114 results on '"Quefeng Li"'
Search Results
2. Wearable Devices, Health Care Use, and Psychological Well‐Being in Patients With Atrial Fibrillation
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Lindsey Rosman, Rachel Lampert, Songcheng Zhuo, Quefeng Li, Niraj Varma, Matthew Burg, Allison E. Gaffey, Tiffany Armbruster, and Anil Gehi
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atrial fibrillation ,digital health ,wearables ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background Wearables are increasingly used by patients with atrial fibrillation (AF) for symptom monitoring and health management, but their impact on patient health care use and psychological well‐being is not well understood. Methods and Results In this retrospective, propensity‐matched study of patients with AF, survey and electronic health record data were merged to compare AF‐specific health care use (outpatient/inpatient visits, rhythm‐related testing, and procedures) and informal health care use (telephone calls and patient portal messages) over a 9‐month period between wearable users and nonusers. We also examined the effects of wearable cardiac monitoring features (eg, heart rate alerts, irregular rhythm notification, and ECG) on patient behavior and well‐being. Of 172 patients with AF in this analysis (age, 72.6±9.0 years; 42% women), 83 used a wearable. Compared with nonusers, wearable users reported higher rates of symptom monitoring and preoccupation (P=0.03) and more AF treatment concerns (P=0.02). Moreover, 20% of wearable users experienced anxiety and always contacted their doctors in response to irregular rhythm notifications. After matching, AF‐specific health care use was significantly greater among wearable users compared with nonusers (P=0.04), including significantly higher rates of ECGs, echocardiograms/transesophageal echocardiogram, and ablation. Wearable users were also significantly more likely to use informal health care resources compared with nonusers (P=0.05). Conclusions Wearables were associated with higher rates of symptom monitoring and preoccupation, AF treatment concerns, AF‐specific health care use, and use of informal health care resources. Prospective, randomized studies are needed to understand the net effects of wearables and their alerts on patients, providers, and the health care system.
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- 2024
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3. Use of mechanical circulatory support and survival for heart and heart-kidney transplant recipients in the new allocation system
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Aurelie Merlo, MD, Hannah F. Bensimhon, MD, Patricia P. Chang, MD, MHS, Zhentao Yu, MS, Randall Watkins, BSEE, SSBB, Quefeng Li, PhD, and Mirnela Byku, MD, PhD
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allocation ,heart-kidney transplant ,LVAD ,MCS ,temporary MCS ,Surgery ,RD1-811 ,Specialties of internal medicine ,RC581-951 - Abstract
Background: The 2018 United Network for Organ Sharing organ allocation change aimed to distribute donor hearts to the sickest patients on the waitlist. Whether this change differentially affected outcomes in heart-only vs heart-kidney transplant recipients is unknown. Methods: This study used the Scientific Registry of Transplant Recipients to compare outcomes, including survival, of heart-only and heart-kidney transplant recipients from 2015 to 2021, from the old vs new allocation system, including use of mechanical circulatory support (MCS), prior to transplant. Results: During the study period, 16,696 patients underwent heart transplant alone (9,320 in the old and 7,376 in the new system) and 1,156 patients underwent heart-kidney transplant (529 in the old and 627 in the new system). For both heart and heart-kidney transplant populations, there was a 3- to 5-fold increase in the use of temporary MCS. Heart-only recipients had worse survival when temporary MCS was used in the old allocation system. Heart-only recipients with durable MCS had worse survival both in the old and the new allocation system. There was no difference in survival in heart-kidney recipients in the old vs new allocation system, regardless of MCS use. Conclusions: The new heart allocation system was associated with increased use of temporary MCS in both heart and heart-kidney recipients. However, this change only differentially affected survival in heart-only recipients with improved survival if on temporary MCS, but worse survival if on durable MCS. Unlike prior studies, heart-kidney recipients did not have different outcomes after the heart allocation change, which may reflect outcomes in more current times.
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- 2024
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4. Lung Ultrasound, Bioimpedance Spectroscopy, and Physical Examination for Volume Assessment in Hospitalized Hemodialysis Patients: A Diagnostic Test Study
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Emily H. Chang, MD, Matthew J. Tugman, BA, Magdalene M. Assimon, PharmD, PhD, Connie A. Gilet, MSN, APRN, NP, Renee Ge, BS, Quefeng Li, PhD, and Jennifer E. Flythe, MD, MPH
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Diseases of the genitourinary system. Urology ,RC870-923 - Published
- 2024
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5. Mapping lesion-specific response and progression dynamics and inter-organ variability in metastatic colorectal cancer
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Jiawei Zhou, Amber Cipriani, Yutong Liu, Gang Fang, Quefeng Li, and Yanguang Cao
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Science - Abstract
Understanding the heterogeneity of growth, response to therapy and progression dynamics in metastatic colorectal cancer (mCRC) remains critical. Here, the authors analyse lesion-specific response heterogeneity in 4,308 mCRC patients and find that organ-level progression sequence is associated with long-term survival.
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- 2023
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6. Integration of clinical parameters, genotype and epistaxis severity score to guide treatment for hereditary hemorrhagic telangiectasia associated bleeding
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Joan D. Beckman, Quefeng Li, Samuel T. Hester, Ofri Leitner, Karen L. Smith, and Raj S. Kasthuri
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Telangiectasia, hereditary hemorrhagic ,Anemia ,Epistaxis, Osler-Rendu-weber disease ,ACVRL1 protein, human ,Endoglin ,Iron ,Medicine - Abstract
Abstract Background Hereditary Hemorrhagic Telangiectasia (HHT) is a rare inherited disorder characterized by development of mucocutaneous telangiectases and visceral organ arteriovenous malformations, which can lead to recurrent, spontaneous bleeding and development of iron deficiency anemia. The primary objective of this study was to ascertain the relationship between epistaxis severity scores (ESS), laboratory values, genotype, and phenotype in HHT. Our secondary objective was to assess efficacy of systemic antifibrinolytic therapy in reducing ESS in HHT. Methodology We conducted a retrospective review of patients seen at the UNC HHT Center from January 1, 2009 to February 28, 2015. ESS, demographics, and results of genetic testing were abstracted from the medical record. Response to antifibrinolytic therapy was evaluated by comparing pre-post ESS. Results One hundred and forty nine patients were eligible with 116 having genetic testing and 33 without. Age, hemoglobin and ferritin levels were predictive of ESS. Of the 116 patients that underwent genetic testing: 63 had an ACVRL1 mutation, 40 had an ENG mutation, 2 had a SMAD4 mutation, and 11 patients had no pathologic HHT genetic variation detected. Compared to patients without a detectable HHT-associated genetic variation, patients with a HHT-associated genetic variation had higher ESS scores (p 4 were started on antifibrinolytic therapy (tranexamic acid or aminocaproic acid) and had a post-treatment ESS recorded. All patients had a decrease in ESS of > 0.71 (minimal meaningful difference), but patients taking antifibrinolytics displayed larger decreases. No patients on antifibrinolytics experienced a VTE with median follow up of 13 months. Conclusions We demonstrate that the ESS correlates with age, hemoglobin and ferritin. Additionally, we demonstrate that HHT patients with genetic mutations have higher ESS scores. Our data demonstrate that antifibrinolytics are effective in decreasing epistaxis severity and safe with long-term use in HHT patients.
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- 2020
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7. Arrhythmia Risk During the 2016 US Presidential Election: The Cost of Stressful Politics
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Lindsey Rosman, Elena Salmoirago‐Blotcher, Rafat Mahmood, Hannan Yang, Quefeng Li, Anthony J. Mazzella, Jeffrey Lawrence Klein, Joseph Bumgarner, and Anil Gehi
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arrhythmia ,implantable cardioverter‐defibrillator ,mental stress ,pacemaker ,triggers ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background Anger and extreme stress can trigger potentially fatal cardiovascular events in susceptible people. Political elections, such as the 2016 US presidential election, are significant stressors. Whether they can trigger cardiac arrhythmias is unknown. Methods and Results In this retrospective case‐crossover study, we linked cardiac device data, electronic health records, and historic voter registration records from 2436 patients with implanted cardiac devices. The incidence of arrhythmias during the election was compared with a control period with Poisson regression. We also tested for effect modification by demographics, comorbidities, political affiliation, and whether an individual's political affiliation was concordant with county‐level election results. Overall, 2592 arrhythmic events occurred in 655 patients during the hazard period compared with 1533 events in 472 patients during the control period. There was a significant increase in the incidence of composite outcomes for any arrhythmia (incidence rate ratio [IRR], 1.77 [95% CI, 1.42–2.21]), supraventricular arrhythmia (IRR, 1.82 [95% CI, 1.36–2.43]), and ventricular arrhythmia (IRR, 1.60 [95% CI, 1.22–2.10]) during the election relative to the control period. There was also an increase in specific types of arrhythmia, including atrial fibrillation (IRR, 1.50 [95% CI, 1.06–2.11]), supraventricular tachycardia (IRR, 3.7 [95% CI, 2.2–6.2]), nonsustained ventricular tachycardia (IRR, 1.7 [95% CI, 1.3–2.2]), and daily atrial fibrillation burden (P
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- 2021
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8. Inferring Regulatory Networks From Mixed Observational Data Using Directed Acyclic Graphs
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Wujuan Zhong, Li Dong, Taylor B. Poston, Toni Darville, Cassandra N. Spracklen, Di Wu, Karen L. Mohlke, Yun Li, Quefeng Li, and Xiaojing Zheng
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regulatory network ,directed acyclic graphs ,mixed observational data ,continuous and categorical variables ,causal regulatory pathways ,Genetics ,QH426-470 - Abstract
Construction of regulatory networks using cross-sectional expression profiling of genes is desired, but challenging. The Directed Acyclic Graph (DAG) provides a general framework to infer causal effects from observational data. However, most existing DAG methods assume that all nodes follow the same type of distribution, which prohibit a joint modeling of continuous gene expression and categorical variables. We present a new mixed DAG (mDAG) algorithm to infer the regulatory pathway from mixed observational data containing both continuous variables (e.g. expression of genes) and categorical variables (e.g. categorical phenotypes or single nucleotide polymorphisms). Our method can identify upstream causal factors and downstream effectors closely linked to a variable and generate hypotheses for causal direction of regulatory pathways. We propose a new permutation method to test the conditional independence of variables of mixed types, which is the key for mDAG. We also utilize an L1 regularization in mDAG to ensure it can recover a large sparse DAG with limited sample size. We demonstrate through extensive simulations that mDAG outperforms two well-known methods in recovering the true underlying DAG. We apply mDAG to a cross-sectional immunological study of Chlamydia trachomatis infection and successfully infer the regularity network of cytokines. We also apply mDAG to a large cohort study, generating sensible mechanistic hypotheses underlying plasma adiponectin level. The R package mDAG is publicly available from CRAN at https://CRAN.R-project.org/package=mDAG.
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- 2020
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9. Correlates of changes in walking during the retirement transition: The Multi-Ethnic Study of Atherosclerosis
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Sydney A. Jones, Quefeng Li, Allison E. Aiello, Angela M. O'Rand, and Kelly R. Evenson
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Medicine - Abstract
Retirement from employment involves disruption in daily routines and has been associated with positive and negative changes in physical activity. Walking is the most common physical activity among older Americans. The factors that influence changes in walking after retirement are unknown. The study objective was to identify correlates of within-person change in recreational walking (for leisure) and transport walking (to get places) during the retirement transition among a multi-ethnic cohort of adults (N = 928) from six US communities. Correlates were measured at the individual (e.g., gender), interpersonal (e.g., social support), and community (e.g., density of walking destinations) levels at study exams between 2000 and 2012. Comparing pre- and post-retirement measures (average 4.5 years apart), 50% of participants increased recreational walking by 60 min or more per week, 31% decreased by 60 min or more per week, and 19% maintained their recreational walking. Forty-one percent of participants increased transport walking by 60 min or more per week, 40% decreased by 60 min or more per week, and 19% maintained their transport walking after retirement. Correlates differed for recreational and transport walking and for increases compared to decreases in walking. Self-rated health, chronic conditions, and perceptions of the neighborhood walking environment were associated with changes in both types of walking after retirement. Further, some correlates differed by gender and retirement age. Findings can inform the targeting of interventions to promote walking during the retirement transition. Keywords: Walking, Retirement, Built environment, Transportation, Leisure activities, Cohort study
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- 2018
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10. Ultrafiltration-profiled hemodialysis to reduce dialysis-related cardiovascular stress: Study protocol for a randomized controlled trial
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Matthew J. Tugman, Julia H. Narendra, Quefeng Li, Yueting Wang, Alan L. Hinderliter, Steven M. Brunelli, and Jennifer E. Flythe
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Medicine (General) ,R5-920 - Abstract
Rapid fluid removal (ultrafiltration, UF) is associated with higher cardiovascular morbidity and mortality among individuals receiving maintenance hemodialysis (HD). Fluid removal rates that exceed vascular refill rates can result in hemodynamic instability, end-organ damage to the heart, kidneys, gut and brain, among other organs, and patient symptoms. There are no known evidence-based HD treatment strategies to reduce harm from higher UF rates. Ultrafiltration profiling, the practice of varying UF rates to maximize fluid removal during periods of greatest hydration and plasma oncotic pressure, has been proposed as an HD treatment intervention that may reduce UF rate-related complications. This study is a randomized 4-phase cross-over trial in which participants are successively alternated between study arms with intervening washout periods, and treatment order is randomized. After 4-week screening and 6-week baseline periods, participants are randomized to HD with conventional UF or HD with UF profiling for a period of 3 weeks followed by a 1-week washout period before crossing over. Participants cross into conventional UF and UF profiling phases twice (2 phases per arm). The primary outcomes of interest are intradialytic hypotension (nadir intradialytic systolic blood pressure
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- 2019
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11. glmmPen: High Dimensional Penalized Generalized Linear Mixed Models.
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Hillary M. Heiling, Naim U. Rashid, Quefeng Li, and Joseph G. Ibrahim
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- 2024
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12. Wearable Devices, Health Care Use, and Psychological Well-Being in Patients With Atrial Fibrillation.
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Rosman, Lindsey, Lampert, Rachel, Songcheng Zhuo, Quefeng Li, Varma, Niraj, Burg, Matthew, Gaffey, Allison E., Armbruster, Tiffany, and Gehi, Anil
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- 2024
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13. Characterizing the Propagation Pattern of Neurodegeneration in Alzheimer's Disease by Longitudinal Network Analysis.
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Yueting Wang, Defu Yang, Quefeng Li, Daniel Kaufer, Martin Styner, and Guorong Wu 0001
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- 2020
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14. An Efficient Greedy Search Algorithm for High-Dimensional Linear Discriminant Analysis
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Hannan Yang, Danyu Lin, and Quefeng Li
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Statistics and Probability ,Statistics, Probability and Uncertainty - Published
- 2024
15. Multi-response Regression for Block-missing Multi-modal Data without Imputation
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Haodong Wang, Quefeng Li, and Yufeng Liu
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Statistics and Probability ,Statistics, Probability and Uncertainty - Published
- 2024
16. Efficient computation of high-dimensional penalized generalized linear mixed models by latent factor modeling of the random effects.
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Heiling, Hillary M., Rashid, Naim U., Quefeng Li, Xianlu L. Peng, Yeh, Jen Jen, and Ibrahim, Joseph G.
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Modern biomedical datasets are increasingly high-dimensional and exhibit complex correlation structures. Generalized linear mixed models (GLMMs) have long been employed to accountforsuch dependencies.However, properspecification ofthe fixed and randomeffectsin GLMMs is increasingly difficult in high dimensions, and computational complexity grows with increasing dimension of the random effects. We present a novel reformulation of the GLMM using a factor model decomposition of the random effects, enabling scalable computation of GLMMsin high dimensions by reducing the latent space from a large number of random effects to a smaller set of latent factors. We also extend our prior work to estimate model parameters using a modified Monte Carlo Expectation Conditional Minimization algorithm, allowing us to perform variable selection on both the fixed and random effects simultaneously. We show through simulation that through this factor model decomposition, our method can fit high-dimensional penalized GLMMs faster than comparable methods and more easily scale to larger dimensions not previously seen in existing approaches. [ABSTRACT FROM AUTHOR]
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- 2024
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17. Sleep, cardiovascular risk factors, and kidney function: The Multi-Ethnic Study of Atherosclerosis (MESA)
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Jinsong Chen, Ana C. Ricardo, Kathryn J Reid, James Lash, Joon Chung, Sanjay R. Patel, Martha L. Daviglus, Tianyi Huang, Lei Liu, Rosalba Hernandez, Quefeng Li, and Susan Redline
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Male ,Hemoglobins ,Behavioral Neuroscience ,Cardiovascular Diseases ,Risk Factors ,Heart Disease Risk Factors ,Albumins ,Humans ,Middle Aged ,Renal Insufficiency, Chronic ,Sleep ,Atherosclerosis ,Kidney - Abstract
Examine the associations of sleep measures with kidney function changes over time among individuals from a community-based study.The sample includes 1657 participants (287 with chronic kidney disease [CKD]) in the Multi-Ethnic Study of Atherosclerosis Sleep Cohort (mean age: 57.7 years, male: 46.0%). We examined associations between a large set of sleep variables (polysomnography, actigraphy, and questionnaires) and cardiovascular disease risk factors and changes in estimated glomerular filtration rate (eGFR) and urinary albumin-to-creatinine ratio over approximately 5 years using high-dimensional regression. We investigated the modifying effect of sleep on the associations between cardiovascular disease risk factors and kidney function.Sleep metrics predicted kidney function decline only among individuals with baseline CKD. Among this group, eGFR decline was associated with decreased stage N3 sleep (0.32 mL/min/1.73 mReduced deep sleep, daytime napping, increased wake bouts, delayed sleep rhythms, and overnight hypoxemia are associated with longitudinal kidney function decline, with effects most apparent in individuals with CKD. Deep sleep, napping, and sleep timing modified the association between hemoglobin A1C and kidney function.
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- 2022
18. Kinetics of basophil hyporesponsiveness during short-course peanut oral immunotherapy
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Michael D, Kulis, Johanna M, Smeekens, Caitlin, Burk, Xiaohong, Yue, Rishu, Guo, Kelly A, Orgel, Ping, Ye, Lauren, Herlihy, Deanna, Hamilton, Quefeng, Li, Corinne, Keet, Wayne, Shreffler, Brian P, Vickery, A Wesley, Burks, and Edwin H, Kim
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Arachis ,Desensitization, Immunologic ,Child, Preschool ,Immunology ,Humans ,Administration, Oral ,Immunologic Factors ,Immunology and Allergy ,Peanut Hypersensitivity ,Allergens ,Child ,Basophils - Abstract
Oral immunotherapy (OIT) leads to suppression of mast cell and basophil degranulation along with changes in the adaptive immune response.This study aimed to determine how rapidly these effects occur during OIT and more broadly, the kinetics of basophil and mast cell suppression throughout the course of therapy.Twenty participants, age 4 to 12 years, were enrolled in a peanut OIT trial and assessed for desensitization and sustained unresponsiveness after 9 months of therapy. Blood was collected 5 times in the first month and then intermittently throughout to quantify immunoglobulins and assess basophil activation by CD63, CD203c, and phosphorylated SYK (pSYK).Twelve of 16 participants that completed the trial were desensitized after OIT, with 9 achieving sustained unresponsiveness after discontinuing OIT for 4 weeks. Basophil hyporesponsiveness, defined by lower CD63 expression, was detected as early as day 90. pSYK was correlated with CD63 expression, and there was a significant decrease in pSYK by day 250. CD203c expression remained unchanged throughout therapy. Interestingly, although basophil activation was decreased across the cohort during OIT, basophil activation did not correlate with individual clinical outcomes. Serum peanut-specific IgGSuppression of basophil activation occurs within the first 90 days of peanut OIT, ultimately leading to suppression of signaling through pSYK.
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- 2022
19. Classification of disease recurrence using transition likelihoods with expectation‐maximization algorithm
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Huijun Jiang, Quefeng Li, Jessica T. Lin, and Feng‐Chang Lin
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Statistics and Probability ,Motivation ,Recurrence ,Epidemiology ,Humans ,Algorithms ,Markov Chains ,Probability - Abstract
When an infectious disease recurs, it may be due to treatment failure or a new infection. Being able to distinguish and classify these two different outcomes is critical in effective disease control. A multi-state model based on Markov processes is a typical approach to estimating the transition probability between the disease states. However, it can perform poorly when the disease state is unknown. This article aims to demonstrate that the transition likelihoods of baseline covariates can distinguish one cause from another with high accuracy in infectious diseases such as malaria. A more general model for disease progression can be constructed to allow for additional disease outcomes. We start from a multinomial logit model to estimate the disease transition probabilities and then utilize the baseline covariate's transition information to provide a more accurate classification result. We apply the expectation-maximization (EM) algorithm to estimate unknown parameters, including the marginal probabilities of disease outcomes. A simulation study comparing our classifier to the existing two-stage method shows that our classifier has better accuracy, especially when the sample size is small. The proposed method is applied to determining relapse vs reinfection outcomes in two Plasmodium vivax treatment studies from Cambodia that used different genotyping approaches to demonstrate its practical use.
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- 2022
20. glmmPen: High Dimensional Penalized Generalized Linear Mixed Models.
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Heiling, Hillary M., Rashid, Naim U., Quefeng Li, and Ibrahim, Joseph G.
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CONDITIONAL expectations ,PANCREATIC cancer - Abstract
Generalized linear mixed models (GLMMs) are widely used in research for their ability to model correlated outcomes with non-Gaussian conditional distributions. The proper selection of fixed and random effects is a critical part of the modeling process since model misspecification may lead to significant bias. However, the joint selection of fixed and random effects has historically been limited to lower-dimensional GLMMs, largely due to the use of criterion-based model selection strategies. Here we present the R package glmmPen, one of the first to select fixed and random effects in higher dimension using a penalized GLMM modeling framework. Model parameters are estimated using a Monte Carlo Expectation Conditional Minimization (MCECM) algorithm, which leverages Stan and RcppArmadillo for increased computational efficiency. Our package supports the Binomial, Gaussian, and Poisson families and multiple penalty functions. In this manuscript we discuss the modeling procedure, estimation scheme, and software implementation through application to a pancreatic cancer subtyping study. Simulation results show our method has good performance in selecting both the fixed and random effects in high dimensional GLMMs. [ABSTRACT FROM AUTHOR]
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- 2023
21. A statistical framework for pathway and gene identification from integrative analysis.
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Quefeng Li, Menggang Yu, and Sijian Wang
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- 2017
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22. Outcomes of implantable cardioverter‐defibrillator implantation in HIV‐infected patients: A single‐center retrospective cohort study
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Venkata A. Narla, Hannan Yang, and Quefeng Li
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Adenosine Triphosphate ,Death, Sudden, Cardiac ,Treatment Outcome ,Humans ,HIV Infections ,General Medicine ,Cardiology and Cardiovascular Medicine ,Defibrillators, Implantable ,Retrospective Studies - Abstract
HIV-infected individuals have a known increased risk of sudden cardiac death (SCD) compared to uninfected individuals. Implantable cardioverter-defibrillators (ICDs) are standard therapy for preventing SCD; however, there is limited data on the outcomes of ICDs in HIV-infected individuals.HIV-infected subjects receive a higher number of appropriate ICD therapies than uninfected controls.This is a retrospective cohort study of 35 consecutive HIV-Infected patients and 36 uninfected controls matched by age, race, and gender who were treated at the University of North Carolina Medical Center in the outpatient or inpatient setting from 2014 to the present and had undergone ICD implantation. For HIV-infected subjects, a multivariate Poisson regression analysis was performed to evaluate the association between covariates and ICD therapies.Among HIV-infected subjects, the mean CD4 count was 582.5 cells/mmHIV-infected subjects had a higher number of appropriate ICD discharge or ATP therapy per person-year than matched uninfected controls.
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- 2022
23. Testing generalized linear models with high-dimensional nuisance parameters
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Jinsong Chen, Quefeng Li, and Hua Yun Chen
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Statistics and Probability ,Applied Mathematics ,General Mathematics ,Statistics, Probability and Uncertainty ,General Agricultural and Biological Sciences ,Agricultural and Biological Sciences (miscellaneous) - Abstract
Summary Generalized linear models often have high-dimensional nuisance parameters, as seen in applications such as testing gene-environment interactions or gene-gene interactions. In these scenarios, it is essential to test the significance of a high-dimensional subvector of the model’s coefficients. Although some existing methods can tackle this problem, they often rely on the bootstrap to approximate the asymptotic distribution of the test statistic, and are thus computationally expensive. Here, we propose a computationally efficient test with a closed-form limiting distribution, which allows the parameter being tested to be either sparse or dense. We show that, under certain regularity conditions, the Type-I error of the proposed method is asymptotically correct, and we establish its power under high-dimensional alternatives. Extensive simulations demonstrate the good performance of the proposed test and its robustness when certain sparsity assumptions are violated. We also apply the proposed method to Chinese famine sample data in order to show its performance when testing the significance of gene-environment interactions.
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- 2022
24. Supplementary Data from Spatiotemporal Heterogeneity across Metastases and Organ-Specific Response Informs Drug Efficacy and Patient Survival in Colorectal Cancer
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Yanguang Cao, Quefeng Li, and Jiawei Zhou
- Abstract
Supplementary Data Online
- Published
- 2023
25. Data from Modeling Tumor Evolutionary Dynamics to Predict Clinical Outcomes for Patients with Metastatic Colorectal Cancer: A Retrospective Analysis
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Yanguang Cao, Quefeng Li, Yubo Zhang, Yutong Liu, and Jiawei Zhou
- Abstract
Over 50% of colorectal cancer patients develop resistance after a transient response to therapy. Understanding tumor resistance from an evolutionary perspective leads to better predictions of treatment outcomes. The objectives of this study were to develop a computational framework to analyze tumor longitudinal measurements and recapitulate the individual evolutionary dynamics in metastatic colorectal cancer (mCRC) patients. A stochastic modeling framework was developed to depict the whole spectrum of tumor evolution prior to diagnosis and during and after therapy. The evolutionary model was optimized using a nonlinear mixed effect (NLME) method based on the longitudinal measurements of liver metastatic lesions from 599 mCRC patients. The deterministic limits in the NLME model were applied to optimize the stochastic model for each patient. Cox proportional hazards models coupled with the least absolute shrinkage and selection operator (LASSO) algorithm were applied to predict patients' progression-free survival (PFS) and overall survival (OS). The stochastic evolutionary model well described the longitudinal profiles of tumor sizes. The evolutionary parameters optimized for each patient indicated substantial interpatient variability. The number of resistant subclones at diagnosis was found to be a significant predictor to survival, and the hazard ratios with 95% CI were 1.09 (0.79–1.49) and 1.54 (1.01–2.34) for patients with three or more resistant subclones. Coupled with several patient characteristics, evolutionary parameters strongly predict patients' PFS and OS. A stochastic computational framework was successfully developed to recapitulate individual patient evolutionary dynamics, which could predict clinical survival outcomes in mCRC patients.Significance:A data analysis framework depicts the individual evolutionary dynamics of mCRC patients and can be generalized to project patient survival outcomes.
- Published
- 2023
26. Supplementary Data from Modeling Tumor Evolutionary Dynamics to Predict Clinical Outcomes for Patients with Metastatic Colorectal Cancer: A Retrospective Analysis
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Yanguang Cao, Quefeng Li, Yubo Zhang, Yutong Liu, and Jiawei Zhou
- Abstract
Supplementary Text S1. Mathematical model and parameter estimation; Supplementary Table 1. Cohen's d point estimate and 95% confidence interval in effect size tests among patients with PD (Progressive Disease), SD (Stable Disease) or PR (Partial Response) responses; Supplementary Figure 1. The individual tumor growth profiles for all 599 individuals; Supplementary Figure 2. Kaplan-Meier curves of the overall survival starting from last tumor observation for each individual patient. The curves were categorized by evolutionary parameters and the number of cell subclones at diagnosis derived from the evolutionary model.
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- 2023
27. Data from Spatiotemporal Heterogeneity across Metastases and Organ-Specific Response Informs Drug Efficacy and Patient Survival in Colorectal Cancer
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Yanguang Cao, Quefeng Li, and Jiawei Zhou
- Abstract
The sum of target lesions is routinely used to evaluate patient objective responses to treatment in the RECIST criteria, but it fails to address response heterogeneity across metastases. This study argues that spatiotemporal heterogeneity across metastases and organ-specific response is informative for drug efficacy and patient survival. We analyzed the longitudinal data of 11,404 metastatic lesions in 2,802 colorectal cancer patients from five phase III clinical trials. Initially, a metric Gower distance was applied to quantify response heterogeneity across metastases. Next, the spatiotemporal response heterogeneity across anatomic sites, therapies, and KRAS mutation status was assessed and examined for its association with drug efficacy and long-term patient survival. The response of metastatic lesions broadly differed across anatomic sites and therapies. About 60% of patients had at least one lesion respond contrarily from total tumor size. High interlesion heterogeneity was associated with shorter progression-free survival and overall survival. Targeted therapies (bevacizumab or panitumumab) combined with standard chemotherapy reduced interlesion heterogeneity and elicited more favorable effects from liver lesions (P < 0.001) than chemotherapy alone. Moreover, the favorable responses in liver metastases (> 30% shrinkage) were associated with extended patient overall survival (P < 0.001), in contrast to lesions in the lungs and lymph nodes. Altogether, the spatiotemporal response heterogeneity across metastases informed drug efficacy and patient survival, which could improve the current methods for treatment evaluation and patient prognosis.Significance:These findings support the modification of RECIST criteria to include individual lesion response to improve assessments of drug efficacy.
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- 2023
28. Open-label study of the efficacy, safety, and durability of peanut sublingual immunotherapy in peanut-allergic children
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Edwin H. Kim, Corinne A. Keet, Yamini V. Virkud, Stacy Chin, Ping Ye, Anusha Penumarti, Johanna Smeekens, Rishu Guo, Xiaohong Yue, Quefeng Li, Michael R. Kosorok, Michael D. Kulis, and A. Wesley Burks
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Immunology ,Immunology and Allergy - Published
- 2023
29. Adaptive supervised learning on data streams in reproducing kernel Hilbert spaces with data sparsity constraint
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Haodong Wang, Quefeng Li, and Yufeng Liu
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Statistics and Probability ,Statistics, Probability and Uncertainty - Published
- 2023
30. High-Dimensional Factor Regression for Heterogeneous Subpopulations
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Peiyao Wang, Quefeng Li, Dinggang Shen, and Yufeng Liu
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Statistics and Probability ,Statistics, Probability and Uncertainty - Published
- 2023
31. CE-452772-3 SELF-PULSE EXAM FOR ATRIAL FIBRILLATION SCREENING: A RANDOMIZED CONTROLLED TRIAL
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Benjamin Chilcutt, Taylor C. Bazemore, Tiffany Armbruster, Ari Becker, Wanting Jin, Quefeng Li, and Anil K. Gehi
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Physiology (medical) ,Cardiology and Cardiovascular Medicine - Published
- 2023
32. Dynamic Classification of Plasmodium vivax Malaria Recurrence: An Application of Classifying Unknown Cause of Failure in Competing Risks
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Yutong Liu, Feng-Chang Lin, Jessica T. Lin, and Quefeng Li
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parasitic diseases - Abstract
A standard competing risks set-up requires both time to event and cause of failure to be fully observable for all subjects. However, in application, the cause of failure may not always be observable, thus impeding the risk assessment. In some extreme cases, none of the causes of failure is observable. In the case of a recurrent episode of Plasmodium vivax malaria following treatment, the patient may have suffered a relapse from a previous infection or acquired a new infection from a mosquito bite. In this case, the time to relapse cannot be modeled when a competing risk, a new infection, is present. The efficacy of a treatment for preventing relapse from a previous infection may be underestimated when the true cause of infection cannot be classified. In this paper, we developed a novel method for classifying the latent cause of failure under a competing risks set-up, which uses not only time to event information but also transition likelihoods between covariates at the baseline and at the time of event occurrence. Our classifier shows superior performance under various scenarios in simulation experiments. The method was applied to Plasmodium vivax infection data to classify recurrent infections of malaria.
- Published
- 2021
33. Uncovering Diverse Mechanistic Spreading Pathways in Disease Progression of Alzheimer's Disease
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Zhentao Yu, Mustaf Dere, Quefeng Li, and Guorong Wu
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Psychiatry and Mental health ,Cellular and Molecular Neuroscience ,Developmental Neuroscience ,Epidemiology ,Health Policy ,Neurology (clinical) ,Geriatrics and Gerontology - Published
- 2022
34. Regularized Buckley–James method for right‐censored outcomes with block‐missing multimodal covariates
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Haodong Wang, Quefeng Li, and Yufeng Liu
- Subjects
Statistics and Probability ,Statistics, Probability and Uncertainty - Published
- 2022
35. Predictors of Post-induction Hypotension for Patients With Pulmonary Hypertension
- Author
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Adriano Bellotti, Simrat Arora, Chelsea Gustafson, Ian Funk, Craig Grossheusch, Carter Simmers, Quefeng Li, Yutong Liu, and Alan Smeltz
- Subjects
General Engineering - Abstract
Purpose The purpose is to identify predictors of post-induction hypotension (PIH) during general anesthesia in a population of patients with varying degrees of pulmonary hypertension (PH). Methods This is a single-center, retrospective, observational study of perioperative data obtained via electronic health records from patients with PH undergoing surgery over a five-year period. Baseline patient characteristics, peri-induction management variables, and pre-induction mean arterial pressure (MAP) were statistically analyzed using Kruskal-Wallis rank sum tests, Pearson's chi-squared tests, and logistic regression analysis to identify risk factors for PIH. We further assessed the relationship between PH and PIH using propensity score matching. Primary outcomes include a percent decrease in post-induction blood pressure as well as a post-induction nadir with a threshold of 55 mm Hg. Results Eight hundred fifty-seven patients in the cohort stratified by severity of PH reveal that advanced age (p0.001), higher BMI (P = 0.002), higher American Society of Anesthesiologists (ASA) score (P = 0.001), and renal and cardiac comorbidities (P0.001) are associated with PH severity. None of our tested parameters were significantly predictive for PIH in patients with PH. Right heart failure was found to be weakly and non-significantly predictive of PIH in patients with PH (P = 0.052, odds ratio [OR] = 1.116). Diabetes (P = 0.007, OR = 0.919) and maintenance of spontaneous ventilation (P = 0.012, OR = 0.925) were associated with decreased rates of PIH. Conclusion Hypotension after induction of general anesthesia in patients with PH is a serious problem, yet statistically significant risk factors were not identified. History of diabetes and preservation of spontaneous ventilation had a significant but weak effect of decreasing rates of PIH. This pilot study was limited by retrospective design and warrants further analysis with a prospective cohort.
- Published
- 2022
36. Chronic E-Cigarette Exposure Alters Human Alveolar Macrophage Morphology and Gene Expression
- Author
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Robert Tarran, Quefeng Li, Raymond D. Coakley, Temperance R. Rowell, Joe A Wrennall, Arunava Ghosh, Neil E. Alexis, Davis Eric, Hong Dang, Erica A. Pawlak, Carla Ribeiro, and Bob A. Lubamba
- Subjects
Cell type ,Lung ,medicine.diagnostic_test ,business.industry ,Vaping ,Immunocytochemistry ,Public Health, Environmental and Occupational Health ,Original Investigations ,Gene Expression ,Tobacco Products ,Electronic Nicotine Delivery Systems ,Bronchoscopies ,medicine.anatomical_structure ,Immune system ,Bronchoalveolar lavage ,Macrophages, Alveolar ,Immunology ,Gene expression ,medicine ,Alveolar macrophage ,Humans ,business - Abstract
Introduction Alveolar macrophages (AMs) are lung-resident immune cells that phagocytose inhaled particles and pathogens, and help coordinate the lung’s immune response to infection. Little is known about the impact of chronic e-cigarette use (ie, vaping) on this important pulmonary cell type. Thus, we determined the effect of vaping on AM phenotype and gene expression. Aims and Methods We recruited never-smokers, smokers, and e-cigarette users (vapers) and performed research bronchoscopies to isolate AMs from bronchoalveolar lavage fluid samples and epithelial cells from bronchial brushings. We then performed morphological analyses and used the Nanostring platform to look for changes in gene expression. Results AMs obtained from smokers and vapers were phenotypically distinct from those obtained from nonsmokers, and from each other. Immunocytochemistry revealed that vapers AMs had significantly elevated inducible nitric oxide synthase (M1) expression and significantly reduced CD301a (M2) expression compared with nonsmokers or smokers. Vapers’ AMs and bronchial epithelia exhibited unique changes in gene expression compared with nonsmokers or smokers. Moreover, vapers’ AMs were the most affected of all groups and had 124 genes uniquely downregulated. Gene ontology analysis revealed that vapers and smokers had opposing changes in biological processes. Conclusions These data indicate that vaping causes unique changes to AMs and bronchial epithelia compared with nonsmokers and smokers which may impact pulmonary host defense. Implications These data indicate that normal “healthy” vapers have altered AMs and may be at risk of developing abnormal immune responses to inflammatory stimuli.
- Published
- 2021
37. Dynamic Classification of
- Author
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Yutong, Liu, Feng-Chang, Lin, Jessica T, Lin, and Quefeng, Li
- Abstract
A standard competing risks set-up requires both time to event and cause of failure to be fully observable for all subjects. However, in application, the cause of failure may not always be observable, thus impeding the risk assessment. In some extreme cases, none of the causes of failure is observable. In the case of a recurrent episode of
- Published
- 2022
38. Supplement of "An Efficient Greedy Search Algorithm for High-dimensional Linear Discriminant Analysis".
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Hannan Yang, Danyu Lin, and Quefeng Li
- Subjects
FISHER discriminant analysis ,SCHWARZ inequality ,MEAN value theorems ,CUMULATIVE distribution function - Abstract
The article focuses on providing proofs and supporting lemmas for "An Efficient Greedy Search Algorithm for High-dimensional Linear Discriminant Analysis." Topics include concentration inequalities for differences in covariance matrices and discriminant vectors; conditions ensuring the convergence of covariance matrix estimates; and results are crucial for validating the efficiency and accuracy of the proposed algorithm in high-dimensional linear discriminant analysis.
- Published
- 2023
39. Hypothermia and Prolonged Time From Procedure End to Extubation After Endovascular Thoracic Aortic Surgery
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Harendra Arora, John A. Encarnacion, Quefeng Li, Yutong Liu, Priya A. Kumar, and Alan M. Smeltz
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Anesthesiology and Pain Medicine ,Hypothermia, Induced ,Humans ,Hypothermia ,Thoracic Surgical Procedures ,Cardiology and Cardiovascular Medicine ,Aorta ,Retrospective Studies - Abstract
Perioperative hypothermia (core temperature36°C) occurs in 50%-to-80% of patients recovering from thoracic aortic surgery, though its effects have not been described fully in this context. The authors, therefore, sought to characterize the incidence of perioperative hypothermia and its association with time from procedure end to extubation in endovascular aortic surgical patients.A retrospective cohort study.At a single academic tertiary center.Patients recovering from thoracic aortic surgery with lumbar drains.None.A total of 196 patients were included in this study, 55 of whom were hypothermic with temperatures35.0°C at the end of surgery. Though the unadjusted time to extubation was not statistically different in the hypothermic group (median 8 minutes, IQR 5-13.5 minutes) compared to the normothermic group (median 7 minutes, IQR 4-12 minutes; p = 0.062), multivariate predictors of increased time from procedure end to extubation included hypothermia (p = 0.011), age (p = 0.009), diabetes (p = 0.015), history of carotid disease (p = 0.040), and crystalloid volume (p = 0.019).Hypothermia in patients recovering from endovascular aortic surgery was associated with prolonged time from procedure end to extubation. Because of the retrospective observational nature of the authors' analysis, it was not possible to determine the extent to which prolonged mechanical ventilation was influenced by low temperature.
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- 2022
40. Efficacy, Safety, and Tolerability of Oral Furosemide Among Patients Receiving Hemodialysis: A Pilot Study
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Jennifer E. Flythe, Magdalene M. Assimon, Matthew J. Tugman, Julia H. Narendra, Simran K. Singh, Wanting Jin, Quefeng Li, Nisha Bansal, Thomas H. Hostetter, and Laura M. Dember
- Subjects
Nephrology - Abstract
Diuretic use may reduce volume-related complications in hemodialysis. We evaluated the efficacy, safety, and tolerability of furosemide in patients with hemodialysis-dependent kidney failure.We conducted an open label, single-arm, 18-week, dose titration pilot study of oral furosemide (maximum dose 320 mg/day) among patients receiving maintenance hemodialysis who reported at least 1 cup of urine output per day. The primary efficacy outcome was an increase from baseline to a specified threshold of 24-hour urine volume, with the threshold based on baseline urine volume (200 ml/dayOf the 39 participants, 28 (72%) received the expected furosemide dose, 3 (8%) underwent dose reduction, 5 (12%) discontinued furosemide without dose reduction, and 3 (8%) underwent dose reduction and subsequently discontinued furosemide. The median (quartile 1, quartile 3) baseline 24-hour urine volume was 290 ml (110, 740), and the maximum, average daily study furosemide dose ranged from 69 mg/day to 320 mg/d. The urine output efficacy outcome was met by 12 (33%), 11 (33%), and 7 (22%) participants at weeks 5, 12, and 18, respectively, in the intention-to-treat analysis, and by 12 (39%), 9 (35%), and 7 (28%) participants at weeks 5, 12, and 18, respectively, in the on-treatment analysis. There were no electrolyte, furosemide level, or patient-reported hearing change safety events.Furosemide was generally safe and well tolerated, but only one-third of participants met the efficacy definition at week 5. The clinical importance of the efficacy findings is uncertain.
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- 2022
41. Spatiotemporal Heterogeneity across Metastases and Organ-Specific Response Informs Drug Efficacy and Patient Survival in Colorectal Cancer
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Jiawei Zhou, Quefeng Li, and Yanguang Cao
- Subjects
Male ,0301 basic medicine ,Oncology ,Cancer Research ,medicine.medical_specialty ,Lung Neoplasms ,Bevacizumab ,Colorectal cancer ,medicine.medical_treatment ,Phases of clinical research ,Article ,Proto-Oncogene Proteins p21(ras) ,Efficacy ,Lesion ,03 medical and health sciences ,Antineoplastic Agents, Immunological ,0302 clinical medicine ,Text mining ,Internal medicine ,Antineoplastic Combined Chemotherapy Protocols ,medicine ,Humans ,Panitumumab ,Longitudinal Studies ,Aged ,Chemotherapy ,business.industry ,Liver Neoplasms ,Middle Aged ,Prognosis ,medicine.disease ,Progression-Free Survival ,030104 developmental biology ,Clinical Trials, Phase III as Topic ,Lymphatic Metastasis ,030220 oncology & carcinogenesis ,Mutation ,Female ,medicine.symptom ,Colorectal Neoplasms ,business ,medicine.drug - Abstract
The sum of target lesions is routinely used to evaluate patient objective responses to treatment in the RECIST criteria, but it fails to address response heterogeneity across metastases. This study argues that spatiotemporal heterogeneity across metastases and organ-specific response is informative for drug efficacy and patient survival. We analyzed the longitudinal data of 11,404 metastatic lesions in 2,802 colorectal cancer patients from five phase III clinical trials. Initially, a metric Gower distance was applied to quantify response heterogeneity across metastases. Next, the spatiotemporal response heterogeneity across anatomic sites, therapies, and KRAS mutation status was assessed and examined for its association with drug efficacy and long-term patient survival. The response of metastatic lesions broadly differed across anatomic sites and therapies. About 60% of patients had at least one lesion respond contrarily from total tumor size. High interlesion heterogeneity was associated with shorter progression-free survival and overall survival. Targeted therapies (bevacizumab or panitumumab) combined with standard chemotherapy reduced interlesion heterogeneity and elicited more favorable effects from liver lesions (P < 0.001) than chemotherapy alone. Moreover, the favorable responses in liver metastases (> 30% shrinkage) were associated with extended patient overall survival (P < 0.001), in contrast to lesions in the lungs and lymph nodes. Altogether, the spatiotemporal response heterogeneity across metastases informed drug efficacy and patient survival, which could improve the current methods for treatment evaluation and patient prognosis. Significance: These findings support the modification of RECIST criteria to include individual lesion response to improve assessments of drug efficacy.
- Published
- 2021
42. Decomposition of variation of mixed variables by a latent mixed Gaussian copula model
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Yutong Liu, Toni Darville, Xiaojing Zheng, and Quefeng Li
- Subjects
Statistics and Probability ,General Immunology and Microbiology ,Applied Mathematics ,General Medicine ,General Agricultural and Biological Sciences ,General Biochemistry, Genetics and Molecular Biology - Abstract
Many biomedical studies collect data of mixed types of variables from multiple groups of subjects. Some of these studies aim to find the group-specific and the common variation among all these variables. Even though similar problems have been studied by some previous works, their methods mainly rely on the Pearson correlation, which cannot handle mixed data. To address this issue, we propose a latent mixed Gaussian copula (LMGC) model that can quantify the correlations among binary, ordinal, continuous, and truncated variables in a unified framework. We also provide a tool to decompose the variation into the group-specific and the common variation over multiple groups via solving a regularized M-estimation problem. We conduct extensive simulation studies to show the advantage of our proposed method over the Pearson correlation-based methods. We also demonstrate that by jointly solving the M-estimation problem over multiple groups, our method is better than decomposing the variation group by group. We also apply our method to a Chlamydia trachomatis genital tract infection study to demonstrate how it can be used to discover informative biomarkers that differentiate patients.
- Published
- 2022
43. Mapping Intrapatient Response Heterogeneity and Lesion-specific Relapse Dynamics in Metastatic Colorectal Cancer
- Author
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Jiawei Zhou, Amber Cipriani, Yutong Liu, Gang Fang, Quefeng Li, and Yanguang Cao
- Abstract
Achieving systemic tumor control across metastases is vital for long-term patient survival but remains intractable in many patients. High intrapatient heterogeneity persists, conferring many dissociated responses across metastatic lesions. Most studies of metastatic disease focus on tumor molecular and cellular features, which are crucial to elucidating the mechanisms underlying intrapatient heterogeneity. However, our understanding of intrapatient heterogeneity on the macroscopic level, such as lesion dynamics in growth, response, and relapse during treatment, remains rudimentary. This study investigated intrapatient heterogeneity through analyzing 116,542 observations of 40,612 lesions in 4,308 metastatic colorectal cancer (mCRC) patients. Despite significant differences in their response and relapse dynamics, metastatic lesions converged on four phenotypes that varied with anatomical site. Importantly, we found that organ-level relapse sequence was closely associated with patient survival, and that patients with the first relapses in the liver often had worse survival. In conclusion, our study provides insights into intrapatient response heterogeneity in mCRC and creates impetus for metastasis-specific therapeutics.
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- 2022
44. Hemodynamic Recovery After Heart Transplantation
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Ian Funk, Chelsea Gustafson, Quefeng Li, Yutong Liu, Emily Teeter, and Alan Smeltz
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Anesthesiology and Pain Medicine ,Hemodynamics ,Heart Transplantation ,Humans ,Heart ,Cardiology and Cardiovascular Medicine - Published
- 2022
45. Characterizing Network Selectiveness to the Dynamic Spreading of Neuropathological Events in Alzheimer's Disease
- Author
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Wenchao, Li, Defu, Yang, Chenggang, Yan, Minghan, Chen, Quefeng, Li, Wentao, Zhu, and Guorong, Wu
- Subjects
Alzheimer Disease ,Connectome ,Brain ,Humans ,Neuroimaging ,Neuropathology ,Article - Abstract
BACKGROUND: Mounting evidence shows that the neuropathological burdens manifest preference in affecting brain regions during the dynamic progression of Alzheimer’s disease (AD). Since the distinct brain regions are physically wired by white matter fibers, it is reasonable to hypothesize the differential spreading pattern of neuropathological burdens may underlie the wiring topology, which can be characterized using neuroimaging and network science technologies. OBJECTIVE: To study the dynamic spreading patterns of neuropathological events in AD. METHODS: We first examine whether hub nodes with high connectivity in the brain network (assemble of white matter wirings) are susceptible to a higher level of pathological burdens than other regions that are less involved in the process of information exchange in the network. Moreover, we propose a novel linear mixed-effect model to characterize the multi-factorial spreading process of neuropathological burdens from hub nodes to non-hub nodes, where age, sex, and APOE4 indicators are considered as confounders. We apply our statistical model to the longitudinal neuroimaging data of amyloid-PET and tau-PET, respectively. RESULTS: Our meta-data analysis results show that 1) AD differentially affects hub nodes with a significantly higher level of pathology, and 2) the longitudinal increase of neuropathological burdens on non-hub nodes is strongly correlated with the connectome distance to hub nodes rather than the spatial proximity. CONCLUSION: The spreading pathway of AD neuropathological burdens might start from hub regions and propagate through the white matter fibers in a prion-like manner.
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- 2022
46. Racial and Ethnic Differences in Acceptability of Urine and Cervico-Vaginal Sample Self-Collection for HPV-Based Cervical Cancer Screening
- Author
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Yutong Liu, John W. Schmitt, Quefeng Li, Lisa Rahangdale, Jennifer S. Smith, LaHoma S. Romocki, Julie A. E. Nelson, Claire Edelman, Vijay Sivaraman, Andrea K. Knittel, Eliane Rohner, Kate Miele, Anna Baker, Samveg A Desai, and F. Hunter McGuire
- Subjects
Adult ,0301 basic medicine ,medicine.medical_specialty ,Ethnic group ,Uterine Cervical Neoplasms ,Sample (statistics) ,Urine ,Self collection ,Urinalysis ,Cervical cancer screening ,Specimen Handling ,03 medical and health sciences ,0302 clinical medicine ,Predictive Value of Tests ,Surveys and Questionnaires ,North Carolina ,medicine ,Humans ,Mass Screening ,Human papillomavirus ,Papillomaviridae ,Early Detection of Cancer ,Aged ,Vaginal Smears ,Obstetrics ,business.industry ,Papillomavirus Infections ,Reproducibility of Results ,Patient Preference ,General Medicine ,Middle Aged ,Patient Acceptance of Health Care ,Uterine Cervical Dysplasia ,Hpv testing ,030104 developmental biology ,Colposcopy ,030220 oncology & carcinogenesis ,Vagina ,Self-Examination ,Female ,business - Abstract
Background: We compared women's acceptability of urine and cervico-vaginal sample self-collection for high-risk (oncogenic) human papillomavirus (hrHPV) testing and assessed whether acceptability v...
- Published
- 2020
47. Relapse or reinfection: Classification of malaria infection using transition likelihoods
- Author
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Quefeng Li, Feng-Chang Lin, and Jessica T. Lin
- Subjects
Statistics and Probability ,medicine.medical_specialty ,Recurrent infections ,Genotype ,Plasmodium vivax ,Mosquito bite ,01 natural sciences ,Article ,General Biochemistry, Genetics and Molecular Biology ,010104 statistics & probability ,03 medical and health sciences ,Recurrence ,Internal medicine ,parasitic diseases ,Malaria, Vivax ,Humans ,Medicine ,In patient ,0101 mathematics ,030304 developmental biology ,0303 health sciences ,General Immunology and Microbiology ,biology ,business.industry ,Applied Mathematics ,Genetic variants ,General Medicine ,biology.organism_classification ,medicine.disease ,Reinfection ,Vivax malaria ,Plasmodium vivax Malaria ,General Agricultural and Biological Sciences ,business ,Malaria - Abstract
In patients with Plasmodium vivax malaria treated with effective blood-stage therapy, the recurrent illness may occur due to relapse from latent liver-stage infection or reinfection from a new mosquito bite. Classification of the recurrent infection as either relapse or reinfection is critical when evaluating the efficacy of an anti-relapse treatment. Although one can use whether a shared genetic variant exists between baseline and recurrence genotypes to classify the outcome, little has been suggested to use both sharing and nonsharing variants to improve the classification accuracy. In this paper, we develop a novel classification criterion that utilizes transition likelihoods to distinguish relapse from reinfection. When tested in extensive simulation experiments with known outcomes, our classifier has superior operating characteristics. A real data set from 78 Cambodian P. vivax malaria patients was analyzed to demonstrate the practical use of our proposed method.
- Published
- 2020
48. Modeling Tumor Evolutionary Dynamics to Predict Clinical Outcomes for Patients with Metastatic Colorectal Cancer: A Retrospective Analysis
- Author
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Yubo Zhang, Yutong Liu, Yanguang Cao, Quefeng Li, and Jiawei Zhou
- Subjects
Male ,0301 basic medicine ,Oncology ,Cancer Research ,medicine.medical_specialty ,Colorectal cancer ,Stochastic modelling ,Leucovorin ,Irinotecan ,Article ,03 medical and health sciences ,0302 clinical medicine ,Lasso (statistics) ,Internal medicine ,Antineoplastic Combined Chemotherapy Protocols ,medicine ,Humans ,Multicenter Studies as Topic ,Longitudinal Studies ,Evolutionary dynamics ,Survival rate ,Randomized Controlled Trials as Topic ,Retrospective Studies ,Proportional hazards model ,business.industry ,Panitumumab ,Liver Neoplasms ,Hazard ratio ,Retrospective cohort study ,Middle Aged ,Models, Theoretical ,Prognosis ,medicine.disease ,Biological Evolution ,Survival Rate ,030104 developmental biology ,Clinical Trials, Phase III as Topic ,030220 oncology & carcinogenesis ,Disease Progression ,Female ,Fluorouracil ,Colorectal Neoplasms ,business ,Follow-Up Studies - Abstract
Over 50% of colorectal cancer patients develop resistance after a transient response to therapy. Understanding tumor resistance from an evolutionary perspective leads to better predictions of treatment outcomes. The objectives of this study were to develop a computational framework to analyze tumor longitudinal measurements and recapitulate the individual evolutionary dynamics in metastatic colorectal cancer (mCRC) patients. A stochastic modeling framework was developed to depict the whole spectrum of tumor evolution prior to diagnosis and during and after therapy. The evolutionary model was optimized using a nonlinear mixed effect (NLME) method based on the longitudinal measurements of liver metastatic lesions from 599 mCRC patients. The deterministic limits in the NLME model were applied to optimize the stochastic model for each patient. Cox proportional hazards models coupled with the least absolute shrinkage and selection operator (LASSO) algorithm were applied to predict patients' progression-free survival (PFS) and overall survival (OS). The stochastic evolutionary model well described the longitudinal profiles of tumor sizes. The evolutionary parameters optimized for each patient indicated substantial interpatient variability. The number of resistant subclones at diagnosis was found to be a significant predictor to survival, and the hazard ratios with 95% CI were 1.09 (0.79–1.49) and 1.54 (1.01–2.34) for patients with three or more resistant subclones. Coupled with several patient characteristics, evolutionary parameters strongly predict patients' PFS and OS. A stochastic computational framework was successfully developed to recapitulate individual patient evolutionary dynamics, which could predict clinical survival outcomes in mCRC patients. Significance: A data analysis framework depicts the individual evolutionary dynamics of mCRC patients and can be generalized to project patient survival outcomes.
- Published
- 2020
49. Abstract 11676: Do Heart Failure Admission Rates Change Around Holidays? The Atherosclerosis Risk in Communities (ARIC) Study
- Author
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David T Saxon, Hannan Yang, Quefeng Li, Matthew S Loop, Stuart D Russell, Joseph Rossi, Richard Stacey, and Patricia Chang
- Subjects
Physiology (medical) ,Cardiology and Cardiovascular Medicine ,human activities - Abstract
Introduction: Heart failure (HF) exacerbations are often precipitated by dietary noncompliance, which is common around holidays. We examined whether HF hospitalizations would increase after major national holidays. Methods: The ARIC Study performed surveillance of HF admissions among patients age ≥55 years in 4 US communities from 2005-2014. HF admissions were identified by ICD-9 codes and validated by physician review. For each holiday (H), 4 days before the holiday (H-4 to H-1), and 4 days after the holiday (H+1 to H+4), we compared average daily HF admission rates, hospital length of stay (LOS), 28-day mortality, and 1-year mortality to the remaining days in each holiday’s month using Poisson regression using a complex sampling design. Results: ARIC identified 92,354 HF admissions (weighted). Patients admitted in holiday months were 46% male and 71% white, with average age 75 years. Compared to the holiday months, patients admitted on H were older (78 years, p Conclusions: HF admission rates, hospital LOS, and mortality were similar in the 4 days following a holiday compared to the remainder of each holiday’s month. However, the day before and/or day of a holiday were associated with lower HF admission rates, shorter hospital LOS, and lower 28-day mortality.
- Published
- 2021
50. Quality of Recovery After Rotator Cuff Repair With Interscalene Liposomal Bupivacaine Versus Interscalene Nerve Catheter
- Author
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Jay W. Schoenherr, Michael Gonzalez, Ricardo Serrano, Meredith Park, Zachary Lee, Kathryn Cobb, Christopher Howard, David Flynn, Quefeng Li, Stuart Grant, and Ty Bullard
- Subjects
Orthopedics and Sports Medicine - Abstract
Background: Interscalene nerve catheters have been proven to be effective in managing pain after rotator cuff repair (RCR) surgery. Liposomal bupivacaine is a newer approved therapy for use around the interscalene brachial plexus, but its analgesic efficacy has limited supporting data in various patient populations. Purpose/Hypothesis: The purpose of this study was to investigate the quality of recovery after arthroscopic RCR in patients who received either single-injection interscalene liposomal bupivacaine or an interscalene peripheral nerve catheter. It was hypothesized that interscalene peripheral nerve catheters would provide more reliable analgesia and improved patient satisfaction 48 hours after surgery. Study Design: Cohort study; Level of evidence, 2. Methods: Enrolled were 93 consecutive patients who underwent arthroscopic rotator cuff surgery at a single ambulatory surgery center between October 2020 and June 2021. Of these patients, 13 were lost to follow-up; thus, 80 patients were included in statistical analysis. One group of patients (n = 48) received a preoperative interscalene nerve block placed with 10 mL 0.5% bupivacaine and 10 mL 1.3% liposomal bupivacaine. The second group (n = 32) received a preoperative interscalene catheter with an initial bolus of 20 mL 0.25% bupivacaine and a 0.2% ropivacaine infusion by an elastomeric pump set at 10 mL/hr for 48 hours. The primary outcome was the difference between preoperative and 48-hour postoperative quality of recovery-15 (QoR-15) scores. Secondary outcomes included visual analog pain scores, opioid use, and patient satisfaction. Complications and adverse effects were also noted. The Kruskal-Wallis test was used to analyze means and standard deviations for continuous endpoints; Fisher exact test was used to analyze counts and proportions for categorical endpoints. Results: The liposomal bupivacaine group had a mean reduction of 3.9 in their postoperative QoR-15 scores, and the catheter group had a mean reduction of 25.1 in their postoperative QoR-15 scores, indicating a significantly worse functional recovery period compared with liposomal bupivacaine within the first 48 hours ( P < .001). Patients who received liposomal bupivacaine also had significantly lower pain scores on the second postoperative day, improved quality of sleep, and improved satisfaction with analgesia ( P < .05 for all). Conclusion: The use of interscalene liposomal bupivacaine demonstrated significantly improved quality of recovery when compared with interscalene nerve catheter after RCR.
- Published
- 2022
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