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August, 2019: Post Doctoral Researchers/Resercah Associates/PhD Candidates

A/Prof Abeyratne is accepting (2021) post-doctoral researchers/covering the areas of: pattern recognition, machine learning, respiratory sound analysis, digital signal processing and smart phone programming. Qualified students are invited to apply for PhD scholarships on a competitve basis.

June 2021:

Snore sound based Sleep Apnea diagnostics intellectual property developed by Dr. Udantha Abeyratne and his team are available for commercialisation. The technology is the culmination of 20 years of ground breaking work leading to four patent applications including two granted ones in the USA (the rest are under examination at various stages) and a large portfolio of peer reviewed publications in international scholarly journals. A Matlab implementation of re-trainable technology and performance comparions against American Academy of Sleep Medicine scoring critera of 2007 (AASM 2007) are available. Prior comparisons on Chicago Criteria ("AASM 1999") are also available via peer-reviewed literature. Our software models indicate that the technology can diagnose sleep apnea at a sensitivity and specificity approching that of a standard facility-based polysomnography (sensitivity, specificity around 90%, 90%-- cross validation studies). Note that the model development data sets available to us (n=100 approx) had been scored per AASM 2007 clinical criteria. Thus, the resulting models require a straight-forward re-training (re-calibration) process on AASM 2012 data before they can be used on subjects diagnosed under AASM 2012 criteria (which is the clinical scoring standard in effect since 2012).

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Assoc./Prof. Udantha Abeyratne is the inventor of the cough-sound based respiratory diagnosis technology (ResApp Health Ltd. (ASX: RAP)) and snore sound based sleep apnea diagnosis technology SnoreSounds.

He earned a PhD (Biomedical Engineering) from Drexel University, USA, and MEng and BScEE degrees in Electrical & Electronic Engineering from Tokushima U, Japan and U Peradeniya, (video here) Sri Lanka respectively. He also received formal post-graduate training in Higher Education (Grad Cert , U of Queensland, Australia) and Paediatric Sleep Science (Grad Cert., U of Western Australia, Australia). He is a Senior Member of the Institute of Electrical & Electronic Engineers (IEEE, USA), and a full Member of the American Academy of Sleep Medicine (AASM).

​Dr. Abeyratne started his research career with a paper on coding techniques for low-bandwidth communication channels. His master's thesis was on a machine learning approach to the human brain activity analysis using electroencephalography (EEG, Brain Waves) and evoked potentials. This approach won the best paper award in ISBET Brain Topography Conference (Osaka, Japan, 1990) and also placed Dr. Abeyratne as a finalist at the Young Investigators' Competition in IFMBE World Congress on Medical Physics and Biomedical Engineering, 1991 (Kyoto, Japan). He completed his PhD (1996) with Prof. Athina Petropulu as the advisor, working on Higher-Order-Spectra and medical ultrasound imaging. The thesis developed slice-based low-complexity algorithms for blind signal identification, tumor detection in ultarsound images, and image deconvolution.

Teaching Activities:

Assoc/Prof. Abeyratne has designed and taught university level courses on digital signal processing, electronic circuits, medical and general instrumentation, medical signal processing, medical imaging, control systems, project management and electromagnetic waves. He has supervised both undergraduate and postgraduate dissertation thesis projects in these areas. Within the last decade five students supervised by him won competitive awards at the UQ Innovation Expo.

Current Research Profile:

Assoc./Prof. Abeyratne's research interests encompass digital signal processing, machine learning, medical instrumentation, medical imaging, electrophysiology, bio-signal analysis and electronics. Over the last two decades A/Prof. Abeyratne has conceptualized, initiated and led the development of a number of innovative technologies funded by prestigious granting agencies such as the Bill & Melinda Gates Foundation, Australian Research Council and the A*-Star Singapore. His research programmes are characteristic of unorthodox approaches resulting in pioneering outcomes that produced spin-off companies, patents and scholarly publications. His research has recieved multiple peer accolades at the international level.

1. Electronic Instrument Design: hand-held ultrasound devices for medical, agricultural and industrial use; stethoscopes for the 21st century (The "Magithescope(c)", winner of two UQ Expo awards in 2013, 2014); biomimetic sensing devices (e.g. electronic nose, e-tongue), low-cost, portable electronic devices ("Tricoders") for diagnosing diseases such as apnea, asthma, pneumonia; wearable electrophysiological devices; real-time fatigue measurement and warning systems; hand-held instruments for the condition monitoring of machinery such as power transformers. Development of diagnostic and treatment devices for sleep apnea. Dr. Abeyratne is especially interested in developing accurate, multi-purpose and low-cost in-situ decision devices for applications in resource-poor regions of the world.

2. Diagnostic and Treatment Technology for Sleep Disorders: speech-like analysis of snore and breathing sounds; sleep diagnostic instrument design; sleep polysomnography, brain wave (EEG) analysis in sleep, quantification of fatigue and sleepiness; sleep apnea; design of apnea treatment devices (CPAP, dental devices); interaction of apnea and chronic diseases. mHealth approaches in sleep diagnostics. A/Prof. Abeyratne pioneered speech-like processing of respiratory sounds, leading to patents, papers and a spin-off company. He conceptualized and led the development of EEG based technology to quantifiy sleepiness in real-time in actual work environments. Outcomes of this program have recieved wide coverage in international media outlets due to its groundbreaking nature and the potential impact.

3. Respiratory Diagnostic Technology: diagnostic instrumentation and algorithm design for respiratory illnesses such as pneumonia, bronchiolitis, asthma, bronchiectasis and COPD; cough sound analysis in respiratory medicine; imaging technology for respiratory diagnosis; Portable diagnostic technologies and mHealth approaches for remote resource-poor areas of the world. About 1 million children below the age of 5 yrs die every year of pneumonia alone, mainly in remote resource-poor areas of the world. Poor access to diagnostics and medical treatment are the major reasons for pneumonia fatalities. A/Prof. Abeyratne proposed a ground-breaking new technology to diagnose pneumonia centred about cough sound analysis. For this research Dr. Abeyratne received funding from UQ, UniQuest and the Bill & Melinda Gates Foundation, which lauded the project (Page 4) as an exmaple for an innovative idea with high impact. Outcomes led to scholarly publications and contributed to patents as well as a spinoff company by UQ.

4. Signal Processing and Machine Intelligence: the analysis of bio-signals such as electroencephalography (EEG), electromyography (EMG); speech and industrial sound analysis, bowel sound analysis and the characterisation of inflammatory bowel disease; cardiovascular signal processing, source localization and blind source separation, higher order spectra, wavelets, pattern recognition, classifier design. Developing technology for monitoring the condition of Left Ventricular Assist Devices (LVAD).

5. mHealth: research on smart phone and other consumer devices as a platform for healthcare delivery. A/Prof Abeyratne is actively engaged in developing mHealth diagnostic solutions, including translating and customising sleep and respiratory technologies. He is also in the process of expanding the work to include meaningful deployment of the technology in both the developed and developing worlds, in collaboration with international NGOs, experts in community medicine, and the UQ spin-off companies resulting from the research program. New national and international collaborations are currently being negotiated to fund and facilitate this work.

The Research Team, Past & Present:

Associate professor Udantha Abeyratne, Dr. Keegan Kosasih (Past PhD graduate); Dr Duleep Herath (past PhD gradute, )Dr. Shahin Akhter (Past PhD graduate), Dr. Vinayak Swarnkar (Past PhD graduate ); Dr. Yusuf Amrulloh (Past PhD graduate); Dr. Shaminda de Silva (Past PhD graduate); Dr. Samantha Karunajeewa (Past PhD graduate); Dr. Suren Rathnayake (Past PhD graduate), Dr. Xiao Di (Past PhD graduate), Dr. T. Emoto (Past PhD work in UQ while at UT), ; Mrunal Markendeya (Current PhD Student); Karen McCloy (current PhD student), Ajith Wakwella (Past MPhil graduate); Lee Teck Hock (Past MPhil Graduate), Tang Xiaoyan (Past MPhil Graduate), Dr. Zhang Guanglan (Past MPhil Graduate), Dr. Syed Adnan (Past MPhil Graduate) and many past and present dissertation thesis students.

Research Collaborators:

Dr. Craig Hukins & Brett Duce (Princess Alexandra Hospital), Prof. Y. Kinouchi & Dr. T. Emoto (U of Tokushima, Japan), Dr. Sarah Biggs (Monash), Dr.Simon Smith (QUT), Dr. Chandima Ekanayake (Griffith U), Dr. Paul Porter (PMH Hospital), Prof. Anne Chang (Menzies School of Health Reserach, CDU), Dr. Scott Mckenzie (Princess Charles Hospital), Dr. Nirmal Weeresekera (JKMRC, UQ), Dr. Rina Triasih (Gadjah Mada U, Indonesia), Dr. K. Puvanendran (1998-2002: Singapore General Hospital, Singapore), Prof.Stanislaw Gubanski (Chalmers U, Sweden).

Experienced materials engineering researcher with proven experience in developing chemically tuned structures for commercial opportunities. My unique skill set spans interfacing technical analysis (morphology, composition, performance, and durability) of sustainable composite materials with economic feasibility and quality system requirements from research and industry associates. I am a team player, and the guiding principles by which I function in all facets of my life include ‘shared values’, ‘shared vision’, ‘complementary expertise’ and ‘diligence’.

Markus graduated from the Vienna University of Technology in Technical Physics in 1995 and was awarded his Doctorate in 1999 after which he worked as postdoctoral research associate and then Assistant Professor at the Department of Radiodiagnostics, Medical University Vienna (AT). From 2004 he worked as Senior Researcher at the Donders Institute for Brain, Cognition and Behaviour (Radboud University Nijmegen, NL) and at the Erwin L. Hahn Institute for Magnetic Resonance Imaging (University Essen-Duisburg, DE). In 2014 he relocated to the University of Queensland to head the Ultra-high Field Human MR Research program at the Centre for Advanced Imaging and was awarded an ARC Future Fellowship. In 2019 he joined the School of Information Technology and Electrical Engineering as Full Professor Biomedical Engineering working on MR Physics and Medical Imaging. He served as Imaging, Sensing and Biomedical Engineering Discipline lead until 2020 when he took up service roles as Deputy Head of School – Research, Director for the National Imaging Facility – Queensland Node, as well as a member of the ARC College of Experts.

Professor Simon Cool is Professor of Bioengineering and Director of the UQ Advanced Cell Therapy Manufacturing Initiative in the School of Chemical Engineering at the University of Queensland.

Professor Cool began his scientific career at the University of Queensland more than 20 years ago. He received his BSc (hons) and PhD degrees from the University of Queensland, where he subsequently held a faculty position in the School of Biomedical Sciences. His areas of studies have included age-related changes in the structure of bone and teeth and the extracellular matrix compartment of skeletal tissue that guide stem cell behaviour and wound repair. Professor Cool was invited to join the Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore in 2003 as a Principal Investigator. He then joined A*STAR’s Institute of Medical Biology (IMB) in 2008, shortly after its inception, to further his research in regenerative medicine, serving as Senior Principal Investigator of the Glycotherapeutics Group. In October 2020, Professor Cool re-joined the Institute of Molecular and Cell Biology (IMCB) as a Research Director, Glycotherapeutics, where he focused on developing novel glycosaminoglycan biomolecules that enhance wound repair and control adult human mesenchymal stem cell activity.

Professor Cool has 117 patent applications across 26 families with 51 granted in the fields of glycosaminoglycan biochemistry, regenerative medicine and stem cell science. He has more than 150 publications and continues to foster strong strategic collaborations both nationally and internationally with academic and industry groups. He has a strong biomanufacturing and translational focus with experience in taking glycosaminoglycan-based devices through discovery RnD on to pre-clinical and clinical testing. Professor Cool also has an entrepreneurial and licensing background having successfully spun-off some of his technology to a US-based regenerative medicine start-up company, SMC Biotechnology Ltd. Professor Cool holds a Visiting Professor appointment at the Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore and an Adjunct Professor (Research) appointment in the Orthopaedic Department at the National University of Singapore (NUS). Prior to his move back to UQ, he previously held the position of Treasurer, Tissue Engineering and Regenerative Medicine International Society, Asia Pacific Chapter (TERMIS-AP) and Treasurer, Stem Cell Society Singapore (SCSS). He also held senior leadership positions in several Singapore-based R&D programmes, notably as Director, Allogeneic Stem Cell Manufacturing (ASTEM) and Theme Leader in Advanced Manufacturing for Biological Materials (AMBM). Prof Cool currently serves on the Editorial Board of the journals Biomaterials, Tissue Engineering and Regenerative Medicine, and is Asia-Pacific Regional Editor for Stem Cells and Development.

Dr. Alejandro Melendez-Calderon has an interdisciplinary background in robotics and biomedical engineering with extensive experience in human augmentation technologies used in medicine (robotics, wearable devices) and computational approaches to understand human neuromuscular control (unimpaired, stroke and SCI population). He has over 19 years of experience gained in academic, clinical and industrial environments.

He leads the NeuroEngineering, Rehabilitation and Medical Robotics Lab at UQ, and is currently a Senior Lecturer within the School of Information Technology and Electrical Engineering and the School of Health and Rehabilitation Sciences (affiliate) at the University of Queensland (Australia; Jan 2020-present). He is also a Principal Research Fellow at the Jamieson Trauma Institute, Queensland Health (Australia, Jun 2022-present) where he leads the Rehabilitaiton and Outcomes theme.

Work experience | Clinical - He was previously a Senior Research Scientist and acting Head of Technology at the cereneo Advanced Rehabilitation Institute / cereneo Center for Neurology and Rehabilitation (Switzerland; 2017-2019), where he led and conducted research in the area of neuromechanics of movement deficits after stroke. He was also an Adjunct Assistant Professor at the Department of Physical Medicine & Rehabilitation, Northwestern University (USA; 2014-2020) and a postdoctoral research fellow at the Shirley Ryan AbilityLab (formerly Rehabilitation Institute of Chicago) (2012-2013), where he conducted research in cross-modal multisensory interactions and assessment of neuromuscular impairments. Medical industry - He led the areas of Robotic Hand Rehabilitation and Assessments, and work on adaptive control of robotic trainers (arm and legs) at Hocoma AG (Switzerland; 2014-2016), one of the world-leading manufacturers of robotic and wearable technologies for rehabilitation. Academic research - He was a Guest Researcher at ETH Zurich (Switzerland; 2016-2019), where he conducted research in biomechanics and motor control/learning. He received his PhD degree from Imperial College London (UK; 2007-2011) for research in robotics, rehabilitation and human motor control.

Interests | Dr. Melendez-Calderon has a scientific interest in understanding principled mechanisms of human behavior, in particular related to movement control/learning and physical interaction; his technical interests are in robotics and computational modeling for medical diagnostics, assistive applications & (bio)medical education.

I completed a PhD in Neuroscience with Jack Pettigrew (FRS) at Vision, Touch & Hearing Research Centre followed by an NHMRC Clinical Research Fellowship at Alfred Health & Monash University.

Back in QLD I'm continuing a transdisciplinary research & innovation program to Bring Discoveries of the Brain to Life!

I'm currently focused on developing novel MedTech Biotech diagnostics & therapeutics for enhancing human performance, recovery & resilience with the following projects:

[1] Precision Pain Medicine — the largest genetic study of persistent (chronic) pain in Australia, in collaboration with QIMR Berghofer & Monash University, aims to identify pharmacogenomics causal pathways for the design of personalised therapeutics & effective early intervention approaches (e.g., screening, education, prevention).

[2] Brain Switcha — A digital transdiagnostic biomarker and cloud-based large-scale population phenotyping & analytics platform to improve early intervention strategies in sleep & mental health conditions (esp. at-risk youth cohorts) and recruitment screening for Defence forces.

[3] VCS — vestibulocortical stimulation: A simple, inexpensive, non-invasive & non-pharmacologic neurotherapeutic treatment technique for fibromyalgia (with US colleagues) and other centralised pain syndromes, sleep apnoea, dementia & mental health conditions (e.g., depression, PTSD, bipolar disorder).

I also have >5 years professional services experience providing specialist research performance evaluation, consultation, reporting & training workshops that successfully delivered several major strategic priorities to a large internal & external client base — such as organisational unit leaders/managers at multiple levels (e.g., Centre/Department) and senior executive business missions for national/international strategic partnerships. This work includes mapping, monitoring & benchmarking of research capacity, capabilities/strengths, gaps & collaboration networks (e.g., clinical, corporate & government) across diverse disciplines for Annual & Septennial Departmental Reviews (e.g., patent, policy & clinical guideline citations; external stakeholder engagement including media); ARC Engagement & Impact assessments; and workforce capability development (e.g., recruitment for senior leadership positions and ranking of NHMRC/ARC funding applicants).

In particular, I enjoy meeting & connecting people with a shared vision & commitment towards building innovative & sustainable public-private partnerships to deliver meaningful solutions for the wider community.

Dr Antonio Padilha L. Bo completed the BEng and MSc at the University of Brasília, Brazil, in 2004 and 2007, respectively, and he was awarded the PhD from the University of Montpellier, France, in 2011. From 2011 to 2019, he has been a tenured assistant professor in electrical engineering at the University of Brasilia, Brazil, where he coordinated Project EMA (Empowering Mobility and Autonomy), which is one of the teams that took part in the Cybathlon competition in 2016 and 2020. He has co-authored over 75 peer-reviewed publications, including awards from societies such as IFAC, IFESS, and MICCAI.

Over the past ten years, Dr Bo has been engaged in research projects concerning the development of technology dedicated to healthcare, particularly in the design of systems to be directly used by a patient in rehabilitation or assistive settings. Every effort featured strong experimental work and was conducted in close collaboration with local rehabilitation centers. In his work, tools from neuroengineering, robotics, control, virtual reality, and instrumentation are often integrated to create devices and algorithms to sense and control human motion. For instance, he has used wearable sensors to segment and estimate parameters of human movement in real-time, a technique that may lead to novel rehabilitation protocols. More importantly, his work has also focused on developing closed-loop control strategies for electrical stimulation applications and prosthetic/orthotic devices. Some examples include systems based on superficial electrical stimulation to enable persons with spinal cord injury to exercise using the lower limbs (e.g. in cycling or rowing) and to attenuate the effects of pathological tremor in essential tremor and Parkinson's Disease.

His long-term research goal is to develop and evaluate the use of noninvasive technology, including electrical stimulation, robotics, virtual reality, and wearable devices, for improving rehabilitation and assistance for persons with motor disabilities.

Dr. Ove A. Peters joined the University of Queensland, Brisbane, Australia, in 2020 after faculty positions in Heidelberg, Germany and Zurich, Switzerland, as well as at the University of California, San Francisco. Most recently, he was the founding director of the postgraduate endodontic program at the Arthur A. Dugoni School of Dentistry in San Francisco, a professor with tenure and the Chair of the Department of Endodontics at that school.

Dr. Peters has wide-ranging clinical and research expertise and has published more than 200 manuscripts related to endodontic technology and biology. He has authored two books and contributed to several leading textbooks in dentistry; he also is an associate editor for the International Endodontic Journal as well as the Australian Endodontic Journal, an academic editor for PLOS One and serves on the review panel of multiple other journals. Among others awards, Dr Peters has received the Hans Genet Award of the European Society of Endodontology and more recently the Louis I. Grossman Award of the American Association of Endodontists. He is a Diplomate of the ABE, a member of OKU and a Fellow of the International and American Colleges of Dentistry.

Dr Abbas Shafiee is a tissue engineering & regenerative medicine scientist interested in translational cell-based and tissue engineering strategies to treat human diseases.

Dr Shafiee completed his PhD in Professor Kiarash Khosrotehrani’s laboratory on stem cell biology. His research career during his PhD had key contributions to delineating endothelial niche and vascular stem cells in the human placental tissues, including the seminal discovery of an entirely new stem cell population, coined as ‘Meso-Endothelial Bipotent Progenitor’ and the identification of key driver signatures for endothelial and bipotential progenitor function (Stem Cell Reports 2018; The FASEB Journal 2017; Stem Cells 2016; Stem Cells Translational Medicine 2015).

In 2016, he joined Distinguished Professor Dietmar Hutmacher’s team and conducted multiple projects on cancer and bone tissue engineering. Dr Shafiee has developed innovative tissue engineered models intersecting concepts from stem cell biology, cancer, and tissue engineering to study species-specific cancer bone metastasis at an unprecedented level of detail. The results of his research have been published in: International Journal of Cancer 2018; Cancers 2018; Biomaterials 2018; Bone Research 2019; Biomaterials 2019; Applied Materials Today 2020; Biomaterials 2020; and Advanced Therapeutics 2020. Utilizing the tissue engineering concept, he was able to better understand the mechanisms of human cancer bone metastasis. Additionally, he was successful in obtaining project grants, including a project grants from Cooperative Research Centers (CRC), and developed a biomimetically designed scaffolds and investigated the interactions of multipotent mesenchymal stem/stromal cell and skin progenitors with 3D printed scaffolds. The application of 3D printed constructs in acute wound models decreased wound contracture and led to a significantly improved skin regeneration.

Dr Shafiee joined Metro North Health (MNH, Queensland Health) in 2020 and started a research program to develop, implement, and evaluate the applications of 3D printing, scanning, cell therapies, and biofabrication technologies in skin wound settings, and dermatology research. Using the 3D printing and organoid technologies he could develop new approaches to enhances physiological wound closure with reduced scar tissue formation (Biomaterials 2021, Small 2021, Advanced Healthcare Materials 2021, Advanced Healthcare Materials 2022) and advance the deramtology research (Advanced healthcare materials 2022, and Small 2024). Dr Shafiee is part of a national program, aiming to develop biofabrication technology to treat skin wounds (funded by MRFF, NHMRC). His groundbreaking organoid research resulted in establishing an international Consortium of Organoid Research in Dermatology, leveraging organoid technology to advance the understanding and treatment of genetic skin diseases. Dr Shafiee has supervised over 10 Masters and PhD students. Honours, Masters and PhD projects are available, please feel free to contact him.

Dr. Susannah Tye joined the Queensland Brain Institute in 2017 and has established a research program within the Asia Pacific Centre for Neuromodulation (QLD, Australia). Before returning to Australia, Dr. Tye directed the Translational Neuroscience Laboratory at the Mayo Clinic (2012-2017). While there she led efforts to develop brain stimulation devices (for rodents and humans) that can quantify neural activity and neurotransmitter dynamics in the living brain. This body of work now forms the basis of the neuropsychiatric arm of the Mayo Clinic’s Deep Brain Stimulation Consortium. Her specific research expertise are in utilising voltammetric (electrochemical) recording techniques to monitor rapid, synaptic neurotransmission in the living brain.

Dr. Tye has over ten years of experience studying neuromodulation in preclinical rodent models and human patients. Her long-term goal is to bridge preclinical and clinical studies to maximise translational impact, specifically in terms of improving patient outcomes for those with severe refractory psychiatric illness. Towards this end, she maintains many international collaborations with both clinical and basic science researchers. Dr. Tye also has a longstanding interest in mentoring young scientists to help them expand their skills in preclinical and basic science research and achieve a successful research career.