BME faculty Senior Projects List 2014

BME Faculty List of Possible Undergraduate Research Projects

Note to students. The projects listed in this matrix represent possible projects available to BME undergraduate students. We encourage you to contact listing faculty members for further information.

First	Last (link to website)	Lab Description	Track	Location	Project title	Project title	Project title	Project title
Jay	Humphrey	Vascular Mechanics and Mechanobiology Lab	Biomechanics	Malone	Quantitative Histology	Computational Hemodynamics	Mechanobiological Assessments using Cell / Tissue Culture	Computer-aided Experimentation
Evan	Morris	Neuroimaging of Addiction and Medications Development	Imaging	PET Center	Imaging the Brain's Dopamine Response to Smoking Cigarettes	Imaging the action of a Medication for Alcoholism.	Build a Mock PET Scanner
Jim	Duncan	Biomedical Image Analysis	Imaging	TAC	Image segmentation of biomedical structures	Quantification of cardiac (left ventricular) deformation from echocardiography	Prediction of tumor growth and response to radiotherapy from Magnetic Resonance Images
Richard	Carson	PET Technology and Applications	Imaging	PET Center	Awake Monkey PET	Novel PET Algorithms for Carotid Arteries	Multimodal Brain Networks in Cocaine Dependence	Improved PET MR image registration
Mark	Saltzman			Malone
Larry	Staib	Medical Image Analysis	Imaging	TAC	Magnetic Resonance Diffusion Weighted Image Analysis	Imaging Biomarkers of Disease	Machine learning for tissue classification
Chi	Liu		Imaging	PET Center
Todd	Constable		Imaging	TAC
Hemant	Tagare		Imaging	TAC
Angelica	Gonzalez			Malone
Andre	Levchenko			West Campus
Stuart	Campbell		Biomechanics	Malone
Fahmeed	Hyder	Functional and Molecular Imaging of the Brain	Imaging	TAC	Calibrated fMRI for basal metabolism	Quantitative metabolic PET	Liposomal BIRDS	Dendrimeric BIRDS
Rong	Fan	Single-cell analysis for cancer research and immunology	All tracks	Malone Engineering Center	Single-cell analysis of T cell response	Genome editing and cancer development	MicroPhysiological Systems	High-content imaging for systems biology
Themis	Kyriakides	Extracellular Matrix, Tissue Engineering, and the Foreign Body Response	Biomolecular Engineering, Tissue Engineering	Amistad	Migration Assays for Testing Next Generation Wound Healing Therapies	Characterizing and Robustly Producing Keratinocyte Extracellular Matrix	Effect of nanotopography on cell fusion
zFirst	zLast	Lab Name	Track	Location	First Project Name	Second Project Name	Third Project Name	Fourth Project Name
zFirst	zLast	Lab Name	Track	Location	First Project Name	Second Project Name	Third Project Name	Fourth Project Name
zFirst	zLast	Lab Name	Track	Location	First Project Name	Second Project Name	Third Project Name	Fourth Project Name
zFirst	zLast	Lab Name	Track	Location	First Project Name	Second Project Name	Third Project Name	Fourth Project Name

---

Lab Descriptions

---

Vascular_Mechanics_and_Mechanobiology_Lab

(Biomechanics Track) Our focus is on (i) developing computational models for understanding vascular disease progression and designing clinical interventions, (ii) using genetic, pharmacologic, and surgical models to elucidate mechanisms that underlie diverse vascular conditions, and (iii) using tissue engineered constructs to test hypotheses of mechanosensing and mechanoregulation of extracellular matrix.

Functional_and_Molecular_Imaging_of_the_Brain

(Bioimaging Track) The societal burden of misdiagnosed brain disorders and diseases is substantial. The Hyder lab is leading breakthroughs in quantitative and translational imaging technologies, based primarily on magnetic resonance methods, to visualize molecular processes of function and dysfunction at the laminar level.

A primary interest of the Hyder lab is to develop functional imaging techniques that relate neural activity to underlying laminar structure in health and disease. Emphasis is on fMRI, but other multi-modal fMRI methods in conjunction with MRS, electrophysiology, optical imaging, and PET are being sought for increased biomarker specificity. Specific areas of interest include (i) understanding the role of the extraordinarily high energy demands of ongoing and intrinsic activity within neural populations as potential for quantitative disease biomarker, (ii) advancing the spatiotemporal resolution of functional imaging to understand the relation of cellular metabolism in health and disease (e.g., healthy aging, Alzheimer’s disease, depression, epilepsy, schizophrenia), and (iii) developing advanced calibrated fMRI methods for using oxidative energy as an absolute index of neural activity, both with task and rest paradigms, across cortical and subcortical regions.

Another active interest in the Hyder lab is molecular imaging with magnetic resonance technologies where several disciplines connect, from chemistry and physics to material science and physiology. A new molecular imaging method, pioneered in the Hyder lab called BIRDS, combines high MRI spatial resolution with high MRS molecular specificity. The method, quite unconventionally, detects the paramagnetically-shifted and non-exchangeable protons from lanthanide (or transition) metal ion probes for high spatiotemporal resolution biosensing. Highly precise molecular imaging of temperature and pH is achievable with BIRDS. Current areas of relevance are (i) design of new molecular probes for BIRDS, (ii) early cancer detection and metastasis using absolute pH imaging, (iii) application of new probes for BIRDS as molecular targets for diseases (e.g., diabetes), and (iv) detection of tumor response to treatments (e.g., radiation, chemotherapy, heat).

Lab_Name

Your text about your lab goes in a paragraph like this.

---

Project Descriptions

Quantitative_Histology

We use histology and immunohistology to quantify regional variations in the distributions of vascular cell phenotype, extracellular matrix, proteases, and cytokines to correlate with computational predictions. Primary focus – image analysis and histopathology.

Computational_Hemodynamics

Working with colleagues in our medical school, we use patient-specific computational models to study vascular disease mechanisms and their treatment. Primary focus - to use image reconstruction methods to create large scale computational models.

Mechanobiological

Assessments using Cell / Tissue Culture – We subject cultured cells and tissue engineered constructs to well defined mechanical stimuli and assess their mechanobiological responses. Primary focus – cell and tissue culture methods.

Computer-aided_Experimentation

We use custom computer-controlled devices to perform theoretically motivated experiments. Primary goal – to design, build, and test new testing systems.

Cardiac_Quantification

Quantification of cardiac (left ventricular) deformation from echocardiography: This work employs image feature detection and matching strategies for estimating local frame-to-frame displacements from image sequences, and then machine learning strategies to integrate the information to quantify strain in the left ventricle under different disease conditions. Biomechanical models of the heart can be used to help with the integration and close collaboration with clinical colleagues in cardiology is a key part of this work.

Biomedical_Segmentation

Image segmentation of biomedical structures: Here, the work involves the use of geometrical and statistical models of shape and mathematical optimization strategies to locate structure in images. The structure can range from finding cells or subcellular particles from high resolution microcope images to locating the endocardial surface of the heart from ultrasound or magnetic resonance images.

Tumor_Prediction

Prediction of tumor growth and response to radiotherapy from Magnetic Resonance Images: Sets of MR images are obtained from patients (in collaboration with Neurosurgeons and Neuroradiologists) and are assembled into a database. Pattern classification strategies can be developed and compared to other work in the literature to try to find parameters that can predict response to treatment.

Calibrated_fMRI_for_basal_metabolism

Simulation studies to assess sensitivities required for fMRI and perfusion data to extract basal metabolism from calibrated fMRI data

Quantitative_metabolic_PET

Analysis of whole brain PET data of glucose and oxidative metabolism in the human brain in relation to blood flow

Liposomal_BIRDS

Development and/or characterization of newly developed probes encapsulated inside liposomes for BIRDS

Dendrimeric_BIRDS

Development and/or characterization of newly developed macromolecular-based probes for BIRDS

Awake_Monkey_PET_Imaging

Perform, analyze, and develop the technology for awake monkey brain PET studies involving combined brain imaging (without head restraint) and behavioral tasks

Carotid_Image_Reconstruction

Develop novel PET Algorithms to measure the activity in the carotid arteries which feed the brain

PET_MR_Cocaine_Brain_Networks

Analysis of PET (Dopamine) and fMRI data in subjects with Cocaine Dependence to determine altered brain networks

PET_MR_Image_Registration

Improve the quality of image registration between PET and MR images for more accurate determination of small brain structures

First_Project

The text about your first project goes in a paragraph like this. Note the format of the title must match the link ("anchor") exactly in the table, above.