A Three-year Comparison of Attitudes Toward Education of Students and Parents of Students Enrolled in an Individualized Reading Program

Purpose. It was the purpose of this study to determine if attitudes toward education of students and parents of students involved in a specific individualized reading program ranging from one to three years in grades four through eight were significantly different from those of students and parents of students enrolled in a traditional reading program in the same school system. (Abstract shortened.

A Measure of Media Bias

In this paper we estimate ADA (Americans for Democratic Action) scores for major media outlets such as the New York Times, USA Today, Fox News' Special Report, and all three network television news shows. Our estimates allow us to answer such questions as “Is the average article in the New York Times more liberal than the average speech by Tom Daschle?” or “Is the average story on Fox News more conservative than the average speech by Bill Frist?” To compute our measure, we count the times that a media outlet cites various think tanks and other policy groups. We compare this with the times that members of Congress cite the same groups in their speeches on the floor of the House and Senate. By comparing the citation patterns we construct an ADA score. As a simplified example, imagine that there were only two think tanks, and suppose that the New York Times cited the first think tank twice as often as the second. Our method asks: What is the typical ADA score of members of Congress who exhibit the same frequency (2:1) in their speeches? This is the score that we would assign to the New York Times. Our results show a strong liberal bias. All of the news outlets except Fox News' Special Report and the Washington Times received a score to the left of the average member of Congress. Consistent with many conservative critics, CBS Evening News and the New York Times received a score far left of center. Outlets such as USA Today, NPR's Morning Edition, NBC's Nightly News and ABC's World News Tonight were moderately left. The most centrist outlets (but still left-leaning) by our measure were the Newshour with Jim Lehrer, CNN's NewsNight with Aaron Brown, and ABC's Good Morning America. Fox News' Special Report, while right of center, was closer to the center than any of the three major networks' evening news broadcasts. All of our findings refer strictly to the news stories of the outlets. That is, we omitted editorials, book reviews, and letters to the editor from our sample

Evaluation of Enzymatic Breakers for the Reduction of Environmental and Health Hazards Associated with Hydraulic Fracturing Fluids

2nd Place, Engineering, 2016 Denman Undergraduate Research ForumHonors Undergraduate Research Scholarship, College of EngineeringHydraulic fracturing ("fracking") is the process in which highly-pressurized fluids are injected underground to obtain energy resources that could not otherwise be accessed. Under high pressures, fissures are created in rock formations, which free trapped energy resources. The fluids used are composed mostly of water with chemical additives, which each add a specific functionality. A polymer increases fluid viscosity to initiate the fracture. A crosslinker may be added to further increase viscosity. Breakers decrease fluid viscosity for flowback. Despite its ability to retrieve critical energy resources, a primary concern with fracturing is its impact to human health and the environment. Many fluid components are toxic and there is fear that the fluid may contaminate groundwater. The goal of the research was to identify alternative components for fracturing fluids. Specifically, breakers were examined. Current breakers are strong oxidizers which degrade the polymer by a free-radical mechanism at high temperatures. Enzymatic breakers, however, are benign to environmental and human health. Two cellulasic enzymes, β-mannanase and α-galactosidase, were proposed as alternative breakers and their performance was compared to that of ammonium persulfate, the industry-standard breaker. Polymer (guar) and crosslinked polymer fluids were broken at well conditions (50oC) and industry-standard concentrations over time (18 hr.). Rheological testing of these fluids included frequency sweeps and steady shear rate sweeps to determine viscosity change over time and breaker kinetics. Filter cake testing was performed to study polymer degradation over time, as the breaker liberated low molecular weight oligomers. Statistical analyses were used to analyze these results. Enzymes show some promise in competing with ammonium persulfate as a breaker, although further testing is necessary. More environmentally-friendly components for fracking fluids may allow fracking, important to the U.S. energy portfolio, to continue with lessened risk and concern.A one-year embargo was granted for this item.Academic Major: Chemical Engineerin

Determination of Biaxial Flow Stress Using Frictionless Dome Test

AbstractThe frictionless dome test can be used to evaluate formability and determine the flow stress curve of sheet materials under biaxial forming conditions. The flow stress curve, obtained from the frictionless dome test can be determined up to larger strains than in tensile test. As a result the need for extrapolation of the stress-strain curve is reduced. The objectives of this study are to (a) for a given sheet material determine K and n values in Hollomon's Law (σ = Kɛn) by using experimental punch force vs. stroke curve and (b) develop the computer program, “PRODOME”, to automate the calculation of K and n values

Engineering Systems of Anti-Repressors for Next-Generation Transcriptional Programming

The ability to control gene expression in more precise, complex, and robust ways is becoming increasingly relevant in biotechnology and medicine. Synthetic biology has sought to accomplish such higher-order gene regulation through the engineering of synthetic gene circuits, whereby a gene’s expression can be controlled via environmental, temporal, or cellular cues. A typical approach to gene regulation is through transcriptional control, using allosteric transcription factors (TFs). TFs are regulatory proteins that interact with operator DNA elements located in proximity to gene promoters to either compromise or activate transcription. For many TFs, including the ones discussed here, this interaction is modulated by binding to a small molecule ligand for which the TF evolved natural specificity and a related metabolism. This modulation can occur with two main phenotypes: a TF shows the repressor (X+) phenotype if its binding to the ligand causes it to dissociate from the DNA, allowing transcription, while a TF shows the anti-repressor (XA) phenotype if its binding to the ligand causes it to associate to the DNA, preventing transcription. While both functional phenotypes are vital components of regulatory gene networks, anti-repressors are quite rare in nature compared to repressors and thus must be engineered. We first developed a generalized workflow for engineering systems of anti-repressors from bacterial TFs in a family of transcription factors related to the ubiquitous lactose repressor (LacI), the LacI/GalR family. Using this workflow, which is based on a re-routing of the TF’s allosteric network, we engineered anti-repressors in the fructose repressor (anti-FruR – responsive to fructose-1,6-phosphate) and ribose repressor (anti-RbsR – responsive to D-ribose) scaffolds, to complement XA TFs engineered previously in the LacI scaffold (anti-LacI – responsive to IPTG). Engineered TFs were then conferred with alternate DNA binding. To demonstrate their utility in synthetic gene circuits, systems of engineered TFs were then deployed to construct transcriptional programs, achieving all of the NOT-oriented Boolean logical operations – NOT, NOR, NAND, and XNOR – in addition to BUFFER and AND. Notably, our gene circuits built using anti-repressors are far simpler in design and, therefore, exert decreased burden on the chassis cells compared to the state-of-the-art as anti-repressors represent compressed logical operations (gates). Further, we extended this workflow to engineer ligand specificity in addition to regulatory phenotype. Performing the engineering workflow with a fourth member of the LacI/GalR family, the galactose isorepressor (GalS – naturally responsive to D-fucose), we engineered IPTG-responsive repressor and anti-repressor GalS mutants in addition to a D-fucose responsive anti-GalS TF. These engineered TFs were then used to create BANDPASS and BANDSTOP biological signal processing filters, themselves compressed compared to the state-of-the-art, and open-loop control systems. These provided facile methods for dynamic turning ‘ON’ and ‘OFF’ of genes in continuous growth in real time. This presents a general advance in gene regulation, moving beyond simple inducible promoters. We then demonstrated the capabilities of our engineered TFs to function in combinatorial logic using a layered logic approach, which currently stands as the state-of-the art. Using our anti-repressors in layered logic had the advantage of reducing cellular metabolic burden, as we were able to create the fundamental NOT/NOR operations with fewer genetic parts. Additionally, we created more TFs to use in layered logic approaches to prevent cellular cross-talk and minimize the number of TFs necessary to create these gene circuits. Here we demonstrated the successful deployment of our XA-built NOR gate system to create the BUFFER, NOT, NOR, OR, AND, and NAND gates. The work presented here describes a workflow for engineering (i) allosteric phenotype, (ii) ligand selectivity, and (iii) DNA specificity in allosteric transcription factors. The products of the workflow themselves serve as vital tools for the construction of next-generation synthetic gene circuits and genetic regulatory devices. Further, from the products of the workflow presented here, certain design heuristics can be gleaned, which should better facilitate the design of allosteric TFs in the future, moving toward a semi-rational engineering approach. Additionally, the work presented here outlines a transcriptional programming structure and metrology which can be broadly adapted and scaled for future applications and expansion. Consequently, this thesis presents a means for advanced control of gene expression, with promise to have long-reaching implications in the future.Ph.D

Application of change point analysis to daily influenza-like illness emergency department visits

Background: The utility of healthcare utilization data from US emergency departments (EDs) for rapid monitoring of changes in influenza-like illness (ILI) activity was highlighted during the recent influenza A (H1N1) pandemic. Monitoring has tended to rely on detection algorithms, such as the Early Aberration Reporting System (EARS), which are limited in their ability to detect subtle changes and identify disease trends. Objective: To evaluate a complementary approach, change point analysis (CPA), for detecting changes in the incidence of ED visits due to ILI. Methodology and principal findings Data collected through the Distribute project (isdsdistribute.org), which aggregates data on ED visits for ILI from over 50 syndromic surveillance systems operated by state or local public health departments were used. The performance was compared of the cumulative sum (CUSUM) CPA method in combination with EARS and the performance of three CPA methods (CUSUM, structural change model and Bayesian) in detecting change points in daily time-series data from four contiguous US states participating in the Distribute network. Simulation data were generated to assess the impact of autocorrelation inherent in these time-series data on CPA performance. The CUSUM CPA method was robust in detecting change points with respect to autocorrelation in time-series data (coverage rates at 90% when −0.2≤ρ≤0.2 and 80% when −0.5≤ρ≤0.5). During the 2008–9 season, 21 change points were detected and ILI trends increased significantly after 12 of these change points and decreased nine times. In the 2009–10 flu season, we detected 11 change points and ILI trends increased significantly after two of these change points and decreased nine times. Using CPA combined with EARS to analyze automatically daily ED-based ILI data, a significant increase was detected of 3% in ILI on April 27, 2009, followed by multiple anomalies in the ensuing days, suggesting the onset of the H1N1 pandemic in the four contiguous states. Conclusions and significance As a complementary approach to EARS and other aberration detection methods, the CPA method can be used as a tool to detect subtle changes in time-series data more effectively and determine the moving direction (ie, up, down, or stable) in ILI trends between change points. The combined use of EARS and CPA might greatly improve the accuracy of outbreak detection in syndromic surveillance systems

Recombinant "IMS TAG" proteins : a new method for validating bottom-up matrix-assisted laser desorption/ionisation ion mobility separation mass spectrometry imaging

Rationale - Matrix assisted laser desorption ionisation mass spectrometry imaging (MALDI-MSI) provides a methodology to map the distribution of peptides generated by in situ tryptic digestion of biological tissue. It is challenging to correlate these peptides to the proteins from which they arise because of the many potentially overlapping and hence interfering peptide signals generated. Methods - A recombinant protein has been synthesised that when cleaved with trypsin yields a range of peptide standards for use as identification and quantification markers for multiple proteins in one MALDI-IMS-MSI experiment. Mass spectrometry images of the distribution of proteins in fresh frozen and formalin fixed paraffin embedded tissue samples following in situ tryptic digestion were generated by isolating signals on the basis of their m/z value and ion mobility drift time which were correlated to matching peptides in the recombinant standard. Results - Tryptic digestion of the IMS-TAG protein and MALDI-MS analysis yielded values for m/z and ion mobility drift time for the signature peptides included in it. MALDI-IMS-MSI images for the distribution of the proteins HSP 90 and Vimentin, in FFPE EMT6 mouse tumours and HSP-90 and Plectin in a fresh frozen mouse fibrosarcoma were generated by extracting ion images at the corresponding m/z and drift time from the tissue samples. Conclusions - The IMS-TAG approach provides a new means to confirm the identity of peptides generated by in situ digestion of biological tissue.</p