Digital Commons Network^™

Molecular Model Of Tfiih Recruitment To The Transcription-Coupled Repair Machinery, Tanmoy Paul, Chunli Yan, Jina Yu, Susan E Tsutakawa, John A Tainer, Dong Wang, Ivaylo Ivanov

Faculty, Staff and Student Publications

Transcription-coupled repair (TCR) is a vital nucleotide excision repair sub-pathway that removes DNA lesions from actively transcribed DNA strands. Binding of CSB to lesion-stalled RNA Polymerase II (Pol II) initiates TCR by triggering the recruitment of downstream repair factors. Yet it remains unknown how transcription factor IIH (TFIIH) is recruited to the intact TCR complex. Combining existing structural data with AlphaFold predictions, we build an integrative model of the initial TFIIH-bound TCR complex. We show how TFIIH can be first recruited in an open repair-inhibited conformation, which requires subsequent CAK module removal and conformational closure to process damaged DNA. In …

Genome-Wide Profiling Of Highly Similar Paralogous Genes Using Hifi Sequencing., Xiao Chen, Daniel Baker, Egor Dolzhenko, Joseph M. Devaney, Jessica Noya, April S. Berlyoung, Rhonda Brandon, Kathleen S. Hruska, Lucas Lochovsky, Paul Kruszka, Scott Newman, Emily G. Farrow, Isabelle Thiffault, Tomi Pastinen, Dalia Kasperaviciute, Christian Gilissen, Lisenka Vissers, Alexander Hoischen, Seth Berger, Eric Vilain, Emmanuèle Délot, Uci Genomics Research To Elucidate The Genetics Of Rare Diseases (Uci Gregor) Consortium, Michael A. Eberle

Manuscripts, Articles, Book Chapters and Other Papers

Variant calling is hindered in segmental duplications by sequence homology. We developed Paraphase, a HiFi-based informatics method that resolves highly similar genes by phasing all haplotypes of paralogous genes together. We applied Paraphase to 160 long (>10 kb) segmental duplication regions across the human genome with high (>99%) sequence similarity, encoding 316 genes. Analysis across five ancestral populations revealed highly variable copy numbers of these regions. We identified 23 paralog groups with exceptionally low within-group diversity, where extensive gene conversion and unequal crossing over contribute to highly similar gene copies. Furthermore, our analysis of 36 trios identified 7 …

Immunotherapy-Related Neurotoxicity In The Central Nervous System Of Children With Cancer, Jiasen He, Jeremy Connors, Andrew Meador, Shuo Xu, Heather Meador, Hong Jiang, Juan Fueyo, Candelaria Gomez-Manzano, Gregory K Friedman, Wafik Zaky, Zsila Sadighi, John M Slopis, Ali H Ahmad

Faculty, Staff and Student Publications

Significant gaps remain in our understanding of immunotherapy-related neurotoxicity in pediatric patients, largely because much of our knowledge comes from studies in adults. Accurately identifying the adverse effects of immunotherapy in children is also challenging, owing to variations in terminology and grading systems. Moreover, the manifestation of immunotherapy-related neurotoxicity differs greatly across different diseases, various modalities, dosages, and delivery methods. Combining immunotherapy with other treatments might improve outcomes but introduces new complexities and potential for increased toxicities. Additionally, pediatric patients with intracranial malignancy have unique responses to immunotherapies and distinct neurotoxicity compared to those with extracranial malignancy. Consequently, we must …

Investigating The Impact Of Electroconvulsive Therapy On Brain Networks And Sleep: An Observational Study Protocol, Mohammadmehdi Kafashan, Lucas Lebovitz, Robby Greenspan, Sijia Zhao, Tae Kim, Masud Husain, Tamara Hershey, Pilar Cristancho, R Edward Hogan, Ben Julian Agustin Palanca, Nuri B Farber, Dns-Ect Study Team

2020-Current year OA Pubs

INTRODUCTION: Electroconvulsive therapy (ECT) is a highly effective treatment for refractory depression, but it may also cause cognitive side effects. Despite decades of use, the mechanisms by which ECT exerts both its antidepressant and cognitive effects are still poorly understood, with the latter substantially limiting referral and adherence to therapy. ECT induces changes in correlated neural activity-functional connectivity-across various brain networks, which may underlie both its clinical efficacy and associated cognitive side effects. Electroencephalography (EEG) could address these knowledge gaps by identifying biomarkers that predict therapeutic outcomes or cognitive side effects. Such developments could ultimately improve patient selection and adherence. …

Emerging Domains For Measuring Health Care Delivery With Electronic Health Record Metadata, Daniel Tawfik, Sunny S Lou, Et Al.

2020-Current year OA Pubs

This article aims to introduce emerging measurement domains made feasible through the electronic health record (EHR) use metadata, to inform the changing landscape of health care delivery. We reviewed emerging domains in which EHR metadata may be used to measure health care delivery, outlining a framework for evaluating measures based on desirability, feasibility, and viability. We argue that EHR use metadata may be leveraged to develop and operationalize novel measures in the domains of team structure and dynamics, workflows, and cognitive environment to provide a clearer understanding of modern health care delivery. Examples of measures feasible using metadata include quantification …

Oncology Provider And Patient Perspectives On A Cardiovascular Health Assessment Tool Used During Posttreatment Survivorship Care In Community Oncology (Results From Wf-1804cd): Mixed Methods Observational Study, Chandylen L Nightingale, Maura Kepper, Randi E Foraker, Et Al.

2020-Current year OA Pubs

BACKGROUND: Most survivors of cancer have multiple cardiovascular risk factors, increasing their risk of poor cardiovascular and cancer outcomes. The Automated Heart-Health Assessment (AH-HA) tool is a novel electronic health record clinical decision support tool based on the American Heart Association's Life's Simple 7 cardiovascular health metrics to promote cardiovascular health assessment and discussion in outpatient oncology. Before proceeding to future implementation trials, it is critical to establish the acceptability of the tool among providers and survivors.

OBJECTIVE: This study aims to assess provider and survivor acceptability of the AH-HA tool and provider training at practices randomized to the AH-HA …

Structure-Function Relationship Of Ash1l And Histone H3k36 And H3k4 Methylation, Kendra R Vann, Rajal Sharma, Chih-Chao Hsu, Maeva Devoucoux, Adam H Tencer, Lei Zeng, Kevin Lin, Li Zhu, Qin Li, Catherine Lachance, Ruben Rosas Ospina, Qiong Tong, Ka Lung Cheung, Shuai Yang, Soumi Biswas, Hongwen Xuan, Jovylyn Gatchalian, Lorena Alamillo, Jianlong Wang, Suk Min Jang, Brianna J Klein, Yue Lu, Patricia Ernst, Brian D Strahl, Scott B Rothbart, Martin J Walsh, Michael L Cleary, Jacques Côté, Xiaobing Shi, Ming-Ming Zhou, Tatiana G Kutateladze

Faculty, Staff and Student Publications

The histone H3K36-specific methyltransferase ASH1L plays a critical role in development and is frequently dysregulated in human diseases, particularly cancer. Here, we report on the biological functions of the C-terminal region of ASH1L encompassing a bromodomain (ASH1LBD), a plant homeodomain (ASH1LPHD) finger, and a bromo-adjacent homology (ASH1LBAH) domain, structurally characterize these domains, describe their mechanisms of action, and explore functional crosstalk between them. We find that ASH1LPHD recognizes H3K4me2/3, whereas the neighboring ASH1LBD and ASH1LBAH have DNA binding activities. The DNA binding function of ASH1LBAH is a driving force for the association of ASH1L with the linker DNA in the …

Drbioright 20: An Llm-Powered Bioinformatics Chatbot For Large-Scale Cancer Functional Proteomics Analysis, Wei Liu, Jun Li, Yitao Tang, Yining Zhao, Chaozhong Liu, Meiyi Song, Zhenlin Ju, Shwetha V Kumar, Yiling Lu, Rehan Akbani, Gordon B Mills, Han Liang

Faculty, Staff and Student Publications

Functional proteomics provides critical insights into cancer mechanisms, facilitating the discovery of novel biomarkers and therapeutic targets. We have developed a comprehensive cancer functional proteomics resource using reverse phase protein arrays, incorporating data from nearly 8000 patient samples from The Cancer Genome Atlas and approximately 900 samples from the Cancer Cell Line Encyclopedia. Our dataset includes a curated panel of nearly 500 high-quality antibodies, covering all major cancer hallmark pathways. To enhance the accessibility and analytic power of this resource, we introduce DrBioRight 2.0 ( https://drbioright.org ), an intuitive bioinformatic platform powered by state-of-the-art large language models. DrBioRight enables researchers …

Carm1 Regulates Tubulin Autoregulation Through Pi3kc2Α R175 Methylation, Yena Cho, Jee Won Hwang, Mark T Bedford, Dae-Geun Song, Su-Nam Kim, Yong Kee Kim

Faculty, Staff and Student Publications

Tubulin is crucial in several cellular processes, including intracellular organization, organelle transport, motility, and chromosome segregation. Intracellular tubulin concentration is tightly regulated by an autoregulation mechanism, in which excess free tubulin promotes tubulin mRNA degradation. However, the details of how changes in free tubulin levels initiate this autoregulation remain unclear. In this study, we identified coactivator-associated arginine methyltransferase 1 (CARM1)-phosphatidylinositol 3-kinase class 2α (PI3KC2α) axis as a novel regulator of tubulin autoregulation. CARM1 stabilizes PI3KC2α by methylating its R175 residue. Once PI3KC2α is not methylated, it becomes unstable, leading to decreased cellular levels. Loss of PI3KC2α results in the release …

Social Media As A Platform For Cancer Care Decision-Making Among Women: Internet Survey-Based Study On Trust, Engagement, And Preferences, Anna Rose Johnson, Grace Anne Longfellow, Clara N Lee, Benjamin Ormseth, Gary B Skolnick, Mary C Politi, Yonaira M Rivera, Terence Myckatyn

2020-Current year OA Pubs

BACKGROUND: Decision aids improve patient and clinician decision-making but are underused and often restricted to clinical settings.

OBJECTIVE: Given limited studies analyzing the feasibility of disseminating decision aids through social media, this study aimed to evaluate the acceptability, trust, and engagement of women with social media as a tool to deliver online decision aids for cancer treatment.

METHODS: To prepare for potential dissemination of a breast cancer decision aid via social media, a cross-sectional survey in February 2023 was conducted via Prime Panels, an online market research platform, of women aged 35-75 years in the United States. Demographics, health, cancer …

Systematic Method For Developing Tailored Strategies For Implementing Point-Of-Care Procalcitonin Testing To Guide Antibiotic Prescribing In Swiss Primary Care: A Protocol For A Mixed-Methods Participatory Approach, Aline Wolfensberger, Sophie Cl Gendolla, Jelena Dunaiceva, Catherine Plüss-Suard, Anne Niquille, Anna Nicolet, Joachim Marti, Byron J Powell, Rahel Naef, Noémie Boillat-Blanco, Yolanda Mueller, Lauren Clack

2020-Current year OA Pubs

INTRODUCTION: Antimicrobial resistance is a major global health threat, driven largely by the misuse and overuse of antibiotics. Point-of-care (POC) tests for inflammatory biomarkers like procalcitonin (PCT) have shown promise in reducing unnecessary antibiotic prescriptions. The hybrid type II ImpPro trial aims to evaluate the implementation and effectiveness of POC-PCT on antibiotic prescriptions by primary care physicians (PCP) in French-speaking Switzerland. Implementation is planned to include a multifaceted strategy delivered mainly, but not exclusively, via PCP quality circles. Currently, little guidance exists on how to best tailor the implementation strategies to a specific context. This study protocol describes the comprehensive …

Scupa: Single-Cell Unified Polarization Assessment Of Immune Cells Using The Single-Cell Foundation Model, Wendao Liu, Zhongming Zhao

Faculty, Staff and Student Publications

MOTIVATION: Immune cells undergo cytokine-driven polarization in response to diverse stimuli, altering their transcriptional profiles and functional states. This dynamic process is central to immune responses in health and diseases, yet a systematic approach to assess cytokine-driven polarization in single-cell RNA sequencing data has been lacking.

RESULTS: To address this gap, we developed single-cell unified polarization assessment (Scupa), the first computational method for comprehensive immune cell polarization assessment. Scupa leverages data from the Immune Dictionary, which characterizes cytokine-driven polarization states across 14 immune cell types. By integrating cell embeddings from the single-cell foundation model Universal Cell Embeddings, Scupa effectively identifies …

Privacy-Preserving Framework For Genomic Computations Via Multi-Key Homomorphic Encryption, Mina Namazi, Mohammadali Farahpoor, Erman Ayday, Fernando Pérez-González

Faculty, Staff and Student Publications

Motivation: The affordability of genome sequencing and the widespread availability of genomic data have opened up new medical possibilities. Nevertheless, they also raise significant concerns regarding privacy due to the sensitive information they encompass. These privacy implications act as barriers to medical research and data availability. Researchers have proposed privacy-preserving techniques to address this, with cryptography-based methods showing the most promise. However, existing cryptography-based designs lack (i) interoperability, (ii) scalability, (iii) a high degree of privacy (i.e. compromise one to have the other), or (iv) multiparty analyses support (as most existing schemes process genomic information of each party individually). Overcoming …

Addressing Health Disparities In Hematologic Malignancies: From Genes To Outreach, Christopher R Flowers, Rachel W Anantha, Veronica Leautaud, Pinkal Desai, Chancellor E Donald, Michelle A T Hildebrandt, Jean L Koff, Rulla M Tamimi, Wendy Cozen, Chijioke Nze, Ari M Melnick

Faculty, Staff and Student Publications

This review underscores our shared responsibility to champion multidimensional strategies rooted in basic and translational science, community involvement, and societal responsiveness for a meaningful impact. Unifying themes include the need to enhance collaborative infrastructure to engage laboratory researchers, epidemiologists, data scientists, clinicians, patients, community leaders, and policymakers; patient-level support services; outreach, education, and navigation for patients at the community level; recruitment and retention of underrepresented groups in the healthcare and research workforce; and funding for these efforts.

Learning Directed Acyclic Graphs For Ligands And Receptors Based On Spatially Resolved Transcriptomic Data Of Ovarian Cancer, Shrabanti Chowdhury, Sammy Ferri-Borgogno, Peng Yang, Wenyi Wang, Jie Peng, Samuel C Mok, Pei Wang

Faculty, Staff and Student Publications

To unravel the mechanism of immune activation and suppression within tumors, a critical step is to identify transcriptional signals governing cell-cell communication between tumor and immune/stromal cells in the tumor microenvironment. Central to this communication are interactions between secreted ligands and cell-surface receptors, creating a highly connected signaling network among cells. Recent advancements in in situ-omics profiling, particularly spatial transcriptomic (ST) technology, provide unique opportunities to directly characterize ligand-receptor signaling networks that power cell-cell communication. In this paper, we propose a novel statistical method, LRnetST, to characterize the ligand-receptor interaction networks between adjacent tumor and immune/stroma cells based on ST …

Developing And Implementing Pediatric Nephrology Milestones 2.0 As An Efficient Tool For Trainee Evaluation And Just-In-Time Feedback., Caroline V. Jackson, Rebecca Hjorten, Laura Edgar, Beatrice Goilav, Roshan P. George, Darcy K. Weidemann

Manuscripts, Articles, Book Chapters and Other Papers

In 2013, the Accreditation Council for Graduate Medical Education (ACGME) implemented Milestones 1.0 as a tool to assess trainee progress towards readiness for independent practice. Critiques of Milestones 1.0 suggested its complexity made the tool difficult to quickly understand and implement in a standardized fashion. This was particularly challenging among subspecialties due to inherent differences in clinical practice settings and make-up of procedural and patient care needs. In response, ACGME launched Milestones 2.0 in 2016 to harmonize competencies applicable to all subspecialties and develop new subspecialty specific competencies to facilitate precise feedback on subspecialty specific content domains. We describe how …

Crisis Communication About The Maui Wildfires On Tiktok: Content Analysis Of Engagement With Maui Wildfire-Related Posts Over 1 Year, Jim P Stimpson, Aditi Srivastava, Ketan Tamirisa, Joseph KeaweʻAimoku Kaholokula, Alexander N Ortega

2020-Current year OA Pubs

BACKGROUND: The August 2023 wildfire in the town of Lāhainā on the island of Maui in Hawai'i caused catastrophic damage, affecting thousands of residents, and killing 102 people. Social media platforms, particularly TikTok, have become essential tools for crisis communication during disasters, providing real-time crisis updates, mobilizing relief efforts, and addressing misinformation. Understanding how disaster-related content is disseminated and engaged with on these platforms can inform strategies for improving emergency communication and community resilience.

OBJECTIVE: Guided by Social-Mediated Crisis Communication theory, this study examined TikTok posts related to the Maui wildfires to assess content themes, public engagement, and the effectiveness …

Spatialge Is A User-Friendly Web Application That Facilitates Spatial Transcriptomics Data Analysis., Oscar E. Ospina, Roberto Manjarres-Betancur, Guillermo Gonzalez-Calderon, Alex C. Soupir, Inna Smalley, Kenneth Y. Tsai, Joseph Markowitz, Mariam L. Khaled, Ethan Vallebuona, Anders E. Berglund, Steven A. Eschrich, Xiaoqing Yu, Brooke L. Fridley

Manuscripts, Articles, Book Chapters and Other Papers

Spatial transcriptomics (ST) is a powerful tool for understanding tissue biology and disease mechanisms. However, the advanced data analysis and programming skills required can hinder researchers from realizing the full potential of ST. To address this, we developed spatialGE, a web application that simplifies the analysis of ST data. The application spatialGE provided a user-friendly interface that guides users without programming expertise through various analysis pipelines, including quality control, normalization, domain detection, phenotyping, and multiple spatial analyses. It also enabled comparative analysis among samples and supported various ST technologies. The utility of spatialGE was demonstrated through its application in studying …

Exploring Social Impairment In Those With Opioid Use Disorder: Linking Impulsivity, Childhood Trauma, And The Prefrontal Cortex, Thais Costa Macedo De Arruda, Laura Sinko, Paul Regier, Altona Tufanoglu, Adrian Curtin, Anne M. Teitelman, Hasan Ayaz, Peter F. Cronholm, Anna Rose Childress

College of Nursing Faculty Papers & Presentations

BACKGROUND: Challenges with social functioning, which is a hallmark of opioid use disorder (OUD), are a drawback in treatment adherence and maintenance. Yet, little research has explored the underlying mechanisms of this impairment. Impulsivity and corresponding neural alterations may be at the center of this issue. Childhood adversity, which has been linked to both impulsivity and poorer treatment outcomes, could also affect this relationship. This study explores the relationship between impulsivity, social functioning, and their neural correlates in the prefrontal cortex, while examining the potential moderating effects of childhood trauma in individuals recovering from OUD.

METHODS: Participants with (N = …

Researcher Perceptions Of Inclusion Of Study Participants Who Use Languages Other Than English., Henry Hoffman, Tran T. Doan, Olivia Migliori, Alisa Khan, Jaime Sidani, Sabrina Liu, Abby Jo Perez, Lani Mears, Benoit Kihumbu, Khara Timsina, Diego Chaves-Gnecco, John Cowden, Maya I. Ragavan

Manuscripts, Articles, Book Chapters and Other Papers

IMPORTANCE: Despite constituting 8% of the US population, people who speak languages other than English (LOE) are consistently underrepresented in health-focused research. To make research more inclusive and generalizable, it is crucial to better understand researcher perspectives on barriers to inclusion of participants using LOE and solutions to promote language justice.

OBJECTIVE: To assess researcher perspectives on barriers to and best practices for inclusion of participants using LOE and to generate strategies to make research more inclusive.

DESIGN, SETTING, AND PARTICIPANTS: This exploratory cross-sectional survey study used an anonymous digital Qualtrics survey distributed between March 1 and June 30, 2023. …

Geographic Access To Cancer Care And Treatment And Outcomes Of Early-Stage Non-Small Cell Lung Cancer, Pratibha Shrestha, Ying Liu, James Struthers, Benjamin Kozower, Min Lian

2020-Current year OA Pubs

IMPORTANCE: Data on the impact of geographic access to cancer care on early-stage non-small cell lung cancer (NSCLC) treatment and outcomes are limited.

OBJECTIVE: To examine the associations of geographic access to cancer care with guideline-recommended treatment and outcomes in patients with early-stage NSCLC.

DESIGN, SETTING, AND PARTICIPANTS: This population-based cohort study included patients with early-stage NSCLC newly diagnosed between January 1, 2007, and December 31, 2015, followed up through December 31, 2016, and identified from the Surveillance, Epidemiology, and End Results dataset. Data analysis was performed from March to November 2024.

EXPOSURES: Geographic access to thoracic surgeons and radiation …

Anesthetic Considerations For Endovascular Repair Of The Thoracic Aorta, Olivia M Valencia, Thomas Powell, Ali Khalifa, Vicente Orozco-Sevilla, Daniel A Tolpin

Faculty, Staff and Students Publications

Thoracic aorta pathologies, especially those of the ascending aorta and aortic arch, were traditionally approached via open surgical repair. This carries risk of ischemic end-organ damage and other complications. Endovascular repair of ascending aorta and aortic arch pathologies is becoming more successful and widespread, thereby posing numerous challenges to the anesthesiologist. This article reviews the anesthesia-pertinent pathophysiology, repair techniques, preoperative evaluation, intraoperative management, and postoperative care of patients presenting for endovascular repair of thoracic aorta pathologies.

Which Systemic Responses Should We Evolve To Help Surgeons Navigate Their Regret Experiences?, Ryan X Lam, Ruhi Thapar, Eric J Silberfein, Lorenzo R Deveza

Faculty, Staff and Students Publications

Regret in surgical practice is typically construed as resulting from the commission or the omission of a specific action at a specific decision point, which leads to a deleterious outcome. This article suggests a need to expand this conception of surgical regret to better account for surgeons' regret experiences arising from factors beyond their control. The commentary accompanying the case investigates these external sources of regret, such as resource limitations or professional interpersonal dynamics that prevent a desired outcome from being realized. It also discusses the normative value of addressing surgeons' experiences of regret, especially as a catalyst to facilitate …

Shifting Tuberculosis Dynamics In The Eu/Eea: Geographical And Drug Resistance Trends Among People Of Foreign Origin, 2019 To 2023, Anca Vasiliu, Veronica Cristea, Krista Stoycheva, Senia Rosales-Klintz, Christoph Lange, Dominik Zenner, Csaba Ködmön

Faculty, Staff and Students Publications

We observed shifting trends in tuberculosis (TB) epidemiology in the EU/EEA between 2019 and 2023. In 2023, TB notifications among people of foreign origin increased by 24.6% after decreasing between 2019 and 2020. The majority originated from African and East Mediterranean regions, with a 316.4% upsurge in TB among Ukrainians in 2022-23. Rifampicin-resistant/multidrug-resistant TB increased by ≥ 60% in 2019-23, mainly among Ukrainians. Rapid response to shifting epidemiological patterns is crucial for efficient TB prevention and control within the EU/EEA.

Convergence On Camk4: A Key Modulator Of Autism-Associated Signaling Pathways In Neurons, Jacqueline Kaiser, Alana Risteska, Abbey G Muller, Haoxiong Sun, Bethany Lei, Kevin Nay, Anthony R Means, Margot A Cousin, David H Drewry, Jonathan S Oakhill, Bruce E Kemp, Anthony J Hannan, Michael Berk, Mark A Febbraio, Andrew L Gundlach, Elisa L Hill-Yardin, John W Scott

Faculty, Staff and Students Publications

Although the precise underlying cause(s) of autism spectrum disorder remain unclear, more than 1000 rare genetic variations are associated with the condition. For many people living with profound autism, this genetic heterogeneity has impeded the identification of common biological targets for therapy development for core and comorbid traits that include significant impairments in social communication and repetitive and restricted behaviors. A substantial number of genes associated with autism encode proteins involved in signal transduction and synaptic transmission that are critical for brain development and function. CAMK4 is an emerging risk gene for autism spectrum disorder that encodes the CaMK4 (calcium/calmodulin-dependent …

Cerebrotendinous Xanthomatosis Occurs At High Frequency In Ashkenazi Jews, Jennifer Hanson, Penelope E Bonnen

Faculty, Staff and Students Publications

Cerebrotendinous Xanthomatosis (CTX) is a treatable, inborn error of bile acids metabolism caused by pathogenic variants in CYP27A1. CTX is a multi-organ system disorder that progresses over decades. Clinical features include cerebellar dysfunction, pyramidal tract dysfunction, cognitive deficits and decline, peripheral neuropathy, chronic diarrhea, bilateral cataracts, and tendon xanthomas. Treatment is effective when started early, but diagnostic delays often result in individuals not being diagnosed until after the window of highest treatment efficacy. CTX is documented to occur in most global populations, however, no CTX-causing genetic variants have been reported in Ashkenazi Jews. We conducted a systematic review of every …

Learning Soft Tissue Deformation From Incremental Simulations, Nathan Lampen, Daeseung Kim, Xuanang Xu, Xi Fang, Jungwook Lee, Tianshu Kuang, Hannah H Deng, Michael A K Liebschner, Jaime Gateno, Pingkun Yan

Faculty, Staff and Students Publications

Background: Surgical planning for orthognathic procedures demands swift and accurate biomechanical modeling of facial soft tissues. Efficient simulations are vital in the clinical pipeline, as surgeons may iterate through multiple plans. Biomechanical simulations typically use the finite element method (FEM). Prior works divide FEM simulations into increments to enhance convergence and accuracy. However, this practice elongates simulation time, thereby impeding clinical integration. To accelerate simulations, deep learning (DL) models have been explored. Yet, previous efforts either perform simulations in a single step or neglect the temporal aspects in incremental simulations.

Purpose: This study investigates the use of spatiotemporal incremental modeling …

Phase 3 Validation Of Paam For Hepatocellular Carcinoma Risk Stratification In Cirrhosis, Naoto Fujiwara, Camden Lopez, Tracey L Marsh, Indu Raman, Cesia A Marquez, Subhojit Paul, Sumit K Mishra, Naoto Kubota, Courtney Katz, Hiroaki Kanzaki, Michael Gonzalez, Lisa Quirk, Sneha Deodhar, Pratibha Selvakumar, Prithvi Raj, Neehar D Parikh, Lewis R Roberts, Myron E Schwartz, Mindie H Nguyen, Alex S Befeler, Stephanie Page-Lester, Sudhir Srivastava, Ziding Feng, K Rajender Reddy, Saira Khaderi, Sumeet K Asrani, Fasiha Kanwal, Hashem B El-Serag, Jorge A Marrero, Amit G Singal, Yujin Hoshida

Faculty, Staff and Students Publications

Background & aims: Hepatocellular carcinoma (HCC) risk stratification is an urgent unmet need for cost-effective HCC screening and early detection in patients with cirrhosis to improve poor HCC prognosis.

Methods: Molecular (prognostic liver secretome signature with α-fetoprotein) and clinical (aMAP [age, male sex, albumin-bilirubin, and platelets] score) variable-based scores were integrated into PAaM (prognostic liver secretome signature with α-fetoprotein plus age, male sex, albumin-bilirubin, and platelets), which was subsequently validated in 2 phase 3 biomarker validation studies: the statewide Texas HCC Consortium and nationwide HCC Early Detection Strategy prospective cohorts, following the prospective specimen collection, retrospective blinded evaluation design. The …

Irisin-Mediated Muscle-Renal Crosstalk As A Protective Mechanism Against Contrast-Induced Acute Kidney Injury Via Cgas-Sting Signalling Inhibition, Long Peng, Suhua Li, Qiang Huang, Yuxiang Sun, Juan Sun, Ting Luo, Yanlin Wang, Zhaoyong Hu, Weiyan Lai, Hui Peng

Faculty, Staff and Students Publications

Background: Contrast-induced acute kidney injury (CI-AKI) continues to pose a pressing clinical challenge during invasive cardiovascular procedures due to the limited availability of preventative strategies. We aimed to demonstrate that irisin, a myokine induced by exercise, protects against CI-AKI by inhibiting the cGAS-STING inflammatory pathway.

Methods and results: We explored the relationship between serum irisin levels and CI-AKI incidence in patients administered the contrast media iohexol. Notably, lower serum irisin levels were strongly associated with an increased incidence of CI-AKI following contrast media administration. To establish a causal link between serum irisin levels and CI-AKI, we utilised a mouse model …

Training Protocol And Calibration Of The International Caries Detection And Assessment System In A School-Based Clinical Trial Of Elementary School-Age Children, Jose-Miguel Yamal, Dania Mofleh, Ru-Jye Chuang, Mengxi Wang, Kila Johnson, Alejandra Garcia-Quintana, Tolulope Titiloye, Suchitra Nelson, Shreela V Sharma

Faculty, Staff and Student Publications

Objectives: This paper demonstrates International Caries Detection and Assessment System (ICDAS) training procedures and inter/intra-examiner reliability for lesion severity, activity, and filling criteria in an elementary school setting.

Methods: ICDAS training was conducted in December 2021 prior to a school-based cluster-randomized controlled trial. A total of 59 children (6-8 years old) in grades 1-2 from one school in Houston, Texas were recruited. Two licensed dentists received a 5-day training from an ICDAS trainer at the participating school. Thirty-eight children were evaluated at least once by each dental trainee, and 18 had repeat examinations. The ICDAS criteria were used to classify …