<p dir="ltr">This dissertation delves into three projects within the realms of image processing, computer vision, and machine/deep learning. The primary objective of the first project is the detection of heavy metal particle concentrations using microfluidic paper-based devices. The second project revolves around the analysis of crystals within microscopic images. The third project centers around zero-shot action recognition in video sequences, utilizing a multi-modality deep learning framework that is refined through prompt tuning to enhance its performance.</p>

<p dir="ltr">Liquid hydrogen peroxide (LHP) and vapor hydrogen peroxide (VHP) efficacy as a sterilant for <i>Bacillus atrophaeus</i> and <i>Geobacillus stearothermophilus</i> spores in aseptic packaging systems under commercial sterilization conditions were evaluated in this research. The work centers on quantifying and modeling the kinetic parameters that impact peroxide sterilization efficacy, including the D and z values, that relate to the change in concentration required for a 1-log reduction in spore population and a novel Z_conc parameter This comprehensive study is divided into four key investigations, each contributing critical insights to the overall understanding of peroxide sterilization processes.</p><p dir="ltr">The first study examined the inactivation kinetics of <i>B. atrophaeus</i> spores in liquid hydrogen peroxide. By evaluating different concentrations (20%, 28%, and 33%) and temperatures (up to 82.2°C), the study revealed that higher concentrations and elevated temperatures significantly enhanced spore inactivation. The Weibull model provided a more accurate fit for the data, indicating a non-linear relationship between spore reduction and exposure time.</p><p dir="ltr">The second part of the research explored the use of VHP for sterilizing <i>B. atrophaeus</i> spores. With VHP concentrations of 2500 ppm and 4450 ppm at various temperatures, the study demonstrated that higher concentrations and temperatures are highly effective for spore inactivation. Both log-linear and Weibull models accurately described the inactivation kinetics, with the Weibull model showing a slightly better fit, emphasizing the potential of VHP in achieving commercial sterility.</p><p dir="ltr">The third investigation focused on developing predictive models for VHP concentration and its efficacy in spore inactivation. The study evaluated VHP concentrations ranging from 2.32 mg/L to 7.35 mg/L and their impact on spore inactivation rates. The Weibull model proved particularly effective in predicting the inactivation of <i>G. stearothermophilus</i> and <i>B. atrophaeus</i> spores, offering a robust tool for optimizing sterilization protocols in aseptic packaging.</p><p dir="ltr">The fourth and final study of the research investigated the influence of surface roughness on spore survival during VHP sterilization cycles on plastic packaging materials. Artificial roughness on high-density polyethylene (HDPE) coupons was created using sandpaper with different grits. <i>B. atrophaeus</i> spores were applied to both roughened and smooth HDPE surfaces. The study finds that rougher surfaces provide more shelter for spores, reducing sterilization efficacy. For example, surfaces roughened with P-36 grit showed a 2.75 log reduction in spore count, whereas smoother surfaces with P-220 grit achieved a 4.42 log reduction. Contact angle measurements indicated that increased roughness led to more hydrophilic surfaces, with water contact angles decreasing from 149.7° for the pristine sample to 105.4° for the P-36 sample. Scanning electron microscopy (SEM) images confirmed that spores were more likely to reside in the valleys of rough surfaces, highlighting the importance of surface characteristics in optimizing VHP sterilization protocols.</p><p dir="ltr">The findings of this dissertation underscore the significant impact of hydrogen peroxide concentration, application conditions, and packaging material surface properties on the efficacy of spore inactivation during sterilization. By providing a comprehensive understanding of these factors, the research contributes to the development of optimized aseptic sterilization protocols, enhancing the reliability and safety of aseptically packaged food and pharmaceutical products. This work will ensure compliance with regulatory standards and improve food safety in commercial manufacturing, laying a solid foundation for future research and practical applications in VHP sterilization technology.</p>

<p dir="ltr">This thesis explores the complex relationship between <i>Listeria</i> <i>monocytogenes</i> and food processing environments (FPEs), focusing on the persistence mechanisms of this pathogen despite rigorous sanitation efforts. <i>L</i>. <i>monocytogenes</i> is a significant public health concern due to its association with high mortality rates in vulnerable populations. Recent studies, including the first chapter of this thesis, have highlighted the challenges in eradicating this pathogen from FPEs, suggesting that biofilms play a crucial role in its persistence. Despite various strategies and enhanced sanitation protocols, the eradication of <i>L</i>. <i>monocytogenes</i> remains elusive, underlining the need for a deeper understanding of its biofilm-associated resilience. Chapter two synthesizes findings from a systematic review and meta-analysis of studies examining the microbial communities on FPE surfaces through metagenomics, aiming to uncover patterns that might explain <i>Listeria</i>'s long-term survival. In chapter three, the thesis delves into the nuanced role of biofilm composition and microbial diversity as factors enabling the persistence of <i>Listeria monocytogenes</i> in food processing environments (FPEs), despite comprehensive sanitation efforts. This section builds on the understanding that <i>L. monocytogenes</i> does not inherently form robust biofilms but thrives within complex microbial communities present on FPE surfaces. The findings presented in this thesis contribute to a more profound comprehension of <i>L. monocytogenes</i>' survival strategies, proposing a shift in focus towards the microbial ecosystem's metabolic interplays for the development of targeted control measures. This approach not only opens new avenues for research but also suggests practical implications for enhancing food safety protocols by considering the broader microbial dynamics at play within biofilms on FPE surfaces.</p>

<p>Maize is one of the top sources of food starch. Industrial use of starch is mostly in its native form and used due to their functional and structural properties. Native starch properties and functionalities have been altered using chemical. An alternative for the development of native starch substituents with desirable starch properties is the use of mutagenesis techniques to increase genetic variation in maize kernels. With this approach, a highly diverse library of native starches with different properties are produced. Traditional analysis of the functional and structural properties requires generous amounts of material as well as a time-consuming and costly breeding process to obtain enough kernels. To address this difficulty, high-throughput techniques are proposed for studying starch properties and functions which includes a 1) single kernel sampling method for the isolation of milligrams of starch, and techniques for studying starch based on functional properties, 2) retrogradation and 3) shear resistance, using low-volume low-concentration starch pastes.</p><p>First, three mechanical approaches were evaluated for the collection of endosperm samples from individual kernels: razor blade, 1.5 mm drill bit, and trephine bur. Furthermore, two methods for the isolation of crude starch from endosperm samples (steeping method and combination of proteases and sonication) were compared. In this study, the mechanical approaches were evaluated using the recovery rate, throughput, and germination rate of sampled kernels. Moreover, yield determination, particle size distribution, and morphological evaluation using a light microscope were performed on crude starch isolated from the endosperm samples. The use of trephine bur to collect endosperm samples and isolation of crude starch using protease digestion and sonication showed the best combination for a high-throughput setting. </p><p>Second, a high-throughput technique using milligram sample for the screening of retrogradation-resistant starch was evaluated by comparing two spectrophotometric techniques: turbidity method and molecular rotor (MR). MRs are fluorescent probes with high sensitivity to the viscosity of their environment, polarity of the media, molecular crowding, and free volume. After excitation, MRs relax through rotational movement and reduces the emission of fluorescence. In this study, hydroxypropylated waxy corn starch (WCS) and hydroxypropylated normal corn starch (NCS) were used and their retrogradation kinetics was compared with retrogradation kinetics of native WCS and NCS. </p><p>It was found that the molecular rotor 9-(2-carboxy-2-cyaovinyl)-julolidine (CCVJ) was effective to sense changes during slow retrogradation of amylose-containing starch pastes. Development of elastic modulus of retrograded NCS pastes obtained from dynamical rheology showed high correlation with the development of fluorescence intensity of the CCVJ. Furthermore, rate of retrogradation using fluorescence intensity was affected by the introduction of a retrogradation inhibitor, hydroxypropyl groups. Accelerated retrogradation of low-concentration WCS pastes was measured using the turbidity method and fluorescence intensity of CCVJ in a microplate. Accelerated retrogradation was performed by subjecting the low-concentration WCS pastes to six freeze-thaw cycles of -20 ºC for 1 hour and 30 ºC for 1 hour. Overall, development of turbidity resulted in the more sensitive technique to detect rate of retrogradation of amylopectin-containing starch. </p><p>The last part of this research studied the use of CCVJ as a technique to identify shear-resistant starch in starch slurries using milligram sample. For this purpose, WCS was cross-linked with sodium trimetaphosphate (STMP) and phosphoryl chloride (POCl₃). Low-volume starch slurries having CCVJ were prepared ranging from 0.5% to 1% starch concentration in a 96-well PCR plates and subjected to heat and shear treatments. It was found that fluorescence intensity measured in native WCS pastes were the lowest. Furthermore, fluorescence intensity of the CCVJ in the gelatinized starch increased as the amount of cross-linker increased in the cross-linked WCS. After shear treatments, the same trend in fluorescence intensity increase was recorded in all the crosslinked WCS. Results obtained using fluorescence intensity were compared with rapid viscosity analyzer (RVA) and images from microscope. Results obtained from both techniques corroborated the findings using fluorescence intensity.</p><p>In general, the findings of this research provide new insights into the possibilities of developing a high-throughput screening platform of milligram starch sample based on their physical properties. </p>

With the advent of industrialization and food processing techniques the sizes of the cereal bran have been drastically reduced. In my thesis, I have tested the effect, if any, of wheat bran and maize bran particle size, in vitro, on the gut microbiota community structure by 16S rRNA sequencing and their function, by Short chain fatty acids (acetate, propionate, butyrate) production. In turn, we also linked the microbiota and SCFA differences to different chemical composition amongst variously sized fractions of wheat and maize bran.

This thesis investigates a newly developed and patented technology for its ability to inactivate spore- forming bacteria and non-spore-forming microorganisms. This new technology “Pressure Assisted Thermal Sterilization©” (PATS) is based on the theory of the thermal expansion of liquids. The efficiency of inactivating spore-forming and non-spore-forming microorganisms by PATS was compared with the thermal treatment alone. A combination treatment consisting of high pressure processing and gaseous carbon dioxide was also investigated for its ability to inactivate bacterial spores in model and real food matrices. The structural damage caused by treatments to the spores and non-spore-forming bacteria was assessed by scanning electron microscopy. Geobacillus stearothermophilus spores suspended in Milli-Q water, UHT milk and pumpkin soup, treated by PATS were found to have significantly lower decimal reduction times (D values) compared with the thermal treatment alone. Spores suspended in UHT milk were more heat resistant compared with those in Milli-Q water and pumpkin soup. Bacillus cereus spores suspended in Milli-Q water and pumpkin soup treated with PATS were more effectively inactivated compared with spores treated by the thermal treatment alone. Clostridium botulinum spores in saline buffer subjected to PATS treatment were inactivated more effectively compared with the thermal treatment alone. Overall, the results show that PATS was a better processing technique for inactivation of bacterial spores compared with thermal treatment alone. However, PATS had no added benefit in inactivating the non-spore-forming bacteria Escherichia coli and Saccharomyces cerevisiae cells compared with the thermal treatment. A shelf life study showed that B. cereus spores in pumpkin soup retained a low spore count (<5 LogCFU/mL) for approximately 40 days in 30oC storage after treatment with PATS. No additional degradation of colour pigments of pumpkin soup and model pumpkin juice was observed following PATS compared with the thermal treatment. Spore-forming microorganisms can be resistant to pressure treatment alone, which limits the application of high pressure processing (HPP). Therefore, a combination approach was investigated. The mechanism of inactivating spores by combining HPP with other treatments is that the pressure assists in spore germination. Then a secondary treatment (thermal or CO2 gas) can be used to inactivate the germinated spores. A combined application of HPP and a consecutive CO2 treatment was investigated for the efficiency of spore inactivation. Results showed that HPP (200 MPa for 30 min) followed by a CO2 treatment inactivated Bacillus subtilis 168 in nutrient broth, tomato juice and liquid whole egg by 2.5, 1.0 and 1.5 LogCFU/mL respectively. These results indicated that this technique is inadequate for practical use. Scanning electron micrographs showed that pressure processing of B. subtilis 168 and B. subtilis natto spores resulted in deformation of the spore structure. This structural deformation of spores may have been due to water absorption during HPP and subsequent release upon decompression. PATS treated G. stearothermophilus and B. cereus spores were more severely damaged compared with the same spores which underwent thermal treatment alone. However, the extent to which E. coli and S. cerevisiae cells were damaged by both PATS and thermal treatment was similar.

This thesis investigates a newly developed and patented technology for its ability to inactivate spore- forming bacteria and non-spore-forming microorganisms. This new technology “Pressure Assisted Thermal Sterilization©” (PATS) is based on the theory of the thermal expansion of liquids. The efficiency of inactivating spore-forming and non-spore-forming microorganisms by PATS was compared with the thermal treatment alone. A combination treatment consisting of high pressure processing and gaseous carbon dioxide was also investigated for its ability to inactivate bacterial spores in model and real food matrices. The structural damage caused by treatments to the spores and non-spore-forming bacteria was assessed by scanning electron microscopy. Geobacillus stearothermophilus spores suspended in Milli-Q water, UHT milk and pumpkin soup, treated by PATS were found to have significantly lower decimal reduction times (D values) compared with the thermal treatment alone. Spores suspended in UHT milk were more heat resistant compared with those in Milli-Q water and pumpkin soup. Bacillus cereus spores suspended in Milli-Q water and pumpkin soup treated with PATS were more effectively inactivated compared with spores treated by the thermal treatment alone. Clostridium botulinum spores in saline buffer subjected to PATS treatment were inactivated more effectively compared with the thermal treatment alone. Overall, the results show that PATS was a better processing technique for inactivation of bacterial spores compared with thermal treatment alone. However, PATS had no added benefit in inactivating the non-spore-forming bacteria Escherichia coli and Saccharomyces cerevisiae cells compared with the thermal treatment. A shelf life study showed that B. cereus spores in pumpkin soup retained a low spore count (<5 LogCFU/mL) for approximately 40 days in 30oC storage after treatment with PATS. No additional degradation of colour pigments of pumpkin soup and model pumpkin juice was observed following PATS compared with the thermal treatment. Spore-forming microorganisms can be resistant to pressure treatment alone, which limits the application of high pressure processing (HPP). Therefore, a combination approach was investigated. The mechanism of inactivating spores by combining HPP with other treatments is that the pressure assists in spore germination. Then a secondary treatment (thermal or CO2 gas) can be used to inactivate the germinated spores. A combined application of HPP and a consecutive CO2 treatment was investigated for the efficiency of spore inactivation. Results showed that HPP (200 MPa for 30 min) followed by a CO2 treatment inactivated Bacillus subtilis 168 in nutrient broth, tomato juice and liquid whole egg by 2.5, 1.0 and 1.5 LogCFU/mL respectively. These results indicated that this technique is inadequate for practical use. Scanning electron micrographs showed that pressure processing of B. subtilis 168 and B. subtilis natto spores resulted in deformation of the spore structure. This structural deformation of spores may have been due to water absorption during HPP and subsequent release upon decompression. PATS treated G. stearothermophilus and B. cereus spores were more severely damaged compared with the same spores which underwent thermal treatment alone. However, the extent to which E. coli and S. cerevisiae cells were damaged by both PATS and thermal treatment was similar.

This thesis investigates a newly developed and patented technology for its ability to inactivate spore- forming bacteria and non-spore-forming microorganisms. This new technology “Pressure Assisted Thermal Sterilization©” (PATS) is based on the theory of the thermal expansion of liquids. The efficiency of inactivating spore-forming and non-spore-forming microorganisms by PATS was compared with the thermal treatment alone. A combination treatment consisting of high pressure processing and gaseous carbon dioxide was also investigated for its ability to inactivate bacterial spores in model and real food matrices. The structural damage caused by treatments to the spores and non-spore-forming bacteria was assessed by scanning electron microscopy. Geobacillus stearothermophilus spores suspended in Milli-Q water, UHT milk and pumpkin soup, treated by PATS were found to have significantly lower decimal reduction times (D values) compared with the thermal treatment alone. Spores suspended in UHT milk were more heat resistant compared with those in Milli-Q water and pumpkin soup. Bacillus cereus spores suspended in Milli-Q water and pumpkin soup treated with PATS were more effectively inactivated compared with spores treated by the thermal treatment alone. Clostridium botulinum spores in saline buffer subjected to PATS treatment were inactivated more effectively compared with the thermal treatment alone. Overall, the results show that PATS was a better processing technique for inactivation of bacterial spores compared with thermal treatment alone. However, PATS had no added benefit in inactivating the non-spore-forming bacteria Escherichia coli and Saccharomyces cerevisiae cells compared with the thermal treatment. A shelf life study showed that B. cereus spores in pumpkin soup retained a low spore count (<5 LogCFU/mL) for approximately 40 days in 30oC storage after treatment with PATS. No additional degradation of colour pigments of pumpkin soup and model pumpkin juice was observed following PATS compared with the thermal treatment. Spore-forming microorganisms can be resistant to pressure treatment alone, which limits the application of high pressure processing (HPP). Therefore, a combination approach was investigated. The mechanism of inactivating spores by combining HPP with other treatments is that the pressure assists in spore germination. Then a secondary treatment (thermal or CO2 gas) can be used to inactivate the germinated spores. A combined application of HPP and a consecutive CO2 treatment was investigated for the efficiency of spore inactivation. Results showed that HPP (200 MPa for 30 min) followed by a CO2 treatment inactivated Bacillus subtilis 168 in nutrient broth, tomato juice and liquid whole egg by 2.5, 1.0 and 1.5 LogCFU/mL respectively. These results indicated that this technique is inadequate for practical use. Scanning electron micrographs showed that pressure processing of B. subtilis 168 and B. subtilis natto spores resulted in deformation of the spore structure. This structural deformation of spores may have been due to water absorption during HPP and subsequent release upon decompression. PATS treated G. stearothermophilus and B. cereus spores were more severely damaged compared with the same spores which underwent thermal treatment alone. However, the extent to which E. coli and S. cerevisiae cells were damaged by both PATS and thermal treatment was similar.

This thesis investigates a newly developed and patented technology for its ability to inactivate spore- forming bacteria and non-spore-forming microorganisms. This new technology “Pressure Assisted Thermal Sterilization©” (PATS) is based on the theory of the thermal expansion of liquids. The efficiency of inactivating spore-forming and non-spore-forming microorganisms by PATS was compared with the thermal treatment alone. A combination treatment consisting of high pressure processing and gaseous carbon dioxide was also investigated for its ability to inactivate bacterial spores in model and real food matrices. The structural damage caused by treatments to the spores and non-spore-forming bacteria was assessed by scanning electron microscopy. Geobacillus stearothermophilus spores suspended in Milli-Q water, UHT milk and pumpkin soup, treated by PATS were found to have significantly lower decimal reduction times (D values) compared with the thermal treatment alone. Spores suspended in UHT milk were more heat resistant compared with those in Milli-Q water and pumpkin soup. Bacillus cereus spores suspended in Milli-Q water and pumpkin soup treated with PATS were more effectively inactivated compared with spores treated by the thermal treatment alone. Clostridium botulinum spores in saline buffer subjected to PATS treatment were inactivated more effectively compared with the thermal treatment alone. Overall, the results show that PATS was a better processing technique for inactivation of bacterial spores compared with thermal treatment alone. However, PATS had no added benefit in inactivating the non-spore-forming bacteria Escherichia coli and Saccharomyces cerevisiae cells compared with the thermal treatment. A shelf life study showed that B. cereus spores in pumpkin soup retained a low spore count (<5 LogCFU/mL) for approximately 40 days in 30oC storage after treatment with PATS. No additional degradation of colour pigments of pumpkin soup and model pumpkin juice was observed following PATS compared with the thermal treatment. Spore-forming microorganisms can be resistant to pressure treatment alone, which limits the application of high pressure processing (HPP). Therefore, a combination approach was investigated. The mechanism of inactivating spores by combining HPP with other treatments is that the pressure assists in spore germination. Then a secondary treatment (thermal or CO2 gas) can be used to inactivate the germinated spores. A combined application of HPP and a consecutive CO2 treatment was investigated for the efficiency of spore inactivation. Results showed that HPP (200 MPa for 30 min) followed by a CO2 treatment inactivated Bacillus subtilis 168 in nutrient broth, tomato juice and liquid whole egg by 2.5, 1.0 and 1.5 LogCFU/mL respectively. These results indicated that this technique is inadequate for practical use. Scanning electron micrographs showed that pressure processing of B. subtilis 168 and B. subtilis natto spores resulted in deformation of the spore structure. This structural deformation of spores may have been due to water absorption during HPP and subsequent release upon decompression. PATS treated G. stearothermophilus and B. cereus spores were more severely damaged compared with the same spores which underwent thermal treatment alone. However, the extent to which E. coli and S. cerevisiae cells were damaged by both PATS and thermal treatment was similar.

In the human gut, bacterial fermentation of dietary fibers and proteins produces metabolites, primarily as short-chain fatty acids (SCFA), that are highly beneficial for host health. However, unlike dietary fiber, bacterial fermentation of protein additionally generates potentially toxic substances such as ammonia, hydrogen sulfide, amines, and indoles. It is believed that most gut bacteria favor utilization of dietary fiber over that of protein for energy. Therefore, when fermentable dietary fiber is readily available to colonic bacteria, protein fermentation, and its subsequent potentially toxic metabolites, remains relatively low. Dietary intake primarily determines the quantity of dietary fiber and protein substrate available to the gut microbiota and the resulting profile of metabolites produced. Increased protein consumption is associated with deleterious health outcomes such as higher risk of colorectal cancer and type II diabetes. Conversely, diets following US dietary recommendations are high in fiber, which promote a healthy microbiome and are protective against disease. Diets following the recommendation are also moderate in protein intake so that, ultimately, far more fiber than protein is available for colonic bacterial fermentation. On the contrary, dietary fiber intake is chronically low in a standard Western diet, while protein consumption is above dietary recommendations, which results in nearly equal amounts of dietary fiber and protein available for gut microbial fermentation. Furthermore, the popularity of high-protein diets for athletes, as well as that of high-protein low-carbohydrate diets for weight loss, may flip fiber and protein substrate proportions upside down, resulting in more protein than fiber available in the gut for fermentation. The objective of this study was to elucidate how substrate ratios in protein-fiber mixtures affect protein fermentation and metabolites, as well as examine the degree to which fiber source may influence these outcomes. Each dietary fiber source [fructooligosaccharides (FOS), apple pectin (Pectin), a wheat bran and raw potato starch mixture (WB+PS), and an even mixture of the three aforementioned fibers (Even Mix)] and protein were combined in three ratios and provided as substrate for in vitro fecal fermentation to understand how low, medium, and high fiber inclusion levels influence fermentation outcomes. They were compared to 100% protein and fiber (each different fiber) controls. Branched-chain fatty acids (BCFAs), metabolites produced exclusively from protein fermentation, were used as a measure of protein fermentation; the data were normalized based on the initial quantity of protein within the substrate. In protein-fiber substrate mixtures, only FOS and Even Mix inhibited BCFAs (mM/g protein basis) and only when they made up at least half of the substrate. Unexpectedly, the rate of protein fermentation was increased when the protein-fiber substrate contained 25% WB+PS fiber, possibly due to the starch component of the fiber. There was evidence that when pH drops during fermentation, as was the case for protein-FOS mixtures, it played a significant role in suppressing protein fermentation. Ammonia production was not largely affected by increasing the proportion of dietary fiber. A significant reduction did not occur until FOS made up at least 50% of the protein-fiber substrate; for Pectin, WB+PS, and Even Mix fibers, 75% inclusion was required for a significant decrease in ammonia. Interestingly, protein was butyrogenic. Protein as the sole substrate produced more butyrate than either Pectin or Even Mix as the sole substrates, and in fact, addition of Pectin to protein significantly reduced butyrate concentrations. However, the possible benefits of butyrate produced via protein fermentation needs to be tempered by the production of potentially toxic compounds and the association between protein fermentation and colorectal cancer. Overall, the thesis findings showed protein fermentation to be relatively stable and not easily influenced by increasing the availability of dietary fiber, and no clear evidence of microbial preference for carbohydrates over protein was found.