32 Institutions 131 Full-Text Articles 238 Authors 19,202 Downloads
Recent Articles in Laboratory and Basic Science Research
Flash4 Dark Reference Images, George McNamara University of Miami
Flash4 Dark Reference Images, 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
Lurking In The Lab: Analysis Of Data From Molecular Biology Laboratory Instruments, Jen Ferguson University of Massachusetts Medical School
Lurking In The Lab: Analysis Of Data From Molecular Biology Laboratory Instruments, Jen Ferguson
Journal of eScience Librarianship
OBJECTIVE: This project examined primary research data files found on instruments in a molecular biology teaching laboratory. Experimental data files were analyzed in order to learn more about the types of data generated by these instruments (e.g. file formats), and to evaluate current laboratory data management practices.
SETTING: This project examined experimental data files from instruments in a teaching laboratory at Brandeis University.
METHODOLOGY: Experimental data files and associated metadata on instrument hard drives were captured and analyzed using Xplorer2 software. Formats were categorized as proprietary or open, and characteristics such as file naming conventions were noted. Discussions with ...
Video Codec Performance (Excel Spreadsheet), George McNamara University of Miami
Video Codec Performance (Excel Spreadsheet), 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).
The Effects Of Blocking Hippocampal Acetylcholine On Meal Onset In Male Rats, Jasmine Nicole Gentry Georgia State University
The Effects Of Blocking Hippocampal Acetylcholine On Meal Onset In Male Rats, Jasmine Nicole Gentry
Georgia State Undergraduate Research Conference
No abstract provided.
Construction Of A Tetracycline-Inducible System For Controlled Gene Expression In Crithidia Fasciculata, Fatima I. Hussain, Sanela Andelija Georgia State University
Construction Of A Tetracycline-Inducible System For Controlled Gene Expression In Crithidia Fasciculata, Fatima I. Hussain, Sanela Andelija
Georgia State Undergraduate Research Conference
No abstract provided.
A Call For Transparent Reporting To Optimize The Predictive Value Of Preclinical Research, Story C. Landis, Marc Fisher University of Massachusetts Medical School
A Call For Transparent Reporting To Optimize The Predictive Value Of Preclinical Research, Story C. Landis, Marc Fisher
Neurology Publications and Presentations
The US National Institute of Neurological Disorders and Stroke convened major stakeholders in June 2012 to discuss how to improve the methodological reporting of animal studies in grant applications and publications. The main workshop recommendation is that at a minimum studies should report on sample-size estimation, whether and how animals were randomized, whether investigators were blind to the treatment, and the handling of data. We recognize that achieving a meaningful improvement in the quality of reporting will require a concerted effort by investigators, reviewers, funding agencies and journal editors. Requiring better reporting of animal studies will raise awareness of the ...
Pubspectra Tattletales, George McNamara University of Miami
Pubspectra Tattletales, George Mcnamara
Tattletales for Multiplex Fluorescent Reporters in Single Cells for Metabolomics
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: firstname.lastname@example.org, email@example.com
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  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 ...
Filtering Efficiency And Feeding Mechanisms Of Daphnia Pulex On Microcystis Aeruginosa And Nannochloropsis, Elizabeth Orlowicz University of New Hampshire
Filtering Efficiency And Feeding Mechanisms Of Daphnia Pulex On Microcystis Aeruginosa And Nannochloropsis, Elizabeth Orlowicz
The filtering and feeding rate of Daphnia pulex from the Old Durham Reservoir, Durham, NH, were measured to determine the feeding efficiency on different concentrations of non-toxic Nannochloropsis (Class Eustigmatophyceae) and toxigenic cyanobacteria Microcystis aeruginosa. Direct observations of thoracic appendage beats and post-abdominal rejections were also measured at 5*105 and 106 cells mL-1 concentrations of Nannochloropsis and M. aeruginosa to examine the feeding mechanisms of the D. pulex. In the presence of increasing Nannochloropsis concentrations, the filtering rates decreased and the feeding rates increased. When exposed to M. aeruginosa, both the filtering and feeding rates decreased ...
The Problem Of Too Many Statistical Tests: Subgroup Analyses In A Study Comparing The Effectiveness Of Online And Live Lectures, David M. Lane University of South Florida
The Problem Of Too Many Statistical Tests: Subgroup Analyses In A Study Comparing The Effectiveness Of Online And Live Lectures, David M. Lane
The more statistical analyses performed in the analysis of research data, the more likely it is that one or more of the conclusions will be in error. Multiple statistical analyses can occur when the sample contains several subgroups and the researchers perform separate analyses for each subgroup. For example, separate analyses may be done for different ethnic groups, different levels of education, and/or for both genders. Media reports of research frequently omit information on the number of subgroup analyses performed thus leaving the reader with insufficient information to assess the validity of the conclusions. This article discusses the problems ...
Light Scattering Study Of Elongated Particles: From Inorganic Nanorice To Polypeptide Micelles, Philip Dee Cleveland State University
Light Scattering Study Of Elongated Particles: From Inorganic Nanorice To Polypeptide Micelles, Philip Dee
Undergraduate Research Posters 2012
Utilizing the powerful experimental technique of Dynamic Light Scattering (DLS) for size characterization of anisotropic particles can be extremely misleading. Unfortunately, this point is often not realized by researchers who strive for particle sizing of nanoparticles in suspensions. We present a consistent analysis of DDLS results on FeOOH nanorice and outline the potential difficulties and challenges of DDLS application for polypeptide micelles.
A Genetic Survey Of English Sole Populations In The Salish Sea, Elizabeth S. Gutierrez, Gary A. Winans, Jon Baker, Amanda Cope California Polytechnic State University
A Genetic Survey Of English Sole Populations In The Salish Sea, Elizabeth S. Gutierrez, Gary A. Winans, Jon Baker, Amanda Cope
STEM Teacher and Researcher (STAR) Program Posters
This summer I interned at the Northwest Fisheries Science Center in Seattle, WA and participated in NOAA’s Salish Sea Project. The Salish Sea Project’s goal is to identify genetically distinctive groups of species in the Salish Sea that may have unique evolutionary and/or adaptive backgrounds. These findings will allow NOAA to promote and monitor the natural production of species in the Salish Sea, to select representative populations for experimental work regarding pollution, ocean acidification and climate change, to contribute to managing the ecosystem for intra- and inter-species diversity, and to help make informed decisions about adaptive management ...
Analyzing Environmental Microbes For Genomic Regions Promoting Ionic Liquid Tolerance In E. Coli, Ann Nguyen, Alison Richins, Thomas Rüegg, Steven Singer, Michael Thelen California Polytechnic State University
Analyzing Environmental Microbes For Genomic Regions Promoting Ionic Liquid Tolerance In E. Coli, Ann Nguyen, Alison Richins, Thomas Rüegg, Steven Singer, Michael Thelen
STEM Teacher and Researcher (STAR) Program Posters
Ionic liquids (ILs) are promising as solvents to increase the efficiency of biofuel production; however, ILs are toxic to microbes used in the fermentation of liquid fuels. To engineer IL resistant biofuel hosts, environmental bacteria were screened for tolerance, and these were used to create gene libraries to test in E. coli. Future characterization of these libraries using molecular techniques will be used to identify genes that contribute IL-tolerance to transformed microbes.
Halloween 2012 Jack O'Lanterns Trick Or Treat, George McNamara University of Miami
Halloween 2012 Jack O'Lanterns Trick Or Treat, 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 ...
An Agent–Based Computational Model For Bank Formation And Interbank Networks, Omneia R.H. Ismail McMaster University
An Agent–Based Computational Model For Bank Formation And Interbank Networks, Omneia R.H. Ismail
Open Access Dissertations and Theses
The aim of this thesis is to study the role of banking in society and the effect of the
interbank market on the performance of the banking system.
It starts by reviewing
several studies conducted on empirical banking networks and highlighting their salient
features in the context of modern network theory. A simulated network resembling the
characteristics documented in the empirical studies is then built and its resilience is
analyzed with a particular emphasis in documenting the crucial role played by highly
It is our belief that the study of systemic risk and contagion in a banking system ...
Mcnamara 20120831fri-20120904tue Cosmic Ray Particles By Ccd Imaging, George McNamara University of Miami
Mcnamara 20120831fri-20120904tue Cosmic Ray Particles By Ccd Imaging, George Mcnamara
McNamara 20120831Fri-20120904Tue Cosmic Ray Particles by CCD imaging.zip contains image files in support of a Microscopy Today article - please see
Targeting Akt/Mtor Signaling Pathways During Murine Skin Tumor Promotion And The Impact Of Dietary Energy Balance Manipulation, Laura A. Checkley Texas Medical Center Library
Targeting Akt/Mtor Signaling Pathways During Murine Skin Tumor Promotion And The Impact Of Dietary Energy Balance Manipulation, Laura A. Checkley
UT GSBS Dissertations and Theses (Open Access)
The prevalence of obesity has continued to rise over the last several decades in the United States lending to overall increases in risk for chronic diseases including many types of cancer. In contrast, reduction in energy consumption via calorie restriction (CR) has been shown to be a potent inhibitor of carcinogenesis across a broad range of species and tumor types. Previous data has demonstrated differential signaling through Akt and mTOR via the IGF-1R and other growth factor receptors across the diet-induced obesity (DIO)/CR spectrum. Furthermore, mTORC1 is known to be regulated directly via nutrient availability, supporting its role in ...
Protein Body Formation In Stable Transgenic Plants Of Nicotiana Tabacum Expressing Elastin-Like Polypeptide And Hydrophobin Fusion Proteins, Sonia P. Gutierrez Western University
Protein Body Formation In Stable Transgenic Plants Of Nicotiana Tabacum Expressing Elastin-Like Polypeptide And Hydrophobin Fusion Proteins, Sonia P. Gutierrez
Electronic Thesis and Dissertation Repository
Plants are recognized as an efficient and inexpensive system to produce valuable recombinant proteins. However, the use of plants still faces two main limitations: the low accumulation levels of some recombinant proteins and the lack of efficient protein purification methods. Two fusion partners, elastin-like polypeptides (ELP) and hydrophobin I (HFBI) were found to increase the accumulation of recombinant proteins and induce the formation of protein bodies (PBs) when targeted to the ER in transient expression assays. In this study I examined the effect of these tags in stable transgenic plants of two Nicotiana tabacum cultivars when fused to green fluorescent ...
Cosmic Ray Particles Images With Orca-Ii Erg, George McNamara University of Miami
Cosmic Ray Particles Images With Orca-Ii Erg, 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 ...
A Study Of Histone Deacetylase Inhibitors: Determination Of The Binding Energetics Of Suberoylanilide Hydroxamic Acid With Zinc And Cobalt And Preliminary Screening Of Nitric Oxide Donors, Erin Gallagher DePaul University
A Study Of Histone Deacetylase Inhibitors: Determination Of The Binding Energetics Of Suberoylanilide Hydroxamic Acid With Zinc And Cobalt And Preliminary Screening Of Nitric Oxide Donors, Erin Gallagher
College of Science and Health Theses and Dissertations
Inhibiting histone deacetylases (HDACs) can suppress tumor cell growth eventually leading to their death, makeing HDACs an important drug target. Therefore, understanding the mechanism behind inhibiting HDACs is imperative. To determine the thermodynamic parameters for the interaction of a known competitive HDAC inhibitor, suberoylanilide hydroxamic acid (SAHA), with zinc(II), the metal ion in the HDAC active site, and cobalt(II), isothermal titration calorimetry (ITC) was used. The results showed that SAHA binds to zinc(II) more strongly than it does to cobalt(II) as the equilibrium binding constants were 4.3 ± 0.5 x 102 M-1 and ...
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Medical Technology: Contexts And Content In Science And Technology, Dr. Anthony Doggett
Post-Exercise Hypotension In Brief Exercise, Jeremiah Bush
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