Search for: All records

Artificial monopoles have been engineered in various systems, yet there has been no systematic study of the singular vector potentials associated with the monopole field. We show that the Dirac string, the line singularity of the vector potential, can be engineered, manipulated, and made manifest in a spinor atomic condensate. We elucidate the connection among spin, orbital degrees of freedom, and the artificial gauge, and show that there exists a mapping between the vortex filament and the Dirac string. We also devise a proposal where preparing initial spin states with relevant symmetries can result in different vortex patterns, revealing an underlying correspondence between the internal spin states and the spherical vortex structures. Such a mapping also leads to a new way of constructing spherical Landau levels, and monopole harmonics. Our observation provides insights into the behavior of quantum matter possessing internal symmetries in curved spaces. Published by the American Physical Society2024 

Epigenetic researchers often evaluate DNA methylation as a potential mediator of the effect of social/environmental exposures on a health outcome. Modern statistical methods for jointly evaluating many mediators have not been widely adopted. We compare seven methods for high-dimensional mediation analysis with continuous outcomes through both diverse simulations and analysis of DNAm data from a large multi-ethnic cohort in the United States, while providing an R package for their seamless implementation and adoption. Among the considered choices, the best-performing methods for detecting active mediators in simulations are the Bayesian sparse linear mixed model (BSLMM) and high-dimensional mediation analysis (HDMA); while the preferred methods for estimating the global mediation effect are high-dimensional linear mediation analysis (HILMA) and principal component mediation analysis (PCMA). We provide guidelines for epigenetic researchers on choosing the best method in practice and offer suggestions for future methodological development. 

Abstract Mediation hypothesis testing for a large number of mediators is challenging due to the composite structure of the null hypothesis, (: effect of the exposure on the mediator after adjusting for confounders; : effect of the mediator on the outcome after adjusting for exposure and confounders). In this paper, we reviewed three classes of methods for large‐scale one at a time mediation hypothesis testing. These methods are commonly used for continuous outcomes and continuous mediators assuming there is no exposure‐mediator interaction so that the product has a causal interpretation as the indirect effect. The first class of methods ignores the impact of different structures under the composite null hypothesis, namely, (1) ; (2) ; and (3) . The second class of methods weights the reference distribution under each case of the null to form a mixture reference distribution. The third class constructs a composite test statistic using the threepvalues obtained under each case of the null so that the reference distribution of the composite statistic is approximately . In addition to these existing methods, we developed the Sobel‐comp method belonging to the second class, which uses a corrected mixture reference distribution for Sobel's test statistic. We performed extensive simulation studies to compare all six methods belonging to these three classes in terms of the false positive rates (FPRs) under the null hypothesis and the true positive rates under the alternative hypothesis. We found that the second class of methods which uses a mixture reference distribution could best maintain the FPRs at the nominal level under the null hypothesis and had the greatest true positive rates under the alternative hypothesis. We applied all methods to study the mediation mechanism of DNA methylation sites in the pathway from adult socioeconomic status to glycated hemoglobin level using data from the Multi‐Ethnic Study of Atherosclerosis (MESA). We provide guidelines for choosing the optimal mediation hypothesis testing method in practice and develop an R packagemedScanavailable on the CRAN for implementing all the six methods. 

Abstract Efficient and accurate modeling of the coupled thermal‐hydraulic‐mechanical‐chemical (THMC) processes in various rock formations is indispensable for designing energy geo‐structures such as underground repositories for high‐level nuclear wastes. This work focuses on developing and verifying an implicit finite element solver for generic coupled THMC problems in geological settings. Starting from the mass, momentum, and energy balance laws, a specialized set of governing equations and a thermoporoelastic constitutive model is derived. This system is then solved by an implicit finite element (FE) scheme. Specifically, the residuals and the Jacobians are scripted in a user‐defined element (UEL) subroutine which is then combined with the general‐purpose FE software Abaqus Standard to solve initial‐boundary value problems. Considering the complexity of the system, the UEL development follows a stepwise manner by first solving the coupled hydraulic‐mechanical (HM) and thermal‐hydraulic‐mechanical (THM) equations before moving on to the full THMC problem. Each implementation step consists of at least one verification test by comparing computed results with closed‐form analytical solutions to ensure that the various coupling effects are correctly realized. To demonstrate the robustness of the algorithm and to validate the UEL, a three‐dimensional case study is performed with reference to the in‐situ heating test of ATLAS at Belgium in 1980s. A hypothetical radionuclide leakage event is then simulated by activating the chemical‐concentration degree of freedom and prescribing a constant high concentration at the heater's surface. The model predicts a limited contaminated regime after six years considering both diffusion and advection effects on species transport. 

Abstract Spatial transcriptomic studies are becoming increasingly common and large, posing important statistical and computational challenges for many analytic tasks. Here, we present SPARK-X, a non-parametric method for rapid and effective detection of spatially expressed genes in large spatial transcriptomic studies. SPARK-X not only produces effective type I error control and high power but also brings orders of magnitude computational savings. We apply SPARK-X to analyze three large datasets, one of which is only analyzable by SPARK-X. In these data, SPARK-X identifies many spatially expressed genes including those that are spatially expressed within the same cell type, revealing new biological insights.