bluuebunny/crossref_metadata_2025 huggingface dataset:
State-Dependent Delay Influenced Drill-String Oscillations and Stability Analysis
Authors: Liu Xianbo , Vlajic Nicholas , Long Xinhua , Meng Guang , Balachandran Balakumar
Published: July 2014

In this paper, the authors present a discrete system model to study the coupled axial–torsional dynamics of a drill string. The model is developed taking into account state-dependent time delay and nonlinearities due to dry friction and loss of contact. Simulations are carried out by using a 32-segment model with 128 states. Bit bounce is observed through time histories of axial vibrations, while stick-slip phenomenon is noted in the torsion response. The normal strain contours of this spatial–temporal system demonstrate the existence of strain wave propagation along the drill string. The shear strain wave exhibits features of wave nodes and wave loops along the drill string, which indicate that the torsional motion has the properties of a standing wave. When the penetration rate is varied, qualitative changes are observed in the system response. The observed behavior includes chaotic and hyperchaotic dynamics. Stability analysis reveals a stable region for the degenerate one-segment model. This stable region becomes infinitesimally small, as the resolution of spatial discretization is increased. This finding suggests that drill-string motions have a high likelihood of being self-exited in practical drilling operations.
Control-Oriented Gas Exchange Model for Diesel Engines Utilizing Variable Intake Valve Actuation
Authors: Kocher Lyle , Koeberlein Ed , Stricker Karla , Van Alstine D. G. , Shaver Greg
Published: July 2014

Modeling and control of the gas exchange process in modern diesel engines is critical for the promotion and control of advanced combustion strategies. However, most modeling efforts to date use complex stand-alone simulation packages that are not easily integrated into, or amenable for the synthesis of, engine control systems. Simpler control-oriented models have been developed; however, in many cases, they do not directly capture the complete dynamic interaction of air handling system components and flows in multicylinder diesel engines with variable geometry turbocharging (VGT), high pressure exhaust gas recirculation (EGR), and flexible intake valve actuation. Flexibility in the valvetrain directly impacts the gas exchange process not only through the effect on volumetric efficiency but also through the combustion process and resulting exhaust gas enthalpy utilized to drive the turbomachinery. This paper describes a low-order, five state model of the air handling system for a multicylinder variable geometry turbocharged diesel engine with cooled EGR and flexible intake valve actuation, validated against 286 steady state and 62 transient engine operating points. The model utilizes engine speed, engine fueling, EGR valve position, VGT nozzle position, and intake valve closing (IVC) time as inputs to the model. The model outputs include calculation of the engine flows as well as the exhaust temperature exiting the cylinders. The gas exchange model captures the dynamic effects of the not only the standard air handling actuators (EGR valve position and VGT position) but also IVC timing, exercised over their useful operating ranges. The model's capabilities are enabled through the use of analytical functions to describe the performance of the turbocharger, eliminating the need to use look-up maps; a physically based control-oriented exhaust gas enthalpy submodel and a physically based volumetric efficiency submodel.
On the Modeling of Steam Methane Reforming
Authors: Mokheimer Esmail M. A. , Ibrar Hussain Muhammad , Ahmed Shakeel , Habib Mohamed A. , Al-Qutub Amro A.
Published: July 2014

Modeling and simulations of steam methane reforming (SMR) process to produce hydrogen and/or syngas are presented in this article. The reduced computational time with high model validity is the main concern in this study. A volume based reaction model is used, instead of surface based model, with careful estimation of mixture's physical properties. The developed model is validated against the reported experimental data and model accuracy as high as 99.75% is achieved. The model is further used to study the effect of different operating parameters on the steam and methane conversion. General behaviors of the reaction are obtained and discussed. The results showed that increasing the conversion thermodynamic limits with the decrease of the pressure results in a need for long reformers so as to achieve the associated fuel reforming thermodynamics limit. It is also shown that not only increasing the steam to methane molar ratio is favorable for higher methane conversion but the way the ratio is changed also matters to a considerable extent.
Numerical Simulation of Aerodynamic Instabilities in a Multistage High-Speed High-Pressure Compressor on Its Test-Rig—Part I: Rotating Stall
Authors: Crevel Flore , Gourdain Nicolas , Moreau Stéphane
Published: July 2014

Aerodynamic instabilities such as stall and surge may lead to mechanical failures. They can be avoided by better understanding and accurate prediction of the associated flow phenomena. Numerical simulations of rotating stall do not often match well the experiments as the number of cells and/or their rotational speed are not correctly predicted. The volumes surrounding the compressor have known effects on rotating stall flow patterns; therefore, an increased need for more realistic simulations has emerged. In that context, this paper addresses a comparison of numerical stall simulation in a compressor alone with a numerical stall simulation including the additional compressor rig. This study investigates the influence of the upstream and downstream volumes of the compressor rig on the rotating stall flow patterns and the consequences on surge inception in a high-pressure, high-speed research compressor. The numerical simulations were conducted using an implicit, time-accurate, 3D compressible Reynolds-averaged Navier–Stokes (URANS) solver. First, rotating stall is simulated in both configurations, and then the outlet nozzles are further closed to bring the compressors to surge. The numerical results show that when the compressor rig is accounted for, fewer cells develop in the third stage and their rotational speed is slightly higher. The major difference linked to the presence of the rig lays in the existence of a 1D low frequency oscillation of the static pressure, which affects the entire flow and modifies surge inception. The analysis of the results leads to a calculation of the thermo-acoustic modes in the whole configuration, which shows that this low frequency corresponds to the third thermo-acoustic mode of the complete test-rig.
MEMS-Scale Turbomachinery Based Vacuum Roughing Pump
Authors: Gannon Anthony J. , Hobson Garth V. , Shea Michael J. , Clay Christopher S. , Millsaps Knox T.
Published: July 2014

This study forms part of a program to develop a micro-electro-mechanical systems (MEMS) scale turbomachinery based vacuum pump and investigates the roughing portion of such a system. Such a machine would have many radial stages with the exhaust stages operating near atmospheric conditions while the inlet stages operate at near vacuum conditions. In low vacuum such as those to the inlet of a roughing pump, the flow can still be treated as a continuum; however, the no-slip boundary condition is not accurate. The Knudsen number becomes a dominant nondimensional parameter in these machines due to their small size and low pressures. As the Knudsen number increases, slip-flow becomes present at the walls. The study begins with a basic overview on implementing the slip wall boundary condition in a commercial code by specifying the wall shear stress based on the mean-free-path of the gas molecules. This is validated against an available micro-Poiseuille classical solution at Knudsen numbers between 0.001 and 0.1 with reasonable agreement found. The method of specifying the wall shear stress is then applied to a generic MEMS scale roughing pump stage that consists of two stators and a rotor operating at a nominal absolute pressure of 500 Pa. The zero flow case was simulated in all cases as the pump down time for these machines is small due to the small volume being evacuated. Initial transient two-dimensional (2D) simulations are used to evaluate three boundary conditions, classical no-slip, specified-shear, and slip-flow. It is found that the stage pressure rise increased as the flow began to slip at the walls. In addition, it was found that at lower pressures the pure slip boundary condition resulted in very similar predictions to the specified-shear simulations. As the specified-shear simulations are computationally expensive it is reasonable to use slip-flow boundary conditions. This approach was used to perform three-dimensional (3D) simulations of the stage. Again the stage pressure increased when slip-flow was present compared with the classical no-slip boundaries. A characteristic of MEMS scale turbomachinery are the large relative tip gaps requiring 3D simulations. A tip gap sensitivity study was performed and it was found that when no-slip boundaries were present the pressure ratio increased significantly with decreasing tip gap. When slip-flow boundaries were present, this relationship was far weaker.
Time-domain simulation of flute-like instruments: Comparison of jet-drive and discrete-vortex models
Authors: Auvray Roman , Ernoult Augustin , Fabre Benoît , Lagrée Pierre-Yves
Published: July 2014

This paper presents two models of sound production in flute-like instruments that allow time-domain simulations. The models are based on different descriptions of the jet flow within the window of the instrument. The jet-drive model depicts the jet by its transverse perturbation that interacts with the labium to produce sound. The discrete-vortex model depicts the jet as two independent shear layers along which vortices are convected and interact with the acoustic field within the window. The limit of validity between both models is usually discussed according to the aspect ratio of the jet W/h, with W the window length and h the flue channel height. The present simulations, compared with experimental data gathered on a recorder, allow to extend the aspect ratio criterion to the notion of dynamic aspect ratio defined as λ/h where λ is the hydrodynamic wavelength that now accounts for geometrical properties, such as W/h, as well as for dynamic properties, such as the Strouhal number. The two models are found to be applicable over neighboring values of geometry and blowing pressure.
Intonation in unaccompanied singing: Accuracy, drift, and a model of reference pitch memory
Authors: Mauch Matthias , Frieler Klaus , Dixon Simon
Published: July 2014

This paper presents a study on intonation and intonation drift in unaccompanied singing, and proposes a simple model of reference pitch memory that accounts for many of the effects observed. Singing experiments were conducted with 24 singers of varying ability under three conditions (Normal, Masked, Imagined). Over the duration of a recording, ∼50 s, a median absolute intonation drift of 11 cents was observed. While smaller than the median note error (19 cents), drift was significant in 22% of recordings. Drift magnitude did not correlate with other measures of singing accuracy, singing experience, or the presence of conditions tested. Furthermore, it is shown that neither a static intonation memory model nor a memoryless interval-based intonation model can account for the accuracy and drift behavior observed. The proposed causal model provides a better explanation as it treats the reference pitch as a changing latent variable.
Acoustic scattering from a water-filled cylindrical shell: Measurements, modeling, and interpretation
Authors: España Aubrey L. , Williams Kevin L. , Plotnick Daniel S. , Marston Philip L.
Published: July 2014

Understanding the physics governing the interaction of sound with targets in an underwater environment is essential to improving existing target detection and classification algorithms. To illustrate techniques for identifying the key physics, an examination is made of the acoustic scattering from a water-filled cylindrical shell. Experiments were conducted that measured the acoustic scattering from a water-filled cylindrical shell in the free field, as well as proud on a sand-water interface. Two modeling techniques are employed to examine these acoustic scattering measurements. The first is a hybrid 2-D/3-D finite element (FE) model, whereby the scattering in close proximity to the target is handled via a 2-D axisymmetric FE model, and the subsequent 3-D propagation to the far field is determined via a Helmholtz integral. This model is characterized by the decomposition of the fluid pressure and its derivative in a series of azimuthal Fourier modes. The second is an analytical solution for an infinitely long cylindrical shell, coupled with a simple approximation that converts the results to an analogous finite length form function. Examining these model results on a mode-by-mode basis offers easy visualization of the mode dynamics and helps distinguish the different physics driving the target response.
Ranging bowhead whale calls in a shallow-water dispersive waveguide
Authors: Abadi Shima H. , Thode Aaron M. , Blackwell Susanna B. , Dowling David R.
Published: July 2014

This paper presents the performance of three methods for estimating the range of broadband (50–500 Hz) bowhead whale calls in a nominally 55-m-deep waveguide: Conventional mode filtering (CMF), synthetic time reversal (STR), and triangulation. The first two methods use a linear vertical array to exploit dispersive propagation effects in the underwater sound channel. The triangulation technique used here, while requiring no knowledge about the propagation environment, relies on a distributed array of directional autonomous seafloor acoustics recorders (DASARs) arranged in triangular grid with 7 km spacing. This study uses simulations and acoustic data collected in 2010 from coastal waters near Kaktovik, Alaska. At that time, a 12-element vertical array, spanning the bottom 63% of the water column, was deployed alongside a distributed array of seven DASARs. The estimated call location-to-array ranges determined from CMF and STR are compared with DASAR triangulation results for 19 whale calls. The vertical-array ranging results are generally within ±10% of the DASAR results with the STR results providing slightly better agreement. The results also indicate that the vertical array can range calls over larger ranges and with greater precision than the particular distributed array discussed here, whenever the call locations are beyond the distributed array boundaries.
Echo statistics of individual and aggregations of scatterers in the water column of a random, oceanic waveguide
Authors: Jones Benjamin A. , Colosi John A. , Stanton Timothy K.
Published: July 2014

The relative contributions of various physical factors to producing non-Rayleigh distributions of echo magnitudes in a waveguide are examined. Factors that are considered include (1) a stochastic, range-dependent sound-speed profile, (2) a directional acoustic source, (3) a variable scattering response, and (4) an extended scattering volume. A two-way parabolic equation model, coupled with a stochastic internal wave model, produces realistic simulations of acoustic propagation through a complex oceanic sound speed field. Simulations are conducted for a single frequency (3 kHz), monostatic sonar with a narrow beam (5° −3 dB beam width). The randomization of the waveguide, range of propagation, directionality of the sonar, and spatial extent of the scatterers each contribute to the degree to which the echo statistics are non-Rayleigh. Of critical importance are the deterministic and stochastic processes that induce multipath and drive the one-way acoustic pressure field to saturation (i.e., complex-Gaussian statistics). In this limit predictable statistics of echo envelopes are obtained at all ranges. A computationally low-budget phasor summation can successfully predict the probability density functions when the beam pattern and number of scatterers ensonified are known quantities.
Assessing the horizontal refraction of ocean acoustic tomography signals using high-resolution ocean state estimates
Authors: Dushaw Brian D.
Published: July 2014

The analysis of signals for acoustic tomography sent between a source and a receiver most often uses the unrefracted geodesic path, an approximation that is justified from theoretical considerations, relying on estimates of horizontal gradients of sound speed, or on simple theoretical models. To quantify the effects of horizontal refraction caused by a realistic ocean environment, horizontal refractions of long-range signals were computed using global ocean state estimates for 2004 from the Estimating the Circulation and Climate of the Ocean (ECCO2) project. Basin-scale paths in the eastern North Pacific Ocean and regional-scale paths in the Philippine Sea were used as examples. At O(5 Mm) basin scales, refracted geodesic and geodesic paths differed by only about 5 km. Gyre-scale features had the greatest refractive influence, but the precise refractive effects depended on the path geometry with respect to oceanographic features. Refraction decreased travel times by 5–10 ms and changed azimuthal angles by about 0.2°. At O(500 km) regional scales, paths deviated from the geodesic by only 250 m, and travel times deviated by less than 0.5 ms. Such effects are of little consequence in the analysis of tomographic data. Refraction details depend only slightly on mode number and frequency.
An efficient probabilistic approach to vibro-acoustic analysis based on the Gaussian orthogonal ensemble
Authors: Reynders Edwin , Legault Julien , Langley Robin S.
Published: July 2014

Vibro-acoustic analysis of complex systems at higher frequencies faces two challenges: how to compute the response without using an excessive number of degrees of freedom (DOFs), and how to quantify the uncertainty of the response due to small spatial variations in geometry, material properties, and boundary conditions, which have a wave scattering effect? In this study, a general method of analysis is presented that provides an answer to both questions while overcoming most limitations of statistical energy analysis. The fundamental idea is to numerically compute an artificial ensemble of realizations for the components of the built-up system that are highly sensitive to small random wave scatterers. This can be efficiently performed because their eigenvalue spacings and mode shapes conform to Gaussian orthogonal ensemble spacings and Gaussian random fields, respectively. The DOFs of the overall system are therefore limited to those of the deterministic components and the interface DOFs of the random components. The method is extensively validated by application to plate structures. Good agreement between the predicted response probability distributions and the results of detailed parametric probabilistic models is obtained, also for cases of low modal overlap, single point loading, and strong subsystem coupling.
Range estimation of bowhead whale (Balaena mysticetus) calls in the Arctic using a single hydrophone
Authors: Bonnel Julien , Thode Aaron M. , Blackwell Susanna B. , Kim Katherine , Michael Macrander A.
Published: July 2014

Bowhead whales generate low-frequency calls in shallow-water Arctic environments, whose dispersive propagation characteristics are well modeled by normal mode theory. As each mode propagates with a different group speed, a call's range can be inferred by the relative time-frequency dispersion of the modal arrivals. Traditionally, at close ranges modal arrivals are separated using synchronized hydrophone arrays. Here a nonlinear signal processing method called “warping” is used to filter the modes on just a single hydrophone. The filtering works even at relatively short source ranges, where distinct modal arrivals are not separable in a conventional spectrogram. However, this warping technique is limited to signals with monotonically increasing or decreasing frequency modulations, a relatively common situation for bowhead calls. Once modal arrivals have been separated, the source range can be estimated using conventional modal dispersion techniques, with the original source signal structure being recovered as a by-product. Twelve bowhead whale vocalizations recorded near Kaktovik (Alaska) in 2010, with signal-to-noise ratios between 6 and 23 dB, are analyzed, and the resulting single-receiver range estimates are consistent with those obtained independently via triangulation from widely-distributed vector sensor arrays. Geoacoustic inversions for each call are necessary in order to obtain the correct ranges.
Compressive beamforming
Authors: Xenaki Angeliki , Gerstoft Peter , Mosegaard Klaus
Published: July 2014

Sound source localization with sensor arrays involves the estimation of the direction-of-arrival (DOA) from a limited number of observations. Compressive sensing (CS) solves such underdetermined problems achieving sparsity, thus improved resolution, and can be solved efficiently with convex optimization. The DOA estimation problem is formulated in the CS framework and it is shown that CS has superior performance compared to traditional DOA estimation methods especially under challenging scenarios such as coherent arrivals and single-snapshot data. An offset and resolution analysis is performed to indicate the limitations of CS. It is shown that the limitations are related to the beampattern, thus can be predicted. The high-resolution capabilities and the robustness of CS are demonstrated on experimental array data from ocean acoustic measurements for source tracking with single-snapshot data.
From acoustic descriptors to evoked quality of car door sounds
Authors: Bezat Marie-Céline , Kronland-Martinet Richard , Roussarie Vincent , Ystad Sølvi
Published: July 2014

This article describes the first part of a study aiming at adapting the mechanical car door construction to the drivers' expectancies in terms of perceived quality of cars deduced from car door sounds. A perceptual cartography of car door sounds is obtained from various listening tests aiming at revealing both ecological and analytical properties linked to evoked car quality. In the first test naive listeners performed absolute evaluations of five ecological properties (i.e., solidity, quality, weight, closure energy, and success of closure). Then experts in the area of automobile doors categorized the sounds according to organic constituents (lock, joints, door panel), in particular whether or not the lock mechanism could be perceived. Further, a sensory panel of naive listeners identified sensory descriptors such as classical descriptors or onomatopoeia that characterize the sounds, hereby providing an analytic description of the sounds. Finally, acoustic descriptors were calculated after decomposition of the signal into a lock and a closure component by the Empirical Mode Decomposition (EMD) method. A statistical relationship between the acoustic descriptors and the perceptual evaluations of the car door sounds could then be obtained through linear regression analysis.
Insertion losses of balconies on a building façade and the underlying wave interactions
Authors: Tang S. K. , Ho C. Y. , Tso T. Y.
Published: July 2014

This study used scale model experiments to investigate the insertion losses of balconies on a building façade in the presence of ground reflections. The experiments measured both A-weighted broad- and narrowband insertion loss spectra. The underlying wave interactions/interferences and their couplings with and without reflections from the balcony ceilings were also examined in detail, and these findings were related to the dimensions and elevations of the balconies. The findings indicate that the ground and ceiling reflections and their interferences with the direct sound play very important roles in shaping the frequency characteristics of the insertion losses. Strong sound attenuation can be attained with a carefully designed geometry and acoustical properties of the balcony and the balcony ceiling.
Time-domain effects of rigid sphere scattering on measurement of transient plane waves
Authors: Muhlestein Michael B. , Thomas Derek C. , Gee Kent L.
Published: July 2014

Transient waves, like all other acoustic waves, will diffract around solid objects, such as measurement instrumentation. A derivation of an impulse response function on the surface of a rigid sphere, based on linear, classical scattering theory, is presented. The theoretical impulse response function is validated using an experiment with blast noise. An application of the impulse response function to a rocket noise measurement is discussed. The impulse response function shows that the presence of the rigid sphere significantly affects the measurement and estimation of rocket-noise waveforms, power spectral densities, and statistical measures.
On the fluid-structure interaction in the cochlea
Authors: Rapson Michael J. , Hamilton Tara J. , Tapson Jonathan C.
Published: July 2014

The cochlea is known to be a nonlinear system that shows strong fluid-structure coupling. In this work, the monolithic state space approach to cochlear modeling [Rapson et al., J. Acoust. Soc. Am. 131, 3925–3952 (2012)] is used to study the inherent nature of this coupling. Mathematical derivations requiring minimal, widely accepted assumptions about cochlear anatomy provide a clear description of the coupling. In particular, the coupling forces between neighboring cochlear partition segments are demonstrated, with implications for theories of cochlear operation that discount the traveling wave hypothesis. The derivations also reaffirm the importance of selecting a physiologically accurate value for the partition mass in any simulation. Numerical results show that considering the fluid properties in isolation can give a misleading impression of the fluid-structure coupling. Linearization of a nonlinear partition model allows the relationship between the linear and nonlinear fluid-structure interaction to be described. Furthermore, the effect of different classes of nonlinearities on the numerical complexity of a cochlear model is assessed. Cochlear models that assume outer hair cells are able to detect pressure will require implicit solver strategies, should the pressure sensitivity be demonstrated. Classical cochlear models in general do not require implicit solver strategies.
ACOUSTICAL STANDARDS NEWS
Authors: Blaeser Susan B. , Schomer Paul D.
Published: July 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.
On the rhythm of infant- versus adult-directed speech in Australian English
Authors: Lee Christopher S. , Kitamura Christine , Burnham Denis , McAngus Todd Neil P.
Published: July 2014

The findings are reported of an investigation into rhythmic differences between infant-directed speech (IDS) and adult-directed speech (ADS) in a corpus of utterances from Australian English mothers speaking to their infants and to another adult. Given the importance of rhythmic cues to stress and word-segmentation in English, the investigation focused on the extent to which IDS makes such cues salient. Two methods of analysis were used: one focused on segmental durational properties, using a variety of durational measures; the other focused on the prominence of vocalic/sonorant segments, as determined by their duration, intensity, pitch, and spectral balance, using individual measures as well as composite measures of prominence derived from auditory-model analyses. There were few IDS/ADS differences/trends on the individual measures, though mean pitch and pitch variability were higher in IDS than ADS, while IDS vowels showed more negative spectral tilt. However, the model-based analyses suggested that differences in the prominence of vowels/sonorant segments were reduced in IDS, with further analysis suggesting that pitch contributed little to prominence. The reduction in prominence contrasts may be due to the importance of mood-regulation in speech to young infants, and may suggest that infants rely on segmental cues to stress and word-segmentation.
De novo formation of a distinct coronary vascular population in neonatal heart
Authors: Tian Xueying , Hu Tianyuan , Zhang Hui , He Lingjuan , Huang Xiuzhen , Liu Qiaozhen , Yu Wei , He Liang , Yang Zhen , Yan Yan , Yang Xiao , Zhong Tao P. , Pu William T. , Zhou Bin
Published: July 2014

The heart needs blood vessels, too

For the newborn heart to grow quickly, the heart's own blood vessels must grow as well. Researchers have assumed that preexisting fetal coronary vessels expand to cause this postnatal coronary vascular growth. Instead, Tian
et al.
now show that, for the most part, brandnew blood vessels form within the neonatal heart (see the Perspective by Burns and Burns). This ability to produce new coronary blood vessels after birth may one day help researchers work out how to promote cardiovascular regeneration after injury or disease.

Science
, this issue p.
90
; see also p.
28
Shaking up volcanoes
Authors: Prejean Stephanie G. , Haney Matthew M.
Published: July 2014

Data from a Japanese seismic network elucidate how large earthquakes may disrupt volcanic systems.

[Also see Report by

Brenguier
et al.

]
A crowning achievement for deciphering coronary origins
Authors: Burns C. Geoffrey , Burns Caroline E.
Published: July 2014

Postnatal maturation of the heart spurs coronary vessel development from an unanticipated source.

[Also see Report by

Tian
et al.

]
Raising the bar
Authors: McNutt Marcia
Published: July 2014

Numbers. Lots and lots of numbers. It is hard to find a paper published in
Science
or any other journal that is not full of numbers. Interpretation of those numbers provides the basis for the conclusions, as well as an assessment of the confidence in those conclusions. But unfortunately, there have been far too many cases where the quantitative analysis of those numbers has been flawed, causing doubt about the authors' interpretation and uncertainty about the result. Furthermore, it is not realistic to expect that a technical reviewer, chosen for her or his expertise in the topical subject matter or experimental protocol, will also be an expert in data analysis. For that reason, with much help from the American Statistical Association,
Science
has established, effective 1 July 2014, a Statistical Board of Reviewing Editors (SBoRE), consisting of experts in various aspects of statistics and data analysis, to provide better oversight of the interpretation of observational data.
High hopes
Authors: Kupferschmidt Kai
Published: July 2014

Psychedelic drugs fell from grace in the 1960s. Now, scientists are rediscovering them as potential treatments for a range of illnesses.
Schistosoma mansoni Soluble Egg Antigens Enhance Listeria monocytogenes Vector HIV-1 Vaccine Induction of Cytotoxic T Cells
Authors: Bui Cac T. , Shollenberger Lisa M. , Paterson Yvonne , Harn Donald A.
Published: July 2014

Vaccines are an important public health measure for prevention and treatment of diseases. In addition to the vaccine immunogen, many vaccines incorporate adjuvants to stimulate the recipient's immune system and enhance vaccine-specific responses. While vaccine development has advanced from attenuated organism to recombinant protein or use of plasmid DNA, the development of new adjuvants that safely increase immune responses has not kept pace. Previous studies have shown that the complex mixture of molecules that comprise saline soluble egg antigens (SEA) fromSchistosoma mansonieggs functions to promote CD4+T helper 2 (Th2) responses. Therefore, we hypothesized that coadministration of SEA with aListeriavector HIV-1 Gag (Lm-Gag) vaccine would suppress host cytotoxic T lymphocyte (CTL) and T helper 1 (Th1) responses to HIV-1 Gag epitopes. Surprisingly, instead of driving HIV-1 Gag-specific responses toward Th2 type, we found that coadministration of SEA with Lm-Gag vaccine significantly increased the frequency of gamma interferon (IFN-γ)-producing Gag-specific Th1 and CTL responses over that seen in mice administered Lm-Gag only. Analysis of the functionality and durability of vaccine responses suggested that SEA not only enlarged different memory T cell compartments but induced functional and long-lasting vaccine-specific responses as well. These results suggest there are components in SEA that can synergize with potent inducers of strong and durable Th1-type responses such as those toListeria. We hypothesize that SEA contains moieties that, if defined, can be used to expand type 1 proinflammatory responses for use in vaccines.
Clones of Streptococcus zooepidemicus from Outbreaks of Hemorrhagic Canine Pneumonia and Associated Immune Responses
Authors: Velineni Sridhar , Timoney John F. , Russell Kim , Hamlen Heidi J. , Pesavento Patricia , Fortney William D. , Crawford P. Cynda
Published: July 2014

Acute hemorrhagic pneumonia caused byStreptococcus zooepidemicushas emerged as a major disease of shelter dogs and greyhounds.S. zooepidemicusstrains differing in multilocus sequence typing (MLST), protective protein (SzP), and M-like protein (SzM) sequences were identified from 9 outbreaks in Texas, Kansas, Florida, Nevada, New Mexico, and Pennsylvania. Clonality based on 2 or more isolates was evident for 7 of these outbreaks. The Pennsylvania and Nevada outbreaks also involved cats. Goat antisera against acutely infected lung tissue as well as convalescent-phase sera reacted with a mucinase (Sz115), hyaluronidase (HylC), InlA domain-containing cell surface-anchored protein (INLA), membrane-anchored protein (MAP), SzP, SzM, and extracellular oligopeptide-binding protein (OppA). The amino acid sequences of SzP and SzM of the isolates varied greatly. Theszpandszmalleles of the closely related Kansas clone (sequence type 129 [ST-129]) and United Kingdom isolate BHS5 (ST-123) were different, indicating that MLST was unreliable as a predictor of virulence phenotype. Combinations of conserved HylC and serine protease (ScpC) and variable SzM and SzP proteins ofS. zooepidemicusstrain NC78 were protectively immunogenic for mice challenged with a virulent canine strain. Thus, although canine pneumonia outbreaks are caused by different strains ofS. zooepidemicus, protective immune responses were elicited in mice by combinations of conserved or variableS. zooepidemicusproteins from a single strain.
Highly Discriminatory Variable-Number Tandem-Repeat Markers for Genotyping of Trichophyton interdigitale Strains
Authors: Drira Ines , Hadrich Ines , Neji Sourour , Mahfouth Nedia , Trabelsi Houaida , Sellami Hayet , Makni Fattouma , Ayadi Ali
Published: July 2014

Trichophyton
interdigitale
is the second most frequent cause of superficial fungal infections of various parts of the human body. Studying the population structure and genotype differentiation of
T. interdigitale
strains may lead to significant improvements in clinical practice. The present study aimed to develop and select suitable variable-number tandem-repeat (VNTR) markers for 92 clinical strains of
T. interdigitale
. On the basis of an analysis of four VNTR markers, four to eight distinct alleles were detected for each marker. The marker with the highest discriminatory power had eight alleles and a
D
value of 0.802. The combination of all four markers yielded a
D
value of 0.969 with 29 distinct multilocus genotypes. VNTR typing revealed the genetic diversity of the strains, identifying three populations according to their colonization sites. A correlation between phenotypic characteristics and multilocus genotypes was observed. Seven patients harbored
T. interdigitale
strains with different genotypes. Typing of clinical
T. interdigitale
samples by VNTR markers displayed excellent discriminatory power and 100% reproducibility.
High-Throughput Ultrasensitive Molecular Techniques for Quantifying Low-Density Malaria Parasitemias
Authors: Imwong Mallika , Hanchana Sarun , Malleret Benoit , Rénia Laurent , Day Nicholas P. J. , Dondorp Arjen , Nosten Francois , Snounou Georges , White Nicholas J.
Published: July 2014

The epidemiology of malaria in “low-transmission” areas has been underestimated. Molecular detection methods have revealed higher prevalences of malaria than conventional microscopy or rapid diagnostic tests, but these typically evaluate finger-prick capillary blood samples (∼5 μl) and therefore cannot detect parasite densities of <200/ml. Their use underestimates true parasite carriage rates. To characterize the epidemiology of malaria in low-transmission settings and plan elimination strategies, more sensitive quantitative PCR (qPCR) is needed to identify and quantify low-density malaria parasitemias. A highly sensitive “high-volume” quantitative PCR (qPCR) method based on
Plasmodium
sp. 18S RNA was adapted for blood sample volumes of ≥250 μl and scaled for high throughput. The methods were validated by assessment of the analytical sensitivity and specificity, diagnostic sensitivity, and specificity, efficiency, precision, analytical and diagnostic accuracies, limit of detection, root cause analysis of false positives, and robustness. The high-volume qPCR method based on
Plasmodium
sp. 18S RNA gave high PCR efficiency of 90 to 105%. Concentrations of parasite DNA from large volumes of blood gave a consistent analytical detection limit (LOD) of 22 parasites/ml (95% CI, 21.79 to 74.9), which is some 2,500 times more sensitive than conventional microscopy and 50 times more sensitive than currently used PCR methods from filter paper blood spots. The diagnostic specificity was 99.75%. Using automated procedures it was possible to process 700 blood samples per week. A very sensitive and specific high-throughput high-volume qPCR method for the detection of low-density parasitemias (>20 parasites/ml) was developed and validated.
Bacterial Nanoscale Cultures for Phenotypic Multiplexed Antibiotic Susceptibility Testing
Authors: Weibull Emilie , Antypas Haris , Kjäll Peter , Brauner Annelie , Andersson-Svahn Helene , Richter-Dahlfors Agneta
Published: July 2014

An optimal antimicrobial drug regimen is the key to successful clinical outcomes of bacterial infections. To direct the choice of antibiotic, access to fast and precise antibiotic susceptibility profiling of the infecting bacteria is critical. We have developed a high-throughput nanowell antibiotic susceptibility testing (AST) device for direct, multiplexed analysis. By processing in real time the optical recordings of nanoscale cultures of reference and clinical uropathogenic
Escherichia coli
strains with a mathematical algorithm, the time point when growth shifts from lag phase to early logarithmic phase (
T
lag
) was identified for each of the several hundreds of cultures tested. Based on
T
lag
, the MIC could be defined within 4 h. Heatmap presentation of data from this high-throughput analysis allowed multiple resistance patterns to be differentiated at a glance. With a possibility to enhance multiplexing capacity, this device serves as a high-throughput diagnostic tool that rapidly aids clinicians in prescribing the optimal antibiotic therapy.
Enterobius vermicularis Salpingitis Seen in the Setting of Ectopic Pregnancy in a Malaysian Patient
Authors: Ngui Romano , Ravindran Sarala , Ong Diana Bee Lan , Chow Tak Kuan , Low Kah Pin , Nureena Zaidi Syeda , Rajoo Yamuna , Chin Yuee Teng , Amir Amirah , Ahmad Arine Fadzlun , Lim Yvonne Ai Lian , Mahmud Rohela
Published: July 2014

We report a rare and unusual case of invasiveEnterobius vermicularisinfection in a fallopian tube. The patient was a 23-year-old Malaysian woman who presented with suprapubic pain and vaginal bleeding. A clinical diagnosis of ruptured right ovarian ectopic pregnancy was made. She underwent a laparotomy with a right salpingo-oophorectomy. Histopathological examination of the right fallopian tube showed eggs and adult remnants ofE. vermicularis, and the results were confirmed using PCR and DNA sequencing.
Neurotropic Astrovirus in Cattle with Nonsuppurative Encephalitis in Europe
Authors: Bouzalas Ilias G. , Wüthrich Daniel , Walland Julia , Drögemüller Cord , Zurbriggen Andreas , Vandevelde Marc , Oevermann Anna , Bruggmann Rémy , Seuberlich Torsten
Published: July 2014

Encephalitis is a frequently diagnosed condition in cattle with neurological diseases. Many affected animals present with a nonsuppurative inflammatory reaction pattern in the brain. While this pattern supports a viral etiology, the causative pathogen remains unknown in a large proportion of cases. Using viral metagenomics, we identified an astrovirus (bovine astrovirus [BoAstV]-CH13) in the brain of a cow with nonsuppurative encephalitis. Additionally, BoAstV RNA was detected with reverse transcription-PCR and
in situ
hybridization in about one fourth (5/22 animals) of cattle with nonsuppurative encephalitis of unknown etiology. Viral RNA was found primarily in neurons and at the site of pathology. These findings support the notion that BoAstV infection is a common cause of encephalitis in cattle. Phylogenetically, BoAstV-CH13 was closely related to rare astrovirus isolates from encephalitis cases in animals and a human patient. Future research needs to be directed toward the pathogenic mechanisms, epidemiology, and potential cross-species transmission of these neurotropic astroviruses.
Psychrobacter sanguinis: an Unusual Bacterium for Nosocomial Meningitis
Authors: Le Guern Rémi , Wallet Frédéric , Vega Emmanuel , Courcol René J. , Loïez Caroline
Published: July 2014

We report the first case of postneurosurgical meningitis due to
Psychrobacter sanguinis
, identified only by 16S rRNA analysis.
Psychrobacter
spp. usually live in deep sea environments and cold habitats. Despite a strict questioning of the patient and the medical staff, we did not find the source of this bacterium.
Genetic Diversity in Enterocytozoon bieneusi Isolates from Dogs and Cats in China: Host Specificity and Public Health Implications
Authors: Karim Md Robiul , Dong Haiju , Yu Fuchang , Jian Fuchun , Zhang Longxian , Wang Rongjun , Zhang Sumei , Rume Farzana Islam , Ning Changshen , Xiao Lihua
Published: July 2014

To explore the genetic diversity, host specificity, and zoonotic potential of
Enterocytozoon bieneusi
, feces from 348 stray and pet dogs and 96 pet cats from different locations in China were examined by internal transcribed spacer (ITS)-based PCR.
E. bieneusi
was detected in 15.5% of the dogs, including 20.5% of stray dogs and 11.7% of pet dogs, and in 11.5% of the pet cats. Higher infection rates were recorded in the >2-year and the 1- to 2-year age groups in dogs and cats, respectively. Altogether, 24 genotypes, including 11 known and 13 new, were detected in 65 infected animals. In 54 positive dogs, 18 genotypes, 9 known (PtEbIX, O, D, CM1, EbpA, Peru8, type IV, EbpC, and PigEBITS5) and 9 new (CD1 to CD9), were found. In contrast, 8 genotypes, 4 known (D, BEB6, I, and PtEbIX) and 4 new (CC1 to CC4), were identified in 11 infected cats. The dominant genotype in dogs was PtEbIX (26/54). Phylogenetic analysis revealed that 8 known genotypes (D, Peru8, type IV, CM1, EbpC, PigEBITS5, O, and EbpA) and 7 new genotypes (CD1 to CD4 and CC2 to CC4) were the members of zoonotic group 1, whereas genotypes CD7, CD8, and CD9 together with PtEbIX belonged to the dog-specific group, and genotypes CD6 and CC1 were placed in group 2 with BEB6 and I. Conversely, genotype CD5 clustered with CM4 without belonging to any previous groups. We conclude that zoonotic genotypes are common in dogs and cats, as are host-specific genotypes in dogs.
H7N9 and Other Pathogenic Avian Influenza Viruses Elicit a Three-Pronged Transcriptomic Signature That Is Reminiscent of 1918 Influenza Virus and Is Associated with Lethal Outcome in Mice
Authors: Morrison Juliet , Josset Laurence , Tchitchek Nicolas , Chang Jean , Belser Jessica A. , Swayne David E. , Pantin-Jackwood Mary J. , Tumpey Terrence M. , Katze Michael G.
Published: July 2014

Modulating the host response is a promising approach to treating influenza, caused by a virus whose pathogenesis is determined in part by the reaction it elicits within the host. Though the pathogenicity of emerging H7N9 influenza virus in several animal models has been reported, these studies have not included a detailed characterization of the host response following infection. Therefore, we characterized the transcriptomic response of BALB/c mice infected with H7N9 (A/Anhui/01/2013) virus and compared it to the responses induced by H5N1 (A/Vietnam/1203/2004), H7N7 (A/Netherlands/219/2003), and pandemic 2009 H1N1 (A/Mexico/4482/2009) influenza viruses. We found that responses to the H7 subtype viruses were intermediate to those elicited by H5N1 and pdm09H1N1 early in infection but that they evolved to resemble the H5N1 response as infection progressed. H5N1, H7N7, and H7N9 viruses were pathogenic in mice, and this pathogenicity correlated with increased transcription of cytokine response genes and decreased transcription of lipid metabolism and coagulation signaling genes. This three-pronged transcriptomic signature was observed in mice infected with pathogenic H1N1 strains such as the 1918 virus, indicating that it may be predictive of pathogenicity across multiple influenza virus strains. Finally, we used host transcriptomic profiling to computationally predict drugs that reverse the host response to H7N9 infection, and we identified six FDA-approved drugs that could potentially be repurposed to treat H7N9 and other pathogenic influenza viruses.

IMPORTANCE
Emerging avian influenza viruses are of global concern because the human population is immunologically naive to them. Current influenza drugs target viral molecules, but the high mutation rate of influenza viruses eventually leads to the development of antiviral resistance. As the host evolves far more slowly than the virus, and influenza pathogenesis is determined in part by the host response, targeting the host response is a promising approach to treating influenza. Here we characterize the host transcriptomic response to emerging H7N9 influenza virus and compare it with the responses to H7N7, H5N1, and pdm09H1N1. All three avian viruses were pathogenic in mice and elicited a transcriptomic signature that also occurs in response to the legendary 1918 influenza virus. Our work identifies host responses that could be targeted to treat severe H7N9 influenza and identifies six FDA-approved drugs that could potentially be repurposed as H7N9 influenza therapeutics.