Physical Sciences and Mathematics Commons^™

Long-Read Sequencing Of The Zebrafish Genome Reorganizes Genomic Architecture, Yelena Chernyavskaya, Xiaofei Zhang, Jinze Liu, Jessica Blackburn

Biostatistics Publications

Background

Nanopore sequencing technology has revolutionized the field of genome biology with its ability to generate extra-long reads that can resolve regions of the genome that were previously inaccessible to short-read sequencing platforms. Over 50% of the zebrafish genome consists of difficult to map, highly repetitive, low complexity elements that pose inherent problems for short-read sequencers and assemblers.

Results

We used long-read nanopore sequencing to generate a de novo assembly of the zebrafish genome and compared our assembly to the current reference genome, GRCz11. The new assembly identified 1697 novel insertions and deletions over one kilobase in length and placed …

Mass Grave Localization Prediction With Geographical Information Systems In Guatemala And Future Impacts, Perla Santillan

Master of Science in Forensic Science Directed Research Projects

Conducting physical searches for mass grave locations based on anecdotal evidence is a time consuming and resource intensive endeavor in circumstances that often pose a threat to personal safety. The development of tools and procedures to speed such searches can greatly reduce the risk involved, increase the number of individuals whose remains are recovered and identified; and, more importantly, reunite these remains with their loved ones to provide them with a proper burial. Geographic information systems (GIS) software, which can analyze and manipulate the spatial characteristics of known mass grave data, represents a powerful tool that can be used to …

The Effect Of Time And Temperature On The Quality Of Latent Fingerprints On Incandescent Lightbulbs, Varying Donors Age And Sex, Kinaysha M. Collazo Maldonado

Master of Science in Forensic Science Directed Research Projects

Fingerprints are used as a means of identification, but there are no established methodologies to determine time since deposition of latent fingerprints by visual means alone. This research considered the influence of age and sex on the quality of recovered latent prints from lit and unlit lightbulbs from 1 to 10 days, using accumulated degree hours (ADH) to account for both heat and time simultaneously. Two male and two female donors (one of each aged40 years) were used. A thermal imaging camera was used to monitor the lightbulbs top and middle regions, which were significantly different (p≤0.05) for the experimental …

The Support Vector Machine And Mixed Integer Linear Programming: Ramp Loss Svm With L1-Norm Regularization, Eric J. Hess, J. Paul Brooks

Statistical Sciences and Operations Research Publications

The support vector machine (SVM) is a flexible classification method that accommodates a kernel trick to learn nonlinear decision rules. The traditional formulation as an optimization problem is a quadratic program. In efforts to reduce computational complexity, some have proposed using an L1-norm regularization to create a linear program (LP). In other efforts aimed at increasing the robustness to outliers, investigators have proposed using the ramp loss which results in what may be expressed as a quadratic integer programming problem (QIP). In this paper, we consider combining these ideas for ramp loss SVM with L1-norm regularization. The result is four …

Principal Component Analysis And Optimization: A Tutorial, Robert Reris, J. Paul Brooks

Statistical Sciences and Operations Research Publications

No abstract provided.

Firing Rate Dynamics In Recurrent Spiking Neural Networks With Intrinsic And Network Heterogeneity, Cheng Ly

Statistical Sciences and Operations Research Publications

Heterogeneity of neural attributes has recently gained a lot of attention and is increasing recognized as a crucial feature in neural processing. Despite its importance, this physiological feature has traditionally been neglected in theoretical studies of cortical neural networks. Thus, there is still a lot unknown about the consequences of cellular and circuit heterogeneity in spiking neural networks. In particular, combining network or synaptic heterogeneity and intrinsic heterogeneity has yet to be considered systematically despite the fact that both are known to exist and likely have significant roles in neural network dynamics. In a canonical recurrent spiking neural network model, …

R Code To Accompany “Principal Component Analysis And Optimization: A Tutorial”, Robert Reris, J. Paul Brooks

Statistical Sciences and Operations Research Data

This data accompanies "Principal Component Analysis and Optimization: A Tutorial" by Robert Reris and J. Paul Brooks, presented at the 2015 INFORMS Computing Society Conference, Operations Research and Computing: Algorithms and Software for Analytics, Richmond, Virginia January 11-13, 2015.

The data contains R code, output, and comments that follow the examples for principal component analysis in the paper.

Data Files To Accompany "The Support Vector Machine And Mixed Integer Linear Programming: Ramp Loss Svm With L1-Norm Regularization", Eric J. Hess, J. Paul Brooks

Statistical Sciences and Operations Research Data

These files accompany, "The Support Vector Machine and Mixed Integer Linear Programming: Ramp Loss SVM with L1-Norm Regularization" by Eric J. Hess and J. Paul Brooks, presented at the 2015 INFORMS Computing Society Conference, Operations Research and Computing: Algorithms and Software for Analytics, Richmond, Virginia January 11-13, 2015.

The files contain instances of optimization problems that are described in the paper and for which results are reported. The files are in CPLEX LP format. The naming convention of the files is as follows: ndBTj0F.lp, where is the number of samples, is the number of attributes, and refers to …

Hypothesis Testing And Power Calculations For Taxonomic-Based Human Microbiome Data, P. S. Larossa, J. Paul Brooks, Elena Deych, Edward L. Boone, David J. Edwards, Qin Wang, Erica Sodergren, George Weinstock, William D. Shannon

Statistical Sciences and Operations Research Publications

This paper presents new biostatistical methods for the analysis of microbiome data based on a fully parametric approach using all the data. The Dirichlet-multinomial distribution allows the analyst to calculate power and sample sizes for experimental design, perform tests of hypotheses (e.g., compare microbiomes across groups), and to estimate parameters describing microbiome properties. The use of a fully parametric model for these data has the benefit over alternative non-parametric approaches such as bootstrapping and permutation testing, in that this model is able to retain more information contained in the data. This paper details the statistical approaches for several tests of …

Is Screening Cargo Containers For Smuggled Nuclear Threats Worthwhile?, Jason R. W. Merrick, Laura A. Mclay

Statistical Sciences and Operations Research Publications

In recent years, Customs and Border Protection (CBP) has installed radiation sensors to screen cargo containers entering theUnited States. They are concerned that terrorists could use containers to smuggle radiological material into the country and carry out attacks with dirty bombs or a nuclear device. Recent studies have questioned the value of improving this screening system with new sensor technology. The cost of delays caused by frequent false alarms outweighs any reduction in the probability of an attack in an expected cost analysis. We extend existing methodology in three ways to demonstrate how additional factors affect the value of screening …