https://research-explorer.ista.ac.at 2000-01-01T00:00+00:00 1 monthly https://research-explorer.ista.ac.at/record/9819 Mallikarjun, B. R. Tewari, Ayush Dib, Abdallah Weyrich, Tim Bickel, Bernd ; https://orcid.org/0000-0001-6511-9385 Seidel, Hans Peter Pfister, Hanspeter Matusik, Wojciech Chevallier, Louis Elgharib, Mohamed A. Theobalt, Christian 2021 Photorealistic editing of head portraits is a challenging task as humans are very sensitive to inconsistencies in faces. We present an approach for high-quality intuitive editing of the camera viewpoint and scene illumination (parameterised with an environment map) in a portrait image. This requires our method to capture and control the full reflectance field of the person in the image. Most editing approaches rely on supervised learning using training data captured with setups such as light and camera stages. Such datasets are expensive to acquire, not readily available and do not capture all the rich variations of in-the-wild portrait images. In addition, most supervised approaches only focus on relighting, and do not allow camera viewpoint editing. Thus, they only capture and control a subset of the reflectance field. Recently, portrait editing has been demonstrated by operating in the generative model space of StyleGAN. While such approaches do not require direct supervision, there is a significant loss of quality when compared to the supervised approaches. In this paper, we present a method which learns from limited supervised training data. The training images only include people in a fixed neutral expression with eyes closed, without much hair or background variations. Each person is captured under 150 one-light-at-a-time conditions and under 8 camera poses. Instead of training directly in the image space, we design a supervised problem which learns transformations in the latent space of StyleGAN. This combines the best of supervised learning and generative adversarial modeling. We show that the StyleGAN prior allows for generalisation to different expressions, hairstyles and backgrounds. This produces high-quality photorealistic results for in-the-wild images and significantly outperforms existing methods. Our approach can edit the illumination and pose simultaneously, and runs at interactive rates. https://research-explorer.ista.ac.at/record/9819 https://research-explorer.ista.ac.at/download/9819/9834 eng Association for Computing Machinery info:eu-repo/semantics/altIdentifier/doi/10.1145/3450626.3459765 info:eu-repo/semantics/altIdentifier/issn/0730-0301 info:eu-repo/semantics/altIdentifier/e-issn/1557-7368 info:eu-repo/semantics/altIdentifier/wos/000674930900011 info:eu-repo/semantics/altIdentifier/arxiv/2103.07658 https://creativecommons.org/licenses/by/4.0/ info:eu-repo/semantics/openAccess Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance editing of head portraits. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href="https://doi.org/10.1145/3450626.3459765">10.1145/3450626.3459765</a> ddc:000 PhotoApp: Photorealistic appearance editing of head portraits info:eu-repo/semantics/article doc-type:article text http://purl.org/coar/resource_type/c_2df8fbb1 https://research-explorer.ista.ac.at/record/19903 Hübner, Valentin ; https://orcid.org/0009-0001-5009-4987 2025 Cooperation, that is, one person paying a cost for another's benefit, is a fundamental principle without which no form of society could exist. The extent to which humans cooperate with each other is also an essential feature that differentiates them from other animals. Cooperation occurs even in the absence of altruistic motivations, when it is selfishly incentivised by the expectation of a future reward. For example, many economic interactions are well described that way. This kind of cooperation requires that people exhibit reciprocal behaviour that acts as a mechanism that rewards cooperation. With game-theoretic models, it is possible to formally study potential such mechanisms and under what conditions they can exist. This thesis contributes to this effort by analysing recently introduced models of cooperation that advance on previous work by taking into account the potential for pre-existing inequality among cooperating individuals as well as the different forms that reciprocity can take. Individuals may differ both intrinsically, in their abilities, as well as extrinsically, in the amount of resources they have available. Allowing for such differences in a model of cooperation helps to understand how inequality affects the potential for, and outcomes of, cooperation among unequals. In this thesis, it is shown that in the presence of intrinsic inequality, a similar unequal distribution of resources can increase the potential for cooperation. This effect is stronger the smaller the group is in which cooperation takes place. It is also shown that under particular assumptions, if the unequal members of a group vary the size of their contributions to a cooperative effort over time, they can thereby increase their efficiency and improve the collective outcome. Cooperative behaviour in a two-person interaction can be rewarded either by direct reciprocation whenever the same two people interact again, or indirectly by a third party who observed the interaction. In the latter case of indirect reciprocity, individuals are proximally rewarded by a good reputation, which ultimately translates to being rewarded with cooperative behaviour by others. This mechanism can enable selfishly motivated cooperation even in circumstances where individuals are unlikely to meet again, akin to how money facilitates trade. While these two forms of reciprocity have mostly been studied in isolation, this thesis analyses both direct and indirect reciprocity in a general model in order to compare their relative effectiveness under different circumstances. The contribution of this thesis is an extension of previous work regarding a specific kind of interaction, whose parameters allow for convenient mathematical analysis, to the most general set of possible interactions. https://research-explorer.ista.ac.at/record/19903 https://research-explorer.ista.ac.at/download/19903/19976 eng Institute of Science and Technology Austria info:eu-repo/semantics/altIdentifier/doi/10.15479/AT-ISTA-19903 info:eu-repo/semantics/altIdentifier/issn/2663-337X https://creativecommons.org/licenses/by-nc/4.0/ info:eu-repo/semantics/openAccess Hübner V. Reciprocity and inequality in social dilemmas. 2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-19903">10.15479/AT-ISTA-19903</a> ddc:519 Reciprocity and inequality in social dilemmas ISTA Thesis info:eu-repo/semantics/doctoralThesis doc-type:doctoralThesis text http://purl.org/coar/resource_type/c_db06 https://research-explorer.ista.ac.at/record/9402 Schmid, Laura ; https://orcid.org/0000-0002-6978-7329 Chatterjee, Krishnendu ; https://orcid.org/0000-0002-4561-241X Hilbe, Christian ; https://orcid.org/0000-0001-5116-955X Nowak, Martin A. 2021 Direct and indirect reciprocity are key mechanisms for the evolution of cooperation. Direct reciprocity means that individuals use their own experience to decide whether to cooperate with another person. Indirect reciprocity means that they also consider the experiences of others. Although these two mechanisms are intertwined, they are typically studied in isolation. Here, we introduce a mathematical framework that allows us to explore both kinds of reciprocity simultaneously. We show that the well-known ‘generous tit-for-tat’ strategy of direct reciprocity has a natural analogue in indirect reciprocity, which we call ‘generous scoring’. Using an equilibrium analysis, we characterize under which conditions either of the two strategies can maintain cooperation. With simulations, we additionally explore which kind of reciprocity evolves when members of a population engage in social learning to adapt to their environment. Our results draw unexpected connections between direct and indirect reciprocity while highlighting important differences regarding their evolvability. https://research-explorer.ista.ac.at/record/9402 https://research-explorer.ista.ac.at/download/9402/14496 eng Springer Nature info:eu-repo/semantics/altIdentifier/doi/10.1038/s41562-021-01114-8 info:eu-repo/semantics/altIdentifier/e-issn/2397-3374 info:eu-repo/semantics/altIdentifier/wos/000650304000002 info:eu-repo/semantics/altIdentifier/pmid/33986519 info:eu-repo/semantics/openAccess Schmid L, Chatterjee K, Hilbe C, Nowak MA. A unified framework of direct and indirect reciprocity. <i>Nature Human Behaviour</i>. 2021;5(10):1292–1302. doi:<a href="https://doi.org/10.1038/s41562-021-01114-8">10.1038/s41562-021-01114-8</a> ddc:000 A unified framework of direct and indirect reciprocity info:eu-repo/semantics/article doc-type:article text http://purl.org/coar/resource_type/c_2df8fbb1 https://research-explorer.ista.ac.at/record/21517 Roques-Carmes, Charles Bodin, N. Monteil, G. Quiniou, J.F. 2001 In our new approach, the notion of conformal equivalent structure is introduced by comparing the slope or gradient distributions of surface topography in 2D or 3D mode, respectively. The stereological approach described in Section 2 is, thus, confirmed by the numerical one which is proposed in this paper. The approach emphasizes the viability of the modeling and the limits observed in some practical applications of the study of rough surfaces via different approximation methods. The few divergences which have been noticed may be explained by the introduction of parameters such as skewness and kurtosis. https://research-explorer.ista.ac.at/record/21517 eng Elsevier info:eu-repo/semantics/altIdentifier/doi/10.1016/s0043-1648(00)00563-9 info:eu-repo/semantics/altIdentifier/issn/0043-1648 info:eu-repo/semantics/altIdentifier/e-issn/1873-2577 info:eu-repo/semantics/closedAccess Roques-Carmes C, Bodin N, Monteil G, Quiniou JF. Description of rough surfaces using conformal equivalent structure concept: Part 2. Numerical approach. <i>Wear</i>. 2001;248(1-2):92-99. doi:<a href="https://doi.org/10.1016/s0043-1648(00)00563-9">10.1016/s0043-1648(00)00563-9</a> Rough surface topography Equivalent structure concept Description of rough surfaces using conformal equivalent structure concept: Part 2. Numerical approach info:eu-repo/semantics/article doc-type:article text http://purl.org/coar/resource_type/c_2df8fbb1 https://research-explorer.ista.ac.at/record/470 Jeschke, Stefan ; https://orcid.org/0000-0003-4330-8884 Wojtan, Christopher J ; https://orcid.org/0000-0001-6646-5546 2017 This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios. https://research-explorer.ista.ac.at/record/470 https://research-explorer.ista.ac.at/download/470/7359 eng ACM info:eu-repo/semantics/altIdentifier/doi/10.1145/3072959.3073678 info:eu-repo/semantics/altIdentifier/issn/0730-0301 info:eu-repo/semantics/altIdentifier/wos/000406432100071 info:eu-repo/semantics/openAccess Jeschke S, Wojtan C. Water wave packets. <i>ACM Transactions on Graphics</i>. 2017;36(4). doi:<a href="https://doi.org/10.1145/3072959.3073678">10.1145/3072959.3073678</a> ddc:006 Water wave packets info:eu-repo/semantics/article doc-type:article text http://purl.org/coar/resource_type/c_2df8fbb1 https://research-explorer.ista.ac.at/record/9826 Auerbach, Benedikt ; https://orcid.org/0000-0002-7553-6606 Chakraborty, Suvradip Klein, Karen Pascual Perez, Guillermo ; https://orcid.org/0000-0001-8630-415X Pietrzak, Krzysztof Z ; https://orcid.org/0000-0002-9139-1654 Walter, Michael ; https://orcid.org/0000-0003-3186-2482 Yeo, Michelle X ; https://orcid.org/0009-0001-3676-4809 2021 Automated contract tracing aims at supporting manual contact tracing during pandemics by alerting users of encounters with infected people. There are currently many proposals for protocols (like the “decentralized” DP-3T and PACT or the “centralized” ROBERT and DESIRE) to be run on mobile phones, where the basic idea is to regularly broadcast (using low energy Bluetooth) some values, and at the same time store (a function of) incoming messages broadcasted by users in their proximity. In the existing proposals one can trigger false positives on a massive scale by an “inverse-Sybil” attack, where a large number of devices (malicious users or hacked phones) pretend to be the same user, such that later, just a single person needs to be diagnosed (and allowed to upload) to trigger an alert for all users who were in proximity to any of this large group of devices. We propose the first protocols that do not succumb to such attacks assuming the devices involved in the attack do not constantly communicate, which we observe is a necessary assumption. The high level idea of the protocols is to derive the values to be broadcasted by a hash chain, so that two (or more) devices who want to launch an inverse-Sybil attack will not be able to connect their respective chains and thus only one of them will be able to upload. Our protocols also achieve security against replay, belated replay, and one of them even against relay attacks. https://research-explorer.ista.ac.at/record/9826 eng Springer Nature info:eu-repo/semantics/altIdentifier/doi/10.1007/978-3-030-75539-3_17 info:eu-repo/semantics/altIdentifier/issn/0302-9743 info:eu-repo/semantics/altIdentifier/e-issn/1611-3349 info:eu-repo/semantics/altIdentifier/isbn/9783030755386 info:eu-repo/semantics/openAccess Auerbach B, Chakraborty S, Klein K, et al. Inverse-Sybil attacks in automated contact tracing. In: <i>Topics in Cryptology – CT-RSA 2021</i>. Vol 12704. Springer Nature; 2021:399-421. doi:<a href="https://doi.org/10.1007/978-3-030-75539-3_17">10.1007/978-3-030-75539-3_17</a> Inverse-Sybil attacks in automated contact tracing LNCS info:eu-repo/semantics/conferenceObject doc-type:conferenceObject text http://purl.org/coar/resource_type/c_5794 https://research-explorer.ista.ac.at/record/6029 Lindner, Marco Tresztenyak, Aliz Fülöp, Gergö Jahr, Wiebke ; https://orcid.org/0000-0003-0201-2315 Prinz, Adrian Prinz, Iris Danzl, Johann G ; https://orcid.org/0000-0001-8559-3973 Schütz, Gerhard J. Sevcsik, Eva 2019 Protein micropatterning has become an important tool for many biomedical applications as well as in academic research. Current techniques that allow to reduce the feature size of patterns below 1 μm are, however, often costly and require sophisticated equipment. We present here a straightforward and convenient method to generate highly condensed nanopatterns of proteins without the need for clean room facilities or expensive equipment. Our approach is based on nanocontact printing and allows for the fabrication of protein patterns with feature sizes of 80 nm and periodicities down to 140 nm. This was made possible by the use of the material X-poly(dimethylsiloxane) (X-PDMS) in a two-layer stamp layout for protein printing. In a proof of principle, different proteins at various scales were printed and the pattern quality was evaluated by atomic force microscopy (AFM) and super-resolution fluorescence microscopy. https://research-explorer.ista.ac.at/record/6029 https://research-explorer.ista.ac.at/download/6029/6039 eng Frontiers Media S.A. info:eu-repo/semantics/altIdentifier/doi/10.3389/fchem.2018.00655 info:eu-repo/semantics/altIdentifier/e-issn/2296-2646 info:eu-repo/semantics/altIdentifier/wos/000456718000001 info:eu-repo/semantics/openAccess Lindner M, Tresztenyak A, Fülöp G, et al. A fast and simple contact printing approach to generate 2D protein nanopatterns. <i>Frontiers in Chemistry</i>. 2019;6. doi:<a href="https://doi.org/10.3389/fchem.2018.00655">10.3389/fchem.2018.00655</a> ddc:540 A fast and simple contact printing approach to generate 2D protein nanopatterns info:eu-repo/semantics/article doc-type:article text http://purl.org/coar/resource_type/c_2df8fbb1 https://research-explorer.ista.ac.at/record/1001 Guseinov, Ruslan ; https://orcid.org/0000-0001-9819-5077 Miguel, Eder Bickel, Bernd ; https://orcid.org/0000-0001-6511-9385 2017 We present a computational approach for designing CurveUps, curvy shells that form from an initially flat state. They consist of small rigid tiles that are tightly held together by two pre-stretched elastic sheets attached to them. Our method allows the realization of smooth, doubly curved surfaces that can be fabricated as a flat piece. Once released, the restoring forces of the pre-stretched sheets support the object to take shape in 3D. CurveUps are structurally stable in their target configuration. The design process starts with a target surface. Our method generates a tile layout in 2D and optimizes the distribution, shape, and attachment areas of the tiles to obtain a configuration that is fabricable and in which the curved up state closely matches the target. Our approach is based on an efficient approximate model and a local optimization strategy for an otherwise intractable nonlinear optimization problem. We demonstrate the effectiveness of our approach for a wide range of shapes, all realized as physical prototypes. https://research-explorer.ista.ac.at/record/1001 https://research-explorer.ista.ac.at/download/1001/4811 eng ACM info:eu-repo/semantics/altIdentifier/doi/10.1145/3072959.3073709 info:eu-repo/semantics/altIdentifier/wos/000406432100032 info:eu-repo/semantics/openAccess Guseinov R, Miguel E, Bickel B. CurveUps: Shaping objects from flat plates with tension-actuated curvature. In: Vol 36. ACM; 2017. doi:<a href="https://doi.org/10.1145/3072959.3073709">10.1145/3072959.3073709</a> ddc:003 ddc:004 CurveUps: Shaping objects from flat plates with tension-actuated curvature ACM Transactions on Graphics info:eu-repo/semantics/conferenceObject doc-type:conferenceObject text http://purl.org/coar/resource_type/c_5794 https://research-explorer.ista.ac.at/record/319 Gerencser, Mate Hairer, Martin 2019 We study spaces of modelled distributions with singular behaviour near the boundary of a domain that, in the context of the theory of regularity structures, allow one to give robust solution theories for singular stochastic PDEs with boundary conditions. The calculus of modelled distributions established in Hairer (Invent Math 198(2):269–504, 2014. https://doi.org/10.1007/s00222-014-0505-4) is extended to this setting. We formulate and solve fixed point problems in these spaces with a class of kernels that is sufficiently large to cover in particular the Dirichlet and Neumann heat kernels. These results are then used to provide solution theories for the KPZ equation with Dirichlet and Neumann boundary conditions and for the 2D generalised parabolic Anderson model with Dirichlet boundary conditions. In the case of the KPZ equation with Neumann boundary conditions, we show that, depending on the class of mollifiers one considers, a “boundary renormalisation” takes place. In other words, there are situations in which a certain boundary condition is applied to an approximation to the KPZ equation, but the limiting process is the Hopf–Cole solution to the KPZ equation with a different boundary condition. https://research-explorer.ista.ac.at/record/319 https://research-explorer.ista.ac.at/download/319/5722 eng Springer info:eu-repo/semantics/altIdentifier/doi/10.1007/s00440-018-0841-1 info:eu-repo/semantics/altIdentifier/issn/0178-8051 info:eu-repo/semantics/altIdentifier/e-issn/1432-2064 info:eu-repo/semantics/altIdentifier/wos/000463613800001 info:eu-repo/semantics/openAccess Gerencser M, Hairer M. Singular SPDEs in domains with boundaries. <i>Probability Theory and Related Fields</i>. 2019;173(3-4):697–758. doi:<a href="https://doi.org/10.1007/s00440-018-0841-1">10.1007/s00440-018-0841-1</a> ddc:510 Singular SPDEs in domains with boundaries info:eu-repo/semantics/article doc-type:article text http://purl.org/coar/resource_type/c_2df8fbb1 https://research-explorer.ista.ac.at/record/11842 Hensel, Sebastian ; https://orcid.org/0000-0001-7252-8072 Marveggio, Alice 2022 We consider the flow of two viscous and incompressible fluids within a bounded domain modeled by means of a two-phase Navier–Stokes system. The two fluids are assumed to be immiscible, meaning that they are separated by an interface. With respect to the motion of the interface, we consider pure transport by the fluid flow. Along the boundary of the domain, a complete slip boundary condition for the fluid velocities and a constant ninety degree contact angle condition for the interface are assumed. In the present work, we devise for the resulting evolution problem a suitable weak solution concept based on the framework of varifolds and establish as the main result a weak-strong uniqueness principle in 2D. The proof is based on a relative entropy argument and requires a non-trivial further development of ideas from the recent work of Fischer and the first author (Arch. Ration. Mech. Anal. 236, 2020) to incorporate the contact angle condition. To focus on the effects of the necessarily singular geometry of the evolving fluid domains, we work for simplicity in the regime of same viscosities for the two fluids. https://research-explorer.ista.ac.at/record/11842 https://research-explorer.ista.ac.at/download/11842/11848 eng Springer Nature info:eu-repo/semantics/altIdentifier/doi/10.1007/s00021-022-00722-2 info:eu-repo/semantics/altIdentifier/issn/1422-6928 info:eu-repo/semantics/altIdentifier/e-issn/1422-6952 info:eu-repo/semantics/altIdentifier/wos/000834834300001 info:eu-repo/semantics/altIdentifier/arxiv/2112.11154 info:eu-repo/semantics/openAccess Hensel S, Marveggio A. Weak-strong uniqueness for the Navier–Stokes equation for two fluids with ninety degree contact angle and same viscosities. <i>Journal of Mathematical Fluid Mechanics</i>. 2022;24(3). doi:<a href="https://doi.org/10.1007/s00021-022-00722-2">10.1007/s00021-022-00722-2</a> ddc:510 Weak-strong uniqueness for the Navier–Stokes equation for two fluids with ninety degree contact angle and same viscosities info:eu-repo/semantics/article doc-type:article text http://purl.org/coar/resource_type/c_2df8fbb1 https://research-explorer.ista.ac.at/record/9820 Serrano, Ana Chen, Bin Wang, Chao Piovarci, Michael ; https://orcid.org/0000-0002-5062-4474 Seidel, Hans Peter Didyk, Piotr Myszkowski, Karol 2021 Material appearance hinges on material reflectance properties but also surface geometry and illumination. The unlimited number of potential combinations between these factors makes understanding and predicting material appearance a very challenging task. In this work, we collect a large-scale dataset of perceptual ratings of appearance attributes with more than 215,680 responses for 42,120 distinct combinations of material, shape, and illumination. The goal of this dataset is twofold. First, we analyze for the first time the effects of illumination and geometry in material perception across such a large collection of varied appearances. We connect our findings to those of the literature, discussing how previous knowledge generalizes across very diverse materials, shapes, and illuminations. Second, we use the collected dataset to train a deep learning architecture for predicting perceptual attributes that correlate with human judgments. We demonstrate the consistent and robust behavior of our predictor in various challenging scenarios, which, for the first time, enables estimating perceived material attributes from general 2D images. Since our predictor relies on the final appearance in an image, it can compare appearance properties across different geometries and illumination conditions. Finally, we demonstrate several applications that use our predictor, including appearance reproduction using 3D printing, BRDF editing by integrating our predictor in a differentiable renderer, illumination design, or material recommendations for scene design. https://research-explorer.ista.ac.at/record/9820 eng Association for Computing Machinery info:eu-repo/semantics/altIdentifier/doi/10.1145/3450626.3459813 info:eu-repo/semantics/altIdentifier/issn/0730-0301 info:eu-repo/semantics/altIdentifier/e-issn/1557-7368 info:eu-repo/semantics/altIdentifier/wos/000674930900090 info:eu-repo/semantics/openAccess Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on material perception: Model and applications. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href="https://doi.org/10.1145/3450626.3459813">10.1145/3450626.3459813</a> The effect of shape and illumination on material perception: Model and applications info:eu-repo/semantics/article doc-type:article text http://purl.org/coar/resource_type/c_2df8fbb1 https://research-explorer.ista.ac.at/record/201 Iglesias Ham, Mabel 2018 We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications. https://research-explorer.ista.ac.at/record/201 https://research-explorer.ista.ac.at/download/201/5919 eng Institute of Science and Technology Austria info:eu-repo/semantics/altIdentifier/doi/10.15479/AT:ISTA:th_1026 info:eu-repo/semantics/altIdentifier/issn/2663-337X info:eu-repo/semantics/openAccess Iglesias Ham M. Multiple covers with balls. 2018. doi:<a href="https://doi.org/10.15479/AT:ISTA:th_1026">10.15479/AT:ISTA:th_1026</a> ddc:514 ddc:516 Multiple covers with balls ISTA Thesis info:eu-repo/semantics/doctoralThesis doc-type:doctoralThesis text http://purl.org/coar/resource_type/c_db06 https://research-explorer.ista.ac.at/record/19593 Hübschmann, Verena Korkut, Medina ; https://orcid.org/0000-0003-4309-2251 Venturino, Alessandro ; https://orcid.org/0000-0003-2356-9403 Maya-Arteaga, Juan Pablo Siegert, Sandra ; https://orcid.org/0000-0001-8635-0877 2025 Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, our knowledge about the safe usage of anti-inflammatory drugs during pregnancy is still limited. While human induced pluripotent stem cells (hIPSC)-derived brain organoid models have started to explore functional consequences upon viral stimulation, these models commonly lack microglia, which are susceptible to and promote inflammation. Furthermore, microglia are actively involved in neuronal development. Here, we generate hIPSC-derived microglia precursor cells and assemble them into retinal organoids. Once the outer plexiform layer forms, these hIPSC-derived microglia (iMG) fully integrate into the retinal organoids. Since the ganglion cell survival declines by this time in 3D-retinal organoids, we adapted the model into 2D and identify that the improved ganglion cell number significantly decreases only with iMG presence. In parallel, we applied the immunostimulant POLY(I:C) to mimic a fetal viral infection. While POLY(I:C) exposure alters the iMG phenotype, it does not hinder their interaction with ganglion cells. Furthermore, iMG significantly enhance the supernatant’s inflammatory secretome and increase retinal cell proliferation. Simultaneous exposure with the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated changes of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG, ibuprofen rescues this effect only if iMG are present. Mechanistically, ibuprofen targets the enzymes cyclooxygenase 1 and 2 (COX1/PTGS1 and COX2/PTGS2) simultaneously, from which iMG mainly express COX1. Selective COX1 blockage fails to restore the calcium peak amplitude upon POLY(I:C) stimulation, suggesting ibuprofen’s beneficial effect depends on the presence and interplay of COX1 and COX2. These findings underscore the importance of microglia in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development. https://research-explorer.ista.ac.at/record/19593 https://research-explorer.ista.ac.at/download/19593/19607 eng Springer Nature info:eu-repo/semantics/altIdentifier/doi/10.1186/s12974-025-03366-x info:eu-repo/semantics/altIdentifier/e-issn/1742-2094 info:eu-repo/semantics/altIdentifier/wos/001459311800002 info:eu-repo/semantics/altIdentifier/pmid/40181459 info:eu-repo/semantics/openAccess Hübschmann V, Korkut M, Venturino A, Maya-Arteaga JP, Siegert S. Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids. <i>Journal of Neuroinflammation</i>. 2025;22(1). doi:<a href="https://doi.org/10.1186/s12974-025-03366-x">10.1186/s12974-025-03366-x</a> ddc:570 Microglia determine an immune-challenged environment and facilitate ibuprofen action in human retinal organoids info:eu-repo/semantics/article doc-type:article text http://purl.org/coar/resource_type/c_2df8fbb1 https://research-explorer.ista.ac.at/record/19763 Rus, Stefanie ; https://orcid.org/0000-0001-8703-1093 2025 Pattern formation in developing organs is controlled by morphogens. These signalling molecules form concentration gradients across tissues, thereby providing positional information that instructs the pattern of cell differentiation. Morphogen gradients are highly dynamic in space and time. Many factors such as morphogen production, spreading, degradation, cellular rearrangements and others could contribute to changes in the gradient shape, yet how the spatiotemporal signalling dynamics arise in many systems is still unclear. We studied the dynamics of morphogen signalling and tissue patterning in the developing vertebrate neural tube. In this system, neural crest, roof plate and distinct dorsal progenitor subtypes are specified in a spatially and temporally ordered manner in response to dorsal-toventral gradients of BMP and WNT signalling activity. How the BMP and WNT gradients are established and interpreted to ensure ordered cell specification is poorly understood. To address this question, we developed a 2D embryonic stem cell differentiation system that captures key features of dorsal neural tube development. In this system, differentiated colonies display remarkable self-organised pattern formation in response to uniformly applied BMP ligand. We established a method of differentiating the colonies using microfabricated stencils, which allowed us to control the initial size and shape of colonies without confining cell migration and colony growth. This led to highly reproducible pattern formation that facilitates quantification. Using this approach, we observed striking two-phase temporal dynamics of BMP signalling in our colonies: a BMP gradient rapidly forms from the periphery to the centre of colonies, subsequently disappears and is re-established again in the second phase. By combining our quantitative data with a data-driven theoretical model, we uncovered a temporal relay mechanism that underlies this biphasic BMP signalling dynamics. The first signalling phase is controlled by fast tissue-autonomous negative feedback that restricts the duration of the initial response to BMP. The early BMP activity gradient moreover controls the spatial organisation of the cell type pattern: the absence of a first phase results in disordered cell type pattern. The second phase is controlled by slow positive regulation of BMP signalling by the transcription factor LMX1A, a key regulator of roof plate identity. WNT promotes the second phase of BMP signalling via positive feedback on LMX1A. Altogether, the mechanism that we uncovered ensures the coupling of sequential developmental events, making pattern formation spatially and temporally organised. Furthermore, this mechanism allows the BMP signalling pathway to be reused in different contexts – first for the establishment of the neural plate border, and subsequently for dorsal neural progenitor patterning. Our study supports a general developmental principle in which multiple morphogens interact with transcriptional networks resulting in complex spatiotemporal signalling dynamics that ultimately drive organised pattern formation. https://research-explorer.ista.ac.at/record/19763 https://research-explorer.ista.ac.at/download/19763/19764 eng Institute of Science and Technology Austria info:eu-repo/semantics/altIdentifier/doi/10.15479/AT-ISTA-19763 info:eu-repo/semantics/altIdentifier/issn/2663-337X https://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess Rus S. Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube. 2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-19763">10.15479/AT-ISTA-19763</a> ddc:570 Dynamics of morphogen signalling and cell fate decisions in the dorsal neural tube ISTA Thesis info:eu-repo/semantics/doctoralThesis doc-type:doctoralThesis text http://purl.org/coar/resource_type/c_db06 https://research-explorer.ista.ac.at/record/20276 Bhargava, Manas ; https://orcid.org/0009-0007-6138-6890 2025 Complex 3D shapes can be created by morphing flat 2D configurations. Such deformations either preserve the intrinsic material geometry (e.g., folding paper) or modify it through localized contraction. Once transformed, the 3D shape can be further controlled to achieve a target functionality. A key challenge is to take the material specifications and the actuation process as input to automatically design the target 3D shape and its functionality. This thesis presents two novel computational pipelines for the design and control of shape-morphing structures used to create functional prototypes. The first pipeline borrows from the art of origami to fold paper into intricate shapes and applies this principle to make 3D lighting displays. We introduce, PCBend a computational design approach that covers a surface with individually addressable RGB LEDs, effectively forming a low-resolution surface by folding rigid printed circuit boards (PCBs). We optimize cut patterns on PCBs to act as hinges and co-design LED placement, circuit routing, and fabrication constraints to produce PCB blueprints. The PCBs are fabricated using automated standard manufacturing services with LEDs embedded on them. Finally, the fabricated PCBs are cut along the contour and folded onto a 3D-printed support. The 3D lighting display is then controlled to display complex surface light patterns. Creating 3D shapes through folding is only possible if their planar configuration, called ”unfolding” exists without any distortion or overlap. Existing methods often permit distortion or require multiple patches, which are unsuitable for fabrication pipelines that rely on folding non-stretchable materials. We reinforce such fabrication pipelines by providing a geometric relaxation to the problem, where the input shape is modified to admit overlap-free unfolding. The second fabrication pipeline extends shape morphing to soft robotics by emulating nature’s blueprint of distributed actuation. Inspired by vertebrates, we build musculoskeletal robots using modular active actuators, employing Liquid Crystal Elastomers (LCEs) as shrinkable artificial muscles integrated with 3D-printed bones. The chemical composition of LCEs is altered to enable untethered actuation through infrared radiation, allowing active control of individual muscles and their corresponding bones. The combined motion of individual bones defines the robot’s overall shape and functionality. Our proposed system significantly expands both the design and control spaces of soft robots, which we harness using our computational design tools. We build several physical robots that exhibit complex shape morphing and varied terrain navigation, showcasing the versatility of our pipeline. This thesis explores applications ranging from intricate light patterns displayed on 3D shapes formed by folding rigid PCBs to untethered robots that use contractile muscles to exhibit shape morphing and locomotion. Through these examples, the thesis highlights how computational design and distributed actuation, integrated with novel materials, can transform passive structures into functional prototypes. https://research-explorer.ista.ac.at/record/20276 https://research-explorer.ista.ac.at/download/20276/20284 eng Institute of Science and Technology Austria info:eu-repo/semantics/altIdentifier/doi/10.15479/AT-ISTA-20276 info:eu-repo/semantics/altIdentifier/issn/2663-337X info:eu-repo/semantics/altIdentifier/isbn/978-3-99078-065-7 info:eu-repo/semantics/openAccess Bhargava M. Design and control of deformable structures: From PCB lighting displays to elastomer robots. 2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-20276">10.15479/AT-ISTA-20276</a> ddc:000 Design and control of deformable structures: From PCB lighting displays to elastomer robots ISTA Thesis info:eu-repo/semantics/doctoralThesis doc-type:doctoralThesis text http://purl.org/coar/resource_type/c_db06 https://research-explorer.ista.ac.at/record/19684 Yalniz, Gökhan ; https://orcid.org/0000-0002-8490-9312 2025 The overarching goal of this thesis is to break down the complexity of turbulent flows in terms of enumerable, coherent structures and patterns. In a five-paper series, we adopt a variety of perspectives and techniques to relate the properties of systems of increasing complexity to their underlying coherent structures. Initially, we take a dynamical systems point of view, seeing turbulent flow as a chaotic trajectory bouncing between exact unstable solutions of the underlying equations of motion. Using persistent homology, the main tool of topological data analysis capturing the persistence across scales of topological features in a point cloud, we introduce a method that quantifies visits of turbulent trajectories to unstable time-periodic solutions, also called periodic orbits. We demonstrate this method first in the Rössler and Kuramoto–Sivashinsky systems. Using this method in 3D Kolmogorov flow, we extract a Markov chain from turbulent data, where each node corresponds to the neighbourhood of a periodic orbit. The invariant distribution of this Markov chain reproduces expectation values on turbulent data when it is used to weight averages on the respective periodic orbits. In more realistic, wall-bounded settings, such as plane-Couette flow (pcf) driven by the relative motion of the walls, or plane-Poiseuille flow (ppf) driven by a pressure gradient, finding exact solutions is difficult. We use dynamic mode decomposition (DMD), a dimensionality reduction method for sequential data, to identify and approximate low-dimensional dynamics without knowing any exact solutions. Most spatially-extended systems are equivariant under translations, and in such cases spatial drifts dominate DMD, hindering its use in the search for and modelling of low-dimensional dynamics. We augment DMD with a symmetry reduction method trained on turbulent data to stop it from seeing translations as a feature, improving its ability to extract dynamical information in translation-equivariant systems. We find segments of turbulent trajectories that linearize well with their symmetry-reduced DMD spectra, akin to dynamics near exact solutions. Searching for harmonics in the spectra gives leads for periodic orbits with spatial drifts, one of which converges to a new solution. In larger domains, turbulence can localize and coexist with surrounding laminar flow. Our preceding approaches are global, taking all of a domain into account at once, and cannot readily treat each localized patch individually. Working first in a minimal oblique domain that can host a single 1D-localized turbulent patch, we find that turbulence in ppf is connected to a stable periodic orbit at a flow velocity much lower than when turbulence is first onset. We show that, well in advance of sustained turbulence, chaos sets in explosively, and for long time horizons, time series are consistent with that of a random process. Finally, in much larger domains, we study and compare 2D-localized turbulence that appears as large-scale inclined structures, called stripes, in ppf and pcf. While appearing similar, we find that stripes in these two settings differ significantly in terms of how they sustain themselves, and in higher velocities, how they proliferate. https://research-explorer.ista.ac.at/record/19684 https://research-explorer.ista.ac.at/download/19684/19685 https://research-explorer.ista.ac.at/download/19684/19686 https://research-explorer.ista.ac.at/download/19684/19687 https://research-explorer.ista.ac.at/download/19684/19688 https://research-explorer.ista.ac.at/download/19684/19689 https://research-explorer.ista.ac.at/download/19684/19690 https://research-explorer.ista.ac.at/download/19684/19691 https://research-explorer.ista.ac.at/download/19684/19692 https://research-explorer.ista.ac.at/download/19684/19693 https://research-explorer.ista.ac.at/download/19684/19694 eng Institute of Science and Technology Austria info:eu-repo/semantics/altIdentifier/doi/10.15479/AT-ISTA-19684 info:eu-repo/semantics/altIdentifier/issn/2663-337X info:eu-repo/semantics/openAccess Yalniz G. Transition to turbulence : Data-, solution-, and pattern-driven approaches. 2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-19684">10.15479/AT-ISTA-19684</a> ddc:514 ddc:519 ddc:532 ddc:004 Transition to turbulence : Data-, solution-, and pattern-driven approaches ISTA Thesis info:eu-repo/semantics/doctoralThesis doc-type:doctoralThesis text http://purl.org/coar/resource_type/c_db06 https://research-explorer.ista.ac.at/record/12964 Boocock, Daniel R ; https://orcid.org/0000-0002-1585-2631 2023 Pattern formation is of great importance for its contribution across different biological behaviours. During developmental processes for example, patterns of chemical gradients are established to determine cell fate and complex tissue patterns emerge to define structures such as limbs and vascular networks. Patterns are also seen in collectively migrating groups, for instance traveling waves of density emerging in moving animal flocks as well as collectively migrating cells and tissues. To what extent these biological patterns arise spontaneously through the local interaction of individual constituents or are dictated by higher level instructions is still an open question however there is evidence for the involvement of both types of process. Where patterns arise spontaneously there is a long standing interest in how far the interplay of mechanics, e.g. force generation and deformation, and chemistry, e.g. gene regulation and signaling, contributes to the behaviour. This is because many systems are able to both chemically regulate mechanical force production and chemically sense mechanical deformation, forming mechano-chemical feedback loops which can potentially become unstable towards spatio and/or temporal patterning. We work with experimental collaborators to investigate the possibility that this type of interaction drives pattern formation in biological systems at different scales. We focus first on tissue-level ERK-density waves observed during the wound healing response across different systems where many previous studies have proposed that patterns depend on polarized cell migration and arise from a mechanical flocking-like mechanism. By combining theory with mechanical and optogenetic perturbation experiments on in vitro monolayers we instead find evidence for mechanochemical pattern formation involving only scalar bilateral feedbacks between ERK signaling and cell contraction. We perform further modeling and experiment to study how this instability couples with polar cell migration in order to produce a robust and efficient wound healing response. In a following chapter we implement ERK-density coupling and cell migration in a 2D active vertex model to investigate the interaction of ERK-density patterning with different tissue rheologies and find that the spatio-temporal dynamics are able to both locally and globally fluidize a tissue across the solid-fluid glass transition. In a last chapter we move towards lower spatial scales in the context of subcellular patterning of the cell cytoskeleton where we investigate the transition between phases of spatially homogeneous temporal oscillations and chaotic spatio-temporal patterning in the dynamics of myosin and ROCK activities (a motor component of the actomyosin cytoskeleton and its activator). Experimental evidence supports an intrinsic chemical oscillator which we encode in a reaction model and couple to a contractile active gel description of the cell cortex. The model exhibits phases of chemical oscillations and contractile spatial patterning which reproduce many features of the dynamics seen in Drosophila oocyte epithelia in vivo. However, additional pharmacological perturbations to inhibit myosin contractility leaves the role of contractile instability unclear. We discuss alternative hypotheses and investigate the possibility of reaction-diffusion instability. https://research-explorer.ista.ac.at/record/12964 https://research-explorer.ista.ac.at/download/12964/12988 eng Institute of Science and Technology Austria info:eu-repo/semantics/altIdentifier/doi/10.15479/at:ista:12964 info:eu-repo/semantics/altIdentifier/issn/2663-337X info:eu-repo/semantics/altIdentifier/isbn/978-3-99078-032-9 https://creativecommons.org/licenses/by-nc-sa/4.0/ info:eu-repo/semantics/openAccess Boocock DR. Mechanochemical pattern formation across biological scales. 2023. doi:<a href="https://doi.org/10.15479/at:ista:12964">10.15479/at:ista:12964</a> ddc:530 Mechanochemical pattern formation across biological scales ISTA Thesis info:eu-repo/semantics/doctoralThesis doc-type:doctoralThesis text http://purl.org/coar/resource_type/c_db06 https://research-explorer.ista.ac.at/record/20074 Hübschmann, Verena 2025 Prenatal immune challenges pose significant risks to human embryonic brain and eye development. However, we still lack knowledge about the safe usage of anti-inflammatory drugs during pregnancy. Human induced pluripotent stem cell (hIPSC)-derived brain organoid models provide a unique opportunity to investigate neuronal development and have started to explore functional consequences upon viral infection. However, brain organoids usually lack microglia, the brain-resident immune cells. They are present in the early human embryonic brain and actively participate in neuronal circuit development. At the same time, microglia are known for their immune-sensing properties and will influence viral-mediated effects. In my thesis, I was interested to study the multifunctional role of human microglia during retinal development. In chapter 1, I characterize the innate occurrence of IBA1+-microglia-like cells within the retinal organoid differentiation (Bartalska et al., 2022). Therefore, we differentiate hIPSC using an unguided retinal organoid differentiation protocol and observe the presence of IBA1+-microglia-like cells alongside retinal cups between week 3 and 4 in 2.5D culture. However, instead of infiltrating the neuroectodermal sides, they enrich within non-pigmented, 3D-cystic compartments that develop in low numbers parallel to 3D-retinal organoids. To enrich for IBA1+-microglia precursors (preMG), we guided the differentiation with a low-dosed BMP4 application, which prevents retinal cup development and enhances microglia and 3D-cysts formation. We characterize the differentiated preMG for their microglia-like identity and validated their functionality. In parallel, mass spectrometry identifies the 3D-cysts to express mesenchymal and epithelial markers. We confirm that comparable 3D-cysts are also the preferential environment for IBA1+-microglia-like cells within the unguided retinal organoid differentiation. In chapter 2, I investigate how microglia influence retinal development and whether they contribute to viral-mediated consequences (Schmied et al., 2025). Here, we assemble preMG, which we have characterized in chapter 1, into 3D-retinal organoids. Once the outer plexiform layer forms, microglia-like cells (iMG) populate them and interact with retinal cell types. However, at this developmental stage, the ganglion cell number decreases in 3D-retinal organoids. Thus, we adapted the model into 2D which promotes their survival. Integrated iMG engulf ganglion cells and control their cell number. In parallel, we apply the immunostimulant POLY(I:C) to mimic a fetal viral infection. Although POLY(I:C) stimulation affects iMG phenotype, it does not influence their interaction with ganglion cells. Furthermore, iMG presence significantly contributes to the supernatant’s inflammatory secretome and increases retinal cell proliferation. Simultaneous exposure to the non-steroidal anti-inflammatory drug (NSAID) ibuprofen dampens POLY(I:C)-mediated consequences of the iMG phenotype and ameliorates cell proliferation. Remarkably, while POLY(I:C) disrupts neuronal calcium dynamics independent of iMG presence, ibuprofen rescues this effect only in the presence of iMG. Mechanistically, ibuprofen blocks the enzymes cyclooxygenase 1 and 2 (COX1/ PTGS1 and COX2/ PTGS2) simultaneously, from which iMG predominantly express COX1. Selective inhibition of COX1 does not restore the calcium peak amplitude upon POLY(I:C) stimulation, indicating ibuprofen’s effect depends on the presence and interplay of both, COX1 and COX2. In summary, we characterized the 3D-retinal organoid model for the occurrence of IBA1+-microglia like cells. As the innately developing IBA1+-cells enrich in mesenchymal over retinal structures, we optimized a protocol to differentiate IBA1+-microglia precursors. By combining these two models we generate microglia-assembled retinal organoids. Our results underscore the importance of microglia during neurodevelopment, in the context of prenatal immune challenges and provide insight into the mechanisms by which ibuprofen exerts its protective effects during embryonic development. https://research-explorer.ista.ac.at/record/20074 https://research-explorer.ista.ac.at/download/20074/20087 eng Institute of Science and Technology Austria info:eu-repo/semantics/altIdentifier/doi/10.15479/AT-ISTA-20074 info:eu-repo/semantics/altIdentifier/issn/2663-337X info:eu-repo/semantics/altIdentifier/isbn/978-3-99078-060-2 info:eu-repo/semantics/openAccess Schmied V. Human microglia impact neuronal development in retinal organoids. 2025. doi:<a href="https://doi.org/10.15479/AT-ISTA-20074">10.15479/AT-ISTA-20074</a> ddc:570 Human microglia impact neuronal development in retinal organoids ISTA Thesis info:eu-repo/semantics/doctoralThesis doc-type:doctoralThesis text http://purl.org/coar/resource_type/c_db06