Digital Commons Network^™

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. …

Impact Of Covid-19 On New Teacher Retention And Perceived Supports In A Northern California Public School District, Rebecka Maxkenzie

Doctoral Dissertations

This qualitative study examined teachers, schools, and district approaches to new teacher retention with a COVID-19 spin. In the changing world of a global pandemic and shifting teaching modalities, including distance or hybrid learning environments, teachers reflected on their experiences of adaptation. Interviews with teachers in their first three years in the profession were conducted to share the stories of new teachers amid COVID-19. New teachers were recruited through a snowball sampling technique from a large school district in the San Francisco Bay Area in Northern California. To answer the research questions, participants were interviewed about the presence or absence …

The Relationship Between Metacognitive Strategies And Listening Comprehension Proficiency In Intensive-Korean-Foreign-Language Setting, Gumok Seo

Doctoral Dissertations

The study investigated the relationship between a metacognitive-listening strategy and listening proficiency and gained insights into students’ perceptions of listening-strategy use among Korean-as-a-foreign-language learners in an intensive-language setting in Northern California. Little research has been carried out in a Korean-as-a-foreign-language (KFL) setting, and investigation in a different context of an intensive-language program is needed where good study habits, such as metacognitive strategy, self-regulation, and autonomous learning are required. Thus, this study aimed to investigate the relationship between metacognitive-listening-strategy use and listening proficiency outcomes by more- and less-proficient students among KFL adult learners and their perception of metacognitive-listening-strategies.

To achieve the …

Voces Of Little Michoacan: A Collective Narrative Of Resistance And Preservation Of Home, Ana Angel Avendaño

Doctoral Dissertations

This empirical study captured the ongoing community organizing, led primarily by Chicanas and young people in a Latinx community in the San Francisco Bay Area. This community has experienced historic neglect, inequities, gentrification, and economic displacement. Through muxersita portraiture, a critical qualitative methodology, with young people as co-researchers, this study captures the collective narrative of the community of North Fair Oaks through platicas, encuentros y acción. In the process, this collective narrative disrupts the negative impact of gentrification by providing a historical context of the contributions of Latinx in North Fair Oaks. This study uses a critical coraje framework; a …

An Exploration Of Learning-At-Home Experiences Among Families And Children Of Color Labeled With Disabilities During Covid-19: A Narrative Inquiry, Nam Ju Han

Doctoral Dissertations

We are living in this historical moment of a COVID-19 global crisis that is continuing to impact marginalized families in our very own communities. Students of color, especially those who are already on the margins, and experience inequities in the classroom and in the community, have been further impacted by the quarantine as the educational system had not prioritized how to support students who face certain vulnerabilities due to lack of government funding, the historical oppressive tendency for schools to function within a medical model of standardization, along with the commodification of learning. Given the novelty of COVID-19 research, the …

Mediating Language Fluency Development: An Action Research Study In A High-School Ap Chinese Second-Or-Foreign-Language Task-Based Language Teaching Classroom, Jing Liang

Doctoral Dissertations

Fluency development is critical in language learning; however, the teacher’s role as a mediator in a learner’s fluency development rarely has been explored in Task-Based Language Teaching (TBLT) classrooms. This study investigated how a teacher, as the human mediator who can be certain that stimuli in the learning environment will be available and benefit the learners, implemented mediation under the guidance of Mediated Learning Experience (MLE) theory in aiding learners’ speaking cognitive and utterance fluency development in one AP Chinese high-school TBLT classroom in the Bay Area. MLE theory, developed by psychologist Reuven Feuerstein, provided a mediation framework for this …

¿Tú Qué Sabes?: Latina Doctoral Women Disrupting And Resisting Dominant Knowledge, Sendy Ramos Madsen

Doctoral Dissertations

Education environments have systematically excluded, silenced, and erroneously spoken on behalf of Women of Color. Linear forms of scholarship and research practices propagate the dominant perspective and fail to address systems of oppression that result in epistemic suppression and academic hostility towards brown minds. Historically, Latina women have not been seen as creators of knowledge, and their access to educational spaces has been restricted. According to census projections, in 2036, Latinas/os will account for the largest minority group in the United States and one-third of the American educational system. Therefore, academic spaces must establish practices to include Latina women as …

Efforts To Create A Trauma-Informed Classroom In Higher Education: Insights From Members Of A Community College Trauma-Informed Teaching Group, Danyelle Marshall

Doctoral Dissertations

BIPOC students attending a community college in the Bay Area bring traumas to school with them and then they relive their traumas in the classroom through professors’ pedagogy and the curriculum. This dissertation which was conducted during twin pandemics of COVID 19 and racism, researched a group of English professors that teach first generation community college students in their second year and above to understand what they know about trauma and their students and how they begin to conceive efforts to develop trauma-informed pedagogy. Data were collected using a focus group and individual interviews. The focus group created an environment …

Reclaiming Our Humanity: Redemption, Reimagining, And Restorying Of The Foundations For Success Of Formerly Incarcerated African American Males, Robert Mossi Alexander Iii

Doctoral Dissertations

Reclaiming Our Humanity: Redemption, Reimagining, and Restorying of the Foundations for Success of Formerly Incarcerated African American Males African American men represent the highest population found in the criminal justice system. Systemic racism contributes to the high recidivism rates of formerly incarcerated Black men. Additional barriers to affordable education, job training, and other services exist for the formerly incarcerated. The purpose of this study was to interview formerly incarcerated African American men and provide a counter-narrative of the foundations for success post-incarceration. This research project explored the narratives of the lived experiences of formerly incarcerated Black men through the lenses …

Erythema Multiforme After Third Covid-19 Vaccination (Pfizer-Biontech), Stephen K Tyring

Faculty, Staff and Student Publications

We present a case of erythema multiforme (EM) associated with a third (booster) dose of COVID-19 vaccination in a patient who had no cutaneous reactions to previous doses. To our knowledge, this is the first documented case of vaccine-associated EM occurring after a third/booster vaccination. Furthermore, our case emphasizes the need to remain vigilant for vaccine-associated EM in any patient recently vaccinated, regardless of whether previous vaccinations were administered without cutaneous reactions.

Real-World Evidence Of An Emollient Device For Atopic And Contact Dermatitis In Pediatric To Adult Patients – Data From A Post-Marketing Surveillance

Faculty, Staff and Student Publications

PURPOSE: Atopic and contact dermatitis have been attributed to skin barrier abnormalities, immune system dysfunction and inflammation leading to pruritus. As these factors may involve oxidative stress, emollient devices containing antioxidants furfuryl palmitate and tocopherol may help reduce itching and inflammation. In this study, a post-marketing questionnaire was carried out of 40 users of a novel emollient device containing furfuryl palmitate and tocopherol (Relizema™ cream), who purchased it from a pharmacy or health-care professional to ascertain the emollient device's action on itching, flushing and moisturizing.

PATIENTS AND METHODS: The post-marketing questionnaire, administered by trained pharmacy and health-care staff, collected data …