Physical Sciences and Mathematics Commons^™

The Proportional Odds Model For Assessing Rater Agreement With Multiple Modalities, Elizabeth Garrett-Mayer, Steven N. Goodman, Ralph H. Hruban

Johns Hopkins University, Dept. of Biostatistics Working Papers

In this paper, we develop a model for evaluating an ordinal rating systems where we assume that the true underlying disease state is continuous in nature. Our approach in motivated by a dataset with 35 microscopic slides with 35 representative duct lesions of the pancreas. Each of the slides was evaluated by eight raters using two novel rating systems (PanIN illustrations and PanIN nomenclature),where each rater used each systems to rate the slide with slide identity masked between evaluations. We find that the two methods perform equally well but that differentiation of higher grade lesions is more consistent across raters …

Cross-Study Validation And Combined Analysis Of Gene Expression Microarray Data, Elizabeth Garrett-Mayer, Giovanni Parmigiani, Xiaogang Zhong, Leslie Cope, Edward Gabrielson

Johns Hopkins University, Dept. of Biostatistics Working Papers

Investigations of transcript levels on a genomic scale using

hybridization-based arrays led to formidable advances in our

understanding of the biology of many human illnesses. At the same time, these investigations have generated controversy, because of the probabilistic nature of the conclusions, and the surfacing of noticeable discrepancies between the results of studies addressing the same biological question. In this article we present simple and effective data analysis and visualization tools for gauging the degree to which

the finding of one study are reproduced by others, and for integrating multiple studies in a single analysis.

We describe these approaches in …

Atrazine Runoff In The Blue River Basin: Geomorphology, Rainfall, And Agronomic Practices, Kundan Dhakal

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Atrazine concentrations in the Big Blue River Basin (BRB) in Nebraska and Kansas periodically exceed the U.S. EPA Maximum Contaminant Level (MCL) of 3 µg L^-1. The present study is focused on watershed variables influencing surface runoff of atrazine. The assessment includes the impact of corn and sorghum planting progress (indicating atrazine application), rainfall, antecedent soil water content, and soil restrictive layer on stream-measured weekly atrazine load in independent BRB subwatersheds for 1997 - 2004. Maximum atrazine loading occurred after most of the corn had been planted but during sorghum planting from mid-May to early June, immediately following …

Divided Culture: Integrating And Conservation Biology Agriculture, John Banks

SIAS Faculty Publications

Production agriculture, with its implied ecosystem simplification, pesticide and fertilizer use, and emphasis on yield, often appears to be at odds with conservation biology. From a farmer's perspective, the weight conservation biology places on wildlife may seem overly idealistic and naive, detached from economic and sociopolitical reality. In fact, these endeavors are two sides of the same coin, with a shared heritage in decades of population and community ecological theory and experimentation. Better integration of the two disciplines requires acknowledging their various goals and working to produce mutually beneficial outcomes. The best examples of this type of integrated approach result …

The Function Of The Stress Hormone Cortisol In Disease Susceptibility Of Channel Catfish, Ictalurus Punctatus, Todd David Sink

Doctoral Dissertations

The purpose of these studies was to examine the roles that the stress hormone cortisol plays in disease susceptibility of channel catfish, Ictalurus punctatus, to enteric septicemia of catfish (ESC). ESC is a serious disease of the channel catfish industry with annual losses in the millions. Few treatment options such as antibiotics and vaccines are available, but efficacy of treatments has proven to be limited. Deeper investigations into the physiological causes of disease in fish that accompany commercial production are needed to promote understanding of disease treatment and prevention.

Disease challenges using Edwardsiella ictaluri, the pathogenic bacterium that …

Metallic Ferroelectricity And Superconductivity In The Transition Metal Oxide Pyrochlore Cd2Re2O7, Jian He

Doctoral Dissertations

Single crystalline samples of transition metal oxide Cd₂Re₂O₇, the first superconductor among pyrochlore oxides with general formula A₂B₂O₇ and the first example of “ferroelectric metal” theoretically proposed by P.W. Anderson and E.I. Blount back in 1960s, have been grown using vapor transport and carefully characterized, regarding its chemical stoichiometry and structure. In addition to the superconductivity transition, two normal state phase transitions and the anomalous high temperature phase have been comprehensively investigated, by means of transport, thermodynamic and spectroscopy techniques. The system undergoes a subtle continuous cubic-to-tetragonal phase transition …

Electrochemical Investigation Of Anthraquinone Tagged Oligonucleotides And Electrodes, Adam N. Mullenix

Doctoral Dissertations

The DNA double helix is one of the most studied structures in modern science. These molecules provide the basic blueprint for all life as it is presently known to exist. Continuing studies of this structure, and the implications that come with them, currently yield a constantly growing base of knowledge for the study of drug interactions, specifics in the role of the sequence of bases in the DNA chain, and an understanding of the small structural abnormalities and the resulting benefits and problems in the human genome. The research presented herein attempts to examine such interactions using anthraquinone-based modifications for …

U.S. Law Of The Sea Cruise To Map The Foot Of The Slope And 2500-M Isobath Of The Northeast Us Atlantic Continental Margin: Legs 1, 2 And 3. Cruise Report, James V. Gardner

Center for Coastal and Ocean Mapping

U.S. Law of the Sea cruise to map the foot of the slope and 2500-m isobath of the Northeast US Atlantic continental margin: Legs 1,2 and 3

CRUISES H04-1, 2 and 3

August 23, to November 30, 2004

Gulfport, MS to Norfolk, VA

Strict Feedforward Form And Symmetries Of Nonlinear Control Systems, Witold Respondek, Issa Amadou Tall

Miscellaneous (presentations, translations, interviews, etc)

We establish a relation between strict feedforward form and symmetries of nonlinear control systems. We prove that a system is feedback equivalent to the strict feedforward form if and only if it gives rise to a sequence of systems, such that each element of the sequence, firstly, possesses an infinitesimal symmetry and, secondly, it is the factor system of the preceding one, i.e., is reduced from the preceding one by its symmetry. We also propose a strict feedforward normal form and prove that a smooth strict feedforward system can be smoothly brought to that form.

Primitive Ideals Of Semigroup Graded Rings, Hema Gopalakrishnan

Mathematics Faculty Publications

Prime ideals of strong semigroup graded rings have been characterized by Bell, Stalder and Teply for some important classes of semigroups. The prime ideals correspond to certain families of ideals of the component rings called prime families. In this paper, we define the notion of a primitive family and show that primitive ideals of such rings correspond to primitive families of ideals of the component rings.

Manganese Oxide Thin Films Prepared By Nonaqueous Sol-Gel Processing: Preferential Formation Of Birnessite, Stanton Ching, Steven M. Hughes, Timothy P. Gray, Eric J. Welch

Chemistry Faculty Publications

High quality manganese oxide thin films with smooth surfaces and even thicknesses have been prepared with a nonaqueous sol–gel process involving reduction of tetraethylammonium permanganate in methanol. Spin-coated films have been cast onto soft glass, quartz, and Ni foil substrates, with two coats being applied for optimum crystallization. The addition of alkali metal cations as dopants results in exclusive formation of the layered birnessite phase. By contrast, analogous reactions in bulk sol–gel reactions yield birnessite, tunneled, and spinel phases depending on the dopant cation. XRD patterns confirm the formation of well-crystallized birnessite. SEM images of Li-, Na-, and K–birnessite reveal …

Spectral Degree Of Coherence Of A Random Three-Dimensional Electromagnetic Field, Olga Korotkova, Emil Wolf

Physics Articles and Papers

The complex spectral degree of coherence of a general random, statistically stationary electromagnetic field is introduced in a manner similar to the way it is defined for a beamlike field, namely, by means of Young’s interference experiment. Both its modulus and its phase are measurable. We illustrate the definition by applying it to blackbody radiation emerging from a cavity. The results are of particular interest for near-field optics.

What Does Height Really Mean? Part I: Introduction, Thomas H. Meyer, Daniel R. Roman, David B. Zilkoski

Thomas H. Meyer's Peer-reviewed Articles

This is the first paper in a four-part series considering the fundamental question, “what does the word height really mean?” National Geodetic Survey (NGS) is embarking on a height modernization program in which, in the future, it will not be necessary for NGS to create new or maintain old orthometric height benchmarks. In their stead, NGS will publish measured ellipsoid heights and computed Helmert orthometric heights for survey markers. Consequently, practicing surveyors will soon be confronted with coping with these changes and the differences between these types of height. Indeed, although “height’” is a commonly used word, an exact definition …

High Statistics Search For The Θ+ (1.54) Pentaquark State, M. J. Longo, Timothy Holmstrom, Hypercp Collaboration

Chemistry & Physics Faculty Publications

We have searched for θ⁺(1.54)→K⁰p decays using data from the 1999 run of the HyperCP experiment at Fermilab. We see no evidence for a narrow peak in the K_S⁰p mass distribution near 1.54  GeV/c among 106 000 K_S⁰p candidates, and obtain an upper limit for the fraction of θ⁺(1.54) to K_S⁰p candidates of

The Other Side Of Silence: Rachel Carson’S Views Of Animals, Marc Bekoff, Jan Nystrom

Animal Welfare Collection

The publication of Rachel Carson’s Silent Spring in 1962 is widely regarded as one of the major events that launched the modern environmental movement. Silent Spring is a compelling blend of stories, natural history, human values, and biological facts. In this essay we consider Carson’s attitude toward animals in Silent Spring and in other texts. Despite the facts that she was raised to love Nature and animals, little direct attention has been given to Carson’s views about our moral responsibilities to, and the moral standing of animals. Carson favored responsible stewardship, was more of an animal welfarist and environmentalist/conservation biologist …

Coral Reef Ecosystem Restoration Off Southeast Florida, David S. Gilliam, Walter Jaap, Richard E. Dodge, Elizabeth Glynn Fahy, Jamie A. Monty, Brian K. Walker, Lauren F. Shuman, B. D. Ettinger, Daniel P. Fahy, Shaun M. Gill, Richard Shaul

Marine & Environmental Sciences Faculty Proceedings, Presentations, Speeches, Lectures

Significant coral reef community development along the eastern shelf of the United States continues northward of the Florida Keys through Miami-Dade, Broward, Palm Beach, and Martin Counties, Florida (to Latitude 27° N). These Southeast Florida high-latitude coral communities have approximately 30 species of stony corals, stony coral coverage of 2-3%, and a diverse assemblage of reef gorgonians, sponges, and fishes.

This system lays within 3 km of the coast offshore a highly urbanized area comprising a population of over 5 million people (the population of Broward County alone exceeds 1.7 million). These reefs are important economic assets: a 2001 economic …

Techniques For Restoring Gorgonians To Coral Reef Injury Areas, Lauren F. Shuman, David S. Gilliam, Richard E. Dodge, B. D. Ettinger, Daniel P. Fahy, Elizabeth Glynn Fahy, Shaun M. Gill, Jamie A. Monty, Brian K. Walker

Marine & Environmental Sciences Faculty Proceedings, Presentations, Speeches, Lectures

Great attention and energy has been spent investigating reattachment techniques for dislodged and fragmented scleractinian corals; however there has been a lack of controlled experimentation on how to restore dislodged gorgonians following a disturbance event, such as a ship grounding. Unfortunately, reef damage events occur frequently off southeast Florida. As an example, since 1998 at least five freighters have grounded on the reefs near Ft. Lauderdale, Broward County. These freighters dislodged many scleractinian and gorgonian corals and often destroyed thousands of square feet of reef habitat. After these events, restoration efforts concentrated on stabilizing loose debris and rubble, and reattaching …

Meeting The Scientific Needs Of Ecological Risk Assessment In A Regulatory Context, Steven P. Bradbury, Tom C. Feitel, Cornelis J. Van Leeuwen

Steven P. Bradbury

During the past decade, the field of ecological risk assessment has progressed considerably. Advances have come from such international bodies as the Organisation for Economic Co-operation and Development (OECD), the World Health Organisation (WHO), the European and Mediterranean Plant Protection Organisation (EPPO), and the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) (1–8). Risk assessments have played a critical role in the development of various regulations within the European Commission (EC) as well as in other parts of the world, including the United States, Canada, and Japan (9–17). But scientists and regulators are faced with three significant challenges: streamlining …

My Life With Polymer Science: Scientific And Personal Memoirs, Otto Vogl

Otto Vogl

My "life story" will begin with my formative years, my childhood and student days at the University of Vienna, including my dissertation. It will be followed by my teaching appointment as an Instructor at the II. Chemical Institute of the University of Vienna. The urge to see other lands, learn other languages and scientific methods led to the Wandering Years that brought me to the United States. After three years spent as a Research Associate at the University of Michigan and at Princeton University I spent more than 13 years in an industrial career at the Du Pont Company in …

Low Background Techniques For The Borexino Nylon Vessels, Andrea Pocar

Andrea Pocar

Borexino is an organic liquid scintillator underground detector for low energy solar neutrinos. The experiment has to satisfy extremely stringent low background requirements. The thin nylon spherical scintillator containment vessel has to meet cleanliness and low radioactivity levels second only, within the detector, to the scintillator itself. Overall, the background from the vessel in the fiducial volume of the detector must be kept at the level of one event per day or better. The requirements, design choices, results from laboratory tests, and fabrication techniques that have been adopted to meet this goal are presented. Details of the precautions taken during …

Adaptation And Sustainability In A Small Arctic Community: Results Of An Agent-Based Simulation Model, Matthew Berman, Craig Nicolson, Gary Kofinas, Joe Tetlichi, Stephanie Martin

Craig Nicolson

Climate warming and resource development could alter key Arctic ecosystem functions that support fish and wildlife resources harvested by local indigenous communities. A different set of global forces—government policies and tourism markets—increasingly directs local cash economies that communities use to support subsistence activities. Agent-based computational models (ABMs) contribute to an integrated assessment of community sustainability by simulating how people interact with each other and adapt to changing economic and environmental conditions. Relying on research and local knowledge to provide rules and parameters for individual and collective decision making, our ABM generates hypothetical social histories as adaptations to scenario-driven changes in …

Effects Of Signal Processing And Antenna Frequency On The Geostatistical Structure Of Ground-Penetrating Radar Data, Greg A. Oldenborger, Michael D. Knoll, Warren Barrash

CGISS Publications and Presentations

Recent research has suggested that the geostatistical structure of ground-penetrating radar data may be representative of the spatial structure of hydraulic properties. However, radar images of the subsurface can change drastically with application of signal processing or by changing the signal frequency. We perform geostatistical analyses of surface radar reflection profiles in order to investigate the effects of data processing and antenna frequency on the semivariogram structure of radar reflection amplitudes. Surface radar reflection data collected at the Boise Hydrogeophysical Research Site illustrate the processing- and antenna-dependence of radar semivariograms for a fluvial, cobble-and-sand aquifer. Compensating for signal attenuation and …

The Rotundity Of Large Planetary Objects, Adesanwo Moradeyo

Graduate Student Papers (Physics)

The most obvious structural feature of planetary bodies is their roundness. This arises because of the dominate roles of the two effects of gravity and case of the deformation of matter, whether gas, liquid or solid. This project is about proving and solving out the time scale (τ ) of flow restoring the body to spherical shape when we consider a slightly deformed self-gravitating sphere and also checking for spherical of different planetary objects.

Neutron Multiplicity Measurements For The Afci Program Quarterly Progress Report September-December 2004, Denis Beller

Transmutation Sciences Physics (TRP)

The U.S. Advanced Fuel Cycle Initiative (AFCI) is a program to develop economic and environmental methods to reduce the impact of waste from commercial nuclear fuel cycles. One concept for near-complete destruction of waste isotopes from used nuclear fuel is accelerator driven transmutation. High-power accelerators would be used to produce high-energy charged particles, which then collide with heavy metal targets to create a cascade of neutrons. These neutrons then cause a nuclear chain reaction in subcritical systems. Fission neutrons then transmute fissile waste isotopes as well as other problematic isotopes such as technetium-99 and iodine-129. To design these systems, complex …

Fundamental Investigations And Analysis Of Chiral Matter Using Simple Spectroscopic Techniques, Rodney Jamel Sullivan

Doctoral Dissertations

Fundamental investigations of circular dichroism were performed on (R)-(+)-3- methylcyclopentanone, (R)-(-)-2-butylamine, and (S)-(+)-2-butylamine in the liquid and vapor phase to show that solvents often have a structure-masking effect on the circular dichroism for a given molecule. Also, the solid state circular dichroism of cubic sodium chlorate crystals was successfully measured in the midst of adverse experimental circumstances. With these single photon circular dichroism studies at hand, a new technique for measuring circular dichroism was introduced for an advanced investigation of (R)-(+)-3-methylcyclopentanone. The resonance enhanced multiphoton ionization of (R)-(+)-3-methylcyclopentanone was performed …

Com- Putational Subset Model Selection Algorithms And Applications, Xinli Bao

Doctoral Dissertations

This dissertation develops new computationally e±cient algorithms for identifying the subset of variables that minimizes any desired information criteria in model selection.

In recent years, the statistical literature has placed more and more empha- sis on information theoretic model selection criteria. A model selection crite- rion chooses model that \closely" approximates the true underlying model. Recent years have also seen many exciting developments in the model se- lection techniques. As demand increases for data mining of massive data sets with many variables, the demand for model selection techniques are be- coming much stronger and needed. To this end, we introduce …

Newton, Maclaurin, And The Authority Of Mathematics, Judith V. Grabiner

Pitzer Faculty Publications and Research

Sir Isaac Newton revolutionized physics and astronomy in his Principia. How did he do it? Would his method work on any area of inquiry, not only in science, but also about society and religion? We look at how some Newtonians, most notably Colin Maclaurin, combined sophisticated mathematical modeling and empirical data in what has come to be called the "Newtonian Style." We argue that this style was responsible not only for Maclaurin’s scientific success but for his ability to solve problems ranging from taxation to insurance to theology. We show how Maclaurin’s work strengthened the prestige of Newtonianism and …

Nichtmonotone, Neuro-Symbolische Und Begriffliche Wissensverarbeitung, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Diese Schrift dient dem Bericht uber die Hauptaspekte meiner Forschertatigkeit an der TU Dresden seit der Promotion. In diesen dreieinhalb Jahren war es mein Bestreben, selbststandig aktuelle, theoretisch fundierte und anwendungsbezogene Fragestellungen zu entwickeln und zu verfolgen.

Naturgemaß war meine Forschung in dieser Zeit vor allem zu Anfang sehr explorativ. Meine Suche konzentrierte sich dabei auf das Herausarbeiten theoretischer Zusammenhange. Ob ich einen Ansatz dann weiterverfolgte entschied sich anschließend aufgrund einer Evaluation aus angewandter Sicht.

Die in dieser Schrift dargestellten Forschungsansatze gedenke ich in Zukunft fortzufuhren. Sie bilden die Keimzellen fur langfristig angelegte angewandte und theoretische Untersuchungen. Ich werde in …

A Statistical Study Of The Global Structure Of The Ring Current, A. M. Jorgensen, Harlan E. Spence, W. J. Hughes, H. J. Singer

Physics & Astronomy

[1] In this paper we derive the average configuration of the ring current as a function of the state of the magnetosphere as indicated by the Dst index. We sort magnetic field data from the Combined Release and Radiation Effects Satellite (CRRES) by spatial location and by the Dst index in order to produce magnetic field maps. From these maps we calculate local current systems by taking the curl of the magnetic field. We find both the westward (outer) and the eastward (inner) components of the ring current. We find that the ring current intensity varies linearly with Dst as …

Accuracy Limitations Introduced By Digital Projection Sources In Profilometric Optical Metrology Systems, Matthew J. Baker, Joe F. Chicharo, Jiangtao Xi, Enbang Li

Faculty of Informatics - Papers (Archive)

The accuracy of profilometric optical metrology systems utilising Digital Fringe Projection (DFP) is analysed. An analytical model to describe theoretical accuracy limitation is derived and given as a function of object distance from the projector, projector resolution, projection angle and also object gradient. Associated limitations of the model are also discussed and analysed. The validity of the new model is demonstrated through practical experimentation.