Digital Commons Network^™

Archaeal Signal Peptide Prediction Through Integration Of Proteomics And Machine Learning, Anjali Kaur

Theses

Signal peptides are short N-terminal amino acid sequences that direct proteins through cellular secretion pathways and play an essential role in protein localization and function. Computational tools such as SignalP are widely used to predict signal peptides. However, prediction accuracy for archaeal proteins remains lower than for bacterial and eukaryotic proteins, likely because relatively few archaeal proteins were available for model training. The goal of this study was to determine whether expanding the archaeal training data used by SignalP 6.0 could improve archaeal signal peptide prediction. Archaeal proteomics datasets from five archaeal species were analyzed to identify proteins with experimentally …

Dynamics Of Microscale Droplets In Respiratory Airways, Md Shamser Ali Javed

Mathematics Theses and Dissertations

We investigate trajectories of microscale evaporating droplets in a stagnation point flow near a wall of a respiratory airway. The configuration is motivated by the problem of advection and deposition of microscale droplets of respiratory fluids in human airways during transmission of infectious diseases such as tuberculosis and COVID-19. Laminar boundary layer equations are solved to describe the air flow while the equations of motion of the droplet include contributions from gravity, aerodynamic drag, and Saffman force. Evaporation is accounted for at both the droplet surface and the wall of the respiratory airway and is shown to delay droplet deposition …

Strengthening Data Privacy For Post-Secondary Students: A Proposal For Revising Ferpa To Provide Meaningful Protections Against Third-Party Data Breaches, Emily Harris

Seton Hall Journal of Legislation and Public Policy

No abstract provided.

Effects Of B422 Bacteriophage Resistance Mutations On Pectobacterium Versatile Fitness And Virulence, Alex Cherry

Undergraduate Honors Theses

This Honors thesis project examines the impact of lipopolysaccharide mutations on the virulence of a bacteria susceptible to a bacteriophage suspected of using LPS structures as the basis for infection. In my prior work in the lab, I isolated a novel lytic bacteriophage against P. versatile. From host range testing performed in the lab, it is known to infect two strains of P. versatile, B422 and B35. The phage was then used to select for resistant mutants in a pool of B422 transposon mutants, and 20 phage-resistant mutants were identified. 60% of these mutants were found to have differences in …

Public Perceptions Regarding Surveillance Of Lyme Disease In Tennessee, Shaheena Yasmin Asad

Walden Dissertations and Doctoral Studies

Lyme disease (LD), a tick-borne illness, has been a growing concern in the state of Tennessee. Studies have established environmental concerns regarding a growing tick population and identified a gap between reported cases and disease burden in Tennessee. Despite this information, it remains classified as a low-incidence reporting state, raising concerns about underreporting that indicate an ineffective current surveillance system. Because the public perception regarding surveillance of LD is unknown, the purpose of this qualitative study was to explore how adults in Tennessee perceived LD as a credible public health threat within the context of the current surveillance system. Guided …

Single Fluorogens And Orientation-Localization Microscopy For Quantifying Chemical And Biomolecular Dynamics At The Nanoscale, Yiyang Chen, Yuanxin Qiu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Many chemical systems look uniform only because ensemble measurements average over their most interesting molecules. Electron-transfer rates vary across electrode surfaces; lipid membranes contain nanodomains with distinct packing and fluidity; peptide aggregates exhibit local polymorphism; and biomolecular condensates contain transient networks of interactions that are blurred in ensemble images. A central challenge in chemical imaging is not simply to see smaller structures, but to measure chemical variables such as polarity, redox potential, and molecular confinement at the single-molecule level. In this Account, we describe how fluorogens, molecules whose brightness, blinking, spectral shifts, orientation, rotational mobility, and motion are directly shaped …

The Prophylactic Landscape: Sand And Typhoid On The Merrimack River, Laila Seewang

School of Architecture Faculty Publication and Presentations

“The first municipal water filter of the rapid sand type was built at Somerville, NJ, and thus began its wonderful history.”  By 1917 the rapid sand filter was the standard defense against typhoid epidemics in the United States.

Algebraic And Topological Methods In Computational Neuroscience, Trong-Thuc Trang

Electronic Theses and Dissertations

Neural data is incredibly rich in combinatorial, topological, and geometrical information, reflecting the intricate shape and connectivity of neural firing patterns. To decipher these structures, neuroscience increasingly relies on advanced mathematical tools to analyze neural activity. Here we study (1) neural codes within the poset P_Code of neural codes and (2) the connectivity of neural population activity within the insular cortex when responding to interoceptive information. In (1), we establish combinatorial constructions for all upward covering relations based on what we call “isolated subsets” with supporting theorems and give a slight modification of the existing downward covering relations. We …

Drivers Of Stopover Distribution Across Two Autumn Migration Routes Of A Long-Distance Afro-Palearctic Migrant, The Common Cuckoo (Cuculus Canorus), Alex Gale, Máire Kirkland, Phil Atkinson, Robert Puschendorf, Chris Hewson

School of Biological and Marine Sciences

Across the globe, many long-distance migratory birds have undergone population declines. Understanding the environmental factors which underly migratory stopover locations can inform conservation strategies for such species. Here, we identify environmental predictors of autumn stopover sites used by UK-breeding male cuckoos (Cuculus canorus) migrating to centralAfrican wintering grounds via two alternative flyways. Between 2011 and 2021, 88 male cuckoos from UK breeding grounds were fitted with <5 g satellite tags connected to the Argos satellite-based tracking system. Filtered stopovers were used to build presence-pseudoabsence distribution models for each flyway, using Boosted Regression Tree and Random Forest algorithms with thirteen climatic, habitat, topographic and anthropogenic variables. Performance was evaluated using 10-fold cross-validation, and weighted ensembles were generated. To assess drought sensitivity, we produced predictions for high- and low-drought years based on Standardised Precipitation–Evapotranspiration Indices (SPEI). Models performed well (AUC=0.79–0.88; TSS=0.50– 0.66) and revealed route-specific environmental predictors. Along the western route, stopover probability was highest in cooler, semi-humid, high-elevation areas with low contemporaneous drought; Iberian mountain ranges emerged as key sites. Along the eastern route, stopover probability was greatest in heterogeneous habitat, with lowlands and uplands favoured over intermediate elevations; the Po watershed appears particularly important. Hunting risk (included to assess anthropogenic threat) was also high at key areas. The spatial extent of stopover regions—and the probability of them being utilised—declined during years ofhigh short-term drought along the western route, and high long-term drought along the eastern route. Whilst Iberian montane stopover regions are sensitive to increasing drought and aridity under climate change, their topographic heterogeneity may provide climatic refuge while limiting intensive land uses. Preference for heterogeneous habitat within the Po watershed highlightsthe need to retain semi-natural habitat within agricultural landscapes. We recommend route-specific conservation measures and higher resolution models using newly available GPS tags to better understand fine-scale site selection within the regions highlighted here.

Hematological, Inflammatory, And Oxidative Stress Biomarker Profiles In Substance Abuse Combinations: A Comprehensive Evidence-Based Review, Teif Naif Freeh Alenezi, Samia Soliman Barghash

Saudi Toxicology Journal

A potential risk of polysubstance use in relation to substance abuse can involve the development of intricate pharmacological interactions affecting the immune system and oxidative stress responses of the body. The current review aims to present a synthesis of the existing literature about hematologic, inflammatory, and oxidative stress markers associated with three patterns of polysubstance use: (1) stimulants and cannabis, (2) stimulants/depressants and CNS depressants, and (3) multi-drug complex usage. This review explores markers such as a neutrophil-to-lymphocyte ratio (NLR), systemic immune-inflammation index (SII), systemic inflammation response index (SIRI), platelet-to-lymphocyte ratio (PLR), monocyte-to-lymphocyte ratio (MLR), eosinophil-to-lymphocyte ratio (ELR), total oxidant …

Immunohistochemical Characterization Of Tumor-Associated Macrophage Polarization In Cutaneous T-Cell Lymphoma, Emma Luong, Wei Han, Xiao Ni

CATALYST Summer Training Program 2026

No abstract provided.

Atomos Komiks - Making Learning Fun With Science Entertainment, Jerome Aizpuro Suplemento Ii, Julius Noah Hernandez Sempio

DLSU Arts Congress Conference Proceedings

With portable digital devices imposing themselves on the already precarious attention span of the Filipino youth, and with raising concerns about degrading literacy of schoolchildren, it is imperative to find creative and entertaining means to inspire the young studentry to engage in dedicated educational materials. This paper explains the methods being used by a small group of artists, scientists and writers to create content for “science entertainment” in comics format. By combining principles of conceptual compression, knowledge indexing and low-elaboration persuasion techniques to develop knowledge “anchors”, the team aims to generate participatory engagement among readers and stimulate their cognitive innovation. …

Indigenous Pedagogies As An Arts-Based Framework For Education 4.0, Andylyn Simeon

DLSU Arts Congress Conference Proceedings

While Education 4.0 promises to cultivate 21st-century skills like creativity and critical thinking, the reality often falls short. Current frameworks are heavily technocentric, prioritizing digital tools and measurable data over the communal, emotional, and spiritual depth that true learning requires. This paper argues that we can restore balance to this digital shift by looking toward Indigenous Pedagogies (IPs). Far from being “obsolete” relics of the past, these are sophisticated, arts-based systems rooted in storytelling, ritual, and land-based creation that can offer a creative blueprint for the human-centered goals that Education 4.0 claims to value. Through a qualitative synthesis, I deconstruct …

Isoperimetric Soft Robots, Mihai Stanciu

Theses and Dissertations

This thesis presents two advances in isoperimetric soft robotic trusses that improve their performance, modularity, and configurability. The first contribution introduces a large-scale modular robotic truss designed as a lightweight, reconfigurable structure for lunar applications. The system consists of inflatable fabric tubes routed through motorized roller units and interconnected by a newly developed spherical joint that enables multiple robotic triangles to connect at a common vertex. The resulting truss can be assembled into structures beyond a single octahedron while retaining compact stowage when deflated and untethered operation after initial inflation. Experimental validation demonstrates modular assembly, long-term pressure retention, load-bearing capabilities …

Quality Improvement Project: Advancing Personalized Depression Care In Outpatient Psychiatry, Jillian K. Benoit

Doctor of Nursing Practice Projects

Depression is a leading cause of disability worldwide, yet inconsistent use of evidence-based assessment and treatment strategies contributes to gaps in the quality of psychiatric care. A needs assessment at a community outpatient psychiatric clinic identified inconsistent documentation of measurement-based care (MBC), shared decision-making (SDM), and patient education during depression treatment. The purpose of this quality improvement project was to evaluate whether implementation of MBC and SDM improved depression treatment documentation among psychiatric providers over a 4-week period. Guided by Lewin’s Change Theory and implemented using the Iowa Model of Evidence-Based Practice as the implementation framework, this quantitative one-group pretest-posttest …

Towards The Synthesis Of Dragonamide E And Analogs Thereof, Dante Glover

Chemistry Theses

Leishmaniasis is a disease caused by a parasite spread through the female sand fly. It is categorized as a Neglected Tropical Disease and can cause very severe symptoms, even death, if left untreated. Symptoms include skin lesions that can cause permanent scarring, and mucosal membrane infections that can cause facial deformities. More aggressive forms of leishmaniasis can lead to infections of internal organs like the liver and/or spleen and can lead to death. Drug resistance of these parasites has rendered treatment limited and the side effects of which can be harmful as well.

Scientists looking towards new treatments for tropical …

Thermophysical Property Studies: 1. Thermodynamic Consistency For Associating Compounds 2. Autoignition Temperature, Cassandra Jane Guffey

Theses and Dissertations

Accurate thermophysical property data are essential for the design, optimization, and safe operation of chemical processes. Properties such as vapor pressure, enthalpy of vaporization, heat capacity, density, and autoignition temperature--which are among the properties studied in this work--are required for equipment sizing, process simulation, hazard assessment, and economic evaluation. A major focus of this dissertation is the application of multi-property thermodynamic consistency techniques to compounds that exhibit strong vapor-phase association. These methods improve confidence in recommended property values by enforcing rigorous thermodynamic relationships among ideal-gas heat capacity, liquid heat capacity, vapor and liquid densities, vapor pressure, and enthalpy of vaporization. …

Stochastic Inverse Problems In Stochastic Elliptic And Parabolic Pdes, Zi-Jia Gong

Theses

This dissertation presents a computational framework for solving stochastic inverse problems in partial differential equations (PDEs) with random data. The objective is to recover unknown random coefficients in parabolic and elliptic diffusion equations, as well as nearly incompressible linear elasticity models. To achieve this, optimization-based approaches are used to minimize regularized Energy Least Squares (ELS) and Output Least Squares (OLS) objective functionals. Both direct and adjoint methods are used to estimate the gradient and Hessian of the objective functionals with respect to the coefficients. To avoid the expensive computation of the full Hessian matrix, the Newton-CG-like method is also adopted, …

Multi-Omic Analysis Of Molecular Changes In Haloferax Volcanii Biofilm Development, Joshua Koller

Theses

Biofilms are the predominant lifestyle of microorganisms and offer protection against environmental stress. Archaeal biofilm development remains poorly understood relative to its bacterial counterpart, and the fundamental differences between these two domains prevent direct extrapolation from bacterial models. To address this gap, we used quantitative proteomics and transcriptomics to characterize the molecular changes accompanying biofilm formation and maturation in the model archaeon Haloferax volcanii. Protein and transcript abundance were measured across seven conditions spanning both lifestyles and multiple timepoints, with glycosylated proteoforms quantified as entities distinct from their unmodified counterparts, covering both established biofilm-associated structures and newly identified candidates. Known …

Evaluation Of Mechanical Properties And Seal Strength Of Medical Packaging Materials Before And After Supercritical Co₂ Sterilization, Camila Madriz Pizarro

Theses

The sterilization of medical devices is critical in the prevention of infections in healthcare settings. Ethylene oxide (EtO), gamma irradiation, and steam sterilization have been the standard sterilization processes in healthcare settings, where the packaging system remains the most important barrier between the sterilized instrument/device. Safety concerns and regulatory pushback on conventional sterilization methods have pushed for further research on new sterilization techniques. Among the emerging sterilization technologies, one candidate that has garnered considerable attention is Supercritical CO2 sterilization. However, there is a lack of literature to support the compatibility between scCO2 and common medical packaging materials. The present study …

Toroidal Plasmonic Nanodimers For Enhanced Near-Infrared Emission In Heterostructured Inp Quantum Dots, Arda Gülücü, Emre Ozan Polat

Turkish Journal of Physics

Near-infrared (NIR) emitters operating in the 650--900 nm spectral range are highly attractive for imaging and sensing in turbid media. However, cadmium-free InP-based quantum dots (QDs) often exhibit limited brightness owing to nonradiative recombination pathways and inefficient photon outcoupling. In particular, heterostructured InP QDs may possess band alignments that induce partial spatial separation of charge carriers, thereby reducing the electron-hole wavefunction overlap. This characteristic modifies the intrinsic recombination dynamics and increases the sensitivity of their emission to the surrounding photonic environment. Here, we investigate silver toroidal plasmonic nanoantenna dimers (Ag TPNDs) using finite-difference time-domain (FDTD) simulations as a geometry-tunable platform …

Effect Of Hydrogel Rectal Spacers On Bladder Wall And Regional Substructure Dose In Prostate Cancer Patients Undergoing Volumetric Modulated Arc Therapy With Simultaneous Integrated Boost: A Retrospective Planning Study, Geronimo Sosa

Masters Projects

Purpose: Hydrogel rectal spacers reduce rectal dose during prostate radiotherapy, but their effect on bladder wall dose is not well characterized, particularly with volumetric modulated arc therapy with simultaneous integrated boost (VMAT-SIB). This study evaluated the effect of spacer placement on whole and regional bladder wall dose.

Methods: Twenty-nine patients treated with VMAT-SIB (70 Gy in 28 fractions) were analyzed retrospectively: 9 with and 20 without a spacer. The bladder wall was defined as the whole bladder minus a 3-mm inner margin. Primary endpoints were D0.03 cc and D1 cc; secondary endpoints included D2 cc, D3 cc, D10 cc, volume-based …

Mathematics Anxiety And Academic Performance In Mathematics, Bradley Vandermissen

Masters Projects

Mathematics anxiety represents a psychological barrier that negatively impacts student academic performance and self-efficacy across all educational levels. Many secondary mathematics students experience physiological stress, self-doubt, and reduced working memory efficiency when encountering mathematical tasks, often leading to disengagement or an over-reliance on artificial intelligence (AI as a learning shortcut rather than an educational tool. Despite the widespread nature of this issue, educators frequently lack the formal training and practical pedagogical strategies necessary to identify, manage, and alleviate mathematics anxiety within their classrooms. Rooted in Bandura’s Social Cognitive Theory, this project addresses the underlying cognitive and biological components of mathematics …

A Topology-Aware Extension Of Guttae Area Ratio In Fuchs Endothelial Corneal Dystrophy, Molly Orlick, Henry Bair

Wills Eye Hospital Papers

No abstract provided.

Non-Enzymatic Hepatic Abhd6 Interacts With Akt-Foxo1 Axis To Regulate Metabolic Health, Guannan Li, Laurence T Maeyens, Jiyuan Yin, Jan-Bernd Funcke, Chanmin Joung, Ruizhen Li, Ziying Xu, Ting Wu, Xin Li, Nisi Jiang, Mbolle Ekane, Maria Paula Lopez, Pengju Cao, Sijia He, Adam B Salmon, S R Murthy Madiraju, Marc Prentki, Juli Bai, James F Nelson, Xianlin Han, Yi Zhu, Shangang Zhao

Children’s Nutrition Research Center Staff Publications

The enzymatic role of ABHD6 in insulin secretion and resistance is well documented. However, its non-enzymatic function, especially its effects on metabolic health, including selective hepatic insulin resistance and metabolic dysfunction-associated steatotic liver disease (MASLD), is poorly understood. To define the role of ABHD6 in liver physiology, we generated liver-specific ABHD6 knockout mice, as well as liver-specific native and enzymatically inactive mutant ABHD6 overexpression mouse models. We demonstrate that non-enzymatic ABHD6 contributes to the regulation of selective hepatic insulin resistance and MASLD progression. Mechanistically, we show that ABHD6 localizes to the nucleus and interacts with Akt/FoxO1 axis to regulate insulin …

Design And Fabrication Of Petri Dish Optimized For High-Frequency Acoustic Microscopy Using 3d Printing, Tuna Pesen, Beyza Ceren Eren, Arda İnanç, Bora Akgün

Turkish Journal of Physics

High-frequency imaging in acoustic microscopy requires the use of Petri dishes with thin and acoustically transparent bottoms to minimize signal attenuation and distortion. Commercially available options suitable for this purpose are often expensive or limited in compatibility with custom setups. Here, we present a cost-effective and easily customizable alternative developed in our laboratory, consisting of a 3D-printed frame combined with commercially available stretch film. The stretch film serves as an ultrathin (8 µm thickness) base that supports efficient high-frequency acoustic transmission, enabling clear and reliable imaging. Beyond acoustic microscopy, the adaptable design is also compatible with other modalities such as …

Mir172-Ap2 Controls Age-Dependent Regeneration Competence In Populus, Kaiwen Lyu, Abdul Azeez, Victor Busov

Michigan Tech Publications

Plants maintain remarkable regenerative potential, yet this capacity declines with developmental age, limiting clonal propagation and biotechnological applications. Here, we show that the miR172-AP2 module serves as a central determinant of regeneration competence in Populus. Regenerative capacity declines progressively along the shoot developmental gradient, correlating with elevated miR172 and reduced AP2 transcript levels. Functional analyses demonstrate that AP2 promotes both shoot and root regeneration by directly activating downstream transcriptional programmes, including AINTEGUMENTA-LIKE1, BIG LEAF and LIKE APETALA1, which regulate organogenic growth and developmental competence. Elevated miR172 or cytokinin signalling represses AP2, reducing regenerative outcomes, indicating that hormonal and developmental signals …

Vetiver Phytoremediation Of Nitrate-Rich Munition Wastewater: Biomass Valorization Within A Circular Economy Framework, Arash Aliasghar, Rupali Datta, Zhiming Zhang, Christos Christodoulatos, Dibyendu Sarkar

Michigan Tech Publications

Industrial munition facilities generate nitrate-rich wastewater that requires effective and sustainable treatment before discharge. While vetiver grass (Chrysopogon zizanioides)-based phytoremediation has shown promise in nitrogen removal, most studies have been limited to small-scale experiments under low nitrogen concentrations, providing limited guidance for system-level design under elevated loading. This study evaluates a greenhouse-scale phytoremediation system using vetiver grass to treat wastewater containing 1000 mg N/L nitrate and 50 mg/L COD. Plant coverage densities of 2%, 4%, and 6% (w/v) were assessed to quantify optimum density as a design parameter for optimizing nitrate removal. A 6% coverage achieved the highest efficiency, reducing …

Nextlongiso: A Comprehensive Nextflow Pipeline For Multi-Dimensional Long-Read Rna-Seq Analysis, Jiang Tan, Yuqing Wu, Yidan Sun

2020-Current year OA Pubs

SUMMARY: Long-read RNA sequencing technologies, including Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), enable direct characterization of full-length transcripts and transcriptome complexity. However, analysis of long-read RNA-seq data remains fragmented across multiple tools, limiting the ability to obtain a unified view of transcript structure, expression, and regulatory variation in long-read transcriptomes. We present NextLongIso, a scalable and reproducible Nextflow pipeline that enables coordinated analysis of multiple layers of transcript regulation. Rather than focusing solely on transcript reconstruction, NextLongIso integrates transcript discovery with downstream regulatory analyses to jointly characterize alternative splicing, isoform switching, transcript boundary dynamics (including alternative promoters and …

Changes In Water Quality And Microbiota Over Two Years In Florida Hard Clam (Mercenaria Mercenaria) Hatcheries, Bonnie Getter

Electronic Theses and Dissertations

This thesis characterized the water quality and bacterial communities in nine hard clam hatcheries over two production years through weekly or biweekly water quality and chemistry monitoring, monthly bacterial plating in the second year of production, and select 16S microbiome sampling at select hatcheries to address production bottlenecks and support the reliable production of high-quality seed for Florida’s growing hard clam aquaculture industry. Logistic regression models showed that water source was distinguished by pH, salinity, alkalinity, and nitrite, whereas geographic location was distinguished by temperature, salinity, nitrate, and calcium; temperature, dissolved oxygen, salinity, and alkalinity distinguished seasons. Vibrio bacteria differed …