Digital Commons Network^™

Effects Of Post-Translational Histone Modifications On Transcription Rate, Aaron Bohn, Sarah Hodson, Sarah Ricks, David Bates Ph.D, Steven M. Johnson Ph.D

Library/Life Sciences Undergraduate Poster Competition 2023

The structural organization of DNA in eukaryotic cells is greatly implicated in the regulation of gene expression and thus cellular properties and behavior. At the most fundamental unit of this organization, ~147 bp of DNA wraps 1.7 times around a histone octamer core, forming a collective unit called the nucleosome. The positioning and occupancy of these nucleosomes around the promoter elements of genes is known to be a strong regulator of transcription in eukaryotic nuclei, and post-translational modifications (PTM’s) to the protruding N-terminal tails of histone proteins are known to influence chromatin structure and thus gene expression; however, relatively little …

February 23, 2023, Caa

Minutes

No abstract provided.

Analysis And Technical Optimization Of Processing Condition For Better Quality Of Robusta Coffee Production, Usman Ahmad, Khalimatus Sa’Diyah, Sathivel Subramaniam

Faculty Publications

The wet processing of robusta coffee starts with harvesting coffee cherries, followed by sorting the cherries, pulping, fermentation, washing, drying, hard skin hulling, bean sorting, and packaging. Soaking fruit before pulping is an alternative for coffee farmers to delay the pulping process if time does not al-low it. The fermentation process aims to remove mucus that is firmly attached to the hard skin. The addition of L. casei bacteria can accelerate the process but affect the final taste. This study aimed to optimize the duration of soaking and fermentation processes for obtaining coffee beans with a minimum number of unpeeled …

A Representation For Many Player Generalized Divide The Dollar Games, Garrison Greenwood, Daniel Ashlock

Electrical and Computer Engineering Faculty Publications and Presentations

Divide the dollar is a simplified version of a two player bargaining problem game devised by John Nash. The generalized divide the dollar game has n > 2 players. Evolutionary algorithms can be used to evolve individual players for this generalized game but representation—i.e., a genome plus a move or search operator(s)—must be carefully chosen since it affects the search process. This paper proposes an entirely new representation called a demand matrix. Each individual in the evolving population now represents a collection of n players rather than just an individual player. Players use previous outcomes to decide their choices (bids) in …

March 2, 2023: Agenda, University Of North Dakota

University Senate Meeting Minutes

Agenda for the March 2, 2023, meeting of the University Senate. 26 pages

Application Of E-Learning In The Smart City Projects, Asma Ghanim Al Arai

Theses

The concept of smart city is getting popular over time. It uses communication of technology and information to maximize operational organization. It shares information among the public to improve citizen welfare and the services of the government. Smart learning or E-learning is also one of the components of a smart city. Cities are the crucible hub of human innovation. Through smart cities, the community strives to integrate and cover environmental, bio, digital and financial technologies to solve urban problems. The E-learning process is based on formalized teaching, and it enhances with the help of electronic resources. Internet and computers play …

Simplified Demonstration Of A New Perivascular Pump Mechanism For Glymphatic Flow Of Interstitial Fluid In The Brain, Charles F. Babbs

Weldon School of Biomedical Engineering Faculty Working Papers

In a previous paper the author presented details of a new mechanism for the perivascular pump driving glymphatic flow—the brain’s waste removal system. The goal was to capture the essence of complex three-dimensional anatomy and physiology of the brain in a reduced order geometric model. The complexity required to make the model even approximately brain-like tended to obscure the most basic features of the perivascular pump. Here a bare-bones, “simplissimo” model of the perivascular pump is presented. It highlights only the most essential features of the pump mechanism. It also reveals components of brain anatomy and physiology that are not …

The Montclarion, February 23, 2023, The Montclarion

The Montclarion

Student Newspaper of Montclair State University

A Robust Stepwise Clustering Approach To Detect Individual Trees In Temperate Hardwood Plantations Using Airborne Lidar Data, Gang Shao, Songlin Fei, Guofan Shao

Purdue University Libraries Open Access Publishing Fund

Precise tree inventory plays a critical role in sustainable forest planting, restoration, and management. LiDAR-based individual tree detection algorithms often focus on finding individual treetops to discern tree positions. However, deliquescent tree forms (broad, flattened crowns) in deciduous forests can make these algorithms ineffective. In this study, we propose a stepwise tree detection approach, by first identifying individual trees using horizontal point density and then analyzing their vertical structure profiles. We first project LiDAR data onto a 2D horizontal plane and apply mean shift clustering to generate candidate tree clusters. Next, we apply a series of structure analyses on the …

Legal Strategies To Minimize Subway Air Pollution In The United States, Maia Foster

Duke Law Journal

Air pollution in U.S. subway systems poses a major threat to public health. People in subway stations breathe in dangerously high levels of dusts, called particulate matter. Current legislation does not effectively address this problem; in fact, the United States does not have a comprehensive indoor air quality law at all. Left unregulated, people regularly exposed to subway air pollution could suffer respiratory and cardiovascular issues and even premature death.

To mitigate these health effects, some countries have imposed PM standards in subway systems and underground spaces. Others have standards covering all indoor spaces. In the United States, many subway …

The Colby Echo (2023-02-23), Colby College

The Colby Echo

Published by the students of Colby College since 1877, The Colby Echo is the weekly, editorially independent student-run newspaper of Colby College in Waterville, Maine. Published monthly, 1877-1886; semi-monthly, 1886-1897; and weekly during the academic year, 1898-present.

Alfalfa In Rotation With Annual Crops Reduced Nitrate Leaching Potential, Arshdeep Singh, Tahseen Afzal, Bryan Woodbury, Charles Wortmann, Javed Iqbal

Department of Agronomy and Horticulture: Faculty Publications

Rotation of perennial alfalfa (Medicago sativa L.) with annual crops has the potential to reduce nitrate-nitrogen (NO₃-N) in the vadose zone and increase soil organic carbon (SOC) sequestration. The objective of this study was to determine the long-term effects on SOC, NO₃-N, ammonium-N (NH₄-N), and soil water in the 7.2 m depth with an alfalfa rotation compared with continuous corn (Zea mays L.). Soils from six pairs of alfalfa rotation versus continuous corn observation points were sampled to 7.2 m depth in 0.3 m increments. The uppermost 0.3 m was divided into …

Natural Killer T Cells And Other Innate-Like T Lymphocytes As Emerging Platforms For Allogeneic Cancer Cell Therapy, Amy N Courtney, Gengwen Tian, Leonid S Metelitsa

Faculty, Staff and Students Publications

T cells expressing chimeric antigen receptors (CARs) have achieved major clinical success in patients with hematologic malignancies. However, these treatments remain largely ineffective for solid cancers and require significant time and resources to be manufactured in an autologous setting. Developing alternative immune effector cells as cancer immunotherapy agents that can be employed in allogeneic settings is crucial for the advancement of cell therapy. Unlike T cells, Vα24-invariant natural killer T cells (NKTs) are not alloreactive and can therefore be generated from allogeneic donors for rapid infusion into numerous patients without the risk of graft-versus-host disease. Additionally, NKT cells demonstrate inherent …

Addressing Barriers In Fair Data Practices For Biomedical Data, Laura D Hughes, Ginger Tsueng, Jack Digiovanna, Thomas D Horvath, Luke V Rasmussen, Tor C Savidge, Thomas Stoeger, Serdar Turkarslan, Qinglong Wu, Chunlei Wu, Andrew I Su, Lars Pache, Niaid Systems Biology Data Dissemination Working Group

Faculty, Staff and Students Publications

No abstract provided.

Developing A Standardized But Extendable Framework To Increase The Findability Of Infectious Disease Datasets, Ginger Tsueng, Marco A Alvarado Cano, José Bento, Candice Czech, Mengjia Kang, Lars Pache, Luke V Rasmussen, Tor C Savidge, Justin Starren, Qinglong Wu, Jiwen Xin, Michael R Yeaman, Xinghua Zhou, Andrew I Su, Chunlei Wu, Liliana Brown, Reed S Shabman, Laura D Hughes

Faculty, Staff and Students Publications

Biomedical datasets are increasing in size, stored in many repositories, and face challenges in FAIRness (findability, accessibility, interoperability, reusability). As a Consortium of infectious disease researchers from 15 Centers, we aim to adopt open science practices to promote transparency, encourage reproducibility, and accelerate research advances through data reuse. To improve FAIRness of our datasets and computational tools, we evaluated metadata standards across established biomedical data repositories. The vast majority do not adhere to a single standard, such as Schema.org, which is widely-adopted by generalist repositories. Consequently, datasets in these repositories are not findable in aggregation projects like Google Dataset Search. …

Macroh2a Histone Variants Modulate Enhancer Activity To Repress Oncogenic Programs And Cellular Reprogramming, Wazim Mohammed Ismail, Amelia Mazzone, Flavia G Ghiraldini, Jagneet Kaur, Manvir Bains, Amik Munankarmy, Monique S Bagwell, Stephanie L Safgren, John Moore-Weiss, Marina Buciuc, Lynzie Shimp, Kelsey A Leach, Luis F Duarte, Chandandeep S Nagi, Saul Carcamo, Chi-Yeh Chung, Dan Hasson, Neda Dadgar, Jian Zhong, Jeong-Heon Lee, Fergus J Couch, Alexander Revzin, Tamas Ordog, Emily Bernstein, Alexandre Gaspar-Maia

Faculty, Staff and Students Publications

Considerable efforts have been made to characterize active enhancer elements, which can be annotated by accessible chromatin and H3 lysine 27 acetylation (H3K27ac). However, apart from poised enhancers that are observed in early stages of development and putative silencers, the functional significance of cis-regulatory elements lacking H3K27ac is poorly understood. Here we show that macroH2A histone variants mark a subset of enhancers in normal and cancer cells, which we coined 'macro-Bound Enhancers', that modulate enhancer activity. We find macroH2A variants localized at enhancer elements that are devoid of H3K27ac in a cell type-specific manner, indicating a role for macroH2A at …

Hochberg, Marc, Sophia Maier Garcia

Bronx Jewish History Project

Marc Hochberg was born 1949. He grew up with parents, both the children of immigrants, in a six story apartment building on Holland Avenue, off the south side of Pelham Parkway. The area is remembered as 90% Jewish, with one Italian friend from elementary school. He attended Castle Hill Junior High School in Parkchester, which still had few non-white students at the time, and the Bronx High School of Science. When he was in high school his parents moved to Grand Concourse and 165th Street. Bronx Science is remembered as a top education, and he would go to Franklin and …

Cytotoxic And Genotoxic Effects Of Waterpipe On Oral Health Status: Systematic Review And Meta-Analysis, Ricardo Grillo, Mehdi Khemiss, Yuri S. Da Silva

Sultan Qaboos University Medical Journal

This systematic review and meta-analysis aimed to assess the cytotoxic and genotoxic impacts of waterpipe smoking on oral health. The databases MEDLINE, Cochrane Library and Dimensions were searched to find studies evaluating whether waterpipe smokers exhibited any cytotoxic or genotoxic effects on their oral cells compared to non-smokers, with regard to mouth neoplasms. Particularly, changes in DNA methylation and p53 expression were assessed. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were adopted for the systematic review. Review Manager was utilised for statistical analysis with a significance level at P <0.05. To assess the grades of the included articles, a risk of bias analysis was summarised. A forest plot, including some of the included articles included, was created regarding the different grades. A total of 20 studies were included in this review. The results showed that waterpipe smoking has cytotoxic and genotoxic effects on oral cells, with a risk difference of 0.16. Although the published articles are few in number, all confirm the devastating effects of waterpipe smoking related to the carcinogenicity. Waterpipe smoking is harmful to oral health. It causes a series of detrimental cellular and genetic modifications such as acanthosis, epithelial dysplasia and hyperparakeratosis. In addition, waterpipe smoke contains several carcinogenic compounds. As it releases many harmful organic compounds, waterpipe smoking increases the incidence of oral cancer.

Radiologic Assessment Of Orbital Dimensions Among Omani Subjects: A Computed Tomography Imaging-Based Study At A Single Tertiary Centre, Eiman Al Ajmi, Marwa Al Subhi, Mallak Al Maamari, Humoud Al Dhuhli, Srinivasa R. Sirasanagandla

Sultan Qaboos University Medical Journal

Objectives: This study aimed to determine the orbital dimensions of Omani subjects who had been referred for computed tomography (CT) of the brain at Sultan Qaboos University Hospital, Muscat, Oman. Good knowledge of the normal orbital dimensions is clinically essential for successful surgical outcomes. Racial, ethnic and regional variations in the orbital dimensions have been reported. Methods: A total of 273 Omani patients referred for CT scans of the brain were retrospectively evaluated using an electronic medical records database. The orbital dimensions were recorded using both axial and sagittal planes of CT images. Results: The mean orbital index (OI) was …

Cilia Ultrastructure Associated With Primary Ciliary Dyskinesia In Omani Patients, Kawther Al Adawi, Taher Baomar, Marwa Al Riyami, Nawal Al Shamli, Khoula Al Shidhani, Aliya Al Ansari, Hussein Al Kindi

Sultan Qaboos University Medical Journal

Objectives: Primary ciliary dyskinesia (PCD) is a disorder affecting the structure and function of the motile cilia of the respiratory system. Transmission electron microscopy is one method that can be used to examine ciliary ultrastructure in airway biopsies. Although the role of ultrastructural findings in PCD has been described in the literature, this role has not been well-studied in the Middle East or, specifically, Oman. This study aimed to describe ultrastructural features in Omani patients with high suspicion of PCD. Methods: This retrospective cross-sectional study included 129 adequate airway biopsies obtained from Omani patients attending pulmonary clinics at Sultan Qaboos …

Faculty Senate Agenda, Georgia Southern University, Faculty Senate

Faculty Senate Agendas

No abstract provided.

February 23, 2023, The Daily Mississippian

Daily Mississippian (all digitized issues)

No abstract provided.

Origination Of The Modern-Style Diversity Gradient 15 Million Years Ago, Isabel S. Fenton, Tracy Aze, Alexander Farnsworth, Paul Valdes, Erin E. Saupe

School of Biological and Marine Sciences

The latitudinal diversity gradient (LDG) is a prevalent feature of modern ecosystems across diverse clades^1–4. Recognized for well over a century, the causal mechanisms for LDGs remain disputed, in part because numerous putative drivers simultaneously covary with latitude^1,3,5. The past provides the opportunity to disentangle LDG mechanisms because the relationships among biodiversity, latitude and possible causal factors have varied over time^6–9. Here we quantify the emergence of the LDG in planktonic foraminifera at high spatiotemporal resolution over the past 40 million years, finding that a modern-style gradient arose only 15 million years ago. Spatial …

Wifi-Based Human Activity Recognition Using Attention-Based Bilstm, Amany Elkelany, Robert J. Ross, Susan Mckeever

Conference papers

Recently, significant efforts have been made to explore human activity recognition (HAR) techniques that use information gathered by existing indoor wireless infrastructures through WiFi signals without demanding the monitored subject to carry a dedicated device. The key intuition is that different activities introduce different multi-paths in WiFi signals and generate different patterns in the time series of channel state information (CSI). In this paper, we propose and evaluate a full pipeline for a CSI-based human activity recognition framework for 12 activities in three different spatial environments using two deep learning models: ABiLSTM and CNN-ABiLSTM. Evaluation experiments have demonstrated that the …

Bispecific T-Cell Engagers Therapies In Solid Tumors: Focusing On Prostate Cancer, Diana C Simão, Kevin K Zarrabi, José L Mendes, Ricardo Luz, Jorge A Garcia, William Kevin Kelly, Pedro C Barata

Department of Medical Oncology Faculty Papers

Over the past decade, immunotherapy has demonstrated an impressive improvement in treatment outcomes for multiple cancers. Following the landmark approvals for use of immune checkpoint inhibitors, new challenges emerged in various clinical settings. Not all tumor types harbor immunogenic characteristics capable of triggering responses. Similarly, many tumors' immune microenvironment allows them to become evasive, leading to resistance and, thus, limiting the durability of responses. To overcome this limitation, new T-cell redirecting strategies such as bispecific T-cell engager (BiTE) have become attractive and promising immunotherapies. Our review provides a comprehensive perspective of the current evidence of BiTE therapies in solid tumors. …

Allogeneic Natural Killer Cell Therapy, Melissa M Berrien-Elliott, Miriam T Jacobs, Todd A Fehniger

2020-Current year OA Pubs

Interest in adoptive cell therapy for treating cancer is exploding owing to early clinical successes of autologous chimeric antigen receptor (CAR) T lymphocyte therapy. However, limitations using T cells and autologous cell products are apparent as they (1) take weeks to generate, (2) utilize a 1:1 donor-to-patient model, (3) are expensive, and (4) are prone to heterogeneity and manufacturing failures. CAR T cells are also associated with significant toxicities, including cytokine release syndrome, immune effector cell-associated neurotoxicity syndrome, and prolonged cytopenias. To overcome these issues, natural killer (NK) cells are being explored as an alternative cell source for allogeneic cell …

Genetic Subgroups Inform On Pathobiology In Adult And Pediatric Burkitt Lymphoma, Nicole Thomas, Nancy L. Bartlett, Lee Ratner, Et Al.

2020-Current year OA Pubs

Burkitt lymphoma (BL) accounts for most pediatric non-Hodgkin lymphomas, being less common but significantly more lethal when diagnosed in adults. Much of the knowledge of the genetics of BL thus far has originated from the study of pediatric BL (pBL), leaving its relationship to adult BL (aBL) and other adult lymphomas not fully explored. We sought to more thoroughly identify the somatic changes that underlie lymphomagenesis in aBL and any molecular features that associate with clinical disparities within and between pBL and aBL. Through comprehensive whole-genome sequencing of 230 BL and 295 diffuse large B-cell lymphoma (DLBCL) tumors, we identified …

Patterns Of Movement Performance Among Japanese Children And Effects Of Parenting Practices: Latent Class Analysis, Zhu Zhu, Cunyoen Kim, Dandan Jiao, Xiang Li, Ammara Ajmal, Munenori Matsumoto, Yuko Sawada, Toshiyuki Kasai, Taeko Watanabe, Etsuko Tomisaki, Emiko Tanaka, Sumio Ito, Rika Okumura, Tokie Anme

Sultan Qaboos University Medical Journal

Objectives: This study aimed to examine the long-term effects of parenting practice during preschool years on children’s movement performance in primary school. Methods: This three-year longitudinal study included 225 children aged 3–6-years-old. Parents reported baseline parenting practice and evaluated children’s movement performance three years later. Latent class analysis was used to explore latent classes of movement performance. A post hoc test was used to identify the characteristics of different patterns. Finally, adjusted multinomial logistic regression models were used to test the influence of parenting practice on identified patterns of movement performance. Results: Children in this study were grouped into three …

The Association Of Human Leukocyte Antigens Complex With Type 1 Diabetes In The Omani Population, Mohammed Al-Balushi, Samiya Al-Badi, Saif Al-Yaarubi, Hamad Al-Riyami, Azza Al-Shidhani, Shaima Al-Hinai, Ali Alshirawi, Sidgi Hasson, Elias Said, Ali Al-Jabri, Aliya Al Ansari

Sultan Qaboos University Medical Journal

Objectives: Identification of the high risk alleles, genotypes and haplotypes of the human leukocyte antigens (HLA) in different populations is beneficial for understanding their roles in type 1 diabetes (T1D) pathogenesis and intervention practices. This study aimed to identify T1D-associated HLA gene alleles in the Omani population. Methods: The present case-control study included 73 diabetic seropositive children (mean age 9.08 ± 3.27 years) attending the paediatric clinic at Sultan Qaboos University Hospital in Muscat, Oman, and 110 healthy controls. HLA–A, -B, -C, -DRB1 and -DQB1 genes were genotyped using a sequence-specific primer polymerase chain reaction (SSP-PCR). Results: Two HLA class …

Intellectual Disability Related To De Novo Germline Loss Of The Distal End Of The P-Arm Of Chromosome 17: A Case Report, Eden Pope, Matthew Huertas, Amar Paul, Braden Cunningham, Matthew Jennings, Ryan Perry, Stephanie Chavez, John A. Kriak, Kyle B. Bills, David W. Sant

Annual Research Symposium

Hypothesis/Purpose: In this report we present a case of a 20-year-old female with congenital intellectual disability, stunted growth, and hypothyroidism. Competitive genetic hybridization (CHG) revealed a loss of 17p13.3, and the deletion was not present in either parent. This deletion has not previously been characterized, but mutations on the p-arm of chromosome 17 are responsible for Miller-Dieker Syndrome and Isolated Lissencephaly Sequence, both of which share symptoms in common with the patient.

Methods: Peripheral mononuclear cells (PBMCs) were used for karyotyping and competitive genetic hybridization (CHG). Bioinformatic analysis was carried out using the Genome Data Viewer (ncbi.nlm.nih.gov/genome/gdv).

Results: Karyotype was …