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  1. Article ; Online: Probing Transcriptome-Wide RNA Structural Changes Dependent on the DEAD-box Helicase Dbp2.

    Lai, Yu-Hsuan / Tran, Elizabeth J

    Methods in molecular biology (Clifton, N.J.)

    2020  Volume 2209, Page(s) 287–305

    Abstract: RNA helicases function in all aspects of RNA biology mainly through remodeling structures of RNA and RNA-protein (RNP) complexes. Among them, DEAD-box proteins form the largest family in eukaryotes and have been shown to remodel RNA/RNP structures and ... ...

    Abstract RNA helicases function in all aspects of RNA biology mainly through remodeling structures of RNA and RNA-protein (RNP) complexes. Among them, DEAD-box proteins form the largest family in eukaryotes and have been shown to remodel RNA/RNP structures and clamping of RNA-binding proteins, both in vitro and in vivo. Nevertheless, for the majority of these enzymes, it is largely unclear what RNAs are targeted and where they modulate RNA/RNP structures to promote RNA metabolism. Several methods have been developed to probe secondary and tertiary structures of specific transcripts or whole transcriptomes in vivo. In this chapter, we describe a protocol for identification of RNA structural changes that are dependent on a Saccharomyces cerevisiae DEAD-box helicase Dbp2. Experiments detailed here can be adapted to the study of other RNA helicases and identification of putative remodeling targets in vivo.
    MeSH term(s) DEAD-box RNA Helicases/chemistry ; Gene Expression Regulation, Fungal ; Nucleic Acid Conformation ; RNA Probes/chemistry ; RNA, Fungal/chemistry ; Ribonucleoproteins/chemistry ; Saccharomyces cerevisiae/chemistry ; Saccharomyces cerevisiae Proteins/chemistry
    Chemical Substances RNA Probes ; RNA, Fungal ; Ribonucleoproteins ; Saccharomyces cerevisiae Proteins ; Dbp2 protein, S cerevisiae (EC 3.6.1.-) ; DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2020-11-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-0935-4_18
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  2. Article ; Online: The genomic region of the 3' untranslated region (3'UTR) of PHO84, rather than the antisense RNA, promotes gene repression.

    Hegazy, Youssef A / Cloutier, Sara C / Utturkar, Sagar M / Das, Subhadeep / Tran, Elizabeth J

    Nucleic acids research

    2023  Volume 51, Issue 15, Page(s) 7900–7913

    Abstract: PHO84 is a budding yeast gene reported to be negatively regulated by its cognate antisense transcripts both in cis and in trans. In this study, we performed Transient-transcriptome sequencing (TT-seq) to investigate the correlation of sense/antisense ... ...

    Abstract PHO84 is a budding yeast gene reported to be negatively regulated by its cognate antisense transcripts both in cis and in trans. In this study, we performed Transient-transcriptome sequencing (TT-seq) to investigate the correlation of sense/antisense pairs in a dbp2Δ strain and found over 700 sense/antisense pairs, including PHO84, to be positively correlated, contrasting the prevailing model. To define what mechanism regulates the PHO84 gene and how this regulation could have been originally attributed to repression by the antisense transcript, we conducted a series of molecular biology and genetics experiments. We now report that the 3' untranslated region (3'UTR) of PHO84 plays a repressive role in sense expression, an activity not linked to the antisense transcripts. Moreover, we provide results of a genetic screen for 3'UTR-dependent repression of PHO84 and show that the vast majority of identified factors are linked to negative regulation. Finally, we show that the PHO84 promoter and terminator form gene loops which correlate with transcriptional repression, and that the RNA-binding protein, Tho1, increases this looping and the 3'UTR-dependent repression. Our results negate the current model for antisense non-coding transcripts of PHO84 and suggest that many of these transcripts are byproducts of open chromatin.
    MeSH term(s) 3' Untranslated Regions/genetics ; Chromatin ; Genomics ; RNA, Antisense/genetics ; RNA, Antisense/metabolism ; Saccharomyces cerevisiae/metabolism ; Gene Expression Regulation, Fungal
    Chemical Substances 3' Untranslated Regions ; Chromatin ; RNA, Antisense ; PHO84 protein, S cerevisiae
    Language English
    Publishing date 2023-06-28
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad579
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  3. Article ; Online: Unemployed, Immigrant, and Older Asian Workers in a U.S.-Based Job-Training Program: Their Experiences and Well-Being, and Strategies for Reaching This Important Population.

    Lai, Patrick Ho Lam / Halvorsen, Cal J / Chang, Kun / Nguyen, Le Ha Tran / Howard, Elizabeth P / Lyons, Karen S

    Journal of gerontological social work

    2024  , Page(s) 1–17

    Abstract: The Senior Community Service Employment Program (SCSEP) is a U.S.-based job-training program that serves unemployed workers aged 55 and older with incomes at or below 125% of the federal poverty level. While federal funds are set aside to serve Asian ... ...

    Abstract The Senior Community Service Employment Program (SCSEP) is a U.S.-based job-training program that serves unemployed workers aged 55 and older with incomes at or below 125% of the federal poverty level. While federal funds are set aside to serve Asian workers in SCSEP, little is known about their characteristics and experiences. In response, this pilot study aimed to document the health, well-being, and experiences of older Asian SCSEP participants in Massachusetts through the completion of a survey. Respondents (
    Language English
    Publishing date 2024-04-10
    Publishing country United States
    Document type Journal Article
    ZDB-ID 779365-0
    ISSN 1540-4048 ; 0163-4372
    ISSN (online) 1540-4048
    ISSN 0163-4372
    DOI 10.1080/01634372.2024.2339980
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  4. Article ; Online: Transcription, translation, and DNA repair: new insights from emerging noncanonical substrates of RNA helicases.

    Russon, Matthew P / Westerhouse, Kirsten M / Tran, Elizabeth J

    Biological chemistry

    2020  Volume 402, Issue 5, Page(s) 637–644

    Abstract: RNA helicases are enzymes that exist in all domains of life whose canonical functions include ATP-dependent remodeling of RNA structures and displacement of proteins from ribonucleoprotein complexes (RNPs). These enzymes play roles in virtually all ... ...

    Abstract RNA helicases are enzymes that exist in all domains of life whose canonical functions include ATP-dependent remodeling of RNA structures and displacement of proteins from ribonucleoprotein complexes (RNPs). These enzymes play roles in virtually all processes of RNA metabolism, including pre-mRNA splicing, rRNA processing, nuclear mRNA export, translation and RNA decay. Here we review emerging noncanonical substrates of RNA helicases including RNA-DNA hybrids (R-loops) and RNA and DNA G-quadruplexes and discuss their biological significance.
    MeSH term(s) DEAD-box RNA Helicases/genetics ; DEAD-box RNA Helicases/metabolism ; DNA Repair ; G-Quadruplexes ; Humans ; Substrate Specificity
    Chemical Substances DEAD-box RNA Helicases (EC 3.6.4.13)
    Language English
    Publishing date 2020-12-14
    Publishing country Germany
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Review
    ZDB-ID 1334659-3
    ISSN 1437-4315 ; 1431-6730 ; 1432-0355
    ISSN (online) 1437-4315
    ISSN 1431-6730 ; 1432-0355
    DOI 10.1515/hsz-2020-0333
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  5. Article: Cutaneous Manifestations of Rheumatoid Arthritis: Diagnosis and Treatment.

    Diaz, Michael J / Natarelli, Nicole / Wei, Aria / Rechdan, Michaela / Botto, Elizabeth / Tran, Jasmine T / Forouzandeh, Mahtab / Plaza, Jose A / Kaffenberger, Benjamin H

    Journal of personalized medicine

    2023  Volume 13, Issue 10

    Abstract: Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disorder characterized by inflammatory arthritis and periarticular structural damage. Available evidence suggests that RA results from complex interactions between genetic susceptibility (e.g., ... ...

    Abstract Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disorder characterized by inflammatory arthritis and periarticular structural damage. Available evidence suggests that RA results from complex interactions between genetic susceptibility (e.g., HLA-DRB1), environmental factors (e.g., smoking), and immune dysregulation. Alongside joint-related symptoms, individuals with RA may also experience a wide array of skin issues, including the development of nodules, neutrophilic dermatoses, vasculitis, and vasculopathy. Treatment strategies for these manifestations vary but routinely involve corticosteroids, disease-modifying anti-rheumatic drugs, and biologics, with individualized approaches guided by disease severity. In this review, we provide comprehensive insights into the skin-related issues associated with RA, outlining their clinical characteristics and histopathological findings. Our aim is to facilitate early diagnosis and personalized treatment to improve the quality of life of affected individuals.
    Language English
    Publishing date 2023-10-10
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2662248-8
    ISSN 2075-4426
    ISSN 2075-4426
    DOI 10.3390/jpm13101479
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  6. Article ; Online: Eating behaviors and estimated body fat percentage among adolescents with type 1 diabetes.

    Tran, Thanh / Igudesman, Daria / Burger, Kyle / Crandell, Jamie / Maahs, David M / Seid, Michael / Mayer-Davis, Elizabeth J

    Diabetes research and clinical practice

    2023  Volume 207, Page(s) 111070

    Abstract: Aims: Estimate associations between select eating behaviors and estimated body fat percentage (eBFP) and explore effect modification by sex among adolescents with type 1 diabetes (T1D).: Methods: This analysis included 257 adolescents (mean age 14.9 ± ...

    Abstract Aims: Estimate associations between select eating behaviors and estimated body fat percentage (eBFP) and explore effect modification by sex among adolescents with type 1 diabetes (T1D).
    Methods: This analysis included 257 adolescents (mean age 14.9 ± 1.14 years; 49.8 % female) with baseline hemoglobin A1c (HbA1c) between 8 and 13 % (64 mmol/mol-119 mmol/mol) from a randomized trial designed to improve glycemia. Eating behaviors and eBFP were determined from surveys and validated equations respectively. Linear mixed models were used to estimate associations. Effect modification was assessed via stratified plots, stratified associations, and interaction terms.
    Results: Disordered eating, dietary restraint, and eBFP were significantly higher among females while external eating was higher among males. Disordered eating (β: 0.49, 95 %CI: 0.24, 0.73, p = 0.0001) and restraint (β: 1.11, 95 %CI: 0.29, 1.92, p = 0.0081) were positively associated with eBFP while external eating was not (β: -0.19, 95 %CI: -0.470, 0.096, p = 0.20). Interactions with sex were not significant (p-value range: 0.28-0.64).
    Conclusion: Disordered eating and dietary restraint were positively associated with eBFP, highlighting the potential salience of these eating behaviors to cardiometabolic risk for both female and male adolescents. Prospective studies should investigate whether these eating behaviors predict eBFP longitudinally to inform obesity prevention strategies in T1D.
    MeSH term(s) Adolescent ; Female ; Humans ; Male ; Adipose Tissue ; Diabetes Mellitus, Type 1/complications ; Feeding Behavior ; Obesity/complications ; Prospective Studies ; Randomized Controlled Trials as Topic
    Language English
    Publishing date 2023-12-22
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 632523-3
    ISSN 1872-8227 ; 0168-8227
    ISSN (online) 1872-8227
    ISSN 0168-8227
    DOI 10.1016/j.diabres.2023.111070
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  7. Article: A Review of Current and Pipeline Drugs for Treatment of Melanoma.

    Natarelli, Nicole / Aleman, Sarah J / Mark, Isabella M / Tran, Jasmine T / Kwak, Sean / Botto, Elizabeth / Aflatooni, Shaliz / Diaz, Michael J / Lipner, Shari R

    Pharmaceuticals (Basel, Switzerland)

    2024  Volume 17, Issue 2

    Abstract: Malignant melanoma is the most aggressive form of skin cancer. Standard treatment options include surgery, radiation therapy, systemic chemotherapy, targeted therapy, and immunotherapy. Combining these modalities often yields better responses. Surgery is ...

    Abstract Malignant melanoma is the most aggressive form of skin cancer. Standard treatment options include surgery, radiation therapy, systemic chemotherapy, targeted therapy, and immunotherapy. Combining these modalities often yields better responses. Surgery is suitable for localized cases, sometimes involving lymph node dissection and biopsy, to assess the spread of the disease. Radiation therapy may be sometimes used as a standalone treatment or following surgical excision. Systemic chemotherapy, while having low response rates, is utilized as part of combination treatments or when other methods fail. The development of resistance to systemic chemotherapies and associated side effects have prompted further research and clinical trials for novel approaches. In the case of advanced-stage melanoma, a comprehensive approach may be necessary, incorporating targeted therapies and immunotherapies that demonstrate significant antitumor activity. Targeted therapies, including inhibitors targeting BRAF, MEK, c-KIT, and NRAS, are designed to block the specific molecules responsible for tumor growth. These therapies show promise, particularly in patients with corresponding mutations. Combination therapy, including BRAF and MEK inhibitors, has been evidenced to improve progression-free survival; however, concerns about resistance and cutaneous toxicities highlight the need for close monitoring. Immunotherapies, leveraging tumor-infiltrating lymphocytes and CAR T cells, enhance immune responses. Lifileucel, an FDA-approved tumor-infiltrating lymphocyte therapy, has demonstrated improved response rates in advanced-stage melanoma. Ongoing trials continue to explore the efficacy of CAR T-cell therapy for advanced melanoma. Checkpoint inhibitors targeting CTLA-4 and PD-1 have enhanced outcomes. Emerging IL-2 therapies boost dendritic cells, enhancing anticancer immunity. Oncolytic virus therapy, approved for advanced melanoma, augments treatment efficacy in combination approaches. While immunotherapy has significantly advanced melanoma treatment, its success varies, prompting research into new drugs and factors influencing outcomes. This review provides insights into current melanoma treatments and recent therapeutic advances.
    Language English
    Publishing date 2024-02-07
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph17020214
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  8. Article ; Online: Predictors of Housing Trajectories Among Young Adults Experiencing Homelessness in Los Angeles.

    Pedersen, Eric R / DiGuiseppi, Graham / D'Amico, Elizabeth J / Rodriguez, Anthony / Tran, Denise D / Jose, Rupa / Tucker, Joan S

    The journal of behavioral health services & research

    2023  Volume 51, Issue 1, Page(s) 31–43

    Abstract: Experiencing homelessness during young adulthood is associated with negative health outcomes and understanding housing trajectories of young adults experiencing homelessness may aid in the development of evidence-based public health programs designed to ... ...

    Abstract Experiencing homelessness during young adulthood is associated with negative health outcomes and understanding housing trajectories of young adults experiencing homelessness may aid in the development of evidence-based public health programs designed to serve this at-risk age group. In the present study, the authors examined baseline predictors of 24-month trajectories of housing stability and unsheltered housing among a sample of 271 young adults aged 18 to 25 recruited from drop-in centers in Los Angeles. In multivariate models, the authors found that identifying as multi-racial/other and better friendship quality at baseline were associated with less steep increases in the likelihood of stable housing over time. Being employed at baseline was associated with a less steep decrease in the probability of being unsheltered over time, while illicit drug use days associated with a steeper decrease in the probability of being unsheltered over time. Continued research is needed to establish important factors determining young adults' long-term housing trajectories in the effort to promote greater access and engagement with housing services.
    MeSH term(s) Humans ; Young Adult ; Adult ; Los Angeles/epidemiology ; Housing ; Ill-Housed Persons ; Substance-Related Disorders/epidemiology
    Language English
    Publishing date 2023-10-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1419909-9
    ISSN 1556-3308 ; 1094-3412
    ISSN (online) 1556-3308
    ISSN 1094-3412
    DOI 10.1007/s11414-023-09863-2
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  9. Article ; Online: Venoarterial Extracorporeal Membrane Oxygenation With or Without Advanced Intervention for Massive Pulmonary Embolism.

    Cardona, Stephanie / Downing, Jessica V / Witting, Michael D / Haase, Daniel J / Powell, Elizabeth K / Dahi, Siamak / Pasrija, Chetan / Tran, Quincy K

    Perfusion

    2023  , Page(s) 2676591231177909

    Abstract: Introduction: Massive pulmonary embolism (MPE) is a rare but highly fatal condition. Our study's objective was to evaluate the association between advanced interventions and survival among patients with MPE treated with venoarterial extracorporeal ... ...

    Abstract Introduction: Massive pulmonary embolism (MPE) is a rare but highly fatal condition. Our study's objective was to evaluate the association between advanced interventions and survival among patients with MPE treated with venoarterial extracorporeal membrane oxygenation (VA-ECMO).
    Methods: This is a retrospective review of the Extracorporeal Life Support Organization (ELSO) registry data. We included adult patients with MPE who were treated with VA-ECMO during 2010-2020. Our Primary outcome was survival to hospital discharge; secondary outcomes were ECMO duration among survivors and rates of ECMO-related complications. Clinical variables were compared using the Pearson chi-square and Kruskal-Wallis H tests.
    Results: We included 802 patients; 80 (10%) received SPE and 18 (2%) received CDT. Overall, 426 (53%) survived to discharge; survival was not significantly different among those treated with SPE or CDT on VA-ECMO (70%) versus VA-ECMO alone (52%) or SPE or CDT before VA-ECMO (52%). Multivariable regression found a trend towards increased survival among those treated with SPE or CDT while on ECMO (AOR 1.8, 95% CI 0.9-3.6), but no significant correlation. There was no association between advanced interventions and ECMO duration among survivors, or rates of ECMO-related complications.
    Conclusion: Our study found no difference in survival in patients with MPE who received advanced interventions prior to ECMO, and a slight non-significant benefit in those who received advanced interventions while on ECMO.
    Language English
    Publishing date 2023-05-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 645038-6
    ISSN 1477-111X ; 0267-6591
    ISSN (online) 1477-111X
    ISSN 0267-6591
    DOI 10.1177/02676591231177909
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  10. Article ; Online: A Student Teaching Assistant Program for Diversity, Equity, Inclusion, and Antiracism Curricular Enhancement.

    Tran, Meagan T / Dillard, Desireé Brionne / Abdelwahab, Rewan M / Abdulwadood, Isra / Wu, Sarah Y / Adeleye, Olufunmilola / Shoukry, Mira M / Alamy, Nadine H / Elegbede, Audrey M / Keddis, Mira T / Valencia, Elizabeth M / Atunah-Jay, Sarah J

    Academic medicine : journal of the Association of American Medical Colleges

    2024  

    Abstract: Problem: In the United States, physician bias is exhibited early in medical training and contributes to systemic inequities within the field of medicine. A lack of diversity, equity, inclusion, and antiracism (DEI-AR) content within medical curricula ... ...

    Abstract Problem: In the United States, physician bias is exhibited early in medical training and contributes to systemic inequities within the field of medicine. A lack of diversity, equity, inclusion, and antiracism (DEI-AR) content within medical curricula drives critical gaps in knowledge and deficiencies when preparing medical students to serve patients of diverse backgrounds. At the Mayo Clinic Alix School of Medicine (MCASOM), student-led curricular reviews between 2017 to 2018 and 2020 to 2021 revealed opportunities to improve DEI-AR content within preclinical courses. Course directors expressed concern of limited expertise and time to enact effective changes.
    Approach: The MCASOM DEI-AR teaching assistant (TA) program aims to curate a collaborative partnership between course directors and compensated student TAs to facilitate course enhancements responsive to the prior preclinical course review while centering standardized DEI-AR best practices.
    Outcomes: As of January 2024, the program has engaged 14 TAs and partnered with 24 preclinical courses. Postcourse student evaluation responses were collected from 8 courses for 2021 to 2022 (before enhancements) and 2022 to 2023 (after enhancements). Student satisfaction with DEI-AR content is tracked through postcourse evaluations, with preliminary data demonstrating improvement after DEI-AR curricular integration (improvement of mean preenhancement and postenhancement scores of 3.81 to 4.05; t12 = 1.79, P = .21). Qualitative student comments were sorted into general categories of positive, negative, or neutral, showing a 6.25% median increase in positive perception of DEI.
    Next steps: Plans for the MCASOM DEI-AR TA program include application of quality improvement strategies to improve program processes and outcomes. Development of a centralized dashboard that integrates course enhancement progress and ongoing feedback from evaluations is anticipated to facilitate this effort. The program additionally aims to develop partnerships with clinical clerkships, which would allow for a more comprehensive enhancement of the overall medical education experience related to DEI-AR.
    Language English
    Publishing date 2024-04-12
    Publishing country United States
    Document type Journal Article
    ZDB-ID 96192-9
    ISSN 1938-808X ; 1040-2446
    ISSN (online) 1938-808X
    ISSN 1040-2446
    DOI 10.1097/ACM.0000000000005736
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