Physical Sciences and Mathematics Commons^™

Improved Peak Detection And Quantification Of Mass Spectrometry Data Acquired From Surface-Enhanced Laser Desorption And Ionization By Denoising Spectra With The Undecimated Discrete Wavelet Transform, Kevin R. Coombes, Spiros Tsavachidis, Jeffrey S. Morris, Keith A. Baggerly, Henry M. Kuerer

Jeffrey S. Morris

Background: Mass spectrometry, especially surface enhanced laser desorption and ionization (SELDI) is increasingly being used to find disease-related proteomic patterns in complex mixtures of proteins derived from tissue samples or from easily obtained biological fluids such as serum, urine, or nipple aspirate fluid. Questions have been raised about the reproducibility and reliability of peak quantifications using this technology. For example, Yasui and colleagues opted to replace continuous measures of the size of a peak by a simple binary indicator of its presence or absence in their analysis of a set of spectra from prostate cancer patients.

Methods: We collected nipple …

Pooling Information Across Different Studies And Oligonucleotide Microarray Chip Types To Identify Prognostic Genes For Lung Cancer., Jeffrey S. Morris, Guosheng Yin, Keith A. Baggerly, Chunlei Wu, Li Zhang

Jeffrey S. Morris

Our goal in this work is to pool information across microarray studies conducted at different institutions using two different versions of Affymetrix chips to identify genes whose expression levels offer information on lung cancer patients’ survival above and beyond the information provided by readily available clinical covariates. We combine information across chip types by identifying “matching probes” present on both chips, and then assembling them into new probesets based on Unigene clusters. This method yields comparable expression level quantifications across chips without sacrificing much precision or significantly altering the relative ordering of the samples. We fit a series of multivariable …

Accounting For Missing Data In End-Of-Life Research, Paula Diehr, Laura Lee Johnson

Paula Diehr

End-of-life studies are likely to have missing data because sicker persons are less likely to provide information and because measurements cannot be made after death. Ignoring missing data may result in data that are too favorable, because the sickest persons are effectively dropped from the analysis. In a comparison of two groups, the group with the most deaths and missing data will tend to have the most favorable data, which is not desirable. Results based on only the available data may not be generalizable to the original study population. If most of the missing data are absent because of death, …

Biosecurity And The Role Of Statisticians, Ron Brookmeyer

Ron Brookmeyer

No abstract provided.

Methods For Incorporating Death Into Health-Related Variables In Longitudinal Studies, Paula Diehr

Paula Diehr

BACKGROUND AND OBJECTIVES: Longitudinal studies of health over time may be misleading if some people die. Self-rated health (excellent to poor) and the SF-36 profile scores have been transformed to incorporate death. We applied the same approaches to incorporate death into activities of daily living difficulties (ADLs), IADLs, mini-mental state examination, depressive symptoms, blocks walked per week, bed days, the timed walk, body mass index and blood pressure. STUDY DESIGN AND SETTING: The Cardiovascular Health Study of 5,888 older adults, was followed up to 9 years. Mean age was 73 at baseline, and 658 had an incident stroke during follow-up. …

Effects Of Gramicidin-A On The Adsorption Of Phospholipids To The Air–Water Interface, Samares C. Biswas, Shankar B. Rananavare, Stephen B. Hall

Chemistry Faculty Publications and Presentations

Prior studies suggest that the hydrophobic surfactant proteins, SP-B and SP-C, promote adsorption of the lipids in pulmonary surfactant to an air–water interface by stabilizing a negatively curved rate-limiting structure that is intermediate between bilayer vesicles and the surface film. This model predicts that other peptides capable of stabilizing negative curvature should also promote lipid adsorption. Previous reports have shown that under appropriate conditions, gramicidin-A (GrA) induces dioleoyl phosphatidylcholine (DOPC), but not dimyristoyl phosphatidylcholine (DMPC), to form the negatively curved hexagonal-II (HII) phase. The studies reported here determined if GrA would produce the same effects on adsorption of DMPC and …

Matlab Code For Bayesian Fitting Of Adaptive P-Splines In Regression, Veera Baladandayuthapani

Veera Baladandayuthapani

No abstract provided.

Synthesis, Structural Studies And Desilylation Reactions Of Some N-2-(Trimethylsilyl)Ethyl-N-Nitrosocarbamates, Arpitha Thakkalapally, Vladimir Benin

Chemistry Faculty Publications

The present report describes the preparation and characterization of several N-2-(trimethylsilyl)ethyl-N-nitrosocarbamates, designed as precursors to thermally unstable secondary N-nitrosocarbamate anions via fluoride-assisted cleavage. X-ray structural studies demonstrate that the core N-nitrosocarbamate moiety has a nearly planar geometry, with an s-E orientation at the N–N bond. DFT calculations (B3LYP/6-31+G(d)) reproduce accurately the structural features of the title compounds and detailed conformational analysis at the same level of theory addresses the long-standing issue of preferred geometries for three classes of related structures: N-nitrosocarbamates, N-nitrosoureas and N-nitrosoamides. Desilylation studies demonstrate that both the …

26Al-Containing Acidic And Basic Sodium Aluminum Phosphate Preparation And Use In Studies Of Oral Aluminum Bioavailability From Foods Utilizing 26Al As An Aluminum Tracer, Robert A. Yokel, Aaron A. Urbas, Robert A. Lodder, John P. Selegue, Rebecca L. Florence

Pharmaceutical Sciences Faculty Publications

We synthesized ²⁶Al-containing acidic and basic (alkaline) sodium aluminum phosphates (SALPs) which are FDA-approved leavening and emulsifying agents, respectively, and used them to determine the oral bioavailability of aluminum incorporated in selected foods. We selected applicable methods from published syntheses (patents) and scaled them down (∼3000- and 850-fold) to prepare ∼300–400 mg of each SALP. The ²⁶Al was incorporated at the beginning of the syntheses to maximize ²⁶Al and ²⁷Al equilibration and incorporate the ²⁶Al in the naturally-occurring Al-containing chemical species of the products. Near infrared spectroscopy (NIR) and X-ray powder diffraction (XRD) were used …

The Importance Of Experimental Design In Proteomic Mass Spectrometry Experiments: Some Cautionary Tales, Jeffrey S. Morris, Jianhua Hu, Kevin R. Coombes, Keith A. Baggerly

Jeffrey S. Morris

Proteomic expression patterns derived from mass spectrometry have been put forward as potential biomarkers for the early diagnosis of cancer and other diseases. This approach has generated much excitement and has led to a large number of new experiments and vast amounts of new data. The data, derived at great expense, can have very little value if careful attention is not paid to the experimental design and analysis. Using examples from surfaceenhanced laser desorption/ionisation time-of-flight (SELDI-TOF) and matrix-assisted laser desorption–ionisation/time-of-flight (MALDI-TOF) experiments, we describe several experimental design issues that can corrupt a dataset. Fortunately, the problems we identify can be …

Serum Proteomics Profiling: A Young Technology Begins To Mature, Kevin R. Coombes, Jeffrey S. Morris, Jianhua Hu, Sarah R. Edmondson, Keith A. Baggerly

Jeffrey S. Morris

No abstract provided.

An Analysis Of Biometric Technology As An Enabler To Information Assurance, Darren A. Deschaine

Theses and Dissertations

The use of and dependence on, Information technology (IT) has grown tremendously in the last two decades. Still, some believe the United States is only in the infancy of this growth. This explosive growth has opened the door to capabilities that were only dreamed of in the past. As easy as it is to see how advantageous this technology is, it also is clear that with its advantages come distinct responsibilities and new problems that must be addressed. For instance, the minute one begins using information processing systems, the world of information assurance (IA) becomes far more complex. As a …

What Communities Should Do Pre-Event To Support Public Health Post-Event Assessments, Surveillance And Monitoring, Thomas Lyons Carr Iii

Thomas Lyons (Thom) Carr III Appl.Sc., CEM

[Abstract written March 2008, TLC] Under worst-case planning assumptions used by some major metropolitan areas, a Neighbor-to-Neighbor self-help program model is the primary link between citizens and the professional response personnel of the responsible government agencies.

In the Neighbor-to-Neighbor self-help program model or a Community Emergency Management Plan (CEMP) calls on the citizens in neighborhoods to identify and establish cluster emergency preparedness committees, Cluster Emergency Coordination Centers (CECC) and Community Emergency Response Teams (CERT). Missing from these plans or what is not articulated is how constant Public Health Post-Event Surveillance, Monitoring and Assessments will be done. Given the worst-case planning …

Signal In Noise: Evaluating Reported Reproducibility Of Serum Proteomic Tests For Ovarian Cancer, Keith A. Baggerly, Jeffrey S. Morris, Sarah R. Edmonson, Kevin R. Coombes

Jeffrey S. Morris

Proteomic profi ling of serum initially appeared to be dramatically effective for diagnosis of early-stage ovarian cancer, but these results have proven diffi cult to reproduce. A recent publication reported good classifi cation in one dataset using results from training on a much earlier dataset, but the authors have since reported that they did not perform the analysis as described. We examined the reproducibility of the proteomic patterns across datasets in more detail. Our analysis reveals that the pattern that enabled successful classifi cation is biologically implausible and that the method, properly applied, does not classify the data accurately. We …

Reliability, Effect Size, And Responsiveness Of Health Status Measures In The Design Of Randomized And Cluster-Randomized Trials, Paula Diehr

Paula Diehr

BACKGROUND: New health status survey instruments are often described by their psychometric (measurement) properties, such as Validity, Reliability, Effect Size, and Responsiveness. For cluster-randomized trials, another important statistic is the Intraclass Correlation (ICC) for the instrument within clusters. Studies using better instruments can be performed with smaller sample sizes, but better instruments may be more expensive in terms of dollars, opportunity cost, or poorer data quality due to the response burden of longer instruments. METHODS: We defined the psychometric statistics in terms of a mathematical model, and examined the power of a two-sample test as a function of the test-retest …

Measuring Shared Information And Coordinated Activity In Neuronal Networks, K L. Klinkner, C R. Shalizi, Marcelo Camperi

Physics and Astronomy

Most nervous systems encode information about stimuli in the respond- ing activity of large neuronal networks. This activity often manifests itself as dynamically coordinated sequences of action potentials. Since multiple electrode recordings are now a standard tool in neuroscience research, it is important to have a measure of such network-wide behav- ioral coordination and information sharing, applicable to multiple neural spike train data. We propose a new statistic, informational coherence , which measures how much better one unit can be predicted by knowing the dynamical state of another. We argue informational coherence is a measure of association and shared information …

Punishment And Rehabilitation Views Of Social Work Majors And Non-Social Work Students: An Exploratory Study, Eric G. Lambert, Sudershan Pasupuleti, Reva I. Allen

Journal of the South Carolina Academy of Science

No abstract provided.

Design And Cloning Of A Hammerhead Ribozyme Targeted Tohiv-1p7fmrna, Katherine L. Anderson, William H. Jackson

Journal of the South Carolina Academy of Science

No abstract provided.