Following extraction of the spore surface, solubilized proteins were separated by one-dimensional PAGE and stained with glycostain to reveal a reactive high-molecular-mass region of approximately 600 kDa. Tandem mass spectrometry analysis of in-gel digests showed this band to contain peptides corresponding to a putative exosporangial glycoprotein (BclA3) and identified a number of glycopeptides modified with multiple N-acetyl hexosamine moieties and, in some cases, capped with novel glycans. In addition, we demonstrate that the glycosyltransferase gene
sgtA
(gene CD3350 in strain 630 and CDR3194 in strain R20291), which is located immediately upstream of the
bclA3
homolog, is involved in the glycosylation of the spore surface, and is cotranscribed with
bclA3
. The presence of anti-β-O-GlcNAc-reactive material was demonstrated on the surface of spores by immunofluorescence and in surface extracts by Western blotting, although each strain produced a distinct pattern of reactivity. Reactivity of the spore surface with the anti-β-O-GlcNAc antibody was abolished in the 630 and R20291 glycosyltransferase mutant strains, while complementation with a wild-type copy of the gene restored the β-O-GlcNAc reactivity. Phenotypic testing of R20291 glycosyltransferase mutant spores revealed no significant change in sensitivity to ethanol or lysozyme. However, a change in the resistance to heat of R20291 glycosyltransferase mutant spores compared to R20291 spores was observed, as was the ability to adhere to and be internalized by macrophages.
HupB, a Nucleoid-Associated Protein of Mycobacterium tuberculosis, Is Modified by Serine/Threonine Protein Kinases
In Vivo
Authors: Gupta Meetu , Sajid Andaleeb , Sharma Kirti , Ghosh Soumitra , Arora Gunjan , Singh Ramandeep , Nagaraja Valakunja , Tandon Vibha , Singh Yogendra
Published: May 2014

HU, a widely conserved bacterial histone-like protein, regulates many genes, including those involved in stress response and virulence. Whereas ample data are available on HU-DNA communication, the knowledge on how HU perceives a signal and transmit it to DNA remains limited. In this study, we identify HupB, the HU homolog of the human pathogen
Mycobacterium tuberculosis
, as a component of serine/threonine protein kinase (STPK) signaling. HupB is extracted in its native state from the exponentially growing cells of
M. tuberculosis
H
37
Ra and is shown to be phosphorylated on both serine and threonine residues. The STPKs capable of modifying HupB are determined
in vitro
and the residues modified by the STPKs are identified for both
in vivo
and the
in vitro
proteins through mass spectrometry. Of the identified phosphosites, Thr
65
and Thr
74
in the DNA-embracing β-strand of the N-terminal domain of HupB (N-HupB) are shown to be crucial for its interaction with DNA. In addition, Arg
55
is also identified as an important residue for N-HupB–DNA interaction. N-HupB is shown to have a diminished interaction with DNA after phosphorylation. Furthermore,
hupB
is shown to be maximally expressed during the stationary phase in
M. tuberculosis
H
37
Ra, while HupB kinases were found to be constitutively expressed (PknE and PknF) or most abundant during the exponential phase (PknB). In conclusion, HupB, a DNA-binding protein, with an ability to modulate chromatin structure is proposed to work in a growth-phase-dependent manner through its phosphorylation carried out by the mycobacterial STPKs.
Acinetobacter baumannii Response to Host-Mediated Zinc Limitation Requires the Transcriptional Regulator Zur
Authors: Mortensen Brittany L. , Rathi Subodh , Chazin Walter J. , Skaar Eric P.
Published: May 2014

Acinetobacter baumannii
is a leading cause of ventilator-associated pneumonia in intensive care units, and the increasing rates of antibiotic resistance make treating these infections challenging. Consequently, there is an urgent need to develop new antimicrobials to treat
A. baumannii
infections. One potential therapeutic option is to target bacterial systems involved in maintaining appropriate metal homeostasis, processes that are critical for the growth of pathogens within the host. The
A. baumannii
inner membrane zinc transporter ZnuABC is required for growth under low-zinc conditions and for
A. baumannii
pathogenesis. The expression of
znuABC
is regulated by the transcriptional repressor Zur. To investigate the role of Zur during the
A. baumannii
response to zinc limitation, a
zur
deletion mutant was generated, and transcriptional changes were analyzed using RNA sequencing. A number of Zur-regulated genes were identified that exhibit increased expression both when
zur
is absent and under low-zinc conditions, and Zur binds to predicted Zur box sequences of several genes affected by zinc levels or the
zur
mutation. Furthermore, the
zur
mutant is impaired for growth in the presence of both high and low zinc levels compared to wild-type
A. baumannii
. Finally, the
zur
mutant exhibits a defect in dissemination in a mouse model of
A. baumannii
pneumonia, establishing zinc sensing as a critical process during
A. baumannii
infection. These results define Zur-regulated genes within
A. baumannii
and demonstrate a requirement for Zur in the
A. baumannii
response to the various zinc levels experienced within the vertebrate host.
Genetic Dissection of the
mamAB
and
mms6
Operons Reveals a Gene Set Essential for Magnetosome Biogenesis in Magnetospirillum gryphiswaldense
Authors: Lohße Anna , Borg Sarah , Raschdorf Oliver , Kolinko Isabel , Tompa Éva , Pósfai Mihály , Faivre Damien , Baumgartner Jens , Schüler Dirk
Published: May 2014

Biosynthesis of bacterial magnetosomes, which are intracellular membrane-enclosed, nanosized magnetic crystals, is controlled by a set of >30 specific genes. In
Magnetospirillum gryphiswaldense
, these are clustered mostly within a large conserved genomic magnetosome island (MAI) comprising the
mms6
,
mamGFDC
,
mamAB
, and
mamXY
operons. Here, we demonstrate that the five previously uncharacterized genes of the
mms6
operon have crucial functions in the regulation of magnetosome biomineralization that partially overlap MamF and other proteins encoded by the adjacent
mamGFDC
operon. While all other deletions resulted in size reduction, elimination of either
mms36
or
mms48
caused the synthesis of magnetite crystals larger than those in the wild type (WT). Whereas the
mms6
operon encodes accessory factors for crystal maturation, the large
mamAB
operon contains several essential and nonessential genes involved in various other steps of magnetosome biosynthesis, as shown by single deletions of all
mamAB
genes. While single deletions of
mamL
, -
P
, -
Q
, -
R
, -
B
, -
S
, -
T
, and -
U
showed phenotypes similar to those of their orthologs in a previous study in the related
M. magneticum
, we found
mamI
and
mamN
to be not required for at least rudimentary iron biomineralization in
M. gryphiswaldense
. Thus, only
mamE
, -
L
, -
M
, -
O
, -
Q
, and -
B
were essential for formation of magnetite, whereas a
mamI
mutant still biomineralized tiny particles which, however, consisted of the nonmagnetic iron oxide hematite, as shown by high-resolution transmission electron microscopy (HRTEM) and the X-ray absorption near-edge structure (XANES). Based on this and previous studies, we propose an extended model for magnetosome biosynthesis in
M. gryphiswaldense
.