Digital Commons Network^™

Integrating Clinical Cancer And Ptm Proteomics Data Identifies A Mechanism Of Ack1 Kinase Activation, Eranga R. Balasooriya, Deshan Madhusanka, Tania P. López-Palacios, Riley J. Eastmond, Dasun Jayatunge, Jake J. Owen, Jack S. Gashler, Christina M. Egbert, Chanaka Bulathsinghalage, Lu Liu, Stephen R. Piccolo, Joshua L. Andersen

Faculty Publications

Beyond the most common oncogenes activated by mutation (mut-drivers), there likely exists a variety of low-frequency mut-drivers, each of which is a possible frontier for targeted therapy. To identify new and understudied mut-drivers, we developed a machine learning (ML) model that integrates curated clinical cancer data and posttranslational modification (PTM) proteomics databases. We applied the approach to 62,746 patient cancers spanning 84 cancer types and predicted 3,964 oncogenic mutations across 1,148 genes, many of which disrupt PTMs of known and unknown function. The list of putative mut-drivers includes established drivers and others with poorly understood roles in cancer. This ML …

Geographic Differences In The Magnitude Of Black-White Disparities In Having Obesity, Steven A. Cohen, Monique J. Brown, Furong Xu, Caitlin C. Nash, Mary L. Greaney

Faculty Publications

Background

Obesity disparities in the United States are well documented, but the limited body of research suggests that geographic factors may alter the magnitude of these disparities. A growing body of evidence has identified a “rural mortality penalty” where morbidity and mortality rates are higher in rural than urban areas, even after controlling for other factors. Black-White differences in health and mortality are more pronounced in rural areas than in urban areas.

Objective

Therefore, the purpose of this study was to explore how rural-urban status and region moderate Black-White health disparities in obesity.

Methods

Data were abstracted from the 2012 …

Understanding Commitment Of Local Food Banks, Faith-Based Organizations, And Schools To Provide Nongovernment Food Programs, Eliza M. Fishbein, Edward A. Frongillo Ph.D., Sharraf Samin, Audrey L. Richards, Christine E. Blake Ph.D., Rd, Ruth P. Saunders, Cheri J. Shapiro

Faculty Publications

Background: Nongovernment food assistance is typically provided to families by faith-based organizations, schools, and food banks. Community organizations appear to be strongly committed to these programs, but little is known about the basis for this commitment. Objectives: The aim of this study was to examine the values and identities of community organizations to understand the reasons for their commitment to providing nongovernment food assistance. Methods: Thirty-three in-depth interviews were conducted with 36 leaders at faith-based organizations (19 participants), schools (14 participants), and a local food bank (3 participants) in South Carolina. Observations were made, and informational documents (e.g., flyers and …

Lightning Forecast From Chaotic And Incomplete Time Series Using Wavelet De-Noising And Spatiotemporal Kriging, Jared K. Nystrom, Raymond Hill, Andrew J. Geyer, Joseph J. Pignatiello Jr., Eric Chicken

Faculty Publications

Purpose: Present a method to impute missing data from a chaotic time series, in this case lightning prediction data, and then use that completed dataset to create lightning prediction forecasts.

Design/Methodology/Approach: Using the technique of spatiotemporal kriging to estimate data that is autocorrelated but in space and time. Using the estimated data in an imputation methodology completes a dataset used in lighting prediction.

Findings: The techniques provided prove robust to the chaotic nature of the data, and the resulting time series displays evidence of smoothing while also preserving the signal of interest for lightning prediction.

Abstract © Emerald Publishing …

Friction-In-Design Regulation As 21st Century Time, Place, And Manner Restriction, Brett Frischmann, Susan Benesch

Faculty Publications

Digital networked society needs friction-in-design regulation that targets the digital architectures, supposedly smart (data-driven, algorithmic) systems, and interfaces that shape human interactions, behavior, and will (beliefs, preferences, values, intentions). The relentless push to eliminate friction for the sake of efficiency has hidden social costs that affect basic human capabilities and society. A general course correction is needed.

Friction in the digital networked environment can come in many forms. It can be as simple as a time delay prior to publishing a social media post, a notice that provides salient information coupled with a nudge toward actual deliberation, or a query …

Conservative Estimation Of Inertial Sensor Errors Using Allan Variance Data, Kyle A. Lethander, Clark N. Taylor

Faculty Publications

To understand the error sources present in inertial sensors, both the white (time-invariant) and correlated noise sources must be properly characterized. To understand both sources, the standard approach (IEEE standards 647-2006, 952-2020) is to compute the Allan variance of the noise and then use human-based interpretation of linear trends to estimate the separate noise sources present in a sensor. Recent work has sought to overcome the graphical nature and visual-inspection basis of this approach leading to more accurate noise estimates. However, when using noise characterization in a filter, it is important that the noise estimates be not only accurate but …

Called To The Work Of Studying, John C. Peckham

Faculty Publications

No abstract provided.

Love God With All Your Mind, John C. Peckham

Faculty Publications

No abstract provided.

A Life-Changing Witness, Denis Fortin

Faculty Publications

No abstract provided.

Editorial: An Unexpected Event Related To The Aquatic Mammals Of Latin America, Daniel Gonzalez-Socoloske

Faculty Publications

No abstract provided.

Deconstructing The Software Factory: A Practical Application Of Interorganizational Network Analysis, Zachary O. Ryan, Mark Reith, Clay Koschnick

Faculty Publications

Over the past 5 years, the number of DoD software organizations that employ nontraditional organizational structures has increased. These organizations, commonly referred to as software factories, often employ the network-based organizational structures found within high-technology industries. This article details ways in which network analysis techniques can be used to create a big picture view of these nontraditional organizations. Drawing on methodologies employed by network researchers, the authors develop and present an interorganizational analysis process that highlights a program's social and economic structures. Following the case history approach, they demonstrate the applicability of this approach by analyzing an emergent DoD software …

Weakly Forced Thunderstorms In The Southeast Us Are Stronger Near Urban Areas, P. Miller, N. Debbage

Faculty Publications

While cities are well documented to enhance precipitation through the urban rainfall effect (URE), the distinguishing characteristics of urban-influenced storms that help establish the URE are poorly understood. The purpose of this study is to examine the morphological traits (i.e., size, duration, intensity, etc.) and near-storm environmental conditions of weakly forced thunderstorms (WFTs) occurring near urban areas in the Southeast US relative to storms forming in surrounding rural areas. Urban WFTs are found to have higher reflectivities, are more likely to contain hail, and produce more lightning than nearby non-urban storms, but their sizes and shapes are statistically indistinguishable. When …

Evaluating A Large Language Model’S Ability To Solve Programming Exercises From An Introductory Bioinformatics Course, Stephen R. Piccolo, Paul Denny, Andrew Luxton-Reilly, Samuel H. Payne, Perry G. Ridge

Faculty Publications

Life scientists frequently write computer code when doing research. Computer programming can aid researchers in performing tasks that are not supported by existing tools. Programming can also help researchers to implement analytical logic in a way that documents their steps and thus enables others to repeat those steps. Many educational resources are available to teach computer programming, but this skill remains challenging for many researchers and students to master. Artificial-intelligence tools like OpenAI’s ChatGPT are able to interpret human-language requests to generate code. Accordingly, we evaluated the extent to which this technology might be used to perform programming tasks described …

Video Based Estimation Of Surface Currents In A Tidal Inlet, Benjamin Middour, George Voulgaris, Douglas Cahl

Faculty Publications

Oceanic surface currents are estimated from analysis of short duration video obtained by a nadir facing camera installed on a bridge over a tidal inlet. Data analyzed consisted of 13 two-minute video clips captured approximately every 40 min over a period of 8 hr, covering a significant portion of the tidal cycle. Surface current speed and direction estimates are obtained from each collected video using (i) a method originally developed for analysis of imagery from drones (CopterCurrents) and (ii) a particle tracking method. The horizontal (u, v) surface current velocity components and total horizontal velocity magnitude, obtained from the two …

Streamlining The Detection Of Human Thyroid Receptor Ligand Interactions With Xl1-Blue Cell-Free Protein Synthesis And Beta-Galactosidase Fusion Protein Biosensors, J. Porter Hunt, Tyler J. Free, Jackelyn Galiardi, Kevin M. Watt, David W. Wood, Bradley Charles Bundy

Faculty Publications

Thyroid receptor signaling controls major physiological processes and disrupted signaling can cause severe disorders that negatively impact human life. Consequently, methods to detect thyroid receptor ligands are of great toxicologic and pharmacologic importance. Previously, we reported thyroid receptor ligand detection with cell-free protein synthesis of a chimeric fusion protein composed of the human thyroid receptor beta (hTRβ) receptor activator and a β-lactamase reporter. Here, we report a 60% reduction in sensing cost by reengineering the chimeric fusion protein biosensor to include a reporter system composed of either the full-length beta galactosidase (β-gal), the alpha fragment of β-gal (β-gal-α), or a …

Examining Cancer Patients' Perceptions Of The Impact Of Covid-19 On Teleoncology: Findings From 15 Nigerian Outpatient Cancer Clinics, Adedayo Joseph, Abdul R. Shour, Nwamaka N. Lasebikan, Mutiu A. Jimoh, Bolanle C. Adegboyega, Emmanuella Nwachukwu, Opeyemi Awofeso, Azeezat Ajose, Abiola Ibraheem, Omolara Aminat Fatiregun, Musa Ali-Gombe, Usman M. Aliyu, Abdallah Elsaid Kotkat, Olusegun Abayomi Biyi-Olutunde, Evaristus Oseiwe Oboh, Ismail H. Zubairu, Mohammad Rifat Haider, Bankole Olatosi Ph.D., David Puthoff, Adedayo A. Onitilo

Faculty Publications

Purpose

To examine cancer patients' perspectives on the impact of COVID-19 on teleoncology in Nigeria.

Methods

Data from a multicenter survey conducted at 15 outpatient clinics to 1,097 patients with cancer from April and July 2020 were analyzed. The study outcome was telemedicine, defined as patients who reported their routine follow-up visits were converted to virtual visits because of COVID-19 (coded yes/no). Covariates included patient age, ethnicity, marital status, income, cancer treatment, service disruption, and cancer diagnosis/type. Stata/SE.v.17 (StataCorp, College Station, TX) was used to perform chi-square and logistic regression analyses. P values ≤ .05 were considered statistically significant.

Results …

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Quantification Of Solution-Free Red Blood Cell Staining By Sorption Kinetics Of Romanowsky Stains To Agarose Gels, Chae Yun Bae, Hamid Esmaeili, Syed A. Zamin, Min Jeong Seol, Eunmi Hwang, Suk Kyung Beak, Younghoon Song, Bhuvnesh Bharti, Jangwook P. Jung

Faculty Publications

The imaging and quantification of stained red blood cells (RBCs) are important for identifying RBCs in hematology and for diagnosing diseased RBCs or parasites in cytopathology. Romanowsky staining has been used traditionally to produce hues in blood cells using a mixture of anionic eosin Y and cationic methylene blue and azure B. While Romanowsky stains have been widely used in cytopathology, end-users have experienced problems with varying results in staining due to the premature precipitation or evaporation of methanol, leading to the inherent inconsistency of solution-based Romanowsky staining. Herein, we demonstrate that the staining and destaining of blood smears are …

Learning Experience Design As An Orienting Guide For Practice: Insights From Designing For Expertise, Jason K. Mcdonald, Tyler J. Westerberg

Faculty Publications

In this paper we consider how learning experience design (LXD) improves designers’ capacities to influence learning. We do this by exploring what LXD offers the design of learning environments that help develop learners’ expertise. We discuss how LXD (a) attunes designers to different learning affordances than are emphasized in traditional ID; (b) challenges the universal applicability of common ID techniques; and (c) expands designers’ views of the outcomes for which they can design. These insights suggest that LXD is useful because it refocuses and reframes designers' work around flexible design approaches that are often deemphasized in traditional ID.

What's All The Fuss About Pickleball? Motivational Profiles Of Middle Age And Older Adult Recreational Pickleball Players, David C. Barney, Zack E. Beddoes, Keven A. Prusak, Brandon Weekes

Faculty Publications

As a person becomes older their physical activity options may change or be reduced. One activity that is proving differently among older adults is pickleball. As of 2022 over 3.1 million people in the United States participate in pickleball (USAPA Pickleball, 2022). From the casual observer, many recreational tennis courts have been modified to accommodate the increase of pickleball players. Also, many of these pickleball players are older (40 +). Thus, the purpose of this study was to investigate the motivational profiles of 40 and older adults towards playing pickleball. Generally, it was learned that 40 and older adults participate …

Greater Male Variability In Daily Energy Expenditure Develops Through Puberty, Lewis G. Halsey, Vincent Careau, Philip N. Ainslie, Heliodoro Alemán-Mateo, Lene F. Andersen, Liam J. Anderson, Leonore Arab, Issad Baddou, Linda Bandini, Kweku Bedu-Addo, Ellen E. Blaak, Stephane Blanc, Alberto G. Bonomi, Carlijn V.C. Bouten, Pascal Bovet, Soren Brage, Maciej S. Buchowski, Nancy Butte, Stephan G. Camps, Regian Casper, Graeme L. Close, Lisa H. Colbert, Jamie A. Cooper, Richard Cooper, Prasangi Dabare, Sai Krupa Das, Peter S.W. Davies, Sanjoy Deb, Christine Delisle Nyström, William Dietz, Lara R. Dugas, Simon Eaton, Ulf Ekelund

Faculty Publications

There is considerably greater variation in metabolic rates between men than between women, in terms of basal, activity and total (daily) energy expenditure (EE). One possible explanation is that EE is associated with male sexual characteristics (which are known to vary more than other traits) such as musculature and athletic capacity. Such traits might be predicted to be most prominent during periods of adolescence and young adulthood, when sexual behaviour develops and peaks. We tested this hypothesis on a large dataset by comparing the amount of male variation and female variation in total EE, activity EE and basal EE, at …

Improving Behavior In An Alternative High School Summer Program Using Class‑Wide Function‑Related Intervention Teams: A Pilot Study, Paul Caldarella, Erika J. Richards, Leslie Williams, Emily J. Warburton

Faculty Publications

Effective interventions are needed to help alternative high school teachers manage challenging student behaviors. One such intervention, class-wide function-related intervention teams (CWFIT), is a classroom management program based on positive behavior interventions and supports principles. CW-FIT involves teaching appropriate classroom behavioral expectations (social skills), using high behavior-specific praise-to-reprimand ratios, and an interdependent group contingency to provide differential reinforcement of appropriate classroom behavior and eliminate potential reinforcement of problem behavior. In this pilot study, four alternative high school teachers implemented CW-FIT during a summer school program. A series of single subject A-B designs were used over a 3-week period. Results supported …

A Probabilistic View Of Protein Stability, Conformational Specificity, And Design, Jacob A. Stern, Tyler J. Free, Kimberlee L. Stern, Spencer Gardiner, Nicholas A. Dalley, Bradley Charles Bundy, Joshua L. Price, David Wingate, Dnnis Della Corte

Faculty Publications

Various approaches have used neural networks as probabilistic models for the design of protein sequences. These "inverse folding" models employ different objective functions, which come with trade-offs that have not been assessed in detail before. This study introduces probabilistic definitions of protein stability and conformational specificity and demonstrates the relationship between these chemical properties and the p(stucture|seq) Boltzmann probability objective. This links the Boltzmann probability objective function to experimentally verifiable outcomes. We propose a novel sequence decoding algorithm, referred to as “BayesDesign”, that leverages Bayes’ Rule to maximize the p(stucture|seq) objective instead of the p(seq|structure) objective common in inverse folding …

Influencing Air Force Logisticians' Information Seeking During The Covid-19 Pandemic: The Role Of Organizational Meetings In An Expanded Prism Framework, Matthew D. Roberts, Christopher T. Price, Seong-Jong Joo

Faculty Publications

Purpose: This research aims to understand how organizational workplace meetings surrounding the COVID-19 pandemic impacted logistics Airmen across the United States Air Force and how these meetings impacted their risk seeking behavior on social media.

Design/methodology/approach: This survey research tested an extended Planned Risk Information Risk Seeking Model (PRISM) with organizational meetings as an antecedent to determine if current meetings influenced an Airman's perceived behavioral control, attitude toward seeking, subjective norms, knowledge sufficiency and intention to seek information regarding COVID-19.

Findings: Results of the CFA showed that the expanded PRISM model had good model fit. Additionally, using …

End Block Dynamics In Unentangled Polymers By Dielectric Spectroscopy, Mengchun Wu, Karin J. Bichler, Bruno Jakobi, Alyssa Grzesiowski, Gerald J. Schneider

Faculty Publications

Dielectric spectroscopy measures the dynamics of polymer melts over a broad frequency range. Developing a theory for the spectral shape can extend the analysis of dielectric spectra beyond determining relaxation times from the peak maxima and adds physical meaning to shape parameters determined with empirical fit functions. Toward this goal, we use the experimental results on unentangled poly(isoprene), and unentangled poly(butylene oxide), polymer melts, to test whether the concept of end blocks could be one reason for the Rouse model deviating from experimental data. These end blocks have been suggested by simulations and neutron spin echo spectroscopy and are a …

Precision E- Beam Polarimetry At An E-E+ B Factory Using Tau-Pair Events, J. P. Lees, V. Poireau, V, Tisserand, E. Grauges, A. Palano, G. Eigen, D. N. Brown, Yu. G. Kolomensky, M. Fritsch, H. Koch, R. Cheaib, C. Hearty, T. S. Mattison, J. A. Mckenna, R. Y. So, V. E. Blinov, A. R. Buzykaev, V. P. Druzhinin, Milind Purohit, Et. Al.

Faculty Publications

We present a new technique, “tau polarimetry,” for measuring the longitudinal beam polarization present in an e⁺e⁻ collider through the analysis of e⁺e⁻ → τ⁺τ⁻ events. By exploiting the sensitivity of τ decay kinematics to the longitudinal polarization of the beams, we demonstrate that the longitudinal polarization can be measured with a 3 per mil systematic uncertainty at the interaction point using a technique that is independent of spin and beam transport modeling. Using 424.2 ± 1.8 fb⁻¹ of BABAR data at √ s = 10.58 GeV, the average longitudinal …

Do Denisonians Have Wild Perceptions Of Who Faces Discrimination, Too?, Paul A. Djupe

Faculty Publications

No abstract provided.

Risks From Spacecraft Breakup Events In Near Rectilinear Halo Orbits, Nathan R. Boone, Robert A. Bettinger, Bryan D. Little

Faculty Publications

Spacecraft breakup events were simulated in the vicinity of the Lunar Gateway’s Near Rectilinear Halo Orbit to evaluate the risk of debris collision with the station. The Monte Carlo simulations model the breakup of an object shortly after deployment from the Gateway, and using the propagated trajectories of over a million particles across 5,000 random breakup events, the likelihood of collision with the Gateway is statistically evaluated. Approaches within 10 km were observed for only 2.4% of the breakup events, suggesting a low risk of collision, but approaches at larger distances that might still generate a debris avoidance maneuver were …

Recent Breakthroughs In Using Quantum Dots For Cancer Imaging And Drug Delivery Purposes, Aisha Hamidu, William G. Pitt, Ghaleb A. Husseini

Faculty Publications

Cancer is one of the leading causes of death worldwide. Because each person’s cancer may be unique, diagnosing and treating cancer is challenging. Advances in nanomedicine have made it possible to detect tumors and quickly investigate tumor cells at a cellular level in contrast to prior diagnostic techniques. Quantum dots (QDs) are functional nanoparticles reported to be useful for diagnosis. QDs are semiconducting tiny nanocrystals, 2–10 nm in diameter, with exceptional and useful optoelectronic properties that can be tailored to sensitively report on their environment. This review highlights these exceptional semiconducting QDs and their properties and synthesis methods when used …

Young Adults’ Cohabitation And Dating Decisions During The Covid-19 Pandemic: A Qualitative Exploration Of Romantic And Developmental Context, Tyler B. Jamison, Jeremy B. Kanter

Faculty Publications

The COVID-19 pandemic caused significant upheaval for couples and families, particularly in terms of living arrangements. Emerging adults had to make quick decisions about where and with whom to shelter in place. In this grounded theory study, we explored how 22 young adults, predominantly living in the United States, navigated relationship decisions during the pandemic. The results suggest that participants were intentional about their choices, particularly in terms of moving in together (or not). The pandemic sometimes changed the timing of cohabitation or the pace of dating relationships; however, these decisions unfolded in tandem with common developmental tasks, such as …

Synthesis, Crystal And Electronic Structure Of The Zintl Phase Ba16sb11. A Case Study Uncovering Greater Structural Complexity Via Monoclinic Distortion Of The Tetragonal Ca16sb11 Structure Type., Sviatoslav Baranets, Alexander Ovchinnikov, S. M.Gayomi K. Samarakoon, Svilen Bobev

Faculty Publications

The binary Zintl phase Ba16Sb11 has been synthesized and structurally characterized. Detailed studies via single-crystal X-ray diffraction methods indicate that although Ba16Sb11 appears to crystallize in the tetragonal Ca16Sb11 structure type (space group P (Figure presented.) 21m with a=13.5647(9) Å, c=12.4124(12) Å, Z=2, R1=3.14 %; wR2=4.77 %), there exists an extensive structural disorder. Some Ba16Sb11 crystals were found to be monoclinic and the structure was solved and refined in space group P21 (a=18.3929(12) Å, b=13.5233(8) Å, c=18.3978(12) Å, β=94.6600(10)°; Z=4, R1=5.84 %; wR2=9.58 %). The latter corresponds to a 2-fold superstructure of the tetragonal one, which provides a disorder-free structural …