Rapid onset of hypercalcemia from high-grade lymphoma in the setting of HIV-related immune reconstitution inflammatory syndrome.

Hypercalcemia in HIV patients has been previously reported, but 1,25-(OH)2 vitamin D-mediated hypercalcemia, due to increased activity of extrarenal 1-alpha hydroxylase, is rarely described with HIV-related infections or malignancies. We describe a case of 1,25-(OH)2 vitamin D-mediated hypercalcemia in a patient presenting with progressive cognitive decline and weakness. Initial evaluation revealed a new diagnosis of HIV, for which he was started on antiretroviral therapy (ART). He was also noted to have mild asymptomatic hypocalcemia, likely from his acute illness and malnutrition, which was not further investigated at the time. While the patient's mental status initially improved with ART, he became progressively delirious and was found to be hypercalcemic approximately 4 weeks after the initiation of ART. Possible etiologies for hypercalcemia were vigorously evaluated, including granulomatous disease, infection, and malignancy, in the setting of suspected immune reconstitution inflammatory syndrome (IRIS), due to recent initiation of ART. Infectious workup was unrevealing, but computed tomography (CT) of the chest, abdomen, and pelvis revealed new extensive diffuse lymphadenopathy and hepatomegaly, not present on admission studies. Cytology and flow cytometry of a liver biopsy specimen revealed CD10 positive high-grade B-cell lymphoma. Chemotherapy was not pursued due to poor performance status. Over the next week, spontaneous tumor lysis developed, and the patient expired. Postmortem, his 1,25-(OH)2 vitamin D level returned as markedly elevated. Immunohistochemical staining of his liver biopsy tissue showed strong expression of CYP27B1. 1,25-(OH)2 vitamin D-mediated hypercalcemia is uncommon in a patient with newly diagnosed HIV and, in this case, was likely due to IRIS unmasking an underlying high-grade lymphoma and restoration of immune function (including T-cells and cytokine production). This case emphasizes the importance of including aggressive lymphomas, capable of progressing over days to weeks, in the evaluation of hypercalcemia in HIV patients at risk for developing IRIS and the rapid dynamic changes in mineral homeostasis that can occur with such an aggressive tumor in an immunocompromised host

Infectious Mimicry Complicates Diagnosis in Hemophagocytic Syndrome Caused by Anaplastic Large-Cell Lymphoma

Hemophagocytic syndrome (HPS) arises secondary to genetic, rheumatologic, neoplastic, and infectious causes. We discuss a patient whose presentation was consistent with systemic infection but was discovered to have HPS of unknown etiology. The presenting symptoms, as well as unremarkable malignancy and rheumatologic workups, led to the pursuit of an infectious cause, but the patient was ultimately discovered to have an occult anaplastic large-cell lymphoma (ALCL). This case demonstrates the diagnostic challenges that result from infectious mimicry in the context of HPS—first, in distinguishing noninfectious HPS from the systemic inflammation that can result from a widespread infectious process, second, in the identification of the precipitating cause of HPS. While evidence of these challenges has been suggested by the limited literature on HPS and ALCL, our case illustrates the diagnostic dilemma that arises when tissue biopsy does not quickly reveal an etiology. It is important that all physicians be aware that HPS can mimic infection and be prepared to redirect the workup when an infectious etiology for HPS cannot be identified

Bidirectional Exchanges of Medical Students Between Institutional Partners in Global Health Clinical Education Programs: Putting Ethical Principles into Practice

BackgroundOne-third of US medical students participate in global health (GH) education, and approximately one-quarter of US medical schools have structured programs that offer special recognition in GH. GH clinical electives (GHCEs) are opportunities for students to experience a medical system and culture different from their own. GHCEs are administered through institutional affiliation agreements, often between an institution in a high-income country (HIC) and one in a low- or middle-income country (LMIC). Although these agreements suggest the exchange of students in both directions, GHCEs are traditionally characterized by students from HICs traveling to LMICs.ObjectivesThe goal of this study was to investigate the availability of opportunities for students from LMICs participating in GHCEs at partner institutions in HICs and to describe the costs of these opportunities for students from LMICs.MethodsWe conducted a web-based search of 30 US institutions previously identified as having structured programs in GH. We determined which of these schools have programs that accept medical students from international schools for GHCEs, as well as the administrative requirements, types of fees, and other costs to the international student based on information available on the web. Descriptive statistics were employed for the quantitative analysis of costs.FindingsWe found that, although the majority of US institutions with structured GH programs sending students to sites abroad accept international students at their sites in the United States, nearly one-fifth of programs do not offer such opportunities for bidirectional exchange. We also characterized the substantial costs of such experiences, because this can represent a significant barrier for students from LMICs.ConclusionsAccess to GHCEs in US partner institutions should be an important underlying ethical principle in the establishment of institutional partnerships. The opportunities available to and experiences of students from LMIC partner institutions are important areas for future GH education research

Comparative Analysis of Tandem Repeats from Hundreds of Species Reveals Unique Insights into Centromere Evolution

Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. The assumption that the most abundant tandem repeat is the centromere DNA was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and in length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond ~50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution, including the appearance of higher order repeat structures in which several polymorphic monomers make up a larger repeating unit. While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animals and plants. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes

Characterizing Symptoms and Identifying Biomarkers of Long COVID in People With and Without HIV: Protocol for a Remotely Conducted Prospective Observational Cohort Study

Background: Living with HIV is a risk factor for severe acute COVID-19, but it is unknown whether it is a risk factor for long COVID./ Objective: This study aims to characterize symptoms, sequelae, and cognition formally and prospectively 12 months following SARS-CoV-2 infection in people living with HIV compared with people without HIV. People with no history of SARS-CoV-2 infection, both with and without HIV, are enrolled as controls. The study also aims to identify blood-based biomarkers or patterns of immune dysregulation associated with long COVID./ Methods: This prospective observational cohort study enrolled participants into 1 of the following 4 study arms: people living with HIV who had SARS-CoV-2 infection for the first time <4 weeks before enrollment (HIV+COVID+ arm), people without HIV who had SARS-CoV-2 infection for the first time within 4 weeks of enrollment (HIV−COVID+ arm), people living with HIV who believed they never had SARS-CoV-2 infection (HIV+COVID− arm), and people without HIV who believed they never had SARS-CoV-2 infection (HIV−COVID− arm). At enrollment, participants in the COVID+ arms recalled their symptoms, mental health status, and quality of life in the month before having SARS-CoV-2 infection via a comprehensive survey administered by telephone or on the web. All participants completed the same comprehensive survey 1, 2, 4, 6, and 12 months after post–acute COVID-19 symptom onset or diagnosis, if asymptomatic, (COVID+ arms) or after enrollment (COVID− arms) on the web or by telephone. In total, 11 cognitive assessments were administered by telephone at 1 and 4 months after symptom onset (COVID+ arms) or after enrollment (COVID− arms). A mobile phlebotomist met the participants at a location of their choice for height and weight measurements, orthostatic vital signs, and a blood draw. Participants in the COVID+ arms donated blood 1 and 4 months after COVID-19, and participants in the COVID− arms donated blood once or none. Blood was then shipped overnight to the receiving study laboratory, processed, and stored./ Results: This project was funded in early 2021, and recruitment began in June 2021. Data analyses will be completed by summer 2023. As of February 2023, a total of 387 participants were enrolled in this study, with 345 participants having completed enrollment or baseline surveys together with at least one other completed study event. The 345 participants includes 76 (22%) HIV+COVID+, 121 (35.1%) HIV−COVID+, 78 (22.6%) HIV+COVID−, and 70 (20.3%) HIV−COVID− participants./ Conclusions: This study will provide longitudinal data to characterize COVID-19 recovery over 12 months in people living with and without HIV. Additionally, this study will determine whether biomarkers or patterns of immune dsyregulation associate with decreased cognitive function or symptoms of long COVID

The impact of acute nutritional interventions on the plasma proteome

Context: Humans respond profoundly to changes in diet, while nutrition and environment have a great impact on population health. It is therefore important to deeply characterize the human nutritional responses. Objective: Endocrine parameters and the metabolome of human plasma are rapidly responding to acute nutritional interventions such as caloric restriction or a glucose challenge. It is less well understood whether the plasma proteome would be equally dynamic, and whether it could be a source of corresponding biomarkers. Methods: We used high-throughput mass spectrometry to determine changes in the plasma proteome of i) 10 healthy, young, male individuals in response to 2 days of acute caloric restriction followed by refeeding; ii) 200 individuals of the Ely epidemiological study before and after a glucose tolerance test at 4 time points (0, 30, 60, 120 minutes); and iii) 200 random individuals from the Generation Scotland study. We compared the proteomic changes detected with metabolome data and endocrine parameters. Results: Both caloric restriction and the glucose challenge substantially impacted the plasma proteome. Proteins responded across individuals or in an individual-specific manner. We identified nutrient-responsive plasma proteins that correlate with changes in the metabolome, as well as with endocrine parameters. In particular, our study highlights the role of apolipoprotein C1 (APOC1), a small, understudied apolipoprotein that was affected by caloric restriction and dominated the response to glucose consumption and differed in abundance between individuals with and without type 2 diabetes. Conclusion: Our study identifies APOC1 as a dominant nutritional responder in humans and highlights the interdependency of acute nutritional response proteins and the endocrine system

Signatures of immune selection in intact and defective proviruses distinguish HIV-1 elite controllers

Increasing evidence suggests that durable drug-free control of HIV-1 replication is enabled by effective cellular immune responses that may induce an attenuated viral reservoir configuration with a weaker ability to drive viral rebound. Here, we comprehensively tracked effects of antiviral immune responses on intact and defective proviral sequences from elite controllers (ECs), analyzing both classical escape mutations and HIV-1 chromosomal integration sites as biomarkers of antiviral immune selection pressure. We observed that, within ECs, defective proviruses were commonly located in permissive genic euchromatin positions, which represented an apparent contrast to autologous intact proviruses that were frequently located in heterochromatin regions; this suggests differential immune selection pressure on intact versus defective proviruses in ECs. In comparison to individuals receiving antiretroviral therapy, intact and defective proviruses from ECs showed reduced frequencies of escape mutations in cytotoxic T cell epitopes and antibody contact regions, possibly due to the small and poorly inducible reservoir that may be insufficient to drive effective viral escape in ECs. About 15% of ECs harbored nef deletions in intact proviruses, consistent with increased viral vulnerability to host immunity in the setting of nef dysfunction. Together, these results suggest a distinct signature of immune footprints in proviral sequences from ECs.This work is supported by NIH grants HL134539 (to X.G.Y.), AI155171 (to X.G.Y.), AI116228 (to X.G.Y.), AI078799 (to X.G.Y.), DA047034 (to X.G.Y.), AI150396 (to X.G.Y.), the Bill and Melinda Gates Foundation (INV-002703) (to X.G.Y.), AI114235 (to M.L.), AI117841 (to M.L.), AI120008 (to M.L.), AI130005 (to M.L.), DK120387 (to M.L.), AI152979 (to M.L.), AI135940 (to M.L.), AI155233 (to M.L.), and the American Foundation for AIDS Research (amfAR#110181) (to M.L.). X.G.Y. and M.L. are members of the DARE Collaboratory (UM1AI126611) and the BEAT-HIV Martin Delaney Collaboratory (UM1 AI126620). E.R.-M. was supported by Consejo Superior de Investigaciones Científicas (CSIC) and by grant PI19/01127, Instituto de Salud Carlos III, Fondos FEDER, and Consejeria de Transformacion Economica, Industria, Conocimiento y Universidades Junta de Andalucia (P20_01276). Support was also provided by the Harvard University and University of California at San Francisco (UCSF)/Gladstone Institute for HIV Cure Research Centers for AIDS Research (P30 AI060354 and P30 AI027763, respectively), which are supported by the following institutes and centers co-funded by and participating with the U.S. National Institutes of Health: NIAID, NCI, NICHD, NHLBI, NIDA, NIMH, NIA, FIC, and OAR. Additional support for the SCOPE cohort was provided by the Delaney AIDS Research Enterprise (DARE; AI096109 and A127966) and the amfAR Institute for HIV Cure Research (amfAR 109301). The International HIV Controller Cohort is supported by the Bill and Melinda Gates Foundation (OPP1066973), the Ragon Institute of MGH, MIT and Harvard, the NIH (R37 AI067073 to B.D.W.), and the Mark and Lisa Schwartz Family Foundation. This project has been funded in whole or in part with federal funds from the Frederick National Laboratory for Cancer Research, under contract no. HHSN261200800001E. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. government. This research was supported in part by the Intramural Research Program of the NIH, Frederick National Lab, Center for Cancer Research

High-resolution 3D X-ray imaging of intracranial nitinol stents

Introduction To assess an optimized 3D imaging protocol for intracranial nitinol stents in 3D C-arm flat detector imaging. For this purpose, an image quality simulation and an in vitro study was carried out. Methods Nitinol stents of various brands were placed inside an anthropomorphic head phantom, using iodine contrast. Experiments with objects were preceded by image quality and dose simulations. We varied X-ray imaging parameters in a commercially interventional X-ray system to set 3D image quality in the contrast–noise–sharpness space. Beam quality was varied to evaluate contrast of the stents while keeping absorbed dose below recommended values. Two detector formats were used, paired with an appropriate pixel size and X-ray focus size. Zoomed reconstructions were carried out and snapshot images acquired. High contrast spatial resolution was assessed with a CT phantom. Results We found an optimal protocol for imaging intracranial nitinol stents. Contrast resolution was optimized for nickel–titanium-containing stents. A high spatial resolution larger than 2.1 lp/mm allows struts to be visualized. We obtained images of stents of various brands and a representative set of images is shown. Independent of the make, struts can be imaged with virtually continuous strokes. Measured absorbed doses are shown to be lower than 50 mGy Computed Tomography Dose Index (CTDI). Conclusion By balancing the modulation transfer of the imaging components and tuning the high-contrast imaging capabilities, we have shown that thin nitinol stent wires can be reconstructed with high contrast-to-noise ratio and good detail, while keeping radiation doses within recommended values. Experimental results compare well with imaging simulations

Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads

The sequence and assembly of human genomes using long-read sequencing technologies has revolutionized our understanding of structural variation and genome organization. We compared the accuracy, continuity, and gene annotation of genome assemblies generated from either high-fidelity (HiFi) or continuous long-read (CLR) datasets from the same complete hydatidiform mole human genome. We find that the HiFi sequence data assemble an additional 10% of duplicated regions and more accurately represent the structure of tandem repeats, as validated with orthogonal analyses. As a result, an additional 5 Mbp of pericentromeric sequences are recovered in the HiFi assembly, resulting in a 2.5-fold increase in the NG50 within 1 Mbp of the centromere (HiFi 480.6 kbp, CLR 191.5 kbp). Additionally, the HiFi genome assembly was generated in significantly less time with fewer computational resources than the CLR assembly. Although the HiFi assembly has significantly improved continuity and accuracy in many complex regions of the genome, it still falls short of the assembly of centromeric DNA and the largest regions of segmental duplication using existing assemblers. Despite these shortcomings, our results suggest that HiFi may be the most effective standalone technology for de novo assembly of human genomes