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These collections showcase journal articles, preprints, book chapters, and other publications and presentations produced by faculty, postdocs, and researchers at UMass Chan Medical School, including a dedicated collection for research on COVID-19 and related viruses.

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  • Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements

    Wirthlin, Morgan E; Schmid, Tobias A; Elie, Julie E; Zhang, Xiaomeng; Kowalczyk, Amanda; Redlich, Ruby; Shvareva, Varvara A; Rakuljic, Ashley; Ji, Maria B; Bhat, Ninad S; et al. (2024-03-29)
    Vocal production learning ("vocal learning") is a convergently evolved trait in vertebrates. To identify brain genomic elements associated with mammalian vocal learning, we integrated genomic, anatomical, and neurophysiological data from the Egyptian fruit bat (Rousettus aegyptiacus) with analyses of the genomes of 215 placental mammals. First, we identified a set of proteins evolving more slowly in vocal learners. Then, we discovered a vocal motor cortical region in the Egyptian fruit bat, an emergent vocal learner, and leveraged that knowledge to identify active cis-regulatory elements in the motor cortex of vocal learners. Machine learning methods applied to motor cortex open chromatin revealed 50 enhancers robustly associated with vocal learning whose activity tended to be lower in vocal learners. Our research implicates convergent losses of motor cortex regulatory elements in mammalian vocal learning evolution.
  • Citizenship status and career self-efficacy: An intersectional study of biomedical trainees in the United States

    Chatterjee, Deepshikha; Nogueira, Ana T; Wefes, Inge; Chalkley, Roger; Sturzenegger Varvayanis, Susi; Fuhrmann, Cynthia N; Varadarajan, Janani; Jacob, Gabrielle A; Gaines, Christiann H; Hubbard, Nisan M; et al. (2024-03-20)
    This study examines the intersectional role of citizenship and gender with career self-efficacy amongst 10,803 doctoral and postdoctoral trainees in US universities. These biomedical trainees completed surveys administered by 17 US institutions that participated in the National Institutes of Health Broadening Experiences in Scientific Training (NIH BEST) Programs. Findings indicate that career self-efficacy of non-citizen trainees is significantly lower than that of US citizen trainees. While lower career efficacy was observed in women compared with men, it was even lower for non-citizen female trainees. Results suggest that specific career interests may be related to career self-efficacy. Relative to US citizen trainees, both male and female non-citizen trainees showed higher interest in pursuing a career as an academic research investigator. In comparison with non-citizen female trainees and citizen trainees of all genders, non-citizen male trainees expressed the highest interest in research-intensive (and especially principal investigator) careers. The authors discuss potential causes for these results and offer recommendations for increasing trainee career self-efficacy which can be incorporated into graduate and postdoctoral training.
  • SM22α deficiency: promoting vascular fibrosis via SRF-SMAD3-mediated activation of transcription following arterial injury [preprint]

    Shen, Jianbin; Ju, Donghong; Wu, Shichao; Zhao, Jiawei; Pham, Lucynda; Ponce, Alejandro; Yang, Maozhou; Li, Hui Joyce; Zhang, Kezhong; Yang, Zhe; et al. (2024-02-27)
    Vascular fibrosis, characterized by increased Type I collagen expression, significantly contributes to vascular remodeling. Our previous studies show that disrupting the expression of SM22α (aka SM22, Tagln) induces extensive vascular remodeling following arterial injury, involving oxidative stress, inflammation, and chondrogenesis within the vessel wall. This study aims to investigate the molecular mechanisms underlying the transcription of Col1a2, a key fibrotic extracellular matrix marker. We observed upregulation of COL1A2 in the arterial wall of Sm22-/- mice following carotid injury. Bioinformatics and molecular analyses reveal that Col1a2 transcription depends on a CArG box in the promoter, activated synergistically by SRF and SMAD3. Notably, we detected enhanced nuclear translocation of both SRF and SMAD3 in the smooth muscle cells of the injured carotid artery in Sm22-/- mice. These findings demonstrate that SM22 deficiency regulates vascular fibrosis through the interaction of SRF and the SMAD3-mediated canonical TGF-β1 signal pathway, suggesting SM22α as a potential therapeutic target for preventing vascular fibrosis.
  • Modeling neurodevelopmental disorder-associated human AGO1 mutations in Caenorhabditis elegans Argonaute alg-1

    Duan, Ye; Li, Li; Panzade, Ganesh Prabhakar; Piton, Amélie; Zinovyeva, Anna; Ambros, Victor R. (2024-02-27)
    MicroRNAs (miRNA) associate with Argonaute (AGO) proteins and repress gene expression by base pairing to sequences in the 3' untranslated regions of target genes. De novo coding variants in the human AGO genes AGO1 and AGO2 cause neurodevelopmental disorders (NDD) with intellectual disability, referred to as Argonaute syndromes. Most of the altered amino acids are conserved between the miRNA-associated AGO in Homo sapiens and Caenorhabditis elegans, suggesting that the human mutations could disrupt conserved functions in miRNA biogenesis or activity. We genetically modeled four human AGO1 mutations in C. elegans by introducing identical mutations into the C. elegans AGO1 homologous gene, alg-1. These alg-1 NDD mutations cause phenotypes in C. elegans indicative of disrupted miRNA processing, miRISC (miRNA silencing complex) formation, and/or target repression. We show that the alg-1 NDD mutations are antimorphic, causing developmental and molecular phenotypes stronger than those of alg-1 null mutants, likely by sequestrating functional miRISC components into non-functional complexes. The alg-1 NDD mutations cause allele-specific disruptions in mature miRNA profiles, accompanied by perturbation of downstream gene expression, including altered translational efficiency and/or messenger RNA abundance. The perturbed genes include those with human orthologs whose dysfunction is associated with NDD. These cross-clade genetic studies illuminate fundamental AGO functions and provide insights into the conservation of miRNA-mediated post-transcriptional regulatory mechanisms.
  • Acceptance of digital phenotyping linked to a digital pill system to measure PrEP adherence among men who have sex with men with substance use

    Albrechta, Hannah; Goodman, Georgia R; Oginni, Elizabeth; Mohamed, Yassir; Venkatasubramanian, Krishna; Dumas, Arlen; Carreiro, Stephanie; Lee, Jasper S; Glynn, Tiffany R; O'Cleirigh, Conall; et al. (2024-02-22)
    Once-daily oral HIV pre-exposure prophylaxis (PrEP) is an effective strategy to prevent HIV, but is highly dependent on adherence. Men who have sex with men (MSM) who use substances face unique challenges maintaining PrEP adherence. Digital pill systems (DPS) allow for real-time adherence measurement through ingestible sensors. Integration of DPS technology with other digital health tools, such as digital phenotyping, may improve understanding of nonadherence triggers and development of personalized adherence interventions based on ingestion behavior. This study explored the willingness of MSM with substance use to share digital phenotypic data and interact with ancillary systems in the context of DPS-measured PrEP adherence. Adult MSM on PrEP with substance use were recruited through a social networking app. Participants were introduced to DPS technology and completed an assessment to measure willingness to participate in DPS-based PrEP adherence research, contribute digital phenotyping data, and interact with ancillary systems in the context of DPS-based research. Medical mistrust, daily worry about PrEP adherence, and substance use were also assessed. Participants who identified as cisgender male and were willing to participate in DPS-based research (N = 131) were included in this subsample analysis. Most were White (76.3%) and non-Hispanic (77.9%). Participants who reported daily PrEP adherence worry had 3.7 times greater odds (95% CI: 1.03, 13.4) of willingness to share biometric data via a wearable device paired to the DPS. Participants with daily PrEP adherence worry were more likely to be willing to share smartphone data (p = 0.006) and receive text messages surrounding their daily activities (p = 0.003), compared to those with less worry. MSM with substance use disorder, who worried about PrEP adherence, were willing to use DPS technology and share data required for digital phenotyping in the context of PrEP adherence measurement. Efforts to address medical mistrust can increase advantages of this technology for HIV prevention.
  • Persistent False Positive Covid-19 Rapid Antigen Tests

    Herbert, Carly; McManus, David D; Soni, Apurv (2024-02-22)
    Rapid antigen tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are effective tools for the diagnosis of acute infection, particularly when used serially. The percentage of rapid antigen tests with false positive results is reported to be less than 1%. However, we have observed persons who repeatedly test positive with rapid antigen tests despite concurrent negative molecular tests; this infrequent phenomenon occurs predominantly among women and persons with autoimmune disorders.
  • Tunable DNMT1 degradation reveals DNMT1/DNMT3B synergy in DNA methylation and genome organization

    Scelfo, Andrea; Barra, Viviana; Abdennur, Nezar; Spracklin, George; Busato, Florence; Salinas-Luypaert, Catalina; Bonaiti, Elena; Velasco, Guillaume; Bonhomme, Frédéric; Chipont, Anna; et al. (2024-02-20)
    DNA methylation (DNAme) is a key epigenetic mark that regulates critical biological processes maintaining overall genome stability. Given its pleiotropic function, studies of DNAme dynamics are crucial, but currently available tools to interfere with DNAme have limitations and major cytotoxic side effects. Here, we present cell models that allow inducible and reversible DNAme modulation through DNMT1 depletion. By dynamically assessing whole genome and locus-specific effects of induced passive demethylation through cell divisions, we reveal a cooperative activity between DNMT1 and DNMT3B, but not of DNMT3A, to maintain and control DNAme. We show that gradual loss of DNAme is accompanied by progressive and reversible changes in heterochromatin, compartmentalization, and peripheral localization. DNA methylation loss coincides with a gradual reduction of cell fitness due to G1 arrest, with minor levels of mitotic failure. Altogether, this system allows DNMTs and DNA methylation studies with fine temporal resolution, which may help to reveal the etiologic link between DNAme dysfunction and human disease.
  • Domain-inlaid Nme2Cas9 adenine base editors with improved activity and targeting scope

    Bamidele, Nathan; Zhang, Han; Dong, Xiaolong; Cheng, Haoyang; Gaston, Nicholas; Feinzig, Hailey; Cao, Hanbing; Kelly, Karen; Watts, Jonathan K; Xie, Jun; et al. (2024-02-17)
    Nme2Cas9 has been established as a genome editing platform with compact size, high accuracy, and broad targeting range, including single-AAV-deliverable adenine base editors. Here, we engineer Nme2Cas9 to further increase the activity and targeting scope of compact Nme2Cas9 base editors. We first use domain insertion to position the deaminase domain nearer the displaced DNA strand in the target-bound complex. These domain-inlaid Nme2Cas9 variants exhibit shifted editing windows and increased activity in comparison to the N-terminally fused Nme2-ABE. We next expand the editing scope by swapping the Nme2Cas9 PAM-interacting domain with that of SmuCas9, which we had previously defined as recognizing a single-cytidine PAM. We then use these enhancements to introduce therapeutically relevant edits in a variety of cell types. Finally, we validate domain-inlaid Nme2-ABEs for single-AAV delivery in vivo.
  • Genome-wide kinetic profiling of pre-mRNA 3' end cleavage

    Torres-Ulloa, Leslie; Calvo-Roitberg, Ezequiel; Pai, Athma A (2024-02-16)
    Cleavage and polyadenylation is necessary for the formation of mature mRNA molecules. The rate at which this process occurs can determine the temporal availability of mRNA for subsequent function throughout the cell and is likely tightly regulated. Despite advances in high-throughput approaches for global kinetic profiling of RNA maturation, genome-wide 3' end cleavage rates have never been measured. Here, we describe a novel approach to estimate the rates of cleavage, using metabolic labeling of nascent RNA, high-throughput sequencing, and mathematical modeling. Using in silico simulations of nascent RNA-seq data, we show that our approach can accurately and precisely estimate cleavage half-lives for both constitutive and alternative sites. We find that 3' end cleavage is fast on average, with half-lives under a minute, but highly variable across individual sites. Rapid cleavage is promoted by the presence of canonical sequence elements and an increased density of polyadenylation signals near a cleavage site. Finally, we find that cleavage rates are associated with the localization of RNA polymerase II at the end of a gene, and faster cleavage leads to quicker degradation of downstream readthrough RNA. Our findings shed light on the features important for efficient 3' end cleavage and the regulation of transcription termination.
  • Contactless Monitoring System Versus Gold Standard for Respiratory Rate Monitoring in Emergency Department Patients: Pilot Comparison Study

    Goldfine, Charlotte E; Oshim, Md Farhan Tasnim; Chapman, Brittany P; Ganesan, Deepak; Rahman, Tauhidur; Carreiro, Stephanie (2024-02-16)
    Background: Respiratory rate is a crucial indicator of disease severity yet is the most neglected vital sign. Subtle changes in respiratory rate may be the first sign of clinical deterioration in a variety of disease states. Current methods of respiratory rate monitoring are labor-intensive and sensitive to motion artifacts, which often leads to inaccurate readings or underreporting; therefore, new methods of respiratory monitoring are needed. The PulsON 440 (P440; TSDR Ultra Wideband Radios and Radars) radar module is a contactless sensor that uses an ultrawideband impulse radar to detect respiratory rate. It has previously demonstrated accuracy in a laboratory setting and may be a useful alternative for contactless respiratory monitoring in clinical settings; however, it has not yet been validated in a clinical setting. Objective: The goal of this study was to (1) compare the P440 radar module to gold standard manual respiratory rate monitoring and standard of care telemetry respiratory monitoring through transthoracic impedance plethysmography and (2) compare the P440 radar to gold standard measurements of respiratory rate in subgroups based on sex and disease state. Methods: This was a pilot study of adults aged 18 years or older being monitored in the emergency department. Participants were monitored with the P440 radar module for 2 hours and had gold standard (manual respiratory counting) and standard of care (telemetry) respiratory rates recorded at 15-minute intervals during that time. Respiratory rates between the P440, gold standard, and standard telemetry were compared using Bland-Altman plots and intraclass correlation coefficients. Results: A total of 14 participants were enrolled in the study. The P440 and gold standard Bland-Altman analysis showed a bias of -0.76 (-11.16 to 9.65) and an intraclass correlation coefficient of 0.38 (95% CI 0.06-0.60). The P440 and gold standard had the best agreement at normal physiologic respiratory rates. There was no change in agreement between the P440 and the gold standard when grouped by admitting diagnosis or sex. Conclusions: Although the P440 did not have statistically significant agreement with gold standard respiratory rate monitoring, it did show a trend of increased agreement in the normal physiologic range, overestimating at low respiratory rates, and underestimating at high respiratory rates. This trend is important for adjusting future models to be able to accurately detect respiratory rates. Once validated, the contactless respiratory monitor provides a unique solution for monitoring patients in a variety of settings.
  • Harmonizing the Generation and Pre-publication Stewardship of FAIR Image data [preprint]

    Bialy, Nikki; Alber, Frank; Andrews, Brenda; Angelo, Michael; Beliveau, Brian; Bintu, Lacramioara; Boettiger, Alistair; Boehm, Ulrike; Brown, Claire M; Maina, Mahmoud Bukar; et al. (2024-02-08)
    Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health. For this potential to be realized, quality-assured image data must be shared among labs at a global scale to be compared, pooled, and reanalyzed, thus unleashing untold potential beyond the original purpose for which the data was generated. There are two broad sets of requirements to enable image data sharing in the life sciences. One set of requirements is articulated in the companion White Paper entitled "Enabling Global Image Data Sharing in the Life Sciences," which is published in parallel and addresses the need to build the cyberinfrastructure for sharing the digital array data (arXiv:2401.13023 [q-bio.OT], https://doi.org/10.48550/arXiv.2401.13023). In this White Paper, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse image data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made considerable progress toward generating community standard practices for imaging Quality Control (QC) and metadata. We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges, and democratize access to common practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.
  • Bigtools: a high-performance BigWig and BigBed library in Rust [preprint]

    Huey, Jack; Abdennur, Nezar (2024-02-08)
    The BigWig and BigBed file formats were originally designed for the visualization of next-generation sequencing data through a genome browser. Due to their versatility, these formats have long since become ubiquitous for the storage of processed sequencing data and regularly serve as the basis for downstream data analysis. As the number and size of sequencing experiments continues to accelerate, there is an increasing demand to efficiently generate and query BigWig and BigBed files in a scalable and robust manner, and to efficiently integrate these functionalities into data analysis environments and third-party applications. Here, we present Bigtools, a feature-complete, high-performance, and integrable software library for generating and querying both BigWig and BigBed files. Bigtools is written in the Rust programming language and includes a flexible suite of command line tools as well as bindings to Python. Bigtools is cross-platform and released under the MIT license. It is distributed on Crates.io and the Python Package Index, and the source code is available at https://github.com/jackh726/bigtools.
  • Genome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever

    Kotliar, Dylan; Raju, Siddharth; Tabrizi, Shervin; Odia, Ikponmwosa; Goba, Augustine; Momoh, Mambu; Sandi, John Demby; Nair, Parvathy; Phelan, Eric; Tariyal, Ridhi; et al. (2024-02-07)
    Infection with Lassa virus (LASV) can cause Lassa fever, a haemorrhagic illness with an estimated fatality rate of 29.7%, but causes no or mild symptoms in many individuals. Here, to investigate whether human genetic variation underlies the heterogeneity of LASV infection, we carried out genome-wide association studies (GWAS) as well as seroprevalence surveys, human leukocyte antigen typing and high-throughput variant functional characterization assays. We analysed Lassa fever susceptibility and fatal outcomes in 533 cases of Lassa fever and 1,986 population controls recruited over a 7 year period in Nigeria and Sierra Leone. We detected genome-wide significant variant associations with Lassa fever fatal outcomes near GRM7 and LIF in the Nigerian cohort. We also show that a haplotype bearing signatures of positive selection and overlapping LARGE1, a required LASV entry factor, is associated with decreased risk of Lassa fever in the Nigerian cohort but not in the Sierra Leone cohort. Overall, we identified variants and genes that may impact the risk of severe Lassa fever, demonstrating how GWAS can provide insight into viral pathogenesis.
  • Bioframe: operations on genomic intervals in Pandas dataframes

    Abdennur, Nezar; Fudenberg, Geoffrey; Flyamer, Ilya M; Galitsyna, Aleksandra A; Goloborodko, Anton; Imakaev, Maxim; Venev, Sergey (2024-02-01)
    Motivation: Genomic intervals are one of the most prevalent data structures in computational genome biology, and used to represent features ranging from genes, to DNA binding sites, to disease variants. Operations on genomic intervals provide a language for asking questions about relationships between features. While there are excellent interval arithmetic tools for the command line, they are not smoothly integrated into Python, one of the most popular general-purpose computational and visualization environments. Results: Bioframe is a library to enable flexible and performant operations on genomic interval dataframes in Python. Bioframe extends the Python data science stack to use cases for computational genome biology by building directly on top of two of the most commonly-used Python libraries, NumPy and Pandas. The bioframe API enables flexible name and column orders, and decouples operations from data formats to avoid unnecessary conversions, a common scourge for bioinformaticians. Bioframe achieves these goals while maintaining high performance and a rich set of features. Availability and implementation: Bioframe is open-source under MIT license, cross-platform, and can be installed from the Python Package Index. The source code is maintained by Open2C on GitHub at https://github.com/open2c/bioframe.
  • Microbiota encoded fatty-acid metabolism expands tuft cells to protect tissues homeostasis during infection in the large intestine [preprint]

    Kellogg, Tasia D; Ceglia, Simona; Mortzfeld, Benedikt M; Zeamer, Abigail L; Foley, Sage E; Ward, Doyle V; Bhattarai, Shakti K; McCormick, Beth A; Reboldi, Andrea; Bucci, Vanni (2024-01-31)
    Metabolic byproducts of the intestinal microbiota are crucial in maintaining host immune tone and shaping inter-species ecological dynamics. Among these metabolites, succinate is a driver of tuft cell (TC) differentiation and consequent type 2 immunity-dependent protection against invading parasites in the small intestine. Succinate is also a growth enhancer of the nosocomial pathogen Clostridioides difficile in the large intestine. To date, no research has shown the role of succinate in modulating TC dynamics in the large intestine, or the relevance of this immune pathway to C. difficile pathophysiology. Here we reveal the existence of a three-way circuit between commensal microbes, C. difficile and host epithelial cells which centers around succinate. Through selective microbiota depletion experiments we demonstrate higher levels of type 2 cytokines leading to expansion of TCs in the colon. We then demonstrate the causal role of the microbiome in modulating colonic TC abundance and subsequent type 2 cytokine induction using rational supplementation experiments with fecal transplants and microbial consortia of succinate-producing bacteria. We show that administration of a succinate-deficient Bacteroides thetaiotaomicron knockout (Δfrd) significantly reduces the enhanced type 2 immunity in mono-colonized mice. Finally, we demonstrate that mice prophylactically administered with the consortium of succinate-producing bacteria show reduced C. difficile-induced morbidity and mortality compared to mice administered with heat-killed bacteria or the vehicle. This effect is reduced in a partial tuft cell knockout mouse, Pou2f3+/-, and nullified in the tuft cell knockout mouse, Pou2f3-/-, confirming that the observed protection occurs via the TC pathway. Succinate is an intermediary metabolite of the production of short-chain fatty acids, and its concentration often increases during dysbiosis. The first barrier to enteric pathogens alike is the intestinal epithelial barrier, and host maintenance and strengthening of barrier integrity is vital to homeostasis. Considering our data, we propose that activation of TC by the microbiota-produced succinate in the colon is a mechanism evolved by the host to counterbalance microbiome-derived cues that facilitate invasion by intestinal pathogens.
  • Association of spatial proximity to fixed-site syringe services programs with HCV serostatus and injection equipment sharing practices among people who inject drugs in rural New England, United States

    Romo, Eric; Stopka, Thomas J; Jesdale, Bill M; Wang, Bo; Mazor, Kathleen M; Friedmann, Peter D (2024-01-28)
    Background: Hepatitis C virus (HCV) disproportionately affects rural communities, where health services are geographically dispersed. It remains unknown whether proximity to a syringe services program (SSP) is associated with HCV infection among rural people who inject drugs (PWID). Methods: Data are from a cross-sectional sample of adults who reported injecting drugs in the past 30 days recruited from rural counties in New Hampshire, Vermont, and Massachusetts (2018-2019). We calculated the road network distance between each participant's address and the nearest fixed-site SSP, categorized as ≤ 1 mile, 1-3 miles, 3-10 miles, and > 10 miles. Staff performed HCV antibody tests and a survey assessed past 30-day injection equipment sharing practices: borrowing used syringes, borrowing other used injection equipment, and backloading. Mixed effects modified Poisson regression estimated prevalence ratios (aPR) and 95% confidence intervals (95% CI). Analyses were also stratified by means of transportation. Results: Among 330 PWID, 25% lived ≤ 1 mile of the nearest SSP, 17% lived 1-3 miles of an SSP, 12% lived 3-10 miles of an SSP, and 46% lived > 10 miles from an SSP. In multivariable models, compared to PWID who lived within 1 mile of an SSP, those who lived 3 to 10 miles away had a higher prevalence of HCV seropositivity (aPR: 1.25, 95% CI 1.06-1.46), borrowing other used injection equipment (aPR: 1.23, 95% CI 1.04-1.46), and backloading (aPR: 1.48, 95% CI 1.17-1.88). Similar results were observed for PWID living > 10 miles from an SSP: aPR [HCV]: 1.19, 95% CI 1.01-1.40; aPR [borrowing other used equipment]:1.45, 95% CI 1.29-1.63; and aPR [backloading]: 1.59, 95% CI 1.13-2.24. Associations between living 1 to 3 miles of an SSP and each outcome did not reach statistical significance. When stratified by means of transportation, associations between distance to SSP and each outcome (except borrowing other used injection equipment) were only observed among PWID who traveled by other means (versus traveled by automobile). Conclusions: Among PWID in rural New England, living farther from a fixed-site SSP was associated with a higher prevalence of HCV seropositivity, borrowing other used injection equipment, and backloading, reinforcing the need to increase SSP accessibility in rural areas. Means of transportation may modify this relationship.
  • Trauma and psychosocial adversity in youth with autism spectrum disorder and intellectual disability

    Palmer, Sarah J; Dvir, Yael (2024-01-26)
    Traumatic experiences contribute significantly to behavioral and mood dysregulation syndromes presenting for treatment to behavioral health settings. Individuals with Autism Spectrum Disorder (ASD), Intellectual Disability (ID) and developmental delay experience traumatic events more frequently than their typically developing peers. However, measures used to identify trauma related disorders and treatment thereof are based on typically developing individuals. Regardless of the baseline characteristics of individuals who experience trauma, trauma exposure is the result of multiple interdependent environmental, social, and familial characteristics. We used the "ecological systems analysis approach" to structure our review of the impact of trauma on those with ASD and ID. In addition, the COVID-19 pandemic which exposed the global population to a collective trauma, has also catalyzed investigations into the challenges faced by members of society most dependent on social services. Children with ASD and ID were among those vulnerable individuals, and the COVID-19 pandemic has allowed researchers to better understand the impact of a collective trauma on those individuals. It is imperative that we understand current research and recommendations for identifying and treating trauma-related disorders in individuals with developmental disorders to best inform clinical practice and directions for future research in this area.
  • Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing

    Levine, Zoë C; Sene, Aita; Mkandawire, Winnie; Deme, Awa B; Ndiaye, Tolla; Sy, Mouhamad; Gaye, Amy; Diedhiou, Younouss; Mbaye, Amadou M; Ndiaye, Ibrahima M; et al. (2024-01-25)
    The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata in a cross-sectional study of febrile patients and healthy controls in a low malaria burden area. Using 16S and untargeted sequencing, we detected viral, bacterial, or eukaryotic pathogens in 23% (38/163) of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15.5% and 3.8% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model that can distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs (F1 score: 0.823). These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.
  • Effect of Paxlovid Treatment on Long COVID Onset: An EHR-Based Target Trial Emulation from N3C [preprint]

    Preiss, Alexander; Bhatia, Abhishek; Zang, Chengxi; Aragon, Leyna V; Baratta, John M; Baskaran, Monika; Blancero, Frank; Brannock, M Daniel; Chew, Robert F; Díaz, Iván; et al. (2024-01-22)
    Preventing and treating post-acute sequelae of SARS-CoV-2 infection (PASC), commonly known as Long COVID, has become a public health priority. In this study, we examined whether treatment with Paxlovid in the acute phase of COVID-19 helps prevent the onset of PASC. We used electronic health records from the National Covid Cohort Collaborative (N3C) to define a cohort of 426,461 patients who had COVID-19 since April 1, 2022, and were eligible for Paxlovid treatment due to risk for progression to severe COVID-19. We used the target trial emulation (TTE) framework to estimate the effect of Paxlovid treatment on PASC incidence. Our primary outcome measure was a PASC computable phenotype. Secondary outcomes were the onset of novel cognitive, fatigue, and respiratory symptoms in the post-acute period. Paxlovid treatment did not have a significant effect on overall PASC incidence (relative risk [RR] = 0.99, 95% confidence interval [CI] 0.96-1.01). However, its effect varied across the cognitive (RR = 0.85, 95% CI 0.79-0.90), fatigue (RR = 0.93, 95% CI 0.89-0.96), and respiratory (RR = 0.99, 95% CI 0.95-1.02) symptom clusters, suggesting that Paxlovid treatment may help prevent post-acute cognitive and fatigue symptoms more than others.
  • Comparative effectiveness of abatacept versus TNF inhibitors in rheumatoid arthritis patients who are ACPA and shared epitope positive

    Harrold, Leslie R; Wittstock, Keith; Kelly, Sheila; Han, Xue; Zhuo, Joe; Schrader, Amy; Middaugh, Nicole; Moore, Page C; Khaychuk, Vadim (2024-01-19)
    Background: The HLA-DRB1 shared epitope (SE) is a risk factor for the development of rheumatoid arthritis (RA) and the production of anti-citrullinated protein antibodies (ACPAs) in RA patients. Our objective was to examine the real-world effectiveness of abatacept versus tumor necrosis factor inhibitors (TNFi) in patients with RA who were SE and anti-cyclic citrullinated peptide antibody (anti-CCP3) positive. Methods: Abatacept or TNFi initiators who were SE + and anti-CCP3+ (> 20 U/mL) at or prior to treatment and had moderate or high CDAI score (> 10) at initiation were identified. The primary outcome was mean change in CDAI score over six months. Analyses were conducted in propensity score (PS)-trimmed and -matched populations overall and a biologic-experienced subgroup. Mixed-effects models were used. Results: In the overall PS-trimmed (abatacept, n = 170; TNFi, n = 157) and PS-matched cohorts (abatacept, n = 111; TNFi, n = 111), there were numerically greater improvements in mean change in CDAI between abatacept and TNFi but were not statistically significant. Similar trends were seen for biologic-experienced patients, except that statistical significance was reached for mean change in CDAI in the PS-trimmed cohort (abatacept, 12.22 [95% confidence interval (95%CI) 10.13 to 14.31]; TNFi, 9.28 [95%CI 7.08 to 11.48]; p = 0.045). Conclusion: In this real world cohort, there were numerical improvements in efficacy outcomes with abatacept over TNFi in patients with RA who were SE + and ACPA+, similar to results from a clinical trial population The only statistically significant finding after adjusting for covariates was greater improvement in CDAI with abatacept versus TNFi in the bio-experienced PS-trimmed cohort..

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