Faculty Scholarship

Permanent URI for this collectionhttps://hdl.handle.net/10829/24371

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Open Access
Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing
(MDPI, 2021-03) Lippa, Geoffrey; Srivastava, Yoshita; Bonn-Breach, Rachel; Chavali, Sai Shashank; Jenkins, Jermaine; Wedekind, Joseph
RNA plays a central role in all organisms and can fold into complex structures to orchestrate function. Visualization of such structures often requires crystallization, which can be a bottleneck in the structure-determination process. To promote crystallization, an RNA-recognition motif (RRM) of the U1A spliceosomal protein has been co-opted as a crystallization module. Specifically, the U1-snRNA hairpin II (hpII) single-stranded loop recognized by U1A can be transplanted into an RNA target to promote crystal contacts and to attain phase information via molecular replacement or anomalous diffraction methods using selenomethionine. Herein, we produced the F37M/F77M mutant of U1A to augment the phasing capability of this powerful crystallization module. Selenomethionine-substituted U1A(F37M/F77M) retains high affinity for hpII (KD of 59.7 ± 11.4 nM). The 2.20 Å resolution crystal structure reveals that the mutated sidechains make new S-π interactions in the hydrophobic core and are useful for single-wavelength anomalous diffraction. Crystals were also attained of U1A(F37M/F77M) in complex with a bacterial preQ1-II riboswitch. The F34M/F37M/F77M mutant was introduced similarly into a lab-evolved U1A variant (TBP6.9) that recognizes the internal bulged loop of HIV-1 TAR RNA. We envision that this short RNA sequence can be placed into non-essential duplex regions to promote crystallization and phasing of target RNAs. We show that selenomethionine-substituted TBP6.9(F34M/F37M/F77M) binds a TAR variant wherein the apical loop was replaced with a GNRA tetraloop (KD of 69.8 ± 2.9 nM), laying the groundwork for use of TBP6.9(F34M/F37M/F77M) as a crystallization module. These new tools are available to the research communit
Open Access
Automating Crochet Patterns for Surfaces of Revolution
(Tessellations Publishing, 2023-07) Lipnicki, Amanda; Martinez, Megan
A surface of revolution is created by taking a curve in the xy-plane and rotating it about some axis. We develop a program which automatically generates crochet patterns for surfaces by revolution when they are obtained by rotating about the x-axis. In order to accomplish this, we invoke the arclength integral to determine where to take measurements for each row. In addition, a distance measure is created to optimally space increases and decreases. The result is a program that will take a function, x-bounds, crochet gauge, and a scale in order to produce a polished crochet pattern.
Open Access
Bounding the tripartite-circle crossing number of complete tripartite graphs
(Wiley, 2021-10) Matson, Elizabeth; Camacho, Charles; Fernandez-Merchant, Silvia; Jelic Milutinovic, Marija; Kirsch, Rachel; Kleist, Linda; White, Jennifer
A tripartite-circle drawing of a tripartite graph is a drawing in the plane, where each part of a vertex partition is placed on one of three disjoint circles, and the edges do not cross the circles. We present upper and lower bounds on the minimum number of crossings in tripartite-circle drawings of Km,n,p and the exact value for K2,2,n. In contrast to 1- and 2-circle drawings, which may attain the Harary–Hill bound, our results imply that balanced restricted 3-circle drawings of the complete graph are not optimal.
Open Access
Cold Roses
(Johns Hopkins University Press, 2023-03) Gray, Juliana
Open Access
Comedic Hermeneutical Injustice
(Cambridge University Press, 2023-02) Butterfield, Paul
This article posits and explores the concept of comedic hermeneutical injustice: a type of hermeneutical injustice that disadvantages members of marginalized groups in the arena of humor-sharing. First I explain the concept of comedic hermeneutical injustice: that agents who are hermeneutically marginalized are less able to successfully participate in the sharing of humor. Then I suggest that, to prove the existence of such an injustice, two things need to be shown: first, that hermeneutically marginalized groups do suffer some disadvantage in how well their attempts at humor are received, and, second, that this disadvantage amounts to a significant harm. In proving the existence of a comedic disadvantage, this article notes that all jokes require some epistemic content to be shared between joke-teller and joke-hearer. Thus, since being hermeneutically marginalized obstructs one from sharing knowledge with proximate speakers, hermeneutical inequalities can lead to inequalities in the sharing of humor. To show that this constitutes a significant disadvantage, the article observes the various ways that sharing humor successfully can serve agents’ social interests. It concludes by noting some idiosyncrasies of comedic hermeneutical injustice, relative to other forms of epistemic injustice, and situating it within the wider framework of humor's general social-ethical influence.
Open Access
Connect to Learn: Assemblage of Pedagogies in Higher Education in a Community of Practice
(Open/Technology in Education, Society, and Scholarship Association (OTESSA), 2021-12) Sedaghatjou, Mina; Fournier, Elaine; Namukasa, Immaculate
In this paper, we report on the ways in which technology and scholarship of pedagogy emerge as interconnected within a technology-facilitated community of practice (CoP), for educators within various Faculties of Education in North American universities. The goal of the Community of Practice is to connect with and learn from one another, discussing, and reflecting on different types of pedagogical practices among members who teach in both graduate and teacher education programs in the onsite, blended, and online environments. We share analysis of interviews, and notes from CoP members’ feedback; how the CoP members made sense of their diverse teaching and social learning landscapes as well as emergent joint meanings. The results of the study suggest that the assemblage of new ideas and pedagogies can be enhanced by a relational trust. A highlighted role of technology in enabling communication and collaboration among CoP members is also discussed through the lens of connectivism.
Open Access
Excerpts from a Scientist’s Notebook: Ancestral Memory in Europan Pseudocephalopods
(Adamant Press, 2023-10) DeGraff, David
Embargo
‘For Men Only:’ Sexual Health Education, Neurasthenia and the Modern YMCA in the Gilded Age
(Oxford University Press, 2023-01) Szymanski, Mallory
In the late-nineteenth century, Young Men’s Christian Association (YMCA) presented medical lectures designated ‘For Men Only’. This article argues that YMCA lectures about sexual health relied on the discourse of neurasthenia to address sexual health and morality in medical terms. By demonstrating that sexual licentiousness could be both a cause and consequence of this common nervous disease, lecturers at the YMCA invited young men to understand themselves as victims of circumstance, corrupted by modern society. While this period in YMCA history is often considered part of the social hygiene movement of the early twentieth century, this article shows that the efforts of health reform in the 1880s and 1890s mobilised an approach unique to Gilded-Age America, one which served the to bolster the legitimacy of physicians and to attract men into YMCA Halls.
Open Access
Hooked on Calculus: Crocheting Quadric Surfaces
(Tessellations Publishing, 2023-07) Lipnicki, Amanda; Martinez, Megan
In an effort to make the surfaces in a multivariable calculus class tangible, this paper provides crochet patterns for 6 small models of quadric surfaces. We broadly outline the mathematical concepts behind our patternmaking process, explain how this led to our research in automating crochet patterns, and provide ideas for future directions. The patterns, discourse, and resources provided are useful for educational and artistic purposes. They provide tactile examples of surfaces discretized into patterns and applications of calculus to materials and design.
Open Access
Investigating Resiliency Among Students with Emotional Disturbance Living in Underserved Urban Communities
(National Association of Therapeutic Schools and Programs, 2021) Curtin, Kevin A.; Benedict, Elizabeth
The purpose of this article is to investigate resiliency found in students with emotional disturbance who grew up in underserved urban communities and served in therapeutic, residential or day treatment programs. Researchers employed a grounded theory approach using key informant interviews to discover both risk and resiliency factors with the intention of adding to the literature on resiliency for students with special needs. Findings revealed several unique factors based on the resiliency constructs of risk, positive social conditions, positive behaviors, and positive personal qualities. Implications and recommendations for strength-based programming are highlighted.
Open Access
Kant's Theory of Laughter
(The British Society of Aesthetics, 2021-03) Kuplen, Mojca
In this paper I offer an alternative interpretation of Immanuel Kant’s theory of laughter that can meet the challenges left behind by the interpretations that have so far been given. I argue that laughter is a reaction to the dissolution of nonsense, which takes the form of realizing our own misconceptions about the object. Laughter reveals something about our cognitive and rational system: namely, that it is insufficient to explain all of our experiences and perceptions of the world and that we often need to revise our expectations in order to make sense of the world. In this respect, laughter stands in a direct opposition to Kant’s notion of the sublime.
Open Access
Lizzie Borden and the Forty Whacks: Notes on a Rhyme
(Bucknell University, 2023-10) Gray, Juliana
Open Access
Ohio Abortion Regulations and Ethical Dilemmas for Obstetrician–Gynecologists
(Wolters Kluwer Health, Inc., 2022-08) Field, Meredith; Gyuras, Hillary; Bessett, Danielle; Pensak, Meredith; Norris, Alison; McGowan, Michelle
OBJECTIVE: To analyze obstetrician–gynecologists' (ob-gyns’) experiences with, and perspectives on, how Ohio's abortion-restrictive regulatory landscape affects their health care practices. METHODS: Between 2019 and 2020, we conducted qualitative interviews and focus groups with ob-gyns (N=35) who had practiced in Ohio for at least 6 months between 2010 and 2020. Discussions were recorded, transcribed, coded, and analyzed thematically using ATLAS.ti software. RESULTS: Participants perceived Ohio abortion regulations affecting their practice in three key ways: abortion regulations framed abortion and physicians who provide abortion as separate and distinct from other medical practices and physicians; many institutional interpretations of abortion regulations undermined physician expertise and professional autonomy; and the constellation of abortion regulations, institutional interpretations, physicians' trepidation, and their perceived inability to exercise clinical judgment worked together to limit abortion access and increase risks to patients' lives and health. The combined factors left participants feeling distraught that they were unable to practice medicine in an ethical and compassionate manner. CONCLUSION: Ohio abortion regulations limit ob-gyns' ability to provide comprehensive reproductive health care, creating ethical dilemmas for these physicians as they attempt to care for their patients. As Ohio's abortion laws increase in number and restrictiveness, they further undermine obstetric and gynecologic ethical practice guidelines. However, medical institutions play a key role in determining abortion provision in Ohio; through their interpretation of the law, institutions can demonstrate support or further limit ob-gyns’ ability to exercise clinical judgment and provide ethical, compassionate care to their patients. Considerable work remains to bring Ohio's abortion regulations, institutional interpretations, and physician practices into alignment with professional clinical practice and ethics guidelines.
Open Access
Project Time! A Course-Based Undergraduate Research Experience, a CURE for the Traditional Organic Lab
(American Chemical Society, 2023-07) D'Angelo, John
In recent years, course-based undergraduate research experiences (CUREs) have been increasing in popularity as replacements for or adjuvants to the traditional laboratory experience. This approach shifts the focus from an exercise-based curriculum to an experiment-based curriculum and provides students with a more authentic and higher-impact scientific experience. Reported herein are the details of a CURE deployed in the organic chemistry II lab at a primarily undergraduate institution. In this instance, students are given nearly free rein regarding their group projects completed during the second semester. Quantitative assessment of the approach through student surveys is provided, though the statistical significance of the results is at best questionable. Qualitatively, one project has resulted in a paper in preparation and others are nearing this milestone, demonstrating the viability of the approach to expose students to doing publishable scientific research and the scientific process. Additionally, free responses to survey questions seem to suggest that the method is a success.
Open Access
Psychology in Neural Networks – In Honor of Professor Tracy Mott
(now publishers, 2022-09) Bedi, Harpreet Singh
This paper introduces psychology into neural networks by building a correspondence between the theory of behavioral economics and the theory of artificial neural networks. The connection between these two disparate branches of knowledge is concretely constructed by designing a dictionary between prospect theory and artificial neural networks. More specifically, the activation functions in neural networks can be converted to a probability weighting functions in prospect theory and vice versa. This approach leads to infinitely many activation functions and allows for their psychological interpretation in terms of risk seeking and risk averse behavior.
Embargo
Review of Marginalized: Southern Women Playwrights Confront Race, Region, and Gender, by Casey Kayser
(University of Tulsa, 2022-11) Mayberry, Susan
Open Access
Review: Dylan and the Beats
(Curfew Gull, 2023-02) Reginio, Robert
Open Access
The double-edged sword of abortion regulations: Decreasing training opportunities while increasing knowledge requirements
(Taylor & Francis, 2022-11) Field, Meredith; Gyuras, Hillary; Thornton, Olivia; Bessett, Danielle; McGowan, Michelle
Purpose: The authors explore how abortion regulations in Ohio, an abortion-restrictive state in the USA, impact obstetrician-gynecologists’ (OB/GYNs) training in reproductive healthcare and describe what OB/GYNs believe to be the broader impact of Ohio’s regulations on skill-building, skills maintenance, and professional retention of reproductive healthcare providers in the state. Authors discuss how their findings foreshadow abortion training limitations in Ohio and other abortion-restrictive states now that abortion regulations have returned to the states. Methods: The authors conducted four semi-structured focus groups and five in-depth interviews between April 2019 and March 2020. Participants included OB/GYNs practicing obstetrics and gynecology in Ohio between 2010 and 2020. Thematic analysis was conducted using Atlas.ti. Results: Twenty attending physicians and 15 fellows and residents participated in the study. Participants discussed the impact of Ohio’s written transfer agreement, gestational-limit, and abortion method and facility bans on training and skill-building opportunities. Participants felt that Ohio’s strict abortion regulations 1) limit opportunities to observe and perform abortion procedures during training; 2) require learning the ever-changing legality of abortion provision; 3) limit the number of abortions OB/GYNs can provide, leading to the atrophy of their skills over time; and 4) may prevent prospective medical students and residents from choosing to study in Ohio and may lead to physician attrition from the state. Conclusion" Prior to the reversal of federal protections for abortion in 2022, OB/GYNs in Ohio and other abortion-hostile states experienced barriers to training in abortion care. In returning abortion regulation to the states, access to training is likely to be increasingly restricted. This research demonstrates how abortion-restrictions hamper physicians’ skills needed to care for patients, particularly in emergent situations. This puts patients at risk and places physicians in precarious ethical positions. Expanding protections and reducing restrictions on abortion will ensure OB/GYNs and trainees have the skills necessary to care for patients presenting for reproductive healthcare.
Embargo
Towards Greener Data Centers via Programmable Data Plane
(IEEE, 2023-06) Grigoryan, Garegin; Kwon, Minseok
The energy demands of data centers are increasing and are expected to grow exponentially. Reducing the energy consumption of data centers decreases operational expenses, as well as their carbon footprint. We design techniques to reduce data center power consumption by leveraging Software-Defined Networking (SDN) and programmable data plane concepts. Relying solely on in-data plane registers, our proposed system P4Green consolidates traffic in the least number of network switches and shifts workloads to the servers with the available renewable energy. Unlike existing SDN-based solutions, P4Green’s operation does not depend on a centralized controller, making the system scalable and failure-resistant. Our proof-of-concept simulations show that traffic consolidation can reduce data centers’ aggregation switch usage by 36% compared to standard data center load balancing techniques, while workload control can boost renewable energy consumption for 46% of the daily traffic.
Embargo
Words, Like Viruses, Spill Over. Consider “Porn.”
(Taylor & Francis, 2023-10) Myers, Robert

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