bluuebunny/crossref_metadata_2025 huggingface dataset:
Robust real-time implementation of adaptive feedback cancellation using noise injection algorithm on smartphone
Authors: Mishra Parth , Tokgoz Serkan , Panahi Issa M.
Published: April 2018

We propose a novel low latency smartphone-based application that demonstrates the real-time operation to cancel the negative effects of acoustic feedback arising from the coupling between the speaker and the microphone of the smartphone or similar device utilizing the robust Noise Injection (NI) method. We make use of multiple noise injections of short durations to estimate the filter coefficients of an appropriate order between the speaker and the microphone, in order to perform the feedback cancellation effectively in real-time. Our motive behind the development of this application is to perform an effective acoustic feedback cancellation irrespective of the position of speaker and the microphone on the platform under consideration. With the proposed application, we can estimate the transfer function between speaker and microphone in the changing room acoustics making the feedback cancellation very effective. Objective and subjective tests were conducted and results of the proposed real-time application indicate significant acoustic feedback suppression in the presence of varying environmental conditions.
Comparison of processing speed between Arduino Due and Teensy 3.6 boards in a system identification application
Authors: Zorzo Artur , Fonseca William D. , Mareze Paulo , Brandao Eric
Published: April 2018

The system identification technique is a powerful real-time signal processing tool when dealing with the characterization of dynamic systems. This approach uses adaptive filtering techniques and the least mean square (LMS) algorithm to estimate the impulse response of a system in a finite impulse response (FIR) filter format. The main purpose of this paper is to compare the results and processing speed of two ARM-based microcontrollers as well as to give a theoretical background and an implementation procedure of the technique. ARM (Advanced RISC Machine) is an architecture of 32-bit processors usually applied in embedded systems due to its processing power, relatively low consumption, cost and small size. The impulse responses obtained by the method for several passive electronic filters were transformed to the frequency domain and compared with simulations of the circuits' frequency responses. This practice was repeated for both boards and for different parameters of the algorithm. The results have shown that the Arduino Due was unable to deal with higher sampling frequencies due to its processor limitations. On the other hand, the Teensy 3.6, a more powerful controller, yields great results even for higher frequencies.
Tracking and classification of targets detected by a moving multibeam sonar
Authors: Cotter Emma D. , Joslin James , Polagye Brian
Published: April 2018

There are multiple applications where tracking and classification of targets detected in multibeam sonar data is required, ranging from environmental studies to marine security. Target tracking from a fixed frame of reference is well-established, but if the sonar is mounted to a surface-following platform or vessel, the tracking task is complicated by the moving frame of reference. Here, accelerometer data is integrated into a Kalman filter-based tracking scheme to correct for the motion of a non-stationary sonar. This technique is first verified using a vessel-mounted sonar and target with known position. Tracking of marine animals from a moving platform is then demonstrated in real-time for the case of a sonar mounted on the hull of a wave energy converter. These target tracks are classified in real time (e.g., diving bird, seal) using a Random Forest algorithm. The effectiveness and limitations of real-time target tracking and classification from a moving multibeam sonar are discussed.
A method of distinguishing between surface and underwater targets based on time delay in deep water
Authors: Zhao Chunpeng , Liang Guolong
Published: April 2018

It is difficult to distinguish between surface and underwater targets in passive detecting with a single sensor or a horizontal linear array in deep water. It is noticed that targets in different depths have different characteristics in time delay difference of rays. This paper takes advantage of this feature to discriminate targets' depths in direct-arrival zone and shadow zone in deep water. And the relation between judgment boundary and depth of sensor is analyzed. The simulation result shows that when the depth of sensor is 50m, the boundary which can distinguish between surface and underwater targets can be set to 10m. And the depth of the boundary decreases with the increase of the depth of sensor.
Direction estimation of coherent signals based on the symmetry of uniform linear array
Authors: Tian Yunqi , Liang Guolong , Jin Fu
Published: April 2018

A large number of coherent signals are generated due to interface reflection in the ocean. A novel algorithm based on the symmetry of uniform linear array (ULA) is proposed to solve the problem of direction of arrival (DOA) estimation in coherent environment. Considering the center sensor as the reference, ULA can be divided into two symmetric parts. Firstly, the conjugate data of one part is rearranged, meanwhile, the other part data is maintained. Secondly, the correlation function calculated by processed data is averaged to construct a full rank Hermitian Toeplitz matrix. Finally, we can estimate the directions of coherent sources by eigen-decomposition. The results of simulation show that the proposed algorithm not only can effectively distinguish coherent signals, but also can improve the resolution, the accuracy and the probability of success in DOA estimation. Furthermore, the proposed algorithm is robust in the case of lower SNR or fewer snapshots.
Generation of ultrasonic waves in vegetable tissue via non-ablative laser pulses
Authors: Collazos-Burbano David A. , Melo-Luna Carlos A. , Ealo Joao L. , Reina John H.
Published: April 2018

The study of vegetable tissue is essential in plant growth analysis. The elasticity is an important characteristic when firmness is studied in fruits or when turgidity is tested in plant leaves. This property gives information about the ripeness of fruits, the water content in leaves, and, in general, the morphological and physiological state of plants. Hence, the propagation of elastic waves in these media is a useful tool that gives information about the developmental stage of the plant. In this sense, laser ultrasonics is a promising method in the characterization of composite materials. In a certain way, vegetable tissues can be thought of as a kind of biological composite abstracted as a stratified plate of several layers. In this work, as a first approximation, we propose a methodology to generate guided waves in vegetable tissues by using laser ultrasonics techniques. We implement a pulsed laser system to induce ultrasonic waves without damage on the samples. Besides, we develop a methodology for processing the propagated acoustic waves. This analysis allows us the assessment of dispersive properties, a useful tool when determining important descriptors such as firmness index, water content, and provide useful information to feed biophysical models, among others.
Elastic constants of self-healing polyethylene co-methacrylic acid determined via resonant ultrasound spectroscopy
Authors: Pestka II Kenneth A. , Hull Jacob W. , Buckley Jonathan D. , Kalista Stephen J.
Published: April 2018

Self-healing polyethylene co-methacrylic acid (EMAA) is a thermoplastic material that can be shaped into structures that are capable of autonomously healing after being cut, punctured, or shot. In this work, we present results from several samples of self-healing EMAA-0.6 Na, with 60% of the methacrylic acid groups neutralized by sodium, known as DuPont Surlyn 8920. This ionomer, unlike typical crystals with extremely high quality factors and easily identifiable ultrasonic resonances, is a relatively soft polymeric material with significant damping, resulting in sample resonances that can overlap and are often difficult to identify and isolate. In this work, we show the resonant spectrum of several different EMAA-0.6 Na samples as well as the methods used to isolate individual resonances and determine the elastic constants.
Timing effects in auditory-related forward predictions
Authors: Varghese Leonard , Shinn-Cunningham Barbara
Published: April 2018

Violation of learned sensory consequences may generate neural “error” signals that inform subsequent behavior. We investigated how this feedback loop might function in human audition, focusing specifically on timing mismatch signals in cortical structures. Participants pressed a button to trigger a sound at an expected, delayed onset. This sound was usually a broadband click (“standard”), but sometimes a low-pass filtered click (“target”). During 100% of trials during the first two experimental blocks, and on >80% of subsequent trials, these sounds occurred ~1 s after a button press. On the remaining <20% of trials, standards were presented slightly early (“early deviants”) or slightly late (“late deviants”) by 150–200 ms. Listeners were told to respond with a button press to targets; they were not informed about the timing manipulation. We used electroencephalography (EEG) to compare responses evoked by the physically identical expected standards, early deviants, and late deviants. EEG responses evoked by standards and temporal deviants appeared to reflect inter-subject differences in baseline auditory encoding strength, differences in mismatch encoding strength, and/or motor-induced suppression. Subsequent analyses will attempt to disambiguate the relative strength of these contributions, with the goal of determining the extent to which forward sensory predictions in audition reflect expected timing.
Behavioral and electrophysiological evidence of incidental learning, generalization, and retention of speech categories from continuous speech
Authors: Wu Yunan C. , Liu Ran , Lim Sung-Joo , Holt Lori L.
Published: April 2018

Speech learning involves discovering appropriate functional speech units (e.g., speech categories) embedded in a continuous stream of speech. However, speech category learning has been mostly investigated with isolated sound tokens. Here, we used a videogame to encourage incidental learning of speech categories from continuous speech input (Lim et al., 2015). Native English participants (N = 17) played the videogame while listening to acoustically-variable continuous Mandarin sentences. Unbeknownst to participants, four acoustically-variable Mandarin keywords were embedded in the continuous sentences. During training, participants were not informed about the keywords, made no overt categorization decisions, and received no feedback. Participants' post-training categorization test demonstrated robust incidental learning of keyword that persisted even 10 days after training, and generalized to novel utterances and talkers. Further, the N100 response in the frontal EEG site evoked by keyword onsets within continuous Mandarin speech during passive listening was greater post-training compared to pre-training. This neural enhancement was specific to the Mandarin keywords functionally useful in videogame training. Our results demonstrate that although participants were not informed about the keywords, they did not make overt categorization decisions during videogame play, they incidentally learn functionally-relevant non-native speech categories from continuous speech input across considerable acoustic variability.
Sequential stream segregation based on spatial cues: Behavioral and neural measurements
Authors: David Marion , Oxenham Andrew J.
Published: April 2018

Differences in simulated spatial cues in the horizontal plane have been shown to enhance both voluntary and obligatory stream segregation of sounds with realistic spectro-temporal variations, such as sequences of syllables. In this experiment, listeners were presented with sequences of speech tokens, each consisting of a fricative consonant and a voiced vowel. The CV tokens were concatenated into interleaved sequences that alternated in simulated spatial positions. The interleaved sequences lasted 1 min. The listeners had to press a button each time they heard a repeated token. In the selective attention task, the listeners were asked to attend only one of the two interleaved sequences; in the global attention task, the listeners had to perceive the interleaved sequences as single stream to detect a repetition between the sequences. Simultaneous EEG measurements were made. The behavioral results confirmed that listeners were able to either attend selectively or globally, depending on the task requirements. The EEG waveforms differed between the two tasks, despite identical physical stimuli, reflecting the difference between global and selective attention. Both behavioral and EEG results reflected the effects of increasing spatial separation in enhancing selective attention and making global attention to the sequences more difficult.
Behavioral measures of cochlear gain reduction and gain reduction in with normal hearing or minimal cochlear hearing loss
Authors: Strickland Elizabeth A. , Morris Hayley , Skaggs Miranda , Salloom William , Holt Alexis
Published: April 2018

This is a continuation of a study examining the relationship between cochlear hearing loss and various psychoacoustic measures thought to be related to cochlear function. In the listeners tested, thresholds for long tones ranged from well within the clinically normal range to just outside this range. Where thresholds were elevated, other clinical tests were consistent with a cochlear origin. Because the medial olivocochlear reflex (MOCR) decreases the gain of the cochlear active process in response to sound, when possible, measures were made with short stimuli. Signal frequencies were 2, 4, and 8 kHz. Maximum gain was estimated by measuring the threshold masker level for a masker at the signal frequency and a masker well below the signal frequency. The effect of signal duration on threshold was measured using 10 and 200-signals. One point on the lower leg of the input/output function was measured by finding the threshold masker level for a masker slightly less than one octave below the signal frequency needed to mask a signal at 5 dB SL. Gain reduction was estimated by presenting a pink noise precursor before the signal and masker, and measuring the change in signal threshold as a function of precursor level. The relationship between these measures will be discussed. [Work supported by NIH(NIDCD)R01 DC008327 (EAS), and grants from the Purdue Office of the Executive Vice President for Research and the Purdue Graduate School (WS).]
Source-filter interaction: A study using vocal-tract data of a soprano singer
Authors: Kaburagi Tokihiko , Ando Momoyo , Uezu Yasufumi
Published: April 2018

When the fundamental frequency of voice is close to a formant frequency, the voice-source system in the larynx and the acoustic filter of the vocal tract can be coupled acoustically. This source-filter interaction (SFI) can cause unsteadiness in vocal fold oscillations, sudden jump of the fundamental frequency, and transitions in voice register. In this study, a magnetic resonance imaging device was used to scan the vocal tract of a soprano singer in three dimensions when she produced sustained vowels with different notes ranging from A3 (220 Hz) to A5 (880 Hz). The cross-sectional area and the input impedance of the vocal tract were then determined from image data. As a result, the frequency and the magnitude of the first impedance peak for the /i/ vowel increased when the note became higher, suggesting that a strong source-filter interaction may take place for high notes when the fundamental frequency is close to the peak frequency. We therefore conducted a computer simulation of voice generation using models of the vocal folds and the vocal tract. Our preliminary results showed different SFI effects depending on the magnitude of the impedance peak. [This work was supported by JSPS KAKENHI Grant No. JP16K00242.]
Stress-sensitive consonant gemination through plural noun reduplication in Tohono O’odham
Authors: Kim Daejin , Cruz Robert
Published: April 2018

This study examines how plural noun reduplication in Tohono O’odham (TO) language is phonetically realized. To make a noun plural, the first CV sequence (i.e., base; e.g., goks “a dog” → gogoks “dogs”) or the first consonant of the base (e.g., pado “a pig” → papdo “pigs”) are reduplicated after the base (Hill & Zepeda, 1998). Base and reduplicant have been regarded phonologically equivalent (i.e., consonant gemination; Fitzgerald, 2003). In a sense that TO has the strong-weak stress pattern across syllables (e.g., tówa “turkey”), stress may influence reduplicants' duration. The CV reduplicant at the second syllable with the weak stress may not be phonologically same as the base and the C reduplicant at the coda of the base with the strong stress. If CV and C reduplicants are equivalent even with stress, an additional prosodic unit (i.e., mora) may exist. The analysis of TO speech supports that the base (CV1) is longer than the reduplicant (CV2 or C2) even with other contextual variables. Reduplication process may be stress-timed, but it is unknown whether speakers equally treat base and reduplicants. This paper will also discuss a need to examine how TO speakers control the timing with rhythm between base and reduplicant.
Using speech stereotypes to assert identity and affinity with a minority group
Authors: Lutzross Auburn
Published: April 2018

Perception-based studies on female speech have demonstrated clear stereotypes associating acoustic qualities and sexual orientation (e.g., Camp 2009, Munson et al. 2005, Pierrehumbert et al. 2004). However, production studies on female speech are rare and inconclusive: though male speakers have been shown to vary their use of stereotypically gay speech according to context (Podesva 2011), female speakers have not been studied. Likewise, there has been little consideration of how other personal attributes can intersect with sexual orientation to affect use of stereotypical speech. This study addresses the following for female speakers: (1) how personal attributes interact with sexual orientation in phonetic variation, (2) why straight or bisexual speakers might take on features of stereotypically lesbian speech, and (3) how these personal factors affect speech in different contexts and the resulting inter-speaker and inter-context variation. Speakers were recorded in both reading and interview speech modes. ANOVA of phonetic variation revealed that for straight and bisexual speakers, their “familiarity with Queer culture” was the most influential attribute on both speech modes. However, there was no such effect for lesbian speakers. I argue that speakers used stereotypical lesbian speech patterns to express outgroup affinity.
The influence of siblings on toddlers’ mean length of utterance
Authors: VanDam Mark , Saur Allison , Anderst Jenna , Olds Daniel , De Palma Paul
Published: April 2018

Linguistic complexity is an indicator of language development in young children. Complexity of a child’s linguistic productions have been shown to increase with development, but may be affected by factors such as disability or environmental variables. Here, we look into the role of family composition as a possible influence on a child’s developing ability to use increasingly complex language. In particular, we ask if a toddler’s mean length of utterance (MLU) is affected by the presence of siblings in the family and whether the sex of the child may play a role. MLU values were extracted from the public HomeBank database [http://homebank.talkbank.org] of transcribed natural child speech for both the target toddler and for siblings present in the recordings. Results indicate a main effect of increased MLU in children without siblings, but interaction effects suggest that differences may be driven by the boys without siblings alone. There was no correlation between the MLU of the target child and the MLU of the sibling. Findings are discussed in terms of family dynamics and joint attention.
Changes in vowel space characteristics during speech development based on longitudinal of measurements of formant frequencies
Authors: Story Brad H. , Bunton Kate , Diamond Rebekkah
Published: April 2018

During speech development, a child’s vocal tract undergoes changes due to growth of anatomic structures. Such changes typically lower the formant frequencies, reshaping the [F1,F2] vowel space. Much of what is known about vowel space change, however, is based on cross-sectional formant measurements averaged over children in various age groups. The purpose of this study was to characterize changes in the vowel space of four children between the ages of 2 and 6 years. Longitudinally-collected audio recordings of four children (2F,2M) were selected from the Arizona Child Acoustic Database. Each child had been recorded every four months from ages 2-6 years, and produced a variety of words, phrases, vowel-vowel progressions, and occasional spontaneous speech. Formant frequencies (F1 and F2 only) were measured from the recordings using a spectral filtering technique. At each age increment, the formant frequencies for each child were plotted as vowel space density, where the “density” dimension indicates the relative tendency of a talker to produce sound in particular region of the vowel space. The change in location and shape of the density cloud during this period of development will be demonstrated. [Research supported by NIH R01-DC011275, NSF BCS-1145011.]
Waveform performance and sidelobe reduction techniques for continuous active sonar (CAS)
Authors: Adams Matthew T. , Bishop Brian B. , Rotker Nicholas A.
Published: April 2018

The ability to conduct surveillance and tracking of targets over a wide area necessitates the use of a distributed sensing network and an appropriate processing scheme. One such technique that may be appropriate for the target tracking problem is continuous active sonar (CAS). In September 2016, an experiment was performed in Narragansett Bay, RI, to assess the performance of CAS for tracking a single unmanned underwater vehicle (UUV). PN sequence-coded chirps and LFM pulses of various bandwidths and center frequencies were transmitted from one transducer and received at two hydrophones in different locations. Following the experiment, several range-doppler sidelobe reduction techniques were experimented with to improve target detections and range-doppler estimations. During processing, waveform properties critical to sidelobe reduction performance were identified, and new waveforms have been chosen which exhibit these properties. A new experiment will be conducted in the coming months to demonstrate the performance of these waveforms, and results are expected to show improved detections and range-doppler estimations for various targets.
Demonstration of a compact quasi-monostatic autonomous underwater vehicle based continuous active sonar
Authors: Waters Zachary J.
Published: April 2018

Monostatic active sonar systems are typically operated in a pulsed transmit configuration, where an acoustic source is first activated to provide ensonification of the environment and then de-activated while scattered and ambient environmental acoustic energy is collected by a receiving sensor. In applications where the transmitter and receiver are in close proximity as with a monostatic configuration, it is typically impracticable to carry out the simultaneous transmission and reception of acoustic energy. Under such conditions, during continuous transmission, the source may saturate the receive sensors, potentially resulting in an overlap of target scattering returns from down-range with the direct acoustic coupling response from the source-to-receiver as well as reverberation, effectively blinding the sonar. Here, we explore the feasibility of techniques to disambiguate lower level target returns from a continuously transmitting autonomous underwater vehicle (AUV) based sonar. We conclude via theoretical studies supported by empirical analysis that the continuous transmission and reception of acoustic energy in a shallow-water waveguide is feasible for a realistic AUV based sonar system and overview demonstrations of these techniques to detect a bottomed target-object at-sea. [Work Supported by the Office of Naval Research.]
Inference regarding the state of a mobile underwater object from narrow band observations on a small aperture vertical array
Authors: Barros Abner C. , Gendron Paul J.
Published: April 2018

A narrowband source ensonifies an area of interest in a refractive undersea environment. A small aperture vertical array is employed to infer the depth, range and speed of the acoustic scatterer by resolving the scattered direct and surface interacting wave fronts. Tracking the target by means of a continuous wave transmission is challenging due to the difficulty of inferring the frequencies and angles of the two returned closely spaced wave vectors. The propagation of sound in a refractive medium presents additional challenges for inversion of the wave vectors to range, depth, and speed. Joint posterior inference is made possible with a computational Bayesian Gibbs sampling scheme over all track parameters taking full advantage of the analytic tractability of the conditional densities of the received amplitudes and phases and of the ambient acoustic noise power. The conditional densities of the ordered wave vectors however are constructed numerically by 2-dimensional inverse quantile sampling. The inferred joint posterior density of the target state is obtained by constructing a numerical inverse transformation of the acoustic propagation model and provides posterior confidence intervals over speed, depth, and range. Simulation results demonstrate the approach at received signal to noise ratios (SNR) well below -9 dB and illuminate the limits of depth and speed estimation as a function of both depth and SNR.
Normal mode coupling through horizontally variable sound speed
Authors: Clark Cathy Ann
Published: April 2018

In conjunction with construction of a normal mode model specifically designed to compute acoustic propagation in shallow water environments, the coupling associated with horizontally variable sound speed is predicted using a closed form solution in a modified Pekeris wave guide with a hard bottom. The code enables analysis of the correspondence between mode summation and the corresponding wave propagation as represented by ray propagation. The closed form solution is being used to provide insights into horizontal mode coupling and as a benchmark for verification of coupling in the shallow water normal mode solution.
An immersed interface method for the solution of the wide-angle parabolic equation in range-dependent ocean environments
Authors: Sabatini Roberto , Cristini Paul
Published: April 2018

Taking into account accurately a complex topography, within the framework of the parabolic equation method in underwater acoustics, is a difficult task. Several methods have been successfully proposed in the literature in order to improve the accuracy of numerical simulations. Nevertheless, despite the recent improvements, finding an accurate solution remains an open problem. In this presentation, we propose a novel approach for the treatment of irregular ocean bottoms within the framework of the wide-angle parabolic equation. This new approach is based on the immersed interface method originally developed by LeVeque and Li [SIAM J. Numer. Anal. 31(4), 1019–1044, (1994)]. It is intrinsically energy-conserving and allows to naturally handle generic range-dependent bathymetries. As an illustration of its capabilities, we provide some promising results based on the solution of different benchmark problems.
Truncation- and motif-based pan-cancer analysis reveals tumor-suppressing kinases
Authors: Hudson Andrew M. , Stephenson Natalie L. , Li Cynthia , Trotter Eleanor , Fletcher Adam J. , Katona Gitta , Bieniasz-Krzywiec Patrycja , Howell Matthew , Wirth Chris , Furney Simon , Miller Crispin J. , Brognard John
Published: April 2018

A kinase domain–focused functional genomic screen reveals loss-of-function mutations in a JNK pathway kinase in gastric cancer.
A switch-variant model integrates the functions of an autoimmune variant of the phosphatase PTPN22
Authors: Vang Torkel , Nielsen Jimmi , Burn Garth L.
Published: April 2018

The functional activity of the R620W variant of the phosphatase PTPN22 may be determined as much by localization as by catalytic activity.
Unexpected Replication Boost by Simeprevir for Simeprevir-Resistant Variants in Genotype 1a Hepatitis C Virus
Authors: Murai Kazuhisa , Shimakami Tetsuro , Welsch Christoph , Shirasaki Takayoshi , Liu Fanwei , Kitabayashi Juria , Tanaka Shiho , Funaki Masaya , Omura Hitoshi , Nishikawa Tomoki , Sumiyadorj Ariunaa , Honda Masao , Kaneko Shuichi
Published: April 2018

Simeprevir is a novel NS3/4A protease inhibitor (PI) of hepatitis C virus (HCV). The baseline polymorphism NS3-Q80K is frequently observed in genotype (GT) 1a HCV and often associated with treatment failure in simeprevir-containing regimens. We aimed to elucidate mechanisms of treatment failure due to NS3-Q80K. We included a Q80R mutation in our study and generated a series of Huh-7.5 cell lines, each of which harbored either wild-type GT 1a strain H77S.3 or the Q80K or Q80R variant. The cells were cultured with increasing concentrations of simeprevir, and NS3 domain sequences were determined. The mutations identified by sequence analyses were subsequently introduced into H77S.3. The sensitivity of each mutant to the NS3/4A PIs simeprevir, asunaprevir, grazoprevir, and paritaprevir was analyzed. We introduced the mutations into GT 1b strain N.2 and compared the sensitivity to simeprevir with that of GT 1a strain H77S.3. While simeprevir treatment selected mutations at residue D168, such as D168A/V in the wild-type virus, an additional mutation at residue R155, R155K, was selected in Q80K/R variants at simeprevir concentrations of <2.5 μM. Sensitivity analyses showed that simeprevir concentrations of <1 μM significantly boosted the replication of Q80K/R R155K variants. Interestingly, this boost was not observed with the other NS3/4A PIs or in Q80R R155Q/G/T/W variants or GT 1b isolates. The boosted replication of the Q80K+R155K variant by simeprevir could be related to treatment failure in simeprevir-containing antiviral treatments in GT 1a HCV-infected patients with the NS3-Q80K polymorphism. This result provides new insight into how resistance-associated variants can cause treatment failure.
Vibrio Ecology in the Neuse River Estuary, North Carolina, Characterized by Next-Generation Amplicon Sequencing of the Gene Encoding Heat Shock Protein 60 (
hsp60
)
Authors: Jesser Kelsey J. , Noble Rachel T.
Published: April 2018

Of marine eubacteria, the genus
Vibrio
is intriguing because member species are relevant to both marine ecology and human health. Many studies have touted the relationships of
Vibrio
to environmental factors, especially temperature and salinity, to predict total
Vibrio
abundance but lacked the taxonomic resolution to identify the relationships among species and the key drivers of
Vibrio
dynamics. To improve next-generation sequencing (NGS) surveys of
Vibrio
, we have conducted both 16S small subunit rRNA and heat shock protein 60 (
hsp60
) amplicon sequencing of water samples collected at two well-studied locations in the Neuse River Estuary, NC. Samples were collected between May and December 2016 with enhanced sampling efforts in response to two named storms. Using
hsp60
sequences, 21
Vibrio
species were identified, including the potential human pathogens
V. cholerae
,
V. parahaemolyticus
, and
V. vulnificus
. Changes in the
Vibrio
community mirrored seasonal and storm-related changes in the water column, especially in response to an influx of nutrient-rich freshwater to the estuary after Hurricane Matthew, which initiated dramatic changes in the overall
Vibrio
community. Individual species dynamics were wide ranging, indicating that individual
Vibrio
taxa have unique ecologies and that total
Vibrio
abundance predictors are insufficient for risk assessments of potentially pathogenic species. Positive relationships between
Vibrio
, dinoflagellates, and
Cyanobacteria
were identified, as were intraspecies associations, which further illuminated the interactions of cooccurring
Vibrio
taxa along environmental gradients.

IMPORTANCE
The objectives of this research were to utilize a novel approach to improve sequence-based surveys of
Vibrio
communities and to demonstrate the usefulness of this approach by presenting an analysis of
Vibrio
dynamics in the context of environmental conditions, with a particular focus on species that cause disease in humans and on storm effects. The methods presented here enabled the analysis of
Vibrio
dynamics with excellent taxonomic resolution and could be incorporated into future ecological studies and risk prediction strategies for potentially pathogenic species. Next-generation sequencing of
hsp60
and other innovative sequence-based approaches are valuable tools and show great promise for studying
Vibrio
ecology and associated public health risks.
Interleukin-22 Immunotherapy during Severe Influenza Enhances Lung Tissue Integrity and Reduces Secondary Bacterial Systemic Invasion
Authors: Barthelemy Adeline , Sencio Valentin , Soulard Daphnée , Deruyter Lucie , Faveeuw Christelle , Le Goffic Ronan , Trottein François
Published: April 2018

Severe bacterial (pneumococcal) infections are commonly associated with influenza and are significant contributors to the excess morbidity and mortality of influenza. Disruption of lung tissue integrity during influenza participates in bacterial pulmonary colonization and dissemination out of the lungs. Interleukin-22 (IL-22) has gained considerable interest in anti-inflammatory and anti-infection immunotherapy over the last decade. In the current study, we investigated the effect of exogenous IL-22 delivery on the outcome of pneumococcal superinfection postinfluenza. Our data show that exogenous treatment of influenza virus-infected mice with recombinant IL-22 reduces bacterial dissemination out of the lungs but is without effect on pulmonary bacterial burden. Reduced systemic bacterial dissemination was linked to reinforced pulmonary barrier functions, as revealed by total protein measurement in the bronchoalveolar fluids, intratracheal fluorescein isothiocyanate-dextran tracking, and histological approaches. We describe an IL-22-specific gene signature in the lung tissue of influenza A virus (IAV)-infected (and naive) mice that might explain the observed effects. Indeed, exogenous IL-22 modulates the gene expression profile in a way that suggests reinforcement of tissue integrity. Our results open the way to alternative approaches for limiting postinfluenza bacterial superinfection, particularly, systemic bacterial invasion.
Transmembrane Domains of Highly Pathogenic Viral Fusion Proteins Exhibit Trimeric Association
In Vitro
Authors: Webb Stacy R. , Smith Stacy E. , Fried Michael G. , Dutch Rebecca Ellis
Published: April 2018

Many important human pathogens are enveloped viruses that utilize membrane-bound glycoproteins to mediate viral entry. Factors that contribute to the stability of these glycoproteins have been identified in the ectodomain of several viral fusion proteins, including residues within the soluble ectodomain. Although it is often thought to simply act as an anchor, the transmembrane domain of viral fusion proteins has been implicated in protein stability and function as well. Here, using a biophysical approach, we demonstrated that the fusion protein transmembrane domains of several deadly pathogens—Ebola virus, influenza virus, SARS CoV, and rabies virus—self-associate. This observation across various viral families suggests that transmembrane domain interactions may be broadly relevant and serve as a new target for therapeutic development.
Influential Parameters for the Analysis of Intracellular Parasite Metabolomics
Authors: Carey Maureen A. , Covelli Vincent , Brown Audrey , Medlock Gregory L. , Haaren Mareike , Cooper Jessica G. , Papin Jason A. , Guler Jennifer L.
Published: April 2018

Molecular characterization of pathogens such as the malaria parasite can lead to improved biological understanding and novel treatment strategies. However, the distinctive biology of thePlasmodiumparasite, including its repetitive genome and the requirement for growth within a host cell, hinders progress toward these goals. Untargeted metabolomics is a promising approach to learn about pathogen biology. By measuring many small molecules in the parasite at once, we gain a better understanding of important pathways that contribute to the parasite’s response to perturbations such as drug treatment. Although increasingly popular, approaches for intracellular parasite metabolomics and subsequent analysis are not well explored. The findings presented in this report emphasize the critical need for improvements in these areas to limit misinterpretation due to host metabolites and to standardize biological interpretation. Such improvements will aid both basic biological investigations and clinical efforts to understand important pathogens.
Depot-specific characteristics of adipose tissue-derived stromal cells in thyroid-associated orbitopathy
Authors: Wong Janice Siu Chong , Chu Wai Kit , Li Benjamin Fuk-Loi , Pang Chi-Pui , Chong Kelvin Kam-lung
Published: April 2018

Background

Thyroid-associated orbitopathy (TAO) causes inflammatory fibroproliferation of periocular connective tissues. We compared adipose tissue-derived stem/stromal cells (ADSCs) from three adipose depots of each patient with TAO on mesenchymal, myofibrogenic, adipogenic properties and associated hyaluronan (HA) synthesis.

Methods

ADSCs were generated from periocular (eyelid, orbital) and subcutaneous (abdominal) adipose tissues of three patients with TAO. Mesenchymal markers were characterised by reverse transcription-PCR and immunofluorescent staining. A 3-week adipogenic induction was evaluated by Nile red staining and quantitative PCR (qPCR) of peroxisome proliferator-activated receptor (PPARγ), adiponectin and hyaluronan synthase (HAS)-2. A 7-day myofibrogenic induction was assayed by immunofluorescent staining and qPCR of α-smooth muscle actin (α-SMA).

Results

ADSCs from all depots expressed similar levels of mesenchymal markers CD44, CD90 and CD105 (p=0.288, p=0.43 and p=0.837, respectively). After adipogenic induction, intracellular lipid increased for more than 32% and PPARγ mRNA showed more than twofold increase from all three depots. However, adiponectin and HAS-2 mRNA levels were significantly higher in the eyelid and orbital ADSCs than those from the subcutaneous ADSCs after induction (2.4×107, 3.9×106 folds vs below detection limit; 63.3-fold, 26.1-fold, vs 33% reduction, respectively; all p=0.002). Significantly more myofibroblasts and higher mRNA level of α-SMA were obtained from the orbital and eyelid compared with the subcutaneous ADSCs during myofibrogenic induction (80.2%, 70.6% vs 29.3%; 30.2-fold, 24.2-fold vs 1.7-fold, respectively; all p=0.002).

Conclusion

ADSCs from different adipose depots of the same donors exhibited similar mesenchymal phenotypes but differed significantly in adipogenic, myofibrogenic potentials and associated HA synthesis. These depot-specific characteristics of ADSCs may contribute to site-specific adipose tissue involvement in TAO.
Domains of health-related quality of life in age-related macular degeneration: a qualitative study in the Chinese cultural context
Authors: Bian Wei , Wan Junli , Smith Graeme , Li Shiying , Tan Mingqiong , Zhou Fengjiao
Published: April 2018

Objective

To explore which areas of health-related quality of life were affected in Chinese patients, and to identify whether the areas are well covered by validated questionnaires.

Design

A qualitative study based on semistructured interviews was conducted. A qualitative thematic analysis following the approach of Colaizzi was used to analyse the interview data for significant statements and phrases. The themes and subthemes organised from the analysis were then compared by using the following current instruments: National Eye Institute Visual Function Questionnaire (NEI-VFQ-25), Macular Disease Quality of life Questionnaire (MacDQoL) and Low-Luminance Questionnaire (LLD).

Participants and setting

Twenty-one patients with age-related macular degeneration were recruited from the eye clinic of Southwest Eye Hospital in Chongqing, mainland China.

Results

The mean age of the participants was 69.8 years (range 57–82 years) and the duration of the disease ranged from 3 months to 6 years. The qualitative analysis revealed nine important domains including symptoms, difficulties with daily activities, depending on others, depression and uncertainty, optimism and hope, social isolation, role change, family support and financial burden. However, all the three questionnaires were insufficient to capture the full extent of quality of life issues of Chinese patients with AMD, and MacDQoL covered more domains when compared with NEI-VFQ-25 and LLD.

Conclusion

The domains of concepts important to people with AMD in the Chinese culture are not fully represented in the three widely used questionnaires. Nine important domains were identified for the assessment of quality of life and should be considered when assessing the impact of AMD on Chinese individuals. Further studies are needed to develop an AMD quality of life questionnaire, better tailored to the needs and culture of Chinese patients.
Adoption of a novel surgical innovation into clinical practice: protocol for a qualitative systematic review examining surgeon views
Authors: Lewis Thomas L , Furness Hugh N , Miller George W , Parsons Nicholas , Seers Kate , Underwood Martin , Metcalfe Andrew J
Published: April 2018

Introduction

Efficient adoption of clinically effective novel surgical innovations has great potential benefits for patients. Factors affecting the adoption of surgical innovation are not well understood and proposed models of adoption do not accurately correlate with historical evidence. This protocol is for a systematic review that aims to identify the qualitative evidence relating to surgeon views regarding the adoption of novel surgical innovation into clinical practice.

Methods and analysis

A systematic review following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidance will be performed. Two independent reviewers will search the following databases: MEDLINE, Embase, Science Direct, Scopus, Web of Science and the Cochrane Library of Systematic Reviews. Inclusion criteria are studies which report on the views of surgeons who adopt a novel surgical innovation into clinical practice. Each article will be screened for inclusion and assessed according to a Critical Appraisal Skills Programme tool. Data will be synthesised and analysed according to thematic analysis. Given the anticipated yield of a small heterogeneous body of evidence meeting the eligibility criteria for the review, a narrative-based summary is planned.

Ethics and dissemination

This review does not require formal ethical approval as it does not involve direct patient contact or patient-identifiable data. The results of this review will be published in a peer-reviewed journal and presented at relevant conferences. The results will also inform an empirical qualitative study exploring surgeon and other stakeholder views regarding the introduction of novel surgical technology and procedures into clinical practice.

PROSPERO registration number

CRD42017076715.
Hospital admissions associated with medication non-adherence: a systematic review of prospective observational studies
Authors: Mongkhon Pajaree , Ashcroft Darren M , Scholfield C Norman , Kongkaew Chuenjid
Published: April 2018

Background

Medication non-adherence in ambulatory care has received substantial attention in the literature, but less so as it affects acute care. Accordingly, we aimed to estimate the frequency with which non-adherence to medication contributes to hospital admissions.

Methods

We searched the Cochrane Library, EMBASE, Cumulative Index to Nursing and Allied Health Literature, International Pharmaceutical Abstracts and PubMed (until December 2017) to identify prospective observational studies that examined prevalence rates of hospital admissions associated with medication non-adherence. A quality assessment was performed using an expanded Crombie checklist. Data extraction covered patterns, circumstances, and patient and other key characteristics of non-adherence. Pooled estimates were obtained using a random-effect model.

Results

Of 24 included studies, 8 were undertaken in North America, 7 from Europe, 6 from Asia and 3 from Australia. Most studies (79%) were rated as low risk of bias. All but three studies used combination measures to detect non-adherence, but approaches to assess preventability varied considerably. Across the studies, there was high heterogeneity among prevalence estimates (χ2=548, df 23, p<0.001, I2=95.8%). The median prevalence rate of hospital admissions associated with non-adherence was 4.29% (IQR 3.22%–7.49%), with prevalence rates ranging from 0.72% to 10.79%. By definition, almost all of these admissions were considered preventable. The underlying causes contributing to these admissions included medication cost and side effects, and non-adherence most often involved cardiovascular medicines.

Conclusions

Hospital admissions associated with non-adherence to medication are a common problem. This systematic review highlights important targets for intervention. Greater attention could be focused on adherence to medication during the hospital stay as part of an enhanced medication reconciliation process. Standardisation in study methods and definitions is needed to allow future comparisons among settings; future studies should also encompass emerging economies.