Medical Sciences Commons^™

Iron Alters Cell Survival In A Mitochondria-Dependent Pathway In Ovarian Cancer Cells., Edward Haller

Edward Haller

ABSTRACT The role of iron in the development of cancer remains unclear. We previously reported that iron reduces cell survival in a Ras/mitogen-activated protein kinase (MAPK)-dependent manner in ovarian cells; however, the underlying downstream pathway leading to reduced survival was unclear. Although levels of intracellular iron, ferritin/CD71 protein and reactive oxygen species did not correlate with iron-induced cell survival changes, we identified mitochondrial damage (via TEM) and reduced expression of outer mitochondrial membrane proteins (translocase of outer membrane: TOM20 and TOM70) in cell lines sensitive to iron. Interestingly, Ru360 (an inhibitor of the mitochondrial calcium uniporter) reversed mitochondrial changes and …

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

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 …

Enhanced Transmission Of Higher Order Plasmon Modes With Random Au Nanoparticles In Periodic Hole Arrays, Fang-Tzu Chuang

Fang-Tzu Chuang

The enhanced transmission of higher order plasmon modes with random gold nanoparticles embedded in periodic hole arrays using asymmetric pair aperture as a unit is investigated in the midinfrared regime. Different thicknesses of gold film were deposited inside holes and then annealed to form randomly sized and distributed nanoparticles. The holes deposited with thin gold film exhibit significantly enhanced transmission in higher order modes after thermal annealing. The enormous local electric field around the nanoparticles enhances the scattering effect that contributes to the enhanced infrared transmission. This unique design, which integrates localized and propagating surface plasmons, provides an easy way …

Effect Of Paired Apertures In A Periodic Hole Array On Higher Order Plasmon Modes, Fang-Tzu Chuang

Fang-Tzu Chuang

We demonstrate that the transmission of higherorder surface plasmon modes in the mid-infrared range can be enhanced through rectangular hole array on the basis of paired apertures. Experiments prove that enhanced high-order transmission can be generated by either identical shapes or combinations of different hole shapes in pairs. The structure factor is adopted to explain the observed intensity of enhanced transmission. Numerical simulations of the enhanced secondorder mode verify a significant field enhancement in a unit cell of pairs. It is clarified that the separation between the paired apertures and the paired resonance is the key to determine certain higher-order …

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 …

Two Infrared Emission Modes With Different Wavelengths And Orthogonal Polarization In A Waveguide Thermal Emitter, Fang-Tzu Chuang

Fang-Tzu Chuang

This study investigates a Au/SiO2/Au waveguide thermal emitter incorporating a metallic grating embedded in the SiO2 layer. The metal grating acts as a beam splitter, dividing the device into two waveguide structures determined by the polarization of the waveguide modes. The thermal radiation spectrum exhibits two peaks with orthogonal polarization. The emitted wavelengths of the two waveguide modes can be adjusted by controlling the thickness of the SiO2 layers on both sides of the metallic grating during the fabrication process. The emission peaks have ratios of the full width at half maximum to the peak wavelength of 0.057 and 0.05 …

Libraries At The University Of Massachusetts Amherst: Seeking An International Perspective, Maxine G. Schmidt

Maxine G Schmidt

Presentation delivered to librarians in China, Japan and South Korea as part of my sabbatical research on the use of libraries by Asian students in their home countries.

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

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 …

Nanoprojection Lithography Using Self-Assembled Interference Modules For Manufacturing Plasmonic Gratings, Fang-Tzu Chuang

Fang-Tzu Chuang

Abstract—A new nanoprojection lithography (NPL) is proposed to manufacture plasmonic nanogratings. Here, low-cost self-assembly elastomeric polydimethylsiloxane wavy structures are used as the interference modules, with their periods and amplitudes largely controlled by the applied mechanical strain in the synthesis process. Well defined plasmonic grating couplers with desired feature sizes and wavelengths of operation were obtained. This NPL may enable large-area and flash manufacturing of plasmonic nanogratings with tunable array periods.

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

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

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

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

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)

Integrative Bayesian Analysis Of High-Dimensional Multi-Platform Genomics Data, Wenting Wang, Veerabhadran Baladandayuthapani, Jeffrey S. Morris, Bradley M. Broom, Ganiraju C. Manyam, Kim-Anh Do

Jeffrey S. Morris

Motivation: Analyzing data from multi-platform genomics experiments combined with patients’ clinical outcomes helps us understand the complex biological processes that characterize a disease, as well as how these processes relate to the development of the disease. Current integration approaches that treat the data are limited in that they do not consider the fundamental biological relationships that exist among the data from platforms.

Statistical Model: We propose an integrative Bayesian analysis of genomics data (iBAG) framework for identifying important genes/biomarkers that are associated with clinical outcome. This framework uses a hierarchical modeling technique to combine the data obtained from multiple platforms …

Synergy Sted Multicolor 3d-Easysted Excel File, George Mcnamara

George McNamara

Excel 2007 file with calculations for multicolor 3D-EasySTED segmented waveplates (SWP) for fluorescence nanoscopy.

Additional explanation in my Introduction statement and in the Excel file. The Excel file uses an interpolation function available from XlXtrFun (http://www.xlxtrfun.com/XlXtrFun/XlXtrFun.htm). My thanks to Goetz Zinner, www.B-Halle.de, for communicating to me that a single 3D-EasySTED segmented waveplate can be used with multiple excitation and depletion wavelengths.

Please give Goetz Zinner full credit for recognizing that STED segmented waveplate can be manufactured to handle multiple excitation and depletion wavelengths. Different sets of wavelengths can be generated by choosing appropriate thickness quartz substrates for manufacturing the SWP. …

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.

Arcane Secrets Of The Umass Libraries, Maxine G. Schmidt

Maxine G Schmidt

No abstract provided.

Self-Assembled Rippling Structure Based On Metal-Elastomer Composite For Tunable Plasmonics, Fang-Tzu Chuang

Fang-Tzu Chuang

We demonstrate that a periodic metallic wavy-structure can be easily fabricated on elastomeric polydymethylsiloxane (PDMS) substrates. The metallic wavy-structures are self-assembly formed by thermal evaporation of Ag on PDMS without any lithography processes. The size of the PDMS substrate with an aspect ratio (the ratio of length to width) higher than 2 are found to be necessary to self-assemble the one-dimensional metallic wavy-structure. The period of the wavy-structure is controllable by varing the thickness of the deposited silver film. The elastomeric- gratings can excite surface plasmon on Ag/air interfaces; the resonant wavelength can be tuned to a range of 3.5% …

Science Boot Camp For Librarians: Cpd On A Shoestring, Maxine G. Schmidt, Rebecca Reznik-Zellen

Maxine G Schmidt

Science Boot Camp for Librarians was envisioned as a casual but intensive immersion event into selected scientific subjects that employ networked computing capabilities for research and collaboration. The goal of the event is to provide librarians with networking opportunities, but more importantly, to give them some of the context and ocabulary of a discipline to enable them to better engage faculty and research scientists with regard to escience. A half-day is devoted to each of three topics chosen for that year’s camp. A local faculty member provides an overview of the research area, and a second describes a single project …

Localized Shape Resonance On Silver Film Perforated By H-Shaped And More Complex Shaped Hole Arrays, Fang-Tzu Chuang

Fang-Tzu Chuang

The experimental results of light transmission through periodic array of H-shaped hole and more complicated hole which is a combination of multiple U shape are demonstrated. The observations indicate that the localized shape resonance in the longest resonant length of unfolded U-shaped part of the hole always appears. However, localized modes resonant in smaller U-shaped length don't always appear. Localized mode with non-U-shaped resonant path cannot be seen in our sample. In addition, localized mode with different order and resonant path can be excited by different polarized light.

Science For The Environment: Examining The Allocation Of The Burden Of Uncertainty, Elisa Vecchione

Elisa Vecchione

The aim of this paper is to review the basic literature on scientific uncertainty in its statistical paradigm in order to provide enlightenment on one pivotal facet of the precautionary principle, i.e. the allocation of the burden of proof to demonstrate that an activity is not harmful to the environment. The purpose is not to explain a new theory of statistical inference, but to show how regulatory policymaking that is properly informed by scientific expertise and designed to avoid one type of error, may actually make other errors more likely and thus expose the public to danger. This problem is …

Ppar Agonists Down-Regulate The Expression Of Atp10c Mrna During Adipogenesis, A Peretich, Maria Cekanova Ms, Rndr, Phd, S Hurst, Sj Baek, Madhu Dahr

Maria Cekanova MS, RNDr, PhD

No abstract provided.

E-Science @ Umass: Anticipating And Supporting E-Science Activities At The University Of Massachusetts, Maxine G. Schmidt, Rebecca Reznik-Zellen

Maxine G Schmidt

In March of 2008 an Ad Hoccommittee of Science Librarians from the University of Massachusetts Five Campus System convened to discuss the challenges of e-science and prepare the Libraries for their role in e-science initiatives. Three primary outcomes intended to support e-science activities emerged from the work of the Ad Hoc committee.

E-Science @ The University Of Massachusetts, Maxine G. Schmidt, Rebecca Reznik-Zellen, Raquel Rivera, Cecilia P. Mullen

Maxine G Schmidt

e-Science @ the University of Massachusetts Abstract: What is e-Science and how can libraries and librarians support it? The University of Massachusetts takes a proactive approach to support network-enabled research on its campuses and provides examples where e-Science is already at work. Statement: “e-Science” is a term commonly used to describe research in a networked environment, a growing trend not only in the sciences, but the arts and humanities as well. e-Science creates both opportunities and challenges for academic libraries. The opportunities lie in leveraging the basic skill set that libraries and librarians already possess: the knowledge of and practical …

Umass Libraries 2009, Maxine G. Schmidt

Maxine G Schmidt

No abstract provided.

Important, But Odd And Obscure, Reasons To Use The Library, Maxine G. Schmidt

Maxine G Schmidt

No abstract provided.