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Statistical Methods For Mendelian Randomization Under Nonlinearity And Non-Normality, Mary Appah

ETDs from 2020-2029

Instrumental variable (IV) methods are widely used for estimating causal effects in observational studies where unmeasured confounding may bias traditional regression estimates. The core idea is to use a variable referred to as an instrument that is associated with the exposure of interest, independent of unmeasured confounders, and influences the outcome only through the exposure. While originally developed in econometrics, IV methods have been increasingly adopted in epidemiology and genetic research under the framework of Mendelian Randomization (MR), where genetic variants, most commonly single nucleotide polymorphisms (SNPs), serve as instruments. MR provides a powerful tool for investigating causal relationships between …

A Nonenzymatic Electrochemical Glucose Sensor Depending On A Ninps/Co3o4/Functionalized Graphene Oxide-Modified Working Electrode, Sümeyra Pekmez, Muhammet Güler

Turkish Journal of Chemistry

In the present research, the aim was to develop a novel electrochemical enzyme-free glucose sensor dependent upon a nickel nanoparticles (NiNPs)/cobalt (II, III) oxide (Co3O4)/carboxylated graphene oxide (GO-COOH)-modified glassy carbon (GC) electrode. The electrocatalytic performance of the electrode was tested using various electrochemical methods such as amperometry and cyclic voltammetry (CV). The NiNPs@Co3O4/GO-COOH/GC electrode showed noticeably superior electrocatalytic behavior for glucose oxidation in 0.1 M NaOH media, ascribed to the good synergistic impact between NiNPs, Co3O4, and GO-COOH. The amperometric response of the NiNPs@Co3O4/GO-COOH/GC electrode to glucose exhibited two linear determination ranges at +0.55 V potential. The first one was …

Production, Purification, And Crystallization Of The Recombinant Her2 Tyrosine Kinase Domain (Her2-Tkd), Edanur Topalan, Hali̇li̇brahi̇m Çi̇ftçi̇, Hasan Demi̇rci̇

Turkish Journal of Chemistry

The human epidermal growth factor receptor 2 tyrosine kinase domain (HER2-TKD) is an important therapeutic target in oncology. In this study, we developed a practical and cost-effective approach for producing soluble recombinant HER2-TKD in Escherichia coli as a basis for structure-based drug discovery. The gene encoding HER2-TKD was cloned into a pET28a(+) expression vector and expressed in E. coli. Since the protein was initially obtained as inclusion bodies, solubilization with 1.5% sarcosyl was applied to recover it in soluble form. The purified protein was obtained through size-exclusion chromatography, followed by tag removal using reverse affinity purification. Crystallization trials were performed …

Quantum Engineered Mxene–Graphene–Plasmonic Nanocomposites For Next-Generation Transparent And Flexible Space Photovoltaics, Arash Vaghef-Koodehi

Turkish Journal of Chemistry

This study presents a quantum‑engineered, tricomponent heterostructure comprising Ti3C2T MXene quantum dots (2–5 nm), single‑layer graphene, and plasmonic gold nanoparticles (15 ± 3 nm) uniformly embedded within electrospun polyacrylonitrile nanofibers. This integrated architecture demonstrates a remarkable combination of optical transparency (89.3 ± 1.1%) and power conversion efficiency (19.7 ± 0.4%) under AM0 solar illumination, representing 340% enhancement over state‑of‑the‑art transparent photovoltaic devices. A multiscale computational framework, bridging density functional theory and device‑level drift-diffusion modeling, identifies optimal interlayer spacing (3.4 ± 0.1 Å) as the key to achieving 89.3% charge‑transfer efficiency. Concurrently, localized surface plasmon resonances at 532 nm generate electromagnetic …

Efficient Heterogeneous Photo-Fenton Degradation Of Azo Dyes Using The Nanocomposite Mgfe2o4/Mos2, Zahra Zeinali, Leila Ershadi Afshar, Naz Chaibakhsh, Farnaz Isapour

Turkish Journal of Chemistry

In the present work, a facile hydrothermal route was employed to synthesize the nanocomposite MgFe2O4/MoS2, which acted as a heterogeneous photo-Fenton catalyst for the degradation of a synthetic diazo dye, Acid Blue 113 (AB113). The nanocatalyst produced underwent analysis using multiple characterization techniques. The parameters influencing the oxidative reaction were statistically modeled and optimized using response surface methodology. Optimal degradation efficiency for AB113 (94.92%) was attained at pH 8.79 using 10 mg of MgFe2O4/MoS2 nanocatalyst, 1.6 mL of H2O2, and a reaction duration of 27 min. The synergistic effect resulting from the formation of electron-hole pairs renders the combined photocatalysis …

Electrochemical Biosensing Of Alpha-Fetoprotein Based On Carboxylated Multi-Walled Nanotube-Polyazur A (In Des)-Gold Nanoparticles, Merve Yilmaz Çilçar, Meli̇ke Bi̇lgi̇ Kamaç

Turkish Journal of Chemistry

AFP, a cancer biomarker, is monitored during fetal development and in the serum of pregnant women. Sensitive and rapid monitoring of AFP is crucial for effective management. In this study, screen-printed carbon electrodes (SPCEs) modified with multi-walled carbon nanotubes (MWCNT-COOH), polyAzur A (PAA), which was prepared in a deep eutectic solution (DES), and gold nanoparticles (AuNP) were fabricated. AFP biosensors were developed for practical, sensitive, low-cost, and rapid detection of AFP. Optimizations of nanostructures (MWCNT-COOH, AuNP) and polymers (PAADES) were performed. The MWCNT-COOH, PAADES, and AuNP-modified SPCEs were characterized by FE-SEM-EDX, FTIR, and XRD techniques. The amounts of 6-MOH, APTES, …

Kernelizing Protein Interaction Languages: Spectral Approximations And Random Fourier Features, Aishik Ghosh

Master’s Dissertations

Protein-peptide interactions play an important role in many biological phenomena, spanning adaptive immunity to disease pathology. In the Sliding Window Interaction Grammar (SWING) framework, interactions are represented as sequences of biochemical tokens embedded using Doc2Vec, allowing robust generalisation to unobserved MHC alleles. However, classification remains limited to a single Euclidean feature space that is incapable of resolving binding landscapes. This dissertation develops SWING for four distinct kernel types: Gaussian, Laplacian, anisotropic (ARD), and the Spectral Mixture (SM) kernel, each approximated using scalable Random Fourier Features. The SM kernel incorporates prior knowledge about secondary structure into its spectral density as biological …

Data-Driven Electrochemistry Reveals The Impact Of Hydrophobicity On Aptamer Cross-Reactivity, Emily Carroll, Michael A. Pence, Elizabeth Winterholler, Taylor D. Sparks, Shelley D. Minteer

Chemistry Faculty Research & Creative Works

Electrochemical aptamer-based (E-AB) biosensors offer a promising platform for reagentless detection of molecular targets, yet aptamer recognition can be limited by cross-reactivity, particularly for hydrophobic analytes such as steroid hormones. To investigate how cross-reactivity influences E-AB sensor performance, we use automation and machine learning to screen a library of possible interferent molecules against a steroid-binding aptamer, with progesterone serving as a physiologically relevant test case. Here, we develop a label-free E-AB sensor for progesterone detection using a methylene blue-modified aptamer anchored with a hexanethiol linker. We then used an automated electrochemistry platform to perform reproducible and high-throughput characterization of our …

Main-Chain Ion-Pair Polybenzimidazole Membranes Enabling Reduced-Temperature Ht-Pemfc Operation (Down To 120°C), Brian C. Benicewicz, Huina Lin

Faculty Publications

Proton exchange membrane (PEM) fuel cells are promising for clean and efficient energy conversion across diverse applications. High-temperature PEM fuel cells (HT-PEMFCs) using phosphoric acid (PA)-doped polybenzimidazole (PBI) can operate up to 200°C, but at lower temperatures, water-induced PA loss often leads to performance degradation and reduced durability. In this work, we present a new class of main-chain ion-pair PBI membranes by integrating the imidazolium-biphosphate ion-pair units directly into the PBI backbone. This design results in membranes with high acid content, stronger acid-polymer interactions and stabilized acid retention. In single-cell tests, the Im+-PBI15-3 wt.% exhibits peak power densities of 0.79 …

High-Throughput Optical Analysis To Inform Design Of Electrochemical Biosensors, Nathan J. Ricks, Michael A. Pence, Monica Brachi, Shelley D. Minteer

Chemistry Faculty Research & Creative Works

Electrochemical biosensors are central to wearable diagnostics, point-of-care testing, and continuous health monitoring due to their low power requirements, compatibility with miniaturized electronics, and proven clinical impact. Despite these advantages, the development of new electrochemical biosensors remains slow, constrained by limited throughput, complex electrode–biomolecule interfaces, and challenges associated with selectivity and performance in chemically complex environments. This perspective outlines how the next generation of electrochemical biosensors can be enabled by decoupling high-throughput front-end discovery and optimization from electrochemical readouts using nonelectrochemical surrogate assays. Optical, affinity, and cell-sorting platforms, including SELEX, fluorescence-activated cell sorting, and chemically coupled fluorescence assays, allow orders-of-magnitude …

The Effect Of Project-Based Learning Model On Entrepreneurship (Pjbl-E) With A Deep Learning Approach On Students' Problem-Solving And Cognitive Skills, Ricce Oktasari, Irwandi Irwandi, Siti Darwa Suryani

Jurnal Pendidikan Sains

This study aims to examine the effect of the Entrepreneurship-based Project Based Learning (PjBL-E) model integrated with a pedagogical Deep Learning approach on students’ problem-solving skills and cognitive learning outcomes in biology learning. The novelty of this study lies in the integration of entrepreneurship values and pedagogical deep learning principles into Project Based Learning to create contextual and meaningful learning experiences. Entrepreneurship integration encourages students to develop innovative products, identify real-world problems, and apply biological concepts in practical and socio-economic contexts. Meanwhile, the pedagogical Deep Learning approach promotes reflective thinking, conceptual understanding, critical analysis, and the ability to connect theory …

Learning In Infants Using Intrinsically Motivated Goal Conditioned Reinforcement Learning, T I Darsan

Master’s Dissertations

Traditional artificial intelligence models learn by passively digesting large datasets. In contrast, human infants discover skills by actively interacting with their bodies and environments without explicit external rewards. This thesis introduces the Composer Architecture, a machine learning framework designed to mimic this autonomous, open-ended development. The Composer architecture operates in a multi-stage loop, the latent model using Contrastive Learning Through Time (CLTT) to compress high-dimensional raw data from visual, proprioceptive, and touch sensors into a low-dimensional space. To preserve data relationships and prevent topological collapse, a Softmax activation forces these latent representations to lie smoothly on a probability simplex. A …

You Mean What? Commognitive Conflict In Resolving Contextual Logarithm Problems, Endrayana Putut Laksminto Emanuel, Fatkul Anam, Radhitya Duta Pradana, Anik Kirana, Sikky El Walida

Jurnal Pendidikan Sains

Students’ approaches to solving contextual mathematics problems involving logarithms vary significantly due to differences in their prior mathematical understanding. These differences may trigger commognitive conflict during the interpretation and reasoning processes when students attempt to construct mathematical meaning from contextual situations. This qualitative study aimed to explore how commognitive conflict emerges as a mechanism of mathematical interpretation in students’ discourse while solving logarithmic contextual problems. Twenty students participated in the study and were grouped based on their performance. One student was selected as the main research subject for an in-depth analysis. The findings reveal that commognitive conflict appeared in two …

Student Worksheets Based On The Local Wisdom Of Besilek Serawai For Sixth-Grade Elementary Science Learning, Mice Agustin, Tomi Hidayat, Irwandi Irwandi

Jurnal Pendidikan Sains

This study aims to develop a Student Worksheet (Lembar Kerja Peserta Didik [LKPD]) based on the local wisdom of Besilek Serawai for sixth-grade elementary science education and to evaluate its validity. The study employed the ADDIE development model, consisting of five stages: Analyze, Design, Develop, Implement, and Evaluate. The developed LKPD integrates Besilek Serawai, a traditional martial art of the Seluma community, with the concept of the human locomotor system in science instruction. The worksheet was validated by two subject-matter experts and two media experts. Material validation yielded an average score of 4.26, equivalent to a validity percentage of 85.2%, …

Improving Approach Of Evolutionary Strategies For Clustering Technique Enhancement, Duaa Mahde Saleh, Hasanen S. Abdullah, Ahmad Zamsuri

Journal of Soft Computing and Computer Applications

The existence of the information has been the essential aspect of the whole society. Information is concentrated in all forms to be effectively utilized. Clustering — an unsupervised learning technique. It is based on data similarity that gives rise to issues in collection, challenges and instability in data structure. It proposes an advanced evolutionary method by combining two approaches. Firstly, it adopts the evolutionary approach and integrates the advantages between two methods to design one. Among them are Differential Evolution (DE) and Genetic Algorithm (GA), Evolutionary Strategy (ES) and Genetic Programming (GP), and Evolutionary Programming (EP) and Particle Swarm Optimization …

Comparative Study On Throughput Optimization In Nfv: Traditional Dissemination Techniques Vs. Swarm Intelligence Approaches, Sanaa Salih Alwan, Asia Ali Salman, Wulfrano Arturo Luna Ramírez

Journal of Soft Computing and Computer Applications

Network Functions Virtualization (NFV) modernizes networks by replacing hardware with software, creating a more flexible network architecture and offering flexibility in dynamic network environments. This foundational technology is essential for creating the networks of the future, including the Internet of Things (IoT) and cellular services. NFV does provide flexibility, but it struggles to maintain system throughput during high traffic loads while achieving high resource utilization efficiency and dynamic packet routing. The problem lies in the fact that traditional request distribution mechanisms, such as flooding and gossip, fail to operate efficiently in complex network topologies (scale-free networks), leading to: (a) random …

Trophic Transfer Of Fluorescent Polyethylene Microplastics In A Simplified Artemia–Oreochromis Aquatic Food Chain, Dativa J. Shilla

Tanzania Journal of Science

Microplastics (MPs) are pervasive contaminants in aquatic ecosystems, yet experimental evidence of their trophic transfer within tropical African food webs remains scarce. This study provides experimental evidence of indirect trophic transfer of microplastics from Artemia salina to Oreochromis urolepis, a cichlid species of ecological and economic importance in African inland and coastal waters. A simplified two-level food chain was established by exposing A. salina nauplii to fluorescent polyethylene microplastics (10–20 µm; 1, 10, and 100 mg L⁻¹) and subsequently feeding them to juvenile O. urolepis under controlled laboratory conditions. These concentrations were selected to represent a range of exposure levels …

Extraction Of High-Quality Cashew Nutshell Liquid Using Carbon Dioxide-Expanded Hexane, Frank N. Jacob, Neema Msuya, Joseph Y.N Philip, Kando Khalifa Janga

Tanzania Journal of Science

Cashew nutshell liquid (CNSL) is a by–product from cashew processing industries containing four naturally occurring phenolic compounds. This study investigated an extraction approach using CO2–expanded hexane. The central composite design (CCD) was employed in experimental design to investigate the effects and interaction of CO 2 mole fractions and extraction temperature on the CNSL yield and quality (Colour) from Steamed CNSL. The dissolution power of the CO2–expanded hexane was assessed by determining the solubility of CNSL during the initial stages of extraction at different extraction conditions. Findings indicated that higher CO2 mole fractions reduced CNSL solubility, while higher temperatures enhanced it. …

Pinnlab: An Interactive Dashboard For Teaching Data-Driven Parameter Estimation In Differential Equations Using Physics-Informed Neural Networks, Mohan J. Parthasarathy, Padmanabhan Seshaiyer

CODEE Journal

Undergraduate instruction in ordinary differential equations (ODEs) is typically organized around the forward problem: finding solution trajectories when the governing equation and its parameters are known. In scientific practice, however, inverse problems are often more relevant, requiring unknown parameters to be inferred from noisy observations while assessing whether a proposed model is consistent with the data. We introduce PINNLab, an open-source MATLAB dashboard designed to help undergraduate students explore inverse modeling through physics-informed neural networks (PINNs). PINNLab presents PINNs as a complementary data-driven framework that connects differential equations, optimization, empirical data, and scientific machine learning. The instructional sequence is organized …

Learning To See Lesions, Not Skin Tone: Counterfactual Multimodal Learning For Fair, Trustworthy, And Text-Free Dermatology Ai, Shivam Jangid

Master’s Dissertations

Recent advances in deep learning have significantly improved the performance of automated skin lesion classification systems, enabling accurate detection of various dermatological conditions from medical images. Despite these achievements, concerns regarding fairness and generalization remain a major challenge for the deployment of such systems in real-world clinical settings. A key factor contributing to these challenges is the presence of bias in training datasets, particularly with respect to skin-tone representation. Most publicly available skin lesion datasets contain a disproportionate number of samples from individuals with lighter skin tones. As a result, deep learning models trained on these datasets often learn representations …

Deep Reinforcement Learning With Directed Asymmetry And Kolmogorov-Arnold Networks For Dismantling Interdependent Multiplex Networks, Soumyajit Dev

Master’s Dissertations

Identifying the minimum-cost node-removal sequence that fragments a complex network - the network dismantling problem is NP-hard and central to infrastructure resilience. In interdependent multiplex networks, this difficulty is compounded by cascading cross-layer failures. While deep reinforcement learning (DRL) agents utilizing graph neural network (GNN) encoders achieve near-optimal dismantling, current state-of-the-art architectures suffer from two critical limitations. Topologically, existing agents strictly assume undirected edges, rendering them inapplicable to directed systems - such as supply chains or gene regulatory cascades - where failure propagation is fundamentally asymmetric. To resolve this, we propose Disassembling Directed Interdependent Networks (DDIN). DDIN introduces an asymmetric …

Antioxidant Potential Of A Non-Heme Iron Complex: Mitigating H2O2-Induced Cellular Damage, Magy A. Mekhail, David M. Freire, Cameron Bowers, Grant Elam, Nora Del Bosque, Hannah K. Pyle, Sarah K. Dunn, Spencer Lanyon, Timothy J. Hubin, Giridhar Akkaraju, Kayla N. Green

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Iron complexes with antioxidant activity have garnered significant interest for both general and medical applications, yet few studies have yielded functional nonheme iron-based mimics for H₂O₂ mitigation in aqueous environments. Here, we investigate water-soluble nonheme iron complexes derived from 12-membered pyridinophanes (^CF₃PyN₃, PyN₃, ^NMe₂PyN₃, and Py₂N₂) to evaluate the impact of ligand scaffolds on H₂O₂ decomposition activity both in vitro and in a cellular model. Speciation and kinetic analyses reveal that both electronic and geometric modulation of the macrocyclic …

Impact On Energy Budgets In Grassland Production And Conservation Of Possible Production Of Energy From Biomass Crops, R J. Wilkins

IGC Proceedings (1977-2023)

There is commonly a conflict between output/unit of area of land and output/unit of support-energy (SE) input. The possibil­ity of using a proportion of the total land area for biomass energy production suggests an approach for calculating grassland out­put/ha unconfounded with differences in SE input. Output can be calculated for an area of land that is devoted to grassland and biomass energy crops in proportions that result in a net demand for SE of zero. Outputs of utilized metabolizable energy (UME) are related to inputs of SE for (1) grazed grass with high application of nitrogen (N) fertilizer and (2) …

Efficiency Of Dairying Under Contrasting Feeding And Management Systems In North America, Israel, Europe, And New Zealand, J.D. J. Scott

IGC Proceedings (1977-2023)

Four different systems of feeding and managing dairy cattle are seen in major milk-producing countries. These are (1) feeding purchased roughages and concentrates to zero-grazed, intensively penned cows; (2) home growing of roughages and most con­centrates for zero-grazed animals; (3) feeding concentrates with conserved pasture and other roughages in winter and reduced concentrates to grazed cattle in spring-summer; and (4) feeding cattle on grazed pasture and conserved pasture throughout the year. The following data on the four systems were obtained from examples in southern California, Wisconsin, England/Wales, and New Zealand. Average fat-corrected milk (FCM)/cow is approximately 7,140, 5,300, 4,670, and …

Potential Contribution Of White Clover To The Economics And Support-Energy Inputs Of Grass-Based Beef-Production Systems, T A. Stewart, R E. Haycock, A S. Laidlaw

IGC Proceedings (1977-2023)

Biological output, gross margins, and efficiency of support-energy usage in an 18-month beef-production system on grass-white clover swards receiving either 50 kg N/ha stocked at 3.3 head/ha (low N) or 300 kg N/ha stocked 4.5 head/ha (high N) were compared. To date, two production cycles (1977-1979 and 1978-1980) at two sites have been completed. Mean live-weight and carcass gains/ha were, respectively, 17.5% and 14% higher from the high-N than from the low-N system. Gross margin/head was higher from the high-N system in the first production cycle but not in the second. In the low-N system as com· pared with the …

An Evaluation Of The Black Walnut- Tall Fescue Pasture-Management System, H E. Garrett, W B. Kurtz

IGC Proceedings (1977-2023)

The economic and biological feasibility. of a black walnut-livestock-grazing multicropping-management regime bas been evaluated for comparison with a similar livestock-management regime conducted in the open. Pure tall fescue plots were established under open and black walnut-shade conditions. Forage yields on a dry-weight basis were estimated for a 3-year period. A concurrent grazing trial was co􀀌ducted on similar sites using 1.2-ha plots. Black walnut seedlings were planted within the plots on a 3 x 12-m spacing and protected from grazing animals by electric fencing. The economic analyses of the alternate grazing systems were based on their respective present net worth and …

Economics Of Renovating Mountain Hay Meadows, J J. Jacobs

IGC Proceedings (1977-2023)

There are approximately 0.5 million hectares (ha) of irrigated native grass hay in the mountain and intermountain regions of California, Oregon, Idaho, Utah, Nevada, Montana, Wyoming, and Colorado. Often these lands are not producing at their full physical or economic potential. The objectives of this study were to identify alternative improvement procedures to increase hay production and to determine the economic feasibility of those alternatives. The principal means of identifying alternative mountain hay-meadow improvement practices and their costs was personal in­terviews with ranchers. The ranchers interviewed were owners and/or operators of mountain ranches in Wyoming who were us­ing or had …

Pasture Demonstration Program For Beef: Economic Considerations, P R. Hasbargen, R H. Craven, N P. Martin

IGC Proceedings (1977-2023)

This study made an economic evaluation of several alternative pasture improvement programs on beef farms in northern Minnesota. Three questions were addressed relative to several pasture improvement systems. These were (1) Will it pay? (2) Is there a cheaper way? and (3) Is there a more profitable system for a particular farm resource situation? Partial budgeting and computerized linear programming techniques were used to analyze pasture cost and return data obtained from several ranches in northern Minnesota. Study results show that rented pastures, when available, provided the cheapest source of additional summer feed, and that legume pastures provide cheaper sources …

Pennsylvania's Alfalfa Growers Program: Four Years Of Success, J E. Baylor, L E. Lanyon, W K. Waters

IGC Proceedings (1977-2023)

Alfalfa (Medicago sativa L.) is the most important perennial forage legume grown in Pennsylvania. However, yields currently reported by farmers are considerably below what might be expected when all production inputs are utilized. Therefore, a pro­gram was developed (1) to measure how much alfalfa hay, protein, and energy can be pro􀀗uced on 1 ha of Pennsylvania land under nonirrigated conditions, (2) to determine the mineral content and uptake by high-yielding alfalfa crops, and (3) to obtain more realistic on-farm estimates of alfalfa production costs. To achieve the program goals, hay production for each harvest from 2.02-ha farm fields was …

Estimation Of Digestibility Of Legume Forages By Means Of Morphological Parameters, W Kuhbauch

IGC Proceedings (1977-2023)

Forage quality is normally evaluated by time-consuming and costly laboratory analyses. It appears promising to use mor­phological parameters to evaluate forage quality in alfalfa and red clover. During progressive growth of white clover, red clover, and alfalfa, the leaf and stem portion was separated to determine the fiber fraction according to the Van Soest method and to

estimate digestibility by the procedure of Tilley and Terry. Stem : leaf ratio and stand height as a measure of stem length were used as morphological parameters. Leaves of the three legumes vary only slightly in concentration of cell-wall material and in digestibility …