Life Sciences Commons^™

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, …

Table Of Contents, Taxonomic Report Of The International Lepidoptera Survey, October 1, 1998–December 20, 2022, International Lepidoptera Survey

The Taxonomic Report of the International Lepidoptera Survey

Table of contents for all issues of the Taxonomic Report of the International Lepidoptera Survey from October 1, 1998 (volume 1, issue 1) through December 20, 2022 (volume 10, issue 10).

Cphelps Et Al. Disease, Natural And Aquaria E. Radiata Microbiome Asv (Amplicon Sequence Variant) Table, Charlie M. Phelps

Research Datasets

This ASV table is the raw sequencing abundances for the Chapter 4 dataset with accompanying metadata.

Discovery Of Inhibitors Of Peptidoglycan O-Acetyltransferase B (Patb) From Neisseria Gonorrhoeae, A New Potential Antibacterial Target, Stefen Stangherlin

Theses and Dissertations (Comprehensive)

Experts project that by 2050, 10 million lives will be lost annually as a result of antimicrobial resistant infections, surpassing all current leading causes of death, and costing the global economy $100 trillion USD on healthcare efforts. To promote research and development of novel antibiotics, the World Health Organization and Centers for Disease Control and Prevention released a list of priority pathogens regarded as serious or urgent threats of antimicrobial resistance. Many pathogenic bacteria, including several priority pathogens, produce O-acetylated peptidoglycan to establish infection and avoid host immune responses. Consequently, the enzymes responsible for producing O-acetylated peptidoglycan in Gram-negative pathogenic …

Changes In Plant Community Composition, Structure, And Function In Response To Permafrost Thaw, Katherine Standen

Theses and Dissertations (Comprehensive)

Air temperature is increasing at three or more times the global average in high latitudes, causing widespread permafrost thaw across the boreal biome. Since the boreal biome stores 30-40% of global terrestrial carbon (C), of which about 30-45% is found in permafrost soils, this temperature increase could cause a large efflux of C to the atmosphere. Climate warming and permafrost thaw are also expected to alter plant community composition and productivity and, given the link between plant functional traits and ecosystem C fluxes, may alter overall ecosystem function. Across the boreal biome of western Canada, we know surprisingly little about …

The Electrophysiological Correlates Of Text Integration And Direct Vs. Indirect Articles: A Centralized And Lateralized Examination, Deanna C. Hall

Theses and Dissertations (Comprehensive)

As we read, we develop mental models of the discourse content called situation models. Situation models are integral to how we keep track of information, and to do so in an ongoing event incoming information needs to be integrated into the model or discarded. The type of information being presented, and its relation to prior data, impacts how that new information is processed. The current research examined discourse passages containing concepts that were either previously mentioned (match), mentioned with a general term (general category), unmentioned in lieu of another concept (mismatch), or completely unmentioned previously (indeterminate), and examined how these …

Arctic Stream Characteristics And Diet Analysis Choice Impact Condition And Diet Estimates Of Ninespine Stickleback (Pungitius Pungitius), Adam Kuhrt

Theses and Dissertations (Comprehensive)

Ninespine stickleback (Pungitius pungitius) are ubiquitous in circumpolar freshwaters, but their ecological role is not well understood. Little research has been conducted on the influence of environmental variables on ninespine stickleback in stream environments, and while they are understood to be generalist feeders, their diet in stream environments is equally understudied. Determining diet is difficult due to biases inherent in all standard diet analysis methods. Morphological gut-content analysis (M-GCA), DNA metabarcoding of gut contents (D-GCA), and stable isotope analysis (SIA) are currently three of the most frequently conducted diet analyses; and while combinations of these methods are commonly …

Impacts Of Changing Permafrost Conditions On Vegetation Productivity In The Northern Boreal Forest, Emily Ogden

Theses and Dissertations (Comprehensive)

Vegetation productivity across the boreal forest has increased over the past several decades. However, at a regional scale there is large variation from increased (greening) to decreased (browning) productivity and large areas with no measured change. Some of this variation can be explained by disturbances, such as wildfire, or by increased climate variability. In northern regions underlain by permafrost, the interactions between climate, disturbance, and vegetation productivity may be more complex. For my thesis, I used a time-series of ground thermal data from permafrost monitoring sites established by the Geological Survey of Canada along a latitudinal transect of the Northwest …

Effects Of 17Α-Ethinylestradiol (Ee2) On Gonadal Development And Gene Expression In Larval Mummichog (Fundulus Heteroclitus), Carly Sing-Judge

Theses and Dissertations (Comprehensive)

The mummichog (Fundulus heteroclitus) is a small-bodied estuarine fish that inhabits the North American east coast and is often used as a model adult saltwater fish in environmental bioassays. This study aimed to describe gonadal development and gene expression levels in five-week-old mummichog under control conditions and following 17α-ethinylestradiol (EE₂) treatment in order to better understand the susceptibility of sex determination (SD) and gonadal differentiation (GD) processes following contaminant exposure. In the first experiment, eggs were fertilized, collected and incubated in the laboratory for three weeks, then yolk-sac larvae were grown out for five weeks and …

Impact Of Orthophosphate As A Corrosion Inhibitor And Chloramine Disinfectant On Drinking Water Biofilm Communities, Mitchell Cooke

Theses and Dissertations (Comprehensive)

A drinking water distribution system (DWDS) must maintain conditions within quality standards which assure the effective and safe transport of finished drinking water from treatment plants to the household tap. Although safe to drink, finished water is not sterile, and may contain hundreds of microorganisms in a single milliliter. These microorganisms are present from the source waters, such as lakes, rivers and aquifers, and have passed through early treatment steps. Final treatment steps, such as the maintenance of disinfectant residuals, are used to further minimize viable cells present and focus on the reduction of harmful organisms. Microbial cells entering the …

Young Adult And Adolescent Balance Control Strategies During A Dual-Task Stone-Stepping Paradigm, Emily Ford

Theses and Dissertations (Comprehensive)

Stone-stepping demands greater attention and visuomotor integration, as it requires precise foot placement. The amount of attention required during locomotion is typically assessed with a secondary task, by analyzing the dual-task cost. Adolescents are suggested to have a greater dual-task cost than young adults and demonstrate balance control impairments while dual-tasking walking. The purpose of the current study was to explore the balance control differences between adolescents and young adults during a stone-stepping paradigm. We hypothesized that adolescents would experience greater balance control deficits while performing the secondary task compared to the young adults, especially while on the uneven terrain. …

The Avian Hippocampal Declarative Memory System, Chelsey C. Damphousse

Theses and Dissertations (Comprehensive)

Across Mammalia, memory has long been dissociated into multiple component systems specialized to process specific facets of experience. Among these segregated systems, declarative memory is processed by the hippocampus and surrounding structures, which have collectively been referred to as the hippocampal declarative memory system (HDMS). The HDMS, in turn, can be further divided into parallel streams dedicated to the processing of spatial versus object identity based information, commonly discussed as the ‘what’ and ‘where’ streams. While we know that the organization of the HDMS is conserved in humans, nonhuman primates, and rats, evidence outside Mammalia is lacking. Here HDMS homology …

Diversity And Evolution Of Inflorescences In Cuscuta, Morgan Glofcheskie

Theses and Dissertations (Comprehensive)

Cuscuta (dodder) includes ca. 200 species of plant obligate stem parasites with both ecological and economical significance. Inflorescences have been historically used in Cuscuta for species descriptions and identification keys, but no comprehensive study exists to date. The main objective of this study was to survey the diversity of inflorescences, and to understand their evolution and possible form-function relationships. The inflorescence architecture of 132 Cuscuta taxa was analyzed using herbarium specimens, and eight species were grown to study their inflorescence development. Inflorescence traits were mapped into a genus phylogeny obtained from a combined analysis of nuclear ITS and plastid trnL-F …

Toxicity Of The Technology Critical Elements Germanium And Yttrium To Daphnia Magna And Hyalella Azteca And The Influence Of Toxicity Modifying Factors, Rashid Shah

Theses and Dissertations (Comprehensive)

Technology critical elements (TCEs) are increasingly used in high and green technologies but there is little aquatic toxicity data for TCEs, particularly in fresh water. The objective of this study was to investigate the toxicity of two TCEs, Ge and Y, to Daphnia magna and Hyalella azteca and to understand the role of natural organic matter and cations on toxicity modification. Testing followed standard methods. The 48 h EC50 for D. magna was 11.6 (95% CI of 9.64-13.8) mg Ge/L based on measured dissolved concentrations at test end. The addition of NOM at 10 mg DOC/L resulted in a significant …

Transformation Of Farmer Resistance In Conservation Areas: Land Occupation By Farmers In Mount Halimun-Salak National Park, West Java, Sulastri Sardjo, Arya Hadi Dharmawan, Dudung Darusman, Ekawati Sri Wahyuni

Masyarakat: Jurnal Sosiologi

A number of studies have shown various agrarian conflicts as a response by local farmers against the policy of national parks that prohibits them from accessing conservation forest areas. However, previous studies had not explained the dynamics of power relations between park authorities and farmers who stand in opposition to these policies. This study employs a qualitative research approach complemented by secondary data to explain the transformation of farmer resistance in the Mount Halimun-Salak National Park (TNGHS) area, namely from their repertoire of everyday resistance to practices of land occupation. Specifically, this study uses the “powercube” analytical framework to explain …

Employers’ General Knowledge, Social Attitudes, Experience, And Employability Of Level 1 Autism Spectrum Disorder Adults, Jennifer C. Kiselica

Walden Dissertations and Doctoral Studies

AbstractAutism spectrum disorders (ASD) is a neurodevelopmental disorder which causes an individual to have abnormalities in socialization and communication, and unusual behaviors and interests. Each year about a half million young adults with ASD transition from high school to adulthood; however, only 57% become employed. The current study’s purpose was to investigate how general knowledge of ASD and social interactions with those with ASD affected employers’ social attitudes and perceptions of those with ASD being employed by them. Social Contact theory employers who have more social interaction with individuals with ASD have more social knowledge about ASD.. The population for …

Emotional Intelligence And Soft Skills: A Case Study On Information Technology Employee Performance, James Tyler

Walden Dissertations and Doctoral Studies

Soft skills such as communication, teamwork, problem-solving, and stress management in recent years have been seen as a new trend in organizations. Even though there is research demonstrating the importance of soft skills, there is little research on how information technology (IT) organizations are training and evaluating their employees in soft skills. The purpose of this qualitative case study was to understand how human resources departments in IT organizations are training employees on soft skills and how they are evaluating employees’ level of performance. The conceptual framework that was used in this study was Goleman’s emotional intelligence model of self-awareness, …