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Backround/Aim: The purpose of this in vitro study is to evaluate the antibiofilm and antimicrobial activities of 5 different restorative materials that release fluoride.

Purpose: To identify factors predicting slow visual recovery following myopic microkeratome assisted in situ keratomileusis (LASIK)., Design: Retrospective study., Methods: This study included consecutive patients who underwent microkeratome-assisted myopic LASIK between January 2005 and December 2019 at Care Vision Laser Center, Tel Aviv, Israel. Patients were divided into three groups according to whether they experienced normal recovery of visual acuity (1 week visit), slow visual recovery (1 month visit) or very slow recovery (>1 month). Normal visual recovery was defined as achieving an efficacy index of 0.9 or greater. Efficacy index was calculated as postoperative uncorrected visual acuity/preoperative best corrected visual acuity. A comparison of baseline and intraoperative parameters was performed., Results: Overall, 10 439 eyes were included. Mean age was 30.8 ± 8.7 years and 47.1% were females. The slower visual recovery groups (slow 11.4%, n = 1191; very slow 8.4%, n = 875) were of older age (p < 0.001), steeper preoperative steep keratometry (p = 0.002) and larger refractive astigmatism (p < 0.001). In binary logistic regression older age (p < 0.001), female gender (p = 0.001), larger astigmatism (p < 0.001) and high myopia (p < 0.001) remained significant predictors of slow visual recovery., Conclusion: Slow visual recovery was observed in 19.8% of patients following myopic LASIK. Older age, female gender, larger astigmatism and high myopia were associated with slow visual recovery. Patients may be advised accordingly., (© 2024 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.)

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is critical for our understanding of the adaptive immune system's dynamics in health and disease. Reliable analysis of AIRR-seq data depends on accurate rearranged immunoglobulin (Ig) sequence alignment. Various Ig sequence aligners exist, but there is no unified benchmarking standard representing the complexities of AIRR-seq data, obscuring objective comparisons of aligners across tasks. Here, we introduce GenAIRR, a modular simulation framework for generating Ig sequences alongside their ground truths. GenAIRR realistically simulates the intricacies of V(D)J recombination, somatic hypermutation, and an array of sequence corruptions. We comprehensively assessed prominent Ig sequence aligners across various metrics, unveiling unique performance characteristics for each aligner. The GenAIRR-produced datasets, combined with the proposed rigorous evaluation criteria, establish a solid basis for unbiased benchmarking of immunogenetics computational tools. It sets up the ground for further improving the crucial task of Ig sequence alignment, ultimately enhancing our understanding of adaptive immunity., (© The Author(s) 2024. Published by Oxford University Press.)

Introduction: Clinical remission is a relatively new concept in asthma but recent research initiatives suggest it could be an ambitious and achievable therapeutic target for patients with asthma., Methods: In this modified Delphi study (comprising two online surveys, completed either side of a virtual scientific workshop), the opinions of a panel of respiratory physicians were evaluated to summarize perspective statements on key therapeutic outcomes and criteria for on-treatment clinical remission in patients with moderate asthma. An agreement threshold was pre-defined as agreement by ≥ 75% of participants., Results: Surveys 1 and 2 were completed by 20 and 18 participants, respectively. Most participants (95%) agreed with the concept of clinical remission in moderate asthma and that this should be a desirable treatment goal (90%). Based on a composite measure of 4-6 desirable therapeutic outcomes, current understanding of clinical remission was considered as 12 months with no exacerbations, no oral corticosteroids, no daytime or night-time asthma symptoms (Asthma Control Test score ≥ 20 or Asthma Control Questionnaire score ≤ 0.75), stable lung function, and no treatment-related adverse events. No agreement was reached on the role of relievers in defining therapeutic outcomes or on the wider use of biomarkers and airway hyperresponsiveness for defining asthma remission in clinical practice., Conclusions: In line with recent consensus statements from the United States and Europe, there was a high level of agreement on the elements of clinical remission among a panel of respiratory physicians from Asia, the Middle East, and South America. Extension of the concept of clinical remission to patients with moderate asthma was considered aligned with the potential of clinical remission as a goal of therapy., (© 2024. The Author(s).)

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: SHK receives consulting fees from Peraton. AP is an employee of Boehringer Ingelheim Pharma GmbH & Co KG and declares no conflict of interest. DL is an employee of oNKo-innate Pty Ltd and declares no conflict of interest. MCK has served on advisory boards and received speaker fees / travel grants from Merck, Sanofi-Genzyme, Novartis, Biogen, Janssen, Alexion, Celgene / Bristol-Myers Squibb and Roche. He has received research grants from Merck, Roche, Novartis, Sanofi-Genzyme and Celgene / Bristol-Myers Squibb. All other authors declare no conflicts of interest., (Copyright: © 2024 Gabernet et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Introduction: Despite the proven benefits of inhaled corticosteroid (ICS)-containing triple therapy for chronic obstructive pulmonary disease (COPD), clinicians limit patient exposure to ICS due to the risk of pneumonia. However, there are multiple factors associated with the risk of pneumonia in patients with COPD. This post hoc analysis of IMPACT trial data aims to set the risks associated with ICS into a context of specific patient-related factors that contribute to the risk of pneumonia., Methods: The 52-week, double-blind IMPACT trial randomized patients with symptomatic COPD and ≥1 exacerbation in the prior year 2:2:1 to once-daily fluticasone furoate (FF)/umeclidinium (UMEC)/vilanterol (VI), FF/VI or UMEC/VI. Annual rate of on-treatment pneumonias in the intent-to-treat population associated with age, body mass index (BMI), percent predicted forced expiratory volume in 1 s (FEV 1 ) and blood eosinophil count (BEC) was evaluated., Results: This analysis revealed that the annual rate of pneumonia showed the lowest risk at the age of 50 years. The 95% confidence intervals (CI) between ICS-containing and non-ICS containing treatments diverged in ages > 63 years, suggesting a significantly increased ICS-related risk in older patients. In contrast, the annual rate of pneumonia rose in both groups below BMI of 22.5 kg/m 2 , but above that, there was no relationship to pneumonia rate and no differential effect between the two groups. The relationship between BEC and pneumonia was flat up to > 300/µL cells with ICS-containing treatment and then rose. In contrast, the rate of pneumonia with non-ICS containing treatment appeared to increase at a lower level of BEC (~ 200/µL)., Conclusions: There was little evidence of a differential effect of older age, lower BMI, lower FEV 1 and BEC on the pneumonia rate between ICS-containing and non-ICS containing treatments. This analysis points to the need for a balanced approach to risk versus benefit in the use of ICS-containing treatments in COPD., Clinical Trial Registration: IMPACT ClinicalTrials.gov number, NCT02164513., (© 2024. The Author(s).)

Background: Radiation reduction is an integral component in the management of a paediatric cardiac catheterization laboratory. Simple and easily implementable protocol changes and technical upgrades have been shown to significantly reduce radiation exposure., Methods: Radiation exposures (2020-2022) at Safra Children's Hospital, Sheba Medical Center, Israel (unit A: n = 672) were retrospectively reviewed, including dose area product (DAP) (μGy m 2 ), DAP/kg, Air Kerma (mGy), and fluoroscopy time (minutes) for 16 procedural types. Median doses were compared with those measured (2011-2014) at the Hospital for Sick Children, Toronto, Canada (unit B: n = 2033). Radiation reduction techniques included fluoroscopy acquisition at 7.5 frames/s, removal of antiscatter grids for children <30 kg, limiting field of view, use of Philips ClarityIQ technology, and an institutional culture of radiation mindedness., Results: Exposure was significantly lower in unit A in 14 of 16 procedure types. Total median doses were lower in unit A (DAP: 91.4 [44.7-205.4] vs 387 [138.2-1339] μGy m 2 [ P < 0.001], DAP/kg: 9.33 [4.3-16.4] vs 29.22 [12.8-65.9] μGy m 2 /kg [ P < 0.001], and Air Kerma: 14.9 [7.8-29] vs 61 [23-176.4] mGy [ P < 0.001]) despite higher fluoroscopy time (14.1 [4.2-24.6] vs 12.3 [6.8-23.3] minutes [ P  = 0.03]). DAP was lower for specific procedures including pulmonary valvuloplasty (46.3 [14.3-219.3] vs 127 [60-323] μGy m 2 [ P < 0.001]) and patent ductus arteriosus closure (51.9 [18.8-111.8] vs 178 [96-410] μGy m 2 [ P < 0.001])., Conclusions: Enhanced radiation reduction techniques can lead to lower than previously published exposure levels across a wide range of procedure types when employing dose-limiting protocols and radiation reduction technology., (© 2024 The Authors.)

Vision restoration is one of the most promising applications of optogenetics. However, it is limited due to the poor-sensitivity, slow-kinetics and narrow band absorption spectra of opsins. Here, a detailed theoretical study of retinal ganglion neurons (RGNs) expressed with ChRmine, ReaChR, CoChR, CatCh and their mutants, with near monochromatic LEDs, and broadband sunlight, halogen lamp, RGB LED light, and pure white light sources has been presented. All the opsins exhibit improved light sensitivity and larger photocurrent on illuminating with broadband light sources compared to narrow band LEDs. ChRmine allows firing at ambient sunlight (1.5 nW/mm 2 ) and pure white light (1.2 nW/mm 2 ), which is lowest among the opsins considered. The broadband activation spectrum of ChRmine and its mutants is also useful to restore color sensitivity. Although ChRmine exhibits slower turn-off kinetics with broadband light, high-fidelity spikes can be evoked upto 50 Hz. This limit extends upto 80 Hz with the improved hsChRmine mutant although it requires double the irradiance compared to ChRmine. The present study shows that ChRmine and its mutants allow activation of RGNs with ambient light which is useful for goggle-free white light optogenetic retinal prostheses with improved quality of restored vision., (© 2024. The Author(s).)

Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency, reproducibility, and collaboration in AIRR-seq data analysis, serving as a model for handling and documenting bioinformatics pipelines in other research domains., (© The Author(s) 2024. Published by Oxford University Press.)

Summary: Knowledge of immunoglobulin and T cell receptor encoding genes is derived from high-quality genomic sequencing. High-throughput sequencing is delivering large volumes of data, and precise, high-throughput approaches to annotation are needed. Digger is an automated tool that identifies coding and regulatory regions of these genes, with results comparable to those obtained by current expert curational methods., Availability and Implementation: Digger is published under open source license at https://github.com/williamdlees/Digger and is available as a Python package and a Docker container., (© The Author(s) 2024. Published by Oxford University Press.)

Introduction: The objective of this Delphi study was to understand and assess the level of consensus among respiratory experts on the clinical application of GOLD 2023 recommendations in management of patients with chronic obstructive pulmonary disease (COPD)., Methods: The study comprised two online surveys and a participant meeting with 34 respiratory experts from 16 countries. Responses of 73 questions were recorded using a Likert scale ranging from 0 (disagreement) to 9 (agreement). The consensus threshold was 75%., Results: Survey 1 and survey 2 had 34 and 32 participants, respectively; and 25 attended the participant meeting. Consensus was reached on survey 1: 28/42; survey 2: 18/30 close-ended questions. A consensus was reached on the clinical relevance of most updates in definitions and diagnosis of COPD. Mixed results for the treatment recommendations by GOLD were noted: 74% agreed with the recommendation to initiate treatment with dual bronchodilators for group E patients; 63% agreed for including inhaled corticosteroids (ICS)/long-acting β 2 agonist(LABA)/ Long-acting muscarinic receptor antagonists (LAMA) as a treatment option for GOLD B patients. Also, consensus lacked on removing ICS + LABA as an initial therapeutic option, in countries with challenges in access to other treatment option;. 88% agreed that they use GOLD recommendations in their daily clinical practice., Conclusions: This Delphi study demonstrated a high level of consensus regarding key concepts of GOLD 2023 report, with most participants favoring recent updates in definitions, diagnosis, management, and prevention of COPD. More evidence on the etiotype based management and treatment options for group B and E are required which could further strengthen clinical application of the GOLD report., (© 2023. The Author(s).)

Introduction: Analysis of an individual's immunoglobulin (IG) gene repertoire requires the use of high-quality germline gene reference sets. When sets only contain alleles supported by strong evidence, AIRR sequencing (AIRR-seq) data analysis is more accurate and studies of the evolution of IG genes, their allelic variants and the expressed immune repertoire is therefore facilitated., Methods: The Adaptive Immune Receptor Repertoire Community (AIRR-C) IG Reference Sets have been developed by including only human IG heavy and light chain alleles that have been confirmed by evidence from multiple high-quality sources. To further improve AIRR-seq analysis, some alleles have been extended to deal with short 3' or 5' truncations that can lead them to be overlooked by alignment utilities. To avoid other challenges for analysis programs, exact paralogs (e.g. IGHV1-69*01 and IGHV1-69D*01) are only represented once in each set, though alternative sequence names are noted in accompanying metadata., Results and Discussion: The Reference Sets include less than half the previously recognised IG alleles (e.g. just 198 IGHV sequences), and also include a number of novel alleles: 8 IGHV alleles, 2 IGKV alleles and 5 IGLV alleles. Despite their smaller sizes, erroneous calls were eliminated, and excellent coverage was achieved when a set of repertoires comprising over 4 million V(D)J rearrangements from 99 individuals were analyzed using the Sets. The version-tracked AIRR-C IG Reference Sets are freely available at the OGRDB website (https://ogrdb.airr-community.org/germline&#95;sets/Human) and will be regularly updated to include newly observed and previously reported sequences that can be confirmed by new high-quality data., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The author(s) declared that they were an editorial board member of Frontiers, at the time of submission. This had no impact on the peer review process and the final decision., (Copyright © 2024 Collins, Ohlin, Corcoran, Heather, Ralph, Law, Martínez-Barnetche, Ye, Richardson, Gibson, Rodriguez, Peres, Yaari, Watson and Lees.)

Giant viruses infect many unicellular eukaryotes, including algae that form massive oceanic blooms. Despite the major impact of viruses on the marine ecosystem, the ability to quantify and assess active viral infection in nature remains a major challenge. We applied single-cell RNA sequencing, to profile virus and host transcriptomes of 12,000 single algal cells from a coccolithophore bloom. Viral infection was detected already at early exponential bloom phase, negatively correlating with the bloom intensity. A consistent percent of infected coccolithophores displayed the early phase of viral replication for several consecutive days, indicating a daily turnover and continuous virocell-associated metabolite production, potentially affecting the surrounding microbiome. Linking single-cell infection state to host physiology revealed that infected cells remained calcified even in the late infection stage. These findings stress the importance of studying host-virus dynamics in natural populations, at single-cell resolution, to better understand virus life cycle and its impact on microbial food webs.

Monitoring astronauts' health during space missions poses many challenges, including rapid assessment of crew health conditions. Sensitive genetic diagnostics are crucial for examining crew members and the spacecraft environment. CRISPR-Cas12a, coupled with isothermal amplification, has proven to be a promising biosensing system for rapid, on-site detection of genomic targets. However, the efficiency and sensitivity of CRISPR-based diagnostics have never been tested in microgravity. We tested the use of recombinase polymerase amplification (RPA) coupled with the collateral cleavage activity of Cas12a for genetic diagnostics onboard the International Space Station. We explored the detection sensitivity of amplified and unamplified target DNA. By coupling RPA with Cas12a, we identified targets in attomolar concentrations. We further assessed the reactions' stability following long-term storage. Our results demonstrate that CRISPR-based detection is a powerful tool for on-site genetic diagnostics in microgravity, and can be further utilized for long-term space endeavors to improve astronauts' health and well-being., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: David Burstein reports a relationship with Mammoth Biosciences that includes a sponsored research agreement on a different project., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is a crucial step. This process is highly impacted by allele annotations. Aligning sequences, assigning them to specific germline alleles, and inferring individual genotypes are challenging when the repertoire is highly mutated, or sequence reads do not cover the whole V region. Here, we propose an alternative naming scheme for the V alleles, as well as a novel method to infer individual genotypes. We demonstrate the strengths of the two by comparing their outcomes to other genotype inference methods. We validate the genotype approach with independent genomic long-read data. The naming scheme is compatible with current annotation tools and pipelines. Analysis results can be converted from the proposed naming scheme to the nomenclature determined by the International Union of Immunological Societies (IUIS). Both the naming scheme and the genotype procedure are implemented in a freely available R package (PIgLET https://bitbucket.org/yaarilab/piglet). To allow researchers to further explore the approach on real data and to adapt it for their uses, we also created an interactive website (https://yaarilab.github.io/IGHV&#95;reference&#95;book)., (© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Neuroblastoma is a lethal childhood solid tumor of developing peripheral nerves. Two percent of children with neuroblastoma develop opsoclonus myoclonus ataxia syndrome (OMAS), a paraneoplastic disease characterized by cerebellar and brainstem-directed autoimmunity but typically with outstanding cancer-related outcomes. We compared tumor transcriptomes and tumor-infiltrating T and B cell repertoires from 38 OMAS subjects with neuroblastoma to 26 non-OMAS-associated neuroblastomas. We found greater B and T cell infiltration in OMAS-associated tumors compared to controls and showed that both were polyclonal expansions. Tertiary lymphoid structures (TLSs) were enriched in OMAS-associated tumors. We identified significant enrichment of the major histocompatibility complex (MHC) class II allele HLA-DOB ∗ 01:01 in OMAS patients. OMAS severity scores were associated with the expression of several candidate autoimmune genes. We propose a model in which polyclonal auto-reactive B lymphocytes act as antigen-presenting cells and drive TLS formation, thereby supporting both sustained polyclonal T cell-mediated anti-tumor immunity and paraneoplastic OMAS neuropathology., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Purpose: Role of triple therapy in chronic obstructive pulmonary disease (COPD) management is supported by growing evidence, but consensus is lacking on various aspects. We conducted a Delphi survey in respiratory experts on the effects of triple therapy on exacerbation reduction, early optimization, pneumonia risk, and mortality benefits in COPD management., Methods: The study comprised 2-round online surveys and a participant meeting with 21 respiratory experts from 10 countries. The 31-statement questionnaire was prepared using Decipher software after literature review. Responses were recorded using Likert scale ranging from 1 (disagreement) to 9 (agreement) with a consensus threshold of 75%., Results: All experts participated in both surveys and 14/21 attended participant meeting. Consensus was reached on 13/31 questions in first survey and 4/14 in second survey on: mortality benefits of triple therapy; comparable pneumonia risk between single inhaler triple therapy (SITT) and multiple inhaler triple therapy (81%); preference of SITT for patients with high eosinophil count (95%); exacerbation risk reduction and healthcare cost benefits with early initiation of SITT post exacerbation-related hospitalization (<30 days) (86%). No consensus was reached on first line SITT use after first exacerbation resulting in COPD diagnosis (62%)., Conclusion: This study demonstrated that there is consensus among experts regarding many of the key concepts about appropriate clinical use and benefits of triple therapy in COPD. More evidence is required for evaluating the benefits of early optimisation of triple therapy., Competing Interests: Marc Miravitlles has received speaker fees from AstraZeneca, Boehringer Ingelheim, Chiesi, Cipla, GSK, Menarini, Kamada, Takeda, Zambon, CSL Behring, Specialty Therapeutics, Janssen, Grifols and Novartis, consulting fees from AstraZeneca, Atriva Therapeutics, Boehringer Ingelheim, Chiesi, GSK, CSL Behring, Inhibrx, Ferrer, Menarini, Mereo Biopharma, Spin Therapeutics, Specialty Therapeutics, ONO Pharma, Palobiofarma SL, Takeda, Novartis, Novo Nordisk, Sanofi, Zambon and Grifols and research grants from Grifols. Sudeep Acharya is an employee of GSK and holds shares in GSK. Bhumika Aggarwal is an employee of GSK and holds shares in GSK. Frederico LA Fernandes has received consulting fees from GSK, Chiesi, AstraZeneca, Zambon, Abbott and Boehringer Ingelheim and speaker fees from Abbott, GSK, ACHE, AstraZeneca, Novartis, Zambon and Boehringer Ingelheim. Jorge Dreyse Dañobeitía has received grants from Boehringer Ingelheim and AstraZeneca and consulting and speaker fees from GSK. José R. Jardim has received grants from GSK and speaker fees from Zambon, Grifols and GSK. Siwasak Juthong declares no conflicts of interest in this work. Gur Levy is an employee of GSK and holds shares in GSK. Martin Sivori has received speaker fees from AstraZeneca, TEVA, ELEA and GSK. The authors report no other conflicts of interest in this work., (© 2023 Miravitlles et al.)

Motivation: T-cell receptor beta chain (TCRB) repertoires are crucial for understanding immune responses. However, their high diversity and complexity present significant challenges in representation and analysis. The main motivation of this study is to develop a unified and compact representation of a TCRB repertoire that can efficiently capture its inherent complexity and diversity and allow for direct inference., Results: We introduce a novel approach to TCRB repertoire encoding and analysis, leveraging the Lempel-Ziv 76 algorithm. This approach allows us to create a graph-like model, identify-specific sequence features, and produce a new encoding approach for an individual's repertoire. The proposed representation enables various applications, including generation probability inference, informative feature vector derivation, sequence generation, a new measure for diversity estimation, and a new sequence centrality measure. The approach was applied to four large-scale public TCRB sequencing datasets, demonstrating its potential for a wide range of applications in big biological sequencing data., Availability and Implementation: Python package for implementation is available https://github.com/MuteJester/LZGraphs., (© The Author(s) 2023. Published by Oxford University Press.)

Analysis of an individual's immunoglobulin or T cell receptor gene repertoire can provide important insights into immune function. High-quality analysis of adaptive immune receptor repertoire sequencing data depends upon accurate and relatively complete germline sets, but current sets are known to be incomplete. Established processes for the review and systematic naming of receptor germline genes and alleles require specific evidence and data types, but the discovery landscape is rapidly changing. To exploit the potential of emerging data, and to provide the field with improved state-of-the-art germline sets, an intermediate approach is needed that will allow the rapid publication of consolidated sets derived from these emerging sources. These sets must use a consistent naming scheme and allow refinement and consolidation into genes as new information emerges. Name changes should be minimised, but, where changes occur, the naming history of a sequence must be traceable. Here we outline the current issues and opportunities for the curation of germline IG/TR genes and present a forward-looking data model for building out more robust germline sets that can dovetail with current established processes. We describe interoperability standards for germline sets, and an approach to transparency based on principles of findability, accessibility, interoperability, and reusability.

Patent ductus arteriosus (PDA) is a frequently encountered defect in infants born extremely premature (≤26 weeks' gestation). Historically, closure of the PDA was performed using cyclooxygenase inhibitor medications or by surgical ligations. However, the benefits of PDA closure using these therapies have never been demonstrated, albeit studies have previously not focused on the extremely premature infants. Therefore, there was a worldwide trend toward conservative management of the PDA. With improved survival of extremely premature infants, comorbidities associated with the PDA has increased, resulting in finding alternate treatments such as transcatheter patent ductus arteriosus closure (TCPC) for this population. Currently, there is a renewed interest toward selective treatment of the PDA in this high-risk cohort of small infants. This Comprehensive Review article inspects the globally changing trends in the management of the PDA in premature infants, with a special focus on the rising adoption of TCPC. Moreover, this article compiles data from several neonatal networks worldwide to help understand the problem at hand. Understanding the current management of premature infants and their outcomes is fundamentally essential if pediatric cardiologists are to offer TCPC as a viable therapeutic option for this population. This article aims to serve as a guide for pediatric cardiologists on this topic by compiling the results on landmark clinical trials on PDA management and the controversies that arise from these trials. Comparative outcomes from several countries are presented, including interpretations and opinions of the data from experts globally. This is a step toward coming to a global consensus in PDA management in premature infants., (© 2023 The Author(s).)

Introduction: The success of the human body in fighting SARS-CoV2 infection relies on lymphocytes and their antigen receptors. Identifying and characterizing clinically relevant receptors is of utmost importance., Methods: We report here the application of a machine learning approach, utilizing B cell receptor repertoire sequencing data from severely and mildly infected individuals with SARS-CoV2 compared with uninfected controls., Results: In contrast to previous studies, our approach successfully stratifies non-infected from infected individuals, as well as disease level of severity. The features that drive this classification are based on somatic hypermutation patterns, and point to alterations in the somatic hypermutation process in COVID-19 patients., Discussion: These features may be used to build and adapt therapeutic strategies to COVID-19, in particular to quantitatively assess potential diagnostic and therapeutic antibodies. These results constitute a proof of concept for future epidemiological challenges., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Safra, Tamari, Polak, Shiber, Matan, Karameh, Helviz, Levy-Barda, Yahalom, Peretz, Ben-Chetrit, Brenner, Tuller, Gal-Tanamy and Yaari.)

Protection from viral infections depends on immunoglobulin isotype switching, which endows antibodies with effector functions. Here, we find that the protein kinase DYRK1A is essential for B cell-mediated protection from viral infection and effective vaccination through regulation of class switch recombination (CSR). Dyrk1a-deficient B cells are impaired in CSR activity in vivo and in vitro. Phosphoproteomic screens and kinase-activity assays identify MSH6, a DNA mismatch repair protein, as a direct substrate for DYRK1A, and deletion of a single phosphorylation site impaired CSR. After CSR and germinal center (GC) seeding, DYRK1A is required for attenuation of B cell proliferation. These findings demonstrate DYRK1A-mediated biological mechanisms of B cell immune responses that may be used for therapeutic manipulation in antibody-mediated autoimmunity., (© 2023. The Author(s).)

Background & Aims: Hepatocellular carcinoma (HCC) is a model of a diverse spectrum of cancers because it is induced by well-known etiologies, mainly hepatitis C virus (HCV) and hepatitis B virus. Here, we aimed to identify HCV-specific mutational signatures and explored the link between the HCV-related regional variation in mutations rates and HCV-induced alterations in genome-wide chromatin organization., Methods: To identify an HCV-specific mutational signature in HCC, we performed high-resolution targeted sequencing to detect passenger mutations on 64 HCC samples from 3 etiology groups: hepatitis B virus, HCV, or other. To explore the link between the genomic signature and genome-wide chromatin organization we performed chromatin immunoprecipitation sequencing for the transcriptionally permissive H3K4Me3, H3K9Ac, and suppressive H3K9Me3 modifications after HCV infection., Results: Regional variation in mutation rate analysis showed significant etiology-dependent regional mutation rates in 12 genes: LRP2, KRT84, TMEM132B, DOCK2, DMD, INADL, JAK2, DNAH6, MTMR9, ATM, SLX4, and ARSD. We found an enrichment of C->T transversion mutations in the HCV-associated HCC cases. Furthermore, these cases showed regional variation in mutation rates associated with genomic intervals in which HCV infection dictated epigenetic alterations. This signature may be related to the HCV-induced decreased expression of genes encoding key enzymes in the base excision repair pathway., Conclusions: We identified novel distinct HCV etiology-dependent mutation signatures in HCC associated with HCV-induced alterations in histone modification. This study presents a link between cancer-causing mutagenesis and the increased predisposition to liver cancer in chronic HCV-infected individuals, and unveils novel etiology-specific mechanisms leading to HCC and cancer in general., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Crohn's disease (CD) is a chronic relapsing-remitting inflammatory disorder of the gastrointestinal tract that is characterized by altered innate and adaptive immune function. Although massively parallel sequencing studies of the T cell receptor repertoire identified oligoclonal expansion of unique clones, much less is known about the B cell receptor (BCR) repertoire in CD. Here, we present a novel BCR repertoire sequencing data set from ileal biopsies from pediatric patients with CD and controls, and identify CD-specific somatic hypermutation (SHM) patterns, revealed by a machine learning (ML) algorithm trained on BCR repertoire sequences. Moreover, ML classification of a different data set from blood samples of adults with CD versus controls identified that V gene usage, clusters, or mutation frequencies yielded excellent results in classifying the disease (F1 > 90%). In summary, we show that an ML algorithm enables the classification of CD based on unique BCR repertoire features with high accuracy., (© 2023 Safra et al.; Published by Cold Spring Harbor Laboratory Press.)

Background: Machine learning (ML) has gained significant attention for classifying immune states in adaptive immune receptor repertoires (AIRRs) to support the advancement of immunodiagnostics and therapeutics. Simulated data are crucial for the rigorous benchmarking of AIRR-ML methods. Existing approaches to generating synthetic benchmarking datasets result in the generation of naive repertoires missing the key feature of many shared receptor sequences (selected for common antigens) found in antigen-experienced repertoires., Results: We demonstrate that a common approach to generating simulated AIRR benchmark datasets can introduce biases, which may be exploited for undesired shortcut learning by certain ML methods. To mitigate undesirable access to true signals in simulated AIRR datasets, we devised a simulation strategy (simAIRR) that constructs antigen-experienced-like repertoires with a realistic overlap of receptor sequences. simAIRR can be used for constructing AIRR-level benchmarks based on a range of assumptions (or experimental data sources) for what constitutes receptor-level immune signals. This includes the possibility of making or not making any prior assumptions regarding the similarity or commonality of immune state-associated sequences that will be used as true signals. We demonstrate the real-world realism of our proposed simulation approach by showing that basic ML strategies perform similarly on simAIRR-generated and real-world experimental AIRR datasets., Conclusions: This study sheds light on the potential shortcut learning opportunities for ML methods that can arise with the state-of-the-art way of simulating AIRR datasets. simAIRR is available as a Python package: https://github.com/KanduriC/simAIRR., (© The Author(s) 2023. Published by Oxford University Press GigaScience.)

Fischer-Tropsch synthesis (FTS), a significant reaction for effective H 2 utilization, is a promising approach for direct production of light olefins from syngas (H 2 + CO). For the FT-Olefin process, an efficient catalyst restricting the product distribution of FTS to light olefins is required. Aligned with this goal, we synthesized 24 catalysts comprising Fe and Cu in combination with rare earth metals (La, Ce, Nd, Ho, Er) and zeolite supports (ultrastable Y and mordenite). FT-Olefin performances of these catalysts were screened using a high-throughput test system at atmospheric pressure, and then promising catalysts were tested under high pressure in a conventional test system. Results show that Nd increases selectivity to light olefins and Ho suppresses C 5 + and coke formation. It is also demonstrated that zeolite-metal interaction, leading to a mixture of both acidic and basic sites, is significant in increasing light olefin production. The mordenite-supported 20 wt % Fe, 0.5 wt % Cu, and 0.5 wt % Ho catalyst provides the highest light olefin yield with the lowest coke and heavier hydrocarbon selectivity., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

The main challenge in cardiac optogenetics is to have low-power, high-fidelity deep excitation of cells with minimal invasiveness and heating. We present a detailed computational study of optogenetic excitation of human ventricular cardiomyocytes (HVCMs) with new ChRmine, bReaChES and CsChrimson red-shifted opsins to overcome the challenge. Action potentials (APs) in ChRmine-expressing HVCMs can be triggered at 6 µW mm -2 (10 ms pulse) and 0.7 µW mm -2 (100 ms pulse) at 585 nm, which is two orders of magnitude lower than ChR2(H134R). This enables safe sustained excitation of deeply situated cardiac cells with ChRmine (7.46 mm) and with bReaChES (6.21 mm) with the light source at the pericardium surface. Deeper excitation up to 10.2 mm can be achieved with ChRmine by illuminating at 650 nm. Photostimulation conditions for minimum charge transfer during APs have been determined, which is important for tissue health under sustained excitation. The AP duration for all the opsins is constant up to 100 ms pulse width but increases thereafter. Interestingly, the AP frequency increases with irradiance under continuous illumination, but APs are suppressed at higher irradiances. The optimal range of irradiance for each opsin to excite HVCMs has been determined. Under optimal photostimulation conditions, each opsin can precisely excite APs up to 2.5 Hz, while latency and power of light pulse for each AP in a sequence remain most stable and an order of magnitude lower, respectively, in ChRmine-expressing HVCMs. The study highlights the importance of ChRmine and bReaChES for resynchronization, termination of ventricular tachycardia and designing optogenetic cardiac pacemakers with enhanced battery life. KEY POINTS: This work is the formulation of accurate theoretical models of optogenetic control of human ventricular cardiomyocytes (HVCMs) expressed with newly discovered opsins (ChRmine, bReaChES and CsChrimson). Under continuous illumination, action potentials in each opsin-expressing HVCMs can only be evoked in a certain range of irradiances. Action potentials in ChRmine-expressing HVCMs can be triggered at ultra-low power (6 µW mm -2 at 10 ms pulse or 0.7 µW mm -2 at 100 ms pulse at 585 nm), which is two to three orders of magnitude lower than reported results. Ongoing action potentials in ChRmine-expressing HVCMs can be suppressed by continuous illumination of 585 nm light at 2 µW mm -2 . ChRmine enables sustained excitation due to its faster recovery from the desensitized state. Optogenetic excitation of deeply situated cardiac cells is possible up to ∼7.46 and 10.2 mm with ChRmine on illuminating the outer surface of pericardium at safe irradiance at 585 nm and 650 nm, respectively. The study opens up prospects for designing energy-efficient light-induced pacemakers, resynchronization and termination of ventricular tachycardia., (© 2022 The Authors. The Journal of Physiology © 2022 The Physiological Society.)

Questions about the different aspects of physical activity (PA) are commonly asked in the clinical setting, yet their compatibility for use with children, particularly children with obesity (OB) is uncertain. Our aim was to investigate different PA-related questions when compared to an objective maximal cardiopulmonary exercise test (CPET) or validated questionnaires. For this study, 33 normal-weight (NW) (5 to less than 85% BMI percentile) and 35 OB (≥95% BMI percentile) children responded to three self-report PA questions evaluating PA domains (exercise capacity, limitations, and the maintenance of an active lifestyle); they also completed a maximal CPET and two validated questionnaires: the New York Heart Association (NYHA) questionnaire and the international physical activity questionnaire (IPAQ). The results regarding the NW children were highly compatible with their self-reports about exercise capacity (85%), whereas the compatibility was low (40%) in the OB group (p < 0.001). Both OB and NW groups had moderate compatibility between the self-report and objective findings regarding their exercise limitations and lifestyle with no significant differences between the groups. These findings suggest that it is inadvisable to rely on a single-item question by which to assess PA in OB children, and no definite conclusions regarding PA status should be drawn. NW children are more compatible with self-reporting their overall exercise capacity, with more limited compatibilities observed when self-reporting their limitations or lifestyle.

Background: Late preterm (340−366 weeks gestational age [GA]) infants may have abnormal pulmonary development and possible exercise physiology parameters. We aim to assess the effect of late prematurity on exercise capacity in childhood and to compare it to early preterm (EP) (born < 300 GA), and to term healthy control (TC) (>370 week GA). Methods: Late preterm and early preterm (7−10 years) completed a cardiopulmonary exercise test (CPET) and spirometry and were compared to EP and to TC. Results: Eighty-four children (age 9.6 ± 1.0 years, 48% girls) participated. Twenty-one former LP were compared to 38 EP (15 with Bronchopulmonary dysplasia (BPD) [EP+], 23 without BPD [EP−]) and to 25 TC children. Peak oxygen uptake (peakV̇O2) was statistically lower than in the TC, but within the normal range, and without difference from the EP (LP 90.2 ± 15.1%, TC 112.4 ± 16.9%, p < 0.001; EP+ 97.3 ± 25.5%, EP− 85.4 ± 20.8%, p = 0.016 and p < 0.001, respectively, when compared with TC). Lung function (FEV1) was lower than normal only in the EP+ (75.6 ± 14.9% predicted, compared with 12.5 ± 87.8 in EP−, 87.5 ± 16.9 in LP and 91.0 ± 11.7 in TC). Respiratory and cardiac limitations were similar between all four study groups. Conclusions: This study demonstrated lower exercise capacity (peakV̇O2) in former LP children compared with healthy term children. Exercise capacity in LP was comparable to that of EP, with and without BPD. However, the exercise test parameters, specifically peakV̇O2, were within the normal range, and no significant physiological exercise limitations were found.

Purpose: Autism is a multifactorial neurodevelopment disease and it has not been disclosed as a hypoglutamatergic or hyperglutamathergic disease. Ceftriaxone is an antibiotic that increases glutamate transporter-1 (GLT-1) expression in the brain in chronic use. In our study we aimed to investigate the effects of different doses of ceftriaxone in postnatal period in male mice exposed to valproic acid (VPA) at 12.5th day of pregnancy. Methods: A total of 96 BALB/c male mice were divided into 12 groups (n = 8 animals per group). Ceftriaxone (50, 100, 200 mg/kg/d) or saline was given to the male offsprings born from pregnant mice administered VPA and/or saline, between days 47 and 55. Dihydrokainic acid (10 mg/kg), a GLT-1 inhibitor, was administered intraperitoneally to evaluate whether GLT-1 mediates the effect of ceftriaxone. Three chamber sociability and social interaction test and the rota rod test were performed in all groups on days 54 and 55. GLT-1 levels in the hippocampus were measured by immunohistochemistry (IHC) and western blotting (WB). Results: In our study, autism-like behaviors were observed in male offsprings that were exposed to VPA in the intrauterine period. Chronic ceftriaxone administration has no curative effect on behavioral impairment seen in autism. Conclusion: Our results show that ceftriaxone did not exert significant therapeutic effect on VPA-induced mouse model of autism., Competing Interests: The authors have no conflicts of interest to declare., (©2022 The Authors.)

The immunoglobulin genes of inbred mouse strains that are commonly used in models of antibody-mediated human diseases are poorly characterized. This compromises data analysis. To infer the immunoglobulin genes of BALB/c mice, we used long-read SMRT sequencing to amplify VDJ-C sequences from F1 (BALB/c x C57BL/6) hybrid animals. Strain variations were identified in the Ighm and Ighg2b genes, and analysis of VDJ rearrangements led to the inference of 278 germline IGHV alleles. 169 alleles are not present in the C57BL/6 genome reference sequence. To establish a set of expressed BALB/c IGHV germline gene sequences, we computationally retrieved IGHV haplotypes from the IgM dataset. Haplotyping led to the confirmation of 162 BALB/c IGHV gene sequences. A musIGHV398 pseudogene variant also appears to be present in the BALB/cByJ substrain, while a functional musIGHV398 gene is highly expressed in the BALB/cJ substrain. Only four of the BALB/c alleles were also observed in the C57BL/6 haplotype. The full set of inferred BALB/c sequences has been used to establish a BALB/c IGHV reference set, hosted at https://ogrdb.airr-community.org. We assessed whether assemblies from the Mouse Genome Project (MGP) are suitable for the determination of the genes of the IGH loci. Only 37 (43.5%) of the 85 confirmed IMGT-named BALB/c IGHV and 33 (42.9%) of the 77 confirmed non-IMGT IGHV were found in a search of the MGP BALB/cJ genome assembly. This suggests that current MGP assemblies are unsuitable for the comprehensive documentation of germline IGHVs and more efforts will be needed to establish strain-specific reference sets., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Jackson, Kos, Lees, Gibson, Smith, Peres, Yaari, Corcoran, Busse, Ohlin, Watson and Collins.)

Saturation mutagenesis is a semi-rational approach for protein engineering where sites are saturated either entirely or partially to include amino acids of interest. We previously reported on a codon compression algorithm, where a set of minimal degenerate codons are selected according to user-defined parameters such as the target organism, type of saturation and usage levels. Here, we communicate an addition to our web tool that considers the distance between the wild-type codon and the library, depending on its purpose. These forms of restricted collections further reduce library size, lowering downstream screening efforts or, in turn, allowing more comprehensive saturation of multiple sites. The library design tool can be accessed via http://www.dynamcc.com/dynamcc&#95;d/. Graphical Abstract., (© The Author(s) 2022. Published by Oxford University Press.)

The tumor microenvironment hosts antibody-secreting cells (ASCs) associated with a favorable prognosis in several types of cancer. Patient-derived antibodies have diagnostic and therapeutic potential; yet, it remains unclear how antibodies gain autoreactivity and target tumors. Here, we found that somatic hypermutations (SHMs) promote antibody antitumor reactivity against surface autoantigens in high-grade serous ovarian carcinoma (HGSOC). Patient-derived tumor cells were frequently coated with IgGs. Intratumoral ASCs in HGSOC were both mutated and clonally expanded and produced tumor-reactive antibodies that targeted MMP14, which is abundantly expressed on the tumor cell surface. The reversion of monoclonal antibodies to their germline configuration revealed two types of classes: one dependent on SHMs for tumor binding and a second with germline-encoded autoreactivity. Thus, tumor-reactive autoantibodies are either naturally occurring or evolve through an antigen-driven selection process. These findings highlight the origin and potential applicability of autoantibodies directed at surface antigens for tumor targeting in cancer patients., Competing Interests: Declaration of interests The antibodies reported in the article are in the process of being patented., (Copyright © 2022 Elsevier Inc. All rights reserved.)

New insights in evolution are available thanks to next-generation sequencing technologies in recent years. However, due to the network of complex relations between species, caused by the intensive horizontal gene transfer (HGT) between different bacterial species, it is difficult to discover bacterial evolution. This difficulty leads to new research in the field of phylogeny, including the gene-based phylogeny, in contrast to sequence-based phylogeny. In previous articles, we presented evolutionary insights of Synteny Index (SI) study on a large biological dataset. We showed that the SI approach naturally clusters 1133 species into 39 cliques of closely related species. In addition, we presented a model that enables calculation of the number of translocation events between genomes based on their SI distance. Here, these two studies are combined together and lead to new insights. A principal result is the relation between two evolutionary clocks: the well-known sequence-based clock influenced by point mutations, and SI distance clock influenced by translocation events. A surprising linear relation between these two evolutionary clocks rising for closely related species across all genus. In other words, these two different clocks are ticking at the same rate inside the genus level. Conversely, a phase-transition manner discovered between these two clocks across non-closely related species. This may suggest a new genus definition based on an analytic approach, since the phase-transition occurs where each gene, on average, undergoes one translocation event. In addition, rare cases of HGT among highly conserved genes can be detected as outliers from the phase-transition pattern., Competing Interests: The author declares that there are no conflicts of interest., (© 2022 The Authors.)

Background: T and B cell receptor (TCR, BCR) repertoires constitute the foundation of adaptive immunity. Adaptive immune receptor repertoire sequencing (AIRR-seq) is a common approach to study immune system dynamics. Understanding the genetic factors influencing the composition and dynamics of these repertoires is of major scientific and clinical importance. The chromosomal loci encoding for the variable regions of TCRs and BCRs are challenging to decipher due to repetitive elements and undocumented structural variants., Methods: To confront this challenge, AIRR-seq-based methods have recently been developed for B cells, enabling genotype and haplotype inference and discovery of undocumented alleles. However, this approach relies on complete coverage of the receptors' variable regions, whereas most T cell studies sequence a small fraction of that region. Here, we adapted a B cell pipeline for undocumented alleles, genotype, and haplotype inference for full and partial AIRR-seq TCR data sets. The pipeline also deals with gene assignment ambiguities, which is especially important in the analysis of data sets of partial sequences., Results: From the full and partial AIRR-seq TCR data sets, we identified 39 undocumented polymorphisms in T cell receptor Beta V (TRBV) and 31 undocumented 5 ' UTR sequences. A subset of these inferences was also observed using independent genomic approaches. We found that a single nucleotide polymorphism differentiating between the two documented T cell receptor Beta D2 (TRBD2) alleles is strongly associated with dramatic changes in the expressed repertoire., Conclusions: We reveal a rich picture of germline variability and demonstrate how a single nucleotide polymorphism dramatically affects the composition of the whole repertoire. Our findings provide a basis for annotation of TCR repertoires for future basic and clinical studies., (© 2021. The Author(s).)

Background: Enzyme replacement therapy (ERT) with alglucosidase alfa improves the prospect of patients with infantile-onset Pompe disease (IOPD). However, a progressive decline has been reported. Objective quantification of the response to ERT when assessing newer strategies is warranted., Methods: This combined retrospective-prospective study assessed the acute and long-term effects of ERT on exercise in IOPD patients. Evaluation included cardiopulmonary exercise testing (CPET), 6-min walking test (6MWT), spirometry, motor function test (GMFM-88) and enzyme blood levels., Results: Thirty-four CPETs (17 pre- and 17 two days-post ERT) over variable follow-up periods were performed in four patients. Two days following ERT, blood enzyme levels increased (median, 1.22 and 10.15 μmol/L/h ( p = 0.003)). However, FEV1, FVC and GMFM-88, the median 6MWD and the peak VO 2 were unchanged. Long-term evaluations showed stabilization in young patients but progressive deterioration in adolescents. Clinical deterioration was associated with more pronounced deterioration in peak VO 2 followed in the decreasing order by 6MWD, FVC and GMFM-88., Conclusions: The peak VO 2 and 6MWD might serve as more sensitive markers to assess clinical deterioration. More studies are needed to clarify the sensitivity of the peak VO 2 and 6MWT for quantification of individualized response. This may be important when assessing newer strategies and formulations in IOPD.

Inference of germline polymorphisms in immunoglobulin genes from B cell receptor repertoires is complicated by somatic hypermutations, sequencing/PCR errors, and by varying length of reference alleles. The light chain inference is particularly challenging owing to large gene duplications and absence of D genes. We analyzed the light chain cDNA sequences from naïve B cell receptor repertoires from 100 individuals. We optimized light chain allele inference by tweaking parameters of the TIgGER functions, extending the germline reference sequences, and establishing mismatch frequency patterns at polymorphic positions to filter out false-positive candidates. We identified 48 previously unreported variants of light chain variable genes. We selected 14 variants for validation and successfully validated 11 by Sanger sequencing. Clustering of light chain 5'UTR, L-PART1, and L-PART2 revealed partial intron retention in 11 kappa and 9 lambda V alleles. Our results provide insight into germline variation in human light chain immunoglobulin loci., Competing Interests: V.G. declares advisory board positions in aiNET GmbH and Enpicom B.V. V.G. is also a consultant for Roche/Genentech. All remaining authors declare no conflict of interests., (© 2021 The Authors.)

The adaptive branch of the immune system learns pathogenic patterns and remembers them for future encounters. It does so through dynamic and diverse repertoires of T- and B- cell receptors (TCR and BCRs, respectively). These huge immune repertoires in each individual present investigators with the challenge of extracting meaningful biological information from multi-dimensional data. The ability to embed these DNA and amino acid textual sequences in a vector-space is an important step towards developing effective analysis methods. Here we present Immune2vec, an adaptation of a natural language processing (NLP)-based embedding technique for BCR repertoire sequencing data. We validate Immune2vec on amino acid 3-gram sequences, continuing to longer BCR sequences, and finally to entire repertoires. Our work demonstrates Immune2vec to be a reliable low-dimensional representation that preserves relevant information of immune sequencing data, such as n-gram properties and IGHV gene family classification. Applying Immune2vec along with machine learning approaches to patient data exemplifies how distinct clinical conditions can be effectively stratified, indicating that the embedding space can be used for feature extraction and exploratory data analysis., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Ostrovsky-Berman, Frankel, Polak and Yaari.)