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A continuous spectral algorithm and computer routines in the R programming environment that enable the simulation of second-order stationary and intrinsic (i.e., with second-order stationary increments or generalized increments) vector Gaussian random fields in Euclidean spaces are presented. The simulation is obtained by computing a weighted sum of cosine and sine waves, with weights that depend on the matrix-valued spectral density associated with the spatial correlation structure of the random field to simulate. The computational cost is proportional to the number of locations targeted for simulation, below that of sequential, matrix decomposition and discrete spectral algorithms. Also, the implementation is versatile, as there is no restriction on the number of vector components, workspace dimension, number and geometrical configuration of the target locations. The computer routines are illustrated with synthetic examples and statistical testing is proposed to check the normality of the distribution of the simulated random field or of its generalized increments. A by-product of this work is a spectral representation of spherical, cubic, penta, Askey, J-Bessel, Cauchy, Laguerre, hypergeometric, iterated exponential, gamma, and stable covariance models in the d-dimensional Euclidean space. [ABSTRACT FROM AUTHOR]

This paper addresses the problem of simulating multivariate random fields with stationary Gaussian increments in a d-dimensional Euclidean space. To this end, one considers a spectral turning-bands algorithm, in which the simulated field is a mixture of basic random fields made of weighted cosine waves associated with random frequencies and random phases. The weights depend on the spectral density of the direct and cross variogram matrices of the desired random field for the specified frequencies. The algorithm is applied to synthetic examples corresponding to different spatial correlation models. The properties of these models and of the algorithm are discussed, highlighting its computational efficiency, accuracy and versatility. [ABSTRACT FROM AUTHOR]

This work pertains to the simulation of an intrinsic random field of order $$k$$ with a given generalized covariance function and multivariate Gaussian generalized increments. An iterative algorithm based on the Gibbs sampler is proposed to simulate such a random field at a finite set of locations, resulting in a sequence of random vectors that converges in distribution to a random vector with the desired distribution. The algorithm is tested on synthetic case studies to experimentally assess its rate of convergence, showing that few iterations are sufficient for convergence to take place. The sequence of random vectors also proves to be strongly mixing, allowing the generation of as many independent realizations as desired with a single run of the algorithm. Another interesting property of this algorithm is its versatility, insofar as it can be adapted to construct realizations conditioned to pre-existing data and can be used for any number and configuration of the target locations and any generalized covariance model. [ABSTRACT FROM AUTHOR]

Chlamydia trachomatis (Ct) is the most common bacterial sexually transmitted infection globally, and a vaccine is urgently needed to stop transmission and disease. Chlamydial Protease Activity Factor (CPAF) is an immunoprevalent and immunodominant antigen for CD4 T cells and B cells, which makes it a strong vaccine candidate. Due to the tolerogenic nature of the female genital tract (FGT) and its lack of secondary lymphoid tissue, effective induction of protective cell-mediated immunity will likely require potent and safe mucosal adjuvants. To address this need, we produced CPAF in a cell-free protein synthesis platform and adjuvanted it with the TLR9-agonist CpG1826, a synthetic cyclic-di-AMP (CDA) STING (stimulator of interferon genes) agonist ADU-S100, and/or the squalene oil-in-water nanoemulsion, AddaS03. We determined that intranasal immunization with CPAF plus ADU-S100 was well tolerated in female mice, induced CD4 T cells characterized by TNFα production alone or in combination with IL-17 A or IFNγ, significantly reduced bacterial shedding, and shortened the duration of infection in mice intravaginally challenged with Chlamydia muridarum. These data demonstrate the potential for CDA as a mucosal adjuvant for vaccines against Chlamydia genital tract infection., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Daisy Arroyo reports financial support was provided by Vaxcyte, Inc. Tony Bruno reports financial support was provided by Vaxcyte, Inc. Manhong Wu reports financial support was provided by Vaxcyte, Inc. James Rozzelle reports financial support was provided by Vaxcyte, Inc. Jeff Fairman reports financial support was provided by Vaxcyte, Inc. Taylor B. Poston has patent Chlamydial Protease-Like Activity Factor and Adjuvant Compositions And Uses Thereof pending to Assignee. Toni Darville has patent Chlamydial Protease-Like Activity Factor and Adjuvant Compositions And Uses Thereof pending to Assignee. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Chlamydia trachomatis (Ct) is the most common bacterial sexually transmitted infection globally, and a vaccine is urgently needed to stop transmission and disease. Chlamydial Protease Activity Factor (CPAF) is an immunoprevalent and immunodominant antigen for CD4 T cells and B cells, which makes it a strong vaccine candidate. Due to the tolerogenic nature of the female genital tract (FGT) and its lack of secondary lymphoid tissue, effective induction of protective cell-mediated immunity will likely require potent and safe mucosal adjuvants. To address this need, we produced CPAF in a cell-free protein synthesis platform and adjuvanted it with the TLR9-agonist CpG1826, STING (stimulator of interferon genes) agonist cyclic-di-AMP (CDA), and/or the squalene oil-in-water nanoemulsion, AddaS03. We determined that intranasal immunization with CPAF plus CDA was well tolerated in female mice, induced CD4 T cells that produced IL-17A or IFNγ, significantly reduced bacterial shedding, and shortened the duration of infection in mice intravaginally challenged with Chlamydia muridarum . These data demonstrate the potential for CDA as a mucosal adjuvant for vaccines against Chlamydia genital tract infection.