@inproceedings{8135, abstract = {Discrete Morse theory has recently lead to new developments in the theory of random geometric complexes. This article surveys the methods and results obtained with this new approach, and discusses some of its shortcomings. It uses simulations to illustrate the results and to form conjectures, getting numerical estimates for combinatorial, topological, and geometric properties of weighted and unweighted Delaunay mosaics, their dual Voronoi tessellations, and the Alpha and Wrap complexes contained in the mosaics.}, author = {Edelsbrunner, Herbert and Nikitenko, Anton and Ölsböck, Katharina and Synak, Peter}, booktitle = {Topological Data Analysis}, isbn = {9783030434076}, issn = {21978549}, pages = {181--218}, publisher = {Springer Nature}, title = {{Radius functions on Poisson–Delaunay mosaics and related complexes experimentally}}, doi = {10.1007/978-3-030-43408-3_8}, volume = {15}, year = {2020}, } @article{8138, abstract = {Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration.}, author = {Zhang, J and Mazur, E and Balla, J and Gallei, Michelle C and Kalousek, P and Medveďová, Z and Li, Y and Wang, Y and Prat, Tomas and Vasileva, Mina K and Reinöhl, V and Procházka, S and Halouzka, R and Tarkowski, P and Luschnig, C and Brewer, PB and Friml, Jiří}, issn = {2041-1723}, journal = {Nature Communications}, number = {1}, pages = {3508}, publisher = {Springer Nature}, title = {{Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization}}, doi = {10.1038/s41467-020-17252-y}, volume = {11}, year = {2020}, } @article{8139, abstract = {Clathrin-mediated endocytosis (CME) is a crucial cellular process implicated in many aspects of plant growth, development, intra- and inter-cellular signaling, nutrient uptake and pathogen defense. Despite these significant roles, little is known about the precise molecular details of how it functions in planta. In order to facilitate the direct quantitative study of plant CME, here we review current routinely used methods and present refined, standardized quantitative imaging protocols which allow the detailed characterization of CME at multiple scales in plant tissues. These include: (i) an efficient electron microscopy protocol for the imaging of Arabidopsis CME vesicles in situ, thus providing a method for the detailed characterization of the ultra-structure of clathrin-coated vesicles; (ii) a detailed protocol and analysis for quantitative live-cell fluorescence microscopy to precisely examine the temporal interplay of endocytosis components during single CME events; (iii) a semi-automated analysis to allow the quantitative characterization of global internalization of cargos in whole plant tissues; and (iv) an overview and validation of useful genetic and pharmacological tools to interrogate the molecular mechanisms and function of CME in intact plant samples.}, author = {Johnson, Alexander J and Gnyliukh, Nataliia and Kaufmann, Walter and Narasimhan, Madhumitha and Vert, G and Bednarek, SY and Friml, Jiří}, issn = {1477-9137}, journal = {Journal of Cell Science}, number = {15}, publisher = {The Company of Biologists}, title = {{Experimental toolbox for quantitative evaluation of clathrin-mediated endocytosis in the plant model Arabidopsis}}, doi = {10.1242/jcs.248062}, volume = {133}, year = {2020}, } @article{8142, abstract = {Cell production and differentiation for the acquisition of specific functions are key features of living systems. The dynamic network of cellular microtubules provides the necessary platform to accommodate processes associated with the transition of cells through the individual phases of cytogenesis. Here, we show that the plant hormone cytokinin fine‐tunes the activity of the microtubular cytoskeleton during cell differentiation and counteracts microtubular rearrangements driven by the hormone auxin. The endogenous upward gradient of cytokinin activity along the longitudinal growth axis in Arabidopsis thaliana roots correlates with robust rearrangements of the microtubule cytoskeleton in epidermal cells progressing from the proliferative to the differentiation stage. Controlled increases in cytokinin activity result in premature re‐organization of the microtubule network from transversal to an oblique disposition in cells prior to their differentiation, whereas attenuated hormone perception delays cytoskeleton conversion into a configuration typical for differentiated cells. Intriguingly, cytokinin can interfere with microtubules also in animal cells, such as leukocytes, suggesting that a cytokinin‐sensitive control pathway for the microtubular cytoskeleton may be at least partially conserved between plant and animal cells.}, author = {Montesinos López, Juan C and Abuzeineh, A and Kopf, Aglaja and Juanes Garcia, Alba and Ötvös, Krisztina and Petrášek, J and Sixt, Michael K and Benková, Eva}, issn = {1460-2075}, journal = {The Embo Journal}, number = {17}, publisher = {Embo Press}, title = {{Phytohormone cytokinin guides microtubule dynamics during cell progression from proliferative to differentiated stage}}, doi = {10.15252/embj.2019104238}, volume = {39}, year = {2020}, } @phdthesis{8155, abstract = {In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as transcriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal non-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters. In the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are hard to evolve or maintain. }, author = {Grah, Rok}, issn = {2663-337X}, pages = {310}, publisher = {Institute of Science and Technology Austria}, title = {{Gene regulation across scales – how biophysical constraints shape evolution}}, doi = {10.15479/AT:ISTA:8155}, year = {2020}, } @phdthesis{8156, abstract = {We present solutions to several problems originating from geometry and discrete mathematics: existence of equipartitions, maps without Tverberg multiple points, and inscribing quadrilaterals. Equivariant obstruction theory is the natural topological approach to these type of questions. However, for the specific problems we consider it had yielded only partial or no results. We get our results by complementing equivariant obstruction theory with other techniques from topology and geometry.}, author = {Avvakumov, Sergey}, issn = {2663-337X}, pages = {119}, publisher = {Institute of Science and Technology Austria}, title = {{Topological methods in geometry and discrete mathematics}}, doi = {10.15479/AT:ISTA:8156}, year = {2020}, } @article{8162, abstract = {In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity.}, author = {Laukoter, Susanne and Pauler, Florian and Beattie, Robert J and Amberg, Nicole and Hansen, Andi H and Streicher, Carmen and Penz, Thomas and Bock, Christoph and Hippenmeyer, Simon}, issn = {0896-6273}, journal = {Neuron}, number = {6}, pages = {1160--1179.e9}, publisher = {Elsevier}, title = {{Cell-type specificity of genomic imprinting in cerebral cortex}}, doi = {10.1016/j.neuron.2020.06.031}, volume = {107}, year = {2020}, } @article{8163, abstract = {Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces.}, author = {Vegter, Gert and Wintraecken, Mathijs}, issn = {1588-2896}, journal = {Studia Scientiarum Mathematicarum Hungarica}, number = {2}, pages = {193--199}, publisher = {Akadémiai Kiadó}, title = {{Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes}}, doi = {10.1556/012.2020.57.2.1454}, volume = {57}, year = {2020}, } @article{8167, abstract = {The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.}, author = {Stankowski, Sean and Westram, Anja M and Zagrodzka, Zuzanna B. and Eyres, Isobel and Broquet, Thomas and Johannesson, Kerstin and Butlin, Roger K.}, issn = {1471-2970}, journal = {Philosophical Transactions of the Royal Society. Series B: Biological Sciences}, number = {1806}, publisher = {The Royal Society}, title = {{The evolution of strong reproductive isolation between sympatric intertidal snails}}, doi = {10.1098/rstb.2019.0545}, volume = {375}, year = {2020}, } @article{8168, abstract = {Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.}, author = {Kulmuni, Jonna and Butlin, Roger K. and Lucek, Kay and Savolainen, Vincent and Westram, Anja M}, issn = {1471-2970}, journal = {Philosophical Transactions of the Royal Society. Series B: Biological sciences}, number = {1806}, publisher = {The Royal Society}, title = {{Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers}}, doi = {10.1098/rstb.2019.0528}, volume = {375}, year = {2020}, } @article{8170, abstract = {Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function of time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct peaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and centrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For CS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the gas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in detail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in helium droplets introduced here should apply to a range of molecules and complexes.}, author = {Chatterley, Adam S. and Christiansen, Lars and Schouder, Constant A. and Jørgensen, Anders V. and Shepperson, Benjamin and Cherepanov, Igor and Bighin, Giacomo and Zillich, Robert E. and Lemeshko, Mikhail and Stapelfeldt, Henrik}, issn = {10797114}, journal = {Physical Review Letters}, number = {1}, publisher = {American Physical Society}, title = {{Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains}}, doi = {10.1103/PhysRevLett.125.013001}, volume = {125}, year = {2020}, } @misc{8181, author = {Hauschild, Robert}, publisher = {IST Austria}, title = {{Amplified centrosomes in dendritic cells promote immune cell effector functions}}, doi = {10.15479/AT:ISTA:8181}, year = {2020}, } @inproceedings{8186, abstract = {Numerous methods have been proposed for probabilistic generative modelling of 3D objects. However, none of these is able to produce textured objects, which renders them of limited use for practical tasks. In this work, we present the first generative model of textured 3D meshes. Training such a model would traditionally require a large dataset of textured meshes, but unfortunately, existing datasets of meshes lack detailed textures. We instead propose a new training methodology that allows learning from collections of 2D images without any 3D information. To do so, we train our model to explain a distribution of images by modelling each image as a 3D foreground object placed in front of a 2D background. Thus, it learns to generate meshes that when rendered, produce images similar to those in its training set. A well-known problem when generating meshes with deep networks is the emergence of self-intersections, which are problematic for many use-cases. As a second contribution we therefore introduce a new generation process for 3D meshes that guarantees no self-intersections arise, based on the physical intuition that faces should push one another out of the way as they move. We conduct extensive experiments on our approach, reporting quantitative and qualitative results on both synthetic data and natural images. These show our method successfully learns to generate plausible and diverse textured 3D samples for five challenging object classes.}, author = {Henderson, Paul M and Tsiminaki, Vagia and Lampert, Christoph}, booktitle = {Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition}, issn = {2575-7075}, location = {Virtual}, pages = {7498--7507}, publisher = {IEEE}, title = {{Leveraging 2D data to learn textured 3D mesh generation}}, doi = {10.1109/CVPR42600.2020.00752}, year = {2020}, } @inproceedings{8188, abstract = {A natural approach to generative modeling of videos is to represent them as a composition of moving objects. Recent works model a set of 2D sprites over a slowly-varying background, but without considering the underlying 3D scene that gives rise to them. We instead propose to model a video as the view seen while moving through a scene with multiple 3D objects and a 3D background. Our model is trained from monocular videos without any supervision, yet learns to generate coherent 3D scenes containing several moving objects. We conduct detailed experiments on two datasets, going beyond the visual complexity supported by state-of-the-art generative approaches. We evaluate our method on depth-prediction and 3D object detection---tasks which cannot be addressed by those earlier works---and show it out-performs them even on 2D instance segmentation and tracking.}, author = {Henderson, Paul M and Lampert, Christoph}, booktitle = {34th Conference on Neural Information Processing Systems}, isbn = {9781713829546}, location = {Vancouver, Canada}, pages = {3106–3117}, publisher = {Curran Associates}, title = {{Unsupervised object-centric video generation and decomposition in 3D}}, volume = {33}, year = {2020}, } @article{8190, author = {Sixt, Michael K and Huttenlocher, Anna}, issn = {1540-8140}, journal = {The Journal of Cell Biology}, number = {8}, publisher = {Rockefeller University Press}, title = {{Zena Werb (1945-2020): Cell biology in context}}, doi = {10.1083/jcb.202007029}, volume = {219}, year = {2020}, } @inproceedings{8194, abstract = {Fixed-point arithmetic is a popular alternative to floating-point arithmetic on embedded systems. Existing work on the verification of fixed-point programs relies on custom formalizations of fixed-point arithmetic, which makes it hard to compare the described techniques or reuse the implementations. In this paper, we address this issue by proposing and formalizing an SMT theory of fixed-point arithmetic. We present an intuitive yet comprehensive syntax of the fixed-point theory, and provide formal semantics for it based on rational arithmetic. We also describe two decision procedures for this theory: one based on the theory of bit-vectors and the other on the theory of reals. We implement the two decision procedures, and evaluate our implementations using existing mature SMT solvers on a benchmark suite we created. Finally, we perform a case study of using the theory we propose to verify properties of quantized neural networks.}, author = {Baranowski, Marek and He, Shaobo and Lechner, Mathias and Nguyen, Thanh Son and Rakamarić, Zvonimir}, booktitle = {Automated Reasoning}, isbn = {9783030510732}, issn = {16113349}, location = {Paris, France}, pages = {13--31}, publisher = {Springer Nature}, title = {{An SMT theory of fixed-point arithmetic}}, doi = {10.1007/978-3-030-51074-9_2}, volume = {12166}, year = {2020}, } @inproceedings{8195, abstract = {This paper presents a foundation for refining concurrent programs with structured control flow. The verification problem is decomposed into subproblems that aid interactive program development, proof reuse, and automation. The formalization in this paper is the basis of a new design and implementation of the Civl verifier.}, author = {Kragl, Bernhard and Qadeer, Shaz and Henzinger, Thomas A}, booktitle = {Computer Aided Verification}, isbn = {9783030532871}, issn = {1611-3349}, pages = {275--298}, publisher = {Springer Nature}, title = {{Refinement for structured concurrent programs}}, doi = {10.1007/978-3-030-53288-8_14}, volume = {12224}, year = {2020}, } @article{8199, abstract = {We investigate a mechanism to transiently stabilize topological phenomena in long-lived quasi-steady states of isolated quantum many-body systems driven at low frequencies. We obtain an analytical bound for the lifetime of the quasi-steady states which is exponentially large in the inverse driving frequency. Within this lifetime, the quasi-steady state is characterized by maximum entropy subject to the constraint of fixed number of particles in the system's Floquet-Bloch bands. In such a state, all the non-universal properties of these bands are washed out, hence only the topological properties persist.}, author = {Gulden, Tobias and Berg, Erez and Rudner, Mark Spencer and Lindner, Netanel}, issn = {2542-4653}, journal = {SciPost Physics}, publisher = {SciPost Foundation}, title = {{Exponentially long lifetime of universal quasi-steady states in topological Floquet pumps}}, doi = {10.21468/scipostphys.9.1.015}, volume = {9}, year = {2020}, } @article{8203, abstract = {Using inelastic cotunneling spectroscopy we observe a zero field splitting within the spin triplet manifold of Ge hut wire quantum dots. The states with spin ±1 in the confinement direction are energetically favored by up to 55 μeV compared to the spin 0 triplet state because of the strong spin–orbit coupling. The reported effect should be observable in a broad class of strongly confined hole quantum-dot systems and might need to be considered when operating hole spin qubits.}, author = {Katsaros, Georgios and Kukucka, Josip and Vukušić, Lada and Watzinger, Hannes and Gao, Fei and Wang, Ting and Zhang, Jian-Jun and Held, Karsten}, issn = {1530-6992}, journal = {Nano Letters}, number = {7}, pages = {5201--5206}, publisher = {American Chemical Society}, title = {{Zero field splitting of heavy-hole states in quantum dots}}, doi = {10.1021/acs.nanolett.0c01466}, volume = {20}, year = {2020}, } @article{8220, abstract = {Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings.}, author = {Corominas-Murtra, Bernat and Scheele, Colinda L.G.J. and Kishi, Kasumi and Ellenbroek, Saskia I.J. and Simons, Benjamin D. and Van Rheenen, Jacco and Hannezo, Edouard B}, issn = {10916490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {29}, pages = {16969--16975}, publisher = {National Academy of Sciences}, title = {{Stem cell lineage survival as a noisy competition for niche access}}, doi = {10.1073/pnas.1921205117}, volume = {117}, year = {2020}, }