Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses.

The recurring spillover of pathogenic coronaviruses and demonstrated capacity of sarbecoviruses, such SARS-CoV-2, to rapidly evolve in humans underscores the need to better understand immune responses to this virus family. For this purpose, we characterized the functional breadth and potency of antibodies targeting the receptor binding domain (RBD) of the spike glycoprotein that exhibited cross-reactivity against SARS-CoV-2 variants, SARS-CoV-1 and sarbecoviruses from diverse clades and animal origins with spillover potential. One neutralizing antibody, C68.61, showed remarkable neutralization breadth against both SARS-CoV-2 variants and viruses from different sarbecovirus clades. C68.61, which targets a conserved RBD class 5 epitope, did not select for escape variants of SARS-CoV-2 or SARS-CoV-1 in culture nor have predicted escape variants among circulating SARS-CoV-2 strains, suggesting this epitope is functionally constrained. We identified 11 additional SARS-CoV-2/SARS-CoV-1 cross-reactive antibodies that target the more sequence conserved class 4 and class 5 epitopes within RBD that show activity against a subset of diverse sarbecoviruses with one antibody binding every single sarbecovirus RBD tested. A subset of these antibodies exhibited Fc-mediated effector functions as potent as antibodies that impact infection outcome in animal models. Thus, our study identified antibodies targeting conserved regions across SARS-CoV-2 variants and sarbecoviruses that may serve as therapeutics for pandemic preparedness as well as blueprints for the design of immunogens capable of eliciting cross-neutralizing responses.

2023 Neer Award for Basic Science: Genetics of Cutibacterium acnes in Revision Shoulder Arthroplasty: A Large-Scale Bacterial Whole-Genome Sequencing Study.

BACKGROUND: Cutibacterium acnes is the bacterium most commonly responsible for shoulder periprosthetic joint infection (PJI) and is often cultured from samples obtained at the time of revision for failed shoulder arthroplasty. We sought to determine whether these bacteria originate from the patient or from exogenous sources. We also sought to identify which C. acnes genetic traits were associated with the development of shoulder PJI. METHODS: We performed bacterial whole-genome sequencing of C. acnes from a single-institution repository of cultures obtained before or during primary and revision shoulder arthroplasty and correlated the molecular epidemiology and genetic content of strains with clinical features of infection. RESULTS: A total of 341 isolates collected over a four-year period from 88 patients were sequenced. C. acnes cultured from surgical specimens demonstrated significant similarity to the strains colonizing the skin of the same patient (p<0.001). Infrequently, there was evidence of strains shared across unrelated patients, suggesting that exogenous sources of C. acnes culture-positivity were uncommon. Phylotypes IB and II were modestly associated with clinical features of PJI, but all phylotypes appeared inherently capable of causing disease. Chronic shoulder PJI was associated with the absence of common C. acnes genes involved in bacterial quorum-sensing (luxS, tqsA). CONCLUSION: C. acnes strains cultured from deep intraoperative sources during revision shoulder arthroplasty demonstrate strong genetic similarity to the strains colonizing a patient's skin. Some phylotypes of C. acnes commonly colonizing human skin are modestly more virulent than others, but all phylotypes have a capacity for PJI. C. acnes cultured from cases of PJI commonly demonstrated genetic hallmarks associated with adaptation from acute to chronic phases of infection. This is the strongest evidence to date supporting the role of the patient's own, cutaneous C. acnes strains in the pathogenesis of shoulder arthroplasty infection. Our findings support the importance of further research focused on perioperative decolonization and management of endogenous bacteria that are likely to be introduced into the arthroplasty wound at the time of skin incision.

How Trustworthy Is Your Tree? Bayesian Phylogenetic Effective Sample Size Through the Lens of Monte Carlo Error.

Bayesian inference is a popular and widely-used approach to infer phylogenies (evolutionary trees). However, despite decades of widespread application, it remains difficult to judge how well a given Bayesian Markov chain Monte Carlo (MCMC) run explores the space of phylogenetic trees. In this paper, we investigate the Monte Carlo error of phylogenies, focusing on high-dimensional summaries of the posterior distribution, including variability in estimated edge/branch (known in phylogenetics as "split") probabilities and tree probabilities, and variability in the estimated summary tree. Specifically, we ask if there is any measure of effective sample size (ESS) applicable to phylogenetic trees which is capable of capturing the Monte Carlo error of these three summary measures. We find that there are some ESS measures capable of capturing the error inherent in using MCMC samples to approximate the posterior distributions on phylogenies. We term these tree ESS measures, and identify a set of three which are useful in practice for assessing the Monte Carlo error. Lastly, we present visualization tools that can improve comparisons between multiple independent MCMC runs by accounting for the Monte Carlo error present in each chain. Our results indicate that common post-MCMC workflows are insufficient to capture the inherent Monte Carlo error of the tree, and highlight the need for both within-chain mixing and between-chain convergence assessments.

Anatomic Total Shoulder: Predictors of Excellent Outcomes at Five Years after Arthroplasty.

PURPOSE: The objectives of this study were to: report minimum 5-year outcomes in patients undergoing TSA and determine characteristics predictive of patients achieving an excellent functional outcome. METHODS: Pre-operative demographic variables and Simple Shoulder Test (SST) scores were obtained pre-operatively and at a minimum of five years after surgery. A final SST ≥ 10 and percentage of maximal possible improvement (% MPI) of ≥ 66.7% were determined to be the thresholds for excellent outcomes. Univariate and multivariate analysis were performed to identify factors associated with excellent five year clinical outcomes. RESULTS: Of 233 eligible patients, 188 (81%) had adequate follow-up for inclusion in this study. Mean SST scores improved from 3.4 ± 2.4 to 9.7 ± 2.2 (p < 0.001). Male sex was an independent predictor of both SST ≥ 10 (OR 3.46, 95% CI 1.70-7.31; p < 0.001) and %MPI ≥ 66.7 (OR 2.27, 95% CI 1.11-4.81, p = 0.027). Workers' Compensation insurance was predictive of not obtaining SST ≥ 10 (OR 0.12, 95% 0.02-0.60; p = 0.016) or %MPI ≥ 66.7 (OR 0.16, 95% CI 0.03-0.77, p = 0.025). MCID was passed by the vast majority (95%) of patients undergoing TSA and did not necessarily indicate an excellent, satisfactory outcome. CONCLUSION: Male sex and commercial insurance coverage were significantly associated with these excellent outcomes, while Workers' Compensation insurance was associated with failure to achieve this result. Thresholds for excellent outcomes, such as final SST ≥ 10 and %MPI ≥ 66.7, may be useful in identifying the characteristics of patients who benefit most from TSA.

Anatomic shoulder arthroplasty: the correlation between patient resilience, mental health, and outcome.

BACKGROUND: Recovery from anatomic shoulder arthroplasty may be enhanced in patients with good mental health and the resilience to participate in the prescribed postoperative rehabilitation program. To test this concept, we utilized validated and reliable scales in determining whether resilience and mental health are associated with the outcome of anatomic arthroplasty. METHODS: Three hundred ninety-nine patients (195 ream and run [RnR] and 204 anatomic total shoulder arthroplasty [aTSA]) were surveyed at a mean follow-up of 6.3 ± 3.3 years. Preoperative variables included age, sex, body mass index, history of prior shoulder surgery, diabetes, visual analog scale for pain, Simple Shoulder Test (SST) scores, and Veteran's RAND 12 Mental Component Score (VR-12 MCS). Outcomes collected included the SST, American Shoulder and Elbow Surgeons (ASES) score, revision rate, and patient satisfaction. Resilience was documented using the Connor-Davidson Resilience Scale 10 (CD-RISC 10) at latest follow-up. Univariable and multivariable regression analyses were used to identify factors significantly associated with follow-up postoperative SST, ASES, and satisfaction. RESULTS: In the univariable analysis, CD-RISC 10 was positively correlated with postoperative SST, ASES, and satisfaction after both RnR and aTSA. The mean CD-RISC 10 scores were higher in the RnR cohort (34.3 ± 4.8 vs. 32.5 ± 6.2 for aTSA, P < .001). Male sex and lower preoperative visual analog scale for pain were correlated with higher ASES after RnR; VR-12 MCS was positively correlated with all outcomes except SST after RnR. In the multivariable linear regression analysis, CD-RISC 10 was independently associated with postoperative SST, ASES and satisfaction scores in aTSA patients. In the RnR cohort, CD-RISC 10 was only correlated with satisfaction. VR-12 MCS was correlated with ASES and satisfaction after RnR. DISCUSSION: In this study of anatomic arthroplasties, increased resilience and better mental health were correlated with better outcomes. RnR patients had higher resilience than aTSA patients. Greater resilience was associated with better outcomes after aTSA. Better mental health was associated with superior outcomes after the ream and run procedure.

Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex.

Lassa virus is estimated to cause thousands of human deaths per year, primarily due to spillovers from its natural host, Mastomys rodents. Efforts to create vaccines and antibody therapeutics must account for the evolutionary variability of Lassa virus's glycoprotein complex (GPC), which mediates viral entry into cells and is the target of neutralizing antibodies. To map the evolutionary space accessible to GPC, we use pseudovirus deep mutational scanning to measure how nearly all GPC amino-acid mutations affect cell entry and antibody neutralization. Our experiments define functional constraints throughout GPC. We quantify how GPC mutations affect neutralization by a panel of monoclonal antibodies and show that all antibodies are escaped by mutations that exist among natural Lassa virus lineages. Overall, our work describes a biosafety-level-2 method to elucidate the mutational space accessible to GPC and shows how prospective characterization of antigenic variation could aid design of therapeutics and vaccines.

Many-core algorithms for high-dimensional gradients on phylogenetic trees.

MOTIVATION: Advancements in high-throughput genomic sequencing are delivering genomic pathogen data at an unprecedented rate, positioning statistical phylogenetics as a critical tool to monitor infectious diseases globally. This rapid growth spurs the need for efficient inference techniques, such as Hamiltonian Monte Carlo (HMC) in a Bayesian framework, to estimate parameters of these phylogenetic models where the dimensions of the parameters increase with the number of sequences N. HMC requires repeated calculation of the gradient of the data log-likelihood with respect to (wrt) all branch-length-specific (BLS) parameters that traditionally takes O(N2) operations using the standard pruning algorithm. A recent study proposes an approach to calculate this gradient in O(N), enabling researchers to take advantage of gradient-based samplers such as HMC. The CPU implementation of this approach makes the calculation of the gradient computationally tractable for nucleotide-based models but falls short in performance for larger state-space size models, such as Markov-modulated and codon models. Here, we describe novel massively parallel algorithms to calculate the gradient of the log-likelihood wrt all BLS parameters that take advantage of graphics processing units (GPUs) and result in many fold higher speedups over previous CPU implementations. RESULTS: We benchmark these GPU algorithms on three computing systems using three evolutionary inference examples exploring complete genomes from 997 dengue viruses, 62 carnivore mitochondria and 49 yeasts, and observe a >128-fold speedup over the CPU implementation for codon-based models and >8-fold speedup for nucleotide-based models. As a practical demonstration, we also estimate the timing of the first introduction of West Nile virus into the continental Unites States under a codon model with a relaxed molecular clock from 104 full viral genomes, an inference task previously intractable. AVAILABILITY AND IMPLEMENTATION: We provide an implementation of our GPU algorithms in BEAGLE v4.0.0 (https://github.com/beagle-dev/beagle-lib), an open-source library for statistical phylogenetics that enables parallel calculations on multi-core CPUs and GPUs. We employ a BEAGLE-implementation using the Bayesian phylogenetics framework BEAST (https://github.com/beast-dev/beast-mcmc).

Managing rotator cuff tear arthropathy: a role for cuff tear arthropathy hemiarthroplasty as well as reverse total shoulder arthroplasty.

BACKGROUND: Disabling cuff tear arthropathy (CTA) is commonly managed with reverse shoulder arthroplasty (RSA). However, for patients with CTA having preserved active elevation, cuff tear arthropathy hemiarthroplasty (CTAH) may offer a cost-effective alternative that avoids the complications unique to RSA. We sought to determine the characteristics and outcomes of a series of patients with CTA managed with these procedures. MATERIALS AND METHODS: We retrospectively reviewed 103 patients with CTA treated with shoulder arthroplasty, the type of which was determined by the patient's ability to actively elevate the arm. Outcome measures included the change in the Simple Shoulder Test (SST), the percent maximum improvement in SST (%MPI), and the percentage of patients exceeding the minimal clinically important difference for the change in SST and %MPI. Postoperative x-rays were evaluated to assess the positions of the center of rotation and the greater tuberosity for each implant. RESULTS: Forty-four percent of the 103 patients were managed with CTAH while 56% were managed with RSA. Both arthroplasties resulted in clinically significant improvement. Patients having RSA improved from a mean preoperative SST score of 1.7 (interquartile range [IQR], 0.0-3.0) to a postoperative score of 6.3 (IQR, 2.3-10.0) (P < .01). Patients having CTAH improved from a preoperative SST score of 3.1 (IQR, 1.0-4.0) to a postoperative score of 7.6 (IQR, 5.0-10.) (P < .001). These improvements exceeded the minimal clinically important difference. Instability accounted for most of the RSA complications; however, it did not account for any CTAH complications. The postoperative position of the center of rotation and greater tuberosity on anteroposterior radiographs did not correlate with the clinical outcomes for either procedure. CONCLUSION: For 103 patients with CTA, clinically significant improvement was achieved with appropriately indicated CTAH and RSA. In view of the lower cost of the CTAH implant, it may provide a cost-effective alternative to RSA for patients with retained active elevation.

Using viral sequence diversity to estimate time of HIV infection in infants.

Age at HIV acquisition may influence viral pathogenesis in infants, and yet infection timing (i.e. date of infection) is not always known. Adult studies have estimated infection timing using rates of HIV RNA diversification, however, it is unknown whether adult-trained models can provide accurate predictions when used for infants due to possible differences in viral dynamics. While rates of viral diversification have been well defined for adults, there are limited data characterizing these dynamics for infants. Here, we performed Illumina sequencing of gag and pol using longitudinal plasma samples from 22 Kenyan infants with well-characterized infection timing. We used these data to characterize viral diversity changes over time by designing an infant-trained Bayesian hierarchical regression model that predicts time since infection using viral diversity. We show that diversity accumulates with time for most infants (median rate within pol = 0.00079 diversity/month), and diversity accumulates much faster than in adults (compare previously-reported adult rate within pol = 0.00024 diversity/month [1]). We find that the infant rate of viral diversification varies by individual, gene region, and relative timing of infection, but not by set-point viral load or rate of CD4+ T cell decline. We compare the predictive performance of this infant-trained Bayesian hierarchical regression model with simple linear regression models trained using the same infant data, as well as existing adult-trained models [1]. Using an independent dataset from an additional 15 infants with frequent HIV testing to define infection timing, we demonstrate that infant-trained models more accurately estimate time since infection than existing adult-trained models. This work will be useful for timing HIV acquisition for infants with unknown infection timing and for refining our understanding of how viral diversity accumulates in infants, both of which may have broad implications for the future development of infant-specific therapeutic and preventive interventions.

phippery: a software suite for PhIP-Seq data analysis.

SUMMARY: We present the phippery software suite for analyzing data from phage display methods that use immunoprecipitation and deep sequencing to capture antibody binding to peptides, often referred to as PhIP-Seq. It has three main components that can be used separately or in conjunction: (i) a Nextflow pipeline, phip-flow, to process raw sequencing data into a compact, multidimensional dataset format and allows for end-to-end automation of reproducible workflows. (ii) a Python API, phippery, which provides interfaces for tasks such as count normalization, enrichment calculation, multidimensional scaling, and more, and (iii) a Streamlit application, phip-viz, as an interactive interface for visualizing the data as a heatmap in a flexible manner. AVAILABILITY AND IMPLEMENTATION: All software packages are publicly available under the MIT License. The phip-flow pipeline: https://github.com/matsengrp/phip-flow. The phippery library: https://github.com/matsengrp/phippery. The phip-viz Streamlit application: https://github.com/matsengrp/phip-viz.

Minimum 10-year follow-up of anatomic total shoulder arthroplasty and ream-and-run arthroplasty for primary glenohumeral osteoarthritis.

BACKGROUND: Reports on long term outcomes and failures of shoulder arthroplasty are uncommon. The purpose of this study is to present minimum 10-year outcomes in consecutive patients undergoing ream-and-run and anatomic total shoulder arthroplasty (TSA) for primary glenohumeral arthritis. METHODS: This study analyzed consecutive patients who had undergone a ream-and-run or TSA with minimum 10-year follow-up. Pain scores and Simple Shoulder Test (SST) values were obtained preoperatively and at a minimum of 10 years postoperatively via e-mail or mail-in response. Percentage of maximum possible improvement (%MPI) was also calculated. RESULTS: Of 127 eligible patients, 63 (50%) responded to a 10-year survey. This included 34 patients undergoing ream-and-run arthroplasty and 29 patients undergoing TSA. The ream-and-run patients were significantly younger than the TSA patients (60 ± 7 vs. 68 ± 8, P < .001), predominantly male (97% vs. 41%, P < .001), and had a lower American Society of Anesthesiologists classification (P = .018). In the ream-and-run group, the mean pain score improved from a preoperative value of 6.5 ± 1.9 to 0.9 ± 1.3 (P < .001), and the mean SST score improved from 5.4 ± 2.4 to 10.3 ± 2.1 at 10-year follow-up (P < .001). Twenty-eight (82%) achieved an SST improvement above the minimally clinically important difference (MCID) of 2.6. Four patients (12%) underwent single-stage exchange to another hemiarthroplasty, whereas 1 (3%) required manipulation under anesthesia. In the TSA group, the pain score improved from a preoperative value of 6.6 ± 2.2 to 1.2 ± 2.3 (P < .001), and the SST score improved from 3.8 ± 2.6 to 8.9 ± 2.6 at 10-year follow-up (P < .001). Of the 29 patients who underwent a TSA, 27 (93%) achieved an SST improvement above the MCID of 1.6. No patient in the TSA group required reoperation. CONCLUSION: Although the characteristics of the patients differ between the 2 groups, excellent functional results can be obtained with the ream-and-run arthroplasty and TSA for glenohumeral osteoarthritis.

Elevated binding and functional antibody responses to SARS-CoV-2 in infants versus mothers.

Infant antibody responses to viral infection can differ from those in adults. However, data on the specificity and function of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in infants, and direct comparisons between infants and adults are limited. Here, we characterize antibody binding and functionality against Wuhan-Hu-1 (B lineage) strain SARS-CoV-2 in convalescent plasma from 36 postpartum women and 14 of their infants infected with SARS-CoV-2 from a vaccine-naïve prospective cohort in Nairobi, Kenya. We find significantly higher antibody titers against SARS-CoV-2 Spike, receptor binding domain and N-terminal domain, and Spike-expressing cell-surface staining levels in infants versus mothers. Plasma antibodies from mothers and infants bind to similar regions of the Spike S2 subunit, including the fusion peptide (FP) and stem helix-heptad repeat 2. However, infants display higher antibody levels and more consistent antibody escape pathways in the FP region compared to mothers. Finally, infants have significantly higher levels of antibody-dependent cellular cytotoxicity (ADCC), though, surprisingly, Spike pseudovirus neutralization titers between infants and mothers are similar. These results suggest infants develop distinct SARS-CoV-2 binding and functional antibody activities and reveal age-related differences in humoral immunity to SARS-CoV-2 infection that could be relevant to protection and COVID-19 disease outcomes.

Passively Acquired Constant Region 5-Specific Antibodies Associated With Improved Survival in Infants Who Acquire Human Immunodeficiency Virus.

Studying vertical human immunodeficiency virus (HIV) transmission enables the impact of passively transferred antibodies on HIV transmission and pathogenesis to be examined. Using phage display of HIV envelope peptides and peptide enzyme-linked immunosorbent assay (ELISA), we found that, in infants who acquired HIV, passive antibody responses to constant region 5 (C5) were associated with improved survival in 2 cohorts. In a combined analysis, C5 peptide ELISA activity was correlated directly with survival and estimated infection time and inversely with set point viral load. These results suggest that preexisting C5-specific antibodies may be correlated with the survival of infants living with HIV, motivating additional research into their protective potential.

A topology-marginal composite likelihood via a generalized phylogenetic pruning algorithm.

Bayesian phylogenetics is a computationally challenging inferential problem. Classical methods are based on random-walk Markov chain Monte Carlo (MCMC), where random proposals are made on the tree parameter and the continuous parameters simultaneously. Variational phylogenetics is a promising alternative to MCMC, in which one fits an approximating distribution to the unnormalized phylogenetic posterior. Previous work fit this variational approximation using stochastic gradient descent, which is the canonical way of fitting general variational approximations. However, phylogenetic trees are special structures, giving opportunities for efficient computation. In this paper we describe a new algorithm that directly generalizes the Felsenstein pruning algorithm (a.k.a. sum-product algorithm) to compute a composite-like likelihood by marginalizing out ancestral states and subtrees simultaneously. We show the utility of this algorithm by rapidly making point estimates for branch lengths of a multi-tree phylogenetic model. These estimates accord with a long MCMC run and with estimates obtained using a variational method, but are much faster to obtain. Thus, although generalized pruning does not lead to a variational algorithm as such, we believe that it will form a useful starting point for variational inference.

Which Components of the Simple Shoulder Test Show Improvement After Scapulothoracic Fusion for Recalcitrant Scapular Winging? Clinical Results at a Minimum of 5 Years of Follow-up.

BACKGROUND: Scapular winging is an uncommon but important cause of shoulder pain and disability. Surgical management can include soft tissue procedures such as split pectoralis major transfer, the Eden-Lange procedure, or a triple tendon transfer. When these procedures do not alleviate symptomatic winging or are inappropriate, scapulothoracic fusion is an alternative, but data on its longer-term effectiveness are sparse. QUESTIONS/PURPOSES: (1) What changes in outcome scores were observed (VAS, Single Assessment Numeric Evaluation [SANE], and Simple Shoulder Test [SST] scores), and what proportion of the patients improved by an amount larger than the minimum clinically important difference (MCID) for the outcome tool in question? (2) Which components of the SST are patients able to perform at a minimum of 5 years? (3) What complications occurred after surgery? METHODS: We performed a retrospective study in a single, large, urban referral medical center of patients who underwent scapulothoracic fusion. Between January 2011 and November 2016, 15 patients underwent scapulothoracic fusion to treat symptomatic scapular winging. Only patients with nondystrophic etiology were included in the analysis (n = 13). Of the 13 remaining patients, one patient was lost to follow-up and another patient died during data collection, leaving 11 patients for the final analysis. Six patients had brachial plexus injuries affecting multiple nerve roots and periscapular muscles, and five had persistent symptoms despite prior tendon transfer. The median age of the patients was 43 years (range 20 to 67 years), and there were six male and five female patients. All patients had a minimum of 5 years of follow-up. There was a median follow-up of 79 months (range 61 to 128 months). The VAS pain score (range 0 to 10, higher scores represent more pain; MCID = 2), SST score (range 0 to 12, higher scores represent less pain and better shoulder function; MCID = 2.3), and SANE score (range 0 to 100, higher scores represent better shoulder function; MCID = 28) were recorded before surgery and at the most recent follow-up. We compared scores from before surgery with those taken at the most recent follow-up and ascertained the proportion of patients whose improvement exceeded the MCID. The number of patients achieving fusion (as confirmed by a CT image), complications, and reoperations was recorded via a record review as well as direct patient query by telephone. RESULTS: The median VAS pain score improved from 7 (range 3 to 10) preoperatively to 3 (range 2 to 5) at the latest follow-up (p < 0.001). The median SANE score improved from 30 (range 0 to 60) preoperatively to 65 (range 40 to 85) at the latest follow-up (p < 0.001). The median SST score improved from 0 (range 0 to 9) to 8 (range 5 to 10) at the latest follow-up (p < 0.001). Ten of 11 patients had improvements exceeding the MCID for VAS, six of 11 had improvements for SANE scores, and nine of 11 had improvements for SST. Preoperative to postoperative improvements in these components of the SST were seen (responses of "yes"): comfort at rest (three of 11 improved to 11 of 11; p < 0.001), sleep comfortably (three of 11 improved to 11 of 11; p < 0.001), place coin on shelf (two of 11 improved to 10 of 11; p < 0.001), lift 1 pound above shoulder (two of 11 improved to eight of 11; p = 0.03), and carry 20 pounds with the arm at side (one of 11 improved to nine of 11; p < 0.001). All 11 patients had successful fusion noted on CT images. There were three complications (progression of glenohumeral arthritis, broken wires, and perioperative chest tube placement) and one reoperation for progression of glenohumeral arthritis with subsequent total shoulder arthroplasty. CONCLUSION: Patients with recalcitrant symptomatic scapular winging often undergo an exhaustive course of clinical examinations, diagnostic tests, physical therapy, and multiple surgical procedures. Those with brachial plexus palsy with involvement of multiple nerves may continue to have symptoms despite nonoperative management and subsequent soft tissue tendon transfers. Scapulothoracic fusion could be considered for patients with persistent pain and decreased function because of recalcitrant scapular winging who are either not candidates for the procedure or have persistent symptoms despite prior soft tissue procedures. LEVEL OF EVIDENCE: Level IV, therapeutic study.

Statistical inference reveals the role of length, GC content, and local sequence in V(D)J nucleotide trimming.

To appropriately defend against a wide array of pathogens, humans somatically generate highly diverse repertoires of B cell and T cell receptors (BCRs and TCRs) through a random process called V(D)J recombination. Receptor diversity is achieved during this process through both the combinatorial assembly of V(D)J-genes and the junctional deletion and insertion of nucleotides. While the Artemis protein is often regarded as the main nuclease involved in V(D)J recombination, the exact mechanism of nucleotide trimming is not understood. Using a previously published TCRß repertoire sequencing data set, we have designed a flexible probabilistic model of nucleotide trimming that allows us to explore various mechanistically interpretable sequence-level features. We show that local sequence context, length, and GC nucleotide content in both directions of the wider sequence, together, can most accurately predict the trimming probabilities of a given V-gene sequence. Because GC nucleotide content is predictive of sequence-breathing, this model provides quantitative statistical evidence regarding the extent to which double-stranded DNA may need to be able to breathe for trimming to occur. We also see evidence of a sequence motif that appears to get preferentially trimmed, independent of GC-content-related effects. Further, we find that the inferred coefficients from this model provide accurate prediction for V- and J-gene sequences from other adaptive immune receptor loci. These results refine our understanding of how the Artemis nuclease may function to trim nucleotides during V(D)J recombination and provide another step toward understanding how V(D)J recombination generates diverse receptors and supports a powerful, unique immune response in healthy humans.

Reconstruction of a polyclonal ADCC antibody repertoire from an HIV-1 non-transmitting mother.

Human natural history and vaccine studies support a protective role of antibody dependent cellular cytotoxicity (ADCC) activity against many infectious diseases. One setting where this has consistently been observed is in HIV-1 vertical transmission, where passively acquired ADCC activity in HIV-exposed infants has correlated with reduced acquisition risk and reduced pathogenesis in HIV+ infants. However, the characteristics of HIV-specific antibodies comprising a maternal plasma ADCC response are not well understood. Here, we reconstructed monoclonal antibodies (mAbs) from memory B cells from late pregnancy in mother MG540, who did not transmit HIV to her infant despite several high-risk factors. Twenty mAbs representing 14 clonal families were reconstructed, which mediated ADCC and recognized multiple HIV Envelope epitopes. In experiments using Fc-defective variants, only combinations of several mAbs accounted for the majority of plasma ADCC of MG540 and her infant. We present these mAbs as evidence of a polyclonal repertoire with potent HIV-directed ADCC activity.

Risk Factors for Stiffness Requiring Intervention After Ream-and-Run Arthroplasty.

Ream-and-run arthroplasty can improve pain and function in patients with glenohumeral arthritis while avoiding the complications and activity restrictions associated with a prosthetic glenoid component. However, stiffness is a known complication after ream-and-run arthroplasty and can lead to repeat procedures such as a manipulation under anesthesia (MUA) or open surgical revision. The objective of this study was to determine risk factors associated with repeat procedures indicated for postoperative stiffness after ream-and-run arthroplasty. Methods: We conducted a retrospective review of our shoulder arthroplasty database to identify patients who underwent ream-and-run arthroplasty and determined which patients underwent subsequent repeat procedures (MUA and/or open revision) indicated for postoperative stiffness. The minimum follow-up was 2 years. We collected baseline demographic information and preoperative and 2-year patient-reported outcome scores and analyzed preoperative radiographs. Univariate and multivariate analyses determined the factors significantly associated with repeat procedures to treat postoperative stiffness. Results: There were 340 patients who underwent ream-and-run arthroplasty. The mean Simple Shoulder Test (SST) scores for all patients improved from 5.0 ± 2.4 preoperatively to 10.2 ± 2.6 postoperatively (p < 0.001). Twenty-six patients (7.6%) underwent open revision for stiffness. An additional 35 patients (10.3%) underwent MUA. Univariate analysis found younger age (p = 0.001), female sex (p = 0.034), lower American Society of Anesthesiologists (ASA) class (p = 0.045), posterior decentering on preoperative radiographs (p = 0.010), and less passive forward elevation at the time of discharge after ream-and-run arthroplasty (p < 0.001) to be significant risk factors for repeat procedures. Multivariate analysis found younger age (p = 0.040), ASA class 1 compared with class 3 (p = 0.020), and less passive forward elevation at discharge (p < 0.001) to be independent risk factors for repeat procedures. Of the patients who underwent open revision for stiffness, 69.2% had multiple positive cultures for Cutibacterium. Conclusions: Younger age, ASA class 1 compared with class 3, and less passive forward elevation in the immediate postoperative period were independent risk factors for repeat procedures to treat postoperative stiffness after ream-and-run arthroplasty. Level of Evidence: Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.

Single B cell transcriptomics identifies multiple isotypes of broadly neutralizing antibodies against flaviviruses.

Sequential dengue virus (DENV) infections often generate neutralizing antibodies against all four DENV serotypes and sometimes, Zika virus. Characterizing cross-flavivirus broadly neutralizing antibody (bnAb) responses can inform countermeasure strategies that avoid infection enhancement associated with non-neutralizing antibodies. Here, we used single cell transcriptomics to mine the bnAb repertoire following secondary DENV infection. We identified several new bnAbs with comparable or superior breadth and potency to known bnAbs, and with distinct recognition determinants. Unlike all known flavivirus bnAbs, which are IgG1, one newly identified cross-flavivirus bnAb (F25.S02) was derived from IgA1. Both IgG1 and IgA1 versions of F25.S02 and known bnAbs displayed neutralizing activity, but only IgG1 enhanced infection in monocytes expressing IgG and IgA Fc receptors. Moreover, IgG-mediated enhancement of infection was inhibited by IgA1 versions of bnAbs. We demonstrate a role for IgA in flavivirus infection and immunity with implications for vaccine and therapeutic strategies.

Dynamics of Cutibacterium repopulation onto the skin surface of the shoulder after chlorhexidine application.

PURPOSE: The objective of this study was to characterize the temporal dynamics of Cutibacterium repopulation of the skin surface after application of chlorhexidine to the shoulder. METHODS: Ten shoulders in five male subjects were used. A skin swab was taken prior to (0 minutes) and then at three, 30, 60, 120, and 240 minutes after skin preparation with 2% chlorhexidine gluconate and 70% isopropyl alcohol. Semi-quantitative bacterial load was measured for each timepoint. RESULTS: From zero minutes (pre-treatment) to three minutes, chlorhexidine-isopropyl alcohol reduced the skin bacterial load in eight out of ten shoulders. Of these eight shoulders, four (50%) had growth by 30 minutes, seven (88%) had growth by 60 minutes, and all eight (100%) had growth by 240 minutes. Compared to the three minutes after chlorhexidine application, bacterial load had significantly increased by 60 minutes but were still significantly lower than the pre-prep bacterial load (0 minutes). CONCLUSION: Following standard surgical skin preparation with chlorhexidine-isopropyl alcohol, the surface of the shoulder is repopulated with Cutibacterium within one hour, presumably from reservoirs in sebaceous glands not penetrated by topical antiseptic agents. Since these dermal glands are transected by skin incision for shoulder arthroplasty, this study suggests that they may be sources of wound contamination during surgery in spite of skin preparation with chlorhexidine.