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HESTIA - Semi-Automatic and Adversary-Aware Risk Assessment of Critical Infrastructure Systems
No full textDue to the characteristics and connectivity of today's critical infrastructure like the Cyber Physical Systems (CPS), cyber-attacks on these systems are currently difficult to prevent in an efficient and sustainable manner. Prevention and mitigation need accurate identification and evaluation of: system vulnerabilities, likely threats and attacks, and applicable hardening measures. Furthermore, the ability to prioritize hardening measures based on accurate assessments of threat risk and consequence and mitigation availability, applicability, and cost is also needed. To address this challenge we created HESTIA: High-level and Extensible System for Training and Infrastructure risk Assessment. We describe the architecture and working principles of HESTIA. We present a formal model of the HESTIA system. We validate the HESTIA system using formal proofs and a case-study based proof tracing. We hope that the HESTIA system model will enable CPS engineers to build software that can iteratively: 1) specify a CPS (system), 2) select applicable attacks and hardening measures from a library (delta), 3) check system and delta specifications for consistency and applicability, and 4) apply deltas on system specifications, forming a new CPS model. HESTIA enables the discovery of attack-defend scenarios through simulation and the design of optimal hardening strategies for a given CPS. The contributions reported in this dissertation are: (a) present a requirement for high-level and reconfigurable system for adversary-aware infrastructure risk assessment by performing a review of the existing literature; (b) present the architecture and workflow of HESTIA: a high-level and extensible system for adversary-aware infrastructure risk assessment; (c) formalize the HESTIA process and workflow; (d) present METICS: a realistic case study of a CPS organization; and (e) validate the HESTIA system using formal verification and proof tracing using the METICS case study.doctoral, Ph.D., Computer Science -- University of Idaho - College of Graduate Studies, 2020-0
Elucidating mechanisms that drive changes in the composition of the human vaginal microbiome
No full textThe influence of the vaginal microbiome on women’s relative risk to disease and reproductive complications has been well documented. In the last decade, extensive cross-sectional and longitudinal studies have shown that many types of vaginal communities are found in healthy women, and that the composition of these communities can change over a matter of days. Currently, we have a poor understanding of the factors that cause compositional differences observed between women and temporal changes within women. Thus, the goal of my work is to fill this gap in knowledge. In the opening chapter, I briefly review what is known about the composition of vaginal communities in reproductive age women. Due to the positive association with Lactobacillus in the vagina and vaginal health, I narrowed the focus on species within this genus. Additionally, I discuss two host factors, namely estrogen and glycogen that have been associated with changes in the abundances of lactobacilli over a woman’s lifespan. Next, I characterized the composition of vaginal bacterial communities in a cohort of black adolescent women based on differences in the total abundances of Lactobacillus. Then I explore the relationships between estrogen, glycogen, stress, and vaginal community composition. I confirmed previous findings that glycogen levels are associated with high abundances of lactobacilli in vaginal communities. I also report that estradiol levels do not correlate with vaginal glycogen measurements, nor vaginal community composition. This finding is noteworthy as it suggests the association between estrogen, glycogen, and vaginal lactobacilli is more complex than previously thought. This study addresses potential developmental factors that influence the composition of vaginal communities and provides new insights into the kinds of communities that are present among black adolescent women. In my third chapter, I differentiated putative amylases in the human vagina, which likely break down glycogen into simpler sugars that are fermented by vaginal lactobacilli. For this work, I designed a pilot study to collect vaginal samples from 23 reproductive age women. Using metagenomics and proteomics, I identified putative amylases expressed in vaginal fluids that mapped to the metagenomes of vaginal bacteria. I report novel findings that there are multiple amylases in the human vagina that are produced by both the host and bacteria within the community. Finally, I explore the transition from pregnancy to postpartum in a cohort of 48 women. I document findings that are consistent with previous studies that showed the composition of vaginal communities changes from pregnancy to postpartum and is marked by reduced abundances of Lactobacillus and increased alpha diversity. I report new findings of host-associated compounds that are significantly associated with the changes observed during postpartum.doctoral, Ph.D., Bioinformatics & Computational Biology -- University of Idaho - College of Graduate Studies, 2020-0
Assessing Outcomes of Selection Using Genetic Panels for Prediction of Carcass Quality in Beef Cattle
No full textMarbling and tenderness are economically important traits that have been shown to be highly heritable in beef cattle. As a result, genetic panel technology has become available for beef producers to use as a selection tool and has grown in popularity in the beef industry since its validation. Therefore, the objectives of the outlined studies were to 1.) determine whether beef cattle genetically selected for tenderness generated a more tender product, and to 2.) evaluate the effectiveness of genetic panel marbling indexes [Igenity (IT) and PredicGEN (PG)] to predict marbling of crossbred cattle. In the first study, Igenity (IT) panel results were provided by a cattle producer for fifty-two steers. Carcasses from those steers were grouped based upon their IT tenderness index scores. Steaks from boneless strip loins collected from the carcasses were analyzed for Warner-Bratzler shear force (WBSF) and consumer sensory evaluations. In the second study, blood samples from twenty-three steers were submitted for genetic panel analysis, and their carcasses were grouped by IT and PG marbling index scores. Steaks from those carcasses were analyzed for WBSF and a consumer sensory panel. Based on results from the first experiment, the cattle that had been selected to be tender were very tender, suggesting a successful selection outcome. Although all the carcasses attained the USDA Certified Tender threshold (masters, M.S., Animal and Veterinary Science -- University of Idaho - College of Graduate Studies, 2020-0
Managing and Monitoring Pythium Leak and Shatter Bruise of Potato (Solanum tuberosum L.) Cultivars
No full textLeak is a devastating storage disease caused by the opportunistic pathogen, Pythium ultimum var. ultimum. The disease is identified by dark grey lesions in the flesh of the potato that exude water from damaged cells. Oospores or other propagules typically infect potatoes through mechanical wounds (shatter bruises) during harvest. The disease contributes to loss in storage but also creates ideal environments for secondary pathogens to further decay. It is recommended to manage leak by implementing cultural controls such as harvesting at tuber temperatures below 21°C, avoiding bruise, and establishing a good skin set. The objectives of this research were to examine these general recommendations for several russet cultivars and understand why cultivars may differ in leak and bruise susceptibility and recommend means to prevent both. Specific studies evaluated (1) the effects of both pulp and storage temperature on leak susceptibility among several russet cultivars, (2) the association of leak development of russet cultivars and tuber shatter bruise and mechanical failure properties, (3) the efficiency of bacterial antagonists and other post-harvest fungicides in managing leak, and (4) methods and tools for bruise mitigation programs. Although potato cultivars vary in susceptibility to leak, the standard recommended control method for all cultivars is to harvest potatoes when pulp temperatures are below 21°C. However, potatoes may be harvested with higher than ideal pulp temperatures or a cultivar may warrant stricter recommendations. Several russet cultivars were equilibrated to pulp temperatures of 12.8, 15.5, 18.3, and 21.1°C, bruised and inoculated with P. ultimum then evaluated four days later. To test how leak development in russet cultivars would respond to a change of temperature in storage, tubers were equilibrated to pulp temperatures of 15.5 and 21.1°C, bruised and inoculated then stored at 12.8, 15.5, 18.3, and 21.1°C for four days. Leak susceptibility was influenced by pulp temperature but the storage temperature had an overriding effect if altered from the original pulp temperature. Leak susceptibility differed among cultivars and by temperature. The results highlight the importance of harvesting susceptible cultivars when pulp temperatures are below 15.5°C or cooling tubers below 15.5°C when adequate refrigeration or cooling air are available to rapidly modify temperatures in storage. Pythium ultimum infects a tuber via wounds or shatter bruises, which occur during mechanical harvesting and handling. To evaluate if cultivar susceptibility to leak is related to shatter bruise susceptibility and tuber mechanical failure properties, tubers were bruised and inoculated to mimic the state of potatoes during harvest. Cultivars varied in susceptibility to leak development, shatter bruise, and mechanical failure properties. Although, leak incidence was not highly correlated to shatter bruise area and number, a relationship between leak and mechanical failure properties of the tuber was observed. Shatter bruise incidence was correlated to tissue mechanical failure properties, and these measurements could provide insight into the shatter bruise potential for a cultivar. The prevalence or susceptibility of shatter bruise could not directly explain a cultivars susceptibility to leak and therefore additional research is needed to further understand the relationship between mechanical failure properties and leak. Post-harvest fungicides can also be important tools in managing storage diseases such as leak. A mixture of bacterial control agents developed by the National Center for Agricultural Utilization Research (NCAUR, USDA-ARS, Peoria, IL) was tested for efficiency against leak compared to other commercial fungicides. The bacterial control agents varied in efficacy of leak control and were not as effective as a commercial chemical fungicide. The bacterial control agent may have contributed to the control of P. ultimum when rehydrated with a nutrient medium and mixed with the commercial chemical fungicide; however, P. ultimum control was not significantly greater than the conventional fungicide alone. Other post-harvest products studied were not effective and did not differ from the inoculated control. Biological antagonists may be an effective post-harvest tool but more research is warranted to realize its potential in managing leak alone or when mixed with conventional fungicides. Minimizing bruise should be part of an integrated management program for storage diseases such as leak. Limiting bruise will also help maintain quality of potatoes. A bulletin was written to outline tools and protocols to monitor the potential for bruise within a potato handling operation. Tools include dipping potatoes in iodine to readily see the blue stained shatter bruises. Another tool outlined how to assess for blackspot bruise as the majority of the blackspot bruises could be visible and evaluated within 3 to 5 hours, which is earlier than previous recommendations. Instrumented spheres are another tool used to record damaging impacts that occur during harvesting and handling operations. These tools and methods help to monitor bruise and aid in making timely mechanical adjustments to further prevent bruisedoctoral, Ph.D., Plant, Soil and Entomological Sciences -- University of Idaho - College of Graduate Studies, 2020-0
Restaurant online reviews and their manipulations
No full textMy thesis contains two separate chapters. In the first chapter, I focus on what consumers express about their dining experience. I present a case study using Yelp restaurant review data on what affects restaurant customers' sentiment responses to dining out. The case study uses a sentiment-analysis method to extract and generate sentiment indices from 175,879 text-based Yelp restaurant reviews. I then examine the relationships between our sentiment indices and ratings and what factors(food, service, expenditure, and social) affect consumer dining experience more than others. In the second chapter, I find that, other than seller manufactured fake reviews, review platforms can also manipulate reviews by changing consumers' leaving review behaviours. Online review platforms are able to attract more satisfied consumers to leave reviews which results in rating inflation in their platforms. In this situation, even if all the reviews are real, consumers still receive biased information from online reviews. My paper provides empirical evidence for information design theory.masters, M.S., Agricultural Economics and Rural Sociology (Applied Economics) -- University of Idaho - College of Graduate Studies, 2020-0
COMPARATIVE QTL MAPPING OF HAGBERG FALLING NUMBER, PRE-HARVEST SPROUTING, AND LATE MATURITY ALPHA-AMYLASE IN UI PLATINUM BY SY CAPSTONE DERIVED POPULATION
No full textThe Hagberg falling number (FN) is an important quality trait in common wheat being used in grain trading business and in end-use quality due to starch damage. Measuring FN can is conducted using flour sample after grain is harvested. Therefore, assessment of FN is very expensive and affected by environments where the grains were produced. Pre-harvest sprouting (PHS) and late maturity α-Amylase (LMA) are the two main sources that cause wheat grain samples with low FN. QTL and tightly linked molecular markers for FN, PHS, and LMA is the best alternative that can be used in early generation selection and improvement of selection efficiency. The present study conducted a comparative QTL mapping for the three related traits in a doubled haploid population derived from two hard white spring wheat cultivars UI Platinum (UIP) and SY Capstone (SYC). FN data from nine trials, PHS data from eight datasets in two experiments, and LMA data from two treatment trials were used in QTL analysis. A total of sixteen QTL for FN were detected on seven chromosome regions and five of them (QFN.UIA-1B-1, QFN.UIA-2B, QFN.UIA-3B-1, QFN.UIA-5A-1, QFN.UIA-7A-1) were detected in three or more data sets, explaining 10 to 34% of phenotypic variation. Nine QTL for PHS were identified in three or more data sets on six chromosome regions, explaining 10 to 25% of phenotypic variation. QTL for LMA were identified on chromosomes 4A (UIP HFN), 5A (UIP HFN), and 7A-1 (SYC HFN). QTL on 5A was associated with all three traits and UIP contributed to higher FN, resistance to PHS and LMA. QTL on 7A-1 was associated with FN and LMA and UIP contributed to lower FN and higher PHS score. QTL on 1B-1 was associated with FN and PHS and UIP contributed to the lower FN and higher PHS score. This study suggests that the three traits may share a little genetic information in common, therefore, selecting one trait may be able to indirectly select other related traits. This study also suggests that resistant lines to FN, PHS, and LMA can be selected through genetic recombination for QTL from the two parents. Compared to the physical map of Chinese Spring, the 5A QTL is the flanking region of Amy 3 gene. This suggests that it is necessary to study the Amy 3 gene in order to understand the genetic control of the three traits assessed in the present study.masters, M.S., Plant, Soil and Entomological Sciences -- University of Idaho - College of Graduate Studies, 2020-0
Analysis of the Temperature Dependent Band-Edge Distribution as a Function of Annealing in ZnO and Zno-Based Thin Film Alloys
No full textThe study of the band edge in UV-Vis absorption spectra has impacted fundamental understanding of semiconductor physics as well as advances in technological application. An analytical approach based on the derivative of the absorption spectra was used to explore the nature of the band-edge of ZnO and MgZnO thin films grown via the sputtering technique. It was found that the band-edge is composed of a Gaussian where the width and peak position were employed to model the electron-phonon (e-p) interaction and defect characteristics of the film. These characteristics were studied via transmission experiments in the temperature range of 77 K to 532 K. The as-grown film was found to exhibit a very weak e-p coupling relative to the static contribution of defects similar to the behavior of amorphous-like semiconductors. Upon successive controlled annealing of the ZnO film, up to 800 C, the defect component diminished and the phonon contribution became dominant. Specifically, the e-p interaction was similar to semiconductors with long range order. X-ray diffraction and imaging studies agree with these results. The defects in the ZnO films are discussed in terms of structural inhomogeneities and Zn interstitials prevalent in ZnO films grown via sputtering. MgZnO showed similar defect and e-p coupling behavior. Furthermore, building on the derivative analysis, we show an analytical technique capable of separating signal-artifact convolution. Finally, we develop an analytic set of models that can be applied to nonlinear band-edges. We show that, in the limiting case of linearity, our model is consistent with and produces the same results as the linear Urbach model. Our new model is capable of bypassing “tailing” as an indirect measure of the spread in the local potential and gives a direct measure of this quantity. The author gratefully acknowledges the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Materials Science and Engineering, Award No. DE-FG02-07ER46386doctoral, Ph.D., Physics -- University of Idaho - College of Graduate Studies, 2020-0
The Effect of Supplemental Butyrate on Passive Transfer of Immunity and on VFA Transporter Abundance During the Weaning Transition
No full textThe acquisition of passive transfer of immunity and weaning transition are two events in early calfhood that are critical to calf health and growth. Without adequate passive transfer calves are more susceptible to disease for the first 6-8 weeks of life and without a successful weaning transition calves may experience weight loss and nutritional stress. Dietary inclusion of sodium butyrate may improve both passive transfer and the weaning transition. In experiment 1, twenty neonatal calves were assigned to either control (CTRL-C) or sodium butyrate supplementation (BUT-C). Butyrate supplementation reduced IgG absorption in BUT-C calves but did not affect average daily gain. It is not recommended to supplement calves with butyrate before the cessation of intestinal immunoglobulin absorption. In experiment 2, thirty-six Holstein bull calves were assigned to milk-only (PRE-M), calf starter and hay (PRE-S), calf starter and hay with a two-week weaning transition (POST-S), or calf starter and hay with a two-week weaning transition plus supplemental sodium butyrate (POST-B). Calves were harvested and rumen epithelial tissue was examined for VFA transporter abundance (MCT1) plus transporters involved in intracellular pH regulation (NHE3 and NBC1). MCT1 abundance was not affected by the addition of solid feed to the diet, weaning, or butyrate supplementation. NBC1 abundance increased with the dietary inclusion of solid feed, suggesting the developing rumen has the capacity to adapt to dietary changes. NHE3 abundance decreased during weaning, suggesting that the rumen epithelium acidifies itself through the weaning transition, though the physiological relevance of this phenomenon is unknown.masters, M.S., Animal and Veterinary Science -- University of Idaho - College of Graduate Studies, 2020-0
Cultural Resources and Wildland Fire Management: An Investigation into the Operational Effects of Prescribed Burning to a Simulated Archaeological Record
No full textWildfire is one of many natural forces that has challenged humans for thousands of years. In just over the last one hundred years, methods to suppress and manage wildfire in the United States were formally developed. Wildfire prevention and suppression is necessary to the management of many natural and cultural resources. Cultural resources are nonrenewable resources that require consideration by those who manage wildland fire. Though there has been previous research conducted on the direct impact of fire to cultural resources, there is a dearth of information on how operational effects, such as fireline construction, impact cultural resources including archaeological sites. What limited information is available on the subject suggests that mechanical fireline construction and rehabilitation are no less of a threat to cultural resources than fire is. Working within the framework of experimental archaeology, I simulated an archaeological site using replica precontact artifacts and authentic historic materials. A fireline was mechanically constructed through the simulated site, a prescribed burn was conducted, and the fireline was mechanically rehabilitated. Data were gathered on the spatial displacement and physical impacts to experimental artifacts. The findings of this study reveal that mechanical fireline construction consistently displaces artifacts by several meters. Fireline rehabilitation also contributes to the displacement of artifacts. Both of these operational effects are no less directly threatening to cultural resources than fire is, and have irreversible impacts that severely inhibit the ability to interpret or recover an archaeological site. Physical impacts to artifacts in this study include breakage and staining from combustive residue. By quantifying the impacts of fireline construction and rehabilitation to the simulated archaeological site, this study provides a means for cultural resource specialists and wildland fire managers to make appropriate decisions towards the preservation of our Nation’s heritage.masters, M.A., Anthropology -- University of Idaho - College of Graduate Studies, 2020-0