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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.

Measurement(s) Transcriptomics • Hemagglutination Inhibition Assay • IgG IgM IgA Total Measurement • Virus-neutralizing Antibody • ELISA Technology Type(s) Microarray • RNA sequencing • Hemagglutination Inhibition Assay • ELISA • Microneutralization Assay • serum neutralization of viral infectivity assay Sample Characteristic - Organism Homo sapiens

SARS-CoV-2 infection can lead to progressive pathology in patients with COVID-19, but information for this disease progression is sparse. Here the authors use multi-omics approach to profile the immune responses of patients, assessing immune repertoire and effects of tocilizumab treatments, to find a dyssynchrony between innate and adaptive immunity in progressive COVID-19.

We propose a novel variable step size predictor design method for a class of linear discrete-time censored system. We divide the censored system into two parts. The system measurement equation in one part doesn't contain the censored data, and the system measurement equation in the other part is the censored signal. For the normal one, we use the Kalman filtering technology to design one-step predictor. For the one that the measurement equation is censored, we determine the predictor step size according to the censored data length and give the gain compensation parameter matrix β(s) for the case predictor with obvious errors applying the minimum error variance trace, projection formula, and empirical analysis, respectively. Finally, a simulation example shows that the variable step size predictor based on empirical analysis has better estimation performance.

It is difficult to adjust the pH of oil acidized wastewater rich in Ca2+, thus hindering the polyacrylamide (PAM) flocculation. This study aims at accelerating the flocculation process by introducing CO2 into the water to induce the formation of CaCO3 nuclei. The order in which CO2 and NaOH were added affected the floc structures. Compared with CO2-NaOH-PAM, the flocs of NaOH-CO2-PAM were more compact and more CaCO3 crystals were formed. The aqueous Ca2+ involved in the reaction reached 20%, and CO2 utilization was enhanced. The settling time was shortened by half (from 20 to 3 min), and NaOH consumption was reduced by one-tenth (from 0.03 to 0.003 mol), hence significantly reducing the costs. Due to the higher settling rate and shorter contact time, the NaOH-CO2-PAM flocs adsorbed less so that the residual oil was 124 mg·L−1, while in the case of CO2-NaOH-PAM it was 88 mg·L−1. As a promising coagulation aid, CO2 can also be used to mineralize pollutants in wastewater.

In order to better understand how the immune system interacts with environmental triggers to produce organ-specific disease, we here address the hypothesis that B and plasma cells are free to migrate through the mucosal surfaces of the upper and lower respiratory tracts, and that their total antibody repertoire is modified in a common respiratory tract disease, in this case atopic asthma. Using Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) we have catalogued the antibody repertoires of B cell clones retrieved near contemporaneously from multiple sites in the upper and lower respiratory tract mucosa of adult volunteers with atopic asthma and non-atopic controls and traced their migration. We show that the lower and upper respiratory tracts are immunologically connected, with trafficking of B cells directionally biased from the upper to the lower respiratory tract and points of selection when migrating from the nasal mucosa and into the bronchial mucosa. The repertoires are characterized by both IgD-only B cells and others undergoing class switch recombination, with restriction of the antibody repertoire distinct in asthmatics compared with controls. We conclude that B cells and plasma cells migrate freely throughout the respiratory tract and exhibit distinct antibody repertoires in health and disease.

The skin lesion erythema migrans (EM) is an initial sign of the Ixodes tick–transmitted Borreliella spirochetal infection known as Lyme disease. T cells and innate immune cells have previously been shown to predominate the EM lesion and promote the reaction. Despite the established importance of B cells and antibodies in preventing infection, the role of B cells in the skin immune response to Borreliella is unknown. Here, we used single-cell RNA-Seq in conjunction with B cell receptor (BCR) sequencing to immunophenotype EM lesions and their associated B cells and BCR repertoires. We found that B cells were more abundant in EM in comparison with autologous uninvolved skin; many were clonally expanded and had circulating relatives. EM-associated B cells upregulated the expression of MHC class II genes and exhibited preferential IgM isotype usage. A subset also exhibited low levels of somatic hypermutation despite a gene expression profile consistent with memory B cells. Our study demonstrates that single-cell gene expression with paired BCR sequencing can be used to interrogate the sparse B cell populations in human skin and reveals that B cells in the skin infection site in early Lyme disease expressed a phenotype consistent with local antigen presentation and antibody production.

The extended Kalman filter (EKF) has a wide range of applications (especially in power battery management systems) with a rapidly increasing market share. It aims to minimize the symmetric loss function (mean square error) and it has high accuracy and efficiency in battery state estimation. This study deals with the second-order extended Kalman filter-based process and the measurement white noise estimation problem for nonlinear continuous-discrete systems. The design of the white noise filter and smoother were, firstly, converted into a linear estimation problem by the second-order Taylor series expansion approximation and the function that makes the second-order term approximately equivalent to the estimation error variance. Secondly, based on the projection formula of the Kalman filtering (KF) theory and the Lemma of expectation for quadratic and quartic product traces of random vectors, the second-order EKF was derived. Then, to generate white noise estimators in the forms of filtering and smoothing, we derived a recursive solution, using an innovation method. Finally, a numerical example is given to show the effectiveness of the proposed method.

The oil and gas in the Palaeogene lacustrine carbonate rock reservoirs in the Bohai Sea accumulated during several periods. The reservoir porosity formed during each period affected the degree of accumulation that occurred. In this paper, the percentages of particles, authigenic minerals and pores in the reservoir bed were calculated with the statistical method of microstructure analysis. The formation time was determined with an isotopic analysis of the authigenic carbonate minerals and the homogenization temperature of the gas–liquid inclusions. The percentages of the primary intergranular pores that formed during the different stages were recovered based on the compaction features both before and after the formation of the major authigenic minerals. The evolution of porosity was thus described quantitatively and chronologically, employing the percentages of the residual primary intergranular pores, visceral cavity pores and dissolved pores at the different burial depths. The results indicate that in the initial sediments of the reservoir rock, the primary intergranular porosity was 32.4%. During the early burial stage, the total reservoir porosity increased by up to 46.9%, due to the addition of another type of primary pore, namely visceral cavity pores, which were generated from the decomposition of bioclasts. During the late, deep burial stage, the compaction reduced only 8.2% of the porosity, due to the support of the pore-lining dolomite precipitating during the early stage. Authigenic minerals occupied 12.6% of the porosity, and the dissolution created the secondary porosity by 3.8%. Good preservation of the visceral cavity pores and the growth of the pore-lining dolomites during the early stages are the major factors leading to the high reservoir porosity. The quantitative and chronological characteristics of the reservoir porosity evolution could be described accurately. The prediction of reservoir beds can be better guided than in previously reported methods by applying high resolution microscopic quantitative analysis technology and authigenic mineral timing analysis technology.

The efficacy of the adaptive humoral immune response likely requires diverse, yet focused regional B cell antibody production throughout the body. Here we address, in the first study of its kind, the B cell repertoire in the bronchial mucosa, an important barrier to antigens inhaled from the atmosphere. To accomplish this, we have applied high-throughput Adaptive Immune Receptor Repertoire Sequencing (AIRR-Seq) to 10 bronchial biopsies from altogether four different sites in the right lungs from an asthmatic patient and a healthy subject. While the majority of identified B cell clones were restricted to a single site, many were disseminated in multiple sites. Members of a clone were shared more between adjacent biopsies than between distal biopsies, suggesting local mucosal migration and/or a homing mechanism for B cells through the blood or lymph. A smaller fraction of clones spanned the bronchial mucosa and peripheral blood, suggesting ongoing trafficking between these compartments. The bronchial mucosal B cell repertoire in the asthmatic patient was geographically more variable but less diverse compared to that of the healthy subject, suggesting an ongoing, antigen-driven humoral immune response in atopic asthma. Whether this is a feature of atopy or disease status remains to be clarified in future studies. We observed a subset of highly mutated and antigen-selected IgD-only cells in the bronchial mucosa. These cells were found in relative high abundance in the asthmatic individual but also, albeit at lower abundance, in the healthy subject. This novel finding merits further exploration using a larger cohort of subjects.

The dolomite reservoirs in the Paleogene Shahejie Formation in the Bozhong area of the Bohai Bay Basin contain a large amount of dolomite cement. Petrologic and mineralogic studies have shown that the dolomite cements can be divided into three types according to their occurrence: coating dolomite (CD), pore-lining dolomite (LD), and pore-filling dolomite (FD). The laser microsampling technique was used to analyze the C and O isotopes in the carbonate minerals. This method is an effective way to produce CO2 gas from a particular carbonate structure in a thin section, and it has a spatial resolution of 20–50 µm and an optimal precision of approximately ±0.22σ for δ13C and δ18O in carbonate standard materials. The carbon and oxygen isotopic compositions and the oxygen isotopic geothermometer results showed that the dolomitization fluid is mainly low temperature fluid, the lake basin environment is relatively closed, and the salinity index Z value is greater than 120, which indicates the invasion of seawater. CD and early-stage LD crystals were mainly very fine crystals with faint cathodoluminescence, which indicates the early formation of diagenesis. The high temperatures of late-stage LD and FD measured by oxygen isotope thermometers indicates that they formed at a deeper depth. The dolomite cements in the study area may have formed in two stages: seepage-reflux dolomitization during the penecontemporaneous period and burial dolomitization.

The pH value of oil acidized wastewater is relatively low (pH = 6.1), which seriously affects the flocculation of polyacrylamide (PAM). NaOH was used to adjust the pH value, but the maximum was only 7.5. The regulation was limited as the Ca2þ in aqueous phase up to 1,350 mg L-1 consumed OH-. A novel formulation of Na2CO3 þ PAM was proposed to form CaCO3 floc core to facilitate PAM coagulation. When the concentration was above 400 mg L-1, the PAM precipitation tended to be maximum, followed by NaOH adjustment of pH to 8.0 that could enhance PAM flocculation successively. The sewage sludge (SS) remained and residue oil reduced to 25 mg L-1 and 34 mg L-1 respectively. The analysis of the species and composition of fatty acids indicated that the coagulation-flocculation selectively effected the sedimentation of saturated fatty acids (SAT). This provides a new idea for recovery of high value-added residual oil. The optimal additive of Na2CO3 is expected as promising coagulant aid to improve the PAM coagulation-flocculation of oil acidized wastewater. [ABSTRACT FROM AUTHOR]

We evaluated in vivo innate immune responses in monocyte populations from 67 young (aged 21-30 years) and older (aged ≥65 years) adults before and after influenza vaccination. CD14+CD16+ inflammatory monocytes were induced after vaccination in both young and older adults. In classical CD14+CD16- and inflammatory monocytes, production of tumor necrosis factor α and interleukin 6, as measured by intracellular staining, was strongly induced after vaccination. Cytokine production was strongly associated with influenza vaccine antibody response; the highest levels were found as late as day 28 after vaccination in young subjects and were substantially diminished in older subjects. Notably, levels of the anti-inflammatory cytokine interleukin 10 (IL-10) were markedly elevated in monocytes from older subjects before and after vaccination. In purified monocytes, we found age-associated elevation in phosphorylated signal transducer and activator of transcription-3, and decreased serine 359 phosphorylation of the negative IL-10 regulator dual-specificity phosphatase 1. These findings for the first time implicate dysregulated IL-10 production in impaired vaccine responses in older adults. [ABSTRACT FROM AUTHOR]

NLRs (nucleotide-binding domain leucine-rich-repeat-containing receptors; NOD-like receptors) are a class of pattern recognition receptor (PRR) that respond to host perturbation from either infectious agents or cellular stress1,2. The function of most NLR family members has not been characterized and their role in instructing adaptive immune responses remains unclear2,3. NLRP10 (also known as PYNOD, NALP10, PAN5 and NOD8) is the only NLR lacking the putative ligand-binding leucine-rich-repeat domain, and has been postulated to be a negative regulator of other NLR members, including NLRP3 (refs 4–6). We did not find evidence that NLRP10 functions through an inflammasome to regulate caspase-1 activity nor that it regulates other inflammasomes. Instead, Nlrp10−/− mice had a profound defect in helper T-cell-driven immune responses to a diverse array of adjuvants, including lipopolysaccharide, aluminium hydroxide and complete Freund’s adjuvant. Adaptive immunity was impaired in the absence of NLRP10 because of a dendritic cell (DC) intrinsic defect in emigration from inflamed tissues, whereas upregulation of DC costimulatory molecules and chemotaxis to CCR7-dependent and -independent ligands remained intact. The loss of antigen transport to the draining lymph nodes by a subset of migratory DCs resulted in an almost absolute loss in naive CD4+ T-cell priming, highlighting the critical link between diverse innate immune stimulation, NLRP10 activity and the immune function of mature DCs. [ABSTRACT FROM AUTHOR]

The seasonal influenza vaccine is an important public health tool but is only effective in a subset of individuals. The identification of molecular signatures provides a mechanism to understand the drivers of vaccine-induced immunity. Most previously reported molecular signatures of human influenza vaccination were derived from a single age group or season, ignoring the effects of immunosenescence or vaccine composition. Thus, it remains unclear how immune signatures of vaccine response change with age across multiple seasons. In this study we profile the transcriptional landscape of young and older adults over five consecutive vaccination seasons to identify shared signatures of vaccine response as well as marked seasonal differences. Along with substantial variability in vaccine-induced signatures across seasons, we uncovered a common transcriptional signature 28 days postvaccination in both young and older adults. However, gene expression patterns associated with vaccine-induced Ab responses were distinct in young and older adults; for example, increased expression of killer cell lactin-like receptor B1 (KLRB1; CD161) 28 days postvaccination positively and negatively predicted vaccine-induced Ab responses in young and older adults, respectively. These findings contribute new insights for developing more effective influenza vaccines, particularly in older adults. [ABSTRACT FROM AUTHOR]

Vaccines formulated with nonreplicating pathogens require adjuvants to help bolster immunogenicity. The role of adjuvants in Ab production has been well studied, but how they influence memory CD8+ T cell differentiation remains poorly defined. In this study we implemented dendritic cell-mediated immunization to study the effects of commonly used adjuvants, TLR ligands, on effector and memory CD8+ T cell differentiation in mice. Intriguingly, we found that the TLR4 ligand LPS was far more superior to other TLR ligands in generating memory CD8+ T cells upon immunization. LPS boosted clonal expansion similar to the other adjuvants, but fewer of the activated CD8+ T cells died during contraction, generating a larger pool of memory cells. Surprisingly, monophosphoryl lipid A (MPLA), another TLR4 ligand, enhanced clonal expansion of effector CD8+ T cells, but it also promoted their terminal differentiation and contraction; thus, fewer memory CD8+ T cells formed, and MPLA-primed animals were less protected against secondary infection compared with those primed with LPS. Furthermore, gene expression profiling revealed that LPS-primed effector cells displayed a stronger pro-memory gene expression signature, whereas the gene expression profile of MPLA-primed effector cells aligned closer with terminal effector CD8+ T cells. Lastly, we demonstrated that the LPS-TLR4-derived "pro-memory" signals were MyD88, but not Toll/IL-1R domain-containing adapter inducing IFN-β, dependent. This study reveals the influential power of adjuvants on the quantity and quality of CD8+ T cell memory, and that attention to adjuvant selection is crucial because boosting effector cell expansion may not always equate with more memory T cells or greater protection. [ABSTRACT FROM AUTHOR]