On a Clear Day You Can See Forever

These are the teaching notes for a case study in which students grapple with the issue of air pollution, specifically the causes and effects of haze and smog as ubiquitous, persistent air quality problems. In analyzing local conditions in one state, they will explore the wider environmental, political, social, and human health implications of air pollution. The case is designed to give students a taste of a real-world situation while dealing with course-related facts and issues. It has been scripted to facilitate students' exposure to authentic problems in their own backyard, but with the wider implications of government regulation and international cooperation on health issues within shared airsheds. Educational levels: High school, Undergraduate lower division

Knowledge-based system V and V in the Space Station Freedom program

Knowledge Based Systems (KBS's) are expected to be heavily used in the Space Station Freedom Program (SSFP). Although SSFP Verification and Validation (V&V) requirements are based on the latest state-of-the-practice in software engineering technology, they may be insufficient for Knowledge Based Systems (KBS's); it is widely stated that there are differences in both approach and execution between KBS V&V and conventional software V&V. In order to better understand this issue, we have surveyed and/or interviewed developers from sixty expert system projects in order to understand the differences and difficulties in KBS V&V. We have used this survey results to analyze the SSFP V&V requirements for conventional software in order to determine which specific requirements are inappropriate for KBS V&V and why they are inappropriate. Further work will result in a set of recommendations that can be used either as guidelines for applying conventional software V&V requirements to KBS's or as modifications to extend the existing SSFP conventional software V&V requirements to include KBS requirements. The results of this work are significant to many projects, in addition to SSFP, which will involve KBS's

Sexual Conflict Over Egg Allocation: A Dynamic Programming Approach to Modeling the Evolution of Male Harm and Female Resistance

Sexual conflict, which is expected to be ubiquitous among polygamous species, is known to occasionally result in male adaptations that are harmful to females. One theoretical model indicates that males may benefit from physically harming their mates by triggering a “terminal investment” reproductive response by them. Using dynamic programming, we explore how females optimize their lifetime egg allocation, how selection acts on males to exploit such allocation, and how females respond to resist this exploitation. The model reveals alternative female response pathways; one of the most effective of which is simply to forgo plasticity in egg allocation. By switching to a fixed reproductive schedule, females reduce their vulnerability to male manipulations. The results predict that terminal investment should be rare. In addition, terminal investment should occur at higher frequency among monogamous species, where male harm is never adaptive, than among polygamous species. Another unique conclusion of our model is that male harm should be exclusively or preferentially directed at older females and/or females in poor condition

Computational methods to improve genome assembly and gene prediction

DNA sequencing is used to read the nucleotides composing the genetic material that forms individual organisms. As 2nd generation sequencing technologies offering high throughput at a feasible cost have matured, sequencing has permeated nearly all areas of biological research. By a combination of large-scale projects led by consortiums and smaller endeavors led by individual labs, the flood of sequencing data will continue, which should provide major insights into how genomes produce physical characteristics, including disease, and evolve. To realize this potential, computer science is required to develop the bioinformatics pipelines to efficiently and accurately process and analyze the data from large and noisy datasets. Here, I focus on two crucial bioinformatics applications: the assembly of a genome from sequencing reads and protein-coding gene prediction. In genome assembly, we form large contiguous genomic sequences from the short sequence fragments generated by current machines. Starting from the raw sequences, we developed software called Quake that corrects sequencing errors more accurately than previous programs by using coverage of k-mers and probabilistic modeling of sequencing errors. My experiments show correcting errors with Quake improves genome assembly and leads to the detection of more polymorphisms in re-sequencing studies. For post-assembly analysis, we designed a method to detect a particular type of mis-assembly where the two copies of each chromosome in diploid genomes diverge. We found thousands of examples in each of the chimpanzee, cow, and chicken public genome assemblies that created false segmental duplications. Shotgun sequencing of environmental DNA (often called metagenomics) has shown tremendous potential to both discover unknown microbes and explore complex environments. We developed software called Scimm that clusters metagenomic sequences based on composition in an unsupervised fashion more accurately than previous approaches. Finally, we extended an approach for predicting protein-coding genes on whole genomes to metagenomic sequences by adding new discriminative features and augmenting the task with taxonomic classification and clustering of the sequences. The program, called Glimmer-MG, predicts genes more accurately than all previous methods. By adding a model for sequencing errors that also allows the program to predict insertions and deletions, accuracy significantly improves on error-prone sequences

Dirty snow: The impact of urban particulates on a mid-latitude seasonal snowpack

This thesis examines the spatial distribution of particulate matter in snow around a mid-size, midlatitude city. Particulates are small, light absorbing impurities that are produced from the incomplete combustion of carbon-based fuel. When deposited on the snowpack, these particles reduce snow albedo and accelerate melt. Two experiments were designed to explore the distribution and effect of urban particulate emissions on snow surrounding Syracuse, NY (43.049897, -76.149102, pop: 149,000). The “directional study” examined the relationship between distribution and cross-city prevailing wind, while, the “transect study” examined the variability of particulate concentration with distance from a busy interstate highway. Fifteen sites were sampled over two winter seasons (2016-2017 and 2017-2018). Eight sites were located in the suburbs roughly aligned to the cardinal directions with respect to the city, one site was located within the city boundaries and six sites were located on a transect across I-90. Snow temperature, air temperature, wind speed/direction and albedo were recorded at each site. A snow core was collected for laboratory analysis using the Light Meter Filter Analysis method and two photos were taken of the snow surface for a second albedo analysis using ImageJ. At the city-scale, trend analyses show that particulate concentration decreases from W to E across the urban center and albedo increases from NW to SE. The small westerly shift between albedo and particulate trend analysis may be explained by a slight difference in measurement parameters. Albedo analysis measures the effect of particulates on the snow surface since the end of snow accumulation. Particulate concentration, however, measures the total quantity of particulates in the entire snowpack. Both analyses align with the WSW to NW prevailing wind that is responsible for the formation of lake effect snow from Lake Ontario and Lake Erie. That said, the observed distribution was found to be opposite expectations. This is likely a result of wind circulation patterns within the urban core. At the local-scale, high particulate concentration/low albedo was found adjacent to the interstate highway. Results show that the concentration does not necessarily decrease with distance from vehicle emissions. Instead, particulate distribution is altered by the presence of any obstacles within 600m of the highway. Snow surface photo analysis was able to determine the relative albedo of each site but not actual albedo value. Despite this, the photo analysis method looks promising for future citizen science based studies of particulate matter. Overall, findings suggest that urban particulate distribution in midlatitude snow is altered by city morphology and proximity to local emission sources. Future research is necessary to examine how this distribution affects climatic processes in the midlatitudes

Angular trapping of a mirror using radiation pressure

Alignment control in gravitational-wave detectors has consistently proven to be a dicult problem due to the stringent noise contamination requirement for the gravitational wave readout and the radiation-pressure induced angular instability in Fabry- Perot cavities (Sidles-Sigg instability). In this thesis, I present optical springs as a tool to damp the motion of a mirror. I discuss the design and implementation of a single degree-of-freedom optical spring system and the importance of the photothermal eect in properly predicting optical spring behavior. I also present the development and implementation of an angular control scheme, attempting to damp two degrees of freedom with two optical cavities. I then extend this understanding into a plausible concept for implementing optical-spring-based angular control in the Advanced LIGO detectors

Comparison of student perceptions of the learning environment during an academic calendar change

This is the second phase of a longitudinal research project to determine the effects on the learning environment of the change from a quarter system to a semester system form of academic calendar at Iowa State University. The null hypotheses for this part of the project were: (1) There will be no change in the student\u27s perception of the learning environment between Year 1 (quarter system) and Year 2 (semester system). (2) The degree of change as reflected by difference scores will not be related to the independent variables studied. (3) Within subgroups of the selected variables, there will be no change between Year 1 and Year 2. The independent variables studied were sex, college affiliation, G.P.A., residential location, full-time/part-time, work, attendance at another school under the semester system and classification;Hypothesis number one was rejected for two factors and many individual items in the survey. In Year 1, the respondents were undecided or slightly favorable toward the Semester Advantages factor. In Year 2, the respondents disagreed with the Semester Advantages factor. With the Quarter Advantages factor, the respondents were on the disagree side of the scale in both years, but the disagreement was less strong in Year 2;Hypothesis number two was rejected for the independent variables of classification, sex, and work. The Semester Advantages factor produced a significant change in all three variables;Hypothesis number three was rejected for sex, work, previous exposure to a semester system and classification. The Semester Advantages factor and Quarter Advantages factor indicated significant change for the first three variables while the Cultural/Community Activities factor was significant for graduate students;A prediction equation was attempted for the Semester Advantages factor. The best predictor was how the person scored on that factor in Year 1. However, only 28% of the variability could be explained

Antigen Trafficking within \u3cem\u3eChlamydia trachomatis\u3c/em\u3e-Infected Polarized Human Endometrial Epithelial Cells.

Chlamydia trachomatis serovars D-K are the leading cause of bacterially-acquired sexually transmitted infections in the United States. As an obligate intracellular pathogen, C. trachomatis infects columnar epithelial cells of the genital mucosae and can cause deleterious sequelae such as pelvic inflammatory disease, infertility, and ectopic pregnancy. Several chlamydial antigens reach the host cell cytosol prior to the natural release of chlamydiae at the end of the developmental cycle. While some of these extra-inclusion antigens traffic to the host cell surface, others remain intracellular where they are proposed to influence vital host cell functions and antigen trafficking and presentation. The research herein examines the escape and trafficking of the immunodominant chlamydial antigens MOMP, LPS, and cHsp60 within C. trachomatis serovar E-infected polarized human endometrial epithelial cells. Studies using high-resolution transmission electron microscopy (TEM) and immuno-TEM report the novel escape mechanism of chlamydial antigens via vesicles everted/pinched off from the inclusion membrane, an occurrence observed both in the presence and absence of the antibiotic azithromycin. These extra-inclusion vesicles were differentiated from Golgi vesicles and were shown to deliver chlamydial heat shock protein 60 (cHsp60)-homologs 2 and 3, but not homolog 1, to the infected cell surface. Examination of the iron-responsiveness of the three cHsp60 homologs by immuno-TEM revealed a significant increase in cHsp60-2 following iron deprivation. Further investigation of the trafficking of chlamydial MOMP and LPS antigens enveloped within the protective everted inclusion membrane vesicles within host cells involved density gradient centrifugation for the separation of epithelial secretory pathway components followed by SDS-PAGE and Western blot to determine whether the chlamydial antigen-containing vesicles could fuse with and deliver the antigens to host cell organelles. Coupled with immuno-TEM, these data confirmed the presence of major chlamydial antigens within the endoplasmic reticulum of infected host cells. Additionally, chlamydial lipopolysaccharide (LPS) was co-localized with CD1d, a lipid antigen-presenting molecule. Collectively, these studies (i) establish a novel escape mechanism for chlamydial antigens, (ii) identify cHsp60-2 as a marker of iron stress response in C. trachomatis, and (iii) define for the first time the host cell ER as a destination for selected chlamydial antigens during infection