Visualization and validation of (Q)SAR models

Analyzing and modeling relationships between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects in chemical datasets is a challenging task for scientific researchers in the field of cheminformatics. Therefore, (Q)SAR model validation is essential to ensure future model predictivity on unseen compounds. Proper validation is also one of the requirements of regulatory authorities in order to approve its use in real-world scenarios as an alternative testing method. However, at the same time, the question of how to validate a (Q)SAR model is still under discussion. In this work, we empirically compare a k-fold cross-validation with external test set validation. The introduced workflow allows to apply the built and validated models to large amounts of unseen data, and to compare the performance of the different validation approaches. Our experimental results indicate that cross-validation produces (Q)SAR models with higher predictivity than external test set validation and reduces the variance of the results. Statistical validation is important to evaluate the performance of (Q)SAR models, but does not support the user in better understanding the properties of the model or the underlying correlations. We present the 3D molecular viewer CheS-Mapper (Chemical Space Mapper) that arranges compounds in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kinds of features, like structural fragments as well as quantitative chemical descriptors. Comprehensive functionalities including clustering, alignment of compounds according to their 3D structure, and feature highlighting aid the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. Even though visualization tools for analyzing (Q)SAR information in small molecule datasets exist, integrated visualization methods that allows for the investigation of model validation results are still lacking. We propose visual validation, as an approach for the graphical inspection of (Q)SAR model validation results. New functionalities in CheS-Mapper 2.0 facilitate the analysis of (Q)SAR information and allow the visual validation of (Q)SAR models. The tool enables the comparison of model predictions to the actual activity in feature space. Our approach reveals if the endpoint is modeled too specific or too generic and highlights common properties of misclassified compounds. Moreover, the researcher can use CheS-Mapper to inspect how the (Q)SAR model predicts activity cliffs. The CheS-Mapper software is freely available at http://ches-mapper.org.

Hadronic correlation functions with quark-disconnected contributions in lattice QCD

One of the fundamental interactions in the Standard Model of particle physicsrnis the strong force, which can be formulated as a non-abelian gauge theoryrncalled Quantum Chromodynamics (QCD). rnIn the low-energy regime, where the QCD coupling becomes strong and quarksrnand gluons are confined to hadrons, a perturbativernexpansion in the coupling constant is not possible.rnHowever, the introduction of a four-dimensional Euclidean space-timernlattice allows for an textit{ab initio} treatment of QCD and provides arnpowerful tool to study the low-energy dynamics of hadrons.rnSome hadronic matrix elements of interest receive contributionsrnfrom diagrams including quark-disconnected loops, i.e. disconnected quarkrnlines from one lattice point back to the same point. The calculation of suchrnquark loops is computationally very demanding, because it requires knowledge ofrnthe all-to-all propagator. In this thesis we use stochastic sources and arnhopping parameter expansion to estimate such propagators.rnWe apply this technique to study two problems which relay crucially on therncalculation of quark-disconnected diagrams, namely the scalar form factor ofrnthe pion and the hadronic vacuum polarization contribution to the anomalousrnmagnet moment of the muon.rnThe scalar form factor of the pion describes the coupling of a charged pion torna scalar particle. We calculate the connected and the disconnected contributionrnto the scalar form factor for three different momentum transfers. The scalarrnradius of the pion is extracted from the momentum dependence of the form factor.rnThe use ofrnseveral different pion masses and lattice spacings allows for an extrapolationrnto the physical point. The chiral extrapolation is done using chiralrnperturbation theory ($chi$PT). We find that our pion mass dependence of thernscalar radius is consistent with $chi$PT at next-to-leading order.rnAdditionally, we are able to extract the low energy constant $ell_4$ from thernextrapolation, and ourrnresult is in agreement with results from other lattice determinations.rnFurthermore, our result for the scalar pion radius at the physical point isrnconsistent with a value that was extracted from $pipi$-scattering data. rnThe hadronic vacuum polarization (HVP) is the leading-order hadronicrncontribution to the anomalous magnetic moment $a_mu$ of the muon. The HVP canrnbe estimated from the correlation of two vector currents in the time-momentumrnrepresentation. We explicitly calculate the corresponding disconnectedrncontribution to the vector correlator. We find that the disconnectedrncontribution is consistent with zero within its statistical errors. This resultrncan be converted into an upper limit for the maximum contribution of therndisconnected diagram to $a_mu$ by using the expected time-dependence of therncorrelator and comparing it to the corresponding connected contribution. Wernfind the disconnected contribution to be smaller than $approx5%$ of thernconnected one. This value can be used as an estimate for a systematic errorrnthat arises from neglecting the disconnected contribution.rn

Visuell-mediale Landschaftskonstruktionen als Bild-Raum-Diskurse

Durch die massenmediale Zunahme von statischen und bewegten Bilder im Laufe des letzten Jahrhunderts vollzieht sich unsere lebensweltliche Wirklichkeitskonstruktion zu Beginn des 21. Jahrhunderts zunehmend über Visualisierungen, die mit den neuen Formen der Digitalisierung noch an Dynamik zunehmen werden. Mit diesen omnipräsenten visuell-medialen Repräsentationen werden meist räumliche Vorstellungen transportiert, denn Räume werden vor allem über Bilder konstruiert. Diese Bildräume zirkulieren dabei nicht als singuläre Bedeutungszuschreibungen, sondern sind in sprachliche und bildliche Diskurse eingebettet. Visuell-mediale Bild-Raum-Diskurse besitzen zunehmend die Fähigkeit, unser Wissen über und unsere Wahrnehmung von Räumen zu kanalisieren und auf stereotype Raumstrukturen zu reduzieren. Dabei verfestigt sich eine normative Ordnung von bestimmten machtvollen Bildräumen, die nicht genügend kritisch hinterfragt werden. Deshalb ist es für die Geographie von entscheidender Wichtigkeit, mediale Raumkonstruktio- nen, ihre Einbettung in diskursive Bildarchive und ihre essentialistische und handlungspraktische gesellschaftliche Wirkung zu verstehen.rnLandschaften können vor diesem Hintergrund als visuell-medial transportierte Bild-Raum-Diskurse konzeptionalisiert werden, deren gesellschaftliche Wirkmächtigkeit mit Hilfe einer visuell ausgerichteten Diskursanalyse hinterfragt werden sollte. Auf Grundlage einer zeichentheoretischen Ikonologie wurde eine Methodik entwickelt, die visuell ausgerichtete Schrift-Bild-Räume angemessen analysieren kann. Am Beispiel der Inszenierung des Mittelrheintals, wurde, neben einer diachronischen Strukturanalyse der diskursrelevanten Medien (Belletristik, Malerei, Postkarten, Druckgrafiken und Fotografien), eine Feinanalyse der fotografischen „Rheinlandschaften“ von August Sander der 1930er Jahre durchgeführt. Als Ergebnis zeigte sich, dass der Landschaftsdiskurs über das Mittelrheintal immer noch durch die gegenseitige Durchdringung der romantischen Literatur und Malerei in der ersten Hälfte des 19. Jahrhunderts und die historischen Fotografien in den ersten Jahrzehnten des 20. Jahrhunderts bestimmt ist, nicht zuletzt forciert durch die Ernennung zum UNESCO-Welterbe 2002. Der stark visuell ausgerichtete Landschaftsdiskurs trägt somit zum einen positiv konnotierte, romantisch-pittoreske Züge, die die Einheit von Mensch und Natur symbolisieren, zum anderen historisch-konservatorische Züge, die eine Mythifizierung zu einer gewachsenen, authentischen Kulturlandschaft evozieren.

Trpv6 mediates intestinal calcium absorption during calcium restriction and contributes to bone homeostasis

Energy-dependent intestinal calcium absorption is important for the maintenance of calcium and bone homeostasis, especially when dietary calcium supply is restricted. The active form of vitamin D, 1,25-dihydroxyvitamin D(3) [1,25(OH)(2)D(3)], is a crucial regulator of this process and increases the expression of the transient receptor potential vanilloid 6 (Trpv6) calcium channel that mediates calcium transfer across the intestinal apical membrane. Genetic inactivation of Trpv6 in mice (Trpv6(-/-)) showed, however, that TRPV6 is redundant for intestinal calcium absorption when dietary calcium content is normal/high and passive diffusion likely contributes to maintain normal serum calcium levels. On the other hand, Trpv6 inactivation impaired the increase in intestinal calcium transport following calcium restriction, however without resulting in hypocalcemia. A possible explanation is that normocalcemia is maintained at the expense of bone homeostasis, a hypothesis investigated in this study. In this study, we thoroughly analyzed the bone phenotype of Trpv6(-/-) mice receiving a normal (approximately 1%) or low (approximately 0.02%) calcium diet from weaning onwards using micro-computed tomography, histomorphometry and serum parameters. When dietary supply of calcium is normal, Trpv6 inactivation did not affect growth plate morphology, bone mass and remodeling parameters in young adult or aging mice. Restricting dietary calcium had no effect on serum calcium levels and resulted in a comparable reduction in bone mass accrual in Trpv6(+/+) and Trpv6(-/-) mice (-35% and 45% respectively). This decrease in bone mass was associated with a similar increase in bone resorption, whereas serum osteocalcin levels and the amount of unmineralized bone matrix were only significantly increased in Trpv6(-/-) mice. Taken together, our findings indicate that TRPV6 contributes to intestinal calcium transport when dietary calcium supply is limited and in this condition indirectly regulates bone formation and/or mineralization.

Körperliche Aktivität und Gesamtsterblichkeit: neue Metaanalyse zur Dosis-Wirkungs-Beziehung

Die Dosis-Wirkungs-Beziehung zwischen der körperlichen Aktivität und der Gesamtsterblichkeit ist nur unzureichend untersucht. Eine neue Metaanalyse von 80 Kohortenstudien mit über 1,3 Millionen Studienteilnehmern fand, dass die Mindestempfehlung der Weltgesundheitsorganisation zur körperlichen Aktivität das Gesamtsterberisiko in der erwachsenen Bevölkerung um 10-11% senkt. Bewegung und Sport mit höherer Intensität sind wirksamer als moderat intensive Alltagsaktivitäten und für Frauen ist der Nutzen grösser als für Männer.