Digital Commons Network^™

October 5, 2023, The Daily Mississippian

Daily Mississippian (all digitized issues)

No abstract provided.

Local, National Talent To Sing The Blues At Annual Festival, Clara Turnage

University of Mississippi News

OXFORD, Miss. – The 12th annual Oxford Blues Festival will kick off three days of blues music with a free-to-the-public event at the University of Mississippi Blues Archive.

Spectator 2023-10-05, Editors Of The Spectator

The Spectator

No abstract provided.

Seasonally Optimized Calibrations Improve Low-Cost Sensor Performance: Long-Term Field Evaluation Of Purpleair Sensors In Urban And Rural India, Mark Joseph Campmier, Jonathan D. Gingrich, Saumya Singh, Nisar Baig, Shahzad Gani, Adithi Upadhya, Pratyush Agrawal, Meenakshi Kushwaha, Harsh Raj Mishra, Ajay Pillarisetti, Sreekanth Vakacherla, Ravi Kant Pathak, Joshua S. Apte

Faculty Work Comprehensive List

Lower-cost air pollution sensors can fill critical air quality data gaps in India, which experiences very high fine particulate matter (PM2.5) air pollution but has sparse regulatory air monitoring. Challenges for low-cost PM2.5 sensors in India include high-aerosol mass concentrations and pronounced regional and seasonal gradients in aerosol composition. Here, we report on a detailed long-time performance evaluation of a popular sensor, the Purple Air PA-II, at multiple sites in India. We established three distinct sites in India across land use categories and population density extremes (in urban Delhi and rural Hamirpur in north India and urban Bengaluru in south …

Neutrosophic Sets And Systems, Vol.58,2023, Florentin Smarandache, Mohamed Abdel-Basset, Said Broumi

Neutrosophic Sets and Systems

No abstract provided.

An Intrinsically Disordered Region Controlling Condensation Of A Circadian Clock Component And Rhythmic Transcription In The Liver, Kun Zhu, Isaac J Celwyn, Dongyin Guan, Yang Xiao, Xiang Wang, Wenxiang Hu, Chunjie Jiang, Lan Cheng, Rafael Casellas, Mitchell A Lazar

Faculty, Staff and Students Publications

Circadian gene transcription is fundamental to metabolic physiology. Here we report that the nuclear receptor REV-ERBα, a repressive component of the molecular clock, forms circadian condensates in the nuclei of mouse liver. These condensates are dictated by an intrinsically disordered region (IDR) located in the protein's hinge region which specifically concentrates nuclear receptor corepressor 1 (NCOR1) at the genome. IDR deletion diminishes the recruitment of NCOR1 and disrupts rhythmic gene transcription in vivo. REV-ERBα condensates are located at high-order transcriptional repressive hubs in the liver genome that are highly correlated with circadian gene repression. Deletion of the IDR disrupts transcriptional …

Sparx: Elucidate Single-Cell Spatial Heterogeneity Of Drug Responses For Personalized Treatment, Ziyang Tang, Xiang Liu, Zuotian Li, Tonglin Zhang, Baijian Yang, Jing Su, Qianqian Song

Publications

Spatial cellular authors heterogeneity contributes to differential drug responses in a tumor lesion and potential therapeutic resistance. Recent emerging spatial technologies such as CosMx, MERSCOPE and Xenium delineate the spatial gene expression patterns at the single cell resolution. This provides unprecedented opportunities to identify spatially localized cellular resistance and to optimize the treatment for individual patients. In this work, we present a graph-based domain adaptation model, SpaRx, to reveal the heterogeneity of spatial cellular response to drugs. SpaRx transfers the knowledge from pharmacogenomics profiles to single-cell spatial transcriptomics data, through hybrid learning with dynamic adversarial adaption. Comprehensive benchmarking demonstrates the …

The Cowl - V. 88 N. 20 - October 5, 2023

The Cowl

The Cowl - student newspaper of Providence College. Vol. 88 No. 20 - October 5, 2023. 20 pages.

A Novel Of Domination In Neutrosophic Over Graphs, R. Narmadadevi, M. Meenu, G. Muthumari

Neutrosophic Sets and Systems

No abstract provided.

Neutrosophic Κ-Structures In An Ag-Groupoid, G. Muhiuddin, K. Porselvi, B. Elavarasan

Neutrosophic Sets and Systems

No abstract provided.

Neutrosophic-Based Correlation Analysis For Fingerprint Image Pattern Recognition And Matching, Vinoth D, Ezhilmaran Devarasan

Neutrosophic Sets and Systems

No abstract provided.

Novel Single Valued Neutrosophic Prioritized Aczel Alsina Aggregation Operators And Their Applications In Multiattribute Decision Making, Sajid Latif, Kifayat Ullah, Abrar Hussain

Neutrosophic Sets and Systems

No abstract provided.

Storytelling For Asian–White Multiracial American College Students’ Racial Identity, Paige Thale Sonoda, Yunkyoung Loh Garrison

All Faculty Scholarship

This pilot study aims to explore how participatory digital storytelling can be used as an intervention to address race-based stress stemming from White supremacy and monoracism and describe the potential experiential effects on racial identity among Asian–White multiracial American college students. Specifically, we employed testimonio, or a liberation psychology-informed approach in a sample of 10 Asian–White multiracial American college students. The intervention consisted of four group sessions: (a) orienting (overview of liberation psychology and storytelling), (b) creating (self-reflection on personal stories and group discussion), (c) narrating (story sharing and filming), and (d) reflecting (watching and reacting to digital stories). Using …

Literature-Based Predictions Of Mendelian Disease Therapies, Cole A Deisseroth, Won-Seok Lee, Jiyoen Kim, Hyun-Hwan Jeong, Ryan S Dhindsa, Julia Wang, Huda Y Zoghbi, Zhandong Liu

Faculty, Staff and Students Publications

In the effort to treat Mendelian disorders, correcting the underlying molecular imbalance may be more effective than symptomatic treatment. Identifying treatments that might accomplish this goal requires extensive and up-to-date knowledge of molecular pathways-including drug-gene and gene-gene relationships. To address this challenge, we present "parsing modifiers via article annotations" (PARMESAN), a computational tool that searches PubMed and PubMed Central for information to assemble these relationships into a central knowledge base. PARMESAN then predicts putatively novel drug-gene relationships, assigning an evidence-based score to each prediction. We compare PARMESAN's drug-gene predictions to all of the drug-gene relationships displayed by the Drug-Gene Interaction …

Disease-Modifying Therapies And Features Linked To Treatment Response In Type 1 Diabetes Prevention: A Systematic Review, Jamie L Felton, Kurt J Griffin, Richard A Oram, Cate Speake, S Alice Long, Suna Onengut-Gumuscu, Stephen S Rich, Gabriela S F Monaco, Carmella Evans-Molina, Linda A Dimeglio, Heba M Ismail, Andrea K Steck, Dana Dabelea, Randi K Johnson, Marzhan Urazbayeva, Stephen Gitelman, John M Wentworth, Maria J Redondo, Emily K Sims, Ada/Easd Pmdi

Faculty, Staff and Students Publications

BACKGROUND: Type 1 diabetes (T1D) results from immune-mediated destruction of insulin-producing beta cells. Prevention efforts have focused on immune modulation and supporting beta cell health before or around diagnosis; however, heterogeneity in disease progression and therapy response has limited translation to clinical practice, highlighting the need for precision medicine approaches to T1D disease modification.

METHODS: To understand the state of knowledge in this area, we performed a systematic review of randomized-controlled trials with ≥50 participants cataloged in PubMed or Embase from the past 25 years testing T1D disease-modifying therapies and/or identifying features linked to treatment response, analyzing bias using a …

Pls3 Missense Variants Affecting The Actin-Binding Domains Cause X-Linked Congenital Diaphragmatic Hernia And Body-Wall Defects, Florence Petit, Mauro Longoni, Julie Wells, Richard S Maser, Eric L Bogenschutz, Matthew J Dysart, Hannah T M Contreras, Frederic Frénois, Barbara R Pober, Robin D Clark, Philip F Giampietro, Hilger H Ropers, Hao Hu, Maria Loscertales, Richard Wagner, Xingbin Ai, Harrison Brand, Anne-Sophie Jourdain, Marie-Ange Delrue, Brigitte Gilbert-Dussardier, Louise Devisme, Boris Keren, David J Mcculley, Lu Qiao, Rebecca Hernan, Julia Wynn, Tiana M Scott, Daniel G Calame, Zeynep Coban-Akdemir, Patricia Hernandez, Andres Hernandez-Garcia, Hagith Yonath, James R Lupski, Yufeng Shen, Wendy K Chung, Daryl A Scott, Carol J Bult, Patricia K Donahoe, Frances A High

Faculty, Staff and Student Publications

Congenital diaphragmatic hernia (CDH) is a relatively common and genetically heterogeneous structural birth defect associated with high mortality and morbidity. We describe eight unrelated families with an X-linked condition characterized by diaphragm defects, variable anterior body-wall anomalies, and/or facial dysmorphism. Using linkage analysis and exome or genome sequencing, we found that missense variants in plastin 3 (PLS3), a gene encoding an actin bundling protein, co-segregate with disease in all families. Loss-of-function variants in PLS3 have been previously associated with X-linked osteoporosis (MIM: 300910), so we used in silico protein modeling and a mouse model to address these seemingly disparate clinical …

Global Effect Of Modifiable Risk Factors On Cardiovascular Disease And Mortality, Global Cardiovascular Risk Consortium, Christina Magnussen, Francisco M Ojeda, Darryl P Leong, Jesus Alegre-Diaz, Philippe Amouyel, Larissa Aviles-Santa, Dirk De Bacquer, Christie M Ballantyne, Antonio Bernabé-Ortiz, Martin Bobak, Hermann Brenner, Rodrigo M Carrillo-Larco, James De Lemos, Annette Dobson, Marcus Dörr, Chiara Donfrancesco, Wojciech Drygas, Robin P Dullaart, Gunnar Engström, Marco M Ferrario, Jean Ferrières, Giovanni De Gaetano, Uri Goldbourt, Clicerio Gonzalez, Guido Grassi, Allison M Hodge, Kristian Hveem, Licia Iacoviello, M Kamran Ikram, Vilma Irazola, Modou Jobe, Pekka Jousilahti, Pontiano Kaleebu, Maryam Kavousi, Frank Kee, Davood Khalili, Wolfgang Koenig, Anna Kontsevaya, Kari Kuulasmaa, Karl J Lackner, David M Leistner, Lars Lind, Allan Linneberg, Thiess Lorenz, Magnus Nakrem Lyngbakken, Reza Malekzadeh, Sofia Malyutina, Ellisiv B Mathiesen, Olle Melander, Andres Metspalu, J Jaime Miranda, Marie Moitry, Joseph Mugisha, Mahdi Nalini, Vijay Nambi, Toshiharu Ninomiya, Karen Oppermann, Eleonora D'Orsi, Andrzej Pająk, Luigi Palmieri, Demosthenes Panagiotakos, Arokiasamy Perianayagam, Annette Peters, Hossein Poustchi, Andrew M Prentice, Eva Prescott, Ulf Risérus, Veikko Salomaa, Susana Sans, Satoko Sakata, Ben Schöttker, Aletta E Schutte, Sadaf G Sepanlou, Sanjib Kumar Sharma, Jonathan E Shaw, Leon A Simons, Stefan Söderberg, Abdonas Tamosiunas, Barbara Thorand, Hugh Tunstall-Pedoe, Raphael Twerenbold, Diego Vanuzzo, Giovanni Veronesi, Julia Waibel, S Goya Wannamethee, Masafumi Watanabe, Philipp S Wild, Yao Yao, Yi Zeng, Andreas Ziegler, Stefan Blankenberg

Faculty, Staff and Students Publications

BACKGROUND: Five modifiable risk factors are associated with cardiovascular disease (CVD) and all-cause mortality. The regional and sex-specific prevalence of these modifiable risk factors and their impact on CVD and all-cause mortality have not been evaluated using individual-level data.

METHODS: The Global Cardiovascular Risk Consortium harmonized individual-level data from 112 cohort studies conducted in 34 countries and 8 geographic regions. Associations between body-mass index, systolic blood pressure, non-high-density lipoprotein cholesterol, smoking, and diabetes with incident CVD and all-cause mortality were examined using Cox regression analyses and stratified by geographic region, age and sex. Population-attributable fractions were estimated for 10-year incident …

Rare Variants In Long Non-Coding Rnas Are Associated With Blood Lipid Levels In The Topmed Whole-Genome Sequencing Study, Yuxuan Wang, Margaret Sunitha Selvaraj, Xihao Li, Zilin Li, Jacob A Holdcraft, Donna K Arnett, Joshua C Bis, John Blangero, Eric Boerwinkle, Donald W Bowden, Brian E Cade, Jenna C Carlson, April P Carson, Yii-Der Ida Chen, Joanne E Curran, Paul S De Vries, Susan K Dutcher, Patrick T Ellinor, James S Floyd, Myriam Fornage, Barry I Freedman, Stacey Gabriel, Soren Germer, Richard A Gibbs, Xiuqing Guo, Jiang He, Nancy Heard-Costa, Bertha Hildalgo, Lifang Hou, Marguerite R Irvin, Roby Joehanes, Robert C Kaplan, Sharon Lr Kardia, Tanika N Kelly, Ryan Kim, Charles Kooperberg, Brian G Kral, Daniel Levy, Changwei Li, Chunyu Liu, Don Lloyd-Jone, Ruth Jf Loos, Michael C Mahaney, Lisa W Martin, Rasika A Mathias, Ryan L Minster, Braxton D Mitchell, May E Montasser, Alanna C Morrison, Joanne M Murabito, Take Naseri, Jeffrey R O'Connell, Nicholette D Palmer, Michael H Preuss, Bruce M Psaty, Laura M Raffield, Dabeeru C Rao, Susan Redline, Alexander P Reiner, Stephen S Rich, Muagututi'a Sefuiva Ruepena, Wayne H-H Sheu, Jennifer A Smith, Albert Smith, Hemant K Tiwari, Michael Y Tsai, Karine A Viaud-Martinez, Zhe Wang, Lisa R Yanek, Wei Zhao, Nhlbi Trans-Omics For Precision Medicine (Topmed) Consortium, Jerome I Rotter, Xihong Lin, Pradeep Natarajan, Gina M Peloso

Faculty, Staff and Student Publications

Long non-coding RNAs (lncRNAs) are known to perform important regulatory functions in lipid metabolism. Large-scale whole-genome sequencing (WGS) studies and new statistical methods for variant set tests now provide an opportunity to assess more associations between rare variants in lncRNA genes and complex traits across the genome. In this study, we used high-coverage WGS from 66,329 participants of diverse ancestries with measurement of blood lipids and lipoproteins (LDL-C, HDL-C, TC, and TG) in the National Heart, Lung, and Blood Institute (NHLBI) Trans-Omics for Precision Medicine (TOPMed) program to investigate the role of lncRNAs in lipid variability. We aggregated rare variants …

Genomic Variant Benchmark: If You Cannot Measure It, You Cannot Improve It, Sina Majidian, Daniel Paiva Agustinho, Chen-Shan Chin, Fritz J Sedlazeck, Medhat Mahmoud

Faculty, Staff and Students Publications

Genomic benchmark datasets are essential to driving the field of genomics and bioinformatics. They provide a snapshot of the performances of sequencing technologies and analytical methods and highlight future challenges. However, they depend on sequencing technology, reference genome, and available benchmarking methods. Thus, creating a genomic benchmark dataset is laborious and highly challenging, often involving multiple sequencing technologies, different variant calling tools, and laborious manual curation. In this review, we discuss the available benchmark datasets and their utility. Additionally, we focus on the most recent benchmark of genes with medical relevance and challenging genomic complexity.

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 …