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84,177 results on '"Markus, M."'

1. Semantic Information Management in Low-Temperature Plasma Science and Technology with VIVO

Author

Siffa, Ihda Chaerony, Wagner, Robert, Scholten, Laura Vilardell, and Becker, Markus M.

Subjects
Physics - Plasma Physics, Computer Science - Digital Libraries
Abstract

Digital research data management is increasingly integrated across universities and research institutions, addressing the handling of research data throughout its lifecycle according to the FAIR data principles (Findable, Accessible, Interoperable, Reusable). Recent emphasis on the semantic and interlinking aspects of research data, e.g., by using ontologies and knowledge graphs further enhances findability and reusability. This work presents a framework for creating and maintaining a knowledge graph specifically for low-temperature plasma (LTP) science and technology. The framework leverages a domain-specific ontology called Plasma-O, along with the VIVO software as a platform for semantic information management in LTP research. While some research fields are already prepared to use ontologies and knowledge graphs for information management, their application in LTP research is nascent. This work aims to bridge this gap by providing a framework that not only improves research data management but also fosters community participation in building the domain-specific ontology and knowledge graph based on the published materials. The results may also support other research fields in the practical use of knowledge graphs for semantic information management.

Published
2024

2. Weak-Lensing Shear-Selected Galaxy Clusters from the Hyper Suprime-Cam Subaru Strategic Program: II. Cosmological Constraints from the Cluster Abundance

Author

Chiu, I-Non, Chen, Kai-Feng, Oguri, Masamune, Rau, Markus M., Hamana, Takashi, Lin, Yen-Ting, Miyatake, Hironao, Miyazaki, Satoshi, More, Surhud, Sunayama, Tomomi, Sugiyama, Sunao, and Takada, Masahiro

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

We present cosmological constraints using the abundance of weak-lensing shear-selected galaxy clusters in the Hyper Suprime-Cam (HSC) Subaru Strategic Program. The clusters are selected on the mass maps constructed using the three-year (Y3) weak-lensing data with an area of $\approx500~$deg$^2$, resulting in a sample size of $129$ clusters with high signal-to-noise ratios $\nu$ of $\nu\geq4.7$. Owing to the deep, wide-field, and uniform imaging of the HSC survey, this is by far the largest sample of shear-selected clusters, in which the selection solely depends on gravity and is free from any assumptions about the dynamical state. Informed by the optical counterparts, the shear-selected clusters span a redshift range of $z\lesssim0.7$ with a median of $z\approx0.3$. The lensing sources are securely selected at $z\gtrsim0.7$ with a median of $z\approx1.3$, leading to nearly zero cluster member contamination. We carefully account for (1) the bias in the photometric redshift of sources, (2) the bias and scatter in the weak-lensing mass using a simulation-based calibration, and (3) the measurement uncertainty that is directly estimated on the mass maps using an injection-based method developed in a companion paper (Chen et al. submitted). In a blind analysis, the fully marginalized posteriors of the cosmological parameters are obtained as $\Omega_{\mathrm{m}} = 0.50^{+0.28}_{-0.24}$, $\sigma_8 = 0.685^{+0.161}_{-0.088}$, $\hat{S}_{8}\equiv\sigma_8\left(\Omega_{\mathrm{m}}/0.3\right)^{0.25} = 0.835^{+0.041}_{-0.044}$, and $\sigma_8\left(\Omega_{\mathrm{m}}/0.3\right)^{0.5} = 0.993^{+0.084}_{-0.126}$ in a flat $\Lambda$CDM model. We compare our cosmological constraints with other studies, including those based on cluster abundances, galaxy-galaxy lensing and clustering, and Cosmic Microwave Background observed by $Planck$, and find good agreement at levels of $\lesssim2\sigma$. [abridged], Comment: Accepted for publication in the Open Journal of Astrophysics. Main results are Figures 11 and 12. The cluster catalog and the cosmological chain are accessible at https://github.com/inonchiu/hsc_shear_selected_clusters

Published
2024
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3. Weak-Lensing Shear-Selected Galaxy Clusters from the Hyper Suprime-Cam Subaru Strategic Program: I. Cluster Catalog, Selection Function and Mass--Observable Relation

Author

Chen, Kai-Feng, Chiu, I-Non, Oguri, Masamune, Lin, Yen-Ting, Miyatake, Hironao, Miyazaki, Satoshi, More, Surhud, Hamana, Takashi, Rau, Markus M., Sunayama, Tomomi, Sugiyama, Sunao, and Takada, Masahiro

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

We present the first step towards deriving cosmological constraints through the abundances of galaxy clusters selected in a $510\,\mathrm{deg}^2$ weak-lensing aperture mass map, constructed with the Year-Three shear catalog from the Hyper Suprime-Cam Subaru Strategic Program. We adopt a conservative source galaxy selection to construct a sample of $129$ weak-lensing peaks with a signal-to-noise ratio above $4.7$. We use semi-analytical injection simulations to derive the selection function and the mass--observable relation of our sample. These results take into account complicated uncertainties associated with weak-lensing measurements, such as the non-uniform survey depth and the complex survey geometry, projection effects from uncorrelated large-scale structures, and the intrinsic alignment of source galaxies. We also propose a novel modeling framework to make parts of the mass--observable relation insensitive to assumed cosmological parameters. Such a framework not only offers a great computational advantage to cosmological studies, but can also benefit future astrophysical studies using shear-selected clusters. Our results are an important step towards utilizing these cluster samples that are constructed nearly independent of any baryonic assumptions in upcoming deep-and-wide lensing surveys from the Vera Rubin Observatory, Euclid, and the Nancy Grace Roman Space Telescope., Comment: 17 pages, 9 figures, submitted to OJA. The cluster catalog of the cosmological sample (signal-to-noise ratio above $4.7$) is accessible at https://github.com/inonchiu/hsc_shear_selected_clusters

Published
2024

4. Nanosecond pulsed barrier discharge in argon for various frequencies and theoretical analysis of 2p states density ratios for E/N determination

Author

Kusýn, Lukáš, Jovanović, Aleksandar P., Loffhagen, Detlef, Becker, Markus M., and Hoder, Tomáš

Subjects
Physics - Plasma Physics
Abstract

Nanosecond pulsed barrier discharges in atmospheric pressure argon are simulated using spatially one- and two-dimensional fluid-Poisson models using the reaction kinetics model presented by Stankov et al. [1], which considers all ten argon 2p states (Paschen notation) separately. The very first (single) discharge and repetitive discharges with frequencies from 5kHz to 100kHz are considered and a semi-automated procedure is utilized to find appropriate 2p states for electric field determination using an intensity ratio method. The proposed method is based on a time-dependent collisional-radiative model enabling a sub-nanosecond plasma diagnostics, it links the 2p state density ratios to the reduced electric field strength E/N by quantifying the excitation rate coefficients and by computing 2p states effective lifetimes from the fluid model simulation. The semi-automated procedure identifies several candidates for determination of E/N from given temporal profiles of the 2p state densities. Different approaches for effective lifetime determination are tested and applied also to measured data. The influence of radial and axial 2p state density integration on the intensity ratio method is discussed. The above mentioned models and procedures result in a flexible theory-based methodology applicable for development of new diagnostic techniques., Comment: 19 pages, 13 figures

Published
2024

5. Joint Modelling of Astrophysical Systematics for Cosmology with LSST

Author

Šarčević, Nikolina, Leonard, C. Danielle, Rau, Markus M., and Collaboration, LSST Dark Energy Science

Subjects
Astrophysics - Cosmology and Nongalactic Astrophysics
Abstract

We present a novel framework for jointly modelling the weak lensing source galaxy redshift distribution and the intrinsic alignment of galaxies via a shared luminosity function (LF). Considering this framework within the context of a Rubin Observatory's Legacy Survey of Space and Time (LSST) Year 1 and Year 10 cosmic shear analysis, we first demonstrate the substantial impact of the LF on both source galaxy redshift distributions and the intrinsic alignment contamination. We establish how the individual parameters of a Schechter LF model impact the redshift distribution of a magnitude-limited sample, and we demonstrate the effect of marginalising over the LF parameters as incorporated in the intrinsic alignment modelling of a standard cosmic shear analysis set-up. We forecast the impact of our joint modelling framework on cosmological parameter constraints. Our preliminary results are promising, indicating that this framework can yield cosmological constraints consistent with those expected from standard analyses, enhanced by the flexibility of not fixing LF parameters. We plan to further validate these findings with comprehensive Markov chain Monte Carlo simulations to robustly quantify bias avoidance and underscore the framework's efficacy. Taking advantage of our forecasting results and the parameter degeneracies, we identify the specific impact of the shape of the LF of source galaxies on the cosmic shear data vector. We also discuss the potential of this method in providing a way to model generic selection functions in redshift distribution estimation, as well as its possibilities for extension to a 3x2pt analysis, particularly with respect to incorporating galaxy bias in this luminosity-function-based framework. Although we consider the context of LSST cosmic shear in this work, the proposed joint modelling framework is generically applicable to weak lensing surveys., Comment: 19 pages, 16 figures, 3 tables; v2: added LSST DESC to arxiv author list

Published
2024

6. Genomic analysis of intracranial and subcortical brain volumes yields polygenic scores accounting for variation across ancestries

Author

García-Marín, Luis M., Campos, Adrian I., Diaz-Torres, Santiago, Rabinowitz, Jill A., Ceja, Zuriel, Mitchell, Brittany L., Grasby, Katrina L., Thorp, Jackson G., Agartz, Ingrid, Alhusaini, Saud, Ames, David, Amouyel, Philippe, Andreassen, Ole A., Arfanakis, Konstantinos, Arias-Vasquez, Alejandro, Armstrong, Nicola J., Athanasiu, Lavinia, Bastin, Mark E., Beiser, Alexa S., Bennett, David A., Bis, Joshua C., Boks, Marco P. M., Boomsma, Dorret I., Brodaty, Henry, Brouwer, Rachel M., Buitelaar, Jan K., Burkhardt, Ralph, Cahn, Wiepke, Calhoun, Vince D., Carmichael, Owen T., Chakravarty, Mallar, Chen, Qiang, Ching, Christopher R. K., Cichon, Sven, Crespo-Facorro, Benedicto, Crivello, Fabrice, Dale, Anders M., Smith, George Davey, de Geus, Eco J. C., De Jager, Philip L., de Zubicaray, Greig I., Debette, Stéphanie, DeCarli, Charles, Depondt, Chantal, Desrivières, Sylvane, Djurovic, Srdjan, Ehrlich, Stefan, Erk, Susanne, Espeseth, Thomas, Fernández, Guillén, Filippi, Irina, Fisher, Simon E., Fleischman, Debra A., Fletcher, Evan, Fornage, Myriam, Forstner, Andreas J., Francks, Clyde, Franke, Barbara, Ge, Tian, Goldman, Aaron L., Grabe, Hans J., Green, Robert C., Grimm, Oliver, Groenewold, Nynke A., Gruber, Oliver, Gudnason, Vilmundur, Håberg, Asta K., Haukvik, Unn K., Heinz, Andreas, Hibar, Derrek P., Hilal, Saima, Himali, Jayandra J., Ho, Beng-Choon, Hoehn, David F., Hoekstra, Pieter J., Hofer, Edith, Hoffmann, Wolfgang, Holmes, Avram J., Homuth, Georg, Hosten, Norbert, Ikram, M. Kamran, Ipser, Jonathan C., Jack Jr, Clifford R., Jahanshad, Neda, Jönsson, Erik G., Kahn, Rene S., Kanai, Ryota, Klein, Marieke, Knol, Maria J., Launer, Lenore J., Lawrie, Stephen M., Hellard, Stephanie Le, Lee, Phil H., Lemaître, Hervé, Li, Shuo, Liewald, David C. M., Lin, Honghuang, Longstreth, Jr, W. T., Lopez, Oscar L., Luciano, Michelle, Maillard, Pauline, Marquand, Andre F., Martin, Nicholas G., Martinot, Jean-Luc, Mather, Karen A., Mattay, Venkata S., McMahon, Katie L., Mecocci, Patrizia, Melle, Ingrid, Meyer-Lindenberg, Andreas, Mirza-Schreiber, Nazanin, Milaneschi, Yuri, Mosley, Thomas H., Mühleisen, Thomas W., Müller-Myhsok, Bertram, Maniega, Susana Muñoz, Nauck, Matthias, Nho, Kwangsik, Niessen, Wiro J., Nöthen, Markus M., Nyquist, Paul A., Oosterlaan, Jaap, Pandolfo, Massimo, Paus, Tomas, Pausova, Zdenka, Penninx, Brenda W. J. H., Pike, G. Bruce, Psaty, Bruce M., Pütz, Benno, Reppermund, Simone, Rietschel, Marcella D., Risacher, Shannon L., Romanczuk-Seiferth, Nina, Romero-Garcia, Rafael, Roshchupkin, Gennady V., Rotter, Jerome I., Sachdev, Perminder S., Sämann, Philipp G., Saremi, Arvin, Sargurupremraj, Muralidharan, Saykin, Andrew J., Schmaal, Lianne, Schmidt, Helena, Schmidt, Reinhold, Schofield, Peter R., Scholz, Markus, Schumann, Gunter, Schwarz, Emanuel, Shen, Li, Shin, Jean, Sisodiya, Sanjay M., Smith, Albert V., Smoller, Jordan W., Soininen, Hilkka S., Steen, Vidar M., Stein, Dan J., Stein, Jason L., Thomopoulos, Sophia I., Toga, Arthur W., Tordesillas-Gutiérrez, Diana, Trollor, Julian N., Valdes-Hernandez, Maria C., van ′t Ent, Dennis, van Bokhoven, Hans, van der Meer, Dennis, van der Wee, Nic J. A., Vázquez-Bourgon, Javier, Veltman, Dick J., Vernooij, Meike W., Villringer, Arno, Vinke, Louis N., Völzke, Henry, Walter, Henrik, Wardlaw, Joanna M., Weinberger, Daniel R., Weiner, Michael W., Wen, Wei, Westlye, Lars T., Westman, Eric, White, Tonya, Witte, A. Veronica, Wolf, Christiane, Yang, Jingyun, Zwiers, Marcel P., Ikram, M. Arfan, Seshadri, Sudha, Thompson, Paul M., Satizabal, Claudia L., Medland, Sarah E., and Rentería, Miguel E.

Published
2024
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8. The interplay between polygenic score for tumor necrosis factor-α, brain structural connectivity, and processing speed in major depression

Author

Flinkenflügel, Kira, Gruber, Marius, Meinert, Susanne, Thiel, Katharina, Winter, Alexandra, Goltermann, Janik, Usemann, Paula, Brosch, Katharina, Stein, Frederike, Thomas-Odenthal, Florian, Wroblewski, Adrian, Pfarr, Julia-Katharina, David, Friederike S., Beins, Eva C., Grotegerd, Dominik, Hahn, Tim, Leehr, Elisabeth J., Dohm, Katharina, Bauer, Jochen, Forstner, Andreas J., Nöthen, Markus M., Jamalabadi, Hamidreza, Straube, Benjamin, Alexander, Nina, Jansen, Andreas, Witt, Stephanie H., Rietschel, Marcella, Nenadić, Igor, van den Heuvel, Martijn P., Kircher, Tilo, Repple, Jonathan, and Dannlowski, Udo

Published
2024
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9. Genetische Diagnostik bei psychischen Erkrankungen im Erwachsenenalter

Author

Kilarski, Laura L., Claus, Isabelle, Binder, Elisabeth B., Degenhardt, Franziska, Domschke, Katharina, Forstner, Andreas J., Grabe, Hans J., Heilbronner, Urs, Müller, Daniel, Nöthen, Markus M., Radtke, Franziska, Rietschel, Marcella, Schulze, Thomas G., Streit, Fabian, Tebartz van Elst, Ludger, Tüscher, Oliver, Deckert, Jürgen, and Schulte, Eva C.

Published
2024
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13. Ground-Based Remote Sensing of Aerosol, Clouds, Dynamics, and Precipitation in Antarctica: First Results from the 1-Year COALA Campaign at Neumayer Station III in 2023

Author

Radenz, Martin, Engelmann, Ronny, Henning, Silvia, Schmithusen, Holger, Baars, Holger, Frey, Markus M., Weller, Rolf, Buhl, Johannes, Jimenez, Cristofer, Roschke, Johanna, Muser, Lukas Ole, Wullenweber, Nellie, Zeppenfeld, Sebastian, Griesche, Hannes, Wandinger, Ulla, and Seifert, Patric

Subjects
Clouds -- Observations, Remote sensing -- Methods -- Usage -- 2023 AD, Aerosols -- Observations -- 2023 AD, Precipitation variability -- Observations -- 2023 AD, Business, Earth sciences
Abstract

Novel observations of aerosol and clouds by means of ground-based remote sensing have been performed in Antarctica over the Ekstrom Ice Shelf on the coast of Dronning Maud Land at Neumayer Station III (70.67[degrees]S, 8.27[degrees]W) from January to December 2023. The deployment of the OCEANET-Atmosphere remote sensing observatory in the framework of the Continuous Observations of Aerosol-Cloud Interaction (COALA) campaign has brought Aerosol, Clouds and Trace Gases Research Infrastructure (ACTRIS) aerosol and cloud profiling capabilities next to meteorological and air chemistry in situ observations at the Antarctic station. We present an overview of the site, the instrumental setup, and data analysis strategy and introduce 3 scientific highlights from austral fall and winter, namely, 1) observations of a persistent mixed-phase cloud embedded in a plume of marine aerosol. Remote sensing-based retrievals of cloud-relevant aerosol properties and cloud microphysical parameters confirm that the free-tropospheric mixed-phase cloud layer formed in an aerosol-limited environment. 2) Two extraordinary warm air intrusions: one with intense snowfall produced the equivalent of 10% of the yearly snow accumulation and a second one with record-breaking maximum temperatures and heavy icing due to supercooled drizzle. 3) Omnipresent aerosol layers in the stratosphere. Our profiling capabilities could show that 50% of the 500-nm aerosol optical depth of 0.06 was caused by stratospheric aerosol, while the troposphere was usually pristine. As demonstrated by these highlights, the 1-yr COALA observations will serve as a reference dataset for the vertical structure of aerosol and clouds above the region, enabling future observational and modeling studies to advance understanding of atmospheric processes in Antarctica. KEYWORDS: Antarctica; Ice shelves; Aerosols; Clouds; Remote sensing; Aerosol-cloud interaction, 1. Introduction The Antarctic continent and its surrounding Southern Ocean are key components of the global climate system. Having been considered rather stable over the last century, the climate of [...]

Published
2024
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17. Hyper Suprime-Cam Year 3 results: Cosmology from cosmic shear two-point correlation functions

Author

Li, Xiangchong, Zhang, Tianqing, Sugiyama, Sunao, Dalal, Roohi, Terasawa, Ryo, Rau, Markus M, Mandelbaum, Rachel, Takada, Masahiro, More, Surhud, Strauss, Michael A, Miyatake, Hironao, Shirasaki, Masato, Hamana, Takashi, Oguri, Masamune, Luo, Wentao, Nishizawa, Atsushi J, Takahashi, Ryuichi, Nicola, Andrina, Osato, Ken, Kannawadi, Arun, Sunayama, Tomomi, Armstrong, Robert, Bosch, James, Komiyama, Yutaka, Lupton, Robert H, Lust, Nate B, MacArthur, Lauren A, Miyazaki, Satoshi, Murayama, Hitoshi, Nishimichi, Takahiro, Okura, Yuki, Price, Paul A, Tait, Philip J, Tanaka, Masayuki, and Wang, Shiang-Yu

Subjects
Particle and High Energy Physics, Physical Sciences
Abstract

We perform a blinded cosmology analysis with cosmic shear two-point correlation functions measured from more than 25 million galaxies in the Hyper Suprime-Cam three-year shear catalog in four tomographic redshift bins ranging from 0.3 to 1.5. After conservative masking and galaxy selection, the survey covers 416 deg2 of the northern sky with an effective galaxy number density of 15 arcmin-2 over the four redshift bins. The 2PCFs adopted for cosmology analysis are measured in the angular range; 7.1

Published
2023

18. Investigation of dog ownership and physical activity on weekdays and weekends using longitudinal data from the SOEP Cohort

Author

Yu TANIGUCHI, Tomoko IKEUCHI, Markus M. Grabka, and Jongsay Yong

Subjects
Dog, Animals, Physical activity, SOEP, Medicine, Science
Abstract

Abstract This study examines the association between dog ownership over a period of 5 years (always, sometimes and no ownership) with physical activity on weekdays and weekends over a period of 6 years using the nationally representative German Socio-Economic Panel. Participants were asked if they had any pets and how many hours they spend on sports, fitness, and exercise. We hypothesized that the length of dog ownership may have different effects on the physical activity of the owner. Overall, 15,240 participants completed the questionnaire on dog ownership in both 2011 and 2016, and reported their physical activity levels at least once between 2013 and 2018. Generalized estimating equation models showed that, compared to no ownership, always dog ownership was associated with higher physical activity on weekdays (Coefficient = 0.106, Standard Error: SE = 0.027, P

Published
2024
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19. Fecal glycoprotein 2 is a marker of gut microbiota dysbiosis and systemic inflammation

Author

Fabian Frost, Stefan Weiss, Johannes Hertel, Malte Rühlemann, Corinna Bang, Andre Franke, Matthias Nauck, Marcus Dörr, Henry Völzke, Dirk Roggenbuck, Peter Schierack, Uwe Völker, Georg Homuth, Ali A. Aghdassi, Matthias Sendler, Markus M. Lerch, and Frank U. Weiss

Subjects
GP2, Exocrine, Pancreas, Pancreatitis, IBD, Biomarker, Diseases of the digestive system. Gastroenterology, RC799-869
Abstract

Abstract Background Antimicrobial autoantigenic glycoprotein 2 (GP2) is an important component of the innate immune system which originates from the exocrine pancreas as well as from the small intestines. The relationship of GP2 with the intestinal microbiome as well as the systemic implications of increased fecal GP2 levels are, however, still unclear. Therefore, fecal samples from 2,812 individuals of the Study of Health in Pomerania (SHIP) were collected to determine GP2 levels (enzyme-linked immunosorbent assay) and gut microbiota profiles (16 S rRNA gene sequencing). These data were correlated and associated with highly standardised and comprehensive phenotypic data of the study participants. Results Fecal GP2 levels were increased in individuals with higher body mass index and smokers, whereas lower levels were found in case of preserved exocrine pancreatic function, female sex or a healthier diet. Moreover, higher GP2 levels were associated with increased serum levels of high-sensitivity C-reactive protein, loss of gut microbial diversity and an increase of potentially detrimental bacteria (Streptococcus, Haemophilus, Clostridium XIVa, or Collinsella). At the same time, predicted microbial pathways for the biosynthesis of beneficial short-chain fatty acids or lactic acid were depleted in individuals with high fecal GP2. Of note, GP2 exhibited a stronger association to overall microbiome variation than calprotectin. Conclusion Fecal GP2 is a biomarker of gut microbiota dysbiosis and associated with increased systemic inflammation. The intestines may be more important as origin for GP2 than pancreatic acinar cells. Future studies need to investigate the potential clinical value in disease specific patient cohorts.

Published
2024
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20. Multi-omics profiling of DNA methylation and gene expression alterations in human cocaine use disorder

Author

Eric Zillich, Hanna Belschner, Diana Avetyan, Diego Andrade-Brito, José Jaime Martínez-Magaña, Josef Frank, Naguib Mechawar, Gustavo Turecki, Judit Cabana-Domínguez, Noèlia Fernàndez-Castillo, Bru Cormand, Janitza L. Montalvo-Ortiz, Markus M. Nöthen, Anita C. Hansson, Marcella Rietschel, Rainer Spanagel, Stephanie H. Witt, and Lea Zillich

Subjects
Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract

Abstract Structural and functional changes of the brain are assumed to contribute to excessive cocaine intake, craving, and relapse in cocaine use disorder (CUD). Epigenetic and transcriptional changes were hypothesized as a molecular basis for CUD-associated brain alterations. Here we performed a multi-omics study of CUD by integrating epigenome-wide methylomic (N = 42) and transcriptomic (N = 25) data from the same individuals using postmortem brain tissue of Brodmann Area 9 (BA9). Of the N = 1 057 differentially expressed genes (p

Published
2024
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21. Associations between antagonistic SNPs for neuropsychiatric disorders and human brain structure

Author

Lydia M. Federmann, Friederike S. David, Christiane Jockwitz, Thomas W. Mühleisen, Dominique I. Pelzer, Markus M. Nöthen, Svenja Caspers, Katrin Amunts, Janik Goltermann, Till F. M. Andlauer, Frederike Stein, Katharina Brosch, Tilo Kircher, Sven Cichon, Udo Dannlowski, Lisa Sindermann, and Andreas J. Forstner

Subjects
Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract

Abstract A previously published genome-wide association study (GWAS) meta-analysis across eight neuropsychiatric disorders identified antagonistic single-nucleotide polymorphisms (SNPs) at eleven genomic loci where the same allele was protective against one neuropsychiatric disorder and increased the risk for another. Until now, these antagonistic SNPs have not been further investigated regarding their link to brain structural phenotypes. Here, we explored their associations with cortical surface area and cortical thickness (in 34 brain regions and one global measure each) as well as the volumes of eight subcortical structures using summary statistics of large-scale GWAS of brain structural phenotypes. We assessed if significantly associated brain structural phenotypes were previously reported to be associated with major neuropsychiatric disorders in large-scale case-control imaging studies by the ENIGMA consortium. We further characterized the effects of the antagonistic SNPs on gene expression in brain tissue and their association with additional cognitive and behavioral phenotypes, and performed an exploratory voxel-based whole-brain analysis in the FOR2107 study (n = 754 patients with major depressive disorder and n = 847 controls). We found that eight antagonistic SNPs were significantly associated with brain structural phenotypes in regions such as anterior parts of the cingulate cortex, the insula, and the superior temporal gyrus. Case-control differences in implicated brain structural phenotypes have previously been reported for bipolar disorder, major depressive disorder, and schizophrenia. In addition, antagonistic SNPs were associated with gene expression changes in brain tissue and linked to several cognitive-behavioral traits. In our exploratory whole-brain analysis, we observed significant associations of gray matter volume in the left superior temporal pole and left superior parietal region with the variants rs301805 and rs1933802, respectively. Our results suggest that multiple antagonistic SNPs for neuropsychiatric disorders are linked to brain structural phenotypes. However, to further elucidate these findings, future case-control genomic imaging studies are required.

Published
2024
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22. Sex-specific molecular signature of mouse podocytes in homeostasis and in response to pharmacological challenge with rapamycin

Author

Ola Al-Diab, Christin Sünkel, Eric Blanc, Rusan Ali Catar, Muhammad Imtiaz Ashraf, Hongfan Zhao, Pinchao Wang, Markus M. Rinschen, Raphaela Fritsche-Guenther, Florian Grahammer, Sebastian Bachmann, Dieter Beule, Jennifer A. Kirwan, Nikolaus Rajewsky, Tobias B. Huber, Dennis Gürgen, and Angelika Kusch

Subjects
Podocytes, Sex differences, Transcriptome, Proteome, Metabolome, mTOR, Medicine, Physiology, QP1-981
Abstract

Abstract Background Sex differences exist in the prevalence and progression of major glomerular diseases. Podocytes are the essential cell-type in the kidney which maintain the physiological blood-urine barrier, and pathological changes in podocyte homeostasis are critical accelerators of impairment of kidney function. However, sex-specific molecular signatures of podocytes under physiological and stress conditions remain unknown. This work aimed at identifying sexual dimorphic molecular signatures of podocytes under physiological condition and pharmacologically challenged homeostasis with mechanistic target of rapamycin (mTOR) inhibition. mTOR is a crucial regulator involved in a variety of physiological and pathological stress responses in the kidney and inhibition of this pathway may therefore serve as a general stress challenger to get fundamental insights into sex differences in podocytes. Methods The genomic ROSAmT/mG-NPHS2 Cre mouse model was used which allows obtaining highly pure podocyte fractions for cell-specific molecular analyses, and vehicle or pharmacologic treatment with the mTOR inhibitor rapamycin was performed for 3 weeks. Subsequently, deep RNA sequencing and proteomics were performed of the isolated podocytes to identify intrinsic sex differences. Studies were supplemented with metabolomics from kidney cortex tissues. Results Although kidney function and morphology remained normal in all experimental groups, RNA sequencing, proteomics and metabolomics revealed strong intrinsic sex differences in the expression levels of mitochondrial, translation and structural transcripts, protein abundances and regulation of metabolic pathways. Interestingly, rapamycin abolished prominent sex-specific clustering of podocyte gene expression and induced major changes only in male transcriptome. Several sex-biased transcription factors could be identified as possible upstream regulators of these sexually dimorphic responses. Concordant to transcriptomics, metabolomic changes were more prominent in males. Remarkably, high number of previously reported kidney disease genes showed intrinsic sexual dimorphism and/or different response patterns towards mTOR inhibition. Conclusions Our results highlight remarkable intrinsic sex-differences and sex-specific response patterns towards pharmacological challenged podocyte homeostasis which might fundamentally contribute to sex differences in kidney disease susceptibilities and progression. This work provides rationale and an in-depth database for novel targets to be tested in specific kidney disease models to advance with sex-specific treatment strategies.

Published
2024
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23. Structured multicellular intestinal spheroids (SMIS) as a standardized model for infection biology

Author

Angelina Kraski, Paweł Migdał, Robert Klopfleisch, Clara Räckel, Jutta Sharbati, Markus M. Heimesaat, Thomas Alter, Carlos Hanisch, Greta Gölz, Ralf Einspanier, and Soroush Sharbati

Subjects
Multilayered spheroid, 3D cell culture, Intestinal mucosa, Infection model, Diseases of the digestive system. Gastroenterology, RC799-869
Abstract

Abstract Background 3D cell culture models have recently garnered increasing attention for replicating organ microarchitecture and eliciting in vivo-like responses, holding significant promise across various biological disciplines. Broadly, 3D cell culture encompasses organoids as well as single- and multicellular spheroids. While the latter have found successful applications in tumor research, there is a notable scarcity of standardized intestinal models for infection biology that mimic the microarchitecture of the intestine. Hence, this study aimed to develop structured multicellular intestinal spheroids (SMIS) specifically tailored for studying molecular basis of infection by intestinal pathogens. Results We have successfully engineered human SMIS comprising four relevant cell types, featuring a fibroblast core enveloped by an outer monolayer of enterocytes and goblet cells along with monocytic cells. These SMIS effectively emulate the in vivo architecture of the intestinal mucosal surface and manifest differentiated morphological characteristics, including the presence of microvilli, within a mere two days of culture. Through analysis of various differentiation factors, we have illustrated that these spheroids attain heightened levels of differentiation compared to 2D monolayers. Moreover, SMIS serve as an optimized intestinal infection model, surpassing the capabilities of traditional 2D cultures, and exhibit a regulatory pattern of immunological markers similar to in vivo infections after Campylobacter jejuni infection. Notably, our protocol extends beyond human spheroids, demonstrating adaptability to other species such as mice and pigs. Conclusion Based on the rapid attainment of enhanced differentiation states, coupled with the emergence of functional brush border features, increased cellular complexity, and replication of the intestinal mucosal microarchitecture, which allows for exposure studies via the medium, we are confident that our innovative SMIS model surpasses conventional cell culture methods as a superior model. Moreover, it offers advantages over stem cell-derived organoids due to scalability and standardization capabilities of the protocol. By showcasing differentiated morphological attributes, our model provides an optimal platform for diverse applications. Furthermore, the investigated differences of several immunological factors compared to monotypic monolayers after Campylobacter jejuni infection underline the refinement of our spheroid model, which closely mimics important features of in vivo infections.

Published
2024
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24. MALDI imaging combined with two-photon microscopy reveals local differences in the heterogeneity of colorectal cancer

Author

Arora Bharti, Kulkarni Ajinkya, Markus M. Andrea, Ramos-Gomes Fernanda, Bohnenberger Hanibal, Ströbel Philipp, Alves Frauke, and Klein Oliver

Subjects
Medical technology, R855-855.5, Medical physics. Medical radiology. Nuclear medicine, R895-920
Abstract

Abstract Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, accentuated by its heterogeneity and complex tumour microenvironment (TME). The role of TME on tumour pathophysiology is pivotal, especially the influence of components of the extracellular matrix (ECM), such as collagen. We introduce a novel multimodal imaging strategy to unravel the complex spatial heterogeneity of CRC by integrating the imaging features from two-photon laser scanning microscopy (2PLSM) and histology with proteomics signatures from matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI MSI). Our study is the first to correlate the structural coherence of collagen fibres and the nuclei distribution profile of tumour tissue with the peptide signatures, offering insights into the proteomic landscape of CRC within regions of high nuclei distribution (HND), as well as chaotic and organised regions of collagen. We use this approach to distinguish the patient tissues originating from left-sided colorectal cancer (LSCC) and from right-sided colorectal cancer (RSCC). This discriminative signature highlights the role of high nuclei distribution and collagen architecture in tumour progression. Complementary m/z values of several proteins associated to components of ECM, such as plectin, vinculin, vimentin, and myosin, have shown differentially intensity distributions between LSCC and RSCC. Our findings demonstrate the potential of combining structural information with peptide features to identify molecular signatures in different tumour regions and retrieve new insights into CRC pathophysiology.

Published
2024
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25. Towards a Machine-Learned Poisson Solver for Low-Temperature Plasma Simulations in Complex Geometries

Author

Siffa, Ihda Chaerony, Becker, Markus M., Weltmann, Klaus-Dieter, and Trieschmann, Jan

Subjects
Physics - Computational Physics, Computer Science - Machine Learning, Mathematics - Numerical Analysis
Abstract

Poisson's equation plays an important role in modeling many physical systems. In electrostatic self-consistent low-temperature plasma (LTP) simulations, Poisson's equation is solved at each simulation time step, which can amount to a significant computational cost for the entire simulation. In this paper, we describe the development of a generic machine-learned Poisson solver specifically designed for the requirements of LTP simulations in complex 2D reactor geometries on structured Cartesian grids. Here, the reactor geometries can consist of inner electrodes and dielectric materials as often found in LTP simulations. The approach leverages a hybrid CNN-transformer network architecture in combination with a weighted multiterm loss function. We train the network using highly-randomized synthetic data to ensure the generalizability of the learned solver to unseen reactor geometries. The results demonstrate that the learned solver is able to produce quantitatively and qualitatively accurate solutions. Furthermore, it generalizes well on new reactor geometries such as reference geometries found in the literature. To increase the numerical accuracy of the solutions required in LTP simulations, we employ a conventional iterative solver to refine the raw predictions, especially to recover the high-frequency features not resolved by the initial prediction. With this, the proposed learned Poisson solver provides the required accuracy and is potentially faster than a pure GPU-based conventional iterative solver. This opens up new possibilities for developing a generic and high-performing learned Poisson solver for LTP systems in complex geometries.

Published
2023
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28. Multi-omics profiling of DNA methylation and gene expression alterations in human cocaine use disorder

Author

Zillich, Eric, Belschner, Hanna, Avetyan, Diana, Andrade-Brito, Diego, Martínez-Magaña, José Jaime, Frank, Josef, Mechawar, Naguib, Turecki, Gustavo, Cabana-Domínguez, Judit, Fernàndez-Castillo, Noèlia, Cormand, Bru, Montalvo-Ortiz, Janitza L., Nöthen, Markus M., Hansson, Anita C., Rietschel, Marcella, Spanagel, Rainer, Witt, Stephanie H., and Zillich, Lea

Published
2024
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32. Sex-specific molecular signature of mouse podocytes in homeostasis and in response to pharmacological challenge with rapamycin

Author

Al-Diab, Ola, Sünkel, Christin, Blanc, Eric, Catar, Rusan Ali, Ashraf, Muhammad Imtiaz, Zhao, Hongfan, Wang, Pinchao, Rinschen, Markus M., Fritsche-Guenther, Raphaela, Grahammer, Florian, Bachmann, Sebastian, Beule, Dieter, Kirwan, Jennifer A., Rajewsky, Nikolaus, Huber, Tobias B., Gürgen, Dennis, and Kusch, Angelika

Published
2024
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36. Exploring the genetics of lithium response in bipolar disorders

Author

Herrera-Rivero, Marisol, Adli, Mazda, Akiyama, Kazufumi, Akula, Nirmala, Amare, Azmeraw T., Ardau, Raffaella, Arias, Bárbara, Aubry, Jean-Michel, Backlund, Lena, Bellivier, Frank, Benabarre, Antonio, Bengesser, Susanne, Bhattacharjee, Abesh Kumar, Biernacka, Joanna M., Birner, Armin, Cearns, Micah, Cervantes, Pablo, Chen, Hsi-Chung, Chillotti, Caterina, Cichon, Sven, Clark, Scott R., Colom, Francesc, Cruceanu, Cristiana, Czerski, Piotr M., Dalkner, Nina, Degenhardt, Franziska, Del Zompo, Maria, DePaulo, J. Raymond, Etain, Bruno, Falkai, Peter, Ferensztajn-Rochowiak, Ewa, Forstner, Andreas J., Frank, Josef, Frisén, Louise, Frye, Mark A., Fullerton, Janice M., Gallo, Carla, Gard, Sébastien, Garnham, Julie S., Goes, Fernando S., Grigoroiu-Serbanescu, Maria, Grof, Paul, Hashimoto, Ryota, Hasler, Roland, Hauser, Joanna, Heilbronner, Urs, Herms, Stefan, Hoffmann, Per, Hou, Liping, Hsu, Yi-Hsiang, Jamain, Stephane, Jiménez, Esther, Kahn, Jean-Pierre, Kassem, Layla, Kato, Tadafumi, Kelsoe, John, Kittel-Schneider, Sarah, Kuo, Po-Hsiu, Kusumi, Ichiro, König, Barbara, Laje, Gonzalo, Landén, Mikael, Lavebratt, Catharina, Leboyer, Marion, Leckband, Susan G., Maj, Mario, Manchia, Mirko, Marie-Claire, Cynthia, Martinsson, Lina, McCarthy, Michael J., McElroy, Susan L., Millischer, Vincent, Mitjans, Marina, Mondimore, Francis M., Monteleone, Palmiero, Nievergelt, Caroline M., Novák, Tomas, Nöthen, Markus M., O’Donovan, Claire, Ozaki, Norio, Papiol, Sergi, Pfennig, Andrea, Pisanu, Claudia, Potash, James B., Reif, Andreas, Reininghaus, Eva, Richard-Lepouriel, Hélène, Roberts, Gloria, Rouleau, Guy A., Rybakowski, Janusz K., Schalling, Martin, Schofield, Peter R., Schubert, Klaus Oliver, Schulte, Eva C., Schweizer, Barbara W., Severino, Giovanni, Shekhtman, Tatyana, Shilling, Paul D., Shimoda, Katzutaka, Simhandl, Christian, Slaney, Claire M., Squassina, Alessio, Stamm, Thomas, Stopkova, Pavla, Streit, Fabian, Tekola-Ayele, Fasil, Thalamuthu, Anbupalam, Tortorella, Alfonso, Turecki, Gustavo, Veeh, Julia, Vieta, Eduard, Viswanath, Biju, Witt, Stephanie H., Zandi, Peter P., Alda, Martin, Bauer, Michael, McMahon, Francis J., Mitchell, Philip B., Rietschel, Marcella, Schulze, Thomas G., and Baune, Bernhard T.

Published
2024
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37. Factor analysis of lifetime psychopathology and its brain morphometric and genetic correlates in a transdiagnostic sample

Author

Krug, Axel, Stein, Frederike, David, Friederike S., Schmitt, Simon, Brosch, Katharina, Pfarr, Julia-Katharina, Ringwald, Kai G., Meller, Tina, Thomas-Odenthal, Florian, Meinert, Susanne, Thiel, Katharina, Winter, Alexandra, Waltemate, Lena, Lemke, Hannah, Grotegerd, Dominik, Opel, Nils, Repple, Jonathan, Hahn, Tim, Streit, Fabian, Witt, Stephanie H., Rietschel, Marcella, Andlauer, Till F. M., Nöthen, Markus M., Philipsen, Alexandra, Nenadić, Igor, Dannlowski, Udo, Kircher, Tilo, and Forstner, Andreas J.

Published
2024
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40. Octyl itaconate enhances VSVΔ51 oncolytic virotherapy by multitarget inhibition of antiviral and inflammatory pathways

Author

Kurmasheva, Naziia, Said, Aida, Wong, Boaz, Kinderman, Priscilla, Han, Xiaoying, Rahimic, Anna H. F., Kress, Alena, Carter-Timofte, Madalina E., Holm, Emilia, van der Horst, Demi, Kollmann, Christoph F., Liu, Zhenlong, Wang, Chen, Hoang, Huy-Dung, Kovalenko, Elina, Chrysopoulou, Maria, Twayana, Krishna Sundar, Ottosen, Rasmus N., Svenningsen, Esben B., Begnini, Fabio, Kiib, Anders E., Kromm, Florian E. H., Weiss, Hauke J., Di Carlo, Daniele, Muscolini, Michela, Higgins, Maureen, van der Heijden, Mirte, Bardoul, Angelina, Tong, Tong, Ozsvar, Attila, Hou, Wen-Hsien, Schack, Vivien R., Holm, Christian K., Zheng, Yunan, Ruzek, Melanie, Kalucka, Joanna, de la Vega, Laureano, Elgaher, Walid A. M., Korshoej, Anders R., Lin, Rongtuan, Hiscott, John, Poulsen, Thomas B., O’Neill, Luke A., Roy, Dominic G., Rinschen, Markus M., van Montfoort, Nadine, Diallo, Jean-Simon, Farin, Henner F., Alain, Tommy, and Olagnier, David

Published
2024
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42. Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung

Author

Dörner, Patrick J., Anandakumar, Harithaa, Röwekamp, Ivo, Fiocca Vernengo, Facundo, Millet Pascual-Leone, Belén, Krzanowski, Marta, Sellmaier, Josua, Brüning, Ulrike, Fritsche-Guenther, Raphaela, Pfannkuch, Lennart, Kurth, Florian, Milek, Miha, Igbokwe, Vanessa, Löber, Ulrike, Gutbier, Birgitt, Holstein, Markus, Heinz, Gitta Anne, Mashreghi, Mir-Farzin, Schulte, Leon N., Klatt, Ann-Brit, Caesar, Sandra, Wienhold, Sandra-Maria, Offermanns, Stefan, Mack, Matthias, Witzenrath, Martin, Jordan, Stefan, Beule, Dieter, Kirwan, Jennifer A., Forslund, Sofia K., Wilck, Nicola, Bartolomaeus, Hendrik, Heimesaat, Markus M., and Opitz, Bastian

Published
2024
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46. Lithium response in bipolar disorder is associated with focal adhesion and PI3K-Akt networks: a multi-omics replication study

Author

Ou, Anna H., Rosenthal, Sara B., Adli, Mazda, Akiyama, Kazufumi, Akula, Nirmala, Alda, Martin, Amare, Azmeraw T., Ardau, Raffaella, Arias, Bárbara, Aubry, Jean-Michel, Backlund, Lena, Bauer, Michael, Baune, Bernhard T., Bellivier, Frank, Benabarre, Antonio, Bengesser, Susanne, Bhattacharjee, Abesh Kumar, Biernacka, Joanna M., Cervantes, Pablo, Chen, Guo-Bo, Chen, Hsi-Chung, Chillotti, Caterina, Cichon, Sven, Clark, Scott R., Colom, Francesc, Cousins, David A., Cruceanu, Cristiana, Czerski, Piotr M., Dantas, Clarissa R., Dayer, Alexandre, Del Zompo, Maria, Degenhardt, Franziska, DePaulo, J. Raymond, Étain, Bruno, Falkai, Peter, Fellendorf, Frederike Tabea, Ferensztajn-Rochowiak, Ewa, Forstner, Andreas J., Frisén, Louise, Frye, Mark A., Fullerton, Janice M., Gard, Sébastien, Garnham, Julie S., Goes, Fernando S., Grigoroiu-Serbanescu, Maria, Grof, Paul, Gruber, Oliver, Hashimoto, Ryota, Hauser, Joanna, Heilbronner, Urs, Herms, Stefan, Hoffmann, Per, Hofmann, Andrea, Hou, Liping, Jamain, Stephane, Jiménez, Esther, Kahn, Jean-Pierre, Kassem, Layla, Kato, Tadafumi, Kittel-Schneider, Sarah, König, Barbara, Kuo, Po-Hsiu, Kusumi, Ichiro, Lackner, Nina, Laje, Gonzalo, Landén, Mikael, Lavebratt, Catharina, Leboyer, Marion, Leckband, Susan G., Jaramillo, Carlos A. López, MacQueen, Glenda, Maj, Mario, Manchia, Mirko, Marie-Claire, Cynthia, Martinsson, Lina, Mattheisen, Manuel, McCarthy, Michael J., McElroy, Susan L., McMahon, Francis J., Mitchell, Philip B., Mitjans, Marina, Mondimore, Francis M., Monteleone, Palmiero, Nievergelt, Caroline M., Nöthen, Markus M., Novák, Tomas, Ösby, Urban, Ozaki, Norio, Papiol, Sergi, Perlis, Roy H., Pisanu, Claudia, Potash, James B., Pfennig, Andrea, Reich-Erkelenz, Daniela, Reif, Andreas, Reininghaus, Eva Z., Rietschel, Marcella, Rouleau, Guy A., Rybakowski, Janusz K., Schalling, Martin, Schofield, Peter R., Schubert, K. Oliver, Schulze, Thomas G., Schweizer, Barbara W., Seemüller, Florian, Severino, Giovanni, Shekhtman, Tatyana, Shilling, Paul D., Shimoda, Kazutaka, Simhandl, Christian, Slaney, Claire M., Squassina, Alessio, Stamm, Thomas, Stopkova, Pavla, Tighe, Sarah K., Tortorella, Alfonso, Turecki, Gustavo, Vieta, Eduard, Volkert, Julia, Witt, Stephanie, Wray, Naomi R., Wright, Adam, Young, L. Trevor, Zandi, Peter P., and Kelsoe, John R.

Published
2024
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