Universität Stuttgart
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Item Open Access ROSIE : RObust Sparse ensemble for outlIEr detection and gene selection in cancer omics data(2022) Jensch, Antje; Lopes, Marta B.; Vinga, Susana; Radde, NicoleThe extraction of novel information from omics data is a challenging task, in particular, since the number of features (e.g. genes) often far exceeds the number of samples. In such a setting, conventional parameter estimation leads to ill-posed optimization problems, and regularization may be required. In addition, outliers can largely impact classification accuracy. Here we introduce ROSIE, an ensemble classification approach, which combines three sparse and robust classification methods for outlier detection and feature selection and further performs a bootstrap-based validity check. Outliers of ROSIE are determined by the rank product test using outlier rankings of all three methods, and important features are selected as features commonly selected by all methods. We apply ROSIE to RNA-Seq data from The Cancer Genome Atlas (TCGA) to classify observations into Triple-Negative Breast Cancer (TNBC) and non-TNBC tissue samples. The pre-processed dataset consists of 16,600 genes and more than 1,000 samples. We demonstrate that ROSIE selects important features and outliers in a robust way. Identified outliers are concordant with the distribution of the commonly selected genes by the three methods, and results are in line with other independent studies. Furthermore, we discuss the association of some of the selected genes with the TNBC subtype in other investigations. In summary, ROSIE constitutes a robust and sparse procedure to identify outliers and important genes through binary classification. Our approach is ad hoc applicable to other datasets, fulfilling the overall goal of simultaneously identifying outliers and candidate disease biomarkers to the targeted in therapy research and personalized medicine frameworks.Item Open Access Heat transport from atmosphere through the subsurface to drinking‐water supply pipes(2023) Nissler, Elisabeth; Scherrer, Samuel; Class, Holger; Müller, Tanja; Hermannspan, Mark; Osmancevic, Esad; Haslauer, ClausDrinking‐water quality in supply pipe networks can be negatively affected by high temperatures during hot summer months due to detrimental bacteria encountering ideal conditions for growth. Thus, water suppliers are interested in estimating the temperature in their distribution networks. We investigate both experimentally and by numerical simulation the heat and water transport from ground surface into the subsurface, (i.e., above drinking‐water pipes). We consider the meteorological forcing functions by a sophisticated approach to model the boundary conditions for the heat balance at the soil-atmosphere interface. From August to December 2020, soil temperatures and soil moisture were measured dependent on soil type, land‐use cover, and weather data at a pilot site, constructed specifically for this purpose at the University of Stuttgart with polyethylene and cast‐iron pipes installed under typical in situ conditions. We included this interface condition at the atmosphere-subsurface boundary into an integrated non‐isothermal, variably saturated (Richards') the numerical simulator DuMux 3. This allowed, after calibration, to match measured soil temperatures with ±2°C accuracy. The land‐use cover influenced the soil temperature in 1.5 m more than the soil material used for back‐filling the trench above the pipe.Item Open Access Alumina and zirconia-reinforced polyamide PA-12 composites for biomedical additive manufacturing(2021) Nakonieczny, Damian S.; Kern, Frank; Dufner, Lukas; Antonowicz, Magdalena; Matus, KrzysztofThis work aimed to prepare a composite with a polyamide (PA) matrix and surface-modified ZrO2 or Al2O3 to be used as ceramic fillers (CFs). Those composites contained 30 wt.% ceramic powder to 70 wt.% polymer. Possible applications for this type of composite include bioengineering applications especially in the fields of dental prosthetics and orthopaedics. The ceramic fillers were subjected to chemical surface modification with Piranha Solution and suspension in 10 M sodium hydroxide and Si3N4 to achieve the highest possible surface development and to introduce additional functional groups. This was to improve the bonding between the CFs and the polymer matrix. Both CFs were examined for particle size distribution (PSD), functional groups (FTIR), chemical composition (XPS), phase composition (XRD), and morphology and chemical composition (SEM/EDS). Filaments were created from the powders prepared in this way and were then used for 3D FDM printing. Samples were subjected to mechanical tests (tensility, hardness) and soaking tests in a high-pressure autoclave in artificial saliva for 14, 21, and 29 days.Item Open Access Designing covalent organic framework‐based light‐driven microswimmers toward therapeutic applications(2023) Sridhar, Varun; Yildiz, Erdost; Rodríguez‐Camargo, Andrés; Lyu, Xianglong; Yao, Liang; Wrede, Paul; Aghakhani, Amirreza; Akolpoglu, Birgul M.; Podjaski, Filip; Lotsch, Bettina V.; Sitti, MetinWhile micromachines with tailored functionalities enable therapeutic applications in biological environments, their controlled motion and targeted drug delivery in biological media require sophisticated designs for practical applications. Covalent organic frameworks (COFs), a new generation of crystalline and nanoporous polymers, offer new perspectives for light‐driven microswimmers in heterogeneous biological environments including intraocular fluids, thus setting the stage for biomedical applications such as retinal drug delivery. Two different types of COFs, uniformly spherical TABP‐PDA‐COF sub‐micrometer particles and texturally nanoporous, micrometer‐sized TpAzo‐COF particles are described and compared as light‐driven microrobots. They can be used as highly efficient visible‐light‐driven drug carriers in aqueous ionic and cellular media. Their absorption ranging down to red light enables phototaxis even in deeper and viscous biological media, while the organic nature of COFs ensures their biocompatibility. Their inherently porous structures with ≈2.6 and ≈3.4 nm pores, and large surface areas allow for targeted and efficient drug loading even for insoluble drugs, which can be released on demand. Additionally, indocyanine green (ICG) dye loading in the pores enables photoacoustic imaging, optical coherence tomography, and hyperthermia in operando conditions. This real‐time visualization of the drug‐loaded COF microswimmers enables unique insights into the action of photoactive porous drug carriers for therapeutic applications.Item Open Access Counterion effects on the mesomorphic and electrochemical properties of guanidinium salts(2024) Ebert, Max; Lange, Alyna; Müller, Michael; Wuckert, Eugen; Gießelmann, Frank; Klamroth, Tillmann; Zens, Anna; Taubert, Andreas; Laschat, SabineIonic liquid crystals (ILCs) combine the ion mobility of ionic liquids with the order and self-assembly of thermotropic mesophases. To understand the role of the anion in ILCs, wedge-shaped arylguanidinium salts with tetradecyloxy side chains were chosen as benchmark systems and their liquid crystalline self-assembly in the bulk phase as well as their electrochemical behavior in solution were studied depending on the anion. Differential scanning calorimetry (DSC), polarizing optical microscopy (POM) and X-ray diffraction (WAXS, SAXS) experiments revealed that for spherical anions, the phase width of the hexagonal columnar mesophase increased with the anion size, while for non-spherical anions, the trends were less clear cut. Depending on the anion, the ILCs showed different stability towards electrochemical oxidation and reduction with the most stable being the PF6 based compound. Cyclic voltammetry (CV) and density functional theory (DFT) calculations suggest a possible contribution of the guanidinium cation to the oxidation processes.Item Open Access Philosophy of action and Its relationship to interactive visualisation and Molière’s theatre(2023) Feige, Daniel M.; Weiskopf, Daniel; Dickhaut, KirstenItem Open Access Editorial - creative metacognition : the chief manager of accurate decisions(2023) Puente-Díaz, Rogelio; Cavazos-Arroyo, Judith; Brem, AlexanderItem Open Access Confirmation of siderazot, Fe3N1.33, the only terrestrial nitride mineral(2021) Bette, Sebastian; Theye, Thomas; Bernhardt, Heinz-Jürgen; Clark, William P.; Niewa, RainerSiderazot, the only terrestrial nitride mineral, was reported only once in 1876 to occur as coating on volcanic rocks in a fumarolic environment from Mt. Etna and, to date, has been neither confirmed nor structurally characterized. We have studied the holotype sample from the Natural History Museum, London, UK, originally collected by O. Silvestri in 1874, and present siderazot with epsilon-Fe3N-type crystal structure and composition of Fe3N1.33(7) according to crystal structure Rietveld refinements, in good agreement with electron microprobe analyses. Crystal structure data, chemical composition, and Raman and reflectance measurements are reported. Possible formation conditions are derived from composition and phase stability data according to synthetic samples.Item Open Access Highly active cooperative Lewis acid : ammonium salt catalyst for the enantioselective hydroboration of ketones(2021) Titze, Marvin; Heitkämper, Juliane; Junge, Thorsten; Kästner, Johannes; Peters, RenéEnantiopure secondary alcohols are fundamental high‐value synthetic building blocks. One of the most attractive ways to get access to this compound class is the catalytic hydroboration. We describe a new concept for this reaction type that allowed for exceptional catalytic turnover numbers (up to 15 400), which were increased by around 1.5-3 orders of magnitude compared to the most active catalysts previously reported. In our concept an aprotic ammonium halide moiety cooperates with an oxophilic Lewis acid within the same catalyst molecule. Control experiments reveal that both catalytic centers are essential for the observed activity. Kinetic, spectroscopic and computational studies show that the hydride transfer is rate limiting and proceeds via a concerted mechanism, in which hydride at Boron is continuously displaced by iodide, reminiscent to an SN2 reaction. The catalyst, which is accessible in high yields in few steps, was found to be stable during catalysis, readily recyclable and could be reused 10 times still efficiently working.Item Open Access Extremely narrow superconducting band with crystal spin 3/2h in LaH10(2023) Krüger, Ekkehard