bluuebunny/crossref_metadata_2025 huggingface dataset:
Relationship among the physiologic channel interactions, spectral-ripple discrimination, and vowel identification in cochlear implant users
Authors: Won Jong Ho , Humphrey Elizabeth L. , Yeager Kelly R. , Martinez Alexis A. , Robinson Camryn H. , Mills Kristen E. , Johnstone Patti M. , Moon Il Joon , Woo Jihwan
Published: November 2014

The hypothesis of this study was that broader patterns of physiological channel interactions in the local region of the cochlea are associated with poorer spectral resolution in the same region. Electrically evoked compound action potentials (ECAPs) were measured for three to six probe electrodes per subject to examine the channel interactions in different regions across the electrode array. To evaluate spectral resolution at a confined location within the cochlea, spectral-ripple discrimination (SRD) was measured using narrowband ripple stimuli with the bandwidth spanning five electrodes: Two electrodes apical and basal to the ECAP probe electrode. The relationship between the physiological channel interactions, spectral resolution in the local cochlear region, and vowel identification was evaluated. Results showed that (1) there was within- and across-subject variability in the widths of ECAP channel interaction functions and in narrowband SRD performance, (2) significant correlations were found between the widths of the ECAP functions and narrowband SRD thresholds, and between mean bandwidths of ECAP functions averaged across multiple probe electrodes and broadband SRD performance across subjects, and (3) the global spectral resolution reflecting the entire electrode array, not the local region, predicts vowel identification.
Perceptual consequences of changes in epilaryngeal area and shape
Authors: Samlan Robin A. , Kreiman Jody
Published: November 2014

The influence of epilaryngeal area on glottal flow and the acoustic signal has been described [Titze, J. Acoust. Soc. Am. 123, 2733–2749 (2008)], but it is not known how (or whether) changes in epilaryngeal area influence perceived voice quality. This study examined these relationships in a kinematic vocal tract model. Epilaryngeal constrictions and expansions were simulated at the levels of the aryepiglottic folds and the ventricular folds in the context of four glottal configurations representing normal vibration to severe vocal fold paralysis, for the three corner vowels /a/, /i/, and /u/. Minimum and maximum glottal flow, maximum flow declination rate, spectral slope, cepstral peak prominence, and the harmonics-to-noise ratio were measured, and listeners completed a perceptual sort-and-rate task for all samples. Epilaryngeal constriction and expansion caused salient differences in voice quality. The location of constriction was also perceivable. Vowels simulated with aryepiglottic constriction demonstrated lower maximum airflow and less noise than the other epilaryngeal shapes, and listeners consistently perceived them as distinct from other stimuli. Acoustic differences decreased with increasing severity of simulated paralysis. Results of epilaryngeal constriction and expansion were similar for /a/ and /i/, and produced slightly different patterns for /u/.
The effects of measurement error and vowel selection on the locus equation measure of coarticulation
Authors: Montgomery Allen , Reed Paul E. , Crass Kimberlee A. , Isabel Hubbard H. , Stith Joanna
Published: November 2014

Effects on the slope of introducing error in the F2 Hz values in locus equations (LEs) and of using fewer than ten vowels were investigated. For each of the initial consonants /b, d, g/, 2000 simulated sets were generated using Monte Carlo techniques. The sets were altered with 50, 100, or 200 Hz error being randomly applied to each F2 value within a set. Selected vowels were then removed from the sets and the effects on the slopes were measured. Results suggest that the LE slopes are generally resistant to error and reduced number of vowels. Effects of adding 50 Hz of random error to the F2 values in sets using eight or ten vowels were minimal, yielding a mean absolute change in slope less than 0.07.
Perception of touch quality in piano tones
Authors: Goebl Werner , Bresin Roberto , Fujinaga Ichiro
Published: November 2014

Both timbre and dynamics of isolated piano tones are determined exclusively by the speed with which the hammer hits the strings. This physical view has been challenged by pianists who emphasize the importance of the way the keyboard is touched. This article presents empirical evidence from two perception experiments showing that touch-dependent sound components make sounds with identical hammer velocities but produced with different touch forms clearly distinguishable. The first experiment focused on finger-key sounds: musicians could identify pressed and struck touches. When the finger-key sounds were removed from the sounds, the effect vanished, suggesting that these sounds were the primary identification cue. The second experiment looked at key-keyframe sounds that occur when the key reaches key-bottom. Key-bottom impact was identified from key motion measured by a computer-controlled piano. Musicians were able to discriminate between piano tones that contain a key-bottom sound from those that do not. However, this effect might be attributable to sounds associated with the mechanical components of the piano action. In addition to the demonstrated acoustical effects of different touch forms, visual and tactile modalities may play important roles during piano performance that influence the production and perception of musical expression on the piano.
Analysis of shear-wave attenuation in unconsolidated sands and glass beads
Authors: Buckingham Michael J.
Published: November 2014

Chotiros and Isakson [J. Acoust. Soc. Am. 135, 3264–3279 (2014)] contend that the physics-based grain-shearing (GS) theories of wave propagation in granular materials are not consistent with one particular shear-attenuation data set for water-saturated angular sand that has appeared in the literature. This provides them with the rationale for developing their own model, an extension of the empirical Biot-Stoll model, which they designate the Extended Biot (EB) model. In this article, the EB model and the grain-shearing theories are briefly reviewed, and it is demonstrated that, in fact, the original GS theory accurately matches the frequency-dependent trends of all the shear attenuation data sets that are currently available, including those for saturated angular sands after random fluctuations are suppressed by averaging over several realizations of the medium. It is also pointed out that Chotiros and Isakson's treatment of the available shear-attenuation data is highly selective, and that the format in which they present the selected data makes their comparisons with theoretical models difficult to interpret. Thus, their attempts at validating the EB model and their conclusions concerning alternative theories should be treated with caution.
Burst spectrum as a cue for the stop voicing contrast in American English
Authors: Chodroff Eleanor , Wilson Colin
Published: November 2014

Voicing contrasts in stop consonants are expressed by a constellation of acoustic cues. This study focused on a spectral cue present at burst onset in American English labial and coronal stops. Spectral shape was examined for word-initial, prevocalic stops of all three places of articulation in a laboratory production study and a large corpus of continuous read speech. Voiceless labial and coronal stops were found to have greater energy at higher frequencies in comparison to homorganic voiced stops, a difference that could not be attributed to aspiration in the voiceless stops or modal phonation in the voiced, while no consistent effect was found for dorsal stops. This pattern was found with various methods of spectral estimation (time-averaged and multitaper spectra) and measures of spectral energy concentration (center of gravity and spectral peak) for both linear and auditorily based frequency scales. Perceptual relevance of the spectral cue was tested in laboratory and online experiments with continua created by crossing burst shape and voice onset time. A trading relation was observed such that voiceless identifications were more likely for tokens with higher frequency bursts. Goodness ratings indicated that burst spectrum influences category typicality for voiceless stops even when voice onset time is unambiguous.
Mixing of collinear plane wave pulses in elastic solids with quadratic nonlinearity
Authors: Chen Zimu , Tang Guangxin , Zhao Youxun , Jacobs Laurence J. , Qu Jianmin
Published: November 2014

This paper derives a set of necessary and sufficient conditions for generating resonant waves by two propagating time-harmonic plane waves. It is shown that in collinear mixing, a resonant wave can be generated either by a pair of longitudinal waves, in which case the resonant mixing wave is also a longitudinal wave, or by a pair of longitudinal and transverse waves, in which case the resonant wave is a transverse wave. In addition, the paper obtains closed-form analytical solutions to the resonant waves generated by two collinearly propagating sinusoidal pulses. The results show that amplitude of the resonant pulse is proportional to the mixing zone size, which is determined by the spatial lengths of the input pulses. Finally, numerical simulations based on the finite element method and experimental measurements using one-way mixing are conducted. It is shown that both numerical and experimental results agree well with the analytical solutions.
Electroacoustic analysis, design, and implementation of a small balanced armature speaker
Authors: Bai Mingsian R. , You Bo-Cheng , Lo Yi-Yang
Published: November 2014

This paper presents a new design and implementation of a balanced armature speaker (BAS), which is composed of permanent magnetic circuits, a moving armature, and a coil. The armature rocks about a pivot with the coil at one end and the permanent magnet on another. A magnetic circuit analysis is conducted for the designed BAS to formulate the force factor, which is required for modeling the coupling between the electrical and mechanical systems. In addition, an electromechanoacoustical analogous circuit is established for the BAS, which bears the same structure as the moving coil loudspeaker, except that the force factor is different. A hybrid model, which combines the lumped parameter model in the electrical and acoustical domains with a finite element model in the mechanical domain, is developed to model the high-frequency response because of the high-order modes of the membrane, the drive rod, and the armature. The electroacoustic analysis is experimentally verified. The results indicate that the sound pressure response that is simulated using the hybrid model is in superior agreement with the measured response to that simulated using the lumped parameter model.
Listening effort and speech intelligibility in listening situations affected by noise and reverberation
Authors: Rennies Jan , Schepker Henning , Holube Inga , Kollmeier Birger
Published: November 2014

This study compared the combined effect of noise and reverberation on listening effort and speech intelligibility to predictions of the speech transmission index (STI). Listening effort was measured in normal-hearing subjects using a scaling procedure. Speech intelligibility scores were measured in the same subjects and conditions: (a) Speech-shaped noise as the only interfering factor, (b) + (c) fixed signal-to-noise ratios (SNRs) of 0 or 7 dB and reverberation as detrimental factors, and (d) reverberation as the only detrimental factor. In each condition, SNR and reverberation were combined to produce STI values of 0.17, 0.30, 0.43, 0.57, and 0.70, respectively. Listening effort always decreased with increasing STI, thus enabling a rough prediction, but a significant bias was observed indicating that listening effort was lower in reverberation only than in noise only at the same STI for one type of impulse responses. Accordingly, speech intelligibility increased with increasing STI and was significantly better in reverberation only than in noise only at the same STI. Further analyses showed that the broadband reverberation time is not always a good estimate of speech degradation in reverberation and that different speech materials may differ in their robustness toward detrimental effects of reverberation.
Scaling of plane-wave functions in statistically optimized near-field acoustic holography
Authors: Hald Jørgen
Published: November 2014

Statistically Optimized Near-field Acoustic Holography (SONAH) is a Patch Holography method, meaning that it can be applied in cases where the measurement area covers only part of the source surface. The method performs projections directly in the spatial domain, avoiding the use of spatial discrete Fourier transforms and the associated errors. First, an inverse problem is solved using regularization. For each calculation point a multiplication must then be performed with two transfer vectors—one to get the sound pressure and the other to get the particle velocity. Considering SONAH based on sound pressure measurements, existing derivations consider only pressure reconstruction when setting up the inverse problem, so the evanescent wave amplification associated with the calculation of particle velocity is not taken into account in the regularized solution of the inverse problem. The present paper introduces a scaling of the applied plane wave functions that takes the amplification into account, and it is shown that the previously published virtual source-plane retraction has almost the same effect. The effectiveness of the different solutions is verified through a set of simulated measurements.
Time-domain delay-and-sum beamforming for time-reversal detection of intermittent acoustic sources in flows
Authors: Rakotoarisoa Ifanila , Fischer Jeoffrey , Valeau Vincent , Marx David , Prax Christian , Brizzi Laurent-Emmanuel
Published: November 2014

This study focuses on the identification of intermittent aeroacoustic sources in flows by using the time-domain beamforming technique. It is first shown that this technique can be seen as a time-reversal (TR) technique, working with approximate Green functions in the case of a shear flow. Some numerical experiments investigate the case of an array measurement of a generic acoustic pulse emitted in a wind-tunnel flow, with a realistic multi-arm spiral array. The results of the time-domain beamforming successfully match those given by a numerical TR technique over a wide range of flow speeds (reaching the transonic regime). It is shown how the results should be analyzed in a focusing plane parallel to the microphone array in order to estimate the location and emission time of the pulse source. An experimental application dealing with the aeroacoustic radiation of a bluff body in a wind-tunnel flow is also considered, and shows that some intermittent events can be clearly identified in the noise radiation. Time-domain beamforming is then an efficient tool for analyzing intermittent acoustic sources in flows, and is a computationally cheaper alternative to the numerical TR technique, which should be used for complex configurations where the Green function is not available.
One-dimensional single-sided acoustic focusing in a Goupillaud layered model
Authors: Zhang Yinquan , Wang Ning , Wang Pengyu
Published: November 2014

Using the single-sided reflection response of an unknown layered medium, one-dimensional single-sided acoustic focusing is a process that constructs a normally incident plane waveform such that the sound field collapses to a point inside this medium at a specified time. A recursive method for finding the incident waveform of the discrete single-sided focusing in the Goupillaud layered model is presented. The method is formulated using the standard Z-transform and provides an intuitive way to understand how single-sided focusing works in an unknown medium. Two numerical scattering experiments, with different layered structures, are simulated to verify the proposed method. In addition, the responses to virtual sources in the examples are reconstructed.
Multi-echo processing by a bottlenose dolphin operating in “packet” transmission mode at long range
Authors: Finneran James J. , Schroth-Miller Maddie , Borror Nancy , Tormey Megan , Brewer Arial , Black Amy , Bakhtiari Kimberly , Goya Gavin
Published: November 2014

Bottlenose dolphins performing echolocation tasks at long ranges may utilize a transmission mode where bursts, or “packets,” of echolocation clicks are emitted rather than single clicks. The clicks within each packet are separated by time intervals well below the two-way travel time, while the packets themselves are emitted at intervals greater than the two-way travel time. Packet use has been shown to increase with range; however, the exact function of packets and the advantages gained by their utilization remain unknown. In this study, the capability for dolphins to utilize multi-echo processing within packets of echoes was investigated by manipulating the number of available echoes within each packet as a dolphin performed a long-range echolocation task. The results showed an improvement in detectability with an increase in the number of echoes in each packet and suggest that packet use is an adaptation to allow multi-echo processing at long ranges without introducing range ambiguity.
Sound source localization identification accuracy: Bandwidth dependencies
Authors: Yost William A. , Zhong Xuan
Published: November 2014

Sound source localization accuracy using a sound source identification task was measured in the front, right quarter of the azimuth plane as rms (root-mean-square) error (degrees) for stimulus conditions in which the bandwidth (1/20 to 2 octaves wide) and center frequency (250, 2000, 4000 Hz) of 200-ms noise bursts were varied. Tones of different frequencies (250, 2000, 4000 Hz) were also used. As stimulus bandwidth increases, there is an increase in sound source localization identification accuracy (i.e., rms error decreases). Wideband stimuli (>1 octave wide) produce best sound source localization accuracy (∼6°–7° rms error), and localization accuracy for these wideband noise stimuli does not depend on center frequency. For narrow bandwidths (<1 octave) and tonal stimuli, accuracy does depend on center frequency such that highest accuracy is obtained for low-frequency stimuli (centered on 250 Hz), worse accuracy for mid-frequency stimuli (centered on 2000 Hz), and intermediate accuracy for high-frequency stimuli (centered on 4000 Hz).
Dipole transducer enhancement from a passive resonator
Authors: Butler John L. , Butler Alexander L. , Curtis Victoria
Published: November 2014

A passive resonator model for enhancing the low frequency performance of dipole transducers is presented using a spherical wave function model. It is shown that because the near field response of a dipole has the same on-axis low frequency dependence as an equivalent monopole, it can effectively excite a nearby monopole passive resonator and do this with enough strength to significantly modify the response of the system. Sample results are presented to demonstrate the performance enhancement and to illustrate the conversion of the dipole beam pattern to a nearly omni-directional beam pattern.
IGF-I and IGF-I Receptor Polymorphisms Among Elite Swimmers
Authors: Ben-Zaken Sigal , Meckel Yoav , Dror Nitzan , Nemet Dan , Eliakim Alon
Published: November 2014

In recent years several genetic polymorphisms related to the GH-IGF-I axis were suggested to promote athletic excellence in endurance and power sports. We studied the presence of the C-1245T SNP (rs35767), a nucleotide substitution in the promoter region of the IGF-I gene, and the presence of the 275124A > C SNP (rs1464430), a common nucleotide substitution in the intron region of the IGF-I receptor (IGF-IR) gene in elite long and short-distance swimmers compared with nonphysically active controls. The rare T/T IGF-I polymorphism was found only in 5.3% of the long-distance swimmers, and was not found at all in the short-distance swimmers or among the control group participants. The prevalence of the IGF-I receptor AA genotype was significantly lower in the swimming group as a whole (35%) compared with the control group (46%), in particularly due to reduced frequency of the AA genotype among short-distance swimmers (26%). In contrast to previous reports in elite endurance and power track and field athletes, single nucleotide polymorphisms of the IGF-I and the IGF-IR were not frequent among elite Israeli short- and long-distance swimmers emphasizing the importance of other factors for excellence in swimming. The results also suggest that despite seemingly similar metabolic characteristics different sports disciplines may have different genetic polymorphisms. Thus, combining different disciplines for sports genetic research purposes should be done with extreme caution.
Overcoming Staph Infections Is Hardwired
Authors: Hurtley Stella M.
Published: November 2014

Cystine-knot proteins play an evolutionarily conserved dual function in nerve development and immunity to staphylococcal infection.
Bone Marrow Dendritic Cells from Mice with an Altered Microbiota Provide Interleukin 17A-Dependent Protection against Entamoeba histolytica Colitis
Authors: Burgess Stacey L. , Buonomo Erica , Carey Maureen , Cowardin Carrie , Naylor Caitlin , Noor Zannatun , Wills-Karp Marsha , Petri William A.
Published: November 2014

There is an emerging paradigm that the human microbiome is central to many aspects of health and may have a role in preventing enteric infection.
Entamoeba histolytica
is a major cause of amebic diarrhea in developing countries. It colonizes the colon lumen in close proximity to the gut microbiota. Interestingly, not all individuals are equally susceptible to 
E. histolytica
 infection. Therefore, as the microbiota is highly variable within individuals, we sought to determine if a component of the microbiota could regulate susceptibility to infection. In studies utilizing a murine model, we demonstrated that colonization of the gut with the commensal
Clostridia
-related bacteria known as segmented filamentous bacteria (SFB) is protective during 
E. histolytica
infection. SFB colonization in this model was associated with elevated cecal levels of interleukin 17A (IL-17A), dendritic cells, and neutrophils. Bone marrow-derived dendritic cells (BMDCs) from SFB-colonized mice had higher levels of IL-23 production in response to stimulation with trophozoites. Adoptive transfer of BMDCs from an SFB
+
to an SFB
−
mouse was sufficient to provide protection against
E. histolytica
. IL-17A induction during BMDC transfer was necessary for this protection. This work demonstrates that intestinal colonization with a specific commensal bacterium can provide protection during amebiasis in a murine model. Most importantly, this work demonstrates that the microbiome can mediate protection against an enteric infection via extraintestinal effects on bone marrow-derived dendritic cells.

IMPORTANCE
Entamoeba histolytica
is the causative agent of amebiasis, an infectious disease that contributes significantly to morbidity and mortality due to diarrhea in the developing world. We showed in a murine model that colonization with the commensal members of the
Clostridia
known as SFB provides protection against
E. histolytica
and that dendritic cells from SFB-colonized mice alone can recapitulate protection. Understanding interactions between enteropathogens, commensal intestinal bacteria, and the mucosal immune response, including dendritic cells, will help in the development of effective treatments for this disease and other infectious and inflammatory diseases. The demonstration of immune-mediated protection due to communication from the microbiome to the bone marrow represents an emerging field of study that will yield unique approaches to the development of these treatments.
Improving Microbial Biogasoline Production in Escherichia coli Using Tolerance Engineering
Authors: Foo Jee Loon , Jensen Heather M. , Dahl Robert H. , George Kevin , Keasling Jay D. , Lee Taek Soon , Leong Susanna , Mukhopadhyay Aindrila
Published: November 2014

Engineering microbial hosts for the production of fungible fuels requires mitigation of limitations posed on the production capacity. One such limitation arises from the inherent toxicity of solvent-like biofuel compounds to production strains, such as
Escherichia coli
. Here we show the importance of host engineering for the production of short-chain alcohols by studying the overexpression of genes upregulated in response to exogenous isopentenol. Using systems biology data, we selected 40 genes that were upregulated following isopentenol exposure and subsequently overexpressed them in
E. coli
. Overexpression of several of these candidates improved tolerance to exogenously added isopentenol. Genes conferring isopentenol tolerance phenotypes belonged to diverse functional groups, such as oxidative stress response (
soxS
,
fpr
, and
nrdH
), general stress response (
metR
,
yqhD
, and
gidB
), heat shock-related response (
ibpA
), and transport (
mdlB
). To determine if these genes could also improve isopentenol production, we coexpressed the tolerance-enhancing genes individually with an isopentenol production pathway. Our data show that expression of 6 of the 8 candidates improved the production of isopentenol in
E. coli
, with the methionine biosynthesis regulator MetR improving the titer for isopentenol production by 55%. Additionally, expression of MdlB, an ABC transporter, facilitated a 12% improvement in isopentenol production. To our knowledge, MdlB is the first example of a transporter that can be used to improve production of a short-chain alcohol and provides a valuable new avenue for host engineering in biogasoline production.

IMPORTANCE
The use of microbial host platforms for the production of bulk commodities, such as chemicals and fuels, is now a focus of many biotechnology efforts. Many of these compounds are inherently toxic to the host microbe, which in turn places a limit on production despite efforts to optimize the bioconversion pathways. In order to achieve economically viable production levels, it is also necessary to engineer production strains with improved tolerance to these compounds. We demonstrate that microbial tolerance engineering using transcriptomics data can also identify targets that improve production. Our results include an exporter and a methionine biosynthesis regulator that improve isopentenol production, providing a starting point to further engineer the host for biogasoline production.
Mass Spectrometric Analysis ofl-Cysteine Metabolism: Physiological Role and Fate ofl-Cysteine in the Enteric Protozoan Parasite Entamoeba histolytica
Authors: Jeelani Ghulam , Sato Dan , Soga Tomoyoshi , Watanabe Haruo , Nozaki Tomoyoshi
Published: November 2014

l-Cysteine is essential for virtually all living organisms, from bacteria to higher eukaryotes. Besides having a role in the synthesis of virtually all proteins and of taurine, cysteamine, glutathione, and other redox-regulating proteins,l-cysteine has important functions under anaerobic/microaerophilic conditions. In anaerobic or microaerophilic protozoan parasites, such asEntamoeba histolytica,l-cysteine has been implicated in growth, attachment, survival, and protection from oxidative stress. However, a specific role of this amino acid or related metabolic intermediates is not well understood. In this study, using stable-isotope-labeledl-cysteine and capillary electrophoresis-time of flight mass spectrometry, we investigated the metabolism ofl-cysteine inE. histolytica. [U-13C3,15N]l-cysteine was rapidly metabolized into three unknown metabolites, besidesl-cystine andl-alanine. These metabolites were identified as thiazolidine-4-carboxylic acid (T4C), 2-methyl thiazolidine-4-carboxylic acid (MT4C), and 2-ethyl-thiazolidine-4-carboxylic acid (ET4C), the condensation products ofl-cysteine with aldehydes. We demonstrated that these 2-(R)-thiazolidine-4-carboxylic acids serve for storage ofl-cysteine. Liberation ofl-cysteine occurred when T4C was incubated with amebic lysates, suggesting enzymatic degradation of thesel-cysteine derivatives. Furthermore, T4C and MT4C significantly enhanced trophozoite growth and reduced intracellular reactive oxygen species (ROS) levels when it was added to cultures, suggesting that 2-(R)-thiazolidine-4-carboxylic acids are involved in the defense against oxidative stress.

IMPORTANCEAmebiasis is a human parasitic disease caused by the protozoan parasiteEntamoeba histolytica. In this parasite,l-cysteine is the principal low-molecular-weight thiol and is assumed to play a significant role in supplying the amino acid during trophozoite invasion, particularly when the parasites move from the anaerobic intestinal lumen to highly oxygenated tissues in the intestine and the liver. It is well known thatE. histolyticaneeds a comparatively high concentration ofl-cysteine for its axenic cultivation. However, the reason for and the metabolic fate ofl-cysteine in this parasite are not well understood. Here, using a metabolomic and stable-isotope-labeled approach, we investigated the metabolic fate of this amino acid in these parasites. We found thatl-cysteine inside the cell rapidly reacts with aldehydes to form 2-(R)-thiazolidine-4-carboxylic acid. We showed that these 2-(R)-thiazolidine-4-carboxylic derivatives serve as anl-cysteine source, promote growth, and protect cells against oxidative stress by scavenging aldehydes and reducing the ROS level. Our findings represent the first demonstration of 2-(R)-thiazolidine-4-carboxylic acids and their roles in protozoan parasites.
Deep Sequencing Identifies Noncanonical Editing of Ebola and Marburg Virus RNAs in Infected Cells
Authors: Shabman Reed S. , Jabado Omar J. , Mire Chad E. , Stockwell Timothy B. , Edwards Megan , Mahajan Milind , Geisbert Thomas W. , Basler Christopher F.
Published: November 2014

Deep sequencing of RNAs produced by Zaire ebolavirus (EBOV) or the Angola strain of Marburgvirus (MARV-Ang) identified novel viral and cellular mechanisms that diversify the coding and noncoding sequences of viral mRNAs and genomic RNAs. We identified previously undescribed sites within the EBOV and MARV-Ang mRNAs where apparent cotranscriptional editing has resulted in the addition of non-template-encoded residues within the EBOV glycoprotein (GP) mRNA, the MARV-Ang nucleoprotein (NP) mRNA, and the MARV-Ang polymerase (L) mRNA, such that novel viral translation products could be produced. Further, we found that the well-characterized EBOV GP mRNA editing site is modified at a high frequency during viral genome RNA replication. Additionally, editing hot spots representing sites of apparent adenosine deaminase activity were found in the MARV-Ang NP 3′-untranslated region. These studies identify novel filovirus-host interactions and reveal production of a greater diversity of filoviral gene products than was previously appreciated.

IMPORTANCE
This study identifies novel mechanisms that alter the protein coding capacities of Ebola and Marburg virus mRNAs. Therefore, filovirus gene expression is more complex and diverse than previously recognized. These observations suggest new directions in understanding the regulation of filovirus gene expression.
Synthetic Biology for Engineering Acetyl Coenzyme A Metabolism in Yeast
Authors: Nielsen Jens
Published: November 2014

The yeast
Saccharomyces cerevisiae
is a widely used cell factory for the production of fuels, chemicals, and pharmaceuticals. The use of this cell factory for cost-efficient production of novel fuels and chemicals requires high yields and low by-product production. Many industrially interesting chemicals are biosynthesized from acetyl coenzyme A (acetyl-CoA), which serves as a central precursor metabolite in yeast. To ensure high yields in production of these chemicals, it is necessary to engineer the central carbon metabolism so that ethanol production is minimized (or eliminated) and acetyl-CoA can be formed from glucose in high yield. Here the perspective of generating yeast platform strains that have such properties is discussed in the context of a major breakthrough with expression of a functional pyruvate dehydrogenase complex in the cytosol.
High-dose tigecycline and colistin for successful treatment of disseminated carbapenem-resistantKlebsiella pneumoniaeinfection in a liver transplant recipient
Authors: Dan Jennifer Marie , Mendler Michel Henry , Hemming Alan W , Aslam Saima
Published: November 2014

Solid organ transplantation (SOT) is a risk factor for the acquisition of carbapenem-resistantKlebsiella pneumoniae. This infection is associated with a high mortality rate given the limited armamentarium of antibiotics for multidrug-resistant organisms along with continued immunosuppression to prevent graft rejection. We report a case of carbapenem-resistantK. pneumoniaepneumonia, bacteraemia and intra-abdominal infection in a newly transplanted liver recipient. The patient was successfully treated with a long course of high-dose tigecycline and colistin, along with surgical drainage. We discuss SOT-relevant epidemiology, therapeutic options and the rationale for our treatment choice.
Paraneoplastic vertigo as the presenting symptom of a testicular seminoma
Authors: Ball Andrea , Greer Emma B , Wong Christopher J
Published: November 2014

Vertigo is a common presenting symptom, but rarely may be caused by a malignancy. We present a case of a 44-year-old man who presented with nystagmus and vertigo precipitated by movement, with accompanying nausea and weight loss. Diagnostic workup revealed a right testicular mass that was resected and found to be a seminoma. The patient's symptoms resolved after surgical resection and treatment with corticosteroids.
Improving incident reporting among junior doctors
Authors: Hotton Emily , Jordan Lesley , Peden Carol
Published: November 2014

To ensure systems in hospitals improve to make patient care safer, learning must occur when things go wrong. Incident reporting is one of the commonest mechanisms used to learn from harm events and near misses. Only a relatively small number of incidents that occur are actually reported and different groups of staff have different rates of reporting. Nationally, junior doctors are low reporters of incidents, a finding supported by our local data. We set out to explore the culture and awareness around incident reporting among our junior doctors, and to improve the incident reporting rate within this important staff group. In order to achieve this we undertook a number of work programmes focused on junior doctors, including: assessment of their knowledge, confidence and understanding of incident reporting, education on how and why to report incidents with a focus on reporting on clinical themes during a specific time period, and evaluation of the experience of those doctors who reported incidents.

Junior doctors were asked to focus on incident reporting during a one week period. Before and after this focussed week, they were invited to complete a questionnaire exploring their confidence about what an incident was and how to report.

Prior to "Incident Reporting Week", on average only two reports were submitted a month by junior doctors compared with an average of 15 per month following the education and awareness week. This project highlights the fact that using a focussed reporting period and/or specific clinical themes as an education tool can benefit a hospital by promoting awareness of incidents and by increasing incident reporting rates. This can only assist in improving hospital systems, and ultimately increase patient safety.
How clean is clean: a new approach to assess and enhance environmental cleaning and disinfection in an acute tertiary care facility
Authors: Ng Wai Khuan
Published: November 2014

Traditional environmental cleaning monitoring through visual assessment can identify gross lapses in practice. However, in recent years the limitations underlying this need for ongoing compliance with cleaning and disinfection policies in the patient's immediate surroundings have become widely recognised.

The value of objectively monitoring and improving environmental cleaning and disinfection in healthcare settings is becoming increasingly identified as a crucial element of strategies to mitigate the transmission of healthcare-associated infections. Mafraq Hospital has adopted a new method using an invisible fluorescent marker system to target on surfaces in patient’s immediate surroundings. Evaluation of at least 30 surfaces and objects in patient rooms revealed that only 11% of targets had been cleaned. Simulation training, educational interventions, empowerment, change involvement and acknowledgment were executed, leading to a sustained improvement of 77% in both quarter 2 and 3 of 2013 in cleaning and disinfecting of all surfaces and objects.
Cilostazol increases patency and reduces adverse outcomes in percutaneous femoropopliteal revascularisation: a meta-analysis of randomised controlled trials
Authors: Benjo Alexandre M , Garcia Daniel C , Jenkins J Stephen , Cardoso Rhanderson M N , Molina Taina P , El-Hayek Georges E , Nadkarni Girish N , Aziz Emad F , Dinicolantonio James J , Collins Tyrone
Published: November 2014

Background

Cilostazol is an oral antiplatelet agent currently indicated for treatment of intermittent claudication. There is evidence that cilostazol may reduce femoropopliteal restenosis after percutaneous endovascular intervention.

Methods

We searched PubMed, Scopus and Cochrane databases from 1966 through September 2013 for randomised controlled trials (RCTs) evaluating the addition of cilostazol to standard care in patients receiving femoropopliteal endovascular treatment. Restenosis, target lesion revascularisation and combined adverse outcomes (death, revascularisation and amputation) within 1–2 years postprocedure were evaluated.

Results

Of 205 articles, three RCTs were included in the analysis. The pooled data provided a total of 396 patients, 195 of whom received cilostazol. When compared to standard medical therapy alone, cilostazol significantly reduced the risk of restenosis (risk difference −0.20; 95% CI −0.29 to −0.11; p<0.0001; number needed to treat 5), target lesion revascularisation (risk difference −0.17; 95% CI −0.25 to −0.09; p<0.0001; number needed to treat 6). Death and amputation were not different in between groups.

Conclusions and limitation

Cilostazol significantly increases femoropopliteal patency and decreases adverse outcomes in percutaneous endovascular intervention. However, further RCTs are needed because of limited sample size; this meta-analysis represents the best current evidence.
Bipartite portosystemic shunt with single insertion: a rare congenital vascular anomaly in a dog
Authors: Carlton Paul Francis , Hammond Gawain
Published: November 2014

A case of a bipartite extra hepatic portosystemic shunt is described in a one‐year‐old, male entire Maltese Terrier breed dog. On CT angiography, one vessel was visibly a portocaval shunt with the other vessel arising from the splenic vein. Both vessels formed a single insertion to the caudal vena cava cranial to the right renal vein which was managed successfully surgically via placement of a 6 mm ameroid constrictor. Multiple portosystemic shunts in dogs have been reported but to the authors’ knowledge this is the first case of a bipartite origin, single insertion portosystemic shunt reported in a dog.
For the love of dogs
Authors: Opperman Shaun
Published: November 2014

Battersea Dogs and Cats Home is featuring in a seven‐part documentary this autumn. The charity's onsite clinic team of five vets and 20 nurses is often at the heart of the Home's most emotive stories and was of particular interest to the TV crew. Veterinary director, Shaun Opperman, explains what was involved
Ten‐minute chat
Authors: Hole Sam Luis
Published: November 2014

Sam Luis Hole has spent over 15 years in the pursuit of providing better oral health care for horses, via dental training in the UK and the USA. He was awarded the RCVS certificate in advanced veterinary practice (CertAVP) for equine dentistry, the first such certificate to be awarded by the RCVS and the first postgraduate qualification in equine veterinary dentistry in the UK.
Ten‐minute chat
Authors: Aldiss Jason
Published: November 2014

Jason Aldiss is a member of the BVA Board, which is responsible for the corporate and financial governance and for setting the strategic direction of the Association
Help I've received a complaint
Authors: Hockey Gordon
Published: November 2014

Gordon Hockey was head of the RCVS professional conduct department before being appointed Head of Legal Services/Registrar. He describes the RCVS disciplinary process from complaint to resolution, while pointing out that complaints about vets are few and far between
Expectations of a new graduate
Authors: Bradshaw Becky
Published: November 2014

Most new graduates hope to get an enjoyable job in the field that they want to work in. They want a boss who understands and supports them; they want to get good at consultations and surgery, and to complete their PDP. And they want to be paid and appreciated for their hard work. Becky Bradshaw offers some tips for achieving this
Ten‐minute chat
Authors: Taylor Gillian
Published: November 2014

Gillian Taylor is a trustee of Canine Partners, a national charity that trains dogs to give people with disabilities greater independence.
New year, new horizons
Authors: Bassett John
Published: November 2014

New Zealander John Bassett has had a varied career, working in practice, government and the food industry. He is currently leading a team of microbiologists and modellers who help R&D ensure safety in the design of food, home care and personal care products for Unilever. In February he will be leaving the company to consider his next role
Ten‐minute chat
Authors: Fowler Vikki
Published: November 2014

Newly qualified vet Vikki Fowler was thrust into the media spotlight when she was involved with the rescue of a shire horse named Hope. Learning to deal with the media was a steep learning curve.
Artificial circulation of a mine pit lake
Authors: Pieters Roger , Coedy William , Ashley Ken I. , Lawrence Gregory A.
Published: November 2014

We describe the artificial circulation (destratification) of a pit lake at the Colomac mine site, 220 km north of Yellowknife, NWT, Canada. The pit lake, with a surface area of 17 ha and depth of 110 m, contained relatively saline water contaminated with the mining-related cyanide by-products, thiocyanate and ammonia. As a result of snow and ice melt, the pit lake was intermittently meromictic and cycling of contaminants through the oxygenated surface layer would have taken many years. To accelerate the oxidation process, the pit was artificially circulated using two air diffusers at a depth of 57 m. The pit lake was circulated during the open-water season, from 12 July 2006 for 57 days, and from 17 June 2007 for 89 days. After the first 12 h of operation of the circulation system, the top 37 m of the pit lake was mixed completely; after 34 h, the pit lake was mixed to the depth of the diffusers (57 m); and after approximately 6.5 days, the pit lake was mixed to the bottom. Upon complete mixing, the temperature and conductivity remained uniform during operation of the circulation system, and the concentration of oxygen in the deep water of the pit lake increased significantly. All thiocyanate was oxidized by the end of the first summer, producing ammonia that was depleted after the second summer of circulation.
Parallel evolutionary divergence in Arctic charSalvelinus alpinuscomplex from Transbaikalia: variation in differentiation degree and segregation of genetic diversity among sympatric forms
Authors: Gordeeva Natalia V. , Alekseyev Sergey S. , Matveev Arkadii N. , Samusenok Vitalii P.
Published: November 2014

Despite the growing recognition of an important role of ecological speciation in evolution, the mechanisms driving sympatric divergence within a single population are not fully understood. We documented a series of parallel divergence events and tried to assess general regularities of the diversification of the ancestral gene pool. For that we analysed variation at microsatellite loci in populations of a highly polymorphic complex species Salvelinus alpinus from 14 Transbaikalian lakes, 10 of them hosting two or three forms: dwarf, small, and large. Our results suggest sympatric or parapatric origin of forms in all 10 lakes (in one lake, two forms out of three). Gene diversity and allelic richness of form populations are positively correlated with lake size and negatively correlated with modal length of mature fish, so that the dwarf form typically has the highest, and the large form, the lowest indices of genetic variation. The latter effect might be caused by differences in life histories, thus reflecting adaptive divergence. Sympatric forms have differently segregated gene pools (FST= 0.030–0.497, RST= 0.011–0.440) and restricted (m = 0.002–0.042) typically asymmetric long-term gene flow. The level of reproductive isolation among forms assessed using putatively neutral microsatellite loci is correlated with their differentiation in morphology, including trophic-related gill raker number, and with lake depth (i.e., with segregation of diets and with habitat diversity), which corresponds to “isolation-by-adaptation” pattern. Our data suggest that the advance in speciation stage apparently more depends upon ecological opportunities of lake ecosystems than upon their age.
Anadromy and residency in steelhead and rainbow trout (Oncorhynchus mykiss): a review of the processes and patterns
Authors: Kendall Neala W. , McMillan John R. , Sloat Matthew R. , Buehrens Thomas W. , Quinn Thomas P. , Pess George R. , Kuzishchin Kirill V. , McClure Michelle M. , Zabel Richard W.
Published: November 2014

Oncorhynchus mykiss form partially migratory populations with anadromous fish that undergo marine migrations and residents that complete their life cycle in fresh water. Many populations’ anadromous components are threatened or endangered, prompting interest in understanding ecological and evolutionary processes underlying anadromy and residency. In this paper, we synthesize information to better understand genetic and environmental influences on O. mykiss life histories, identify critical knowledge gaps, and suggest next steps. Anadromy and residency appear to reflect interactions among genetics, individual condition, and environmental influences. First, an increasing body of literature suggests that anadromous and resident individuals differ in the expression of genes related to growth, smoltification, and metabolism. Second, the literature supports the conditional strategy theory, where individuals adopt a life history pattern based on their conditional status relative to genetic thresholds along with ultimate effects of size and age at maturation and iteroparity. However, except for a generally positive association between residency and high lipid content plus a large attainable size in fresh water, the effects of body size and growth are inconsistent. Thus, individuals can exhibit plasticity in variable environments. Finally, patterns in anadromy and residency among and within populations suggested a wide range of possible environmental influences at different life stages, from freshwater temperature to marine survival. Although we document a number of interesting correlations, direct tests of mechanisms are scarce and little data exist on the extent of residency and anadromy. Consequently, we identified as many data gaps as conclusions, leaving ample room for future research.