Research Opportunities for Grad Students

Overview   Neural Micro/Nano Systems   Neural Signal Analysis  
Neural Imaging   Neural Prosthesis   Clinical Neuorengineering

OVERVIEW

A prerequisite for participation by graduate students is a strong motivation to solve biomedical problems in general, and neuroscience (basic/clinical) in particular, using engineering, instrumentation, computing or mathematical tools and techniques. Graduate students are encouraged to define their own problem and to innovate, taking into consideration the synergy offered by the many ongoing projects as well as resources (and not limit themselves to the listed projects). In fact, graduate students are welcome to interact extensively and brainstorm on new ideas. Historically, the work done by graduate students has led invariably to new directions for the lab as well as numerous publication as well as participation in national conferences and student paper competitions.

The following research synopsis includes some ongoing projects and some new ideas and projects under consideration. This list is an ever-evolving one and is usually tailored to the individual student or research fellow, and should only also serve as a starting point for discussion.  The projects listed below are also likely to change or even get dated; hence, after reviewing, please contact Prof. Thakor (nitish@jhu.edu; Tel: 410-955-7093).

NEURAL MICRO/NANO SYSTEMS

Student/post docs with interests in Neuroscience and strong EE, MEMS, or instrumentation background and hands on skills are encouraged and invited to take part in these projects. Students are strongly encouraged to establish new collaborations and work in teams (e.g. engineers working with cell/molecular biologists or neurophysiologists.

• Dynamically Adaptable Neural Networks
  Ph.D. student Nirveek Bhattacharjee is developing the viral transfection and switchable surfaces for altering gene expression “where and when” it is needed. We are interested in future students continuing this work to develop genetically modifiable, dynamic neural networks.

• Self-Assembly of Biological and Physical Systems Into Multiscale Functional 3D Networks (with Andreou, Gracias, JHU)
  This collaborative project with Dr. Andreou in ECE and Dr. Gracias in ChemE is in early stages of development.

• Integrated Electronics Interface to Neurotransmitter Sensor Array
  Ph.D. student Kartikeya Murari has developed a VLSI circuit interface, namely a potentiostat, with very low power and high dynamic range design. Currently the chip is being tested with micro/nanosensors for eventual use in implantable neural probes.

• Power Harvesting in Implantable Neural Probes (with J. Harb, BYU)
  Masters student, Chris Sauer, and Ph.D. student Moshen Mollazadeh have developed an implantable circuit for low data rate telemetry and for power harvesting. Future work will involve design of fully integrated neural probe for recording electrical/ chemical activity in a wireless, fully implanted package.

• Microdialysis for Neuroscience Research
  In a recently awarded project, our goal is to develop a microfluidic system for sampling neurochemicals and subsequently interface this device for in vivo recording in rodents and eventually in man.

NEURAL SIGNAL ANALYSIS

We are interested in the involvement of students with strong quantitative background who are looking for clinical applications of their work. These projects will allow students/fellows to gather considerable experimental skills, development of animal models, recording and surgery, as well as electrical recording and analysis. The translational, clinically applicable research work should be of great interested to pre-meds and clinical collaborators.

• Brain Electrical Signal (EEG, Evoked Potentials, Spikes) Analysis
  This is a long standing interest area for our lab. Previous students and post doctoral fellows have developed signal processing algorithms for EEG analysis (method of entropy/wavelet entropy/information quantity), Evoked Potential (spectral, coherence and wavelet method) and neural spike analysis.

• QEEG and QSpike: Brain Indicators of Temperature Manipulation after Cardiac Arrest (with R. Geocadin)
  This newly awarded grant, being worked on by post doctoral fellows, Drs. Hyunchool Shin and Xiaofeng Jia, utilizes signal analysis methods to quantify brain’s electrical response (EEG, neural firing patterns or spikes) to cardiac arrest brain injury and hypothermia therapy.

• Traumatic Brain Injury Detection in Neurocritical Care (with Infinite Biomedical Technologies)
  This is a Small Business Innovations Research (SBIR) funded project to develop neural signal analysis algorithms and patient monitoring instruments. The work currently continues through studies of patients at Johns Hopkins Hospital.

• Cortical Health Index (with Infinite Biomedical Technologies)
  Another SBIR application award has now reached a very advanced stage of clinical testing. Cortical Health Index is a comprehensive algorithm for providing an index of brain injury and recovery. This project should be of great interested to pre-meds and clinical collaborators.

NEURAL IMAGING

Our neural imaging work provides unusual opportunity to develop novel optical instrumentation and carry out in vivo experimental evaluation. The speckle imaging of blood flow and microvessel structure is opening new directions for grads and post docs interested in the field of in vivo imaging and novel applications in functional imaging and microvessel structures in brain, tumor and retina.

• Functional Laser Speckle Brain Imaging
  Optical imaging method offers the advantage of high resolution and non-ionizing/ inexpensive imaging. Laser speckle imaging is used by graduate students Li Nan and Abhishek Rege to obtain blood flow distribution in brain. Currently, we are interested in developing spectroscopic and image analysis methods to identify blood vessels (arterioles, venules). Future work will involve development of an on chip imager to carry out optical imaging in awake, behaving animals.

• Mechanism of Neurovascular Coupling
  One application of laser speckle imaing could be functional brain imaging. This involves the study of coupling between blood flow and neural activity. We have started to set up a rodent preparation of whisker barrel stimulation and recording and studying response of neural activity and blood flow to stimulation.

• Imaging and Modeling of Cortical Microvascular Dynamics
  In collaboration with colleagues at UCSD (Drs. Cauwenburghs and Kleinfeld), Ph.D. student Kartikeya Murari proposes to develop novel optical imager and computational and experimental methods to image microvessel dynamics. Laser speckle imaging will be correlated with high resolution images using two photon imaging.

NEURAL PROSTHESIS

The overall scope of this project is quite extensive. A number of research opportunities exist inall aspects – neural signal analysis, control algorithms, telemetry/controller design, arm design and tactile sensor/feedback. In addition, post doctoral and clinical research collaborators will be needed to translate the non-invasive approach to invasive prosthetic control. A number of undergraduate students have joined this project to develop a virtual reality environment, brain control of cursor and development of natural language processor. Graduate students and post docs are encouraged to form teams and provide mentoring.

• Revolutionary Prosthesis (with S. Harshbarger, APL, DARPA)
  This project involves a large consortium of 10 Universities and 30 or more investigators being managed and coordinated by Johns Hopkins Applied Physics Lab. The project has a bold vision of creating a neurally (peripheral nerve or cortical) controlled 21 degrees of freedom arm with numerous technological advances. The project raises numerous challenges in hardware, algorithmic and human interfaces. Our group currently consists of several graduate and undergraduates focusing currently on non-invasive brain computer/machine interface, first generation multi-fingered hand and prosthesis design, and testing and incorporation of sensory feedback. Graduate students Soumyadipta Acharya and John Ferguson are developing algorithms for EEG and event related potential analysis. Graduate students Vikram Aggarwal and Yoonju Cho are developing the controllers and telemetry for the neurally controlled prosthesis. In addition, Aniruddha Chatterjee and Kelvin Liang have developed the first generation tactile sensor/haptic feedback system.

• Central Pattern Generator for Spinal Neuroprosthesis (with Etienne-Cummings, Cohen, JHU)
  Graduate student Jacob Vogelstein has taken on a very interesting and challenging project to study the central pattern generator (CPG) as a model of locomotion. He has implemented the CPG model in silicon, mimicking the algorithms in computational/silicon model which will eventually be useful in testing a functional spinal prosthetic device. He is also continuing work on spinal cord preparation using lampreys to study neural basis to CPG and its modulation. Further hardware, deeper neurophysiological studies and translation to higher mammalian models remain to be developed.

CLINICAL NEUROENGINEERING

This is an experimentally rich area of research with an opportunity to take the research to clinical practice on the bedside. The projects below heavily depend on clinical partnership and team work of experimentally oriented post docs and computer/ quantitative oriented graduate students and undergrads. Students interested in hands on experimental biological/physiological studies, pre-meds and medical collaborators are invited to participate. Students and post-docs with strong signal processing theory are welcome in this collaborative endeavor.

• Consequences of Cardiac Arrest: Brain Injury
  With the help of our Neurology collaborators, Dr. Geocadin and Hanley, we have developed a rodent model of graded CA injury in which we have shown that the neurological response as monitored by quantitative EEG (Q-EEG) is proportional to the duration of arrest and cardiopulmonary resuscitation. We monitor the electrophysiologic output from the brain using advanced signal processing algorithms. The significance lies in the expected discovery of the mechanism of recovery of cellular electrophysiological function and the molecular basis in glutamate-mediated excitability.

• Cardiac Arrest: Neuroprotection by Hypothermia
  Recently hypothermic treatment, administered properly and timely manner has shown some promise towards improving the neurological outcome after cardiac arrest. In a model of hypoxic-asphyxic cardiac arrest and resuscitation in rodents, post-doctoral fellow Dr. X. Jia assesses brain’s electrical activity measured by quantitative EEG (qEEG) and neurodeficit scoring to assess the injury and outcome. Since our proposed model is modeled after clinical protocols and our methods are equally clinically applicable, we expect this work to have strong translational appeal, to take this research from bench to bedside.

• Spinal Cord Injury: Structure (Diffusion Tensor MRI) and Function (Evoked Potential)
  The long-term goal of our research led by Dr. All and graduate student, Manisha Aggarwal, is to develop technologies for monitoring and measuring the injury to the spinal cord for basic scientists as well as clinicians. We propose a two-pronged 1) determine the electrophysiological response as well as the recovery of the sensory and motor pathways, and 2) non-invasively image the site of injury and monitor status of the axonal pathways.

• Image Guided Gene Expression in Spinal Cord Injury
  Research Associate Dr. All and graduate student Manisha Aggarwal, along with collaborators at Washington Center and Dr. Mori in Radiology, are developing novel technology and quantitative methods to determine the injury extent and recovery of the axonal pathways in a two-pronged approach: 1) interactive segmentation of the injury and sparse survived axonal tracts using advanced diffusion tensor imaging algorithms and fiber tracking methods and 2) gene expression in the injured spinal cord in the regions of injury to axonal track identified through imaging.