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

Methylation array data can simultaneously identify individuals and convey protected health information: an unrecognized ethical concern

BACKGROUND: Genome-wide methylation arrays are increasingly used tools in studies of complex medical disorders. Because of their expense and potential utility to the scientific community, current federal policy dictates that data from these arrays, like those from genome-wide genotyping arrays, be deposited in publicly available databases. Unlike the genotyping information, access to the expression data is not restricted. An underlying supposition in the current nonrestricted access to methylation data is the belief that protected health and personal identifying information cannot be simultaneously extracted from these arrays. RESULTS: In this communication, we analyze methylation data from the Illumina HumanMethylation450 array and show that genotype at 1,069 highly informative loci, and both alcohol and smoking consumption information, can be derived from the array data. CONCLUSIONS: We conclude that both potentially personally identifying information and substance-use histories can be simultaneously derived from methylation array data. Because access to genetic information about a database subject or one of their relatives is critical to the de-identification process, this risk of de-identification is limited at the current time. We propose that access to genome-wide methylation data be restricted to institutionally approved investigators who accede to data use agreements prohibiting re-identification

DNA methylation age is accelerated in alcohol dependence.

Alcohol dependence (ALC) is a chronic, relapsing disorder that increases the burden of chronic disease and significantly contributes to numerous premature deaths each year. Previous research suggests that chronic, heavy alcohol consumption is associated with differential DNA methylation patterns. In addition, DNA methylation levels at certain CpG sites have been correlated with age. We used an epigenetic clock to investigate the potential role of excessive alcohol consumption in epigenetic aging. We explored this question in five independent cohorts, including DNA methylation data derived from datasets from blood (n = 129, n = 329), liver (n = 92, n = 49), and postmortem prefrontal cortex (n = 46). One blood dataset and one liver tissue dataset of individuals with ALC exhibited positive age acceleration (p < 0.0001 and p = 0.0069, respectively), whereas the other blood and liver tissue datasets both exhibited trends of positive age acceleration that were not significant (p = 0.83 and p = 0.57, respectively). Prefrontal cortex tissue exhibited a trend of negative age acceleration (p = 0.19). These results suggest that excessive alcohol consumption may be associated with epigenetic aging in a tissue-specific manner and warrants further investigation using multiple tissue samples from the same individuals

Valorization of surface-water RO brines via Assisted-Reverse Electrodialysis for minerals recovery: Performance analysis and scale-up perspectives

Reverse osmosis (RO) processes have been recently identified as mostly capable of quantitative removal of salts and contaminants from saline and surface waters, though posing the problem of a concentrated brine to be disposed of and a produced permeate too low in minerals, thus requiring a sometimes expensive remineralization step. In the present paper, Assisted-Reverse Electrodialysis (A-RED) has been proposed for the remineralization of surface-water RO permeate by recovering minerals from its brine. A purposely developed and validated model has been adopted to carry out a parametric analysis for design and optimization of an industrial-scale plant. The techno-economic analysis underlined that full permeate remineralization can be achieved with minimum specific energy consumption of 0.08 kWh m(-3), while a minimum remineralization cost of 2.2 c(sic) m(-3) was found applying a permeate by-pass and feed & bleed scheme to (i) increase the plant remineralization capacity and (ii) maintain a stack inlet conductivity above 100-160 mu S cm(-1) (starting from a permeate similar to 10 mu S cm(-1)). Compared to current post-treatment techniques, results appear very promising thanks to the reduction of chemicals and total costs as well as environmental concerns related to brine disposal

Effects of Genotype and Child Abuse on DNA Methylation and Gene Expression at the Serotonin Transporter

Altered regulation of the serotonin transporter (SLC6A4) is hypothesized to be a key event in many forms of neuropsychiatric illness, yet our understanding of the molecular mechanisms through which changes in gene function could lead to illness remains incomplete. In prior studies, we and others have demonstrated that methylation of CpG residues in the promoter associated CpG island alters SLC6A4 gene expression, that the extent of that DNA methylation in child abuse is genotype dependent, and that adverse childhood experiences such as child sex abuse are related to methylation. However, we have not examined whether these effects are splice variant specific, whether the association of methylation to gene expression varies as a function of genotype, and whether methylation in other SLC6A4 gene regions are more likely candidates for GxE effects. In the current investigation we measured methylation in lymphoblast DNA from 158 female subjects in the Iowa Adoption Studies at 16 CpG residues spread across the SLC6A4 locus, and analyzed their relationship to gene expression for two SLC6A4 splice variants. Methylation of two CpG residues in the shore of the CpG island (cg22584138 and cg05951817), a location immediately upstream from exon 1A, predicted gene expression for the splice variant containing Exon 1A + 1B. Methylation at two residues in the CpG island itself (cg 25769822 and cg05016953) was associated with total SLC6A4 expression. Examination of these four CpG residues indicated that methylation of cg22584138 was influenced by both genotype and sex abuse, whereas methylation of cg05016953 was influenced only by sex abuse history. Factors influencing methylation at other CpG dinucleotide pairs were not identified. We conclude that methylation effects on transcription may vary as a function of underlying gene motif and splice variant, and that the shore of CpG islands, upstream of TSS, may be of particular interest in examining environmental effects on methylation

Characterization of B-doped polycrystalline diamond films using thermally stimulated luminescence

International audienceThe effect of different rates of boron incorporation during the growth in diamond on the thermoluminescence (TL) features of this material is investigated. TL studies performed between liquid nitrogen temperature (LNT) and 320 K show some phosphorescence and two other peaks at 226 and 266 K. For the first time, boron level in polycrystalline diamond films was identified by TL by an intense glow peak at 226 K and activation energy of about 0.35 eV. For this main peak, spectral analysis shows a prominent broad band luminescence peaking at 2.56 eV. At 77 K, another emission band was observed at 2.22 eV. This is in agreement with the fact that the recombination mechanisms involve two different recombination centers and, therefore, phosphorescence at 77 K and the main peak at 226 K are of different nature, i.e. the TL peak at 226 K is due to boron while phosphorescence is hence, probably due to a shallow donor level. The behavior of TL intensity relative to the main component at 226 K observed on all the films and linked to boron level decreases with increasing boron concentration

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

Methylation Array Data Can Simultaneously Identify Individual and Convey Protected Health Information: an Unrecognized Ethical Concern

Background: Genome-wide methylation arrays are increasingly used tools in studies of complex medical disorders. Because of their expense and potential utility to the scientific community, current federal policy dictates that data from these arrays, like those from genome-wide genotyping arrays, be deposited in publicly available databases. Unlike the genotyping information, access to the expression data is not restricted. An underlying supposition in the current nonrestricted access to methylation data is the belief that protected health and personal identifying information cannot be simultaneously extracted from these arrays. Results: In this communication, we analyze methylation data from the Illumina HumanMethylation450 array and show that genotype at 1,069 highly informative loci, and both alcohol and smoking consumption information, can be derived from the array data. Conclusions: We conclude that both potentially personally identifying information and substance-use histories can be simultaneously derived from methylation array data. Because access to genetic information about a database subject or one of their relatives is critical to the de-identification process, this risk of de-identification is limited at the current time. We propose that access to genome-wide methylation data be restricted to institutionally approved investigators who accede to data use agreements prohibiting re-identification

Methylation of MTHFR Moderates the Effect of Smoking on Genomewide Methylation Among Middle Age African Americans

Differential methylation at MTHFR (mMTHFR) has been examined previously as a moderator of changes in methylation among nascent smokers, but the effects of mMTHFR on genomewide patterns of methylation among established smokers in middle age are unknown. In the current investigation we examined a sample of 180 African American middle-aged smokers and non-smokers to test for patterns indicative of three different potential mechanisms of impact on epigenetic remodeling in response to long-term smoking. We found that mMTHFR moderated the association between smoking and changes in methylation for more than 25% of the 909 loci previously identified as being associated with smoking at a genomewide level of significance in middle-aged African Americans. Observed patterns of effect indicated amplification of both hyper and hypo methylating responses to smoking among those with lower mMTHFR. Moderating effects were robust to controls for sex, age, diet, and cell-type variation. Implications for potential mechanisms conferring effects are discussed. Of particular potential practical importance was a strong effect of mMTHFR on hypomethylation at GPR15 in response to smoking, indicative of the differential impact of MTHFR activity on changes in a specific cell population linked to inflammatory disease in smokers

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