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1. Towards Principled, Practical Policy Gradient for Bandits and Tabular MDPs

Author

Lu, Michael, Aghaei, Matin, Raj, Anant, and Vaswani, Sharan

Subjects
Computer Science - Machine Learning
Abstract

We consider (stochastic) softmax policy gradient (PG) methods for bandits and tabular Markov decision processes (MDPs). While the PG objective is non-concave, recent research has used the objective's smoothness and gradient domination properties to achieve convergence to an optimal policy. However, these theoretical results require setting the algorithm parameters according to unknown problem-dependent quantities (e.g. the optimal action or the true reward vector in a bandit problem). To address this issue, we borrow ideas from the optimization literature to design practical, principled PG methods in both the exact and stochastic settings. In the exact setting, we employ an Armijo line-search to set the step-size for softmax PG and demonstrate a linear convergence rate. In the stochastic setting, we utilize exponentially decreasing step-sizes, and characterize the convergence rate of the resulting algorithm. We show that the proposed algorithm offers similar theoretical guarantees as the state-of-the art results, but does not require the knowledge of oracle-like quantities. For the multi-armed bandit setting, our techniques result in a theoretically-principled PG algorithm that does not require explicit exploration, the knowledge of the reward gap, the reward distributions, or the noise. Finally, we empirically compare the proposed methods to PG approaches that require oracle knowledge, and demonstrate competitive performance., Comment: Accepted at RLC 2024

Published
2024

3. Empirical Evaluation of the Segment Anything Model (SAM) for Brain Tumor Segmentation

Author

Peivandi, Mohammad, Zhang, Jason, Lu, Michael, Zhu, Dongxiao, and Kou, Zhifeng

Subjects
Electrical Engineering and Systems Science - Image and Video Processing
Abstract

Brain tumor segmentation presents a formidable challenge in the field of Medical Image Segmentation. While deep-learning models have been useful, human expert segmentation remains the most accurate method. The recently released Segment Anything Model (SAM) has opened up the opportunity to apply foundation models to this difficult task. However, SAM was primarily trained on diverse natural images. This makes applying SAM to biomedical segmentation, such as brain tumors with less defined boundaries, challenging. In this paper, we enhanced SAM's mask decoder using transfer learning with the Decathlon brain tumor dataset. We developed three methods to encapsulate the four-dimensional data into three dimensions for SAM. An on-the-fly data augmentation approach has been used with a combination of rotations and elastic deformations to increase the size of the training dataset. Two key metrics: the Dice Similarity Coefficient (DSC) and the Hausdorff Distance 95th Percentile (HD95), have been applied to assess the performance of our segmentation models. These metrics provided valuable insights into the quality of the segmentation results. In our evaluation, we compared this improved model to two benchmarks: the pretrained SAM and the widely used model, nnUNetv2. We find that the improved SAM shows considerable improvement over the pretrained SAM, while nnUNetv2 outperformed the improved SAM in terms of overall segmentation accuracy. Nevertheless, the improved SAM demonstrated slightly more consistent results than nnUNetv2, especially on challenging cases that can lead to larger Hausdorff distances. In the future, more advanced techniques can be applied in order to further improve the performance of SAM on brain tumor segmentation.

Published
2023

4. Pericoronary Adipose Tissue Density, Inflammation, and Subclinical Coronary Artery Disease Among People With HIV in the REPRIEVE Cohort

Author

Foldyna, Borek, Mayrhofer, Thomas, Zanni, Markella V, Lyass, Asya, Barve, Radhika, Karady, Julia, McCallum, Sara, Burdo, Tricia H, Fitch, Kathleen V, Paradis, Kayla, Fulda, Evelynne S, Diggs, Marissa R, Bloomfield, Gerald S, Malvestutto, Carlos D, Fichtenbaum, Carl J, Aberg, Judith A, Currier, Judith S, Ribaudo, Heather J, Hoffmann, Udo, Lu, Michael T, Douglas, Pamela S, and Grinspoon, Steven K

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Clinical Trials and Supportive Activities, Cardiovascular, Aging, Clinical Research, Sexually Transmitted Infections, Heart Disease, HIV/AIDS, Prevention, Heart Disease - Coronary Heart Disease, Atherosclerosis, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Humans, Male, Middle Aged, Adipose Tissue, Biomarkers, Coronary Angiography, Coronary Artery Disease, Coronary Vessels, HIV, HIV Infections, Inflammation, Plaque, Atherosclerotic, pericoronary adipose tissue, coronary plaque, coronary artery disease, inflammation, Biological Sciences, Medical and Health Sciences, Microbiology, Clinical sciences
Abstract

BackgroundPericoronary adipose tissue (PCAT) may influence plaque development through inflammatory mechanisms. We assessed PCAT density, as a measure of pericoronary inflammation, in relationship to coronary plaque among people with human immunodeficiency virus (HIV [PWH]) and to a matched control population.MethodsIn this baseline analysis of 727 participants of the Randomized Trial to Prevent Vascular Events in HIV (REPRIEVE) Mechanistic Substudy, we related computed tomography-derived PCAT density to presence and extent (Leaman score) of coronary artery disease (CAD), noncalcified plaque, coronary artery calcium (CAC), and vulnerable plaque features using multivariable logistic regression analyses. We further compared the PCAT density between PWH and age, sex, body mass index, CAC score, and statin use-matched controls from the community-based Framingham Heart Study (N = 464), adjusting for relevant clinical covariates.ResultsAmong 727 REPRIEVE participants (age 50.8 ± 5.8 years; 83.6% [608/727] male), PCAT density was higher in those with (vs without) coronary plaque, noncalcified plaque, CAC >0, vulnerable plaque, and high CAD burden (Leaman score >5) (P < .001 for each comparison). PCAT density related to prevalent coronary plaque (adjusted odds ratio [per 10 HU]: 1.44; 95% confidence interval, 1.22-1.70; P < .001), adjusted for clinical cardiovascular risk factors, body mass index, and systemic immune/inflammatory biomarkers. Similarly, PCAT density related to CAC >0, noncalcified plaque, vulnerable plaque, and Leaman score >5 (all P ≤ .002). PCAT density was greater among REPRIEVE participants versus Framingham Heart Study (-88.2 ± 0.5 HU versus -90.6 ± 0.4 HU; P < .001).ConclusionsAmong PWH in REPRIEVE, a large primary cardiovascular disease prevention cohort, increased PCAT density independently associated with prevalence and severity of coronary plaque, linking increased coronary inflammation to CAD in PWH.

Published
2023

5. A Comparison of Self-Supervised Pretraining Approaches for Predicting Disease Risk from Chest Radiograph Images

Author

Chen, Yanru, Lu, Michael T, and Raghu, Vineet K

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

Deep learning is the state-of-the-art for medical imaging tasks, but requires large, labeled datasets. For risk prediction, large datasets are rare since they require both imaging and follow-up (e.g., diagnosis codes). However, the release of publicly available imaging data with diagnostic labels presents an opportunity for self and semi-supervised approaches to improve label efficiency for risk prediction. Though several studies have compared self-supervised approaches in natural image classification, object detection, and medical image interpretation, there is limited data on which approaches learn robust representations for risk prediction. We present a comparison of semi- and self-supervised learning to predict mortality risk using chest x-ray images. We find that a semi-supervised autoencoder outperforms contrastive and transfer learning in internal and external validation., Comment: 33 pages, 22 figures, Accepted for publication at MIDL 2023

Published
2023

6. Biological and Clinical Implications of the Vascular Endothelial Growth Factor Coreceptor Neuropilin-1 in Human Immunodeficiency Virus

Author

Schnittman, Samuel R, Kolossváry, Márton, Beck-Engeser, Gabriele, Fitch, Kathleen V, Ambayec, Gabrielle C, Nance, Robin M, Zanni, Markella V, Diggs, Marissa, Chan, Fay, McCallum, Sara, Toribio, Mabel, Bamford, Laura, Fichtenbaum, Carl J, Eron, Joseph J, Jacobson, Jeffrey M, Mayer, Kenneth H, Malvestutto, Carlos, Bloomfield, Gerald S, Moore, Richard D, Umbleja, Triin, Saag, Michael S, Aberg, Judith A, Currier, Judith S, Delaney, Joseph AC, Martin, Jeffrey N, Lu, Michael T, Douglas, Pamela S, Ribaudo, Heather J, Crane, Heidi M, Hunt, Peter W, and Grinspoon, Steven K

Subjects
Biomedical and Clinical Sciences, Immunology, Heart Disease, HIV/AIDS, Infectious Diseases, Aging, Sexually Transmitted Infections, Heart Disease - Coronary Heart Disease, Prevention, Cardiovascular, 2.1 Biological and endogenous factors, Aetiology, Cancer, Good Health and Well Being, cancer, cardiovascular disease, HIV, neuropilin-1, VEGF, Clinical sciences, Medical microbiology
Abstract

Plasma vascular endothelial growth factor (VEGF) coreceptor neuropilin-1 (NRP-1) had the largest association with coronary plaque in the Randomized Trial to Prevent Vascular Events in HIV (REPRIEVE) proteomics analysis. With little known about NRP-1 in people with human immunodeficiency virus (PWH), we explored its relation to other proteins in REPRIEVE and validated our findings through a Centers for AIDS Research Network of Integrated Clinical Systems (CNICS) case-cohort study by assessing its relation to host factors and incident cardiovascular disease and cancer. Within REPRIEVE, NRP-1 was associated with proteins involved in angiogenesis, signal transduction, immunoregulation, and cell migration/adhesion. Within CNICS, NRP-1 was associated with key host factors, including older age and male sex. NRP-1 was associated with an increased hazard of multiple cancers but a decreased prostate cancer risk. Finally, NRP-1 was most strongly associated with mortality and type 2 myocardial infarction. These data suggest that NRP-1 is part of a clinically relevant immunoregulatory pathway related to multiple comorbidities in PWH. Clinical Trials Registration. NCT02344290.

Published
2023

8. Coronary Artery Plaque Composition and Severity Relate to the Inflammasome in People With Treated Human Immunodeficiency Virus

Author

Schnittman, Samuel R, Kitch, Douglas W, Swartz, Talia H, Burdo, Tricia H, Fitch, Kathleen V, McCallum, Sara, Flynn, Jacqueline M, Fulda, Evelynne S, Diggs, Marissa R, Stapleton, Jack T, Casado, José L, Taron, Jana, Currier, Judith S, Zanni, Markella V, Malvestutto, Carlos, Fichtenbaum, Carl J, Aberg, Judith A, Ribaudo, Heather J, Lu, Michael T, Douglas, Pamela S, and Grinspoon, Steven K

Subjects
Biomedical and Clinical Sciences, Dentistry, Prevention, Clinical Research, Heart Disease, Atherosclerosis, Heart Disease - Coronary Heart Disease, Cardiovascular, atherosclerosis, HIV, inflammasome, Leaman score, Clinical sciences, Medical microbiology
Abstract

BackgroundInflammasome activation is increased in people with human immunodeficiency virus (PWH), but its relationship with coronary plaque is poorly understood in this setting.MethodsIn a large human immunodeficiency virus cardiovascular prevention cohort, relationships between caspase-1, interleukin (IL)-1β, and IL-18 and coronary plaque indices were assessed by multivariate logistic regression.ResultsHigher IL-18 and IL-1β were associated with Leaman score, an integrative measure of plaque burden and composition.ConclusionsAs Leaman score >5 is associated with cardiovascular events in the general population, future work is needed to determine how the inflammasome relates to events and whether strategies to reduce its activation affect events or plaque progression among PWH.

Published
2023

9. Cytomegalovirus Immunoglobulin G (IgG) Titer and Coronary Artery Disease in People With Human Immunodeficiency Virus (HIV)

Author

Schnittman, Samuel R, Lu, Michael T, Mayrhofer, Thomas, Burdo, Tricia H, Fitch, Kathleen V, McCallum, Sara, Fulda, Evelynne S, Zanni, Markella V, Foldyna, Borek, Malvestutto, Carlos, Fichtenbaum, Carl J, Aberg, Judith A, Bloomfield, Gerald S, Overton, Edgar T, Currier, Judith, Tebas, Pablo, Sha, Beverly E, Ribaudo, Heather J, Flynn, Jacqueline M, Douglas, Pamela S, Erlandson, Kristine M, and Grinspoon, Steven K

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, Prevention, Atherosclerosis, Infectious Diseases, HIV/AIDS, Cardiovascular, Patient Safety, Clinical Research, Clinical Trials and Supportive Activities, Heart Disease - Coronary Heart Disease, Heart Disease, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Inflammatory and immune system, Infection, Good Health and Well Being, Male, Humans, Middle Aged, Female, Cytomegalovirus, Coronary Artery Disease, Immunoglobulin G, HIV, Cardiovascular Diseases, Cytomegalovirus Infections, HIV Infections, Biomarkers, human immunodeficiency virus, cytomegalovirus, cardiovascular disease, coronary artery disease, inflammation, Biological Sciences, Medical and Health Sciences, Microbiology, Clinical sciences
Abstract

BackgroundCytomegalovirus (CMV) infection is thought to result in increased immune activation in people with human immunodeficiency virus (HIV, PWH). Although some data have linked asymptomatic CMV infection to cardiovascular disease among PWH, it remains unknown whether CMV is associated with increased or high-risk coronary plaque.MethodsThe Randomized Trial to Prevent Vascular Events in HIV (REPRIEVE) enrolled PWH aged 40-75 years on stable antiretroviral therapy (ART) with low-to-moderate atherosclerotic cardiovascular disease (ASCVD) risk. Among a subset of US REPRIEVE participants, coronary plaque was assessed by coronary computed tomography angiography. Here, we assessed the relationship between CMV immunoglobulin G (IgG) titer and (1) levels of immune activation, (2) inflammatory biomarkers, and (3) coronary plaque phenotypes at study entry.ResultsOf 672 participants, mean age was 51 years, 83% were men, median ASCVD risk score was 4.5%, and 66% had current CD4+ T-cell count ≥500 cells/mm3. Higher CMV IgG quartile group was associated with older age and lower current and nadir CD4+ T-cell counts. CMV IgG titer was associated with specific inflammatory biomarkers (sCD163, MCP-1, interleukin [IL]-6, hsCRP) in univariate analysis, but not after controlling for HIV-specific factors. In contrast, CMV IgG titer was not associated with coronary artery disease indexes, including presence of plaque, coronary artery calcium (CAC) score >0, vulnerable plaque presence, or Leaman score >5.ConclusionsNo meaningful association was seen between CMV IgG titer and coronary artery disease indexes among ART-treated PWH at study enrollment. Longitudinal assessments in REPRIEVE will determine the relationship of CMV IgG titer to plaque progression and cardiovascular events.Clinical trials registrationNCT02344290.

Published
2023

10. Sex Differences in Subclinical Atherosclerosis and Systemic Immune Activation/Inflammation Among People With Human Immunodeficiency Virus in the United States

Author

Zanni, Markella V, Foldyna, Borek, McCallum, Sara, Burdo, Tricia H, Looby, Sara E, Fitch, Kathleen V, Fulda, Evelynne S, Autissier, Patrick, Bloomfield, Gerald S, Malvestutto, Carlos D, Fichtenbaum, Carl J, Overton, Edgar T, Aberg, Judith A, Erlandson, Kristine M, Campbell, Thomas B, Ellsworth, Grant B, Sheth, Anandi N, Taiwo, Babafemi, Currier, Judith S, Hoffmann, Udo, Lu, Michael T, Douglas, Pamela S, Ribaudo, Heather J, and Grinspoon, Steven K

Subjects
Biomedical and Clinical Sciences, Immunology, Infectious Diseases, Prevention, Atherosclerosis, Heart Disease, Cardiovascular, Clinical Research, Clinical Trials and Supportive Activities, Good Health and Well Being, Humans, Female, Male, United States, HIV, Sex Characteristics, 1-Alkyl-2-acetylglycerophosphocholine Esterase, Plaque, Atherosclerotic, Risk Factors, Inflammation, Biomarkers, Coronary Artery Disease, coronary atherosclerosis, inflammation, women, reproductive aging, Biological Sciences, Medical and Health Sciences, Microbiology, Clinical sciences
Abstract

BackgroundAmong people with HIV (PWH), sex differences in presentations of atherosclerotic cardiovascular disease (ASCVD) may be influenced by differences in coronary plaque parameters, immune/inflammatory biomarkers, or relationships therein.MethodsREPRIEVE, a primary ASCVD prevention trial, enrolled antiretroviral therapy (ART)-treated PWH. At entry, a subset of US participants underwent coronary computed tomography angiography (CTA) and immune phenotyping (n = 755 CTA; n = 725 CTA + immune). We characterized sex differences in coronary plaque and immune/inflammatory biomarkers and compared immune-plaque relationships by sex. Unless noted otherwise, analyses adjust for ASCVD risk score.ResultsThe primary analysis cohort included 631 males and 124 females. ASCVD risk was higher among males (median: 4.9% vs 2.1%), while obesity rates were higher among females (48% vs 21%). Prevalence of any plaque and of plaque with either ≥1 visible noncalcified portion or vulnerable features (NC/V-P) was lower among females overall and controlling for relevant risk factors (RR [95% CI] for any plaque: .67 [.50, .92]; RR for NC/V-P: .71 [.51, 1.00] [adjusted for ASCVD risk score and body mass index]). Females showed higher levels of IL-6, hs-CRP, and D-dimer and lower levels of Lp-PLA2 (P < .001 for all). Higher levels of Lp-PLA2, MCP-1, and oxLDL were associated with higher plaque (P < .02) and NC/V-P prevalence, with no differences by sex. Among females but not males, D-dimer was associated with higher prevalence of NC/V-P (interaction P = .055).ConclusionsAmong US PWH, females had a lower prevalence of plaque and NC/V-P, as well as differences in key immune/inflammatory biomarkers. Immune-plaque relationships differed by sex for D-dimer but not other tested parameters. Clinical Trial Registration. ClinicalTrials.gov; identifier: NCT0234429 (date of initial registration: 22 January 2015).

Published
2023

11. Leading Change at Berkeley Public Health: Building the Anti-racist Community for Justice and Social Transformative Change

Author

Allen, Amani M, Abram, Ché, Pothamsetty, Navya, Jacobo, Andrea, Lewis, Leanna, Maddali, Sai Ramya, Azurin, Michelle, Chow, Emily, Sholinbeck, Michael, Rincón, Abby, Team, for the ARC4JSTC Action, Keller, Ann, and Lu, Michael

Subjects
Peace, Justice and Strong Institutions, Humans, Public Health, Racism, Curriculum, Health Equity, Social Justice, ARC4JSTC Action Team, Public Health and Health Services
Abstract

A transformative change grounded in a commitment to antiracism and racial and health equity is underway at the University of California, Berkeley, School of Public Health. Responding to a confluence of national, state, and local circumstances, bold leadership, and a moral and disciplinary imperative to name and address racism as a root cause of health inequities, our community united around a common vision of becoming an antiracist institution. Berkeley Public Health has a long history of efforts supporting diversity, equity, inclusion, belonging, and justice. Building upon those efforts, we pursued an institution-wide initiative, one that creates a more equitable and inclusive school of public health that models and supports the development of future public health leaders, practitioners, scholars, and educators. Grounded in the principles of cultural humility, we recognized that our vision was a journey, not a destination. This article describes our efforts from June 2020 through June 2022 in developing and implementing ARC4JSTC (Anti-racist Community for Justice and Social Transformative Change), a comprehensive, multiyear antiracist change initiative encompassing faculty and workforce development, student experience, curriculum and pedagogy, community engagement outreach, and business processes. Our work is data informed, grounded in principles of change management, and focused on building internal capacity to promote long-term change. Our discussion of lessons learned and next steps helps to inform our ongoing work and antiracist institutional change efforts at other schools and programs of public health.

Published
2023

12. Stop, Think, Plan, Reflect

Author

Ingram, Taylor, Pecheny, Yuliya, Kim, Andy, Bodkin, Ryan, Paternack, Julie, Picard, Lindsay, Lu, Michael, Rotoli, Jason, Nobay, Flavia, and Spillane, Linda

Published
2023

13. Proteomic Signature of Subclinical Coronary Artery Disease in People With HIV: Analysis of the REPRIEVE Mechanistic Substudy

Author

Kolossváry, Márton, deFilippi, Chris, Lu, Michael T, Zanni, Markella V, Fulda, Evelynne S, Foldyna, Borek, Ribaudo, Heather, Mayrhofer, Thomas, Collier, Ann C, Bloomfield, Gerald S, Fichtenbaum, Carl, Overton, Edgar T, Aberg, Judith A, Currier, Judith, Fitch, Kathleen V, Douglas, Pamela S, and Grinspoon, Steven K

Subjects
Epidemiology, Biomedical and Clinical Sciences, Health Sciences, Cardiovascular, Heart Disease, Prevention, Atherosclerosis, Clinical Research, Heart Disease - Coronary Heart Disease, Detection, screening and diagnosis, 2.1 Biological and endogenous factors, 4.1 Discovery and preclinical testing of markers and technologies, Aetiology, Good Health and Well Being, Humans, Coronary Artery Disease, Cardiovascular Diseases, Proteomics, Plaque, Atherosclerotic, Risk Factors, HIV Infections, Risk Assessment, proteomics, HIV, coronary artery disease, plaque, CTA, Biological Sciences, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundPeople with HIV (PWH) have subclinical coronary artery disease (CAD) despite low traditional atherosclerotic cardiovascular disease (ASCVD) risk scores. Coronary plaque in PWH presents as a unique phenotype, but little is known about the contributions of specific inflammatory pathways to plaque phenotypes in PWH.MethodsThe REPRIEVE Mechanistic Substudy enrolled PWH on ART without known cardiovascular disease. We used a targeted discovery proteomics approach to evaluate 246 unique proteins representing cardiovascular, inflammatory, and immune pathways. Proteomic signatures were determined for presence of coronary artery calcium (CAC > 0) and presence of coronary plaque.ResultsData were available for 662 participants (aged 51 [SD 6] years, ASCVD risk score 4.9% [SD 3.1%]). Among 12 proteins associated with both CAC and presence of coronary plaque, independent of ASCVD risk score, the odds ratios were highest for NRP1: 5.1 (95% confidence interval [CI], 2.3-11.4) for CAC and 2.9 (95% CI, 1.4-6.1) for presence of plaque. Proteins uniquely related to presence of plaque were CST3, LTBR, MEPE, PLC, SERPINA5, and TNFSF13B; in contrast, DCN, IL-6RA, OSMR, ST2, and VCAM1 were only related to CAC.ConclusionsDistinct immune and inflammatory pathways are differentially associated with subclinical CAD phenotypes among PWH. This comprehensive set of targets should be further investigated to reduce atherosclerosis and ASCVD in PWH.Clinical trials registrationNCT02344290.

Published
2022

14. Factors Associated With Systemic Immune Activation Indices in a Global Primary Cardiovascular Disease Prevention Cohort of People With Human Immunodeficiency Virus on Antiretroviral Therapy

Author

Looby, Sara E, Kantor, Amy, Burdo, Tricia H, Currier, Judith S, Fichtenbaum, Carl J, Overton, Edgar T, Aberg, Judith A, Malvestutto, Carlos D, Bloomfield, Gerald S, Erlandson, Kristine M, Cespedes, Michelle, Kallas, Esper G, Masiá, Mar, Thornton, Alice C, Smith, Mandy D, Flynn, Jacqueline M, Kileel, Emma M, Fulda, Evelynne, Fitch, Kathleen V, Lu, Michael T, Douglas, Pamela S, Grinspoon, Steven K, Ribaudo, Heather J, and Zanni, Markella V

Subjects
Biomedical and Clinical Sciences, Immunology, Clinical Research, Infectious Diseases, HIV/AIDS, Cardiovascular, Atherosclerosis, Clinical Trials and Supportive Activities, Heart Disease, Prevention, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Good Health and Well Being, Biomarkers, Cardiovascular Diseases, Female, HIV, HIV Infections, Humans, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Integrases, Lipopolysaccharide Receptors, Lipoproteins, LDL, Male, Middle Aged, Nucleosides, Reverse Transcriptase Inhibitors, cardiovascular disease risk, immune activation markers, women, reproductive aging, Biological Sciences, Medical and Health Sciences, Microbiology, Clinical sciences
Abstract

BackgroundAmong antiretroviral therapy (ART)-treated people with human immunodeficiency virus (PWH), persistent systemic immune activation contributes to atherogenesis atherosclerotic, cardiovascular disease (CVD) events, and mortality. Factors associated with key immune activation indices have not previously been characterized among a global primary CVD prevention cohort of PWH.MethodsLeveraging baseline Randomized Trial to Prevent Vascular Events in HIV (REPRIEVE) data, we evaluated factors associated with soluble CD14 (sCD14) and oxidized low-density lipoprotein (oxLDL).ResultsThe primary analysis cohort included 4907 participants from 5 global-burden-of-disease regions (38% female, 48% Black, median age 50 years). In fully adjusted models for sCD14, female sex and White race (among those in high-income regions) were associated with higher sCD14 levels, while higher body mass index (BMI) and current use of nucleoside reverse transcriptase inhibitor + integrase strand transfer inhibitor ART were associated with lower sCD14 levels. In fully adjusted models for oxLDL, male sex, residence in high-income regions, White race (among those in high-income regions), and higher BMI were associated with higher oxLDL levels. In a subanalysis cohort of 1396 women with HIV, increased reproductive age was associated with higher sCD14 levels but not with higher oxLDL levels.ConclusionsFactors associated with sCD14 and oxLDL, 2 key indices of immune-mediated CVD risk, differ. Future studies will elucidate ways in which medications (eg, statins) and behavioral modifications influence sCD14 and oxLDL and the extent to which dampening of these markers mediates CVD-protective effects.Clinical trials registrationNCT0234429.

Published
2022

18. Histopathology images predict multi-omics aberrations and prognoses in colorectal cancer patients

Author

Tsai, Pei-Chen, Lee, Tsung-Hua, Kuo, Kun-Chi, Su, Fang-Yi, Lee, Tsung-Lu Michael, Marostica, Eliana, Ugai, Tomotaka, Zhao, Melissa, Lau, Mai Chan, Väyrynen, Juha P., Giannakis, Marios, Takashima, Yasutoshi, Kahaki, Seyed Mousavi, Wu, Kana, Song, Mingyang, Meyerhardt, Jeffrey A., Chan, Andrew T., Chiang, Jung-Hsien, Nowak, Jonathan, Ogino, Shuji, and Yu, Kun-Hsing

Published
2023
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19. InfraredTags: Embedding Invisible AR Markers and Barcodes Using Low-Cost, Infrared-Based 3D Printing and Imaging Tools

Author

Dogan, Mustafa Doga, Taka, Ahmad, Lu, Michael, Zhu, Yunyi, Kumar, Akshat, Gupta, Aakar, and Mueller, Stefanie

Subjects
Computer Science - Human-Computer Interaction, Computer Science - Computer Vision and Pattern Recognition, H.5.0, H.5.2
Abstract

Existing approaches for embedding unobtrusive tags inside 3D objects require either complex fabrication or high-cost imaging equipment. We present InfraredTags, which are 2D markers and barcodes imperceptible to the naked eye that can be 3D printed as part of objects, and detected rapidly by low-cost near-infrared cameras. We achieve this by printing objects from an infrared-transmitting filament, which infrared cameras can see through, and by having air gaps inside for the tag's bits, which appear at a different intensity in the infrared image. We built a user interface that facilitates the integration of common tags (QR codes, ArUco markers) with the object geometry to make them 3D printable as InfraredTags. We also developed a low-cost infrared imaging module that augments existing mobile devices and decodes tags using our image processing pipeline. Our evaluation shows that the tags can be detected with little near-infrared illumination (0.2lux) and from distances as far as 250cm. We demonstrate how our method enables various applications, such as object tracking and embedding metadata for augmented reality and tangible interactions., Comment: 12 pages, 10 figures. To appear in the Proceedings of the 2022 ACM Conference on Human Factors in Computing Systems

Published
2022
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20. Deep Learning-based Assessment of Hepatic Steatosis on chest CT

Author

Zhang, Zhongyi, Weiss, Jakob, Taron, Jana, Zeleznik, Roman, Lu, Michael T., and Aerts, Hugo J. W. L.

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Purpose: Automatic methods are required for the early detection of hepatic steatosis to avoid progression to cirrhosis and cancer. Here, we developed a fully automated deep learning pipeline to quantify hepatic steatosis on non-contrast enhanced chest computed tomography (CT) scans. Materials and Methods: We developed and evaluated our pipeline on chest CT images of 1,431 randomly selected National Lung Screening Trial (NLST) participants. A dataset of 451 CT scans with volumetric liver segmentations of expert readers was used for training a deep learning model. For testing, in an independent dataset of 980 CT scans hepatic attenuation was manually measured by an expert reader on three cross-sectional images at different hepatic levels by selecting three circular regions of interest. Additionally, 100 randomly selected cases of the test set were volumetrically segmented by expert readers. Hepatic steatosis on the test set was defined as mean hepatic attenuation of < 40 Hounsfield unit. Spearman correlation was conducted to analyze liver fat quantification accuracy and the Cohen's Kappa coefficient was calculated for hepatic steatosis prediction reliability. Results: Our pipeline demonstrated strong performance and achieved a mean dice score of 0.970 for the volumetric liver segmentation. The spearman correlation of the liver fat quantification was 0.954 (P <0.0001) between the automated and expert reader measurements. The cohen's kappa coefficient was 0.875 for automatic assessment of hepatic steatosis. Conclusion: We developed a fully automatic deep learning-based pipeline for the assessment of hepatic steatosis in chest CT images. With the fast and cheap screening of hepatic steatosis, our pipeline has the potential to help initiate preventive measures to avoid progression to cirrhosis and cancer.

Published
2022

21. Developing an Anti-Racist Foundations Course in MCH for MPH Students.

Author

Marshall, Cassondra, Bakal, Michael, Deardorff, Julianna, Pies, Cheri, and Lu, Michael C

Subjects
Humans, Students, Child, Maternal-Child Health Centers, Pandemics, Racism, Child Health, COVID-19, Anti-racist pedagogy, Graduate education, MCH education, Basic Behavioral and Social Science, Behavioral and Social Science, Good Health and Well Being, Medical and Health Sciences, Studies in Human Society, Public Health
Abstract

IntroductionOver the past decade, foundational courses in MCH have been revised and revamped to integrate the life course perspective and social determinants of health in ways that bring these essential issues to the core of the learning experience. Yet the racial reckoning of 2020 and the racially disparate health impacts of the COVID-19 pandemic underscore that a deeper, more focused approach to anti-racist pedagogy is now imperative for MCH educators and others responsible for developing the MCH workforce.MethodsIn this paper, we discuss our experience of building a 'community of practice' of anti-racist MCH trainees through our course, 'Foundations of Maternal and Child Health Policy, Practice, and Science.'ResultsWe identify four principles which guided our course: (1) building on students' experience, knowledge, identities and social justice commitments; (2) creating a common purpose and shared vocabulary related to racism; (3) organizing classroom activities to reflect real-world problems and professional practices related to addressing structural racism as a root cause of health inequities; and (4) building students' skills and confidence to recognize and address structural racism as MCH professionals.DiscussionWe hope that this description of our principles, along with examples of how they were put into practice, will be useful to MCH educators who seek to build anti-racist frameworks to guide MCH workforce development.

Published
2022

22. Coronary Plaque in People With HIV vs Non-HIV Asymptomatic Community and Symptomatic Higher-Risk Populations

Author

Karady, Julia, Lu, Michael T., Bergström, Göran, Mayrhofer, Thomas, Taron, Jana, Foldyna, Borek, Paradis, Kayla, McCallum, Sara, Aberg, Judith A., Currier, Judith S., Fitch, Kathleen V., Fulda, Evelynne S., Bloomfield, Gerald S., Overton, Edgar T., Lind, Lars, Östgren, Carl Johan, Elvstam, Olof, Söderberg, Stefan, Jernberg, Tomas, Pepe, Rosalie, Dubé, Michael P., Mushatt, David, Fichtenbaum, Carl J., Malvestutto, Carlos, Zanni, Markella V., Hoffmann, Udo, Ribaudo, Heather, Grinspoon, Steven K., and Douglas, Pamela S.

Published
2024
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23. Lipoprotein subclasses are associated with Hepatic steatosis: insights from the prospective multicenter imaging study for the evaluation of chest pain (PROMISE) clinical trial

Author

Karady, Julia, McGarrah, Robert W, Nguyen, Maggie, Giamberardino, Stephanie N, Meyersohn, Nandini, Lu, Michael T, Staziaki, Pedro V, Puchner, Stefan B, Bittner, Daniel O, Foldyna, Borek, Mayrhofer, Thomas, Connelly, Margery A, Tchernof, Andre, White, Phillip J, Nasir, Khurram, Corey, Kathleen, Voora, Deepak, Pagidipati, Neha, Ginsburg, Geoffrey S, Kraus, William E, Hoffmann, Udo, Douglas, Pamela S, Shah, Svati H, and Ferencik, Maros

Published
2024
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25. COVID-19 Vaccination Rates in a Global HIV Cohort

Author

Fulda, Evelynne S, Fitch, Kathleen V, Overton, Edgar T, Zanni, Markella V, Aberg, Judith A, Currier, Judith S, Lu, Michael T, Malvestutto, Carlos, Fichtenbaum, Carl J, Martinez, Esteban, Umbleja, Triin, Douglas, Pamela S, Ribaudo, Heather J, and Grinspoon, Steven K

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Patient Safety, Infectious Diseases, Cardiovascular, Immunization, Clinical Research, Clinical Trials and Supportive Activities, HIV/AIDS, Vaccine Related, Prevention, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Infection, Good Health and Well Being, COVID-19, COVID-19 Vaccines, HIV Infections, Humans, Male, Randomized Controlled Trials as Topic, Vaccination, human immunodeficiency virus, vaccination, Global Burden of Disease region, Biological Sciences, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Little is known regarding coronavirus disease 2019 (COVID-19) vaccination rates in people with HIV (PWH), a vulnerable population with significant morbidity from COVID-19. We assessed COVID-19 vaccination rates among 6952 PWH in the Randomized Trial to Prevent Vascular Events in HIV (REPRIEVE) compared to region- and country-specific vaccination data. The global probability of COVID-19 vaccination through end of July 2021 was 55% among REPRIEVE participants with rates varying substantially by Global Burden of Disease (GBD) superregion. Among PWH, factors associated with COVID-19 vaccination included residence in high-income regions, age, white race, male sex, body mass index, and higher cardiovascular risk. Clinical Trials Registration. NCT02344290.

Published
2022

26. Novel assays to investigate the mechanisms of latent infection with HIV-2

Author

Lu, Michael D, Telwatte, Sushama, Kumar, Nitasha, Ferreira, Fernanda, Martin, Holly Anne, Kadiyala, Gayatri Nikhila, Wedrychowski, Adam, Moron-Lopez, Sara, Chen, Tsui-Hua, Goecker, Erin A, Coombs, Robert W, Lu, Chuanyi M, Wong, Joseph K, Tsibris, Athe, and Yukl, Steven A

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Immunology, HIV/AIDS, Genetics, Infectious Diseases, Aetiology, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being, HIV Infections, HIV Seropositivity, HIV-1, HIV-2, Humans, Latent Infection, Virus Latency, General Science & Technology
Abstract

Although there have been great advancements in the field of HIV treatment and prevention, there is no cure. There are two types of HIV: HIV-1 and HIV-2. In addition to genetic differences between the two types of HIV, HIV-2 infection causes a slower disease progression, and the rate of new HIV-2 infections has dramatically decreased since 2003. Like HIV-1, HIV-2 is capable of establishing latent infection in CD4+ T cells, thereby allowing the virus to evade viral cytopathic effects and detection by the immune system. The mechanisms underlying HIV latency are not fully understood, rendering this a significant barrier to development of a cure. Using RT-ddPCR, we previously demonstrated that latent infection with HIV-1 may be due to blocks to HIV transcriptional elongation, distal transcription/polyadenylation, and multiple splicing. In this study, we describe the development of seven highly-specific RT-ddPCR assays for HIV-2 that can be applied to the study of HIV-2 infections and latency. We designed and validated seven assays targeting different HIV-2 RNA regions along the genome that can be used to measure the degree of progression through different blocks to HIV-2 transcription and splicing. Given that HIV-2 is vastly understudied relative to HIV-1 and that it can be considered a model of a less virulent infection, application of these assays to studies of HIV-2 latency may inform new therapies for HIV-2, HIV-1, and other retroviruses.

Published
2022

27. CUAB: Convolutional Uncertainty Attention Block Enhanced the Chest X-ray Image Analysis

Author

Wang, Chi-Shiang, Su, Fang-Yi, Lee, Tsung-Lu Michael, Tsai, Yi-Shan, and Chiang, Jung-Hsien

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition, Computer Science - Machine Learning
Abstract

In recent years, convolutional neural networks (CNNs) have been successfully implemented to various image recognition applications, such as medical image analysis, object detection, and image segmentation. Many studies and applications have been working on improving the performance of CNN algorithms and models. The strategies that aim to improve the performance of CNNs can be grouped into three major approaches: (1) deeper and wider network architecture, (2) automatic architecture search, and (3) convolutional attention block. Unlike approaches (1) and (2), the convolutional attention block approach is more flexible with lower cost. It enhances the CNN performance by extracting more efficient features. However, the existing attention blocks focus on enhancing the significant features, which lose some potential features in the uncertainty information. Inspired by the test time augmentation and test-time dropout approaches, we developed a novel convolutional uncertainty attention block (CUAB) that can leverage the uncertainty information to improve CNN-based models. The proposed module discovers potential information from the uncertain regions on feature maps in computer vision tasks. It is a flexible functional attention block that can be applied to any position in the convolutional block in CNN models. We evaluated the CUAB with notable backbone models, ResNet and ResNeXt, on a medical image segmentation task. The CUAB achieved a dice score of 73% and 84% in pneumonia and pneumothorax segmentation, respectively, thereby outperforming the original model and other notable attention approaches. The results demonstrated that the CUAB can efficiently utilize the uncertainty information to improve the model performance.

Published
2021

28. Risk factors for clonal hematopoiesis of indeterminate potential in people with HIV: a report from the REPRIEVE trial

Author

Bhattacharya, Romit, Uddin, Md Mesbah, Patel, Aniruddh P., Niroula, Abhishek, Finneran, Phoebe, Bernardo, Rachel, Fitch, Kathleen V., Lu, Michael T., Bloomfield, Gerald S., Malvestutto, Carlos, Aberg, Judy A., Fichtenbaum, Carl J., Hornsby, Whitney, Ribaudo, Heather J., Libby, Peter, Ebert, Benjamin L., Zanni, Markella V., Douglas, Pamela S., Grinspoon, Steven K., and Natarajan, Pradeep

Published
2024
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29. Standards for quantitative assessments by coronary computed tomography angiography (CCTA): An expert consensus document of the society of cardiovascular computed tomography (SCCT)

Author

Nieman, Koen, García-García, Hector M., Hideo-Kajita, Alexandre, Collet, Carlos, Dey, Damini, Pugliese, Francesca, Weissman, Gaby, Tijssen, Jan G.P., Leipsic, Jonathon, Opolski, Maksymilian P., Ferencik, Maros, Lu, Michael T., Williams, Michelle C., Bruining, Nico, Blanco, Pablo Javier, Maurovich-Horvat, Pal, and Achenbach, Stephan

Published
2024
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31. Real-Time Formal Verification of Autonomous Systems With An FPGA

Author

Bui, Minh, Lu, Michael, Hojabr, Reza, Chen, Mo, and Shriraman, Arrvindh

Subjects
Electrical Engineering and Systems Science - Systems and Control, Computer Science - Robotics
Abstract

Hamilton-Jacobi reachability analysis is a powerful technique used to verify the safety of autonomous systems. This method is very good at handling non-linear system dynamics with disturbances and flexible set representations. A drawback to this approach is that it suffers from the curse of dimensionality, which prevents real-time deployment on safety-critical systems. In this paper, we show that a customized hardware design on a Field Programmable Gate Array (FPGA) could accelerate 4D grid-based Hamilton-Jacobi (HJ) reachability analysis up to 16 times compared to an optimized implementation and 142 times compared to MATLAB ToolboxLS on a 16-thread CPU. Our design can overcome the complex data access pattern while taking advantage of the parallel nature of the HJ PDE computation. Because of this, we are able to achieve real-time formal verification with a 4D car model by re-solving the HJ PDE at a frequency of 5Hz on the FPGA as the environment changes. The latency of our computation is deterministic, which is crucial for safetycritical systems. Our approach presented here can be applied to different systems dynamics, and moreover, potentially leveraged for higher dimensions systems. We also demonstrate obstacle avoidance with a robot car in a changing environment.

Published
2020

32. Trajectories of Host-Response Subphenotypes in Patients With COVID-19 Across the Spectrum of Respiratory Support

Author

Lu, Michael, Drohan, Callie, Bain, William, Shah, Faraaz A., Bittner, Matthew, Evankovich, John, Prendergast, Niall T., Hensley, Matthew, Suber, Tomeka L., Fitzpatrick, Meghan, Ramanan, Raj, Murray, Holt, Schaefer, Caitlin, Qin, Shulin, Wang, Xiaohong, Zhang, Yingze, Nouraie, Seyed M., Gentry, Heather, Murray, Cathy, Patel, Asha, Macatangay, Bernard J., Jacobs, Jana, Mellors, John W., Lee, Janet S., Ray, Prabir, Ray, Anuradha, Methé, Barbara, Morris, Alison, McVerry, Bryan J., and Kitsios, Georgios D.

Published
2023
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34. Coronary Artery Disease Reporting and Data System (CAD-RADS) Adoption: Analysis of Local Trends in a Large Academic Medical Center.

Author

Takigami, Angelo, Thondapu, Vikas, Goiffon, Reece, Depetris, Jena, Gupta, Sumit, Garrana, Sherief, Knyazev, Veniamin, Tower-Rader, Albree, Lu, Michael, Meyersohn, Nandini, Hoffmann, Udo, Hedgire, Sandeep, and Ghoshhajra, Brian

Subjects
CT Angiography, Coronary Arteries
Abstract

PURPOSE: To perform a retrospective review of Coronary Artery Disease Reporting and Data System (CAD-RADS) adoption at a high-volume cardiac CT service. MATERIALS AND METHODS: In this retrospective study, the adoption of CAD-RADS in 6562 coronary CT angiography (CTA) reports from January 1, 2017, to February 13, 2020, was evaluated. Reports without CAD-RADS were classified as opt-outs or exceptions to CAD-RADS. CAD-RADS classifications were retrospectively assigned to the opt-outs and the clinical indications for coronary CTA. RESULTS: CAD-RADS scores were reported in 95% (6264 of 6562) of cases. Among the 5% (n = 298) of reports not reported according to CAD-RADS, 58% (n = 172) were considered opt-outs and 42% (n = 126) were exceptions. Cases with higher degree of stenosis, stents, and coronary artery bypass grafts (CABGs) occurred more often in opt-outs versus reports with CAD-RADS (odds ratio [OR], 8.3 [95% CI: 1.6, 42.1]; P < .001). The quarterly opt-out rate decreased over consecutive quarters in the 1st year (OR, 0.77 [95% CI: 0.61, 0.96]; P = .01), then stabilized. Quarterly opt-out rate for patients with stents decreased over time (OR, 0.82 [95% CI: 0.73, 0.92]; P = .008), as did the opt-out rates in patients with CABG (OR, 0.83 [95% CI: 0.76, 0.91]; P < .001). Exceptions (n = 126) included coronary dissections (44%), anomalous coronary arteries (41%), coronary artery aneurysms or pseudoaneurysms (10%), vasculitis (2%), stent complications (2%), and extrinsic compression of grafts (2%). CONCLUSION: CAD-RADS was adopted rapidly and widely. Readers opted out of its use most often in complex cases of CAD, and the most common exceptions were coronary dissections and anomalous coronary artery.Keywords: Coronary Arteries, CT Angiography© RSNA, 2021.

Published
2021

35. Histopathology images predict multi-omics aberrations and prognoses in colorectal cancer patients

Author

Pei-Chen Tsai, Tsung-Hua Lee, Kun-Chi Kuo, Fang-Yi Su, Tsung-Lu Michael Lee, Eliana Marostica, Tomotaka Ugai, Melissa Zhao, Mai Chan Lau, Juha P. Väyrynen, Marios Giannakis, Yasutoshi Takashima, Seyed Mousavi Kahaki, Kana Wu, Mingyang Song, Jeffrey A. Meyerhardt, Andrew T. Chan, Jung-Hsien Chiang, Jonathan Nowak, Shuji Ogino, and Kun-Hsing Yu

Subjects
Science
Abstract

Abstract Histopathologic assessment is indispensable for diagnosing colorectal cancer (CRC). However, manual evaluation of the diseased tissues under the microscope cannot reliably inform patient prognosis or genomic variations crucial for treatment selections. To address these challenges, we develop the Multi-omics Multi-cohort Assessment (MOMA) platform, an explainable machine learning approach, to systematically identify and interpret the relationship between patients’ histologic patterns, multi-omics, and clinical profiles in three large patient cohorts (n = 1888). MOMA successfully predicts the overall survival, disease-free survival (log-rank test P-value

Published
2023
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36. ModelHub.AI: Dissemination Platform for Deep Learning Models

Author

Hosny, Ahmed, Schwier, Michael, Berger, Christoph, Örnek, Evin P, Turan, Mehmet, Tran, Phi V, Weninger, Leon, Isensee, Fabian, Maier-Hein, Klaus H, McKinley, Richard, Lu, Michael T, Hoffmann, Udo, Menze, Bjoern, Bakas, Spyridon, Fedorov, Andriy, and Aerts, Hugo JWL

Subjects
Computer Science - Machine Learning, Electrical Engineering and Systems Science - Image and Video Processing
Abstract

Recent advances in artificial intelligence research have led to a profusion of studies that apply deep learning to problems in image analysis and natural language processing among others. Additionally, the availability of open-source computational frameworks has lowered the barriers to implementing state-of-the-art methods across multiple domains. Albeit leading to major performance breakthroughs in some tasks, effective dissemination of deep learning algorithms remains challenging, inhibiting reproducibility and benchmarking studies, impeding further validation, and ultimately hindering their effectiveness in the cumulative scientific progress. In developing a platform for sharing research outputs, we present ModelHub.AI (www.modelhub.ai), a community-driven container-based software engine and platform for the structured dissemination of deep learning models. For contributors, the engine controls data flow throughout the inference cycle, while the contributor-facing standard template exposes model-specific functions including inference, as well as pre- and post-processing. Python and RESTful Application programming interfaces (APIs) enable users to interact with models hosted on ModelHub.AI and allows both researchers and developers to utilize models out-of-the-box. ModelHub.AI is domain-, data-, and framework-agnostic, catering to different workflows and contributors' preferences.

Published
2019

39. Noninvasive diagnosis of secondary infections in COVID-19 by sequencing of plasma microbial cell-free DNA

Author

Lisius, Grace, Duttagupta, Radha, Ahmed, Asim A., Hensley, Matthew, Al-Yousif, Nameer, Lu, Michael, Bain, William, Shah, Faraaz, Blauwkamp, Timothy A., Bercovici, Sivan, Schaefer, Caitlin, Qin, Shulin, Wang, Xiaohong, Zhang, Yingze, Mitchell, Kevin J., Hughes, Ellen K., Jacobs, Jana L., Naqvi, Asma, Haidar, Ghady, Mellors, John W., Methé, Barbara, McVerry, Bryan J., Morris, Alison, and Kitsios, Georgios D.

Published
2023
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40. Evolving the Preconception Health Framework

Author

Dehlendorf, Christine, Akers, Aletha Y, Borrero, Sonya, Callegari, Lisa S, Cadena, Denicia, Gomez, Anu Manchikanti, Hart, Jamie, Jimenez, Laura, Kuppermann, Miriam, Levy, Barbara, Lu, Michael C, Malin, Kiko, Simpson, Monica, Verbiest, Sarah, Yeung, Miriam, and Crear-Perry, Joia

Subjects
Reproductive Medicine, Biomedical and Clinical Sciences, Contraception/Reproduction, Behavioral and Social Science, Basic Behavioral and Social Science, Reproductive health and childbirth, Good Health and Well Being, Peace, Justice and Strong Institutions, Health Equity, Humans, Personal Autonomy, Preconception Care, Reproductive Health, Sexual Health, Social Justice, Paediatrics and Reproductive Medicine, Obstetrics & Reproductive Medicine, Reproductive medicine
Abstract

Over the past decade, increasing attention has been paid to intervening in individuals' health in the "preconception" period as an approach to optimizing pregnancy outcomes. Increasing attention to the structural and social determinants of health and to the need to prioritize reproductive autonomy has underscored the need to evolve the preconception health framework to center race equity and to engage with the historical and social context in which reproduction and reproductive health care occur. In this commentary, we describe the results of a meeting with a multidisciplinary group of maternal and child health experts, reproductive health researchers and practitioners, and Reproductive Justice leaders to define a new approach for clinical and public health systems to engage with the health of nonpregnant people. We describe a novel "Reproductive and Sexual Health Equity" framework, defined as an approach to comprehensively meet people's reproductive and sexual health needs, with explicit attention to structural influences on health and health care and grounded in a desire to achieve the highest level of health for all people and address inequities in health outcomes. Principles of the framework include centering the needs of and redistributing power to communities, having clinical and public health systems acknowledge historical and ongoing harms related to reproductive and sexual health, and addressing root causes of inequities. We conclude with a call to action for a multisectoral effort centered in equity to advance reproductive and sexual health across the reproductive life course.

Published
2021

41. Piloting an integrated SARS-CoV-2 testing and data system for outbreak containment among college students: A prospective cohort study.

Author

Packel, Laura, Reingold, Arthur, Hunter, Lauren, Facente, Shelley, Li, Yi, Harte, Anna, Nicolette, Guy, Urnov, Fyodor D, Lu, Michael, Petersen, Maya, and IGI Testing Consortium

Subjects
IGI Testing Consortium, Humans, Contact Tracing, Cohort Studies, Prospective Studies, Communicable Disease Control, Students, Universities, California, Surveys and Questionnaires, COVID-19, SARS-CoV-2, COVID-19 Nucleic Acid Testing, General Science & Technology
Abstract

BackgroundColleges and universities across the country are struggling to develop strategies for effective control of COVID-19 transmission as students return to campus.Methods and findingsWe conducted a prospective cohort study with students living on or near the UC Berkeley campus from June 1st through August 18th, 2020 with the goal of providing guidance for campus reopening in the safest possible manner. In this cohort, we piloted an alternative testing model to provide access to low-barrier, high-touch testing and augment student-driven testing with data-driven adaptive surveillance that targets higher-risk students and triggers testing notifications based on reported symptoms, exposures, or other relevant information. A total of 2,180 students enrolled in the study, 51% of them undergraduates. Overall, 6,247 PCR tests were administered to 2,178 students over the two-month period. Overall test positivity rate was 0.9%; 2.6% of students tested positive. Uptake and acceptability of regular symptom and exposure surveys was high; 98% of students completed at least one survey, and average completion rate was 67% (Median: 74%, IQR: 39%) for daily reporting of symptoms and 68% (Median: 75%, IQR: 40%) for weekly reporting of exposures. Of symptom-triggered tests, 5% were PCR-positive; of exposure-triggered tests, 10% were PCR-positive. The integrated study database augmented traditional contact tracing during an outbreak; 17 potentially exposed students were contacted the following day and sent testing notifications. At study end, 81% of students selected their desire "to contribute to UC Berkeley's response to COVID-19" as a reason for their participation in the Safe Campus study.ConclusionsOur results illustrate the synergy created by bringing together a student-friendly, harm reduction approach to COVID-19 testing with an integrated data system and analytics. We recommend the use of a confidential, consequence-free, incentive-based daily symptom and exposure reporting system, coupled with low-barrier, easy access, no stigma testing. Testing should be implemented alongside a system that integrates multiple data sources to effectively trigger testing notifications to those at higher risk of infection and encourages students to come in for low-barrier testing when needed.

Published
2021

42. Hepatic steatosis and nonalcoholic fatty liver disease are common and associated with cardiometabolic risk in a primary prevention cohort of people with HIV

Author

Lake, Jordan E., Taron, Jana, Ribaudo, Heather J., Leon-Cruz, Jorge, Utay, Netanya S., Swaminathan, Shobha, Fitch, Kathleen V., Kileel, Emma M., Paradis, Kayla, Fulda, Evelynne S., Ho, Ken S., Luetkemeyer, Anne F., Johnston, Carrie D., Zanni, Markella V., Douglas, Pamela S., Grinspoon, Steven K., Lu, Michael T., and Fichtenbaum, Carl J.

Published
2023
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48. Correlates and Timing of Reproductive Aging Transitions in a Global Cohort of Midlife Women With Human Immunodeficiency Virus: Insights From the REPRIEVE Trial

Author

Zanni, Markella V, Currier, Judith S, Kantor, Amy, Smeaton, Laura, Rivard, Corinne, Taron, Jana, Burdo, Tricia H, Badal-Faesen, Sharlaa, Lalloo, Umesh G, Pinto, Jorge A, Samaneka, Wadzanai, Valencia, Javier, Klingman, Karin, Allston-Smith, Beverly, Cooper-Arnold, Katharine, Desvigne-Nickens, Patrice, Lu, Michael T, Fitch, Kathleen V, Hoffman, Udo, Grinspoon, Steven K, Douglas, Pamela S, and Looby, Sara E

Subjects
Reproductive Medicine, Biomedical and Clinical Sciences, Contraception/Reproduction, Clinical Research, Aging, Estrogen, Reproductive health and childbirth, Good Health and Well Being, Adult, Anti-Mullerian Hormone, Biomarkers, Cardiometabolic Risk Factors, Cohort Studies, Female, HIV Infections, Humans, Menopause, Middle Aged, Reproduction, Residence Characteristics, HIV, Women, Sex, Reproductive Aging, Cardiometabolic Risk, Biological Sciences, Medical and Health Sciences, Microbiology, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

BackgroundReproductive aging may contribute to cardiometabolic comorbid conditions. We integrated data on gynecologic history with levels of an ovarian reserve marker (anti-müllerian hormone [AMH)] to interrogate reproductive aging patterns and associated factors among a subset of cisgender women with human immunodeficiency virus (WWH) enrolled in the REPRIEVE trial.MethodsA total of 1449 WWH were classified as premenopausal (n = 482) (menses within 12 months; AMH level ≥20 pg/mL; group 1), premenopausal with reduced ovarian reserve (n = 224) (menses within 12 months; AMH 12 months of amenorrhea). Excluding WWH with surgical menopause, age at final menstrual period was summarized for postmenopausal WWH (group 3) and estimated among all WWH (groups 1-3) using an accelerated failure-time model.ResultsCardiometabolic and demographic parameters associated with advanced reproductive age (controlling for chronologic age) included waist circumference (>88 vs ≤88 cm) (odds ratio [OR], 1.38; 95% confidence interval, 1.06-1.80; P = .02), hemoglobin (≥12 vs

Published
2020

49. Prognostic Value of Coronary CTA in Stable Chest Pain CAD-RADS, CAC, and Cardiovascular Events in PROMISE

Author

Bittner, Daniel O, Mayrhofer, Thomas, Budoff, Matt, Szilveszter, Balint, Foldyna, Borek, Hallett, Travis R, Ivanov, Alexander, Janjua, Sumbal, Meyersohn, Nandini M, Staziaki, Pedro V, Achenbach, Stephan, Ferencik, Maros, Douglas, Pamela S, Hoffmann, Udo, Lu, Michael T, and Investigators, PROMISE

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Biomedical Imaging, Atherosclerosis, Pain Research, Heart Disease, Cardiovascular, Heart Disease - Coronary Heart Disease, Patient Safety, Clinical Research, Detection, screening and diagnosis, 4.2 Evaluation of markers and technologies, Good Health and Well Being, Aged, Angiotensin Receptor Antagonists, Angiotensin-Converting Enzyme Inhibitors, Chest Pain, Computed Tomography Angiography, Coronary Artery Disease, Ethnicity, Female, Humans, Male, Middle Aged, Minority Groups, Predictive Value of Tests, Prognosis, Prospective Studies, Risk Assessment, United States, coronary CT angiography, coronary artery disease, coronary stenosis, coronary artery calcium, CAD-RADS, prognosis, high-risk plaque, PROMISE Investigators, Cardiorespiratory Medicine and Haematology, Cardiovascular System & Hematology, Cardiovascular medicine and haematology, Clinical sciences
Abstract

ObjectivesThe purpose of this study was to compare Coronary Artery Disease Reporting and Data System (CAD-RADS) to traditional stenosis categories and the coronary artery calcium score (CACS) for predicting cardiovascular events in patients with stable chest pain and suspected coronary artery disease (CAD).BackgroundThe 2016 CAD-RADS has been established to standardize the reporting of CAD on coronary CT angiography (CTA).MethodsPROMISE (Prospective Multicenter Imaging Study for Evaluation of Chest Pain) trial participants' CTAs were assessed by a central CT core laboratory for CACS, traditional stenosis-based categories, and modified CAD-RADS grade including high-risk coronary plaque (HRP) features. Traditional stenosis categories and CAD-RADS grade were compared for the prediction of the composite endpoint of death, myocardial infarction, or hospitalization for unstable angina over a median follow-up of 25 months. Incremental prognostic value over traditional risk factors and CACS was assessed.ResultsIn 3,840 eligible patients (mean age: 60.4 ± 8.2 years; 49% men), 3.0% (115) experienced events. CAD-RADS (concordance statistic [C-statistic] 0.747) had significantly higher discriminatory value than traditional stenosis-based assessments (C-statistic 0.698 to 0.717; all p for comparison ≤0.001). With no plaque (CAD-RADS 0) as the baseline, the hazard ratio (HR) for an event increased from 2.43 (95% confidence interval [CI]: 1.16 to 5.08) for CAD-RADS 1 to 21.84 (95% CI: 8.63 to 55.26) for CAD-RADS 4b and 5. In stepwise nested models, CAD-RADS added incremental prognostic value beyond ASCVD risk score and CACS (C-statistic 0.776 vs. 0.682; p

Published
2020

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