1,084 results on '"Waldmann, P."'
Search Results
2. Knobs and dials of retrieving JWST transmission spectra. I. The importance of p-T profile complexity
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Schleich, Simon, Saikia, Sudeshna Boro, Changeat, Quentin, Güdel, Manuel, Voigt, Aiko, and Waldmann, Ingo
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
We investigate the impact of using multipoint p-T profiles of varying complexity on the retrieval of synthetically generated hot Jupiter transmission spectra modelled after state-of-the-art observations of the hot Jupiter WASP-39~b with JWST. We perform homogenised atmospheric retrievals with the TauREx retrieval framework on a sample of synthetically generated transmission spectra, accounting for varying cases of underlying p-T profiles, cloud-top pressures, and expected noise levels. These retrievals are performed using a fixed-pressure multipoint p-T prescription with increasing complexity, ranging from isothermal to an eleven-point profile. We evaluate the performance of the retrievals based on the Bayesian model evidence, and the accuracy of the retrievals compared to the known input parameters. We find that performing atmospheric retrievals using an isothermal prescription for the pressure-temperature profile consistently results in wrongly retrieved atmospheric parameters when compared to the known input parameters. For an underlying p-T profile with a fully positive lapse rate, we find that a two-point profile is sufficient to retrieve the known atmospheric parameters, while under the presence of an atmospheric temperature inversion, we find that a more complex profile is necessary. Our investigation shows that, for a data quality scenario mirroring state-of-the-art observations of a hot Jupiter with JWST, an isothermal p-T prescription is insufficient to correctly retrieve the known atmospheric parameters. We find a model complexity preference dependent on the underlying pressure-temperature structure, but argue that a p-T prescription on the complexity level of a four-point profile should be preferred. This represents the overlap between the lowest number of free parameters and highest model preference in the cases investigated in this work., Comment: 16 pages, 14 figures, accepted for publication in A&A
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- 2024
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3. Operational range bounding of spectroscopy models with anomaly detection
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Simões, Luís F., Casale, Pierluigi, Felismino, Marília, Yip, Kai Hou, Waldmann, Ingo P., Tinetti, Giovanna, and Lueftinger, Theresa
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Computer Science - Machine Learning ,Astrophysics - Instrumentation and Methods for Astrophysics ,I.2.6 ,I.5.1 ,I.6.4 ,J.2 - Abstract
Safe operation of machine learning models requires architectures that explicitly delimit their operational ranges. We evaluate the ability of anomaly detection algorithms to provide indicators correlated with degraded model performance. By placing acceptance thresholds over such indicators, hard boundaries are formed that define the model's coverage. As a use case, we consider the extraction of exoplanetary spectra from transit light curves, specifically within the context of ESA's upcoming Ariel mission. Isolation Forests are shown to effectively identify contexts where prediction models are likely to fail. Coverage/error trade-offs are evaluated under conditions of data and concept drift. The best performance is seen when Isolation Forests model projections of the prediction model's explainability SHAP values., Comment: To appear in "Proceedings of SPAICE 2024: 1st ESA/IAA conference on AI in and for Space". Conference page at https://spaice.esa.int/
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- 2024
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4. The effect of spectroscopic binning on atmospheric retrievals
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Davey, Jack J., Yip, Kai Hou, Al-Refaie, Ahmed F., and Waldmann, Ingo P.
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
With the James Webb Space Telescope (JWST) offering higher resolution data in space-based transmission spectroscopy, understanding the capabilities of our current atmospheric retrieval pipelines is essential. These new data cover wider wavelength ranges and at much higher spectral resolution than previous instruments have been able to offer. Therefore, it is often appealing to bin spectra to fewer points, better constrained in their transit depth, before using them as inputs for atmospheric retrievals. However, little quantitative analysis of the trade-off between spectral resolution and signal-to-noise ratio has been conducted thus far. As such, we produce a simulation replicating the observations of WASP-39b by the NIRSpec PRISM instrument on board JWST and assess the accuracy and consistency of retrievals while varying resolution and the average photometric error. While this probes a specific case we also plot `binning paths' in the resulting sensitivity maps to demonstrate the best attainable atmospheric parameter estimations starting from the position of the real JWST Early Release Science observation. We repeat this analysis on three different simulation setups where each includes an opaque cloud layer at a different height in the atmosphere. We find that a much greater resolution is needed in the case of a high cloud deck since features are already heavily muted by the presence of the clouds. In the other two cases, there are large `safe zones' in the parameter space. If these maps can be generalised, binning paths could inform future observations on how to achieve the most accurate retrieval results., Comment: Submitted to Monthly Notices of the Royal Astronomical Society, 25 pages, 27 figures
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- 2024
5. Enhancing 3D Planetary Atmosphere Simulations with a Surrogate Radiative Transfer Model
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Tahseen, Tara P. A., Mendonça, João M., Yip, Kai Hou, and Waldmann, Ingo P.
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics ,Physics - Atmospheric and Oceanic Physics - Abstract
This work introduces an approach to enhancing the computational efficiency of 3D atmospheric simulations by integrating a machine-learned surrogate model into the OASIS global circulation model (GCM). Traditional GCMs, which are based on repeatedly numerically integrating physical equations governing atmospheric processes across a series of time-steps, are time-intensive, leading to compromises in spatial and temporal resolution of simulations. This research improves upon this limitation, enabling higher resolution simulations within practical timeframes. Speeding up 3D simulations holds significant implications in multiple domains. Firstly, it facilitates the integration of 3D models into exoplanet inference pipelines, allowing for robust characterisation of exoplanets from a previously unseen wealth of data anticipated from JWST and post-JWST instruments. Secondly, acceleration of 3D models will enable higher resolution atmospheric simulations of Earth and Solar System planets, enabling more detailed insights into their atmospheric physics and chemistry. Our method replaces the radiative transfer module in OASIS with a recurrent neural network-based model trained on simulation inputs and outputs. Radiative transfer is typically one of the slowest components of a GCM, thus providing the largest scope for overall model speed-up. The surrogate model was trained and tested on the specific test case of the Venusian atmosphere, to benchmark the utility of this approach in the case of non-terrestrial atmospheres. This approach yields promising results, with the surrogate-integrated GCM demonstrating above 99.0% accuracy and 147 factor GPU speed-up of the entire simulation compared to using the matched original GCM under Venus-like conditions., Comment: 20 pages, 14 figures
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- 2024
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6. On the (In-)Completeness of Destructive Equality Resolution in the Superposition Calculus
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Waldmann, Uwe
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Computer Science - Logic in Computer Science ,F.4.1 - Abstract
Bachmair's and Ganzinger's abstract redundancy concept for the Superposition Calculus justifies almost all operations that are used in superposition provers to delete or simplify clauses, and thus to keep the clause set manageable. Typical examples are tautology deletion, subsumption deletion, and demodulation, and with a more refined definition of redundancy joinability and connectedness can be covered as well. The notable exception is Destructive Equality Resolution, that is, the replacement of a clause $x \not\approx t \lor C$ with $x \notin \mathrm{vars}(t)$ by $C\{x \mapsto t\}$. This operation is implemented in state-of-the-art provers, and it is clearly useful in practice, but little is known about how it affects refutational completeness. We demonstrate on the one hand that the naive addition of Destructive Equality Resolution to the standard abstract redundancy concept renders the calculus refutationally incomplete. On the other hand, we present several restricted variants of the Superposition Calculus that are refutationally complete even with Destructive Equality Resolution., Comment: 22 pages; shortened version to appear in Proc. IJCAR 2024, Springer
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- 2024
7. 3D-MuPPET: 3D Multi-Pigeon Pose Estimation and Tracking
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Waldmann, Urs, Chan, Alex Hoi Hang, Naik, Hemal, Nagy, Máté, Couzin, Iain D., Deussen, Oliver, Goldluecke, Bastian, and Kano, Fumihiro
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- 2024
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8. Is the atmosphere of the ultra-hot Jupiter WASP-121b variable?
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Changeat, Quentin, Skinner, Jack W., Cho, James Y-K., Nättilä, Joonas, Waldmann, Ingo P., Al-Refaie, Ahmed F., Dyrek, Achrène, Edwards, Billy, Mikal-Evans, Thomas, Joshua, Max, Morello, Giuseppe, Skaf, Nour, Tsiaras, Angelos, Venot, Olivia, and Yip, Kai Hou
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Astrophysics - Earth and Planetary Astrophysics - Abstract
We present a comprehensive analysis of the Hubble Space Telescope observations of the atmosphere of WASP-121 b, a ultra-hot Jupiter. After reducing the transit, eclipse, and phase-curve observations with a uniform methodology and addressing the biases from instrument systematics, sophisticated atmospheric retrievals are used to extract robust constraints on the thermal structure, chemistry, and cloud properties of the atmosphere. Our analysis shows that the observations are consistent with a strong thermal inversion beginning at ~0.1 bar on the dayside, solar to subsolar metallicity Z (i.e., -0.77 < log(Z) < 0.05), and super-solar C/O ratio (i.e., 0.59 < C/O < 0.87). More importantly, utilizing the high signal-to-noise ratio and repeated observations of the planet, we identify the following unambiguous time-varying signals in the data: i) a shift of the putative hotspot offset between the two phase-curves and ii) varying spectral signatures in the transits and eclipses. By simulating the global dynamics of WASP-121 b atmosphere at high-resolution, we show that the identified signals are consistent with quasi-periodic weather patterns, hence atmospheric variability, with signatures at the level probed by the observations (~5% to ~10%) that change on a timescale of ~5 planet days; in the simulations, the weather patterns arise from the formation and movement of storms and fronts, causing hot (as well as cold) patches of atmosphere to deform, separate, and mix in time., Comment: Accepted for publication in ApJS. 43 pages, 31 figures, 2 animations (available online at the journal)
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- 2024
9. Hydrogen storage and geo-methanation in a depleted underground hydrocarbon reservoir
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Hellerschmied, Cathrine, Schritter, Johanna, Waldmann, Niels, Zaduryan, Artur B, Rachbauer, Lydia, Scherr, Kerstin E, Andiappan, Anitha, Bauer, Stephan, Pichler, Markus, and Loibner, Andreas P
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Engineering ,Electrical Engineering ,Mechanical Engineering ,Affordable and Clean Energy ,Electrical and Electronic Engineering ,Environmental Engineering ,Electrical engineering ,Mechanical engineering - Abstract
Coupling of power-to-gas processes with underground gas storage could effectively allow surplus electricity to be stored for later use. Depleted hydrocarbon reservoirs could be used as stores, but practical experience of hydrogen storage in such sites is limited. Here we present data from a field trial that stored 119,353 m3 of hydrogen admixed to natural gas in a depleted hydrocarbon reservoir. After 285 days, hydrogen recovery was 84.3%, indicating the process’s technical feasibility. Additionally, we report that microbes mediated hydrogen conversion to methane. In laboratory experiments studying mesocosms that mimic real reservoirs, hydrogen and carbon dioxide were converted to methane (0.26 mmol l−1 h−1 evolution rate) reproducibly over 14 cycles in 357 days. This rate theoretically allows 114,648 m3 of methane per year to be produced in the test reservoir (equivalent to ~1.08 GWh). Our research demonstrates the efficiency of hydrogen storage and the importance of geo-methanation in depleted hydrocarbon reservoirs.
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- 2024
10. Tracing the Longitudinal Role of Orthographic Knowledge in Spelling Development from Primary to Upper-Secondary School
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Jakob Åsberg Johnels, Christian Waldmann, and Maria Levlin
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Background: Phonological processing skills have been found to contribute to spelling development across different orthographies; however, less is known about the role of orthographic knowledge. This longitudinal study explores the contribution of phonological and orthographic knowledge to spelling development in a semi-transparent orthography (Swedish) across a period of 10 years. Methods: A group of Swedish speaking children were assessed on phonological recoding (phonological choice-task), orthographic knowledge (choice-task) and spelling (dictation task) in primary school (grade 2, age 8, total N = 99), secondary school (grade 8, age 14, N = 99) and again in upper secondary school (year 2, age 17, N = 79). Furthermore, spelling in a natural writing assignment was collected in upper secondary school. Spelling scores from grade 8 (dictation) and year 2 in upper secondary school (dictation and text) were included as dependent variables in three sets of hierarchical regression analyses. In the first step spelling performance in grade 2 was included to control for the autoregressive effect. In the second step, orthographic knowledge and phonological recoding from grade 2 were entered into the model in order to test for the longitudinal prediction. Results: Test scores within and across ages were significantly correlated in bivariate analysis. Regression analysis revealed that orthographic knowledge in grade 2 was a unique longitudinal predictor of spelling performance across time-points (secondary and upper secondary school) and assessment formats (dictation and text), beyond the contribution of the control variables. Conclusions: This study confirms the role of early orthographic knowledge in Swedish spelling development throughout the school years assessed in standardized dictation tasks as well as in naturalistic writing assignments.
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- 2024
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11. Factsheet: Epidemiologie von Krebserkrankungen der Vulva und Vagina in Deutschland
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Buttmann-Schweiger, Nina, Waldmann, Annika, Sówka, Sarah, and Kraywinkel, Klaus
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- 2024
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12. Sediment-redox dynamics in an oligotrophic deep-water lake in Tierra del Fuego: insights from Fe isotopes
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Ordoñez Rendón, Luis Gabriel, Neugebauer, Ina, Thomas, Camille, Chiaradia, Massimo, Waldmann, Nicolas, and Ariztegui, Daniel
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- 2024
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13. Leadless pacemaker implantation following tricuspid interventions: multicenter collaboration of feasibility and safety
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Gul, Enes Elvin, Baudinaud, Pierre, Waldmann, Victor, Sabbag, Avi, Jubeh, Yousef, Clementy, Nicholas, Bisson, Arnaud, Ollitrault, Pierre, Conti, Sergio, Carabelli, Adrian, and Dogan, Zeki
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- 2024
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14. Live-Ortung von Beschäftigten in der agilen Personaleinsatzplanung: Umsetzung des Datenschutzes in der Intralogistik
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Johannhörster, Volker, Kohn, Matthias, Kunz, Thomas, Schleper, Janine, and Waldmann, Ulrich
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- 2024
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15. Psychische Gesundheit am Arbeitsplatz – Welche Rolle spielen sozioökonomische, geschlechterspezifische und migrationsbedingte Ungleichheiten?
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Herold, Regina, Feißt, Manuel, Morawa, Eva, Hondong, Sinja, Rothermund, Eva, Waldmann, Tamara, Heming, Meike, Weber, Jeannette, Hander, Nicole R., Mulfinger, Nadine, Kröger, Christoph, and Erim, Yesim
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- 2024
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16. Psychische Belastungen bei Erwerbstätigen: Leistungsinanspruchnahme und Kosten für das deutsche Gesundheitssystem
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Mulfinger, Nadine, Angerer, Peter, Erim, Yesim, Hander, Nicole, Hansmann, Marieke, Herold, Regina, Kilian, Reinhold, Kröger, Christoph, Rothermund, Eva, Weber, Jeannette, and Waldmann, Tamara
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- 2024
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17. A divergent intermediate strategy yields biologically diverse pseudo-natural products
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Bag, Sukdev, Liu, Jie, Patil, Sohan, Bonowski, Jana, Koska, Sandra, Schölermann, Beate, Zhang, Ruirui, Wang, Lin, Pahl, Axel, Sievers, Sonja, Brieger, Lukas, Strohmann, Carsten, Ziegler, Slava, Grigalunas, Michael, and Waldmann, Herbert
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- 2024
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18. SO$_2$, silicate clouds, but no CH$_4$ detected in a warm Neptune
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Dyrek, Achrène, Min, Michiel, Decin, Leen, Bouwman, Jeroen, Crouzet, Nicolas, Mollière, Paul, Lagage, Pierre-Olivier, Konings, Thomas, Tremblin, Pascal, Güdel, Manuel, Pye, John, Waters, Rens, Henning, Thomas, Vandenbussche, Bart, Martinez, Francisco Ardevol, Argyriou, Ioannis, Ducrot, Elsa, Heinke, Linus, Van Looveren, Gwenael, Absil, Olivier, Barrado, David, Baudoz, Pierre, Boccaletti, Anthony, Cossou, Christophe, Coulais, Alain, Edwards, Billy, Gastaud, René, Glasse, Alistair, Glauser, Adrian, Greene, Thomas P., Kendrew, Sarah, Krause, Oliver, Lahuis, Fred, Mueller, Michael, Olofsson, Goran, Patapis, Polychronis, Rouan, Daniel, Royer, Pierre, Scheithauer, Silvia, Waldmann, Ingo, Whiteford, Niall, Colina, Luis, van Dishoeck, Ewine F., Greve, Thomas, Ostlin, Göran, Ray, Tom P., and Wright, Gillian
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
WASP-107b is a warm ($\sim$740 K) transiting planet with a Neptune-like mass of $\sim$30.5 $M_{\oplus}$ and Jupiter-like radius of $\sim$0.94 $R_{\rm J}$, whose extended atmosphere is eroding. Previous observations showed evidence for water vapour and a thick high-altitude condensate layer in WASP-107b's atmosphere. Recently, photochemically produced sulphur dioxide (SO$_2$) was detected in the atmosphere of a hot ($\sim$1,200 K) Saturn-mass planet from transmission spectroscopy near 4.05 $\mu$m, but for temperatures below $\sim$1,000 K sulphur is predicted to preferably form sulphur allotropes instead of SO$_2$. Here we report the 9$\sigma$-detection of two fundamental vibration bands of SO$_2$, at 7.35 $\mu$m and 8.69 $\mu$m, in the transmission spectrum of WASP-107b using the Mid-Infrared Instrument (MIRI) of the JWST. This discovery establishes WASP-107b as the second irradiated exoplanet with confirmed photochemistry, extending the temperature range of exoplanets exhibiting detected photochemistry from $\sim$1,200 K down to $\sim$740 K. Additionally, our spectral analysis reveals the presence of silicate clouds, which are strongly favoured ($\sim$7$\sigma$) over simpler cloud setups. Furthermore, water is detected ($\sim$12$\sigma$), but methane is not. These findings provide evidence of disequilibrium chemistry and indicate a dynamically active atmosphere with a super-solar metallicity.
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- 2023
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19. 15NH3 in the atmosphere of a cool brown dwarf
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Barrado, David, Mollière, Paul, Patapis, Polychronis, Min, Michiel, Tremblin, Pascal, Martinez, Francisco Ardevol, Whiteford, Niall, Vasist, Malavika, Argyriou, Ioannis, Samland, Matthias, Lagage, Pierre-Olivier, Decin, Leen, Waters, Rens, Henning, Thomas, Morales-Calderón, María, Guedel, Manuel, Vandenbussche, Bart, Absil, Olivier, Baudoz, Pierre, Boccaletti, Anthony, Bouwman, Jeroen, Cossou, Christophe, Coulais, Alain, Crouzet, Nicolas, Gastaud, René, Glasse, Alistair, Glauser, Adrian M., Kamp, Inga, Kendrew, Sarah, Krause, Oliver, Lahuis, Fred, Mueller, Michael, Olofsson, Göran, Pye, John, Rouan, Daniel, Royer, Pierre, Scheithauer, Silvia, Waldmann, Ingo, Colina, Luis, van Dishoeck, Ewine F., Ray, Tom, Östlin, Göran, and Wright, Gillian
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Solar and Stellar Astrophysics - Abstract
Brown dwarfs serve as ideal laboratories for studying the atmospheres of giant exoplanets on wide orbits as the governing physical and chemical processes in them are nearly identical. Understanding the formation of gas giant planets is challenging, often involving the endeavour to link atmospheric abundance ratios, such as the carbon-to-oxygen (C/O) ratio, to formation scenarios. However, the complexity of planet formation requires additional tracers, as the unambiguous interpretation of the measured C/O ratio is fraught with complexity. Isotope ratios, such as deuterium-to-hydrogen and 14N/15N, offer a promising avenue to gain further insight into this formation process, mirroring their utility within the solar system. For exoplanets only a handful of constraints on 12C/13C exist, pointing to the accretion of 13C-rich ice from beyond the disks' CO iceline. Here we report on the mid-infrared detection of the 14NH3 and 15NH3 isotopologues in the atmosphere of a cool brown dwarf with an effective temperature of 380 K in a spectrum taken with the Mid-InfraRed Instrument of the James Webb Space Telescope. As expected, our results reveal a 14N/15N value consistent with star-like formation by gravitational collapse, demonstrating that this ratio can be accurately constrained. Since young stars and their planets should be more strongly enriched in the 15N isotope, we expect that 15NH3 will be detectable in a number of cold, wide-separation exoplanets., Comment: Accepted by Nature. 28 pages, 7 figures, uses nature3.cls
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- 2023
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20. Learning Linear Gaussian Polytree Models with Interventions
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Tramontano, D., Waldmann, L., Drton, M., and Duarte, E.
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Statistics - Machine Learning ,Computer Science - Machine Learning - Abstract
We present a consistent and highly scalable local approach to learn the causal structure of a linear Gaussian polytree using data from interventional experiments with known intervention targets. Our methods first learn the skeleton of the polytree and then orient its edges. The output is a CPDAG representing the interventional equivalence class of the polytree of the true underlying distribution. The skeleton and orientation recovery procedures we use rely on second order statistics and low-dimensional marginal distributions. We assess the performance of our methods under different scenarios in synthetic data sets and apply our algorithm to learn a polytree in a gene expression interventional data set. Our simulation studies demonstrate that our approach is fast, has good accuracy in terms of structural Hamming distance, and handles problems with thousands of nodes., Comment: To be published in: IEEE Journal on Selected Areas in Information Theory, Special Issue: Causality: Fundamental Limits and Applications
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- 2023
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21. Qualitative and quantitative assessment of infraoccluded deciduous teeth: a systematic review
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Teresa Temming, Susanne Waldmann, Anahita Jablonski-Momeni, and Heike Korbmacher-Steiner
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Tooth ankylosis ,Deciduous teeth ,Infraocclusion ,Alveolar bone growth ,Systematic review ,Specialties of internal medicine ,RC581-951 - Abstract
Abstract Background Infraocclusion of deciduous teeth is a frequent dental anomaly caused by ankylosis accompanied by local growth disturbance. During puberal growth spurt an increasing progression of infraocclusion is detected. The clinical classification of ankylosed deciduous teeth varies considerably among scientific studies. The aim of this paper is to present an up-to-date overview of the variety of methods. Methods The systematic literature search followed the PRISMA guidelines and included the analysis of the following databases and study registries: PubMed (MEDLINE), the Cochrane Library, Web of Science, Embase.com and ClinicalTrials.gov from database inception until September 23, 2024. Studies that investigated at least one ankylosed deciduous tooth per participant in a quantitative or qualitative manner were included. Studies that evaluated only histological data were excluded. Controlled and uncontrolled clinical studies, retrospective studies, observational studies and cross-sectional studies were included. The studies were restricted to English and German languages. Case reports, case series, comments, expert opinions, letters to the editor, literature reviews and studies enrolling less than 10 patients or 10 infraoccluded teeth in total were excluded. Results Of 5645 records, 42 papers qualified for the final analysis. The evaluation of infraoccluded deciduous teeth was mainly (n = 37) performed by quantitative and semiquantitative assessment of the extent of infraposition at the occlusal level. The measurement reference differed considerably. Fewer studies have analyzed ankylosed deciduous teeth at the alveolar level by examining the contour of the alveolar ridge (n = 7) or the height of the alveolar process (n = 5). Even fewer studies (n = 4) have performed qualitative analysis at the skeletal level by evaluating the influence of the vertical skeletal growth pattern on the incidence of ankylosed deciduous teeth. Conclusions To carry out a comprehensive evaluation of infraoccluded deciduous teeth, an assessment of the occlusal, alveolar and potentially skeletal levels is advisable. Radiographic investigations i.e. panoramic radiographs are therefore essential as a supplement to clinical examination. There is a need for standardization and objectification of the methods for the classification of infraoccluded deciduous teeth to give a general recommendation of clinical performance. Registration This systematic review has been registered in the international prospective register of systematic reviews (PROSPERO) under the registration number: CRD42024555842.
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- 2024
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22. A compound-target pairs dataset: differences between drugs, clinical candidates and other bioactive compounds
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A. Lina Heinzke, Barbara Zdrazil, Paul D. Leeson, Robert J. Young, Axel Pahl, Herbert Waldmann, and Andrew R. Leach
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Science - Abstract
Abstract Providing a better understanding of what makes a compound a successful drug candidate is crucial for reducing the high attrition rates in drug discovery. Analyses of the differences between active compounds, clinical candidates and drugs require high-quality datasets. However, most datasets of drug discovery programs are not openly available. This work introduces a dataset of compound-target pairs extracted from the open-source bioactivity database ChEMBL (release 32). Compound-target pairs in the dataset either have at least one measured activity or are part of the manually curated set of known interactions in ChEMBL. Known interactions between drugs or clinical candidates and targets are specifically annotated to facilitate analyses of differences between drugs, clinical candidates, and other active compounds. In total, the dataset comprises 614,594 compound-target pairs, 5,109 (3,932) of which are known interactions between drugs (clinical candidates) and targets. The extraction is performed in an automated manner and fully reproducible. We are providing not only the datasets but also the code to rerun the analyses with other ChEMBL releases.
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- 2024
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23. Tabular deep learning: a comparative study applied to multi-task genome-wide prediction
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Yuhua Fan and Patrik Waldmann
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Tabular data ,Multi-trait ,Genome-wide prediction (GWP) ,Non-linear models ,Computer applications to medicine. Medical informatics ,R858-859.7 ,Biology (General) ,QH301-705.5 - Abstract
Abstract Purpose More accurate prediction of phenotype traits can increase the success of genomic selection in both plant and animal breeding studies and provide more reliable disease risk prediction in humans. Traditional approaches typically use regression models based on linear assumptions between the genetic markers and the traits of interest. Non-linear models have been considered as an alternative tool for modeling genomic interactions (i.e. non-additive effects) and other subtle non-linear patterns between markers and phenotype. Deep learning has become a state-of-the-art non-linear prediction method for sound, image and language data. However, genomic data is better represented in a tabular format. The existing literature on deep learning for tabular data proposes a wide range of novel architectures and reports successful results on various datasets. Tabular deep learning applications in genome-wide prediction (GWP) are still rare. In this work, we perform an overview of the main families of recent deep learning architectures for tabular data and apply them to multi-trait regression and multi-class classification for GWP on real gene datasets. Methods The study involves an extensive overview of recent deep learning architectures for tabular data learning: NODE, TabNet, TabR, TabTransformer, FT-Transformer, AutoInt, GANDALF, SAINT and LassoNet. These architectures are applied to multi-trait GWP. Comprehensive benchmarks of various tabular deep learning methods are conducted to identify best practices and determine their effectiveness compared to traditional methods. Results Extensive experimental results on several genomic datasets (three for multi-trait regression and two for multi-class classification) highlight LassoNet as a standout performer, surpassing both other tabular deep learning models and the highly efficient tree based LightGBM method in terms of both best prediction accuracy and computing efficiency. Conclusion Through series of evaluations on real-world genomic datasets, the study identifies LassoNet as a standout performer, surpassing decision tree methods like LightGBM and other tabular deep learning architectures in terms of both predictive accuracy and computing efficiency. Moreover, the inherent variable selection property of LassoNet provides a systematic way to find important genetic markers that contribute to phenotype expression.
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- 2024
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24. 3D-MuPPET: 3D Multi-Pigeon Pose Estimation and Tracking
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Waldmann, Urs, Chan, Alex Hoi Hang, Naik, Hemal, Nagy, Máté, Couzin, Iain D., Deussen, Oliver, Goldluecke, Bastian, and Kano, Fumihiro
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning - Abstract
Markerless methods for animal posture tracking have been rapidly developing recently, but frameworks and benchmarks for tracking large animal groups in 3D are still lacking. To overcome this gap in the literature, we present 3D-MuPPET, a framework to estimate and track 3D poses of up to 10 pigeons at interactive speed using multiple camera views. We train a pose estimator to infer 2D keypoints and bounding boxes of multiple pigeons, then triangulate the keypoints to 3D. For identity matching of individuals in all views, we first dynamically match 2D detections to global identities in the first frame, then use a 2D tracker to maintain IDs across views in subsequent frames. We achieve comparable accuracy to a state of the art 3D pose estimator in terms of median error and Percentage of Correct Keypoints. Additionally, we benchmark the inference speed of 3D-MuPPET, with up to 9.45 fps in 2D and 1.89 fps in 3D, and perform quantitative tracking evaluation, which yields encouraging results. Finally, we showcase two novel applications for 3D-MuPPET. First, we train a model with data of single pigeons and achieve comparable results in 2D and 3D posture estimation for up to 5 pigeons. Second, we show that 3D-MuPPET also works in outdoors without additional annotations from natural environments. Both use cases simplify the domain shift to new species and environments, largely reducing annotation effort needed for 3D posture tracking. To the best of our knowledge we are the first to present a framework for 2D/3D animal posture and trajectory tracking that works in both indoor and outdoor environments for up to 10 individuals. We hope that the framework can open up new opportunities in studying animal collective behaviour and encourages further developments in 3D multi-animal posture tracking.
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- 2023
25. Strict Wick-type deformation quantization on Riemann surfaces: Rigidity and Obstructions
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Kraus, Daniela, Roth, Oliver, Schleissinger, Sebastian, and Waldmann, Stefan
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Mathematics - Complex Variables ,Mathematical Physics ,Mathematics - Functional Analysis ,Primary 30F45, 30F35, 53D55, Secondary 53A55 - Abstract
Let $X$ be a hyperbolic Riemann surface. We study a convergent Wick-type star product $\star_X$ on $X$ which is induced by the canonical convergent star product $\star_{\mathbb{D}}$ on the unit disk $\mathbb{D}$ via Uniformization Theory. While by construction, the resulting Fr\'echet algebras $(\mathcal{A}(X),\star_X)$ are strongly isomorphic for conformally equivalent Riemann surfaces, our work exhibits additional severe topological obstructions. In particular, we show that the Fr\'echet algebra $(\mathcal{A}(X),\star_X)$ degenerates if and only if the connectivity of $X$ is at least $3$, and $(\mathcal{A}(X),\star_X)$ is noncommutative if and only if $X$ is simply connected. We also explicitly determine the algebra $\mathcal{A}_X$ and the star product $\star_X$ for the intermediate case of doubly connected Riemann surfaces $X$. As a perhaps surprinsing result, we deduce that two such Fr\'echet algebras are strongly isomorphic if and only if either both Riemann surfaces are conformally equivalent to an (not neccesarily the same) annulus or both are conformally equivalent to a punctured disk., Comment: References updated
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- 2023
26. Old and New Benchmarks for Relative Termination of String Rewrite Systems
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Hofbauer, Dieter and Waldmann, Johannes
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Computer Science - Logic in Computer Science - Abstract
We provide a critical assessment of the current set of benchmarks for relative SRS termination in the Termination Problems Database (TPDB): most of the benchmarks in Waldmann_19 and ICFP_10_relative are, in fact, strictly terminating (i. e., terminating when non-strict rules are considered strict), so these benchmarks should be removed, or relabelled. To fill this gap, we enumerate small relative string rewrite systems. At present, we have complete enumerations for a 2-letter alphabet up to size 11, and for a 3-letter alphabet up to size 8. For some selected benchmarks, old and new, we discuss how to prove termination, automated or not., Comment: Presented at WST 2023
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- 2023
27. Impact of the gas choice and the geometry on the breakdown limits in Micromegas detectors
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Gasik, P., Waldmann, T., Fabbietti, L., Klemenz, T., Lautner, L., and Ulukutlu, B.
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Physics - Instrumentation and Detectors - Abstract
In this study we investigate the stability limits of Micromegas detectors upon irradiation with alpha particles. The results are obtained with meshes with different optical transparency and geometry of wires. The measurements are performed in Ar- and Ne- based mixtures with different CO$_2$ content. We observe that the breakdown limit strongly depends on the gas and that a higher amount of quencher in the mixture does not necessarily correlate with higher stability. In addition, we observe discharge probability scaling with the wire pitch. This suggests that a Micromegas mesh cell can be treated as an independent amplification unit, similar to a hole in a GEM foil. The outcome of these studies provides valuable input for further optimization of MPGD detectors, multi-layer stacks in particular., Comment: 6 pages, 3 figures Part of MPGD 2022 proceedings
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- 2023
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28. A spectroscopic thermometer: individual vibrational band spectroscopy with the example of OH in the atmosphere of WASP-33b
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Wright, Sam O. M., Nugroho, Stevanus K., Brogi, Matteo, Gibson, Neale P., de Mooij, Ernst J. W., Waldmann, Ingo, Tennyson, Jonathan, Kawahara, Hajime, Kuzuhara, Masayuki, Hirano, Teruyuki, Kotani, Takayuki, Kawashima, Yui, Masuda, Kento, Birkby, Jayne L., Watson, Chris A., Tamura, Motohide, Zwintz, Konstanze, Harakawa, Hiroki, Kudo, Tomoyuki, Hodapp, Klaus, Jacobson, Shane, Konishi, Mihoko, Kurokawa, Takashi, Nishikawa, Jun, Omiya, Masashi, Serizawa, Takuma, Ueda, Akitoshi, Vievard, Sébastien, and Yurchenko, Sergei N.
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Astrophysics - Earth and Planetary Astrophysics - Abstract
Individual vibrational band spectroscopy presents an opportunity to examine exoplanet atmospheres in detail by distinguishing where the vibrational state populations of molecules differ from the current assumption of a Boltzmann distribution. Here, retrieving vibrational bands of OH in exoplanet atmospheres is explored using the hot Jupiter WASP-33b as an example. We simulate low-resolution spectroscopic data for observations with the JWST's NIRSpec instrument and use high resolution observational data obtained from the Subaru InfraRed Doppler instrument (IRD). Vibrational band-specific OH cross section sets are constructed and used in retrievals on the (simulated) low and (real) high resolution data. Low resolution observations are simulated for two WASP-33b emission scenarios: under the assumption of local thermal equilibrium (LTE) and a toy non-LTE model for vibrational excitation of selected bands. We show that mixing ratios for individual bands can be retrieved with sufficient precision to allow the vibrational population distributions of the forward models to be reconstructed. A simple fit for the Boltzmann distribution in the LTE case shows that the vibrational temperature is recoverable in this manner. For high resolution, cross-correlation applications, we apply the individual vibrational band analysis to an IRD spectrum of WASP-33b, applying an 'un-peeling' technique. Individual detection significances for the two strongest bands are shown to be in line with Boltzmann distributed vibrational state populations consistent with the effective temperature of the WASP-33b atmosphere reported previously. We show the viability of this approach for analysing the individual vibrational state populations behind observed and simulated spectra including reconstructing state population distributions., Comment: Submitted for publication in AJ
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- 2023
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29. Disentangling influences of climate variability and lake-system evolution on climate proxies derived from isoprenoid and branched glycerol dialkyl glycerol tetraethers (GDGTs): the 250 kyr Lake Chala record
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A. J. Baxter, F. Peterse, D. Verschuren, A. Maitituerdi, N. Waldmann, and J. S. Sinninghe Damsté
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Ecology ,QH540-549.5 ,Life ,QH501-531 ,Geology ,QE1-996.5 - Abstract
High-resolution paleoclimate records from tropical continental settings are greatly needed to advance understanding of global climate dynamics. The International Continental Scientific Drilling Program (ICDP) project DeepCHALLA recovered a 214.8 m long sediment sequence from Lake Chala, a deep and permanently stratified (meromictic) crater lake in eastern equatorial Africa, covering the past ca. 250 000 years (250 kyr) of continuous lacustrine deposition since the earliest phase of lake-basin development. Lipid biomarker analyses on the sediments of Lake Chala can provide quantitative records of past variation in temperature and moisture balance from this poorly documented region. However, the degree to which climate proxies derived from aquatically produced biomarkers are affected by aspects of lake developmental history is rarely considered, even though it may critically influence their ability to consistently register a particular climate variable through time. Modern-system studies of Lake Chala revealed crucial information about the mechanisms underpinning relationships between proxies based on isoprenoid (iso-) and branched (br-) glycerol dialkyl glycerol tetraethers (GDGTs) and the targeted climate variables, but the persistence of these relationships in the past remains unclear. Here we assess the reliability of long-term climate signals registered in the sediments of Lake Chala by comparing downcore variations in GDGT distributions with major phases in lake-system evolution as reflected by independent proxies of lake depth, mixing regime and nutrient dynamics: seismic reflection data, lithology and fossil diatom assemblages. Together, these records suggest that during early lake history (before ca. 180–200 ka) the distinct mixing-related depth zones with which specific GDGT producers are associated in the modern-day lake were not yet formed, likely due to more open lake hydrology and absence of chemical water-column stratification. Consequently absolute GDGT concentrations dating to this period are relatively low, proxies sensitive to water-column stratification (e.g., branched versus isoprenoid tetraether (BIT) index) display highly irregular temporal variability, and correlations between proxies are dissimilar to expectations based on modern-system understanding. A sequence of lake-system changes between ca. 180–200 and ca. 80 ka first established and then strengthened the chemical density gradient, promoting meromictic conditions despite the overall decrease in lake depth due to the basin gradually being filled up with sediments. From ca. 180 ka onward some GDGTs and derived proxies (e.g., crenarchaeol concentration, BIT index and IR6Me) display strong ∼ 23 kyr periodicity, likely reflecting the predominantly precession-driven insolation forcing of Quaternary climate variability in low-latitude regions. Our results suggest that GDGT-based temperature and moisture-balance proxies in Lake Chala sediments reflect the climate history of eastern equatorial Africa from at least ca. 160 ka onwards, i.e., covering the complete last glacial–interglacial cycle and the penultimate glacial maximum. This work confirms the potential of lacustrine GDGTs for elucidating the climate history of tropical regions at Quaternary timescales, provided they are applied to suitably high-quality sediment archives. Additionally, their interpretation should incorporate a broader understanding of the extent to which lake-system evolution limits the extrapolation back in time of proxy-climate relationships established in the modern system.
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- 2024
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30. Retrieval study of cool, directly imaged exoplanet 51 Eri b
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Whiteford, Niall, Glasse, Alistair, Chubb, Katy L., Kitzmann, Daniel, Ray, Shrishmoy, Phillips, Mark W., Biller, Beth A., Palmer, Paul I., Rice, Ken, Waldmann, Ingo P., Changeat, Quentin, Skaf, Nour, Wang, Jason, Edwards, Billy, and Al-Refaie, Ahmed
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics ,Astrophysics - Solar and Stellar Astrophysics - Abstract
Retrieval methods are a powerful analysis technique for modelling exoplanetary atmospheres by estimating the bulk physical and chemical properties that combine in a forward model to best-fit an observed spectrum, and they are increasingly being applied to observations of directly-imaged exoplanets. We have adapted TauREx3, the Bayesian retrieval suite, for the analysis of near-infrared spectrophotometry from directly-imaged gas giant exoplanets and brown dwarfs. We demonstrate TauREx3's applicability to sub-stellar atmospheres by presenting results for brown dwarf benchmark GJ 570D which are consistent with previous retrieval studies, whilst also exhibiting systematic biases associated with the presence of alkali lines. We also present results for the cool exoplanet 51 Eri b, the first application of a free chemistry retrieval analysis to this object, using spectroscopic observations from GPI and SPHERE. While our retrieval analysis is able to explain spectroscopic and photometric observations without employing cloud extinction, we conclude this may be a result of employing a flexible temperature-pressure profile which is able to mimic the presence of clouds. We present Bayesian evidence for an ammonia detection with a 2.7$\sigma$ confidence, the first indication of ammonia in an exoplanetary atmosphere. This is consistent with this molecule being present in brown dwarfs of a similar spectral type. We demonstrate the chemical similarities between 51 Eri b and GJ 570D in relation to their retrieved molecular abundances. Finally, we show that overall retrieval conclusions for 51 Eri b can vary when employing different spectral data and modelling components, such as temperature-pressure and cloud structures.
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- 2023
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31. Wake Tail Plane Interactions for a Tandem Wing Configuration in High-Speed Stall Conditions
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Kleinert, Johannes, Ehrle, Maximilian, Waldmann, Andreas, and Lutz, Thorsten
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Physics - Fluid Dynamics - Abstract
In this work, wake-tail plane interactions are investigated for a tandem wing configuration in buffet conditions using hybrid RANS/LES simulations with the Automated Zonal Detached Eddy Simulation (AZDES) method. The analyzed configuration consists of two untapered and unswept wing segments, representative of a wing-tail plane configuration. The shock oscillation on the front wing segment and the development of its turbulent wake are characterized, including a spectral analysis of the pressure and velocity fluctuations in the wake and a modal analysis of the flow field applying Proper Orthogonal Decomposition (POD). The impact of the wake on the aerodynamics and loads of the rear wing segment is then studied, with a spectral analysis of its lift and surface pressure oscillations. Finally, the influence of the position and the incidence angle of the rear wing segment are investigated. For the considered flow conditions, 2D buffet is present on the front wing segment. During the downstream movement of the shock, the amount of separation reaches its minimum and small vortices are present in the wake. During the upstream movement of the shock, the amount of separation is at its maximum and larger turbulent structures are present together with high fluctuation levels of velocity and pressure. A distinct peak can be associated with the meandering motion of wake vortices, identified by means of a modal analysis of the flow field using Proper Orthogonal Decomposition. The impingement of the wake causes a strong variation of the loading of the rear wing segment. A comparably low-frequent oscillation of the lift coefficient, attributed to the change of intensity of the downwash caused by the front segment, can be distinguished from fluctuations of high frequency that are caused by the impingement of the turbulent structures in the wake., Comment: Updated arXiv version to version published in CEAS Aeronautical Journal
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- 2023
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32. Mach and Reynolds Number Effects on Transonic Buffet on the XRF-1 Transport Aircraft Wing at Flight Reynolds Number
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Waldmann, Andreas, Ehrle, Maximilian C., Kleinert, Johannes, Yorita, Daisuke, and Lutz, Thorsten
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Physics - Fluid Dynamics - Abstract
This work provides an overview of aerodynamic data acquired in the European Transonic Windtunnel using an XRF-1 transport aircraft configuration both at cruise conditions and at the edges of the flight envelope. The goals and design of the wind tunnel test was described, highlighting the use of the cryogenic wind tunnel's capability to isolate the effects of Mach and Reynolds numbers and the dynamic pressure. The resulting dataset includes an aerodynamic baseline characterization of the full span model with vertical and horizontal tailplanes and without engine nacelles. The effects of different inflow conditions were studied using data from continuous polars, evaluating the changes in aeroelastic deformation which are proportional to $q/E$ and the influence of $M$ and $Re$ on the shock position. Off-design data was analyzed at the lowest and highest measured Mach numbers of 0.84 and 0.90, respectively. Wing lower surface flow and underside shock motion was analyzed at negative angles of attack using $c_p$ distribution and unsteady pressure transducer fluctuation data, identifying significant upstream displacement of the shock close to the leading edge. Wing upper side flow and the shock motion near buffet onset and beyond was analyzed using unsteady pressure data from point transducers and unsteady pressure sensitive paint (PSP) measurements. Buffet occurs at lower angles of attack at high Mach number, and without clearly defined lift break. Spectral contents at the acquired data points in the buffet range suggest broadband fluctuations at Strouhal numbers between 0.2 and 0.6, which is consistent with recent literature. The spanwise shock propagation velocities were determined independently via analysis of unsteady PSP and pressure transducers to be in the range between $u_s / u_{\infty} = 0.24$ and $0.32$.
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- 2022
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33. Release kinetics of growth factors loaded into β-TCP ceramics in an in vitro model
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Marco Waldmann, Marc Bohner, Anna Baghnavi, Bianca Riedel, and Michael Seidenstuecker
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β-TCP ,PRP ,ceramic ,growth factor ,TGF-beta ,IGF-1 ,Biotechnology ,TP248.13-248.65 - Abstract
Introductionβ-TCP ceramics are bone replacement materials that have recently been tested as a drug delivery system that can potentially be applied to endogenous substances like growth factors found in blood platelets to facilitate positive attributes.MethodsIn this work, we used flow chamber loading to load β-TCP dowels with blood suspensions of platelet-rich plasma (PRP), platelet-poor plasma (PPP), or buffy coat (BC) character. PRP and BC platelet counts were adjusted to the same level by dilution. Concentrations of TGF-β1, PDGF-AB, and IGF-1 from dowel-surrounding culture medium were subsequently determined using ELISA over 5 days. The influence of alginate was additionally tested to modify the release.ResultsConcentrations of TGF-β1 and PDGF-AB increased and conclusively showed a release from platelets in PRP and BC compared to PPP. The alginate coating reduced the PDGF-AB release but did not reduce TGF-β1 and instead even increased TGF-β1 in the BC samples. IGF-1 concentrations were highest in PPP, suggesting circulating levels rather than platelet release as the driving factor. Alginate samples tended to have lower IGF-1 concentrations, but the difference was not shown to be significant.DiscussionThe release of growth factors from different blood suspensions was successfully demonstrated for β-TCP as a drug delivery system with release patterns that correspond to PRP activation after Ca2+-triggered activation. The release pattern was partially modified by alginate coating.
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- 2024
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34. Exploring the Ability of HST WFC3 G141 to Uncover Trends in Populations of Exoplanet Atmospheres Through a Homogeneous Transmission Survey of 70 Gaseous Planets
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Edwards, Billy, Changeat, Quentin, Tsiaras, Angelos, Yip, Kai Hou, Al-Refaie, Ahmed F., Anisman, Lara, Bieger, Michelle F., Gressier, Amelie, Shibata, Sho, Skaf, Nour, Bouwman, Jeroen, Cho, James Y-K., Ikoma, Masahiro, Venot, Olivia, Waldmann, Ingo, Lagage, Pierre-Olivier, and Tinetti, Giovanna
- Subjects
Astrophysics - Earth and Planetary Astrophysics - Abstract
We present the analysis of the atmospheres of 70 gaseous extrasolar planets via transit spectroscopy with Hubble's Wide Field Camera 3 (WFC3). For over half of these, we statistically detect spectral modulation which our retrievals attribute to molecular species. Among these, we use Bayesian Hierarchical Modelling to search for chemical trends with bulk parameters. We use the extracted water abundance to infer the atmospheric metallicity and compare it to the planet's mass. We also run chemical equilibrium retrievals, fitting for the atmospheric metallicity directly. However, although previous studies have found evidence of a mass-metallicity trend, we find no such relation within our data. For the hotter planets within our sample, we find evidence for thermal dissociation of dihydrogen and water via the H$^-$ opacity. We suggest that the general lack of trends seen across this population study could be due to i) the insufficient spectral coverage offered by HST WFC3 G141, ii) the lack of a simple trend across the whole population, iii) the essentially random nature of the target selection for this study or iv) a combination of all the above. We set out how we can learn from this vast dataset going forward in an attempt to ensure comparative planetology can be undertaken in the future with facilities such as JWST, Twinkle and Ariel. We conclude that a wider simultaneous spectral coverage is required as well as a more structured approach to target selection., Comment: Accepted for publication in ApJS
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- 2022
35. Epidemiologie des geriatrischen Krebsgeschehens in Deutschland
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Hübner, Joachim, Eberle, Andrea, Kraywinkel, Klaus, Luttmann, Sabine, and Waldmann, Annika
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- 2024
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36. SO2, silicate clouds, but no CH4 detected in a warm Neptune
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Dyrek, Achrène, Min, Michiel, Decin, Leen, Bouwman, Jeroen, Crouzet, Nicolas, Mollière, Paul, Lagage, Pierre-Olivier, Konings, Thomas, Tremblin, Pascal, Güdel, Manuel, Pye, John, Waters, Rens, Henning, Thomas, Vandenbussche, Bart, Ardevol Martinez, Francisco, Argyriou, Ioannis, Ducrot, Elsa, Heinke, Linus, van Looveren, Gwenael, Absil, Olivier, Barrado, David, Baudoz, Pierre, Boccaletti, Anthony, Cossou, Christophe, Coulais, Alain, Edwards, Billy, Gastaud, René, Glasse, Alistair, Glauser, Adrian, Greene, Thomas P., Kendrew, Sarah, Krause, Oliver, Lahuis, Fred, Mueller, Michael, Olofsson, Goran, Patapis, Polychronis, Rouan, Daniel, Royer, Pierre, Scheithauer, Silvia, Waldmann, Ingo, Whiteford, Niall, Colina, Luis, van Dishoeck, Ewine F., Östlin, Göran, Ray, Tom P., and Wright, Gillian
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- 2024
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37. Wake tail plane interactions for a tandem wing configuration in high-speed stall conditions
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Kleinert, Johannes, Ehrle, Maximilian, Waldmann, Andreas, and Lutz, Thorsten
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- 2024
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38. A model approach to show that monocytes can enter microporous β-TCP ceramics
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Marco Waldmann, Marc Bohner, Long-Quan R. V. Le, Anna Baghnavi, Bianca Riedel, and Michael Seidenstuecker
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β-TCP ,PRP ,Ceramic ,Monocyte ,Immunofluorescence ,Live/Dead ,Biotechnology ,TP248.13-248.65 - Abstract
Abstract β-TCP ceramics are versatile bone substitute materials and show many interactions with cells of the monocyte-macrophage-lineage. The possibility of monocytes entering microporous β-TCP ceramics has however not yet been researched. In this study, we used a model approach to investigate whether monocytes might enter β-TCP, providing a possible explanation for the origin of CD68-positive osteoclast-like giant cells found in earlier works. We used flow chambers to unidirectionally load BC, PRP, or PPP into slice models of either 2 mm or 6 mm β-TCP. Immunofluorescence for CD68 and live/dead staining was performed after the loading process. Our results show that monocytes were present in a relevant number of PRP and BC slices representing the inside of our 2 mm slice model and also present on the actual inside of our 6 mm model. For PPP, monocytes were not found beyond the surface in either model. Our results indicate the possibility of a new and so far neglected constituent in β-TCP degradation, perhaps causing the process of ceramic degradation also starting from inside the ceramics as opposed to the current understanding. We also demonstrated flow chambers as a possible new in vitro model for interactions between blood and β-TCP.
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- 2024
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39. Awareness for artifacts in fluorescence microscopy of β-TCP
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Marco Waldmann, Marc Bohner, Anna Baghnavi, Bianca Riedel, and Michael Seidenstuecker
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β-TCP ,Ceramic ,Fluorescence, Immunofluorescence ,Live/Dead ,Artifacts, Technovit ,Medicine ,Biology (General) ,QH301-705.5 ,Science (General) ,Q1-390 - Abstract
Abstract Fluorescence analysis of β-TCP ceramics is often used to describe cells found on said ceramics. However, we found, to our knowledge, so far undescribed artifacts which might sometimes be hard to differentiate from cells due to shape and fluorescence behavior. We tried prolonged ultrasound washing as well as Technovit 9100 fixation to reduce these artifacts. While untreated dowels showed no reduction in artifacts no matter the further treatment, Technovit fixation reduced the artifacts with even further reduction achieved by mechanical cleaning. As a consequence, scientists working with these dowels and likely even other types should try to avoid creating false positive results by considering the existence of these artifacts, checking additional filters for unusual fluorescence and by reducing them by using Technovit fixation when possible.
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- 2024
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40. Identification of carbon dioxide in an exoplanet atmosphere
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The JWST Transiting Exoplanet Community Early Release Science Team, Ahrer, Eva-Maria, Alderson, Lili, Batalha, Natalie M., Batalha, Natasha E., Bean, Jacob L., Beatty, Thomas G., Bell, Taylor J., Benneke, Björn, Berta-Thompson, Zachory K., Carter, Aarynn L., Crossfield, Ian J. M., Espinoza, Néstor, Feinstein, Adina D., Fortney, Jonathan J., Gibson, Neale P., Goyal, Jayesh M., Kempton, Eliza M. -R., Kirk, James, Kreidberg, Laura, López-Morales, Mercedes, Line, Michael R., Lothringer, Joshua D., Moran, Sarah E., Mukherjee, Sagnick, Ohno, Kazumasa, Parmentier, Vivien, Piaulet, Caroline, Rustamkulov, Zafar, Schlawin, Everett, Sing, David K., Stevenson, Kevin B., Wakeford, Hannah R., Allen, Natalie H., Birkmann, Stephan M., Brande, Jonathan, Crouzet, Nicolas, Cubillos, Patricio E., Damiano, Mario, Désert, Jean-Michel, Gao, Peter, Harrington, Joseph, Hu, Renyu, Kendrew, Sarah, Knutson, Heather A., Lagage, Pierre-Olivier, Leconte, Jérémy, Lendl, Monika, MacDonald, Ryan J., May, E. M., Miguel, Yamila, Molaverdikhani, Karan, Moses, Julianne I., Murray, Catriona Anne, Nehring, Molly, Nikolov, Nikolay K., de la Roche, D. J. M. Petit dit, Radica, Michael, Roy, Pierre-Alexis, Stassun, Keivan G., Taylor, Jake, Waalkes, William C., Wachiraphan, Patcharapol, Welbanks, Luis, Wheatley, Peter J., Aggarwal, Keshav, Alam, Munazza K., Banerjee, Agnibha, Barstow, Joanna K., Blecic, Jasmina, Casewell, S. L., Changeat, Quentin, Chubb, K. L., Colón, Knicole D., Coulombe, Louis-Philippe, Daylan, Tansu, de Val-Borro, Miguel, Decin, Leen, Santos, Leonardo A. Dos, Flagg, Laura, France, Kevin, Fu, Guangwei, Muñoz, A. García, Gizis, John E., Glidden, Ana, Grant, David, Heng, Kevin, Henning, Thomas, Hong, Yu-Cian, Inglis, Julie, Iro, Nicolas, Kataria, Tiffany, Komacek, Thaddeus D., Krick, Jessica E., Lee, Elspeth K. H., Lewis, Nikole K., Lillo-Box, Jorge, Lustig-Yaeger, Jacob, Mancini, Luigi, Mandell, Avi M., Mansfield, Megan, Marley, Mark S., Mikal-Evans, Thomas, Morello, Giuseppe, Nixon, Matthew C., Ceballos, Kevin Ortiz, Piette, Anjali A. A., Powell, Diana, Rackham, Benjamin V., Ramos-Rosado, Lakeisha, Rauscher, Emily, Redfield, Seth, Rogers, Laura K., Roman, Michael T., Roudier, Gael M., Scarsdale, Nicholas, Shkolnik, Evgenya L., Southworth, John, Spake, Jessica J., Steinrueck, Maria E, Tan, Xianyu, Teske, Johanna K., Tremblin, Pascal, Tsai, Shang-Min, Tucker, Gregory S., Turner, Jake D., Valenti, Jeff A., Venot, Olivia, Waldmann, Ingo P., Wallack, Nicole L., Zhang, Xi, and Zieba, Sebastian
- Subjects
Astrophysics - Earth and Planetary Astrophysics - Abstract
Carbon dioxide (CO2) is a key chemical species that is found in a wide range of planetary atmospheres. In the context of exoplanets, CO2 is an indicator of the metal enrichment (i.e., elements heavier than helium, also called "metallicity"), and thus formation processes of the primary atmospheres of hot gas giants. It is also one of the most promising species to detect in the secondary atmospheres of terrestrial exoplanets. Previous photometric measurements of transiting planets with the Spitzer Space Telescope have given hints of the presence of CO2 but have not yielded definitive detections due to the lack of unambiguous spectroscopic identification. Here we present the detection of CO2 in the atmosphere of the gas giant exoplanet WASP-39b from transmission spectroscopy observations obtained with JWST as part of the Early Release Science Program (ERS). The data used in this study span 3.0 to 5.5 {\mu}m in wavelength and show a prominent CO2 absorption feature at 4.3 {\mu}m (26{\sigma} significance). The overall spectrum is well matched by one-dimensional, 10x solar metallicity models that assume radiative-convective-thermochemical equilibrium and have moderate cloud opacity. These models predict that the atmosphere should have water, carbon monoxide, and hydrogen sulfide in addition to CO2, but little methane. Furthermore, we also tentatively detect a small absorption feature near 4.0 {\mu}m that is not reproduced by these models., Comment: 27 pages, 6 figures, Accepted for publication in Nature, data and models available at https://doi.10.5281/zenodo.6959427
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- 2022
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41. Don't Pay Attention to the Noise: Learning Self-supervised Representations of Light Curves with a Denoising Time Series Transformer
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Morvan, Mario, Nikolaou, Nikolaos, Yip, Kai Hou, and Waldmann, Ingo
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Astrophysics - Instrumentation and Methods for Astrophysics ,Statistics - Machine Learning - Abstract
Astrophysical light curves are particularly challenging data objects due to the intensity and variety of noise contaminating them. Yet, despite the astronomical volumes of light curves available, the majority of algorithms used to process them are still operating on a per-sample basis. To remedy this, we propose a simple Transformer model -- called Denoising Time Series Transformer (DTST) -- and show that it excels at removing the noise and outliers in datasets of time series when trained with a masked objective, even when no clean targets are available. Moreover, the use of self-attention enables rich and illustrative queries into the learned representations. We present experiments on real stellar light curves from the Transiting Exoplanet Space Satellite (TESS), showing advantages of our approach compared to traditional denoising techniques., Comment: ICML 2022 Workshop: Machine Learning for Astrophysics
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- 2022
42. A library of quantitative markers of seizure severity
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Gascoigne, Sarah J., Waldmann, Leonard, Panagiotopoulou, Mariella, Chowdhury, Fahmida, Cronie, Alison, Diehl, Beate, Duncan, John S., Falconer, Jennifer, Guan, Yu, Leach, Veronica, Livingstone, Shona, Papasavvas, Christoforos, Faulder, Ryan, Blickwedel, Jess, Schroeder, Gabrielle M., Thomas, Rhys H., Wilson, Kevin, Taylor, Peter N., and Wang, Yujiang
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Quantitative Biology - Neurons and Cognition - Abstract
Purpose: Understanding fluctuations of seizure severity within individuals is important for defining treatment outcomes and response to therapy, as well as developing novel treatments for epilepsy. Current methods for grading seizure severity rely on qualitative interpretations from patients and clinicians. Quantitative measures of seizure severity would complement existing approaches, for EEG monitoring, outcome monitoring, and seizure prediction. Therefore, we developed a library of quantitative electroencephalographic (EEG) markers that assess the spread and intensity of abnormal electrical activity during and after seizures. Methods: We analysed intracranial EEG (iEEG) recordings of 1056 seizures from 63 patients. For each seizure, we computed 16 markers of seizure severity that capture the signal magnitude, spread, duration, and post-ictal suppression of seizures. Results: Quantitative EEG markers of seizure severity distinguished focal vs. subclinical and focal vs. FTBTC seizures across patients. In individual patients, 71% had a moderate to large difference (ranksum r > 0.3) between focal and subclinical seizures in three or more markers. Circadian and longer-term changes in severity were found for 67% and 53% of patients, respectively. Conclusion: We demonstrate the feasibility of using quantitative iEEG markers to measure seizure severity. Our quantitative markers distinguish between seizure types and are therefore sensitive to established qualitative differences in seizure severity. Our results also suggest that seizure severity is modulated over different timescales. We envisage that our proposed seizure severity library will be expanded and updated in collaboration with the epilepsy research community to include more measures and modalities., Comment: 30 pages main text, 18 pages supplementary. Six main figures, two supplementary figures
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- 2022
43. ESA-Ariel Data Challenge NeurIPS 2022: Inferring Physical Properties of Exoplanets From Next-Generation Telescopes
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Yip, Kai Hou, Waldmann, Ingo P., Changeat, Quentin, Morvan, Mario, Al-Refaie, Ahmed F., Edwards, Billy, Nikolaou, Nikolaos, Tsiaras, Angelos, de Oliveira, Catarina Alves, Lagage, Pierre-Olivier, Jenner, Clare, Cho, James Y-K., Thiyagalingam, Jeyan, and Tinetti, Giovanna
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics ,Physics - Data Analysis, Statistics and Probability - Abstract
The study of extra-solar planets, or simply, exoplanets, planets outside our own Solar System, is fundamentally a grand quest to understand our place in the Universe. Discoveries in the last two decades have re-defined our understanding of planets, and helped us comprehend the uniqueness of our very own Earth. In recent years the focus has shifted from planet detection to planet characterisation, where key planetary properties are inferred from telescope observations using Monte Carlo-based methods. However, the efficiency of sampling-based methodologies is put under strain by the high-resolution observational data from next generation telescopes, such as the James Webb Space Telescope and the Ariel Space Mission. We are delighted to announce the acceptance of the Ariel ML Data Challenge 2022 as part of the NeurIPS competition track. The goal of this challenge is to identify a reliable and scalable method to perform planetary characterisation. Depending on the chosen track, participants are tasked to provide either quartile estimates or the approximate distribution of key planetary properties. To this end, a synthetic spectroscopic dataset has been generated from the official simulators for the ESA Ariel Space Mission. The aims of the competition are three-fold. 1) To offer a challenging application for comparing and advancing conditional density estimation methods. 2) To provide a valuable contribution towards reliable and efficient analysis of spectroscopic data, enabling astronomers to build a better picture of planetary demographics, and 3) To promote the interaction between ML and exoplanetary science. The competition is open from 15th June and will run until early October, participants of all skill levels are more than welcomed!, Comment: 13 pages, Accepted in the Conference on Neural Information Processing Systems 2022 (NeurIPS 2022), Competition hosted on https://www.ariel-datachallenge.space/
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- 2022
44. Mortality from upper gastrointestinal tumors in colorectal cancer screening patients
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Jasmin Zessner-Spitzenberg, Elisabeth Waldmann, Lisa-Maria Rockenbauer, Daniela Penz, Anna Hinterberger, Barbara Majcher, Arno Asaturi, Michael Trauner, and Monika Ferlitsch
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Endoscopy Lower GI Tract ,Polyps / adenomas / ... ,CRC screening ,Epidemiology ,Endoscopic ultrasonography ,Gastric cancer ,Esophageal cancer ,Diseases of the digestive system. Gastroenterology ,RC799-869 - Published
- 2024
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45. Abwerten, Aussortieren, Separieren
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Maximilian Waldmann
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Algorithmische Ungleichheit ,Maschinenhabitus ,Algorithmische Apparate ,Pierre Bourdieu ,Karen Barad ,Reflexion ,Special aspects of education ,LC8-6691 - Abstract
Lernende Algorithmen gelten aufgrund ihrer irreduziblen Opazität als eigenständige Akteure/Performanzen, die bestehende soziale Gefälle digital amplifizieren, neue Barrieren in technisierten sozialen Ordnungen erzeugen oder Grenzen verschieben können, die den Zugang zu gesellschaftlichen Ressourcen beschränken. Der Artikel vergleicht die beiden dominierenden Ansätze miteinander, die sich mit Entstehung und Effekten dieser automatisierten Mechanismen kritisch auseinandersetzen. Auf Basis der Gegenüberstellung werden schliesslich unterschiedliche reflexive Implikationen und eine diffraktive Lesart medienbildungstheoretischer Interventionen ausgelotet.
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- 2024
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46. Discovery of a Novel Pseudo‐Natural Product Aurora Kinase Inhibitor Chemotype through Morphological Profiling
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Lin Wang, Furkan Yilmaz, Okan Yildirim, Beate Schölermann, Sukdev Bag, Luca Greiner, Axel Pahl, Sonja Sievers, Rebecca Scheel, Carsten Strohmann, Christopher Squire, Daniel J. Foley, Slava Ziegler, Michael Grigalunas, and Herbert Waldmann
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Aurora kinase inhibitor ,indole dearomatization ,interrupted fischer indole ,morphological profiling ,pseudo‐natural products ,Science - Abstract
Abstract The pseudo‐natural product (pseudo‐NP) concept aims to combine NP fragments in arrangements that are not accessible through known biosynthetic pathways. The resulting compounds retain the biological relevance of NPs but are not yet linked to bioactivities and may therefore be best evaluated by unbiased screening methods resulting in the identification of unexpected or unprecedented bioactivities. Herein, various NP fragments are combined with a tricyclic core connectivity via interrupted Fischer indole and indole dearomatization reactions to provide a collection of highly three‐dimensional pseudo‐NPs. Target hypothesis generation by morphological profiling via the cell painting assay guides the identification of an unprecedented chemotype for Aurora kinase inhibition with both its relatively highly 3D structure and its physicochemical properties being very different from known inhibitors. Biochemical and cell biological characterization indicate that the phenotype identified by the cell painting assay corresponds to the inhibition of Aurora kinase B.
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- 2024
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47. Evaluation of commercial 18650 and 26700 sodium-ion cells and comparison with well-established lithium-ion cells
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Katharina Bischof, Vittorio Marangon, Michael Kasper, Aislim Aracil Regalado, Margret Wohlfahrt-Mehrens, Markus Hölzle, Dominic Bresser, and Thomas Waldmann
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Na-ion batteries ,Li-ion batteries ,Commercial cells ,Heating ,Specific energy ,Industrial electrochemistry ,TP250-261 ,Electric apparatus and materials. Electric circuits. Electric networks ,TK452-454.4 - Abstract
Recently, the first sodium-ion cells have been commercialized and have become available for consumers. Given, moreover, the exciting announcements by several producers of such battery cells, it is of great interest to analyze these first commercial cells in order to understand which materials are used and how these cells are designed. Herein, two types of commercially available sodium-ion battery cells (cylindrical 1.5 Ah 18650 and 3.5 Ah 26700 cells) are investigated regarding (i) their electrode chemistry, (ii) their thermal properties upon discharge as a function of the applied C rate, (iii) the available specific energy, and (iv) their cell impedance. The data are correlated with the electrode thickness and electrode area obtained from an ex situ (ante-mortem) analysis of the 18650 cells, and discussed in comparison with the performance metrics reported for commercial lithium-ion cells. This comparison reveals that the herein studied 18650 sodium-ion cells (hard carbon⎪⎪NaxNiyFezMn1-y-zO2) provide a comparable or even higher specific energy (∼128 Wh kg−1) than that of graphite⎪⎪LiFePO4 lithium-ion cells.
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- 2024
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48. To Sample or Not To Sample: Retrieving Exoplanetary Spectra with Variational Inference and Normalising Flows
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Yip, Kai Hou, Changeat, Quentin, Al-Refaie, Ahmed, and Waldmann, Ingo
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
Current endeavours in exoplanet characterisation rely on atmospheric retrieval to quantify crucial physical properties of remote exoplanets from observations. However, the scalability and efficiency of the technique are under strain with increasing spectroscopic resolution and forward model complexity. The situation becomes more acute with the recent launch of the James Webb Space Telescope and other upcoming missions. Recent advances in Machine Learning provide optimisation-based Variational Inference as an alternative approach to perform approximate Bayesian Posterior Inference. In this investigation we combined Normalising Flow-based neural network with our newly developed differentiable forward model, Diff-Tau, to perform Bayesian Inference in the context of atmospheric retrieval. Using examples from real and simulated spectroscopic data, we demonstrated the superiority of our proposed framework: 1) Training Our neural network only requires a single observation; 2) It produces high-fidelity posterior distributions similar to sampling-based retrieval and; 3) It requires 75% less forward model computation to converge. 4.) We performed, for the first time, Bayesian model selection on our trained neural network. Our proposed framework contribute towards the latest development of a neural-powered atmospheric retrieval. Its flexibility and speed hold the potential to complement sampling-based approaches in large and complex data sets in the future., Comment: 16 pages, 4 figures, Published in ApJ
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- 2022
49. Five key exoplanet questions answered via the analysis of 25 hot Jupiter atmospheres in eclipse
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Changeat, Quentin, Edwards, Billy, Al-Refaie, Ahmed F., Tsiaras, Angelos, Skinner, Jack W., Cho, James Y-K, Yip, Kai H., Anisman, Lara, Ikoma, Masahiro, Bieger, Michelle F., Venot, Olivia, Shibata, Sho, Waldmann, Ingo P., and Tinetti, Giovanna
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Astrophysics - Earth and Planetary Astrophysics ,Astrophysics - Instrumentation and Methods for Astrophysics - Abstract
Population studies of exoplanets are key to unlocking their statistical properties. So far the inferred properties have been mostly limited to planetary, orbital and stellar parameters extracted from, e.g., Kepler, radial velocity, and GAIA data. More recently an increasing number of exoplanet atmospheres have been observed in detail from space and the ground. Generally, however, these atmospheric studies have focused on individual planets, with the exception of a couple of works which have detected the presence of water vapor and clouds in populations of gaseous planets via transmission spectroscopy. Here, using a suite of retrieval tools, we analyse spectroscopic and photometric data of 25 hot Jupiters, obtained with the Hubble and Spitzer Space Telescopes via the eclipse technique. By applying the tools uniformly across the entire set of 25 planets, we extract robust trends in the thermal structure and chemical properties of hot Jupiters not obtained in past studies. With the recent launch of JWST and the upcoming missions Twinkle, and Ariel, population based studies of exoplanet atmospheres, such as the one presented here, will be a key approach to understanding planet characteristics, formation, and evolution in our galaxy., Comment: 66 pages, 23 figures, 7 tables. Published in The Astrophysical Journal Supplement Series
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- 2022
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50. Systematic investigation of critical charge limits in Thick GEMs
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Gasik, P., Lautner, L., Fabbietti, L., Fribert, H., Klemenz, T., Mathis, A., Ulukutlu, B., and Waldmann, T.
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Physics - Plasma Physics ,Physics - Instrumentation and Detectors - Abstract
We present discharge probability studies performed with a single Thick Gas Electron Multiplier (THGEM) irradiated with alpha particles in Ar-CO$_2$ and Ne-CO$_2$ mixtures. We observe a clear dependency of the discharge stability on the noble gas and quencher content pointing to lighter gases being more stable against the development of streamer discharges. A detailed comparison of the measurements with Geant4 simulations allowed us to extract the critical charge value leading to the formation of a spark in a THGEM hole, which is found to be within the range of 3-7$\times10^6$ electrons, depending on the gas mixture. Our experimental findings are compared to previous GEM results. We show that the discharge probability of THGEMs exceeds the one measured with GEMs by orders of magnitude. This can be explained with simple geometrical considerations, where primary ionization is collected by a lower number of holes available in a THGEM structure, reaching higher primary charge densities and thus increasing the probability of a spark occurrence. However, we show that the critical charge limits are similar for both amplification structures., Comment: 10 pages, 8 figures
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- 2022
- Full Text
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