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 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 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 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 Lernen und üben wir das Richtige? : Kritische Erfolgsfaktoren der Bewältigung des Massenanfalls von Verletzten : Ergebnisse einer FMEA und einer Analyse von MANV-bezogenen Curricula(2021) Drews, Patrick; Berger, Maximilian; Sautter, Johannes; Rohde, AnnikaDer Massenanfall von Verletzten (MANV) ist eine Ausnahmesituation für Rettungsdienst und andere Einsatzkräfte. Trotz niedriger Inzidenz müssen sich die Einsatzkräfte sowohl auf ärztlicher als auch auf nichtärztlicher Seite auf diesen Einsatzfall vorbereiten. In der vorliegenden Pilotstudie wurden anhand einer Fehlermöglichkeits- und -einflussanalyse (FMEA) die kritischen Einsatzfaktoren im MANV ermittelt und mit den Ausbildungscurricula verglichen. Die herangezogenen Curricula waren Notfallsanitäter:in, organisatorische:r Leiter:in, Konzept zur katastrophenmedizinischen Ausbildung im studentischen Unterricht an deutschen Hochschulen, Nationaler Kompetenz-basierter Lernzielkatalog Medizin (NKLM), Zusatz-Weiterbildung Notfallmedizin und Fortbildung zum:zur leitenden Notarzt:ärztin. Die Ergebnisse lassen vermuten, dass in der praktischen Ausbildung der MANV eine eher untergeordnete Rolle spielt. Weitere empirische Untersuchungen sind aus Sicht der Autoren notwendig.Item Open Access Touching data with PropellerHand(2022) Achberger, Alexander; Heyen, Frank; Vidackovic, Kresimir; Sedlmair, MichaelImmersive analytics often takes place in virtual environments which promise the users immersion. To fulfill this promise, sensory feedback, such as haptics, is an important component, which is however not well supported yet. Existing haptic devices are often expensive, stationary, or occupy the user’s hand, preventing them from grasping objects or using a controller. We propose PropellerHand, an ungrounded hand-mounted haptic device with two rotatable propellers, that allows exerting forces on the hand without obstructing hand use. PropellerHand is able to simulate feedback such as weight and torque by generating thrust up to 11 N in 2-DOF and a torque of 1.87 Nm in 2-DOF. Its design builds on our experience from quantitative and qualitative experiments with different form factors and parts. We evaluated our prototype through a qualitative user study in various VR scenarios that required participants to manipulate virtual objects in different ways, while changing between torques and directional forces. Results show that PropellerHand improves users’ immersion in virtual reality. Additionally, we conducted a second user study in the field of immersive visualization to investigate the potential benefits of PropellerHand there.Item Open Access Magnetic resonance imaging of water content and flow processes in natural soils by pulse sequences with ultrashort detection(2021) Haber-Pohlmeier, Sabina; Caterina, David; Blümich, Bernhard; Pohlmeier, AndreasMagnetic resonance imaging is a valuable tool for three-dimensional mapping of soil water processes due to its sensitivity to the substance of interest: water. Since conventional gradient- or spin-echo based pulse sequences do not detect rapidly relaxing fractions of water in natural porous media with transverse relaxation times in the millisecond range, pulse sequences with ultrafast detection open a way out. In this work, we compare a spin-echo multislice pulse sequence with ultrashort (UTE) and zero-TE (ZTE) sequences for their suitability to map water content and its changes in 3D in natural soil materials. Longitudinal and transverse relaxation times were found in the ranges around 80 ms and 1 to 50 ms, respectively, so that the spin echo sequence misses larger fractions of water. In contrast, ZTE and UTE could detect all water, if the excitation and detection bandwidths were set sufficiently broad. More precisely, with ZTE we could map water contents down to 0.1 cm3/cm3. Finally, we employed ZTE to monitor the development of film flow in a natural soil core with high temporal resolution. This opens the route for further quantitative imaging of soil water processes.Item Open Access Stereoretentive regio‐ und enantioselektive Allylierung von Isoxazolinonen per planar chiralem Palladacyclus‐Katalysator(2022) Yu, Xin; Hu, Lingfei; Frey, Wolfgang; Lu, Gang; Peters, RenéDie katalytische allylische Substitution ist eines der wichtigsten Werkzeuge in der asymmetrischen Synthese zur enantioselektiven Bildung von C-C-Bindungen. Während in vorigen Arbeiten eine hohe Effizienz in Bezug auf Enantio- und Regiokontrolle unter Verwendung verschiedener Katalysatortypen erreicht wurde, besteht eine starke allgemeine Einschränkung in einer sehr ausgeprägten Präferenz für die Bildung von allylischen Substitutionsprodukten mit (E)-konfigurierten C=C-Doppelbindungen. Hier berichten wir, dass mit einem planar-chiralen Palladacyclus-Katalysator unter Verwendung von Isoxazolinonen und Allylimidaten als Substrate ein diastereospezifisches Reaktionsergebnis erzielt wird, wodurch die C=C-Doppelbindungsgeometrie der Allylsubstrate in den hoch enantiomerenangereicherten Produkten beibehalten wird. DFT-Rechnungen zeigen, dass die Reaktionen über einen SN2-Mechanismus und nicht über π-Allyl-Pd-Komplexe ablaufen. Entscheidend für die hohe Kontrolle ist die Stabilisierung des allylischen Fragments im SN2-Übergangszustand durch π-Wechselwirkungen mit den Phenylsubstituenten des Pentaphenylferrocen-Katalysatorkerns.Item Open Access Unpacking stakeholder perceptions of the benefits and challenges associated with urban greenspaces in Sub-Saharan Africa(2021) Guenat, Solène; Porras Lopez, Gabriel; Mkwambisi, David D; Dallimer, MartinUrban greenspaces underpin ecosystem service provision in cities and are therefore indispensable for human well-being. Nevertheless, they are increasingly disappearing from cities in Sub-Saharan Africa. Understanding how the stakeholders influencing urban greenspace management perceive the benefits provided by urban greenspaces and the challenges to its conservation and management is critical for reversing this trend. Using Malawi’s capital city, Lilongwe, as a case study, we conducted 44 semi-structured interviews to explore the profiles and perceptions of stakeholders who currently hold influence over greenspace planning, conservation and management. Stakeholders with influence over urban greenspace management described the main focus of their organisation as relating to urban planning, natural resources protection and management, development work, or the hospitality business sector. Critically, only a third of all stakeholders focused on natural resources protection and management. Stakeholders had nuanced and varied appreciations of the benefits that greenspaces provide. Regulation and maintenance ecosystem services, as well as cultural services were frequently mentioned. However, provisioning services were mostly mentioned by those in development work. Stakeholders also identified an additional suite of societal benefits that do not directly map onto ecosystem service frameworks, such as the generation of financial income and the provision of employment opportunities. Challenges identified as hampering the planning, conservation and management of greenspaces included inappropriate urbanisation, lack of coordination and participation, and population growth. Lack of coordination was however not widely acknowledged among those focusing on natural resources protection, who conversely identified population growth more often than any other groups. Highlighting how stakeholders with varying priorities perceive ecosystem services a first step towards improving greenspaces management both for their better acceptation and for improving their potential for biodiversity conservation. Specifically, we bring attention to need for stakeholders working with natural resources protection to recognise more the need for collaborations and engagement. Additional research is also necessary to understand how those different perspectives might be integrated into ongoing processes and procedures to manage greenspaces in Sub-Saharan Africa.Item Open Access Finite-temperature interplay of structural stability, chemical complexity, and elastic properties of bcc multicomponent alloys from ab initio trained machine-learning potentials(2021) Gubaev, Konstantin; Ikeda, Yuji; Tasnádi, Ferenc; Neugebauer, Jörg; Shapeev, Alexander V.; Grabowski, Blazej; Körmann, FritzAn active learning approach to train machine-learning interatomic potentials (moment tensor potentials) for multicomponent alloys to ab initio data is presented. Employing this approach, the disordered body-centered cubic (bcc) TiZrHfTax system with varying Ta concentration is investigated via molecular dynamics simulations. Our results show a strong interplay between elastic properties and the structural ω phase stability, strongly affecting the mechanical properties. Based on these insights we systematically screen composition space for regimes where elastic constants show little or no temperature dependence (elinvar effect).