Ashu Guru

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 Web-based interface for storing and executing simulation models

The dominance of the Internet in the development of information and communication technology has made Web-based distributed solutions increasingly attractive. Apart from providing other services, the World Wide Web is being looked upon as an environment for hosting modeling and simulation applications. SIMAN is a simulation language that allows users to simulate discrete and continuous systems. In this research, a Web-based interface or toolkit has been developed for storing and executing SIMAN simulation models over the Internet. This toolkit consists of a World Wide Web interface to SIMAN and a Web-accessible database for storing user models. It provides users an easy-to-use environment for developing text-based simulation models using the SIMAN simulation language. It also allows users to test the functionality of a SIMAN model using the SIMAN debugger/run controller.

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 nuclear matrix associated proteins. ISPTM increased the MS/MS spectral identification rate substantially, displayed significantly better sensitivity for systematic PTM identification compared with that of 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.

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. Proteins 2014; 82:2597–2608.

A template-based data specification framework for modeling physical security systems

Simulation studies often fail to provide any useful result 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 15 templates built on top of 14 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 parameters.

An integrated modeling framework for crop and biofuel systems using the DSSAT and GREET models

Abstract As global demand for food, energy, and water resources continues to increase, decision-makers in these sectors must find sustainable ways to produce and provide for the growing population. While many models have been created to aid in decision-making in these systems, there is a lack of robust integrated models that enable an understanding of the interconnections of these systems. This study develops a modeling framework that explores the connections of the corn and ethanol systems, two major food and energy resources. A crop modeling tool (DSSAT) and a biofuel life cycle assessment tool (GREET) are connected using a service-oriented architecture programming approach. A Python program is developed to connect these two models and run scenario analyses to assess environmental impacts of the integrated system. This paper explores the impact of decisions such as fertilizer use and plant population on environmental effects of greenhouse gases, energy use, and water in the integrated system.

Predictive analytics for learning and usage of the plant sciences E-library

This study examines learning and usage of the Plant Sciences E-Library (PASSEL, passel.unl.edu), a large international, open-source multidisciplinary learning object repository (7793 users from 14 countries). The analyses employ predictive analytics to isolate usage variables which predict learning from the instructional material. Specifically, the study focuses on student engagement as measured by total time online and time spent with different content modality material. This paper describes the analytic process, reports data on usage of learning object modules and module elements, identifies significant predictors of learning, and discusses future research directions.

A novel way to study muscle anatomy of the beef animal

In an academic and industrial setting, it is difficult to teach the anatomy of a beef animal. It has required a beef carcass fabricated into wholesale and retail cuts or dissection of individual muscles. This could only happen in a laboratory, and substantial cost would be incurred for each lab session. Books or manuals can assist somewhat but these are only twodimensional in nature, making it difficult to understand some of the spatial relationships between muscles. It is now possible to use a web site (http://bovine.unl.edu) as a resource for the muscular anatomy of the beef animal. The site helps users understand bovine muscular and skeletal anatomy through the use of interactive 3D and 2D graphics simulations, pictures, drawings, and navigation through a series of well-defined information modules. The sections below describe the procedures and methodology followed to develop the content, material, and online infrastructure.