Data Science Commons^™

Analyzing The Effects Of Data Variability & Volume On Predicting Particulate Matter (Pm2.5): Insights From A Machine Learning Approach, Jada A. Macharie

Theses and Dissertations

Accurately predicting PM_2.5 concentrations are imperative to the future of public health and environmental policies. Machine learning models incorporating spatial and temporal datasets to predict PM_2.5 are often limited by data availability constraints and poor resolution satellite imagery.

Safety, Immunogenicity, And Mechanism Of A Rotavirus Mrna-Lnp Vaccine In Mice, Chenxing Lu, Yan Li, Rong Chen, Xiaoqing Hu, Qingmei Leng, Xiaopeng Song, Xiaochen Lin, Jun Ye, Jinlan Wang, Jinmei Li, Lida Yao, Xianqiong Tang, Xiangjun Kuang, Guangming Zhang, Maosheng Sun, Yan Zhou, Hongjun Li

Faculty, Staff and Student Publications

Rotaviruses (RVs) are a major cause of diarrhea in young children worldwide. The currently available and licensed vaccines contain live attenuated RVs. Optimization of live attenuated RV vaccines or developing non-replicating RV (e.g., mRNA) vaccines is crucial for reducing the morbidity and mortality from RV infections. Herein, a nucleoside-modified mRNA vaccine encapsulated in lipid nanoparticles (LNP) and encoding the VP7 protein from the G1 type of RV was developed. The 5' untranslated region of an isolated human RV was utilized for the mRNA vaccine. After undergoing quality inspection, the VP7-mRNA vaccine was injected by subcutaneous or intramuscular routes into mice. …

The Impact Of Accessible Data On Cyberstalking, Elise Kwan

The Journal of Purdue Undergraduate Research

No abstract provided.

Model Selection Through Cross-Validation For Supervised Learning Tasks With Manifold Data, Derek Brown

The Journal of Purdue Undergraduate Research

No abstract provided.

Machine Learning Of Big Data: A Gaussian Regression Model To Predict The Spatiotemporal Distribution Of Ground Ozone, Jerry Gu

The Journal of Purdue Undergraduate Research

Tracking pollution levels on the ground is important to the environment and public health. One of the pollutants of concern is ozone, which, at high concentrations, can cause respiratory and cardiovascular problems. The National Center for Atmospheric Research (NCAR) has published valuable ozone data obtained from ground-based sensors installed at selected locations. Because it is unfeasible to measure the exact ozone levels everywhere at any time, it would be valuable to predict the temporal-spatial distributions of ozone concentration based on existing data. This would help us better understand the patterns and trends in the data and make better decisions to …

A Computational Profile Of Invasive Lionfish In Belize: A New Insight On A Destructive Species, Joshua E. Balan

The Journal of Purdue Undergraduate Research

Since their discovery in the region in 2009, invasive Indonesian-native lionfish have been taking over the Belize Barrier Reef. As a result, populations of local species have dwindled as they are either eaten or outcompeted by the invaders. This has led to devastating losses ecologically and economically; massive industries in the local nations, such as fisheries and tourism, have suffered greatly. Attempting to combat this, local organizations, from nonprofits to ecotourism companies, have been manually spear-hunting them on scuba dives to cull the population. One such company, Reef Conservation Institute (ReefCI), operating out of Tom Owens Caye outside of Placencia, …

Prevention And Potential Treatment Strategies For Respiratory Syncytial Virus, Bo-Wen Sun, Peng-Peng Zhang, Zong-Hao Wang, Xia Yao, Meng-Lan He, Rui-Ting Bai, Hao Che, Jing Lin, Tian Xie, Zi Hui, Xiang-Yang Ye, Li-Wei Wang

Faculty, Staff and Student Publications

Respiratory syncytial virus (RSV) is a significant viral pathogen that causes respiratory infections in infants, the elderly, and immunocompromised individuals. RSV-related illnesses impose a substantial economic burden worldwide annually. The molecular structure, function, and in vivo interaction mechanisms of RSV have received more comprehensive attention in recent times, and significant progress has been made in developing inhibitors targeting various stages of the RSV replication cycle. These include fusion inhibitors, RSV polymerase inhibitors, and nucleoprotein inhibitors, as well as FDA-approved RSV prophylactic drugs palivizumab and nirsevimab. The research community is hopeful that these developments might provide easier access to knowledge and …

Dementia Prediction In Older Adults Using Sex-Specific Health Trajectory Clustering, Omar A Ibrahim, Muskan Garg, Sunyang Fu, Maria Vassilaki, Ronald C Petersen, Jennifer St Sauver, Sunghwan Sohn

Faculty, Staff and Student Publications

With increasing number of people living with dementia, the problem of late diagnosis significantly impacts a person's quality of life while early signs of dementia may provide useful insights to facilitate better treatment plans. With time, this progressive neurodegenerative syndrome could progress from mild cognitive impairment to dementia. A pattern of health conditions can be characterized in unsupervised manner to help predict this progress. As a significant extension to our previous work with streaming clustering model, we consider additional information for predicting dementia onset. With empirical observations, we discover the importance of examining sex and age to predict dementia onset. …

Fusionnw, A Potential Clinical Impact Assessment Of Kinases In Pan-Cancer Fusion Gene Network, Chengyuan Yang, Himansu Kumar, Pora Kim

Faculty, Staff and Student Publications

Kinase fusion genes are the most active fusion gene group in human cancer fusion genes. To help choose the clinically significant kinase so that the cancer patients that have fusion genes can be better diagnosed, we need a metric to infer the assessment of kinases in pan-cancer fusion genes rather than relying on the sample frequency expressed fusion genes. Most of all, multiple studies assessed human kinases as the drug targets using multiple types of genomic and clinical information, but none used the kinase fusion genes in their study. The assessment studies of kinase without kinase fusion gene events can …

Current Status And Applications Of Microbial Chassis Strains For Chinese Biomanufacturing Industry, Guoqiang Chen, Fuqing Wu, Shuang Zheng, Jun Ding, Junting Sheng

Bulletin of Chinese Academy of Sciences (Chinese Version)

Biomanufacturing is an important component of new quality productive forces, representing the commanding height of the new round of technological revolution and serving as a new engine for industrial transformation following information technology. It demonstrates vast application prospects in fields such as renewable energy, advanced materials, biomedicine, green food, and environmental protection. Biomanufacturing utilizes chassis microorganisms similar as “microchip” to produce various bioproducts via processes including chassis design and construction, large-scale cell cultivation, and product purifications. Most chassis microorganisms in biomanufacturing were not domestically identified. This study summarizes the types of common chassis microorganisms both domestically and internationally, as well …

Research Progress In High-Throughput Phenotype Testing Technology And Equipment For Engineering Cells Based On Microfluidics, Shuang Li, Xiaojie Guo, Haibo Chen, Sisi Chen, Xin Da, Zhenghui Li, Qinxiu Liu, Yi Wang, Xinhui Xing, Chong Zhang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Engineering cells are a core component of green bio-manufacturing. The efficient testing and acquisition of engineering cells with the desired phenotype is a critical factor in the successful implementation of bio-manufacturing. In recent years, based on microfluidics technologies, non-culture type single-cell phenotype high-throughput test equipment and culture type phenotype high-throughput test equipment for the growth and metabolism of single cell in a bioreactor have been developed such as microdroplet and microchamber, realizing high-throughput, automated, miniaturized, and integrated testing of the phenotypes of engineering cells and providing a powerful tool for the breeding of engineering cells. This review systematically compiles the …

Analysis And Reflections On Key Platform Facilities Construction Of Global Biomanufacturing Industry, Xiaoyan Wu, Fang Chen, Yaoying Shan, Anjing Lu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Biomanufacturing, an emerging production method, is becoming a significant trend in global economic development and has garnered widespread international attention. Platform facilities are vital to the biomanufacturing industry’s development, serving as both the foundation for technological innovation and the bridge between research outcomes and practical applications. This study analyzes three key types of platform facilities and their operational mechanisms: technology innovation platforms (exemplified by the U.S. Agile BioFoundry), pilot-scale platforms (represented by European Bio Base Europe Pilot Plant), and industry incubation platforms (illustrated by the UK SynbiCITE). Drawing from these successful examples and examining China’s current platform infrastructure, this paper …

Research On Innovative Development Path And Policy Guarantee Of China’S Synthetic Biology Industry, Hongjun Geng, Chang Wang

Bulletin of Chinese Academy of Sciences (Chinese Version)

Synthetic biology is hailed as the third revolution in life sciences after the discovery of the DNA double helix structure and genomic technology, and is the core driving force for the leapfrog development of next-generation biomanufacturing and the future bioeconomy, opening up an opportunity window for the reshaping of the global manufacturing map. How to strategically position the synthesis biology industry and seize the strategic high ground in the industry is a core topic of interest for global science and technology powers and manufacturing powers. Based on the identification of problems in the development of China’s synthesis biology industry, this …

Internal Logic And Policy Recommendations Of Big Data To Support High-Quality Development Of Modern Agricultural Industry, Yingming Li, Zitong Wang, Mingyue Wang, Shiyi Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Clarifying the internal logic of big data to support modern agricultural production is helpful to cultivate and develop new quality productive forces in agriculture. From the perspective of economics, this study proposes that the role of big data in modern agricultural production is mainly reflected in two levels. Firstly, it improves the total factor productivity of the traditional agricultural production function. Secondly, it changes the factor endowment structure of agricultural production and forms a new agricultural production function. Based on these, the realization form of big data to support modern agricultural production can be summarized as improving the efficiency of …

Recent Progress And Perspectives On Development Of Gene Editing Tools, Zixian Liu, Chengping Li, Gogo Jun-Jie Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

The gene editing field has witnessed remarkable advancements in recent years, leading to the establishment and refinement of multidimensional gene editing platforms. These innovations have enabled precise targeted gene knockout, repair, and insertion. These tools have stimulated significant progress in fundamental research, therapeutics, agriculture, environment protection, and industrial applications. In this review, we provide a comprehensive overview of the milestones in gene editing tool development and offer perspectives on potential future directions for this rapidly evolving field.

Microbial Production Of Feed Amino Acids Promotes Reduction And Replacement Of Soybean Meal, Jia Liu, Qi Sheng, Kaifang Liu, Liming Liu

Bulletin of Chinese Academy of Sciences (Chinese Version)

With the promotion of soybean meal reduction and substitution as well as lower-protein diet technologies, China has become a leading global producer of feed amino acids. However, the amino acid industry faces significant challenges due to its relatively late start in independently developing industrial strains, resulting in relatively lagging key economic and technical parameters and a less robust intellectual property framework. The rapid progress of synthetic biology has provided promising avenues for the design and optimization of industrial amino acid-producing strains, offering new opportunities for the amino acid fermentation industry to enhance the global competitiveness. This study offers an in-depth …

Current Status And Prospect Of Industrial Filamentous Fungi In Biomanufacturing, Zhiqiang Du, Ping Men, Yu Zhou, Xuan Zhang, Xuenian Huang, Xuefeng Lyu

Bulletin of Chinese Academy of Sciences (Chinese Version)

Filamentous fungi, a critical class of industrial microorganisms pivotal to the biomanufacturing industry, has extensive applications in various fields such as pharmaceuticals, food, agriculture, and chemical materials, which are playing a vital role in human life. Recently, innovations in synthetic biology have further driven the application of industrial filamentous fungi in biomanufacturing, highlighting their critical role in this field. This article presents a comprehensive review of the recent progress in the field, covering the latest developments in genetic modification techniques for industrial filamentous fungi, successful cases of rational strain improvement strategies aimed to enhance the quality and efficiency of current …

Digitalized Design Of Cell Factory Enables Green Biomanufacturing, Fanze Meng, Rui Cao, Bing Hu, Lei Qin, Chun Li

Bulletin of Chinese Academy of Sciences (Chinese Version)

Green manufacturing is a modern manufacturing mode in the consideration of both environmental impact and efficiency of resource utilization, it represents a significant component of the “new productive force”. Centered on cell factories, green biomanufacturing leverages renewable resources to efficiently produce products that conform to the concepts of low-carbon, green, and sustainable development. The design of high-performance cell factories is pivotal for achieving efficient green biomanufacturing. Nevertheless, traditional cell factory design processes are complex, time-consuming, and labor-intensive. With advancements in artificial intelligence, digital-assisted cell factory design has emerged as a solution to save time and reduce costs. By integrating technologies …

Bioprocess Engineering And Intelligent Biomanufacturing, Guan Wang, Yingping Zhuang

Bulletin of Chinese Academy of Sciences (Chinese Version)

In the era of rapid development of synthetic biology, biomanufacturing, as a bridge between life sciences and engineering technologies, is gradually demonstrating its extraordinary potential to reshape industrial landscapes. However, challenges such as production efficiency, cost control, and process monitoring still hinder the smooth transition from laboratory innovations to industrial-scale implementation. Intelligent biomanufacturing has emerged as a new form of productive force, offering innovative solutions to these problems. This study reviews the latest advances in bioprocess engineering and intelligent biomanufacturing, focusing on three key technological systems: intelligent sensing, intelligent analysis, and intelligent control. Intelligent sensing technology acts as the “eyes” …

Artificial Intelligence Driven Information Technology System Restructuring And Reconstruction—Review Of Information Science & Technology In China: A Roadmap To 2050, Xuehai Hong

Bulletin of Chinese Academy of Sciences (Chinese Version)

The Information Science & Technology in China: A Roadmap to 2050 and Information Technology: Accelerating the Integration of Human Machine Things have predicted the long-term development of China’s information technology field. This study reviews the development and changes in the field of information technology in the past 15 years, and compares them with the initial predictions, pointing out that some important judgments made at the beginning were in line with expectations. In recent years, the global development of information technology has entered a slow period, while the rapid evolution of the new generation of artificial intelligence will bring new opportunities …

Revealing Chronic Disease Progression Patterns Using Gaussian Process For Stage Inference, Yanfei Wang, Weiling Zhao, Angela Ross, Lei You, Hongyu Wang, Xiaobo Zhou

Faculty, Staff and Student Publications

OBJECTIVE: The early stages of chronic disease typically progress slowly, so symptoms are usually only noticed until the disease is advanced. Slow progression and heterogeneous manifestations make it challenging to model the transition from normal to disease status. As patient conditions are only observed at discrete timestamps with varying intervals, an incomplete understanding of disease progression and heterogeneity affects clinical practice and drug development.

MATERIALS AND METHODS: We developed the Gaussian Process for Stage Inference (GPSI) approach to uncover chronic disease progression patterns and assess the dynamic contribution of clinical features. We tested the ability of the GPSI to reliably …

Development And Validation Of A Nomogram For Predicting Pulmonary Infection In Patients Receiving Immunosuppressive Drugs, Chuxuan Luo, Yue Zhang, Jiajie Zhang, Chen Jin, Xiaolan Ye, Yan Ren, Huajuan Shen, Maosheng Chen, Yiwen Li, Qiang He, Guangbiao Xu, Lina Shao

Faculty, Staff and Student Publications

Objective: Pulmonary infection (PI), a severe complication of immunosuppressive therapy, affects patients' prognosis. As part of this study, we aimed to construct a pulmonary infection prediction (PIP) model and validate it in patients receiving immunosuppressive drugs (ISDs). Methods: Totally, 7,977 patients being treated with ISDs were randomised 7:3 to the developing (n = 5,583) versus validation datasets (n = 2,394). Our predictive nomogram was established using the least absolute shrinkage and selection operator (LASSO) and multivariate COX regression analyses. With the use of the concordance index (C-index) and calibration curve, the prediction performance of the final model was …

Expanded T Lymphocytes In The Cerebrospinal Fluid Of Multiple Sclerosis Patients Are Specific For Epstein-Barr-Virus-Infected B Cells, Assaf Gottlieb, H Phuong T Pham, Jerome G Saltarrelli, J William Lindsey

Faculty, Staff and Student Publications

Epstein-Barr virus (EBV) infection has long been associated with multiple sclerosis (MS), but the role of EBV in the pathogenesis of MS is not clear. Our hypothesis is that a major fraction of the expanded clones of T lymphocytes in the cerebrospinal fluid (CSF) are specific for autologous EBV-infected B cells. We obtained blood and CSF samples from eight relapsing-remitting patients in the process of diagnosis. We stimulated cells from the blood with autologous EBV-infected lymphoblastoid cell lines (LCL), EBV, varicella zoster virus, influenza, and candida and sorted the responding cells with flow cytometry after 6 d. We sequenced the …

Qiditangshen Granules Alleviates Diabetic Nephropathy Podocyte Injury: A Network Pharmacology Study And Experimental Validation In Vivo And Vitro, Fei Gao, Ying Zhou, Borui Yu, Huidi Xie, Yang Shi, Xianhui Zhang, Hongfang Liu

Faculty, Staff and Student Publications

BACKGROUND: QiDiTangShen granules (QDTS), a traditional Chinese medicine (TCM) compound prescription, have remarkable efficacy in diabetic nephropathy (DN) patients, and their pharmacological mechanism needs further exploration.

METHODS: According to the active ingredients and targets of the QDTS in the TCMSP database, the network pharmacology of QDTS was investigated. The potential active ingredients were chosen based on the oral bioavailability and the drug similarity index. At the same time, targets for DN-related disease were obtained from GeneCards, OMIM, PharmGKB, TTD, and DrugBank. The TCM-component-target network and the protein-protein interaction (PPI) network were constructed with the Cytoscape and STRING platforms, respectively, and …

Regulation Of Polysaccharide In Wu-Tou Decoction On Intestinal Microflora And Pharmacokinetics Of Small Molecular Compounds In Aia Rats, Di Yang, Xiaoxu Cheng, Meiling Fan, Dong Xie, Zhiqiang Liu, Fei Zheng, Yulin Dai, Zifeng Pi, Hao Yue

Faculty, Staff and Student Publications

Wu-tou decoction (WTD), a traditional Chinese medicine prescription, is used to treat rheumatoid arthritis (RA). It works by controlling intestinal flora and its metabolites, which in turn modulates the inflammatory response and intestinal barrier function. Small molecular compounds (SM) and polysaccharides (PS) were the primary constituents of WTD extract. In this work, a model of adjuvant-induced arthritis (AIA) in rats was established and treated with WTD, SM, and PS, respectively. 16S rRNA gene sequencing was used to examine the regulatory impact of the various groups on the disturbance of the gut flora induced by RA. Further, since PS cannot be …

Henderson Named One Of The Most Influential People In Legal Education, James Owsley Boyd

Keep Up With the Latest News from the Law School (blog)

Indiana University Maurer School of Law Professor Bill Henderson has once again been recognized as one of the most influential people in legal education, but he’s not the only one with ties to the Law School on this year’s list.

The National Jurist ranked Henderson #18 on its list. Kellye Testy, a 1991 alumna of the Law School and president and CEO of the Law School Admission Council, is ranked second.

Prediction Of Hydrogel Degradation Time Based On Central Composite Design, Ying Wang, Deji Liu, Ruiquan Liao, Guangming Zhang, Manlai Zhang, Xiaohui Li

Faculty, Staff and Student Publications

In this study, a self-degrading hydrogel was formed by free-radical-initiated copolymerization, which can be used for oil and gas well strip pressure operations. Fourier transform infrared spectroscopy (FTIR), nuclear magnetic resonance (1H NMR), scanning electron microscopy (SEM), and thermogravimetry-mass spectrometry (TGA-MS) were used to study the reaction mechanism as well as the microstructure of the gels. Then, the effects of the four factors and their interactions on gel degradation time were determined by central composite design (CCD). Then, the effects of copolymer concentration, cross-linker, initiator, and reaction temperature and their interactions on gel degradation time were determined by central composite …

Fusionneoantigen: : A Resource Of Fusion Gene-Specific Neoantigens, Himansu Kumar, Ruihan Luo, Jianguo Wen, Chengyuan Yang, Xiaobo Zhou, Pora Kim

Faculty, Staff and Student Publications

Among the diverse sources of neoantigens (i.e. single-nucleotide variants (SNVs), insertions or deletions (Indels) and fusion genes), fusion gene-derived neoantigens are generally more immunogenic, have multiple targets per mutation and are more widely distributed across various cancer types. Therefore, fusion gene-derived neoantigens are a potential source of highly immunogenic neoantigens and hold great promise for cancer immunotherapy. However, the lack of fusion protein sequence resources and knowledge prevents this application. We introduce 'FusionNeoAntigen', a dedicated resource for fusion-specific neoantigens, accessible at https://compbio.uth.edu/FusionNeoAntigen. In this resource, we provide fusion gene breakpoint crossing neoantigens focused on ∼43K fusion proteins of ∼16K in-frame …

Drmref: Comprehensive Reference Map Of Drug Resistance Mechanisms In Human Cancer, Xiaona Liu, Jiahao Yi, Tina Li, Jianguo Wen, Kexin Huang, Jiajia Liu, Grant Wang, Pora Kim, Qianqian Song, Xiaobo Zhou

Faculty, Staff and Student Publications

Drug resistance poses a significant challenge in cancer treatment. Despite the initial effectiveness of therapies such as chemotherapy, targeted therapy and immunotherapy, many patients eventually develop resistance. To gain deep insights into the underlying mechanisms, single-cell profiling has been performed to interrogate drug resistance at cell level. Herein, we have built the DRMref database (https://ccsm.uth.edu/DRMref/) to provide comprehensive characterization of drug resistance using single-cell data from drug treatment settings. The current version of DRMref includes 42 single-cell datasets from 30 studies, covering 382 samples, 13 major cancer types, 26 cancer subtypes, 35 treatment regimens and 42 drugs. All datasets in …

Cov2var, A Function Annotation Database Of Sars-Cov-2 Genetic Variation, Yuzhou Feng, Jiahao Yi, Lin Yang, Yanfei Wang, Jianguo Wen, Weiling Zhao, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has resulted in the loss of millions of lives and severe global economic consequences. Every time SARS-CoV-2 replicates, the viruses acquire new mutations in their genomes. Mutations in SARS-CoV-2 genomes led to increased transmissibility, severe disease outcomes, evasion of the immune response, changes in clinical manifestations and reducing the efficacy of vaccines or treatments. To date, the multiple resources provide lists of detected mutations without key functional annotations. There is a lack of research examining the relationship between mutations and various factors such as disease severity, pathogenicity, patient age, patient gender, cross-species …