Dynamic tuning of lymphocytes: physiological basis, mechanisms, and function.

Dynamic tuning of cellular responsiveness as a result of repeated stimuli improves the ability of cells to distinguish physiologically meaningful signals from each other and from noise. In particular, lymphocyte activation thresholds are subject to tuning, which contributes to maintaining tolerance to self-antigens and persisting foreign antigens, averting autoimmunity and immune pathogenesis, but allowing responses to strong, structured perturbations that are typically associated with acute infection. Such tuning is also implicated in conferring flexibility to positive selection in the thymus, in controlling the magnitude of the immune response, and in generating memory cells. Additional functional properties are dynamically and differentially tuned in parallel via subthreshold contact interactions between developing or mature lymphocytes and self-antigen-presenting cells. These interactions facilitate and regulate lymphocyte viability, maintain their functional integrity, and influence their responses to foreign antigens and accessory signals, qualitatively and quantitatively. Bidirectional tuning of T cells and antigen-presenting cells leads to the definition of homeostatic set points, thus maximizing clonal diversity.

Endless fascination.

Each of us fortunate enough to have had a career in experimental science has a tale to tell, often one with surprising twists and turns, full of lessons that can help guide those embarking on a similar journey. At the very least, a well-written recounting of a career can be entertaining. I offer my memory's version of my career in immunology and hope the readers will find it of value or at least of interest.

Differentiation of effector CD4 T cell populations (*).

CD4 T cells play critical roles in mediating adaptive immunity to a variety of pathogens. They are also involved in autoimmunity, asthma, and allergic responses as well as in tumor immunity. During TCR activation in a particular cytokine milieu, naive CD4 T cells may differentiate into one of several lineages of T helper (Th) cells, including Th1, Th2, Th17, and iTreg, as defined by their pattern of cytokine production and function. In this review, we summarize the discovery, functions, and relationships among Th cells; the cytokine and signaling requirements for their development; the networks of transcription factors involved in their differentiation; the epigenetic regulation of their key cytokines and transcription factors; and human diseases involving defective CD4 T cell differentiation.

Innate immunological function of TH2 cells in vivo.

Type 2 helper T cells (TH2 cells) produce interleukin 13 (IL-13) when stimulated by papain or house dust mite extract (HDM) and induce eosinophilic inflammation. This innate response is dependent on IL-33 but not T cell antigen receptors (TCRs). While type 2 innate lymphoid cells (ILC2 cells) are the dominant innate producers of IL-13 in naive mice, we found here that helminth-infected mice had more TH2 cells compared to uninfected mice, and thes e cells became major mediators of innate type 2 responses. TH2 cells made important contributions to HDM-induced antigen-nonspecific eosinophilic inflammation and protected mice recovering from infection with Ascaris suum against subsequent infection with the phylogenetically distant nematode Nippostrongylus brasiliensis. Our findings reveal a previously unappreciated role for effector TH2 cells during TCR-independent innate-like immune responses.

IL-25-responsive, lineage-negative KLRG1(hi) cells are multipotential 'inflammatory' type 2 innate lymphoid cells.

Innate lymphoid cells (ILCs) are lymphocyte-like cells that lack T cell or B cell antigen receptors and mediate protective and repair functions through cytokine secretion. Among these, type 2 ILCs (ILC2 cells) are able to produce type 2 cytokines. We report the existence of an inflammatory ILC2 (iILC2) population responsive to interleukin 25 (IL-25) that complemented IL-33-responsive natural ILC2 (nILC2) cells. iILC2 cells developed into nILC2-like cells in vitro and in vivo and contributed to the expulsion of Nippostrongylus brasiliensis. They also acquired IL-17-producing ability and provided partial protection against Candida albicans. We propose that iILC2 cells are transient progenitors of ILCs mobilized by inflammation and infection that develop into nILC2-like cells or ILC3-like cells and contribute to immunity to both helminths and fungi.

Bridging innate and adaptive immunity.

The Nobel Prize in Physiology or Medicine for 2011 to Jules Hoffmann, Bruce Beutler, and the late Ralph Steinman recognizes accomplishments in understanding and unifying the two strands of immunology, the evolutionarily ancient innate immune response and modern adaptive immunity.

Cutaneous immunosurveillance and regulation of inflammation by group 2 innate lymphoid cells.

Type 2 immunity is critical for defense against cutaneous infections but also underlies the development of allergic skin diseases. We report the identification in normal mouse dermis of an abundant, phenotypically unique group 2 innate lymphoid cell (ILC2) subset that depended on interleukin 7 (IL-7) and constitutively produced IL-13. Intravital multiphoton microscopy showed that dermal ILC2 cells specifically interacted with mast cells, whose function was suppressed by IL-13. Treatment of mice deficient in recombination-activating gene 1 (Rag1(-/-)) with IL-2 resulted in the population expansion of activated, IL-5-producing dermal ILC2 cells, which led to spontaneous dermatitis characterized by eosinophil infiltrates and activated mast cells. Our data show that ILC2 cells have both pro- and anti-inflammatory properties and identify a previously unknown interactive pathway between two innate populations of cells of the immune system linked to type 2 immunity and allergic diseases.

Cytokines of the γ(c) family control CD4+ T cell differentiation and function.

Naive CD4(+) T cells undergo massive proliferation and differentiation into at least four distinct helper T cell subsets after recognition of foreign antigen-derived peptides presented by dendritic cells. Each helper T cell subset expresses a distinct set of genes that encode unique transcription factor(s), as well as hallmark cytokines. The cytokine environment created by activated CD4(+) T cells, dendritic cells and/or other cell types during the course of differentiation is a major determinant for the helper T cell fate. This Review focuses on the role of cytokines of the common γ-chain (γ(c)) family in the determination of the effector helper T cell phenotype that naive CD4(+) T cells adopt after being activated and in the function of these helper T cells.

Individual T helper cells have a quantitative cytokine memory.

The probabilistic expression of cytokine genes in differentiated T helper (Th) cell populations remains ill defined. By single-cell analyses and mathematical modeling, we show that one stimulation featured stable cytokine nonproducers as well as stable producers with wide cell-to-cell variability in the magnitude of expression. Focusing on interferon-γ (IFN-γ) expression by Th1 cells, mathematical modeling predicted that this behavior reflected different cell-intrinsic capacities and not mere gene-expression noise. In vivo, Th1 cells sort purified by secreted IFN-γ amounts preserved a quantitative memory for both probability and magnitude of IFN-γ re-expression for at least 1 month. Mechanistically, this memory resulted from quantitatively distinct transcription of individual alleles and was controlled by stable expression differences of the Th1 cell lineage-specifying transcription factor T-bet. Functionally, Th1 cells with graded IFN-γ production competence differentially activated Salmonella-infected macrophages for bacterial killing. Thus, individual Th cells commit to produce distinct amounts of a given cytokine, thereby generating functional intrapopulation heterogeneity.

Reading and writing single-atom magnets.

The single-atom bit represents the ultimate limit of the classical approach to high-density magnetic storage media. So far, the smallest individually addressable bistable magnetic bits have consisted of 3-12 atoms. Long magnetic relaxation times have been demonstrated for single lanthanide atoms in molecular magnets, for lanthanides diluted in bulk crystals, and recently for ensembles of holmium (Ho) atoms supported on magnesium oxide (MgO). These experiments suggest a path towards data storage at the atomic limit, but the way in which individual magnetic centres are accessed remains unclear. Here we demonstrate the reading and writing of the magnetism of individual Ho atoms on MgO, and show that they independently retain their magnetic information over many hours. We read the Ho states using tunnel magnetoresistance and write the states with current pulses using a scanning tunnelling microscope. The magnetic origin of the long-lived states is confirmed by single-atom electron spin resonance on a nearby iron sensor atom, which also shows that Ho has a large out-of-plane moment of 10.1 ± 0.1 Bohr magnetons on this surface. To demonstrate independent reading and writing, we built an atomic-scale structure with two Ho bits, to which we write the four possible states and which we read out both magnetoresistively and remotely by electron spin resonance. The high magnetic stability combined with electrical reading and writing shows that single-atom magnetic memory is indeed possible.

TARA: Training and Representation Alteration for AI Fairness and Domain Generalization.

We propose a novel method for enforcing AI fairness with respect to protected or sensitive factors. This method uses a dual strategy performing training and representation alteration (TARA) for the mitigation of prominent causes of AI bias. It includes the use of representation learning alteration via adversarial independence to suppress the bias-inducing dependence of the data representation from protected factors and training set alteration via intelligent augmentation to address bias-causing data imbalance by using generative models that allow the fine control of sensitive factors related to underrepresented populations via domain adaptation and latent space manipulation. When testing our methods on image analytics, experiments demonstrate that TARA significantly or fully debiases baseline models while outperforming competing debiasing methods that have the same amount of information-for example, with (% overall accuracy, % accuracy gap) = (78.8, 0.5) versus the baseline method's score of (71.8, 10.5) for Eye-PACS, and (73.7, 11.8) versus (69.1, 21.7) for CelebA. Furthermore, recognizing certain limitations in current metrics used for assessing debiasing performance, we propose novel conjunctive debiasing metrics. Our experiments also demonstrate the ability of these novel metrics in assessing the Pareto efficiency of the proposed methods.

Diversity and Pathogenicity of Pythium Species Associated with Reduced Yields of Processing Tomatoes (Solanum lycopersicum) in Victoria, Australia.

Yield decline associated with poor crop establishment, stunting, wilting, and diminished root systems was reported in processing tomato crops in Victoria, Australia. During surveys between 2016 and 2018 Pythium species were isolated by soil baiting and by culturing from the diseased roots and collars of plants exhibiting these symptoms. Eleven species of Pythium were identified based on cultural characteristics and phylogenetic analysis with ITS, Cox-1, and Cox-2 gene sequences. None of the 11 Pythium species had been reported previously from processing or fresh tomatoes in Australia. Pythium dissotocum was the most abundant and widespread species isolated during surveys in each of two growing seasons. In pathogenicity tests, these Pythium species ranged from nonpathogenic to highly aggressive. P. aphanidermatum, P. ultimum, and P. irregulare were consistently the most aggressive species, causing serious damage or death at the pregermination, postgermination, and later stages of plant growth. Five processing tomato cultivars varied significantly in their susceptibility to Pythium disease. These results suggest that Pythium species could be contributing to yield loss in processing tomatoes in Victoria both in the crop establishment phase and through the season.

Retrospective SARS-CoV-2 IgG screening during the first wave (March-June 2020) of the COVID-19 pandemic in the United Kingdom.

During the "first wave" of the coronavirus disease 2019 (COVID-19) pandemic in the United Kingdom (March-June 2020), the city of Leicester was particularly hard hit, resulting in reimposed lockdown measures. Although initial polymerase chain reaction testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was attempted within the community, testing was soon abandoned due to an inability to keep up with demand by local laboratories. It is therefore feasible that undiagnosed transmission of COVID-19 in the community by asymptomatic individuals was a real possibility. Therefore, retrospective SARS-CoV-2 immunoglobulin G (IgG) testing of archived sera from out-patients visiting University Hospitals of Leicester NHS Trust service was performed to investigate the transmission of SARS-CoV-2 in the community. A total of 1779 sera samples were tested from samples collected between 16th March and 3rd June 2020, of which 202 (11.35%) were SARS-CoV-2 IgG positive. Positivity was lowest in March (2.54%) at the beginning of the pandemic before peaking in April (17.16%) before a decline in May and June (11.16% and 12.68%, respectively). This retrospective screening offers some insight into the early patterns of SARS-CoV-2 transmission within a sampled community population during the first wave of the COVID-19 pandemic; supporting the argument for more community screening during high incidences of pandemics.

Least kth-Order and Rényi Generative Adversarial Networks.

We investigate the use of parameterized families of information-theoretic measures to generalize the loss functions of generative adversarial networks (GANs) with the objective of improving performance. A new generator loss function, least kth-order GAN (LkGAN), is introduced, generalizing the least squares GANs (LSGANs) by using a kth-order absolute error distortion measure with k≥1 (which recovers the LSGAN loss function when k=2). It is shown that minimizing this generalized loss function under an (unconstrained) optimal discriminator is equivalent to minimizing the kth-order Pearson-Vajda divergence. Another novel GAN generator loss function is next proposed in terms of Rényi cross-entropy functionals with order α>0, α≠1. It is demonstrated that this Rényi-centric generalized loss function, which provably reduces to the original GAN loss function as α→1, preserves the equilibrium point satisfied by the original GAN based on the Jensen-Rényi divergence, a natural extension of the Jensen-Shannon divergence. Experimental results indicate that the proposed loss functions, applied to the MNIST and CelebA data sets, under both DCGAN and StyleGAN architectures, confer performance benefits by virtue of the extra degrees of freedom provided by the parameters k and α, respectively. More specifically, experiments show improvements with regard to the quality of the generated images as measured by the Fréchet inception distance score and training stability. While it was applied to GANs in this study, the proposed approach is generic and can be used in other applications of information theory to deep learning, for example, the issues of fairness or privacy in artificial intelligence.

Unsupervised Discovery, Control, and Disentanglement of Semantic Attributes With Applications to Anomaly Detection.

Our work focuses on unsupervised and generative methods that address the following goals: (1) learning unsupervised generative representations that discover latent factors controlling image semantic attributes, (2) studying how this ability to control attributes formally relates to the issue of latent factor disentanglement, clarifying related but dissimilar concepts that had been confounded in the past, and (3) developing anomaly detection methods that leverage representations learned in the first goal. For goal 1, we propose a network architecture that exploits the combination of multiscale generative models with mutual information (MI) maximization. For goal 2, we derive an analytical result, lemma 1, that brings clarity to two related but distinct concepts: the ability of generative networks to control semantic attributes of images they generate, resulting from MI maximization, and the ability to disentangle latent space representations, obtained via total correlation minimization. More specifically, we demonstrate that maximizing semantic attribute control encourages disentanglement of latent factors. Using lemma 1 and adopting MI in our loss function, we then show empirically that for image generation tasks, the proposed approach exhibits superior performance as measured in the quality and disentanglement of the generated images when compared to other state-of-the-art methods, with quality assessed via the Fréchet inception distance (FID) and disentanglement via mutual information gap. For goal 3, we design several systems for anomaly detection exploiting representations learned in goal 1 and demonstrate their performance benefits when compared to state-of-the-art generative and discriminative algorithms. Our contributions in representation learning have potential applications in addressing other important problems in computer vision, such as bias and privacy in AI.

The transcription factor T-bet is induced by multiple pathways and prevents an endogenous Th2 cell program during Th1 cell responses.

T-bet is a critical transcription factor for T helper 1 (Th1) cell differentiation. To study the regulation and functions of T-bet, we developed a T-bet-ZsGreen reporter mouse strain. We determined that interleukin-12 (IL-12) and interferon-γ (IFN-γ) were redundant in inducing T-bet in mice infected with Toxoplasma gondii and that T-bet did not contribute to its own expression when induced by IL-12 and IFN-γ. By contrast, T-bet and the transcription factor Stat4 were critical for IFN-γ production whereas IFN-γ signaling was dispensable for inducing IFN-γ. Loss of T-bet resulted in activation of an endogenous program driving Th2 cell differentiation in cells expressing T-bet-ZsGreen. Genome-wide analyses indicated that T-bet directly induced many Th1 cell-related genes but indirectly suppressed Th2 cell-related genes. Our study revealed redundancy and synergy among several Th1 cell-inducing pathways in regulating the expression of T-bet and IFN-γ, and a critical role of T-bet in suppressing an endogenous Th2 cell-associated program.

Endurance training-induced increase in muscle oxidative capacity without loss of muscle mass in younger and older resistance-trained men.

While concurrent training is regularly used in older populations, the inverse relationship between fibre size and oxidative capacity suggests that endurance training in resistance-trained individuals may result in some loss of resistance training-induced gains in muscle mass, which may be more pronounced in older people. We investigated the impact of superimposed endurance training in younger (28.5 ± 4.8 years; n = 8) and older (67.5 ± 5.5 years; n = 7) highly resistance-trained men. Participants underwent a 10-week endurance cycling training programme consisting of five 6-min intervals at 75% max heart rate (HRmax) separated by 4-min intervals at 90% HRmax. The anatomical cross-sectional area (ACSA) of the thigh muscles, as determined with MRI, was 24% smaller in older compared to younger participants (p < 0.001). Although maximal oxygen consumption (VO2max) was also lower in the older group (p < 0.001), VO2max per kg body mass did not differ significantly between younger and older participants. Histological analyses of biopsies of the m. vastus lateralis showed that endurance training induced an increase in succinate dehydrogenase activity in both younger and older participants (p ≤ 0.043), and an increase in the number of capillaries around type I fibres (p = 0.017). The superimposed endurance training did not induce a significant decrease in thigh ACSA, fibre cross-sectional area, or knee extensor maximum voluntary isometric force. These observations indicate that adding endurance training to resistance training can lead to positive endurance-related adaptations without negative consequences for muscle size and strength in older and younger resistance-trained people.

Effect of a Consumer-Focused Website for Low Back Pain on Health Literacy, Treatment Choices, and Clinical Outcomes: Randomized Controlled Trial.

BACKGROUND: The internet is used for information related to health conditions, including low back pain (LBP), but most LBP websites provide inaccurate information. Few studies have investigated the effectiveness of internet resources in changing health literacy or treatment choices. OBJECTIVE: This study aims to evaluate the effectiveness of the MyBackPain website compared with unguided internet use on health literacy, choice of treatments, and clinical outcomes in people with LBP. METHODS: This was a pragmatic, web-based, participant- and assessor-blinded randomized trial of individuals with LBP stratified by duration. Participants were randomly allocated to have access to the evidence-based MyBackPain website, which was designed with input from consumers and expert consensus or unguided internet use. The coprimary outcomes were two dimensions of the Health Literacy Questionnaire (dimension 2: "having sufficient information to manage my health;" dimension 3: "actively managing my health;" converted to scores 1-100) at 3 months. Secondary outcomes included additional Health Literacy Questionnaire dimensions, quality of treatment choices, and clinical outcomes. RESULTS: A total of 453 participants were recruited, and 321 (70.9%) completed the primary outcomes. Access to MyBackPain was not superior to unguided internet use on primary outcomes (dimension 2: mean difference -0.87 units, 95% CI -3.56 to 1.82; dimension 3: mean difference -0.41 units, 95% CI -2.78 to 1.96). Between-group differences in other secondary outcomes had inconsistent directions and were unlikely to be clinically important, although a small improvement of unclear importance in the quality of stated treatment choices at 1 month was found (mean difference 0.93 units, 95% CI 0.03 to 1.84). CONCLUSIONS: MyBackPain was not superior to unguided internet use for health literacy, but data suggest some short-term improvement in treatment choices. Future research should investigate if greater interactivity and engagement with the website may enhance its impact. TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (ANZCTR) ACTRN12617001292369; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=372926. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.1136/bmjopen-2018-027516.

Distinct functions for the transcription factors GATA-3 and ThPOK during intrathymic differentiation of CD4(+) T cells.

The transcription factors GATA-3 and ThPOK are required for intrathymic differentiation of CD4(+) T cells, but their precise functions in this process remain unclear. Here we show that, contrary to previous findings, Gata3 disruption blocked differentiation into the CD4(+) T cell lineage before commitment to the CD4(+) lineage and in some contexts permitted the 'redirection' of major histocompatibility complex class II-restricted thymocytes into the CD8(+) lineage. GATA-3 promoted ThPOK expression and bound to a region of the locus encoding ThPOK established as being critical for ThPOK expression. Finally, ThPOK promoted differentiation into the CD4(+) lineage in a way dependent on GATA-3 but inhibited differentiation into the CD8(+) lineage independently of GATA-3. We propose that GATA-3 acts as a specification factor for the CD4(+) lineage 'upstream' of the ThPOK-controlled CD4(+) commitment checkpoint.

COVID-19 multisystem inflammatory syndrome in three teenagers with confirmed SARS-CoV-2 infection.

Coronavirus disease 2019 (COVID-19) is generally a relatively mild illness in children. An emerging disease entity coined as pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) has been reported recently, but is very rare and only affects a very small minority of children. Here we describe the clinical presentations and outcomes of three teenagers with serologically-confirmed SARS-CoV-2 infection admitted to a pediatric intensive care unit for PIMS-TS. Although their initial presentations were very similar, their COVID-19-related disease varied in severity.