bluuebunny/crossref_metadata_2025 huggingface dataset:
Are phylogenies derived from family‐level supertrees robust for studies on macroecological patterns along environmental gradients?
Authors: Qian Hong , Zhang Jian
Published: May 2015

Ecologists frequently use a supertree method to generate phylogenies in ecological studies. However, the robustness of research results based on phylogenies generated with a supertree method has not been well evaluated. Here, we use the angiosperm tree flora of North America as a model system to test the robustness of phylogenies generated with a supertree method for studies on the relationship between phylogenetic properties and environment, by comparing the relationship between phylogenetic metrics and environmental variables derived from a phylogeny reconstructed with a supertree method to that derived from a phylogeny resolved at species level. North America was divided into equal area quadrats of 12 100 km2. Nine indices of phylogenetic structure were calculated for angiosperm tree assemblages in each quadrat using two phylogenies resolved at different levels (one resolved at the family level and the other resolved at the species level). Scores of phylogenetic indices were related to two major climatic variables (temperature and precipitation) using correlation and regression analyses. Scores of phylogenetic indices resulting from the two phylogenies are perfectly or nearly perfectly correlated. On average, there is no difference in the variation explained by the two climatic variables between scores of phylogenetic indices derived from the two phylogenies. Our study suggests that a phylogeny derived from a well resolved family‐level supertree as backbone with genera and species attached to the backbone as polytomies is robust for studies investigating the relationship between phylogenetic structure and environment in biological assemblages at a broad spatial scale.
Metabolic responses to predation risk in a jumping spider
Authors: Okuyama T.
Published: May 2015

Predators not only consume prey but also modify the traits of prey (e.g. physiology and behaviour). This study examined how the metabolic rate of prey (measured by CO2 release) changes as they perceive the presence of a predator in a laboratory setting. The jumping spider Hasarius adansoni was used as the study subject. Two species of jumping spiders, Plexippus paykulli and Ptocasius strupifer, and the oriental fruit fly Bactocera dorsalis were used as visual cues. Pl. paykulli is larger than H. adansoni and was used as a cue of predators. Pt. strupifer (smaller than H. adansoni) and B. dorsalis were used as reference controls. The response of H. adansoni to Pl. paykulli was dynamic, with CO2 release first increasing with the detection of the predator and then decreasing to a low level. Similar responses were not observed when H. adansoni detected the other species. The results show that H. adansoni reacts to visual cues of predation threat by rapidly changing its metabolic rate and suggest that the dynamic expressions of metabolism contain rich information about how H. adansoni perceives the environment.
High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment
Authors: Ford Antonia G. P. , Dasmahapatra Kanchon K. , Rüber Lukas , Gharbi Karim , Cezard Timothee , Day Julia J.
Published: May 2015

Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (FST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.
Evaluation of Disturbances in Mechanized Tunneling Using Process Simulation
Authors: Rahm Tobias , Scheffer Markus , Thewes Markus , König Markus , Duhme Ruben
Published: May 2015

Production in mechanized tunneling frequently encounters disruptions due to sensitive process interdependencies. Reasons can be technical failures, insufficient capacity dimensioning, organizational deficiencies, or sensitive supply chains. These unproductive times could be reduced by an adequately designed project setup including logistical aspects. Therefore, possible disturbances must be identified and analyzed in detail. Based on this investigation, the machine and logistics setup can be changed to cope with unforeseen events. We present a modeling and simulation approach to analyze production and logistic processes of mechanized tunneling processes in a transparent and understandable way. The system is formalized in the modeling standard SysML. Thereby, we consider relevant system elements and process interdependencies to assess the effect of disturbances and to identify bottlenecks. We distinguish three kinds of disruptions: (i) technical failure of main elements related to the production processes, (ii) issues resulting from an insufficient supply chain, and (iii) cascading disturbances. The implementation in a simulation environment and the processing of relevant input data are presented hereupon. The presented approach is then illustrated by means of an application example based on a completed metro project. Three extending simulation studies quantify the impact of the identified disturbance categories.
Detection of Orthobunyavirus in mosquitoes collected in Argentina
Authors: TAURO L. B. , BATALLAN G. P. , RIVAROLA M. E. , VISINTIN A. , BERRÓN C. I. , SOUSA E. C. , DIAZ L. A. , ALMIRON W. R. , NUNES M. R. , CONTIGIANI M. S.
Published: May 2015

Bunyamwera virus (BUNV) (Bunyaviridae, genus Orthobunyavirus, serogroup Bunyamwera) is considered an emerging pathogen for humans and animals in American countries. The CbaAr‐426 strain of BUNV was recovered from mosquitoes Ochlerotatus albifasciatus (Diptera: Culicidae) collected in Córdoba province (Argentina), where serological studies detected high seroprevalences in humans and animals. Molecular detection of Orthobunyavirus was performed in mosquitoes collected in Córdoba province. Seventeen mosquito pools of Oc. albifasciatus, Ochlerotatus scapularis and Culex quinquefasciatus (Diptera: Culicidae) showed positive results; four of these positive pools, all of Oc. scapularis, were sequenced. All amplicons grouped with BUNV in the Bunyamwera serogroup. The findings highlight the circulation of BUNV in Córdoba province and represent the first report of BUNV‐infected Oc. scapularis mosquitoes in Argentina.
Dynamic evolution of Geranium mitochondrial genomes through multiple horizontal and intracellular gene transfers
Authors: Park Seongjun , Grewe Felix , Zhu Andan , Ruhlman Tracey A. , Sabir Jamal , Mower Jeffrey P. , Jansen Robert K.
Published: May 2015

The exchange of genetic material between cellular organelles through intracellular gene transfer (IGT) or between species by horizontal gene transfer (HGT) has played an important role in plant mitochondrial genome evolution. The mitochondrial genomes of Geraniaceae display a number of unusual phenomena including highly accelerated rates of synonymous substitutions, extensive gene loss and reduction in RNA editing.

Mitochondrial DNA sequences assembled for 17 species of Geranium revealed substantial reduction in gene and intron content relative to the ancestor of the Geranium lineage. Comparative analyses of nuclear transcriptome data suggest that a number of these sequences have been functionally relocated to the nucleus via IGT.

Evidence for rampant HGT was detected in several Geranium species containing foreign organellar DNA from diverse eudicots, including many transfers from parasitic plants. One lineage has experienced multiple, independent HGT episodes, many of which occurred within the past 5.5 Myr.

Both duplicative and recapture HGT were documented in Geranium lineages. The mitochondrial genome of Geranium brycei contains at least four independent HGT tracts that are absent in its nearest relative. Furthermore, G. brycei mitochondria carry two copies of the cox1 gene that differ in intron content, providing insight into contrasting hypotheses on cox1 intron evolution.
Genes and networks regulating root anatomy and architecture
Authors: Wachsman Guy , Sparks Erin E. , Benfey Philip N.
Published: May 2015

The root is an excellent model for studying developmental processes that underlie plant anatomy and architecture. Its modular structure, the lack of cell movement and relative accessibility to microscopic visualization facilitate research in a number of areas of plant biology. In this review, we describe several examples that demonstrate how cell type‐specific developmental mechanisms determine cell fate and the formation of defined tissues with unique characteristics. In the last 10 yr, advances in genome‐wide technologies have led to the sequencing of thousands of plant genomes, transcriptomes and proteomes. In parallel with the development of these high‐throughput technologies, biologists have had to establish computational, statistical and bioinformatic tools that can deal with the wealth of data generated by them. These resources provide a foundation for posing more complex questions about molecular interactions, and have led to the discovery of new mechanisms that control phenotypic differences. Here we review several recent studies that shed new light on developmental processes, which are involved in establishing root anatomy and architecture. We highlight the power of combining large‐scale experiments with classical techniques to uncover new pathways in root development.

Contents

Summary
26

I.
Introduction
26

II.
Signaling modules that regulate cell fate
27

III.
Understanding global connections through gene regulatory networks
29

IV.
Signaling mechanism of organ formation: lateral root formation
32

V.
Genetic regulation of global root architecture
33

VI.
Conclusions
35

References
36
Possible World Semantics and True‐True Counterfactuals
Authors: Walters Lee
Published: May 2015

The standard semantics for counterfactuals ensures that any counterfactual with a true antecedent and true consequent is itself true. There have been many recent attempts to amend the standard semantics to avoid this result. I show that these proposals invalidate a number of further principles of the standard logic of counterfactuals. The case against the automatic truth of counterfactuals with true components does not extend to these further principles, however, so it is not clear that rejecting the latter should be a consequence of rejecting the former. Instead I consider how one might defuse putative counterexamples to the truth of true‐true counterfactuals.
How Long Has the Earth Existed? Persuasion and World‐Picture in Wittgenstein's On Certainty
Authors: Perissinotto Luigi
Published: May 2015

In some sections of On Certainty, Wittgenstein uses the term “persuasion,” pitting it, on the one hand, against “giving reasons” (proving and justifying), and comparing it, on the other, to conversion (also in the religious sense of the term), while, finally, defining it as “giving someone one's own picture of the world.” In this essay, I analyse these sections, in an effort to fit them into the broader context of On Certainty, and to clarify the meaning and the limits of the comparison between persuasion and conversion. My aim is to show that persuasion as Wittgenstein understands it here is quite similar to what we could call “re‐education.”
The Duty of Clarity: A Persuasion Effort. Continuity and Physics from Boltzmann to Wittgenstein
Authors: Montibeller Marcello
Published: May 2015

Despite several scholars referring to the relationships between the philosophy of Boltzmann and Wittgenstein, this topic is still to be explored. The aim of this paper is to analyse the similarities between their views on mathematical continuum and on the meaning of physical theories and phenomenological states of affairs. In several arguments, they both aim to achieve a similar task: by clarifying the meaning of theories in their concrete use, both authors persuade the reader to abandon an apparently intuitive way of thinking in order to overcome theoretical problems by dissolving them.
Do All Activities “Weigh” Equally? How Different Physical Activities Differ as Predictors of Weight
Authors: Lordan Grace , Pakrashi Debayan
Published: May 2015

In Britain, it is recommended that, to stay healthy, adults should do 150 minutes of moderate‐intensity physical activity every week. The recommendations provided by the U.K. government, however, remain silent in regard to the type of activity that should be done. Using the annual Health Survey for England we compare how different types of physical activities predict a person's weight. In particular, we consider clinically measured body mass index and waist circumference. We document mean slopes emanating from ordinary least squares regressions with these measures as the dependent variables. We show that individuals who walk at a brisk or fast pace are more likely to have a lower weight when compared to individuals doing other activities. Additionally, we highlight that the association between physical activity and weight is stronger for females and individuals over the age of 50. Our overall conclusions are robust to a number of specifications.
Risk Communication, Values Clarification, and Vaccination Decisions
Authors: Witteman Holly O. , Chipenda Dansokho Selma , Exe Nicole , Dupuis Audrey , Provencher Thierry , Zikmund‐Fisher Brian J.
Published: May 2015

Many health‐related decisions require choosing between two options, each with risks and benefits. When presented with such tradeoffs, people often make choices that fail to align with scientific evidence or with their own values. This study tested whether risk communication and values clarification methods could help parents and guardians make evidence‐based, values‐congruent decisions about children's influenza vaccinations. In 2013–2014 we conducted an online 2×2 factorial experiment in which a diverse sample of U.S. parents and guardians (n = 407) were randomly assigned to view either standard information about influenza vaccines or risk communication using absolute and incremental risk formats. Participants were then either presented or not presented with an interactive values clarification interface with constrained sliders and dynamic visual feedback. Participants randomized to the risk communication condition combined with the values clarification interface were more likely to indicate intentions to vaccinate (β = 2.10, t(399) = 2.63, p < 0.01). The effect was particularly notable among participants who had previously demonstrated less interest in having their children vaccinated against influenza (β = –2.14, t(399) = –2.06, p < 0.05). When assessing vaccination status reported by participants who agreed to participate in a follow‐up study six months later (n = 116), vaccination intentions significantly predicted vaccination status (OR = 1.66, 95%CI (1.13, 2.44), p < 0.05) and rates of informed choice (OR = 1.51, 95%CI (1.07, 2.13), p < 0.012), although there were no direct effects of experimental factors on vaccination rates. Qualitative analysis suggested that logistical barriers impeded immunization rates. Risk communication and values clarification methods may contribute to increased vaccination intentions, which may, in turn, predict vaccination status if logistical barriers are also addressed.
Conical Fluidized Bed with Arc Design for Improved Performance of Gas Distributor
Authors: Hamawand Ihsan , Da Silva W. P. , Jawad Ali H.
Published: May 2015

Particles distributions along a conical fluidized bed were predicted by an alternative arrangement of the minimum fluidization velocity equation. The proposed approach introduces two new equations which present the particle diameter in the bed as function of: height in the bed (Z), angle of inclination of the fluidized bed wall (θ), input flow rate (Qo), and gas distributor diameter (Do, 2ro). A novel arc-shaped design of the gas distributor was suggested, which provides enhanced distribution of the gas and enables greater control on the direction of the gas inlet. The model showed that the inclination of the fluidized bed wall should not exceed a critical angle, which can be determined with the set of equations specially developed for this purpose, to prevent inhomogeneous fluidization across the bed and accumulation of particles along the walls. By applying the Box Wilson Method, theoretical data were obtained for constant column diameter at the base (0.05 m), and varying bed height, Z, (range: 0.5 to 1.5 m), velocity of gas inlet, U, (range 0.25 to 1 m s-1), and balance factor, a, (range: 0.5 to 1, a new factor), respectively. The angle of inclination of the wall was first predicted based on the above parameters, and subsequently, the particle size distribution along the column was determined. Theoretically the novel arc-shaped distributor design has shown the potential of generating homogeneous fluidization regimes along the bed.
Bespoke finite difference schemes that preserve multiple conservation laws
Authors: Grant Timothy J.
Published: May 2015

Conservation laws provide important constraints on the solutions of partial differential equations (PDEs), therefore it is important to preserve them when discretizing such equations. In this paper, a new systematic method for discretizing a PDE, so as to preserve the local form of multiple conservation laws, is presented. The technique, which uses symbolic computation, is applied to the Korteweg–de Vries (KdV) equation to find novel explicit and implicit schemes that have finite difference analogues of its first and second conservation laws and its first and third conservation laws. The resulting schemes are numerically compared with a multisymplectic scheme.
Stability Analysis of a Schistosomiasis Transmission Model with Control Strategies
Authors: Diaby Mouhamadou
Published: May 2015

We have established and rigorously analyzed a new mathematical model that describes the dynamics schistosomiasis infection. This model incorporates several realistic features including density-dependent births rate of snails and reduced fecundity in snail hosts. Our qualitative analysis of the deterministic model is made with respect to the stability of the disease free equilibrium and the unique endemic equilibrium. Some biological consequences and control strategies are discussed. We have derived the basic reproduction number above which the infection will be controlled under certain levels. We have shown that the disease free equilibrium is globally asymptotically stable when the basic reproduction number ...
Generalized equipartition theorem and confining walls
Authors: Rey Rossend
Published: May 2015

It is shown that the generalized equipartition theorem as applied to the momentum may fail, even though the usual conditions of validity are met. This failure is linked to the nature of the confining walls, with ideal walls constituting a singular case. The corresponding analysis illustrates the use of proper sets of canonical coordinates, and the utility of canonical transformations other than point transformations.
Passive acoustic mapping utilizing optimal beamforming in ultrasound therapy monitoring
Authors: Coviello Christian , Kozick Richard , Choi James , Gyöngy Miklós , Jensen Carl , Smith Penny Probert , Coussios Constantin-C.
Published: May 2015

Passive acoustic mapping (PAM) is a promising imaging method that enables real-time three-dimensional monitoring of ultrasound therapy through the reconstruction of acoustic emissions passively received on an array of ultrasonic sensors. A passive beamforming method is presented that provides greatly improved spatial accuracy over the conventionally used time exposure acoustics (TEA) PAM reconstruction algorithm. Both the Capon beamformer and the robust Capon beamformer (RCB) for PAM are suggested as methods to reduce interference artifacts and improve resolution, which has been one of the experimental issues previously observed with TEA. Simulation results that replicate the experimental artifacts are shown to suggest that bubble interactions are the chief cause. Analysis is provided to show that these multiple bubble artifacts are generally not reduced by TEA, while Capon-based methods are able to reduce the artifacts. This is followed by experimental results from in vitro experiments and in vivo oncolytic viral therapy trials that show improved results in PAM, where RCB is able to more accurately localize the acoustic activity than TEA.
Effects of real-time cochlear implant simulation on speech production
Authors: Casserly Elizabeth D.
Published: May 2015

Investigations using normal-hearing subjects listening to simulations of cochlear implant (CI) acoustic processing have provided substantial information about the impact of these distorted listening conditions on the accuracy of auditory perception, but extensions of this method to the domain of speech production have been limited. In the present study, a portable, real-time vocoder was used to simulate conditions of CI auditory feedback during speech production in NH subjects. Acoustic-phonetic characteristics of sibilant fricatives, aspirated stops, and F1/F2 vowel qualities were analyzed for changes as a result of CI simulation of acoustic speech feedback. Significant changes specific to F1 were observed; speakers reduced their phonological vowel height contrast, typically via talker-specific raising of the low vowels [æ] and [ɑ] or lowering of high vowels [i] and [u]. Comparisons to the results of both localized feedback perturbation procedures and investigations of speech production in deaf adults with CIs are discussed.
Spatial-temporal ultrasound imaging of residual cavitation bubbles around a fluid–tissue interface in histotripsy
Authors: Hu Hong , Xu Shanshan , Yuan Yuan , Liu Runna , Wang Supin , Wan Mingxi
Published: May 2015

Cavitation is considered as the primary mechanism of soft tissue fragmentation (histotripsy) by pulsed high-intensity focused ultrasound. The residual cavitation bubbles have a dual influence on the histotripsy pulses: these serve as nuclei for easy generation of new cavitation, and act as strong scatterers causing energy “shadowing.” To monitor the residual cavitation bubbles in histotripsy, an ultrafast active cavitation imaging method with relatively high signal-to-noise ratio and good spatial-temporal resolution was proposed in this paper, which combined plane wave transmission, minimum variance beamforming, and coherence factor weighting. The spatial-temporal evolutions of residual cavitation bubbles around a fluid–tissue interface in histotripsy under pulse duration (PD) of 10–40 μs and pulse repetition frequency (PRF) of 0.67–2 kHz were monitored by this method. The integrated bubble area curves inside the tissue interface were acquired from the bubble image sequence, and the formation process of histotripsy damage was estimated. It was observed that the histotripsy efficiency decreased with both longer PDs and higher PRFs. A direct relationship with a coefficient of 1.0365 between histotripsy lesion area and inner residual bubble area was found. These results can assist in monitoring and optimization of the histotripsy treatment further.
Mathematical models for the acoustic response of a solids-loaded encapsulated bubble
Authors: Spencer Steven J.
Published: May 2015

A method of active acoustic resonance interference spectroscopy is introduced for estimation of bubble properties. A modified form of Rayleigh–Plesset equation for forced oscillation of either a single free bubble or elastic shell encapsulated microbubble with attached solids loading is solved by the regular perturbation method for steady oscillatory solutions as a result of small amplitude acoustic excitation by a point sinusoidal oscillator. A model for the total pressure field at an acoustic receiver in an incompressible liquid is then solved by the regular perturbation method. Closed-form analytical solutions are found for pressure power at the acoustic receiver as a function of the excitation frequency and strength; the properties of the bubble, liquid, and encapsulating shell; and the geometry of the active monitoring system. The receiver pressure power exhibits a maximum due to bubble resonance and a minimum due to destructive interference between source and bubble response pressure fields at higher excitation frequencies. The inverse problem is solved to derive unique closed-form analytical estimators for bubble equilibrium size, attached solids mass loading, and encapsulating layer dilatational viscosity as a function of the frequencies of the fundamental resonance maximum, interference minimum, second harmonic maximum total average acoustic power, monitoring system, and phase properties.
Material properties of Pacific hake, Humboldt squid, and two species of myctophids in the California Current
Authors: Becker Kaylyn N. , Warren Joseph D.
Published: May 2015

Material properties of the flesh from three fish species (Merluccius productus, Symbolophorus californiensis, and Diaphus theta), and several body parts of the Humboldt squid (Dosidicus gigas) collected from the California Current ecosystem were measured. The density contrast relative to seawater varied within and among taxa for fish flesh (0.9919−1.036), squid soft body parts (mantle, arms, tentacle, braincase, eyes; 1.009−1.057), and squid hard body parts (beak and pen; 1.085−1.459). Effects of animal length and environmental conditions on nekton density contrast were investigated. The sound speed contrast relative to seawater varied within and among taxa for fish flesh (0.986−1.027) and Humboldt squid mantle and braincase (0.937−1.028). Material properties in this study are similar to values from previous studies on species with similar life histories. In general, the sound speed and density of soft body parts of fish and squid were 1%−3% and 1%−6%, respectively, greater than the surrounding seawater. Hard parts of the squid were significantly more dense (6%−46%) than seawater. The material properties reported here can be used to improve target strength estimates from acoustic scattering models, which could increase the accuracy of biomass estimates from acoustic surveys for these nekton.
The role of excitation-pattern cues in the detection of frequency shifts in bandpass-filtered complex tones
Authors: Marmel Frederic , Plack Christopher J. , Hopkins Kathryn , Carlyon Robert P. , Gockel Hedwig E. , Moore Brian C. J.
Published: May 2015

One task intended to measure sensitivity to temporal fine structure (TFS) involves the discrimination of a harmonic complex tone from a tone in which all harmonics are shifted upwards by the same amount in hertz. Both tones are passed through a fixed bandpass filter centered on the high harmonics to reduce the availability of excitation-pattern cues and a background noise is used to mask combination tones. The role of frequency selectivity in this “TFS1” task was investigated by varying level. Experiment 1 showed that listeners performed more poorly at a high level than at a low level. Experiment 2 included intermediate levels and showed that performance deteriorated for levels above about 57 dB sound pressure level. Experiment 3 estimated the magnitude of excitation-pattern cues from the variation in forward masking of a pure tone as a function of frequency shift in the complex tones. There was negligible variation, except for the lowest level used. The results indicate that the changes in excitation level at threshold for the TFS1 task would be too small to be usable. The results are consistent with the TFS1 task being performed using TFS cues, and with frequency selectivity having an indirect effect on performance via its influence on TFS cues.
Speech perception of sine-wave signals by children with cochlear implants
Authors: Nittrouer Susan , Kuess Jamie , Lowenstein Joanna H.
Published: May 2015

Children need to discover linguistically meaningful structures in the acoustic speech signal. Being attentive to recurring, time-varying formant patterns helps in that process. However, that kind of acoustic structure may not be available to children with cochlear implants (CIs), thus hindering development. The major goal of this study was to examine whether children with CIs are as sensitive to time-varying formant structure as children with normal hearing (NH) by asking them to recognize sine-wave speech. The same materials were presented as speech in noise, as well, to evaluate whether any group differences might simply reflect general perceptual deficits on the part of children with CIs. Vocabulary knowledge, phonemic awareness, and “top-down” language effects were all also assessed. Finally, treatment factors were examined as possible predictors of outcomes. Results showed that children with CIs were as accurate as children with NH at recognizing sine-wave speech, but poorer at recognizing speech in noise. Phonemic awareness was related to that recognition. Top-down effects were similar across groups. Having had a period of bimodal stimulation near the time of receiving a first CI facilitated these effects. Results suggest that children with CIs have access to the important time-varying structure of vocal-tract formants.
Expectations and speech intelligibility
Authors: Babel Molly , Russell Jamie
Published: May 2015

Socio-indexical cues and paralinguistic information are often beneficial to speech processing as this information assists listeners in parsing the speech stream. Associations that particular populations speak in a certain speech style can, however, make it such that socio-indexical cues have a cost. In this study, native speakers of Canadian English who identify as Chinese Canadian and White Canadian read sentences that were presented to listeners in noise. Half of the sentences were presented with a visual-prime in the form of a photo of the speaker and half were presented in control trials with fixation crosses. Sentences produced by Chinese Canadians showed an intelligibility cost in the face-prime condition, whereas sentences produced by White Canadians did not. In an accentedness rating task, listeners rated White Canadians as less accented in the face-prime trials, but Chinese Canadians showed no such change in perceived accentedness. These results suggest a misalignment between an expected and an observed speech signal for the face-prime trials, which indicates that social information about a speaker can trigger linguistic associations that come with processing benefits and costs.
A sidelobe suppressing near-field beamforming approach for ultrasound array imaging
Authors: He Zhengyao , Zheng Fan , Ma Yuanliang , Kim Hyung Ham , Zhou Qifa , Shung K. Kirk
Published: May 2015

A method is proposed to suppress sidelobe level for near-field beamforming in ultrasound array imaging. An optimization problem is established, and the second-order cone algorithm is used to solve the problem to obtain the weight vector based on the near-field response vector of a transducer array. The weight vector calculation results show that the proposed method can be used to suppress the sidelobe level of the near-field beam pattern of a transducer array. Ultrasound images following the application of weight vector to the array of a wire phantom are obtained by simulation with the Field II program, and the images of a wire phantom and anechoic sphere phantom are obtained experimentally with a 64-element 26 MHz linear phased array. The experimental and simulation results agree well and show that the proposed method can achieve a much lower sidelobe level than the conventional delay and sum beamforming method. The wire phantom image is demonstrated to focus much better and the contrast of the anechoic sphere phantom image improved by applying the proposed beamforming method.
Minke whales (Balaenoptera acutorostrata) respond to navy training
Authors: Martin Stephen W. , Martin Cameron R. , Matsuyama Brian M. , Henderson E. Elizabeth
Published: May 2015

Minke whales (Balaenoptera acutorostrata) were acoustically detected and localized via their boing calls using 766 h of recorded data from 24 hydrophones at the U.S. Navy's Pacific Missile Range Facility located off Kauai, Hawaii. Data were collected before, during, and after naval undersea warfare training events, which occurred in February over three consecutive years (2011–2013). Data collection in the during periods were further categorized as phase A and phase B with the latter being the only period with naval surface ship activities (e.g., frigate and destroyer maneuvers including the use of mid-frequency active sonar). Minimum minke whale densities were estimated for all data periods based upon the numbers of whales acoustically localized within the 3780 km2 study area. The 2011 minimum densities in the study area were: 3.64 whales [confidence interval (CI) 3.31–4.01] before the training activity, 2.81 whales (CI 2.31–3.42) for phase A, 0.69 whales (CI 0.27–1.8) for phase B and 4.44 whales (CI 4.04–4.88) after. The minimum densities for the phase B periods were highly statistically significantly lower (p < 0.001) from all other periods within each year, suggesting a clear response to the phase B training. The phase A period results were mixed when compared to other non-training periods.
Integration over song classification replicates: Song variant analysis in the hihi
Authors: Ranjard Louis , Withers Sarah J. , Brunton Dianne H. , Ross Howard A. , Parsons Stuart
Published: May 2015

Human expert analyses are commonly used in bioacoustic studies and can potentially limit the reproducibility of these results. In this paper, a machine learning method is presented to statistically classify avian vocalizations. Automated approaches were applied to isolate bird songs from long field recordings, assess song similarities, and classify songs into distinct variants. Because no positive controls were available to assess the true classification of variants, multiple replicates of automatic classification of song variants were analyzed to investigate clustering uncertainty. The automatic classifications were more similar to the expert classifications than expected by chance. Application of these methods demonstrated the presence of discrete song variants in an island population of the New Zealand hihi (Notiomystis cincta). The geographic patterns of song variation were then revealed by integrating over classification replicates. Because this automated approach considers variation in song variant classification, it reduces potential human bias and facilitates the reproducibility of the results.
Changes in otoacoustic emissions during selective auditory and visual attention
Authors: Walsh Kyle P. , Pasanen Edward G. , McFadden Dennis
Published: May 2015

Previous studies have demonstrated that the otoacoustic emissions (OAEs) measured during behavioral tasks can have different magnitudes when subjects are attending selectively or not attending. The implication is that the cognitive and perceptual demands of a task can affect the first neural stage of auditory processing—the sensory receptors themselves. However, the directions of the reported attentional effects have been inconsistent, the magnitudes of the observed differences typically have been small, and comparisons across studies have been made difficult by significant procedural differences. In this study, a nonlinear version of the stimulus-frequency OAE (SFOAE), called the nSFOAE, was used to measure cochlear responses from human subjects while they simultaneously performed behavioral tasks requiring selective auditory attention (dichotic or diotic listening), selective visual attention, or relative inattention. Within subjects, the differences in nSFOAE magnitude between inattention and attention conditions were about 2–3 dB for both auditory and visual modalities, and the effect sizes for the differences typically were large for both nSFOAE magnitude and phase. These results reveal that the cochlear efferent reflex is differentially active during selective attention and inattention, for both auditory and visual tasks, although they do not reveal how attention is improved when efferent activity is greater.
A multi-hypothesis tracker for clicking whales
Authors: Baggenstoss Paul M.
Published: May 2015

This paper describes a tracker specially designed to track clicking beaked whales using widely spaced bottom-mounted hydrophones, although it can be adapted to different species and sensors. The input to the tracker is a sequence of static localization solutions obtained using time difference of arrival information at widely spaced hydrophones. To effectively handle input localizations with high ambiguity, the tracker is based on multi-hypothesis tracker concepts, so it considers all potential association hypotheses and keeps a large number of potential tracks in memory. The method is demonstrated on actual data and shown to successfully track multiple beaked whales at depth.
Targeting phosphatase-dependent proteoglycan switch for rheumatoid arthritis therapy
Authors: Doody Karen M. , Stanford Stephanie M. , Sacchetti Cristiano , D. Svensson Mattias N. , Coles Charlotte H. , Mitakidis Nikolaos , Kiosses William B. , Bartok Beatrix , Fos Camille , Cory Esther , Sah Robert L. , Liu-Bryan Ru , Boyle David L. , Arnett Heather A. , Mustelin Tomas , Corr Maripat , Esko Jeffrey D. , Tremblay Michel L. , Firestein Gary S. , Aricescu A. Radu , Bottini Nunzio
Published: May 2015

Targeting joint-lining fibroblast-like synoviocytes reduces the severity of arthritis.
Clostridium clariflavum: Key Cellulosome Players Are Revealed by Proteomic Analysis
Authors: Artzi Lior , Morag Ely , Barak Yoav , Lamed Raphael , Bayer Edward A.
Published: May 2015

Clostridium clariflavum
is an anaerobic, cellulosome-forming thermophile, containing in its genome genes for a large number of cellulosomal enzyme and a complex scaffoldin system. Previously, we described the major cohesin-dockerin interactions of the cellulosome components, and on this basis a model of diverse cellulosome assemblies was derived. In this work, we cultivated
C. clariflavum
on cellobiose-, microcrystalline cellulose-, and switchgrass-containing media and isolated cell-free cellulosome complexes from each culture. Gel filtration separation of the cellulosome samples revealed two major fractions, which were analyzed by label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) in order to identify the key players of the cellulosome assemblies therein. From the 13 scaffoldins present in the
C. clariflavum
genome, 11 were identified, and a variety of enzymes from different glycoside hydrolase and carbohydrate esterase families were identified, including the glycoside hydrolase families GH48, GH9, GH5, GH30, GH11, and GH10. The expression level of the cellulosomal proteins varied as a function of the carbon source used for cultivation of the bacterium. In addition, the catalytic activity of each cellulosome was examined on different cellulosic substrates, xylan and switchgrass. The cellulosome isolated from the microcrystalline cellulose-containing medium was the most active of all the cellulosomes that were tested. The results suggest that the expression of the cellulosome proteins is regulated by the type of substrate in the growth medium. Moreover, both cell-free and cell-bound cellulosome complexes were produced which together may degrade the substrate in a synergistic manner. These observations are compatible with our previously published model of cellulosome assemblies in this bacterium.

IMPORTANCE
Because the reservoir of unsustainable fossil fuels, such as coal, petroleum, and natural gas, is overutilized and continues to contribute to environmental pollution and CO
2
emission, the need for appropriate alternative energy sources becomes more crucial. Bioethanol produced from dedicated crops and cellulosic waste can provide a partial answer, yet a cost-effective production method must be developed. The cellulosome system of the anaerobic thermophile
C. clariflavum
comprises a large number of cellulolytic and hemicellulolytic enzymes, which self-assemble in a number of different cellulosome architectures for enhanced cellulosic biomass degradation. Identification of the major cellulosomal components expressed during growth of the bacterium and their influence on its catalytic capabilities provide insight into the performance of the remarkable cellulosome of this intriguing bacterium. The findings, together with the thermophilic characteristics of the proteins, render
C. clariflavum
of great interest for future use in industrial cellulose conversion processes.
A Novel Pathogenic Mammalian Orthoreovirus from Diarrheic Pigs and Swine Blood Meal in the United States
Authors: Thimmasandra Narayanappa Athmaram , Sooryanarain Harini , Deventhiran Jagadeeswaran , Cao Dianjun , Ammayappan Venkatachalam Backiyalakshmi , Kambiranda Devaiah , LeRoith Tanya , Heffron Connie Lynn , Lindstrom Nicole , Hall Karen , Jobst Peter , Sexton Cary , Meng Xiang-Jin , Elankumaran Subbiah
Published: May 2015

Since May 2013, outbreaks of porcine epidemic diarrhea have devastated the U.S. swine industry, causing immense economic losses. Two different swine enteric coronaviruses (porcine epidemic diarrhea virus and Delta coronavirus) have been isolated from the affected swine population. The disease has been reported from at least 32 states of the United States and other countries, including Mexico, Peru, Dominican Republic, Canada, Columbia, Ecuador, and Ukraine, with repeated outbreaks in previously infected herds. Here we report the isolation and characterization of a novel mammalian orthoreovirus 3 (MRV3) from diarrheic feces of piglets from these outbreaks in three states and ring-dried swine blood meal from multiple sources. MRV3 could not be isolated from healthy or pigs that had recovered from epidemic diarrhea from four states. Several MRV3 isolates were obtained from chloroform-extracted pig feces or blood meal in cell cultures or developing chicken embryos. Biological characterization of two representative isolates revealed trypsin resistance and thermostability at 90°C. NextGen sequencing of ultrapurified viruses indicated a strong homology of the S1 segment to mammalian and bat MRV3. Neonatal piglets experimentally infected with these viruses or a chloroform extract of swine blood meal developed severe diarrhea and acute gastroenteritis with 100% mortality within 3 days postinfection. Therefore, the novel porcine MRV3 may contribute to enteric disease along with other swine enteric viruses. The role of MRV3 in the current outbreaks of porcine epidemic diarrhea in the United States remains to be determined, but the pathogenic nature of the virus warrants further investigations on its epidemiology and prevalence.

IMPORTANCE
Porcine orthoreoviruses causing diarrhea have been reported in China and Korea but not in the United States. We have isolated and characterized two pathogenic reassortant MRV3 isolates from swine fecal samples from porcine epidemic diarrhea outbreaks and ring-dried swine blood meal in the United States. These fecal and blood meal isolates or a chloroform extract of blood meal induced severe diarrhea and mortality in experimentally infected neonatal pigs. Genetic and phylogenetic analyses of two MRV3 isolates revealed that they are identical but differed significantly from nonpathogenic mammalian orthoreoviruses circulating in the United States. The present study provides a platform for immediate development of suitable vaccines and diagnostics to prevent and control porcine orthoreovirus diarrhea.
Management of developmental speech and language disorders. Part 2: acquired conditions
Authors: O'Hare Anne
Published: May 2015

Many children who present with these acquired impairments of communication have a clear preceding event such as an acquired brain injury from a road traffic accident. Children often respond differently in this situation to adult presentations. They may have a period of mutism when the prognosis might look poor and yet they subsequently make rapid progress and recover speech. They have greater potential for neural plasticity and language recovery, although they often have persisting difficulties in oral and written language. Alternatively, there may be a presentation with a paroxysmal event such as a seizure or a period of depressed consciousness, and the unusual behaviour that may accompany dysphasia and dysarthria may be misinterpreted in the child, whereas for the adult with the more common ‘stroke-like’ presentation, it would be immediately considered. Rarely the aphasia/dysphasia may itself be the paroxysmal event where actually recognising that the child's disrupted communication is the basis of any observed behaviours can be the greater challenge.
Breast cancer in male-to-female (MtF) transgender patients: is hormone receptor negativity a feature?
Authors: Teoh Zhi Hao , Archampong David , Gate Tim
Published: May 2015

A 41-year-old male-to-female (MtF) transgender patient presented with a symptomatic tender lump in the left breast. There was no family history of breast cancer. She had been receiving estrogen therapy for 14 years to maintain her secondary sexual characteristics. Triple assessment revealed a 13 mm triple-negative grade 3 invasive ductal carcinoma. The tumour was completely excised following a left wide local excision and sentinel lymph node biopsy. There was no regional lymph node involvement. She was referred to the oncologist for adjuvant chemotherapy and radiotherapy.
Fishbone-induced perforated appendicitis
Authors: Bababekov Yanik J , Stanelle Eric J , Abujudeh Hani H , Kaafarani Haytham M A
Published: May 2015

We review the literature and describe a case of fishbone-induced appendicitis. A 63-year-old man presented with abdominal pain. Work up including a focused history and imaging revealed fishbone-induced perforated appendicitis. The patient was managed safely and successfully with laparoscopic removal of the foreign body and appendectomy.
Radial shaft stress fracture after internal fixation using a titanium plate
Authors: Nagoshi Narihito , Yamanaka Kazuyoshi , Sasaki Takashi
Published: May 2015

A 22-year-old man, a boxer, presented with acute right forearm pain after striking a punch mitt. The patient had sustained a diaphyseal fracture of the right radius 19 months previously and was treated by minimally invasive plate osteosynthesis using a titanium reconstruction plate. Radiography revealed stress fractures beneath a proximal screw hole of the plate. The forearm was protected in a splint for 6 weeks and the fracture healed. Titanium plates are superior to stainless steel plates, due to various properties of titanium including corrosion resistance and biocompatibility. Removal of such plates is not routinely performed in our hospital, but plate removal may be warranted for patients who actively participate in certain sports.