Digital Commons Network^™

Deep Learning Approaches For Cancer Prognosis Prediction Using Histopathological, Omics, And Clinical Data, Shuai Jiang

Dartmouth College Ph.D Dissertations

Accurate prediction of patient outcomes is crucial for shared clinical decision-making, treatment planning, and patients' psychological adjustment. Histopathological features of cancer, including tumor size, lymph node involvement, and metastasis, are commonly incorporated into survival prediction models, underscoring the prognostic value of whole slide images (WSIs). Concurrently, studies have highlighted the significance of omics data, such as transcriptomics, in providing valuable insights into cancer prognosis.

The emerging deep learning methods have brought new opportunities in biomedical informatics. Despite a growing body of studies on the application of deep learning methods for predicting prognosis using WSIs, the results are varied, primarily due …

Improving Human Recognition Of Deepfakes, Jeremy Mumford

Undergraduate Honors Theses

This thesis is focused on deepfakes, a new term given to fake videos and images generated by deep learning algorithms and models. Deepfakes pose a considerable threat to society by raising the bar for quality in misinformation while also lowering the amount of skill and effort required. Deepfakes threaten to undermine democratic societies by swaying public opinion through misinformation. While many researchers are working hard to develop automated tools to combat deepfakes, this thesis used a 10-item IRB approved survey to examine whether two separate interventions could successfully improve an individual’s ability to recognize deepfakes. Demographic differences in recognizing deepfakes …

Alternative Robust Ways Of Witnessing Nonclassicality In The Simplest Scenario, Massy Khoshbin, Lorenzo Catani, Matthew Leifer

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this paper we relate notions of nonclassicality in what is known as the simplest nontrivial scenario (a prepare and measure scenario composed of four preparations and two binary-outcome tomographically complete measurements). Specifically, we relate the established method developed by Pusey [M. F. Pusey, Phys. Rev. A 98, 022112 (2018)] to witness a violation of preparation noncontextuality, that is not suitable in experiments where the operational equivalences to be tested are specified in advance, with an approach based on the notion of bounded ontological distinctness for preparations, defined by Chaturvedi and Saha [A. Chaturvedi and D. Saha, Quantum …

Single Dual-Specific Anti-Pd-L1/Tgf-Β Antibody Synergizes With Chemotherapy As Neoadjuvant Treatment For Pancreatic Ductal Adenocarcinoma: A Preclinical Experimental Study, Haoxiang Zhang, Jiaoshun Chen, Jianwei Bai, Jing Zhang, Shaoyi Huang, Liang Zeng, Pengfei Zhou, Qiang Shen, Tao Yin

School of Medicine Faculty Publications

AIMS: Chemotherapy resistance is an important cause of neoadjuvant therapy failure in pancreatic ductal adenocarcinoma (PDAC). BiTP is a single antibody that can simultaneously and dually target transforming growth factor-beta (TGF-β) and programmed cell death 1 ligand 1 (PD-L1). We attempted in this study to investigate the efficacy of BiTP in combination with first-line chemotherapy in PDAC. METHODS: Preclinical assessments of BiTP plus gemcitabine and nab-paclitaxel were completed through a resectable KPC mouse model (C57BL/6J). Spectral flow cytometry, tissue section staining, enzyme-linked immunosorbent assays, Counting Kit-8, transwell, and Western blot assays were used to investigate the synergistic effects. RESULTS: BiTP …

Exploring Student Self-Assessment In General Education: A Pilot Study Using Surveying Tools, Cristo E. Yáñez León, James Lipuma, Jeremy P. Reich, Yi Meng

STEM for Success Resources

PResented at: Congreso Internacional de Investigación Academia Journals Tláhuac 2023 Venue: Instituto Tecnológico de Tláhuac II, CDMX, México Date: September 13-14, 2023.

This research article delves into an innovative pilot study examining student self-assessment in the realm of General Education Requirements (GER) within a STEM-focused university. Employing a tailored survey based on AAC&U VALUE Rubrics and utilizing a 5-point Likert scale, the study contributes to the Middle States Commission on Higher Education (MSCHE) accreditation review. Our findings explore the congruence between self-assessed student awareness and institutional benchmarks, shedding light on the efficacy of out-of-course pre-and post-tests. The research unveils pivotal …

Consensus-Based Virtual Leader Tracking Algorithm For Flight Formation Control Of Swarm Uavs, Berat Yıldız, Akif Durdu, Ahmet Kayabaşi

Turkish Journal of Electrical Engineering and Computer Sciences

Technological developments in industrial areas also impact unmanned aerial vehicles (UAVs). Recent improvements in both software and hardware have significantly increased the use of many UAVs in social and military fields. In particular, the widespread use of these vehicles in social areas such as entertainment, shipping, transportation, and delivery and military areas such as surveillance, tracking, and offensive measures has accelerated the research on swarm systems. This study examined the previous investigations on swarm UAVs and aimed to create a more efficient algorithm. The effectiveness of the proposed algorithm was compared with other leader-based applications. A swarm consisting of 5 …

Cascade Controller Design Via Controller Synthesis For Load Frequency Control Of Electrical Power Systems, Yavuz Güler, Mustafa Nalbantoğlu, Ibrahim Kaya

Turkish Journal of Electrical Engineering and Computer Sciences

The regulation of tie-line electricity flow and frequency of electrical power systems (EPS) is crucial for ensuring their robustness to parameter changes and efficient management of disturbances. To this end, a novel cascade control design approach utilizing a serial Proportional-Integral-Derivative controller with a filter (PIDF) is proposed in this paper. The parameters of the controllers are derived analytically, and it is employed in both loops of the cascade control system to regulate the Load Frequency Control (LFC) of EPS. The implementation of PIDF controllers in both loops is utilized in the cascade control scheme for various power systems featuring different …

Label-Aware Distance Mitigates Temporal And Spatial Variability For Clustering And Visualization Of Single-Cell Gene Expression Data, Shaoheng Liang, Jinzhuang Dou, Ramiz Iqbal, Ken Chen

Faculty, Staff and Student Publications

Clustering and visualization are essential parts of single-cell gene expression data analysis. The Euclidean distance used in most distance-based methods is not optimal. The batch effect, i.e., the variability among samples gathered from different times, tissues, and patients, introduces large between-group distance and obscures the true identities of cells. To solve this problem, we introduce Label-Aware Distance (LAD), a metric using temporal/spatial locality of the batch effect to control for such factors. We validate LAD on simulated data as well as apply it to a mouse retina development dataset and a lung dataset. We also found the utility of our …

A Historical Contingency Hypothesis For Population Ecology, Sarah Hoy, Rolf O. Peterson, John A. Vucetich

Michigan Tech Publications

Assessments of historical contingency have advanced our understanding of adaptive radiation and community ecology, but little attention has been given to assessing the importance of historical contingency in population ecology. An obstacle has been the unmet need to conceptualize historical contingencies for populations in a manner that allows for their explanatory power to be assessed and quantified so that it can be directly compared with the explanatory power of statistical models representing other hypotheses or theory-based explanations. Here we conceptualize historical contingencies as a series of random events characterized by (1) significant legacy effects that are comparable in length to …

Montana Kaimin, March 14, 2024, Students Of The University Of Montana, Missoula

Montana Kaimin, 1898-present

Student newspaper of the University of Montana, Missoula.

Utilizing Machine Learning Techniques For Accurate Diagnosis Of Breast Cancer And Comprehensive Statistical Analysis Of Clinical Data, Myat Ei Ei Phyo

USF Tampa Graduate Theses and Dissertations

Breast cancer represents a formidable malignancy, presenting a substantial threat to global health and individual well-being. Conventionally, it is widely held that the prognosis for breast cancer patients hinges predominantly upon the timing of diagnosis and the extent of cancer progression, typically delineated by its stage. However, emerging evidence from robust regression and machine learning analyses challenges this prevailing notion. The results indicate that survival months cannot be solely attributed to diagnosis and socio-economic factors. Instead, additional variables such as existing diseases and treatment complexities may contribute to the intricate landscape of breast cancer outcomes.

This research aims to delve …

Exploring Educational Equity: An Ethnographic Case Study Of Non-Profit Initiatives In Early Childhood Education, Jovana Jovanovic

USF Tampa Graduate Theses and Dissertations

Quality early childhood education is acknowledged as a crucial factor in paving the way for academic success and societal contribution. Childhood experiences greatly influence individual life trajectories, significantly shaping future endeavors. This research delves into the intricate dynamics between socioeconomic status (SES), educational outcomes, and non-profit organizations, emphasizing the challenges faced by students from economically disadvantaged backgrounds. While factors such as limited resources, financial constraints, and substandard living conditions have been linked to negative consequences on educational attainment, this research seeks to understand the specific role of non-profits in enhancing educational opportunities. By shedding light on collaborative efforts between local …

Nutrient Removal Of Biochar Amended Modified Bioretention Systems Treating Nursery Runoff, Nicholas Richardson

USF Tampa Graduate Theses and Dissertations

Excess inputs of nutrients, such as nitrogen and phosphorus, to surface water bodies can lead to the presence of harmful algal blooms (HABs). HABs can damage their surrounding environments and the economies dependent on them. Nutrient pollution can be properly controlled and monitored at point-sources, such as wastewater treatment plants, but is more difficult to control for non-point sources, such as fertilizer runoff. One form of fertilizer runoff that remains overlooked is runoff from plant nurseries. Controlled release fertilizers (CRFs) embedded in plant containers at nurseries can leach excess nutrients into the runoff. For nurseries in Florida, best management practices …

Investigating Gulf Coast Aquifer System: Stratigraphy Reconstruction, Inverse Modeling, And Groundwater Stress Assessment, Shuo Yang

LSU Doctoral Dissertations

The Mississippi Embayment aquifer system (MEAS) and the Coastal Lowlands aquifer system (CLAS) provide substantial groundwater resources for human activities in the U.S. Gulf Coastal Plain. However, the overexploitation has led to groundwater depletion in the MEAS and the CLAS, threatening sustainable groundwater use. Such concern highlights the crucial need for an advanced understanding of stratigraphy and groundwater in these aquifer systems, which is essential for effective regional groundwater management. This dissertation presents a comprehensive investigation of MEAS and CLAS in the Louisiana and southwestern Mississippi region, encompassing three fundamental dimensions: stratigraphy reconstruction, groundwater modeling, and groundwater stress assessments. A …

In-Person, Hybrid, Or Remote: Exploring The Effectiveness Of Teacher Practices On Student Performance During The Covid-19 Pandemic, Ashley M. Segalla

LSU Doctoral Dissertations

Schools and universities had to make unexpected changes beginning in Spring 2020 because of the COVID-19 pandemic. In Spring 2021, one university in the southern region of the United States implemented hybrid teaching formats in College Algebra courses, where students attended half of the classes in-person, and the remaining half of classes were attended synchronously and remotely. The purpose of this mixed methods study was to determine if students’ attendance methods (virtual or in-person) impacted their academic performance in the course. Additionally, the study sought to determine how students and the instructor felt student performance was impacted by hybrid attendance. …

Method For Securely Merging Uniform Lists, Peter Rindal Visa, Srinivasan Raghuraman Visa, Gayathri Annapurna Garimella Visa

Defensive Publications Series

Present disclosure the present disclosure is directed to secure computation and data encryption. In particular, the present disclosure is directed to secure computation that enables computation while keeping data encrypted. More particularly, the present disclosure is directed to a secure protocol that can merge two encrypted lists given that they are ordered. In a modern data analysis process, data is transferred to, stored in, and computed by a server. During these three processes, encryption protects the data when it is transferred and stored.

Books And Media

Appalachia

Reviews of: The Race that Changed Running: The Inside Story of the UTMB, by Doug Mayer; Been Outside: Adventures of Black Women, Nonbinary, and Gender Nonconforming People in Nature, edited by Amber Wendler and Shaz Zamore; AMC's Best Day Hikes in the White Mountains, by Robert N. Buchsbaum; AMC's Best Day Hikes Near Boston, by Michael Tougias, John S. Burk, and Alison O'Leary; AMC's Best Day Hikes Near Washington, D.C., by Jennifer Adach and Beth Homicz; Campfire Stories: Tales from America's National Parks and Trails, Volume II, edited by Dave Kyu and Ilyssa Kyu; …

Seamless Ink-Graphics Interleaving And Authoring Via Structural Decompilation Of Smart Documents, Daniel Kiecza

Defensive Publications Series

This disclosure describes a digital educational environment that provides a frictionless editing experience for students and enables them to focus on their learning and can also be used in other settings. Traditional multimedia content is seamlessly blended with handwritten content and semantically interpreted by content type to provide scaffolded learning. Interactive learning experiences in text, charts, tables, shapes, mathematics, games, diagrams, graphs, images, drawings, data visualization, etc. are supported in a multi-representational form. A student can solve an equation using either stylus/ink or math equations rendered from ink strokes, and the solution can be automatically and parallelly tested for correctness. …

Gt-Ches And Dycon: Improved Classification For Human Evolutionary Systems, Joseph S. Johnson

Theses and Dissertations

The purpose of this work is to rethink the process of learning in human evolutionary systems. We take a sober look at how game theory, network theory, and chaos theory pertain specifically to the modeling, data, and training components of generalization in human systems. The value of our research is three-fold. First, our work is a direct approach to align machine learning generalization with core behavioral theories. We made our best effort to directly reconcile the axioms of these heretofore incompatible disciplines -- rather than moving from AI/ML towards the behavioral theories while building exclusively on AI/ML intuition. Second, this …

March 13, 2024 Faculty Senate Minutes, University Of South Carolina

Faculty Senate

No abstract provided.

Predicting Gender Of Author Using Large Language Models (Llms), Satya Uday Sanku

USF Tampa Graduate Theses and Dissertations

The advent of text data from social media, blogs, movie reviews, and other textual sources has opened new avenues for research, particularly in the domain of Author Profiling. Author Profiling helps in Capturing the Stylistic features and also useful for analyzing the required elements in the written text. This Study addresses one of the tasks in Author Profiling which is termed as gender detection or Classification of Gender from Text. The main goal of this research is to obtain valuable and relevant gender characteristics that will accurately classify the Author’s gender of a review extracted from an Anime Review website. …

Miniature Optical Fiber Fabry-Perot Interferometer Based On A Single-Crystal Metal-Organic Framework For The Detection And Quantification Of Benzene And Ethanol At Low Concentrations In Nitrogen Gas, Farhan Mumtaz, Bohong Zhang, Narasimman Subramaniyam, Mohammad Roman, Peter Holtmann, Abhishek Prakash Hungund, Ryan O'Malley, Thomas M. Spudich, Michael Davis, Rex E. Gerald, Jie Huang

Electrical and Computer Engineering Faculty Research & Creative Works

This study reports for the first time, to the best of our knowledge, a real-time detection of ultralow-concentration chemical gases using fiber-optic technology, combining a miniaturized Fabry-Perot interferometer (FPI) with metal-organic frameworks (MOFs). The sensor consists of a short and thick-walled silica capillary segment spliced to a lead-in single-mode fiber (SMF), housing a tiny single crystal of HKUST-1 MOF, imparting chemo selectivity features. Ethanol and benzene gases were tested, resulting in a shift in the FPI interference signal. The sensor demonstrated high sensitivity, detecting ethanol gas concentrations (EGCs) with a sensitivity of 0.428 nm/ppm between 24.9 and 40.11 ppm and …

March 13, 2024 (Vol. 108, No. 23), Daily Eastern News

Daily Eastern News: 2023-2024

No abstract provided.

Β-Sheets Mediate The Conformational Change And Allosteric Signal Transmission Between The Aslov2 Termini, Sian Xiao, Mayar Terek Ibrahim, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

Avena sativa phototropin 1 light-oxygen-voltage 2 domain (AsLOV2) is a model protein of Per-Arnt-Sim (PAS) superfamily, characterized by conformational changes in response to external environmental stimuli. This conformational change begins with the unfolding of the N-terminal A'α helix in the dark state followed by the unfolding of the C-terminal Jα helix. The light state is characterized by the unfolded termini and the subsequent modifications in hydrogen bond patterns. In this photoreceptor, β-sheets are identified as crucial components for mediating allosteric signal transmission between the two termini. Through combined experimental and computational investigations, the Hβ …

Density And Magnetic Field Asymmetric Kelvin‐Helmholtz Instability, Xuanye Ma, Peter Delamere, Katariina Nykyri, Antonius Otto, Stefan Eriksson, Lihui Chai, Brandon Burkholder, Andrew Dimmock, Yu-Lun Liou, Shiva Kavosi

Publications

The Kelvin‐Helmholtz (KH) instability can transport mass, momentum, magnetic flux, and energy between the magnetosheath and magnetosphere, which plays an important role in the solar‐wind‐ magnetosphere coupling process for different planets. Meanwhile, strong density and magnetic field asymmetry are often present between the magnetosheath (MSH) and magnetosphere (MSP), which could affect the transport processes driven by the KH instability. Our magnetohydrodynamics simulation shows that the KH growth rate is insensitive to the density ratio between the MSP and the MSH in the compressible regime, which is different than the prediction from linear incompressible theory. When the interplanetary magnetic field (IMF) …

Reconsidering The Reliability Of Chemical Process Simulators I: Implementation Of The Murphree And Vaporization Efficiencies, Zachary Braswell, Brian F. Hanley, Holt Ragsdale

Faculty Publications

Most chemical process simulators in widespread use today allow users to apply some type of efficiency correction to individual equilibrium stages or to equilibrium stage sections in order to align the stage or section separation performance more closely to actual tray performance in the field. Some simulators even allow for the use of component efficiencies on individual stages or in stage sections. It is our contention, however, that two of the more commonly available efficiency models, the vaporization efficiency and Murphree vapor phase efficiency, have generally been implemented incorrectly. The three major conceptual inconsistencies are (1) the assumption that the …

An Exposome Atlas Of Serum Reveals The Risk Of Chronic Diseases In The Chinese Population, Lei You, Jing Kou, Mengdie Wang, Guoqin Ji, Xiang Li, Chang Su, Fujian Zheng, Mingye Zhang, Yuting Wang, Tiantian Chen, Ting Li, Lina Zhou, Xianzhe Shi, Chunxia Zhao, Xinyu Liu, Surong Mei, Guowang Xu

Faculty, Staff and Student Publications

Although adverse environmental exposures are considered a major cause of chronic diseases, current studies provide limited information on real-world chemical exposures and related risks. For this study, we collected serum samples from 5696 healthy people and patients, including those with 12 chronic diseases, in China and completed serum biomonitoring including 267 chemicals via gas and liquid chromatography-tandem mass spectrometry. Seventy-four highly frequently detected exposures were used for exposure characterization and risk analysis. The results show that region is the most critical factor influencing human exposure levels, followed by age. Organochlorine pesticides and perfluoroalkyl substances are associated with multiple chronic diseases, …

Genomic Evolution Shapes Prostate Cancer Disease Type, Dan J Woodcock, Atef Sahli, Ruxandra Teslo, Vinayak Bhandari, Andreas J Gruber, Aleksandra Ziubroniewicz, Gunes Gundem, Yaobo Xu, Adam Butler, Ezequiel Anokian, Bernard J Pope, Chol-Hee Jung, Maxime Tarabichi, Stefan C Dentro, J Henry R Farmery, Cruk Icgc Prostate Group, Peter Van Loo, Anne Y Warren, Vincent Gnanapragasam, Freddie C Hamdy, G Steven Bova, Christopher S Foster, David E Neal, Yong-Jie Lu, Zsofia Kote-Jarai, Michael Fraser, Robert G Bristow, Paul C Boutros, Anthony J Costello, Niall M Corcoran, Christopher M Hovens, Charlie E Massie, Andy G Lynch, Daniel S Brewer, Rosalind A Eeles, Colin S Cooper, David C Wedge

Faculty, Staff and Student Publications

The development of cancer is an evolutionary process involving the sequential acquisition of genetic alterations that disrupt normal biological processes, enabling tumor cells to rapidly proliferate and eventually invade and metastasize to other tissues. We investigated the genomic evolution of prostate cancer through the application of three separate classification methods, each designed to investigate a different aspect of tumor evolution. Integrating the results revealed the existence of two distinct types of prostate cancer that arise from divergent evolutionary trajectories, designated as the Canonical and Alternative evolutionary disease types. We therefore propose the evotype model for prostate cancer evolution wherein Alternative-evotype …

Resolving The Nanoscale Structure Of Β-Sheet Peptide Self-Assemblies Using Single-Molecule Orientation–Localization Microscopy, Weiyan Zhou, Conor L. O'Neill, Tianben Ding, Oumeng Zhang, Jai S. Rudra, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Synthetic peptides that self-assemble into cross-β fibrils are versatile building blocks for engineered biomaterials due to their modularity and biocompatibility, but their structural and morphological similarities to amyloid species have been a long-standing concern for their translation. Further, their polymorphs are difficult to characterize using spectroscopic and imaging techniques that rely on ensemble averaging to achieve high resolution. Here, we utilize Nile red (NR), an amyloidophilic fluorogenic probe, and single-molecule orientation-localization microscopy (SMOLM) to characterize fibrils formed by the designed amphipathic enantiomers KFE8^L and KFE8^D and the pathological amyloid-beta peptide Aβ42. Importantly, NR SMOLM reveals the helical (bilayer) …

“Educational Facials”: A Healing Tool For The Beautiful Struggle, Kari Kokka, Michelle Cody

Teaching and Learning Faculty Research

Critical educators of Color often work to support their students to work toward justice. However, because we live and work in a society imbued with white supremacy, cisheteropatriarchy, and additional systems of oppression, students and colleagues may resist efforts toward equity and racial justice, especially in mathematics education with women of Color instructors. In this paper, two mathematics educators, a Japanese American woman and a Black woman, elaborate a theory of educational facials, first coined by the second author in 2015. The theory of educational facials is an analytic tool for healing from and navigating harmful school climates. The authors …