A Template-Based Data Specification Framework For Modeling Physical Security Systems

Simulation studies often fail to provide any useful results due to its success being highly dependent on the skills of the analyst to understand a system and then correctly identify all the required data parameters and dependent variables. This paper describes a template-based framework to help identify and specify the components and data parameters for developing models of physical security systems. The layered framework consists of fifteen templates built on top of fourteen data primitives representing 119 data parameters. The modeling framework has been programmed as an internet-based web application and is simulation language independent. The usefulness of the framework was tested and shown to have a significant impact on improving the identification of system components and their associated data parameter

Functional Evolution of PLP-dependent Enzymes based on Active-Site Structural Similarities

Families of distantly related proteins typically have very low sequence identity, which hinders evolutionary analysis and functional annotation. Slowly evolving features of proteins, such as an active site, are therefore valuable for annotating putative and distantly related proteins. To date, a complete evolutionary analysis of the functional relationship of an entire enzyme family based on active-site structural similarities has not yet been undertaken. Pyridoxal-5’-phosphate (PLP) dependent enzymes are primordial enzymes that diversified in the last universal ancestor. Using the Comparison of Protein Active Site Structures (CPASS) software and database, we show that the active site structures of PLP-dependent enzymes can be used to infer evolutionary relationships based on functional similarity. The enzymes successfully clustered together based on substrate specificity, function, and three-dimensional fold. This study demonstrates the value of using active site structures for functional evolutionary analysis and the effectiveness of CPASS

ISPTM: an Iterative Search Algorithm for Systematic Identification of Post-translational Modifications from Complex Proteome Mixtures

Identifying protein post-translational modifications (PTMs) from tandem mass spectrometry data of complex proteome mixtures is a highly challenging task. Here we present a new strategy, named iterative search for identifying PTMs (ISPTM), for tackling this challenge. The ISPTM approach consists of a basic search with no variable modification, followed by iterative searches of many PTMs using a small number of them (usually two) in each search. The performance of the ISPTM approach was evaluated on mixtures of 70 synthetic peptides with known modifications, on an 18-protein standard mixture with unknown modifications and on real, complex biological samples of mouse nuclear matrix proteins with unknown modifications. ISPTM revealed that many chemical PTMs were introduced by urea and iodoacetamide during sample preparation and many biological PTMs, including dimethylation of arginine and lysine, were significantly activated by Adriamycin treatment in NM associated proteins. ISPTM increased the MS/MS spectral identification rate substantially, displayed significantly better sensitivity for systematic PTM identification than the conventional all-in-one search approach and offered PTM identification results that were complementary to InsPecT and MODa, both of which are established PTM identification algorithms. In summary, ISPTM is a new and powerful tool for unbiased identification of many different PTMs with high confidence from complex proteome mixtures

Science Literacy: Using Research-Based Facts to Make Real-World Decisions

Science Literacy: Using Research-Based Facts to Make Real-World Decisions As the next generation of leaders is entering the educational pipeline, it’s important to have an emphasis on science, technology, engineering and mathematics (STEM) to solve the grand challenge of feeding 9 billion people by 2050

Searching the protein structure database for ligand-binding site similarities using CPASS v.2

<p>Abstract</p> <p>Background</p> <p>A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as "hypothetical" or "uncharacterized" protein. Our Comparison of Protein Active-Site Structures (CPASS v.2) database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR) protocol and has been successfully applied to aid the annotation of a number of proteins of unknown function.</p> <p>Findings</p> <p>We report a major upgrade to our CPASS software and database that significantly improves its broad utility. CPASS v.2 is designed with a layered architecture to increase flexibility and portability that also enables job distribution over the Open Science Grid (OSG) to increase speed. Similarly, the CPASS interface was enhanced to provide more user flexibility in submitting a CPASS query. CPASS v.2 now allows for both automatic and manual definition of ligand-binding sites and permits pair-wise, one versus all, one versus list, or list versus list comparisons. Solvent accessible surface area, ligand root-mean square difference, and Cβ distances have been incorporated into the CPASS similarity function to improve the quality of the results. The CPASS database has also been updated.</p> <p>Conclusions</p> <p>CPASS v.2 is more than an order of magnitude faster than the original implementation, and allows for multiple simultaneous job submissions. Similarly, the CPASS database of ligand-defined binding sites has increased in size by ~ 38%, dramatically increasing the likelihood of a positive search result. The modification to the CPASS similarity function is effective in reducing CPASS similarity scores for false positives by ~30%, while leaving true positives unaffected. Importantly, receiver operating characteristics (ROC) curves demonstrate the high correlation between CPASS similarity scores and an accurate functional assignment. As indicated by distribution curves, scores ≥ 30% infer a functional similarity. Software URL: <url>http://cpass.unl.edu</url>.</p

A template-based conceptual modeling infrastructure for simulation of physical security systems

Although simulation is one of the most innovative and cost-effective tools for modeling and analyzing a system, simulation studies often fail to provide any useful results. One reason is attributed to the fact that model formulation depends on the skills of the analyst. This paper describes a research to develop a conceptual modeling infrastructure to assist a simulation analyst in specifying components for studying physical security systems. The modeling framework has been programmed as an internet-based web application. Using the application, the successful development and implementation of a physical security simulation model will be aided by a defined scientific methodology rather than simply the skills of the analyst. Further the modeling framework is simulation language independent, thus allowing for a top-down or bottom-up approach to developing the conceptual model. This offers support for an object-oriented modeling design

A template-based approach for simulation model specification of physical security systems

Although simulation is one of the most innovative and cost-effective tools for modeling and analyzing a system, simulation studies often fail to provide any useful results. One reason is attributed to the fact that model formulation depends on the skills of the analyst and her domain knowledge of the system under study. The objective of this research is to develop a conceptual modeling framework to assist a simulation analyst in specifying components for studying physical security systems. By doing so it is expected to make simulation less modeler dependent. The described work resulted in development of a layered, modeling language independent framework with a total of 15 templates built on top of 14 primitives having 119 parameters. The modeling framework has been programmed as an internet-based web application and is simulation language independent. It allows for a top-down or bottom-up approach in developing the conceptual model. The usefulness of the framework is evaluated empirically through 45 participants having undergraduate and graduate level background in Industrial Engineering. It was found that conceptual models developed by the participants failed to identify at least 82% of the parameters when compared to the conceptual models developed using the web application of the developed framework

A web-based interface for storing and executing simulation model

The dominance of the Internet in the development ofinformation and communication technology has madeWeb-based distributed solutions increasingly attractive.Apart from providing other services, the World Wide Webis being looked upon as an environment for hostingmodeling and simulation applications. SIMAN is asimulation language that allows users to simulate discreteand continuous systems. In this research, a web-basedinterface or toolkit has been developed for storing andexecuting SIMAN simulation models over the Internet.This toolkit consists of a World Wide Web interface toSIMAN and a web-accessible database for storing usermodels. It provides users an easy-to-use environment fordeveloping text-based simulation models using the SIMANsimulation language. It also allows users to test thefunctionality of a SIMAN model using the SIMANdebugger/run controller

Correlation Using the R Statistical Package - Part 3: R Functions and Scripts

Objectives In this lesson module we will calculate the correlation coefficient between one of the Canopy Spectral Reflectance (CSR) indices with yield and/or yield components under water stressed and non-stressed treatments in 300 winter wheat lines. As we analyze one aspect of the recorded data we will demonstrate the concepts of R programming and computational thinking to accomplish this goal. After completing this lesson, you will be able to: 1. Prepare experimental data for analysis using the R functions. 2. Using R and actual data, calculate correlation coefficient values. 3. Demonstrate how to use Computational Thinking for problem-solving in a typical domain scenario in a plant breeding experiment. Modules: Lesson home Objectives The R Functions The R Script Summary Video

Correlation Using the R Statistical Package - Part 3: R Functions and Scripts

Objectives In this lesson module we will calculate the correlation coefficient between one of the Canopy Spectral Reflectance (CSR) indices with yield and/or yield components under water stressed and non-stressed treatments in 300 winter wheat lines. As we analyze one aspect of the recorded data we will demonstrate the concepts of R programming and computational thinking to accomplish this goal. After completing this lesson, you will be able to: 1. Prepare experimental data for analysis using the R functions. 2. Using R and actual data, calculate correlation coefficient values. 3. Demonstrate how to use Computational Thinking for problem-solving in a typical domain scenario in a plant breeding experiment. Modules: Lesson home Objectives The R Functions The R Script Summary Video