Engineering Commons^™

Modeling Heat Transfer During Cooling Of Ready-To-Eat Meat And Poultry Products Using Three-Dimensional Finite Element Analysis And Web-Based Simulation, Jihan F. Cepeda Jimenez

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

The meat industry is required to comply with processing performance standards for preventing the growth of foodborne pathogens in products. These performance standards, established by the United States Department of Agriculture - Food Safety and Inspection Service (USDA-FSIS) require a reduction of Salmonella spp (lethality standard) and limit the growth of sporeforming bacteria (stabilization standard) in certain processed meat products. In general, strategies used to comply with these standards are associated with thermal processing. Meat processors have difficulties complying with these performance standards. Moreover, thermal processing deviations are an issue in the meat industry that generate uncertainty regarding the safety …

Network Science: Using Information Technology To Enable Collaboration, Arden L. Bement Jr.

PPRI Digital Library

No abstract provided.

The River Discontinuum: Applying Beaver Modifications To Baseline Conditions For Restoration Of Forested Headwaters, Denise Burchsted, Melinda Daniels, Robert Thorson, Jason Vokoun

Center for Integrative Geosciences

Billions of dollars are being spent in the United States to restore rivers to a desired, yet often unknown, reference condition. In lieu of a known reference, practitioners typically assume the paradigm of a connected watercourse. Geological and ecological processes, however, create patchy and discontinuous fluvial systems. One of these processes, dam building by North American beavers (Castor canadensis), generated discontinuities throughout precolonial river systems of northern North America. Under modern conditions, beaver dams create dynamic sequences of ponds and wet meadows among free-flowing segments. One beaver impoundment alone can exceed 1000 meters along the river, flood the valley laterally, …

The Gel Documentation System: A Cornerstone To The Implementation Of The Introduction To Biotechnology And Introduction To Bioinformatics Cross-Disciplinary Course Series (Final Report), Marcy Kelly, Gregory Lampard, Constance Knapp

Cornerstone 3 Reports : Interdisciplinary Informatics

Our original goal was to offer Pace undergraduate students opportunities to be introduced to both Biotechnology and Computer Science as it relates to Bioinformatics. We proposed a two course series, offered to both computer science and biology students that will increase both biological and computer science literacy of our students. The two courses are Introduction to Biotechnology (BIO 372) and Introduction to Bioinformatics.

Hydraulic Conductivity, Infiltration, And Runoff From No-Till And Tilled Cropland, Jessica H. Deck

Department of Environmental Engineering: Theses and Student Research

Infiltration and runoff are important processes that affect the efficiency of center pivot irrigation systems. No-till planting systems potentially influence the hydraulic properties of soils and the soil surface conditions. The result of long-term use of no-till could be higher infiltration and lower runoff from rainfall and irrigation.

This potential was investigated in Nebraska on two center pivot irrigated sites; Fillmore County and Phelps County, one furrow irrigated site; South Central Agriculture Laboratory (SCAL), and one dryland site; Rogers Farm. Paired treatments were used at each location, one that was no-till planted and one that used two to three operations …

Terminology Enhanced Ehr: Integration Of Archetypes And Terminology, An Implementation Experience, Sheng Yu, Damon Berry

Reports

The integration of terminology and EHR information models is an important step in the journey towards semantic interoperability. Archetypes and two-level models for EHRs provide a mechanism that not only applies constraints on clinical content but also ensures effective terminology binding. However the lack of a standardised mechanism to bind terminology to the EHR and the difficulty of systematically coding clinical content, has led to a number of possible implementation choices. This study presents a review of the problems that may occur when working with modern terminology systems and discusses some related state of art technologies. The paper aims to …

Endogenous Sirnas And Noncoding Rna-Derived Small Rnas Are Expressed In Adult Mouse Hippocampus And Are Up-Regulated In Olfactory Discrimination Training., Neil Smalheiser, G Lugli, Jyothi Thimmapuram, E.H. Cook, J Larson

Cyber Center Publications

We previously proposed that endogenous siRNAs may regulate synaptic plasticity and long-term gene expression in the mammalian brain. Here, a hippocampal-dependent task was employed in which adult mice were trained to execute a nose-poke in a port containing one of two simultaneously present odors in order to obtain a reward. Mice demonstrating olfactory discrimination training were compared to pseudo-training and nose-poke control groups; size-selected hippocampal RNA was subjected to Illumina deep sequencing. Sequences that aligned uniquely and exactly to the genome without uncertain nucleotide assignments, within exons or introns of MGI annotated genes, were examined further. The data confirm that …

Structures Of Human Thymidylate Synthase R163k With Dump, Fdump And Glutathione Show Asymmetric Ligand Binding, Lydia M. Gibson, Lesa R. Celeste, Leslie L. Lovelace, Lukasz Lebioda

Faculty Publications

Thymidylate synthase (TS) is a well validated target in cancer chemotherapy. Here, a new crystal form of the R163K variant of human TS (hTS) with five subunits per asymmetric part of the unit cell, all with loop 181-197 in the active conformation, is reported. This form allows binding studies by soaking crystals in artificial mother liquors containing ligands that bind in the active site. Using this approach, crystal structures of hTS complexes with FdUMP and dUMP were obtained, indicating that this form should facilitate high-throughput analysis of hTS complexes with drug candidates. Crystal soaking experiments using oxidized glutathione revealed that …

Determining Optimal Storage Arrangements For Open Access Data Sets, As For Nsf Data Management Plan Requirements, David B. Lowe

Published Works

Document is a proposed draft of a decision tree to be used in determining what approach to take for making data available in order to comply with open access requirements for data management, as per National Science Foundation requirements.

Deletion Of The Cel48s Cellulase From Clostridium Thermocellum, Daniel G. Olson, Shital A. Tripathi, Richard J. Giannone, Jonathan Lo, Nicky C. Caiazza, David A. Hogsett, Robert L. Hettich, Adam M. Guss, Genia Dubrovsky, Lee R. Lynd

Dartmouth Scholarship

Clostridium thermocellum is a thermophilic anaerobic bacterium that rapidly solubilizes cellulose with the aid of a multienzyme cellulosome complex. Creation of knockout mutants for Cel48S (also known as CelS, S(S), and S8), the most abundant cellulosome subunit, was undertaken to gain insight into its role in enzymatic and microbial cellulose solubilization. Cultures of the Cel48S deletion mutant (S mutant) were able to completely solubilize 10 g/L crystalline cellulose. The cellulose hydrolysis rate of the S mutant strain was 60% lower than the parent strain, with the S mutant strain also exhibiting a 40% reduction in cell yield. The cellulosome produced …

Green Technology: Think Globally, Act Locally, Arden L. Bement Jr.

PPRI Digital Library

No abstract provided.

Use Of Oids And Iis In En13606, Damon Berry, Jostein Ven, Gerard Freriks, David Moner

Reports

No abstract provided.

Discovering Gene Functional Relationships Using Faun (Feature Annotation Using Nonnegative Matrix Factorization), Elina Tjioe, Michael W. Berry, Ramin Homayouni

Faculty Publications and Other Works -- EECS

Background

Searching the enormous amount of information available in biomedical literature to extract novel functional relationships among genes remains a challenge in the field of bioinformatics. While numerous (software) tools have been developed to extract and identify gene relationships from biological databases, few effectively deal with extracting new (or implied) gene relationships, a process which is useful in interpretation of discovery-oriented genome-wide experiments.

Results

In this study, we develop a Web-based bioinformatics software environment called FAUN or Feature Annotation Using Nonnegative matrix factorization (NMF) to facilitate both the discovery and classification of functional relationships among genes. Both the computational complexity …

Hrc Enews — 2010 Fall, Megan K. Svarz

Publications (HRC)

This issue contains staff accomplishments and announcements, event listings, and a "new faces" listing for new staff, affiliates, and researchers.

Selective Biochlorination Of Hydroxyquinolines By A Flavin-Dependent Halogenase, Fuchao Xu, Amanda Merkley, Dayu Yu, Jixun Zhan

Biological Engineering Faculty Publications

Rdc2 is a flavin-dependent halogenase from Pochonia chlamydosporia. Through the introduction of a His₆-tag to both the N- and C-termini, the isolation yield of Rdc2 from Escherichia coli using Ni-NTA affinity chromatography was increased by three-fold. In vitro reaction of Rdc2 and a flavin reductase (Fre) with seven different hydroxyquinolines revealed that 3-hydroxyquinoline (3), 5-hydroxyquinoline (5), 6-hydroxyquinoline (6), and 7-hydroxyquinoline (7) can be specifically halogenated. These products were prepared by incubating the corresponding substrates with IPTG-induced E. coli BL21(DE3)/Rdc2. They were respectively characterized as 3-hydroxy-4-chloroquinoline (3a), 5-hydroxy-6-chloroquinoline (5a), 5-chloro-6-hydroxyquinoline (6a), and 7-hydroxy-8-chloroquinoline (7a) by NMR and MS …

Alterations In Multiple Measures Of White Matter Integrity In Normal Women At High Risk For Alzheimer's Disease, Brian T. Gold, David K. Powell, Anders H. Andersen, Charles D. Smith

Neuroscience Faculty Publications

There is evidence that disruption of white matter (WM) microstructure is an early event in the course of Alzheimer's disease (AD). However, the neurobiological bases of WM microstructural declines in presymptomatic AD are unknown. In the present study we address this issue using a multimodal imaging approach to the study of presymptomatic AD. Participants were 37 high-risk (both family history of dementia and one or more APOE4 alleles) women and 20 low-risk (neither family history nor APOE4) women. Groups were matched for age, education, neuropsychological performance, and vascular factors that could affect white matter. Whole-brain analyses of diffusion tensor imaging …

Identification Of An Archaeal Presenilin-Like Intramembrane Protease, Celia Torres-Arancivia, Carolyn M. Ross, Jose Chavez, Zahra Assur, Georgia Dolios, Filippo Mancia, Iban Ubarretxena-Belandia

Publications and Research

Background: The GXGD-type diaspartyl intramembrane protease, presenilin, constitutes the catalytic core of the c-secretase multi-protein complex responsible for activating critical signaling cascades during development and for the production of b-amyloid peptides (Ab) implicated in Alzheimer’s disease. The only other known GXGD-type diaspartyl intramembrane proteases are the eukaryotic signal peptide peptidases (SPPs). The presence of presenilin-like enzymes outside eukaryots has not been demonstrated. Here we report the existence of presenilin-like GXGD-type diaspartyl intramembrane proteases in archaea.

Methodology and Principal Findings: We have employed in vitro activity assays to show that MCMJR1, a polytopic membrane protein from the archaeon Methanoculleus marisnigri JR1, …

Biological Computation, Melanie Mitchell

Computer Science Faculty Publications and Presentations

In this article, the term biological computation refers to the proposal that living organisms themselves perform computations, and, more specifically, that the abstract ideas of information and computation may be key to understanding biology in a more unified manner. It is important to point out that the study of biological computation is typically not the focus of the field of computational biology, which applies computing tools to the solution of specific biological problems. Likewise, biological computation is distinct from the field of biologically-inspired computing, which borrows ideas from biological systems such as the brain, insect colonies, and the immune system …

Negative Dielectrophoretic Capture Of Bacterial Spores In Food Matrices, Mehti Koklu, Seungkyung Park, Suresh D. Pillai, Ali Beskok

Mechanical & Aerospace Engineering Faculty Publications

A microfluidic device with planar square electrodes is developed for capturing particles from high conductivity media using negative dielectrophoresis (n-DEP). Specifically, Bacillus subtilis and Clostridium sporogenes spores, and polystyrene particles are tested in NaCl solution (0.05 and 0.225 S/m), apple juice (0.225 S/m), and milk (0.525 S/m). Depending on the conductivity of the medium, the Joule heating produces electrothermal flow (ETF), which continuously circulates and transports the particles to the DEP capture sites. Combination of the ETF and n-DEP results in different particle capture efficiencies as a function of the conductivity. Utilizing 20 μm height DEP chambers, “almost complete” and …

Development Of Pyrf-Based Genetic System For Targeted Gene Deletion In Clostridium Thermocellum And Creation Of A Pta Mutant, Shital A. Tripathi, Daniel G. Olson, D. Aaron Argyros, Bethany B. Miller, Trisha F. Barrett, Daniel M. Murphy, Jesse D. Mccool, Anne K. Warner, Vineet B. Rajgarhia, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza

Dartmouth Scholarship

We report development of a genetic system for making targeted gene knockouts in Clostridium thermocellum, a thermophilic anaerobic bacterium that rapidly solubilizes cellulose. A toxic uracil analog, 5-fluoroorotic acid (5-FOA), was used to select for deletion of the pyrF gene. The ΔpyrF strain is a uracil auxotroph that could be restored to a prototroph via ectopic expression of pyrF from a plasmid, providing a positive genetic selection. Furthermore, 5-FOA was used to select against plasmid-expressed pyrF, creating a negative selection for plasmid loss. This technology was used to delete a gene involved in organic acid production, namely pta, which encodes …

Pre-Swing Deficits In Forward Propulsion, Swing Initiation And Power Generation By Individual Muscles In Hemiparetic Walking, Carrie L. Peterson, Allison Kinney, Steven A. Kautz, Richard R. Neptune

Mechanical and Aerospace Engineering Faculty Publications

Clinical studies of hemiparetic walking have shown pre-swing abnormalities in the paretic leg suggesting that paretic muscle contributions to important biomechanical walking subtasks are different than those of non-disabled individuals. Three-dimensional forward dynamics simulations of two representative hemiparetic subjects with different levels of walking function classified by self-selected walking speed (i.e., limited community=0.4–0.8 m/s and community walkers=>0.8 m/s) and a speed-matched control were generated to quantify individual muscle contributions to forward propulsion, swing initiation and power generation during the pre-swing phase (i.e., double support phase proceeding toe-off). Simulation analyses identified decreased paretic soleus and gastrocnemius contributions to forward propulsion …

Relationships Between Muscle Contributions To Walking Subtasks And Functional Walking Status In Persons With Post-Stroke Hemiparesis, Allison Kinney, Carrie L. Peterson, Steven A. Kautz, Richard R. Neptune

Mechanical and Aerospace Engineering Faculty Publications

Walking speed is commonly used to predict stroke severity and assess functional walking status (i.e., household, limited community and community walking status) post-stroke. The underlying mechanisms that limit walking speed (and functional walking status by extension) need to be understood to improve post-stroke rehabilitation. Previous experimental studies have shown correlations between paretic plantarflexor output during the pre-swing phase and walking speed and suggest that the paretic hip flexors can compensate in some hemiparetic subjects. Modeling and simulation studies of healthy walking have shown that the ankle plantarflexors, soleus (SOL) and gastrocnemius (GAS), and uniarticular hip flexors (IL) are essential contributors …

Graph Algorithms For Machine Learning: A Case-Control Study Based On Prostate Cancer Populations And High Throughput Transcriptomic Data, Gary L. Rogers, Pablo Moscato, Michael A. Langston

Faculty Publications and Other Works -- EECS

Background

The continuing proliferation of high-throughput biological data promises to revolutionize personalized medicine. Confirming the presence or absence of disease is an important goal. In this study, we seek to identify genes, gene products and biological pathways that are crucial to human health, with prostate cancer chosen as the target disease.

Materials and methods

Using case-control transcriptomic data, we devise a graph theoretical toolkit for this task. It employs both innovative algorithms and novel two-way correlations to pinpoint putative biomarkers that classify unknown samples as cancerous or normal.

Results and conclusion

Observed accuracy on real data suggests that we are …

Rapid Diagnosis Of Tuberculosis In A Peripheral Setting, Elsje Pienaar

Department of Chemical and Biomolecular Engineering: Theses and Student Research

Tuberculosis is an ancient and worldwide epidemic affecting millions of people in mainly the developing world, killing almost 2 million people in 2008. Current diagnostic techniques are outdated and have proven insufficient to control the disease. Smear microscopy has poor sensitivity and culture is slow to yield results. Modern diagnostic techniques are making great strides in shortening time to result but are restricted by two qualities: 1) prohibitively high costs prevent implementation in resource poor areas, and 2) equipment and technician requirements limit application to centralized laboratories. There exists a divide between new technologies and the people that need them …

Crystallization Of Community-Acquired Respiratory Distress Syndrome Toxin From Mycoplasma Pneumonia, Olga N. Pakhomova, Alexander B. Taylor, Argentina Becker, Stephen P. Holloway, T. R. Kannan, Joel B. Baseman, P. John Hart

Bioelectrics Publications

Community-acquired respiratory distress syndrome toxin (CARDS TX) is a 591-amino-acid protein with ADP-ribosyltransferase and vacuolating activities that damages the cells lining the respiratory tracts of patients infected with the bacterial pathogen Mycoplasma pneumoniae. Crystals of CARDS TX were grown in space group C2, with unit-cell parameters a = 191.4, b = 107.4, c = 222.1 A, beta = 90.6 degrees. A complete 2.2 A data set was obtained from a single CARDS TX crystal.

Electrically Mediated Delivery Of Plasmid Dna To The Skin, Using A Multielectrode Array, Richard Heller, Yolmari Criz, Loree C. Heller, Richard A. Gilbert, Mark J. Jaroszeski

Bioelectrics Publications

The easy accessibility of skin makes it an excellent target for gene transfer protocols. To take full advantage of skin as a target for gene transfer, it is important to establish an efficient and reproducible delivery system. Electroporation is a strong candidate to meet this delivery criterion. Electroporation of the skin is a simple, direct, in vivo method to deliver genes for therapy. Previously, delivery to the skin was performed by means of applicators with relatively large distances between electrodes, resulting in significant muscle stimulation and pain. These applicators also had limitations in controlling the directionality of the applied field. …

Expanding Ethics Education In Science & Engineering, Jane E. Fountain

Ethics in Science and Engineering National Clearinghouse

This presentation was part of the AAAS Annual Conference professional development workshop, National Science Foundation and Ethics Education in Science and Engineering, during the recent meeting in San Diego, California (18-22 February). Dr. Michael Gorman, Program Director, Science, Technology & Society, National Science Foundation, moderated the workshop presentations and the discussion that followed. In addition, he contributed a set of powerpoint slides outlining the role of NSF in its response to the America Competes Act, including a commitment to support an online resource in ethics education. Dr. Philip Langlais, Vice Provost for Graduate Studies & Research, Old Dominion University, presented …

Nsf Supported Case-Studies Done By Systems Engineering Graduate Students At Uva, Michael Gorman

Ethics in Science and Engineering National Clearinghouse

This presentation was part of the AAAS Annual Conference professional development workshop, National Science Foundation and Ethics Education in Science and Engineering, during the recent meeting in San Diego, California (18-22 February). Dr. Michael Gorman, Program Director, Science, Technology & Society, National Science Foundation, moderated the workshop presentations and the discussion that followed. In addition, he contributed a set of powerpoint slides outlining the role of NSF in its response to the America Competes Act, including a commitment to support an online resource in ethics education. Dr. Philip Langlais, Vice Provost for Graduate Studies & Research, Old Dominion University, presented …

Science And Engineering Ethics Education: Recipes For Success, Philip J. Langlais

Ethics in Science and Engineering National Clearinghouse

This presentation was part of the AAAS Annual Conference professional development workshop, National Science Foundation and Ethics Education in Science and Engineering, during the recent meeting in San Diego, California (18-22 February). Dr. Michael Gorman, Program Director, Science, Technology & Society, National Science Foundation, moderated the workshop presentations and the discussion that followed. In addition, he contributed a set of powerpoint slides outlining the role of NSF in its response to the America Competes Act, including a commitment to support an online resource in ethics education. Dr. Philip Langlais, Vice Provost for Graduate Studies & Research, Old Dominion University, presented …

Rcr For Postdocs: Promoting Ethical Professional Development, Kathleen Flint

Ethics in Science and Engineering National Clearinghouse

This presentation was part of the AAAS Annual Conference professional development workshop, National Science Foundation and Ethics Education in Science and Engineering, during the recent meeting in San Diego, California (18-22 February). Dr. Michael Gorman, Program Director, Science, Technology & Society, National Science Foundation, moderated the workshop presentations and the discussion that followed. In addition, he contributed a set of powerpoint slides outlining the role of NSF in its response to the America Competes Act, including a commitment to support an online resource in ethics education. Dr. Philip Langlais, Vice Provost for Graduate Studies & Research, Old Dominion University, presented …