Physical Sciences and Mathematics Commons^™

Detection Of 2,4,6-Trinitrotoluene Using A Colorimetric Gold Nanoparticle Air Cassette Filter, Andrea I. Ferrer Vega

Master of Science in Forensic Science Directed Research Projects

Trinitrotoluene (TNT) is an explosive commonly used during military and terrorist activities. Current methods to identify this compound require sampling, transport and analysis at a forensic lab using analytical instrumentation. However, on-site detection is needed to assist efforts to prevent detonation. Gold nanoparticles have been used as sensors throughout the years due to their versatility and surface enhanced Raman scattering properties in the presence of an analyte and low limits of detection. By taking advantage of the Meisenheimer complex that TNT forms in the presence of amines, it is possible to determine its presence at picogram levels. Subsequently, adhering amine …

In Defense Of Science—What Would John Do?, Mohamed Gad-El-Hak

Mechanical and Nuclear Engineering Publications

Recent onslaughts on the importance of pure research to our collective well-being are trending. In this essay, I discuss the issues involved and offer a rebuttal. The thoughts are inspired by my mentor, academic sibling, and idol John Leask Lumley.

An Annotated Corpus With Nanomedicine And Pharmacokinetic Parameters, Nastassja Lewinski, Ivan Jimenez, Bridget Mcinnes

Chemical and Life Science Engineering Publications

A vast amount of data on nanomedicines is being generated and published, and natural language processing (NLP) approaches can automate the extraction of unstructured text-based data. Annotated corpora are a key resource for NLP and information extraction methods which employ machine learning. Although corpora are available for pharmaceuticals, resources for nanomedicines and nanotechnology are still limited. To foster nanotechnology text mining (NanoNLP) efforts, we have constructed a corpus of annotated drug product inserts taken from the US Food and Drug Administration’s Drugs@FDA online database. In this work, we present the development of the Engineered Nanomedicine Database corpus to support the …

Parsing Metamap Files In Hadoop, Amy Olex, Alberto Cano, Bridget T. Mcinnes

Computer Science Publications

The UMLS::Association CUICollector module identifies UMLS Concept Unique Identifier bigrams and their frequencies in a biomedical text corpus. CUICollector was re-implemented in Hadoop MapReduce to improve algorithm speed, flexibility, and scalability. Evaluation of the Hadoop implementation compared to the serial module produced equivalent results and achieved a 28x speedup on a single-node Hadoop system.

Gap Detection For Genome-Scale Constraint-Based Models, J. Paul Brooks, William P. Burns, Stephen S. Fong, Chris M. Gowen, Seth B. Roberts

Statistical Sciences and Operations Research Publications

Constraint-based metabolic models are currently the most comprehensive system-wide models of cellular metabolism. Several challenges arise when building an in silico constraint-based model of an organism that need to be addressed before flux balance analysis (FBA) can be applied for simulations. An algorithm called FBA-Gap is presented here that aids the construction of a working model based on plausible modifications to a given list of reactions that are known to occur in the organism. When applied to a working model, the algorithm gives a hypothesis concerning a minimal medium for sustaining the cell in culture. The utility of the algorithm …

Genome-Scale Metabolic Analysis Of Clostridium Thermocellum For Bioethanol Production, Seth B. Roberts, Christopher M. Gowen, J. Paul Brooks, Stephen S. Fong

Chemical and Life Science Engineering Publications

Background

Microorganisms possess diverse metabolic capabilities that can potentially be leveraged for efficient production of biofuels. Clostridium thermocellum (ATCC 27405) is a thermophilic anaerobe that is both cellulolytic and ethanologenic, meaning that it can directly use the plant sugar, cellulose, and biochemically convert it to ethanol. A major challenge in using microorganisms for chemical production is the need to modify the organism to increase production efficiency. The process of properly engineering an organism is typically arduous.

Results

Here we present a genome-scale model of C. thermocellum metabolism, iSR432, for the purpose of establishing a computational tool to study the …