136879 research outputs found
Sort by
Salmonella Survival, Growth, and Presence in Onion Bulbs, Extracts, and Production Environment
No full textThe purpose of this research was to investigate the presence, survival, and growth of Salmonella in onions and their environment as a prerequisite to understanding the risk that Salmonella poses to the consumer. Extracts from red and white onions grown under blue light significantly (P < 0.05) inhibited the growth of Salmonella. Extracts from genotype 1104 showed an optical density (OD) that was significantly lower than all other extracts, with total inhibition in extracts from the outer scales. Salmonella Newport was inoculated at various depths using a syringe (wounding) in and on red, white, and yellow onions and stored at room temperature for up to 18 days. At intervals, samples were collected from the top layer (skin) and inner layers of each onion and were tested for Salmonella. In all cases, the outer layer of all onion varieties not only inhibited S. Newport growth, but the populations of this pathogen were reduced by 3.2, 2.4, and 2.5 log cycles on red, white, and yellow onions, respectively within the first 3 days of storage, with no significant further changes in counts over 18 days. In contrast, Salmonella Newport grew by 1.7, 2.3, and 2.5 log cycles over the 18-d storage time in the inner layers of red, white, and yellow onions. In the trials to track the presence of Salmonella in onion-producing environments, a total of 255 samples (101 from fields, and 154 from packing plants) were collected and subjected to qualitative and quantitative Salmonella assay in a BAX system with the SalQuant kit. Salmonella was detected in 3 (13%) of 23 samples of well water collected from one onion field, 3 (4%) of 75 samples of soil collected from 3 fields, and 16 (10%) of 151 surface samples collected from 3 onion packing plants. In field samples that tested positive, the quantitative assay gave mean counts of 0.1 log CFU/50 L in water and 1.2 log CFU/g in soil. For environmental samples from packing plants, the mean counts for positive samples ranged between 1.9 and 3.2 CFU/cm2 , no significant differences between types of surfaces were found in the Salmonella counts
Advanced Autonomous Algorithms for Versatile Terrain Navigation and Multirobot Coverage Control
No full textThe primary objective of this research is to develop robust autonomous navigation and multirobot coverage control algorithms with broad applicability. To achieve this objective, this dissertation delves into three core topics: 1) terrain-aware path planning, 2) real-time stair detection, and 3) multi-robot coverage control. To address the challenges associated with autonomous navigation using vision-based terrain classification, a novel technique, the uncertainty rejection filter, is introduced. This filter, when combined with a neural networks-based terrain classification model, enhances the reliability of autonomous navigation by identifying uncertain regions and assigning appropriate traversal costs. Simulations and field tests demonstrate the effectiveness of this path-planning scheme. This dissertation also presents a real-time stair detection algorithm based on a decision boundary-aware model. Leveraging a support vector machine trained on RGB images, the algorithm outperforms existing models. Lastly, novel algorithms for multi-robot coverage control are proposed for both homogeneous and heterogeneous systems. A centralized approach incorporating agent dropout and reinsertion processes improves overall coverage, while a decentralized version achieves desired outcomes without a central computer. These algorithms exhibit improved coverage performance in diverse non-convex environments. Additionally, a user interface is introduced to enable users to define target areas for coverage by the proposed algorithms. Field experiments showcase the successful integration of the user interface with the coverage control algorithms
NAC1 Restrains T Cell Memory Formation through Metabolism Regulation During Viral Infection
No full textOur recent studies uncovered the important roles of nucleus accumbens-associated protein 1 (NAC1), a transcriptional co-factor, in regulating the activity of regulatory T cells, and antitumor immunity. Little is known about how NAC1 interrupts T cell memory, despite its significance in the host's defensive response to invading pathogens. Many factors interrupt T cell memory formation, such as transcriptional factors, virus types, cell metabolism, and autophagic status.
In the current study, we analyzed T cells from wild-type (WT) and NAC1-deficient (-/-) mice and observed that NAC1 is essential for both CD8��� and CD4��� T cell metabolism including glycolysis and oxidative phosphorylation and supports T cell survival in vitro.
In vivo, compared with wild-type (WT) mice, NAC1-/- mice exhibit a slow decrease of viral antigen (Ag)-specific CD8��� T cells. Additionally, we observed that the NAC1-/- mice demonstrated a stronger memory formation of VACV-specific CD8��� T cells post-viral infection. Mechanically, we identified that compared with WT CD8��� T cells, the Interferon Regulatory Factor 4 (IRF4), a key transcription factor in T cell development, was highly expressed in NAC1-/- CD8��� T cells. For CD4��� T cells, we further demonstrated that deficiency of NAC1 downregulates glycolysis in CD4��� T cells through modulation of the AMPK-mTOR pathway. Moreover, loss of NAC1 reduces the expression of ROCK1, the phosphorylation and stabilization of BECLIN1. Furthermore, forced expression of ROCK1 in NAC1-/- CD4��� T cells results in the restoration of autophagy as well as the activity of the AMPK-mTOR pathway. In animal experiments, adoptively transferred NAC1-/- CD4��� T cells or NAC1-/- mice challenged with VACV show enhanced formation of the VACV-specific CD4��� memory T cells as compared with adoptively transferred WT CD4��� T cells or WT mice, but this enhancement of memory T cell formation can be abrogated by forced expression of ROCK1.
Overall, the results of this study reveal the novel role of NAC1 as a suppressor of T cell memory formation and imply that targeting NAC1 may be exploited as a new approach to promoting memory T cell development
Spatial Patterns, Drivers, and Impacts of the Urban Land Expansion in Nigeria from 1985 to 2015
No full textUrbanization is reshaping landscapes worldwide, posing considerable challenges to ecosystems, climate patterns, and resource utilization. This dissertation studies the spatio-temporal patterns of urban land change, its drivers, and its implications for biodiversity and flood exposure in Nigeria from 1985 to 2015. A pivotal aspect of the methodology is the evaluation of global urban land cover products to facilitate the understanding of urban land expansion in a context where specific national data on land cover is scarce or not available. This evaluation revealed each product's ability and limitations in accurately reflecting the reality of Nigeria's urban development. The specific findings of this research also reveal significant environmental implications, such as the loss and fragmentation of natural habitats and the exposure of urban land to flooding. Thus, the dissertation provides valuable insights that can inform urban management, policy formulation, and conservation strategies in developing urban landscapes, that are particularly tailored to Nigeria, but also indicative of other rapidly urbanizing countries across Sub-Saharan Africa
John Bickham field notebook: Herp_AK900-AK1000.pdf
No full textEach page/AK number corresponds to a karyotype slide data and/or unique specimen.Data pages for Herp_AK900-AK1000 corresponding to unique identifiers of specimens/samples examined for biological research. Specimens are primarily housed at Texas A&M University; Biodiverstiy Research and Teaching Collection
Management Decisions for U.S. Ranches
No full textRanchers face many challenging decisions impacting operational longevity. This dissertation examines rancher decisions regarding 1) generational transfer of a family-operated ranch and 2) cow herd rebuilding strategies after drought. Chapter 1 provides an analysis of survey responses from U.S. ranchers regarding plans to transition their ranch to the next generation. Less than 40% of survey participants have a transition plan in place. Participants shared the details of their ranch transition plans or the roadblocks preventing them from developing a plan. Transition plan scenarios were developed based on producer responses to the survey.
In Chapter 2, transition plan scenarios from Chapter 1 were imposed on representative ranches, and financial performance was evaluated under each scenario. Ranch transition scenarios considered the use of business entities vs. sole proprietorships; willingness of parents to relinquish management or ownership to heirs; gifting vs. selling assets to heirs; buyouts between siblings; and asset balancing between on-farm and off-farm heirs.
For Chapter 3, different scenarios for cow herd rebuilding after drought were imposed on the representative ranches. The most common drought management response was partial liquidation of the cow herd. In this analysis, each representative ranch liquidated 20% of their mature cows during the drought. Post-drought herd rebuilding scenarios included slow-rebuild versus quick-rebuild strategies and strategies to rebuild with ranch-raised replacements versus rebuilding by purchasing females. Ranch financial performance was evaluated under each scenario, and results showed the optimal scenarios included retained replacement heifers during drought. For scenarios that did not include retained replacements during drought, quick-rebuild scenarios with purchased females were considered optimal; ranches under these scenarios were able to capitalize more on high cattle prices in the early post-drought years
Three Essays on Climate Change Impacts on the U.S. Livestock Sector
No full textThis dissertation contains three essays and their contents are summarized as follows. The first essay contains a literature review regarding climate and climate change related decision possibilities as they impact livestock productivity and decisions. We covered impacts, emissions, adaptation possibilities and mitigation alternatives. We pointed out research gaps on non-ruminant animals and on settings involving developing countries.
The second essay reports on an application of econometric models to explore how climate affects livestock performance. We investigated climate impacts on the productive and reproductive performance for US cattle, hogs and chickens, using temperature humidity index (THI) as a proxy of heat stress. Our results show that climate factors play an important role in livestock productivity. Future climate projections reveal a decrease in all major livestock yield metrics, with the projected changes in yield showing geographical variations across the country.
The third essay reports on an analysis of implications of omitting or including livestock impacts within an agricultural-sector-based climate change impact appraisal. Previous agricultural sector studies have largely ignored impacts on livestock just concentrating on crops. By integrating the livestock impact projections from the second essay, we find introducing livestock impacts causes a 2.5B (22.1%) decline under RCP 4.5
Design and Evaluation of Scancap: A Low-Cost, Reusable Tethered Capsule Endoscope with Digital Chromo-Endoscopy Imaging for Unsedated Screening and Early Detection of Barrett���s Esophagus
No full textEsophageal adenocarcinoma (EAC) is the sixth leading cause of cancer death worldwide. Early detection and treatment of Barrett���s esophagus (BE), a precursor to EAC, increases the five-year survival rate from 18% to 98%. BE is a global challenge; however, current endoscopes for early detection of BE are costly and require extensive infrastructure for patient examination and sedation. We describe the design and evaluation of the first prototype of ScanCap, a high-resolution optical endoscopy system with a reusable, low-cost tethered capsule designed to provide high-definition, digital chromoendoscopic imaging for early detection of BE in unsedated patients. The tethered capsule (12.8 mm diameter, 35.5 mm length) contains a color camera and rotating mirror and is designed to be swallowed; images are collected as the capsule is retracted manually via the tether. The tether provides electrical power and illumination at wavelengths of 415 nm and 565 nm and transmits data from the camera to a tablet. The ScanCap prototype capsule was used to image the oral mucosa in normal volunteers and ex vivo esophageal resections; images were compared to those obtained using an Olympus CV-180 endoscope. Images of superficial capillaries in intact oral mucosa were clearly visible in ScanCap images. Diagnostically relevant features of BE, including irregular Z-lines, distorted mucosa, and dilated vasculature, were clearly visible in ScanCap images of ex-vivo esophageal specimens
Optimization-based Scheduling in Multi-service Appointment Systems with Application to College Counseling Centers
No full textAppointment scheduling is a crucial problem in various domains such as healthcare and logistics. In practice, several complicating factors make the decision-making process challenging. In this work, we study multi-service appointment scheduling systems having non-stationary arrival processes, with a special focus on college Counseling and Psychological Service (CAPS) centers. Given the increasing prevalence of mental health issues among college students and the resource constraints faced by CAPS centers in addressing the rise in demand, our goal is to propose data-driven solutions that improve students��� access to these vital services.
To achieve this, we adopt a two-step methodology. First, we develop a comprehensive discrete-event simulation (DES) model that accurately reflects the complexities of CAPS center operations. This model acts as a testing ground for evaluating the performances of different scheduling-related policies. Second, we construct optimization-based frameworks that leverage historical demand to identify data-driven schedules that lead to good-performing systems, while incorporating several realistic factors like multiple customer classes and their associated importance, time-varying demands, resource limitations, and implementability. To address the challenge of characterizing system performance for such complex stochastic systems, we develop stylized optimization models based on approximation schemes that capture the transient behavior of the original system. Further analysis leads to key structural properties, which we use to devise efficient globally convergent solution schemes for the stylized models. Our numerical experiments, based on data obtained from Texas A&M University���s CAPS center, demonstrate the benefits of the proposed scheduling methodologies, leading to policies that significantly enhance system performance compared to current scheduling practices
Targeted Therapeutic Strategies Against Triple-Negative and Metaplastic Breast Cancers
No full textBreast cancer is the second most common cause of cancer mortality in women in the United States. As a heterogenous disease, breast cancer is clinically classified by expression of estrogen receptor (ER), progesterone receptor (PR), and overexpression/amplification of human epidermal growth factor receptor 2 (HER2). Triple-negative breast cancer (TNBC), i.e., those not expressing ER, PR, or HER2, represent ~10-20% of all breast cancer cases, has the worst prognosis in comparison to ER+ or HER2+ breast cancers.
Gene profiling analysis has identified TNBC subtypes with unique molecular signatures that may be therapeutically targeted. Among the six known TNBC molecular subtypes, the mesenchymal subtype comprises 30% of all TNBCs and has the worst disease-free survival compared to other TNBC subtypes. Metaplastic breast cancer (MpBC) is a highly aggressive, and metastatic breast cancer malignancy that typically falls under the mesenchymal TNBC subtype, accounting for <5% of all invasive breast cancers. Patients with MpBC are generally diagnosed at a later age with a more aggressive disease, likely contributing to their dismal median survival of 8 months after metastasis. There are no standardized therapeutic options for patients with MpBC.
MpBC is characterized by one or more cell populations that have undergone metaplastic differentiation, i.e. cells convert from glandular to non-glandular morphology. MpBCs are enriched with epithelial-to-mesenchymal (EMT) and cancer stem cell (CSC) markers, with hyperactivation of phosphoinositide-3-kinase (PI3K) pathway and enhanced nitric oxide (NO) production. Patients diagnosed with metaplastic TNBC have a significantly worse prognosis compared to non-metaplastic TNBC (non-MpTNBC). Thus, the development of effective therapies for women with MpBC and non-MpTNBC represents a significant unmet clinical need.
The focus of my dissertation has been on evaluating novel therapeutic strategies in the preclinical setting to treat MpBC and non-MpTNBC. Using human breast cancer cell lines and patient-derived xenograft (PDX) models, my preclinical studies focused on evaluating targeted therapies, such as utilizing monoclonal antibodies against EGFR to treat TNBC, as well as combining PI3K and nitric oxide synthase (NOS) inhibitors to treat MpBC. I found that combined PI3K and NOS inhibition reverses EMT, decreases CSC populations, rendering MpBC tumors more chemosensitive