Medical Biophysics Commons^™

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

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: gtmcnamara@mdanderson.org, 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 …

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

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 PET AC of …

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 …

Rescuing Acetylcholinesterase From Nerve Agent Inhibition: Protein Dynamics Driven Drug Discovery, Aiyana M. Emigh, Brian Bennion

STAR Program Research Presentations

Severe morbidity and mortality consequences result from irreversible inhibition of human acetylcholinesterase by organophosphates (OPs). Oxime-based reactivators are currently the only available treatments but lack efficacy in the central nervous system (CNS) where the most damage occurs. Computational docking and molecular dynamics (MD) simulations reveal complex structural barriers that may reduce oxime efficacy. These results may guide future drug designs of more effective countermeasures.

Mechanistic Basis For Atrial And Ventricular Arrhythmias Caused By Kcnq1 Mutations, Daniel C. Bartos

Theses and Dissertations--Physiology

Cardiac arrhythmias are caused by a disruption of the normal initiation or propagation of electrical impulses in the heart. Hundreds of mutations in genes encoding ion channels or ion channel regulatory proteins are linked to congenital arrhythmia syndromes that increase the risk for sudden cardiac death. This dissertation focuses on how mutations in a gene (KCNQ1) that encodes a voltage-gated K⁺ ion channel (Kv7.1) can disrupt proper channel function and lead to abnormal repolarization of atrial and ventricular cardiomyocytes.

In the heart, Kv7.1 coassembles with a regulatory protein to conduct the slowly activating delayed rectifier K^{+ …}

Prophylactic Cranial Irradiation For Patients With Limited-Stage Small-Cell Lung Cancer With Response To Chemoradiation, Patricia Tai, Avi Assouline, Kurian Joseph, Larry Stitt, Edward Yu

Edward Yu

Background Previous clinical studies have generally reported that prophylactic cranial irradiation (PCI) was given to patients with a complete response (CR) to chemotherapy and chest radiotherapy in limited-stage small-cell lung cancer (SCLC). It is not clear if those with incomplete response (IR) would benefit from PCI. Patients and Methods The Saskatchewan experience from 1981 through 2007 was reviewed. Patients were treated with chest radiotherapy and chemotherapy with or without PCI (typical doses: 2500 cGy in 10 fractions over 2 weeks, 3000 cGy in 15 fractions over 3 weeks, or 3000 cGy in 10 fractions over 2 weeks). Results There were …

Peptide-Mediated Targeting Of Angiogenesis For Molecular Imaging And Treatment Of Cancer, Choi-Fong Cho

Electronic Thesis and Dissertation Repository

The development of screening approaches to identify novel affinity ligands has paved the way for a new generation of molecular targeted nanomedicines. To identify novel targeting ligands, several studies have demonstrated the advantages in screening one-bead-one-compound (OBOC) libraries. Conventional methods typically bias the display of the target protein to ligands during the screening process. We have developed an unbiased multiplex ‘beads on a bead’ strategy to isolate, characterize, and validate high affinity ligands from OBOC libraries. In addition, due to the advantages associated with screening OBOC libraries directly against living cells, we sought to combine cell-based screen methods with automated …

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 …

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

Dissertations & 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 …

The Impact Of Post-Mastectomy Radiation Therapy On Male Breast Cancer Patients--A Case Series, Edward Yu, Hiromichi Suzuki, Jawaid Younus, Tarek Elfiki, Larry Stitt, Gary Yau, Olga Vujovic, Francisco Perera, Michael Lock, Patricia Tai

Michael Lock

OBJECTIVE: To assess the impact of radiation management on male breast cancer (MBC) at London Regional Cancer Program (LRCP).

METHODS AND MATERIALS: Men with a diagnosis of breast cancer referred to LRCP were reviewed. The seventh American Joint Committee on Cancer staging system was used. Patients treated with and without post-mastectomy radiation therapy (PMRT) were analyzed. Disease-free survival (DFS) was defined as time duration from diagnosis to first recurrence. Overall survival (OS) was defined as time duration from pathologic diagnosis to death or last follow-up with any death defined as an event. Survival estimates were obtained using Kaplan-Meier methodology.

RESULTS: …

Technology Assessment Of Automated Atlas Based Segmentation In Prostate Bed Contouring, Jeremiah Hwee, Alexander Louie, Stewart Gaede, Glenn Bauman, David D'Souza, Tracy Sexton, Michael Lock, Belal Ahmad, George Rodrigues

Michael Lock

BACKGROUND: Prostate bed (PB) contouring is time consuming and associated with inter-observer variability. We evaluated an automated atlas-based segmentation (AABS) engine in its potential to reduce contouring time and inter-observer variability.

METHODS: An atlas builder (AB) manually contoured the prostate bed, rectum, left femoral head (LFH), right femoral head (RFH), bladder, and penile bulb of 75 post-prostatectomy cases to create an atlas according to the recent RTOG guidelines. 5 other Radiation Oncologists (RO) and the AABS contoured 5 new cases. A STAPLE contour for each of the 5 patients was generated. All contours were anonymized and sent back to the …

Evidence Of Adult Lung Growth In Humans., Miranda Kirby, David G Mccormack, Grace Parraga

Medical Biophysics Publications

A 33-year-old woman underwent a right-sided pneumonectomy in 1995 for treatment of a lung adenocarcinoma. As expected, there was an abrupt decrease in her vital capacity, but unexpectedly, it increased during the subsequent 15 years. Serial computed tomographic (CT) scans showed progressive enlargement of the remaining left lung and an increase in tissue density. Magnetic resonance imaging (MRI) with the use of hyperpolarized helium-3 gas showed overall acinar-airway dimensions that were consistent with an increase in the alveolar number rather than the enlargement of existing alveoli, but the alveoli in the growing lung were shallower than in normal lungs. This …

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 …

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 somatic …

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/

Hyperpolarized 3he And 129xe Mr Imaging In Healthy Volunteers And Patients With Chronic Obstructive Pulmonary Disease, Miranda Kirby, Sarah Svenningsen, Amir Owrangi, Andrew Wheatley, Adam Farag, Alexei Ouriadov, Giles E Santyr, Roya Etemad-Rezai, Harvey O Coxson, David G Mccormack, Grace Parraga

Medical Biophysics Publications

PURPOSE: To quantitatively compare hyperpolarized helium 3 (3He) and xenon 129 (129Xe) magnetic resonance (MR) images obtained within 5 minutes in healthy volunteers and patients with chronic obstructive pulmonary disease (COPD) and to evaluate the correlations between 3He and 129Xe MR imaging measurements and those from spirometry and plethysmography.

MATERIALS AND METHODS: This study was approved by an ethics board and compliant with HIPAA. Written informed consent was obtained from all subjects. Eight healthy volunteers and 10 patients with COPD underwent MR imaging, spirometry, and plethysmography. Ventilation defect percentages (VDPs) at 3He and 129Xe imaging were obtained by using semiautomated …

What Can Computed Tomography And Magnetic Resonance Imaging Tell Us About Ventilation?, Brett A Simon, David W Kaczka, Alexander A Bankier, Grace Parraga

Medical Biophysics Publications

This review provides a summary of pulmonary functional imaging approaches for determining pulmonary ventilation, with a specific focus on multi-detector x-ray computed tomography and magnetic resonance imaging (MRI). We provide the important functional definitions of pulmonary ventilation typically used in medicine and physiology and discuss the fact that some of the imaging literature describes gas distribution abnormalities in pulmonary disease that may or may not be related to the physiological definition or clinical interpretation of ventilation. We also review the current state-of-the-field in terms of the key physiological questions yet unanswered related to ventilation and gas distribution in lung disease. …

Cosmic Ray Particles Images With Orca-Ii Erg, George Mcnamara

George McNamara

Cosmic ray particles image series acquired using a Hamamatsu ORCA-II ERG scientific grade CCD camera, cooled to -60 C. Each image is a consecutive 600 second (10 minute) exposure time with no light to the camera.

While processing the data, I discoverd that the background changed around planes 25 and 227 (see Excel file and jpeg screenshots), so I also processed only planes 025-227 (203 planes total, 2030 minutes, 33.83 hours). the CCD industry "rule of thumb" for a "typical" CCD sensor (i.e. 1/3" CCD) is that one cosmic ray particle strikes a sensor approximately every 30 seconds (assuming not …

Shift Work And Vascular Events: Systematic Review And Meta-Analysis., Manav V Vyas, Amit X Garg, Arthur V Iansavichus, John Costella, Allan Donner, Lars E Laugsand, Imre Janszky, Marko Mrkobrada, Grace Parraga, Daniel G Hackam

Medical Biophysics Publications

OBJECTIVE: To synthesise the association of shift work with major vascular events as reported in the literature.

DATA SOURCES: Systematic searches of major bibliographic databases, contact with experts in the field, and review of reference lists of primary articles, review papers, and guidelines.

STUDY SELECTION: Observational studies that reported risk ratios for vascular morbidity, vascular mortality, or all cause mortality in relation to shift work were included; control groups could be non-shift ("day") workers or the general population.

DATA EXTRACTION: Study quality was assessed with the Downs and Black scale for observational studies. The three primary outcomes were myocardial infarction, …