Digital Commons Network^™

Compass: Joint Copy Number And Mutation Phylogeny Reconstruction From Amplicon Single-Cell Sequencing Data, Etienne Sollier, Jack Kuipers, Koichi Takahashi, Niko Beerenwinkel, Katharina Jahn

Faculty, Staff and Student Publications

Reconstructing the history of somatic DNA alterations can help understand the evolution of a tumor and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, most existing phylogenetic methods for scDNAseq data are designed either for single nucleotide variants (SNVs) or for large copy number alterations (CNAs), or are not applicable to targeted sequencing. Here, we develop COMPASS, a computational method for inferring the joint phylogeny of SNVs and CNAs from targeted scDNAseq data. We evaluate COMPASS on simulated data and apply it to several datasets including …

The Forbidden Fruit: A Case Of Tejocote (Crataegus Mexicana) Supplement Toxicity, Cali Clark, Terrence Kelly, Kyle Mense, Shane Miller, Ashley Broce

GME Publications

Supplement use continues to increase throughout the United States and as these compounds are not approved by the Food and Drug Administration, the side effect profiles are not well studied. Tejocote (Crataegus mexicana) is part of the hawthorn family and is a Mexican root supplement that is marketed for weight loss. We describe the case of a patient who ingested tejocote and presented with weakness, nausea, bradycardia with an atrioventricular block, and drug-induced thrombocytopenia.

Delayed Discovery: The Covid-19 Pandemic’S Influence On Osteoarthritis Clinical Trials, Nicholas B. Sajjadi, J. Michael Anderson, Griffin K. Hughes, Christena Abraham, Jamal Malik, Micah Hartwell, Matt Vassar

Student Publications

Context: The COVID-19 pandemic disrupted clinical research in many medical and surgical fields, resulting in research waste and loss of treatment for patients. Although other areas have been explored, the extent of the pandemic’s influence on osteoarthritis (OA) trials is currently unknown.

Objectives: This study aims to explore the reasons for termination of clinical trials investigating OA during the COVID-19 pandemic.

Methods: We searched ClinicalTrials.gov for OA trials and characterized their reason for discontinuation, noting where trialists directly cited the COVID-19 pandemic as the reason for trial discontinuation. We also coded other common reasons for trial discontinuation. Descriptive and inferential …

Atypical Intraparenchymal Meningioma With Yap1-Maml2 Fusion In A Young Adult Male: A Case Report And Mini Literature Review., Alisa Nobee, Mei Xu, Anjali Seth, Yuan Rong

PCOM Scholarly Works

Oncogenic Yes-associated protein (YAP) 1 fusions have been recently identified in several cases of meningioma mostly involving pediatric patients. The meningiomas harboring YAP1-MAML2, which is the most frequent fusion subtype, exhibit activated YAP1 signaling and share similarities with NF2 (neurofibromatosis type 2 gene) mutant meningiomas. We reported a rare case of atypical intraparenchymal meningioma with YAP1-MAML2 fusion in a 20-year-old male. The patient presented with an episode of seizure without a medical history. MRI revealed a lesion in the right temporal lobe without extra-axial involvement. The radiological and morphological findings, however, were indistinctive from other intracranial diseases, e.g., vascular malformation …

Placebo Effects Of Transcranial Direct Current Stimulation On Motor Skill Acquisition, Nicole K. Haikalis, Andrew Hooyman, Peiyuan Wang, Ayoub Daliri, Sydney Y. Schaefer

Physical Therapy Faculty Articles and Research

Transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation technique used in neurorehabilitation to enhance motor training. However, its benefits to motor training can be difficult to reproduce across research studies. It is possible that the observed benefits of tDCS are not directly related to the intervention itself but rather to the brain-mind responses elicited by the treatment context, commonly known as a placebo effect. This study investigated the presence of a placebo effect of tDCS on motor training and explored potential underlying factors. Sixty-eight participants who were right-handed were randomly assigned to active tDCS, sham tDCS, or a …

Kinase Inhibitor Pulldown Assay Identifies A Chemotherapy Response Signature In Triple-Negative Breast Cancer Based On Purine-Binding Proteins, Junkai Wang, Alexander B Saltzman, Eric J Jaehnig, Jonathan T Lei, Anna Malovannaya, Matthew V Holt, Meggie N Young, Mothaffar F Rimawi, Foluso O Ademuyiwa, Meenakshi Anurag, Beom-Jun Kim, Matthew J Ellis

2020-Current year OA Pubs

UNLABELLED: Triple-negative breast cancer (TNBC) constitutes 10%-15% of all breast tumors. The current standard of care is multiagent chemotherapy, which is effective in only a subset of patients. The original objective of this study was to deploy a mass spectrometry (MS)-based kinase inhibitor pulldown assay (KIPA) to identify kinases elevated in non-pCR (pathologic complete response) cases for therapeutic targeting. Frozen optimal cutting temperature compound-embedded core needle biopsies were obtained from 43 patients with TNBC before docetaxel- and carboplatin-based neoadjuvant chemotherapy. KIPA was applied to the native tumor lysates that were extracted from samples with high tumor content. Seven percent of …

Impact Of Geroscience On Therapeutic Strategies For Older Adults With Cardiovascular Disease: Jacc Scientific Statement, Daniel E Forman, George A Kuchel, John C Newman, James L Kirkland, Elena Volpi, George E Taffet, Nir Barzilai, Ambarish Pandey, Dalane W Kitzman, Peter Libby, Luigi Ferrucci

Faculty, Staff and Students Publications

Geroscience posits that cardiovascular disease (CVD) and other chronic diseases result from progressive erosion of the effectiveness of homeostatic mechanisms that oppose age-related accumulation of molecular damage. This hypothetical common root to chronic diseases explains why patients with CVD are often affected by multimorbidity and frailty and why older age negatively affects CVD prognosis and treatment response. Gerotherapeutics enhance resilience mechanisms that counter age-related molecular damage to prevent chronic diseases, frailty, and disability, thereby extending healthspan. Here, we describe the main resilience mechanisms of mammalian aging, with a focus on how they can affect CVD pathophysiology. We next present novel …

Insight Into The Mechanism Of H+-Coupled Nucleobase Transport, Jun Weng, Xiaoming Zhou, Pattama Wiriyasermkul, Zhenning Ren, Kehan Chen, Eva Gil-Iturbe, Ming Zhou, Matthias Quick

Faculty, Staff and Students Publications

The nucleobase/ascorbic acid transporter (NAT) family comprises proteins in all kingdoms of life. Their substrates, nucleobases and their analogs, have special attention in therapeutic applications, such as the treatment of solid tumors, lymphoproliferative diseases, viral infections, and inflammatory diseases. Here, we present the crystal structure of a bacterial NAT member, PurT of Colwellia psychrerythraea (PurTCp) at 2.80 Å resolution that, together with functional data, provide insight into the transport mechanism of NAT family members.

Oleoylethanolamide Facilitates Pparα And Tfeb Signaling And Attenuates Aβ Pathology In A Mouse Model Of Alzheimer’S Disease, Michele M Comerota, Manasee Gedam, Wen Xiong, Feng Jin, Lisheng Deng, Meng C Wang, Jin Wang, Hui Zheng

Faculty, Staff and Students Publications

BACKGROUND: Age is the strongest risk factor for the development of Alzheimer's disease (AD). Besides the pathological hallmarks of β-amyloid (Aβ) plaques and neurofibrillary tangles, emerging evidence demonstrates a critical role of microglia and neuroinflammation in AD pathogenesis. Oleoylethanolamide (OEA) is an endogenous lipid amide that has been shown to promote lifespan and healthspan in C. elegans through regulation of lysosome-to-nucleus signaling and cellular metabolism. The goal of our study was to determine the role of OEA in the mediation of microglial activity and AD pathology using its stable analog, KDS-5104.

METHODS: We used primary microglial cultures and genetic and …

Spatial Organization Of The Mouse Retina At Single Cell Resolution By Merfish, Jongsu Choi, Jin Li, Salma Ferdous, Qingnan Liang, Jeffrey R Moffitt, Rui Chen

Faculty, Staff and Students Publications

The visual signal processing in the retina requires the precise organization of diverse neuronal types working in concert. While single-cell omics studies have identified more than 120 different neuronal subtypes in the mouse retina, little is known about their spatial organization. Here, we generated the single-cell spatial atlas of the mouse retina using multiplexed error-robust fluorescence in situ hybridization (MERFISH). We profiled over 390,000 cells and identified all major cell types and nearly all subtypes through the integration with reference single-cell RNA sequencing (scRNA-seq) data. Our spatial atlas allowed simultaneous examination of nearly all cell subtypes in the retina, revealing …

A Multiparameter Molecular Classifier To Predict Response To Neoadjuvant Lapatinib Plus Trastuzumab Without Chemotherapy In Her2+ Breast Cancer, Jamunarani Veeraraghavan, Carolina Gutierrez, Carmine De Angelis, Robert Davis, Tao Wang, Tomas Pascual, Pier Selenica, Katherine Sanchez, Hiroaki Nitta, Monesh Kapadia, Anne C Pavlick, Patricia Galvan, Brent Rexer, Andres Forero-Torres, Rita Nanda, Anna M Storniolo, Ian E Krop, Matthew P Goetz, Julie R Nangia, Antonio C Wolff, Britta Weigelt, Jorge S Reis-Filho, Susan G Hilsenbeck, Aleix Prat, C Kent Osborne, Rachel Schiff, Mothaffar F Rimawi

Faculty, Staff and Student Publications

PURPOSE: Clinical trials reported 25% to 30% pathologic complete response (pCR) rates in HER2+ patients with breast cancer treated with anti-HER2 therapies without chemotherapy. We hypothesize that a multiparameter classifier can identify patients with HER2-"addicted" tumors who may benefit from a chemotherapy-sparing strategy.

EXPERIMENTAL DESIGN: Baseline HER2+ breast cancer specimens from the TBCRC023 and PAMELA trials, which included neoadjuvant treatment with lapatinib and trastuzumab, were used. In the case of estrogen receptor-positive (ER+) tumors, endocrine therapy was also administered. HER2 protein and gene amplification (ratio), HER2-enriched (HER2-E), and PIK3CA mutation status were assessed by dual gene protein assay (GPA), research-based …

Discovery And Targeting Of A Noncanonical Mechanism Of Sarcoma Resistance To Adi-Peg20 Mediated By The Microenvironment, Leonard C Rogers, Jeff C Kremer, Caitlyn B Brashears, Zongtao Lin, Alliny C S Bastos, Adriana Baker, Nicole Fettig, Dong Zhou, Kooresh I Shoghi, Carina A Dehner, John S A Chrisinger, Benjamin A Garcia, Toshinao Oyama, Brian A Van Tine, Et Al.

2020-Current year OA Pubs

PURPOSE: Many cancers lack argininosuccinate synthetase 1 (ASS1), the rate-limiting enzyme of arginine biosynthesis. This deficiency causes arginine auxotrophy, targetable by extracellular arginine-degrading enzymes such as ADI-PEG20. Long-term tumor resistance has thus far been attributed solely to ASS1 reexpression. This study examines the role of ASS1 silencing on tumor growth and initiation and identifies a noncanonical mechanism of resistance, aiming to improve clinical responses to ADI-PEG20.

EXPERIMENTAL DESIGN: Tumor initiation and growth rates were measured for a spontaneous Ass1 knockout (KO) murine sarcoma model. Tumor cell lines were generated, and resistance to arginine deprivation therapy was studied in vitro and …

Policy Formulation For Managing Ship-Generated Plastic Waste Via Improved Port Reception Facility Governance, Rika Kurniaty, Setyo Widagdo, Yasniar Rachmawati Madjid, Rafly Reyhan Al Kharji, Arsella Imanda Putri

Indonesian Journal of International Law

Plastic is a significant portion of marine debris, ranging from 60% to 80%. Historically, ships have been a major contributor to plastic pollution in the ocean, followed by Indonesia, which is acknowledged as the second-largest originator. Global efforts to combat marine pollution, including plastic waste, have been undertaken through international agreements like MARPOL Annex V. This agreement has mandated countries to establish suitable port facilities for ship-generated wastes. However, an assessment of Indonesian ports indicated insufficient compliance with environmental management standards, particularly in waste handling. The current direct fee policy for waste disposal may disincentivize proper waste disposal by ship …

Full Issue

Insights: The Newsletter of the Neal A. Maxwell Institute for Religious Scholarship

No abstract provided.

Farms Will Publish More Books, Noel B. Reynolds

Insights: The Newsletter of the Neal A. Maxwell Institute for Religious Scholarship

This year marks the first time that FARMS has published its own books intended for the general LDS market. The first two were Book of Mormon Authorship Revisited: The Evidence for Ancient Origins and LDS Perspectives on the Dead Sea Scrolls. With this issue of the newsletter we release a third: Ancient Scrolls from the Dead Sea: Photographs and Commentary on a Unique Collection of Scrolls. Before 1997 is over we expect to release three more books (described on page 8).

Farms Dead Sea Scrolls Database Now Available To Farms Subscribers

Insights: The Newsletter of the Neal A. Maxwell Institute for Religious Scholarship

After several years of research, scanning, text marking, and preparation of photographs, FARMS is pleased to announce that The Dead Sea Scrolls on CD: The FARMS Electronic Database is now available for sale to FARMS subscribers for $249. It is intended primarily for scholars with sufficient skills in biblical Hebrew to do research on the scrolls. Windows 3.1 (or higher) or OS2 is required.

Repairing Mechanism In Bone, Ahmed M. Al-Mukhtar

Maaen Journal for Medical Sciences

This work aims to explain the behavior of cracks in bones because the bone repairing mechanism is still somehow unknown. In this matter, different issues exist, such as the biological parameters (e.g., osteoblasts and osteoclasts), and the physical parameters (e.g., microcracks and defects). Traditionally, the bones respond to any load or defect within their microstructures. The defects and microcracks are increasing in the aged bone. Therefore, the damage increases unless the remodeling is completed. Remolded bones have increased fracture toughness. Hence, it is a basic mechanism for repair based on Wolff’s law. The smaller crack lengths (e.g., less than 1 …

Drug Delivery System Using A Buccal Film, Zainab Thabit Salih, Asia Al-Mahmood, Sumayah Al-Mahmood

Maaen Journal for Medical Sciences

The pharmaceutical industry has recently adopted a revolutionary strategy concerning the dosage form's composition and delivery methods, it is necessary to generate unique dosage forms in order to increase patient compliance, safety, and effectiveness. Enzymes are responsible for both the first-pass digestion and subsequent degradation of common oral dosage forms, although mucoadhesive films can prevent this issue, so, the creation of the buccal film is just one of the cutting-edge technologies that serve as an alternative to the conventional oral solid dosage form particularly for young children and elderly patients who have trouble swallowing. The buccal film is easier to …

Potential Benefits And Challenges Of Chatgpt In Future Nursing Education, Ahmed Lateef Alkhaqani

Maaen Journal for Medical Sciences

ChatGPT is a language model that has the potential to revolutionize nursing education and research by making it a quick and time-efficient process. This article highlights the challenges and opportunities this technology presents to nursing and health science education, including concerns around academic integrity and privacy and the need for educators to adapt quickly to ensure staff training and comprehensive policies are in place. Furthermore, educators and educational institutions firmly oppose the utilization of ChatGPT, perceiving its application as a direct menace to academic honesty, which might have an impact on academic, educational, and public well-being.

Advanced Mesoporous Silica Nanoparticles: Synthesis, Characteristics And Applications, Asmaa Abdelaziz Mohamed, Marwa Malik Kamil, Firas Aziz Rahi, Noor Zuhair Kbah

Maaen Journal for Medical Sciences

Recent breakthroughs in pharmaceutical delivery methods employing a range of carriers have radically transformed modern diagnostic and therapeutic practices. Mesoporous silica nanoparticles (MSNs) were created due to the demand for substances with superior thermal and chemical capabilities. These ordered porous substances have generated a lot of interest as carriers due to their distinct advantages over the competition. They may be made economically using a simple process. Moreover, the shape, pore size, and particle size may all be changed by modifying the synthesis's conditions. Investigations on MSNs as drug carriers have reportedly accelerated in recent years, highlighting the potential benefits of …

Severe Covid-19 Following Rituximab And Nirmatrelvir/Ritonavir Treatment In A Patient With Mctd, Case Report, Rohail A. Baig, Faieja Chowdhury, Omar Siddiqui, Adnaan Sheikh, Varun Mehta, Pranjali Dakwale

Advances in Clinical Medical Research and Healthcare Delivery

This is an article about how the use of medications such as nirmatrelvir/ritonavir can cause rebound COVID-19 and how the use of Rituximab, a biologic agent, can prolong the duration and increase severity of symptoms of COVID-19 in patients with pre-disposed autoimmune diseases that are on chronic pharmacotherapy.

Encephalopathy Tango: When Beta-Lactam Antibiotics Waltz With Gaba Receptor, Ali Mohamed, Nagesh Jadhav, Mohamed Elbathani, Abubaker Farah

Advances in Clinical Medical Research and Healthcare Delivery

Beta-lactam antibiotics are a class of drugs that are widely used to treat a variety of infections. They are generally well-tolerated, but they can cause a variety of side effects, including allergic reactions, acute interstitial nephritis (AIN) and neurotoxicity.

We present a patient who developed neurotoxicity after being treated with cephalosporin and carbapenem antibiotics. A 76-year-old female was admitted to the hospital with osteomyelitis of the right foot. She was initially treated with cefepime and daptomycin. She was discharged and then began to experience delirium with visual hallucinations and acute kidney injury. After common causes of confusion were excluded, the …

Cystic Fibrosis - An Ever Evolving Challenge, Abdullah A. Orakzai, Osama Sherjeel Khan, Syeda Sarah Raza, Muhammad H. Sharif, Mehr A. Orakzai

Advances in Clinical Medical Research and Healthcare Delivery

Cystic fibrosis (CF) is a genetic disease that results from mutations in a large single gene located on chromosome 7. More than 2000 different mutations in the gene have been identified to have caused the disease. Most of these mutations are exceedingly rare and therefore not a part of CF screening or all testing panels. This case discusses an adult female with a history of asthma, bronchiectasis, pseudomonas colonization, and respiratory failure on chronic oxygen who presented to the ED with sudden onset shortness of breath, fever, chills, body aches, nonproductive cough, and headache. The patient's condition clinically improved with …

Goofus And Gallant’S Guide To Textbook Cataloging, Scott M. Dutkiewicz, Tomeka Jackson

South Carolina Libraries

This article presents an overview of the 2022 SCLA presentation "Goofus and Gallant's Guide to Textbook Cataloging," presented by Scott Dutkiewicz. This presentation was inspired by the Highlights for Children comic strip “Goofus and Gallant. The reader will learn about five common cataloging mistakes associated with textbooks. Areas discussed are call numbers and classification, editions, pagination, subject and genre access, and indication of audience.

Euscorpius Sulfur Sp. N. (Scorpiones: Euscorpiidae), A New Cave Scorpion From Albania And Northwestern Greece, František Kovařík, Marek Audy, Serban M. Sarbu, Victor Fet

Euscorpius

A new species of cave scorpion, Euscorpius sulfur sp. n. (Scorpiones: Euscorpiidae) from Albania and northwestern Greece is described, fully complemented with color photographs of both live and preserved specimens, as well as their habitats.

The Degree Of Double Bind And Feigned Affection In Predicting Emotional Cutoff Among Spouses From Wives’ Perspective, Esraa Al-Rawashdeh, Hussein Salem Alsharah

Jordan Journal of Applied Science-Humanities Series

This study investigated the levels of emotional cutoff, double bind communication, and feigned affection among Jordanian wives who utilize family reform offices in religious courts. Employing a descriptive and predictive approach, data were collected from a sample of 130 wives in Amman. Results indicated an “average” level of emotional cutoff, a “high” level of double bind communication, and a “medium” level of feigned affection. Furthermore, double bind communication and feigned affection were found to significantly predict emotional cutoff. No significant difference in emotional cutoff was observed based on educational attainment; however, a significant difference was found based on marriage duration. …

Development Of An Attitude Scale Using A Combination Of Likert And Thurstone Scaling Techniques, Yazan Qawaqneh, Ahmad Odeh

Jordan Journal of Applied Science-Humanities Series

The current study aimed to develop an attitude scale using a combination of Likert and Thurstone scaling techniques to integrate the two methods and address the issues of non-response to all items on the Thurstone scale and the equal relative weight of all items on the Likert scale. The study sample comprised 50 arbitrators and 150 students from the ninth and tenth grades in Ajloun Governorate, selected randomly with one grade level as the unit of choice. To achieve the study's objectives, a descriptive-analytical and correlational approach was employed, and study tools were developed following both traditional Likert methods and …

High-Throughput Bioprinting Of The Nasal Epithelium Using Patient-Derived Nasal Epithelial Cells., I Deniz Derman, Miji Yeo, Diana Cadena, Megan Callender, Mian Horvath, Zengshuo Mo, Ruoyun Xiong, Elizabeth Fleming, Phylip Chen, Mark E Peeples, Karolina Palucka, Julia Oh, Ibrahim T Ozbolat

Faculty Research 2023

Progenitor human nasal epithelial cells (hNECs) are an essential cell source for the reconstruction of the respiratory pseudostratified columnar epithelium composed of multiple cell types in the context of infection studies and disease modeling. Hitherto, manual seeding has been the dominant method for creating nasal epithelial tissue models through biofabrication. However, this approach has limitations in terms of achieving the intricate three-dimensional (3D) structure of the natural nasal epithelium. 3D bioprinting has been utilized to reconstruct various epithelial tissue models, such as cutaneous, intestinal, alveolar, and bronchial epithelium, but there has been no attempt to use of 3D bioprinting technologies …

Affordable Learning Resources With Usu Libraries: Oer, Course Reserves, And Ebooks, Stephanie Western

Library Faculty & Staff Presentations

What is OER?

"Open Educational Resources are teaching, learning, and research materials in any medium--digital or otherwise--that reside in the public domain or have been released under an open license that permits no-cost access, use, adaptation, and redistribution by others with no or limited restrictions."

Organizational Information Systems (Is) Strategy, It Governance, And Firm Performance: Two Essays On How It Firms Utilize The Roles Of Is Strategy And It Governance To Improve Firm Performance, Xiaqing He

Information Systems & Operations Management Dissertations - Archive

This dissertation includes two essays. For essay one, we investigate the implications of organizational wireless and mobile strategy on firm performance in the context of publicly traded information technology firms in the United States. A research model is developed to examine the roles of information technology investment and chief information officer compensation in moderating the relationship between wireless and mobile strategy and firm performance. Topic modeling techniques and ordinary least squares regression are employed to analyze the data. The results support the positive effects of wireless and mobile strategy on firm performance. Additionally, chief information officer compensation is found to …