Mass Transport in Nanoporous Materials: New Insights from Micro-Imaging by Interference Microscopy

This thesis presents the recent progress of diffusion measurements in nanoporous host systems by micro-imaging. Interference microscopy is applied as a powerful tool to record transient, intracrystalline concentration profiles of different sorbate species in the porous framework of two different zeolites, viz. ZSM-5 (MFI) and ZSM-58 (DDR). These profiles, yielding high temporal and spatial resolutions of about 10 s and 0.45 μm, follow the change of the refractive index of the host-guest system during uptake and release of certain guest molecules. With the thus accessible changes of concentration and particle fluxes, mass transport parameters, such as intracrystalline diffusivity and surface permeability, can be obtained by the use of the very fundamental equations on diffusion. Additionally, in two examples of never before performed types of experiments, further insights into challenging fields of host-guest interactions are provided: The well known phase transition in MFI type zeolites covering high benzene loadings is investigated in a single crystal study, allowing to follow the change of the sorbate phase in great detail. Furthermore, in DDR zeolites, a new way of data analysis facilitates to study the uptake and release of binary mixtures. Here, from the two-dimension profiles obtained by interference microscopy, the local concentrations of the sorbate species could be retrieved by using the so-called ideal adsorbed solution theory

Inverse of the Gaussian multiplicative chaos: Lehto welding of Independent Quantum disks

In this article, we use the framework of "Random conformal weldings" (by K. Astala, P. Jones, A. Kupiainen, E. Saksman) to prove the existence of Lehto-welding for the inverse for $\gamma<0.1818$ and independent copies for $\gamma_{2}\leq\gamma_{1}<0.1818$. In particular, we obtain the existence of some conformaly invariant loop $\Gamma$ that glues two disks with boundary length given by independent copies of GMC on the unit circle. It is still unclear how to show that those loops $\Gamma$ are in fact SLE-loops in a parallel proof to "Integrability of SLE via conformal welding of random surfaces" (by Morris Ang, Nina Holden, and Xin Sun).Comment: arXiv admin note: text overlap with arXiv:0909.1003 by other author

Machine learning extracts marks of thiamine’s role in cold acclimation in the transcriptome of Vitis vinifera

IntroductionThe escalating challenge of climate change has underscored the critical need to understand cold defense mechanisms in cultivated grapevine Vitis vinifera. Temperature variations can affect the growth and overall health of vine.MethodsWe used Self Organizing Maps machine learning method to analyze gene expression data from leaves of five Vitis vinifera cultivars each treated by four different temperature conditions. The algorithm generated sample-specific “portraits” of the normalized gene expression data, revealing distinct patterns related to the temperature conditions applied.ResultsOur analysis unveiled a connection with vitamin B1 (thiamine) biosynthesis, suggesting a link between temperature regulation and thiamine metabolism, in agreement with thiamine related stress response established in Arabidopsis before. Furthermore, we found that epigenetic mechanisms play a crucial role in regulating the expression of stress-responsive genes at low temperatures in grapevines.DiscussionApplication of Self Organizing Maps portrayal to vine transcriptomics identified modules of coregulated genes triggered under cold stress. Our machine learning approach provides a promising option for transcriptomics studies in plants

The wealth of information from transient guest profiles

The application of interference microscopy (IFM) and infrared microscopy (IRM) to monitor the evolution of the concentration of guest molecules in nanoporous host materials opens a new field of diffusion research in condensed matter. It combines the methodical virtues of the profiling methods of solid-state diffusion studies with the benefit of the mobility enhancement in fluids. We are going to illustrate the rich options of diffusion studies provided by this novel experimental approach

Machine learned-based visualization of the diversity of grapevine genomes worldwide and in Armenia using SOMmelier

In the proposed study three major issues have been addressed: Firstly, the diversity of grapevine accessions worldwide and particularly in Armenia, a small country located in the largely volcanic Armenian Highlands, is incredibly rich in cultivated and especially wild grapes; secondly, the information hidden in their (whole) genomes, e.g., about the domestication history of grapevine over the last 11,000 years and phenotypic traits such as cultivar utilization and a putative resistance against powdery mildew, and, thirdly machine learning methods to extract and to visualize this information in an easy to percept way. We shortly describe the Self Origanizing Maps (SOM) portrayal method called “SOMmelier” (as the vine-genome “waiter”) and illustrate its power by applying it to whole genome data of hundreds of grapevine accessions. We also give a short outlook on possible future directions of machine learning in grapevine transcriptomics and ampelogaphy

Association of candidate pharmacogenetic markers with platinum-induced ototoxicity:PanCareLIFE dataset

Genetic association studies suggest a genetic predisposi- tion for cisplatin-induced ototoxicity. Among other candidate genes, thiopurine methyltransferase ( TPMT ) is considered a critical gene for susceptibility to cisplatin-induced hearing loss in a pharmacogenetic guideline. The PanCareLIFE cross- sectional cohort study evaluated the genetic associations in a large pan-European population and assessed the diagnos- tic accuracy of the genetic markers. 1,112 pediatric cancer survivors who had provided biomaterial for genotyping were screened for participation in the pharmacogenetic association study. 900 participants qualified for inclusion. Based on the assessment of original audiograms, patients were assigned to three phenotype categories: no, minor, and clinically relevant hearing loss. Fourteen variants in eleven candidate genes ( ABCC3, OTOS, TPMT, SLC22A2, NFE2L2, SLC16A5, LRP2, GSTP1, SOD2, WFS1, and ACYP2 ) were genotyped. The genotype and phenotype data represent a resource for conducting meta- analyses to derive a more precise pooled estimate of the ef- fects of genes on the risk of hearing loss due to platinum treatment

Association of candidate pharmacogenetic markers with platinum-induced ototoxicity: PanCareLIFE dataset

Genetic association studies suggest a genetic predisposition for cisplatin-induced ototoxicity. Among other candidate genes, thiopurine methyltransferase (TPMT) is considered a critical gene for susceptibility to cisplatin-induced hearing loss in a pharmacogenetic guideline. The PanCareLIFE cross-sectional cohort study evaluated the genetic associations in a large pan-European population and assessed the diagnostic accuracy of the genetic markers. 1,112 pediatric cancer survivors who had provided biomaterial for genotyping were screened for participation in the pharmacogenetic association study. 900 participants qualified for inclusion. Based on the assessment of original audiograms, patients were assigned to three phenotype categories: no, minor, and clinically relevant hearing loss. Fourteen variants in eleven candidate genes (ABCC3, OTOS, TPMT, SLC22A2, NFE2L2, SLC16A5, LRP2, GSTP1, SOD2, WFS1, and ACYP2) were genotyped. The genotype and phenotype data represent a resource for conducting meta-analyses to derive a more precise pooled estimate of the effects of genes on the risk of hearing loss due to platinum treatment

Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes:findings from the ENIGMA Epigenetics Working Group

DNA methylation, which is modulated by both genetic factors and environmental exposures, may offer a unique opportunity to discover novel biomarkers of disease-related brain phenotypes, even when measured in other tissues than brain, such as blood. A few studies of small sample sizes have revealed associations between blood DNA methylation and neuropsychopathology, however, large-scale epigenome-wide association studies (EWAS) are needed to investigate the utility of DNA methylation profiling as a peripheral marker for the brain. Here, in an analysis of eleven international cohorts, totalling 3337 individuals, we report epigenome-wide meta-analyses of blood DNA methylation with volumes of the hippocampus, thalamus and nucleus accumbens (NAcc)-three subcortical regions selected for their associations with disease and heritability and volumetric variability. Analyses of individual CpGs revealed genome-wide significant associations with hippocampal volume at two loci. No significant associations were found for analyses of thalamus and nucleus accumbens volumes. Cluster-based analyses revealed additional differentially methylated regions (DMRs) associated with hippocampal volume. DNA methylation at these loci affected expression of proximal genes involved in learning and memory, stem cell maintenance and differentiation, fatty acid metabolism and type-2 diabetes. These DNA methylation marks, their interaction with genetic variants and their impact on gene expression offer new insights into the relationship between epigenetic variation and brain structure and may provide the basis for biomarker discovery in neurodegeneration and neuropsychiatric conditions