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Probabilistic Modeling and Regression Analysis of Experimental Data for Structural Systems

Description

The Experimental Data Processing (EDP) software is a C++ GUI-based application to streamline the process of creating a model for structural systems based on experimental data. EDP is designed to process raw data, filter the data for noise and outliers, create a fitted model to describe that data, complete a…

The Experimental Data Processing (EDP) software is a C++ GUI-based application to streamline the process of creating a model for structural systems based on experimental data. EDP is designed to process raw data, filter the data for noise and outliers, create a fitted model to describe that data, complete a probabilistic analysis to describe the variation between replicates of the experimental process, and analyze reliability of a structural system based on that model. In order to help design the EDP software to perform the full analysis, the probabilistic and regression modeling aspects of this analysis have been explored. The focus has been on creating and analyzing probabilistic models for the data, adding multivariate and nonparametric fits to raw data, and developing computational techniques that allow for these methods to be properly implemented within EDP. For creating a probabilistic model of replicate data, the normal, lognormal, gamma, Weibull, and generalized exponential distributions have been explored. Goodness-of-fit tests, including the chi-squared, Anderson-Darling, and Kolmogorov-Smirnoff tests, have been used in order to analyze the effectiveness of any of these probabilistic models in describing the variation of parameters between replicates of an experimental test. An example using Young's modulus data for a Kevlar-49 Swath stress-strain test was used in order to demonstrate how this analysis is performed within EDP. In order to implement the distributions, numerical solutions for the gamma, beta, and hypergeometric functions were implemented, along with an arbitrary precision library to store numbers that exceed the maximum size of double-precision floating point digits. To create a multivariate fit, the multilinear solution was created as the simplest solution to the multivariate regression problem. This solution was then extended to solve nonlinear problems that can be linearized into multiple separable terms. These problems were solved analytically with the closed-form solution for the multilinear regression, and then by using a QR decomposition to solve numerically while avoiding numerical instabilities associated with matrix inversion. For nonparametric regression, or smoothing, the loess method was developed as a robust technique for filtering noise while maintaining the general structure of the data points. The loess solution was created by addressing concerns associated with simpler smoothing methods, including the running mean, running line, and kernel smoothing techniques, and combining the ability of each of these methods to resolve those issues. The loess smoothing method involves weighting each point in a partition of the data set, and then adding either a line or a polynomial fit within that partition. Both linear and quadratic methods were applied to a carbon fiber compression test, showing that the quadratic model was more accurate but the linear model had a shape that was more effective for analyzing the experimental data. Finally, the EDP program itself was explored to consider its current functionalities for processing data, as described by shear tests on carbon fiber data, and the future functionalities to be developed. The probabilistic and raw data processing capabilities were demonstrated within EDP, and the multivariate and loess analysis was demonstrated using R. As the functionality and relevant considerations for these methods have been developed, the immediate goal is to finish implementing and integrating these additional features into a version of EDP that performs a full streamlined structural analysis on experimental data.

ContributorsMarkov, Elan Richard (Author) / Rajan, Subramaniam (Thesis director) / Khaled, Bilal (Committee member) / Chemical Engineering Program (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Ira A. Fulton School of Engineering (Contributor) / Barrett, The Honors College (Contributor)

Created2016-05

Joseph Rotblat, the Physicist Who Left the Manhattan Project: a Biography of Scientific Responsibility

Description

Joseph Rotblat (1908-2005) was the only physicist to leave the Manhattan Project for moral reasons before its completion. He would spend the rest of his life advocating for nuclear disarmament. His activities for disarmament resulted in the formation, in 1957, of the Pugwash conferences, which emerged as the leading global…

Joseph Rotblat (1908-2005) was the only physicist to leave the Manhattan Project for moral reasons before its completion. He would spend the rest of his life advocating for nuclear disarmament. His activities for disarmament resulted in the formation, in 1957, of the Pugwash conferences, which emerged as the leading global forum to advance limits on nuclear weapons during the Cold War. Rotblat's efforts, and the activities of Pugwash, resulted in both being awarded the Nobel Peace Prize in 1995. Rotblat is a central figure in the global history of resistance to the spread of nuclear weapons. He also was an important figure in the emergence, after World War II, of a counter-movement to introduce new social justifications for scientific research and new models for ethics and professionalism among scientists. Rotblat embodies the power of the individual scientist to say "no" and thus, at least individually, put limits of conscience on his or her scientific activity. This paper explores the political and ethical choices scientists make as part of their effort to behave responsibly and to influence the outcomes of their work. By analyzing three phases of Rotblat's life, I demonstrate how he pursued his ideal of beneficial science, or science that appears to benefit humanity. The three phases are: (1) his decision to leave the Manhattan Project in 1944, (2) his role in the creation of Pugwash in 1957 and his role in the rise of the organization into international prominence and (3) his winning the Nobel Peace Prize in 1995. These three phases of Rotblat's life provide a singular window of the history of nuclear weapons and the international movement for scientific responsibility in the 50 years since the bombing of Hiroshima in 1945. While this paper does not provide a complete picture of Rotblat's life and times, I argue that his experiences shed important light on the difficult question of the individual responsibility of scientists.

ContributorsEvans, Alison Dawn (Author) / Zachary, Gregg (Thesis director) / Hurlbut, Ben (Committee member) / Francis, Sybil (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)

Created2015-05

Perceived Ratio of Vegetable to Fruit in Juice Diets: A Case Study of the Online Juicing Population

Description

The purpose of this study was to determine the ratio of vegetable to fruit incorporated during a fresh vegetable and/or fruit juice diet. Juicing is the process of extracting the liquid part of a plant, fruit, or vegetable. Food can be ground, pressed, and spun to separate the liquid from…

The purpose of this study was to determine the ratio of vegetable to fruit incorporated during a fresh vegetable and/or fruit juice diet. Juicing is the process of extracting the liquid part of a plant, fruit, or vegetable. Food can be ground, pressed, and spun to separate the liquid from the pulp. A juice diet involves juicing and consuming a variety of vegetables and fruits. The primary objective of this study was to gather information about the ratio of vegetable to fruit incorporated in freshly made juices during a juice diet. Therefore, the study survey inquired about various topics related to ingredient ratio during a juice diet. The survey data allowed for examination of the relationships between ingredient ratio and certain variables (e.g. gender, age, length of time juicing, juice fast participation, health effects, etc.). The study participants were recruited using online social media. Facebook was the primary method for reaching the online juicing community. A written invitation was distributed in several health related Facebook groups encouraging any person with experience juicing to complete an anonymous survey. This post was also shared via Twitter and various health related websites. The study survey data was used to examine the relationships between ingredient ratio and specific variables. The survey data showed participants had varying levels of experience with juicing. The responses indicated many participants were familiar with juice fasting and many participants completed more than one juice fast. Based on the survey response data, the most common ratio of vegetable to fruit incorporated by the participants during a juice diet was 80% vegetable to 20% fruit. The majority of participants indicated daily consumption of freshly made juice containing 70% -100% vegetables. Based on the survey response data, beginner juicers may be less inclined to incorporate organic produce into their juice diet compared to advanced juicers. The majority of participants reported positive health benefits during a juice diet. Some of the positive health benefits indicated by participants include weight loss, increased energy, and a positive impact on disease symptoms. Some of the negative side effects experienced by participants during a juice diet include frequent urination, headache, and cravings. Cross tabulation calculations between the ratio of ingredients and several variables covered by the study survey demonstrated statistical significance (i.e. length of time juicing, frequency of drinking juice, juice fast participation, number of juice fasts completed, servings of vegetables/fruit in a juice, percent of organic vegetables/fruit used in a juice, perceived positive side effects, and perceived negative side effects). This study provided insight about the average ratio of vegetable to fruit incorporated by participants during a juice diet. When analyzing the data it is important to consider the survey data was self-reported. Therefore, every result and conclusion is based on the individual perceptions of the study participants. In future experimentation, the use of medical tests and blood work would be useful to determine the biological and biochemical effects of drinking raw vegetable and/or fruit juice on the human body.

ContributorsMata, Sara Ann (Author) / Mayol-Kreiser, Sandra (Thesis director) / Shepard, Christina (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor)

Created2015-05

Microbiota Transfer Therapy Alters Gut Ecosystem and Improves Gastrointestinal and Autism Symptoms: An Open-Label Study

Description

Background: Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and activities. The causes of these disorders remain poorly understood, but gut microbiota, the 1013 bacteria in the human intestines, have been implicated because children…

Background: Autism spectrum disorders (ASD) are complex neurobiological disorders that impair social interactions and communication and lead to restricted, repetitive, and stereotyped patterns of behavior, interests, and activities. The causes of these disorders remain poorly understood, but gut microbiota, the 1013 bacteria in the human intestines, have been implicated because children with ASD often suffer gastrointestinal (GI) problems that correlate with ASD severity. Several previous studies have reported abnormal gut bacteria in children with ASD. The gut microbiome-ASD connection has been tested in a mouse model of ASD, where the microbiome was mechanistically linked to abnormal metabolites and behavior. Similarly, a study of children with ASD found that oral non-absorbable antibiotic treatment improved GI and ASD symptoms, albeit temporarily. Here, a small open-label clinical trial evaluated the impact of Microbiota Transfer Therapy (MTT) on gut microbiota composition and GI and ASD symptoms of 18 ASD-diagnosed children.

Results: MTT involved a 2-week antibiotic treatment, a bowel cleanse, and then an extended fecal microbiota transplant (FMT) using a high initial dose followed by daily and lower maintenance doses for 7–8 weeks. The Gastrointestinal Symptom Rating Scale revealed an approximately 80% reduction of GI symptoms at the end of treatment, including significant improvements in symptoms of constipation, diarrhea, indigestion, and abdominal pain. Improvements persisted 8 weeks after treatment. Similarly, clinical assessments showed that behavioral ASD symptoms improved significantly and remained improved 8 weeks after treatment ended. Bacterial and phage deep sequencing analyses revealed successful partial engraftment of donor microbiota and beneficial changes in the gut environment. Specifically, overall bacterial diversity and the abundance of Bifidobacterium, Prevotella, and Desulfovibrio among other taxa increased following MTT, and these changes persisted after treatment stopped (followed for 8 weeks).

Conclusions: This exploratory, extended-duration treatment protocol thus appears to be a promising approach to alter the gut microbiome and virome and improve GI and behavioral symptoms of ASD. Improvements in GI symptoms, ASD symptoms, and the microbiome all persisted for at least 8 weeks after treatment ended, suggesting a long-term impact.

ContributorsKang, Dae Wook (Author) / Adams, James (Author) / Gregory, Ann C. (Author) / Borody, Thomas (Author) / Chittick, Lauren (Author) / Fasano, Alessio (Author) / Khoruts, Alexander (Author) / Geis, Elizabeth (Author) / Maldonado Ortiz, Juan (Author) / McDonough-Means, Sharon (Author) / Pollard, Elena (Author) / Roux, Simon (Author) / Sadowsky, Michael J. (Author) / Schwarzberg Lipson, Karen (Author) / Sullivan, Matthew B. (Author) / Caporaso, J. Gregory (Author) / Krajmalnik-Brown, Rosa (Author) / Biodesign Institute (Contributor)

Created2017-01-23

Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children

Description

High proportions of autistic children suffer from gastrointestinal (GI) disorders, implying a link between autism and abnormalities in gut microbial functions. Increasing evidence from recent high-throughput sequencing analyses indicates that disturbances in composition and diversity of gut microbiome are associated with various disease conditions. However, microbiome-level studies on autism are…

High proportions of autistic children suffer from gastrointestinal (GI) disorders, implying a link between autism and abnormalities in gut microbial functions. Increasing evidence from recent high-throughput sequencing analyses indicates that disturbances in composition and diversity of gut microbiome are associated with various disease conditions. However, microbiome-level studies on autism are limited and mostly focused on pathogenic bacteria. Therefore, here we aimed to define systemic changes in gut microbiome associated with autism and autism-related GI problems. We recruited 20 neurotypical and 20 autistic children accompanied by a survey of both autistic severity and GI symptoms. By pyrosequencing the V2/V3 regions in bacterial 16S rDNA from fecal DNA samples, we compared gut microbiomes of GI symptom-free neurotypical children with those of autistic children mostly presenting GI symptoms. Unexpectedly, the presence of autistic symptoms, rather than the severity of GI symptoms, was associated with less diverse gut microbiomes. Further, rigorous statistical tests with multiple testing corrections showed significantly lower abundances of the genera Prevotella, Coprococcus, and unclassified Veillonellaceae in autistic samples. These are intriguingly versatile carbohydrate-degrading and/or fermenting bacteria, suggesting a potential influence of unusual diet patterns observed in autistic children. However, multivariate analyses showed that autism-related changes in both overall diversity and individual genus abundances were correlated with the presence of autistic symptoms but not with their diet patterns. Taken together, autism and accompanying GI symptoms were characterized by distinct and less diverse gut microbial compositions with lower levels of Prevotella, Coprococcus, and unclassified Veillonellaceae.

ContributorsKang, Dae Wook (Author) / Park, Jin (Author) / Ilhan, Zehra (Author) / Wallstrom, Garrick (Author) / LaBaer, Joshua (Author) / Adams, James (Author) / Krajmalnik-Brown, Rosa (Author) / Biodesign Institute (Contributor)

Created2013-06-03

Evaluating The Effects of Fumonisin B1 on the Human Gut Microbiome with in vitro Bioreactors

Description

Fumonisins are fungal metabolites found in corn and cereals. Fumonisins pose health risks, including suspected carcinogenicity, yet their mechanism of toxicity remains unclear. While modifications in the human gut microbiome can impact host health, the effects of fumonisins on the microbiome are not well understood. Thus, our study aimed to…

Fumonisins are fungal metabolites found in corn and cereals. Fumonisins pose health risks, including suspected carcinogenicity, yet their mechanism of toxicity remains unclear. While modifications in the human gut microbiome can impact host health, the effects of fumonisins on the microbiome are not well understood. Thus, our study aimed to assess a possible dose-response relationship between fumonisin B1 (FB1) and the gut microbiome. We utilized in vitro anaerobic bioreactors with media simulating most of the nutrients in the human large intestine, inoculated them with fecal samples from 19 healthy adults and treated them with FB1 at concentrations of 0, 10, 100, and 1000 ppb. Analyses of bioreactor headspace revealed declining methane production over time, possibly influenced by the addition of dimethyl sulfoxide (DMSO). Significant differences in acetic acid production were observed in 10 ppb reactor (Day 2) and 100 ppb reactor (Day 8) when compared to 0 ppb control. Microbiome analysis showed minimal shifts in microbial relative abundances during FB1 treatment, except for Desulfovibrio desulfuricans C at Day 8 when compared between 0 ppb and 10 ppb as well as 10 ppb and 1000 ppb at Day 16. Alpha diversity analyses indicated significant differences in observed features within bioreactors of different treatments, with some variation in Faith’s Phylogenetic Diversity between the 0 ppb and 10 ppb bioreactors. Beta diversity analyses, however, revealed no significant differences between bioreactors. Overall, our findings suggest no clear dose-response relationship between FB1 treatment and gut microbiome composition/functions. The presence of DMSO may have obscured potential effects. This research will help contribute to our understanding of mycotoxicity influence on the human gut microbiome.

ContributorsSanchez Carreon, Aurely (Author) / Krajmalnik-Brown, Rosa (Thesis director) / Cheng, Qiwen (Committee member) / Barrett, The Honors College (Contributor) / School of Molecular Sciences (Contributor)

Created2024-05

The Impact of Diet on Skin Elasticity

Description

Skin elasticity, a key indicator of skin health, is influenced by various factors including diet and body composition. This study, led by Myka Williams as part of her Barrett, The Honors College Thesis Project at Arizona State University under the guidance of Dr. Carol Johnston and Dr. Sandy Mayol-Kreiser, investigates…

Skin elasticity, a key indicator of skin health, is influenced by various factors including diet and body composition. This study, led by Myka Williams as part of her Barrett, The Honors College Thesis Project at Arizona State University under the guidance of Dr. Carol Johnston and Dr. Sandy Mayol-Kreiser, investigates the relationship between diet—specifically vegetarian and omnivorous patterns—and skin elasticity. Utilizing the ElastiMeter from Delfin Technologies, we assessed the skin elasticity of 38 individuals from the ASU community. Our findings revealed no significant difference in skin elasticity between the dietary groups. However, intriguing correlations emerged between participants' Body Mass Index (BMI) and skin elasticity. These initial findings suggest the potential influence of body composition on skin health, warranting further research with additional parameters to strengthen and expand upon these observations.

ContributorsWilliams, Myka (Author) / Johnston, Carol (Thesis director) / Mayol-Kreiser, Sandy (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / School of Human Evolution & Social Change (Contributor)

Created2024-05