Convergent Structures Illuminate Features for Germline Antibody Binding and Pan-Lassa Virus Neutralization.

Lassa virus (LASV) causes hemorrhagic fever and is endemic in West Africa. Protective antibody responses primarily target the LASV surface glycoprotein (GPC), and GPC-B competition group antibodies often show potent neutralizing activity in humans. However, which features confer potent and broadly neutralizing antibody responses is unclear. Here, we compared three crystal structures of LASV GPC complexed with GPC-B antibodies of varying neutralization potency. Each GPC-B antibody recognized an overlapping epitope involved in binding of two adjacent GPC monomers and preserved the prefusion trimeric conformation. Differences among GPC-antibody interactions highlighted specific residues that enhance neutralization. Using structure-guided amino acid substitutions, we increased the neutralization potency and breadth of these antibodies to include all major LASV lineages. The ability to define antibody residues that allow potent and broad neutralizing activity, together with findings from analyses of inferred germline precursors, is critical to develop potent therapeutics and for vaccine design and assessment.

Cohesin Loss Eliminates All Loop Domains.

The human genome folds to create thousands of intervals, called "contact domains," that exhibit enhanced contact frequency within themselves. "Loop domains" form because of tethering between two loci-almost always bound by CTCF and cohesin-lying on the same chromosome. "Compartment domains" form when genomic intervals with similar histone marks co-segregate. Here, we explore the effects of degrading cohesin. All loop domains are eliminated, but neither compartment domains nor histone marks are affected. Loss of loop domains does not lead to widespread ectopic gene activation but does affect a significant minority of active genes. In particular, cohesin loss causes superenhancers to co-localize, forming hundreds of links within and across chromosomes and affecting the regulation of nearby genes. We then restore cohesin and monitor the re-formation of each loop. Although re-formation rates vary greatly, many megabase-sized loops recovered in under an hour, consistent with a model where loop extrusion is rapid.

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.

RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here, we develop PARIS, a method based on reversible psoralen crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher-order architectures, and RNA-RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on an individual-molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures and discovered conserved long-range and alternative structures. XIST, a long noncoding RNA (lncRNA) essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher-order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome. VIDEO ABSTRACT.

A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ∼10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs "facing" one another. The inactive X chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats.

Hospital Prices for Physician-Administered Drugs for Patients with Private Insurance.

BACKGROUND: Hospitals can leverage their position between the ultimate buyers and sellers of drugs to retain a substantial share of insurer pharmaceutical expenditures. METHODS: In this study, we used 2020-2021 national Blue Cross Blue Shield claims data regarding patients in the United States who had drug-infusion visits for oncologic conditions, inflammatory conditions, or blood-cell deficiency disorders. Markups of the reimbursement prices were measured in terms of amounts paid by Blue Cross Blue Shield plans to hospitals and physician practices relative to the amounts paid by these providers to drug manufacturers. Acquisition-price reductions in hospital payments to drug manufacturers were measured in terms of discounts under the federal 340B Drug Pricing Program. We estimated the percentage of Blue Cross Blue Shield drug spending that was received by drug manufacturers and the percentage retained by provider organizations. RESULTS: The study included 404,443 patients in the United States who had 4,727,189 drug-infusion visits. The median price markup (defined as the ratio of the reimbursement price to the acquisition price) for hospitals eligible for 340B discounts was 3.08 (interquartile range, 1.87 to 6.38). After adjustment for drug, patient, and geographic factors, price markups at hospitals eligible for 340B discounts were 6.59 times (95% confidence interval [CI], 6.02 to 7.16) as high as those in independent physician practices, and price markups at noneligible hospitals were 4.34 times (95% CI, 3.77 to 4.90) as high as those in physician practices. Hospitals eligible for 340B discounts retained 64.3% of insurer drug expenditures, whereas hospitals not eligible for 340B discounts retained 44.8% and independent physician practices retained 19.1%. CONCLUSIONS: This study showed that hospitals imposed large price markups and retained a substantial share of total insurer spending on physician-administered drugs for patients with private insurance. The effects were especially large for hospitals eligible for discounts under the federal 340B Drug Pricing Program on acquisition costs paid to manufacturers. (Funded by Arnold Ventures and the National Institute for Health Care Management.).

Cooperative transitions involving hydrophobic polyelectrolytes.

Hydrophobic polyelectrolytes (HPEs) can solubilize bilayer membranes, form micelles, or can reversibly aggregate as a function of pH. The transitions are often remarkably sharp. We show that these cooperative transitions occur by a competition between two or more conformational states and can be explained within the framework of Monod-Wymann-Changeux (MWC) theory that was originally formulated for allosteric interactions. Here, we focus on the pH-dependent destabilization and permeation of bilayer membranes by HPEs. We formulate the general conditions that lead to sharp conformational transitions involving simple macromolecules mediated by concentration variations of molecular ligands. That opens up potential applications ranging from medicine to the development of switchable materials.

Prenatal Infection by Respiratory Viruses Is Associated with Immunoinflammatory Responses in the Fetus.

Rationale: Respiratory viral infections can be transmitted from pregnant women to their offspring, but frequency, mechanisms, and postnatal outcomes remain unclear. Objectives: The aims of this prospective cohort study were to compare the frequencies of transplacental transmission of respiratory syncytial virus (RSV) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), analyze the concentrations of inflammatory mediators in maternal and fetal blood, and assess clinical consequences. Methods: We recruited pregnant women who developed upper respiratory infections or tested positive for SARS-CoV-2. Maternal and cord blood samples were collected at delivery. Study questionnaires and electronic medical records were used to document demographic and medical information. Measurements and Main Results: From October 2020 to June 2022, droplet digital PCR was used to test blood mononuclear cells from 103 mother-baby dyads. Twice more newborns in our sample were vertically infected with RSV compared with SARS-CoV-2 (25.2% [26 of 103] vs. 11.9% [12 of 101]; P = 0.019). Multiplex ELISA measured significantly increased concentrations of several inflammatory cytokines and chemokines in maternal and cord blood from newborns, with evidence of viral exposure in utero compared with control dyads. Prenatal infection was associated with significantly lower birth weight and postnatal weight growth. Conclusions: Data suggest a higher frequency of vertical transmission for RSV than SARS-CoV-2. Intrauterine exposure is associated with fetal inflammation driven by soluble inflammatory mediators, with expression profiles dependent on the virus type and affecting the rate of viral transmission. Virus-induced inflammation may have pathological consequences already in the first days of life, as shown by its effects on birth weight and postnatal weight growth.

The IPD-IMGT/HLA Database.

It is 24 years since the IPD-IMGT/HLA Database, http://www.ebi.ac.uk/ipd/imgt/hla/, was first released, providing the HLA community with a searchable repository of highly curated HLA sequences. The database now contains over 35 000 alleles of the human Major Histocompatibility Complex (MHC) named by the WHO Nomenclature Committee for Factors of the HLA System. This complex contains the most polymorphic genes in the human genome and is now considered hyperpolymorphic. The IPD-IMGT/HLA Database provides a stable and user-friendly repository for this information. Uptake of Next Generation Sequencing technology in recent years has driven an increase in the number of alleles and the length of sequences submitted. As the size of the database has grown the traditional methods of accessing and presenting this data have been challenged, in response, we have developed a suite of tools providing an enhanced user experience to our traditional web-based users while creating new programmatic access for our bioinformatics user base. This suite of tools is powered by the IPD-API, an Application Programming Interface (API), providing scalable and flexible access to the database. The IPD-API provides a stable platform for our future development allowing us to meet the future challenges of the HLA field and needs of the community.

COVID-19 Vaccine Side Effects and Long-Term Neutralizing Antibody Response : A Prospective Cohort Study.

BACKGROUND: Concern about side effects is a common reason for SARS-CoV-2 vaccine hesitancy. OBJECTIVE: To determine whether short-term side effects of SARS-CoV-2 messenger RNA (mRNA) vaccination are associated with subsequent neutralizing antibody (nAB) response. DESIGN: Prospective cohort study. SETTING: San Francisco Bay Area. PARTICIPANTS: Adults who had not been vaccinated against or exposed to SARS-CoV-2, who then received 2 doses of either BNT162b2 or mRNA-1273. MEASUREMENTS: Serum nAB titer at 1 month and 6 months after the second vaccine dose. Daily symptom surveys and objective biometric measurements at each dose. RESULTS: 363 participants were included in symptom-related analyses (65.6% female; mean age, 52.4 years [SD, 11.9]), and 147 were included in biometric-related analyses (66.0% female; mean age, 58.8 years [SD, 5.3]). Chills, tiredness, feeling unwell, and headache after the second dose were each associated with 1.4 to 1.6 fold higher nAB at 1 and 6 months after vaccination. Symptom count and vaccination-induced change in skin temperature and heart rate were all positively associated with nAB across both follow-up time points. Each 1 °C increase in skin temperature after dose 2 was associated with 1.8 fold higher nAB 1 month later and 3.1 fold higher nAB 6 months later. LIMITATIONS: The study was conducted in 2021 in people receiving the primary vaccine series, making generalizability to people with prior SARS-CoV-2 vaccination or exposure unclear. Whether the observed associations would also apply for neutralizing activity against non-ancestral SARS-CoV-2 strains is also unknown. CONCLUSION: Convergent self-report and objective biometric findings indicate that short-term systemic side effects of SARS-CoV-2 mRNA vaccination are associated with greater long-lasting nAB responses. This may be relevant in addressing negative attitudes toward vaccine side effects, which are a barrier to vaccine uptake. PRIMARY FUNDING SOURCE: National Institute on Aging.

Ebola Virus-Specific Neutralizing Antibody Persists at High Levels in Survivors 2 Years After Resolution of Disease in a Sierra Leonean Cohort.

Ebola virus (EBOV) infection results in Ebola virus disease (EVD), an often severe disease with a nonspecific presentation. Since its recognition, periodic outbreaks of EVD continue to occur in sub-Saharan Africa. The 2013-2016 West African EVD outbreak was the largest recorded, resulting in a substantial cohort of EVD survivors with persistent health complaints and variable immune responses. In this study, we characterize humoral immune responses in EVD survivors and their contacts in Eastern Sierra Leone. We found high levels of EBOV IgG in EVD survivors and lower yet substantial antibody levels in household contacts, suggesting subclinical transmission. Neutralizing antibody function was prevalent but variable in EVD survivors, raising questions about the durability of immune responses from natural infection with EBOV. Additionally, we found that certain discrete symptoms-ophthalmologic and auditory-are associated with EBOV IgG seropositivity, while an array of symptoms are associated with the presence of neutralizing antibody.

Multicomponent Synthesis of α-Branched Amines via a Zinc-Mediated Carbonyl Alkylative Amination Reaction.

Methods for the synthesis of α-branched alkylamines are important due to their ubiquity in biologically active molecules. Despite the development of many methods for amine preparation, C(sp3)-rich nitrogen-containing compounds continue to pose challenges for synthesis. While carbonyl reductive amination (CRA) between ketones and alkylamines is the cornerstone method for α-branched alkylamine synthesis, it is sometimes limited by the sterically demanding condensation step between dialkyl ketones and amines and the more restricted availability of ketones compared to aldehydes. We recently reported a "higher-order" variant of this transformation, carbonyl alkylative amination (CAA), which utilized a halogen atom transfer (XAT)-mediated radical mechanism, enabling the streamlined synthesis of complex α-branched alkylamines. Despite the efficacy of this visible-light-driven approach, it displayed scalability issues, and competitive reductive amination was a problem for certain substrate classes, limiting applicability. Here, we report a change in the reaction regime that expands the CAA platform through the realization of an extremely broad zinc-mediated CAA reaction. This new strategy enabled elimination of competitive CRA, simplified purification, and improved reaction scope. Furthermore, this new reaction harnessed carboxylic acid derivatives as alkyl donors and facilitated the synthesis of α-trialkyl tertiary amines, which cannot be accessed via CRA. This Zn-mediated CAA reaction can be carried out at a variety of scales, from a 10 µmol setup in microtiter plates enabling high-throughput experimentation, to the gram-scale synthesis of medicinally-relevant compounds. We believe that this transformation enables robust, efficient, and economical access to α-branched alkylamines and provides a viable alternative to the current benchmark methods.

igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV).

SUMMARY: igv.js is an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). It can be easily dropped into any web page with a single line of code and has no external dependencies. The viewer runs completely in the web browser, with no backend server and no data pre-processing required. AVAILABILITY AND IMPLEMENTATION: The igv.js JavaScript component can be installed from NPM at https://www.npmjs.com/package/igv. The source code is available at https://github.com/igvteam/igv.js under the MIT open-source license. IGV-Web, the end-user application built around igv.js, is available at https://igv.org/app. The source code is available at https://github.com/igvteam/igv-webapp under the MIT open-source license. SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.

An ACE2-dependent Sarbecovirus in Russian bats is resistant to SARS-CoV-2 vaccines.

Spillover of sarbecoviruses from animals to humans has resulted in outbreaks of severe acute respiratory syndrome SARS-CoVs and the ongoing COVID-19 pandemic. Efforts to identify the origins of SARS-CoV-1 and -2 has resulted in the discovery of numerous animal sarbecoviruses-the majority of which are only distantly related to known human pathogens and do not infect human cells. The receptor binding domain (RBD) on sarbecoviruses engages receptor molecules on the host cell and mediates cell invasion. Here, we tested the receptor tropism and serological cross reactivity for RBDs from two sarbecoviruses found in Russian horseshoe bats. While these two viruses are in a viral lineage distinct from SARS-CoV-1 and -2, the RBD from one virus, Khosta 2, was capable of using human ACE2 to facilitate cell entry. Viral pseudotypes with a recombinant, SARS-CoV-2 spike encoding for the Khosta 2 RBD were resistant to both SARS-CoV-2 monoclonal antibodies and serum from individuals vaccinated for SARS-CoV-2. Our findings further demonstrate that sarbecoviruses circulating in wildlife outside of Asia also pose a threat to global health and ongoing vaccine campaigns against SARS-CoV-2.

Barriers to Office Hysteroscopy in Fellowship Education and Practice.

STUDY OBJECTIVE: To identify the top 3 perceived barriers to performing office hysteroscopy (OH) by minimally invasive gynecologic surgery (MIGS) faculty and fellows and identify opportunities for education on this key topic that will be most effective in fellowship training and MIGS practice. DESIGN: Cross-sectional survey study targeted at all American Association of Gynecologic Laparoscopists-accredited Fellowship in Minimally Invasive Gynecologic Surgery fellows, program directors, and associate program directors in February to April 2022. The survey was designed by faculty who have extensive experience in OH procedures. In addition, a literature search was performed to aid with question design. SETTING, PATIENTS, AND INTERVENTIONS: This was a REDCap electronic survey administered through the Fellowship in Minimally Invasive Gynecologic Surgery listserv. No additional follow-up was performed after survey completion. The 15-minute survey was sent to 60 program directors, 92 assistant program directors, and 158 fellows, including the incoming class of 2024 and the 2022 fellowship graduates. MEASUREMENTS AND MAIN RESULTS: A total of 93 responses were received; 67% of respondents performed OH but 73% of those performed 5 procedures or less per month. Most participants controlled pain with nonsteroidal anti-inflammatory drugs +/- paracervical block. The most common perceived barrier to performing OH was concern over pain management. Other commonly cited concerns were equipment costs, sterilization costs, and office staff training; 37% to 44% of respondents also cited lack of departmental support and insufficient clinic time, respectively, as barriers, and 56% indicated they are interested in educational materials on OH. CONCLUSION: Our study suggests general interest in, but a low volume of, OH among MIGS fellows and faculty. The most common perceived barrier was concern regarding pain management. This has been well studied in the literature and likely presents an area for greater education to improve OH utilization. We also uncovered concerns regarding systemic barriers, such as equipment costs, departmental support, and clinic structure. This is an area for further research and advocacy efforts to address barriers to OH on a system level.

Satisfactory 5-year functional outcomes following primary ACL reconstructions from the UK National Ligament Registry.

PURPOSE: The aim of this study was to describe the 10-year findings from the UK National Ligament Registry (NLR). METHODS: A retrospective review was performed for prospectively collected data on the NLR between January 2013 and December 2022. All patients who underwent primary ACL reconstruction (ACLR) on the registry were included. Surgical characteristics were analysed, including surgeon grade and case volume, concomitant knee procedures, venous thromboembolic prophylaxis, graft characteristics, femoral and tibial tunnel drilling, and fixation methods. Clinical outcomes were collected preoperatively and at 6 months, 1 year, 2 years and 5 years following the index procedure. RESULTS: During the study period, 17,492 unilateral ACLR procedures were recorded. Autograft was used in 98%, most commonly a combined semitendinosus and gracilis graft (77%) or patella tendon graft (31%). Allograft was used in only 1% of the patients. In 52% of cases, ACLR was associated with an additional procedure, with isolated medial meniscal surgery being the most common (21%). Femoral tunnel drilling was mostly performed through an anteromedial portal (73%) and tibial tunnel drilling using an outside-in technique (92%). The most common method of femoral graft fixation was with an Endobutton fixed loop suspensory device (77%), while interference screws predominated for tibial tunnel fixation (86%). Patients who underwent ACLR surgery showed significant improvement in their functional outcome scores at six months, 1 year, 2 years and 5 years postoperatively. CONCLUSION: Data from the NLR shows a detailed description of the current trends and evolution of ACLR in the United Kingdom over the last 10 years. Satisfactory functional outcomes were observed 5 years postoperatively. This study provides useful information on the prevalence of ACL-associated injuries and current surgical techniques with the aim of improving the quality of clinical care and patients' outcomes. Moreover, it provides surgeons with a benchmark against which to compare current practices and functional outcomes following ACLR across the United Kingdom. LEVEL OF EVIDENCE: Level III.

Ten-year results from the UK National Ligament Registry: Patient characteristics and factors predicting nonresponders for completion of outcome scores.

PURPOSE: The aim of this study was to report the demographic and mechanism of injury data in the UK National Ligament Registry (NLR) at 10 years and determine factors leading to poor compliance with completion of Patient-Reported Outcome Scores (PROMs). METHODS: A retrospective review was performed for prospectively collected data on the NLR between January 2013 and December 2022. All patients who underwent primary anterior cruciate ligament reconstruction (ACLR) were included. Patient demographics, mechanism of injury and patient compliance with completing PROMs were analysed. Patient characteristics were further analysed in relation to compliance with completing the different PROMs at the predefined time points. Patients were identified as nonresponders if they had not completed either 1- or 2-year postoperative Knee injury and Osteoarthritis Outcome Score (KOOS). RESULTS: A total of 17,492 patients were included in this study. The average age for patients undergoing ACLR between 2013 and 2022 was 29.4 (SD, 10.3). Seventy percent were men and 30% women. Football was the most common activity associated with an ACL injury. Patient compliance with recording PROMs was 55% preoperatively and 37%, 32% and 24% at 1-, 2- and 5-year postoperative follow-up, respectively. Nonresponders represented 54% of eligible patients. Multivariate analyses showed that sex, age, smoking, time interval between injury and surgery and low socioeconomic status were associated with low compliance with postoperative PROM completion (p < 0.001). CONCLUSION: This study reports the demographic characteristics for patients on the NLR since 2013. Male sex, young age, increased waiting time between injury and surgery, smoking and lower socioeconomic class were predictors of low compliance with completion of postoperative PROMs on the UK NLR. Understanding the factors that affect patient compliance with PROMs improves our ability to provide targeted interventions and information to specific patient populations with the aim of enhancing inclusiveness and representation of population in the registry. LEVEL OF EVIDENCE: Level III.

Isometry of anteromedial reconstructions mimicking the deep medial collateral ligament depends on the femoral insertion.

PURPOSE: This study aimed to investigate the length change patterns of the native deep medial collateral ligament (dMCL) and potential anteromedial reconstructions (AMs) that might be added to a reconstruction of the superficial MCL (sMCL) to better understand the control of anteromedial rotatory instability (AMRI). METHODS: Insertion points of the dMCL and potential AM reconstructions were marked with pins (tibial) and eyelets (femoral) in 11 cadaveric knee specimens. Length changes between the pins and eyelets were then tested using threads in a validated kinematics rig with muscle loading of the quadriceps and iliotibial tract. Between 0° and 100° knee flexion, length change pattern of the anterior, middle and posterior part of the dMCL and simulated AM reconstructions were analysed using a rotary encoder. Isometry was tested using the total strain range (TSR). RESULTS: The tibiofemoral distance of the anterior dMCL part lengthened with flexion (+12.7% at 100°), whereas the posterior part slackened with flexion (-12.9% at 100°). The middle part behaved almost isometrically (maximum length: +2.8% at 100°). Depending on the femoral position within the sMCL footprint, AM reconstructions resulted in an increase in length as the knee flexed when a more centred position was used, irrespective of the tibial attachment position. Femoral positioning in the posterior aspect of the sMCL footprint exhibited <4% length change and was slightly less tight in flexion (min TSR = 3.6 ± 1.5%), irrespective of the tibial attachment position. CONCLUSION: The length change behaviour of potential AM reconstructions in a functionally intact knee is mainly influenced by the position of the femoral attachment, with different tibial attachments having a minimal effect on length change. Surgeons performing AM reconstructions to control AMRI would be advised to choose a femoral graft position in the posterior part of the native sMCL attachment to optimise graft length change behaviour. Given the high frequency of MCL injuries, sufficient restoration of AMRI is essential in isolated and combined ligamentous knee injuries. LEVEL OF EVIDENCE: There is no level of evidence as this study was an experimental laboratory study.

The impact of bariatric surgery on liver enzymes in people with obesity: A 5-year observational study.

BACKGROUND AND PURPOSE: Non-alcoholic fatty liver disease (NAFLD) has increasing worldwide prevalence, fuelled by rising obesity rates, and weight reduction is the mainstay of its management. We sought to study the effect of bariatric surgery, the most effective long-term treatment for obesity and associated metabolic disorders, on liver function in people with obesity. METHODS: We performed a retrospective longitudinal cohort study of 511 patients who had undergone bariatric surgery (71 sleeve gastrectomy and 440 gastric bypass) over 60 months of follow-up. Patients were stratified into groups based on their baseline alanine aminotransferase (ALT) into Group A (ALT < 40 U/L) and Group B (ALT > 40 U/L). Postoperative follow-up weight loss, liver function tests, HbA1c, blood pressure and lipid profiles were collected. FINDINGS: Bariatric surgery resulted in nadir total weight loss of 33.1% by 24 months (p < 0.001) with no significant difference between groups. In people with raised baseline ALT (Group B), ALT and gamma glutamyl transferase (GGT) levels decreased significantly by 4 months postoperatively (p < 0.001) and sustained over 60 months of follow-up. There was also significant and sustained reduction in HbA1c, blood pressure, total cholesterol, and non-HDL cholesterol overall with no differences between groups. CONCLUSIONS: Bariatric surgery results in significant weight loss, improves liver function tests and metabolic outcomes in people with obesity. Bariatric surgery could be a therapeutic consideration for patients with NAFLD associated with severe obesity who have otherwise been unresponsive to conservative management.

Facilitating knowledge transfer to policy makers and front-line workers during a pandemic: Implementation, impact and lessons learned.

BACKGROUND: Stakeholders working on the COVID-19 pandemic response needed access to evidence, requiring a systematic approach to identify and disseminate relevant research. OBJECTIVES: Outline the stages of development of a COVID-19 Literature Digest; demonstrate the impact the Digest had on decision-making and knowledge gain; identify the lessons learned. METHODS: A standardised process was developed to identify and select papers. The main sources for content were PubMed, bioRxiv and medRxiv. A shared EndNote library was used to deduplicate and organise papers. Three user surveys obtained feedback from subscribers to determine if the Digest remained valuable, and explore the benefits to individuals. RESULTS: 40-60 papers were summarised each week. 211 Digests were produced from March 2020 to March 2022, with around 10,000 papers included altogether. Survey results suggest benefits of the Digest were gaining new knowledge, saving time and contributing to evidence-based decision making. DISCUSSION: Digest procedures constantly evolved and were adapted in response to survey feedback. Lessons identified: learn from failure, communication is key, measure your impact, work collaboratively, reflect and be flexible. CONCLUSION: The Digest was successfully produced within the limits of available resource. The learning from this Digest will inform evidence monitoring, selection and dissemination for future health crises.

Structural Framework for Analysis of CD4+ T-Cell Epitope Dominance in Viral Fusion Proteins.

Antigen conformation shapes CD4+ T-cell specificity through mechanisms of antigen processing, and the consequences for immunity may rival those from conformational effects on antibody specificity. CD4+ T cells initiate and control immunity to pathogens and cancer and are at least partly responsible for immunopathology associated with infection, autoimmunity, and allergy. The primary trigger for CD4+ T-cell maturation is the presentation of an epitope peptide in the MHC class II antigen-presenting protein (MHCII), most commonly on an activated dendritic cell, and then the T-cell responses are recalled by subsequent presentations of the epitope peptide by the same or other antigen-presenting cells. Peptide presentation depends on the proteolytic fragmentation of the antigen in an endosomal/lysosomal compartment and concomitant loading of the fragments into the MHCII, a multistep mechanism called antigen processing and presentation. Although the role of peptide affinity for MHCII has been well studied, the role of proteolytic fragmentation has received less attention. In this Perspective, we will briefly summarize evidence that antigen resistance to unfolding and proteolytic fragmentation shapes the specificity of the CD4+ T-cell response to selected viral envelope proteins, identify several remarkable examples in which the immunodominant CD4+ epitopes most likely depend on the interaction of processing machinery with antigen conformation, and outline how knowledge of antigen conformation can inform future efforts to design vaccines.