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Challenges To Informed Peer Review Matching Algorithms, Matthew Verleger, Heidi Diefes-Dux, Matthew W. Ohland, Mary Besterfield-Sacre, Sean Brophy

Publications

Background Peer review is a beneficial pedagogical tool. Despite the abundance of data instructors often have about their students, most peer review matching is by simple random assignment. In fall 2008, a study was conducted to investigate the impact of an informed algorithmic assignment method, called Un‐weighted Overall Need (UON), in a course involving Model‐Eliciting Activities (MEAs). The algorithm showed no statistically significant impact on the MEA Final Response scores. A study was then conducted to examine the assumptions underlying the algorithm.

Purpose (Hypothesis) This research addressed the question: To what extent do the assumptions used in making informed peer …

The Circuit, Fall 2010, Department Of Electrical And Computer Engineering, Michigan Technological University

Department of Electrical and Computer Engineering Newsletters

Table of Contents

• Strategic Faculty Hiring Initiatives at Michigan Tech
• Tech Receives $3 Million to Develop EV Education Programs
• ECE Student Brings Laptops to Ghana
• Tech's Online Power Engineering Program Marks 10th Anniversary
• Dave House: Why Research is Key to the Future of Tech and to ECE
• Alumni Gifts Fund New Center for Computer Systems Research
• Faculty and Student News

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 …

An Automated Phenotype-Driven Approach (Geneforce) For Refining Metabolic And Regulatory Models, Dipak Barua, Joonhoon Kim, Jennifer L. Reed

Chemical and Biochemical Engineering Faculty Research & Creative Works

Integrated constraint-based metabolic and regulatory models can accurately predict cellular growth phenotypes arising from genetic and environmental perturbations. Challenges in constructing such models involve the limited availability of information about transcription factor-gene target interactions and computational methods to quickly refine models based on additional datasets. In this study, we developed an algorithm, GeneForce, to identify incorrect regulatory rules and gene-protein-reaction associations in integrated metabolic and regulatory models. We applied the algorithm to refine integrated models of Escherichia coli and Salmonella typhimurium, and experimentally validated some of the algorithm's suggested refinements. The adjusted E. coli model showed improved accuracy …

Electroencephalogram Artifact Removal Using A Wavelet Neural Network, Hoang-Anh T. Nguyen

Electrical & Computer Engineering Theses & Dissertations

A wavelet neural network (WNN) technique rs developed for electroencephalogram (EEG) artifact removal without electrooculographic (EOG) recordings. The algorithm combines the universal approximation characteristics of neural networks and the time/frequency property of wavelet, where the neural network was trained on a simulated dataset with known ground truths. The contribution of this thesis is two-fold. First, many EEG artifact removal algorithms, including regression based methods, require reference EOG signals, which are not always available. To remove EEG ai1ifacts, a WNN tries to learn the characteristics of the artifacts first and does not need reference EOG signals once trained. Second, WNNs are …

Development Of Sustainability Indicators For Products And Processes, Sundeep Bodapati

Mechanical & Aerospace Engineering Theses & Dissertations

Significant increase in industrialization is a leading cause for the depletion of global resources and changes in the earth's atmosphere due to global warming. There has been a major concern for the manufacturing industry to deal with the above problems and this had led the researchers to focus on the area of sustainability. Sustainable development aims for the future, which is characterized by the interaction of the economic, environment and society. To enable the manufacturing companies to measure sustainability performance, developing the metrics for sustainability is critical. The purpose of this thesis is to review the indicators published in the …

A Novel Piezoelectric Device With Dual Functions Of Studying Biological Soft Tissues, Avin A. Jamadagni

Mechanical & Aerospace Engineering Theses & Dissertations

This thesis presents the design of a novel piezoelectric device with dual functions of studying soft biological tissues. The device consists of a central circular plate and a set of flexural beams. The flexural beams are partially covered with piezoelectric film for integrated transduction. It can function as a force sensor for measuring the mechanical behavior of a tissue sample and a load applier for mimicking physiological loads experienced by the tissue sample in vivo, while the mechanical behavior can be visually observed under a microscope simultaneously. By combining the classic theories in solid mechanics and piezoelectricity, the performance of …

Dispersion Of Cytotoxic Properties Of Multi-Walled Carbon Nanotubes Suspended In Biological Solutions With Tween 80: Their Role In Enhancing Killing Effects Of Nanosecond Pulse Electric Fields On Tumor Cell Lines, Bhargava S. Kalluri

Biological Sciences Theses & Dissertations

The objective of this study was to determine whether multi-walled carbon nanotubes (MWCNTs) suspended in the surfactant Tween 80 give an additive killing effect on tumor cells when exposed to nsPEFs. In this study, MWCNTs were suspended in DMEM and RPMI with or without T80 (surfactant). The size distribution of MWCNTs suspended in these solutions was evaluated with a Delsa™ Nano Zeta potential and sub micro particle Size Analyzer and confirmed with microscopy. The cytotoxicity of MWCNTs dispersed in different concentrations of T80 was evaluated in PANC1 (Human pancreatic cancer cell line) and Jurkat cell lines (Human T-cell lymphoblast cell …

Intracellular Localisation, Geno- And Cytotoxic Response Of Poly N-Isopropylacrylamide (Pnipam) Nanoparticles To Human Keratinocyte (Hacat) And Colon Cells (Sw 480), Pratap Naha, Kunal Bhattacharya, Tiziana Tenuta, Kenneth Dawson, Iseult Lynch, Amaya Gracia, Fiona Lyng, Hugh Byrne

Articles

PNIPAM nanoparticles, with and without a covalentlylinked fluorescent label, were prepared by a free radical polymerisation technique. The cyto and genotoxicity of PNIPAM nanoparticles were analysed in two representative mammalian cell lines, SW480, a colon, and HaCaT, a dermal cell line. Physical characterisation in terms of particle size and zeta potential of the PNIPAM nanoparticles was carried out both in aqueous solution and in the appropriate cell culture media. Uptake and colocalisation of fluorescently labelled PNIPAM nanoparticles was monitored in both cell lines using confocal laser scanning microscopy. Genotoxicity analysis using the Comet assay was performed in both cell lines …

Distributed Power Balancing For The Freedm System, Rav Akella, Fanjun Meng, Derek Ditch, Bruce M. Mcmillin, Mariesa Crow

Computer Science Faculty Research & Creative Works

The FREEDM microgrid is a test bed for a smart grid integrated with Distributed Grid Intelligence (DGI) to efficiently manage the distribution and storage of renewable energy. Within the FREEDM system, DGI applies distributed algorithms in a unique way to achieve economically feasible utilization and storage of alternative energy sources in a distributed fashion. The FREEDM microgrid consists of residential or industrial nodes with each node running a portion of the DGI process called Intelligent Energy Management (IEM). Such IEM nodes within FREEDM coordinate among themselves to efficiently and economically manage their power generation, utility and storage. Among a variety …

The Effect Of Ionic Dissolution Products Of Ca-Sr-Na-Zn-Si Bioactive Glass On In Vitro Cytocompatibility, S. Murphy, A. W. Wren, Mark R. Towler, D. Boyd

Chemical and Biochemical Engineering Faculty Research & Creative Works

Many commercial bone grafts cannot regenerate healthy bone in place of diseased bone. Bioactive glasses have received much attention in this regard due to the ability of their ionic dissolution products to promote cell proliferation, cell differentiation and activate gene expression. Through the incorporation of certain ions, bioactive glasses can become therapeutic for specific pathological situations. Calcium-strontium-sodium-zinc-silicate glass bone grafts have been shown to release therapeutic levels of zinc and strontium, however the in vitro compatibility of these materials is yet to be reported. In this study, the in vitro cytocompatibility of three different calcium-strontium-sodium-zinc-silicate glasses was examined as a …

Comparison Of Antibacterial Properties Of Commercial Bone Cements And Fillers With A Zinc-Based Glass Polyalkenoate Cement, A. W. Wren, N. M. Cummins, Mark R. Towler

Chemical and Biochemical Engineering Faculty Research & Creative Works

Postoperative infection following invasive surgical procedures is a significant cause for concern, particularly in spinal reconstructive surgery. The objective of this study is to compare the antibacterial efficacy of a novel zinc-based glass polyalkenoate cement (Zn-GPC) based on 0.04SrO-0.12CaO-0.36ZnO- 0.48SiO₂ glass, to a number of commercially available bone cements and fillers including Simplex P + Tobramycin (S_Tob), Spineplex (S_pine) and Novabone Putty (N_Put). The agar diffusion test was performed on each material against Escherichia coli, Staphlococcus epidermidis, Pseudomonas aeruginosa and Staphlococcus Aureus. S_Tob was found to produce large inhibition zones in each …

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, …

Joint Loop End Modeling Improves Covariance Model Based Non-Coding Rna Gene Search, Jennifer Smith

Electrical and Computer Engineering Faculty Publications and Presentations

The effect of more detailed modeling of the interface between stem and loop in non-coding RNA hairpin structures on efficacy of covariance-model-based non-coding RNA gene search is examined. Currently, the prior probabilities of the two stem nucleotides and two loop-end nucleotides at the interface are treated the same as any other stem and loop nucleotides respectively. Laboratory thermodynamic studies show that hairpin stability is dependent on the identities of these four nucleotides, but this is not taken into account in current covariance models. It is shown that separate estimation of emission priors for these nucleotides and joint treatment of substitution …

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 …

Fetal Breathing Movement And Its Distinctive Characteristics In Bio-Magnetic Data, Umit Deniz Ulusar

Theses and Dissertations

Magnetoencephalography (MEG) is widely used to study magnetic fields generated by the electrical activity of the human brain and can also be applied for fetal neurological health assessment. The fetal MEG (fMEG) signals are often contaminated with other bio-magnetic signals such as fetal breathing movement (FBM), which acts as an interfering factor for fetal neurological signals. This study was carried out to identify the bio-magnetic signals pertinent to the FBM. The fMEG signals were captured using superconducting quantum interference devices (SQUIDs) and the FBMs were recorded by an ultrasound-based video technique. The simultaneous recording is challenging since SQUIDs are extremely …

Signal Detection Framework Using Semantic Text Mining Techniques, Sithu D. Sudarsan

Theses and Dissertations

Signal detection is a challenging task for regulatory and intelligence agencies. Subject matter experts in those agencies analyze documents, generally containing narrative text in a time bound manner for signals by identification, evaluation and confirmation, leading to follow-up action e.g., recalling a defective product or public advisory for potential flu outbreak. Technical challenges to achieve effective signal detection include mining unstructured data, increasing document collections, and presence of multi-domain vocabulary. Lack of annotation and multi-domain vocabulary makes traditional semantic web mining ineffective. Use of heuristics to enhance bag-of-words type text mining to semantic text mining is a novel idea attempted …

Predicting Stability Of Alpha-Helical, Orthogonal-Bundle Proteins On Surfaces, Shuai Wei, Thomas A. Knotts

Faculty Publications

The interaction of proteins with surfaces is a key phenomenon in many applications, but current understanding of the biophysics involved is lacking. At present, rational design of such emerging technologies is difficult as no methods or theories exist that correctly predict how surfaces influence protein behavior. Using molecular simulation and a coarse-grain model, this study illustrates for the first time that stability of proteins on surfaces can be correlated with tertiary structural elements for alpha-helical, orthogonal-bundle proteins. Results show that several factors contribute to stability on surfaces including the nature of the loop region where the tether is placed and …

Field-Structured Chemiresistors : Tunable Sensors For Chemical-Switch Arrays, Douglas Read

Chemical and Biological Engineering ETDs

We have developed a significantly improved composite material for applications to chemiresistors, which are resistance-based sensors for volatile organic compounds. This material is a polymer composite containing Au-coated magnetic particles organized into electrically conducting pathways by magnetic fields. This improved material overcomes the various problems inherent to conventional carbon-black chemiresistors, while achieving an unprecedented magnitude of response. When exposed to chemical vapors, the polymer swells only slightly, yet this is amplified into large, reversible resistance changes—as much as 9 decades at a swelling of only 1.5 %. These conductor-insulator transitions occur over such a narrow range of analyte vapor concentration …

Sintering Of Metal Nanoparticles On Model Substrates, Levi R. Houk

Chemical and Biological Engineering ETDs

The sintering of precious metal catalysts is an important problem for the automotive and chemical process industry. As these precious metal catalysts sinter, the metal nanoparticles grow, which in return causes a loss in the overall surface area from loss of the number of available reaction sites. At high temperatures, sintering as a thermally activated process occurs more rapidly and the energetics of the sample changes. In automotive catalysis, for the catalytic converter, the exhaust gases from automobiles contain carbon monoxide, nitrogen oxide compounds, and other hydrogen compounds, which are detrimental to the atmosphere, and a catalyst is required to …

Providing A Theoretical Basis For Nanotoxicity Risk Analysis Departing From Traditional Physiologically-Based Pharmacokinetic (Pbpk) Modeling, Dirk P. Yamamoto

Theses and Dissertations

The same novel properties of engineered nanoparticles that make them attractive may also present unique exposure risks. But, the traditional physiologically-based pharmacokinetic (PBPK) modeling assumption of instantaneous equilibration likely does not apply to nanoparticles. This simulation-based research begins with development of a model that includes diffusion, active transport, and carrier mediated transport. An eigenvalue analysis methodology was developed to examine model behavior to focus future research. Simulations using the physicochemical properties of size, shape, surface coating, and surface charge were performed and an equation was determined which estimates area under the curve for arterial blood concentration, which is a surrogate …

Analysis Of Alternative Methods For Long-Term Wind Speed And Initial Site Assessment For Purposes Of Wind Energy Production Estimation, Ryan Mcdevitt

Theses and Dissertations

A need exists for identification and evaluation of viable sites for wind energy. However, this is made difficult by the site-specific nature of the wind. A review of current industry practices shows that linear regression is the preferred method, although little work has been done to investigate alternative approaches. To address this, various methods were tested on 23 target sites with data measured over a long-term period. Each site was analyzed with the chosen best reference station, across 10 data periods for each method with results classified as mean absolute percentage error in energy density between the projected and measured …

Model Electrode Structures For Studies Of Electrocatalyst Degradation, Ronald Goeke

Chemical and Biological Engineering ETDs

Proton exchange membrane fuel cells (PEMFCs) are being extensively studied as power sources because of their technological advantages such as high energy efficiency, high energy and power densities, environmental friendliness, low noise, rapid refueling, and fuel flexibility. The most effective catalyst in these systems consists of nanoparticles of Pt or Pt-based alloys on carbon supports. Understanding the role of the nanoparticle size and structure on the catalytic activity and degradation is needed to optimize the fuel cell performance and reduce the noble metal loading. Electrocatalyst degradation is believed to occur by four mechanisms; particle sintering (Ostwald ripening and migration and …

Programmable Periodicity Of Quantum Dot Arrays With Dna Origami Nanotubes, Hieu Bui, Craig Onodera, Carson Kidwell, Yerpeng Tan, Elton Graugnard, Wan Kuang, Jeunghoon Lee, William B. Knowlton, Bernard Yurke, William L. Hughes

Materials Science and Engineering Faculty Publications and Presentations

To fabricate quantum dot arrays with programmable periodicity, functionalized DNA origami nanotubes were developed. Selected DNA staple strands were biotin-labeled to form periodic binding sites for streptavidin-conjugated quantum dots. Successful formation of arrays with periods of 43 and 71 nm demonstrates precise, programmable, large-scale nanoparticle patterning; however, limitations in array periodicity were also observed. Statistical analysis of AFM images revealed evidence for steric hindrance or site bridging that limited the minimum array periodicity.

Dna Translocation Through An Array Of Kinked Nanopores, Zh Chen

Chemical and Biological Engineering ETDs

Synthetic solid-state nanopores are being intensively investigated as single-molecule sensors for detection and characterization of DNA, RNA, and proteins. This field has been inspired by the exquisite selectivity and flux demonstrated by natural biological channels and the dream of emulating these behaviors in more robust synthetic materials that are more readily integrated into practical devices. To date, the guided etching of polymer films, focused ion beam sculpting, and electron-beam lithography and tuning of silicon nitride membranes have emerged as three promising approaches to define synthetic solid-state pores with sub-nanometer resolution. These procedures have in common the formation of nominally cylindrical …

Chemical Changes In Soil And Soil Solution After Calcium Silicate Addition To A Northern Hardwood Forest, Youngil Cho, Charles T. Driscoll, Chris E. Johnson, Thomas G. Siccama

Civil and Environmental Engineering - All Scholarship

Liming has been used to mitigate effects of acidic deposition in forest ecosystems. This study was designed to examine the effects of calcium (Ca) supply on the spatial patterns and the relations between soil and soil solution chemistry in a base-poor forest watershed. Watershed 1 at the Hubbard Brook Experimental Forest in New Hampshire, USA was experimentally treated with wollastonite (CaSiO₃) in October, 1999. Exchangeable Ca (Ex-Ca), soil pH_s (in 0.01 M CaCl₂), effective cation exchange capacity (CEC_e), and effective base saturation (BS_e) increased, while exchangeable acidity (Ex-Acid) decreased …

Quantitative Imaging Reveals Heterogeneous Growth Dynamics And Treatment-Dependent Residual Tumor Distributions In A Three-Dimensional Ovarian Cancer Model, Jonathan P. Celli, Imran Rizvi, Conor L. Evans, Adnan O. Abu-Yousif, Tayyaba Hasan

Dartmouth Scholarship

Three-dimensional tumor models have emerged as valuable in vitro research tools, though the power of such systems as quantitative reporters of tumor growth and treatment response has not been adequately explored. We introduce an approach combining a 3-D model of disseminated ovarian cancer with high-throughput processing of image data for quantification of growth characteristics and cytotoxic response. We developed custom MATLAB routines to analyze longitudinally acquired dark-field microscopy images containing thousands of 3-D nodules. These data reveal a reproducible bimodal log-normal size distribution. Growth behavior is driven by migration and assembly, causing an exponential decay in spatial density concomitant with …

Kinetics Of Dna And Rna Hybridization In Serum And Serum-Sds, Elton Graugnard, Amber Cox, Jeunghoon Lee, Cheryl Jorcyk, Bernard Yurke, William L. Hughes

Materials Science and Engineering Faculty Publications and Presentations

Cancer is recognized as a serious health challenge both in the United States and throughout the world. While early detection and diagnosis of cancer leads to decreased mortality rates, current screening methods require significant time and costly equipment. Recently, increased levels of certain micro-ribonucleic acids (miRNAs) in the blood have been linked to the presence of cancer. While blood-based biomarkers have been used for years in cancer detection, studies analyzing trace amounts of miRNAs in blood and serum samples are just the beginning. Recent developments in deoxyribonucleic acid (DNA) nanotechnology and DNA computing have shown that it is possible to …

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 …

Differential Regulation Of Immature Articular Cartilage Compressive Moduli And Poisson’S Ratios By In Vitro Stimulation With Igf-1 And Tgf-Β1, Gregory M. Williams, Kristin J. Dills, Christian R. Flores, Michael E. Stender, Kevin M. Stewart, Lauren M. Nelson, Albert C. Chen, Koichi Masuda, Scott J. Hazelwood, Stephen M. Klisch, Robert L. Sah

Mechanical Engineering

Mechanisms of articular cartilage growth and maturation have been elucidated by studying composition-function dynamics during in vivo development and in vitro culture with stimuli such as insulin-like growth factor-1 (IGF-1) and transforming growth factor-beta 1 (TGF-β1). This study tested the hypothesis that IGF-1 and TGF-β1 regulate immature cartilage compressive moduli and Poisson’s ratios in a manner consistent with known effects on tensile properties. Bovine calf articular cartilage from superficial-articular (S) and middle-growth (M) regions were analyzed fresh or following culture in medium with IGF-1 or TGF-β1. Mechanical properties in confined (CC) and unconfined (UCC) compression, cartilage matrix composition, and explant …