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Integrated Mrna Sequence Optimization Using Deep Learning, Haoran Gong, Jianguo Wen, Ruihan Luo, Yuzhou Feng, Jingjing Guo, Hongguang Fu, Xiaobo Zhou Jan 2023

Integrated Mrna Sequence Optimization Using Deep Learning, Haoran Gong, Jianguo Wen, Ruihan Luo, Yuzhou Feng, Jingjing Guo, Hongguang Fu, Xiaobo Zhou

Faculty, Staff and Student Publications

The coronavirus disease of 2019 pandemic has catalyzed the rapid development of mRNA vaccines, whereas, how to optimize the mRNA sequence of exogenous gene such as severe acute respiratory syndrome coronavirus 2 spike to fit human cells remains a critical challenge. A new algorithm, iDRO (integrated deep-learning-based mRNA optimization), is developed to optimize multiple components of mRNA sequences based on given amino acid sequences of target protein. Considering the biological constraints, we divided iDRO into two steps: open reading frame (ORF) optimization and 5' untranslated region (UTR) and 3'UTR generation. In ORF optimization, BiLSTM-CRF (bidirectional long-short-term memory with conditional random …


Kif6 Trp719arg Genetic Variant Increases Risk For Thoracic Aortic Dissection, Juan J Velasco, Yupeng Li, Bulat A Ziganshin, Mohammad A Zafar, John A Rizzo, Deqiong Ma, Hui Zang, Asanish Kalyanasundaram, John A Elefteriades Jan 2023

Kif6 Trp719arg Genetic Variant Increases Risk For Thoracic Aortic Dissection, Juan J Velasco, Yupeng Li, Bulat A Ziganshin, Mohammad A Zafar, John A Rizzo, Deqiong Ma, Hui Zang, Asanish Kalyanasundaram, John A Elefteriades

College of Science & Mathematics Departmental Research

Background: KIF6 (kinesin family member 6), a protein coded by the KIF6 gene, serves an important intracellular function to transport organelles along microtubules. In a pilot study, we found that a common KIF6 Trp719Arg variant increased the propensity of thoracic aortic aneurysms (TAA) to suffer dissection (AD). The present study aims for a definite investigation of the predictive ability of KIF6 719Arg vis à vis AD. Confirmatory findings would enhance natural history prediction in TAA. Methods: 1108 subjects (899 aneurysm and 209 dissection patients) had KIF6 719Arg variant status determined. Results: The 719Arg variant in the KIF6 gene correlated strongly …


Wrapper-Based Deep Feature Optimization For Activity Recognition In The Wearable Sensor Networks Of Healthcare Systems, Karam Kumar Sahoo, Raghunath Ghosh, Saurav Mallik, Arup Roy, Pawan Kumar Singh, Zhongming Zhao Jan 2023

Wrapper-Based Deep Feature Optimization For Activity Recognition In The Wearable Sensor Networks Of Healthcare Systems, Karam Kumar Sahoo, Raghunath Ghosh, Saurav Mallik, Arup Roy, Pawan Kumar Singh, Zhongming Zhao

Faculty, Staff and Student Publications

The Human Activity Recognition (HAR) problem leverages pattern recognition to classify physical human activities as they are captured by several sensor modalities. Remote monitoring of an individual's activities has gained importance due to the reduction in travel and physical activities during the pandemic. Research on HAR enables one person to either remotely monitor or recognize another person's activity via the ubiquitous mobile device or by using sensor-based Internet of Things (IoT). Our proposed work focuses on the accurate classification of daily human activities from both accelerometer and gyroscope sensor data after converting into spectrogram images. The feature extraction process follows …


Oxphos Defects Cause Hypermetabolism And Reduce Lifespan In Cells And In Patients With Mitochondrial Diseases, Gabriel Sturm, Kalpita R Karan, Anna S Monzel, Balaji Santhanam, Tanja Taivassalo, Céline Bris, Sarah A Ware, Marissa Cross, Atif Towheed, Albert Higgins-Chen, Meagan J Mcmanus, Andres Cardenas, Jue Lin, Elissa S Epel, Shamima Rahman, John Vissing, Bruno Grassi, Morgan Levine, Steve Horvath, Ronald G Haller, Guy Lenaers, Douglas C Wallace, Marie-Pierre St-Onge, Saeed Tavazoie, Vincent Procaccio, Brett A Kaufman, Erin L. Seifert, Michio Hirano, Martin Picard Jan 2023

Oxphos Defects Cause Hypermetabolism And Reduce Lifespan In Cells And In Patients With Mitochondrial Diseases, Gabriel Sturm, Kalpita R Karan, Anna S Monzel, Balaji Santhanam, Tanja Taivassalo, Céline Bris, Sarah A Ware, Marissa Cross, Atif Towheed, Albert Higgins-Chen, Meagan J Mcmanus, Andres Cardenas, Jue Lin, Elissa S Epel, Shamima Rahman, John Vissing, Bruno Grassi, Morgan Levine, Steve Horvath, Ronald G Haller, Guy Lenaers, Douglas C Wallace, Marie-Pierre St-Onge, Saeed Tavazoie, Vincent Procaccio, Brett A Kaufman, Erin L. Seifert, Michio Hirano, Martin Picard

Department of Pediatrics Faculty Papers

Patients with primary mitochondrial oxidative phosphorylation (OxPhos) defects present with fatigue and multi-system disorders, are often lean, and die prematurely, but the mechanistic basis for this clinical picture remains unclear. By integrating data from 17 cohorts of patients with mitochondrial diseases (n = 690) we find evidence that these disorders increase resting energy expenditure, a state termed hypermetabolism. We examine this phenomenon longitudinally in patient-derived fibroblasts from multiple donors. Genetically or pharmacologically disrupting OxPhos approximately doubles cellular energy expenditure. This cell-autonomous state of hypermetabolism occurs despite near-normal OxPhos coupling efficiency, excluding uncoupling as a general mechanism. Instead, hypermetabolism is associated …


An Age-Dependent Immuno-Epidemiological Model With Distributed Recovery And Death Rates, Samiran Ghosh, Vitaly Volpert, Malay Banerjee Jan 2023

An Age-Dependent Immuno-Epidemiological Model With Distributed Recovery And Death Rates, Samiran Ghosh, Vitaly Volpert, Malay Banerjee

Faculty, Staff and Student Publications

The work is devoted to a new immuno-epidemiological model with distributed recovery and death rates considered as functions of time after the infection onset. Disease transmission rate depends on the intra-subject viral load determined from the immunological submodel. The age-dependent model includes the viral load, recovery and death rates as functions of age considered as a continuous variable. Equations for susceptible, infected, recovered and dead compartments are expressed in terms of the number of newly infected cases. The analysis of the model includes the proof of the existence and uniqueness of solution. Furthermore, it is shown how the model can …


Relations Of Current And Past Cancer With Severe Outcomes Among 104,590 Hospitalized Covid-19 Patients: The Covid Ehr Cohort At The University Of Wisconsin, Margaret B Nolan, Li-Shiun Chen, Et Al. Jan 2023

Relations Of Current And Past Cancer With Severe Outcomes Among 104,590 Hospitalized Covid-19 Patients: The Covid Ehr Cohort At The University Of Wisconsin, Margaret B Nolan, Li-Shiun Chen, Et Al.

2020-Current year OA Pubs

BACKGROUND: There is mixed evidence about the relations of current versus past cancer with severe COVID-19 outcomes and how they vary by patient and cancer characteristics.

METHODS: Electronic health record data of 104,590 adult hospitalized patients with COVID-19 were obtained from 21 United States health systems from February 2020 through September 2021. In-hospital mortality and ICU admission were predicted from current and past cancer diagnoses. Moderation by patient characteristics, vaccination status, cancer type, and year of the pandemic was examined.

RESULTS: 6.8% of the patients had current (n = 7,141) and 6.5% had past (n = 6,749) cancer diagnoses. Current …


Ageanno: A Knowledgebase Of Single-Cell Annotation Of Aging In Human, Kexin Huang, Hoaran Gong, Jingjing Guan, Lingxiao Zhang, Changbao Hu, Weiling Zhao, Liyu Huang, Wei Zhang, Pora Kim, Xiaobo Zhou Jan 2023

Ageanno: A Knowledgebase Of Single-Cell Annotation Of Aging In Human, Kexin Huang, Hoaran Gong, Jingjing Guan, Lingxiao Zhang, Changbao Hu, Weiling Zhao, Liyu Huang, Wei Zhang, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

Aging is a complex process that accompanied by molecular and cellular alterations. The identification of tissue-/cell type-specific biomarkers of aging and elucidation of the detailed biological mechanisms of aging-related genes at the single-cell level can help to understand the heterogeneous aging process and design targeted anti-aging therapeutics. Here, we built AgeAnno (https://relab.xidian.edu.cn/AgeAnno/#/), a knowledgebase of single cell annotation of aging in human, aiming to provide comprehensive characterizations for aging-related genes across diverse tissue-cell types in human by using single-cell RNA and ATAC sequencing data (scRNA and scATAC). The current version of AgeAnno houses 1 678 610 cells from 28 healthy …


Spascer: Spatial Transcriptomics Annotation At Single-Cell Resolution, Zhiwei Fan, Yangyang Luo, Huifen Lu, Tiangang Wang, Yuzhou Feng, Weiling Zhao, Pora Kim, Xiaobo Zhou Jan 2023

Spascer: Spatial Transcriptomics Annotation At Single-Cell Resolution, Zhiwei Fan, Yangyang Luo, Huifen Lu, Tiangang Wang, Yuzhou Feng, Weiling Zhao, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

In recent years, the explosive growth of spatial technologies has enabled the characterization of spatial heterogeneity of tissue architectures. Compared to traditional sequencing, spatial transcriptomics reserves the spatial information of each captured location and provides novel insights into diverse spatially related biological contexts. Even though two spatial transcriptomics databases exist, they provide limited analytical information. Information such as spatial heterogeneity of genes and cells, cell-cell communication activities in space, and the cell type compositions in the microenvironment are critical clues to unveil the mechanism of tumorigenesis and embryo differentiation. Therefore, we constructed a new spatial transcriptomics database, named SPASCER (https://ccsm.uth.edu/SPASCER), …


Pickles V3: The Updated Database Of Pooled In Vitro Crispr Knockout Library Essentiality Screens, Lance C Novak, Juihsuan Chou, Medina Colic, Christopher A Bristow, Traver Hart Jan 2023

Pickles V3: The Updated Database Of Pooled In Vitro Crispr Knockout Library Essentiality Screens, Lance C Novak, Juihsuan Chou, Medina Colic, Christopher A Bristow, Traver Hart

Faculty, Staff and Student Publications

PICKLES (https://pickles.hart-lab.org) is an updated web interface to a freely available database of genome-scale CRISPR knockout fitness screens in human cell lines. Using a completely rewritten interface, researchers can explore gene knockout fitness phenotypes across cell lines and tissue types and compare fitness profiles with fitness, expression, or mutation profiles of other genes. The database has been updated to include data from three CRISPR libraries (Avana, Score, and TKOv3), and includes information from 1162 whole-genome screens probing the knockout fitness phenotype of 18 959 genes. Source code for the interface and the integrated database are available for download.


Longitudinal Assessment Of Multimorbidity Medication Patterns Among Smokers In The Copdgene Cohort, Yisha Li, Sarah J. Schmiege, Heather Anderson, Nicole E. Richmond, Kendra A. Young, John E. Hokanson, Stephen I. Rennard, Tessa L. Crume, Erin Austin, Katherine A. Pratte, Rebecca Conway, Gregory L. Kinney Jan 2023

Longitudinal Assessment Of Multimorbidity Medication Patterns Among Smokers In The Copdgene Cohort, Yisha Li, Sarah J. Schmiege, Heather Anderson, Nicole E. Richmond, Kendra A. Young, John E. Hokanson, Stephen I. Rennard, Tessa L. Crume, Erin Austin, Katherine A. Pratte, Rebecca Conway, Gregory L. Kinney

Journal Articles: Pulmonary & Critical Care Med

Background and objectives: Chronic obstructive pulmonary disease (COPD) is usually comorbid with other chronic diseases. We aimed to assess the multimorbidity medication patterns and explore if the patterns are similar for phase 1 (P1) and 5-year follow-up phase 2 (P2) in the COPDGene cohort. Materials and Methods: A total of 5564 out of 10,198 smokers from the COPDGene cohort who completed 2 visits, P1 and P2 visits, with complete medication use history were included in the study. We conducted latent class analysis (LCA) among the 27 categories of chronic disease medications, excluding COPD treatments and cancer medications at P1 and …


Safely Correct Hyponatremia With Continuous Renal Replacement Therapy: A Flexible, All-Purpose Method Based On The Mixing Paradigm, Sheldon Chen, Jerry Yee, Robert Chiaramonte Jan 2023

Safely Correct Hyponatremia With Continuous Renal Replacement Therapy: A Flexible, All-Purpose Method Based On The Mixing Paradigm, Sheldon Chen, Jerry Yee, Robert Chiaramonte

Nephrology Articles

Treating chronic hyponatremia by continuous renal replacement therapy (CRRT) is challenging because the gradient between a replacement fluid's [sodium] and a patient's serum sodium can be steep, risking too rapid of a correction rate with possible consequences. Besides CRRT, other gains and losses of sodium- and potassium-containing solutions, like intravenous fluid and urine output, affect the correction of serum sodium over time, known as osmotherapy. The way these fluids interact and contribute to the sodium/potassium/water balance can be parsed as a mixing problem. As Na/K/H(2) O are added, mixed in the body, and drained via CRRT, the net balance of …


A Review Of Piezoelectric Footwear Energy Harvesters: Principles, Methods, And Applications, Bingqi Zhao, Feng Qian, Alexander Hatfield, Lei Zuo, Tian-Bing Xu Jan 2023

A Review Of Piezoelectric Footwear Energy Harvesters: Principles, Methods, And Applications, Bingqi Zhao, Feng Qian, Alexander Hatfield, Lei Zuo, Tian-Bing Xu

Mechanical & Aerospace Engineering Faculty Publications

Over the last couple of decades, numerous piezoelectric footwear energy harvesters (PFEHs) have been reported in the literature. This paper reviews the principles, methods, and applications of PFEH technologies. First, the popular piezoelectric materials used and their properties for PEEHs are summarized. Then, the force interaction with the ground and dynamic energy distribution on the footprint as well as accelerations are analyzed and summarized to provide the baseline, constraints, potential, and limitations for PFEH design. Furthermore, the energy flow from human walking to the usable energy by the PFEHs and the methods to improve the energy conversion efficiency are presented. …


Use Gpt-J Prompt Generation With Roberta For Ner Models On Diagnosis Extraction Of Periodontal Diagnosis From Electronic Dental Records, Yao-Shun Chuang, Xiaoqian Jiang, Chun-Teh Lee, Ryan Brandon, Duong Tran, Oluwabunmi Tokede, Muhammad F Walji Jan 2023

Use Gpt-J Prompt Generation With Roberta For Ner Models On Diagnosis Extraction Of Periodontal Diagnosis From Electronic Dental Records, Yao-Shun Chuang, Xiaoqian Jiang, Chun-Teh Lee, Ryan Brandon, Duong Tran, Oluwabunmi Tokede, Muhammad F Walji

Faculty, Staff and Student Publications

This study explored the usability of prompt generation on named entity recognition (NER) tasks and the performance in different settings of the prompt. The prompt generation by GPT-J models was utilized to directly test the gold standard as well as to generate the seed and further fed to the RoBERTa model with the spaCy package. In the direct test, a lower ratio of negative examples with higher numbers of examples in prompt achieved the best results with a F1 score of 0.72. The performance revealed consistency, 0.92-0.97 in the F1 score, in all settings after training with the RoBERTa model. …


Towards Fair Patient-Trial Matching Via Patient-Criterion Level Fairness Constraint, Chia-Yuan Chang, Jiayi Yuan, Sirui Ding, Qiaoyu Tan, Kai Zhang, Xiaoqian Jiang, Xia Hu, Na Zou Jan 2023

Towards Fair Patient-Trial Matching Via Patient-Criterion Level Fairness Constraint, Chia-Yuan Chang, Jiayi Yuan, Sirui Ding, Qiaoyu Tan, Kai Zhang, Xiaoqian Jiang, Xia Hu, Na Zou

Faculty, Staff and Student Publications

Clinical trials are indispensable in developing new treatments, but they face obstacles in patient recruitment and retention, hindering the enrollment of necessary participants. To tackle these challenges, deep learning frameworks have been created to match patients to trials. These frameworks calculate the similarity between patients and clinical trial eligibility criteria, considering the discrepancy between inclusion and exclusion criteria. Recent studies have shown that these frameworks outperform earlier approaches. However, deep learning models may raise fairness issues in patient-trial matching when certain sensitive groups of individuals are underrepresented in clinical trials, leading to incomplete or inaccurate data and potential harm. To …


Architectural Design Of A Blockchain-Enabled, Federated Learning Platform For Algorithmic Fairness In Predictive Health Care: Design Science Study, Xueping Liang, Juan Zhao, Yan Chen, Eranga Bandara, Sachin Shetty Jan 2023

Architectural Design Of A Blockchain-Enabled, Federated Learning Platform For Algorithmic Fairness In Predictive Health Care: Design Science Study, Xueping Liang, Juan Zhao, Yan Chen, Eranga Bandara, Sachin Shetty

VMASC Publications

Background: Developing effective and generalizable predictive models is critical for disease prediction and clinical decision-making, often requiring diverse samples to mitigate population bias and address algorithmic fairness. However, a major challenge is to retrieve learning models across multiple institutions without bringing in local biases and inequity, while preserving individual patients' privacy at each site.

Objective: This study aims to understand the issues of bias and fairness in the machine learning process used in the predictive health care domain. We proposed a software architecture that integrates federated learning and blockchain to improve fairness, while maintaining acceptable prediction accuracy and minimizing overhead …


The Shortfalls Of Vulnerability Indexes For Public Health Decision-Making In The Face Of Emergent Crises: The Case Of Covid-19 Vaccine Uptake In Virginia, Lydia Cleveland Sa, Erika Frydenlund Jan 2023

The Shortfalls Of Vulnerability Indexes For Public Health Decision-Making In The Face Of Emergent Crises: The Case Of Covid-19 Vaccine Uptake In Virginia, Lydia Cleveland Sa, Erika Frydenlund

VMASC Publications

Equitable and effective vaccine uptake is a key issue in addressing COVID-19. To achieve this, we must comprehensively characterize the context-specific socio-behavioral and structural determinants of vaccine uptake. However, to quickly focus public health interventions, state agencies and planners often rely on already existing indexes of "vulnerability." Many such "vulnerability indexes" exist and become benchmarks for targeting interventions in wide ranging scenarios, but they vary considerably in the factors and themes that they cover. Some are even uncritical of the use of the word "vulnerable," which should take on different meanings in different contexts. The objective of this study is …


Population Variations Of Cheiloscopy Patterns: A Cross-Sectional Observation Pilot Study, Emily Smith Regan, Brenda T. Bradshaw, Ann M. Bruhn, Walter Melvin, Sinjini Sikdar Jan 2023

Population Variations Of Cheiloscopy Patterns: A Cross-Sectional Observation Pilot Study, Emily Smith Regan, Brenda T. Bradshaw, Ann M. Bruhn, Walter Melvin, Sinjini Sikdar

Dental Hygiene Faculty Publications

Purpose Lip prints are unique and have potential for use as a human identifier. The purpose of this study was to observe possible cheiloscopy differences of individuals with and without parafunctional oral habits such as smoking, vaping, playing a wind instrument or using an asthma inhaler.

Methods This IRB approved blinded cross-sectional observation pilot study collected lip prints from sixty-six individuals, three of which were excluded. Participants cleansed their lips, then lipstick was applied to the vermillion zones of the upper and lower lips. Adhesive tape was applied to the lips and prints were transferred to white bond paper for …


Dental Hygiene And Dental Assistant Students' Simulated Dvi Radiographic Match Accuracy: A Pilot Study, Samantha C. Vest, Brenda T. Bradshaw, Marsha A. Voelker, Ann M. Bruhn, Tara L. Newcomb, Sinjini Sikdar Jan 2023

Dental Hygiene And Dental Assistant Students' Simulated Dvi Radiographic Match Accuracy: A Pilot Study, Samantha C. Vest, Brenda T. Bradshaw, Marsha A. Voelker, Ann M. Bruhn, Tara L. Newcomb, Sinjini Sikdar

Dental Hygiene Faculty Publications

Purpose Allied dental health care professionals have served on disaster victim identification (DVI) teams; however, the literature is void of statistical measures regarding transferable skills and disaster preparedness. The purpose of this study was to assess second year dental hygiene and dental assistant students’ match accuracy for simulated DVI radiographs and compare the match accuracy between the student groups.

Methods Five patient cases were chosen at random to retrospectively collect sets of digital bitewing radiographs from two time periods. The five retrospectively selected sets of images served as simulated antemortem (AM) and postmortem (PM) radiographs. A convenience sample of second …


Sensitive Data Detection With High-Throughput Machine Learning Models In Electrical Health Records, Kai Zhang, Xiaoqian Jiang Jan 2023

Sensitive Data Detection With High-Throughput Machine Learning Models In Electrical Health Records, Kai Zhang, Xiaoqian Jiang

Faculty, Staff and Student Publications

In the era of big data, there is an increasing need for healthcare providers, communities, and researchers to share data and collaborate to improve health outcomes, generate valuable insights, and advance research. The Health Insurance Portability and Accountability Act of 1996 (HIPAA) is a federal law designed to protect sensitive health information by defining regulations for protected health information (PHI). However, it does not provide efficient tools for detecting or removing PHI before data sharing. One of the challenges in this area of research is the heterogeneous nature of PHI fields in data across different parties. This variability makes rule-based …


Large Language Models For Healthcare Data Augmentation: An Example On Patient-Trial Matching, Jiayi Yuan, Ruixiang Tang, Xiaoqian Jiang, Xia Hu Jan 2023

Large Language Models For Healthcare Data Augmentation: An Example On Patient-Trial Matching, Jiayi Yuan, Ruixiang Tang, Xiaoqian Jiang, Xia Hu

Faculty, Staff and Student Publications

The process of matching patients with suitable clinical trials is essential for advancing medical research and providing optimal care. However, current approaches face challenges such as data standardization, ethical considerations, and a lack of interoperability between Electronic Health Records (EHRs) and clinical trial criteria. In this paper, we explore the potential of large language models (LLMs) to address these challenges by leveraging their advanced natural language generation capabilities to improve compatibility between EHRs and clinical trial descriptions. We propose an innovative privacy-aware data augmentation approach for LLM-based patient-trial matching (LLM-PTM), which balances the benefits of LLMs while ensuring the security …


Split Learning For Distributed Collaborative Training Of Deep Learning Models In Health Informatics, Zhuohang Li, Chao Yan, Xinmeng Zhang, Gharib Gharibi, Zhijun Yin, Xiaoqian Jiang, Bradley A Malin Jan 2023

Split Learning For Distributed Collaborative Training Of Deep Learning Models In Health Informatics, Zhuohang Li, Chao Yan, Xinmeng Zhang, Gharib Gharibi, Zhijun Yin, Xiaoqian Jiang, Bradley A Malin

Faculty, Staff and Student Publications

Deep learning continues to rapidly evolve and is now demonstrating remarkable potential for numerous medical prediction tasks. However, realizing deep learning models that generalize across healthcare organizations is challenging. This is due, in part, to the inherent siloed nature of these organizations and patient privacy requirements. To address this problem, we illustrate how split learning can enable collaborative training of deep learning models across disparate and privately maintained health datasets, while keeping the original records and model parameters private. We introduce a new privacy-preserving distributed learning framework that offers a higher level of privacy compared to conventional federated learning. We …


Local Contrastive Learning For Medical Image Recognition, Syed A Rizvi, Ruixiang Tang, Xiaoqian Jiang, Xiaotian Ma, Xia Hu Jan 2023

Local Contrastive Learning For Medical Image Recognition, Syed A Rizvi, Ruixiang Tang, Xiaoqian Jiang, Xiaotian Ma, Xia Hu

Faculty, Staff and Student Publications

The proliferation of Deep Learning (DL)-based methods for radiographic image analysis has created a great demand for expert-labeled radiology data. Recent self-supervised frameworks have alleviated the need for expert labeling by obtaining supervision from associated radiology reports. These frameworks, however, struggle to distinguish the subtle differences between different pathologies in medical images. Additionally, many of them do not provide interpretation between image regions and text, making it difficult for radiologists to assess model predictions. In this work, we propose Local Region Contrastive Learning (LRCLR), a flexible fine-tuning framework that adds layers for significant image region selection as well as cross-modality …


Text Classification Of Cancer Clinical Trial Eligibility Criteria, Yumeng Yang, Soumya Jayaraj, Ethan Ludmir, Kirk Roberts Jan 2023

Text Classification Of Cancer Clinical Trial Eligibility Criteria, Yumeng Yang, Soumya Jayaraj, Ethan Ludmir, Kirk Roberts

Faculty, Staff and Student Publications

Automatic identification of clinical trials for which a patient is eligible is complicated by the fact that trial eligibility are stated in natural language. A potential solution to this problem is to employ text classification methods for common types of eligibility criteria. In this study, we focus on seven common exclusion criteria in cancer trials: prior malignancy, human immunodeficiency virus, hepatitis B, hepatitis C, psychiatric illness, drug/substance abuse, and autoimmune illness. Our dataset consists of 764 phase III cancer trials with these exclusions annotated at the trial level. We experiment with common transformer models as well as a new pre-trained …


Transiently Impaired Endothelial Function During Thyroid Hormone Withdrawal In Differentiated Thyroid Cancer Patients, Li-Ying Hou, Xiao Li, Guo-Qiang Zhang, Chuang Xi, Chen-Tian Shen, Hong-Jun Song, Wen-Kun Bai, Zhong-Ling Qiu, Quan-Yong Luo Jan 2023

Transiently Impaired Endothelial Function During Thyroid Hormone Withdrawal In Differentiated Thyroid Cancer Patients, Li-Ying Hou, Xiao Li, Guo-Qiang Zhang, Chuang Xi, Chen-Tian Shen, Hong-Jun Song, Wen-Kun Bai, Zhong-Ling Qiu, Quan-Yong Luo

Faculty, Staff and Student Publications

PURPOSE: Endothelial dysfunction, which was associated with chronic hypothyroidism, was an early event in atherosclerosis. Whether short-term hypothyroidism following thyroxine withdrawal during radioiodine (RAI) therapy was associated with endothelial dysfunction in patients with differentiated thyroid cancer (DTC) was unclear. Aim of the study was to assess whether short-term hypothyroidism could impair endothelial function and the accompanied metabolic changes in the whole process of RAI therapy.

METHODS: We recruited fifty-one patients who underwent total thyroidectomy surgery and would accept RAI therapy for DTC. We analyzed thyroid function, endothelial function and serum lipids levels of the patients at three time points: the …


A Gcn-Based Approach To Uncover Misaligned Synonymous Terms In The Umls Metathesaurus, Xubing Hao, Rashmie Abeysinghe, Jay Shi, Licong Cui Jan 2023

A Gcn-Based Approach To Uncover Misaligned Synonymous Terms In The Umls Metathesaurus, Xubing Hao, Rashmie Abeysinghe, Jay Shi, Licong Cui

Faculty, Staff and Student Publications

The Unified Medical Language System (UMLS), a large repository of biomedical vocabularies, has been used for supporting various biomedical applications. Ensuring the quality of the UMLS is critical to maintain both the accuracy of its content and the reliability of downstream applications. In this work, we present a Graph Convolutional Network (GCN)-based approach to identify misaligned synonymous terms organized under different UMLS concepts. We used synonymous terms grouped under the same concept as positive samples and top lexically similar terms as negative samples to train the GCN model. We applied the model to a test set and suggested those negative …


Digital Solutions Observed In Clinical Trials: A Formative Feasibility Scoping Review, Taylor M Harrison, Sungrim Moon, Liwei Wang, Sunyang Fu, Hongfang Liu Jan 2023

Digital Solutions Observed In Clinical Trials: A Formative Feasibility Scoping Review, Taylor M Harrison, Sungrim Moon, Liwei Wang, Sunyang Fu, Hongfang Liu

Faculty, Staff and Student Publications

Growing digital access accelerates digital transformation of clinical trials where digital solutions (DSs) are increasingly and widely leveraged for improving trial efficiency, effectiveness, and accessibility. Many factors impact DS success including technology barriers, privacy concerns, or user engagement activities. It is unclear how those factors are considered or reported in the literature. Here, we perform a formative feasibility scoping review to identify gaps impacting DS quality and reproducibility in trials. Articles containing digital terms published in English from 2009 to 2022 were collected (n=4,167). 130 articles published between 2016 and 2022 were randomly selected for full-text review. Eligible articles (n=100) …


Contextual Variation Of Clinical Notes Induced By Ehr Migration, Kurt Miller, Sungrim Moon, Sunyang Fu, Hongfang Liu Jan 2023

Contextual Variation Of Clinical Notes Induced By Ehr Migration, Kurt Miller, Sungrim Moon, Sunyang Fu, Hongfang Liu

Faculty, Staff and Student Publications

The structure and semantics of clinical notes vary considerably across different Electronic Health Record (EHR) systems, sites, and institutions. Such heterogeneity hampers the portability of natural language processing (NLP) models in extracting information from the text for clinical research or practice. In this study, we evaluate the contextual variation of clinical notes by measuring the semantic and syntactic similarity of the notes of two sets of physicians comprising four medical specialties across EHR migrations at two Mayo Clinic sites. We find significant semantic and syntactic variation imposed by the context of the EHR system and between medical specialties whereas only …


Characterizing Performance Gaps Of A Code-Based Dementia Algorithm In A Population-Based Cohort Of Cognitive Aging, Maria Vassilaki, Sunyang Fu, Luke R Christenson, Muskan Garg, Ronald C Petersen, Jennifer St Sauver, Sunghwan Sohn Jan 2023

Characterizing Performance Gaps Of A Code-Based Dementia Algorithm In A Population-Based Cohort Of Cognitive Aging, Maria Vassilaki, Sunyang Fu, Luke R Christenson, Muskan Garg, Ronald C Petersen, Jennifer St Sauver, Sunghwan Sohn

Faculty, Staff and Student Publications

BACKGROUND: Multiple algorithms with variable performance have been developed to identify dementia using combinations of billing codes and medication data that are widely available from electronic health records (EHR). If the characteristics of misclassified patients are clearly identified, modifying existing algorithms to improve performance may be possible.

OBJECTIVE: To examine the performance of a code-based algorithm to identify dementia cases in the population-based Mayo Clinic Study of Aging (MCSA) where dementia diagnosis (i.e., reference standard) is actively assessed through routine follow-up and describe the characteristics of persons incorrectly categorized.

METHODS: There were 5,316 participants (age at baseline (mean (SD)): 73.3 …


Segmentation Of Acute Stroke Infarct Core Using Image-Level Labels On Ct-Angiography, Luca Giancardo, Arash Niktabe, Laura Ocasio, Rania Abdelkhaleq, Sergio Salazar-Marioni, Sunil A Sheth Jan 2023

Segmentation Of Acute Stroke Infarct Core Using Image-Level Labels On Ct-Angiography, Luca Giancardo, Arash Niktabe, Laura Ocasio, Rania Abdelkhaleq, Sergio Salazar-Marioni, Sunil A Sheth

Faculty, Staff and Student Publications

Acute ischemic stroke is a leading cause of death and disability in the world. Treatment decisions, especially around emergent revascularization procedures, rely heavily on size and location of the infarct core. Currently, accurate assessment of this measure is challenging. While MRI-DWI is considered the gold standard, its availability is limited for most patients suffering from stroke. Another well-studied imaging modality is CT-Perfusion (CTP) which is much more common than MRI-DWI in acute stroke care, but not as precise as MRI-DWI, and it is still unavailable in many stroke hospitals. A method to determine infarct core using CT-Angiography (CTA), a much …


Keystroke-Dynamics For Parkinson's Disease Signs Detection In An At-Home Uncontrolled Population: A New Benchmark And Method, Shikha Tripathi, Teresa Arroyo-Gallego, Luca Giancardo Jan 2023

Keystroke-Dynamics For Parkinson's Disease Signs Detection In An At-Home Uncontrolled Population: A New Benchmark And Method, Shikha Tripathi, Teresa Arroyo-Gallego, Luca Giancardo

Faculty, Staff and Student Publications

Parkinson's disease (PD) is the second most prevalent neurodegenerative disease disorder in the world. A prompt diagnosis would enable clinical trials for disease-modifying neuroprotective therapies. Recent research efforts have unveiled imaging and blood markers that have the potential to be used to identify PD patients promptly, however, the idiopathic nature of PD makes these tests very hard to scale to the general population. To this end, we need an easily deployable tool that would enable screening for PD signs in the general population. In this work, we propose a new set of features based on keystroke dynamics, i.e., the time …