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Mcnamara 20120831fri-20120904tue Cosmic Ray Particles By Ccd Imaging, George McNamara 2012 M.D. Anderson Cancer Center

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/


Cosmic Ray Particles Images With Orca-Ii Erg, George McNamara 2012 M.D. Anderson Cancer Center

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 ...


Transcription Factor Activator Protein 2 In Development And Disease Of The Neural Crest, Eric Scott Van Otterloo 2012 University of Iowa

Transcription Factor Activator Protein 2 In Development And Disease Of The Neural Crest, Eric Scott Van Otterloo

Theses and Dissertations

The neural crest (NC) is a vertebrate specific early embryonic stem-cell population that forms an array of derivatives in the developing embryo. These cells are induced from the developing ectoderm at the boundary of the neural plate and non-neural ectoderm (termed the neural plate border). After initial induction the NC migrate along predefined routes within the developing embryo and upon reaching their destination begin to differentiate into this myriad of derivatives. These derivatives include neurons, glia, cartilage, bone, connective tissue and pigmented melanocytes, among others. Through genetic studies a variety of genes important in these various stages of NC development ...


Ral Gtpases Regulate Biogenesis Of Cell Polarity, C. Clayton Hazelett 2012 University of Iowa

Ral Gtpases Regulate Biogenesis Of Cell Polarity, C. Clayton Hazelett

Theses and Dissertations

Cell polarity is the asymmetric distribution of organelles that almost all cells use to separate individual processes and perform complex functions. Although the manner in which cells are polarized is very diverse, the processes necessary to assume polarized phenotypes are similar in many cell types. Epithelial cell polarization is of particular importance, as these cells serve form linings of organs and act as barriers distinguishing different compartments. Furthermore, loss of epithelial polarization occurs in some disease states and may result in cell invasion through underlying matrix. During initial polarization, vesicle trafficking is indispensible for assembly of structures, including apical junctional ...


Identification Of Genes Contributing To Preterm Birth: Insights From Genetic, Transcriptomic, And Epigenetic Analyses, Jinsil Kim 2012 University of Iowa

Identification Of Genes Contributing To Preterm Birth: Insights From Genetic, Transcriptomic, And Epigenetic Analyses, Jinsil Kim

Theses and Dissertations

Preterm birth (PTB) is a global public health problem that has significant adverse effects on neonatal mortality and morbidity. Progress in understanding the pathological mechanisms underlying PTB has been greatly hampered by the complex and polygenic nature of the disease. As a result, a multifaceted approach may hold promise for identifying true causal factors. The main objective of this thesis is to identify genes that play a role in the etiology of PTB using experimental data derived from different molecular levels (genome, transcriptome, and epigenome). To achieve this goal, we performed association studies using a candidate gene approach to identify ...


Flatbed Scanner Report - Optical Density Dynamic Range, George McNamara 2012 M.D. Anderson Cancer Center

Flatbed Scanner Report - Optical Density Dynamic Range, George Mcnamara

George McNamara

George McNamara (now at University of Miami) report for Hua Yu and Richard Jove, City of Hope National Medical Center, on optical density dynamic range of several flatbed scanners.


Introduction To Nanoscopy Nano-Talk, George McNamara 2012 M.D. Anderson Cancer Center

Introduction To Nanoscopy Nano-Talk, George Mcnamara

George McNamara

T7-1 is the designation for the LMRG Nanoscopy session at ABRF in Orlando, FL, on March 20, 2012. The PDF file here is a draft of my presentation.

May not be very helpful since (1) would probably help to know what is in my head and each slide will [hopefully] prompt me to say, and (2) 10 minute talk so I am going to push the "next slide" button after saying very little.

__________________

Publisher statement:

The T7-1 Introduction to Nanoscopy Nano Talk is copyrighted (c) George McNamara, 2012. Except for (1) screenshots from research articles (which are copyrighted by ...


Pubspectra - Open Data Access Fluorescence Spectra, George McNamara 2012 M.D. Anderson Cancer Center

Pubspectra - Open Data Access Fluorescence Spectra, George Mcnamara

George McNamara

The Internet is enabling greater access to spectral imaging publications, spectral graphs, and data than that was available a generation ago. The spectral imaging systems discussed in this issue of Cytometry work because reagent and hardware spectra are reproducible, reusable, and provide input to spectral unmixing and spectral components recognition algorithms. These spectra need to be readily available in order to determine what to purchase, how to use it, and what the output means. We refer to several commercially sponsored and academic spectral web sites and discuss our spectral graphing and data sites. Sites include fluorescent dye graph servers from ...


Mcnamara 2011 Feature Extraction (Image Analysis), George McNamara 2012 M.D. Anderson Cancer Center

Mcnamara 2011 Feature Extraction (Image Analysis), George Mcnamara

George McNamara

Feature Extraction presentation and movies in a ZIP file from a presentation I gave at ISAC 2011 in Baltomore, Md.

Feature extraction is one phrase for image analysis.


Rogers Pmn Movie - Background Information, George McNamara 2012 M.D. Anderson Cancer Center

Rogers Pmn Movie - Background Information, George Mcnamara

George McNamara

Please see

http://mdc.custhelp.com/app/answers/detail/a_id/18689/~/metamatters-newsletters

for my series of MetaMorph MetaMatters articles in volume 2, numbers 3 through 6, on the Rogers PMN Panorama data set.

http://mdc.custhelp.com/app/answers/detail/a_id/18689/~/metamatters-newsletters

Brief summary (for more, see the Word doc)


Single Cell Wound Healing In Drosophila Melanogaster Embryos, John Rosasco 2012 University of Puget Sound

Single Cell Wound Healing In Drosophila Melanogaster Embryos, John Rosasco

Summer Research

The role of contractile actin and myosin filaments filaments and the links they form with other proteins are vitally important to single cell wound healing, Which occurs in synctial Drosophila embryos as well as in vertebrates. Previous work by Wayne Rickoll has concentrated on determining the orientations of actin during wound healing during dorsal closure in Drosophila, a morphogenetic process in which epidermal cells extend to cover the embryonic gut during development. Transmission electron microscope analysis of cells undergoing dorsal closure revealed that actin is oriented parallel and perpendicular to the leading edge of the wound. Based on this observation ...


Effective Non-Viral Delivery Of Sirna To Acute Myeloid Leukemia Cells With Lipid-Substituted Polyethylenimines, Breanne Landry 2012 University of Alberta

Effective Non-Viral Delivery Of Sirna To Acute Myeloid Leukemia Cells With Lipid-Substituted Polyethylenimines, Breanne Landry

Pharmacy Faculty Articles and Research

Use of small interfering RNA (siRNA) is a promising approach for AML treatment as the siRNA molecule can be designed to specifically target proteins that contribute to aberrant cell proliferation in this disease. However, a clinical-relevant means of delivering siRNA molecules must be developed, as the cellular delivery of siRNA is problematic. Here, we report amphiphilic carriers combining a cationic polymer (2 kDa polyethyleneimine, PEI2) with lipophilic moieties to facilitate intracellular delivery of siRNA to AML cell lines. Complete binding of siRNA by the designed carriers was achieved at a polymer:siRNA ratio of ~0.5 and led to siRNA ...


The Developmental Regulator Gon4-Like Functions Within The Transcriptional Networks That Control B Lymphopoiesis And Cd4+ T Cell Responses, Isaiah Luke Hankel 2011 University of Iowa

The Developmental Regulator Gon4-Like Functions Within The Transcriptional Networks That Control B Lymphopoiesis And Cd4+ T Cell Responses, Isaiah Luke Hankel

Theses and Dissertations

B and T lymphocytes are critical to the adaptive immune response against invading microorganisms. B and T cells develop in the bone marrow and thymus, respectively, and initiate a series of proliferative responses once they encounter their cognate antigen in the peripheral lymphoid organs. These developmental and functional processes are controlled by different networks of transcriptional regulators that repress and activate gene expression. Identifying proteins that activate or repress specific genes and integrating these proteins into their transcriptional networks is critical to understanding lymphocyte development and function. The study of B lymphopoiesis and CD4+ T cell functional responses has greatly ...


Dissection Of A Type I Interferon Pathway In Controlling Bacterial Intracellular Infection In Mice, Juliane Lippmann, Holger Müller, Jan Naujoks, Christoph Tabeling, Sunny Shin, Martin Witzenrath, Katharina Hellwig, Carsten J. Kirschning, Gregory A. Taylor, Winfried Barchet, Stefan Bauer, Norbert Suttorp, Craig A. Roy, Bastian Opitz 2011 University of Pennsylvania

Dissection Of A Type I Interferon Pathway In Controlling Bacterial Intracellular Infection In Mice, Juliane Lippmann, Holger Müller, Jan Naujoks, Christoph Tabeling, Sunny Shin, Martin Witzenrath, Katharina Hellwig, Carsten J. Kirschning, Gregory A. Taylor, Winfried Barchet, Stefan Bauer, Norbert Suttorp, Craig A. Roy, Bastian Opitz

Department of Microbiology Papers

Defense mechanisms against intracellular bacterial pathogens are incompletely understood. Our study characterizes a type I IFN-dependent cell-autonomous defense pathway directed against Legionella pneumophila, an intracellular model organism and frequent cause of pneumonia. We show that macrophages infected with L. pneumophila produced IFNβ in a STING- and IRF3- dependent manner. Paracrine type I IFNs stimulated up-regulation of IFN-stimulated genes and a cell-autonomous defense pathway acting on replicating and non-replicating Legionella within their specialized vacuole. Our infection experiments in mice lacking receptors for type I and/or II IFNs show that type I IFNs contribute to expression of IFN-stimulated genes and to ...


Mcnamara 2011 Mpmicro - Multi-Probe Microscopy (10/31/2011), George McNamara 2011 M.D. Anderson Cancer Center

Mcnamara 2011 Mpmicro - Multi-Probe Microscopy (10/31/2011), George Mcnamara

George McNamara

Multi-Probe Microscopy is an ~1500 page Word document summarizing what I know and/or found interesting in light microscopy, fluorescence microscopy and digital image analysis, from 1995-2005. Very little has been updated since 2005.


Forward Osmosis Bag: Ground Testing The Prospect Of Using Alternative Water Sources For Drinking Water, Michaela Marie Brant, Ariella Yendler, Mona Hammoudeh, Michael T. Flynn 2011 California Polytechnic State University - San Luis Obispo

Forward Osmosis Bag: Ground Testing The Prospect Of Using Alternative Water Sources For Drinking Water, Michaela Marie Brant, Ariella Yendler, Mona Hammoudeh, Michael T. Flynn

STAR Program Research Presentations

On the STS-135 Space Shuttle mission, to be launched July 8, 2011, a forward osmosis bag (FOB) study will be conducted. At NASA Ames this summer, the ground truth testing is being conducted for results comparisons. The FOB technology is derived from a commercial product, the X-Pack water filter. Forward osmosis operates by utilizing an established concentration gradient across a semi-permeable membrane to move water molecules from one side of the membrane to the other. This concept is exploited to harvest drinking water from grey water sources such as urine, sea water, or vehicle water. In this experiment, potassium chloride ...


Multimodal Spectral Imaging Of Cells Using A Transmission Diffraction Grating On A Light Microscope, Dragan Isailovic, Yang Xu, Tyler Copus, Suraj Saraswat, Surya M. Nauli 2011 University of Toledo

Multimodal Spectral Imaging Of Cells Using A Transmission Diffraction Grating On A Light Microscope, Dragan Isailovic, Yang Xu, Tyler Copus, Suraj Saraswat, Surya M. Nauli

Pharmacy Faculty Articles and Research

A multimodal methodology for spectral imaging of cells is presented. The spectral imaging setup uses a transmission diffraction grating on a light microscope to concurrently record spectral images of cells and cellular organelles by fluorescence, darkfield, brightfield, and differential interference contrast (DIC) spectral microscopy. Initially, the setup was applied for fluorescence spectral imaging of yeast and mammalian cells labeled with multiple fluorophores. Fluorescence signals originating from fluorescently labeled biomolecules in cells were collected through triple or single filter cubes, separated by the grating, and imaged using a charge-coupled device (CCD) camera. Cellular components such as nuclei, cytoskeleton, and mitochondria were ...


Biology Of Redox Active Endosomal Signaling In Response To Il-1-Beta, Fredrick Daniel Oakley 2011 University of Iowa

Biology Of Redox Active Endosomal Signaling In Response To Il-1-Beta, Fredrick Daniel Oakley

Theses and Dissertations

Interleukin-1-beta (IL-1β) is a potent proinflammatory cytokine. A primary outcome of IL-1β signaling is the activation of NFκB, a transcription factor that induces a large number of immune molecules, apoptotic factors, anti-apoptotic factors, and other transcription factors. Recent work has demonstrated that the activation of NFκB involves a multistep redox-signaling cascade that requires endocytosis of the interleukin receptor (IL-1R1)/ligand pair and superoxide production by NADPH oxidase 2 (Nox2) within the resulting newly formed early endosome. Hydrogen peroxide produced by the rapid dismutation of superoxide is necessary for the subsequent downstream recruitment of IL-1R1 effectors (TRAF6, IKK kinases) and ultimately ...


Using A Focus Measure To Automate The Location Of Biological Tissue Surfaces In Brightfield Microscopy, Daniel Toby Elozory 2011 University of South Florida

Using A Focus Measure To Automate The Location Of Biological Tissue Surfaces In Brightfield Microscopy, Daniel Toby Elozory

Graduate Theses and Dissertations

The study of microstructures in brightfield microscopy using unbiased stereology plays a large and growing role in bioscience research. Stereology enables objective quantitative analysis of biological structures within a tissue sample. A first step in the stereology process is to calculate the thickness of a tissue sample by locating the top and bottom surfaces of the sample. The aim of this project is to fully automate this location process by using the relative optical focus measure as an indicator of tissue surface boundary.

The current method for identification of focus bounding planes requires a trained user to manually select the ...


An Upper Limit For Macromolecular Crowding Effects, Andrew C. Miklos, Congang Li, Courtney D. Sorell, L. Andrew Lyon, Gary J. Pielak 2011 University of North Carolina

An Upper Limit For Macromolecular Crowding Effects, Andrew C. Miklos, Congang Li, Courtney D. Sorell, L. Andrew Lyon, Gary J. Pielak

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Background: Solutions containing high macromolecule concentrations are predicted to affect a number of protein properties compared to those properties in dilute solution. In cells, these macromolecular crowders have a large range of sizes and can occupy 30% or more of the available volume. We chose to study the stability and ps-ns internal dynamics of a globular protein whose radius is similar to 2 nm when crowded by a synthetic microgel composed of poly(N-isopropylacrylamide-co-acrylic acid) with particle radii of similar to 300 nm.

Results: Our studies revealed no change in protein rotational or ps-ns backbone dynamics and only mild (similar ...


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