Digital Commons Network^™

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 …

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 …

Morphometric, Physiological, And Environmental Health Assessments Of Enhalus Acoroides From The Southeast Coast Of Bali, Indonesia, Made Pharmawati, Luh Putu Wrasiati, Ni Made Gari

Journal of King Abdulaziz University: Marine Science

Seagrasses function as primary producers and as spawning grounds and shelter for marine biota. Regardless of their relevance, seagrasses are under threat due to anthropogenic impacts and an increasing frequency of extreme climate events. Enhalus acoroides is a species of seagrass that is spread in the east and southeast waters of Bali, from Sanur Beach to Nusa Dua Beach. This study aims to analyze the differences in morphometry and the chlorophyll, proline, and malondialdehyde (MDA) content, a marker for oxidative stress in E. acoroides leaves at Pengastian Beach, Semawang Beach, and Samuh Beach, Bali. Samples were collected using line transect …

Electrochemical Characterization And Modulation Of Biological Processes, Yue-Qi Li, Wei-Hua Huang, De-Chen Jiang, Bao-Hong Liu, Bin Su, Yang Tian, Jing-Juan Xu, Ping Yu, Feng Zhao, Huang-Xian Ju, Jing-Hong Li

Journal of Electrochemistry

Electrochemical processes lie at the core of biological function, governing energy transduction, metabolic flux, and molecular signaling. Recent advances in electrochemical science now allow these processes to be probed and controlled with unprecedented spatial, temporal, and chemical resolution. In this review, we present an integrated framework that progresses from fundamental mechanisms to analytical technologies and functional modulation. We begin by outlining electron transfer pathways in mitochondrial respiration, microbial extracellular electron transfer, and DNA- and protein-based charge conduction, followed by the principles of photon-electron conversion in photosynthesis and the central role of redox equilibrium in coordinating cellular responses. We then highlight …

Synthesis, Characterization, Antioxidant Content And Antibacterial Study Of New Ligand And Its Complexes From Sulfonic Acid And 2-Phthalaldehyde, Mawlood Khalid Mawlood, Wurood Ali Jaafar

Baghdad Science Journal

The research includes preparation of a new Schiff base from the condensation of sulfonic acid with 2-phthalaldehyde by dissolving (0.2 g, 0.346 mmole) of the ligand (L) in (10 ml) of absolute ethanol, then 0.06 g of potassium hydroxide (KOH) dissolved in 10 ml of distilled water added to it and reacting the product with some binary metal salts (Mn, Co, Ni, Cu, Cd, Zn, Pt, Hg). The biological study was conducted against two types of gram-positive and gram-negative bacteria, Staphylococcus. aureus and Escherichia coli, and the fungus Candida albicans was also used. All the prepared complexes showed …

2021u_Sm22_Approved_Cd_Bio-4611-Radiation-In-Our-World, Undergraduate Curriculum Committee

All Approved Curriculum

No abstract provided.

2022g_Sm26_Approved_Cd_Bio_5684-Biological-Data-Analyses, Graduate Council

All Approved Curriculum

No abstract provided.

2022g_Sm10_Approved_Cm_Bio_5833-Collections-Curation-And-Research-Design, Graduate Council

All Approved Curriculum

No abstract provided.

2d-Nanosilicate Carriers For Sustained Delivery Of Vaccine Components, Chih Yun Liu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Laponite® 2D Nanosilicates (NS) are disc-shaped platelets (~30 nm diameter, ~1 nm thick) with positively charged edges and negatively charged faces, capable of loading proteins, drugs, and nucleic acids via electrostatic interactions to form a house-of-cards gel that sequesters cargo. Here, we evaluated NS for sustained delivery of antigens and Toll-like receptor (TLR) agonists to extend germinal center duration and enhance antibody quality. The model antigen ovalbumin (OVA) was adsorbed onto NS at acidic pH in a ~1:1 ratio, with partial unfolding that remained stable at physiological pH. NS-OVA complexes were efficiently internalized by dendritic cells, with uptake driven primarily …

Development Of An Evidence-Based Nutrition Protocol For Professional Pickleball Athletes, Laura Morales

Department of Nutrition Student Projects

Professional pickleball has expanded rapidly, yet sport-specific nutrition guidance remains absent. Current information available to athletes comes largely from non-professional or industry sources and lacks an evidence-based foundation. This project aims to address that gap by developing a nutrition protocol tailored specifically for professional pickleball players. The approach synthesizes data from pickleball workload studies, racket-sport physiology, and established sports nutrition consensus statements. Key focus areas include fueling strategies, protein distribution for recovery, hydration and sodium planning, heat acclimation and cooling practices, travel and jet-lag management, altitude considerations, and evidence-based supplementation. By integrating findings from racket-sport analogs and intermittent high-intensity training …

A Novel Of Bounded Zeghdoudi Distribution: Estimations, Simulation And Applications, Mohammed Elgarhy, Hanene Hamdani, Laxmi Prasad Sapkota, Ahmed M. Gemeay

Mesopotamian Journal of CyberSecurity

In this article, we introduce a new unit Zeghoudi distribution, which is called the bounded Zeghoudi distribution (BZD), an innovative modification of the Zeghoudi distribution (ZD). This new suggested distribution retains the original ZD’s simplicity while improving modeling flexibility and accuracy for data constrained to the unit interval. The BZD displays numerous significant characteristics, including decreased, left-skewed, right-skewed, and unimodal probability density functions, but the hazard rate function can be J-shaped, U-shaped, and bathtub-shaped. Some important statistical features of the BZD, such as moments, mean, variance, moment generating function, lower and upper incomplete moments, mean residual life, mean inactivity time, …

Statistical Validation Of The Microplate Reader For Antioxidant Activity Measurement Using The Dpph Assay, Rismawati Rismawati, Dikdik Kurnia, Ersanda Hafiz, Muhammad Ihda H. L. Zein

Chimica et Natura Acta

Antioxidants research has been garnering increased interest among researchers, particularly in the fields of medicine and health, focusing on both natural and synthetic antioxidants. The DPPH method is the most used approach for antioxidant analysis due to its efficiency, simplicity, and accuracy. This study aims to validate the sensitivity of the microplate reader compared to UV-Vis spectrophotometer, both used for measuring absorbance in the DPPH antioxidant test. The samples used in this study include ascorbic acid, gallic acid, and quercetin standards. Statistical validation in the DPPH antioxidant test includes precision testing, T-test, and % recovery test. Based on the statistically …

Mitochondrial Insoluble Aggregates In Aging And Alzheimer’S Disease Models: Cross-Species Proteomic Integration, Identification Of Conserved Candidates, And Pharmacological Disruption Of Eef-2 Interactions, Sonu Pahal

Theses and Dissertations

Protein aggregation within mitochondria emerges early in both aging and Alzheimer’s disease (AD) and contributes to progressive loss of proteostasis. Insoluble mitochondrial aggregate fractions from Caenorhabditis elegans revealed extensive enrichment of metabolic and translational proteins that also appear in human Alzheimer hippocampal aggregates. Comparative analysis across age and genotype identified a conserved subset of aggregation-prone proteins, several of which cluster around elongation factor 2 (eEF-2), a regulator of ribosomal translocation and energy coupling. Cross-species integration defined a network in which eEF-2 links chaperones, metabolic enzymes, and RNA-binding proteins that co-aggregate in both human Alzheimer material and nematode models. Functional tests …

A Reflective Lab Journal For Biodesign: Navigating More-Than-Human Sensibilities And Disciplinary Tensions, Jiho Kim, Iohanna Nicenboim, Joana Martins, Elvin Karana

IASDR Conference Series

This paper introduces reflective journaling as a tool for advancing biodesign practices, merging documentation methods from biology and design while integrating more-than-human sensibilities into laboratory practices. It highlights the need for tools that can flexibly support record-keeping across biology and design, balancing precision and accountability with iteration, creativity, and collaboration. Furthermore, it critically addresses calls to support care ethics and nurturing multispecies interactions within biodesign. Through an explorative review of diverse documentation formats, including laboratory notebooks and annotated portfolios, and informed by our own biodesign experiences, we introduce the Reflective Biodesign Lab Journal as a potential approach to address these …

Kinship Infrastructure Design: Evaluating Diversity And Resilience In Emergency Response Systems Through Agent-Based Modeling, Fayruz Maysha

Doctoral Dissertations and Master's Theses

Traditional infrastructure systems are often designed for predictable scenarios, making them vulnerable to disruption when real-world conditions change unexpectedly. This research addresses that limitation by introducing Kinship Infrastructure Design (KID), a bioinspired framework based on the kinship coefficient (Φ). Adapted from studies of genetic relatedness in eusocial insects, the kinship coefficient (Φ) measures similarity and diversity among system components by calculating the degree to which their functional traits—encoded as a synthetic genome—match. This research investigates whether a system design can achieve a “Goldilocks Zone” of functional diversity where systems achieve optimal adaptability and coordination under uncertainty."

Rather than relying on …

The Malonate Template: The Key To Unlocking Novel Amino Acids, Thomas Owens

Dissertations

The “Malonate Template” provides access to various amino acids, all from a common intermediate. Herein, demonstrates the use of the malonate template to establish a synthetic route to both 2-thiohistidine and 2-thio-3-N-methyl-histidine from a benzyl methyl malonate derived intermediate. Furthermore, efforts exploiting the applicability of the malonate template for the of both 2-thiohistidine and 2-thio-3-N-methyl-histidine as a suitable alternative to methods previously described by Erdelmeier are described.

The method presented incorporates modifications to the biomimetic pathway described by Erdelmeier for the synthesis of 2-thiohisidine. By exploiting the biomimetic formation of 2-thiohisitidne’s mechanism via mass spectrometry, we …

The Mayfly Newsletter, Donna Giberson

The Mayfly Newsletter

The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.

G2pdeep-V2: A Web-Based Deep-Learning Framework For Phenotype Prediction And Biomarker Discovery For All Organisms Using Multi-Omics Data, Shuai Zeng, Trinath Adusumilli, Sania Zafar Awan, Manish Sridhar Immadi, Dong Xu, Trupti Joshi

Biomedical Sciences

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm …

Embodied Encounters With Plankton: Ground Truth Methods As Sites For Human-Ocean Entanglement, Clarissa Chevalier

Study of Women, Gender, & Sexuality: Faculty Publications

This article examines shifting methods of plankton research within contemporary oceanography through direct participatory engagement on a ten-day research cruise off the Santa Lucia Escarp- ment in February 2025. As a feminist visual science studies researcher, I reflect on how seasick- ness, sensory immersion, and embodied participation shaped my experience of plankton sampling and reveal the entanglement of oceanographic knowledge with its contexts. While remote sensing technologies – such as satellites, digital twins, and remotely operated vehicles – are increasingly shaping oceanography and producing intensified modes of ocean quantification, I argue that tactile, physical sampling methods remain indispensable in plankton …

Computational Study On Protein Docking With Vascular Disease Application, Lohitha Reddy Shanigaram

Master's Theses

This thesis investigates how computational methods can help us understand protein docking and vascular diseases by integrating machine learning. The main goal of this research is to develop a system that can predict whether variants in the SOX17 gene are associated to Pulmonary Arterial Hypertension (PAH), a significant vascular condition. To do this, a dataset of 1,063 SOX17 variants was created using publicly available sources such as ClinVar, gnomAD, LOVD, and Ensembl. The study included cleaning and structuring the dataset, encoding genomic data and training a Random Forest classifier to classify variants as positive, negative, or unknown for disease association. …

Sertraline To Reduce Recidivism In Impulsive Violent Offenders (Reinvest): A Randomised Double Blind Clinical Trial, Tony Butler, Emaediong I. Akpanekpo, Lee Knight, Kristy Robledo, David Greenberg, Andrew Ellis, Stephen Allnutt, Kay Wilhelm, Alison Jones, Rodney Scott, Bianca Ton, Luke Grant, Philip Mitchell, Ross Tynan, Jocelyn Jones, Dominic Villa, Duncan Chappell, Carolynn Dixon, Alison Churchill, Val Gebski, Tony Keech, Peter W. Schofield

Research outputs 2022 to 2026

Background: Biological studies suggest serotonin modulation via selective serotonin reuptake inhibitors (SSRIs) might reduce impulsive violence, however, robust evidence in offender populations is limited. We aimed to determine whether sertraline reduces violent reoffending compared with placebo in highly impulsive men with recurrent violent offending.

Methods: We conducted a double-blind, placebo-controlled, randomised clinical trial in community settings in New South Wales, Australia. Eligible participants were men aged 18 years or older with ≥2 prior violent convictions and a Barratt Impulsiveness Scale score ≥70. Following a 4-week single-blind active run-in phase with sertraline, participants were randomly assigned (1:1, minimization stratified by key …

"Gross Normality" And "Marked Deviation": A Qualitative Study Of Disability Theory In Three Periods Of Sociological Literature, Kelsey Sullivan

Masters Theses

In the 20th century, three theoretical perspectives concurrently dominated sociological discussions of disability. Functionalism and Talcott Parsons argued for a pathologized framework in the form of a “sick role” occupied by disabled people. Interactionism and Erving Goffman emphasized the stigmas faced by individual disabled people, and the ripple-effects of those stigmas. Finally, disabled activists, inspired by social constructionism, championed the social model of disability. This model purported that disability is a social condition, resulting from systemic barriers imposed upon people who do not fit the mental or physiological norm. This project, through a content analysis of 30 historical journal articles, …

Developing A Metabolic Engineering Chassis From A Metabolically Versatile Organism, Rhodopseudomonas Palustris Cga009, Mark William Kathol

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Metabolic engineering has made it possible to develop biological processes that were once considered economically unfeasible or uncompetitive. This field has enabled both a robust niche market, whereby products, such as pharmaceutical substances like monoclonal antibodies, are produced exclusively through biological means, as well as an emerging commodity production market. Nonetheless, significant challenges remain in harnessing the unique metabolic capabilities of genetically non-tractable organisms. This dissertation focuses on Rhodopseudomonas palustris CGA009 as a potential chassis for metabolic engineering. To address the issue of genetic intractability, a synthetic biology toolkit was developed to facilitate the expression of heterologous proteins in R …

Synthesis, Characterization And Biological Activity Studies Of New Metal Ion Complexes With Schiff Base Derived From (Z)-3-Hydrazineylidene-1-Phenylpyrazolidine And Evaluating Them As Antioxidants, Zahra Mounir Ahmed, Naser Shaalan

Baghdad Science Journal

The research includes the preparation of several complexes of the transition elements and zinc where M(II) = Co, Ni, Cu, and Zn, containing the 3d shell, with ligand (LH)was synthesized by treating the (Z)-3-hydrazineylidene-1-phenylpyrazolidine and Salicylaldehyde. Ligand (LH) was identified using FT-IR spectra,¹H-¹³C-NMR, UV-Vis spectroscopy, elemental microanalysis CHN and mass spectrometry. The complexes were studied and identified with elemental microanalysis CHN, FT-IR spectroscopy, UV-Vis spectroscopy, conductivity measurement, and magnetic sensitivity. The result showed that, these complexes were classified as homogeneous tridentate complexes with the formula [M(LH) (H₂O)₂Cl] or [M(LH)₂]. xH …

Nanodiamonds In Advancing Biomedical Sciences, Ebenezer Owusu, Sofia Lerma, Jinhyeong Jang, Deepa Roy, Shizue Mito, Upal Roy, Elena A. Rozhkova

Health & Biomedical Sciences Faculty Publications

Nanodiamonds (NDs), tetrahedral carbon structures with a size ranging from 1 to 100 nm, have gained growing attention in recent years due to their distinct optical, thermal, and mechanical properties compared to other carbon nanomaterials (e.g., graphene, carbon nanotubes, carbon dots). Combined with a high surface-to-volume ratio and tunable and chemically versatile surfaces, these support broad applications across catalysis, electronics, and life sciences. Moreover, the biocompatible characteristics of NDs enable their controllable interfacial interactions with biological systems, positioning them as excellent candidates for advancing cutting-edge biomedical sciences, particularly through the engineering of efficient material biointerfaces that facilitate optimal interactions with …

Developing Optogenetic Approaches To Study Ca2+ Signaling Processes, Tatsuki Nonomura, Xiaoxuan Liu, Megan Chiu, Zhi Tan, Tien-Hung Lan, Yubin Zhou

Faculty, Staff and Students Publications

Calcium ions (Ca2+) are essential second messengers intimately implicated in a variety of biological processes, ranging from short-term events such as muscle contraction to long-term effects like gene expression. Dysregulated Ca2+ signaling can disrupt cellular function and contribute to the development of various human diseases, including developmental, neurological, immunoinflammatory, metabolic, and cardiovascular disorders. To study the mechanisms and biological consequences of Ca2+ signaling, optogenetic approaches have proven invaluable, as they offer exceptional spatiotemporal resolution compared to traditional methods. Recent progress in non-opsin-based optogenetics, particularly those engineered from Ca2+ release–activated Ca2+ (CRAC) channels, has substantially advanced our understanding of Ca2+ signaling …

Synthesis And Evaluation Of Bodipy-, Azabodipy- And Chlorin-Based Conjugates For Imaging And Photodynamic Therapy Of Egfr-Overexpressing Cancers, Simran Dhingra

LSU Doctoral Dissertations

This dissertation discusses the design of EGFR-targeted small-molecule agents that unite molecular imaging with photodynamic therapy. Chapter 1 frames the clinical need for early detection and selective treatment and surveys BODIPY, aza-BODIPY, and chlorin scaffolds as tunable chromophores for near-infrared imaging and photosensitization. It also outlines EGFR as a validated target and compares two ligand classes used throughout this work: the tyrosine kinase inhibitor erlotinib and the cyclic peptide KLARLLT.

Chapter 2 describes the synthesis of a near-IR BODIPY bearing either one or two erlotinib units. Docking and SPR show specific interactions with the EGFR kinase domain, and both conjugates …

Depression Polygenicity And Disease Activity And Disability Worsening In Multiple Sclerosis, Ali Manouchehrinia, Kathryn C Fitzgerald, Amber Salter, Ruth Ann Marrie, Lars Alfredsson, Charles N Bernstein, James M Bolton, Gary Cutter, John D Fisk, Lesley A Graff, Carol A Hitchon, Jan Hillert, Ingrid Kockum, Yi Lu, Fred D Lublin, Kyla Mckay, Tomas Olsson, Scott Patten, Amit Patki, Hayley Riel, Klementy Shchetynsky, Pernilla Stridh, Hemant K Tiwari, Jerry S Wolinsky, Kaarina Kowalec

Faculty, Staff and Student Publications

Objective: A better understanding of factors associated with multiple sclerosis (MS) disease activity and disability is needed. Given the strong link between comorbid depression and MS disease activity and disability, we aimed to determine whether the depression genetic burden, as modelled using its polygenic score, is associated with MS disease activity and disability worsening.

Methods: In this cohort study, we used samples from neurologist-defined adult people with MS (PwMS) followed in clinical care or during a clinical trial from existing cohorts: Canada, the United States (US), and Sweden with extensive longitudinal phenotypes. We computed the depression polygenic score (PGS) and …

Catalytic Removal Of Synozol Blue Dye From Aqueous Solution Through Green Synthesized Iron Nps With H2o2: With Addition Of Ecosar And Biological Investigation, Rabiya Kousar, Zia Ul Haq Khan, Jingyu Sun, Sana Sabahat, Noor Samad Shah, Jibran Iqbal, Mahmood M.S. Abdullah, Rabia Naz, Zia Ullah Khan

All Works

This bioinspired study explores the fascinating realm of clean and green chemistry by unveiling the potential of FeO NPs fabricated by taking advantage of botanical extract obtained from the leaves of Justicia adhatoda as a reducing agent because it reduced Fe (II) to Fe (0). FeONPs have been fabricated successfully with distinctive structural and morphological features that have been characterized through multiple analytical techniques, like UV/Vis, FTIR, XRD, SEM, TEM, BET, and Zeta potential. The surface plasmonic resonance peak appeared at 268 nm, which was measured through the UV/Vis spectra of synthesized NPs. XRD analysis discovered the crystalline nature of …

A Bibliometric Analysis Of The 100 Most Cited Papers In Molecular Biology Studies Of Oral Submucous Fibrosis, Sahil Thuse, Abhirami Premarajan, Gargi Sarode, Muhammad Ruslin, Rajesh Shetty, Sachin Sarode

Journal of Dentomaxillofacial Science

Objective: To systematically map the existing research about molecular biology of OSF along with the notable amount of research in the past and the future insights of the same.

Material and Method: The analysis evaluates the research trends in OSF using Scopus as a primary source due to its comprehensive coverage of peer reviewed literature. The search was performed on 25 April 2025. Only original and review articles were selected wherein "molecular biology" and "oral submucous fibrosis" were the Boolean terms applied. Hundred most cited articles were shortlisted. Network visualisation and bibliometric mapping was performed by VOS viewer. Keyword co-occurrence …