Coordinating Hand-Eye Decisions across the Parietal Cortex through Coherent Neuronal Ensembles
Date: Wednesday 4 November 2015
Speaker: Dr Yan Wong
Foraging through the environment we gather information about our surroundings through combinations of eye and arm movements. The posterior parietal cortex (PPC) is involved in the spatial representation of movement plans for these saccades and reaches. Within the PPC, specialized neurons are involved in guiding saccadic eye movements and their activity is modulated by the value of saccade targets. However, it is unknown how these valuation signals are utilized to select, plan and coordinate movements of different effectors. Further, selecting and planning arm and eye movements recruits neurons in many different areas of the brain but how ensembles of neurons work together to make a single choice is also unknown.
This talk will explore how an effector-specific reinforcement learning model of choice behaviour can be used to accurately infer a subjects valuations of different choices, and how firing of PPC neurons are modulated by these valuations. Dr Wong will then show how these neurons can be classified based on the presence of significant spike-field coherence between different brain areas to identify neurons that have unique information about upcoming choices. Dr Wong proposes that coherent patterns of neural firing could play an important role in how we make decisions, and that temporally-coherent neural activity may provide a mechanism by which neurons coordinate their activity in order to make choices.
What can we learn from local field potentials (LFPs) recorded in the brain?
Date: Wednesday 12 August 2015
Speaker: Professor Gaute Einevoll
While extracellular electrical recordings are the work horse in in vivo electrophysiology, the interpretation of such recordings is not trivial. The recorded extracellular potentials in general stem from a complicated sum of contributions from all transmembrane currents of the neurons in the vicinity of the electrode contact.
The high-frequency part of the recorded signal contains information about action-potential firing (spikes), and the signal can often be sorted into spiking contributions from individual neurons surrounding the electrode. The interpretation of the low-frequency part of the low-frequency part, the local field potential (LFP), is more challenging as thousands of neurons in general will contribute to the measured signal (Lindén et al., Neuron, 2011). To take full advantage of the new generation of silicon-based multielectrodes recording LFPs from tens, hundreds or even thousands of contact positions simultaneously, we thus need to develop new data analysis methods (Einevoll et al., Nat Rev Neurosci, 2013). From volume conduction theory it follows that the extracellular potentials can be calculated by adding contributions from the transmembrane currents around the electrode contact, and a forward-modeling scheme for calculating the extracellular potential generated by activity in biophysically detailed neuron models has been developed (Holt & Koch, J Comp Neurosci 1999).
Professor Gaute Einevoll will discuss results from our group where this scheme has been used to explore the neural activity underlying LFPs and to develop new analysis methods for the signal.
Gaute T. Einevoll is a professor of physics at the at the Norwegian University of Life Sciences and University of Oslo. His main research interests are on (i) biophysical modelling of electrical signals, (ii) various aspects of multiscale modeling of early sensory pathways, (iii) biophysical modeling of astrocytes and their interactions with neurons, as well as (iv) development of neuroinformatics tools for analysis of neural data. Prof. Einevoll received his master’s in physics from the Norwegian University of Science and Technology in Trondheim in 1985 and his doctoral degree in theoretical physics from the same university in 1991. He is currently serving as the vice-president of the Organization of Computational Neurosciences, and is also a co-leader of the Norwegian national node of the International Neuroinformatics Coordinating Society (INCF).
Network Inference using Data Based Modelling: Challenges and Pitfalls
Date: Wednesday 29 July 2015
Speaker: Professor Bjoern Schelter
Complex networks are powerful representations of spatially extended systems and can advance our understanding of their dynamics. A large number of analysis techniques is available that aim at inferring the underlying network structure from data. Despite great successes in various fields, there still exist a number of problems for which there are currently no satisfactory solutions. This seminar will provide an overview of analysis techniques with particular emphasis on challenges and pitfalls when applying these techniques to data.
Bjoern Schelter assumed the position as Chair Professor in the Institute for Complex Systems and Mathematical Biology, the Institute for Pure and Applied Mathematics, and the Department of Physics at King’s College, University of Aberdeen, in 2014 after being a Senior Lecturer for 2 years. Before he was running his group “Multivariate Time Series Analysis in Neurology” at the Freiburg Centre for Data Analysis and Modelling and the Department of Physics at the University of Freiburg. His main focus of research is in data-based modelling and model-based data analysis in the Life Sciences. Prof Schelter looks back to roughly 15 years of experience in developing and applying mathematical methods for the analysis of time series with particular focus on bridging linear stochastic systems and nonlinear dynamics. Complementing his theoretical research, the spectrum of applications he has contributed to include various fields in the Neurosciences, in particular epilepsy research, tremor research with focus on Parkinson’s disease as well as dementia research. To achieve this, several theoretical developments became necessary. He has contributed to the development of mathematical methods, ranging from linear approaches to non-linear dynamics. The methods cover parametric as well as non-parametric techniques. Statistical aspects present an important part of the developments. His mathematical/ theoretical contributions are documented in roughly 30 publications. Software tools have been developed to enable a user-friendly interface to the techniques developed. Another 30 publications document Prof Schelter’s successful applications in the Life Sciences. His research has not only elicited a number of international collaborations to University partners but also several collaborations to industry partners to exploit his ideas commercially
Date: Monday 27 July 2015
Speaker: Associate Professor Cameron R. ‘Dale’ Bass
Brain injury is a conundrum. Brain injuries are common from falls, traffic crashes, military scenarios, approaching an epidemic. Mild traumatic brain injury (mTBI) or “concussive” injuries are a major societal issue and are associated with activities at all ages including sports, motor vehicle crashes, and falls. Recent emphasis on sports-related concussions (~1.6-3.8 million annually) highlights the need to understand the etiology of mTBI. Over 40 years of investigations from the early skull fracture studies to modern cellular, subcellular mechanophysiological and electrophysiological studies have left us with practical and teleological confusion. Fundamental questions such as How do we treat mild/moderate neurotrauma?, What is the human injury tolerance for repeated impact?, Is there a difference between blast and blunt neurotrauma?, Can we use animals to biofidelically model human neurotrauma? or even What causes a human to lose consciousness from impact? remain unanswered along with many others. This lack of knowledge prevents effective treatment, injury countermeasures and understanding of risks. What is the state of injury biomechanics of the brain for both blast and blunt neurotrauma? This superficial and wide-ranging discussion will touch on recent results in injury biomechanics of blunt trauma and blast trauma. This will include results and inferences on pathophysiology from the cellular to the organismal level, histopathological and biophysical results. Along the way, I will outline approaches for basic brain material characterization and modeling, including a novel fractional calculus approach to characterize viscoelasticity.
Associate Professor Cameron Bass, Duke University will discuss phenomenology and notional injury criteria for blunt and blast neurotrauma and outline approaches for mild neurotrauma biomarkers including behavioral approaches and biochemical approaches. This seminar will explore animal models and scaling to human impact conditions, physiologically, immunologically and biomechanically. Finally, the lecture will address approaches to biomechanical instrumentation for blunt impact epidemiology outlining the principal challenges in obtaining and assessing impact data in the field.
Cameron R. ‘Dale’ Bass is a Doctor of Philosophy and Associate Research Professor/Director of the Injury Biomechanics Laboratory at Duke University with many students in biomechanics, including studies in viscoelasticity imaging, blunt neurotrauma and spinal injury, and blast neurotrauma. Currently, this is 10 PhD students, all of them quite intelligent. By now, the students do all the work and Dr. Bass provides the Philosophy, often ad infinitum.
Neural mechanisms of eye-hand coordination in the posterior parietal
Date: Monday 13 July 2015
Speaker: Dr Maureen Hagan
Everyday activities like reaching for our morning coffee depend on a well-orchestrated coupling of where we look with our eyes and where we reach with our hand. A wealth of behavioural research has contributed to our understanding of how eye movements occur in concert with arm and hand movements. However, little is known about how the brain computes the necessary transformations to link eye and hand movements.
The posterior parietal cortex (PPC) has a well-established role in visually guided behaviour and contains areas that are specialized for guiding eye movements (area LIP) as well as reaches (Parietal reach region, PRR). This research recorded spiking and local field potential activity during coordinated eye-hand tasks. The synchronization of spiking activity with the local field potential may serve as a mechanism by which the timing of neural events within and across brain areas is able to coordinate complex behaviours. This presentation is able to show that many of the behavioural features of eye-hand coordination can be directly linked to the synchronization of neural activity in the PPC.
Dr Maureen Hagan received her PhD in 2013 at the Center for Neural Science at New York University. Her thesis examined the mechanisms of eye-hand coordination by studying the interactions of spiking and LFP activity in the posterior parietal cortex. Her thesis was awarded the Dean’s dissertation award for outstanding research. She has recently joined the Physiology Department at Monash University as a postdoctoral research fellow, studying the neural basis of visual perception.
Differential changes in synaptic inputs to ON & OFF retinal ganglion cells during retinal degeneration
Date: Monday 11 May 2015
Speaker: Susmita Saha
The results of clinical testing of the electrical retinal implants are encouragingly successful in restoring some kind of useful vision in blind patients with inherited retinal disorders like Retinitis Pigmentosa (RP). However many challenges remain for its implementation in large population. For example, to mimic the normal retinal mechanism, we need to differentially stimulate the ON and OFF ganglion cells (GCs), which is not possible with the current technology. In order to achieve that, it is utterly important to know about the functional conditions of these two types of cells at different stages of RP especially at advanced stages. The overall aim of Susmita Saha's PhD project was to demonstrate the differential effect of complete photoreceptor loss on the synapse densities, synaptic currents and spiking activities of ON and OFF retinal ganglion cells using rd1 mouse as a model of degeneration.
Susmita Saha is currently completing PhD study in the National Vision Research Institute under the department of Electrical and Electronic Engineering (EEE) and the department of Anatomy and Neuroscience in the University of Melbourne. Susmita completed my BSc in EEE from the Bangladesh University of Engineering and Technology in 2004. Then she joined the leading mobile operator company of Bangladesh as a system Engineer and worked there until Jan, 2011. During PhD study, she also did a summer internship job with Victorian Life Sciences Computation Initiative (VLSCI), Parkville in an image processing and machine learning related project.
Bilateral Cochlear Implants: Recent Advances and Future Directions
Date: Monday 27 April 2015
Speaker: Professor Ruth Litovsky
In the field of audiology, the standard of care is to provide patients who are deaf or hard-of-hearing with cochlear implants (CIs) in both ears. The goal of bilateral implantation is to take advantage of binaural neural circuitry, which enables humans to localize sounds and to hear speech in noise at poor signal-to-noise ratios. Although bilateral CIs seem to improve performance relative to that seen with a single CI, most users show notable decrement compared to normal hearing people. The factors that are responsible for these gaps in performance will be discussed. For example, we observe limitation in the signal processing and speech coding strategies utilized by today’s clinical CIs, which do not coordinate the inputs from the two devices. Another issue to consider is the effects of auditory deprivation early in life on neural degeneration in the binaural circuitry. This talk will focus on approaches that may be needed for restoring binaural sensitivity in CI processors, the role of auditory plasticity due to congenital vs. later-onset of deafness, the potential importance of training and top-down processing such as executive function, working memory and attention).
Ruth Litovsky, PhD is Professor at the University of Wisconsin-Madison, in the Departments of Communication Sciences and Disorders, and Surgery/Division of Otolaryngology. She directs the Doctorate in Audiology Program, and the Binaural Hearing and Speech Laboratory at the Waisman Center. Professor Litovsky is actively involved in the fields of hearing research and auditory implants. She has served on numerous grant review panels and editorial boards, chaired the Conference on Implantable Auditory Prostheses at Asilomar in 2011, elected Councilor for the Association for Research in Otolaryngology and is Program Committee Chair of the Midwinter Meeting of the Association for Research in Otolaryngology, Associate Editor for Journal of the Association for Research in Otolaryngology and the Journal of the Acoustical Society of America. Litovsky received her PhD in 1991 in Developmental Psychology, with post-doctoral training in auditory neurophysiology and psychoacoustics. Her research focuses on binaural hearing, covering lifespan of humans to include infants and elderly adults, with populations of normal-hearing persons and those who are deaf and use cochlear implants. At the heart of her research questions is the issue of bilateral cochlear implants. In adults the research questions focus on the ability of people with onset of deafness in childhood vs. adulthood to integrate information from the two ears with fidelity and precision, and the extent to which functional outcomes such as sound localization and speech understanding in complex environments is similar in these individuals compared with normal hearing listeners. This research program has been funded continuously by grants from the NIH-NIDCD since 1995.
Reading with retinal prostheses: targeted stimulation strategies harnessing phosphene orientation
Date: Monday 13 April 2015
Venue: Newton Rooms, Fifth Floor, Electrical and Electronic Engineering Building 193, The University of Melbourne
Speaker: Isabell Kirak-Kornek, The University of Melbourne
Conventional stimulation strategies for retinal implants generally assume evenly distributed, round, black-and-white phosphenes, whose intensity can be modulated to reflect different brightness levels in the image that is being presented to the implantee. However, psychophysical experiments with patients have shown that phosphenes can be very complex and can differ in size, shape, and even colour. In this talk, results are presented to demonstrate how a user could benefit from a targeted stimulation strategy that uses more than just phosphene intensity to convey information. In particular, methods to harness the phosphene shape and orientation in order to facilitate letter recognition with retinal implants and increase reading speed were investigated. The results of two psychophysical studies are presented that were conducted to assess how phosphene direction could help or hinder reading performance for simulated phosphene vision with normal-sighted subjects. This work has implications for the wider field of simulation-based psychophysical experiments to assess and improve the retinal implant user experience.
Isabell Kiral-Kornek is currently undertaking research towards a Ph.D. at The University of Melbourne. As part of Bionic Vision Australia, her research focuses on how to best convey visual information to an implant recipient to help in daily tasks, such as reading. Before she moved to Australia, she received a Diploma (Master's equivalent) in electrical engineering from the University of Hanover, Germany.
Quantitative imaging metrics for diagnosis, prediction and monitoring of arthritis in preclinical and clinical conditions
Date: Monday 30 March 2015
Venue: Newton Rooms, Fifth Floor, Electrical and Electronic Engineering Building 193, The University of Melbourne. (please turn left as you exit the lift, then left again) Speaker: Kathryn Stok, Swiss Federal Institute of Technology
Diseased joints are often no longer capable of providing normal function; i.e. load bearing, stabilisation, painless and unrestricted activity. Today there is no truly effective procedure to regenerate articular cartilage and tissue defects induced by arthritis are often irreversible. As such research groups around the world are exploring therapeutic targets for cartilage regeneration, biomarkers for understanding joint breakdown, and reconstructive approaches for restoring joint health. Dr Kathryn Stok investigates the morphology, function, disease and repair of cartilage and joints, in order to decode the interplay between mechanical, structural and biological responses, as well as interactions with neighbouring tissues. One primary avenue for development is novel mechanical and imaging methods for preclinical animal models. The first part of this seminar will describe a study which demonstrates new metrics for sensitive discrimination of structural deterioration with traumatic osteoarthritis, and the scalability of these metrics in two different animal models and in clinical datasets. A road map to clinical use will also be described. In the second part, an overview of other methods and protocols are described, which support the ongoing effort to give new insight into the progression and monitoring of disease models.
Dr Kathryn Stok is Head of the Integrative Cartilage Research Group at the Swiss Federal Institute of Technology in Zurich (ETH Zurich) since 2009, and a Senior Scientist for Cartilage & Arthritis Imaging Development at Scanco Medical AG since January 2015. She completed her PhD in the Department of Information Technology and Electrical Engineering at ETH Zurich in 2007. Prior to that she spent a year as a research assistant at Nanyang Technological University, Singapore, and completed her undergraduate and Master degrees in Mechanical Engineering at QUT in Brisbane. Kathryn is an innovative biomedical engineer in microstructural imaging and biomechanics of cartilage and joint structures using a variety of experimental and computational approaches. Her research work merges solid engineering approaches with biological advancement, and she has worked for over twelve years in biomedical engineering research (biomechanics and bioimaging); exploring global health challenges from both a basic science and a technological perspective. Her current research interests are investigating imaging strategies for quantitative multiscale assessment of joints, cartilage tissue and tissue-engineered cartilage constructs. Additionally she is developing a technological platform for standardised production of materials for tissue engineering models; specifically for use in the cosmetic and orthopaedic industries. She has previous and ongoing collaborations within the academic, business and health sectors in order to support this vision. Kathryn currently serves on the Osteoarthritis Research Society International’s (OARSI) communications committee, and is a co-chair of the international SPECTRA collaboration (Study grouP for xtrEme-Computed Tomography in Rheumatoid Arthritis).
Neural network models of pitch perception in normal and cochlear implant (CI) hearing
Date: Monday 16 March 2015
Venue: Newton Rooms, Fifth Floor, Electrical and Electronic Engineering Building 193, The University of Melbourne. (please turn left as you exit the lift, then left again) Speaker: Nina Erfanian, The University of Melbourne
Pitch is the perceptual correlate of sound frequency and is important for using speech prosody, understanding tonal languages, and appreciating music. The goal of this study was to develop computational models of normal and CI hearing to investigate the mechanisms of pitch perception in both cases. An artificial neural network (ANN) constituted the core of the model. Inputs to the ANN were spectral and/or temporal cues for pitch perception extracted from simulated auditory peripheral inputs. Temporal cues were extracted from the activity of the auditory nerve through a spiking neural network. Validation of the model was performed by comparing its performance with psychophysical results. The model was then applied to investigate the impact of stimulation field spread on pitch perception in CI hearing and to explore the role of and interaction between spectral and temporal cues in performing simulated pitch-related tasks. Results showed that different CI sound processing strategies were affected differently by the extent of stimulation field. It was also revealed that temporal cues for pitch perception compensated for missing spectral cues in listening conditions such as telephone conversation. Computational models of auditory perception such as this can serve as human substitutes in auditory perception studies. Since such human studies are very expensive and time consuming, these models can assist in the more rapid development of cochlear implant sound processing strategies.
Nafise (Nina) Erfanian Saeedi is a PhD student in the Electrical and Electronic Engineering department of Melbourne University. She received her Bachelor and Master of Science degree with distinction in Biomedical Engineering from Amirkabir University of Technology (Tehran Polytechnic), Iran, in 2007 and 2010, respectively. In 2011, she joined the NeuroEngineering lab in Melbourne University to undertake research towards a PhD. Her research focuses on computational models of auditory perception in normal and cochlear implant hearing.
A model of inner hair cell ion channels can explain nonrenewal properties of auditory nerve spike trains
Date: Monday 2 March 2015
Venue: Newton Rooms, Fifth Floor, Electrical and Electronic Engineering Building 193, The University of Melbourne. (please turn left as you exit the lift, then left again) Speaker: Bahar Moezzi, The University of South Australia
We propose several modifications to an existing computational model of stochastic vesicle release in the inner hair cell ribbon synapses, with the aim of producing simulated auditory nerve fibre spiking data that more closely matches empirical data. Specifically, we studied long and short term inter-spike interval correlations in the spiking of post-synaptic auditory nerve fibres. We introduced a standard biophysical stochastic model of calcium channel opening and closing, but showed that this model is insufficient for generating a match with empirically observed spike correlations. Instead, we incorporated a stochastic fractal model of potassium channel opening and closing and produced a qualitative match with empirically observed firing correlations. By combining the fractal potassium channel model with the standard calcium channel model and changing the model’s auditory nerve refractory properties, we produced long and short term correlations in the simulated auditory nerve spike trains that matched empirical observations quantitatively.
Bahar Moezzi received her bachelor’s degree in physics from Sharif University of Technology in Iran. Later, she received two Master’s degrees in physics from Columbia University in the USA. She spent several years at the Centre for Theoretical Neuroscience at Columbia University as a research assistant before going back to Iran to work as a software developer. In 2013, she joined the Computational and Theoretical Neuroscience Laboratory of Associate Professor Mark McDonnell at the University of South Australia, as a PhD candidate.
Affordable Healthcare Technologies For South East Asia Countries
Date: Monday 23 Feb 2015
Venue: Newton Rooms, Fifth Floor, Electrical and Electronic Engineering Building 193, The University of Melbourne. (please turn left as you exit the lift, then left again) Speaker: Prof. Eko Supriyanto, Johor Bahru University,
Cardiovascular disease and cancer are responsible for more than 55% death in South East Asia. Unhealthy life style and environment are the most common causes of these diseases. As an effort to improve the healthy life expectancy, affordable healthcare technologies for healthcare management of more than 600 Million populations with GDP per-capita around USD 4400 are required. Low cost telehealth, diagnosis and treatment technologies have been proposed to enable the quality affordable technologies. This includes the use of low cost nanosensor and ultrasound device to detect cancer and cardiovascular diseases, application of herbal medicine for cancer and cardiovascular disease prevention and treatment and low cost biodegradable polymer stent for cardiovascular system management. Low cost nanosensor has been successfully developed and tested in our laboratory, to detect human papilloma virus (HPV) DNA in the menstrual blood. We have also successfully extracted and applied some active compounds from mistletoe to validate its anticancer activity. Prospective technologies for cardiovascular diagnosis using ultrasound and treatment using newly developed biodegradable stent have been also investigated. In this lecture, these technologies will be presented.
Eko Supriyanto is a professor in medical imaging and electronics at Universiti Teknologi Malaysia (UTM). He is also the Director of Cardiovascular Engineering Centre UTM-National Heart Institute as well as the Head of Advanced Diagnostics and E-Health Research Group. He obtained Doctor of Engineering from University of Federal Armed Forces Hamburg, Germany. His research interest encloses the application of computer, electronics and material for management of cardiovascular diseases, cancer, fetal and children development. He has published more than 140 international journal papers and 6 books in the area of biomedical engineering. He has 23 patents and 35 international awards for his research achievement.
The artificial placenta and womb: Can medical technology offer a way forward for infants born at the border of viability?
Date: Monday 9 February 2015
Speaker: Dr Stephen Bird, Department of Obstetrics and Gynaecology, Melbourne Medical School
Preterm birth is the delivery of infants at less than 37 weeks of a full term, and is now the second major cause of death for infants under 5 years. Preterm birth can occur without warning and has many causes. Particularly concerning is the high numbers of infants born on the border of viability, between 22 and 25 week. For these infants there are few options and approximately 70% of 270,000 infants born each year do not survive to leave hospital. These babies cannot cope with life outside the womb due to the immaturity of their lungs and hearts. Those that do survive are currently at significant risk of severe, lifelong ill health. Given the technological advances in recent years, this seminar explores whether new technology approaches could overcome the current barriers to survival and give these extremely preterm infants a chance at life.
Stephen Bird has a Masters in analytical chemistry and PhD in biomedical science and more than 20 years of research experience and teaching in tertiary education. Formally, Stephen worked in New Zealand in kidney research investigating the longevity of the peritoneal membrane used in artificial renal replacement therapy. Stephen’s interest in developmental biology was inspired in the Netherlands whilst working at the Hubrecht Institute, where He helped develop a culture model of adult cardiomyocytes for regenerative heart research. These themes continued in Australia and now Stephen is focused on developing awareness of extreme prematurity and artificial placentation to help extremely preterm infants. Dr Bird holds an Honorary appointment in the Department of Obstetrics and Gynaecology, The University of Melbourne, Australia, and is a member of STC Australia. He is passionate about developing Medtech solutions for the most pressing medical problems.
Technology for reverse-engineering cortical circuits
Date: Monday 8 December
Speaker: Dr Simon Schultz, Department of Bioengineering, Imperial College London
Recent years have seen a step up in efforts to develop technology for reverse-engineering brain circuitry, with for instance the recent Obama BRAIN initiative in the USA. In this talk, I will describe efforts in my laboratory to develop, and scale up, technology for studying cortical circuits. We are currently focusing on (i) improving scanning technology for multiphoton microscopy in order to acquire high signal to noise ratio measurements of activity from large numbers of neurons simultaneously, (ii) the development of improved algorithms for action potential detection from calcium imaging using GCamp6 and OGB-1 AM indicators, (iii) the development of algorithms for decoding neural ensemble activity patterns that scale well to hundreds or thousands of neurons, and (iv) the development of a novel multi-photon targeted robotic in vivo patch-clamping platform. We are applying these tools to study information processing in the cerebellum and in mammalian neocortical circuits. A major driver of research into cortical circuits is the increasing prevalence and social cost of dementias such as Alzheimer’s Disease, which disrupt information processing in the cortical circuit. An important outcome of our research is thus the development of technologies which allow information processing deficiencies to be detected at earlier stages in Alzheimer Disease models, and for therapeutic strategies to be directly assessed in terms of their effect on cortical circuit function.
SimonSchultz is Royal Society Industry Fellow, Reader in Neurotechnology, and Director of the Centre for Neurotechnology at Imperial College London. He received Bachelor degrees in electrical engineering and physics at Monash University, and a Masters degree in electrical engineering at Sydney University, before completing a DPhil in computational neuroscience at Oxford University in 1998. This was followed by postdoctoral stints in experimental neuroscience with Tony Movshon at New York University, and Michael Häusser at UCL. He joined Imperial College in 2004, and has led the development of Imperial’s critical mass in the area of Neurotechnology. He is widely known for work on neural coding. He has been amongst the pioneers in the use of two-photon imaging to study neural coding and has also worked on large-scale computational models of cortical circuits. He has been the PI or Co-PI of grants totalling over £20M, including being on the executive board of the EU FP7 Marie-Curie Training Network “NETT - Neural Engineering Transformative Technologies”, and PI of the £10M EPSRC Centre for Doctoral Training in Neurotechnology for Life and Health. He acts as Associate Editor for the Journal of Computational Neuroscience.
Development of a high-dimensional brain machine interface
Date: Monday 24 November
Speaker: Dr Yan Wong, The University of Melbourne
Over the last few decades neural prosthetics such as the cochlear implants and deep brain stimulators have greatly improved the lives of tens of thousands of patients. In recent years, there has been a push to translate this early success into new therapeutic devices to help those suffering from a broader range of sensory and motor deficits. One such device is the brain machine interface targeted towards upper limb amputees. Current state-of-the-art brain machine interface devices suffer limitations due to an inability to extract enough information from neural signals as well as instability in the neural signals under examination. In this talk I will outline work towards the utilization of movement synergies as well as the incorporation of the local field potential into decoding algorithms. I will present a novel test system that allows recording from multiple depths of the frontal motor cortices simultaneously with all the movements of the arm and hand. Finally, I will present results showing the successful decoding of high-dimensional upper limb movements both offline and online.
Dr Yan Wong received his PhD for work towards the design and development of a vision prosthetic microchip and novel electrode organizations for current focusing from the University of New South Wales in 2009. For his postdoctoral work, he joined the Center for Neural Science at New York University studying the role of spike-LFP interactions in the Parietal cortex on movement planning, as well as developing a Brain Machine Interface for high-dimensional upper limb control. He has recently joined the Biomedical Engineering department at the University of Melbourne. During his career, Dr Wong has received grants from the NIH and DARPA, as well as many prestigious accolades such as twice being awarded the best student paper at the annual IEEE International EMBC meeting and the AusBiotech National Student Excellence award.
Improving our understanding of cardiovascular disease through innovations in coronary artery imaging and fluid dynamics research
Date: Monday 17 November
Speaker: Associate Professor of Medicine Peter Barlis, Melbourne Medical School, University of Melbourne
Cardiovascular disease remains the leading cause of morbidity and mortality in our community. Several advances in the diagnosis and treatment of heart disease have played an instrumental role in improving outcomes for patients. Nevertheless, a number of challenges still exist. Over the last 5 years, a novel intracoronary imaging technology called optical coherence tomography (OCT) has been increasingly used. With a super-high resolution of 15 microns, this light-based imaging modality permits detailed interrogation of within the coronary arteries to look at the features that go on to cause build up of plaque. This imaging modality is also best suited to visualize coronary stents, the devices used to prop open blocked arteries and used to identify predictors of why stents may fail once they have been implanted. This seminar will examine the utility of OCT in contemporary clinical practice and showcase some of the innovative applications and studies currently under way within the Faculty of Medicine, Dentistry & Health Sciences and the School of Engineering at the University of Melbourne.
Peter Barlis, MBBS, MPH, PhD, FESC, FRSA, FACC, FCSANZ, FRACP. Peter is an internationally recognised Interventional Cardiologist and Associate Professor of Medicine with the Melbourne Medical School, University of Melbourne and holds an Honorary Principal Fellow appointment with the Department of Mechanical Engineering, the University of Melbourne. After graduating from the University of Melbourne (MBBS), he completed his advanced cardiology training at Austin Health and then completed a Master of Public Health with the Department of Epidemiology and Preventative Medicine, Monash University. He then undertook his interventional fellowship at the National Heart & Lung Institute, Royal Brompton Hospital, UK supervised by Professor Carlo Di Mario and then went on to complete his PhD at the Thoraxcentre in the Netherlands on the use of optical coherence tomography (OCT) in interventional cardiology, supervised by Professor Patrick W. Serruys.
Since returning back to Australia in 2008, he has introduced this novel imaging modality into the country and has pioneered its use and uptake across the region. He is an investigator on numerous clinical trials and is a reviewer for multiple cardiovascular journals. Peter is frequently invited to give lecturers nationally and internationally on the application of light based imaging for the assessment of atherosclerotic plaque and coronary stents. He has published over 90 peer-reviewed manuscripts, many of which he is first or senior author and in 2011 was co-Editor of the ‘Textbook of interventional cardiology: Principles & Practice’ (Wiley-Blackwell Publishing). He is holder of a prestigious NHMRC Health Professional Fellowship allowing him to undertake in-depth analytical research using OCT to better understand the reasons behind coronary stent failures and in 2011, with the Department of Mechanical Engineering group, was awarded a $1M ARC Linkage Grant examining cutting-edge imaging and fluid mechanics techniques to help improve future coronary stent designs. In addition to being a Fellow of the Cardiac Society of Australia and New Zealand and the European Society of Cardiology, in February 2014, Peter was awarded Fellowship status of the American College of Cardiology in recognition of his clinical and research impact.
Information theoretically estimating the performance of cochlear implants
Date: Monday 10 November
Speaker: Xiao (Demi) Gao, The Institute for Telecommunications Research, University of South Australia
Information theory has been used in estimating the performance of cochlear implants. Previously, a channel model of cochlear implant stimulation was developed and the performance of cochlear implants was numerically estimated from an information theoretic perspective. Here, we propose an improvement to the biological accuracy of a crucial component of the overall modelling framework, a revised model of the channel output. We estimate the stochastic information transfer from cochlear implant electrodes to auditory nerve fibres, and infer the optimal number of electrodes by calculating the mutual information between channel input (choice of electrode) and channel output (defined as a function of the active nerve fibres in response to an electrode choice). We also investigate to what extent the positions and the usage probabilities of electrodes could impact on the performance of cochlear implants based on this modelling framework.
Xiao (Demi) Gao is currently a PhD student at the Institute for Telecommunications Research, University of South Australia under the supervision of Dr Mark D. McDonnell and Assoc Prof David B. Grayden. Her PhD research is focused on modelling the cochlear implant system and theoretically estimating the performance of cochlear implants. Demi received a Bachelor of Science in Computer Science in Central China Normal University in 2006, and a Master of Science in Biology in Huazhong Agricultural University in 2009. Since graduating she worked at the Institute of Hydrobiology, Chinese Academy of Science as a research assistant from 2007 to 2010. Then she worked as a research engineer in Chinese Maritime Academy from 2011 to 2012.
Biomechanics of knee joint injuries using cutting-edge musculoskeletal models and gaming technologies
Date: Monday 20 October
Speaker: Dr Hossein Mokhtarzadeh, the University of Melbourne and Australian Institute for Musculoskeletal Science (AIMSS)
The aim of this presentation is to address the biomechanics of anterior cruciate ligament injury (ACL) and its consequences. The ACL is one of the main spring-like ligaments of the knee joint that plays a major role in stabilizing the knee joint. ACL rupture is a comMonday sporting injury that may lead to an early knee osteoarthritis (OA). OA following ACL injury is a debilitating cartilage disease which has no cure yet. ACL reconstruction (ACLR) surgery is a costly method that is performed in order to help patients to return to sport and reduce the likelihood of OA. However, it has been shown that ACLR may not prevent OA. This talk will present some our recent work on the role of lower limb muscle function on the knee joint loading that is believed to contribute to initiation of OA. In addition, some novel methodologies using gaming technologies to enhance our understanding of the long term effect of ACL injury will be presented.
Dr Hossein Mokhtarzadeh has recently completed a PhD in Mechanical Engineering specialising in biomechanics at the University of Melbourne under the supervision of A/Prof. Peter Lee and Dr Denny Oetomo. Dr Mokhtarzadeh is currently doing his postdoctoral research fellow at the University of Melbourne and Australian Institute for Musculoskeletal Science (AIMSS) and leading musculoskeletal modelling group at AIMSS. He directly works with A/Prof. Peter Pivonka who is an internationally expert in computational bone biology. Hossein’s main area of research is in mechanobiology and particularly neuromusculoskeletal modelling , computational biomechanics, drug delivery in bone, and in-vitro and animal studies. Throughout his PhD, he received a number of awards including one of the top 12 early career researchers in Australia in 2013 as a Fresh Scientist, an Inspiring Scientist to present his work in Museum Victoria, and first place in 3 minute thesis competition in 2010. He received the Outstanding Researcher Award from the NIH center at Stanford University in 2014. Dr Mokhtarzadeh received a huge amount of media attention for his PhD related research, including articles in Herald Sun, The Age, ABC science show to name a few. He presented his work on biomechanics of knee injury at the World Congress of Biomechanics, 2014 as an invited speaker in the ANZSB Young Investigator session. He has recently come back from visiting major Universities in the US including Harvard and MIT Universities, Cornell University, Boston University, Northeastern University, and Stanford University.
Neuromorphic approaches to computing acoustic information
Date: Monday 13 October
Speaker: Associate Professor Neil McLachlan, Melbourne School of Psychological Sciences
During the 1890’s Ivan Pavlov observed that dogs could be conditioned to salivate at the sound of a bell. The association of conditioned stimuli to behaviours (or unconditioned stimuli) has been studied in a wide range of animals for over a century, however practically no research has been undertaken on how animals learn to recognize the conditioned stimuli in the first place. This is important because sound recognition likely occurs early in auditory processing, and underpins most other auditory functions. More specifically, previous research has shown that conditioned reflexive responses to sound involve ponto-cerebellar pathways, and so these pathways likely underpin sound recognition more generally. High level computational models of these pathways have been used to recognize human speech, music, environmental sounds and animal calls, and to act as adaptive filters for integrating pitch information. This paper will outline a new neurocognitive account of the auditory pathways and provide examples of computational algorithms based on this model. More broadly, it will discuss the possibility that neuro-cognition based on memory processes may provide the operating systems for future generations neuromorphic computers based on memsistors. These computers will learn and adapt to natural environments just like animals, but can “inherit” (or share) their memories from other computers at any time.
Dr McLachlan is an Associate Professor in Psychological Sciences at The University of Melbourne and has broad professional experience in music, acoustic design, engineering, and auditory neuroscience. In 2000 he designed the World’s first harmonic bells, and more recently has designed a new harmonic percussion ensemble for use in educational and a range of community contexts. To establish better design criteria for musical instrument design he has developed the first end-end neurobiological model of auditory processing. He has computationally implemented aspects of this model leading to the development of new sound segregation and recognition algorithms for hearing prosthetics and automated sensing systems.
Diamonds are Electronics’ Best Friend: An all-diamond packaging for a bionic vision prosthesis
Date: Monday 22 September
Speaker: Samantha Lichter, The University of Melbourne
Bionic vision through electrical stimulation of the retina is fast becoming a reality. To date, clinical trials have allowed blind patients to see a lover’s smile and navigate night scenes. This data has encouraged an abundance of research activity. Bionic Vision Australia, among others, is developing a retinal prosthesis to restore high visual acuity. One of its flagship technologies is a diamond electrode array, which will form part of the encapsulation for the implanted electronics. The remainder of the encapsulation also needs to be constructed from leak-proof, or hermetic, materials. The PhD’s aim was to design and test the feasibility of a hermetic encapsulation that incorporated the diamond electrode array. An all-diamond hermetic encapsulation design was proposed, in which a diamond box-shaped capsule was bonded to the diamond array, with the electronics contained inside.
Diamond capsules were made from polycrystalline diamond. Laser micromachining was found to be the optimal fabrication method. Hermetic joints were made in diamond using vacuum brazing with precious metal braze alloys. Bond interfaces were studied for morphology, chemical composition and hermeticity. Brazed diamond capsules were sealed at room temperature using laser microwelding. Welds were optimised for smooth surfaces and hermeticity.
The results demonstrated a hermetic all-diamond encapsulation. Combining the hermetic capsule, the brazing technique, and the welding technique with the diamond electrode array formed a retinal prosthesis technology that can protect against degradation for the lifetime of the patient.
Samantha Lichter is doing her PhD with the Bionic Vision Australia team at the University of Melbourne. Her thesis is entitled “An All-Diamond Hermetic Encapsulation for a High-Acuity Retinal Prosthesis”. Samantha completed a Bachelor of Science and Bachelor of Materials Engineering (Hons) from Monash University in 2007. She has designed, prototyped and proved in concept a novel leak-proof encapsulation technology for implantable electronics, to prevent inflammatory response due to CMOS materials and moisture damage to the device components.
The Revolutions of Scientific Structure
Date: Monday 8 September
Speaker: Colin Hales, The University of Melbourne
This is the debut seminar detailing the first of the two main scientific outcomes of the new book “The Revolutions of Scientific Structure”. The book resulted from an examination of what it would take to build an artificial scientist. In presenting this seminar the audience will be introduced to what might be the first formal act of science self-governance in the modern era. Until this book it can be claimed that self-governance is absent from science, whereas science self-regulation is brilliantly integrated into the daily life of all of us. The first scientific outcome in the book is measurement and documentation of a “Law of Scientific Behaviour”. It is a law of nature about the natural world of construction of laws of nature by their constructors: us (scientists). In the process a formal framework for the kind of science we currently do is created and named ‘appearance-aspect’ science.
That done, the fundamental limitation of appearance aspect science is identified. Science, as it is currently practised, will permanently fail to deliver an adequate science of the scientific observer. This science is currently operating under the name ‘science of consciousness’. The character of the failure is that unlike anywhere else in science, when it is done, we will be unable to hand to engineers the usual science deliverables. As a result, engineers will be unable to design and create an artificial scientist and then prove it. This is a procedural failure due to science operating at a scientific evidence boundary condition intrinsic to what we all assume is the only way to do science. The book then sets about an act of science self governance that adds a new kind of scientific behaviour that does not suffer the same problem. It is the only kind that will deliver a the necessary principled scientific account of the scientific observer. As a result engineers will be able to build an artificial scientist/scientific observer and prove it. The practical methods and interpretation of the new kind of science are outlined. Some scientists are already using it in other areas and don’t realise it. The new framework for science is called DUAL-ASPECT science.
The book is available here: https://www.worldscientific.com/worldscibooks/10.1142/9211.The Front-Matter (preface) and preamble (Chapter 1) are already accessible free from the publisher. Press release here: https://www.worldscientific.com/page/pressroom/2014-07-11-01
Nanites, drug delivery and microfluidics: simple complexity
Date: Monday 1 September
Speaker: Mattias Björnmalm, Department of Chemical and Biomolecular Engineering, The University of Melbourne
Through nanotechnology, synthetic structures can be engineered at the nanometer-level, thus creating materials that can interact with, and influence, biological systems at their very core. Intelligent ‘nanobots’ or ‘nanites’ are still far from reality, but in recent years sophisticated nano-systems have started to emerge. A prominent example is the use of responsive nanoparticles for drug delivery to increase the efficacy of current therapies, as well as to enable new ones. But despite the great promise of biomedical nanoparticles, only a few have made it to the clinic. In this talk, we discuss how new technologies can be used to overcome or circumvent key challenges facing particle-based drug delivery. We focus on microfluidics and lithography-based methods and present recent results demonstrating the potential of these techniques for the engineering of new and improved particles, as well as for evaluating their biological performance using biomimetic models. The ability of these methods to simplify both engineering and evaluation of increasingly complex particle-systems has helped to start the slow process of scratching away the latter half of the label ‘science fiction’ from concepts such as ‘nanites’.
Mattias Björnmalm obtained his MSc in Engineering within Nanotechnology from Lund University, Sweden, in 2012. Before coming to Australia he was a lab engineer within biotechnology at the KTH Royal Institute of Technology, Sweden, working within protein engineering of antibody-like molecules. Currently, he is a PhD student in Prof. Frank Caruso’s group at the Department of Chemical and Biomolecular Engineering, The University of Melbourne, and his research is primarily focused on microfluidic methods for engineering and evaluating drug delivery particles.
Biomaterials for Musculoskeletal Functional Tissue Regeneration
Date: Monday 25 August
Speaker: James C.-H. Goh, Department of Biomedical Engineering, National University of Singapore
Biomaterials including polymers, hydrogels, ceramics, metals and self-assembled materials have been widely used for bone, cartilage, ligament, tendon and dental tissue regeneration. Most importantly, nano scaled biomaterials provide some important and interesting properties to the traditional biomaterials, including high ratio of surface area to volume, enhanced mechanical properties, high purity and homogeneity, and outstanding magnetic, optical and electrical properties. Taking advantages of these novel properties, the nano-biomaterials can be manipulated to stimulate the chemical and structural similarities to natural musculoskeletal tissues. For instance, cartilage is hard to be regenerated due to lack of an efficient vascular system, limited progenitor cells and chondrocyte mobility in the dense cartilage extracellular matrix. However, nano-biomaterials can provide a biomimetic interface (or environment) to improve functions of chondrocyte, inhabiting and differentiation of progenitor cells. Moreover, the nano-biomaterials will enhance the lifetime and performance of tissue engineered scaffolds for cartilage regeneration (such as improved mechanical properties and hierarchical structures). On the other hand, the development of nano-biomaterials on bone regeneration is now focusing on two different directions: scaffolds for treatment of segmental defects (with structural functions) and cavity defects (such as fillers and injectable scaffolds). The utilization of nano-biomaterials in orthopedic applications has been proved to be an effective and innovative technique to enhance osseointegration and bone regeneration. Further, the nano-biomaterials have also been applied in dental applications, including dental implants and dental adhesives. Similar to bone implants, such dental implants will enhance osseointegration. Further, the nano-biomaterials based dental adhesives can also provide significant properties such as strong durability of the bond between teeth and adhesive, leading to new choices for dental restoration. The nano-biomaterials also have significant impacts on ligament/tendon regeneration. For example, nanostructured scaffolds are extremely helpful that can serve as structural and mechanical support for cellular function and tissue regeneration. In conclusion, countless opportunities and approaches have been brought by the development of nano-biomaterials to solve the current difficulties of implant materials, providing lots of success for nano-biomaterials in a variety of musculoskeletal tissue regeneration applications.
James C.-H. Goh is Professor and Head of Department, Department of Biomedical Engineering, National University of Singapore (NUS), Singapore. He was awarded BSc (1st Class) in Mechanical Engineering and PhD in Bioengineering by University of Strathclyde, UK. He has been conducting cutting edge research at NUS. He has published widely in musculoskeletal biomechanics and tissue engineering, and has given numerous invited/plenary talks in international conferences. He has organized many international conferences and was International Vice-President of the World Congress on Medical Physics and Biomedical Engineering (Seoul, Korea, 2006), Chairman of the Organizing Committee of the 3rd WACBE World Congress on Bioengineering (Bangkok, Thailand, 2007), Chairman of the Organizing Committee of the 6th World Congress of Biomechanics (Singapore, 2010), and Chairman of the Organizing Committee of TERMIS-AP Conference (Singapore, 2011). He currently serves as President of the Biomedical Engineering Society (Singapore), Vice-President of the International Federation of Medical and Biological Engineering, Member of the World Council of Biomechanics, and Secretary General of the Asia-Pacific Association for Biomechanics.
The role of macroscopic brain networks in seizure initiation
Date: Monday 4 August
Speaker: John Terry, College of Engineering, Mathematics and Physical Sciences, University of Exeter
In this talk we introduce the mathematical language of graph theory, which has evolved into a useful tool for studying complex brain networks inferred from a variety of measures of neural activity such as fMRI, DTI, MEG and EEG. In the context of neurological disorders, recent work has discovered differences in the structure of graphs inferred from patient and control cohorts. However, most of these studies pursue a purely observational approach; identifying correlations between properties of graphs and the cohort which they describe, without consideration of the underlying mechanisms. To move beyond this necessitates the development of mathematical modelling approaches to appropriately interpret network interactions and the alterations in brain dynamics they permit. In the talk we introduce some of the mathematical and computational modelling approaches we have taken to study epilepsy, exploring how differences in the properties of functional networks inferred from resting state EEG recordings of people with idiopathic generalised epilepsies can lead to a heighten probability of seizures. Our findings demonstrate the potential for a mathematical model based analysis of routine clinical EEG to provide significant additional information beyond standard clinical interpretation, which should ultimately enable a more appropriate mechanistic stratification of people with epilepsy leading to improved diagnostics and therapeutics.
Multiscale modelling of epileptic seizures, from macro- to micro-scopic dynamics.
Date: Monday 21 July
Speaker: Sebastian Naze, Institute of Systems Neurosciences, Marseille
Epileptic seizure dynamics span multiple scales in space and time. Understanding seizure mechanisms requires identifying the relations between seizure components within and across these scales, together with the analysis of their dynamical repertoire. Mathematical models have been developed to reproduce seizure dynamics from the micro-scale of a single neuron to a neural mass macro-scale, as either driven or autonomous processes. In this study, we start from a phenomenological model displaying features of electrical epileptic neural activity (i.e. macroscopic), and we move towards a more biologically realistic network of neurons (i.e. microscopic), while keeping track of the dynamical repertoire exhibited by the macroscopic system. Our model is composed of two neuronal populations, characterized by fast excitatory bursting neurons and regular spiking inhibitory neurons, embedded in a comMonday extracellular environment represented by a slow variable. By systematically analyzing the parameter landscape offered by the simulation framework, we reproduce typical sequences of neural activity observed during status epilepticus. We find that exogenous fluctuations from extracellular environment and electro-tonic couplings play a major role in the progress of the seizure, which supports previous studies and further validates our model. Simulated traces are compared with in vivo experimental data from rodents at different stages of the disorder. We discuss potential mechanisms underlying such machinery and the relevance of our approach within a multi-scale paradigm, supporting previous detailed modelling studies and reflecting on the limitations of our methodology.
Sebastian Naze studied Networks and Telecommunications at the University of Tours, France, followed by a Bachelor degree in Computer Science at the Heriot-Watt University, Edinburgh, Scotland, and a Master degree in Information Science at the Vrije University, Amsterdam, The Netherlands. Following courses in Artificial Intelligence, Sebastian gained interests in modelling cognitive processes in the context of psychiatric disorder so he completed Master thesis on Computational modelling of post-traumatic stress (PTSD), under the supervision on Jan Treur at the Agent systems department. Then further motivated in modelling biological processes, Sebastian Naze started a PhD in 2012 under the supervision of Viktor Jirsa and Christophe Bernard at the Institute of Systems Neurosciences in Marseille, working on multi-scale modelling of epileptic seizures.
A conductance based model of intrinsic sensory neurons of the gastrointestinal tract
Date: Monday 21 July
Speaker: Jordan Chambers, University of Melbourne
The enteric nervous system regulates function of the gastrointestinal tract. Intrinsic sensory neurons (ISNs) of the enteric nervous system play a crucial role in this regulation because they respond to stimuli and drive many intestinal motor patterns and reflexes. ISNs express a large number of voltage and calcium gated ion channels, but how interactions between different ionic currents in ISNs produce both normal and pathological behaviours in the intestine remains unclear. A conductance based model of ISNs was constructed based on electrophysiological recordings and data from the literature. The model included voltage-gated sodium and potassium channels, N-type calcium channels, big conductance calcium dependent potassium channels, calcium dependent non-specific cation channels, intermediate conductance calcium dependent potassium channels, hyperpolarisation activated cation channels and internal calcium dynamics. The model reproduced several key physiological observations. A sensitivity analysis indicated which conductances have the largest influence on the excitability of ISNs. In conclusion, the model identifies how interactions between different iconic currents influence the excitability of ISNs and highlights an important role for Ih in enteric neuroplasticity resulting from disease.
Jordan completed his Bachelor of Science (Hons.) and PhD in the Department of Physiology, University of Melbourne. He then joined the Ion Channels and Disease Group at Howard Florey in 2010 before returning to the Department of Physiology 2011. Recently, Jordan has joined BME to work on attention in auditory perception.
Towards closed-loop stimulation strategies in bionic devices
Date: Monday 14 July
Speaker: Matias Maturana, University of Melbourne
Currently, retinal prosthesis and many other medical bionics devices use open-loop stimulation strategies. That is, the level of stimulation does not depend on any continuous measurements of neural activity. Closed-loop stimulation strategies have been implemented in some medical bionics devices, such as functional electrical stimulation, with great success, and have shown the benefits of closed-loop systems. We propose that a closed-loop stimulation strategy in a retinal prosthesis could improve reliability of retinal ganglion cell responses, mitigate neural fatigue, require lower power consumption, and lead to a better visual perception. We present a model for predicting neural responses to electrical stimulation derived using in vitro data. We show how this type of generalised model can be used to design a model-based controller for the control of neural responses, and propose that this method could also be implemented in other medical bionic devices.
Matias completed Bachelor of Arts and Science at the University of Melbourne in 2006 and Master of Engineering (Electrical) in 2012. During his Masters, Matias worked part-time at Bionic Vision Australia doing computational modelling of the intrinsic properties of retinal ganglion cells. His interest in visual neuroscience led him to commence his PhD in 2013, where he is looking at improving stimulation strategies for the bionic eye.
Mapping the human connectome with MRI: Promise, progress and pitfalls
Date: Monday 7 July
Speaker: Assoc Prof Alex Fornito, Monash University
The human brain is an extraordinarily complex network, comprising billions of neurons connected by trillions of synapses. Generating a comprehensive map of these connections‹a so-called human connectome‹across multiple spatial resolution scales has become a central goal for neuroscientists.
Magnetic resonance imaging (MRI) has featured prominently in such attempts, representing the only technique allowing in vivo mapping of whole-brain connectivity in human volunteers. The application of graph theory and complex network science to such data has driven rapid advances in our capacity to map and model brain structure and function in both health and disease. This talk will provide an overview of the basic principles underlying a connectomic approach to the human brain, discuss recent progress and highlight limitations that must be addressed if we are to make further gains in our understanding of the brain.
Alex completed his Masters (Clinical Neuropsychology) and PhD in 2007 in the Departments of Psychiatry and Psychology at The University of Melbourne, followed by Post-Doctoral training in the Brain Mapping Unit at the University of Cambridge, UK. He joined the School of Psychological Sciences at Monash University in 2013 and is currently Deputy Director of Monash Clinical and Imaging Neuroscience and an ARC Future Fellow.
Behavioural Performance and Neural Activation Patterns in Partial Hearing Cochlear Implanted Cat Model
Date: Monday 23rd June
Speaker: Yuri Benovitski, Bionics Institute
Animal behavioural studies make a significant contribution to hearing research and provide vital information which is not available from human subjects. Animal psychoacoustics are usually extremely time consuming and labour intensive; in addition, animals may become stressed, especially if restraints or negative reinforcers such as electric shocks are used. To address these issues, a novel psychoacoustic experiment was designed and vigorously tested. Measured frequency discrimination thresholds were stable, repeatable and comparable with previously published results. The same psychoacoustic experimental setup was used to study chronic performance of partially deafened cats using a cochlear implant. Four cats were systematically tested on different reference frequencies with intra-cochlear electrical stimulation turned on and off. This study was able to show, for the first time, that cats can utilize information provided by a CI in performing a behavioural frequency discrimination task. Moving up the auditory processing pathway, behavioural performance was compared to acute neural activation patterns in primary auditory cortices of the same animals. A new data analysis technique allowing direct comparison of psychoacoustical and electrophysiological recordings was developed. This behaving animal model allows studying how electric and acoustic stimulation of the cochlea are combined. This is particularly important as more people with significant amount of residual hearing receive cochlear implants.
Yuri Benovitski is currently submitting his PhD thesis with the Bionic Institute and the department of Engineering at La-Trobe University. He holds a bachelor of Electronic Engineering (Hons) from RMIT University. His research objectives are combining Biomedical Engineering and Neuroscience by using novel experimental setups and data analysis techniques.
Optimal Control of an Epileptic Neural Population Model
Date: Monday 16th June
Speaker: Assistant Professor Justin Ruth, Singapore University of Technology and Design
Neural population models describe the macroscopic neural activity that can be clinically recorded by an electroencephalogram (EEG). Such models are relevant for the investigation of many pathological neurological phenomena including epilepsy and Parkinson's disease because the models operate on the same scale as the recorded data. Although several models exist in the neuroscience literature, none have leveraged the systematic approach of optimal control theory to design stimuli to treat such neurological conditions. In this talk, I will present the model and a formulation of the seizure abatement goal expressed as an optimal control problem. I will show several results including a realistic, noise-driven simulation where the control is applied as needed in a moving window.
Justin Ruths is an assistant professor at the Singapore University of Technology and Design with the faculty of Engineering Systems and Design. Justin holds degrees in Physics (BS, Rice University), Mechanical Engineering (MS, Columbia University), Electrical Engineering (MS, Washington University in Saint Louis), and Systems Science and Applied Math (PhD, Washington University in Saint Louis). His research themes include casting problems in the natural sciences and medicine as optimal control problems and investigating the control of large-scale complex systems. Towards this latter goal, some of his recent work is at the interface of control and network science.
Modelling and identification by Cellular Nonlinear Networks: seizure prediction in epilepsy?
Date: Monday 2 June
Speaker: Prof Ronald Tetzlaff, Technische Universität Dresden, Germany
Approximately 1% of the world’s population is affected by epilepsy, which is the most comMonday chronical neurological disorder worldwide. The problem of detecting a pre-seizure state in epilepsy using EEG signals has been addressed in many contributions by various authors over the past decades. Recently, Chua has shown that the emergence of complex behavior (e.g. pattern formation) in reaction-diffusion networks is based on local activity and especially on a subset called the “edge of chaos” in the parameter space of these networks. In the presentation, the theory of local activity will be introduced. Furthermore, an identification procedure for reaction-diffusion networks will be proposed based on the theory Cellular Nonlinear Networks which are characterized by local couplings of dynamical systems of comparably low complexity. By using Electroencephalogram (EEG) signal segments in epilepsy, Reaction-Diffusion Cellular Nonlinear Networks (RD-CNN) have been determined and analyzed. Results will be given discussed in the presentation.
Ronald Tetzlaff is a Full Professor of Fundamentals of Electrical Engineering at the Technische Universität Dresden, Germany. His scientific interests include problems in the theory of signals and systems, stochastic processes, physical fluctuation phenomena, system modelling, system identification, Volterra systems, Cellular Nonlinear Networks, and Memristive Systems. From 1999 to 2003 Ronald Tetzlaff was Associate Editor of the IEEE, Transactions on Circuits and Systems: part I. He was "Distinguished Lecturer" of the IEEE CAS Society (2001-2002). He is a member of the scientific committee of different international conferences. He was the chair of the 7th IEEE International Workshop on Cellular Neural Networks and their Applications (CNNA 2002), of the 18th IEEE Workshop on Nonlinear Dynamics of Electronic Systems (NDES 2010), of the 5th International Workshop on Seizure Prediction (IWSP 2011) and of the 21st European Conference on Circuit Theory and Design (ECCTD 2013). Ronald Tetzlaff is in the Editorial Board of the International Journal of Circuit Theory and Applications since 2007 and he is also in the Editorial Board of the AEÜ —International Journal of Electronics and Communications since 2008. He serves as a reviewer for several journals and for the European Commission. From 2005 to 2007 he was the chair of the IEEE Technical Committee Cellular Neural Networks & Array Computing. He is a member of the Informationstechnische Gesellschaft (ITG) and the German Society of Electrical Engineers and of the German URSI Committee.
Circuits and Systems for Electroceuticals
Date: Friday 30 May
Speaker: Prof Wouter Serdijn, TU Delft
In the design process of electroceuticals, such as hearing instruments, pacemakers, cochlear implants and neurostimulators, the tradeoff between performance and power consumption is a delicate balancing act. In this presentation I will cover techniques to deal with the acquisition and generation of electrophysiological signals and to provide reliable communication with and through the body. We will discuss signal-specific analog-to-digital converters, morphological filters, arbitrary-waveform neurostimulators, energy harvesting and ultra wideband wireless communication from a low-power circuits and system perspective. Design examples and their performance will be discussed and an avenue sketched for treatment of various neurological disorders, such as tinnitus and addiction.
Wouter A. Serdijn (M'98, SM'08, F'11) was born in Zoetermeer ('Sweet Lake City'), the Netherlands, in 1966. He received the M.Sc. (cum laude) and Ph.D. degrees from Delft University of Technology, Delft, The Netherlands, in 1989 and 1994, respectively.
His research interests include low-voltage, ultra-low-power and ultra wideband integrated circuits and systems for biosignal conditioning and detection, neuroprosthetics, transcutaneous wireless communication, power management and energy harvesting as applied in, e.g., hearing instruments, cardiac pacemakers, cochlear implants, neurostimulators, portable, wearable, implantable and injectable medical devices and electroceuticals.
He is co-editor and co-author of the books EMI-Resilient Amplifier Circuits (Springer 2013), Ultra Low-Power Biomedical Signal Processing: an analog wavelet filter approach for pacemakers (Springer, 2009), Circuits and Systems for Future Generations of Wireless Communications (Springer, 2009), Power Aware Architecting for data dominated applications (Springer, 2007), Adaptive Low-Power Circuits for Wireless Communications (Springer, 2006), Research Perspectives on Dynamic Translinear and Log-Domain Circuits (Kluwer, 2000), Dynamic Translinear and Log-Domain Circuits (Kluwer, 1998) and Low-Voltage Low-Power Analog Integrated Circuits (Kluwer, 1995). He authored and co-authored 7 book chapters and more than 250 scientific publications and presentations. He teaches Circuit Theory, Analog Signal Processing, Micropower Analog IC Design and Bioelectronics. He received the Electrical Engineering Best Teacher Award in 2001 and 2004.
He has served, a.o., as General Chair for IEEE BioCAS 2013, Technical Program Chair for IEEE BioCAS 2010 and as Technical Program Chair for IEEE ISCAS 2010 and 2012, as a member of the Board of Governors (BoG) of the IEEE Circuits and Systems Society (2006—2011), as chair of the Analog Signal Processing Technical Committee of the IEEE Circuits and Systems society, as a member of the Steering Committee of the IEEE Transactions on Biomedical Circuits and Systems (T-BioCAS) and as Editor-in-Chief for IEEE Transactions on Circuits and Systems—I: Regular Papers (2010—2011). He currently is TPC Co-Chair for IEEE ISCAS 2014 and General Co-Chair for IEEE ISCAS 2015.
Wouter A. Serdijn is an IEEE Fellow, an IEEE Distinguished Lecturer and a mentor of the IEEE.
Capturing Light-Fields on Chip: lens-less 3-D imaging in standard CMOS
Date: Wednesday 21 May
Speaker: Alyosha Molnar, Cornell University
Whereas traditional image sensors map the intensity of light at a particular plane, significantly more information is present in a field of light rays. In particular, by mapping the distribution of incident angle in a scene, “light-field” imaging permits passive extraction of 3-D structure from a single frame. I will present a new class of pixel, the “angle-sensitive pixel” (ASP) built in a standard CMOS manufacturing process. ASPs use pixel-scale diffraction gratings built from metal interconnect layers to generate a strongly angle-sensitive light response.
An appropriately chosen mosaic of ASPs provides a much richer description of incoming light and does so in a computationally compact format, similar to the Gabor filters used in many image-processing applications. I will discuss several applications for arrays of ASPs, including digital light-field photography, lensless far-field imaging, and near-field lensless 3-D imaging of fluorescent microscale sources. I will also discuss several recently developed variants on the ASP, especially applicable to problems in biomedical imaging.
Alyosha Molnar received his BS from Swarthmore College in 1997, and after spending a season as a deck-hand on a commercial Tuna fishing boat, worked for Conexant Systems for 3 years as an RFIC design engineer. He was co-responsible engineer developing their first-generation direct-conversion receiver for the GSM cellular standard. Starting graduate school at U.C. Berkeley in 2001, Molnar worked on an early, ultra-low-power radio transceiver for wireless sensor networks, and then joined a retinal neurophysiology group where he worked on dissecting the structure and function of neural circuits in the mammalian retina, using a combination of electrophysiology, pharmacology and anatomy. He joined the Faculty at Cornell University in 2007, and presently works on low-power software-defined radios, neural interface circuits, and new integrated imaging techniques. He is recipient of the DARPA Young Faculty Award in 2010, NSF CAREER Award in 2012, and Lewis Winner outstanding paper award at ISSCC in 2012. He is presently associated with the University of Melbourne as a visiting professor.
Bionic Voice — Restoring Natural Voice for the Severely Speech Impaired
Date: Monday 19 May
Speaker: Farzaneh Ahmadi, University of Sydney
The most important mechanism of human communications is speech and the larynx is the only source of voice production in the human speech generation mechanism. When a person speaks, the sound waves generated at his larynx pass through the vocal tract and are shaped into different phonemes by the changes in the shape of the vocal tract. If for any reason the larynx fails to function (e.g. as the result of larynx cancer or aphonia), the person will lose the ability to generate voice and will remain merely with the possibility of producing limited whispers. These “voice loss” patients suffer greatly from unintelligibility issues and have difficulty communicating in daily life and over the phone. During the process of speech generation, motor neural signals are generated in the speech and larynx motor cortex of the brain and are transferred to the face and larynx muscles to control their movements. Despite the vast amount of research in modelling human speech production mechanism, limited effort has been made in discovering how the underlying neural activity controls the face, neck and larynx muscles in the speech production. This research aims to discover the neuromuscular mechanism of larynx movement generation and control and use this understanding to implement a Bionic Voice (voice prosthesis with neural interface) prototype which can be tested in-situ in a variety of users. As the first stage, the research correlates the human larynx movements with neuromascular activity of face and neck muscles during voice production. The project aims to be the first in Australia to apply these findings to develop a Bionic Voice Prosthesis that will significantly enhance voice generation and intelligibility of speech for the voice loss patients.
Dr Farzaneh Ahmadi has a background in Electrical engineering. Her area of expertise is signal processing in general and her areas of interest are bio-signals processing, computational neuroscience, brain dynamics and bionic systems. She has a main interest in biomedical research and especially bionic technologies to aid the disabled. She has started working on Bionic Voice research since her PhD at Nanyang Technological University of Singapore and subsequently has decided a research career to develop a working bionic voice solution for voice loss patients. Farzaneh Ahmadi has been the highest ranked awardee of two research grants including the GPRW research fellowships at the University of Sydney in 2013, She is currently working on the question of how to control a bionic voice solution using a combination of physiological attributes. Bionic voice will act as an artificial larynx for patients who lose their larynx functionality.
Opportunities and Pitfalls in Biology for Engineers
Date: Monday 19 May
Speaker: Tristan Croll, Queensland University of Technology
With apologies to Albert Einstein:
Biology without engineering is lame; bioengineering without biology is blind
For much of its history, biological science has held a reputation as a field of study for people who can’t handle physics, chemistry or math. For a great deal of time this was, in a sense, true – but not because these fields are irrelevant to biology. Far from it: rather, the “big problems” in biology were so far beyond the scope of the tools available as to make them effectively intractable. Thus, biology was relegated to a “soft” observational science, while the “hard” scientists honed their skills on easier problems.
The status quo has, of course, changed dramatically in the past few decades, as computational and theoretical resources have grown to the point where we can begin to seriously tackle what is, in reality, perhaps the hardest of all hard sciences – and engineers are well placed to excel in this space. After all, what is protein folding if not the world’s most challenging structural engineering challenge? What is a cell if not the world’s most complex chemical processing plant? What is a protein interaction network if not the most tangled spaghetti code, generated not by the work of an incompetent programmer but by the better part of 4 billion years of blind evolution? Such challenges are well within the scope of engineering principles and, in fact, must be met if the nascent field of bioengineering is to truly succeed and flourish.
However, there are pitfalls here for the unwary engineer. In particular, in the world of biology where the sole guiding principle is, in effect, “what works, works” the engineer’s training in making simplifying assumptions can prove disastrously counterproductive. Conversely, important problems in biology may go unsolved for decades simply because those active in the field lack the necessary background to understand concepts that to a suitably qualified engineer would seem trivial.
In a deliberately provocative talk cast through the lens of my various research projects spanning much of the past decade, I will discuss examples of each of these cases, and expand on the challenges and potential opportunities they represent, the need for both biologists and engineers to work together with mutual respect, and the need for a new generation of research scientists to explicitly treat biology with a hard-science approach. Particular scientific topics to discuss include:
- Why are most solid polymers (the primary focus of a few decades of tissue engineering research) probably dead ends for most tissue engineering applications?
- Why is surface immobilization of normally cell-bound ligands such as stem cell factor probably insufficient to improve hematopoietic stem cell culture?
- Why are transglutaminases probably some of the most important enzymes you’ve never heard of?
- What can be done to accelerate both teaching and research in the challenging field of structural biology?
- What bioengineering problems can we most successfully attack right now while we gather the necessary understanding for the more complex challenges?
Dr Tristan Croll began his academic career with a first-class Honours degree in Chemical Engineering at the University of Queensland. Having developed a growing appreciation of the potential benefits of applying engineering techniques to biological and medical problems, he leaped at the opportunity to become one of the inaugural PhD students of the Tissue Engineering group in the University of Melbourne Department of Chemical Engineering. After graduating in mid-2006, his subsequent postdoctoral experience in the Australian Institute of Bioengineering and Nanotechnology at UQ added to his growing appreciation of the many fundamental biological unknowns hampering progress in bioengineering. This ultimately led to the difficult choice to make a substantial change in the direction of his career. With this in mind, he moved to QUT’s Institute of Health and Biomedical Innovation in 2008, and since that time has focused his research primarily on questions regarding the fundamental biology of the wound healing process, while maintaining an interest in the development of enabling technologies for study of processes relevant to biomedical engineering. He has active research projects in the structural biology of cell surface receptors, understanding of novel interactions modulating the signalling of insulin-like growth factor I, and probing the in vivo biological roles of transglutaminases, a critically important yet poorly understood family of enzymes. In addition, he has spent the past few years developing a low-cost, large-volume 3D bioreactor design to eventually be released on an “open source” basis to facilitate study in the challenging field of 3D cell culture.
Dr Croll is currently a teaching/research lecturer at QUT, where he spends his non-research time teaching students concepts in molecular structure, enzymology, cell signalling pathways and general cell biology.
Threshold Concepts and Disciplinarity in Biomedical Engineering Education
Date: Monday 12 May
Speaker: Paul Junor, Senior Lecturer, Electronics & Biomedical Engineering La Trobe University
The task of consolidating and streamlining the multidisciplinary strands of Biomedical Engineering poses a challenge for course design. A relatively contemporary development in education, the Threshold Concepts Framework (Meyer and Land, 2003) offers some potential assistance to this ongoing process: “It has been discovered that, not only can threshold concept theory help in focusing students’ and teachers’ attention, it can also be a tool for curriculum development where there is a tendency to overcrowd the curriculum” (Male & Baillie, 2011).
The threshold concepts notion has attracted widespread interest and has been used in a number of disciplines such as mainstream engineering (Entwistle et al, 2005; Flanagan et al, 2010; Male & Baillie, 2011; Scott & Harlow, 2012). There are also number of publications emerging relating to applications in healthcare education, but an initial survey revealed no existing literature applying threshold concepts to Biomedical Engineering.
Tempered by considerations of disciplinarity (Shulman, 2005; Donald, 2011), this presentation considers the appropriation of suitable proxies from acknowledged threshold concepts of related fields such as Physiology, Biology, Medicine and Surgery in addition to those of the established engineering disciplines, to inform and guide further planning for specific threshold concept identification for Biomedical Engineering.
Paul Junor is a Senior Lecturer in Electronics & Biomedical Engineering at La Trobe University. Immediately prior to joining the Department of Electronic Engineering there in 1993, he had been a Biomedical Engineer at Peter MacCallum Cancer Institute from 1982, before which he had worked for a private radiology company, and had held teaching and research positions (RMIT and Monash Medical School). He is immediate past-president of the Society for Medical & Biological Engineering (Vic.) (2005-2010); a Senior Member of IEEE (currently chair of the Victorian IEEE Education Society Chapter) and a Fellow of Engineers Australia (currently Victorian representative to the EA Biomedical Engineering College Board).
The Human Connectome in Health and Disease
Date: Monday 5 May
Speaker: Andrew Zalesky, University of Melbourne
A central goal in neuroscience is to comprehensively map the network architecture of the human brain, known as the human connectome. Mapping and deciphering this amazingly complex neural wiring diagram will reveal much about what makes us uniquely human and provide novel insights into disorders of the brain and mind. From the perspective of an engineer that has been working in human connectomics soon after the field’s inception in 2005, I will present some of the unique computational and modelling challenges associated with mapping brain networks and give examples of how these challenges have been solved using traditional computer science and engineering approaches. In this talk, I will specifically focus on mapping the large-scale connectome with magnetic resonance imaging (MRI) techniques. I will discuss shortest path approaches that I have developed for tracking the trajectories of axonal fibre bundles in a computational process known as tractography. I will also discuss the network-based statistic and applications in neuropsychiatric disorders, including schizophrenia and addiction.
Andrew Zalesky is a senior research fellow at the University of Melbourne. He currently holds an NHMRC research fellowship and previously held numerous ARC fellowships. Dr Zalesky is known for publishing some of the first neuroimaging evidence of connectome pathology in schizophrenia. He is also recognised for developing the network-based statistic, a statistical method that is now widely implemented in brain image analysis software. He has published more than 70 peer reviewed articles; including two articles in the top 0.01% cited papers in the same year and field. Dr Zalesky is an editor of Brain Topography and currently serves on the editorial board of NeuroImage.
Salience and a task-based objective measure of image quality
Date: Monday 28 April
Speaker: Prof Murray Loew, Director of the Biomedical Engineering Program in the Department of Electrical and Computer Engineering at George Washington University
We present an objective image-quality measure that is correlated with perceived image quality as a function of the most conspicuous features contained within an image. Those salient features are determined by combining aspects of multiple disciplines (including psychology, vision science, and image engineering) to define a new measure that emphasizes the importance of contrast-based features as a function of spatial frequency, i.e., scale. Visual search models and visual psychophysics provide the framework for our channel model. We leverage previous work on just-noticeable discrimination models to develop a salience model for single images. Signal detection and estimation theory is used to develop a statistical basis for our scale-based salience measure.
The new measure is applied to medical images; salient features within mammograms are studied extensively. Our new salience measure has multiple potential applications. The development of a perceptually-correlated metric that is useful for quantifying the conspicuity of local, low-level or bottom-up visual cues can be used to improve reader training. This could be accomplished by presenting technicians, residents, etc., with images that are processed to enhance or degrade perceptually important frequency bands, thereby increasing or decreasing the perceptual “pop-out” within regions-of-interest. Further, images that can be grouped by known perceptual difficulty can be used as training and testing aids because selection is based upon perceptually-correlated image similarities or differences. This would complement the selection of cases based upon anatomical, histological or clinical requirements by providing a means of selecting cases using an image (contrast and scale) similarity measure. The salience metric was evaluated using a set of 40 mammograms and registered eye-position data from nine observers.
Murray Loew is a professor and director of the Biomedical Engineering Program in the Department of Electrical and Computer Engineering at George Washington University (Washington, D.C. USA). He is the inaugural recipient of the Fulbright Distinguished Chair in Advanced Science and Technology, sponsored by the Defence Science and Technology Organisation (DSTO). His research is in the area of medical imaging and image analysis, image registration, and image compression. Through his Fulbright, Prof. Loew will come to the DSTO laboratories in Adelaide for five months to work on object tracking and image and data fusion. He is a Fellow of the IEEE and of AIMBE.
Bistable Dynamics of Perceiving Ambiguous Stimuli
Date: Monday 14 April
Speaker: John Rinzel, Center for Neural Science and Courant Institute of Mathematical Sciences, New York University
When experiencing an ambiguous sensory stimulus (e.g., the vase-faces image), subjects may report haphazard alternations (time scale, seconds) between the possible interpretations. I will describe dynamical models for neuronal populations that compete through mutual inhibition for dominance - showing alternations, behaving as noisy oscillators or as multistable systems subject to noise-driven switching. In highly idealized formulations networks are percept specific without direct representation of stimulus features. Our recent work involves perception of ambiguous auditory stimuli, the models incorporate feature specificity, tonotopy, so that perceptual selectivity is emergent rather than built-in.
Reduced-order modelling of perinatal cardiovascular dynamics and congenital heart disease
Date: Monday 7 April
Speaker: Dr Jonathan Mynard, University of Melbourne
In newborns with congenital heart disease, the cardiovascular system often displays 1) heart and vascular abnormalities that disturb normal blood flow patterns, and 2) a survival-dependent persistence of some features of the fetal circulation. For example, in pulmonary atresia with intact ventricular septum (PAIVS), the right ventricular outflow path fails to develop and pulmonary flow is dependent on a patent ductus arteriosus; in addition, profound coronary abnormalities may be present. Reduced order numerical modelling allows complex cardiovascular dynamics to be investigated with more flexibility and less ethical concern than in clinical or experimental settings. This talk will provide an overview of the development of numerical models of the entire circulation of the normal fetus and neonate, these being derived from a reference model of the adult circulation. A model of PAIVS is also developed to elucidate the determinants of coronary blood flow before and after surgical opening of the right-ventricular outflow path.
Jonathan Mynard completed undergraduate degrees in Medical Biophysics and Electronic Engineering at Swinburne University in 2005. He then earned a Master of Research in Computer Modelling at Swansea University, Wales, where he developed a one-dimensional model of the adult systemic arterial circulation. Jonathan completed his PhD at Melbourne University in conjuction with the Murdoch Children’s Research Institute, with his thesis focusing on cardiovascular dynamics in the perinatal period. He currently holds a CJ Martin Overseas Biomedical Fellowship from NHMRC, and he recently returned from two years at the University of Toronto, Canada where he worked in the Biomedical Simulation Laboratory gaining skills in image-based computational fluid dynamics.
Neural Network Model of Visual Cortex for Perception of Motion Transparency
Date: Monday 31 March
Speaker: Parvin Zarei Eskikand, University of Melbourne
Motion transparency relates to the situation where there are multiple motions perceived in only one spatial location. One of the main challenges of motion processing systems is that local motion signals do not represent accurately direction of the whole object. This is known as the “aperture problem”. The small receptive fields of individual neurons can only measure motion components orthogonal to their preferred direction. This problem makes the processing of motion transparency very challenging, because solving the aperture problem requires uniqueness in the motion domain, but perception of a transparent motion is based on the representation of multiple objects. The aim of this project is to model different layers of the visual cortex to demonstrate the neural processing that underlies the perception of motion transparency. In this talk, I will introduce a model that is able to detect the motion signals and discriminate these signals resulting from different objects in the input. The initial local motion components will be extracted at the first stage by a motion detector and then these components will be analyzed in higher layers to form an accurate estimation of motion of the individual objects.
Low power wireless transceivers for implanted medical devices and neural prostheses
Date: Monday 17 March
Speaker: Farhad Goodarzy, University of Melbourne
In this session a wireless transceiver for implantable medical devices (IMD), Neural prostheses (NP) and embedded neural systems is discussed. We'll talk about modulation schemes and a new modified technique, called saturated amplified signal (SAS). We analyze the system based on the underlying circuitry and the modulation scheme which provides a theoretical basis to compare and produce optimal low power wireless transceivers for biomedical applications. We also present a low power wireless transceiver in the MICS frequency band based on the modified modulation and present the results. The design is capable of being fully integrated on single chip solutions for surgically implanted bionic systems, wearable devices and neural embedded systems.
Towards a biophysically inspired model of the cerebellum
Date: Wednesday 5 February
Speaker: Tom Close
Despite much of the distinct regular structure and neurophysiology of the cerebellum being known from the time of Eccles fifty years ago, we still do not understand how the elegant motor control systems found in nature could arise from this neural circuitry. The most well known theory, proposed by Marr and Albus in the late 60's, draws an analogy between an adaptive filter and the arrangement Purkinje cells and parallel fibres. However, this explanation doesn't agree with many recent biophysical observations, such as the relatively short delays that occur in spike transmission along the parallel fibres and the timing of the "error signal" from the climbing fibre axon. Therefore, to work towards a theory of cerebellar function that can explain the neurological basis of highly skilful motor actions that currently cannot be reproduced by artificial systems, we are building a biophysically detailed model of the cerebellum to capture key biophysical characteristics with potential functional implications. However, highly detailed network simulations quickly become unmanageable using standard simulation software practices. Therefore, we have developed a software framework that separates the biophysically derived parameters from the algorithmic code required to initialise the simulation on large computer clusters. We then demonstrate how this framework can be used to quickly identify the effect of parallel fibre feedback on the input layer of the cerebellum.
Tom Close was awarded a PhD on "Advanced techniques in diffusion MRI tractography" from the Department of Electronic and Electrical Engineering at the University of Melbourne in 2011, under the wise tutelage of Leigh Johnston and Iven Mareels amongst many other supervisors. He is currently a post-doctoral researcher in the Computational Neuroscience Unit of the Okinawa Institute of Science and Technology, Japan, where he is following his passion of studying the behaviour of the cerebella network in between staring out his window at blue coral-filled waters.
Mathematical Modelling of Brain Networks: From Synaptic Plasticity to Behaviour
Date: Monday 20 January
Speaker: Rob Kerr
Date: Monday 2 December 2013
Micelles and vesicles have long been proposed as carriers for low molecular weight molecules including drugs. The core-shell systems are found to be useful for the encapsulation of hydrophobic drugs in the core while maintaining the water solubility of the system with the hydrophilic shell. In addition, their sizes between 20–100 nm makes them perfect to target the drug passively to the tumour. Despite their high stability, micelles still tend to break up upon dilution once they reached their lower critical aggregation concentration. Several approaches have been undertaken to stabilise these structures using the crosslinking of the core or shell.
This talk will discuss how the synthesis of the underlying block copolymers, which build up these core-shell nanoparticles. The chemistry of these polymers does not only determine how big these particles are, but it can also influence drug encapsulation and the …
Date: Monday 25 November 2013
The pattern of cortical folding that is unique to each human brain arises during development from a series of physiological and biomechanical factors that remain the focus of on-going research. To analyse patterns of cortical folding, MRI has been widely used in the computation of metrics based on morphometric analyses.
This talk will firstly present the use of a Spherical Harmonic representation of the cortical surface to measure cortical complexity, including prediction of intermediate folding states during development. Secondly, a modified gyrification index computed using the Laplace Beltrami operator will be presented. This method uses the intrinsic geometry of the cortex, rather than being constrained by slice orientation. Cortical folding is quantified using a metric based on eigenvalues of the Laplace Beltrami operator. It will be demonstrated that such metrics are useful measures of cortical gyrification …
Biomedical Engineering Seminar: Biological and engineering challenges in biomanufacture of human platelets for transfusion
Date: Monday 11 November 2013
Platelets are small, enucleated blood cells that play critical roles in maintaining blood vessel integrity and tissue repair. Platelets survive for only 5–7 days and their number within blood needs to be maintained above a critical threshold to prevent spontaneous bleeding. In severe cases of low platelet counts, platelet transfusion is the treatment of choice. However, globally, the supply of fresh human platelets from volunteer donors often outstrips demand.
This talk discusses technology developed for large-scale biomanufacture of these cells from haemopoietic stem cells. An underpinning aspect of this technology development is the desire to replicate the process of platelet production in vivo. This is a truly amazing biological process involving controlled differentiation of stem cells to ultimately produce a large polyploid cell, the megakaryocyte and the final conversion of these cells to platelets. …
Date: Monday 21 October 2013
The use of surface initiated polymerisation (SIP) methods have become widespread as a method of modifying surfaces, particularly in the formation of polymer brush coatings and to produce coatings with advanced functionality. In the last six years CSIRO has developed and implemented a method of SIP which relies on the use of macro-initiators/iniferters (mI) or macro-chain transfer agents (mCTA) that are covalently bonded to a surface and act as initiator or chain growth sites for the formation of polymer brush coatings with very well defined properties. The method is particularly useful for controlled or living polymerisation mechanisms such as Radical Addition-Fragmentation chain Transfer (RAFT), Atom Transfer Radical Polymerisation (ATRP) and Initiator-Transfer-Termination (Iniferter) and can be applied to a variety of substrate materials with either simple or complex geometries.
This talk will discuss the …
Date: Monday 14 October 2013
In 2012 about 50,000 Australians suffered a stroke, and about 65% of them remain with a physical disability. In order to improve the neurorehabilitation efficiency, and the patients recovery, therapists are naturally trying to use new technologies in the rehabilitation process. Robotics systems were thus introduced in the field of neurorehabilitation in the seventies.
This talk will deal with the particular interest of robotics exoskeletons which have the ability to interact with the human limb at several contact points, not only at the hand level. This specific ability constitutes a serious advantage for rehabilitation applications but also bring new problems and more complexity in terms of control. Two new exoskeleton control methods dedicated to neurorehabilitation have thus been developed to fully take advantage of this specific structure. The first one provide a passive mobilization of the patient limb …
Continuous Wave Nuclear Magnetic Resonance - Investigation of off-resonance effects of Rabi modulated excitation
Date: Monday 7 October 2013
In this biomedical engineering seminar magnetic resonance imaging (MRI) will be considered and how it has been adopted as a common scanning technique for medical diagnostic use. MRI uses pulsed excitation protocols, in which the object of interest is excited by short-lived pulses, and measurements taken as the object’s magnetisation returns to equilibrium. Researchers are investigating an alternative method of continuous wave excitation, in which the object is continuously excited and measurements are simultaneously performed, to provide a potentially richer information source about the object.
Preliminary work has focused on characterisation of the nuclear magnetic resonance signal during Rabi modulated continuous wave excitation. Under this form of excitation, the bulk magnetisation reaches a periodic steady-state, which can be approximated by a Fourier expansion of the Bloch equation, restricted to harmonics …
Date: Monday 23 September 2013
The aim of this project is to model the effect of electrical stimulation on local neural activity in the brain. This will contribute to a larger project of systematic controlling of epileptic seizures through a model-based strategy. Epileptic seizures are the result of an uncontrolled burst of electrical activity in the brain, which can lead to convulsions or loss of consciousness. The most common form of treatment for epilepsy is via drugs. However, they are not effective for approximately one third of epilepsy patients. An alternative therapy is to apply electrical stimulation to control abnormal brain activity.
In order for the developed model to be clinically applicable, the appropriate functional form and physiological parameters need to be identified to make it applicable to cortical tissue stimulated by surface electrode arrays. The whole model will then …
Date: Monday 9 September 2013
Venue: Room 202 (Masters Seminar Room 2) , Old Metallurgy Building
Presbyopia is a condition in which the aging eye loses its ability to focus on close objects (accommodation), due to hardening of the natural lens. While wearing reading glasses remains the most common solution to this condition they cannot provide dynamic accommodation due to their fixed focal length. An attractive potential solution to presbyopia involves replacing the hardened natural lens with a gel soft enough to allow accommodation.
In this study, functional polysiloxanes macromonomers have been investigated as possible candidate materials to replace the hardened natural lens for correction of presbyopia. This requires a biostable and biocompatible polysiloxane to be injected into the capsular bag in a liquid form and cured in situ to form a soft gel. These polymers are designed to mimic the optical and mechanical properties of a young person’s natural lens by having a …
Date: Monday 2 September 2013
Stochasticity is an essential aspect of biochemical processes at the cellular level. We now know that living cells take advantage of stochasticity in some cases and counteract stochastic effects in others.The presenter will use examples to discuss how cells process information and discuss the relative roles that analog and digital signal processing play in cellular systems. In the response of Escherichia coli to nitrogen starvation, for example, researchers find strong evidence for both types of information processing. Using time-resolved proteomic, metabolomic and transcriptomic data researchers can show that the nitrogen state can be computed with high fidelity. The high accuracy - the channel capacity amounts to approximately 10 bits - reflects a strong evolutionary impetus on optimizing sensing and correctly responding to the environmental nitrogen state. Combining different …
Biomedical Engineering Seminar: Systems Biology of drug response and metastasis through multi-scale modeling, novel biomaterials and high-throughput imaging
Date: Monday 26 August 2013
Cancer cell migration, signaling and response to therapeutics have historically been carried out in two-dimensional environments that are far from in vivo. These environments create artificial polarities, mediate unrealistic cell-matrix interactions and lead to signaling cascades that paint an incomplete and inaccurate picture of cancer cell behavior in vivo. Consequently, our understanding of matrix mechanical regulation of therapeutic efficacy and chemoresistance is qualitative and fragmented. Additionally, current computational models are unable to connect biochemical signaling events at the molecular level with biomechanical processes observed in native like 3D environments making the predictive power of models limited in their scope.
Using a combination of multi-scale modeling approaches (deterministic, finite element, molecular simulations) with development …
Date: Monday 19 August 2013
Layer-by-layer (LbL)-assembled carriers have recently emerged as a promising class of materials for applications in biology with studies progressing from in vitro to in vivo. The versatility of LbL assembly coupled with particle templating allows the generation of capsules with specific properties (eg., stimuli-responsive, efficient cargo encapsulation), thus offering new opportunities in drug delivery. In this presentation, the interactions between human cancer cells and the LbL capsules will be discussed. The focus will be placed on the internalization and intracellular trafficking of these particles. Based on the cellular interactions, several approached for drug encapsulation and controlled intracellular released will also be addressed in the talk. Taken together, these studies have highlighted the importance of understanding the complex cellular dynamics of particles in advanced …
Date: Monday 12 August 2013
This presentation will discuss methods for developing subject-specific mesoscopic neural models. The ability to create subject-specific models will enable estimation of normally hidden aspects of physiology. Imaging physiological parameters will lead to a greater understanding of diseases and provide new targets for novel therapies. The model-data fusion framework in this presentation is based on nonlinear Kalman filtering. In particular, we will demonstrate estimation accuracy using synthetic data before showing results from real intracranial EEG data. …
Biomedical Engineering Seminar: Atomic Force Microscopy Measurement of Fluid-Solid Interactions within Aggrecan Proteoglycan Networks
Date: Monday 29 July 2013
Venue: Greenwood Theatre, Building 193, Electrical and Electronic Engineering
The molecular structure and nanomechanical properties of aggrecan monomers extracted and purified from human articular cartilage from donors of different ages have recently been visualized and quantified via atomic force microscopy (AFM)-based imaging, force spectroscopy, and high bandwidth nano-rheology. AFM imaging enabled direct comparison of full length monomers at different ages. The demonstrably shorter glycosaminoglycan (GAG) chains observed in adult full length aggrecan monomers, compared to newborn monomers reflects markedly altered biosynthesis with age. These results provide molecular-level evidence of the effects of age on the conformational and nanomechanical properties of aggrecan, with direct implications for the effects of aggrecan nanostructure on macro-level properties of cartilage tissue. The presenter will discuss recent studies of brush layers of aggrecan from these …
Biomedical Engineering Seminar: The effect of morphology and intrinsic electrophysiology in shaping retinal ganglion cell responses
Date: Monday 24 June 2013
Venue: Greenwood Theatre, Building 193, Electrical and Electronic Engineering
Retinal ganglion cells (RGCs) display differences in their morphology and intrinsic electrophysiology. Matias Maturana will explore realistic, morphologically correct models of 200 ON and OFF RGCs, and test ionic channel densities in morphological compartments that are necessary to capture experimentally recorded phenomena. He will investigate the effect of the cell’s morphology on its impulse waveform, using the first and second-order time derivatives as well as phase plot features. Matias Maturana proposes that a combination of morphological and ionic features shape the cell’s impulse response and confirm that by simulations. In addition, he explore the ability of the constrained models of RGCs to respond to high frequency bi-phasic pulse train stimulation and show that cells’ morphology plays an important role in shaping cell responses.…
Biomedical Engineering Seminar: Vision processing for safe and efficient navigation with a visual prosthesis
Date: Monday 17 June 2013
Current and near-term visual prostheses are severely limited in their capacity to convey visual information about the scene to implantees. This has motivated consideration of how vision processing algorithms can be designed and used to maximise the bandwidth available, in order to improve functional outcomes for patients. In this talk the speaker will present an overview of recent and ongoing work at NICTA CRL towards the development of computer vision algorithms and novel visual representations to enhance the perception of scene structure in prosthetic vision. In particular, the presentation will outline recent work demonstrating how such algorithms may be used to emphasise low contrast ground obstacles, and encode the time-to-contact of objects posing an imminent threat of collision. Obstacle avoidance work has been shown to reduce collisions by close to 50% compared with …
Date: Monday 3 June 2013
The aim of this research seminar is to propose a framework to obtain patient-specific models for people with epilepsy who have focal seizures. Different biologically plausible models of the brain are reviewed, including methods that have been used to analyse and identify them. A novel framework is proposed to construct patient-specific models using Electrocorticographic (ECoG) data. To this end, the Jansen and Rit (1995) model of a cortical column is extended such that the model emulates transitions to and from seizures states. The extended model will be fitted (by an identification and validation method) to ECoG data. This framework may help us to describe the underlying mechanisms of initiation and termination of seizures in individual patients. Our next goal is to generalise our proposed frameworks by interconnecting the extended models, and fit them to multi-channel ECoG data …
Biomedical Engineering Seminar: The stellate microcircuit of the cochlear nucleus — design and optimisation of a biophysically-realistic neural network model
Date: Monday 29 April 2013
Biophysically-realistic neural network (BNN) models require quality design and optimisation methods in order to best advance understanding of complex neural processing. This talk presents a novel BNN model of the cochlear nucleus stellate microcircuit, which provides a robust spectral representation of sound and plays an essential part in speech communication. The model was optimised using rigorous sequential methods and simultaneous genetic algorithms. The results of the analysis demonstrate the utility of this approach for improving BNN models.…
Date: Monday 8 April 2013
Exercise renders a disproportionate load on the cardiac ventricles. Animal and human studies are concordant in demonstrating that right ventricle load (wall stress, work and oxygen demand), which is considerably less than for the left ventricle at rest, increases disproportionately during exercise. The result is that the right ventricle may be injured by prolonged intense exercise creating the potential for long term heart problems including serious arrhythmias.
This presentation describes possible mechanisms for arrhythmic heart remodelling by combining echocardiography and magnetic resonance imaging in real-time exercise studies. Repeatedly, the obtained results demonstrate that the focus of exercise changes in the heart should focus on the right ventricle and pulmonary circulation. The right ventricle’s unique shape, location and loading present specific issues …
Biomedical Engineering Seminar: Validating MEG/EEG finite element head models using a controlled rabbit experiment
Date: Monday 25 March 2013
In focal epilepsy, it is essential to accurately determine the location of the seizure focus for each patient. Electroencephalography (EEG) and magnetoencephalography (MEG) based source localisation is a promising non-invasive method to determine the location of the seizure focus. Validation of realistic MEG/EEG finite element head models for source localisation will be presented using a self-developed controlled in vivo rabbit experiment. The original findings are that skull defects influence the MEG and finite element head models can be used to account for skull defects in MEG and EEG.…
Biomedical Engineering Seminar: Requirements for the Robust Operant Conditioning of Neural Firing Rates
Date: Monday 18 March 2013
Operant conditioning experiments have shown that changes in the firing rates of individual neurons in the motor cortex of monkeys can be elicited. In these experiments, the firing rates of the neurons were measured using an implanted electrode, and the monkeys were presented with feedback based on these rates and rewarded for increasing them. Behavioural learning such as this is assumed to occur at the synaptic level and reward-modulated spike-timing-dependent plasticity (RSTDP) has previously been proposed as such a model.
In this study, the presenter will propose a generalization of the classical RSTDP model that can account for experiments where dopamine changes the amplitude of long-term potentiation and depression. Using analytical techniques and numerical simulations, classical RSTDP is compared with the proposed generalized model. The requirements for these models …
Biomedical Engineering Seminar: Realistic spiking models of octopus cell circuits of the mammalian auditory brainstem
Date: Monday 11 March 2013
Octopus cells are named after their unique shape, with dendrites oriented in one direction. They receive input from a large number of Auditory Nerve Fibers (>60) representing a broad frequency band. The talk covers three topics relating to the computational modelling of the behaviour and function of octopus cells:
- A multi-compartmental Hodgkin-Huxley model, combined with a realistic model of the auditory periphery was used to determine the importance of the octopus cells' dendritic delay. We found that this dendritic delay might compensate for systematic asynchrony across ANFs with different CFs.
- A modified leaky integrate-and-fire model with a simple dendritic delay to investigate the function of octopus cells output in the ventral nucleus of the lateral lemniscus. In particular, we used realistic sounds to investigate the effect when octopus …
Date: Monday 25 February 2013
Hossein Mokhtarzadeh (PhD student in Biomechanics) will be presenting the first seminar in our new Biomedical Engineering Seminar Series.
Landing is an inevitable physical activity in many sports such as basketball, soccer, and gymnastics. Upon landing, the anterior cruciate ligament (ACL) is one of the most susceptible knee structures to injury with a higher rate of incidence among female athletes.
Hossein Mokhtarzadeh will outline his study to investigate the biomechanics of landing maneuver to understand ACL injury mechanism. In this study, two experimental approaches were used to quantify the effects of muscle forces and impact loads on ACL loading: human motion capture and in-vitro experiments. It was found that it was not only the knee joint muscles but also the coordination of muscles surrounding the ankle joint that together play a major role in protecting ACL from injury; also the results …
Date: 2:00pm Tuesday 29 January 2013
The NeuroEngineering Laboratory Seminars recommence for 2013 with a guest speaker from Pennsylvania State University, Pro. Steven Schiff. This promises to be an excellent seminar so anyone interested is encouraged to attend.
Title: Adventures in Control Theory: Hydrocephalus, Seizures, Climate, Dung, and the Neonatal Septisome
Abstract: Modern model-based control theory brings us optimal estimation of state of dynamical systems, even when those dynamics are floridly nonlinear as in many biological processes. Because our understanding of biology and disease has only relatively recently given us models of sufficient fidelity to warrant inclusion in control models, and because the engineering methods to incorporate complex nonlinear models are also recently developed, there are vast applications to consider exploring. This talk will …
Date: 11:00am Wednesday 12 December 2012
Venue: Main Conference Room (Ground Floor), Centre for Neural Engineering Building #261
The Melbourne School of Engineering presents a special NeuroEngineering Laboratory Seminar, with a guest speaker from the University of Exeter, UK, Professor John Terry. Professor Terry is an excellent speaker and his work is of the highest quality. ProfessorTerry is a world leader in computational and theoretical neuroscience, and nonlinear dynamics. His work focuses on studying oscillatory systems in the brain, with strong clinical implications.
In this seminar Professor Terry explores two classes of models (biophysically inspired and phenomenologically derived) to study network mechanisms of seizure initiation and evolution. He first introduces a biophysically inspired model, based on the principles of mass action, and demonstrate that transitions in the model precisely correspond to those observed in the EEG recordings of patients with absences. He describes …
Date: 11:00am Wednesday 24 October 2012
Venue: Main Conference Room (Ground Floor), Centre for Neural Engineering Building #261
The NeuroEngineering Laboratory Seminar Series continues with a PhD Completion Seminar by Amanda Ng.
Magnetic Resonance Imaging phase data contains information about the magnetic properties and chemical composition of tissue and demonstrates novel contrast compared to the magnitude data more commonly used in MRI studies. Current methods for processing phase data and their limitations will be discussed, and new methods for artifact removal and analysis of phase data will be presented. Particular focus will be placed on Quantitative Susceptibility Mapping, in which localised magnetic susceptibilities are estimated from the phase data. This technique holds great promise in clinical studies of neurodegenerative diseases in which iron accumulates in the brain.
Amanda is completing her PhD at the University of Melbourne in collaboration with the Florey …
Date: 11:00am Tuesday 11 September 2012
Venue: Brown Theatre, Electrical and Electronic Engineering Building, Building number 193
NeuroEngineering is about using scientific methods to understand and model the nervous system, and to use this knowledge to engineer systems that interact with, augment, or mimic nervous system functionality. This seminar will provide an overview of the research activity of the NeuroEngineering Laboratory in the Department of Electrical and Electronic Engineering at the University of Melbourne. The areas of research are: Audition, Speech and Bionic Ear Design, which aims to develop improved technology for the hearing impaired. Bionic Eye Design and Vision, which aims to develop a bionic eye to aid the vision impaired. Computational Neuroscience, which aims to develop mathematical models and computational analyses of neural systems. Epilepsy, which aims to develop technology that can detect, predict and stop epileptic seizures. Neuroimaging, which aims to develop MRI acquisition …
Date: 11:00am Wednesday 22 August 2012
Venue: Main Conference Room, Ground Floor, Centre for Neural Engineering Building, Building Number 261
Neurons in the brain engage in collective oscillations in a range of frequencies that span several orders of magnitude. In particular, gamma and high-gamma oscillations (40-100 Hz and above) have been associated with neuronal activation in several brain regions, and are altered in cognitive disorders such as schizophrenia. First proposed as a psychophysiological mechanism for perceptual binding, gamma oscillations are now acknowledged as a general and versatile mechanism of neuronal processing. Gamma oscillations have been shown to be critically dependent on the activity of inhibitory interneurons. In contrast to excitatory neurons, inhibitory interneurons are present in many different subtypes, which differ in their molecular, electrophysiological and anatomical properties. In particular, interneuronal types that are responsible for gamma generation often exhibit …
Date: 11:00am Wednesday 15 August 2012
Venue: Main Conference Room (Ground Floor), Centre for Neural Engineering, Building Number 261
Every aspect of modern science relies upon creating representations of things. And when we do, we pick the signals that interest us and the behavior that interests us. From that, we determine how to interpret the way input is converted into output in a system. Our description of that process is our understanding of the system. The same is true for mental processes and reverse engineering their implementation in neural circuitry.
The feasible approach to this is called (whole) brain emulation and relies on determining precisely which signals we care about and then breaking the problem down into a collection of smaller system identification problems. To tackle those, there is a roadmap that includes structural scanning (connectomics) as well as new tools for functional recording – some of which are now in development in collaboration with laboratories at …
Date: 11:00am Wednesday 1 August 2012
Venue: Main Conference Room (Ground Floor), Centre for Neural Engineering Building, Building Number 261
Professor Peter Gawthrop, visiting researcher to National ICT Australia (NICTA) in the Department of Electrical & Electronic Engineering will be presenting a seminar as part of the NeuroEngineering Laboratory seminar series, titled "Intermittent Control: a Computational Theory of Human Control Systems". The term "Intermittent" has been used since the 1940s to describe human motion control as a sequence of open-loop trajectories punctuated by intermittent feedback. This seminar formulates a computational model to capture this behaviour whilst also explaining why human motion often appears to be continuous in nature. The use of the model to explain experimental data will be discussed.…
Date: 11:00am Wednesday 25 July 2012
Venue: Main Conference Room (Ground Floor), Centre for Neural Engineering Building, Building No. 261
The NeuroEngineering Laboratory Seminar Series continues with a talk by Associate Professor Jeremy Crook on Stem Cell Translation: Tools & Therapies.…
Date: 11:00am Wednesday 30 May 2012
Venue: Main Conference Room (Ground Floor), Centre for Neural Engineering Building, Building number 261
In this seminar, PhD student, Nina Saeedi will report on her research project which creates a physiologically-inspired neural network model of auditory perception and evaluates its performance in perceiving different aspects of sound. In this network, acoustic and electric models of the auditory system are applied as models of normal hearing and hearing with cochlear implants.
The project assesses model performance in different tasks like pitch perception, vowel recognition and consonant recognition to ensure that it is similar to human performance reported in the literature. It uses this model as a test platform to investigate the effect of the limiting factors on the auditory performance of cochlear implants. These include insufficient temporal resolution, limited number of electrodes and current spread, as well as the inability of the brain …
Date: 11:00am Wednesday 16 May 2012
Venue: Main Conference Room (Ground Floor), Centre for Neural Engineering Building, Building number 261
The capabilities of Smartphone platforms will play major roles in driving the practicality of mHealth applications, which are expected to impact prevention and treatment methods in diverse medical fields. This talk opens the concept of Mobile Health (mHealth) from the biomedical applications, Quality of Service (QoS), security, and cloud computing perspectives. The number of operational mobile subscribers is expected to pass the 6 billion mark by mid 2012 and the number of wearable wireless sensors is expected to grow to 400 million by the year 2014. Such a tremendous growth in the mobile space will result in an increasing number of mobile-based applications deployments, such as: Machine-to-Machine (M2M) communications, Electronic-Health (eHealth), and Mobile-Health (mHealth). These emerging mobile applications will require 3G and 4G mobile networks for biomedical …
Algorithms for current steering in retinal prostheses
Presenter: Evgeni Sergeev, The NeuroEngineering Laboratory, Department of Electrical and Electronic Engineering, University of Melbourne.
Date: Wednesday 13 June
The current emitted by each electrode of a retinal prosthesis can be independently controlled. The problem of current steering is to select appropriate currents in order to shape the firing pattern of the target neurons as required. Before this is possible, a link between the tissue current and the response of a retinal neuron must be established. Several in vitro results from the literature with be discussed, which will help us develop a relevant model. Then preliminary results will be presented.
Neural Network Model of Auditory Perception
Speaker: Nina Saeedi, The NeuroEngineering Laboratory, Department of Electrical and Electronic Engineering, University of Melbourne.
Date: Wednesday 30 May 2012
There are different factors limiting the auditory performance of cochlear implant recipients. From a signal processing point of view, some of these factors are: insufficient temporal resolution, limited number of electrodes and current spread. Also, poor performance might be a result of inability of the brain to adapt to the information provided by the implant.
Investigating the effects of any of the above factors by observing patients' performance is very expensive and time-consuming. The goal of this project is to create a physiologically- inspired neural network model of auditory perception and evaluate its performance in perceiving different aspects of sound. In this network, acoustic and electric models of the auditory system are applied as models of normal hearing and hearing with cochlear implants. Model performance will be assessed in different tasks like pitch perception, vowel recognition and consonant recognition to ensure that it is similar to human performance reported in the literature. After the model is validated, it will be used as a test platform to investigate the effect of the limiting factors mentioned above.
Functional changes of the ganglion cells following photoreceptor degeneration in a mouse model of retinitis pigmentosa
Speaker: Susmita Saha
Date: Wednesday 9 May
In order to use a retinal implant to restore vision in Retinitis Pigmentosa (RP), the ganglion cells need to be intact since they are the output cells of the retina. However, few studies have investigated how photoreceptor loss in retinitis pigmentosa affects the synaptic activity and output of the ganglion cells during different stages of degeneration. Also, very little is known about the synaptic activity of the ganglion cells in response to electrical stimulation in a RP-degenerated retina. The objective of this PhD project is to investigate the changes in the spontaneous excitatory and inhibitory synaptic activity of the alpha-ON and alpha-OFF ganglion cells in the degenerate retina at different stages of the disease. This involves investigating the anatomical distribution and electrophysiological properties of synapses of the ganglion cells in an animal model.
Adult neurogenesis and mental health: A summary of recent results
Speaker: Prof. Joachim Diederich
Date: Wednesday 2 May 2012
Adult neurogenesis is one of the most active and vibrant areas in the neurosciences. While it was believed for decades that “no new neurons” are being formed in the adult mammalian brain, it has been confirmed now that the generation of new neurons and synapses does occur in both the hippocampus and the olfactory bulb. Even more importantly, new neurons are being recruited into functional circuits and the process appears to be highly relevant for learning and memory. Impaired neurogenesis has been associated with mental health problems such as depression and schizophrenia. This informal presentation will provide an overview of recent results on adult neurogenesis and the link to mental health problems.
The Neural Tissue Simulator: An Ultrascalable Solution to Large-Scale Structural and Electrophysiological Simulations of Neuronal Circuit Function
Speaker: Dr. James Kozloski, Research Staff Member, Master Inventor, Biometaphorical Computing Thomas J. Watson Research Center, Yorktown Heights, NY USA
Date: Wednesday 18 April 2012
We have developed a novel tissue volume decomposition, and a hybrid branched cable equation solver for performing large-scale simulations of neural tissue (2011). The decomposition divides the simulation into regular tissue blocks and distributes them on a parallel multithreaded machine. The solver computes neurons that have been divided arbitrarily across blocks and can be considered a tunable hybrid of Hines’ fully implicit method (1984), and the explicit predictor-corrector method of Rempe and Chopp (2006). We demonstrate thread, strong, and weak scaling of our approach on a machine of 4,096 nodes with 4 threads per node. Scaling synapses to physiological numbers had little effect on performance, since our decomposition approach generates synapses that are almost always computed locally. The largest simulation included in our scaling results comprised 1 million neurons, 1 billion compartments, and 10 billion conductance based synapses and gap junctions. Based on results from the ultra-scalable Neural Tissue Simulator, we estimate requirements for a simulation at the scale of a human brain and derive an approach to scaling computational neuroscience together with expected supercomputational resources over the next decade.
Biomolecular Structure Determination without Crystallography: Bright Prospects for X-ray Free-Electron Laser Imaging
Speaker: Dr. Harry Quiney, ARC Centre of Excellence for Coherent X-ray Science, School of Physics, The University of Melbourne
Date: Wednesday 4 April 2012
The structures of biomolecules are currently determined crystallographically using coherent X-ray or electron sources. This process naturally requires the availability of high quality crystals, the production of which frequently presents formidable difficulties. Membrane proteins, which mediate communication between the interior and exterior environments of cells, typically form two-dimensional structures and have proven resistant to the methods that are used to grow samples suitable for crystallography. Periodic structures amplify high-resolution information about the unit cell structures, so any structure determination scheme using aperiodic samples must trade off this amplification against an increased incident flux of photons or electrons. The X-ray Free-Electron Laser (XFEL) sources in the US, Japan and Germany are being developed to determine biomolecular structures by interacting intense femtosecond X-ray pulses with nanocrystals or single-molecule targets. The pulses are so bright that the electronic damage caused by the interaction inevitably leads to the Coulomb explosion of the target. If the pulses are short enough, however, sufficient structural information can be gathered before this disintegration, an approach that is now generally known as “diffract and destroy” imaging. This presentation will survey the potential uses of emerging XFEL source technologies in the determination of structure and dynamics in biomolecular systems.
Exploring the Human Default Mode Network with Intracranial Electrophysiology
Speaker: Dr. Brett Foster, Stanford Human Intracranial Cognitive Electrophysiology Program & Laboratory of Behavioral and Cognitive Neurology. Department of Neurology and Neurological
Sciences, School of Medicine, Stanford University
Date: Tuesday 27 March 2012
Since its discovery over a decade ago, the human “Default-Mode Network” (DMN) has received an incredible amount of research interest and skepticism in the field of neuroimaging. With many early criticisms being addressed, the scientific debate now focuses on adjudicating the specific functional role(s) of this network and its unique contribution to cognition. While neuroimaging studies have made progress in this respect, more refined methods are required for anatomically and temporally resolving the functional dynamics of DMN activity. Indeed the electrophysiological correlates of DMN function remain relatively unknown. Our group has tackled this specific question using human intracranial recordings from the posteromedial cortex (PMC), a core node of the DMN. This talk will summaries our progress so far in studying the cognitive electrophysiology of the PMC and the novel insights obtained by using intracranial recordings.
Modelling the impact of complex network structure on balanced excitation and inhibition in large networks of cortical neurons
Speaker: Mark McDonnell
Date: Wednesday 21 March 2012
The developing interdisciplinary field of network science is proving highly fruitful in revealing complex structure in the connections between the components of many complex systems. Examples of “complex networks” include small-world networks and scale-free networks, and example systems where they have been observed include genomes, social groups, financial markets, and the brain. Network science also seeks to develop mathematical analysis of the influence of complex structure on system dynamics, by combining empirical connectivity data with theory from statistical and nonlinear physics.
Physiology and Modelling of complex cells in primate Visual cortex
Speaker: Shaun Cloherty
Date: Wednesday 7 March 2012
One of the enduring dichotomies in visual neuroscience is the classification of visual cortical neurons into simple and complex types. These cell types are distinguished by the way they spatially and temporally integrate visual stimuli, i.e., their receptive field properties. Simple cells exhibit spatially distinct subregions within their receptive fields, which respond selectively to either luminance increments (bright stimuli) or decrements (dark stimuli). In contrast, complex cells exhibit bright and dark receptive fields that are largely overlapping. As a result, complex cells are often considered to be phase invariant energy detectors. I will present results from single unit recordings in primate visual cortex demonstrating that complex cell receptive fields are dynamic and, in fact, complex cells can encode phase information. In light of these data I will review and assess the prevailing models of cortical complex cells.
Fluorescence guided resection of glioma using 5-aminolevulinic acid-Quantitative Methods
Speaker: Neda Haj-Hosseini
Date: Wednesday 29 February 2012
Total tumor resection in patients with glioblastoma multiforme (GBM) is difficult to achieve due to the tumor's infiltrative way of growing and morphological similarity to the surrounding functioning brain tissue. The diagnosis is usually subjectively performed using a surgical microscope. A hand-held optical touch pointer using a fluorescence spectroscopy system is developed and evaluated for distinguishing healthy from malignant brain tissue intraoperatively.
Inferring neuronal network connectivity from multiunit tetrode recordings in live animals
Speaker: Dr. Patrick O’Brien
Date: Wednesday 8 February 2012
Safety of Wide-Field Retinal Prosthesis
Speaker: Joel Villalobos
Date: Wednesday 25 January 2012
Within the research effort to develop a clinically viable retinal implant, there is a pre-clinical program being conducted. This session will present a summary of the PhD research efforts, which involved design of a spherically contoured implant substrate and passive chronic suprachoroidal implantation in a cat model. Results of the histopathology assessment indicated the implant was well tolerated in the eye's suprachoroidal space. Electrode impedances and electrical stimulation thresholds showed that this technology is viable and could continue progression towards a clinical program.
Representation of input signals in recurrently connected neuronal networks
Speaker: Matthieu Gilson
Date: Wednesday 18 January 2012
Spike-timing-dependent plasticity (STDP) has been observed in many brain areas, such as sensory cortices, where it is hypothesised to develop the structure of synaptic connections between neurons. Previous studies have demonstrated how STDP can capture spiking information at a short timescale, such as coincident spiking, spike patterns and oscillatory spike trains. However, it is not yet clear how STDP stores this information in detail in the synaptic structure of recurrently connected neuronal networks. We use a theoretical framework to investigate the learning dynamics induced by STDP based on the temporal cross-correlograms between input spike trains. The key to understand the computation scheme is the interplay between the properties of STDP, neuronal response and input correlograms. In the case of a single neuron, STDP can extract the strongest spectral components of the input correlation structure in a similar fashion to principal component analysis (PCA). In a recurrent network, STDP can encode different features of input stimuli relying on partial connectivity and heterogeneities in the synaptic connections (e.g., conduction delays). Our mathematical study of the STDP dynamics aims to bridge the gap between physiology and machine learning, thus shedding light on possible neuronal encoding schemes. On the application side, such spiking neuronal networks that behave as self-adapting filters can be used for the representation, categorisation and detection of spatio-temporal stimuli.
The frequency of oscillatory inputs is encoded in the connection strengths of networks of spiking neurons by STDP
Speaker: Rob Kerr
Date: Wednesday 7 December 2011
Spike-timing-dependent plasticity (STDP) is a learning rule that updates synaptic strengths based on the relative timing of pre- and post-synaptic spikes. Unlike classical, rate-based Hebbian learning, STDP can potentially encode fast temporal correlations in neuronal activity, such as oscillations, in the functional structure of networks of neurons that have axonal and dendritic propagation delays. In this study, the changes made by STDP to synaptic strengths in recurrent networks with axonal delays receiving oscillatory inputs were investigated analytically with Poisson neuron models and verified through simulations with leaky integrate-and-fire neurons. The motivation behind this was to understand how general spatiotemporal patterns can be learnt by a network of neurons with STDP present. An application of this specific model might be in explaining how the brain can perceive the pitch of complex sounds up to 300Hz, even when the fundamental frequency is missing. Both the analytical description and simulations found that connections were selectively potentiated and depressed based on their axonal delay in such a way that the delays of the strong connections in the network “resonated” with the input frequency.