Life Sciences Commons^™

A Structural, Cognitive, And Behavioral Model For Error Analysis Of Group B Streptococcus Prophylaxis In Pregnancy

Faculty, Staff and Student Publications

The objective of this study was to develop a structural-cognitive-behavioral model for error analysis of group B streptococcus (GBS) prophylaxis failure, classify delivery cases into this model, and examine compliance with treatment guidelines. A retrospective, cohort study was conducted of women with liveborn pregnancies greater than 24 weeks in April 2018 at a single hospital. We created a structural-cognitive-behavioral model of five assessments for adherence to GBS prophylaxis guidelines and then classified these into four distinct error stages. A descriptive analysis was performed to determine if the pregnancy had a perfect process, a GBS prophylaxis failure, or a fortuitous outcome. …

Improving Pharmacovigilance Signal Detection From Clinical Notes With Locality Sensitive Neural Concept Embeddings, Devika Subramanian, Trevor Cohen

Faculty, Staff and Student Publications

Although pharmaceutical products undergo clinical trials to profile efficacy and safety, some adverse drug reactions (ADRs) are only discovered after release to market. Post-market drug safety surveillance - pharmacovigilance - leverages information from various sources to proactively identify such ADRs. Clinical notes are one source of observational data that could assist this process, but their inherent complexity can obfuscate possible ADR signals. In previous research, embeddings trained on observational reports have improved detection of such signals over commonly used statistical measures. Moreover, neural embedding methods which further encode juxtapositional information have shown promise on analogical retrieval tasks, suggesting proximity-based alternatives …

P-Smoother: Efficient Pbwt Smoothing Of Large Haplotype Panels, Shaojie Zhang, Degui Zhi

Faculty, Staff and Student Publications

MOTIVATION: As large haplotype panels become increasingly available, efficient string matching algorithms such as positional Burrows-Wheeler transformation (PBWT) are promising for identifying shared haplotypes. However, recent mutations and genotyping errors create occasional mismatches, presenting challenges for exact haplotype matching. Previous solutions are based on probabilistic models or seed-and-extension algorithms that passively tolerate mismatches.

RESULTS: Here, we propose a PBWT-based smoothing algorithm, P-smoother, to actively 'correct' these mismatches and thus 'smooth' the panel. P-smoother runs a bidirectional PBWT-based panel scanning that flips mismatching alleles based on the overall haplotype matching context, which we call the IBD (identical-by-descent) prior. In a simulated …

Enhancing Diagnosis Through Technology: Decision Support, Artificial Intelligence, And Beyond

Faculty, Staff and Student Publications

Patient care in intensive care environments is complex, time-sensitive, and data-rich, factors that make these settings particularly well-suited to clinical decision support (CDS). A wide range of CDS interventions have been used in intensive care unit environments. The field needs well-designed studies to identify the most effective CDS approaches. Evolving artificial intelligence and machine learning models may reduce information-overload and enable teams to take better advantage of the large volume of patient data available to them. It is vital to effectively integrate new CDS into clinical workflows and to align closely with the cognitive processes of frontline clinicians.

Metabolic Imaging Using Hyperpolarization For Assessment Of Premalignancy, Dontrey Bourgeois, Prasanta Dutta, Mark Titus, Shayan Shams, Priya Bhosale, Michael Kim, Florencia Mcallister, Pratip K Bhattacharya

Faculty, Staff and Student Publications

There is an unmet need for noninvasive surrogate markers that can help identify premalignant lesions across different tumor types. Here we describe the methodology and technical details of protocols employed for in vivo

Advances In Non-Invasive Biosensing Measures To Monitor Wound Healing Progression, Daniel Colchado, Hima Vangapandu, Shayan Shams, Taiyun Chi, Jangwook P Jung, Swathi Balaji

Faculty, Staff and Student Publications

Impaired wound healing is a significant financial and medical burden. The synthesis and deposition of extracellular matrix (ECM) in a new wound is a dynamic process that is constantly changing and adapting to the biochemical and biomechanical signaling from the extracellular microenvironments of the wound. This drives either a regenerative or fibrotic and scar-forming healing outcome. Disruptions in ECM deposition, structure, and composition lead to impaired healing in diseased states, such as in diabetes. Valid measures of the principal determinants of successful ECM deposition and wound healing include lack of bacterial contamination, good tissue perfusion, and reduced mechanical injury and …

A Novel Group Of Genes That Cause Endocrine Resistance In Breast Cancer Identified By Dynamic Gene Expression Analysis, Farnaz Allahbakhsh, Jacky Wu, Nan Deng, W Jim Zheng, Hulin Wu, Michihisa Umetani, Vahed Maroufy

Faculty, Staff and Student Publications

Breast cancer (BC) is the most common type of cancer diagnosed in women. Among female cancer deaths, BC is the second leading cause of death worldwide. For estrogen receptor-positive (ER-positive) breast cancers, endocrine therapy is an effective therapeutic approach. However, in many cases, an ER-positive tumor becomes unresponsive to endocrine therapy, and tumor regrowth occurs after treatment. While some genetic mutations contribute to resistance in some patients, the underlying causes of resistance to endocrine therapy are mostly undetermined. In this study, we utilized a recently developed statistical approach to investigate the dynamic behavior of gene expression during the development of …

Effects Of Tamoxifen Inducible Mercremer On Gene Expression In Cardiac Myocytes In Mice, Hyun-Hwan Jeong, Zhongming Zhao, Priyatansh Gurha, Ali J Marian

Faculty, Staff and Student Publications

The Cre-LoxP technology, including the tamoxifen (TAM) inducible MerCreMer (MCM), is increasingly used to delineate gene function, understand the disease mechanisms, and test therapeutic interventions. We set to determine the effects of TAM-MCM on cardiac myocyte transcriptome. Expression of the MCM was induced specifically in cardiac myocytes upon injection of TAM to myosin heavy chain 6-MCM (Myh6-Mcm) mice for 5 consecutive days. Cardiac function, myocardial histology, and gene expression (RNA-sequencing) were analyzed 2 weeks after TAM injection. A total of 346 protein coding genes (168 up- and 178 down-regulated) were differentially expressed. Transcript levels of 85 genes, analyzed …

Rural Feminism And Perspectives Of Women Farmers In The Agriculture Industry: "I Don't Think I'D Want To Be A Man In This Industry", Cassie M. Duncan

College of Graduate Studies: Theses & Dissertations

Women currently make up 36% of the workforce in the agriculture industry and are actively growing in number (National Agricultural Statistics Service, 2017). Historically, women’s roles in the agriculture industry were silent or ignored, which has had consequences for women, such as poorer quality of life (Meares, 1997). Today, women are becoming more and more involved in the agriculture industry, but still face inequality in the workplace due to their gender. This research aims to understand the day-to-day experiences and impact of gender for women who work in the production agriculture industry; and by doing so, expand Feminist Theory to …

Applying Conservation Genomic Techniques To Guide Management Of The Reticulated Flatwoods Salamander (Ambystoma Bishopi), Miranda Gaupp

College of Graduate Studies: Theses & Dissertations

The Reticulated flatwoods salamander (Ambystoma bishopi) is a federally endangered amphibian endemic to the longleaf-pine ecosystem of the southeastern U.S. This study used analyses of single-nucleotide polymorphism (SNP) data, collected from 2,255 unique individuals across 5 breeding seasons, spread across the known extant range of A. bishopi, to characterize the genetic diversity and demographics of populations, genetic relationships among populations, and patterns and spatial extents of gene flow, and to evaluate potential effects of management on A. bishopi’s resiliency. Population structure was strongly hierarchical, with individual breeding ponds (n = 38) acting as semi-connected subpopulations …

The Essence Of Soil Biodiversity, Loren B. Byrne

Arts & Sciences Faculty Publications

Soil ecologists and conservationists should focus on raising people’s awareness of the essence of soil biodiversity: its complex ecologicalwebs and emergent ecosystemservices that support aboveground life and human well-being. Conservation and communication efforts regarding soil biodiversity must consider local-scale ecological contexts and different audiences. Engaging educational and outreach materials and methods should be prioritized to advance preservation of soil systems and their biodiversity.

Population Genomics Of Redbreast Sunfish (Lepomis Auritus): Exploring Gene Flow And Local Adaptation In A Widely Distributed Freshwater Fish, Garret J. Strickland

College of Graduate Studies: Theses & Dissertations

Little information is available concerning the distribution of genetic diversity in non-salmonid, non-imperiled, freshwater fish. In order to fill in this knowledge gap, I conducted a population genomics survey in Redbreast Sunfish (Lepomis auritus; RBS), a widespread, generalist species distributed along the Atlantic slope rivers of eastern North America. I sampled four basins (ACF, Savannah, Roanoke, and James) at eight sites each with a factorial experimental design. Sites were distributed among coastal plain, Piedmont, or mountain ecoregions in order to capture the greatest range of environmental states experienced by RBS, with the intention of finding evidence for local adaptation to …

Behavior And Chemical Signals As Markers Of Colony Identification In Argentine Ants (Linepithema Humile), Stephanie A. Rohrbach

College of Graduate Studies: Theses & Dissertations

Argentine ants, Linepithema humile, are a highly successful invasive species around the globe and are especially prominent in states such as California and the southeastern United States. L.humile have a unique form of unicoloniality, called “supercolonies”. L. humile can detect colonymates through scent markers in their outer cuticle. With these chemical markers, ants will exhibit high aggression if they smell different from one another. In our study, we performed aggression assays among ten different nest sites and analyzed their CHCs through gas chromatography mass spectrometry, or GC-MS, analysis. For our behavior results, while within-nest interactions displayed low aggression as …

Of Course Crustaceans Are Sentient: But There's More To The Story, Arthur S. Reber, Frantisek Baluska, William B. Miller Jr.

Animal Sentience

We are in basic agreement with Crump et al. that animal welfare, particularly with regard to the experience of pain, is a topic of importance. However, we come to the issue from a different perspective, one in which all species are sentient and can feel pain. The implications of this theory are discussed.

All Living Organisms Are Sentient, Arthur S. Reber, Frantisek Baluska, William B. Miller Jr.

Animal Sentience

We argue that all living organisms, from the simplest unicellular prokaryotes to Homo sapiens, have valenced experiences—feelings as states of preference—and are capable of cognitive representations. Bacteria can learn, form stable memories, and communicate, hence solve problems. Rowan et al.'s statement that "Subjective feelings are just that — subjective — and are available only to the animal (or human) experiencing them" is true but irrelevant. When we see a fish flopping about in the bottom of a boat we immediately recognize suffering without having a glimpse of the nature of piscine distress. Some controlled anthropomorphism can go a …

Molecular Detection Of Novel Anaplasma Sp. And Zoonotic Hemopathogens In Livestock And Their Hematophagous Biting Keds (Genus Hippobosca) From Laisamis, Northern Kenya, Daniel M. Mwaki, Kevin O. Kidambasi, Johnson Kinyua, Kenneth Ogila, Collins Kigen, Dennis Getange, Jandouwe Villinger, Daniel K. Masiga, Mark Carrington, Joel L. Bargul

All Peer-Reviewed Publications

Background: Livestock are key sources of livelihood among pastoral communities. Livestock productivity is chiefly constrained by pests and diseases. Due to inadequate disease surveillance in northern Kenya, little is known about pathogens circulating within livestock and the role of livestock-associated biting keds (genus Hippobosca) in disease transmission. We aimed to identify the prevalence of selected hemopathogens in livestock and their associated blood-feeding keds. Methods: We randomly collected 389 blood samples from goats (245), sheep (108), and donkeys (36), as well as 235 keds from both goats and sheep (116), donkeys (11), and dogs (108) in Laisamis, Marsabit County, northern Kenya. …

Potential Of Entomocomposting Toward Soil Pathogen Suppression, Dennis Beesigamukama, María Gómez-Brandón, Chrysantus Mbi Tanga

All Peer-Reviewed Publications

Waste accumulation and microbial pollution are key environmental challenges in most developing countries. Land filling, the commonest waste disposal method, is not sustainable due to land scarcity and point source pollution. Thus, a large fraction of organic wastes is not properly disposed, yet the conventional methods of waste recycling are less effective. The degradation of waste using insect life stages (entomocomposting) has emerged as a novel tool that is fast, affordable, and sustainable in recycling organic wastes with maximum pathogen suppression. This bioconversion process also generates an organic fertilizer with potential to enhance soil remediation and provide additional benefits on …

Integrated Pest Management Of Tuta Absoluta: Practical Implementations Across Different World Regions, Nicolas Desneux, Peng Han, Ramzi Mansour, Judit Arnó, Thierry Brévault, Mateus R. Campos, Anais Chailleux, Raul N.C. Guedes, Javad Karimi, Kouassi Arthur J. Konan, Anne Violette Lavoir, María G. Luna, Meritxell Perez-Hedo, Alberto Urbaneja, François J. Verheggen, Lucia Zappalà, Khaled Abbes, Abid Ali, Yunus Bayram, Fernando Cantor, Andrew G.S. Cuthbertson, Raf De Vis, Fedai Erler, Dnyaneshwar M. Firake, Khalid Haddi, M. Jamal Hajjar, Khasan Ismoilov, Coline C. Jaworski

All Peer-Reviewed Publications

The South American tomato pinworm, Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae), has invaded most Afro-Eurasian countries and is threatening worldwide tomato production. Various strategies have been developed and implemented to manage this pest. Here, we present a timely review on the up-to-date development and practical implementation of integrated pest management (IPM) programs for tomato crops across different world regions infested by T. absoluta. While insecticide resistance is a growing concern, biological control via releasing or conserving arthropod natural enemies and sex pheromone-based biotechnical control are the most successful management practices. Agronomic control-related research is an emerging area where the soil fertilization …

Characterization Of L-Malic Acid-Capped Cds Quantum Dots And Examination Of The Nanoncrystal's Biosensor Ability, Andrei A. Potapenko

Honors Theses and Capstones

Ligand-capped quantum dots are microscopic semiconductors commonly used in biomedical research and therapy for cell imaging and drug delivery. Despite the abundance of in vivo applications, the nature of interactions between the nanocrystals and the amino acids comprising human proteins remains insufficiently investigated. In this work, we report on the synthesis, ligand exchange, and characterization of the L-malic acid-capped CdS quantum dots via various spectroscopic techniques. We also assess the ligand-capped nanocrystals as potential probes for some amino acids. We determine that in the presence of L-cysteine, the L-malic acid-capped CdS quantum dots fluorescence signal quenches drastically, thus indicating a …

Screening Ocean Samples From Georgia For The Presence Of Msx And Dermo Using Pcr And Qpcr Methods, Olivia Michelle Williams

Honors Theses and Capstones

This Senior Thesis project aimed to be able to screen samples that came in from a PhD student in Georgia for the presence of two oyster diseases, MSX and Dermo. This study was done using PCR followed by visualizing on E-gels for initial presence of disease. These were then followed by qPCR and visualization on Criterion gels. These Criterion gels were able to be analyzed in order to calculate the pg/uL of MSX and Dermo in the original ocean samples. Since the samples were sent in over the course of February-August ‘21 the presence over time was also able to …

The Effect Of Post-Meal Walking On 24-Hour Central Blood Pressure In Young Women With And Without Excess Adiposity, Maison P. D'Amelio, Bilal A. Chaudhry, Ciana B. Lazu

Honors Theses and Capstones

Post-meal walking (PMW) performed after breakfast, lunch, and dinner has been demonstrated to reduce blood glucose. However, no studies have examined the potential additive benefits of post-meal walking exercise on daytime central blood pressure (BP) in young women. METHODS: Thirteen physically inactive, non-hypertensive women (Age: 20±1 years; percent body fat: 28.2±13%) completed the study during the early follicular or placebo phase of their contraceptive cycle. Participants completed a control day (CON; no exercise/excess physical activity) and PMW day (3 bouts x 15 minutes of brisk walking) over five days in random order. Daytime ambulatory BP and accelerometry data (to estimate …

Impact Of Drought Stress On Oak Stomatal Size And Density At Thompson Farm, Nh, Emily Chen

Honors Theses and Capstones

Global climate change is likely to affect northeastern U.S. forests by increasing the frequency and severity of drought events. Historically, droughts rarely occurred in this region, so native tree species are not well-adapted to extreme moisture stress. In the future, the changing climate will likely cause unprecedented levels of low water availability which may have implications on future forest composition. It is hypothesized that trees can respond to these environmental changes by altering their functional traits, also referred to as phenotypic plasticity; for example, by producing leaves with fewer and smaller stomata.

To determine the capacity to which oak trees …

Developmental Plasticity Of Stress Tolerance And Life-History Strategy To Artificial Light At Night, Alyssa M. Bonfoey

University of the Pacific Theses and Dissertations

Artificial light at night (ALAN), or ecological light pollution, is increasingly prevalent worldwide. Exposure to ALAN tends to negatively impact animals—particularly, nocturnal animals—but life-history strategies may mitigate these costs. Animals in many regions are also increasingly exposed to climate-related stressors, such as heat and drought. Yet, interactions among ALAN, life-history strategy, and stress tolerance are unknown. Therefore, I determined if developmental ALAN exposure (1) affects development, (2) affects adult phenotype, including heat and desiccation tolerance, and (3) affects and/or interacts with life-history strategy. To address my aims, I used the variable field cricket (Gryllus lineaticeps) because its geographic range is …

The Role Of Rad51 In Trichomonas Vaginalis, Dominique Hall

University of the Pacific Theses and Dissertations

Drug resistance to the current treatments on the market is on the rise, therefore there is strong interest in understanding what could be causing the resistance, how resistance could be spreading through the population, and finding some possible new drug targets. One protein of interest is Radiation Sensitive Protein 51 (Rad51). It is a protein that is involved in homologous recombination as well as other processes such as DNA damage repair. While Trichomonas vaginalis traditionally has been known to replicate via binary fission, a modified form of closed mitosis, there is some evidence that meiosis, or at least some form …

Examining Soil Microbial Diversity In Transition Zones Between Corn Fields And Restored Prairie In The Upper Midwest, Anna M. Burns

Scripps Senior Theses

Prairies were once the largest ecosystem in North America, but agriculture and settlement has destroyed up to 99% of their pre-colonization extent. Prairie restorations are a strategy to recover the biodiversity and carbon sequestration functions of these grasslands, but typically occur in isolated strips between agricultural fields. My thesis analyzes how effective prairie restorations in the Liberty Prairie (northeastern Illinois) are at recovering the diversity of the prairie soil microbiome, focusing on verrucomicrobia abundance, alpha diversity, and soil physical characteristics.

Footprints On The Prairie: Examining The Interlocking Land Histories Of The Liberty Prairie Reserve, Illinois, Anna M. Burns

Scripps Senior Theses

This thesis begins with the local history of the Liberty Prairie, the land where I conducted the ecological field-work that I later discuss in my second thesis on soil microbiome diversity (“Examining Soil Microbial Diversity in Transition Zones Between Corn Fields and Restored Prairie in the Upper Midwest"). I examine the Indigenous histories of the land, and the conflicts between the Bodwéwadmi and Euro-American settlers that resulted in the land being farmed for cattle, corn, and soy for over a hundred and fifty years. I then take a step back and analyze the broader historical contexts of Midwestern Corn Belt …

The Effect Of Acute And Chronic Arsenic Exposure On Malignant Transformation Of The Human Bronchial Epithelial Cell (Beas-2b), Bandar Almutairy

Wayne State University Dissertations

Arsenic (As3+), a metalloid abundant in the environment, is classified as a group I carcinogen associated with several common human cancers, including cancers in the lung, skin, bladder, liver, and prostate (Wei, Zhang & Tao, 2019b). The mechanisms of As3+-induced carcinogenesis had been extensively studied, and different mechanisms might be involved in various types of cancer (Wei, Zhang & Tao, 2019b). Recent studies showed that exposure to a high dose of arsenic is able to induce lung cancer. Moreover, arsenic activates oncogenic signaling pathways such as MAPKs, EGFR/RAS/RAF, PI3K/AKT, and JNK/STAT3 pathways as well as epigenetic alterations such as miRNAs …

Assessing The Environmental And Economic Sustainability Of Functional Food Ingredient Production Process, Anushree Priyadarshini, Brijesh K. Tiwari, Gaurav Rajauria

Articles

Development and application of novel technologies in food processing is vital for ensuring the availability of adequate, safe, and convenient food with the desired quality and functional properties. Environmental and economic sustainability of technologies is essential prior to their application in the food processing sector. The objective of this research is to determine the environmental and economic feasibility of ultrasound-assisted extraction (UAE) for recovering functional food ingredients from seaweed. Experimental data is used to conduct a life cycle assessment (LCA) to investigate the environmental performance with a functional unit (FU) of obtaining 1 g of extracted polyphenols, measured as gallic …

Application Of High-Intensity Ultrasound To Improve Food Processing Efficiency: A Review, Prasad Chavan, Pallavi Sharma, Sajeev Rattan Sharma, Tarsem Chand Mittal, Amit Jaiswal

Articles

The use of non-thermal processing technologies has grown in response to an ever-increasing demand for high-quality, convenient meals with natural taste and flavour that are free of chemical additions and preservatives. Food processing plays a crucial role in addressing food security issues by reducing loss and controlling spoilage. Among the several non-thermal processing methods, ultrasound technology has shown to be very beneficial. Ultrasound processing, whether used alone or in combination with other methods, improves food quality significantly and is thus considered beneficial. Cutting, freezing, drying, homogenization, foaming and defoaming, filtration, emulsification, and extraction are just a few of the applications …

Advances In Emerging Technologies For The Decontamination Of The Food Contact Surfaces, Shubham Sharma, Swarna Jaiswal, Brendan Duffy, Amit Jaiswal

Articles

Foodborne pathogens could be transferred to food from food contact surfaces contaminated by poor hygiene or biofilm formation. The food processing industry has various conditions favouring microbes' adherence, such as moisture, nutrients, and the microbial inoculums obtained from the raw material. The function of the ideal antimicrobial surface is preventing initial attachment of the microbes, killing the microbes or/and removing the dead bacteria. This review article provides detail about the challenges food industries are facing with respect to food contact materials. It also summarises the merits and demerits of several sanitizing methods developed for industrial use. Furthermore, it reviews the …