Physical Sciences and Mathematics Commons^™

Model Checking For Roc Regression Analysis, Tianxi Cai, Yingye Zheng

Harvard University Biostatistics Working Paper Series

The Receiver Operating Characteristic (ROC) curve is a prominent tool for characterizing the accuracy of continuous diagnostic test. To account for factors that might invluence the test accuracy, various ROC regression methods have been proposed. However, as in any regression analysis, when the assumed models do not fit the data well, these methods may render invalid and misleading results. To date practical model checking techniques suitable for validating existing ROC regression models are not yet available. In this paper, we develop cumulative residual based procedures to graphically and numerically assess the goodness-of-fit for some commonly used ROC regression models, and …

Expert Testimony In Capital Sentencing: Juror Responses, John H. Montgomery, J. Richard Ciccone, Stephen P. Garvey, Theodore Eisenberg

Cornell Law Faculty Publications

The U.S. Supreme Court, in Furman v. Georgia (1972), held that the death penalty is constitutional only when applied on an individualized basis. The resultant changes in the laws in death penalty states fostered the involvement of psychiatric and psychologic expert witnesses at the sentencing phase of the trial, to testify on two major issues: (1) the mitigating factor of a defendant’s abnormal mental state and (2) the aggravating factor of a defendant’s potential for future violence. This study was an exploration of the responses of capital jurors to psychiatric/psychologic expert testimony during capital sentencing. The Capital Jury Project is …

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 …

2005 Scholars And Artists Bibliography, Stephen D. Slane Dr., Michael Schwartz Library, Cleveland State University, Friends Of The Michael Schwartz Library

Scholars and Artists Bibliographies

This bibliography was created for the annual Friends of the Michael Schwartz Library Scholars and Artists Reception, recognizing scholarly and creative achievements of Cleveland State University faculty, staff and emeriti. Dr, Steve Slane was the guest speaker.

Population Intervention Models In Causal Inference, Alan E. Hubbard, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

Marginal structural models (MSM) provide a powerful tool for estimating the causal effect of a] treatment variable or risk variable on the distribution of a disease in a population. These models, as originally introduced by Robins (e.g., Robins (2000a), Robins (2000b), van der Laan and Robins (2002)), model the marginal distributions of treatment-specific counterfactual outcomes, possibly conditional on a subset of the baseline covariates, and its dependence on treatment. Marginal structural models are particularly useful in the context of longitudinal data structures, in which each subject's treatment and covariate history are measured over time, and an outcome is recorded at …

Gauss-Seidel Estimation Of Generalized Linear Mixed Models With Application To Poisson Modeling Of Spatially Varying Disease Rates, Subharup Guha, Louise Ryan

Harvard University Biostatistics Working Paper Series

Generalized linear mixed models (GLMMs) provide an elegant framework for the analysis of correlated data. Due to the non-closed form of the likelihood, GLMMs are often fit by computational procedures like penalized quasi-likelihood (PQL). Special cases of these models are generalized linear models (GLMs), which are often fit using algorithms like iterative weighted least squares (IWLS). High computational costs and memory space constraints often make it difficult to apply these iterative procedures to data sets with very large number of cases.

This paper proposes a computationally efficient strategy based on the Gauss-Seidel algorithm that iteratively fits sub-models of the GLMM …

Computational Techniques For Spatial Logistic Regression With Large Datasets, Christopher J. Paciorek, Louise Ryan

Harvard University Biostatistics Working Paper Series

In epidemiological work, outcomes are frequently non-normal, sample sizes may be large, and effects are often small. To relate health outcomes to geographic risk factors, fast and powerful methods for fitting spatial models, particularly for non-normal data, are required. We focus on binary outcomes, with the risk surface a smooth function of space. We compare penalized likelihood models, including the penalized quasi-likelihood (PQL) approach, and Bayesian models based on fit, speed, and ease of implementation.

A Bayesian model using a spectral basis representation of the spatial surface provides the best tradeoff of sensitivity and specificity in simulations, detecting real spatial …

Is The Number Of Sick Persons In A Cohort Constant Over Time?, Paula Diehr, Ann Derleth, Anne Newman, Liming Cai

UW Biostatistics Working Paper Series

Objectives: To estimate the number of persons in a cohort who are sick, over time.

Methods: We calculated the number of sick persons in the Cardiovascular Health Study (CHS), a cohort study of older adults followed up to 14 years, using eight definitions of “healthy” and “sick”. We projected the number in each health state over time for a birth cohort.

Results: The number of sick persons in CHS was approximately constant for 14 years, for all definitions of “sick”. The estimated number of sick persons in the birth cohort was approximately constant from ages 55-75, after which it decreased. …

A Nonstationary Negative Binomial Time Series With Time-Dependent Covariates: Enterococcus Counts In Boston Harbor, E. Andres Houseman, Brent Coull, James P. Shine

Harvard University Biostatistics Working Paper Series

Boston Harbor has had a history of poor water quality, including contamination by enteric pathogens. We conduct a statistical analysis of data collected by the Massachusetts Water Resources Authority (MWRA) between 1996 and 2002 to evaluate the effects of court-mandated improvements in sewage treatment. Motivated by the ineffectiveness of standard Poisson mixture models and their zero-inflated counterparts, we propose a new negative binomial model for time series of Enterococcus counts in Boston Harbor, where nonstationarity and autocorrelation are modeled using a nonparametric smooth function of time in the predictor. Without further restrictions, this function is not identifiable in the presence …

Synthesis Of Lanthanum-Strontium Magnanites By A Hydroxide-Precursor Co-Precipitation Method In Solution And In Reverse Micellar Microemulsion, Vuk Uskoković, Darko Makovec, Miha Drofenik

Pharmacy Faculty Articles and Research

Nanostructured lanthanum-strontium manganites have been synthesized using two different co-precipitation approaches, one in bulk solution, and the other in reverse micelles of CTAB/1-hexanol/1-butanol/water microemulsion. In both cases, precursor cations were precipitated by alkali precipitating agents. The properties of the material synthesized by using these two methods were compared in order to reveal potential advantages of microemulsion-assisted approach. The influence of the annealing conditions on the properties of synthesized manganites was investigated by using X-ray diffraction, transmission electron microscopy, differential thermal analysis, thermogravimetric analysis and magnetic measurements.

Direct Effect Models, Mark J. Van Der Laan, Maya L. Petersen

U.C. Berkeley Division of Biostatistics Working Paper Series

The causal effect of a treatment on an outcome is generally mediated by several intermediate variables. Estimation of the component of the causal effect of a treatment that is mediated by a given intermediate variable (the indirect effect of the treatment), and the component that is not mediated by that intermediate variable (the direct effect of the treatment) is often relevant to mechanistic understanding and to the design of clinical and public health interventions. Under the assumption of no-unmeasured confounders for treatment and the intermediate variable, Robins & Greenland (1992) define an individual direct effect as the counterfactual effect of …

Effects Of Information And Machine Learning Algorithms On Word Sense Disambiguation With Small Datasets, Gondy Leroy, Thomas C. Rindflesch

CGU Faculty Publications and Research

Current approaches to word sense disambiguation use (and often combine) various machine learning techniques. Most refer to characteristics of the ambiguity and its surrounding words and are based on thousands of examples. Unfortunately, developing large training sets is burdensome, and in response to this challenge, we investigate the use of symbolic knowledge for small datasets. A naïve Bayes classifier was trained for 15 words with 100 examples for each. Unified Medical Language System (UMLS) semantic types assigned to concepts found in the sentence and relationships between these semantic types form the knowledge base. The most frequent sense of a word …

Summer 2005 Research Symposium Abstract Book, Trinity College

Science Symposia Abstracts

Summer 2005 volume of abstracts for science research projects conducted by Trinity College students.

Development Of Dose Conversion Coefficients For Radionuclides Produced In Spallation Neutron Sources Quarterly Progress Report 4/01/05 – 6/30/05, Phillip W. Patton, Mark Rudin

Transmutation Sciences Physics (TRP)

The research consortium comprised of representatives from several universities and national laboratories has successfully generated internal and external dose conversion coefficients for twenty radionuclides produced in spallation neutron sources. These dose coefficients fill data gaps exist in Federal Guide Report No. 11 and in Publications 68 and 72 of the International Commission on Radiological Protection (ICRP), and two articles containing the data have been accepted for publication in the Journal of Health Physics. Currently, more nuclear data is needed for the rare radionuclides produced from a mercury target. While attempting to develop a workable plan to acquire this missing data, …

Weast Nile Virus Serosurveillance In Iowa White-Tailed Deer (1999-2003), Julian Santatella, Robert Mclean, Jeffrey S. Hall, James S. Gill, Richard A. Bowen, Harlo H. Hadow, Larry Clark

USDA Wildlife Services: Staff Publications

Sera from white-tailed deer (Odocoileus virginianus) were collected in Iowa during the winter months (1999-2003), 2 years before and after West Nile virus (WNV) was first reported in Iowa (2001), and were analyzed for antibodies to WNV. Samples from 1999 to 2001 were antibody negalive by blocking enzyme-linikedI immunosorbent assay (bELISA) and plaque reduction neutralization test (PRNT₉₀). Prevalence derived from bELISA (2002, 12.7%; 2003. 11.2%) and WNV PRNT₉₀ (2002,7.9%; 2003, 8.5%) assays were similar. All sanlples were negative for antibodies against St. Louis encephalitis virus as determined by PRNT₉₀. Antibodies to flaviviruses were …

Attributable Risk Function In The Proportional Hazards Model, Ying Qing Chen, Chengcheng Hu, Yan Wang

UW Biostatistics Working Paper Series

As an epidemiological parameter, the population attributable fraction is an important measure to quantify the public health attributable risk of an exposure to morbidity and mortality. In this article, we extend this parameter to the attributable fraction function in survival analysis of time-to-event outcomes, and further establish its estimation and inference procedures based on the widely used proportional hazards models. Numerical examples and simulations studies are presented to validate and demonstrate the proposed methods.

Prognosis Of Stage Ii Colon Cancer By Non-Neoplastic Mucosa Gene Expresssion Profiling, Alain Barrier, Sandrine Dudoit, Et Al.

U.C. Berkeley Division of Biostatistics Working Paper Series

Aims. This study assessed the possibility to build a prognosis predictor, based on non-neoplastic mucosa microarray gene expression measures, in stage II colon cancer patients. Materials and Methods. Non-neoplastic colonic mucosa mRNA samples from 24 patients (10 with a metachronous metastasis, 14 with no recurrence) were profiled using the Affymetrix HGU133A GeneChip. The k-nearest neighbor method was used for prognosis prediction using microarray gene expression measures. Leave-one-out cross-validation was used to select the number of neighbors and number of informative genes to include in the predictor. Based on this information, a prognosis predictor was proposed and its accuracy estimated by …

Colon Cancer Prognosis Prediction By Gene Expression Profiling, Alain Barrier, Sandrine Dudoit, Et Al.

U.C. Berkeley Division of Biostatistics Working Paper Series

Aims. This study assessed the possibility to build a prognosis predictor, based on microarray gene expression measures, in stage II and III colon cancer patients. Materials and Methods. Tumour (T) and non-neoplastic mucosa (NM) mRNA samples from 18 patients (9 with a recurrence, 9 with no recurrence) were profiled using the Affymetrix HGU133A GeneChip. The k-nearest neighbour method was used for prognosis prediction using T and NM gene expression measures. Six-fold cross-validation was applied to select the number of neighbours and the number of informative genes to include in the predictors. Based on this information, one T-based and one NM-based …

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 …

Relationships Between Environmental Factors And Fungi On Occupants' Perceptions Of Indoor Air Quality, Monica Rodriguez

Masters Theses & Specialist Projects

In recent decades, concerns about potential health effects resulting from exposure to contaminants that cause indoor air pollution have dramatically increased. The purpose of this study was to assess the indoor air quality of three buildings at Western Kentucky University and to examine and characterize indoor levels of basic comfort parameters, carbon dioxide, and fungi as well as occupants' perceptions of poor indoor air quality and the role of fungi on reported health symptoms. The three buildings included in the study were: Tate Page Hall (TPH), Jones Jagger Hall (JJH) and Science and Technology Hall (STH). Fifty-three questionnaires were completed …

Exposure Assessment Of Mercury In Fish From Kentucky Surface Waters, Najla Gubari

Masters Theses & Specialist Projects

Consumption of fish contaminated with mercury is the primary exposure pathway by which humans are exposed to mercury. Mercury is known to be a neurological toxin that can cause attention and language deficits, impaired memory, and impaired visual and motor function, especially in children under the age of six. In addition, mercury exposure can lead to other health problems in adults, such as damage to the kidney and increased risk of coronary heart disease. This study assesses the exposure to mercury through consumption of fish from Kentucky surface waters. The exposure assessment is based on data collected by the Kentucky …

Causal Inference In Longitudinal Studies With History-Restricted Marginal Structural Models, Romain Neugebauer, Mark J. Van Der Laan, Ira B. Tager

U.C. Berkeley Division of Biostatistics Working Paper Series

Causal Inference based on Marginal Structural Models (MSMs) is particularly attractive to subject-matter investigators because MSM parameters provide explicit representations of causal effects. We introduce History-Restricted Marginal Structural Models (HRMSMs) for longitudinal data for the purpose of defining causal parameters which may often be better suited for Public Health research. This new class of MSMs allows investigators to analyze the causal effect of a treatment on an outcome based on a fixed, shorter and user-specified history of exposure compared to MSMs. By default, the latter represents the treatment causal effect of interest based on a treatment history defined by the …

The Sensitivity And Specificity Of Markers For Event Times, Tianxi Cai, Margaret S. Pepe, Thomas Lumley, Yingye Zheng, Nancy Swords Jenny

Harvard University Biostatistics Working Paper Series

No abstract provided.

2005 Annual Research Symposium Abstract Book, Trinity College

Science Symposia Abstracts

2005 annual volume of abstracts for science research projects conducted by students at Trinity College.

A Mathematical Model For Treatment-Resistant Mutations Of Hiv, Helen Moore, Weiqing Gu

All HMC Faculty Publications and Research

In this paper, we propose and analyze a mathematical model, in the form of a system of ordinary differential equations, governing mutated strains of human immunodeficiency virus (HIV) and their interactions with the immune system and treatments. Our model incorporates two types of resistant mutations: strains that are not responsive to protease inhibitors, and strains that are not responsive to reverse transcriptase inhibitors. It also includes strains that do not have either of these two types of resistance (wild-type virus) and strains that have both types. We perform our analysis by changing the system of ordinary differential equations (ODEs) to …

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 …

Development Of Dose Conversion Coefficients For Radionuclides Produced In Spallation Neutron Sources Quarterly Progress Report 1/1/05 – 3/31/05, Phillip W. Patton, Mark Rudin

Transmutation Sciences Physics (TRP)

The research consortium comprised of representatives from several universities and national laboratories has successfully generated internal and external dose conversion coefficients for twenty radionuclides produced in spallation neutron sources. In addition, the group has identified twenty radionuclide that are missing electron capture files and eighteen additional radionuclides missing substantial physical data. The goal for the current year is to develop a methodology that will allow for producing the dose coefficients for these radionuclides with missing data. Methods to obtain these data are being investigated.

Acute Toxicity Testing Without Animals: More Scientific And Less Of A Gamble, Gillian R. Langley

Application of Alternative Methods Collection

In this report, we argue specifically that acute toxicity data should not be sought from animal tests. The underlying principle of such tests on rats and mice is that the results can be effectively extrapolated to humans. In fact, after nearly 80 years of use of these tests, the predictivity of rodent data for human acute toxic effects has been disputed but never proven.

Against 'Individual Risk': A Sympathetic Critique Of Risk Assessment, Matthew D. Adler

All Faculty Scholarship

"Individual risk" currently plays a major role in risk assessment and in the regulatory practices of the health and safety agencies that employ risk assessment, such as EPA, FDA, OSHA, NRC, CPSC, and others. Risk assessors use the term "population risk" to mean the number of deaths caused by some hazard. By contrast, "individual risk" is the incremental probability of death that the hazard imposes on some particular person. Regulatory decision procedures keyed to individual risk are widespread. This is true both for the regulation of toxic chemicals (the heartland of risk assessment), and for other health hazards, such as …

Insights Into Latent Class Analysis, Margaret S. Pepe, Holly Janes

UW Biostatistics Working Paper Series

Latent class analysis is a popular statistical technique for estimating disease prevalence and test sensitivity and specificity. It is used when a gold standard assessment of disease is not available but results of multiple imperfect tests are. We derive analytic expressions for the parameter estimates in terms of the raw data, under the conditional independence assumption. These expressions indicate explicitly how observed two- and three-way associations between test results are used to infer disease prevalence and test operating characteristics. Although reasonable if the conditional independence model holds, the estimators have no basis when it fails. We therefore caution against using …