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Rare antinuclear antibody (ANA) pattern recognition has been a widely applied technology for routine ANA screening in clinical laboratories. In recent years, the application of deep learning methods in recognizing ANA patterns has witnessed remarkable advancements. However, the majority of studies in this field have primarily focused on the classification of the most common ANA patterns, while another subset has concentrated on the detection of mitotic metaphase cells. To date, no prior research has been specifically dedicated to the identification of rare ANA patterns. In the present paper, we introduce a novel attention-based enhancement framework, which was designed for the recognition of rare ANA patterns in ANA-indirect immunofluorescence images. More specifically, we selected the algorithm with the best performance as our target detection network by conducting comparative experiments. We then further developed and enhanced the chosen algorithm through a series of optimizations. Then, attention mechanism was introduced to facilitate neural networks in expediting the learning process, extracting more essential and distinctive features for the target features that belong to the specific patterns. The proposed approach has helped to obtained high precision rate of 86.40%, 82.75% recall, 84.24% F1 score and 84.64% mean average precision for a 9-category rare ANA pattern detection task on our dataset. Finally, we evaluated the potential of the model as medical technologist assistant and observed that the technologist's performance improved after referring to the results of the model prediction. These promising results highlighted its potential as an efficient and reliable tool to assist medical technologists in their clinical practice. [ABSTRACT FROM AUTHOR]

Classifying epitopes is essential since they can be applied in various fields, including therapeutics, diagnostics and peptide-based vaccines. To determine the epitope or peptide against an antibody, epitope mapping with peptides is the most extensively used method. However, this method is more time-consuming and inefficient than using present methods. The ability to retrieve data on protein sequences through laboratory procedures has led to the development of computational models that predict epitope binding based on machine learning and deep learning (DL). It has also evolved to become a crucial part of developing effective cancer immunotherapies. This paper proposes an architecture to generalize this case since various research strives to solve a low-performance classification problem. A proposed DL model is the fusion architecture, which combines two architectures: Transformer architecture and convolutional neural network (CNN), called MITNet and MITNet-Fusion. Combining these two architectures enriches feature space to correlate epitope labels with the binary classification method. The selected epitope–T-cell receptor (TCR) interactions are GILG, GLCT and NLVP, acquired from three databases: IEDB, VDJdb and McPAS-TCR. The previous input data was extracted using amino acid composition, dipeptide composition, spectrum descriptor and the combination of all those features called AADIP composition to encode the input data to DL architecture. For ensuring consistency, fivefold cross-validations were performed using the area under curve metric. Results showed that GILG, GLCT and NLVP received scores of 0.85, 0.87 and 0.86, respectively. Those results were compared to prior architecture and outperformed other similar deep learning models. [ABSTRACT FROM AUTHOR]

The haemagglutination test (HAT)-field protocol described here is an optimization of the recently published HAT, for the detection of antibodies directed against the receptor binding domain (RBD) of the SARS-Cov-2 virus. HAT and HAT-field are both based on haemagglutination triggered by a single reagent, the IH4-RBD recombinant protein. A sample of IH4-RBD sufficient for several thousand tests or a plasmid encoding IH4-RBD can be obtained from the authors of our first paper. Using titration of IH4-RBD, HAT-field now allows a quantitative assessment of antibody levels in a single step, using a few microliters of whole blood, such as can be obtained by finger prick, and requires only very simple disposable equipment. Because it is based on a single soluble reagent, the test can be adapted very simply and rapidly to detect antibodies against variants of the SARS-CoV-2, or conceivably against different pathogens. HAT-field appears well suited to provide quantitative assessments of the serological protection of populations as well as individuals, and given its very low cost, the stability of the IH4-RBD reagent in the adapted buffer and the simplicity of the procedure, could be deployed pretty much anywhere, including in the poorest countries and the most remote corners of the globe. [ABSTRACT FROM AUTHOR]

Summary Antibody repertoires reveal insights into the biology of the adaptive immune system and empower diagnostics and therapeutics. There are currently multiple tools available for the annotation of antibody sequences. All downstream analyses such as choosing lead drug candidates depend on the correct annotation of these sequences; however, a thorough comparison of the performance of these tools has not been investigated. Here, we benchmark the performance of commonly used immunoinformatic tools, i.e. IMGT/HighV-QUEST, IgBLAST and MiXCR, in terms of reproducibility of annotation output, accuracy and speed using simulated and experimental high-throughput sequencing datasets. We analyzed changes in IMGT reference germline database in the last 10 years in order to assess the reproducibility of the annotation output. We found that only 73/183 (40%) V, D and J human genes were shared between the reference germline sets used by the tools. We found that the annotation results differed between tools. In terms of alignment accuracy, MiXCR had the highest average frequency of gene mishits, 0.02 mishit frequency and IgBLAST the lowest, 0.004 mishit frequency. Reproducibility in the output of complementarity determining three regions (CDR3 amino acids) ranged from 4.3% to 77.6% with preprocessed data. In addition, run time of the tools was assessed: MiXCR was the fastest tool for number of sequences processed per unit of time. These results indicate that immunoinformatic analyses greatly depend on the choice of bioinformatics tool. Our results support informed decision-making to immunoinformaticians based on repertoire composition and sequencing platforms. Availability and implementation All tools utilized in the paper are free for academic use. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Background Home-care robots have been developed as one of the assistive technologies, and benefits and challenges of their use have been debated in many countries. Research teams in Japan, Finland and Ireland carried out a questionnaire to explore perceptions of potential users (older people, family caregivers, and health and social care professionals (HSCPs)) towards the use of home-care robots. As part of a larger tri-country comparative study, this paper reports preliminary findings from the data collected from the online survey of HSCPs in Ireland. Methods Questionnaire was developed iteratively among the research teams in three countries. Questions related to the use of advocates in deciding whether to use home-care robots, desirable functions in such robots, and perceptions of privacy protection. Based on networks of professional and advocacy groups, HSCPs were contacted and 123 respondents took part in the questionnaire, and 46 fully completed the questionnaire. Results Out of 46 respondents (44 female, 1 male and 1 did not wish to specify), 80% answered that they are open to the use of home-care robots. Safety monitoring and alert functions were considered to be most desirable in home-care robots. 76% of the respondents placed importance on the guarantee of entitlement to receiving human care, irrespective of the use of home-care robots. 30% answered that they have a negative impression of robots, to some extent. The overall majority (N=39, 85%) felt strongly that a decision as to whether to use home-care robots should be made by the user, and that the access to data collected in any form by robots requires extra care. Conclusion While there was generally a positive perception of the use of home-care robots among Irish HSCPs, cautious attitudes were evident in the areas of decision-making and privacy. This study was funded by the Pfizer Health Research Foundation. [ABSTRACT FROM AUTHOR]

The presence or absence of terminal sialic acid residues in the sugar moiety attached to the Fc-domain of IgG molecules modulates IgG activity and is associated with autoimmune or infection related inflammation. In a recent paper, Oswald and colleagues suggest that IgG sialylation may occur post IgG secretion from plasma cells, which would be a major issue for therapeutic antibodies injected into patients. In contrast, we argue that previous work rather demonstrates that IgG sialylation occurs within B cells and that the experimental system used by the authors is not suitable to address this critical question. [ABSTRACT FROM AUTHOR]

Objectives The European Single Hub and Access point for paediatric Rheumatology in Europe initiative aimed to optimize care for children with rheumatic diseases. Kawasaki disease (KD) is the most common cause of acquired heart disease in children and an important cause of long-term cardiac disease into adulthood. Prompt diagnosis and treatment of KD is difficult due to the heterogeneity of the disease but is crucial for improving outcome. To date, there are no European internationally agreed, evidence-based guidelines concerning the diagnosis and treatment of KD in children. Accordingly, treatment regimens differ widely. The aim of this study is to provide consensus-based, European-wide evidence-informed recommendations for diagnosis and treatment of children with KD. Methods Recommendations were developed using the EULAR's standard operating procedures. An extensive systematic literature search was performed, and evidence-based recommendations were extrapolated from the included papers. These were evaluated by a panel of international experts via online surveys and subsequently discussed in three consensus meetings, using nominal group technique. Recommendations were accepted when ⩾80% agreed. Results In total, 17 recommendations for diagnosis and 14 for treatment of KD in children were accepted. Diagnostic recommendations included laboratory and imaging workup for complete as well as incomplete KD. Treatment recommendations included the importance of early treatment in both complete and incomplete KD, use of intravenous immunoglobulin, aspirin, corticosteroids for high-risk cases, and other treatment options for those with resistant disease. Conclusion The Single Hub and Access point for paediatric Rheumatology in Europe initiative provides international evidence-based recommendations for diagnosing and treating KD in children, facilitating improvement and uniformity of care. [ABSTRACT FROM AUTHOR]

It has been observed that converting scFv formatted antibodies to full-length IgG often associates with loss of affinity. We aim to address this issue in this paper by establishing an integrated affinity maturation method applying yeast display technology platform. To demonstrate that, we employed a human thrombopoietin receptor targeting antibody named 3D9 which was identified previously from a combinational antibody library in scFv-Fc fusion protein form. We have observed that significant potency loss happened when 3D9 was transformed to full-length IgG form. In this study, we tested whether the potency of the full-length IgG can be improved by affinity maturation of 3D9 using a modified Fab yeast display platform. An efficient CDR3 targeted mutagenesis strategy was designed for Fab library with pre-designed CDR diversity. Next generation sequencing was also used for evaluation of the enrichment process and investigation of sequence-function relationship of the antibody. A variant with improved affinity and higher potency was identified. The study demonstrates that the strategy we used here are efficient for optimizing affinity and activity of full-length IgGs. [ABSTRACT FROM AUTHOR]

The extent of the role of N-linked glycans (N-glycans) in shielding influenza A hemagglutinin (HA) against host antibodies has proved controversial, with different authors making widely different assumptions. One common assumption is that N-glycans physically shield surface residues that are near to glycosylation sites, thereby preventing antibodies from binding to them. However, it is unclear, from existing experimental evidence, whether antibodies that bind close to N-glycans are a rare or commonplace feature of human herd immune responses to influenza AHA. The aim of this paper is to present a computational analysis of mutations in the vicinity of N-glycans that will facilitate a better understanding of their protective role. We identify, from an analysis of over 6000 influenza A H3N2 sequences, a set of residues adjacent to N-glycosylation sites that are highly likely to be involved in antigenic escape from host antibodies. Fifteen of these residues occur within 10 Å of an N-glycosylation site. Hence, we conclude that it is relatively common for antibodies to bind in close proximity to N-glycans on the surface ofHA, with any shielding effect largely attributable to the inability of host antibodies to bind across an N-glycan attachment site, rather than to the physical masking of neighboring residues. [ABSTRACT FROM PUBLISHER]

Motivation The emergence of a novel strain of betacoronavirus, SARS-CoV-2, has led to a pandemic that has been associated with over 700 000 deaths as of August 5, 2020. Research is ongoing around the world to create vaccines and therapies to minimize rates of disease spread and mortality. Crucial to these efforts are molecular characterizations of neutralizing antibodies to SARS-CoV-2. Such antibodies would be valuable for measuring vaccine efficacy, diagnosing exposure and developing effective biotherapeutics. Here, we describe our new database, CoV-AbDab, which already contains data on over 1400 published/patented antibodies and nanobodies known to bind to at least one betacoronavirus. This database is the first consolidation of antibodies known to bind SARS-CoV-2 as well as other betacoronaviruses such as SARS-CoV-1 and MERS-CoV. It contains relevant metadata including evidence of cross-neutralization, antibody/nanobody origin, full variable domain sequence (where available) and germline assignments, epitope region, links to relevant PDB entries, homology models and source literature. Results On August 5, 2020, CoV-AbDab referenced sequence information on 1402 anti-coronavirus antibodies and nanobodies, spanning 66 papers and 21 patents. Of these, 1131 bind to SARS-CoV-2. Availabilityand implementation CoV-AbDab is free to access and download without registration at http://opig.stats.ox.ac.uk/webapps/coronavirus. Community submissions are encouraged. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

I International Immunology i , dxab111, https://doi.org/10.1093/intimm/dxab111 After this paper was accepted, the authors realized that the data in the middle and bottom histograms of Fig. 3C and the right-hand flow cytometry plot of Fig. [Extracted from the article]

Background Rituximab is an anti-CD20 chimeric monoclonal antibody that depletes pre-plasma B cells. It is used in paediatric rheumatology for conditions including juvenile systemic lupus erythematosus (jSLE), juvenile dermatomyositis (JDM), vasculitides and refractory juvenile idiopathic arthritis (JIA). We aim to describe the cohort of patients treated with rituximab in the Scottish Paediatric and Adolescent Rheumatology Network (SPARN) in a 5-year period, and assess the need for a network guideline. Methods A review of paper and electronic case records. Patients seen within the SPARN network who received Rituximab between 2014 and 2018 were included. Results Vasculitis Rituximab was given to 16 patients in 5 different SPARN centres between 2014 and 2018. Male: Female ratio was 1:4.3. Mean age at first dose of rituximab was 12.75 years. Mean disease duration pre rituximab was 1 year. 8 (50%) patients had jSLE, 7 multisystem and 1 isolated lupus nephritis. 3 had ANCA-positive vasculitis and 5 had other conditions. (1 had RF+ve JIA; 1 severe panuveitis; 1 had an unspecified autoinflammatory condition; 1 had COPA syndrome with severe interstitial lung disease and 1 had autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). Documentation of pre-rituximab checks was poor. Baseline bloods were done in all 16 patients. 11 patients had lymphocyte subsets and 13 immunoglobulins documented. Disease-specific antibodies were measured in all patients in whom applicable (11). 11 had a chest x-ray prior to rituximab. In 9 cases a pre-rituximab pregnancy test was indicated: none were documented. In only 3 patients was a pre-rituximab history of recent infections documented. In 8 patients a discussion regarding treatment risks and benefits was documented. Post-infusion lymphocyte subset monitoring was variable but documented in 15. 1 patient was never B cell deplete. 9 never fully reconstituted. RTX dose information was available for 14. All received doses of 750mg/m2 with 6 having the dose capped at 1g. Dose frequency information was available for all. The majority (9) received 2 doses. Of the rest, 1 patient received a single dose. 3 received 3 doses, 2 had 4 and 1 had 5. All patients in whom information was available, received pre-medication with paracetamol, chlorphenamine and methylprednisolone (n = 14). 4 patients had side effects noted (rash/itch in 1, anaphylaxis in 1, facial flushing in 1 and post-infusion infection in 1). Clinical response was clearly documented in 8 patients, 7 of whom showed clinical improvement (2 had systemic jSLE, 2 had ANCA +ve vasculitis, 1 had isolated lupus nephritis, 1 had COPA syndrome and 1 had RF+ JIA). Conclusion Rituximab is used for a range of conditions and in a number of centres within SPARN. This review highlights variation in and poor documentation of pre-rituximab discussions and investigations, prescribing, monitoring and response. A SPARN rituximab protocol is being developed to address this. Conflicts of Interest The authors declare no conflicts of interest. [ABSTRACT FROM AUTHOR]