Point mutations in Arf1 reveal cooperative effects of the N-terminal extension and myristate for GTPase-activating protein catalytic activity.

The ADP-ribosylation factors (Arfs) constitute a family of small GTPases within the Ras superfamily, with a distinguishing structural feature of a hypervariable N-terminal extension of the G domain modified with myristate. Arf proteins, including Arf1, have roles in membrane trafficking and cytoskeletal dynamics. While screening for Arf1:small molecule co-crystals, we serendipitously solved the crystal structure of the non-myristoylated engineered mutation [L8K]Arf1 in complex with a GDP analogue. Like wild-type (WT) non-myristoylated Arf1•GDP, we observed that [L8K]Arf1 exhibited an N-terminal helix that occludes the hydrophobic cavity that is occupied by the myristoyl group in the GDP-bound state of the native protein. However, the helices were offset from one another due to the L8K mutation, with a significant change in position of the hinge region connecting the N-terminus to the G domain. Hypothesizing that the observed effects on behavior of the N-terminus affects interaction with regulatory proteins, we mutated two hydrophobic residues to examine the role of the N-terminal extension for interaction with guanine nucleotide exchange factors (GEFs) and GTPase Activating Proteins (GAPs. Different than previous studies, all mutations were examined in the context of myristoylated Arf. Mutations had little or no effect on spontaneous or GEF-catalyzed guanine nucleotide exchange but did affect interaction with GAPs. [F13A]myrArf1 was less than 1/2500, 1/1500, and 1/200 efficient as substrate for the GAPs ASAP1, ARAP1 and AGAP1; however, [L8A/F13A]myrArf1 was similar to WT myrArf1. Using molecular dynamics simulations, the effect of the mutations on forming alpha helices adjacent to a membrane surface was examined, yet no differences were detected. The results indicate that lipid modifications of GTPases and consequent anchoring to a membrane influences protein function beyond simple membrane localization. Hypothetical mechanisms are discussed.

Chamber shallowing technique for challenging DMEK cases: Tucking cellulose spears under the speculum to augment posterior pressure.

Some anterior chambers do not readily shallow because of insufficient posterior pressure and/or very deep anterior chamber anatomy, which can make unscrolling descemet membrane endothelial keratoplasty (DMEK) tissue more challenging with an unmodified tap technique. We present a hands-free method for augmenting posterior pressure by temporarily tucking cellulose sponges under the blades of the eyelid speculum. The sponges transfer some of the eyelid speculum's weight onto the bulbar surface posterior to the iris, thereby indenting the sclera and causing the iris diaphragm to bulge further forward. This hands-free technique can transform a potentially challenging DMEK case into a more straightforward one by facilitating both a shallow anterior chamber and a bimanual unscrolling technique. However, it only works in bicameral eyes with a vitreous body (e.g., an eye with penetrating keratoplasty, vitreous syneresis, and axial myopia) and will not work in unicameral eyes after vitrectomy (e.g., an eye with an Anterior Chamber Intraocular Lens (ACIOL)).

A VRC13-like bNAb response is associated with complex escape pathways in HIV-1 envelope.

The rational design of HIV-1 immunogens to trigger the development of broadly neutralizing antibodies (bNAbs) requires understanding the viral evolutionary pathways influencing this process. An acute HIV-1-infected individual exhibiting >50% plasma neutralization breadth developed neutralizing antibody specificities against the CD4-binding site (CD4bs) and V1V2 regions of Env gp120. Comparison of pseudoviruses derived from early and late autologous env sequences demonstrated the development of >2 log resistance to VRC13 but not to other CD4bs-specific bNAbs. Mapping studies indicated that the V3 and CD4-binding loops of Env gp120 contributed significantly to developing resistance to the autologous neutralizing response and that the CD4-binding loop (CD4BL) specifically was responsible for the developing resistance to VRC13. Tracking viral evolution during the development of this cross-neutralizing CD4bs response identified amino acid substitutions arising at only 4 of 11 known VRC13 contact sites (K282, T283, K421, and V471). However, each of these mutations was external to the V3 and CD4BL regions conferring resistance to VRC13 and was transient in nature. Rather, complete resistance to VRC13 was achieved through the cooperative expression of a cluster of single amino acid changes within and immediately adjacent to the CD4BL, including a T359I substitution, exchange of a potential N-linked glycosylation (PNLG) site to residue S362 from N363, and a P369L substitution. Collectively, our data characterize complex HIV-1 env evolution in an individual developing resistance to a VRC13-like neutralizing antibody response and identify novel VRC13-associated escape mutations that may be important to inducing VRC13-like bNAbs for lineage-based immunogens.IMPORTANCEThe pursuit of eliciting broadly neutralizing antibodies (bNAbs) through vaccination and their use as therapeutics remains a significant focus in the effort to eradicate HIV-1. Key to our understanding of this approach is a more extensive understanding of bNAb contact sites and susceptible escape mutations in HIV-1 envelope (env). We identified a broad neutralizer exhibiting VRC13-like responses, a non-germline restricted class of CD4-binding site antibody distinct from the well-studied VRC01-class. Through longitudinal envelope sequencing and Env-pseudotyped neutralization assays, we characterized a complex escape pathway requiring the cooperative evolution of four amino acid changes to confer complete resistance to VRC13. This suggests that VRC13-class bNAbs may be refractory to rapid escape and attractive for therapeutic applications. Furthermore, the identification of longitudinal viral changes concomitant with the development of neutralization breadth may help identify the viral intermediates needed for the maturation of VRC13-like responses and the design of lineage-based immunogens.

Light as a drug: prospective randomized evaluation and comparison of the effect of decreased illumination on visual recovery after cataract surgery.

PURPOSE: To compare the effect of decreased illumination on the rate of postoperative visual recovery, and the incidence of cystoid macular edema (CME) with surgical visualization achieved with a traditional analog operating microscope compared with a 3D digital visualization system. SETTING: Ambulatory surgery center, New York. DESIGN: Prospective, randomized, consecutive, single-surgeon series. METHODS: Patients undergoing routine cataract surgery were randomized into either (1) visualization through the binoculars of a standard operating microscope ("traditional group") or (2) visualization through a 3D digital visualization system affixed to the same operating microscope ("digital group"). Note was made in each case of light intensity used, light exposure time, cumulative dissipated energy (CDE), femtosecond laser use, preoperative medical and ocular conditions, intraoperative and/or postoperative complications, and preoperative and postoperative visual acuities and optical coherence tomography confirmed CME. RESULTS: The study comprised 118 eyes in the traditional group and 96 eyes in the digital group. There were no differences in preoperative visual acuity, light exposure time, CDE, or femtosecond laser use between groups, but the light intensity used in the digital group was significantly less (19.5% ± 0.5%) than in the traditional group (48.6% ± 0.6%; P < .001). Furthermore, the digital group achieved a better decimal postoperative day 1 visual acuity (0.60 ± 0.03) with less rates of CME (2.1%) when compared with that of the traditional group (0.51 ± 0.02, P = .03; and 9.2%, P = .03), respectively. CONCLUSIONS: Visual recovery and CME rates were significantly better in patients who underwent cataract surgery assisted by the 3D digital visualization platform without an increase in complications or surgical time.

A Fair Individualized Polysocial Risk Score for Identifying Increased Social Risk in Type 2 Diabetes.

Background: Racial and ethnic minority groups and individuals facing social disadvantages, which often stem from their social determinants of health (SDoH), bear a disproportionate burden of type 2 diabetes (T2D) and its complications. It is crucial to implement effective social risk management strategies at the point of care. Objective: To develop an electronic health records (EHR)-based machine learning (ML) analytical pipeline to address unmet social needs associated with hospitalization risk in patients with T2D. Methods: We identified real-world patients with T2D from the EHR data from University of Florida (UF) Health Integrated Data Repository (IDR), incorporating both contextual SDoH (e.g., neighborhood deprivation) and individual-level SDoH (e.g., housing instability). The 2015-2020 data were used for training and validation and 2021-2022 data for independent testing. We developed a machine learning analytic pipeline, namely individualized polysocial risk score (iPsRS), to identify high social risk associated with hospitalizations in T2D patients, along with explainable AI (XAI) and fairness optimization. Results: The study cohort included 10,192 real-world patients with T2D, with a mean age of 59 years and 58% female. Of the cohort, 50% were non-Hispanic White, 39% were non-Hispanic Black, 6% were Hispanic, and 5% were other races/ethnicities. Our iPsRS, including both contextual and individual-level SDoH as input factors, achieved a C statistic of 0.72 in predicting 1-year hospitalization after fairness optimization across racial and ethnic groups. The iPsRS showed excellent utility for capturing individuals at high hospitalization risk because of SDoH, that is, the actual 1-year hospitalization rate in the top 5% of iPsRS was 28.1%, ~13 times as high as the bottom decile (2.2% for 1-year hospitalization rate). Conclusion: Our ML pipeline iPsRS can fairly and accurately screen for patients who have increased social risk leading to hospitalization in real word patients with T2D.

Intracanalicular dexamethasone insert for post-corneal crosslinking inflammation and pain: the LINK study.

PURPOSE: To compare the efficacy of an intracanalicular dexamethasone insert with tapered topical steroid over 28 days after corneal cross-linking (CXL). SETTING: Single private practice, outpatient setting. DESIGN: Prospective observational randomized study. METHODS: This prospective randomized study investigated the efficacy of a dexamethasone intracanalicular insert on post-CXL pain and inflammation in progressive keratoconus patients. 20 patients (40 eyes) were enrolled; half were randomized to the dexamethasone intracanalicular insert group; half were prescribed a 28-day topical tapering steroid regimen. All patients were evaluated for pain scores, rate of re-epithelialization, ease of the post-CXL regimen, and need for rescue pain medication after standard bilateral epithelium-off CXL on postoperative day (POD) 1, POD3, and POD4 to 7, as well as postoperative week (POW) 1, POW2, POW3, and POW4. RESULTS: 20 patients (40 eyes) underwent standard-of-care epithelium-off bilateral CXL for progressive keratoconus. 10 patients were randomized to receive prednisolone eyedrops on a tapering schedule after CXL; 10 patients received dexamethasone intracanalicular inserts at the time of CXL. Regardless of the postoperative steroid regimen, there was no significant difference in the rate of re-epithelialization or use of rescue pain medication between groups. There was a nominal, however, statistical difference in pain scores between groups, favoring prednisolone eyedrops. Both groups stated no difficulty in following postoperative regimens. There were no adverse events noted in relation to treatment or the CXL procedure. CONCLUSIONS: Using a dexamethasone insert to alleviate pain and inflammation can be considered as a safe and efficacious part of a post-CXL regimen.

Association Between Weight Reduction and Employees' Healthcare Cost.

OBJECTIVE: The aim of the study is to assess the impact of ≥15% body mass index (BMI) reduction on employees' health expenditures. METHODS: We retrospectively analyzed health risk assessment surveys combined with insurance claims from January 2014 to December 2019. We compared costs of employees with baseline BMI > 30 who reported ≥15% BMI reduction in subsequent health risk assessment reports with employees who lost ≤5% BMI within the same period, matching the two cohorts on demographics and costs. RESULTS: The study cohort of 197 lost an average of 23% of their BMI from baseline. The average age was 44 years with majority females (approximately 80%). Group health insurance payments were similar at baseline; at year 1, the study cohort had a 33% payment reduction compared with 10% reduction in the control group. CONCLUSIONS: A ≥15% BMI reduction was associated with a substantial medical cost savings.

Future of virtual education and telementoring.

PURPOSE OF REVIEW: To summarize recent technological advancements in medical and surgical education and explore what the future of medicine might be as it relates to blockchain technology, the metaverse, and web3. RECENT FINDINGS: Through the use of digitally assisted ophthalmic surgery and high dynamic range 3D cameras, it is now possible to record and live stream 3D video content. Although the 'metaverse' is still in its early stages, there are a variety of proto-metaverse technologies that exist to facilitate user interactions that can mimic the real world through the use of shared digital environments and 3D spatial audio. Advanced blockchain technologies can allow for further development of interoperable virtual worlds where a user has an on-chain identity, credentials, data, assets, and much more that they can carry across platforms seamlessly. SUMMARY: As remote real-time communication becomes an integral part of human interaction, 3D live streaming has the potential to revolutionize ophthalmic education by removing traditional geographic and physical constraints of in-person surgical viewing. The incorporation of metaverse and web3 technologies has created new outlets for knowledge sharing that may improve how we operate, teach, learn, and transfer knowledge.

The small molecule inhibitor NAV-2729 has a complex target profile including multiple ADP-ribosylation factor regulatory proteins.

The ADP-ribosylation factor (Arf) GTPases and their regulatory proteins are implicated in cancer progression. NAV-2729 was previously identified as a specific inhibitor of Arf6 that reduced progression of uveal melanoma in an orthotopic xenograft. Here, our goal was to assess the inhibitory effects of NAV-2729 on the proliferation of additional cell types. We found NAV-2729 inhibited proliferation of multiple cell lines, but Arf6 expression did not correlate with NAV-2729 sensitivity, and knockdown of Arf6 affected neither cell viability nor sensitivity to NAV-2729. Furthermore, binding to native Arf6 was not detected; however, we determined that NAV-2729 inhibited both Arf exchange factors and Arf GTPase-activating proteins. ASAP1, a GTPase-activating protein linked to cancer progression, was further investigated. We demonstrated that NAV-2729 bound to the PH domain of ASAP1 and changed ASAP1 cellular distribution. However, ASAP1 knockdown did not fully recapitulate the cytoskeletal effects of NAV-2729 nor affect cell proliferation. Finally, our screens identified 48 other possible targets of NAV-2729. These results illustrate the complexities of defining targets of small molecules and identify NAV-2729 as a model PH domain-binding inhibitor.

Phenotypic signatures of immune selection in HIV-1 reservoir cells.

Human immunodeficiency virus 1 (HIV-1) reservoir cells persist lifelong despite antiretroviral treatment1,2 but may be vulnerable to host immune responses that could be exploited in strategies to cure HIV-1. Here we used a single-cell, next-generation sequencing approach for the direct ex vivo phenotypic profiling of individual HIV-1-infected memory CD4+ T cells from peripheral blood and lymph nodes of people living with HIV-1 and receiving antiretroviral treatment for approximately 10 years. We demonstrate that in peripheral blood, cells harbouring genome-intact proviruses and large clones of virally infected cells frequently express ensemble signatures of surface markers conferring increased resistance to immune-mediated killing by cytotoxic T and natural killer cells, paired with elevated levels of expression of immune checkpoint markers likely to limit proviral gene transcription; this phenotypic profile might reduce HIV-1 reservoir cell exposure to and killing by cellular host immune responses. Viral reservoir cells harbouring intact HIV-1 from lymph nodes exhibited a phenotypic signature primarily characterized by upregulation of surface markers promoting cell survival, including CD44, CD28, CD127 and the IL-21 receptor. Together, these results suggest compartmentalized phenotypic signatures of immune selection in HIV-1 reservoir cells, implying that only small subsets of infected cells with optimal adaptation to their anatomical immune microenvironment are able to survive during long-term antiretroviral treatment. The identification of phenotypic markers distinguishing viral reservoir cells may inform future approaches for strategies to cure and eradicate HIV-1.

Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy.

HIV-1 establishes a life-long reservoir of virally infected cells which cannot be eliminated by antiretroviral therapy (ART). Here, we demonstrate a markedly altered viral reservoir profile of long-term ART-treated individuals, characterized by large clones of intact proviruses preferentially integrated in heterochromatin locations, most prominently in centromeric satellite/micro-satellite DNA. Longitudinal evaluations suggested that this specific reservoir configuration results from selection processes that promote the persistence of intact proviruses in repressive chromatin positions, while proviruses in permissive chromosomal locations are more likely to be eliminated. A bias toward chromosomal integration sites in heterochromatin locations was also observed for intact proviruses in study participants who maintained viral control after discontinuation of antiretroviral therapy. Together, these results raise the possibility that antiviral selection mechanisms during long-term ART may induce an HIV-1 reservoir structure with features of deep latency and, possibly, more limited abilities to drive rebound viremia upon treatment interruptions.

Distinguishing Severe Acute Respiratory Syndrome Coronavirus 2 Persistence and Reinfection: A Retrospective Cohort Study.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reinfection is poorly understood, partly because few studies have systematically applied genomic analysis to distinguish reinfection from persistent RNA detection related to initial infection. We aimed to evaluate the characteristics of SARS-CoV-2 reinfection and persistent RNA detection using independent genomic, clinical, and laboratory assessments. METHODS: All individuals at a large academic medical center who underwent a SARS-CoV-2 nucleic acid amplification test (NAAT) ≥45 days after an initial positive test, with both tests between 14 March and 30 December 2020, were analyzed for potential reinfection. Inclusion criteria required having ≥2 positive NAATs collected ≥45 days apart with a cycle threshold (Ct) value <35 at repeat testing. For each included subject, likelihood of reinfection was assessed by viral genomic analysis of all available specimens with a Ct value <35, structured Ct trajectory criteria, and case-by-case review by infectious diseases physicians. RESULTS: Among 1569 individuals with repeat SARS-CoV-2 testing ≥45 days after an initial positive NAAT, 65 (4%) met cohort inclusion criteria. Viral genomic analysis characterized mutations present and was successful for 14/65 (22%) subjects. Six subjects had genomically supported reinfection, and 8 subjects had genomically supported persistent RNA detection. Compared to viral genomic analysis, clinical and laboratory assessments correctly distinguished reinfection from persistent RNA detection in 12/14 (86%) subjects but missed 2/6 (33%) genomically supported reinfections. CONCLUSIONS: Despite good overall concordance with viral genomic analysis, clinical and Ct value-based assessments failed to identify 33% of genomically supported reinfections. Scaling-up genomic analysis for clinical use would improve detection of SARS-CoV-2 reinfections.

Vasculopathy and Increased Vascular Congestion in Fatal COVID-19 and Acute Respiratory Distress Syndrome.

Rationale: The leading cause of death in coronavirus disease 2019 (COVID-19) is severe pneumonia, with many patients developing acute respiratory distress syndrome (ARDS) and diffuse alveolar damage (DAD). Whether DAD in fatal COVID-19 is distinct from other causes of DAD remains unknown. Objective: To compare lung parenchymal and vascular alterations between patients with fatal COVID-19 pneumonia and other DAD-causing etiologies using a multidimensional approach. Methods: This autopsy cohort consisted of consecutive patients with COVID-19 pneumonia (n = 20) and with respiratory failure and histologic DAD (n = 21; non-COVID-19 viral and nonviral etiologies). Premortem chest computed tomography (CT) scans were evaluated for vascular changes. Postmortem lung tissues were compared using histopathological and computational analyses. Machine-learning-derived morphometric analysis of the microvasculature was performed, with a random forest classifier quantifying vascular congestion (CVasc) in different microscopic compartments. Respiratory mechanics and gas-exchange parameters were evaluated longitudinally in patients with ARDS. Measurements and Main Results: In premortem CT, patients with COVID-19 showed more dilated vasculature when all lung segments were evaluated (P = 0.001) compared with controls with DAD. Histopathology revealed vasculopathic changes, including hemangiomatosis-like changes (P = 0.043), thromboemboli (P = 0.0038), pulmonary infarcts (P = 0.047), and perivascular inflammation (P < 0.001). Generalized estimating equations revealed significant regional differences in the lung microarchitecture among all DAD-causing entities. COVID-19 showed a larger overall CVasc range (P = 0.002). Alveolar-septal congestion was associated with a significantly shorter time to death from symptom onset (P = 0.03), length of hospital stay (P = 0.02), and increased ventilatory ratio [an estimate for pulmonary dead space fraction (Vd); p = 0.043] in all cases of ARDS. Conclusions: Severe COVID-19 pneumonia is characterized by significant vasculopathy and aberrant alveolar-septal congestion. Our findings also highlight the role that vascular alterations may play in Vd and clinical outcomes in ARDS in general.

Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants.

The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses and their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable the identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.

Three or four levels of hierarchy minimize hydraulic power in leaves with pinnate dendritic venation.

We present a model of the hydraulic power required by the network of veins in a leaf with pinnate venation. The pinnate networks we study are dendritic networks with a single midrib and L levels of hierarchy, where L=2 corresponds to secondary veins branching from the midrib, L=3 additionally has tertiary veins branching from secondary veins, L=4 additionally has quaternary veins branching from tertiary veins, etc.We begin by utilizing the classic results of Murray to show that the minimal power required in a pipe of constant radius depends only on the length of the pipe and the volume flow rate to the 2/3 power. After then showing that the power required by the midrib is essentially independent of the number of secondary and higher order veins, we provide an explicit formula for the minimal total power required with L levels of hierarchy. The critical parameters in this model are the height and width of the leaf and the density ρ of vein terminations. We show how ρ can be estimated from published data on leaf vein density, and that for a very wide range of ρ the value of L minimizing the total power required is either 3 or 4. That is, three or four levels of leaf vein hierarchy suffice to minimize the required hydraulic power.

Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses.

HIV-1-infected cells that persist despite antiretroviral therapy (ART) are frequently considered "transcriptionally silent," but active viral gene expression may occur in some cells, challenging the concept of viral latency. Applying an assay for profiling the transcriptional activity and the chromosomal locations of individual proviruses, we describe a global genomic and epigenetic map of transcriptionally active and silent proviral species and evaluate their longitudinal evolution in persons receiving suppressive ART. Using genome-wide epigenetic reference data, we show that proviral transcriptional activity is associated with activating epigenetic chromatin features in linear proximity of integration sites and in their inter- and intrachromosomal contact regions. Transcriptionally active proviruses were actively selected against during prolonged ART; however, this pattern was violated by large clones of virally infected cells that may outcompete negative selection forces through elevated intrinsic proliferative activity. Our results suggest that transcriptionally active proviruses are dynamically evolving under selection pressure by host factors.