REYNOLDS STRESS CORRECTION BY MACHINE LEARNING METHODS WITH PHYSICAL CONSTRAINTS

For the past three decade, Reynolds Average Navier-Stokes models have been widely used in the industry to simulate complex flows. However, these models suffer from limitations. Indeed there are still large discrepancies in the Reynolds stresses between the RANS model and high-fidelity data provided by DNS or experiments. This paper presents a strategy to correct the Menter SST model using an explicit algebraic model and two different neural networks: An multilayer perceptron (MLP) and a generative adversarial network (GAN). Moreover, in order to preserve the physical properties of the Reynolds stress tensor, we introduce a penalisation term in the loss of the GAN

Calibration of thickness-dependent k-factors for germanium X-ray lines to improve energy-dispersive X-ray spectroscopy of SiGe layers in analytical transmission electron microscopy

We show that the accuracy of energy-dispersive X-ray spectroscopy can be improved by analysing and comparing multiple lines from the same element. For each line, an effective k-factor can be defined that varies as a function of the intensity ratio of multiple lines (e.g. K/L) from the same element. This basically performs an internal self-consistency check in the quantification using differently absorbed X-ray lines, which is in principle equivalent to an absorption correction as a function of specimen thickness but has the practical advantage that the specimen thickness itself does not actually need to be measured

Diffusion and jump-length distribution in liquid and amorphous Cu33_{33}Zr67_{67}

Using molecular dynamics simulation, we calculate the distribution of atomic jum ps in Cu$_{33}$Zr$_{67}$ in the liquid and glassy states. In both states the distribution of jump lengths can be described by a temperature independent exponential of the length and an effective activation energy plus a contribution of elastic displacements at short distances. Upon cooling the contribution of shorter jumps dominates. No indication of an enhanced probability to jump over a nearest neighbor distance was found. We find a smooth transition from flow in the liquid to jumps in the g lass. The correlation factor of the diffusion constant decreases with decreasing temperature, causing a drop of diffusion below the Arrhenius value, despite an apparent Arrhenius law for the jump probability

Survey of overnight academic hospitalist supervision of trainees

In 2003, Accreditation Council for Graduate Medical Education (ACGME) announced the first in a series of guidelines related to the residency training. The most recent recommendations include explicit recommendations regarding the provision of on‐site clinical supervision for trainees of internal medicine. To meet these standards, many internal medicine residency programs turned to hospitalist programs to fill that need. However, much is unknown about the current relationships between hospitalist and residency programs, specifically with regard to supervisory roles and supervision policies. We aimed to describe how academic hospitalists currently supervise housestaff during the on‐call, or overnight, period and hospitalist program leader their perceptions of how these new policies would impact trainee‐hospitalist interactions. Journal of Hospital Medicine 2012; © 2012 Society of Hospital MedicinePeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/93713/1/1961_ftp.pd

Screening of MAMLD1 Mutations in 70 Children with 46,XY DSD: Identification and Functional Analysis of Two New Mutations

More than 50% of children with severe 46,XY disorders of sex development (DSD) do not have a definitive etiological diagnosis. Besides gonadal dysgenesis, defects in androgen biosynthesis, and abnormalities in androgen sensitivity, the Mastermind-like domain containing 1 (MAMLD1) gene, which was identified as critical for the development of male genitalia, may be implicated. The present study investigated whether MAMLD1 is implicated in cases of severe 46,XY DSD and whether routine sequencing of MAMLD1 should be performed in these patients

Effect of strain on surface diffusion in semiconductor heteroepitaxy

We present a first-principles analysis of the strain renormalization of the cation diffusivity on the GaAs(001) surface. For the example of In/GaAs(001)-c(4x4) it is shown that the binding of In is increased when the substrate lattice is expanded. The diffusion barrier \Delta E(e) has a non-monotonic strain dependence with a maximum at compressive strain values (e 0) studied. We discuss the consequences of spatial variations of both the binding energy and the diffusion barrier of an adatom caused by the strain field around a heteroepitaxial island. For a simplified geometry, we evaluate the speed of growth of two coherently strained islands on the GaAs(001) surface and identify a growth regime where island sizes tend to equalize during growth due to the strain dependence of surface diffusion.Comment: 10 pages, 8 figures, LaTeX2e, to appear in Phys. Rev. B (2001). Other related publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm

Establishing a generalized polyepigenetic biomarker for tobacco smoking

Large-scale epigenome-wide association meta-analyses have identified multiple 'signatures'' of smoking. Drawing on these findings, we describe the construction of a polyepigenetic DNA methylation score that indexes smoking behavior and that can be utilized for multiple purposes in population health research. To validate the score, we use data from two birth cohort studies: The Dunedin Longitudinal Study, followed to age-38 years, and the Environmental Risk Study, followed to age-18 years. Longitudinal data show that changes in DNA methylation accumulate with increased exposure to tobacco smoking and attenuate with quitting. Data from twins discordant for smoking behavior show that smoking influences DNA methylation independently of genetic and environmental risk factors. Physiological data show that changes in DNA methylation track smoking-related changes in lung function and gum health over time. Moreover, DNA methylation changes predict corresponding changes in gene expression in pathways related to inflammation, immune response, and cellular trafficking. Finally, we present prospective data about the link between adverse childhood experiences (ACEs) and epigenetic modifications; these findings document the importance of controlling for smoking-related DNA methylation changes when studying biological embedding of stress in life-course research. We introduce the polyepigenetic DNA methylation score as a tool both for discovery and theory-guided research in epigenetic epidemiology.This article is freely available via Open Access. Click on the Publisher URL to access it via the publisher's site.The Dunedin Longitudinal Study is funded by the New Zealand Health Research Council, the New Zealand Ministry of Business, Innovation, and Employment, the National Institute on Aging (AG032282), and the Medical Research Council (MR/P005918/1). The E-Risk Study is funded by the Medical Research Council (G1002190) and the National Institute of Child Health and Human Development (HD077482). Additional support was provided by a Distinguished Investigator Award from the American Asthma Foundation to Dr. Mill, and by the Jacobs Foundation and the Avielle Foundation. Dr. Arseneault is the Mental Health Leadership Fellow for the U.K. Economic and Social Research Council. Dr. Belsky is a Jacobs Foundation Fellow. This work used a high-performance computing facility partially supported by grant 2016-IDG-1013 (“HARDAC + : Reproducible HPC for Next-generation Genomics”) from the North Carolina Biotechnology Center. Illumina DNA methylation data are accessible from the Gene Expression Omnibus (accession code: GSE105018).pre-print, post-print, publisher's PD

The regulation of monoamine oxidase: a gene expression by distinct variable number tandem repeats

The monoamine oxidase A (MAOA) uVNTR (upstream variable number tandem repeat) is one of the most often cited examples of a gene by environment interaction (GxE) in relation to behavioral traits. However, MAOA possesses a second VNTR, 500 bp upstream of the uVNTR, which is termed d- or distal VNTR. Furthermore, genomic analysis indicates that there are a minimum of two transcriptional start sites (TSSs) for MAOA, one of which encompasses the uVNTR within the 5′ untranslated region of one of the isoforms. Through expression analysis in semi-haploid HAP1 cell lines genetically engineered in order to knockout (KO) either the uVNTR, dVNTR, or both VNTRs, we assessed the effect of the two MAOA VNTRs, either alone or in combination, on gene expression directed from the different TSSs. Complementing our functional analysis, we determined the haplotype variation of these VNTRs in the general population. The expression of the two MAOA isoforms was differentially modulated by the two VNTRs located in the promoter region. The most extensively studied uVNTR, previously considered a positive regulator of the MAOA gene, did not modulate the expression of what it is considered the canonical isoform, while we found that the dVNTR positively regulated this isoform in our model. In contrast, both the uVNTR and the dVNTR were found to act as negative regulators of the second less abundant MAOA isoform. The haplotype analysis for these two VNTRs demonstrated a bias against the presence of one of the potential variants. The uVNTR and dVNTR differentially affect expression of distinct MAOA isoforms, and thus, their combined profiling offers new insights into gene-regulation, GxE interaction, and ultimately MAOA-driven behavior