ExPT: Synthetic Pretraining for Few-Shot Experimental Design

Experimental design is a fundamental problem in many science and engineering fields. In this problem, sample efficiency is crucial due to the time, money, and safety costs of real-world design evaluations. Existing approaches either rely on active data collection or access to large, labeled datasets of past experiments, making them impractical in many real-world scenarios. In this work, we address the more challenging yet realistic setting of few-shot experimental design, where only a few labeled data points of input designs and their corresponding values are available. We approach this problem as a conditional generation task, where a model conditions on a few labeled examples and the desired output to generate an optimal input design. To this end, we introduce Experiment Pretrained Transformers (ExPT), a foundation model for few-shot experimental design that employs a novel combination of synthetic pretraining with in-context learning. In ExPT, we only assume knowledge of a finite collection of unlabelled data points from the input domain and pretrain a transformer neural network to optimize diverse synthetic functions defined over this domain. Unsupervised pretraining allows ExPT to adapt to any design task at test time in an in-context fashion by conditioning on a few labeled data points from the target task and generating the candidate optima. We evaluate ExPT on few-shot experimental design in challenging domains and demonstrate its superior generality and performance compared to existing methods. The source code is available at https://github.com/tung-nd/ExPT.git.Comment: 2023 Conference on Neural Information Processing Systems (NeurIPS

A paradox of immunodeficiency and inflammation in human aging: lessons learned from apoptosis

Aging is associated with a paradox of immunodeficiency and inflammation (an evidence of hyperactive immune system). Apoptosis is associated with cellular depletion and suppression of inflammatory response. In this brief review, we will present evidence for the role of increased apoptosis in immunodeficiency and paradoxical increased inflammation associated with human aging. In particular, a role of apoptotic cells in failure to generate anti-inflammatory responses and directly activating inflammatory responses will be discussed

Age-associated epigenetic modifications in human DNA increase its immunogenicity

Chronic inflammation, increased reactivity to self-antigens and incidences of cancer are hallmarks of aging. However, the underlying mechanisms are not well understood. Age-associated alterations in the DNA either due to oxidative damage, defects in DNA repair or epigenetic modifications such as methylation that lead to mutations and changes in the expression of genes are thought to be partially responsible. Here we report that epigenetic modifications in aged DNA also increase its immunogenicity rendering it more reactive to innate immune system cells such as the dendritic cells. We observed increased upregulation of costimulatory molecules as well as enhanced secretion of IFN-α from dendritic cells in response to DNA from aged donors as compared to DNA from young donors when it was delivered intracellularly via Lipofectamine. Investigations into the mechanisms revealed that DNA from aged subjects is not degraded, neither is it more damaged compared to DNA from young subjects. However, there is significantly decreased global level of methylation suggesting that age-associated hypomethylation of the DNA may be the cause of its increased immunogenicity. Increased immunogenicity of self DNA may thus be another mechanism that may contribute to the increase in age-associated chronic inflammation, autoimmunity and cancer

Life and death of lymphocytes: a role in immunesenescence

Human aging is associated with progressive decline in immune functions, increased frequency of infections. Among immune functions, a decline in T cell functions during aging predominates. In this review, we will discuss the molecular signaling in two major pathways of apoptosis, namely death receptor pathway and mitochondrial pathway, and their alterations in both T and B lymphocytes in human aging with a special emphasis on naïve and different memory subsets of CD8+ T cells. We will also discuss a possible role of lymphocyte apoptosis in immune senescence

Cytomegalovirus Colitis in Primary Hypogammaglobulinemia With Normal CD4+ T Cells: Deficiency of CMV-Specific CD8+ T Cells

CMV colitis has been reported in immunocompromized patients with severe deficiency of CD4+ T cells and T cell functions. In this study we present an extensive immunological analysis in a patient with primary hypogammaglobulinemia and CMV colitis who had normal numbers of CD3+T, CD4+T and CD8+T cells, and normal T cell proliferative responses to mitogens and recall antigens. Naïve (TN), central (TCM), and effector (TEM) memory subsets of CD4+ and CD8+ T cells, Granzyme+ and Perforin+ CD8+ T cells, PD-1+ T cells, CD4 Treg, CD8 Treg, and CMV tetramer specific CD8+ T cells were analyzed with specific antibodies and isotype controls using multicolor flow cytometry. CD8 TEM, Granzyme+ and Perforin+, and PD-1 CD8+T cells were increased, whereas CD8 TN and CD8 TCM cells were decreased in the patient as compared to controls. CMV tetramer+ CD8+ T cells were decreased in the patient. These data demonstrate that a deficiency of CMV-specific CD8+ T cells even in the presence of normal CD4+ T cell numbers and normal T cell functions may predispose patients with primary hypogammaglobulinemia to CMV colitis

Role of 0.5 M mannitol as an adjuvant with lidocaine with or without epinephrine for inferior alveolar nerve block : a randomized control trial

Background: The most commonly used local anesthetic in dentistry is lidocaine. For decades, mannitol is the most widely used agent in the management of raised intracranial pressure and as prophylaxis against acute renal failure surgeries. Material and Methods: 120 patients were randomly divided into four groups, 30 patients in each group. Group A was administered 2% lidocaine with 1:80000 epinephrine; group B, 2% lidocaine with 1:80000 epinephrine and 0.5 M mannitol; group C, 2% lidocaine and 0.5 M mannitol; and group D (control group), 2% lidocaine for achieving local anesthesia. Extraction of lower erupted tooth was done under inferior alveolar nerve block. Parameters taken were onset of anesthesia, duration of anesthesia and pain. Heft-Parker visual analogue scale was taken to evaluate the pain response during procedure after every 10 minutes until complete return of sensation by probing. The Chi-square test was used to compare the pain among the groups. The continuous variables were compared among the groups by one way analysis of variance (ANOVA) followed by Tukey?s post-hoc comparison tests. The p-value 0.05). The total time in return of sensation was higher among the patients of group C (70.30±4.34) than group A (65.94±3.45), group B (62.23±7.47) and group D (47.70±8.04) but difference among the groups was found to be statistically significant (p=0.0001). There was no significant (p>0.05) difference in the pain at baseline and at start. No pain was found among all the patients from 10 minutes to subsequent time intervals. Conclusions: Mannitol was effective in increasing the efficacy of lidocaine as an adjuvant to local anesthetic solution in inferior alveolar nerve block

Dendritic Cells from Aged Subjects Display Enhanced Inflammatory Responses to Chlamydophila pneumoniae

Chlamydophila pneumoniae (CPn) is a common respiratory pathogen that causes a chronic and persistent airway infection. The elderly display an increased susceptibility and severity to this infection. However, the underlying mechanisms are not well understood. Dendritic cells (DCs) are the initiators and regulators of immune responses. Therefore, we investigated the role of DCs in the age-associated increased CPn infection in vitro in humans. Though the expression of activation markers was comparable between the two age groups, DCs from aged subjects secreted enhanced levels of proinflammatory mediators such as TNF-α and CXCL-10 in response to CPn. In contrast, the secretion of IL-10 and innate interferons, IFN-α and IFN-λ, was severely impaired in DCs from aged donors. The increased activation of DCs from aged subjects to CPn also resulted in enhanced proliferation of CD4 and CD8 T cells in a DC-T coculture. Furthermore, T cells primed with CPn-stimulated DCs from aged subjects secreted increased levels of IFN-γ and reduced levels of IL-10 compared to DCs obtained from young subjects. In summary, DCs from the elderly displayed enhanced inflammatory response to CPn which may result in airway remodeling and increase the susceptibility of the elderly to respiratory diseases such as asthma

Adaptive and Innate Immune Responses in Autism: Rationale for Therapeutic Use of Intravenous Immunoglobulin

Autism is a complex polygenic neurodevelopmental disorder characterized by deficits in communication and social interactions as well as specific stereotypical behaviors. Both genetic and environmental factors appear to contribute to the pathogenesis of autism. Accumulating data including changes in immune responses, linkage to major histocompatibility complex antigens, and the presence of autoantibodies to neural tissues/antigens suggest that the immune system plays an important role in its pathogenesis. In this brief review, we discuss the data regarding changes in both innate and adaptive immunity in autism and the evidence in favor of the role of the immune system, especially of maternal autoantibodies in the pathogenesis of a subset of patients with autism. The rationale for possible therapeutic use of intravenous immunoglobulin is also discussed

Impaired Functions of Peripheral Blood Monocyte Subpopulations in Aged Humans

Aging is associated with increased susceptibility to microbial infections, and monocytes play an important role in microbial defense. In this study, we have identified and compared four subpopulations of monocytes (CD14++(high)CD16−, CD14+(low)CD16−, CD14++(high)CD16+, and CD14+(low)CD16+) in the peripheral blood of young and aged subjects with regard to their numbers, cytokine production, TLR expression, and phosphorylation of ERK1/2 in response to pam3Cys a TLR-1/2 ligand. Proportions and numbers of CD14++(high)CD16+ and CD14+(low)CD16+ monocytes were significantly increased, whereas proportions of CD14+(low)CD16− monocytes were decreased in aged subjects as compared to young subjects. In aged subjects, IL-6 production by all four subsets of monocytes was significantly decreased, whereas TNF-α production was decreased in monocyte subsets, except the CD14+(low)CD16− subset. A significantly reduced expression of TLR1 was observed in CD14++(high)CD16+ and CD14+(low)CD16+ monocyte subsets in aged subjects. Furthermore, following pam3Cys stimulation, ERK1/2 phosphorylation was significantly lower in CD14+(low)CD16+, CD14++(high)CD16+, and CD14+(low)CD16− subsets of monocytes from aged subjects. This is the first study of four subpopulations of monocytes in aging, which demonstrates that their functions are differentially impaired with regard to the production of cytokines, expression of TLR, and signaling via the ERK–MAPK pathway. Finally, changes in the number of monocyte subsets, and impairment of TLR1 expression, TNF-α production, and EK1/2 phosphorylation was more consistent in CD16+ monocyte subsets regardless of expression of CD14high or CD14+low, therefore highlighting the significance of further subdivision of monocytes into four subpopulations