Connected Health Living Lab

The school of computing, in collaboration with the institute of nursing and health research and the school of engineering, recently established the connected health living lab (CH:LL) at Ulster University. CH:LL offers a dedicated environment to support user and clinical engagement, access to state-of-the-art technology to assess usability and interaction with innovative technologies, in addition to being a dedicated environment to record user behaviours with new connected health solutions. The creation of such a dedicated environment offers a range of benefits to support multi-disciplinary research in the area of connected health. This paper illustrates the design, development, and implementation of CH:LL, including a description of the various technologies associated with the living lab at Ulster University. To conclude, the paper highlights how these resources have been used to date within various research projects

Reduced phase error through optimized control of a superconducting qubit

Minimizing phase and other errors in experimental quantum gates allows higher fidelity quantum processing. To quantify and correct for phase errors in particular, we have developed a new experimental metrology --- amplified phase error (APE) pulses --- that amplifies and helps identify phase errors in general multi-level qubit architectures. In order to correct for both phase and amplitude errors specific to virtual transitions and leakage outside of the qubit manifold, we implement "half derivative" an experimental simplification of derivative reduction by adiabatic gate (DRAG) control theory. The phase errors are lowered by about a factor of five using this method to $\sim 1.6^{\circ}$ per gate, and can be tuned to zero. Leakage outside the qubit manifold, to the qubit $|2\rangle$ state, is also reduced to $\sim 10^{-4}$ for $20\%$ faster gates.Comment: 4 pages, 4 figures with 2 page supplementa

An ultrasound protocol for comparing tongue contours: upright vs. supine

A study is described that employs ultrasound to measure the effects of gravity on production of vowels. The materials are designed to encourage consistent production over repetitions. A recording and analysis protocol is described which allows for correction for probe movement or rejection of data where correction is not possible. Results indicate a slight superior and posterior displacement of the tongue root in supine posture, consistent with a shift in the support structure of the tongue.caslUltraxpub2507pu

Comparing articulatory images: An MRI / Ultrasound Tongue Image database

This work was supported by an EPSRC grant (EP/I027696/1). Thanks to our ULTRAX project colleagues Steve Renals and Korin Richmond. Scott Semple is supported by the British Heart Foundation Centre of Research Excellence Award. Thanks to Steve Cowen for technical assistance and Annette Cooper for MRI data acquisition.We report the development of a database that will contain paired ultrasound and MRI of tongue movements and shapes from 12 adults, illustrated with pilot data from one speaker. The primary purpose of the database will be to evaluate the informational content of ultrasound tongue images on the basis of the richer articulatory structures visible with MRI, and to provide tongue shape information that can later be incorporated into an image processing algorithm to enhance ultrasound tongue images. Ultrasound is an increasingly popular technique for studying speech production since it provides a real-time image of tongue movements. Its potential as a visualfeedback speech therapy tool has been recognised but has not yet been exploited to any great extent. In part this is because obstruents like /t/ /k/ /ch/,which are important targets for therapy, have tongue shapes in both canonical and common error productions which ultrasound displays rather poorly compared to the more easily-imaged vowels, glides and liquids. By enhancing ultrasound images in real time with information based on our corpus, we aim to create images which we hypothesise will A) be more easily understood by children for clinical feedback B) extend the range and utility of ultrasound generally.caslUltraxArticulate Instruments Ltd. Articulate Assistant Advanced Ultrasound Module User Manual, Revision 2.12, [manual]. Author, Edinburgh, 2010. Bernhardt, B., Gick, B., Bacsfalvi, P., and Adler-Bock, M. Ultrasound in speech therapy with adolescents and adults. Clinical Linguistics & Phonetics, 19: 605-617, 2005. Engwall, O. Assessing Magnetic Resonance Imaging Measurements: Effects of Sustenation, Gravitation, and Coarticulation. In: Harrington, J., Tabain, M., editors, Speech Production: Models, Phonetic Processes, and Techniques. Hove: Psychology Press, 301-314, 2006. ICPLA (International Clinical Phonetics and Linguistics Association). ExtIPA Symbols for Disordered Speech, 2002. IPA (The International Phonetic Association). The International Phonetic Alphabet, 2005. Michi K-I, Yamashita Y, Imai S, Suzuki N and Yoshida H. Role of visual feedback treatment for defective /s/ sounds in patients with cleft palate. Journal of Speech and Hearing Research, 36: 277-285, 1993. Lee, J. and Stone, M. Overlaying Ultrasound to MRI Sequences. Paper presented at Ultrafest V (March, 2010) retrieved May 19th, 2011 from http://www.haskins.yale.edu/conferences/UltrafestV/abstracts.html Scobbie, J.M., Lawson, E., Cowen, S. Cleland, J. and Wrench, A.A. A common coordinate system for mid-sagittal articulatory measurement. Proceedings of Interspeech, Florence, 2011in press. Stone, M. A Guide to Analysing Tongue Motion from Ultrasound Images. Clinical Linguistics and Phonetics, 19: 455-501, 2005. Wrench, A.A., Cleland, J. and Scobbie, J.M. An Ultrasound Protocol for Comparing Tongue Contours: Upright vs. Supine. Proceedings ofpub2477pu

Helping children learn non-native articulations: The implications for ultrasound-based clinical intervention

An increasing number of studies are examining the effectiveness of ultrasound as a visual biofeedback device for speech production training or therapy. However, no randomised control trials exist. We compared the success of typically-developing children learning new articulations with and without ultrasound biofeedback. Thirty children aged 6-12 were randomly assigned to 2 groups: Group U were taught novel (non-English) consonants and vowels using ultrasound in addition to imitation, modelling, articulatory descriptions and feedback on performance. Group A were taught the same speech sounds, using the same methods but in the absence of ultrasound visual biofeedback. Results showed that both groups of children improved in their production of the novel sounds with the exception of the high back vowels [u,]. No advantage for Group U was found, except for the palatal stop [c].https://www.internationalphoneticassociation.org/icphs/icphs2015caslpub3962pub69

SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies

<p>Abstract</p> <p>Background</p> <p>Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for contemporary biological assays. For example, RT-PCR validation of gene expression microarray results may be unsuccessful if the two technologies target different splice variants. Effective use of sequence-based technologies requires knowledge of the specific splice variant(s) that are targeted. In addition, the critical roles of alternative splice forms in biological function and in disease suggest that assay results may be more informative if analyzed in the context of the targeted splice variant.</p> <p>Results</p> <p>A number of contemporary technologies are used for analyzing transcripts or proteins. To enable investigation of the impact of splice variation on the interpretation of data derived from those technologies, we have developed SpliceCenter. SpliceCenter is a suite of user-friendly, web-based applications that includes programs for analysis of RT-PCR primer/probe sets, effectors of RNAi, microarrays, and protein-targeting technologies. Both interactive and high-throughput implementations of the tools are provided. The interactive versions of SpliceCenter tools provide visualizations of a gene's alternative transcripts and probe target positions, enabling the user to identify which splice variants are or are not targeted. The high-throughput batch versions accept user query files and provide results in tabular form. When, for example, we used SpliceCenter's batch siRNA-Check to process the Cancer Genome Anatomy Project's large-scale shRNA library, we found that only 59% of the 50,766 shRNAs in the library target all known splice variants of the target gene, 32% target some but not all, and 9% do not target any currently annotated transcript.</p> <p>Conclusion</p> <p>SpliceCenter <url>http://discover.nci.nih.gov/splicecenter</url> provides unique, user-friendly applications for assessing the impact of transcript variation on the design and interpretation of RT-PCR, RNAi, gene expression microarrays, antibody-based detection, and mass spectrometry proteomics. The tools are intended for use by bench biologists as well as bioinformaticists.</p

A common co-ordinate system for mid-sagittal articulatory measurement

A standard practice in EMA articulatory measurement is to set the origin of the measurement space near the boundary of the upper incisors and gum, on a standard reference coil. A conventional horizontal dimension is defined as being parallel to the speaker's unique bite (occlusal) plane. We propose that this convention be extended to other instrumentation, with a focus on how it can be achieved for ultrasound tongue imaging (UTI) in particular, using a disposable and hygienic vacuum-formed bite plate of known size. A bite plane trace, like a palate trace, provides a consistent reference to allow images to be rotated and translated in case the probe is in a new location relative to a speaker's cranial space. The bite plane also allows speakers with differently shaped palates to be overlaid, and for ultrasound data to share a coordinate space with EMA. We illustrate the proposal using a sample of six speakers. The average bite plane slope could be used to retrospectively rotate ultrasound data that lacks bite-plane measurementcaslpub3597pu

Enabling new articulatory gestures in children with persistent speech sound disorders using ultrasound visual biofeedback

Deposited in University of Strathclyde (Strathprints) repository on 26 September 2018 at: https://strathprints.strath.ac.uk/id/eprint/65547Purpose: This study evaluated ultrasound visual biofeedback treatment for teaching new articulations to children with a wide variety of Speech Sound Disorders. It was hypothesized that motor-based intervention incorporating ultrasound would lead to rapid acquisition of a range of target lingual gestures with generalization to untreated words. Method: Twenty children aged 6-15 with a range of mild to severe speech disorders affecting a variety of lingual targets enrolled in a case series with replication. Of these, fifteen children completed the intervention. All of the children presented with a variety of errors. We therefore employed a target selection strategy to treat the most frequent lingual error. These individual speech targets were treated using ultrasound visual biofeedback as part of 10 to 12 one hour intervention sessions. The primary outcome measure was percentage target segment correct in untreated wordlists. Results: Six children were treated for velar fronting; three for post-alveolar fronting; two for backing alveolars to pharyngeal or glottal place; one for debuccalisation (production of all onsets as [h]); one for vowel merger; and two for lateralised sibilants. Ten achieved the new articulation in the first or second session of intervention despite no children being readily stimulable for their target articulation before intervention. In terms of generalization, effect sizes for percentage target segments correct ranged from no effect (five children); small effect (one child); medium effect (four children) and large effect (five children). Conclusion: Ultrasound visual biofeedback can be used to treat a wide range of lingual errors in children with various speech sound disorders, from mild to severe. Visual feedback may be useful for establishing new articulations; however, generalization is more variable.Funding: This study was supported by a grant from the Chief Scientist Office of Scotland (ETM/402) awarded to James M. Scobbie and Joanne Cleland.62pubpub

Covert contrast and covert errors in persistent velar fronting

Special Issue on Covert ContrastsThis is an Accepted Manuscript of an article published by Taylor & Francis in Clinical Linguistics & Phonetics on 09/09/2016, available online: https://doi.org/10.1080/02699206.2016.1209788Acoustic and articulatory studies demonstrate covert contrast in perceptually neutralised phonemic contrasts in both typical children and children with speech disorders. These covert contrasts are thought to be relatively common and symptomatic of phonetic speech disorders. However, clinicians in the speech therapy clinic have had no easy way of identifying this covertness. This study uses ultrasound tongue imaging to compare tongue contours for /t/and /k/in seven children with persistent velar fronting. We present a method of overlaying tongue contours to identify covert contrast at the articulatory level. Results show that all seven children, contrary to expectations, produced both /t/and /k/with near-identical tongue shapes showing no evidence of covert contrast. However, further analysis of one of the participants showed highly variable tongue shapes for /t/and /k/, including retroflex productions of both. Although not phonologically conditioned, this covert error is evidence of speech disorder at the phonetic level.This work was funded by grants EP/I027696/1(Engineering and Physical Sciences Research Council, UK) and ETM/402 (Chief Scientist Office, Scotland).casl31pub4523pub