Data Science Commons^™

The Protective Efficacy Of A Sars-Cov-2 Vaccine Candidate B1351v Against Several Variant Challenges In K18-Hace2 Mice, Xin Wan, Fengjie Lin, Dongsheng Yang, Jie Wu, Kaiwen Wang, Wei Li, Qian Cai, Lei You, Deqin Pang, Jia Lu, Changfu Guo, Jinrong Shi, Yan Sun, Xinguo Li, Kai Duan, Shuo Shen, Shengli Meng, Jing Guo, Zejun Wang

Faculty, Staff and Student Publications

The emergence of SARS-CoV-2 variants of concern (VOCs) with increased transmissibility and partial resistance to neutralization by antibodies has been observed globally. There is an urgent need for an effective vaccine to combat these variants. Our study demonstrated that the B.1.351 variant inactivated vaccine candidate (B.1.351V) generated strong binding and neutralizing antibody responses in BALB/c mice against the B.1.351 virus and other SARS-CoV-2 variants after two doses within 28 days. Immunized K18-hACE2 mice also exhibited elevated levels of live virus-neutralizing antibodies against various SARS-CoV-2 viruses. Following infection with these viruses, K18-hACE2 mice displayed a stable body weight, a high survival …

Influence Of Polypyrrole On Phosphorus- And Tio2-Based Anode Nanomaterials For Li-Ion Batteries, Yejin Kim, Keun-Young Shin, Byung Hyo Kim

Faculty, Staff and Student Publications

Phosphorus (P) and TiO2 have been extensively studied as anode materials for lithium-ion batteries (LIBs) due to their high specific capacities. However, P is limited by low electrical conductivity and significant volume changes during charge and discharge cycles, while TiO2 is hindered by low electrical conductivity and slow Li-ion diffusion. To address these issues, we synthesized organic–inorganic hybrid anode materials of P–polypyrrole (PPy) and TiO2–PPy, through in situ polymerization of pyrrole monomer in the presence of the nanoscale inorganic materials. These hybrid anode materials showed higher cycling stability and capacity compared to pure P and TiO2. The enhancements are attributed …

A/B Testing Of User Enrollment Forms To Enhance Diversity In The Biomedical Workforce Via The National Research Mentoring Network: User-Centered Design Case Study, Nan Kennedy, Damaris Javier, Katie Stinson, Jamboor K Vishwanatha

Faculty, Staff and Student Publications

BACKGROUND: The National Research Mentoring Network (NRMN) is a National Institutes of Health-funded program for diversifying the science, technology, engineering, math, and medicine research workforce through the provision of mentoring, networking, and professional development resources. The NRMN provides mentoring resources to members through its online platform-MyNRMN.

OBJECTIVE: MyNRMN helps members build a network of mentors. Our goal was to expand enrollment and mentoring connections, especially among those who have been historically underrepresented in biomedical training and the biomedical workforce.

METHODS: To improve the ease of enrollment, we implemented the split testing of iterations of our user interface for platform registration. …

Development Of The Roadway Pothole Management Program, Dingxin Cheng

Mineta Transportation Institute

Addressing the issue of potholes is a primary concern for maintaining urban infrastructure. The research team has developed a prototype pothole management program. The program includes a mobile application and two machine learning models. The mobile app enables users to upload images of potholes, report relevant information, and provide driving directions to the pothole location. With the help of this application, the user can seamlessly capture images of the potholes, record pertinent information, and submit the data for necessary action. The mobile application is an essential tool in the Pothole Management Program (PMP), as it enhances the program's efficiency, effectiveness, …

Enacting Data Context: Fixing Meaning In Transparency Data Initiatives, Lindsay Poirier

Statistical and Data Sciences: Faculty Publications

This article documents the “context cultures” underpinning efforts to develop regulations for collecting and reporting data in a United States public database known as Open Payments. Open Payments is a dataset published annually by the US Center for Medicare and Medicaid Services that documents the transfers of value from pharmaceutical and medical device manufacturers to physicians, prescribing non-physicians, and teaching hospitals. In the article, I show context became a manifold concern as differentially-situated actors engaged in modes of public advocacy and social action around not only what data meant, but also what it meant to make data meaningful. I show …

Identification Of Immune-Associated Biomarkers Of Diabetes Nephropathy Tubulointerstitial Injury Based On Machine Learning: A Bioinformatics Multi-Chip Integrated Analysis, Yaotan Li, Baoluo Hou, Yuxin Hu, Zhaoxi Dong, Jingyi Tang, Hongfang Liu, Weijing Liu

Faculty, Staff and Student Publications

BACKGROUND: Diabetic nephropathy (DN) is a major microvascular complication of diabetes and has become the leading cause of end-stage renal disease worldwide. A considerable number of DN patients have experienced irreversible end-stage renal disease progression due to the inability to diagnose the disease early. Therefore, reliable biomarkers that are helpful for early diagnosis and treatment are identified. The migration of immune cells to the kidney is considered to be a key step in the progression of DN-related vascular injury. Therefore, finding markers in this process may be more helpful for the early diagnosis and progression prediction of DN.

METHODS: The …

Ghcu, A Molecular Chaperone, Regulates Leaf Curling By Modulating The Distribution Of Kngh1 In Cotton, Lisha Xuan, Sunyi Yan, Yayao Zhang, Yiwen Cao, Xiaoran Li, Zhanfeng Si, Jieqiong Deng, Tianzhen Zhang, Yan Hu

Faculty, Staff and Student Publications

Leaf shape is considered to be one of the most significant agronomic traits in crop breeding. However, the molecular basis underlying leaf morphogenesis in cotton is still largely unknown. In this study, through genetic mapping and molecular investigation using a natural cotton mutant cu with leaves curling upward, the causal gene GHCU is successfully identified as the key regulator of leaf flattening. Knockout of GHCU or its homolog in cotton and tobacco using CRISPR results in abnormal leaf shape. It is further discovered that GHCU facilitates the transport of the HD protein KNOTTED1-like (KNGH1) from the adaxial to the abaxial …

Genetic Analysis Of Seven Patients With Inherited Ichthyosis And Nagashima-Type Palmoplantar Keratoderma, Lin-Xi Zeng, Guo-Qiang Zhang

Faculty, Staff and Student Publications

Inherited ichthyosis comprises a series of heterogeneous dermal conditions; it mainly manifests as widespread hyperkeratosis, xerosis and scaling of the skin. At times, overlapping symptoms require differential diagnosis between ichthyosis and several other similar disorders. The present study reports seven patients with confirmed or suspected to be associated with ichthyosis by conducting a thorough clinical and genetic investigation. Genetic testing was conducted using whole-exome sequencing, with Sanger sequencing as the validation method. The MEGA7 program was used to analyze the conservation of amino acid residues affected by the detected missense variants. The enrolled patients exhibited ichthyosis-like but distinct clinical manifestations. …

Fedgmmat: Federated Generalized Linear Mixed Model Association Tests

Faculty, Staff and Student Publications

Increasing genetic and phenotypic data size is critical for understanding the genetic determinants of diseases. Evidently, establishing practical means for collaboration and data sharing among institutions is a fundamental methodological barrier for performing high-powered studies. As the sample sizes become more heterogeneous, complex statistical approaches, such as generalized linear mixed effects models, must be used to correct for the confounders that may bias results. On another front, due to the privacy concerns around Protected Health Information (PHI), genetic information is restrictively protected by sharing according to regulations such as Health Insurance Portability and Accountability Act (HIPAA). This limits data sharing …

Streaminghub - A Realtime Biosignal Processing Framework For Lab Scale Experimentation, Yasith Jayawardana

Computer Science Theses & Dissertations

In human subjects research, biosignals such as eye movements, heart rate, and brain activity, are often collected and analyzed to find patterns with tangible real-world implications. Modern advancements in technology have sparked interest towards analyzing biosignals in realtime. When developing such algorithms, one may expect to find free, open-source tools that provide easy access to live, recorded, and simulated data streams. Yet, biosignal interfaces are often vendor-specific, making cross-vendor biosignal streaming non-trivial. Likewise, reading biosignal datasets is also non-trivial, as their content may be arranged quite differently.

To combat this divide, we provide the scientific community with a realtime biosignal …

An Integrated Space Test Lexicon: A Taxonomy For The Integrated Test And Evaluation Of Space Systems, Stephen K. Tullino, Andrew S. Keys, Robert A. Bettinger, Amy M. Cox, David R. Jacques

Faculty Publications

The proposed Integrated Space Test Lexicon is intended to amalgamate the numerous definitions of integrated (IT or IT&E), development test (DT or DT&E), and operational test (OT or OT&E) into unified, service-wide definitions, aligned with the Space Test Enterprise Vision. Refining such definitions will help distill the core characteristics of these fundamental test types to first identify space system activities composing what is traditionally known as DT and OT, then to provide a means of how these activities fit into the IT paradigm and support space system development. In forging a common understanding of how DT and OT support space …

Metabolomics Analysis Reveals Metabolite Diversity Of The Rare Cliff Plant Oresitrophe Rupifraga Unge, Guangming Zhang

Faculty, Staff and Student Publications

Oresitrophe is monotypic, with the only species, Oresitrophe rupifraga Bunge, which is exclusive to China, having special growth and developmental traits due to its habitat. Furthermore, it has bright flowers and medicinal benefits. This study investigated the metabolites present in various tissues of Oresitrophe rupifraga Bunge. Using a widely targeted metabolomics approach, 1965 different metabolites were identified in Oresitrophe rupifraga Bunge. Based on principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA), the aboveground and underground metabolites of Oresitrophe rupifraga differed significantly. The comparison between bulblets and leaves revealed the differential expression of 461 metabolites, whereas the …

Considerations For Quality Control Monitoring Of Machine Learning Models In Clinical Practice, Hongfang Liu, Xiaoyang Ruan, Curt Storlie

Faculty, Staff and Student Publications

Integrating machine learning (ML) models into clinical practice presents a challenge of maintaining their efficacy over time. While existing literature offers valuable strategies for detecting declining model performance, there is a need to document the broader challenges and solutions associated with the real-world development and integration of model monitoring solutions. This work details the development and use of a platform for monitoring the performance of a production-level ML model operating in Mayo Clinic. In this paper, we aimed to provide a series of considerations and guidelines necessary for integrating such a platform into a team's technical infrastructure and workflow. We …

Discovery Of Runs-Of-Homozygosity Diplotype Clusters And Their Associations With Diseases In Uk Biobank

Faculty, Staff and Student Publications

Runs-of-homozygosity (ROH) segments, contiguous homozygous regions in a genome were traditionally linked to families and inbred populations. However, a growing literature suggests that ROHs are ubiquitous in outbred populations. Still, most existing genetic studies of ROH in populations are limited to aggregated ROH content across the genome, which does not offer the resolution for mapping causal loci. This limitation is mainly due to a lack of methods for the efficient identification of shared ROH diplotypes. Here, we present a new method, ROH-DICE (runs-of-homozygous diplotype cluster enumerator), to find large ROH diplotype clusters, sufficiently long ROHs shared by a sufficient number …

Study Of Prognostic Splicing Factors In Cancer Using Machine Learning Approaches

Faculty, Staff and Student Publications

Splicing factors (SFs) are the major RNA-binding proteins (RBPs) and key molecules that regulate the splicing of mRNA molecules through binding to mRNAs. The expression of splicing factors is frequently deregulated in different cancer types, causing the generation of oncogenic proteins involved in cancer hallmarks. In this study, we investigated the genes that encode RNA-binding proteins and identified potential splicing factors that contribute to the aberrant splicing applying a random forest classification model. The result suggested 56 splicing factors were related to the prognosis of 13 cancers, two SF complexes in liver hepatocellular carcinoma, and one SF complex in esophageal …

Successful Management Of Chromoblastomycosis Utilizing Conventional Antifungal Agents And Imiquimod Therapy, Liyan Xi, Hongfang Liu, Yinghui Liu

Faculty, Staff and Student Publications

Chromoblastomycosis (CBM), a chronic fungal infection affecting the skin and subcutaneous tissues, is predominantly caused by dematiaceous fungi in tropical and subtropical areas. Characteristically, CBM presents as plaques and nodules, often leading to scarring post-healing. Besides traditional diagnostic methods such as fungal microscopy, culture, and histopathology, dermatoscopy and reflectance confocal microscopy can aid in diagnosis. The treatment of CBM is an extended and protracted process. Imiquimod, acting as an immune response modifier, boosts the host's immune response against CBM, and controls scar hyperplasia, thereby reducing the treatment duration. We present a case of CBM in Guangdong with characteristic reflectance confocal …

Extreme Value Statistics Analysis Of Process Defects In Additive Manufacturing Materials, Ayorinde E. Olatunde, Kristen Hernandez, Austin Ngo, Arafath Nihar, Thomas G. Ciardi, Rachel Yamamoto, Pawan K. Tripathi, Roger H. French, John J. Lewandowski, Anirban Mondal

Faculty Scholarship

Fatigue and fracture studies focused on process defects that occur in Additive Manufacturing (AM) materials have shown that defect populations possess features which are better measured with extreme value statistics (EVS). In AM alloys, defect occurrences increase with material volume. This situation facilitates the need to model process defects in the path of fatigue crack growth with suitable statistical tools, such as EVS, which is more cost-effective when compared to destructive experiments. The application of EVS on defect space features helps determine the difference in defects present on fracture surfaces. As the fatigue quality of any material depends on its …

Diverse Mentoring Connections Across Institutional Boundaries In The Biomedical Sciences: Innovative Graph Database Analysis, Damaris Javier, Katie Stinson, Gabrielle Saleh, Jamboor K Vishwanatha

Faculty, Staff and Student Publications

BACKGROUND: With an overarching goal of increasing diversity and inclusion in biomedical sciences, the National Research Mentoring Network (NRMN) developed a web-based national mentoring platform (MyNRMN) that seeks to connect mentors and mentees to support the persistence of underrepresented minorities in the biomedical sciences. As of May 15, 2024, the MyNRMN platform, which provides mentoring, networking, and professional development tools, has facilitated more than 12,100 unique mentoring connections between faculty, students, and researchers in the biomedical domain.

OBJECTIVE: This study aimed to examine the large-scale mentoring connections facilitated by our web-based platform between students (mentees) and faculty (mentors) across institutional …

Sre-Yolov8: : An Improved Uav Object Detection Model Utilizing Swin Transformer And Re-Fpn

Faculty, Staff and Student Publications

To tackle the intricate challenges associated with the low detection accuracy of images taken by unmanned aerial vehicles (UAVs), arising from the diverse sizes and types of objects coupled with limited feature information, we present the SRE-YOLOv8 as an advanced method. Our method enhances the YOLOv8 object detection algorithm by leveraging the Swin Transformer and a lightweight residual feature pyramid network (RE-FPN) structure. Firstly, we introduce an optimized Swin Transformer module into the backbone network to preserve ample global contextual information during feature extraction and to extract a broader spectrum of features using self-attention mechanisms. Subsequently, we integrate a Residual …

Examining The Interaction Between Calcium Supplement Use, Demographics, And Lifestyle Factors On Bone Health In Women, Vix Talbot

University Honors Theses

Osteoporosis is a condition which poses a significant health threat, particularly among women during the menopause transition, where accelerated bone loss increases fracture risk. Calcium supplementation has been shown to be an important intervention to mitigate bone mineral density (BMD) decline during this and other periods of life. However, the efficacy of calcium supplementation is influenced by various individual factors, including demographics and lifestyle habits. This study investigates the interaction between calcium supplement use, and several interaction terms on bone health in women. Multiple linear regression analysis is employed to assess the impact of these factors on BMD. Data from …