Deep Mutational Scanning of SARS-CoV-2 Receptor Binding Domain Reveals Constraints on Folding and ACE2 Binding.

The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor and is a major determinant of host range and a dominant target of neutralizing antibodies. Here, we experimentally measure how all amino acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBD's surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity-enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.

Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases.

PURPOSE: This study aims to assess the diagnostic utility and provide reporting recommendations for clinical DNA methylation episignature testing based on the cohort of patients tested through the EpiSign Clinical Testing Network. METHODS: The EpiSign assay utilized unsupervised clustering techniques and a support vector machine-based classification algorithm to compare each patient's genome-wide DNA methylation profile with the EpiSign Knowledge Database, yielding the result that was reported. An international working group, representing distinct EpiSign Clinical Testing Network health jurisdictions, collaborated to establish recommendations for interpretation and reporting of episignature testing. RESULTS: Among 2399 cases analyzed, 1667 cases underwent a comprehensive screen of validated episignatures, imprinting, and promoter regions, resulting in 18.7% (312/1667) positive reports. The remaining 732 referrals underwent targeted episignature analysis for assessment of sequence or copy-number variants (CNVs) of uncertain significance or for assessment of clinical diagnoses without confirmed molecular findings, and 32.4% (237/732) were positive. Cases with detailed clinical information were highlighted to describe various utility scenarios for episignature testing. CONCLUSION: Clinical DNA methylation testing including episignatures, imprinting, and promoter analysis provided by an integrated network of clinical laboratories enables test standardization and demonstrates significant diagnostic yield and clinical utility beyond DNA sequence analysis in rare diseases.

Robustness of Phylogenetic Inference to Model Misspecification Caused by Pairwise Epistasis.

Likelihood-based phylogenetic inference posits a probabilistic model of character state change along branches of a phylogenetic tree. These models typically assume statistical independence of sites in the sequence alignment. This is a restrictive assumption that facilitates computational tractability, but ignores how epistasis, the effect of genetic background on mutational effects, influences the evolution of functional sequences. We consider the effect of using a misspecified site-independent model on the accuracy of Bayesian phylogenetic inference in the setting of pairwise-site epistasis. Previous work has shown that as alignment length increases, tree reconstruction accuracy also increases. Here, we present a simulation study demonstrating that accuracy increases with alignment size even if the additional sites are epistatically coupled. We introduce an alignment-based test statistic that is a diagnostic for pairwise epistasis and can be used in posterior predictive checks.

Lung function improves after delayed treatment with CNP-miR146a following acute lung injury.

Acute respiratory distress syndrome (ARDS) is a highly morbid pulmonary disease characterized by hypoxic respiratory failure. Its pathogenesis is characterized by unrestrained oxidative stress and inflammation, with long-term sequelae of pulmonary fibrosis and diminished lung function. Unfortunately, prior therapeutic ARDS trials have failed and therapy is limited to supportive measures. Free radical scavenging cerium oxide nanoparticles (CNP) conjugated to the anti-inflammatory microRNA-146a (miR146a), termed CNP-miR146a, have been shown to prevent acute lung injury in a pre-clinical model. In this study, we evaluated the potential of delayed treatment with CNP-miR146a at three or seven days after injury to rescue the lung from acute injury. We found that intratracheal CNP-miR146a administered three days after injury lowers pulmonary leukocyte infiltration, reduce inflammation and oxidative stress, lower pro-fibrotic gene expression and collagen deposition in the lung, and ultimately improve pulmonary function.

Cerium oxide nanoparticle conjugation to microRNA-146a mechanism of correction for impaired diabetic wound healing.

Diabetic wounds represent a significant healthcare burden and are characterized by impaired wound healing due to increased oxidative stress and persistent inflammation. We have shown that CNP-miR146a synthesized by the conjugation of cerium oxide nanoparticles (CNP) to microRNA (miR)-146a improves diabetic wound healing. CNP are divalent metal oxides that act as free radical scavenger, while miR146a inhibits the pro-inflammatory NFκB pathway, so CNP-miR146a has a synergistic role in modulating both oxidative stress and inflammation. In this study, we define the mechanism(s) by which CNP-miR146a improves diabetic wound healing by examining immunohistochemical and gene expression analysis of markers of inflammation, oxidative stress, fibrosis, and angiogenesis. We have found that intradermal injection of CNP-miR146a increases wound collagen, enhances angiogenesis, and lowers inflammation and oxidative stress, ultimately promoting faster closure of diabetic wounds.

Cerium oxide nanoparticle delivery of microRNA-146a for local treatment of acute lung injury.

Acute respiratory distress syndrome (ARDS) is a devastating pulmonary disease with significant in-hospital mortality and is the leading cause of death in COVID-19 patients. Excessive leukocyte recruitment, unregulated inflammation, and resultant fibrosis contribute to poor ARDS outcomes. Nanoparticle technology with cerium oxide nanoparticles (CNP) offers a mechanism by which unstable therapeutics such as the anti-inflammatory microRNA-146a can be locally delivered to the injured lung without systemic uptake. In this study, we evaluated the potential of the radical scavenging CNP conjugated to microRNA-146a (termed CNP-miR146a) in preventing acute lung injury (ALI) following exposure to bleomycin. We have found that intratracheal delivery of CNP-miR146a increases pulmonary levels of miR146a without systemic increases, and prevents ALI by altering leukocyte recruitment, reducing inflammation and oxidative stress, and decreasing collagen deposition, ultimately improving pulmonary biomechanics.

Is Tapering Enteroplasty an Alternative to Resection of Dilated Bowel in Small Intestinal Atresia?

BACKGROUND: Intestinal atresia is a congenital defect resulting in intestinal discontinuity and can be associated with significant morbidity related to intestinal failure. The bowel proximal to the atresia is often significantly dilated and dysfunctional. The treatment approaches of this dilated bowel include resection with primary anastomosis versus tapering enteroplasty with preservation of bowel length. The purpose of this study was to compare these two approaches in regard to bowel function as characterized by the time to full enteral feeding. METHODS: A retrospective review was performed of intestinal atresia repair performed at a tertiary referral pediatric hospital from 2007 to 2017. Length of stay, time to full enteral feeds, and complications were assessed in patients who underwent repair with tapering enteroplasty (n = 8) and compared with those who underwent resection and anastomosis (n = 39). RESULTS: The median age at surgery, gender distribution, weeks gestational age (WGA), location of the atresia, and comorbidities were similar between the two groups. Overall, there was no statistically significant difference in length of stay and time to full enteral feeds between groups. Three of eight (38%) patients in the tapered group and five of 39 patients (13%; P = 0.12) in the nontapered group underwent further surgical exploration because of bowel dysmotility. Factors associated with longer length of hospital stay were abdominal reoperation and WGA, and factors associated with longer time to full enteral feeds were WGA, abdominal reoperation, and gastroschisis. CONCLUSIONS: Tapering enteroplasty at initial operation for intestinal atresias preserves bowel length and has statistically equivalent outcomes to resection and anastomosis in regard to the length of stay and time to full enteral feeds.

Thromboelastography-guided management of coagulopathy in neonates with congenital diaphragmatic hernia supported by extracorporeal membrane oxygenation.

PURPOSE: Congenital diaphragmatic hernia (CDH) can cause severe hemodynamic deterioration requiring support with extracorporeal membrane oxygenation (ECMO). ECMO is associated with hemorrhagic and thromboembolic complications. In 2015, we standardized anti-coagulation management on ECMO, incorporating thromboelastography (TEG) as an adjunct to manage hemostasis of CDH patients. The purpose of this study is to evaluate our blood product utilization, choice of blood product use in response to abnormal TEG parameters, and the associated effect on bleeding and thrombotic complications. METHODS: We retrospectively reviewed all CDH neonates supported by ECMO between 2008 and 2018. Blood product administration, TEG data, and hemorrhagic and thrombotic complications data were collected. We divided subjects into two groups pre-2015 and post-2015. RESULTS: After 2015, platelet transfusion was administered for a low maximum amplitude (MA) more frequently (77% compared to 65%, p = 0.0007). Cryoprecipitate was administered less frequently for a low alpha-angle (28% compared to 41%, p = 0.0016). There was no difference in fresh frozen plasma use over time. After standardizing the use of TEG, we observed a significant reduction in hemothoraces (18% compared to 54%, p = 0.026). CONCLUSION: Institutional standardization of anti-coagulation management of CDH neonates on ECMO, including the use of goal-directed TEG monitoring may lead to improved blood product utilization and a decrease in bleeding complications in neonates with CDH supported by ECMO. LEVEL OF EVIDENCE/TYPE OF STUDY: Level III, Retrospective comparative study.

Examination of Prenatal Sonographic Findings: Intra-Abdominal Bowel Dilation Predicts Poor Gastroschisis Outcomes.

BACKGROUND: Gastroschisis is an anterior abdominal wall defect with variable outcomes. There are conflicting data regarding the prognostic value of sonographic findings. OBJECTIVES: The aim of this study was to identify prenatal ultrasonographic features associated with poor neonatal outcomes. METHOD: A retrospective review of 55 patients with gastroschisis from 2007 to 2017 was completed. Ultrasounds were reviewed for extra-abdominal intestinal diameter (EAID) and intra-abdominal intestinal diameter (IAID), echogenicity, visceral content within the herniation, amniotic fluid index, defect size, and abdominal circumference (AC). Ultrasound variables were correlated with full enteral feeding and the diagnosis of a complex gastroschisis. RESULTS: Bivariate analysis demonstrated an increased time to full enteral feeds with increasing number of surgeries, EAID, and IAID. Additionally, there was a significant relationship between IAID and AC percentile with the diagnosis of complex gastroschisis. On multivariate analysis, only IAID was significant and increasing diameter had a 2.82 (95% CI 1.02-7.78) higher odds of a longer time to full enteral feeds and a 1.2 (95% CI 1.05-1.36) greater odds of the diagnosis of a complex gastroschisis. CONCLUSIONS: Based on these findings, IAID is associated with a longer time to full enteral feeding and the diagnosis of complex gastroschisis.

MOMS Plus: Single-Institution Review of Outcomes for Extended BMI Criteria for Open Fetal Repair of Myelomeningocele.

BACKGROUND: In utero repair has become an accepted therapy to decrease the rate of ventriculoperitoneal shunting and improve neurologic function in select cases of myelomeningocele. The Management of Myelomeningocele Study (MOMS) trial excluded patients with a BMI >35 due to concerns for increased maternal complications and preterm delivery, limiting the population that may benefit from this intervention. OBJECTIVES: The aim of this study was to evaluate outcomes associated with extending the maternal BMI criteria to 40 in open fetal repair of myelomeningocele. METHOD: Retrospective review of fetal closure of myelomeningocele at a quaternary referral center between 2013 and 2016 with maternal BMI ranging from 35 to 40. RESULTS: Eleven patients with a BMI >35 were identified. The average BMI was 37. The average maternal age at the time of evaluation was 27 years. The average gestational age at fetal surgery was 24 weeks. Gestational age at birth was an average of 32 weeks. There was one perinatal death immediately following the fetal intervention. The shunt rate at 1 year was 45% (5/11 patients). CONCLUSIONS: In this single-institution review of expanded BMI criteria for fetal repair of myelomeningocele, we did not observe any adverse maternal outcomes associated with maternal obesity; however, the gestational age at delivery was 2 weeks earlier compared to the MOMS trial.

Hand-to-hand coupling and strategies to minimize unintentional energy transfer during laparoscopic surgery.

BACKGROUND: Energy-based devices are used in nearly every laparoscopic operation. Radiofrequency energy can transfer to nearby instruments via antenna and capacitive coupling without direct contact. Previous studies have described inadvertent energy transfer through bundled cords and nonelectrically active wires. The purpose of this study was to describe a new mechanism of stray energy transfer from the monopolar instrument through the operating surgeon to the laparoscopic telescope and propose practical measures to decrease the risk of injury. METHODS: Radiofrequency energy was delivered to a laparoscopic L-hook (monopolar "bovie"), an advanced bipolar device, and an ultrasonic device in a laparoscopic simulator. The tip of a 10-mm telescope was placed adjacent but not touching bovine liver in a standard four-port laparoscopic cholecystectomy setup. Temperature increase was measured as tissue temperature from baseline nearest the tip of the telescope which was never in contact with the energy-based device after a 5-s open-air activation. RESULTS: The monopolar L-hook increased tissue temperature adjacent to the camera/telescope tip by 47 ± 8°C from baseline (P < 0.001). By having an assistant surgeon hold the camera/telescope (rather than one surgeon holding both the active electrode and the camera/telescope), temperature change was reduced to 26 ± 7°C (P < 0.001). Alternative energy devices significantly reduced temperature change in comparison to the monopolar instrument (47 ± 8°C) for both the advanced bipolar (1.2 ± 0.5°C; P < 0.001) and ultrasonic (0.6 ± 0.3°C; P < 0.001) devices. CONCLUSIONS: Stray energy transfers from the monopolar "bovie" instrument through the operating surgeon to standard electrically inactive laparoscopic instruments. Hand-to-hand coupling describes a new form of capacitive coupling where the surgeon's body acts as an electrical conductor to transmit energy. Strategies to reduce stray energy transfer include avoiding the same surgeon holding the active electrode and laparoscopic camera or using alternative energy devices.

Single-molecule long-read 16S sequencing to characterize the lung microbiome from mechanically ventilated patients with suspected pneumonia.

In critically ill patients, the development of pneumonia results in significant morbidity and mortality and additional health care costs. The accurate and rapid identification of the microbial pathogens in patients with pulmonary infections might lead to targeted antimicrobial therapy with potentially fewer adverse effects and lower costs. Major advances in next-generation sequencing (NGS) allow culture-independent identification of pathogens. The present study used NGS of essentially full-length PCR-amplified 16S ribosomal DNA from the bronchial aspirates of intubated patients with suspected pneumonia. The results from 61 patients demonstrated that sufficient DNA was obtained from 72% of samples, 44% of which (27 samples) yielded PCR amplimers suitable for NGS. Out of the 27 sequenced samples, only 20 had bacterial culture growth, while the microbiological and NGS identification of bacteria coincided in 17 (85%) of these samples. Despite the lack of bacterial growth in 7 samples that yielded amplimers and were sequenced, the NGS identified a number of bacterial species in these samples. Overall, a significant diversity of bacterial species was identified from the same genus as the predominant cultured pathogens. The numbers of NGS-identifiable bacterial genera were consistently higher than identified by standard microbiological methods. As technical advances reduce the processing and sequencing times, NGS-based methods will ultimately be able to provide clinicians with rapid, precise, culture-independent identification of bacterial, fungal, and viral pathogens and their antimicrobial sensitivity profiles.

Muscle Flap Technique Safe for On-ECMO Congenital Diaphragmatic Hernia Repair.

INTRODUCTION: Prosthetic patches (patch) and muscle flaps (flap) are techniques used for repair of congenital diaphragmatic hernia (CDH) with a large defect unamenable to primary closure. We hypothesized that the flap technique for CDH repair while on extra-corporeal membrane oxygenation (on-ECMO) would have decreased bleeding complications compared to patch due to the hemostatic advantage of native tissue. METHODS: A single-center retrospective comparative study of patients who underwent on-ECMO CDH repair between 2008 and 2022 was performed. RESULTS: Fifty-two patients met inclusion criteria: 18 patch (34.6%) and 34 flap (65.4%). There was no difference in CDH severity between groups. On univariate analysis, reoperation for surgical bleeding was lower following flap repair compared to patch (23.5% vs 55.6%, respectively; p = 0.045), 48-h postoperative blood product transfusion was lower after flap repair (132 mL/kg vs 273.5 mL/kg patch; p = 0.006), and two-year survival was increased in the flap repair group compared to patch (53.1% vs 17.7%, respectively; p = 0.036). On multivariate analysis adjusting for CDH side, day on ECMO repaired, and day of life CDH repaired, flap repair was significantly associated with lower five-day postoperative packed red blood cell transfusion amount, improved survival to hospital discharge, and improved two-year survival. CONCLUSIONS: Our experience suggests that the muscle flap technique for on-ECMO CDH repair is associated with reduced bleeding complications compared to prosthetic patch repair, which may in part be responsible for the improved survival seen in the flap repair group. These results support the flap repair technique as a favored method for on-ECMO CDH repair. LEVEL OF EVIDENCE: Level III.

Drug-regulated CD33-targeted CAR T cells control AML using clinically optimized rapamycin dosing.

Chimeric antigen receptor (CAR) designs that incorporate pharmacologic control are desirable; however, designs suitable for clinical translation are needed. We designed a fully human, rapamycin-regulated drug product for targeting CD33+ tumors called dimerizaing agent-regulated immunoreceptor complex (DARIC33). T cell products demonstrated target-specific and rapamycin-dependent cytokine release, transcriptional responses, cytotoxicity, and in vivo antileukemic activity in the presence of as little as 1 nM rapamycin. Rapamycin withdrawal paused DARIC33-stimulated T cell effector functions, which were restored following reexposure to rapamycin, demonstrating reversible effector function control. While rapamycin-regulated DARIC33 T cells were highly sensitive to target antigen, CD34+ stem cell colony-forming capacity was not impacted. We benchmarked DARIC33 potency relative to CD19 CAR T cells to estimate a T cell dose for clinical testing. In addition, we integrated in vitro and preclinical in vivo drug concentration thresholds for off-on state transitions, as well as murine and human rapamycin pharmacokinetics, to estimate a clinically applicable rapamycin dosing schedule. A phase I DARIC33 trial has been initiated (PLAT-08, NCT05105152), with initial evidence of rapamycin-regulated T cell activation and antitumor impact. Our findings provide evidence that the DARIC platform exhibits sensitive regulation and potency needed for clinical application to other important immunotherapy targets.

Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features.

Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.

Success and Pitfalls of Genetic Testing in Undiagnosed Diseases: Whole Exome Sequencing and Beyond.

Novel approaches to uncover the molecular etiology of neurodevelopmental disorders (NDD) are highly needed. Even using a powerful tool such as whole exome sequencing (WES), the diagnostic process may still prove long and arduous due to the high clinical and genetic heterogeneity of these conditions. The main strategies to improve the diagnostic rate are based on family segregation, re-evaluation of the clinical features by reverse-phenotyping, re-analysis of unsolved NGS-based cases and epigenetic functional studies. In this article, we described three selected cases from a cohort of patients with NDD in which trio WES was applied, in order to underline the typical challenges encountered during the diagnostic process: (1) an ultra-rare condition caused by a missense variant in MEIS2, identified through the updated Solve-RD re-analysis; (2) a patient with Noonan-like features in which the NGS analysis revealed a novel variant in NIPBL causing Cornelia de Lange syndrome; and (3) a case with de novo variants in genes involved in the chromatin-remodeling complex, for which the study of the epigenetic signature excluded a pathogenic role. In this perspective, we aimed to (i) provide an example of the relevance of the genetic re-analysis of all unsolved cases through network projects on rare diseases; (ii) point out the role and the uncertainties of the reverse phenotyping in the interpretation of the genetic results; and (iii) describe the use of methylation signatures in neurodevelopmental syndromes for the validation of the variants of uncertain significance.

Systematic identification of disease-causing promoter and untranslated region variants in 8,040 undiagnosed individuals with rare disease.

Background: Both promoters and untranslated regions (UTRs) have critical regulatory roles, yet variants in these regions are largely excluded from clinical genetic testing due to difficulty in interpreting pathogenicity. The extent to which these regions may harbour diagnoses for individuals with rare disease is currently unknown. Methods: We present a framework for the identification and annotation of potentially deleterious proximal promoter and UTR variants in known dominant disease genes. We use this framework to annotate de novo variants (DNVs) in 8,040 undiagnosed individuals in the Genomics England 100,000 genomes project, which were subject to strict region-based filtering, clinical review, and validation studies where possible. In addition, we performed region and variant annotation-based burden testing in 7,862 unrelated probands against matched unaffected controls. Results: We prioritised eleven DNVs and identified an additional variant overlapping one of the eleven. Ten of these twelve variants (82%) are in genes that are a strong match to the individual's phenotype and six had not previously been identified. Through burden testing, we did not observe a significant enrichment of potentially deleterious promoter and/or UTR variants in individuals with rare disease collectively across any of our region or variant annotations. Conclusions: Overall, we demonstrate the value of screening promoters and UTRs to uncover additional diagnoses for previously undiagnosed individuals with rare disease and provide a framework for doing so without dramatically increasing interpretation burden.

Heterozygous loss-of-function SMC3 variants are associated with variable and incompletely penetrant growth and developmental features.

Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 13 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated a milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, some instead having intriguing symptomatologies with rational biological links to SMC3 including bone marrow failure, acute myeloid leukemia, and Coats retinal vasculopathy. Analyses of transcriptomic and epigenetic data suggest that SMC3 pLoF variants reduce SMC3 expression but do not result in a blood DNA methylation signature clustering with that of CdLS, and that the global transcriptional signature of SMC3 loss is model-dependent. Our finding of substantial population-scale LoF intolerance in concert with variable penetrance in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multi-layered genomic data paired with careful phenotyping.

Impact of an emergency department observation unit transient ischemic attack protocol on length of stay and cost.

This study examined the impact of an emergency department (ED) observation unit's accelerated diagnostic protocol (ADP) on hospital length of stay (LOS), cost of care, and clinical outcome of patients who had sustained a transient ischemic attack (TIA). All patients with TIA presenting to the ED over a 18-consecutive month period were eligible for the study. During the initial 11 months of the study (pre-ADP period), all patients were admitted to the neurology service. Over the subsequent 7 months (post-ADP period), patients were either managed using the ADP or were admitted based on ADP exclusion criteria or at a physician's discretion. All patients had orders for serial clinical examinations, neurologic evaluation, cardiac monitoring, vascular imaging of the brain and neck, and echocardiography. A total of 142 patients were included in the study (mean age, 67.9 ± 13.9 years; 61% female; mean ABCD(2) score, 4.3 ± 1.4). In the post-ADP period, 68% of the patients were managed using the ADP. Of these patients, 79% were discharged with a median LOS of 25.5 hours (ED + observation unit). Compared with the pre-ADP patients, the post-ADP patients (ADP and non-ADP) had a 20.8-hour shorter median LOS (95% confidence interval, 16.3-25.1 hours; P < .01) than pre-ADP patients and lower median associated costs (cost difference, $1643; 95% confidence interval, $1047-$2238). The stroke rate at 90 days was low in both groups (pre-ADP, 0%; post-ADP, 1.2%). Our findings indicate that introduction of an ED observation unit ADP for patients with TIA at a primary stroke center is associated with a significantly shorter LOS and lower costs compared with inpatient admission, with comparable clinical outcomes.

High-resolution mapping of the neutralizing and binding specificities of polyclonal sera post-HIV Env trimer vaccination.

Mapping polyclonal serum responses is critical to rational vaccine design. However, most high-resolution mapping approaches involve isolating and characterizing individual antibodies, which incompletely defines the polyclonal response. Here we use two complementary approaches to directly map the specificities of the neutralizing and binding antibodies of polyclonal anti-HIV-1 sera from rabbits immunized with BG505 Env SOSIP trimers. We used mutational antigenic profiling to determine how all mutations in Env affected viral neutralization and electron microscopy polyclonal epitope mapping (EMPEM) to directly visualize serum Fabs bound to Env trimers. The dominant neutralizing specificities were generally only a subset of the more diverse binding specificities. Additional differences between binding and neutralization reflected antigenicity differences between virus and soluble Env trimer. Furthermore, we refined residue-level epitope specificity directly from sera, revealing subtle differences across sera. Together, mutational antigenic profiling and EMPEM yield a holistic view of the binding and neutralizing specificity of polyclonal sera.

Vaccines work by stimulating the immune system to produce proteins called antibodies. These antibodies bind to the virus targeted by the vaccine and block the virus from infecting cells. It has been difficult to develop a vaccine for HIV because frequent mutations allow it to evade antibodies. Understanding exactly how these proteins bind to HIV and how various mutations enable the virus to escape them is crucial to designing a successful HIV vaccine. Over the last decade, scientists have developed new techniques for studying individual antibodies and how they bind to viruses. Now, they are using these insights to design vaccines. Most vaccines result in the production of many antibodies that bind to different parts of the virus, making it harder for a virus to escape. But studying many antibodies with different targets on the virus simultaneously remains challenging. By combining two-cutting edge approaches, Dingens et al. catalogued the many antibodies that rabbits produce in response to an experimental vaccine for HIV. In the experiments, they mapped how two types of rabbit antibodies target the virus: those that could bind to the virus, and those that could both bind and neutralize the virus (i.e., block it from infecting cells). The experiments showed that small differences between the HIV virus and the vaccine explained why some rabbit antibodies created in response to the vaccine could bind but not neutralize the virus. Moreover, the ability to stop HIV from infecting the cells appeared to be reserved to antibodies that could bind to several different locations at the virus. Dingens et al. further documented all the virus mutations that would allow it to evade neutralizing antibodies. The techniques used in the experiments may help scientists identify the best sites on the HIV virus to target with vaccines and to better understand the binding and neutralizing activity of antibodies. The results of the experiments may also help to redesign the experimental HIV vaccine ­ which is currently being tested in humans ­ to be even more effective.