Normalizer: Augmenting Code Clone Detectors using Source Code Normalization

Code clones are duplicate fragments of code that perform the same task. As software code bases increase in size, the number of code clones also tends to increase. These code clones, possibly created through copy-and-paste methods or unintentional duplication of effort, increase maintenance cost over the lifespan of the software. Code clone detection tools exist to identify clones where a human search would prove unfeasible, however the quality of the clones found may vary. I demonstrate that the performance of such tools can be improved by normalizing the source code before usage. I developed Normalizer, a tool to transform C source code to normalized source code where the code is written as consistently as possible. By maintaining the code\u27s function while enforcing a strict format, the variability of the programmer\u27s style will be taken out. Thus, code clones may be easier to detect by tools regardless of how it was written. Reordering statements, removing useless code, and renaming identifiers are used to achieve normalized code. Normalizer was used to show that more clones can be found in Introduction to Computer Networks assignments by normalizing the source code versus the original source code using a small variety of code clone detection tools

ANGLE OF ATTACK DETERMINATION USING INERTIAL NAVIGATION SYSTEM DATA FROM FLIGHT TESTS

Engineers and pilots rely on mechanical flow angle vanes on air data probes to determine the angle of attack of the aircraft in flight. These probes, however, are costly, come with inherent measurement errors, affect the flight characteristics of the aircraft, and are potentially dangerous in envelope expansion flights. Advances in the accuracy, usability, and affordability of inertial navigation systems allow for angle of attack to be determined accurately without direct measurement of the airflow around the aircraft. Utilizing an algorithm developed from aircraft equations of motion, a post-flight data review is completed as the first step in proving the low cost feasibility of utilizing inertial navigation data for such analysis. Flight tests were conducted with the UTSI Cessna 210 research aircraft to calibrate an angle of attack flow angle vane and obtain inertial navigation data from a commercial INS system in typical flight scenarios. The results of the angle of attack algorithm are compared to the measured angle of attack flow angle vane. Discussed in this thesis are the feasibility and potential applications of angle of attack determination from inertial data

Forest Sign Maker

Executive Summary: The Inyo National Forest is arguably one of the most beautiful locations in California, containing natural masterpieces such as Mount Whitney and the Ancient Bristlecone Pine Forest. Despite its magnificence, the Inyo National Forest can be a treacherous region. The Friends of the Inyo take pride in being able to facilitate the viewing experience for all outdoorsmen by maintaining the mountain trails, which includes providing adequate trail signage. Unfortunately, there is a fundamental issue with the recent state of trail signage in the Inyo National Forest: the rate at which signs are being vandalized or naturally destroyed is greater than the rate at which signs can be produced. More specifically, the problem is that the current sign production process is completely manual; the process of routing the necessary letters and symbols consumes the majority of the production time, since it takes approximately two days to complete. Without adequate signage on the mountain trails, hikers and explorers are at a heightened risk for injury. We, the Cal Poly Forest Friends, have been commissioned by the Friends of the Inyo to resolve the issue of manufacturing trail signs. We plan on designing, building, and testing a prototype CNC machine for Paul McFarland, an employee of the Friends of the Inyo whom is responsible for replacing signs. This CNC machine can automatically produce a trail sign from a wooden blank so as to expedite the sign replacement process. By comparing different industry methods of etching letters into a wood substrate, researching all applicable signage guidelines for compliance, and optimizing the prototype design for the intended use cases, we have developed a low cost, high capacity CNC router that can be installed directly in Paul McFarland’s workshop. There has been much work done in the field of CNC machinery, so we believe it is feasible to design a functioning prototype that has been optimized for this purpose. The positional accuracy range of the machine will be broadened from the industry standard of ±0.0005 in to our requirement of ±0.063 inches. This optimized accuracy will allow for emphasis on increased workpiece capacity at a lower total cost. Additionally, by building the prototype CNC router as part of the Cal Poly Multidisciplinary Senior Project class, we will be able to adhere to the revised $3,500 budget. With a successful prototype in hand by June 2015, the sign production rate for the Friends of the Inyo will potentially increase tenfold, and provide the Friends of the Inyo with the ability to replace illegible trail signs within the Inyo National Forest

Phase Contrast Imaging of Laser-Induced Microcavitation

As the medical field becomes more advanced, the scale of operation becomes increasingly smaller. Due to this trend, traditional mechanical tools like a scalpel may not become fine enough to be used for such manipulation. As a result, laser based medical surgeries such as LASIK (Laser assisted in situ keratomileusis) have become popular in recent decades. The associated laser tissue interactions, in particular photoablation, have become an important field of study to reduce unpredictable aftereffects of laser surgery. A consequence of photoablation is laser-induced microcavitation. Laser – induced microcavitation is a process in which optical energy from a laser converts to thermal energy of the tissue and creates a shockwave and a vapor bubble inside a liquid rich environment. As most bio-tissue is liquid rich, laser-induced microcavitation is an important field to study. There have been a number of theoretical and experimental studies regarding laser-induced microcavitation. However most theoretical studies are semi-analytical and focus on the oscillation of the cavitation bubble after it has formed. Additionally, most visual experimental studies use brightfield microscopy to image the microcavitation process. In order to supplement the existing theoretical and experimental studies, this thesis will develop a thermodynamic numerical simulation for the early (< 1 μs) microcavitation process and an experimental setup to image microcavitation develop with phase contrast microscopy. The goal of the numerical simulation is to accurately model the microcavitation process. The corresponding goal of the experimental setup is to identify additional features not visible in brightfield microscopy. The numerical simulation developed in this study was able to model the bubble and shockwave features, but still needs refinement due to only considering linear light absorption instead of plasma induced ablation. The pulsed illumination phase contrast microscopy developed in this study was able to image the vapor bubble boundary with higher contrast and resolve additional features in the high pressure region between the bubble and shockwave. As phase contrast microscopy is a qualitative imaging rather than a quantitative imaging process, the next step is to use differential interference contrast (DIC) microscopy to quantify the features resolved in phase contrast microscopy

On Enabling Integrated Process Compliance with Semantic Constraints in Process Management Systems

Key to broad use of process management systems (PrMS) in practice is their ability to foster and ease the implementation, execution, monitoring, and adaptation of business processes while still being able to ensure robust and error-free process enactment. To meet these demands a variety of mechanisms has been developed to prevent errors at the structural level (e.g., deadlocks). In many application domains, however, processes often have to comply with business level rules and policies (i.e., semantic constraints) as well. Hence, to ensure error-free executions at the semantic level, PrMS need certain control mechanisms for validating and ensuring the compliance with semantic constraints. In this paper, we discuss fundamental requirements for a comprehensive support of semantic constraints in PrMS. Moreover, we provide a survey on existing approaches and discuss to what extent they are able to meet the requirements and which challenges still have to be tackled. In order to tackle the particular challenge of providing integrated compliance support over the process lifecycle, we introduce the SeaFlows framework. The framework introduces a behavioural level view on processes which serves a conceptual process representation for constraint specification approaches. Further, it provides general compliance criteria for static compliance validation but also for dealing with process changes. Altogether, the SeaFlows framework can serve as formal basis for realizing integrated support of semantic constraints in PrMS

Compliance of Semantic Constraints - A Requirements Analysis for Process Management Systems

Key to the use of process management systems (PrMS) in practice is their ability to facilitate the implementation, execution, and adaptation of business processes while still being able to ensure error-free process executions. Mechanisms have been developed to prevent errors at the syntactic level such as deadlocks. In many application domains, processes often have to comply with business level rules and policies (i.e., semantic constraints). Hence, in order to ensure error-free executions at the semantic level, PrMS need certain control mechanisms for validating and ensuring the compliance with semantic constraints throughout the process lifecycle. In this paper, we discuss fundamental requirements for a comprehensive support of semantic constraints in PrMS. Moreover, we provide a survey on existing approaches and discuss to what extent they meet the requirements and which challenges still have to be tackled. Finally, we show how the challenge of life time compliance can be dealt with by integrating design time and runtime process validation

Cancer: The Role of Bax Inhibitor in C. elegans

Ibrahim Abaherah ’20 Major: Biology Michael Bittner \u2721Major: Biology Kevin Ly \u2723Major: Biology Faculty Mentor: Dr. Melissa Silvestrini, Biology Bax inhibitor-1 is an evolutionarily conserved regulator of apoptosis and ER stress in cells. Bax inhibitor-1 is regulated by IRE-1, a transmembrane protein in the ER that is responsible for detection of ER-induced stress and activation of downstream targets involved in the unfolded protein response (UPR) to maintain homeostasis. Our goal is to determine whether the C. elegans Bax inhibitor-1 homolog tmbi-4 is dependent on the IRE1 pathway in C. elegans. Our preliminary data in the lab suggest that tbmi-4 mutants exhibits similar developmental defects and increased sensitivity to ER stress as observed in animals with impaired IRE-1 function. To do so we will perform an ER stress assay to determine how loss of tmbi-4 effects development, thermotolerance and lifespan in C. elegans in the presence and absence of ER stress. These studies will reveal the cellular role of the C. elegans BAX inhibitor tmbi-4

Shared and Distinct Features of Human Milk and Infant Stool Viromes.

Infants acquire many of their microbes from their mothers during the birth process. The acquisition of these microbes is believed to be critical in the development of the infant immune system. Bacteria also are transmitted to the infant through breastfeeding, and help to form the microbiome of the infant gastrointestinal (GI) tract; it is unknown whether viruses in human milk serve to establish an infant GI virome. We examined the virome contents of milk and infant stool in a cohort of mother-infant pairs to discern whether milk viruses colonize the infant GI tract. We observed greater viral alpha diversity in milk than in infant stool, similar to the trend we found for bacterial communities from both sites. When comparing beta diversity, viral communities were mostly distinguishable between milk and infant stool, but each was quite distinct from adult stool, urine, and salivary viromes. There were significant differences in viral families in the infant stool (abundant bacteriophages from the family Siphoviridae) compared to milk (abundant bacteriophages from the family Myoviridae), which may reflect significant differences in the bacterial families identified from both sites. Despite the differences in viral taxonomy, we identified a significant number of shared viruses in the milk and stool from all mother-infant pairs. Because of the significant proportion of bacteriophages transmitted in these mother-infant pairs, we believe the transmission of milk phages to the infant GI tract may help to shape the infant GI microbiome

X-ray protection, surface chemistry and rheology of ball-milled submicron Gd2O3 aqueous suspension

X-ray protective garments are typically comprised of lead-based materials, which are toxic to both people and the environment. Developing alternative lightweight radiation shielding materials is a priority for protecting people working with radiation. Gadolinium, with an electron configuration typical of radiation shielding elements, is proposed as a non-toxic replacement for lead. This study provides new insights into the potential for a gadolinium suspension for replacing lead and proposes an inexpensive and effective preparation method. Submicron gadolinium oxide (Gd2O3) was generated using a cost effective ball milling method involving addition of NaCl. Then, the dispersed-flocculated behaviour of Gd2O3 aqueous slurries was studied via yield stress and zeta potential techniques to stabilise the dispersion. The relationship of the transmission-volume fraction at different kVp from an interventional radiology source was established to investigate radiation attenuation performance of the suspension. At a low volume fraction (0.082), the gadolinium slurry attenuated more than 95% of the X-ray load from a 50⬜100 kVp source. The equivalent weight-thickness at the same attenuation of 95% (5% transmission) of the Gd2O3 suspension was 1.5 g/cm2, which is comparable to that of equivalent commercial lead-based materials (\u3e1 g/cm2). This research is significant for developing a non-lead-based material, Gd2O3 suspension, which offers effective radiation attenuation with weight-thickness minimisation and safe use and disposal