Electrophysiological and behavioural processing of complex acoustic cues

OBJECTIVES

To examine behavioural and neural processing of pitch cues in adults with normal hearing (NH) and adults with sensorineural hearing loss (SNHL).

METHODS

All participants completed a test of behavioural sensitivity to pitch cues using the TFS1 test (Moore and Sek, 2009a). Cortical potentials (N1, P2 and acoustic change complex) were recorded in response to frequency shifted (deltaF) tone complexes in an 'ABA' pattern.

RESULTS

The SNHL group performed more poorly than the NH group for the TFS1 test. P2 was more reflective of pitch differences between the complexes than N1. The presence of acoustic change complex in response to the TFS transitions in the ABA stimulus varied with deltaF. Acoustic change complex amplitudes were reduced for the group with SNHL compared to controls.

CONCLUSION

Behavioural performance and cortical responses reflect pitch processing depending on the salience of pitch cues.

SIGNIFICANCE

These data support the use of cortical potentials and behavioural sensitivity tests to measure processing of complex acoustic cues in people with hearing loss. This approach has potential for evaluation of benefit from auditory training and hearing instrument digital signal processing strategies.

Construction of mouse phantoms from segmented CT scan data for radiation dosimetry studies

We present the complete construction methodology for an anatomically accurate mouse phantom made using materials which mimic the characteristics of tissue, lung, and bone for radiation dosimetry studies. Phantoms were constructed using 2 mm thick slices of tissue equivalent material which was precision machined to clear regions for insertion of lung and bone equivalent material where appropriate. Images obtained using a 3D computed tomography (CT) scan clearly indicate regions of tissue, lung, and bone that match their position within the original mouse CT scan. Additionally, radiographic films are used with the phantom to demonstrate dose mapping capabilities. The construction methodology presented here can be quickly and easily adapted to create a phantom of any specific small animal given a segmented CT scan of the animal. These physical phantoms are a useful tool to examine individual organ dose and dosimetry within mouse systems that are complicated by density inhomogeneity due to bone and lung regions.

Surface Treatments that Demonstrate a Significant Positive Effect on the Shear Bond Strength of Repaired Resin-modified Glass Ionomer

This study examined surface treatment options used to repair resin-modified glass ionomer (RMGI; GC Fuji II LC, GC America). Two hundred forty specimens were equally divided into four different water/temperature cycling environmental conditions. The conditions were 1) five-minute delay, 2) one-week delay with one thermocycle, 3) 500 thermocycles, and 4) 24-hour delay in a dry environment, followed by 500 thermocycles. Within each of the condition groups, the specimens were equally divided again into three different surface treatment groups with 20 specimens in each. The treatment groups comprised A) sanding, B) sanding and acid etch, and C) sanding, acid etch, and dental bonding agent. Our results suggest that RMGI is extremely susceptible to the simultaneous exposure of temperature cycling and water during the first 24 hours. Our main results reflect that 1) during the first five minutes after the initial placement, the surface treatments made no difference in terms of the shear bond strength (NS); and 2) when we weakened the RMGI by exposing it to water and temperature cycling immediately after initial placement, each of the treatments (A<B<C) had a significant incremental increase in bond strength (p<0.05). As such, given that a RMGI is partially a composite resin, the surface treatment with a dental bonding agent did have a significant positive effect on the micromechanical bond strength of the repair.

Bayesian inference of sampled ancestor trees for epidemiology and fossil calibration

Phylogenetic analyses which include fossils or molecular sequences that are sampled through time require models that allow one sample to be a direct ancestor of another sample. As previously available phylogenetic inference tools assume that all samples are tips, they do not allow for this possibility. We have developed and implemented a Bayesian Markov Chain Monte Carlo (MCMC) algorithm to infer what we call sampled ancestor trees, that is, trees in which sampled individuals can be direct ancestors of other sampled individuals. We use a family of birth-death models where individuals may remain in the tree process after sampling, in particular we extend the birth-death skyline model [Stadler et al., 2013] to sampled ancestor trees. This method allows the detection of sampled ancestors as well as estimation of the probability that an individual will be removed from the process when it is sampled. We show that even if sampled ancestors are not of specific interest in an analysis, failing to account for them leads to significant bias in parameter estimates. We also show that sampled ancestor birth-death models where every sample comes from a different time point are non-identifiable and thus require one parameter to be known in order to infer other parameters. We apply our phylogenetic inference accounting for sampled ancestors to epidemiological data, where the possibility of sampled ancestors enables us to identify individuals that infected other individuals after being sampled and to infer fundamental epidemiological parameters. We also apply the method to infer divergence times and diversification rates when fossils are included along with extant species samples, so that fossilisation events are modelled as a part of the tree branching process. Such modelling has many advantages as argued in the literature. The sampler is available as an open-source BEAST2 package (https://github.com/CompEvol/sampled-ancestors).

A central goal of phylogenetic analysis is to estimate evolutionary relationships and the dynamical parameters underlying the evolutionary branching process (e.g. macroevolutionary or epidemiological parameters) from molecular data. The statistical methods used in these analyses require that the underlying tree branching process is specified. Standard models for the branching process which were originally designed to describe the evolutionary past of present day species do not allow one sampled taxon to be the ancestor of another. However the probability of sampling a direct ancestor is not negligible for many types of data. For example, when fossil and living species are analysed together to infer species divergence times, fossil species may or may not be direct ancestors of living species. In epidemiology, a sampled individual (a host from which a pathogen sequence was obtained) can infect other individuals after sampling, which then go on to be sampled themselves. The models that account for direct ancestors produce phylogenetic trees with a different structure from classic phylogenetic trees and so using these models in inference requires new computational methods. Here we developed a method for phylogenetic analysis that accounts for the possibility of direct ancestors.

Factors influencing bank geomorphology and erosion of the Haw River, a high order river in North Carolina, since European settlement

The Haw River, a high order river in the southeastern United States, is characterized by severe bank erosion and geomorphic change from historical conditions of clear waters and connected floodplains. In 2014 it was named one of the 10 most threatened rivers in the United States by American Rivers. Like many developed areas, the region has a history of disturbance including extensive upland soil loss from agriculture, dams, and upstream urbanization. The primary objective of this study was to identify the mechanisms controlling channel form and erosion of the Haw River. Field measurements including bank height, bankfull height, bank angle, root depth and density, riparian land cover and slope, surface protection, river width, and bank retreat were collected at 87 sites along 43.5 km of river. A Bank Erosion Hazard Index (BEHI) was calculated for each study site. Mean bank height was 11.8 m, mean width was 84.3 m, and bank retreat for 2005/2007-2011/2013 was 2.3 m. The greatest bank heights, BEHI values, and bank retreat were adjacent to riparian areas with low slope (<2). This is in contrast to previous studies which identify high slope as a risk factor for erosion. Most of the soils in low slope riparian areas were alluvial, suggesting sediment deposition from upland row crop agriculture and/or flooding. Bank retreat was not correlated to bank heights or BEHI values. Historical dams (1.2–3 m height) were not a significant factor. Erosion of the Haw River in the study section of the river (25% of the river length) contributed 205,320 m³ of sediment and 3759 kg of P annually. Concentration of suspended solids in the river increased with discharge. In conclusion, the Haw River is an unstable system, with river bank erosion and geomodification potential influenced by riparian slope and varied flows.

Are hearing losses among young Maori different to those found in the young NZ European population?

AIM

This study was undertaken to determine if young Maori have more permanent bilateral hearing loss, or less severe and profound hearing loss than New Zealand (NZ) Europeans.

METHODS

Data include hearing-impaired children from birth to 19 years of age from the New Zealand Deafness Notification Database (DND) and covering the periods 1982-2005 and 2009-2013. These were retrospectively analysed, as was information on children and young people with cochlear implants.

RESULTS

Young Maori are more likely to be diagnosed with permanent hearing loss greater than 26 dB HL, averaged across speech frequencies, with 39-43% of hearing loss notifications listed as Maori. Maori have a lower prevalence of severe/profound losses (n=1571, chi squared=22.08, p=0.01) but significantly more bilateral losses than their NZ European peers (n=595, Chi-squared=9.05, p=0.01). The difference in severity profile is supported by cochlear implant data showing Maori are less likely to receive a cochlear implant.

CONCLUSIONS

There are significant differences in the proportion of bilateral (compared to unilateral) losses and in the rates and severity profile of hearing loss among young Maori when compared with their NZ European peers. This has implications for screening and other hearing services in NZ.

Comparisons of dense-plasma-focus kinetic simulations with experimental measurements

Dense-plasma-focus (DPF) Z-pinch devices are sources of copious high-energy electrons and ions, x rays, and neutrons. The mechanisms through which these physically simple devices generate such high-energy beams in a relatively short distance are not fully understood and past optimization efforts of these devices have been largely empirical. Previously we reported on fully kinetic simulations of a DPF and compared them with hybrid and fluid simulations of the same device. Here we present detailed comparisons between fully kinetic simulations and experimental data on a 1.2 kJ DPF with two electrode geometries, including neutron yield and ion beam energy distributions. A more intensive third calculation is presented which examines the effects of a fully detailed pulsed power driver model. We also compare simulated electromagnetic fluctuations with direct measurement of radiofrequency electromagnetic fluctuations in a DPF plasma. These comparisons indicate that the fully kinetic model captures the essential physics of these plasmas with high fidelity, and provide further evidence that anomalous resistivity in the plasma arises due to a kinetic instability near the lower hybrid frequency.

Efficient Bayesian inference under the structured coalescent

Motivation: Population structure significantly affects evolutionary dynamics. Such structure may be due to spatial segregation, but may also reflect any other gene-flow-limiting aspect of a model. In combination with the structured coalescent, this fact can be used to inform phylogenetic tree reconstruction, as well as to infer parameters such as migration rates and subpopulation sizes from annotated sequence data. However, conducting Bayesian inference under the structured coalescent is impeded by the difficulty of constructing Markov Chain Monte Carlo (MCMC) sampling algorithms (samplers) capable of efficiently exploring the state space.

Results: In this article, we present a new MCMC sampler capable of sampling from posterior distributions over structured trees: timed phylogenetic trees in which lineages are associated with the distinct subpopulation in which they lie. The sampler includes a set of MCMC proposal functions that offer significant mixing improvements over a previously published method. Furthermore, its implementation as a BEAST 2 package ensures maximum flexibility with respect to model and prior specification. We demonstrate the usefulness of this new sampler by using it to infer migration rates and effective population sizes of H3N2 influenza between New Zealand, New York and Hong Kong from publicly available hemagglutinin (HA) gene sequences under the structured coalescent.

Availability and implementation: The sampler has been implemented as a publicly available BEAST 2 package that is distributed under version 3 of the GNU General Public License at http://compevol.github.io/MultiTypeTree.

Contact:tgvaughan@gmail.com

Supplementary information:Supplementary data are available at Bioinformatics online.

Real-time feedback control of pH within microfluidics using integrated sensing and actuation

We demonstrate a microfluidic system which applies engineering feedback principles to control the pH of a solution with a high degree of precision. The system utilizes an extended-gate ion-sensitive field-effect transistor (ISFET) along with an integrated pseudo-reference electrode to monitor pH values within a microfluidic reaction chamber. The monitored reaction chamber has an approximate volume of 90 nL. The pH value is controlled by adjusting the flow through two input channels using a pulse-width modulated signal applied to on-chip integrated valves. We demonstrate real-time control of pH through the feedback-controlled stepping of 0.14 pH increments in both the increasing and decreasing direction. The system converges to the pH setpoint within approximately 20 seconds of a step change. The integration of feedback theory into a microfluidic environment is a necessary step for achieving complete control over the microenvironment.

Development of the hearing protection assessment (HPA-2) questionnaire

BACKGROUND

Noise-induced hearing loss (NIHL) remains an important occupational health issue as the second most commonly self-reported occupational injury or illness. The incorrect and inconsistent use of hearing protection devices (HPDs) compromises their effectiveness in preventing NIHL.

AIMS

To describe the development of an easily administered yet robust questionnaire to investigate factors that influence HPD use.

METHODS

A hearing protection assessment (HPA-2) questionnaire was developed using items based on themes identified in our previous research. These fell into two classes: supports and barriers to wearing HPD, which formed two scales within the questionnaire. The questionnaire, which also included demographic items, was administered to workers from 34 manufacturing companies. The internal consistency of the scales was tested, and factor analysis was conducted to investigate the underlying structure of the scales.

RESULTS

Of the 1053 questionnaires distributed, 555 completed questionnaires were received giving a response rate of 53%. The Cronbach's alpha for the barriers scale (α = 0.740) and supports scale (α = 0.771) indicated strong internal reliability of the questionnaire. The supports and barriers were further described as five key factors (risk justification, HPD constraints, hazard recognition, behaviour motivation and safety culture) that influence hearing protection behaviour. Workers who reported always using HPDs had more supports across these factors, while those who did not always wear HPDs reported more barriers.

CONCLUSIONS

The HPA-2 questionnaire may be useful in both research and interventions to understand and motivate hearing protection behaviour by identifying and targeting supports and barriers to HPD use at different levels of the ecological model.

Noise exposure of workers and the use of hearing protection equipment in New Zealand

Hearing loss from occupational noise exposure is a significant occupational health problem, requiring effective health and safety strategies. Essential to this is an understanding of the noise exposure of workers and the use of hearing protection equipment (HPE). This study reports on data collected in New Zealand. Visits were made to companies in each economic sector. Personal dosimetry was used to assess individual noise exposure of 529 workers. Workers were also interviewed about their use of HPE. Overall, 40.4% of production workers had a daily noise exposure greater than 1 Pa(2)h, exceeding the New Zealand National Standard for occupational noise exposure without HPE. Of these, 88.5% reported to use HPE when working in noise; however, some observations suggested that workers do not consistently use the devices. These data add to the overall picture of noise exposure of workers in New Zealand and are especially useful in areas where data did not previously exist or were difficult to access.

Recursive algorithms for phylogenetic tree counting

BACKGROUND

In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior distributions. When all samples come from the same time point and no prior information available on divergence times, the tree counting problem is easy. However, when fossil evidence is used in the inference to constrain the tree or data are sampled serially, new tree spaces arise and counting the number of trees is more difficult.

RESULTS

We describe an algorithm that is polynomial in the number of sampled individuals for counting of resolutions of a constraint tree assuming that the number of constraints is fixed. We generalise this algorithm to counting resolutions of a fully ranked constraint tree. We describe a quadratic algorithm for counting the number of possible fully ranked trees on n sampled individuals. We introduce a new type of tree, called a fully ranked tree with sampled ancestors, and describe a cubic time algorithm for counting the number of such trees on n sampled individuals.

CONCLUSIONS

These algorithms should be employed for Bayesian Markov chain Monte Carlo inference when fossil data are included or data are serially sampled.

Road traffic noise and health-related quality of life: a cross-sectional study

Evidence is emerging linking environmental noise to health problems. Noise can affect health directly and indirectly: For example, noise sensitivity moderates the effects of noise annoyance, which in turn mediates the effects of noise exposure. An alternative hypothesis is that noise sensitivity marks the presence of susceptibility to health problems in general, including annoyance from noise. Whether noise sensitivity causes poor health or whether it is a marker of susceptibility to health problems was addressed by comparing the results of a community-based survey of people with similar noise sensitivity profiles but different environmental noise exposures. A questionnaire was delivered to people living in two socio-economically-matched areas: One was within 50 m of a motorway and the other was away from any significant source of environmental noise. The questionnaire contained 58 questions comprised of the World Health Organization health-related quality of life questionnaire (WHOQOL), and questions about amenity, neighborhood issues, environmental annoyances, demographics, and noise sensitivity. Noise sensitivity did not vary with proximity to the motorway but annoyance with traffic noise and fumes was greater in those living close to the motorway than in those who were not. Scores on the four WHOQOL domains (physical, psychological, social, and environmental) were lower in those living close to the motorway, and the WHOQOL domain scores correlated negatively with noise sensitivity in those who lived near motorways but not in those who lived in the quieter areas. This suggests that noise sensitivity is related to poor health outcomes rather than being a trait marker of susceptibility to health problems in general.

Health effects of cochlear implants

AIM

To investigate whether people on a waiting list for cochlear implantation are more likely than those who have cochlear implants to suffer from illnesses which are potentially mediated by stress.

METHOD

A questionnaire, designed to assess the presence, persistence, and medication use associated with stress-related illnesses, was administered to two groups: those on a waiting list for cochlear implantation and adult users of cochlear implants.

RESULTS

Those on the cochlear implant waiting list had significantly poorer health as indicated by: a greater number of conditions experienced in the past year, longer illness length when affected by a condition, medication use for a greater number of conditions, and poorer mental health.

CONCLUSION

There are lengthy waiting lists for adult cochlear implantation. The need to wait and the lack of a known date for surgery, in combination with having a profound hearing loss is likely to result in chronic stress. Chronic stress may increase the risk of physical and mental illness via physiological systems which mediate response to environmental threats. Cochlear implantation may alleviate chronic stress in people on the waiting list, and these findings support the hypothesis that this influences physical health.

Do quiet areas afford greater health-related quality of life than noisy areas?

People typically choose to live in quiet areas in order to safeguard their health and wellbeing. However, the benefits of living in quiet areas are relatively understudied compared to the burdens associated with living in noisy areas. Additionally, research is increasingly focusing on the relationship between the human response to noise and measures of health and wellbeing, complementing traditional dose-response approaches, and further elucidating the impact of noise and health by incorporating human factors as mediators and moderators. To further explore the benefits of living in quiet areas, we compared the results of health-related quality of life (HRQOL) questionnaire datasets collected from households in localities differentiated by their soundscapes and population density: noisy city, quiet city, quiet rural, and noisy rural. The dose-response relationships between noise annoyance and HRQOL measures indicated an inverse relationship between the two. Additionally, quiet areas were found to have higher mean HRQOL domain scores than noisy areas. This research further supports the protection of quiet locales and ongoing noise abatement in noisy areas.

CMOS biosensor system for on-chip cell culture with read-out circuitry and microfluidic packaging

A 1.5 mm × 3 mm CMOS chip with sensors for monitoring on-chip cell cultures has been designed. The chip is designed in a 0.5 µm CMOS process which has 3 metal layers and 2 poly layers and is a 5 volt process. The chip contains ion sensitive field effect transistors (ISFETs), as well as ISFETs with read-out circuitry, for monitoring the pH of solutions placed on top of the chip. Interdigitated electrode structures (IDESs) are made using the top metal of the process to be used for sensing cellular attachment and proliferation via impendence. IDES read-out circuits and IDES test structures are included. The chip also contains test amplifiers, bandgap reference test structures, and connections for post-processing. We designed the chip to accommodate packaging into an environment where it will be directly exposed to a cell culture environment. Specifically we designed the chip to have the incorporated sensors near the center of the chip allowing for connections made around the edge of the chip to be sealed off using an epoxy or similar material to prevent shorting. Preliminary electrical characterization results for our amplifier indicate a gain of 48 dB, a bandwidth of 1.65 kHz, and a common mode rejection ratio (CMRR) of 72 dB. We also present a packaging technique using a flexible pcb substrate.

Fully kinetic simulations of dense plasma focus Z-pinch devices

Dense plasma focus Z-pinch devices are sources of copious high energy electrons and ions, x rays, and neutrons. The mechanisms through which these physically simple devices generate such high-energy beams in a relatively short distance are not fully understood. We now have, for the first time, demonstrated a capability to model these plasmas fully kinetically, allowing us to simulate the pinch process at the particle scale. We present here the results of the initial kinetic simulations, which reproduce experimental neutron yields (~10(7)) and high-energy (MeV) beams for the first time. We compare our fluid, hybrid (kinetic ions and fluid electrons), and fully kinetic simulations. Fluid simulations predict no neutrons and do not allow for nonthermal ions, while hybrid simulations underpredict neutron yield by ~100x and exhibit an ion tail that does not exceed 200 keV. Only fully kinetic simulations predict MeV-energy ions and experimental neutron yields. A frequency analysis in a fully kinetic simulation shows plasma fluctuations near the lower hybrid frequency, possibly implicating lower hybrid drift instability as a contributor to anomalous resistivity in the plasma.

Tinnitus pitch, masking, and the effectiveness of hearing aids for tinnitus therapy

OBJECTIVE

To assess the benefits of hearing aids on tinnitus according to the tinnitus reaction questionnaire (TRQ; Wilson et al, 1991), to verify whether the degree of masking provided by the hearing aid influenced the TRQ score, to examine whether the matched tinnitus pitch predicted the effectiveness of hearing aids in masking tinnitus, and to determine whether prescription of high-frequency amplification might be desirable in tinnitus management when tinnitus pitch is high.

DESIGN AND STUDY SAMPLE

A retrospective evaluation of the clinical outcomes of 70 tinnitus patients fitted with hearing aids was undertaken. The primary outcome measure was the TRQ, with a secondary subjective measure of tinnitus masking.

RESULTS

Participants who achieved masking with their hearing aids had greater reduction in TRQ scores. Masking was more likely to be achieved when participants had good low-frequency hearing and tinnitus pitch fell into the frequency range of the hearing aids.

CONCLUSIONS

The results support the use of hearing aids for tinnitus management, and suggest that masking may be a significant contributor to hearing aid success, implying that high-frequency amplification may be effective in high-pitch tinnitus.

A network-based analysis of the 1861 Hagelloch measles data

In this article, we demonstrate a statistical method for fitting the parameters of a sophisticated network and epidemic model to disease data. The pattern of contacts between hosts is described by a class of dyadic independence exponential-family random graph models (ERGMs), whereas the transmission process that runs over the network is modeled as a stochastic susceptible-exposed-infectious-removed (SEIR) epidemic. We fit these models to very detailed data from the 1861 measles outbreak in Hagelloch, Germany. The network models include parameters for all recorded host covariates including age, sex, household, and classroom membership and household location whereas the SEIR epidemic model has exponentially distributed transmission times with gamma-distributed latent and infective periods. This approach allows us to make meaningful statements about the structure of the population-separate from the transmission process-as well as to provide estimates of various biological quantities of interest, such as the effective reproductive number, R. Using reversible jump Markov chain Monte Carlo, we produce samples from the joint posterior distribution of all the parameters of this model-the network, transmission tree, network parameters, and SEIR parameters-and perform Bayesian model selection to find the best-fitting network model. We compare our results with those of previous analyses and show that the ERGM network model better fits the data than a Bernoulli network model previously used. We also provide a software package, written in R, that performs this type of analysis.