Publications by authors named "Stephanie Yu"

This qualitative study explored how Asian Americans, Native Hawaiians, and Pacific Islanders (AANHPIs) responded to anti-Asian racism during COVID-19. Participants (n = 459; M = 26.4 years; 77.

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  • The study focuses on analyzing cell-free DNA (cfDNA) to determine its tissue origin, which is important for research and diagnostics, utilizing a new technique called FRAGHA that looks at fragmentation patterns linked to histone modifications.
  • The research demonstrated strong correlations between specific histone modification signals, such as H3K27ac, and various medical conditions, including fetal DNA presence in maternal plasma and liver cancer detection.
  • Machine learning algorithms were employed to improve early detection of liver cancer, showcasing how cfDNA fragmentomics can enhance the effectiveness of liquid biopsies in clinical settings.
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Background: COVID-19 disproportionately impacted marginalized populations early in the pandemic. Families of patients admitted to the intensive care unit (ICU) experienced significant psychological effects. Little is known about whether individual and patient psychological outcomes after a loved ones stay in the ICU differs by socioeconomic status, as measured by the area deprivation index (ADI).

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  • Cell-free DNA (cfDNA) analysis, particularly through a method called FRAGMAXR, can detect and monitor diseases by examining nucleosomal patterns linked to DNA methylation around CpG sites.* -
  • The study found that patients with hepatocellular carcinoma (HCC) exhibited distinct cfDNA nucleosomal patterns that changed based on tumor stage, allowing for effective cancer detection using machine learning.* -
  • The research indicates that these cfDNA patterns could serve as valuable biomarkers for cancer detection and noninvasive prenatal testing, demonstrating strong correlation with established genetic measurements.*
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Recombinant adeno-associated virus (rAAV) vector gene delivery systems have demonstrated great promise in clinical trials but continue to face durability and dose-related challenges. Unlike rAAV gene therapy, integrating gene addition approaches can provide curative expression in mitotically active cells and pediatric populations. We explored a novel in vivo delivery approach based on an engineered transposase, Sleeping Beauty (SB100X), delivered as an mRNA within a lipid nanoparticle (LNP), in combination with an rAAV-delivered transposable transgene.

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Background: The analysis of haplotypes of variants is important for pharmacogenomics analysis and noninvasive prenatal testing for monogenic diseases. However, there is a lack of robust methods for targeted haplotyping.

Methods: We developed digital PCR haplotype sequencing (dHapSeq) for targeted haplotyping of variants, which is a method that compartmentalizes long DNA molecules into droplets.

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A Objectives: Dopamine is known to cause negative interference on enzymatic creatinine measurement. However, its effect on the Jaffe reaction, and its concentration required to interfere with enzymatic reactions, remain uncertain. This study was designed to study the interference of stable dopamine infusion on Jaffe and enzymatic creatinine assays, as well as the effect of dopamine infusion drip arm contamination on both creatinine assays.

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Recent studies have revealed an unexplored population of long cell-free DNA (cfDNA) molecules in human plasma using long-read sequencing technologies. However, the biological properties of long cfDNA molecules (>500 bp) remain largely unknown. To this end, we have investigated the origins of long cfDNA molecules from different genomic elements.

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Objective: Long cell-free DNA (cfDNA) can be found in the plasma of pregnant women and cancer patients. We investigated if droplet digital PCR (ddPCR) can analyze such molecules for diagnostic purposes using preeclampsia as a model.

Method: Plasma samples from ten preeclamptic and sixteen normal pregnancies were analyzed.

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Liquid biopsy using cell-free DNA (cfDNA) has gained global interest as a molecular diagnostic tool. However, the analysis of cfDNA in cancer patients and pregnant women has been focused on short DNA molecules (e.g.

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Evidence-based practices (EBPs) are often adapted during community implementation to improve EBP fit for clients and the service context. Augmenting EBPs with additional dosing and content may improve fit. However, reducing EBP content can reduce EBP effectiveness.

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In value-based decision making, options are selected according to subjective values assigned by the individual to available goods and actions. Despite the importance of this faculty of the mind, the neural mechanisms of value assignments, and how choices are directed by them, remain obscure. To investigate this problem, we used a classic measure of utility maximization, the Generalized Axiom of Revealed Preference, to quantify internal consistency of food preferences in , a nematode worm with a nervous system of only 302 neurons.

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Cell-free DNA (cfDNA) fragmentation is nonrandom, at least partially mediated by various DNA nucleases, forming characteristic cfDNA end motifs. However, there is a paucity of tools for deciphering the relative contributions of cfDNA cleavage patterns related to underlying fragmentation factors. In this study, through non-negative matrix factorization algorithm, we used 256 5' 4-mer end motifs to identify distinct types of cfDNA cleavage patterns, referred to as "founder" end-motif profiles (F-profiles).

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Understanding patient responsiveness, a component of fidelity, is essential as it impacts treatment outcome and ongoing use of treatment elements. This study evaluated patient responsiveness-operationalized as receptivity to treatment modules and ratings of the usefulness and the utilization of treatment elements-to the Transdiagnostic Intervention for Sleep and Circadian Dysfunction (TranS-C) in a sample of adults with serious mental illness (SMI) and sleep/circadian dysfunction. Adults with SMI and sleep/circadian dysfunction (N = 104) received TranS-C in a community mental health setting.

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Background: Nuclear-derived cell-free DNA (cfDNA) molecules in blood plasma are nonrandomly fragmented, bearing a wealth of information related to tissues of origin. DNASE1L3 (deoxyribonuclease 1 like 3) is an important player in shaping the fragmentation of nuclear-derived cfDNA molecules, preferentially generating molecules with 5 CC dinucleotide termini (i.e.

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Family members of critically ill patients with coronavirus disease (COVID-19) have described increased symptoms of posttraumatic stress disorder (PTSD). Little is known about how these symptoms may change over time. We studied changes in PTSD symptoms in family members of critically ill patients with COVID-19 over 12 months.

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Glucokinase-maturity-onset diabetes of the young (GCK-MODY) is often misdiagnosed as other forms of diabetes. A 42-year-old pregnant lady with pre-existing diabetes was treated with insulin during first trimester. Fetal growth restriction was noted since mid-second trimester.

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Background: Recent studies using single molecule, real-time (SMRT) sequencing revealed a substantial population of analyzable long cell-free DNA (cfDNA) in plasma. Potential clinical utilities of such long cfDNA in pregnancy and cancer have been demonstrated. However, the performance of different long-read sequencing platforms for the analysis of long cfDNA remains unknown.

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Objectives: Racial/ethnic discrimination has been linked to behavioral and emotional problems in youth from marginalized groups. However, the psychological experience associated with discrimination may differ between immigrant and nonimmigrant youth. Race-based discrimination may impact an adolescent's view of their own group (private regard) and/or their sense of how others view their group (public regard).

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Cell-free DNA (cfDNA) fragmentation patterns contain important molecular information linked to tissues of origin. We explored the possibility of using fragmentation patterns to predict cytosine-phosphate-guanine (CpG) methylation of cfDNA, obviating the use of bisulfite treatment and associated risks of DNA degradation. This study investigated the cfDNA cleavage profile surrounding a CpG (i.

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Background: Analysis of circulating tumor DNA has become increasingly important as a tool for cancer care. However, the focus of previous studies has been on short fragments of DNA. Also, bisulfite sequencing, a conventional approach for methylation analysis, causes DNA degradation, which is not ideal for the assessment of long DNA properties and methylation patterns.

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