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Oligonychus Trichardti (Acari: Tetranychidae) Associated With Urochloa Grasses In Kenya: An Integrative Taxonomic Approach, Paula Espitia-Buitrago, Claudia Perea, Lavender A. Odhiambo, Rosa N. Jauregui, Frank Chidawanyika Jan 2026

Oligonychus Trichardti (Acari: Tetranychidae) Associated With Urochloa Grasses In Kenya: An Integrative Taxonomic Approach, Paula Espitia-Buitrago, Claudia Perea, Lavender A. Odhiambo, Rosa N. Jauregui, Frank Chidawanyika

All Peer-Reviewed Publications

Spider mites represent a significant constraint to improved forage grass adoption in East Africa, particularly affecting Urochloa cultivars that are crucial for addressing the region’s 40% livestock feed gap. This study employed an integrative taxonomic approach combining morphological and molecular analyses to identify a spider mite species infesting Urochloa interspecific grasses in Kenya. A colony of 80 spider mites was established from symptomatic Urochloa hybrid cv. Cayman plants collected from Mbita Point, Kenya, showing characteristic foliar chlorosis and necrotic spots. Morphological examination of 46 slide-mounted specimens using Hoyer’s medium revealed consistent morphotypical features characteristic of Oligonychus (Reckiella) trichardti Meyer, 1974. …


Trident-Bladder: A Resolution-Aware Multimodal System For Robust, Calibrated Bladder Cancer Diagnosis Across Endoscopy, Histopathology, And Liquid Biopsy, K. Sankar, S. Venkata Lakshmi, Gummadi Reshma, V. Gokula Krishnan, M. Ganesan, V. Vijayaraja Jan 2026

Trident-Bladder: A Resolution-Aware Multimodal System For Robust, Calibrated Bladder Cancer Diagnosis Across Endoscopy, Histopathology, And Liquid Biopsy, K. Sankar, S. Venkata Lakshmi, Gummadi Reshma, V. Gokula Krishnan, M. Ganesan, V. Vijayaraja

Mansoura Engineering Journal

Bladder cancer diagnosis demands the integration of cystoscopy, histopathology, and biomarker testing, yet the majority of AI systems continue to be modality, specific and sensitive to acquisition variations. TRIDENT, Bladder is a resolution, aware multimodal framework that we have developed to address this issue. The method combines cystoscopic lesion segmentation, whole, slide image (WSI) molecular subtype prediction, and urine miRNAclinical data through reliability, weighted fusion and a utility, aware decision policy. The endoscopic branch features a quality, gated super, resolution component, resulting in mDice 87.5, sensitivity 92.1%, precision 91.4%, boundary, F1 85.3%, and ECE 0.023 at 32 FPS. mDice on …


Effect Of Two Cut Off Rows On Seepage Underneath Hy-Draulic Structures Using Weak Form Differential Quadra-Ture Element Method: A Theoretical Approach, Esraa Ahmed, El-Masry A. A, Hossam A.A. Abdel Gawad, Ahmed Elhamrawy Jan 2026

Effect Of Two Cut Off Rows On Seepage Underneath Hy-Draulic Structures Using Weak Form Differential Quadra-Ture Element Method: A Theoretical Approach, Esraa Ahmed, El-Masry A. A, Hossam A.A. Abdel Gawad, Ahmed Elhamrawy

Mansoura Engineering Journal

Investigating confined seepage underneath hydraulic structures is crucial to ensure the safety of these structures. The Weak Form Quadrature Element Method (WFQEM) is the basis of this paper, which explores the behavior of confined flow. The seepage flow governing equation is solved numerically to estimate the uplift pressure underneath the hydraulic structures and the exit gradient.The Gauss–Lobatto–Legendre (GLL) type is used as nodal and integration points. Several models were solved to validate the applied numerical method. The obtained results are compared with theoretical and preceding numerical solutions mentioned in the literature. The system of equations generated from applying the WFQEM …


Comparing Autodissemination, Soil Inoculation And Their Combination As Modes Of Application Of Metarhizium Anisopliae Icipe 69 On The Melon Fly Infesting Courgette In Kenya Under Semi-Field Conditions, Rehemah Gwokyalya, Thomas Dubois, Susan K. Onsongo, Joseph A. Odhiambo, Komivi Senyo Akutse, Samira A. Mohamed Jan 2026

Comparing Autodissemination, Soil Inoculation And Their Combination As Modes Of Application Of Metarhizium Anisopliae Icipe 69 On The Melon Fly Infesting Courgette In Kenya Under Semi-Field Conditions, Rehemah Gwokyalya, Thomas Dubois, Susan K. Onsongo, Joseph A. Odhiambo, Komivi Senyo Akutse, Samira A. Mohamed

All Peer-Reviewed Publications

The melon fly Zeugodacus cucurbitae (Coquillett) (Diptera: Tephritidae) is a significant pest of cucurbit crops, responsible for substantial yield losses and economic damage across Asia and Sub-Saharan Africa. Control of this pest currently relies heavily on synthetic insecticides, which are associated with environmental and human health risks, and contribute to the development of insecticide resistance. Entomopathogenic fungi offer a promising eco-friendly alternative, yet effectiveness of delivery methods remains a critical limitation in their widespread adoption. This study evaluated the efficacy of three application modes of Metarhizium anisopliae (Mechnikov) Sorokin (Hypocreales: Clavicipitaceae) isolate ICIPE 69, autodissemination devices (AD), soil inoculation (soil), …


Thermal Requirements And Phenology Modelling Of A Drosophila Suzukii Population: Implications For Pest Risk Under A Changing Climate, Shepard Ndlela, Abdelmutalab G.A. Azrag, Esther Owino Awuor, Ibrahim Maholidy Farid, Samira Abuelgasim Mohamed Jan 2026

Thermal Requirements And Phenology Modelling Of A Drosophila Suzukii Population: Implications For Pest Risk Under A Changing Climate, Shepard Ndlela, Abdelmutalab G.A. Azrag, Esther Owino Awuor, Ibrahim Maholidy Farid, Samira Abuelgasim Mohamed

All Peer-Reviewed Publications

Drosophila suzukii (spotted-wing drosophila) is an invasive pest causing significant economic losses in soft-skinned fruit crops globally. This study presents comprehensive temperature-dependent life table data and phenology models for an African D. suzukii population collected in Kenya. Developmental time, mortality, fecundity, and adult longevity were assessed under constant temperatures from 12 to 30 °C. Using Insect Life Cycle Modelling (ILCYM) software, linear and nonlinear models were applied to characterise the effects of temperature on life history traits. Additionally, spatial risk indices including Establishment Risk Index (ERI), Generation Index (GI), and Activity Index (AI) were mapped globally for current and future …


Sustainable Control Of Pests And Striga Weed Through Intensified Push-Pull Technology And Frass-Based Soil Amendments, Evanson R. Omuse, Honest Machekano, Daniel M. Mutyambai, Dennis Beesigamukama, Chrysantus M. Tanga, Samwel O. Ogaji, Sevgan Subramanian, Frank Chidawanyika Jan 2026

Sustainable Control Of Pests And Striga Weed Through Intensified Push-Pull Technology And Frass-Based Soil Amendments, Evanson R. Omuse, Honest Machekano, Daniel M. Mutyambai, Dennis Beesigamukama, Chrysantus M. Tanga, Samwel O. Ogaji, Sevgan Subramanian, Frank Chidawanyika

All Peer-Reviewed Publications

Crop productivity under African smallholder farming systems is faced by numerous challenges, including insect pests, weeds, low soil fertility, and climate change. Sustainable intensification, such as push-pull (PP) technology and vegetable-integrated push-pull (VIPP) technology, coupled with soil organic amendments such as black soldier fly frass fertilizer (BSFFF), can address these agricultural constraints. We investigated the individual and synergistic effects of cropping systems comprising two crops [maize (DK777 variety) and cowpea (KVU27 variety)] and agroecological strategies (PP, VIPP and BSFFF) on the management of pests and Striga weeds and crop productivity in three different geographical areas. Diversified cropping systems (PP and …


Intensified Push-Pull Technology Enhances Above-Ground Arthropod Assemblages And Ecological Balance, Evanson R. Omuse, Honest Machekano, Daniel M. Mutyambai, Bonoukpoe M. Sokame, Chrysantus M. Tanga, Johnson O. Nyasani, Sevgan Subramanian, Frank Chidawanyika Jan 2026

Intensified Push-Pull Technology Enhances Above-Ground Arthropod Assemblages And Ecological Balance, Evanson R. Omuse, Honest Machekano, Daniel M. Mutyambai, Bonoukpoe M. Sokame, Chrysantus M. Tanga, Johnson O. Nyasani, Sevgan Subramanian, Frank Chidawanyika

All Peer-Reviewed Publications

Agroecological intensification aims to increase farm productivity, reduce dependency on external inputs, and enhance biodiversity conservation. However, the contribution of recent sustainable agricultural practices to arthropod assemblages and their ecosystem services remains underexplored. Through a 2-year multilocation trial, we investigated the response of above-ground arthropod assemblages and their ecological functions in cowpea and maize grown under monocropping systems and diversified systems (pure and intensified push-pull technologies). Using three sampling methods (visual observations, pitfall traps, sticky traps), a total of 65, 307 arthropod specimens were collected. The most dominant arthropod taxa were Hemiptera (true bugs; 47%), followed by Thysanoptera (thrips; 17%), …


Impacts Of Multitrophic Interactions In Diversified Cropping Systems For Sustainable Management Of Spodoptera Frugiperda, Abdul A. Jalloh, Abdullahi Ahmed Yusuf, Fathiya M. Khamis, Subramanian Sevgan, Daniel Munyao Mutyambai Jan 2026

Impacts Of Multitrophic Interactions In Diversified Cropping Systems For Sustainable Management Of Spodoptera Frugiperda, Abdul A. Jalloh, Abdullahi Ahmed Yusuf, Fathiya M. Khamis, Subramanian Sevgan, Daniel Munyao Mutyambai

All Peer-Reviewed Publications

Background: Rapid population growth has made the sustainable intensification of agricultural productivity essential for meeting global food demands while maintaining environmental integrity and biodiversity. Diversified cropping systems, such as intercropping, push-pull systems, and cover cropping, are recognized as agroecological strategies to enhance plant growth and protection, and suppress major pests, including the fall armyworm (FAW, Spodoptera frugiperda). These systems influence complex above-and-below ground interactions among herbivorous pests, plants, soil microbes, and their natural enemies. Aims: This review synthesizes current knowledge on how diversified cropping systems shape multitrophic interactions that affect soil health, plant performance, S. frugiperda suppression, and biocontrol within …


Adolescent Binge-Like Feeding And Neuroinflammation: Effects Of Intermittent Palatable Diet Access On Microglial Activation In The Brain In Adolescents, Jaimie T. Yu Jan 2026

Adolescent Binge-Like Feeding And Neuroinflammation: Effects Of Intermittent Palatable Diet Access On Microglial Activation In The Brain In Adolescents, Jaimie T. Yu

CMC Senior Theses

Binge eating disorder (BED), one of the most common eating disorders in the United States (Definition & Facts for Binge Eating Disorder - NIDDK, n.d.), is characterized by recurrent episodes of consuming large quantities of food in a short period of time accompanied by a sense of loss of control. The intermittent access (INT) model reliably produces binge-like eating in adult rodents, with animals showing episodic hyperphagia upon time-limited access to a high-fat, high-sugar (HFHS) diet. In adult female rats, INT access produces elevated meal size and reduced satiety ratio relative to controls (Maske et al., 2020), and promotes microglial …


Microbial Community Structure In Global Soils, Matthew Jabro Jan 2026

Microbial Community Structure In Global Soils, Matthew Jabro

CMC Senior Theses

Soil harbors the most diverse microbial communities on Earth, yet whether predictable community types exist across biomes and whether taxonomic composition encodes habitat of origin remain open questions at global scale. This thesis addresses both questions by applying unsupervised clustering and supervised classification to transformed 16S ribosomal RNA (rRNA) amplicon profiles from two independent datasets: the global topsoil survey of Bahram et al. (193 samples) and the Earth Microbiome Project (EMP) soil subset of Thompson et al. (2,209 samples). Application of a sample clustering method based on a mixture of Gaussian Graphical Models (MixGGM) identified 19 clusters in the topsoil …


Neuroimaging Correlates Of Differences In Learning From Repeated Probabilistic Outcomes, Allison E. Rudolph Jan 2026

Neuroimaging Correlates Of Differences In Learning From Repeated Probabilistic Outcomes, Allison E. Rudolph

CMC Senior Theses

Learning from experience requires integrating feedback over time, yet individuals vary widely in how effectively they extract structure from probabilistic environments. This study examined how such variability relates to neural responses in the ventral striatum (vStr), caudate nucleus, hippocampus, and medial prefrontal cortex (mPFC). Seventy-four participants across childhood, adolescence, and adulthood completed a modified Iowa Gambling Task during fMRI scanning, choosing whether to play or pass on four machines differing in expected value and variance. Behavioral learning slopes, calculated across six runs for each machine, were used to classify participants as learners or non-learners. Learners showed clearer improvement over time …


Psr Impacts Chromatin Condensation During Spermatogenesis In Nasonia Vitripennis, Jacqueline R. Solomon Jan 2026

Psr Impacts Chromatin Condensation During Spermatogenesis In Nasonia Vitripennis, Jacqueline R. Solomon

CMC Senior Theses

Paternal Sex Ratio (PSR) is a supernumerary, selfish B chromosome found in the jewel wasp (Nasonia vitripennis). PSR is transmitted strictly paternally to progeny, and when present, it causes paternal genome elimination (PGE) just after fertilization. Due to the haplo-diploid reproduction of N. vitripennis, this PGE event results in all-male broods of progeny, ~90% of which carry and transmit PSR. Thus, PGE is beneficial for PSR’s transmission.  A previous study showed that PSR induces PGE by expressing a gene called haploidizer during spermatogenesis. Although how haploidizer functions in PGE is unknown, this finding suggests two basic models: that (i) the …


Exploration Of The Use Of Radiocarbon Time-Series Records As Indicators Of Upwelling Areas, Rena Reshmi Mukherjee Jan 2026

Exploration Of The Use Of Radiocarbon Time-Series Records As Indicators Of Upwelling Areas, Rena Reshmi Mukherjee

CMC Senior Theses

The Earth’s oceans buffer climate change, regulate weather patterns, sustain global food security, and support biomedical research. Ocean currents redistribute heat and nutrients while promoting genetic diversity, which can serve as a source of novel compounds for biomedical research. Understanding ocean circulation is essential for maintaining these ecosystem services as the climate continues to change. Upwelling, a form of vertical water movement that transports nutrient-rich deep water to the surface, plays a key role in marine productivity and carbon cycling. However, global upwelling patterns remain incompletely mapped. Radiocarbon (14C), a radioactive isotope of carbon, provides a useful tracer of ocean …


Modulating Oran Nitrate-Reducing Bacteria To Enhance Nitric Oxide Bioavailability As A Therapeutic Target For Atherosclerosis, Donovan C. Davidson Jan 2026

Modulating Oran Nitrate-Reducing Bacteria To Enhance Nitric Oxide Bioavailability As A Therapeutic Target For Atherosclerosis, Donovan C. Davidson

CMC Senior Theses

Atherosclerosis remains the primary driver of global cardiovascular disease, yet clinical interventions are largely restricted to high-cost, invasive procedures only after it has reached a critical stage. Recent research has identified a connection between the oral microbiome and vascular health via the enterosalivary nitrate-nitrite-nitic oxide (NO) pathway. Oral nitrate-reducing bacteria (ONRB) drive the synthesization of NO by reducing dietary nitrate into nitrite, which is then converted into bioavailable NO. NO is a potent vasodilator that maintains endothelial health by suppressing inflammation through inhibiting the expression of adhesion molecules VCAM-1 and ICAM-1. However, this pathway is easily compromised by dysbiotic oral …


Not Biological, But Built: Structural And Metabolic Pathways Driving Black Maternal Health Disparities In The United States, Alexandra I. Umegboh Jan 2026

Not Biological, But Built: Structural And Metabolic Pathways Driving Black Maternal Health Disparities In The United States, Alexandra I. Umegboh

CMC Senior Theses

Black infants in the United States are more than twice as likely to die before their first birthday than white infants, a disparity often attributed to genetics, behavior, or individual health choices. However, this idea is challenged by a key contradiction: African immigrant women consistently experience better birth outcomes than U.S.-born Black women despite being similarly racialized. This thesis investigates the origins of this reproductive advantage and the factors contributing to its decline over time. By drawing on epidemiological data, metabolic health research, and literature on African diasporic healing traditions, it argues that the “healthy immigrant effect” is not biological, …


Roles Of Cytokines In Modulating Trypanosoma Brucei Rhodesiense Infection Outcomes In Vervet Monkeys, Clarah Jebet, John Kibuthu Thuita, Daniel Masiga, Benedict Owino Orindi, John Oidho, Mark C. Field, Enock Matovu, Vincent Owino Adung’A Jan 2026

Roles Of Cytokines In Modulating Trypanosoma Brucei Rhodesiense Infection Outcomes In Vervet Monkeys, Clarah Jebet, John Kibuthu Thuita, Daniel Masiga, Benedict Owino Orindi, John Oidho, Mark C. Field, Enock Matovu, Vincent Owino Adung’A

All Peer-Reviewed Publications

Introduction:

Human African trypanosomiasis (HAT), caused by Trypanosoma brucei rhodesiense, is categorized as acute due to rapid disease progression but presents varying clinical outcomes. Although the mechanisms underpinning differential clinical progression are poorly understood, both host and parasite factors are implicated. Therefore, we sought to elucidate roles of primate host factors in mediating varying T. b. rhodesiense infection outcomes.

Methods:

Here, we assessed the roles of selected host cytokines in disease progression using a tsetse-mediated infection in a non-human primate (NHP) vervet monkey model that closely mimics HAT and natural infection. We quantified eight cytokines, including TNF-α, IFN-γ, IL-10, IL-6, …


Impact Of Environmental Microparticles On Insect Olfaction, Steve B.S. Baleba, Danube K.N. Wandji, Yves H. Tchiechoua, Komi Mensah Agboka, Iman B. Hassaballa, Victor O. Omondi, Beatrice T. Nganso, Saliou Niassy, Souleymane Diallo, Merid N. Getahun Jan 2026

Impact Of Environmental Microparticles On Insect Olfaction, Steve B.S. Baleba, Danube K.N. Wandji, Yves H. Tchiechoua, Komi Mensah Agboka, Iman B. Hassaballa, Victor O. Omondi, Beatrice T. Nganso, Saliou Niassy, Souleymane Diallo, Merid N. Getahun

All Peer-Reviewed Publications

Terrestrial insects underpin key ecosystem services, including pollination, herbivory regulation, decomposition, nutrient cycling, and disease control. These functions depend on chemical communication that guides insects to food, mates, hosts, shelters, and oviposition sites while helping them avoid threats. Environmental microparticles, such as micro- and nanoplastics, tyre wear particles, soot, mineral dust, and agricultural residues, are now widespread across air, soil, vegetation, and indoor environments, exposing insects through contact, deposition, and ingestion. Growing evidence shows that these particles disrupt insect olfaction by adsorbing volatile compounds, blocking antennal sensilla, and interfering with receptor and neuronal processes. These disruptions impair foraging, mating, oviposition, …


Effects Of Temperature On The Life-History Traits Of Myzus Persicae And Its Efficiency In Transmitting Potato Virus Y (Pvy) In Potato Crops, Bonoukpoè M. Sokame, Henri E. Tonnang, Heidy Gamarra, Pablo Carhuapoma, Jan Kreuze, Leah R. Johnson, Ali Arab, Peter A. Armbruster, Oswaldo C. Villena Jan 2026

Effects Of Temperature On The Life-History Traits Of Myzus Persicae And Its Efficiency In Transmitting Potato Virus Y (Pvy) In Potato Crops, Bonoukpoè M. Sokame, Henri E. Tonnang, Heidy Gamarra, Pablo Carhuapoma, Jan Kreuze, Leah R. Johnson, Ali Arab, Peter A. Armbruster, Oswaldo C. Villena

All Peer-Reviewed Publications

Aphids are highly sensitive to temperature changes and play a crucial role in transmitting plant viruses, accounting for the transmission of more than 50% of viruses that cause disease in crops. Among them, Myzus persicae is a major global pest, affecting over 400 plant species and transmitting more than 100 plant viruses, including potato virus Y (PVY), which poses a severe threat to potato crops. This study examines how temperature influences the life-history traits of M. persicae and its efficiency in transmitting PVY. Our research revealed that temperature significantly affects developmental duration, survival, and fecundity of M. persicae. The aphids …


The Rna-Binding Protein Hur Modulates The Expression Of The Disease-Linked Ccl2 Rs1024611g-Rs13900t Haplotype, Feroz Akhtar, Joselin Hernandez-Ruiz, Ya-Guang Liu, Roy G. Resendez, Denis Feliers, Liza D. Morales, Alvaro Diaz-Badillo, Donna M. Lehman, Rector Arya, Juan Carlos Lopez-Alvarenga, John Blangero, Ravi Duggirala, Srinivas Mummidi Jan 2026

The Rna-Binding Protein Hur Modulates The Expression Of The Disease-Linked Ccl2 Rs1024611g-Rs13900t Haplotype, Feroz Akhtar, Joselin Hernandez-Ruiz, Ya-Guang Liu, Roy G. Resendez, Denis Feliers, Liza D. Morales, Alvaro Diaz-Badillo, Donna M. Lehman, Rector Arya, Juan Carlos Lopez-Alvarenga, John Blangero, Ravi Duggirala, Srinivas Mummidi

School of Medicine Publications

CC-chemokine ligand 2 (CCL2) is involved in the pathogenesis of several diseases associated with monocyte/macrophage recruitment, such as HIV-associated neurocognitive disorder (HAND), tuberculosis, and atherosclerosis. The rs1024611 (alleles: A>G; G is the risk allele) polymorphism in the CCL2 cis-regulatory region is associated with increased CCL2 expression in vitro and ex vivo, leukocyte mobilization in vivo, and deleterious disease outcomes. However, the molecular basis for the rs1024611-associated differential CCL2 expression remains poorly characterized. It is conceivable that genetic variant(s) in linkage disequilibrium (LD) with rs1024611 could mediate such effects. Previously, we used rs13900 (alleles: C>T) in the CCL2 …


Reduced Threat-Related Neural Efficiency: A Possible Biomarker For Pediatric Anxiety Disorders, Julia O. Linke, Reut Naim, Simona P. Haller, Parmis Khosravi, Beck Scheinberg, Meghan E. Byrne, Anita Harrewijn, Ellen Leibenluft, Melissa A. Brotman, Anderson M. Winkler, Daniel Samuel Pine Jan 2026

Reduced Threat-Related Neural Efficiency: A Possible Biomarker For Pediatric Anxiety Disorders, Julia O. Linke, Reut Naim, Simona P. Haller, Parmis Khosravi, Beck Scheinberg, Meghan E. Byrne, Anita Harrewijn, Ellen Leibenluft, Melissa A. Brotman, Anderson M. Winkler, Daniel Samuel Pine

School of Medicine Publications

Objective: Pediatric anxiety disorders are common and predict adult psychopathology, yet current treatments, such as cognitive-behavioral therapy (CBT), produce lasting remission in less than 50% of affected youths. To support the search for improved, mechanistically grounded interventions, this study evaluated neural efficiency, defined as similarity in functional connectivity between a threat task and rest, as a potential biomarker. The study evaluated neural efficiency in relation to anxiety diagnosis and treatment response.

Methods: The authors compared 103 youths with an anxiety disorder diagnosis (mean age, 12.5 years [SD=2.91], 62% female) to 103 youths with no psychiatric diagnosis (mean age, 13.4 years …


Green Connectivity In Metropolitan Jabodetabek: Climate Change And The Challenge Of Urban Forest, Safira Maharani Putri, Hendricus Andy Simarmata Dec 2025

Green Connectivity In Metropolitan Jabodetabek: Climate Change And The Challenge Of Urban Forest, Safira Maharani Putri, Hendricus Andy Simarmata

CSID Journal of Infrastructure Development

Urban areas in Indonesia, particularly the Greater Jakarta metropolitan region (Jabodetabek), are increasingly experiencing the adverse effects of climate change, such as the Urban Heat Island (UHI) phenomenon. Rapid urbanization has contributed significantly to rising greenhouse gas emissions and deteriorating environmental quality. Urban forests are one of the key solutions to mitigate these impacts; however, their spatial distribution in Jabodetabek remains suboptimal and poorly connected. This study uses NDVI as a proxy for urban forest density, where “urban forest” refers to vegetated areas within cities as defined by Presidential Regulation No. 60/2020. The research addresses the following question: How has …


Semi-Supervised Learning For Annotation And Representation Of Single-Cell Rna Sequencing And Spatial Transcriptomics Data, Haoran Liu Dec 2025

Semi-Supervised Learning For Annotation And Representation Of Single-Cell Rna Sequencing And Spatial Transcriptomics Data, Haoran Liu

Dissertations

Semi-supervised learning has emerged as a powerful paradigm for analyzing single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) data, where full annotation is often costly or impractical. scRNA-seq technologies measure the expression of thousands of genes across tens of thousands of cells, whereas ST additionally captures the spatial coordinates of gene expression within intact tissue sections. Annotation is a key step in both scRNA-seq and ST analysis pipelines, aiming to identify cell types, spatial domains, and latent biological structures. However, most existing annotation approaches rely on separate clustering methods that are typically fully unsupervised and fail to leverage side information …


Entropic Forces Near Fluctuating Surfaces, Rubayet Hassan Dec 2025

Entropic Forces Near Fluctuating Surfaces, Rubayet Hassan

Dissertations

Nanoscale structures are inherently dynamic due to persistent thermal fluctuations. Even in solid materials, these random deformations, driven by ambient thermal energy, can become significant when their characteristic scale approaches that of the structure itself and strongly influence their overall mechanical behavior. Examples of such structures include crystalline membranes, appearing in diverse forms such as nanotubes, nanoribbons, and kirigami/origami structures. Similarly, biological nanostructures, including lipid membranes, microtubules, actin filaments, and DNA, exhibit extreme flexibility and responsiveness due to their low bending rigidity. Numerous physiological processes are intrinsically linked to these thermal fluctuations, including exocytosis and endocytosis, membrane fusion, pore formation, …


Computational Methods For Single-Cell And Multi-Omic Data Integration And Regulatory Network Inference, Jianlan Ren Dec 2025

Computational Methods For Single-Cell And Multi-Omic Data Integration And Regulatory Network Inference, Jianlan Ren

Dissertations

Single-cell and multi-omic technologies have transformed the dissection of cellular heterogeneity and regulatory dynamics in health and disease. However, the high dimensionality, technical variability, and biological complexity of these datasets present significant challenges for integration, annotation, and interpretation. In this dissertation, a suite of computational approaches is introduced to address key problems in single-cell and multi-omic data analysis through model-based innovations and applied statistical frameworks.

First, a constrained deep learning framework for single-cell data integration, label transfer, and clustering is proposed. By incorporating biologically motivated constraints into the training process, robust performance is achieved across simulated and benchmark datasets spanning …


Investigating The Role Of Cornichon-Homolog 3 (Cnih3) In Opioid Use, Contributing Risk Factors, And Associated Neural Substrates, Tania Lintz Dec 2025

Investigating The Role Of Cornichon-Homolog 3 (Cnih3) In Opioid Use, Contributing Risk Factors, And Associated Neural Substrates, Tania Lintz

Arts & Sciences Graduate Student Theses and Dissertations

Opioid misuse remains rampant as potent synthetic opioids such as fentanyl flood the market. Large-scale genetic tools like the GWAS identify previously unrecognized targets and biomarkers in opioid misuse with the hopes of combating the opioid epidemic and opioid use disorder (OUD). One such target is the AMPA receptor (AMPAR) auxiliary protein Cornichon Homolog-3 (CNIH3), which determines AMPAR subunit composition and kinetics. Though CNIH3 was identified as a gene of interest in OUD, its role in opioid use and accompanying risk factors has not been studied. Using mice with a CNIH3 deletion, we assess the role of CNIH3 in risk …


The Effect Of Withering Methods On Physicochemical And Sensory Properties Of Liberica Coffee Leaf Tea (Coffea Liberica), Surhaini Surhaini, Indriyani Indriyani, Rahayu Suseno, Rinaldi Rinaldi, Ferry Jie, Huda Wazzan Dec 2025

The Effect Of Withering Methods On Physicochemical And Sensory Properties Of Liberica Coffee Leaf Tea (Coffea Liberica), Surhaini Surhaini, Indriyani Indriyani, Rahayu Suseno, Rinaldi Rinaldi, Ferry Jie, Huda Wazzan

Research outputs 2022 to 2026

This study aims to evaluate the effect of different withering methods on physicochemical and organoleptic properties of Liberica coffee leaf tea (Coffea liberica) and to identify the optimal treatment. The experiment was conducted using a Completely Randomized Design (CRD) with five withering treatments, including no withering, room temperature withering for 10 h, air withering for 10 h, oven withering at 60°C for 30 min, and steaming for 2 min, each with four replications. The observed parameters included powder moisture content, pH, color (L*, a*, b*), antioxidant activity, total phenols, total tannins, flavonoids, and sensory attributes, namely color, aroma, acidity, taste, …


Construction And Data-Driven Analysis Of A Stochastic, Individual-Based Opioid Epidemiology Network Model, Leigh Bennett Pearcy, Owen Queen, Vincent Jodoin, Suzanne Lenhart, Christopher Strickland Dec 2025

Construction And Data-Driven Analysis Of A Stochastic, Individual-Based Opioid Epidemiology Network Model, Leigh Bennett Pearcy, Owen Queen, Vincent Jodoin, Suzanne Lenhart, Christopher Strickland

Mathematical Modelling and Numerical Simulation with Applications

While substance use epidemiology has been an active area of mathematical research in recent years, the social and mental processes that are involved in the development of substance use disorders have presented challenges to advancing the epidemiological theory and how they differ from the contraction of pathogenic disease. Such distinction is especially pertinent in the context of the current United States opioid epidemic and its intersection with the recent COVID-19 pandemic, as both prescription drugs and social influence play major roles in the development of opioid use disorder. In this paper, we construct a stochastic network model capturing how individual …


Baseline Assessment Of Insect Biodiversity And Distribution In La Salle Botanical Gardens, Pampanga, Philippines, Amir Lyndon Gavriell C. Beup, Kaleela Euan G. Jayson, Alyssa Ira Z. Tan, Ronielle Elisha S. Pascual, Alexi Gabrielle S. Henson, Esperidion Josef P. Ladao Iii, Juan Carlo T. Gumangan Dec 2025

Baseline Assessment Of Insect Biodiversity And Distribution In La Salle Botanical Gardens, Pampanga, Philippines, Amir Lyndon Gavriell C. Beup, Kaleela Euan G. Jayson, Alyssa Ira Z. Tan, Ronielle Elisha S. Pascual, Alexi Gabrielle S. Henson, Esperidion Josef P. Ladao Iii, Juan Carlo T. Gumangan

Sinaya: A Philippine Journal for Senior High School Teachers and Students

Insects are crucial for ecosystem functions, such as pollination and food web maintenance. This study aims to assess insect biodiversity in La Salle Botanical Gardens (LSBG) in Porac, Pampanga, focusing on its grassland and forestland areas. Using rapid biodiversity assessment, this study provides baseline data on insect diversity, abundance, dominance, and evenness for conservation. Sampling employed transect line intercept and quadrat methods. Specimens were collected using different collection and preservation techniques. Insects (n = 184) were collected from August to October 2024, with specimens (n = 46) belonging to seven insect orders in the grassland and specimens (n = 138) …


Comparing Individual Vs Mixed Treatments Of Chicken Bone Meal And Crab Shell Meal On The Growth Of Capsicum Annuum (Bell Pepper), Allthur Rudy R. Arroyo, John Rafael V. Capinia, Ethan Jude R. Reyes, Elnathan Jethro B. Sumalbag, Karl Benedict E. Viri, John Ray Cordova Estrellado, Kerry P. Cabral Dec 2025

Comparing Individual Vs Mixed Treatments Of Chicken Bone Meal And Crab Shell Meal On The Growth Of Capsicum Annuum (Bell Pepper), Allthur Rudy R. Arroyo, John Rafael V. Capinia, Ethan Jude R. Reyes, Elnathan Jethro B. Sumalbag, Karl Benedict E. Viri, John Ray Cordova Estrellado, Kerry P. Cabral

Sinaya: A Philippine Journal for Senior High School Teachers and Students

The recycling of nutrient-rich food waste reduces reliance on synthetic fertilizers, enhances soil quality, and improves plant growth. Existing studies have demonstrated the effectiveness of food waste, such as bone meal (B) and crab shell meal (S), as fertilizers; however, their combined use has not been investigated. This study aims to evaluate the effect of varying proportions of B and S fertilizers on the growth of Capsicum annuum (bell pepper) employing a random complete block design with 10 treatments (pure B, pure S, and a 50:50 BS mix, each at 7 g, 14 g, and 21 g) plus a control …


Cesium-137 Accumulation In Marine Fish And Associated Dose Exposure: A Global Review, N.A.A. Kamarulzaman, M.S.M. Sanusi, H.N. Idris Dec 2025

Cesium-137 Accumulation In Marine Fish And Associated Dose Exposure: A Global Review, N.A.A. Kamarulzaman, M.S.M. Sanusi, H.N. Idris

Journal of King Abdulaziz University: Marine Science

Establishing baseline data for natural radiation exposure and radioactivity levels is essential for radiological health and safety programs, particularly during the implementation and development of nuclear power initiatives. This review evaluates gamma radiation exposure and anthropogenic cesium-137 (137Cs) levels in the world’s oceans and marine fish, analyzing their radioecological impact. Data from 30 peer-reviewed publications indicate that 137Cs activity concentrations in seawater range from 0.07 Bq kg–1 to 6.4 kBq kg–1, with fish values between 0.01–3.50 kBq kg–1. Regression models developed from these studies predict the correlation between 137Cs levels in …