Physical Sciences and Mathematics Commons^™

Semiparametric Quantitative-Trait-Locus Mapping: Ii. On Censored Age-At-Onset, Ying Qing Chen, Chengcheng Hu, Rongling Wu

U.C. Berkeley Division of Biostatistics Working Paper Series

In genetic studies, the variation in genotypes may not only affect different inheritance patterns in qualitative traits, but may also affect the age-at-onset as quantitative trait. In this article, we use standard cross designs, such as backcross or F2, to propose some hazard regression models, namely, the additive hazards model in quantitative trait loci mapping for age-at-onset, although the developed method can be extended to more complex designs. With additive invariance of the additive hazards models in mixture probabilities, we develop flexible semiparametric methodologies in interval regression mapping without heavy computing burden. A recently developed multiple comparison procedures is adapted …

Santa Clara Magazine, Volume 46 Number 1, Summer 2004, Santa Clara University

Santa Clara Magazine

8 - A PUZZLING PROFESSOR By Adam Breen. Byron Walden, an assistant professor of mathematics at SCU, draws on his knowledge of numerical analysis to create crossword puzzles for The New York Times.

10 - THE LAUNCHING PAD By Larry Sokoloff J.D. '92. Top government agencies, other universities, and companies are relying on the University's Robotics Systems Lab-and its students-to build and monitor satellites.

16 - A NOVEL TEAM By Kristin Lenore '04. The University's publishing partnership with Heyday Books aims to help preserve California's cultural legacy.

Australian Backyard Gardens And The Journey Of Migration, Lesley M. Head, Pat Muir, E. Hampel

Faculty of Science - Papers (Archive)

Gardens have been an important site of environmental engagement in Australia since the British colonization. They are places where immigrant people and plants carry on traditions from their homelands, and work out an accommodation with new social and biophysical environments. We examine the backyard gardens of three contemporary migrant groups in suburban Australia, Macedonian, Vietnamese and British-born, and a fourth group of first generation Australians with both parents born overseas. There is strong emphasis on the production of vegetables in Macedonian backyards, and herbs and fruit in Vietnamese backyards. British backyards were more diverse, some focusing on non-native ornamental flowers …

A High -Order Finite Difference Method For Solving Bioheat Transfer Equations In Three-Dimensional Triple -Layered Skin Structure, Haofeng Yu

Doctoral Dissertations

Investigations on instantaneous skin burns are useful for an accurate assessment of burn-evaluation and for establishing thermal protections for various purposes. Meanwhile, hyperthermia with radiation is important in the treatment of cancer, and it is essential for developers and users of hyperthermia systems to predict, and interpret correctly the biomass thermal and vascular response to heating. In this dissertation, we employ the well-known Pennes' bioheat transfer equation to predict the degree of skin burn and the temperature distribution in hyperthermia cancer treatment.

A fourth-order compact finite difference scheme is developed to solve Pennes' bioheat transfer equation in a three-dimensional single …

Workflow Management Systems And Erp Systems: Differences, Commonalities, And Applications, Jorge Cardoso, Robert P. Bostrom, Amit P. Sheth

Kno.e.sis Publications

Two important classes of information systems, Workflow Management Systems(WfMSs) and Enterprise Resource Planning (ERP) systems, have been used to support e-business process redesign, integration, and management. While both technologies can help with business process automation, data transfer, and information sharing, the technological approach and features of solutions provided by WfMS and ERP are different. Currently, there is a lack of understanding of these two classes of information systems in the industry and academia, thus hindering their effective applications. In this paper, we present a comprehensive comparison between these two classes of systems. We discuss how the two types of systems …

Discovery Of Web Services In A Federated Registry Environment, Kaarthik Sivashanmugam, Kunal Verma, Amit P. Sheth

Kno.e.sis Publications

The potential of a large scale growth of private and semi-private registries is creating the need for an infrastructure which can support discovery and publication over a group of autonomous registries. Recent versions of UDDI have made changes to accommodate interactions between distributed registries. In this paper, we discuss METEOR-S Web service Discovery Infrastructure, which provides an ontology-based infrastructure to access a group of registries that are divided based on business domains and grouped into federations. We also discuss how Web service discovery is carried out within a federation.

Southeast Florida Coral Reef Evaluation And Monitoring Project 2003 Year 1 Final Report, Jennifer Wheaton, Carl Beaver, Walter Jaap, Michael Callahan, Selena Kupfner, Shannon Wade, Jim Kidney, Stopher Slade, Erin Mcdevitt, Eric Ault, Fred Voss, David S. Gilliam, B. D. Ettinger, Daniel P. Fahy, Elizabeth Glynn Fahy, Shaun M. Gill, Jamie A. Monty, Lauren F. Shuman, Brian K. Walker, Richard E. Dodge, Tim Mcintosh, Steven Blair, Kenneth Banks, Louis E. Fisher, David Stout, Joe Ligas, Janet Phipps

Marine & Environmental Sciences Faculty Reports

No abstract provided.

Quantification And Visualization Of Ld Patterns And Identification Of Haplotype Blocks, Yan Wang, Sandrine Dudoit

U.C. Berkeley Division of Biostatistics Working Paper Series

Classical measures of linkage disequilibrium (LD) between two loci, based only on the joint distribution of alleles at these loci, present noisy patterns. In this paper, we propose a new distance-based LD measure, R, which takes into account multilocus haplotypes around the two loci in order to exploit information from neighboring loci. The LD measure R yields a matrix of pairwise distances between markers, based on the correlation between the lengths of shared haplotypes among chromosomes around these markers. Data analysis demonstrates that visualization of LD patterns through the R matrix reveals more deterministic patterns, with much less noise, than …

Differential Expression With The Bioconductor Project, Anja Von Heydebreck, Wolfgang Huber, Robert Gentleman

Bioconductor Project Working Papers

A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We discuss different approaches to this task and illustrate how they can be applied using software from the Bioconductor Project. A central problem is the high dimensionality of gene expression space, which prohibits a comprehensive statistical analysis without focusing on particular aspects of the joint distribution of the genes expression levels. Possible strategies are to do univariate gene-by-gene analysis, and to perform data-driven nonspecific filtering of genes before the actual statistical analysis. …

A Physiochemically Constrained Seawater Culturing System For Production Of Benthic Foraminifera, Christopher J. Hintz, G. Thomas Chandler, Jay M. Bernhardt, Daniel C. Mccorkle, Suzanne M. Havach, Jessica K. Blanks, Timothy J. Shaw

Faculty Publications

No abstract provided.

Nonparametric Methods For Analyzing Replication Origins In Genomewide Data, Debashis Ghosh

The University of Michigan Department of Biostatistics Working Paper Series

Due to the advent of high-throughput genomic technology, it has become possible to globally monitor cellular activities on a genomewide basis. With these new methods, scientists can begin to address important biological questions. One such question involves the identification of replication origins, which are regions in chromosomes where DNA replication is initiated. In addition, one hypothesis regarding replication origins is that their locations are non-random throughout the genome. In this article, we develop methods for identification of and cluster inference regarding replication origins involving genomewide expression data. We compare several nonparametric regression methods for the identification of replication origin locations. …

Oliver Ranch Core Group Meeting: June 15, 2004, Red Rock Desert Learning Center

Reports (RRLC)

1. Approval of Minutes from May 18 Meeting
2. UNLV/CESU Update – Peg Rees/Nancy Flagg
   A. ORSS History and Talking Points
   B. Presentations to Civic Groups
3. Line and Space Update – Les Wallach/Henry Tom
4. RRCNRA Capital Improvements Update – Mark Morse
5. ORSS Project Timeline – Michael Reiland
6. Linkages Between ORSS Curriculum and Building Design – Paul Buck
7. Video Interviews of CCSD 5th Graders – CCSD Staff
8. ORSS Sub-Committee Reports
   -- Status of Committee Mission Statements
   -- Committee Responses to L&S Draft
   -- Proposal to Establish a Building Committee
   A. Operations – Jack Ramsey
   B. Wild Horse & Burro – Billie Young
   C. …

Emissions From Miombo Woodland And Dambo Grassland Savanna Fires, Parikhit Sinha, Peter V. Hobbs, Robert J. Yokelson, Donald R. Blake, Song Gao, Thomas W. Kirschsetter

Chemistry and Biochemistry Faculty Publications

[1] Airborne measurements of trace gases and particles over and downwind of two prescribed savanna fires in Zambia are described. The measurements include profiles through the smoke plumes of condensation nucleus concentrations and normalized excess mixing ratios of particles and gases, emission factors for 42 trace gases and seven particulate species, and vertical profiles of ambient conditions. The fires were ignited in plots of miombo woodland savanna, the most prevalent savanna type in southern Africa, and dambo grassland savanna, an important enclave of miombo woodland ecosystems. Emission factors for the two fires are combined with measurements of fuel loading, combustion …

Modeling Holistic Behavior Of Biological Systems For Analysis By Systems Theory, Steven M. Gollmer

Science and Mathematics Faculty Presentations

Due to the complexity of biological systems it is not possible to capture the richness of their interactions by purely studying the individual parts. Only a subset of all possible interactions between individual parts results in functional behavior. This restriction of functional possibilities is sometimes described as an emergent property of the system and emphasizes a holistic approach to the study of biological systems.

By using concepts from systems theory a systemic approach to modeling biological systems is possible. This approach is currently used successfully in such areas as niche theory and organism biology. This presentation looks at a framework …

Semiparametric Methods For Identification Of Tumor Progression Genes From Microarray Data, Debashis Ghosh, Arul Chinnaiyan

The University of Michigan Department of Biostatistics Working Paper Series

The use of microarray data has become quite commonplace in medical and scientific experiments. We focus here on microarray data generated from cancer studies. It is potentially important for the discovery of biomarkers to identify genes whose expression levels correlate with tumor progression. In this article, we develop statistical procedures for the identification of such genes, which we term tumor progression genes. Two methods are considered in this paper. The first is use of a proportional odds procedure, combined with false discovery rate estimation techniques to adjust for the multiple testing problem. The second method is based on order-restricted estimation …

The False Discovery Rate: A Variable Selection Perspective, Debashis Ghosh, Wei Chen, Trivellore E. Raghuanthan

The University of Michigan Department of Biostatistics Working Paper Series

In many scientific and medical settings, large-scale experiments are generating large quantities of data that lead to inferential problems involving multiple hypotheses. This has led to recent tremendous interest in statistical methods regarding the false discovery rate (FDR). Several authors have studied the properties involving FDR in a univariate mixture model setting. In this article, we turn the problem on its side; in this manuscript, we show that FDR is a by-product of Bayesian analysis of variable selection problem for a hierarchical linear regression model. This equivalence gives many Bayesian insights as to why FDR is a natural quantity to …

A Graph Theoretic Approach To Testing Associations Between Disparate Sources Of Functional Genomic Data, Raji Balasubramanian, Thomas Laframboise, Denise Scholtens, Robert Gentleman

Bioconductor Project Working Papers

The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data sources, or lack thereof, can shed light on the mechanisms that govern cellular function. A central challenge for bioinformatics research is to develop a unified framework for combining the multiple sources of functional genomics information and testing associations between them, thus obtaining a robust and integrated view of the underlying biology.

We present a graph theoretic approach to test the significance of the association between multiple disparate sources of functional genomics …

Animal Model Research: The Apples And Oranges Quandary, Kenneth J. Shapiro

Experimentation Collection

In this paper, I explore the premises underlying the problem of the evaluation of animal models. I argue that the presence of similarities and differences between the model and the modelled, although historically and currently a dominant antinomy framing evaluation, is not a bottom-line consideration. What is critical is 1) whether we learn and 2) whether we improve treatment through the animal model research. Similarity between model and modelled and the closely related concept of validity are not coterminus with these critical evaluative measures. In fact, differences between the model and modelled also can provide impetus to new understanding and …

Thickness Dependence Of Magneto-Transport In Cu-Co Granular Thin Films, Jian Qing Wang, Ngocnga Dao, Ham H. Kim, Scott L. Whittenburg

Chemistry and Biochemistry Faculty Publications

This work explores the thickness dependence of magneto-transport properties in granular thin films with different thickness. These results are compared with silver-based film series studied earlier. It was observed that the thickness dependence of the GMReffect was sensitive to the surface chemistry of the films. The extraordinary Hall effect (EHE) in these films was measured and found to be different from the Ag-based system. In the Cu-based system, the EHE is a weak function of film thickness over the range studied. When the variation of the spontaneous magnetization is taken into account the effective EHE has a universal thickness dependence

Analysis Of Phytoplankton Nutrient Limitation In Farmington Bay And The Great Salt Lake, Wayne A. Wurtsbaugh, Amy M. Marcarelli

Watershed Sciences Faculty Publications

The Great Salt Lake is bordered to the south and east by a growing metropolitan area that contributes high nutrients to Farmington Bay. This large bay is eutrophic, and there is concern that continued increases in effluents from the Salt Lake City area could extend to impact the much larger, and currently less productive, Gilbert Bay. This study focused on determining how nutrient supplies might limit, and therefore control, algal populations in Farmington Bay and Gilbert Bay at different salinities. We tested both short and long-term responses of algal growth using laboratory nutrient addition bioassays in the summer and fall …

Development Of Web Tools For Nlx Simulation Software, Daniel Chai Siriphongs

Loma Linda University Electronic Theses, Dissertations & Projects

Valuable mathematical equations have developed within biology and other sciences (physics, chemistry, etc.) that model various processes, but the complexity of the equations are not easily understood by students, scientists, and those with limited knowledge of the subject area. Simulation software used to visually explain a model is normally proprietary to the specific model equations and cannot be easily adapted to new models by non-programmers. Simulation software needs to be modular and based upon web technologies so that the software can be run on multiple platforms. The NLX simulation software is a group of Java-based objects that can be combined …

Evaluating Recruitment Of American Eel, Anguilla Rostrata, To The Potomac River Spring 2004, Marcel M. Montane, Wendy A. Lowery, Hank Brooks, Aimee D. Halvorson

Reports

The Atlantic States Marine Fisheries Commission (ASMFC) adopted the Interstate Fishery Management Plan (FMP) for the American eel in November 1999. The FMP focuses on increasing the states’ efforts to collect data on the resource and the fishery it supports through both fishery dependent and fishery independent studies. To this end, member jurisdictions (including the PRFC) agreed to implement an annual abundance survey for young of year (YOY) American eels. The survey is intended to “…characterize trends in annual recruitment of young of year eels over time [to produce a] qualitative appraisal of the annual recruitment of American eel to …

Status Of The Major Oyster Diseases In Virginia 2003 A Summary Of The Annual Monitoring Program, Ryan Carnegie, Lisa M. Ragone Calvo, Eugene M. Burreson

Reports

Low temperatures and salinities brought abatement in the oyster diseases caused by Perkinsus marinus (Dermo) and Haplosporidium nelsoni (MSX) for the first time since 1998. In the James River, P. marinus prevalences were the lowest they had been since 1998. In summer and fall, when P. marinus is normally most prevalent, it was found in a maximum of 72% of oysters at Wreck Shoal and in less than half the oysters at Horsehead Rock and Point of Shoals. Advanced infections were very rare. Haplosporidium nelsoni had disappeared completely from quarterly James River samples by July

The Prairie Naturalist Volume 36, No.2 June 2004

The Prairie Naturalist

PREDICTING NEONATAL AGE OF WHITE-TAILED DEER IN THE NORTHERN GREAT PLAINS . . T. J. Brinkman, K. L. Monteith, J. A. Jenks, and C. S. DePemo

DUCK NESTING ON ROTATIONAL AND CONTINUOUS GRAZED PASTURES IN NORTH DAKOTA . R. K. Murphy, D. J. Schindler, and R. D. Crawford

MORPHOLOGY OF LESSER PRAIRIE-CHICKENS IN KANSAS ▪ C. A. Hagen, J. C. Pitman, R. J. Robel, and R. D. Applegate

DAILY AND SEASONAL BEHAVIOR OF BISON ON AN OKLAHOMA TALLGRASS PRAIRIE . E. J. Maichak, K. L. Schuler, and M. E. Payton

CHRISTMAS BIRD COUNTS FOR NORTH DAKOTA 2003 ▪ R. N. …

Sweto: Large-Scale Semantic Web Test-Bed, Boanerges Aleman-Meza, Chris Halaschek, Amit P. Sheth, I. Budak Arpinar, Gowtham Sannapareddy

Kno.e.sis Publications

The emergent Semantic Web community needs a common infrastructure for testing the scalability and quality of new techniques and software which use machine processable data. Since ontologies are a centerpiece of most approaches, we believe that for an accurate evaluation of tools for quality, scalability and performance, the research community needs a freely available ontology with a large description base. If the use of tools is to be for advanced semantic applications, such as those in business intelligence and national security, then instances in the knowledge base should be highly interconnected. Thus, we propose and describe a Semantic WEb Technology …

Science-Based Organic Farming: A Resource For Educators, Charles A. Francis, Mindi Schneider, Brad Kindler

Publications from the Center for Applied Rural Innovation (CARI)

Organic farming is an important and growing part of the United States food system. The organic sector has grown by at least 20% per year for the past two decades, and currently shows no indication of slowing in this growth. There is increasing consumer concern about where and how food is produced, and people want to be assured access to safe and healthy food products. Interest and concern about food security, and discussion about the merits of a local food system as compared to the vulnerable globalized marketplace are also becoming increasingly important. In Nebraska we have only limited local …

Impactos Da Exploração Madeireira E Do Fogo Em Florestas De Transição Da Amazônia Legal, André Luiz Silva Monteiro, Carlos Moreira De Souza Jr., Paulo Gonçalves Barreto, Frank Leone De Sousa Pantoja, Jeffrey J. Gerwing

Environmental Science and Management Faculty Publications and Presentations

A exploração de madeira e os incendios têm causado severos danos a florestas na Amazonia. Faltavam estudos sobre os impactos da exploração e do fogo em florestas de transição entre a floresta ombrófila densa e florestas de cerrado. Neste estudo, foram quantificados os impactos de várias intensidades de exploração madeireira e fogo na estrutura e composição de florestas de transição -- em termos de densidade de árvores e de cipós, cobertura do dossel e perturbação do solo e da biomassa acima do solo -- na regiao de Claudia, Mato Grosso. O estudo foi conduzido em 12 propriedades, através de inventários …

Relative Validity Of A Food Frequency Questionnaire Used To Assess Food And Nutrient Intake In A Dietary Intervention Study, Gina Segovia Siapco

Loma Linda University Electronic Theses, Dissertations & Projects

Food frequency questionnaire is a cost effective alternative for measuring dietary intake when conducting large scale surveys. We investigated the validity of a 171-item semi-quantitative food frequency questionnaire in assessing food and nutrient intakes and the prescribed intervention measure during a randomized field trial. Eighty-seven free-living adults (48 females and 39 males) aged 30-72 years provided dietary information by self-administering the Walnut Study Dietary Assessment Questionnaire (WSDAQ), which assessed intake over the past six months, and through seven unannounced non-consecutive 24-hour dietary recalls by telephone. Participants were randomly assigned to either a walnut or habitual diet at baseline. For six …

Food Based Approaches For A Healthy Nutrition In Africa, Mamoudou Hama Dicko

Pr. Mamoudou H. DICKO, PhD

The latest estimates of the FAO demonstrate the problems of the fight against hunger. These problems are manifested by the ever-increasing number of chronically undernourished people worldwide. Their numbers during the 1999-2001 period were estimated at about 840 million of which 798 million live in developing countries. Sub-Saharan Africa alone represented 198 million of those. In this part of Africa the prevalence of undernourishment ranges from 5-34%, causing growth retardation and insufficient weight gain among one third of the children under five years of age and resulting in a mortality of 5-15% among these children. Malnutrition resulting from undernourishment is …

Statistical Analyses And Reproducible Research, Robert Gentleman, Duncan Temple Lang

Bioconductor Project Working Papers

For various reasons, it is important, if not essential, to integrate the computations and code used in data analyses, methodological descriptions, simulations, etc. with the documents that describe and rely on them. This integration allows readers to both verify and adapt the statements in the documents. Authors can easily reproduce them in the future, and they can present the document's contents in a different medium, e.g. with interactive controls. This paper describes a software framework for authoring and distributing these integrated, dynamic documents that contain text, code, data, and any auxiliary content needed to recreate the computations. The documents are …