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RNA splicing patterns contribute to burst size variation among HIV-1-infected Jurkat cell clones.
Get PDFAccurately quantifying virus release from HIV-1-infected cells is central to predicting infection outcomes and evaluating treatment strategies. Recent studies suggest that viral shedding can vary strikingly among infected cells. To identify predictors of virus release levels, a previously developed high-throughput molecular barcoding system was used to track the expression properties of individual infected clones within a polyclonal population. Consistent with previous reports, virus release spanned four orders of magnitude among clonal integrants. While reporter gene expression correlated poorly with virus release, intracellular viral RNA levels correlated well, and levels of unspliced HIV-1 RNA correlated most closely. Comparing clones with different virus release levels showed that they varied not only in total intracellular HIV-1 RNA levels but also in levels of viral RNA splicing. Remobilizing proviruses revealed that splicing differences were largely due to cell-intrinsic properties, although splicing differences were due to heritable features of the parent provirus for at least one clone. This clone displayed high levels of reporter gene expression from an HIV-1spliced RNA, but low levels of unspliced viral RNA and virus release. This over-splicing clone, which contained a non-synonymous substitution in rev, did not respond to treatment with the latency-reversing agent JQ1 but displayed increased virus release in response to treatment with pladienolide B, a splicing inhibitor. These findings demonstrate that splicing differences can contribute to virus production levels and suggest that future studies on proviral populations that include expanded clones may benefit from assessing clone-specific splicing properties. IMPORTANCE: Many models of HIV-1 infection rely on the assumption that actively infected cells release similar amounts of virus, despite recent reports that suggest shedding differs drastically among infected cells. In this study, the expression phenotypes of hundreds of integrant clones were analyzed to identify factors contributing to burst size variation. In agreement with previous reports, virus release spanned over four orders of magnitude within the infected pool. Both proviral expression levels and variation in splicing contributed to these burst size differences. While cell-intrinsic factors appeared to be the primary contributors to heterogeneous shedding patterns, viral point mutations were also observed and, in at least one case, contributed to particle release levels. Together, these findings demonstrate that expression variation among proviruses is both large and multifaceted and suggest that clone-specific differences in HIV-1 expression properties may contribute to unpredicted responses to treatment interventions
An Integrative Framework of Intersectional Stereotyping: Merging the Lens Model and MOSAIC to Explain Variations in Black-Threat Stereotyping.
Get PDFBlack-threat stereotyping, or the tendency to disproportionately associate Black individuals with threat-related concepts, is an artifact of American psychology. Nonetheless, most of what psychologists know about this topic concerns how Black-threat stereotypes are applied to young, straight Black men. In the present analysis, we review existing research on intersectional Black-threat stereotyping: broadly, how Black-threat stereotyping depends on the multiple, intersecting social categories to which targets belong. Although the existing literature is at times contradictory, we argue that it can be well-explained by an Integrative Framework of Intersectional Stereotyping that merges the core assumptions of two recent theories of intersectional stereotyping: the lens model and MOSAIC. The central contribution of the proposed framework is that intersectional stereotypes may at times be retrieved from memory and at other times be dynamically generated. We conclude with a roadmap for future research in this consequential domain.In the United States, Black Americans are killed by police at over twice the rate of White Americans. There are many reasons for this racial disparity, not the least of which is that Black Americans are often stereotyped as threatening. In the present paper, we review what scientists currently know about these inaccurate perceptions, and we discuss the question of whether these perceptions depend on the multiple social groups to which Black Americans belong (for example, Black Americans' age, gender, and sexual orientation groups). We argue that although research on this topic is messy, it can be "cleaned up" with the help of what we call an Integrative Framework of Intersectional Stereotyping. This framework merges insights from two recent theories of intersectional stereotyping: the lens model and MOSAIC
Understanding the pathogenesis of uveitis in Ebola virus disease survivors: an observational cohort and cross-sectional study protocol for clinical, molecular virologic and immunologic characterisation
Get PDFINTRODUCTION: The 2013-2016 Western African outbreak of the Ebola virus disease (EVD), the largest recorded outbreak since the discovery of Ebola virus (EBOV) in 1976, destabilised local health systems and left thousands of survivors at risk for postacute sequelae, including vision-threatening uveitis. In an EVD survivor with severe panuveitis, the detection of persistent EBOV in the aqueous humour, long after clearance of acute viremia, focused clinical and research attention on the host-EBOV interaction in the unique terrain of ocular immune privilege. Despite the recognition that uveitis is common and consequential in EVD survivors, our understanding of pathogenesis is extremely limited, including the contributions of viral persistence and ocular-specific and systemic immune responses to disease expression. In this study protocol, we outline a multifaceted approach to characterise EVD-associated intraocular inflammation, including the clinical phenotype and complications; the presence of EBOV (or EBOV RNA/antigen) in ocular fluids and tissues; and associated local ocular-specific and peripheral immune responses. METHODS AND ANALYSIS: We use an observational cohort design, which includes EVD survivors and close contacts of EVD survivors (ie, no documented history of EVD), and we propose disease (clinical examination and imaging), as well as molecular, virologic and immunologic characterisation, to meet research objectives. ETHICS AND DISSEMINATION: This study has received Institutional Review Board approval from University of Nebraska Medical Centre, Emory University and Sierra Leone Ministry of Health. Findings will be disseminated through peer-reviewed publications
Semiparametric Regression Analysis of Interval-Censored Multi-State Data with An Absorbing State
Get PDFIn studies of chronic diseases, the health status of a subject can often be characterized by a finite number of transient disease states and an absorbing state, such as death. The times of transitions among the transient states are ascertained through periodic examinations and thus interval-censored. The time of reaching the absorbing state is known or right-censored, with the transient state at the previous instant being unobserved. In this article, we provide a general framework for analyzing such multi-state data. We formulate the effects of potentially time-dependent covariates on the multi-state disease process through semiparametric proportional intensity models with random effects. We combine nonparametric maximum likelihood estimation with sieve estimation and develop a stable expectation-maximization algorithm. We establish the asymptotic properties of the proposed estimators through novel use of modern empirical process theory, sieve estimation theory, and semiparametric efficiency theory. In addition, we dynamically predict future states and survival time using the evolving disease history. Finally, we assess the performance of the proposed methods through extensive simulation studies and provide an illustration with a cardiac allograft vasculopathy study. Supplementary materials for this article are available online, including a standardized description of the materials available for reproducing the work
Learning from Peers: A Qualitative Study to Inform the Development of a Community Tailored Peer Support Intervention to Support Healthy Infant Growth
Get PDFBackground: Obesity is a chronic disease that has negative health consequences for children. Peer support models have been used to manage chronic diseases like diabetes; however, little is known about how a peer support intervention might promote healthy infant growth to prevent pediatric obesity. The aim of this project was to explore parental perspectives on how a peer support intervention might be developed to support healthy infant weight gain and nutrition. Methods: Data were collected from November 2022 to October 2023 at a single pediatric primary care clinic. Semi-structured interviews explored parents’ perspectives of how a peer parent coach could promote healthy infant nutrition and growth. Interviews focused on (1) common infant feeding and nutrition questions, (2) the role and importance of peer support during the newborn period, and (3) strategies for addressing and facilitating connections to food-related resources and addressing food insecurity. Results: A total of 18 interviews were conducted. Average parental age was 32.1 years (range 20–46 years). Thirty-three percent of the participants identified as Black, 28% identified as White, 11% identified as Asian, and the remaining identified as Other or preferred not to report. Half of the sample reported a household income of <$20,000, 67% reported having public insurance, and 11% reported household food insecurity. Themes that emerged included: peer parent coaches can (1) provide emotional support to families with young infants, (2) education focused on infant nutrition, and (3) facilitate connections with nutrition resources. Participants also noted the importance of understanding a family’s unique culture when counseling on infant growth and nutrition. Conclusions: Multiple themes were identified about how a peer support intervention could support healthy infant nutrition and growth. Future work should test the feasibility and acceptability of a peer support intervention to promote healthy infant weight gain
Deep learning for Alzheimer’s disease: advances in classification, segmentation, subtyping, and explainability
Get PDFAlzheimer’s disease (AD) poses urgent significant challenges for early detection and personalized prognostication. Deep learning (DL) is now regarded as a pivotal technology for extracting subtle imaging and non-imaging biomarkers; yet translating these advances into clinical practice demands a coherent framework. In this review, we first survey input modalities from structural and functional MRI to PET, genetic profiles, and cognitive tests and the key public cohorts that supply multimodal data. We then categorize DL architectures into three complementary pillars: (1) end-to-end classification networks for direct diagnosis; (2) multimodal fusion strategies that integrate heterogeneous biomarkers; and (3) automated segmentation pipelines for precise anatomical delineation. We also examine subtyping algorithms that uncover latent AD phenotypes via clustering and decision-tree models. In order to fill the gap between high-performance DL and real-world adoption, we detail explainable AI methods that render model decisions transparent, and we review performance benchmarks including accuracy, sensitivity/specificity, Dice and Jaccard indices to contextualize efficacy. Finally, we discuss clinical translation, covering prospective validation, workflow integration, and regulatory/privacy considerations, before outlining challenges and future directions such as data heterogeneity, interpretability–accuracy trade-offs, early/preclinical detection, and federated learning. Our roadmap highlights the interdisciplinary collaborations and technical innovations needed to deliver robust, trustworthy, and scalable DL-based tools for Alzheimer’s care
TOPICS IN CONFORMATIONAL ANALYSIS AND MEDICINAL CHEMISTRY: I. HFIP SOLVATION MODULATES CONFORMATIONAL AND CONFIGURATIONAL EQUILIBRIA; II. SMALL MOLECULE APPROACHES IN TARGETING RNA AND RNA BINDING PROTEINS; AND III. BACKBONE EDITING OF OXIDIZED POLYETHYLENE VIA THE INTRAMOLECULAR SCHMIDT REACTION
Get PDFThis dissertation explores applications of physical organic chemistry, spanning solvent effects on conformational equilibrium, targeted drug discovery, and polymer functionalization. Chapter 1 establishes HFIP as a privileged solvent for controlling conformational equilibria, demonstrating its ability to impose substantial energetic penalties (ΔG up to 1.93 kcal/mol) on axial substituents in 1,3-dioxanes and other heterocycles through specific hydrogen-bonding interactions. Chapters 2–4 focus on drug discovery. Chapter 2 reveals fundamental challenges in designing HuR-targeting PROTACs, as the protein aberrantly engages linker moieties, precluding productive ternary complex formation. Chapter 3 addresses some of these limitations through replacement of the promiscuous hydroxamic acid warhead of KH-39 with amino acids, yielding selective HuR inhibitors (e.g., 3.04b, Ki = 530 nM) that avoid off-target HDAC inhibition and mutagenicity associated with hydroxamates. Chapter 4 deciphers structure-activity relationships of TPP riboswitch binders, identifying critical electrostatic and conformational requirements. This investigation enabled development of a second generation inhibitor, 4.17 (Kd = 57 nM), and serves as a proof-of-concept for RNA-targeted drug discovery. Chapter 5 transitions to polymer chemistry, demonstrating a tandem C–H oxidation/azide-mediated rearrangement to convert polyethylene into “PE-like” materials with tunable properties (e.g., crystallinity, degradability). This backbone-editing strategy enables modular installation of functional groups (esters, amides, chirality) and highlights potential for upcycling commodity plastics.Doctor of Philosoph
Identifying Intimate Partner Violence Patterns and Risk Factors Among Men in Tanzania: A Latent Class Analysis
Get PDFIntroduction: High rates of intimate partner violence (IPV) are reported in Tanzania. Individuals experiencing IPV are typically categorized as victims-only (typically women) or perpetrators-only (typically men). However, studies suggest individuals can both experience and perpetrate IPV. Violence typology frameworks suggest that there are patterns of IPV that differ by victimization and perpetration experience, severity, type of violence, and the risk factors for violence. Person-centered analyses, like latent class analysis (LCA), are well-suited to exploring multiple aspects of IPV and associating risk factors with engagement in different IPV patterns. Methods: Data were collected as part of a randomized controlled trial of men in Dar es Salaam, Tanzania. Endline data from a subsample of n=987 men who reported at least one sexual partner in the past year were included in these analyses. In Study 1, an LCA was conducted to identify IPV patterns. In Studies 2 and 3, Vermunt’s three-step method was used to identify individual-level risk factors, and interpersonal- or community-level risk factors, respectively, associated with engagement in varying patterns of IPV. Results: In Study 1, 53.8% of men reported any IPV victimization, perpetration, or both. The best-fitting model was a three-class model that included a low violence pattern (LV), a moderate psychological violence pattern (MPV), and a severe multiform violence pattern (SMV). Study 2 found that greater childhood adversity and household hunger were associated with engaging in MPV or SMV compared to LV. Worse mental health and lower self-control were associated with engaging in SMV compared to LV. Study 3 found that childhood exposure to parental violence and increased exposure to past year neighborhood disorder were associated with engaging in MPV or SMV compared to LV. No risk factors differentiated between patterns of SMV and MPV at p-value <0.05. However, consistent dose-responses indicate that an increase in each risk factor is predictive of patterns of SMV compared to MPV. Conclusions: There are distinct IPV patterns that differ by severity and type of violence and their associated risk factors. More research is needed to determine if there are risk factors that differentiate between patterns of moderate psychological and severe multiform IPV.Doctor of Philosoph
WHITE RACIAL IDENTITIES, RACIAL IDEOLOGIES, AND NEIGHBORHOOD BELONGING IN A CHANGING SOUTHERN CITY
Get PDFPersistent racial inequality structures all facets of social life in the United States, including healthcare, education, the criminal legal system, employment, wealth accumulation, housing, and neighborhoods. Researchers seeking to theorize structural racial inequality must understand how White people operate, as they are the primary creators and beneficiaries of this inequality. Much scholarly attention has been devoted to this subject; however, gaps remain in our knowledge of how White people experience their own racial identities, explain racial inequality, and feel they belong in differently racialized spaces. Gentrification, or the racialized process of class change, represents an understudied way to examine these topics, because its racial inequality can heighten White adults’ racial salience. This project draws on analysis of in-depth, semi-structured interviews with 98 Durham, North Carolina residents–with a focus on 69 White residents of Durham’s gentrifying neighborhoods–as well as on 67 observation hours in these neighborhoods. It investigates three interrelated topics: how White adults not involved in formal race-related organizing construct their racial identities, how politically left-of-center White adults explain racial inequality post 2020, and how White gentrifiers feel they belong in differently racialized neighborhoods. In so doing, it documents the divergent frameworks of White racial identity work undertaken by White adults not involved in formal race-related organizing, how color-evasive and color-conscious racial ideologies can coexist with politically left-of-center White adults’ acceptance of structural racism, and how both neighborhood racialization and racial composition influence White gentrifiers’ neighborhood belonging. This research thus improves academic knowledge of how racially privileged adults experience and understand the racial and socioeconomic changes that largely benefit them.Doctor of Philosoph
IMPACT OF THE L421P MUTATION IN PENICILLIN-BINDING PROTEIN 1 ON FITNESS AND ANTIBIOTIC RESISTANCE IN Neisseria gonorrhoeae
Get PDFThe L421P mutation in penicillin-binding protein 1 (PBP1), encoded by ponA, is a key resistant determinant involved in chromosomally mediated penicillin resistance in Neisseria gonorrhoeae. Although penicillin has not been used to treat gonococcal infections in the United States since the 1980s, ponAL421P remains present in ~50% of isolates in the PubMLST database. The persistence of ponAL421P is not well understood. In this study we evaluated of the evolutionary origins of ponAL421P to understand its prevalence in the gonococcal population and its involvement in antibiotic resistance. Findings from our phylogenic analysis of the L421P mutation in ponA strongly support the idea that this mutation arose and was selected for in N. gonorrhoeae isolates as a result of penicillin use. Comparative genomics revealed that ponAL421P is exclusive to N. gonorrhoeae, while leucine at position 421 is fully conserved in other Neisseria species.To understand the involvement of ponAL421P in antibiotic resistance, we introduced ponA variants encoding 16 different amino acids at position-421 into FA6140, a penicillin-resistant gonococcal isolate naturally harboring ponAL421P. Proline-421 was the only mutation that increased the penicillin MIC (MICPEN) to the same level as FA6140. We also assessed the fitness of strains with the 16 mutant ponA alleles over multiple serial passages, both with and without sub- MICPEN concentrations. There was no fitness defect attributed to ponAL421P under these experimental conditions; instead, our analyses suggest that the widespread occurrence of ponAL421P is driven by its capacity to increase the MICPEN above the clinical breakpoint. In FA6140 transformed with the mosaic penA allele from strain H041, a ceftriaxone-resistant isolate, ponAL421P increased the MIC of ceftriaxone, suggesting that ceftriaxone targets PBP1 in this strain.Here, we investigated the impact of a key resistance mutation, ponAL421P. We conclude that ponAL421P emerged in gonococcal isolates, increasing the MICPEN above the clinical breakpoint, and has remained in the population even after the removal of penicillin from treatment guidelines. This work highlights the role of the ponAL421P allele in shaping the current antibiotic resistance landscape and supports the need for ongoing surveillance and evolutionary studies of such mutations in the gonococcal population.Doctor of Philosoph