Antibody sequence determinants of viral antigen specificity.

Throughout life, humans experience repeated exposure to viral antigens through infection and vaccination, resulting in the generation of diverse, antigen-specific antibody repertoires. A paramount feature of antibodies that enables their critical contributions in counteracting recurrent and novel pathogens, and consequently fostering their utility as valuable targets for therapeutic and vaccine development, is the exquisite specificity displayed against their target antigens. Yet, there is still limited understanding of the determinants of antibody-antigen specificity, particularly as a function of antibody sequence. In recent years, experimental characterization of antibody repertoires has led to novel insights into fundamental properties of antibody sequences but has been largely decoupled from at-scale antigen specificity analysis. Here, using the LIBRA-seq technology, we generated a large data set mapping antibody sequence to antigen specificity for thousands of B cells, by screening the repertoires of a set of healthy individuals against 20 viral antigens representing diverse pathogens of biomedical significance. Analysis uncovered virus-specific patterns in variable gene usage, gene pairing, somatic hypermutation, as well as the presence of convergent antiviral signatures across multiple individuals, including the presence of public antibody clonotypes. Notably, our results showed that, for B-cell receptors originating from different individuals but leveraging an identical combination of heavy and light chain variable genes, there is a specific CDRH3 identity threshold above which B cells appear to exclusively share the same antigen specificity. This finding provides a quantifiable measure of the relationship between antibody sequence and antigen specificity and further defines experimentally grounded criteria for defining public antibody clonality.IMPORTANCEThe B-cell compartment of the humoral immune system plays a critical role in the generation of antibodies upon new and repeated pathogen exposure. This study provides an unprecedented level of detail on the molecular characteristics of antibody repertoires that are specific to each of the different target pathogens studied here and provides empirical evidence in support of a 70% CDRH3 amino acid identity threshold in pairs of B cells encoded by identical IGHV:IGL(K)V genes, as a means of defining public clonality and therefore predicting B-cell antigen specificity in different individuals. This is of exceptional importance when leveraging public clonality as a method to annotate B-cell receptor data otherwise lacking antigen specificity information. Understanding the fundamental rules of antibody-antigen interactions can lead to transformative new approaches for the development of antibody therapeutics and vaccines against current and emerging viruses.

Testing the optical components for the National Ignition Facility time-resolved soft x-ray opacity spectrometer (OpSpecTR).

Opacity measurements are being carried out at the Z-facility at Sandia National Laboratories and at the National Ignition Facility (NIF) at Lawrence Livermore National Laboratory. The current soft x-ray Opacity Spectrometer (OpSpec) used on the NIF uses two elliptically bent crystals in time-integrated mode on either an image plate or a film. Plans are under way to expand these opacity measurements into a mode of time-resolved detection, called OpSpecTR. Previously, considerations for the available hCMOS detector size and photometrics led to a crystal geometry redesign and the use of a grazing angle x-ray mirror. The mirror acts as a low-pass x-ray energy filter, reducing the contribution of higher energy x rays. The first tests of the mirror and the crystal for OpSpecTR are presented here. The size of the mirror reflection and the reflectivity is tested using a Manson x-ray source. The mirror coupled with the new elliptical crystal shape demonstrates OpSpecTR's spectral coverage. The results from the x-ray optics performance testing are shown along with the intended design.

A spectroscopic analysis code for spatially resolved x-ray absorption data from the COAX platform.

Sophisticated tools such as computer vision techniques in combination with 1D lineout type analyses have been used in automating the analysis of spectral data for high energy density (HED) plasmas. Standardized automation can solve the problems posed by the complexity of HED spectra and the quantity of data. We present a spectroscopic code written for automated and streamlined analysis of spatially resolved x-ray absorption data from the COAX platform on Omega-60. COAX uses radiographs and spectroscopic diagnostics to provide shock position and density information. We also obtain the more novel spectral-derived spatial profile of the supersonic radiation flow into a low-density foam. Considerable effort has been spent modernizing our previous spectroscopic analysis method, including the development of new tools characterized by a faster runtime and minimal user input to reduce bias and a testing suite for verifying the accuracy of the various functions within the code. The new code analyzes our spectroscopic images in 1-2 min, with added uncertainty and confidence.

Relative sensitivity of plastic scintillator: A comparative analysis with 60Co gamma rays, deuterium-deuterium, and deuterium-tritium neutrons.

A plastic scintillator has found extensive application in the realm of high-energy physics and national security science. Many applications in those fields often involve the simultaneous production of photons, neutrons, and charged particles, which makes the relative sensitivity information for these different radiation types important. In this study, we have adopted a multi-head detector comprised of a plastic scintillator and high gain phototubes, which provides a large dynamic range and linearity. A comparative study on the relative sensitivities of plastic scintillators was facilitated by adopting three distinct radiation calibration sources (i.e., 60Co γ rays, DD neutrons, and DT neutrons). Neutrons from a DD source generate a comparable level of scintillation to gamma rays emitted by 60Co (i.e., 60Co-γ/DD-n = 0.92 ± 16%). DT neutrons induce ∼3.5 times the scintillation observed with DD neutrons (i.e., DT-n/DD-n = 3.5 ± 28%). In addition, the Geant4 simulation granted us valuable insights into the relative sensitivity of the scintillator. This comparative study will provide a useful database for users in diverse applications.

Design and characterization of the time-resolved opacity spectrometer (OpSpecTR) for the NIF iron opacity campaign.

A new time-resolved opacity spectrometer (OpSpecTR) is currently under development for the National Ignition Facility (NIF) opacity campaign. The spectrometer utilizes Icarus version 2 (IV2) hybridized complementary metal-oxide-semiconductor sensors to collect gated data at the time of the opacity transmission signal, unlocking the ability to collect higher-temperature measurements on NIF. Experimental conditions to achieve higher temperatures are feasible; however, backgrounds will dominate the data collected by the current time-integrating opacity spectrometer. The shortest available OpSpecTR integration time of ∼2 ns is predicted to reduce self-emission and other late-time backgrounds by up to 80%. Initially, three Icarus sensors will be used to collect data in the self-emission, backlighter, and absorption regions of the transmission spectrum, with plans to upgrade to five Daedalus sensors in future implementations with integration times of ∼1.3 ns. We present the details of the diagnostic design along with recent characterization results of the IV2 sensors.

Development of improved higher-order correction for the NIF opacity spectrometer.

X-ray opacity measurements on the National Ignition Facility (NIF) are in the process of reproducing earlier measurements from the Sandia Z Facility, in particular for oxygen and iron plasmas. These measurements have the potential to revise our understanding of the "solar problem" and of the hot degenerate Q class white dwarf structure by probing plasma conditions near the base of their convection zones. Accurate opacity measurements using soft x-ray Bragg crystal spectrometers require correction for higher-order diffraction effects. Extending prior work in this area [Dutra et al., Review of Scientific Instruments 93, 113527 (2022)], we have developed a new method to remove higher-order spectral components from NIF opacity spectrometer data. By modeling absorption and backlighting continuum spectra and subtracting the second- and third-order components from the measured data, we are able to perform this correction while avoiding imprinting first-order model line features onto the data.

Comparison of uridine and N1-methylpseudouridine mRNA platforms in development of an Andes virus vaccine.

The rodent-borne Andes virus (ANDV) causes a severe disease in humans. We developed an ANDV mRNA vaccine based on the M segment of the viral genome, either with regular uridine (U-mRNA) or N1-methylpseudouridine (m1Ψ-mRNA). Female mice immunized by m1Ψ-mRNA developed slightly greater germinal center (GC) responses than U-mRNA-immunized mice. Single cell RNA and BCR sequencing of the GC B cells revealed similar levels of activation, except an additional cluster of cells exhibiting interferon response in animals vaccinated with U-mRNA but not m1Ψ-mRNA. Similar immunoglobulin class-switching and somatic hypermutations were observed in response to the vaccines. Female Syrian hamsters were immunized via a prime-boost regimen with two doses of each vaccine. The titers of glycoprotein-binding antibodies were greater for U-mRNA construct than for m1Ψ-mRNA construct; however, the titers of ANDV-neutralizing antibodies were similar. Vaccinated animals were challenged with a lethal dose of ANDV, along with a naïve control group. All control animals and two animals vaccinated with a lower dose of m1Ψ-mRNA succumbed to infection whereas other vaccinated animals survived without evidence of virus replication. The data demonstrate the development of a protective vaccine against ANDV and the lack of a substantial effect of m1Ψ modification on immunogenicity and protection in rodents.

Magnetic Nanoparticle-Assisted Non-Viral CRISPR-Cas9 for Enhanced Genome Editing to Treat Rett Syndrome.

The CRISPR-Cas9 technology has the potential to revolutionize the treatment of various diseases, including Rett syndrome, by enabling the correction of genes or mutations in human patient cells. However, several challenges need to be addressed before its widespread clinical application. These challenges include the low delivery efficiencies to target cells, the actual efficiency of the genome-editing process, and the precision with which the CRISPR-Cas system operates. Herein, the study presents a Magnetic Nanoparticle-Assisted Genome Editing (MAGE) platform, which significantly improves the transfection efficiency, biocompatibility, and genome-editing accuracy of CRISPR-Cas9 technology. To demonstrate the feasibility of the developed technology, MAGE is applied to correct the mutated MeCP2 gene in induced pluripotent stem cell-derived neural progenitor cells (iPSC-NPCs) from a Rett syndrome patient. By combining magnetofection and magnetic-activated cell sorting, MAGE achieves higher multi-plasmid delivery (99.3%) and repairing efficiencies (42.95%) with significantly shorter incubation times than conventional transfection agents without size limitations on plasmids. The repaired iPSC-NPCs showed similar characteristics as wild-type neurons when they differentiated into neurons, further validating MAGE and its potential for future clinical applications. In short, the developed nanobio-combined CRISPR-Cas9 technology offers the potential for various clinical applications, particularly in stem cell therapies targeting different genetic diseases.

Surgical sensation during caesarean section: a qualitative analysis.

BACKGROUND: Caesarean section (CS) is a major abdominal surgery performed usually on a young and healthy population under neuraxial anesthesia with little to no sedation. This creates a distinct surgical experience whereby patients are aware of the surgical process, physical sensations, and their environment. This study aimed to provide an in-depth descriptive assessment of subjective surgical experience during CS under regional anaesthesia. We expected the information gained would enhance our current understanding and better alleviate patient anxiety through informed counselling. METHODS: This qualitative descriptive study was conducted at a Canadian academic centre. Twenty patients participated in semi-structured interviews within a week of CS, using an interview guide developed for this study. Patient medical records were reviewed to collect demographic and surgical information. Thematic analysis was conducted using an inductive approach to determine common themes. RESULTS: Nine themes were identified. Five themes were identified in the category of surgical sensation and four themes were identified in the category of peri-operative education. CONCLUSIONS: Patients commonly experienced pressure and movement sensations at varying intensity, and most did not experience pain. Environmental factors, including sounds and distraction by the newborn, affected perception of surgical sensation. Patients wish to receive pre-operative counselling regarding potential surgical sensations, as well as ongoing communication from their anaesthesiologist. These results can be used to guide informed discussions with patients and direct further investigation in this area.

Development of LIBRA-seq for the guinea pig model system as a tool for the evaluation of antibody responses to multivalent HIV-1 vaccines.

Consistent elicitation of serum antibody responses that neutralize diverse clades of HIV-1 remains a primary goal of HIV-1 vaccine research. Prior work has defined key features of soluble HIV-1 Envelope (Env) immunogen cocktails that influence the neutralization breadth and potency of multivalent vaccine-elicited antibody responses including the number of Env strains in the regimen. We designed immunization groups that consisted of different numbers of SOSIP Env strains to be used in a cocktail immunization strategy: the smallest cocktail (group 2) consisted of a set of two Env strains, which were a subset of the three Env strains that made up group 3, which, in turn, were a subset of the six Env strains that made up group 4. Serum neutralizing titers were modestly broader in guinea pigs that were immunized with a cocktail of three Envs compared to cocktails of two and six, suggesting that multivalent Env immunization could provide a benefit but may be detrimental when the cocktail size is too large. We then adapted the LIBRA-seq platform for antibody discovery to be compatible with guinea pigs, and isolated several tier 2 neutralizing monoclonal antibodies. Three antibodies isolated from two separate guinea pigs were similar in their gene usage and CDR3s, establishing evidence for a guinea pig public clonotype elicited through vaccination. Taken together, this work investigated multivalent HIV-1 Env immunization strategies and provides a novel methodology for screening guinea pig B cell receptor antigen specificity at a high-throughput level using LIBRA-seq.IMPORTANCEMultivalent vaccination with soluble Env immunogens is at the forefront of HIV-1 vaccination strategies but little is known about the influence of the number of Env strains included in vaccine cocktails. Our results suggest that adding more strains is sometimes beneficial but may be detrimental when the number of strains is too high. In addition, we adapted the LIBRA-seq platform to be compatible with guinea pig samples and isolated several tier 2 neutralizing monoclonal antibodies, some of which share V and J gene usage and >70% CDR3 identity, thus establishing the existence of public clonotypes in guinea pigs elicited through vaccination.

Plasma proteomic analysis on neuropathic pain in idiopathic peripheral neuropathy patients.

BACKGROUND AND AIMS: Why only half of the idiopathic peripheral neuropathy (IPN) patients develop neuropathic pain remains unknown. By conducting a proteomics analysis on IPN patients, we aimed to discover proteins and new pathways that are associated with neuropathic pain. METHODS: We conducted unbiased mass-spectrometry proteomics analysis on blood plasma from 31 IPN patients with severe neuropathic pain and 29 IPN patients with no pain, to investigate protein biomarkers and protein-protein interactions associated with neuropathic pain. Univariate modeling was done with linear mixed modeling (LMM) and corrected for multiple testing. Multivariate modeling was performed using elastic net analysis and validated with internal cross-validation and bootstrapping. RESULTS: In the univariate analysis, 73 proteins showed a p-value <.05 and 12 proteins showed a p-value <.01. None were significant after Benjamini-Hochberg adjustment for multiple testing. Elastic net analysis created a model containing 12 proteins with reasonable discriminatory power to differentiate between painful and painless IPN (false-negative rate 0.10, false-positive rate 0.18, and an area under the curve 0.75). Eight of these 12 proteins were clustered into one interaction network, significantly enriched for the complement and coagulation pathway (Benjamini-Hochberg adjusted p-value = .0057), with complement component 3 (C3) as the central node. Bootstrap validation identified insulin-like growth factor-binding protein 2 (IGFBP2), complement factor H-related protein 4 (CFHR4), and ferritin light chain (FTL), as the most discriminatory proteins of the original 12 identified. INTERPRETATION: This proteomics analysis suggests a role for the complement system in neuropathic pain in IPN.

SARS-CoV-2 antibodies from children exhibit broad neutralization and belong to adult public clonotypes.

From the beginning of the COVID-19 pandemic, children have exhibited different susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, reinfection, and disease compared with adults. Motivated by the established significance of SARS-CoV-2-neutralizing antibodies in adults, here we characterize SARS-CoV-2-specific antibody repertoires in a young cohort of individuals aged from 5 months to 18 years old. Our results show that neutralizing antibodies in children possess similar genetic features compared to antibodies identified in adults, with multiple antibodies from children belonging to previously established public antibody clonotypes in adults. Notably, antibodies from children show potent neutralization of circulating SARS-CoV-2 variants that have cumulatively resulted in resistance to virtually all approved monoclonal antibody therapeutics. Our results show that children can rely on similar SARS-CoV-2 antibody neutralization mechanisms compared to adults and are an underutilized source for the discovery of effective antibody therapeutics to counteract the ever-evolving pandemic.

Negative Binomial Mixture Model for Identification of Noise in Antigen-Specificity Predictions by LIBRA-seq.

Motivation: LIBRA-seq (linking B cell receptor to antigen specificity by sequencing) provides a powerful tool for interrogating the antigen-specific B cell compartment and identifying antibodies against antigen targets of interest. Identification of noise in LIBRA-seq antigen count data is critical for improving antigen binding predictions for downstream applications including antibody discovery and machine learning technologies. Results: In this study, we present a method for denoising LIBRA-seq data by clustering antigen counts into signal and noise components with a negative binomial mixture model. This approach leverages the VRC01 negative control cells included in a recent LIBRA-seq study(Abu-Shmais et al.) to provide a data-driven means for identification of technical noise. We apply this method to a dataset of nine donors representing separate LIBRA-seq experiments and show that our approach provides improved predictions for in vitro antibody-antigen binding when compared to the standard scoring method used in LIBRA-seq, despite variance in data size and noise structure across samples. This development will improve the ability of LIBRA-seq to identify antigen-specific B cells and contribute to providing more reliable datasets for future machine learning based approaches to predicting antibody-antigen binding as the corpus of LIBRA-seq data continues to grow.

IgM anti-MAG± peripheral neuropathy (IMAGiNe) study protocol: An international, observational, prospective registry of patients with IgM M-protein peripheral neuropathies.

BACKGROUND: International consensus on IgM ± anti-MAG ± PNP (IgM PNP) is lacking. Despite increasing interest in clinical trials, validated disease-specific measures are needed to adequately capture limitations and changes over time. The IMAGiNe (IgM ± anti-myelin associated glycoprotein [MAG] peripheral neuropathy) study surges as an international collaboration to create a standardized registry of patients with IgM ± anti-MAG PNP. The consortium, which currently consists of 11 institutions from 7 countries, presents here the IMAGiNe study design and protocol. AIMS: Functional outcome measures will be constructed at the level of impairment, as well as activity and participation. We aim to describe the natural history of the cohort, the role of anti-MAG antibodies, the presence of clinical subtypes, and potential biomarkers. METHODS: The IMAGiNe study is a prospective, observational cohort study with a 3-year follow-up. At each assessment, researchers collect clinical data and subjects complete a list of preselected outcome measures. Among these, the "Pre-Rasch-built Overall Disability Scale (Pre-RODS)" questionnaire will be submitted to Rasch analysis to assess classic and modern clinimetric requirements. RESULTS: The final measures will include the IgM-PNP-specific RODS and Ataxia Rating Scale (IgM-PNP-ARS). Descriptions of the disease course, clinical heterogeneity, treatment regimes, variations in laboratory values, and antibody titers will help reach consensus on diagnosis and follow-up strategies. CONCLUSION: The constructed interval scales will be cross-culturally valid and suitable for use in future clinical trials and daily practice. The ultimate goals are to improve functional individualized assessment, reach international consensus, and lay the foundations for successful designs in future studies.

[Loss of sight in the postpartum period]. / Verminderd zicht in het kraambed.

BACKGROUND: Vision problems in case of pre-eclampsia or Hemolysis, Elevated Liver, Low Platelets syndrome (HELLP) occur in 25-40% of the cases. Ablatio retinae as a complication occurs in only 0,1-2%. CASE DESCRIPTION: This article describes the case of a healthy 31-year-old woman who gave birth to her first child. A few hours after delivery she experienced vision loss. HELLP was diagnosed. Because of persistent vision loss combined with headache, the ophthalmologist and neurologist were consulted. A bilateral ablatio retinae as a complication of HELLP was diagnosed. Headache was most likely due to the side effect of nifedipine tablets, tension headache or a symptom of HELLP. Vision loss recovered spontaneously within a few weeks. CONCLUSION: Ablatio retinae due to preeclampsia or HELLP is very rare. For all concerned health care providers it is essential to pay attention to vision loss being the first symptom of possible acute underlying diagnosis postpartum.

Density measurements for the National Ignition Facility (NIF) opacity platform.

The Opacity Platform on the National Ignition Facility (NIF) has been developed to measure opacities at varying densities and temperatures relevant to the solar interior and thermal cooling rates in white dwarf stars. The typical temperatures reached at NIF range between 150 and 210 eV, which allow these measurements to be performed experimentally. The captured opacities are crucial to validating radiation-hydrodynamic models that are used in astrophysics. The NIF opacity platform has a unique new capability that allows in situ measurement of the sample expansion. The sample expansion data are used to better understand the plasma conditions in our experiments by inferring the sample density throughout the duration of the laser drive. We present the details of the density measurement technique, data analysis, and recent results for Fe and MgO.

2nd and 3rd order spectral energy corrections with penumbral de-blurring methodology for opacity platform used on the National Ignition Facility.

The Opacity Spectrometer (OpSpec) used in the National Ignition Facility's opacity experiments measures x-ray spectra from 0.9 to 2.1 keV from the different experimental regions: the backlight source, emission source, and the absorption region with the transmission calculated from these regions. The OpSpec designs have gone through several iterations to help improve the signal-to-noise ratio, remove alternate crystal plane reflections, and improve spectral resolution, which helps to increase the validity of the opacity measurements. However, the source spans well outside the current working spectral range, and higher-order reflections are intrinsic to the crystal, which increases the overall signal seen in the data regions. The recorded data are the convolution of 1st order transmission, higher-order reflections, and the penumbra blurring. This work represents the details for deconvolving the 2nd and 3rd order spectral energy corrections with a penumbral de-blurring to correct the relative measurement of x-ray intensity of different spectral energies and further analysis of datasets relevant to the opacity experiments.

Sub-keV design for the National Ignition Facility's soft x-ray Opacity Spectrometer (OpSpec) and expansion plans for time-resolved measurements.

When compared with the National Ignition Facility's (NIF) original soft x-ray opacity spectrometer, which used a convex cylindrical design, an elliptically shaped design has helped to increase the signal-to-noise ratio and eliminated nearly all reflections from alternate crystal planes. The success of the elliptical geometry in the opacity experiments has driven a new elliptical geometry crystal with a spectral range covering 520-1100 eV. When coupled with the primary elliptical geometry, which spans 1000-2100 eV, the new sub-keV elliptical geometry helps to cover the full iron L-shell and major oxygen transitions important to solar opacity experimentation. The new design has been built and tested by using a Henke x-ray source and shows the desired spectral coverage. Additional plans are underway to expand these opacity measurements into a mode of time-resolved detection, ∼1 ns gated, but considerations for the detector size and photometrics mean a crystal geometry redesign. The new low-energy geometry, including preliminary results from the NIF opacity experiments, is presented along with the expansion plans into a time-resolved platform.

Physician perceptions of drug utilization management: Results of a national survey.

The use of drug utilization management techniques such as formulary exclusions, prior authorizations, and step edits has risen sharply during the last decade, contributing to the growing burden on physicians and patients. Limited quantitative data exist, however, on physician perceptions of drug utilization management. A national survey was conducted between February 9 and March 30, 2021, targeting office-based physicians working in the United States to assess their perceptions on drug utilization management in their practice. Of the 742 physicians that participated in the study, over 80% reported deciding against prescribing certain treatments in anticipation of drug utilization management at least sometimes (>50% of the time). Despite utilization management having an impact on prescribing decisions, about half of physicians said that the utilization management policies they encounter rarely or never (0-25% of the time) align with clinical evidence.

Archetype tasks link intratumoral heterogeneity to plasticity and cancer hallmarks in small cell lung cancer.

Small cell lung cancer (SCLC) tumors comprise heterogeneous mixtures of cell states, categorized into neuroendocrine (NE) and non-neuroendocrine (non-NE) transcriptional subtypes. NE to non-NE state transitions, fueled by plasticity, likely underlie adaptability to treatment and dismal survival rates. Here, we apply an archetypal analysis to model plasticity by recasting SCLC phenotypic heterogeneity through multi-task evolutionary theory. Cell line and tumor transcriptomics data fit well in a five-dimensional convex polytope whose vertices optimize tasks reminiscent of pulmonary NE cells, the SCLC normal counterparts. These tasks, supported by knowledge and experimental data, include proliferation, slithering, metabolism, secretion, and injury repair, reflecting cancer hallmarks. SCLC subtypes, either at the population or single-cell level, can be positioned in archetypal space by bulk or single-cell transcriptomics, respectively, and characterized as task specialists or multi-task generalists by the distance from archetype vertex signatures. In the archetype space, modeling single-cell plasticity as a Markovian process along an underlying state manifold indicates that task trade-offs, in response to microenvironmental perturbations or treatment, may drive cell plasticity. Stifling phenotypic transitions and plasticity may provide new targets for much-needed translational advances in SCLC. A record of this paper's Transparent Peer Review process is included in the supplemental information.