Digital Commons Network^™

Yeast Rad52 Is A Homodecamer And Possesses Brca2-Like Bipartite Rad51 Binding Modes, Jaigeeth Deveryshetty, Rahul Chadda, Jenna R Mattice, Simrithaa Karunakaran, Michael J Rau, Katherine Basore, Nilisha Pokhrel, Noah Englander, James A J Fitzpatrick, Brian Bothner, Edwin Antony

2020-Current year OA Pubs

Homologous recombination (HR) is an essential double-stranded DNA break repair pathway. In HR, Rad52 facilitates the formation of Rad51 nucleoprotein filaments on RPA-coated ssDNA. Here, we decipher how Rad52 functions using single-particle cryo-electron microscopy and biophysical approaches. We report that Rad52 is a homodecameric ring and each subunit possesses an ordered N-terminal and disordered C-terminal half. An intrinsic structural asymmetry is observed where a few of the C-terminal halves interact with the ordered ring. We describe two conserved charged patches in the C-terminal half that harbor Rad51 and RPA interacting motifs. Interactions between these patches regulate ssDNA binding. Surprisingly, Rad51 …

Immune Cell Deconvolution Reveals Possible Association Of Γδ T Cells With Poor Survival In Head And Neck Squamous Cell Carcinoma, Anuraag S Parikh, Yize Li, Angela Mazul, Wade Thorstad, Jason Rich, Randal C Paniello, Ryan S Jackson, Patrik Pipkorn, Paul Zolkind, Zongtai Qi, Douglas Adkins, Li Ding, Sidharth V Puram, Et Al.

2020-Current year OA Pubs

(1) Background: The role of rare immune cell subtypes in many solid tumors, chief among them head and neck squamous cell carcinoma (HNSCC), has not been well defined. The objective of this study was to assess the association between proportions of common and rare immune cell subtypes and survival outcomes in HNSCC. (2) Methods: In this cohort study, we utilized a deconvolution approach based on the CIBERSORT algorithm and the LM22 signature matrix to infer proportions of immune cell subtypes from 517 patients with untreated HPV-negative HNSCC from The Cancer Genome Atlas. We performed univariate and multivariable survival analysis, integrating …

Sars-Cov-2: Tale Of A Microscopic Murderer, Josiah P. Garner

Quest

Independent Study

Research in progress for BIOL1406: Biology for Science Majors I

Faculty Mentor: Amina Tassa, Ph.D.

I am delighted to introduce Josiah Garner’s “SARS-CoV-2: Tale of a Microscopic Murderer.” This independent study assignment explores the impact of a novel, deadly, and worldwide virus. The assignment also examines the fast development of vaccines to control the spread and reduce the symptoms of the virus.

Josiah’s paper focuses on the early history of the emergence of COVID-19, the world response, and vaccine development. He demonstrates critical thinking skills and effectively utilizes various research methods to obtain and communicate his information. Josiah …

Teaching Science To Students With Disabilities Using Socio-Scientific Issues, Rachel Juergensen, Laura Zangori, Pat Friedrichsen, Troy D. Sadler

Journal of Science Education for Students with Disabilities

Students with disabilities experience inequitable learning opportunities in science classrooms. To create equitable learning environments, science teachers must embed supports within their curriculum units. Teachers rely on their beliefs about the capabilities of their students, their role as science teachers, and the goals of science education to adapt their curriculum units. Curricular changes occur through their pedagogical design capacity (PDC) during lesson planning and enactments, in which their beliefs inform their PDC choices. Yet there is little research regarding science teachers’ beliefs about teaching students with disabilities and how they enact their science curriculum materials in general education science classrooms. …

Confusion Matrix In Three-Class Classification Problems: A Step-By-Step Tutorial, Mahmoud Fahmy Amin

Journal of Engineering Research

The confusion matrix is a specific table used in machine learning to describe and assess the performance of a classification model (e.g., an artificial neural network) for a set of test data whose actual distinguishing features are known. The confusion matrix for an n-class classification problem is square, with n rows and n columns. The rows represent the class actual samples (instances), which are the classifier inputs, and the columns represent the class predicted samples, which are the classifier outputs. Binary class classifiers have been presented in a previous paper, where in this paper, we are concerned with three-class classification …

Extraction Of Blood Vessels Geometric Shape Features With Catheter Localization And Geodesic Distance Transform For Right Coronary Artery Detection., Ahmed Hawas

Journal of Engineering Research

X-ray angiography is considered the standard imaging sensory system for diagnosing coronary artery diseases. For automated, accurate diagnosis of such diseases, coronary vessels’ detection from the captured low quality and noisy angiography images is challenging. It is essential to detect the main branch of the coronary artery, to resolve such limitations along with the problems due to the sudden changes in the lumen diameter, and the abrupt changes in local artery direction. Accordingly, this paper solved these limitations by proposing a computer-aided detection system for the right coronary artery (RCA) extraction, where geometric shape features with catheter localization and geodesic …

Nanoparticles Additives For Diesel/Biodiesel Fuel Blends As A Performance And Emissions Enhancer In The Applications Of Direct Injection Diesel Engines: A Comparative Review, Medhat Elkelawy

Journal of Engineering Research

Nanomaterials (NMs) like copper oxides, titanium oxides, and aluminum oxides have been developing into some of the most promising fuel additives for diesel engines in recent years. in order to create a practical nano fuel. A significant amount of laboratory testing has been conducted up to this point to investigate the impact of using nano fuels on several aspects of diesel engine characteristics, particularly on hazardous emissions and engine performance (brake specific fuel consumption, effective power, brake thermal efficiency). This study provides an overview of the findings so far and the current situation regarding the use of nano fuels in …

Pneumatic Artificial Muscles (Pams) Identification For Actuating A Wrist-Joint Rehabilitation Robot, Omer Omer

Journal of Engineering Research

Pneumatic Artificial Muscles (PAMs) are the most promising type of pneumatic-based actuators. Recently, they have been widely used in medical and rehabilitation robotic systems due to their flexibility, reliability, and high load-to-weight ratio. The aim of this work is to introduce an accurate mathematical model for describing the performance of the pneumatic artificial muscles under different applied pressures and loads by examining different previously proposed models. Being motivated by the muscles’ usage in a wearable robotic device for wrist rehabilitation where the required muscle force is not so large, it is interesting to consider the model that best expresses the …

Evaluation Of Different Atmospheric Correction ‎Methods Prior To The Estimation Of Total Dissolved ‎Solids Concentrations From Satellite Imagery, Ahmed Aboelnaga

Journal of Engineering Research

Surface water quality is degraded by the presence of numerous types of pollution produced by anthropogenic activities. Hence, surface water quality monitoring and assessment is essential. Conventional approaches of surface water quality monitoring are costly, time-consuming, and labor-intensive. On the other hand, remote sensing is an effective tool for monitoring surface water quality. Satellite images should be atmospherically corrected prior to using them in the estimation of surface water quality parameters (SWQPs). Therefore, The purpose of this study is to evaluate the outputs from several atmospheric correction methods, such as Dark Object Subtraction (DOS), Quick Atmospheric Correction (QUAC), Fast Line …

How Can Transformational Leadership Be Unbound From The Gender Binary Paradigm?, Jody Condit Fagan, Michelle Hamilton-Page

Libraries

Disrupting binary conceptions of gender could be one of the most needed paradigmatic shifts in leadership studies. Nonbinary leadership paradigms can liberate people of all genders from a framework that forces them to describe their leader behaviors as aligned with or transgressive of a binary gender. Academic leadership studies has generally focused on differences between men and women and discrimination against women, with trans and nonbinary gender identities notably absent. Traditional models of leadership need to be interrogated to see if they hold up under a nonbinary lens. In this presentation, we will examine two dimensions of the iconic model …

Reimagining Large River Management Using The Resist–Accept–Direct (Rad) Framework In The Upper Mississippi River, Nicole K. Ward, Abigail J. Lynch, Erik A. Beever, Joshua Booker, Kristen L. Bouska, Holly Embke, Jeffrey N. Houser, John F. Kocik, David J. Lawrence, Mary Grace Lemon, Doug Limpinsel, Madeline R. Magee, Bryan M. Maitland, Owen Mckenna, Andrew Meier, John M. Morton, Jeffrey D. Muehlbauer, Robert Newman, Devon C. Oliver, Heidi M. Rantala, Greg G. Sass, Aaron Shultz, Laura M. Thompson, Jennifer L. Wilkening

Biology Faculty Publications

Background Large-river decision-makers are charged with maintaining diverse ecosystem services through unprecedented social-ecological transformations as climate change and other global stressors intensify. The interconnected, dendritic habitats of rivers, which often demarcate jurisdictional boundaries, generate complex management challenges. Here, we explore how the Resist–Accept–Direct (RAD) framework may enhance large-river management by promoting coordinated and deliberate responses to social-ecological trajectories of change. The RAD framework identifies the full decision space of potential management approaches, wherein managers may resist change to maintain historical conditions, accept change toward different conditions, or direct change to a specified future with novel conditions. In the Upper Mississippi …

The Rattler (Volume 112, Issue 2), St. Mary's University

The Rattler (Previous issues)

Founded in 1919, The Rattler is the student voice of St. Mary’s University in San Antonio, Texas. The newspaper documents campus life, academic and social issues, student opinion, and local and national events as they relate to the University community. Content typically includes news articles, editorial commentary, arts and culture coverage, sports reporting, and advertisements.

October 4, 2023 Greenmail, University Of Alabama At Birmingham

GreenMail (student newsletter through 2024)

No abstract provided.

Biochemical Pathways Represented By Gene Ontology-Causal Activity Models Identify Distinct Phenotypes Resulting From Mutations In Pathways., David P. Hill, Harold J. Drabkin, Cynthia Smith, Kimberly M Van Auken, Peter D'Eustachio

Faculty Research 2023

Gene inactivation can affect the process(es) in which that gene acts and causally downstream ones, yielding diverse mutant phenotypes. Identifying the genetic pathways resulting in a given phenotype helps us understand how individual genes interact in a functional network. Computable representations of biological pathways include detailed process descriptions in the Reactome Knowledgebase and causal activity flows between molecular functions in Gene Ontology-Causal Activity Models (GO-CAMs). A computational process has been developed to convert Reactome pathways to GO-CAMs. Laboratory mice are widely used models of normal and pathological human processes. We have converted human Reactome GO-CAMs to orthologous mouse GO-CAMs, as …

The College Voice, Vol. 58, No. 2 [October 4, 2023], Connecticut College

2023-2024

No abstract provided.

Validation Of Automated Data Abstraction For Sccm Discovery Virus Covid-19 Registry: Practical Ehr Export Pathways (Virus-Peep), Diana J. Valencia Morales, Vikas Bansal, Smith F. Heavner, Janna C. Castro, Mayank Sharma, Aysun Tekin, Marija Bogojevic, Simon Zec, Nikhil Sharma, Rodrigo Cartin-Ceba, Rahul S. Nanchal, Devang K. Sanghavi, Abigail T. La Nou, Syed A. Khan, Katherine A. Belden, Jen-Ting Chen, Roman R. Melamed, Imran A. Sayed, Ronald A. Reilkoff, Vitaly Herasevich, Juan Pablo Domecq Garces, Allan J. Walkey, Karen Boman, Vishakha K. Kumar, Rahul Kashyap

Division of Infectious Diseases and Environmental Medicine Faculty Papers

BACKGROUND: The gold standard for gathering data from electronic health records (EHR) has been manual data extraction; however, this requires vast resources and personnel. Automation of this process reduces resource burdens and expands research opportunities.

OBJECTIVE: This study aimed to determine the feasibility and reliability of automated data extraction in a large registry of adult COVID-19 patients.

MATERIALS AND METHODS: This observational study included data from sites participating in the SCCM Discovery VIRUS COVID-19 registry. Important demographic, comorbidity, and outcome variables were chosen for manual and automated extraction for the feasibility dataset. We quantified the degree of agreement with Cohen's …

The Effects Of A High-Carbohydrate Versus A High-Fat Shake On Biomarkers Of Metabolism And Glycemic Control When Used To Interrupt A 38-Hour Fast: A Randomized Crossover Study, Landon S. Deru

Theses and Dissertations

Purpose: The primary aim of this study was to determine the impact of various fast-interrupting shakes on markers of glycemic control including glucose, β-hydroxybutyrate (BHB), insulin, glucagon, GLP-1, and GIP. Methods: Twenty-seven adults (12 female, 15 male) completed all three conditions of this study. One condition consisted of a 38-hour water-only fast, and the other two conditions were similar but the fasts were interrupted at 24 hours by either a high carbohydrate/low fat (HC/LF) or a low carbohydrate/high fat (LC/HF) shake. Results: The water only fast resulted in 135.3% more BHB compared to the HC/LF condition (t = 7.77, p < 0.0001) and 69.6% more compared to the LC/HF condition (t = 5.12, p < 0.0001). Conversely, the LC/HF condition exhibited a 38.8% higher BHB level than the HC/LF condition (t = 2.70, p = 0.0086). Additionally, the area under the curve (AUC) for glucose was 14.2% higher in the HC/LF condition than in the water condition (t = 6.23, p < 0.0001) and 6.9% higher compared to the LC/HF condition (t = 3.14, p = 0.0024), with the LC/HF condition yielding 7.8% more glucose than the water condition (t = 3.21, p = 0.0020). At the 25-hour mark, insulin and glucose-dependent insulinotropic polypeptide (GIP) were significantly elevated in the HC/LF condition compared to the LC/HF condition (F = 3.84, p = 0.0002 and F = 2.27, p = 0.0244, respectively) and compared to the water condition (F = 7.00, p < 0.0001 and F = 9.96, p < 0.0001, respectively). Furthermore, insulin, glucagon-like peptide-1 (GLP-1), and GIP were increased in the LC/HF condition compared to the water condition at 25 hours (F = 3.19, p = 0.0016, F = 2.43, p = 0.0158, and F = 12.13, p < 0.0001, respectively). Notably, glucagon concentrations at the 25-hour mark decreased in the HC/LF group compared to the LC/HF condition (F = 3.37, p = 0.0009). However, by the 38-hour time point, no statistically significant differences were observed among the conditions for any of the analyzed hormones. Conclusions: While a LC/HF shake does not mimic a fast completely, it does preserve some of the metabolic changes including elevated BHB and glucagon, and decreased glucose and insulin compared to a HC/LF shake.

October 4, 2023 Faculty Senate Minutes, University Of South Carolina

Faculty Senate

No abstract provided.

2023-10-04 The Cost Of Living Places Financial Burden On Seattle Students, Amelia Carey

The Spectator Online

No abstract provided.

Commonwealth Times 2023-10-04

Commonwealth Times, 1969-

No abstract provided.

Chapter Viii — Derailed Modernization: The Derg’S Phase, Messay Kebede

Ethiopian Modernization: Opportunities and Derailments

The cultural trait making higher social positions into contested temporary occupations (see Chapter III on idil) should have found, in the modernization process of evicting outdated, anti-modern occupants, an even better opportunity to vent itself. In the traditional system, power struggles opposed ambitious individuals who shared common values and a mutual understanding of social life. The struggle did not go beyond the act of changing places in a fixed social framework. However, as a result of the impact of exogenous modern ideas, the struggle shifted to a confrontation between elites with different ideologies and social programs. These elites want to …

Leveraging Osteoclast Genetic Regulatory Data To Identify Genes With A Role In Osteoarthritis., Benjamin H. Mullin, Kun Zhu, Suzanne J. Brown, Shelby Mullin, Frank Dudbridge, Nathan J. Pavlos, J Brent Richards, Elin Grundberg, Jordana T. Bell, Eleftheria Zeggini, John P. Walsh, Jiake Xu, Scott G. Wilson

Manuscripts, Articles, Book Chapters and Other Papers

There has been a growing interest in the role of the subchondral bone and its resident osteoclasts in the progression of osteoarthritis (OA). A recent genome-wide association study (GWAS) identified 100 independent association signals for OA traits. Most of these signals are led by noncoding variants, suggesting that genetic regulatory effects may drive many of the associations. We have generated a unique human osteoclast-like cell-specific expression quantitative trait locus (eQTL) resource for studying the genetics of bone disease. Considering the potential role of osteoclasts in the pathogenesis of OA, we performed an integrative analysis of this dataset with the recently …

Reiterated Empathy In Ba Director Training, Alex Cahill

School of Art, Design and Architecture

In 2019, the University of Plymouth started the only current BA Directing degree program in the United Kingdom. As programme creator/lead and curriculum designer, I was interviewed in 2021 by The Stage to discuss whether the craft of directing can be taught in a classroom. While some may argue the ‘director’s eye (that is – the mental ability to coherently visualise the whole production) cannot be taught, I argue that directing skills, specifically collaboration skills through reiterated empathy, can both be taught and should also be the basis of director training. Therefore, I created a series of exercises based on …

Functional Behaviour Of Flocs Explained By Observed 3d Structure And Porosity, Tj Lawrence, Sj Carr, Aj Manning, Jat Wheatland, Aj Bushby, Kl Spencer

School of Biological and Marine Sciences

Clay-rich flocculated suspended sediments are an important constituent of estuarine and coastal systems globally. They are responsible for the host, movement and deposition of a variety of pollutants, contaminants and sediment itself. Accurate modelling of the movement of these sediments is crucial for a number of industries including fisheries, aquaculture, shipping and waste management. This requires an accurate and reliable measurements of the physical properties of flocs and their behaviour. Porosity is a key element in floc structures, and this research provides updated 3D quantified porosity and pore space morphological data in relation to influences on floc settling behaviour. We …

Analysis And Prediction Of Liver Volume Change Maps Derived From Computational Tomography Scans Acquired Pre- And Post-Radiation Therapy, Guillaume Cazoulat, Aashish C Gupta, Mais M Al Taie, Eugene J Koay, Kristy K Brock

Faculty, Staff and Student Publications

External beam radiation therapy (EBRT) of liver cancers can cause local liver atrophy as a result of tissue damage or hypertrophy as a result of liver regeneration. Predicting those volumetric changes would enable new strategies for liver function preservation during treatment planning. However, understanding of the spatial dose/volume relationship is still limited. This study leverages the use of deep learning-based segmentation and biomechanical deformable image registration (DIR) to analyze and predict this relationship. Pre- and Post-EBRT imaging data were collected for 100 patients treated for hepatocellular carcinomas, cholangiocarcinoma or CRC with intensity-modulated radiotherapy (IMRT) with prescription doses ranging from 50 …

Detection Of Early Myocardial Dysfunction By Imaging Biomarkers In Cancer Patients Undergoing Photon Beam Vs Proton Beam Radiotherapy: A Prospective Study, Muhannad Aboud Abbasi, Giulia Bruno, Cristina Di Stefano, Laura Garcia Bello, Nadia N Laack, Kimberly S Corbin, Thomas J Whitaker, Patricia A Pellikka, Robert W Mutter, Hector R Villarraga

Faculty, Staff and Student Publications

1. Background: We sought to determine acute and subacute changes in cardiac function after proton beam (PBT) and photon beam (PhT) radiotherapy (RT) using conventional and two-dimensional speckle tracking echocardiography (2D-STE) in patients with malignant breast and thoracic tumors. 2. Methods: Between March 2016 and March 2017, 70 patients with breast or thoracic cancer were prospectively enrolled and underwent transthoracic echocardiography with comprehensive strain analysis at pretreatment, mid-treatment, end of treatment, and 3 months after RT. 3. Results: PBT was used to treat 44 patients; PhT 26 patients. Mean ± SD age was 55 ± 12 years; most patients (93%) …

Use Of Social Media For Information Sharing In The Management Of People Living With Hiv In Nigeria, Farida Sani Stores [email protected], Farida Sani Stores Dr, Farida Sani Stores Dr, Farida Sani Stores Dr

Library Philosophy and Practice (e-journal)

Abstract

The study investigates the use of Social Media for information sharing in the management of people living with HIV in Nigeria. The specific objectives of the study were to find out the information needs of the PLHIV, the sources of their information, the types of information shared and the challenges. The study had four research questions. A Cross-sectional research design was employed. Questionnaires and interview were the instruments used to collect the data. Four hundred (400) respondents were selected as the sample, The Director General; of the National Agency for the Control of AIDS was also interviewed. The quantitative …

Toni Novak Oral History, Toni Novak, Lorenzo Spaccarelli

Raymond College

No abstract provided.

Disrupted Stiffness Ratio Alters Nuclear Mechanosensing, Brandon K Walther, Adam P Sears, Anahita Mojiri, Reza Avazmohammadi, Jianhua Gu, Olga V Chumakova, Navaneeth Krishna Rajeeva Pandian, Abishai Dominic, Jean-Louis Martiel, Saami K Yazdani, John P Cooke, Jacques Ohayon, Roderic I Pettigrew

Faculty, Staff and Student Publications

The ability of endothelial cells to sense and respond to dynamic changes in blood flow is critical for vascular homeostasis and cardiovascular health. The mechanical and geometric properties of the nuclear and cytoplasmic compartments affect mechanotransduction. We hypothesized that alterations to these parameters have resulting mechanosensory consequences. Using atomic force microscopy and mathematical modeling, we assessed how the nuclear and cytoplasmic compartment stiffnesses modulate shear stress transfer to the nucleus within aging endothelial cells. Our computational studies revealed that the critical parameter controlling shear transfer is not the individual mechanics of these compartments, but the stiffness ratio between them. Replicatively …

Gut Microbiota Aggravates Neutrophil Extracellular Traps-Induced Pancreatic Injury In Hypertriglyceridemic Pancreatitis, Guanqun Li, Liwei Liu, Tianqi Lu, Yuhang Sui, Can Zhang, Yongwei Wang, Tao Zhang, Yu Xie, Peng Xiao, Zhongjie Zhao, Chundong Cheng, Jisheng Hu, Hongze Chen, Dongbo Xue, Hua Chen, Gang Wang, Rui Kong, Hongtao Tan, Xuewei Bai, Zhibo Li, Florencia Mcallister, Le Li, Bei Sun

Faculty, Staff and Student Publications

Hypertriglyceridemic pancreatitis (HTGP) is featured by higher incidence of complications and poor clinical outcomes. Gut microbiota dysbiosis is associated with pancreatic injury in HTGP and the mechanism remains unclear. Here, we observe lower diversity of gut microbiota and absence of beneficial bacteria in HTGP patients. In a fecal microbiota transplantation mouse model, the colonization of gut microbiota from HTGP patients recruits neutrophils and increases neutrophil extracellular traps (NETs) formation that exacerbates pancreatic injury and systemic inflammation. We find that decreased abundance of Bacteroides uniformis in gut microbiota impairs taurine production and increases IL-17 release in colon that triggers NETs formation. …