Digital Commons Network^™

Closing The Crop Yield Gap Between Organic And Conventional Farming Systems In Kenya: Long-Term Trial Research Indicates Agronomic Viability, David Bautze, Edward Karanja, Martha Musyoka, Johanna Rüegg, Eva Goldmann, Milka Kiboi, Ivonne Kampermann, Marc Cotter, Amritbir Riar, Felix Matheri, Edwin Mwangi, Monicah Mucheru-Muna, Hottensiah Wambui, John J. Anyango, Samuel Ndung'u, Chrysantus Tanga, Komi K.M. Fiaboe, Jesca Mbaka, Anne Muriuki, David Kamau, Noah Adamtey

All Peer-Reviewed Publications

The production gap between current and attainable yields is highest on Africa's smallholder farms, and some studies indicate that they might not benefit from the yield gains offered by conventional farming. Simultaneously, alternative farming systems like organic provide biodiversity and soil fertility advantages, but their ability to produce sufficient food is still under debate. Additionally, comparative data on the productivity of organic versus conventional in tropical regions are scarce or short-term. We investigated the crop productivity of organic and conventional farming systems using 15 years in two long-term systems comparison trials in Kenya. The trials were established in 2007 at …

Sampdetox : Black-Box Backdoor Defense Via Perturbation-Based Sample Detoxification, Yanxin Yang, Chentao Jia, Dengke Yan, Ming Hu, Tianlin Li, Xiaofei Xie, Xian Wei, Mingsong Chen

Research Collection School Of Computing and Information Systems

The advancement of Machine Learning has enabled the widespread deployment of Machine Learning as a Service (MLaaS) applications. However, the untrustworthy nature of third-party ML services poses backdoor threats. Existing defenses in MLaaS are limited by their reliance on training samples or white-box model analysis, highlighting the need for a black-box backdoor purification method. In our paper, we attempt to use diffusion models for purification by introducing noise in a forward diffusion process to destroy backdoors and recover clean samples through a reverse generative process. However, since a higher noise also destroys the semantics of the original samples, it still …

Revisiting Masked Auto-Encoders For Ecg-Language Representation Learning, Hung Manh Pham, Aaqib Saeed, Dong Ma

Research Collection School Of Computing and Information Systems

We propose C-MELT, a novel framework for multimodal self-supervised learning of Electrocardiogram (ECG) and text encoders. C-MELT pre-trains a contrastive-enhanced masked auto-encoder architecture using ECG-text paired data. It exploits the generative strengths with improved discriminative capabilities to enable robust cross-modal alignment. This is accomplished through a carefully designed model, loss functions, and a novel negative sampling strategy. Our preliminary experiments demonstrate significant performance improvements with up to 12% in downstream cardiac arrhythmia classification and patient identification tasks. Our findings demonstrate C-MELT's capacity to extract rich, clinically relevant features from ECG-text pairs, paving the way for more accurate and efficient cardiac …

From A Timeline Contact Graph To Close Contact Tracing And Infection Diffusion Intervention, Yipeng Zhang, Zhifeng Bao, Yuchen Li, Baihua Zheng, Xiaoli Wang

Research Collection School Of Computing and Information Systems

This paper proposes a novel graph structure to address the problems of information spreading in a real-world, frequently updating graph, with two main contributions at hand: accurately tracing infection diffusion according to fine-grained user movements and finding vulnerable vertices under the virus immunization scenario to mitigate infection diffusion. Unlike previous work that primarily predicts the long-term epidemic trend at the census level, this study aims to intervene in the short-term at the individual level. Therefore, two downstream tasks are formulated to illustrate practicalities: Epidemic Mitigating in Public Area problem (EMA) and Epidemic Maximized Spread in Public Area problem (ESA), where …

Unearthing Lactococcus Lactis And Scheffersomyeces Symbionts From Edible Wood-Boring Beetle Larvae As A Bio-Resource For Industrial Applications, Shadrack Kibet, Cynthia M. Mudalungu, Njogu M. Kimani, John Mark O. Makwatta, James Kabii, Subramanian Sevgan, Segenet Kelemu, Chrysantus M. Tanga

All Peer-Reviewed Publications

Background: Gut microbiota have several advantages in influencing the host nutrition, metabolism, immunity and growth. However, the understanding of the gut microbiota in key edible wood-boring beetle larvae remain largely undefined. In the present study, the characteristics of the gut microbiota of two edible wood-boring species (Titocerus jaspideus and Passalus punctiger) from two indigenous forested areas were investigated. Results: Over 50% of Amplicon Sequence Variants (ASVs) constituted of Firmicutes in T. jaspideus. The dominant phyla in both beetle species were Bacteroidota (4.20–19.79%) and Proteobacteria (15.10–23.90%). Lactococcus lactis was the most abundant and core prokaryote in the guts of T. jaspideus. …

Biological Reinforcement Learning Simulation For Natural Enemy -Host Behavior: Exploring Deep Learning Algorithms For Population Dynamics, Komi Mensah Agboka, Emmanuel Peter, Erion Bwambale, Bonoukpoè Mawuko Sokame

All Peer-Reviewed Publications

This study introduces a simulation of biological reinforcement learning to explore the behavior of natural enemies in the presence of host pests, aiming to analyze the population dynamics between natural enemies and insect pests within an ecological context. The simulation leverages on Q-learning, a reinforcement learning algorithm, to model the decision-making processes of both parasitoids/predators and pests, thereby assessing the impact of varying parasitism and predation rates on pest population growth. Simulation parameters, such as episode count, duration in months, steps, learning rate, and discount factor, were set arbitrarily. Environmental and reward matrices, representing climatic conditions, crop availability, and the …

Biostimulant And Antagonistic Potential Of Endophytic Fungi Against Fusarium Wilt Pathogen Of Tomato Fusarium Oxysporum F. Sp. Lycopersici, Marie Cecile Muhorakeye, Everlyne Samita Namikoye, Fathiya M. Khamis, Waceke Wanjohi, Komivi S. Akutse

All Peer-Reviewed Publications

Endophytic fungal-based biopesticides are sustainable and ecologically-friendly biocontrol agents of several pests and diseases. However, their potential in managing tomato fusarium wilt disease (FWD) remains unexploited. This study therefore evaluated effectiveness of nine fungal isolates against tomato fusarium wilt pathogen, Fusarium oxysporum f. sp. lycopersici (FOL) in vitro using dual culture and co-culture assays. The efficacy of three potent endophytes that inhibited the pathogen in vitro was assessed against FWD incidence, severity, and ability to enhance growth and yield of tomatoes in planta. The ability of endophytically-colonized tomato (Solanum lycopersicum L.) plants to systemically defend themselves upon exposure to FOL …

Multimodal Interactions In Stomoxys Navigation Reveal Synergy Between Olfaction And Vision, Merid N. Getahun, Steve B.S. Baleba, John Ngiela, Peter Ahuya, Daniel Masiga

All Peer-Reviewed Publications

Stomoxys flies exhibit an attraction toward objects that offer no rewards, such as traps and targets devoid of blood or nectar incentives. This behavior provides an opportunity to develop effective tools for vector control and monitoring. However, for these systems to be sustainable and eco-friendly, the visual cues used must be specific to target vector(s). In this study, we modified the existing blue Vavoua trap, which was originally designed to attract biting flies, to create a deceptive host attraction system specifically biased toward attracting Stomoxys. Our research revealed that Stomoxys flies are attracted to various colors, with red proving to …

Long-Term Push–Pull Cropping System Shifts Soil And Maize-Root Microbiome Diversity Paving Way To Resilient Farming System, Abdul A. Jalloh, Fathiya Mbarak Khamis, Abdullahi Ahmed Yusuf, Sevgan Subramanian, Daniel Munyao Mutyambai

All Peer-Reviewed Publications

Background: The soil biota consists of a complex assembly of microbial communities and other organisms that vary significantly across farming systems, impacting soil health and plant productivity. Despite its importance, there has been limited exploration of how different cropping systems influence soil and plant root microbiomes. In this study, we investigated soil physicochemical properties, along with soil and maize-root microbiomes, in an agroecological cereal-legume companion cropping system known as push–pull technology (PPT). This system has been used in agriculture for over two decades for insect-pest management, soil health improvement, and weed control in sub-Saharan Africa. We compared the results with …

Biochemistry And Transcriptomic Analyses Of Phthorimaeaabsoluta (Lepidoptera: Gelechiidae) Response To Insecticides, Samantha W. Karanu, Inusa J. Ajene, Elijah K. Lelmen, Maureen A. Ong’Onge, Komivi S. Akutse, Fathiya M. Khamis

All Peer-Reviewed Publications

Phthorimaeaabsoluta is an invasive solanaceous plant pest with highly devastating effects on tomato plant. Heavy reliance on insecticide use to tackle the pest has been linked to insecticide resistance selection in P.absoluta populations. To underline insights on P.absoluta insecticide resistance mechanisms to diamides and avermectins, we evaluated the transcriptomic profile of parental (field-collected) and F8 (lab-reared) populations. Furthermore, to screen for the presence of organophosphate and pyrethroid resistance, we assessed the gene expression levels of acetylcholinesterase (ace1) and para-type voltage-gated sodium channel (VGSG) genes in the F1 to F8 lab-reared progeny of diamide and avermectin exposed P.absoluta field-collected populations. The …

Designing And Delivering Bioinformatics Project-Based Learning In East Africa, Caleb K. Kibet, Jean Baka Domelevo Entfellner, Daudi Jjingo, Etienne Pierre De Villiers, Santie De Villiers, Karen Wambui, Sam Kinyanjui, Daniel Masiga

All Peer-Reviewed Publications

Background: The Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We highlight how the program has evolved to meet challenges and achieve its goals and how experiential learning through mini projects enhances the acquisition of skills and collaboration. We continued to learn and grow through honest feedback and evaluation of the program, trainers, and modules, enabling us to provide robust training even during the Coronavirus disease 2019 (COVID-19) pandemic, when we had to redesign the program due to restricted travel and in person group meetings. Results: In response to the pandemic, we developed …

Community Perceptions, Acceptability, And The Durability Of House Screening Interventions Against Exposure To Malaria Vectors In Nyimba District, Zambia, Kochelani Saili, Christiaan De Jager, Freddie Masaninga, Brian Chisanga, Andy Sinyolo, Japhet Chiwaula, Jacob Chirwa, Busiku Hamainza, Emmanuel Chanda, Nathan N. Bakyaita, Clifford Maina Mutero

All Peer-Reviewed Publications

Background: House screening remains conspicuously absent in national malaria programs despite its recognition by the World Health Organization as a supplementary malaria vector-control intervention. This may be attributed, in part, to the knowledge gap in screen durability or longevity in local climatic conditions and community acceptance under specific cultural practices and socio-economic contexts. The objectives of this study were to assess the durability of window and door wire mesh screens a year after full house screening and to assess the acceptability of the house screening intervention to the participants involved. Methods: This study was conducted in Nyimba district, Zambia and …

A Mathematical Model For Mapping The Insecticide Resistance Trend In The Anopheles Gambiae Mosquito Population Under Climate Variability In Africa, Komi Mensah Agboka, Mark Wamalwa, James Mutuku Mutunga, Henri E.Z. Tonnang

All Peer-Reviewed Publications

The control of arthropod disease vectors using chemical insecticides is vital in combating malaria, however the increasing insecticide resistance (IR) poses a challenge. Furthermore, climate variability affects mosquito population dynamics and subsequently IR propagation. We present a mathematical model to decipher the relationship between IR in Anopheles gambiae populations and climate variability. By adapting the susceptible-infected-resistant (SIR) framework and integrating temperature and rainfall data, our model examines the connection between mosquito dynamics, IR, and climate. Model validation using field data achieved 92% accuracy, and the sensitivity of model parameters on the transmission potential of IR was elucidated (e.g. μPRCC = …

Precision And Efficacy Of Rna-Guided Dna Integration In High-Expressing Muscle Loci, Made Harumi Padmaswari, Gabrielle Bulliard, Shilpi Agrawal, Mary S. Jia, Sabin Khadgi, Kevin A. Murach, Christopher E. Nelson

Biomedical Engineering Faculty Publications and Presentations

Gene replacement therapies primarily rely on adeno-associated virus (AAV) vectors for transgene expression. However, episomal expression can decline over time due to vector loss or epigenetic silencing. CRISPR-based integration methods offer promise for long-term transgene insertion. While the development of transgene integration methods has made substantial progress, identifying optimal insertion loci remains challenging. Skeletal muscle is a promising tissue for gene replacement owing to low invasiveness of intramuscular injections, relative proportion of body mass, the multinucleated nature of muscle, and the potential for reduced adverse effects. Leveraging endogenous promoters in skeletal muscle, we evaluated two highly expressing loci using homology-independent …

Evaluation Of Industrial Hemp Cultivar And Biochar Rate To Remediate Heavy-Metal-Contaminated Soil From The Tar Creek Superfund Site, Usa, Dietrich V. Thurston, Kristofor R. Brye, David M. Miller, Philip A. Moore Jr., Donald M. Johnson, Mike Richardson

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Soil contamination by cadmium (Cd), lead (Pb), and zinc (Zn) at the Tar Creek superfund site in northeast Oklahoma, United States, remains a threat to the environment and local ecosystem. Phytoremediation with industrial hemp (Cannabis sativa L.) and the use of biochar (BC) have been independently shown to be effective methods to remediate heavy-metal-contaminated soils. The objective of this greenhouse study was to evaluate the effects of industrial hemp cultivar (‘Carmagnola’ and ‘Jinma’), biochar rate (0, 2, 5, and 10% by volume), soil contamination level (low, medium, and high), and their interactions on above- (AG) and belowground dry matter …

Use Of A Capsule Suspension Formulation Of S-Metolachlor In Fenclorim-Treated Rice, Jason K. Norsworthy, Samuel C. Noe, Thomas R. Butts, Trenton L. Roberts

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

As herbicide resistance continues to render commonly used rice herbicides ineffective, alternative sites of action are paramount to maintaining yield and producer profitability. Combining a slow-release formulation and a fenclorim seed treatment might allow the safe use of S-metolachlor in rice. Experiments were initiated in 2022 and 2023 near Colt, AR, on a silt loam soil to evaluate crop safety using a capsule suspension (CS) formulation of S-metolachlor and a fenclorim seed treatment in rice. The first experiment assessed the tolerance of two cultivars (‘Diamond’ and ‘DG263L’) to three rates (0.42, 0.84, and 1.68 kg ai ha^{−1 …}

Interpreting The Spatial Distribution Of Soil Properties With A Physically-Based Distributed Hydrological Model, Zamir Libohova, Marcelo Mancini, Hans Edwin Winzeler, Quentin D. Read, Ning Sun, Dylan Beaudette, Candiss Williams, Joshua Michael Blackstock, Sergio H.G. Silva, Nilton Curi, Kabindra Adhikari, Amanda Ashworth, Joshua O. Minai, Phillip R. Owens

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Digital soil maps are commonly data-driven as the development of physically-based models for soil mapping is difficult due to the complexity of soils. However, physically-based hydrologic models have been successful in simulating water dynamics. Since water movement is a major driver of pedogenesis, the physical rules that govern water movement might help explain and predict the spatial variation of soil properties. Here, we demonstrate the novel use of a physically-based, distributed hydrologic model to inform the spatial distribution of soil properties. The Distributed Hydrology Soil Vegetation Model (DHSVM) was utilized to simulate soil moisture content (SM) and water table …

Foraging Behavior And Age Affect Maternal Transfer Of Mercury To Northern Elephant Seal Pups, Sarah H. Peterson, Michael G. Peterson, Joshua T. Ackerman, Cathy Debier, Chandra Goetsch, Rachel R. Holser, Luis A. Hückstädt, Jennifer C. Johnson, Theresa R. Keates, Birgitte I. Mcdonald, Elizabeth A. Mchuron, Daniel P. Costa

Faculty Research, Scholarly, and Creative Activity

Deep ocean foraging northern elephant seals (Mirounga angustirostris) consume fish and squid in remote depths of the North Pacific Ocean. Contaminants bioaccumulated from prey are subsequently transferred by adult females to pups during gestation and lactation, linking pups to mercury contamination in mesopelagic food webs (200–1000 m depths). Maternal transfer of mercury to developing seal pups was related to maternal mercury contamination and was strongly correlated with maternal foraging behavior (biotelemetry and isotopes). Mercury concentrations in lanugo (hair grown in utero) were among the highest observed worldwide for young pinnipeds (geometric mean 23.01 μg/g dw, range 8.03–63.09 μg/g dw; n …

Benefits Of Teaching Pre-Literacy In Waldorf Education In Early Childhood, April Guerrero

Capstone Projects and Master's Theses

This senior capstone research project examines the benefits of teaching pre-literacy in Waldorf education in early childhood. In Waldorf Education, literacy development incorporates differentiated instructions that fosters cognitive and social emotional learning of their students. Through the use of literature review and several teachers in various grades of Waldorf schools, the result findings revealed that pedagogical practices around literacy instructions promote critical thinking skills, nurtures children’s creative expression, and imagination. Literacy curriculum in Waldorf schools allows students to create tangible evidence of self-expressions and communication skills. Given its emphasis on holistic curriculum, it allows teachers to engage with their diverse …

Roman History In Sibylline Oracle 13: A Palestinian Jewish Perspective On Emperors, Usurpers, And Saviors During The Third Century Ce (Part Two: From Decius To Odenath Of Palmyra), Kenneth Atkinson

Faculty Publications

Sibylline Oracle 13 is a remarkable historical document that contains a unique perspective on the poorly documented period of Roman history known as the “Crisis of the Third Century (235-284 CE), which began with the assassination of the Roman emperor Severus Alexander (222-235 CE), the last ruler of the Severan dynasty. This turbulent era was marked by nearly fifty years of civil wars, barbarian invasions, rebellions, and approximately twenty-six claimants to the throne. Although the end of this turmoil under Diocletian (284-305 CE) is well known, we have little information about much of this century, particularly its first decades. The …

Deep Learning Approach For Accurate Segmentation Of Oil Spills In Marine Systems, Mohamed Elsheref

LSU New Orleans Theses and Dissertations

Oil spills present critical environmental hazards, threatening marine ecosystems and necessitating fast, accurate detection for effective mitigation. Synthetic Aperture Radar (SAR) imagery has been instrumental in detecting oil spills, but manual interpretation is often inefficient and prone to errors. This study addresses the limitations of manual methods by proposing a deep learning approach for automated oil spill detection and segmentation.

Utilizing a novel transfer learning-based semantic segmentation model, this research focuses on detecting oil slicks on the sea surface with higher accuracy and efficiency. The model leverages pre-trained networks and incorporates U-Net variants, including UNet++ and MultiResUNet, to optimize spatial …

Examining The Impact Of Eds And Meds Anchor Institutions On Local Communities: A Mixed Methods Case Study On University Medical Center New Orleans, Samuel P. Firmin

LSU New Orleans Theses and Dissertations

The purpose of this study was to examine how the University Medical Center New Orleans (UMCNO), a major Eds and Meds anchor institution, has contributed to the well-being outcomes of surrounding communities within the New Orleans BioDistrict since its opening in 2015. Eds and Meds institutions often have mixed impacts on their local communities, and little research has focused on their effects in the Deep South, particularly in New Orleans, a region with pronounced socioeconomic disparities. This study aimed to address this research gap by investigating the following question: to what extent does UMCNO's Community Health Needs Assessments align with …

Benefits Of After School Programs On The Academic Success On Lower Elementary School Students, Jessica Rodriguez Rodriguez

Capstone Projects and Master's Theses

After School programs offer significant benefits to students. They support students by offering tutoring, homework assistance, enrichment activities that reinforce classroom learning, and helping young students develop essential skills in reading, math, and critical thinking. The purpose of my capstone project is to examine the benefits of afterschool programs on the academic success of lower elementary school students. Through literature review, interviews with teachers, a coordinator, an academic coordinator, an administrator, and anonymous student surveys, the result findings indicated that afterschool programs are important and have benefited students in meeting their needs to foster their success. It also highlights the …

Disposal Deficiency: Single-Use Battery-Powered Smoking Devices, Isaiah A. Zuniga

Capstone Projects and Master's Theses

There exists a critical issue in the disposal process for single-use battery-operated smoking devices, including cannabinoid and tobacco products in Monterey County, which pose significant social and health ramifications. The County of Monterey Health Department’s Tobacco Prevention Program aims to educate youth and adults and support cessation services. This project focuses on spreading awareness through educational media about the proper disposal of single-use battery-operated smoking devices, with the long-term aspiration of developing a comprehensive disposal process to reduce environmental contamination and encourage healthier habits. Initial findings revealed that many users are unaware that vapes and similar devices cannot be disposed …

Enhanced Care Management, James Love

Capstone Projects and Master's Theses

Santa Cruz County’s Enhanced Care Management (ECM) program assists Medi-Cal recipients who are unhoused, have substance use disorders/serious mental illness, or are high utilizers of medical services, obtain and maintain medical care coordination services. This population faces many challenges living in Santa Cruz, and the ECM team needs additional resources to continue the supportive work the care management program provides.

The needs assessment documents the ECM team’s desired physical and emotional resources to support their health and identifies the current barriers to supporting clients. The ECM team responded to a Google form survey and the responses were analyzed for common …

The Forgotten S.O.P., Kamille Stevens

Capstone Projects and Master's Theses

The Institute for Innovation and Entrepreneurship Development (iiED) is dedicated to cultivating entrepreneurship and economic growth within the Monterey Bay. Its goal is to create a pipeline of entrepreneurs from the Monterey Bay region who remain local and are able to increase the number of businesses and high-paying jobs in the area. To reach this goal, iiED provides multiple opportunities to its participants and tailors those opportunities based on their feedback.

Recently, iiED’s management has begun to experience turnover as individuals retire or reduce their work hours. As a result, iiED has begun to depend on the specialized knowledge of …

Addressing The Lack Of Parental Involvement With Spanish-Speaking Parents In Education, Zaira Cortez-Zacarias

Capstone Projects and Master's Theses

Student achievement and engagement at an independent studies school must be improved by the lack of parental involvement among Spanish-speaking parents. Learning for Life charter school provides an alternative, flexible learning environment for middle and high school students (grades 7-12) who require more individualized attention and they serve students in Monterey, Salinas, San Benito, and Santa Cruz school districts. Identifying obstacles to parental involvement in Spanish-speaking families and creating plans to improve engagement and communication were the goals of this project. The project's main objectives were to develop outreach strategies that are sensitive to cultural differences, provide language assistance, and …

Career Readiness, Jeanette Quezada

Capstone Projects and Master's Theses

This project aimed to address the lack of job experience among adolescents, which often leaves them feeling unprepared for the job market or higher education. Career readiness workshops were conducted with 7th-12th grade students at Learning For Life Charter School to enhance their job preparation skills. It was hypothesized that the workshops would boost students’ confidence in tasks such as filling out job and college applications, creating resumes, and writing cover letters. Pre- and post-workshop surveys revealed significant improvements in self-assessed confidence levels. Based on these findings, the workshops were beneficial for students. To further leverage these results, it is …

Addressing The Needs Of Survivors In Domestic Violence Shelters, Diana Edith Hernandez Saldivar

Capstone Projects and Master's Theses

Survivors of domestic violence, sexual assault, and human trafficking often face significant barriers to accessing basic hygiene items when seeking shelter. Monarch Services, a nonprofit in Santa Cruz County, addresses these challenges at its Mariposa House. The agency offers various services for survivors, including advocacy, case management, and emergency shelter. This project involved organizing a donation drive, enhancing the intake process with a needs assessment, and gathering client feedback through surveys on hygiene items received. The expected outcomes were collecting hygiene products, integrating a needs assessment into the intake form, and client feedback. The shelter successfully received hygiene donations, updated …

Harvesting Hope: How La Casa De La Cultura Serves Migrant Families Through Health And Advocacy Programs, Ana Ruiz

Capstone Projects and Master's Theses

This project aims to enhance community engagement in Pajaro through strategic outreach and marketing efforts for weekly meetings hosted at La Casa de la Cultura. By increasing awareness and participation, the initiative seeks to empower residents, especially those from marginalized backgrounds, to access vital resources and services. The project will collect data on attendance and community interests, leading to more tailored presentations that address pressing concerns. Ultimately, this outreach aims to foster a unified, informed community capable of advocating for its needs and accessing available support systems effectively.