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 Precision 3D‐printed cell scaffolds mimicking native tissue composition and mechanics(2020) Erben, Amelie; Hörning, Marcel; Hartmann, Bastian; Becke, Tanja; Eisler, Stephan A.; Southan, Alexander; Cranz, Séverine; Hayden, Oliver; Kneidinger, Nikolaus; Königshoff, Melanie; Lindner, Michael; Tovar, Günter E. M.; Burgstaller, Gerald; Clausen‐Schaumann, Hauke; Sudhop, Stefanie; Heymann, MichaelCellular dynamics are modeled by the 3D architecture and mechanics of the extracellular matrix (ECM) and vice versa. These bidirectional cell‐ECM interactions are the basis for all vital tissues, many of which have been investigated in 2D environments over the last decades. Experimental approaches to mimic in vivo cell niches in 3D with the highest biological conformity and resolution can enable new insights into these cell‐ECM interactions including proliferation, differentiation, migration, and invasion assays. Here, two‐photon stereolithography is adopted to print up to mm‐sized high‐precision 3D cell scaffolds at micrometer resolution with defined mechanical properties from protein‐based resins, such as bovine serum albumin or gelatin methacryloyl. By modifying the manufacturing process including two‐pass printing or post‐print crosslinking, high precision scaffolds with varying Young's moduli ranging from 7‐300 kPa are printed and quantified through atomic force microscopy. The impact of varying scaffold topographies on the dynamics of colonizing cells is observed using mouse myoblast cells and a 3D‐lung microtissue replica colonized with primary human lung fibroblast. This approach will allow for a systematic investigation of single‐cell and tissue dynamics in response to defined mechanical and bio‐molecular cues and is ultimately scalable to full organs.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 Batch studies of phosphonate and phosphate adsorption on granular ferric hydroxide (GFH) with membrane concentrate and its synthetic replicas(2020) Reinhardt, Tobias; Veizaga Campero, Adriana Noelia; Minke, Ralf; Schönberger, Harald; Rott, EduardPhosphonates are widely used as antiscalants for softening processes in drinking water treatment. To prevent eutrophication and accumulation in the sediment, it is desirable to remove them from the membrane concentrate before they are discharged into receiving water bodies. This study describes batch experiments with synthetic solutions and real membrane concentrate, both in the presence of and absence of granular ferric hydroxide (GFH), to better understand the influence of ions on phosphonate and phosphate adsorption. To this end, experiments were conducted with six different phosphonates, using different molar Ca:phosphonate ratios. The calcium already contained in the GFH plays an essential role in the elimination process, as it can be re-dissolved, and, therefore, increase the molar Ca:phosphonate ratio. (Hydrogen-)carbonate ions had a competitive effect on the adsorption of phosphonates and phosphate, whereas the influence of sulfate and nitrate ions was negligible. Up to pH 8, the presence of CaII had a positive effect on adsorption, probably due to the formation of ternary complexes. At pH > 8, increased removal was observed, with either direct precipitation of Ca:phosphonate complexes or the presence of inorganic precipitates of calcium, magnesium, and phosphate serving as adsorbents for the phosphorus compounds. In addition, the presence of (hydrogen-)carbonate ions resulted in precipitation of CaCO3 and/or dolomite, which also acted as adsorbents for the phosphorus compounds.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 Unknown 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.