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 …

Graduate Colloquium, Borbala Mazzag

Borbala Mazzag

No abstract provided.

Update On Ethanol Processing Residue Properties, Kurt A. Rosentrater, Kasiviswanathan Muthukumarappan, James Julson, Padmanaban Krishnan

Kurt A. Rosentrater

The production of corn-based ethanol in the U.S. is dramatically increasing, and consequently so is the amount of byproduct materials generated from this processing sector. These coproduct streams are currently solely utilized as livestock feed, which is a route that provides ethanol processors with a substantial revenue source and significantly increases the profitability of the production process. With the construction and operation of many new plants in recent years, these residuals do, however, have much potential for value-added processing and utilization in other sectors as well. This option holds promise of economic benefit for corn processors, especially if the livestock …

Renewable Energy Alternatives: Current Status And Capacities, Kurt A. Rosentrater, Youakim Al-Kalaani

Kurt A. Rosentrater

A key to the United States’ economic growth is an ever-increasing demand for energy, which has traditionally been met primarily by combusting the hydrocarbons found in fossil fuels. As environmental concerns grow, renewable energy resources are gaining increasing attention. To aid both researchers as well as educators, this paper examines historical energy data for both traditional as well as alternative energy sources. Even with the progressive developments of non-traditional energy sources over the years, the U.S. still receives more than 90% of its energy from fossil and nuclear fuels. Explicit examination of the alternative energy sector has revealed that hydroelectric …

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.

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 …

Thermodynamics, Structure, And Dynamics Of Water Confined Between Hydrophobic Plates, Francis Starr, P. Kumar, S. Buldyrev, N. Giovambattista, H. Stanley

Francis Starr

No abstract provided.

Mathematical Modeling Of The Hypothalamic-Pituitary-Adrenal System Activity, Zeljko D. Cupic

Zeljko D Cupic

No abstract provided.

Severe Wind And Fire Regimes In Northern Forests: Historic Variability At The Regional Scale, Lisa A. Schulte-Moore, David J. Mladenoff

Lisa A. Schulte Moore

Within the northern Great Lakes region, mesoscale (10s to 100s of km2) forest patterning is driven by disturbance dynamics. Using original Public Land Survey (PLS) records in northern Wisconsin, USA, we study spatial patterns of wind and fire disturbances during the pre-Euroamerican settlement period (ca. 1850). Our goals were: (1) to determine how effectively wind and fire disturbance can be econstructed from the PLS, (2) to assess the roles of wind and fire in shaping vegetation patterns, (3) to evaluate landscape to regional controls of wind and fire regimes, and (4) to assess the potential for interactions between these disturbances. …

The Ivory-Billed Woodpecker In Mississippi?, Stephen J. Dinsmore

Stephen J Dinsmore

In April the environmental community received a real surprise--the Ivory-billed Woodpecker, long thought to be extinct, had apparently been rediscovered in Arkansas! As the news unfolded, the world learned that a team of researchers had been tracking at least one woodpecker, a lone male, for more than a year in the Cache River region of east-central Arkansas. The rediscovery of a bird presumed extinct for more than 60 years subsequently galvanized the environmental community and garnered much-needed support for the preservation of the Southeast's remaining old growth bottomland forests and endangered species recovery.

Waterfowl Abundance And Distribution In The Mississippi Delta, Stephen J. Dinsmore, Aaron T. Pearse, Richard M. Kaminski, Kenneth J. Reinecke

Stephen J Dinsmore

During mornings of empty skies, a duck hunter has plenty of time to ponder the question, "Where are all the ducks?" Invariable, the distraught hunter arrives at an unhappy conclusion: the ducks are not going to show up, so they must be elsewhere. The typical progression of an unsuccessful morning of hunting leads to multiple explanations as to why there weren't any ducks, such as mild winter temperatures in and north of Mississippi, not enough rain to attract ducks, too much rain and the ducks are scattered, the region doesn't have enough food to attract and hold ducks, the ducks …

Hamiota, A New Genus Of Freshwater Mussel (Bivalvia: Unionidae) From The Gulf Of Mexico Drainages Of The Southeastern United States, Kevin J. Roe, Paul D. Hartfield

Kevin J. Roe

Hamiota, a new genus of freshwater mussel containing four species formerly assigned to the genus Lampsilis Rafinesque, 1820, is described. In addition to the genus Lampsilis, members of Hamiota had previously been placed in the genera Villosa Frierson, 1927, and Ligumia Swainson, 1840. Several characters including the packaging of their larvae in a superconglutinate lure to attract host fishes, placement and shape of the marsupia, and release of glochidia through the excurrent siphon, support the recognition of these species as a distinct genus.

Pre-Euroamerican Distribution Of Pine Warblers (Dendroica Pinus) In Wisconsin: A Tool For Setting Regional Conservation Priorities, Lisa A. Schulte, Anna M. Pidgeon, David J. Mladenoff

Lisa A. Schulte Moore

A common goal of conservation and management plans is to maintain populations of species of conservation concern at some historic level that was a product of environmental conditions at a time when they were less influenced by humans than at present. Conservation planning also includes consideration of the distribution, abundance, and reproductive success of a species, all of which are affected by both the amount and spatial pattern of habitat. In this work, we have fused the fields of spatial and historical ecology to provide a perspective that includes an estimate of a bird species’ distribution just prior to Euroamerican …

Who Believes What? Clearing Up Confusion Over Intelligent Design And Young-Earth Creationism, Marcus R. Ross

Marcus R. Ross

The question of what differentiates young-Earth creationism (YEC) from Intelligent Design (ID) has resulted in inaccurate and confusing terminology, and hinders both understanding and dialogue. Though both YEC and ID groups have drawn distinctions between themselves, previous attempts to classify design-based positions on origins have been unable to adequately resolve their relationships. The Nested Hierarchy of Design, a multiple-character classification system, categorizes teleological positions according to the strength of claims regarding the reality, detectability, source, method, and timing of design, and results in an accurate and robust classification of numerous positions. This method avoids the philosophical and theological pitfalls of …

Reduced Macrophage Apoptosis Is Associated With Accelerated Atherosclerosis In Low-Denstiy Lipoprotein Receptor-Null Mice, Michael Sinensky, J. Liu, D. P. Thweke, Y. R. Su, M. F. Linton, S. Fazio

Michael Sinensky

Objective— The majority of apoptotic cells in atherosclerotic lesions are macrophages. However, the pathogenic role of macrophage apoptosis in the development of atherosclerosis remains unclear. Elevated expression of Bax, one of the pivotal proapoptotic proteins of the Bcl-2 family, has been found in human atherosclerotic plaques. Activation of Bax also occurs in free cholesterol-loaded and oxysterol-treated mouse macrophages. In this study, we examined the effect of Bax deficiency in bone marrow-derived leukocytes on the development of atherosclerosis in low-density lipoprotein receptor-null (LDLR−/−) mice. Methods and Results— Fourteen 8-week-old male LDLR−/− mice were lethally irradiated and reconstituted with either wild-type (WT) …

The Reflection Of Karst In The Online Mirror: A Survey Within Scientific Databases, 1960-2005, Lee J. Florea, Beth Fratesi, Todd A. Chavez

Todd A. Chavez

The field of cave and karst science is served by a literature that is dispersed across far-flung topical journals, government publications, and club newsletters. As part of an inter-institutional project to globalize karst information (KIP, the Karst Information Portal), the USF Library undertook a structured battery of literature searches to map the domain of karst literature. The study used 4,300 individual searches and four literature databases: GeoRef, BIOSIS, Anthropology Plus, and GPO Access. The searches were based on a list of 632 terms including 321 karst-related keywords culled from three leading encyclopedias and glossaries of cave and karst science. An …

Interaction Between The Dorsal And Ventral Pathways In Mental Rotation: An Fmri Study, Hideya Koshino, Patricia Carpenter, Timothy Keller, Marcel Just

Marcel Adam Just

No abstract provided.

Imagining Material Versus Geometric Properties Of Objects: An Fmri Study, Sharlene Newman, Roberta Klatzky, Susan Lederman, Marcel Just

Marcel Adam Just

No abstract provided.

Functional Connectivity In An Fmri Working Memory Task In High-Functioning Autism, Hideya Koshino, Patricia Carpenter, Nancy Minshew, Vladimir Cherkassky, Timothy Keller, Marcel Just

Marcel Adam Just

No abstract provided.

The Framing Effect And Risky Decisions: Examining Cognitive Functions With Fmri, Cleotilde Gonzalez, Jason Dana, Hideya Koshino, Marcel Adam Just

Marcel Adam Just

No abstract provided.