Digital Commons Network^™

Trending Tubes: A Social Media Analysis Of Tympanostomy Tubes In Children, Luis D Neve, Harold S Pine

Faculty, Staff and Student Publications

OBJECTIVE: To investigate the popular social media platforms Instagram and Facebook for public posts related to tympanostomy tubes in children, to discern attitudes and perceptions surrounding tympanostomy tubes, and to evaluate the content of social media posts related to tympanostomy tubes.

STUDY DESIGN: Qualitative study.

SETTING: Instagram and Facebook social media platforms.

METHODS: Instagram and Facebook were searched for public posts from 2018 and 2019 including the search terms "ear tubes,""ear tube surgery,""tympanostomy," and "myringotomy." Posts were excluded if they were unrelated to pediatric tympanostomy tubes or written in a non-English language. Relevant posts underwent subgroup analysis based on 6 …

Dysregulated Hypothalamic-Pituitary-Adrenal Axis Is Associated With Increased Inflammation And Worse Outcomes After Ischemic Stroke In Diabetic Mice

Faculty, Staff and Student Publications

Diabetic patients have larger infarcts, worse neurological deficits, and higher mortality rate after an ischemic stroke. Evidence shows that in diabetes, the hypothalamic-pituitary-adrenal (HPA) axis was dysregulated and levels of cortisol increased. Based on the role of the HPA axis in immunity, we hypothesized that diabetes-dysregulated stress response exacerbates stroke outcomes via regulation of inflammation. To test this hypothesis, we assessed the regulation of the HPA axis in diabetic mice before and after stroke and determined its relevance in the regulation of post-stroke injury and inflammation. Diabetes was induced in C57BL/6 mice by feeding a high-fat diet and intraperitoneal injection …

Dysphagia Is Associated With Worse Clinical Outcomes In Geriatric Trauma Patients, Michael W Wandling, Lillian S Kao, Thaddeus J Puzio

Faculty, Staff and Student Publications

INTRODUCTION: Dysphagia is associated with increased morbidity, mortality, and resource utilization in hospitalized patients, but studies on outcomes in geriatric trauma patients with dysphagia are limited. We hypothesized that geriatric trauma patients with dysphagia would have worse clinical outcomes compared with those without dysphagia.

METHODS: Patients with and without dysphagia were compared in a single-center retrospective cohort study of trauma patients aged ≥65 years admitted in 2019. The primary outcome was mortality. Secondary outcomes included intensive care unit (ICU) length of stay (LOS), hospital LOS, discharge destination, and unplanned ICU admission. Multivariable regression analyses and Bayesian analyses adjusted for age, …

Occurrence, Toxicity And Adsorptive Removal Of The Chloramphenicol Antibiotic In Water: A Review, Duyen Thi Cam Nguyen

Faculty, Staff and Student Publications

Chloramphenicol is a broad-spectrum bacterial antibiotic used against conjunctivitis, meningitis, plague, cholera, and typhoid fever. As a consequence, chloramphenicol ends up polluting the aquatic environment, wastewater treatment plants, and hospital wastewaters, thus disrupting ecosystems and inducing microbial resistance. Here, we review the occurrence, toxicity, and removal of chloramphenicol with emphasis on adsorption techniques. We present the adsorption performance of adsorbents such as biochar, activated carbon, porous carbon, metal-organic framework, composites, zeolites, minerals, molecularly imprinted polymers, and multi-walled carbon nanotubes. The effect of dose, pH, temperature, initial concentration, and contact time is discussed. Adsorption is controlled by π-π interactions, donor-acceptor interactions, …

Pain Management And Telemedicine: A Look At The Covid Experience And Beyond

Faculty, Staff and Student Publications

COVID-19 caused a drastic change in clinical medicine around the globe. In the United States, telemedicine was rapidly adopted on a wide scale to minimize direct patient interaction and to reduce the spread of the COVID-19 virus. Telemedicine also went hand in hand with the rapid movement of working remotely. This has provided several challenges to chronic pain management clinics along with other subspecialties. Telemedicine has also opened opportunities for providing valuable care for patients with significant barriers to healthcare professionals. Given the benefits and downfalls of telemedicine, it is ultimately up to the provider who has an established patient-physician …

Formation, Antimicrobial Activity, And Biomedical Performance Of Plant-Based Nanoparticles: A Review, Duyen Thi Cam Nguyen

Faculty, Staff and Student Publications

Because many engineered nanoparticles are toxic, there is a need for methods to fabricate safe nanoparticles such as plant-based nanoparticles. Indeed, plant extracts contain flavonoids, amino acids, proteins, polysaccharides, enzymes, polyphenols, steroids, and reducing sugars that facilitate the reduction, formation, and stabilization of nanoparticles. Moreover, synthesizing nanoparticles from plant extracts is fast, safe, and cost-effective because it does not consume much energy, and non-toxic derivatives are generated. These nanoparticles have diverse and unique properties of interest for applications in many fields. Here, we review the synthesis of metal/metal oxide nanoparticles with plant extracts. These nanoparticles display antibacterial, antifungal, anticancer, and …

Dat3m: A Data Tracker For Multi-Faceted Management Of Multi-Site Clinical Research Data Submission, Curation, Master Inventorying, And Sharing, Guo-Qiang Zhang

Faculty, Staff and Student Publications

Managing research data is an important and challenging aspect of clinical studies, especially for multi-site collaboratives. To address this challenge, we designed, developed and deployed a multi-faceted, multi-level interactive data tracker (DaT3M) for multi-site clinical research data submission, curation, master inventorying, and sharing. Components of DaT3M include data overview, data portal, data status panel, data query engine, and data downloader. DaT3M managed clinical research data for the Center for SUDEP Research (CSR). The CSR instance of DaT3M includes 2,743 subjects from seven data contributing institutions, 7 data modalities and 10,678 data components: 3,398 Epilepsy Monitoring Unit reports, 3,440 electroencephalography recordings, …

Temporal Cohort Logic

Faculty, Staff and Student Publications

We introduce a new logic, called Temporal Cohort Logic (TCL), for cohort specification and discovery in clinical and population health research. TCL is created to fill a conceptual gap in formalizing temporal reasoning in biomedicine, in a similar role that temporal logics play for computer science and its applications. We provide formal syntax and semantics for TCL and illustrate the various logical constructs using examples related to human health. Relationships and distinctions with existing temporal logical frameworks are discussed. Applications in electronic health record (EHR) and in neurophysiological data resource are provided. Our approach differs from existing temporal logics, in …

Causal Inference Of Genetic Variants And Genes In Amyotrophic Lateral Sclerosis, Yulin Dai, Yin-Ying Wang, Peilin Jia, Fan Liu

Faculty, Staff and Student Publications

Amyotrophic lateral sclerosis (ALS) is a fatal progressive multisystem disorder with limited therapeutic options. Although genome-wide association studies (GWASs) have revealed multiple ALS susceptibility loci, the exact identities of causal variants, genes, cell types, tissues, and their functional roles in the development of ALS remain largely unknown. Here, we reported a comprehensive post-GWAS analysis of the recent large ALS GWAS (n = 80,610), including functional mapping and annotation (FUMA), transcriptome-wide association study (TWAS), colocalization (COLOC), and summary data-based Mendelian randomization analyses (SMR) in extensive multi-omics datasets. Gene property analysis highlighted inhibitory neuron 6, oligodendrocytes, and GABAergic neurons (Gad1/Gad2) as …

An Ensemble-Based Deep Convolutional Neural Network For Computer-Aided Polyps Identification From Colonoscopy, Kunio Kasugai, Zhongming Zhao

Faculty, Staff and Student Publications

Colorectal cancer (CRC) is the third leading cause of cancer death globally. Early detection and removal of precancerous polyps can significantly reduce the chance of CRC patient death. Currently, the polyp detection rate mainly depends on the skill and expertise of gastroenterologists. Over time, unidentified polyps can develop into cancer. Machine learning has recently emerged as a powerful method in assisting clinical diagnosis. Several classification models have been proposed to identify polyps, but their performance has not been comparable to an expert endoscopist yet. Here, we propose a multiple classifier consultation strategy to create an effective and powerful classifier for …

A Deep Learning-Based Framework For Supporting Clinical Diagnosis Of Glioblastoma Subtypes, Zhongming Zhao

Faculty, Staff and Student Publications

Understanding molecular features that facilitate aggressive phenotypes in glioblastoma multiforme (GBM) remains a major clinical challenge. Accurate diagnosis of GBM subtypes, namely classical, proneural, and mesenchymal, and identification of specific molecular features are crucial for clinicians for systematic treatment. We develop a biologically interpretable and highly efficient deep learning framework based on a convolutional neural network for subtype identification. The classifiers were generated from high-throughput data of different molecular levels, i.e., transcriptome and methylome. Furthermore, an integrated subsystem of transcriptome and methylome data was also used to build the biologically relevant model. Our results show that deep learning model outperforms …

Crucial Roles Of Microrna-16-5p And Microrna-27b-3p In Ameloblast Differentiation Through Regulation Of Genes Associated With Amelogenesis Imperfecta, Naina Singh, Thanh Le, Zhongming Zhao, Junichi Iwata

Faculty, Staff and Student Publications

Amelogenesis imperfecta is a congenital disorder within a heterogeneous group of conditions characterized by enamel hypoplasia. Patients suffer from early tooth loss, social embarrassment, eating difficulties, and pain due to an abnormally thin, soft, fragile, and discolored enamel with poor aesthetics and functionality. The etiology of amelogenesis imperfecta is complicated by genetic interactions. To identify mouse amelogenesis imperfecta-related genes (mAIGenes) and their respective phenotypes, we conducted a systematic literature review and database search and found and curated 70 mAIGenes across all of the databases. Our pathway enrichment analysis indicated that these genes were enriched in tooth development-associated pathways, forming four …

Dimensionality Reduction And Louvain Agglomerative Hierarchical Clustering For Cluster-Specified Frequent Biomarker Discovery In Single-Cell Sequencing Data

Faculty, Staff and Student Publications

The major interest domains of single-cell RNA sequential analysis are identification of existing and novel types of cells, depiction of cells, cell fate prediction, classification of several types of tumor, and investigation of heterogeneity in different cells. Single-cell clustering plays an important role to solve the aforementioned questions of interest. Cluster identification in high dimensional single-cell sequencing data faces some challenges due to its nature. Dimensionality reduction models can solve the problem. Here, we introduce a potential cluster specified frequent biomarkers discovery framework using dimensionality reduction and hierarchical agglomerative clustering Louvain for single-cell RNA sequencing data analysis. First, we pre-filtered …

Explanation-Driven Deep Learning Model For Prediction Of Brain Tumour Status Using Mri Image Data, Zhongming Zhao

Faculty, Staff and Student Publications

Cancer research has seen explosive development exploring deep learning (DL) techniques for analysing magnetic resonance imaging (MRI) images for predicting brain tumours. We have observed a substantial gap in explanation, interpretability, and high accuracy for DL models. Consequently, we propose an explanation-driven DL model by utilising a convolutional neural network (CNN), local interpretable model-agnostic explanation (LIME), and Shapley additive explanation (SHAP) for the prediction of discrete subtypes of brain tumours (meningioma, glioma, and pituitary) using an MRI image dataset. Unlike previous models, our model used a dual-input CNN approach to prevail over the classification challenge with images of inferior quality …

Breast Cancer Detection: Shallow Convolutional Neural Network Against Deep Convolutional Neural Networks Based Approach, Kangkana Bora, Zhongming Zhao

Faculty, Staff and Student Publications

Introduction: Of all the cancers that afflict women, breast cancer (BC) has the second-highest mortality rate, and it is also believed to be the primary cause of the high death rate. Breast cancer is the most common cancer that affects women globally. There are two types of breast tumors: benign (less harmful and unlikely to become breast cancer) and malignant (which are very dangerous and might result in aberrant cells that could result in cancer).

Methods: To find breast abnormalities like masses and micro-calcifications, competent and educated radiologists often examine mammographic images. This study focuses on computer-aided diagnosis to help …

The Wnt/Β-Catenin Pathway Regulates Expression Of The Genes Involved In Cell Cycle Progression And Mitochondrial Oxidative Phosphorylation In The Postmitotic Cardiac Myocytes, Hyun-Hwan Jeong, Zhongming Zhao, Priyatansh Gurha, Ali J Marian

Faculty, Staff and Student Publications

INTRODUCTION: Aging is associated with cardiac myocyte loss, sarcopenia, and cardiac dysfunction. Adult cardiac myocytes are postmitotic cells with an insufficient proliferative capacity to compensate for myocyte loss. The canonical WNT (cWNT) pathway is involved in the regulation of cell cycle reentry in various cell types. The effects of the cWNT pathway on the expression of genes involved in cell cycle reentry in the postmitotic cardiac myocytes are unknown.

AIM: The aim of the study was to identify genes whose expression is regulated by the β-catenin, the indispensable component to the cWNT signaling, in the postmitotic myocytes.

METHODS AND RESULTS: …

Prediction Of Intensive Care Unit Admission (>24h) After Surgery In Elective Noncardiac Surgical Patients Using Machine Learning Algorithms, Xuechao Hao, Yao Hu, Jin Yin, Tao Zhu, Xiaobo Zhou

Faculty, Staff and Student Publications

BACKGROUND: To develop a highly discriminative machine learning model for the prediction of intensive care unit admission (>24h) using the easily available preoperative information from electronic health records. An accurate prediction model for ICU admission after surgery is of great importance for surgical risk assessment and appropriate utilization of ICU resources.

METHOD: Data were collected retrospectively from a large hospital, comprising 135,442 adult patients who underwent surgery except for cardiac surgery between 1 January 2014, and 31 July 2018 in China. Multiple existing predictive machine learning algorithms were explored to construct the prediction model, including logistic regression, random forest, …

Distinguish Bipolar And Major Depressive Disorder In Adolescents Based On Multimodal Neuroimaging: Results From The Adolescent Brain Cognitive Development Stud, Qu Xiang, Li Peng, Jian Zhang, Weiling Zhao, Mingliang Li, Xiaobo Zhou

Faculty, Staff and Student Publications

BACKGROUND: Major depressive disorder and bipolar disorder in adolescents are prevalent and are associated with cognitive impairment, executive dysfunction, and increased mortality. Early intervention in the initial stages of major depressive disorder and bipolar disorder can significantly improve personal health.

METHODS: We collected 309 samples from the Adolescent Brain Cognitive Development study, including 116 adolescents with bipolar disorder, 64 adolescents with major depressive disorder, and 129 healthy adolescents, and employed a support vector machine to develop classification models for identification. We developed a multimodal model, which combined functional connectivity of resting-state functional magnetic resonance imaging and four anatomical measures of …

Prediction Of Fluid Intelligence From T1-W Mri Images: A Precise Two-Step Deep Learning Framework, Xiaobo Zhou

Faculty, Staff and Student Publications

The Adolescent Brain Cognitive Development (ABCD) Neurocognitive Prediction Challenge (ABCD-NP-Challenge) is a community-driven competition that challenges competitors to develop algorithms to predict fluid intelligence scores from T1-w MRI images. In this work, a two-step deep learning pipeline is proposed to improve the prediction accuracy of fluid intelligence scores. In terms of the first step, the main contributions of this study include the following: (1) the concepts of the residual network (ResNet) and the squeeze-and-excitation network (SENet) are utilized to improve the original 3D U-Net; (2) in the segmentation process, the pixels in symmetrical brain regions are assigned the same label; …

Apaview: A Web-Based Platform For Alternative Polyadenylation Analyses In Hematological Cancers, Xiaoyan Wang, Jianqiang Du, Junbo Duan, Huqin Zhang, Xiaobo Zhou, Xiaoming Wu

Faculty, Staff and Student Publications

Background: Hematologic malignancies, such as acute promyelocytic leukemia (APL) and acute myeloid leukemia (AML), are cancers that start in blood-forming tissues and can affect the blood, bone marrow, and lymph nodes. They are often caused by genetic and molecular alterations such as mutations and gene expression changes. Alternative polyadenylation (APA) is a post-transcriptional process that regulates gene expression, and dysregulation of APA contributes to hematological malignancies. RNA-sequencing-based bioinformatic methods can identify APA sites and quantify APA usages as molecular indexes to study APA roles in disease development, diagnosis, and treatment. Unfortunately, APA data pre-processing, analysis, and visualization are time-consuming, inconsistent, …

Whole Lung Lavage: Treating Pulmonary Alveolar Proteinosis At The Time Of Covid Pandemic, Pralay Kumar Sarkar, Pedro Piedra, Neda Zarrin-Khameh

Faculty, Staff and Students Publications

Pulmonary alveolar proteinosis (PAP) is a rare syndrome due to increased production or decreased clearance of surfactant in alveoli and terminal bronchi that cause hypoxemic respiratory insufficiency. Here we present a patient with PAP whose disease was exacerbated by superimposed COVID-19 pneumonia. He underwent whole lung lavage (WLL). Evaluation of the viral count of the first and the last lavage of the left lung showed viral load in the alveolar space dropped by approximately 10-folds, however the magnitude of the viral load was substantial in both lavage samples. Whole pulmonary lavage may be used as a treatment option on patients …

Emerging Roles Of Alternative Cleavage And Polyadenylation (Apa) In Human Disease, Prakash Dharmalingam, Rajasekaran Mahalingam, Hari Krishna Yalamanchili, Tingting Weng, Harry Karmouty-Quintana, Ashrith Guha, Rajarajan A Thandavarayan

Duncan NRI Faculty and Staff Publications

In the messenger RNA (mRNA) maturation process, the 3'-end of pre-mRNA is cleaved and a poly(A) sequence is added, this is an important determinant of mRNA stability and its cellular functions. More than 60%-70% of human genes have three or more polyadenylation (APA) sites and can be cleaved at different sites, generating mRNA transcripts of varying lengths. This phenomenon is termed as alternative cleavage and polyadenylation (APA) and it plays role in key biological processes like gene regulation, cell proliferation, senescence, and also in various human diseases. Loss of regulatory microRNA binding sites and interactions with RNA-binding proteins leading to …

Creation Of A Global Vaccine Risk Index, Tasmiah Nuzhath, Peter J Hotez, Ashish Damania, P Shuling Liu, Brian Colwell

Center for Medical Ethics and Health Policy Staff Publications

The World Health Organization has identified vaccine hesitancy as one of its top ten global health threats for 2019. Efforts are underway to define the factors responsible for reductions in vaccine confidence. However, as global measles cases accelerated beginning in 2018, it became evident that additional factors were promoting measles re-emergence, including war, political and socio-economic collapse, shifting poverty, and vulnerability to weather events and climate change. Accordingly, we propose a Global Vaccine Risk Index (VRI) to consider these variables as a more comprehensive means to identify vulnerable nations where we might expect measles and other vaccine-preventable diseases to emerge …

Genocide In East Turkestan: Exploring The Perspectives Of Uyghurs In The Diaspora And Their Resistance To Chinese State Violence, Lina Semyonovna Lenberg

Doctoral Dissertations

The Uyghurs of Xinjiang Uyghur Autonomous Region—or East Turkestan, as many Uyghurs call their Indigenous homeland in northwestern China, are a Muslim ethnic group whose culture and identity are being systematically destroyed by the Chinese state. Since 2016, Uyghurs have been imprisoned in China’s “re-education camps” on an enormous scale, numbering up to three million. Uyghurs have experienced discrimination and marginalization in China for many years, yet relatively little attention has been given to what has now become a set of gross human rights violations amounting to crimes against humanity and genocide. The purpose of this study was twofold. First, …

Understanding The Perspectives, Practices, And Expectations Of Korean American Parents Toward The Heritage Language Education Of Their Children, Yunhee Choi

Doctoral Dissertations

The purpose of this qualitative study, conducted with parents of a Bay Area Korean school, was to explore how Korean American parents perceive, practice, and expect from the heritage language education of their children. The parents shared their experiences as Korean immigrants in raising their children in two languages. First, a survey was distributed and collected to apprehend the demographics of 24 Korean American parents in a West Coast metropolitan area who sent their children to a Korean heritage language school on weekends. Then one-on-one in-depth interviews were conducted with seven of these parents. Seven themes emerged from the data: …

Teaching Solidarity: Popular Education In Grassroots U.S. Social Movements, Tenaya Summers Lafore

Doctoral Dissertations

Fifty years after he wrote Pedagogy of the Oppressed (1970), Brazilian educator Paulo Freire’s work is as relevant as ever. But while many of Freire’s ideas are well known in the United States, there is limited research on their application in social movement settings, a practice commonly known as popular education. This comparative case study draws on Freire’s theory of popular education to analyze two U.S.-based grassroots education programs, one with low-income residents in the Tenderloin neighborhood of San Francisco and one with front-line hospital and public school employees on the East Coast. Through six months of participant observation and …

Effects Of Teaching Argument To First-Year Community-College Students Using A Structural And Dialectical Approach, Sharon Radcliff

Doctoral Dissertations

The purpose of this study was to measure to what extent an experimental method of teaching argument incorporating elements from both Toulmin’s (2004) structural approach and Walton’s (2013) dialectical approach effects first-year college students’ ability to write strong arguments. This experimental instruction used critical questioning as a strategy in building a strong argument, incorporating alternative viewpoints, and creating a dialogue between claims and counterclaims, backed logically by verifiable evidence from reliable sources.

Using the Analytic Scoring Rubric of Argumentative Writing (ASRAW; Stapleton & Wu, 2015) that includes the argument elements of claims, data, counterclaim, counterclaim data, rebuttal claim, and rebuttal …

Using Peer Review To Improve English As A Second Language College Students' Writing Scores, Mengjie Wei

Doctoral Dissertations

This study was conducted to examine the effectiveness of peer-review in college English as Second Language writing classes to improve ESL students’ writing scores. It also investigated a statistically significant difference in college ESL students’ writing scores between those who use the self-check list and peer review worksheet and those who only use the self-check list in writing paragraphs and essays. More specifically, this study was conducted to determine the influence of different areas on students’ English writing scores, i.e., format/content/structure, grammar, vocabulary, and spelling. In addition, this study explored students’ attitudes and opinions on peer-review in writing class.

This …

The Effects Of Curriculum-Integrated Explicit Learning Strategy Instruction On Reading Comprehension For English As A Second Language (Esl) Learners At The Community College, Sylvia Chaiyeon Lee

Doctoral Dissertations

Reading skills are critical for English as a Second Language (ESL) students in higher education to achieve academic success. However, effective ways to promote student success in ESL reading courses are under-researched. Identifying factors that may enhance the quality and outcomes of learning ESL reading is essential. One such factor identified by previous research is learning strategies. Explicit instruction on learning strategies may lessen the problems and difficulties that international students encounter. Explicit strategy instruction can bring a systematic scaffold into a language learning process, guide students toward proper learning strategies, and promote constructive cognitive processing during learning.

This study …

Cuentos Criollos: Colombian Internally Displaced Families As Knowledge Producers, Liliana Salazar De Deck

Doctoral Dissertations

Colombia continues to report the highest number of internally displaced people (IDPs) with over eight million registered in 2021 (UNHCR, 2021). The majority of the internally displaced people are campesinos, AfroColombians, and members of Indigenous communities. Historically, people in these demographic groups have been excluded from political participation and wealth accumulation, and their identities are minoritized (Bello, 2003). Urban schools have become contact zones (Pratt, 1991) for internally displaced families and various economic, social, and political discourses attempt to explore and explain their experiences. However, the voices of the families themselves are not often found within this body of scholarship. …