Digital Commons Network^™

Learning Data-Driven Representations For Biomolecular Analysis, Optimization, And Design, Egbert Castro

Yale Graduate School of Arts and Sciences Dissertations

Recently, the study of biomolecules has undergone a shift toward high-throughput experimentation, leveraging advancements across various fields to produce datasets of unprecedented scale. Within these datasets, there are undiscovered truths that carry major implications for our understanding of biology and our ability to treat disease. However, innovative approaches are needed to distill signals from noise and enable the next generation of discoveries. Deep learning methods have excelled in their ability to learn from complex and large datasets in many domains, but their potential for biomolecular data has yet to be fully realized. To do so requires the ability to integrate …

Functionalized Dna Nanostructures For Membrane Engineering, Qiancheng Xiong

Yale Graduate School of Arts and Sciences Dissertations

DNA nanotechnology is a powerful tool for constructing precisely designed nanostructures with applications in diverse fields, including synthetic biology, nanomedicine, and biomolecular engineering. This dissertation explores the use of DNA nanotechnology in membrane engineering, focusing on developing DNA endoskeleton-supported membranes and large functionalized DNA-toxin nanopores. The first approach encountered challenges while constructing interlocked DNA nanostructures for endoskeleton-supported membranes. The negative results highlighted the need to optimize the interlocked DNA endoskeleton cage design further to ensure its practical application in templating fully exposed, continuous membranes. The second approach incorporated pneumolysins into DNA-origami channels to create large, functionalized DNA-toxin nanopores. These hybrid …

Bacterial Cell Surface Characterization By Phage Display Coupled To High-Throughput Sequencing, Casey Grun

Yale Graduate School of Arts and Sciences Dissertations

Antimicrobial resistance is a looming threat that reflects the remarkable capacity of bacteria to adapt and change in response to selective pressures. The versatile pathogen P. aeruginosa is a model case---already intrinsically resistant to many antibiotics, it can establish decades-long chronic infections, during which it evolves to survive antimicrobial treatment and evade host defenses. Many changes occur on its cell surface, a key location for both virulence and antibiotic resistance, but our technologies for studying these adaptive phenotypes are limited. Here we combined phage display with high-throughput DNA sequencing to create a high throughput, highly multiplexed technology for surveying bacterial …

Beyond Bias: Three Papers On Bias In Social Networks And Mitigating Bias In Social Science Research, Jeffrey K. Sachs

Yale Graduate School of Arts and Sciences Dissertations

The dissertation consists of three relational-based approaches to analyzing bias in socialnetworks and social data. The first study introduces two group fairness metrics that incorporate network structure, revealing its substantial impact on fairness outcomes, which is often overlooked by traditional metrics. The second study investigates information diffusion processes, highlighting the potential for inequality generated by conventional seeding strategies. It focuses on designing equitable network interventions, considering each group’s relative influence. I calibrate the diffusion models to actual diffusion processes to assess various network influence measures and their likelihood of producing equitable outcomes under a set of fairness constraints. The analysis …

Methods And Complexity In Phage-Bacteria Ecology And Evolution, Michael Blazanin

Yale Graduate School of Arts and Sciences Dissertations

Chapter I:Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the development of computational tools to handle and analyze these data to produce insights. However, existing tools are limited. Many use parametric analyses that require mathematical assumptions about the microbial growth characteristics. Those that use non-parametric or model-free analyses often can only quantify a few traits of interest, and none are capable of importing and reshaping all known growth curve data formats. To address this gap, here I present a newly-developed R package: gcplyr. gcplyr can flexibly …

Outbreak Dynamics Of Emerging Sars-Cov-2 Variants In Human And Animal Populations, Rebecca Lynn Earnest

Yale Graduate School of Arts and Sciences Dissertations

The COVID-19 pandemic is characterized by cycles of SARS-CoV-2 viral variant emergence followed by surges of infections and deaths. In the United States, the most notable variants to date are Alpha (B.1.1.7), Delta (B.1.617.2 and AY.x sub-lineages), and Omicron (BA.1, BA.2, BA.4, BA.5, and various sub-lineages). Pandemic response evolved along with the virus, raising three overarching research questions with each new variant that correspond to the chapters of this dissertation. When a new variant emerges, how is it different from the previously dominant variant(s) in circulation? The set of mutations that define a SARS-CoV-2 variant can affect viral properties such …

Error Detection In Bosonic Circuit Quantum Electrodynamics, James David Teoh

Yale Graduate School of Arts and Sciences Dissertations

Any useful quantum computer must be robust to errors on the individual qubits. This means a quantum algorithm can still reliably give the correct answer despite the qubits suffering from decoherence. Quantum error correction provides a means for achieving this, by encoding logical qubits redundantly in many additional physical qubits and/or additional energy levels. In the presence of errors the logical information is still preserved, but this remains a monumentally difficult task to achieve in practice. But what can we do with quantum error detection? Rather than trying to recover from a quantum error we instead reset qubits that are …

How To Make Machine Learning Financial Recommendations More Fair: Theoretical Explanation, Tho M. Nguyen, Saeid Tizpaz-Niari, Vladik Kreinovich

Departmental Technical Reports (CS)

Machine learning has been actively and successfully used to make financial decisions. In general, these systems work reasonably well. However, in some cases, these systems show unexpected bias towards minority groups -- the bias that is sometime much larger than the bias in the data on which they were trained. A recent paper analyzed whether a proper selection of hyperparameters can decrease this bias. It turned out that while the selection of hyperparameters indeed affect the system's fairness, only a few of the hyperparameters lead to consistent improvement of fairness: the number of features used for training and the number …

Gold & Blue Law Edition, Fall 2023, St. Mary's University - San Antonio, Texas

Gold & Blue Law Edition

This is the Fall 2023 edition of Gold & Blue Law Edition which is St. Mary's University's official School of Law publication.

Gold & Blue, Fall 2023, St. Mary's University - San Antonio, Texas

Gold & Blue

This is the Fall 2023 edition of Gold & Blue which is St. Mary's University's official school publication.

Csci 632/Csci 492: Machine Learning, David Harrison

GMAS Course Syllabi

No abstract provided.

Editorial: Research Advances Of Modification And Nutrition Properties Of Food Carbohydrates, Volume I, Yanjun Zhang, Jianhua Xie, Bin Li, Srinivas Janaswamy

Dairy Science and Food Science Faculty Publications: 2022 to Present

As a group of essential biopolymers, carbohydrates exist widely in living organisms and play many known and unknown biological roles in life activities via different pathways. Carbohydrates are widely used in foodstuffs, pharmaceuticals, biofuels, and biomaterials, to name a few. Parallelly, a growing understanding and deeper investigation drive the development of natural carbohydrates for novel applications, especially for treating chronic diseases, e.g., hyperlipidemia, obesity, and diabetes. The emerging evidence indicates that carbohydrates are effective for modulating gut microbiota, a vital organ in health and diseases. In addition, modifying carbohydrates alters and/or enhances nutrition properties, further expanding their application potential. Notably, …

Overview Of Hil Co-Simulation For Very Large Distribution Systems And Power Electronic Converters With A Dc Fast Charging Ev Benchmark Study On An Ieee Test Feeder, Rosemary E. Alden, Donovin D. Lewis, Dan M. Ionel

Electrical and Computer Engineering Graduate Research

Current development towards implementation of the future smart grid includes advanced controller and power hardware-in-the-loop (CHIL/PHIL) testing of new technology. The impact of new loads, distributed energy resources (DER) equipment, and controls spans two fields, both electric distribution power systems modeling, typically completed in the phasor domain, and electromagnetic transient (EMT) analysis across the frequency domain. The co-simulation of distribution power systems and power electronic converter controls is a growing field of research for improved design using real-time HIL capability. Within this paper, over fifty references are reviewed to summarize the current state of HIL technology, specifically with co-simulation in …

Metropolitan Transportation Commission Discretionary Transit Funding Methods Evaluation, Christopher E. Ferrell, John M. Eells, David Reinke, Richard Lee

Mineta Transportation Institute

In 2021, the Santa Clara Valley Transportation Authority (VTA) approached the Mineta Transportation Institute (MTI) with a proposal to have MTI provide an evaluation of the Metropolitan Transportation Commission’s (MTC’s) operational discretionary funding allocation policies and methods for Bay Area transit operators. The research was done in two parts. Part 1 investigated MTC’s past and current allocation methods for discretionary operational transit funding programs; Part 2 involved the evaluation of outcomes if MTC employed alternative allocation methods. After the Part 1 review of MTC’s various transit funding programs, the federal pandemic relief funds and the Transportation Development Act/State Transit Assistance …

Virus Control Aboard A Commuter Bus, Hamid Rahai, Jeremy Bonifacio

Mineta Transportation Institute

A major health concern for public transit users is exposure to viruses from other passengers. This numerical study examines virus containment aboard a public bus with changes to the bus ventilation system. The virus was modeled as a 2.5 µm round solid particle released from the mouth of the infectious passenger at a rate of 21 particles per second at a mouth velocity of 0.278 m/sec. The air delivery to the cabin was two linear ceiling slots spanning the length of the bus delivering 59.38 m3/min (2,097 CFM) of air at a mean velocity of 1 m/sec. Two different axial …

Understanding How To Diversify The Cybersecurity Workforce: A Qualitative Analysis, Maria Chaparro Osman, Maureen Namukasa, Cherrise Ficke, Isabella Piasecki, Tj Oconnor, Meredith Carroll

Aeronautics Faculty Publications

A robust cybersecurity workforce is critical for protection against a range of malicious attacks. However, it has been noted that there are many vacancies and a shortage of individuals entering the cybersecurity workforce. The workforce shortage has been partially attributed to the lack of diversity in the cybersecurity domain, with women, African Americans, and Hispanics remaining underrepresented in educational and professional settings. Using a qualitative approach, this work sought to investigate what led underrepresented minorities currently involved in cybersecurity to the industry, with the goal of determining methods to attract underrepresented minorities and diversify the workforce. A thematic analysis was …

Explicit Theory-Informed Clinical Reasoning Curriculum In A Hybrid Learning Physical Therapy Program, Stephanie M. Thurmond, Evan J. Petersen, Steven G. Lesh, Tricia R. Prokop, Allison J. Durham

School of Physical and Occupational Therapy Faculty Publications

Despite agreement among educators that clinical reasoning (CR) is an essential skill for health care professionals, use of explicit, theory-informed CR strategies and tools are lacking in Doctor of Physical Therapy (DPT) educational programs. The purpose of this commentary is to describe a four-step process whereby CR is implemented as an explicit curricular component in an accelerated, hybrid DPT program. Our process utilized four steps: 1) Identifying relevant literature and theories that informed our current understanding of CR, 2) Creating a programmatic definition of CR, 3) Delineating educational principles and curricular components that operationalize the teaching and assessment of CR, …

Mata Pencaharian Berkelanjutan Kondisi Masyarakat Adat Lekuk 50 Tumbi Dan Peran Lembaga Adat, Muhamamd Hasan Izzurrahman, Muhammad Azami Nasri

Jurnal Ilmu Kesejahteraan Sosial

Sustainable livelihoods are key for communities to sustain their lives. However, limited access to and utilisation of natural resources, particularly customary forests, has led to a decline in the livelihoods of the Lekuk 50 Tumbi indigenous community. Difficulty in clearing land is a major obstacle for them in finding alternative income. This research aims to evaluate the quality of life of the Lekuk 50 Tumbi indigenous community with a focus on indigenous institutions' initiatives based on sustainable livelihoods, considering the five aspects of capital. Through in-depth interviews and qualitative analysis, natural capital, physical capital, human capital, financial capital and social …

Whole School Improvement Programme (Wsip): A Female Headteacher, Serving In Public School Perspectives, Sultan Alam

Professional Development Centre, Gilgit

The research centered on delving into the experiences of a female headteacher in a public school who participated in a WSIP initiative and effectively implemented its teachings within her educational institution. This initiative stands as a flagship program of AKU-IED, PDCN in the specific context of Gilgit-Baltistan. Its aim is to introduce educational reforms in the region through formal in-person and distance education modes for headteachers.
The results revealed that the WSIP intervention wielded a substantial influence over the female headteacher's professional methodologies. This led to a transformation in her mindset and a noticeable enhancement of her skills. The headteacher …

Nursing News & Views - October 2023, Joanne Miller Rn

Nursing Newsletters

No abstract provided.

The Great Displacement: Climate Change And The Next American Migration, Minnesota State University, Mankato

Weather/Natural Disasters

Bibliography and photographs of a display of government documents from Minnesota State University, Mankato.

2023 Commencement Program - Fall, Morehead State University. Registrar's Office.

Morehead State Commencement Programs

2023 Fall Commencement program for Morehead State University.

Factors Influencing Instructors’ Adoption And Continued Use Of Computing Science Technologies: A Case Study In The Context Of Cell Collective, Changsoo Song, Resa M. Helikar, Wendy Smith, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Acquiring computational modeling and simulation skills has become ever more critical for students in life sciences courses at the secondary and tertiary levels. Many modeling and simulation tools have been created to help instructors nurture those skills in their classrooms. Understanding the factors that may motivate instructors to use such tools is crucial to improve students’ learning, especially for having authentic modeling and simulation learning experiences. This study designed and tested a decomposed technology acceptance model in which the perceived usefulness and perceived ease of use constructs are split between the teaching and learning sides of the technology to examine …

Redefining “No Evidence Of A Breach” In Election Security, Yunsieg P. Kim

SMU Law Review Forum

For legal purposes, we rightly understand the lack of evidence to mean a lack of existence. For example, many candidates in the 2022 elections baselessly claimed that the 2020 presidential election was stolen. But, absent evidence of systemic fraud, the law correctly determines that President Biden was duly elected. If the law entertained any outlandish assertion regardless of evidentiary support, accusers could peddle whatever claims they please, forcing the accused to disprove them. Similar to the legal understanding of “no evidence,” many appear to believe that no evidence of a security breach in our voting equipment indicates no breach. For …

Nbc Peacock North Fall 2023, Peacock North Staff

NBC Peacock North Newsletter

Highlights include: Marilyn's Page -- Chuck Todd Leaving Meet the Press -- Nightly News Celebrates its 75th Anniversary -- Audio Group Leads SNL Emmy Nominations -- Summer 2023 -- Peacock History

Exoskeletons - Designing For Social Justice, Grace Cd Murphy

College of Engineering Summer Undergraduate Research Program

Many engineering professionals believe that discussions surrounding diversity, equity, and inclusion (DEI), and social justice do not belong in engineering because engineering is supposed to be a neutral or objective field. Through an extensive review of the literature and a survey sent out to potential users, the need for DEI in engineering was examined. Many current engineering projects do not take into consideration social justice principles which leaves certain groups further marginalized and disempowered while empowering a select few. Engineering has the opportunity to be a field of service, but first risks and benefits must be weighed and the outcome …

Communicating The Need To Communicate - Lessons Learned From Failure Point To A Need For Systems Perspectives, Calvin J. Fong, Elizabeth Matranga, Dianne J. Deturris

College of Engineering Summer Undergraduate Research Program

Failure investigation reports indicate that a systems perspective is needed to reduce failure in aerospace missions.

The failures occurred not because of a technical problem but because not enough communication was occurring.

Robotic Origami Worm, Carter Josef, Michael Freeman, Mohammad Hasan

College of Engineering Summer Undergraduate Research Program

Soft robotics can solve many unique engineering problems. The ancient art of origami has inspired design for a new breed of robots. In this research, a novel fold design was created which has high linear stiffness, high bending stiffness, and the ability to deform omnidirectionally in order to turn. The robot is operated using a DC motor to expand and contract and electromagnets to control friction. The robot moves very quickly compared with many other origami robots in the literature. Other interesting ways to control friction were explored including expansion mechanisms. An origami design was created and tested that expands …

Exploring And Operationalizing Inclusive Teaching In Engineering Education, Keith Fouch, Ellie Abundo

College of Engineering Summer Undergraduate Research Program

Inclusive teaching is vital in engineering education because of its potential to enhance learning for all students. The purpose of this research is to explore faculty experiences with inclusive teaching, specifically focused on engineering settings. Our findings highlight dominant beliefs, practices, and challenges that emerged from our preliminary analysis. Future work will corroborate these findings with additional faculty as well as engineering student perspectives and beliefs.

Student’S Conceptualization Of Engineering Design Over Multiple Design Experiences, Caitlyn Berryhill

College of Engineering Summer Undergraduate Research Program

Cal Poly’s undergraduate engineering program requires a design experience for each of the four years. This research project's focus is to better understand how students are conceptualizing engineering design over their multiple design projects. Data was collected through a comprehensive survey given to 73 engineering students. The questions in this survey targeted student’s comprehension and relationship with design, as well as their demographics and course history. Open-ended questions were organized using a thematic coding system which were then compared to the demographics and course history information. This process resulted in four separate comparisons between the survey questions. Interpreting these results …