Medical Biophysics Commons^™

Delta Relaxation Enhanced Magnetic Resonance - Development And Application Of A Field-Cycling Contrast Mechanism, Yonathan Araya

University of Western Ontario - Electronic Thesis and Dissertation Repository

Delta relaxation enhanced magnetic resonance (dreMR) is a novel imaging method capable of producing contrast proportional only to the concentration of the bound form of the targetable contrast agent using a dynamic field-cycling technique. The characteristic high relaxivity magnetic field dependence of bound paramagnetic contrast agents enables suppression of tissue contrast from unbound agents and unenhanced tissue, thereby increasing probe specificity. The dreMR technique requires an auxiliary actively shielded field-shifting insert electromagnet to modulate the strength of the main clinical magnetic field as a function of time during the relaxation and evolution periods of a pulse sequence.

Ablavar (approved for ...

Improving Acute Stroke Management With Ct Perfusion Imaging: Approaches To Treatment Guidance And Brain Tissue Salvage, Christopher D. D'Esterre

University of Western Ontario - Electronic Thesis and Dissertation Repository

CT Perfusion (CTP) provides measurement of perfusion at the capillary level which can be used to characterize tissue viability, and blood-brain-barrier (BBB) compromise. Using CTP, the goals of this research are to: 1) select patients that will benefit from acute stroke treatment, and 2) determine if pre-stroke neuroprotection reduces stroke severity.

Chapter two investigates the cerebral blood volume (CBV) parameter in a small acute ischemic stroke (AIS) patient set. Overestimation of the acute CBV defect is caused by incomplete wash-out of the CT contrast due to a shortened CTP acquisition time (“truncation artifact”).

In chapter three we examine the prognostic ...

Magnetic Resonance Imaging Of Brain Tissue Abnormalities: Transverse Relaxation Time In Autism And Tourette Syndrome And Development Of A Novel Whole-Brain Myelin Mapping Technique, Yann Gagnon

University of Western Ontario - Electronic Thesis and Dissertation Repository

The transverse relaxation time (T2) is a fundamental parameter of magnetic resonance imaging sensitive to tissue microstructure and water content, thus offering a non-invasive approach to evaluate abnormalities of brain tissue in-vivo. Prevailing hypotheses of two childhood psychiatric disorders were tested using quantitative T2 imaging and automated region of interest (ROI) analyses. In autism, the under-connectivity theory, which proposes aberrant connectivity within white matter (WM) was assessed, finding T2 to be eleveted in the frontal and parietal lobes, while dividing whole brain data into neurodevelopmentally relevant WM ROIs found increased T2 in bridging and radiate WM. In Tourette syndrome, tissue ...

Flash4 Dark Reference Images, George Mcnamara

George McNamara

Hamamatsu FLASH4.0 dark reference images, acquired with 10 second exposure times, no light to camera. Camera offset (set by Hamamatsu( is ~100 (the average intensity of the first image is always ~1 intensity level higher - an odd feature, but trivial in practice for a 16-bit camera).

George McNamara, Ph.D.

Single Cells Analyst at L.J.N. Cooper Lab

University of Texas M.D. Anderson Cancer Center

Improving Cervical Cancer Nodal Boost Radiation Therapy By Quantifying Uncertainties And Exploring Advanced Radiation Therapy Modalities, Zhiqian Yu

UT GSBS Dissertations and Theses (Open Access)

Radiation therapy for patients with intact cervical cancer is frequently delivered using primary external beam radiation therapy (EBRT) followed by two fractions of intracavitary brachytherapy (ICBT). Although the tumor is the primary radiation target, controlling microscopic disease in the lymph nodes is just as critical to patient treatment outcome. In patients where gross lymphadenopathy is discovered, an extra EBRT boost course is delivered between the two ICBT fractions. Since the nodal boost is an addendum to primary EBRT and ICBT, the prescription and delivery must be performed considering previously delivered dose. This project aims to address the major issues of ...

Atlas-Based Attenuation Correction For Pet/Mri, John Christian Patrick

University of Western Ontario - Electronic Thesis and Dissertation Repository

Attenuation correction (AC) in PET/MRI is difficult as there is no clear relationship between MR signal and 511 keV attenuation coefficients (μ). One strategy is to align a pre-defined atlas of μ to the PET/MRI for AC. However, atlas design may influence quantitative accuracy of AC. In this thesis we compare 3 atlas design strategies and evaluate their performance in an oncology patient population. The 3 strategies were: correction with BMI-dependent atlases; gender-dependent atlases, and a gender- and sex-independent atlas. Patients were imaged with FDG PET/CT and 3T MRI. The atlases were created and then used for ...

Raman Micro Spectroscopy For The Characterisation Of Cervical Cancer., Nosheen Rashid

Doctoral

The primary purpose of this study is to evaluate the potential of FTIR and Confocal Raman micro spectroscopy (CRM) in elucidating the biochemical changes occurring in different layers of the cervical epithelium including basal, superficial and the underlying connective tissue known as stroma during the progression of Cervical Intraepithelial Neoplasia (CIN) to cancer. Initially the two techniques were compared and Raman was chosen based on its higher spatial and spectral resolution. The sample preparation and spectral measurement procedures were optimised and all samples were formalin fixed paraffin processed, dewaxed using xylene, and measured on calcium fluoride windows. Raman spectra were ...

Video Codec Performance (Excel Spreadsheet), George Mcnamara

George McNamara

Video codec performance (Excel spreadsheet). Movie was made in 2005-2006 when I worked at City of Hope National Medical Center. VTLF refers to Video Timelapse Light Facility. Videos were outputted from MetaMorph as AVI files. Personally, I always recommend uncompressed video files fro scientific uses. I also encourage posting the original scientific data format (ex. .lsm, .zvi, .lif, .stk).

Pubspectra Tattletales, George Mcnamara

George McNamara

Tattletales for Multiplex Fluorescent Reporters in Single Cells for Metabolomics

George McNamara

Analytical Imaging Core Facility, University of Miami, Miller School of Medicine, Miami, FL

As of April 2013: L.J.N. Cooper & D.A. Lee Cellular Immunotherapy Lab, University of Texas M.D. Anderson Cancer Center, Houston, TX

Email: gmcnamara@med.miami.edu, geomcnamara@earthlink.net

Tattletales is my concept for spatial multiplexing many fluorescent protein (FP) biosensors in the same live cell. For example, there are excellent FP biosensors to Ca++ ions, pH, glucose, ribose, glutamine, glutamate, ATP, redox, ROS, pyruvate, cAMP, cGMP, IP3, PI(3,4,5)P3, cell cycle indicators (Fucci2), PKA, PKC, photsphatases, caspase(s) [1, 2]. However, these are typically used one biosensor per experiment, due in part to flooding the cell with soluble biosensor. That is, conventionally, either a metabolite (glucose) reporter or a signal transduction (Ca++) reporter can be imaged. By flooding the cell with the reporter, signal to noise ratio is compromized by autofluorescence.

Tattletales takes advantage of spatial multiplexing to both increase the number of different reporters, and improve signal to noise ratio by localizing each biosensor to a small volume. I started with the observation by Robinett et al [3] who localized 512 GFP-nls-LacI to a 256 LacO array as a 200 nm diameter diffraction limited spot (nuclear background due to overexpression). Many thousands of DNA binding proteins, of known sequence specifities, exist (LacI, TetR, GalR, etc for cell line studies; ZF-FPs, TALE-FPs to STRs, telomere repeat binding factors-FPs, etc for primary cells) and can be fused (as cDNAs) to different fluorescent proteins and FP biosensors.

Many biosensors are available as affinity series [1, 4], now enabling extended dynamic range. I realized that spatial multiplexing of many DNA binding protein-reporters by localizing to different spots in the cell nucleus and distinguished by combinatorial addressing, where N address colors ...

Investigating Adenosine’S Role In Controlling The Cerebral Metabolic Rate Of Oxygen Following Hypoxia-Ischemia, Mustafa Ridha

Electronic Thesis and Dissertation Repository

The cerebral metabolic rate of oxygen (CMRO2) has been shown to be an early indicator of hypoxia-ischemia (HI); however, the mechanisms controlling post-HI CMRO2 are not clear. One potential mechanism is the activation of the adenosine A1 receptor due to increased adenosine concentrations during the insult. The present study investigated if the specific adenosine A1 antagonist, DPCPX, would reduce the typical reduction in CMRO2 and electrical cortical activity following HI. Measurements of CMRO2 and electrical cortical activity were obtained on piglets by near-infrared spectroscopy (NIRS) and amplitude-integrated electroencephalography (aEEG), respectively. The post-HI measurements of CMRO2 and mean aEEG background voltage ...

Development Of A Beam-Specific Planning Target Volume And A Robust Plan Analysis Tool For Proton Therapy, Peter Park

UT GSBS Dissertations and Theses (Open Access)

Proton therapy is growing increasingly popular due to its superior dose characteristics compared to conventional photon therapy. Protons travel a finite range in the patient body and stop, thereby delivering no dose beyond their range. However, because the range of a proton beam is heavily dependent on the tissue density along its beam path, uncertainties in patient setup position and inherent range calculation can degrade thedose distribution significantly. Despite these challenges that are unique to proton therapy, current management of the uncertainties during treatment planning of proton therapy has been similar to that of conventional photon therapy. The goal of ...

Neurophysiological Impact And Modeling-Independent Elucidation Of Inactivation Pathways In A-Type K+ Channels, J.D. Fineberg, David Ritter, Manuel Covarrubias

Department of Molecular Physiology and Biophysics Faculty Papers

Poster presented at Society for Neuroscience

Abstract:

A-type voltage-gated K⁺ channels auto-regulate their function by undergoing fast inactivation. Independent of molecular mechanisms, this inactivation can proceed after channel opening (open-state inactivation, OSI) or from a closed state prior to opening (closed-state inactivation, CSI). We hypothesize that the specific neurophysiological roles of A-type Kv channels depend on whether they undergo OSI, CSI or both (CSI+OSI). To explore these possibilities, we introduced Markov kinetic schemes of the A-type Kv4 conductance into a computational model of the hippocamcal CA1 neuron assuming either CSI or CSI+OSI and compared the properties of the ...

Halloween 2012 Jack O'Lanterns Trick Or Treat, George Mcnamara

George McNamara

Halloween 2012 makes trick or treating more visual and interactive than in past years.

the download is a ZIP file containing three files.

Print out the (unnumbered) image on as large and nice printer paper as possible - I used glossy 44" wide here in Miami (University of Miami, MillerSchool of Medicine, Calder Library, Biomedical Communications dept - I also made another print on "fabric", also 44" wide to take with me to an HHMI Janelia Farm conference on 'turning images into knowledge' that ends on Oct 31 - might stay up for a second conference, "GFP..." that start Nov 4).

The other ...

Development Of A Monte Carlo Simulation Tool For Light Transport Inside Scintillation Crystals, Xin Yang

Open Access Dissertations and Theses

The scintillation crystal is a critical component in positron emission tomography (PET) systems. It impacts a number of PET system performance parameters, including spatial, energy, and time resolution. Our goal is to develop a new simulation tool to achieve improved accuracy by addressing several limitations in the existing packages, including more advanced surface treatments, temporal dependency of photon arrival, and rigorous experimental validations. The comparison of preliminary Monte Carlo simulation results and analytical calculations for specular reflection suggest that the simulation model is working well. The time-resolved light output was studied for various crystal surface treatment configurations. The measured energy ...

The Identification And Differentiation Between Normal And Secondary Colorectal Cancer In Human Liver Tissue Using X-Ray Interaction Techniques, Sahar Darvish Molla

Open Access Dissertations and Theses

As secondary colorectal liver cancer is the most widespread malignancy in patients with colorectal cancer, the main aim of this study is to identify and differentiate between benign and malignant secondary colorectal liver cancer tissue. Low energy X-ray interaction techniques were used. XRF and coherent scattering data were collected for all 24 normal and 24 tumour matched pair tissues. Measurements of these parameters were made using a laboratory experimental set-up comprising a Mo X-ray tube, Si Drift detector and Scintillation (NaI) detector.

Twelve elements of interest were statistically explored for normal and tumour samples. Comparing normal and tumour tissues, statistically ...

In-Vivo X-Ray Fluorescence Assessment Of Iron Levels In The Skin For Β-Thalassemia Patients, Ibrahim Abu Atiya

Open Access Dissertations and Theses

The purpose of this study is to assess the feasibility of a non-invasive, reliable, and cheap method to evaluate iron-overload in beta-thalassemia major patients. The approach taken was through the possibility of in-vivo measurement of iron in the skin using a technique called x-ray fluorescence. It was hoped that the quantification of iron levels in the skin will correlate with those levels in major parenchymal organs, such as the liver and the heart – where most iron deposition occurs in thalassemic patients. Water phantoms were used to produce a calibration line with an R² value of 0.998. Skin, liver ...

The Fractal Nature And Functional Connectivity Of Brain Function As Measured By Bold Mri In Alzheimer’S Disease, Mohammed A. Warsi

Open Access Dissertations and Theses

Alzheimer’s disease (AD) is a degenerative disease with progressive deterioration of neural networks in the brain. Fractal dimension analysis (FD) of resting state blood oxygen level dependent (BOLD) signals acquired using functional magnetic resonance imaging (fMRI) allows us to quantify complex signalling in the brain and may offer a window into the network erosion. This novel approach can provide a sensitive tool to examine early stages of AD. As AD progresses, we expect to see a reduction in brain connectivity and signal complexity concurrent with biochemical changes (e.g. altered levels of N-acetyl aspartate (NAA), myoinositol (mI) and glutamate ...

Dose-Based Evaluation Of A Prostate Bed Protocol, Olga M. Dona Lemus

Open Access Dissertations and Theses

The image-guided radiation therapy (IGRT) protocol used at Juravinski Cancer Center for post-prostatectomy patients involves acquiring a kV cone beam computed tomography (CBCT) image at each fraction and shifting the treatment couch to align surgical clips. This IGRT strategy is promising but its dosimetric impact is unknown, it requires significant resources, and delivers non-negligible doses to normal tissues. The objective of this work is to evaluate this IGRT protocol and investigate possible alternatives.

IGRT delivered dose is reconstructed by deforming the planning CT to the CBCT images acquired at each fraction, computing dose on the deformed images, and inversely transforming ...

Optimal Strategy For Prophylactic Cranial Irradiation In Limited Stage Small Cell Lung Cancer, Edward Yu, Patricia Tai, Avi Assouline, Kurian Joseph

Edward Yu

No abstract provided.

Mcnamara 20120831fri-20120904tue Cosmic Ray Particles By Ccd Imaging, George Mcnamara

George McNamara

McNamara 20120831Fri-20120904Tue Cosmic Ray Particles by CCD imaging.zip contains image files in support of a Microscopy Today article - please see

http://www.microscopy-today.com/