@misc{11542, author = {Schulz, Rouven}, publisher = {Institute of Science and Technology Austria}, title = {{Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses)}}, doi = {10.15479/AT:ISTA:11542}, year = {2022}, } @article{11556, abstract = {We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the oscillations with respect to fluctuations and noise.}, author = {Kalinov, Aleksei and Osinskiy, A.I. and Matveev, S.A. and Otieno, W. and Brilliantov, N.V.}, issn = {0021-9991}, journal = {Journal of Computational Physics}, keywords = {Computer Science Applications, Physics and Astronomy (miscellaneous), Applied Mathematics, Computational Mathematics, Modeling and Simulation, Numerical Analysis}, publisher = {Elsevier}, title = {{Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics}}, doi = {10.1016/j.jcp.2022.111439}, volume = {467}, year = {2022}, } @phdthesis{11626, abstract = {Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.}, author = {Gallei, Michelle C}, isbn = {978-3-99078-019-0}, issn = {2663-337X}, pages = {248}, publisher = {Institute of Science and Technology Austria}, title = {{Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana}}, doi = {10.15479/at:ista:11626}, year = {2022}, } @misc{11653, abstract = {Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.}, author = {Elkrewi, Marwan N}, publisher = {Institute of Science and Technology Austria}, title = {{Data from Elkrewi, Khauratovich, Toups et al. 2022, "ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp"}}, doi = {10.15479/AT:ISTA:11653}, year = {2022}, } @article{11658, abstract = {The depth of a cell in an arrangement of n (non-vertical) great-spheres in Sd is the number of great-spheres that pass above the cell. We prove Euler-type relations, which imply extensions of the classic Dehn–Sommerville relations for convex polytopes to sublevel sets of the depth function, and we use the relations to extend the expressions for the number of faces of neighborly polytopes to the number of cells of levels in neighborly arrangements.}, author = {Biswas, Ranita and Cultrera di Montesano, Sebastiano and Edelsbrunner, Herbert and Saghafian, Morteza}, journal = {Leibniz International Proceedings on Mathematics}, publisher = {Schloss Dagstuhl - Leibniz Zentrum für Informatik}, title = {{Depth in arrangements: Dehn–Sommerville–Euler relations with applications}}, year = {2022}, } @article{11660, abstract = {We characterize critical points of 1-dimensional maps paired in persistent homology geometrically and this way get elementary proofs of theorems about the symmetry of persistence diagrams and the variation of such maps. In particular, we identify branching points and endpoints of networks as the sole source of asymmetry and relate the cycle basis in persistent homology with a version of the stable marriage problem. Our analysis provides the foundations of fast algorithms for maintaining collections of interrelated sorted lists together with their persistence diagrams. }, author = {Biswas, Ranita and Cultrera di Montesano, Sebastiano and Edelsbrunner, Herbert and Saghafian, Morteza}, journal = {LIPIcs}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs}}, year = {2022}, } @article{11723, abstract = {Plant cell growth responds rapidly to various stimuli, adapting architecture to environmental changes. Two major endogenous signals regulating growth are the phytohormone auxin and the secreted peptides rapid alkalinization factors (RALFs). Both trigger very rapid cellular responses and also exert long-term effects [Du et al., Annu. Rev. Plant Biol. 71, 379–402 (2020); Blackburn et al., Plant Physiol. 182, 1657–1666 (2020)]. However, the way, in which these distinct signaling pathways converge to regulate growth, remains unknown. Here, using vertical confocal microscopy combined with a microfluidic chip, we addressed the mechanism of RALF action on growth. We observed correlation between RALF1-induced rapid Arabidopsis thaliana root growth inhibition and apoplast alkalinization during the initial phase of the response, and revealed that RALF1 reversibly inhibits primary root growth through apoplast alkalinization faster than within 1 min. This rapid apoplast alkalinization was the result of RALF1-induced net H+ influx and was mediated by the receptor FERONIA (FER). Furthermore, we investigated the cross-talk between RALF1 and the auxin signaling pathways during root growth regulation. The results showed that RALF-FER signaling triggered auxin signaling with a delay of approximately 1 h by up-regulating auxin biosynthesis, thus contributing to sustained RALF1-induced growth inhibition. This biphasic RALF1 action on growth allows plants to respond rapidly to environmental stimuli and also reprogram growth and development in the long term.}, author = {Li, Lanxin and Chen, Huihuang and Alotaibi, Saqer S. and Pěnčík, Aleš and Adamowski, Maciek and Novák, Ondřej and Friml, Jiří}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Multidisciplinary}, number = {31}, publisher = {Proceedings of the National Academy of Sciences}, title = {{RALF1 peptide triggers biphasic root growth inhibition upstream of auxin biosynthesis}}, doi = {10.1073/pnas.2121058119}, volume = {119}, year = {2022}, } @article{11732, abstract = {We study the BCS energy gap Ξ in the high–density limit and derive an asymptotic formula, which strongly depends on the strength of the interaction potential V on the Fermi surface. In combination with the recent result by one of us (Math. Phys. Anal. Geom. 25, 3, 2022) on the critical temperature Tc at high densities, we prove the universality of the ratio of the energy gap and the critical temperature.}, author = {Henheik, Sven Joscha and Lauritsen, Asbjørn Bækgaard}, issn = {1572-9613}, journal = {Journal of Statistical Physics}, keywords = {Mathematical Physics, Statistical and Nonlinear Physics}, publisher = {Springer Nature}, title = {{The BCS energy gap at high density}}, doi = {10.1007/s10955-022-02965-9}, volume = {189}, year = {2022}, } @inproceedings{11775, abstract = {Quantitative monitoring can be universal and approximate: For every finite sequence of observations, the specification provides a value and the monitor outputs a best-effort approximation of it. The quality of the approximation may depend on the resources that are available to the monitor. By taking to the limit the sequences of specification values and monitor outputs, we obtain precision-resource trade-offs also for limit monitoring. This paper provides a formal framework for studying such trade-offs using an abstract interpretation for monitors: For each natural number n, the aggregate semantics of a monitor at time n is an equivalence relation over all sequences of at most n observations so that two equivalent sequences are indistinguishable to the monitor and thus mapped to the same output. This abstract interpretation of quantitative monitors allows us to measure the number of equivalence classes (or “resource use”) that is necessary for a certain precision up to a certain time, or at any time. Our framework offers several insights. For example, we identify a family of specifications for which any resource-optimal exact limit monitor is independent of any error permitted over finite traces. Moreover, we present a specification for which any resource-optimal approximate limit monitor does not minimize its resource use at any time. }, author = {Henzinger, Thomas A and Mazzocchi, Nicolas Adrien and Sarac, Naci E}, booktitle = {22nd International Conference on Runtime Verification}, issn = {0302-9743}, location = {Tbilisi, Georgia}, pages = {200--220}, publisher = {Springer Nature}, title = {{Abstract monitors for quantitative specifications}}, doi = {10.1007/978-3-031-17196-3_11}, volume = {13498}, year = {2022}, } @phdthesis{11777, abstract = {In this dissertation we study coboundary expansion of simplicial complex with a view of giving geometric applications. Our main novel tool is an equivariant version of Gromov's celebrated Topological Overlap Theorem. The equivariant topological overlap theorem leads to various geometric applications including a quantitative non-embeddability result for sufficiently thick buildings (which partially resolves a conjecture of Tancer and Vorwerk) and an improved lower bound on the pair-crossing number of (bounded degree) expander graphs. Additionally, we will give new proofs for several known lower bounds for geometric problems such as the number of Tverberg partitions or the crossing number of complete bipartite graphs. For the aforementioned applications one is naturally lead to study expansion properties of joins of simplicial complexes. In the presence of a special certificate for expansion (as it is the case, e.g., for spherical buildings), the join of two expanders is an expander. On the flip-side, we report quite some evidence that coboundary expansion exhibits very non-product-like behaviour under taking joins. For instance, we exhibit infinite families of graphs $(G_n)_{n\in \mathbb{N}}$ and $(H_n)_{n\in\mathbb{N}}$ whose join $G_n*H_n$ has expansion of lower order than the product of the expansion constant of the graphs. Moreover, we show an upper bound of $(d+1)/2^d$ on the normalized coboundary expansion constants for the complete multipartite complex $[n]^{*(d+1)}$ (under a mild divisibility condition on $n$). Via the probabilistic method the latter result extends to an upper bound of $(d+1)/2^d+\varepsilon$ on the coboundary expansion constant of the spherical building associated with $\mathrm{PGL}_{d+2}(\mathbb{F}_q)$ for any $\varepsilon>0$ and sufficiently large $q=q(\varepsilon)$. This disproves a conjecture of Lubotzky, Meshulam and Mozes -- in a rather strong sense. By improving on existing lower bounds we make further progress towards closing the gap between the known lower and upper bounds on the coboundary expansion constants of $[n]^{*(d+1)}$. The best improvements we achieve using computer-aided proofs and flag algebras. The exact value even for the complete $3$-partite $2$-dimensional complex $[n]^{*3}$ remains unknown but we are happy to conjecture a precise value for every $n$. %Moreover, we show that a previously shown lower bound on the expansion constant of the spherical building associated with $\mathrm{PGL}_{2}(\mathbb{F}_q)$ is not tight. In a loosely structured, last chapter of this thesis we collect further smaller observations related to expansion. We point out a link between discrete Morse theory and a technique for showing coboundary expansion, elaborate a bit on the hardness of computing coboundary expansion constants, propose a new criterion for coboundary expansion (in a very dense setting) and give one way of making the folklore result that expansion of links is a necessary condition for a simplicial complex to be an expander precise.}, author = {Wild, Pascal}, isbn = {978-3-99078-021-3}, issn = {2663-337X}, pages = {170}, publisher = {Institute of Science and Technology}, title = {{High-dimensional expansion and crossing numbers of simplicial complexes}}, doi = {10.15479/at:ista:11777}, year = {2022}, } @inproceedings{11839, abstract = {It is a highly desirable property for deep networks to be robust against small input changes. One popular way to achieve this property is by designing networks with a small Lipschitz constant. In this work, we propose a new technique for constructing such Lipschitz networks that has a number of desirable properties: it can be applied to any linear network layer (fully-connected or convolutional), it provides formal guarantees on the Lipschitz constant, it is easy to implement and efficient to run, and it can be combined with any training objective and optimization method. In fact, our technique is the first one in the literature that achieves all of these properties simultaneously. Our main contribution is a rescaling-based weight matrix parametrization that guarantees each network layer to have a Lipschitz constant of at most 1 and results in the learned weight matrices to be close to orthogonal. Hence we call such layers almost-orthogonal Lipschitz (AOL). Experiments and ablation studies in the context of image classification with certified robust accuracy confirm that AOL layers achieve results that are on par with most existing methods. Yet, they are simpler to implement and more broadly applicable, because they do not require computationally expensive matrix orthogonalization or inversion steps as part of the network architecture. We provide code at https://github.com/berndprach/AOL.}, author = {Prach, Bernd and Lampert, Christoph}, booktitle = {Computer Vision – ECCV 2022}, isbn = {9783031198021}, location = {Tel Aviv, Israel}, pages = {350--365}, publisher = {Springer Nature}, title = {{Almost-orthogonal layers for efficient general-purpose Lipschitz networks}}, doi = {10.1007/978-3-031-19803-8_21}, volume = {13681}, year = {2022}, } @phdthesis{11879, abstract = {As the overall global mean surface temperature is increasing due to climate change, plant adaptation to those stressful conditions is of utmost importance for their survival. Plants are sessile organisms, thus to compensate for their lack of mobility, they evolved a variety of mechanisms enabling them to flexibly adjust their physiological, growth and developmental processes to fluctuating temperatures and to survive in harsh environments. While these unique adaptation abilities provide an important evolutionary advantage, overall modulation of plant growth and developmental program due to non-optimal temperature negatively affects biomass production, crop productivity or sensitivity to pathogens. Thus, understanding molecular processes underlying plant adaptation to increased temperature can provide important resources for breeding strategies to ensure sufficient agricultural food production. An increase in ambient temperature by a few degrees leads to profound changes in organ growth including enhanced hypocotyl elongation, expansion of petioles, hyponastic growth of leaves and cotyledons, collectively named thermomorphogenesis (Casal & Balasubramanian, 2019). Auxin, one of the best-studied growth hormones, plays an essential role in this process by direct activation of transcriptional and non-transcriptional processes resulting in elongation growth (Majda & Robert, 2018).To modulate hypocotyl growth in response to high ambient temperature (hAT), auxin needs to be redistributed accordingly. PINs, auxin efflux transporters, are key components of the polar auxin transport (PAT) machinery, which controls the amount and direction of auxin translocated in the plant tissues and organs(Adamowski & Friml, 2015). Hence, PIN-mediated transport is tightly linked with thermo-morphogenesis, and interference with PAT through either chemical or genetic means dramatically affecting the adaptive responses to hAT. Intriguingly, despite the key role of PIN mediated transport in growth response to hAT, whether and how PINs at the level of expression adapt to fluctuation in temperature is scarcely understood. With genetic, molecular and advanced bio-imaging approaches, we demonstrate the role of PIN auxin transporters in the regulation of hypocotyl growth in response to hAT. We show that via adjustment of PIN3, PIN4 and PIN7 expression in cotyledons and hypocotyls, auxin distribution is modulated thereby determining elongation pattern of epidermal cells at hAT. Furthermore, we identified three Zinc-Finger (ZF) transcription factors as novel molecular components of the thermo-regulatory network, which through negative regulation of PIN transcription adjust the transport of auxin at hAT. Our results suggest that the ZF-PIN module might be a part of the negative feedback loop attenuating the activity of the thermo-sensing pathway to restrain exaggerated growth and developmental responses to hAT.}, author = {Artner, Christina}, isbn = {978-3-99078-022-0}, issn = {2663-337X}, keywords = {high ambient temperature, auxin, PINs, Zinc-Finger proteins, thermomorphogenesis, stress}, pages = {128}, publisher = {Institute of Science and Technology Austria}, title = {{Modulation of auxin transport via ZF proteins adjust plant response to high ambient temperature}}, doi = {10.15479/at:ista:11879}, year = {2022}, } @phdthesis{11932, abstract = {The ability to form and retrieve memories is central to survival. In mammals, the hippocampus is a brain region essential to the acquisition and consolidation of new memories. It is also involved in keeping track of one’s position in space and aids navigation. Although this space-memory has been a source of contradiction, evidence supports the view that the role of the hippocampus in navigation is memory, thanks to the formation of cognitive maps. First introduced by Tolman in 1948, cognitive maps are generally used to organize experiences in memory; however, the detailed mechanisms by which these maps are formed and stored are not yet agreed upon. Some influential theories describe this process as involving three fundamental steps: initial encoding by the hippocampus, interactions between the hippocampus and other cortical areas, and long-term extra-hippocampal consolidation. In this thesis, I will show how the investigation of cognitive maps of space helped to shed light on each of these three memory processes. The first study included in this thesis deals with the initial encoding of spatial memories in the hippocampus. Much is known about encoding at the level of single cells, but less about their co-activity or joint contribution to the encoding of novel spatial information. I will describe the structure of an interaction network that allows for efficient encoding of noisy spatial information during the first exploration of a novel environment. The second study describes the interactions between the hippocampus and the prefrontal cortex (PFC), two areas directly and indirectly connected. It is known that the PFC, in concert with the hippocampus, is involved in various processes, including memory storage and spatial navigation. Nonetheless, the detailed mechanisms by which PFC receives information from the hippocampus are not clear. I will show how a transient improvement in theta phase locking of PFC cells enables interactions of cell pairs across the two regions. The third study describes the learning of behaviorally-relevant spatial locations in the hippocampus and the medial entorhinal cortex. I will show how the accumulation of firing around goal locations, a correlate of learning, can shed light on the transition from short- to long-term spatial memories and the speed of consolidation in different brain areas. The studies included in this thesis represent the main scientific contributions of my Ph.D. They involve statistical analyses and models of neural responses of cells in different brain areas of rats executing spatial tasks. I will conclude the thesis by discussing the impact of the findings on principles of memory formation and retention, including the mechanisms, the speed, and the duration of these processes.}, author = {Nardin, Michele}, issn = {2663-337X}, pages = {136}, publisher = {Institute of Science and Technology Austria}, title = {{On the encoding, transfer, and consolidation of spatial memories}}, doi = {10.15479/at:ista:11932}, year = {2022}, } @phdthesis{11945, abstract = {G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type. We validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact. Our DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level.}, author = {Schulz, Rouven}, issn = {2663-337X}, pages = {133}, publisher = {Institute of Science and Technology Austria}, title = {{Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function}}, doi = {10.15479/at:ista:11945}, year = {2022}, } @phdthesis{12072, abstract = {In this thesis, we study two of the most important questions in Arithmetic geometry: that of the existence and density of solutions to Diophantine equations. In order for a Diophantine equation to have any solutions over the rational numbers, it must have solutions everywhere locally, i.e., over R and over Qp for every prime p. The converse, called the Hasse principle, is known to fail in general. However, it is still a central question in Arithmetic geometry to determine for which varieties the Hasse principle does hold. In this work, we establish the Hasse principle for a wide new family of varieties of the form f(t) = NK/Q(x) ̸= 0, where f is a polynomial with integer coefficients and NK/Q denotes the norm form associated to a number field K. Our results cover products of arbitrarily many linear, quadratic or cubic factors, and generalise an argument of Irving [69], which makes use of the beta sieve of Rosser and Iwaniec. We also demonstrate how our main sieve results can be applied to treat new cases of a conjecture of Harpaz and Wittenberg on locally split values of polynomials over number fields, and discuss consequences for rational points in fibrations. In the second question, about the density of solutions, one defines a height function and seeks to estimate asymptotically the number of points of height bounded by B as B → ∞. Traditionally, one either counts rational points, or integral points with respect to a suitable model. However, in this thesis, we study an emerging area of interest in Arithmetic geometry known as Campana points, which in some sense interpolate between rational and integral points. More precisely, we count the number of nonzero integers z1, z2, z3 such that gcd(z1, z2, z3) = 1, and z1, z2, z3, z1 + z2 + z3 are all squareful and bounded by B. Using the circle method, we obtain an asymptotic formula which agrees in the power of B and log B with a bold new generalisation of Manin’s conjecture to the setting of Campana points, recently formulated by Pieropan, Smeets, Tanimoto and Várilly-Alvarado [96]. However, in this thesis we also provide the first known counterexamples to leading constant predicted by their conjecture. }, author = {Shute, Alec L}, isbn = {978-3-99078-023-7}, issn = {2663-337X}, pages = {208}, publisher = {Institute of Science and Technology Austria}, title = {{Existence and density problems in Diophantine geometry: From norm forms to Campana points}}, doi = {10.15479/at:ista:12072}, year = {2022}, } @inproceedings{12102, abstract = {Given a Markov chain M = (V, v_0, δ), with state space V and a starting state v_0, and a probability threshold ε, an ε-core is a subset C of states that is left with probability at most ε. More formally, C ⊆ V is an ε-core, iff ℙ[reach (V\C)] ≤ ε. Cores have been applied in a wide variety of verification problems over Markov chains, Markov decision processes, and probabilistic programs, as a means of discarding uninteresting and low-probability parts of a probabilistic system and instead being able to focus on the states that are likely to be encountered in a real-world run. In this work, we focus on the problem of computing a minimal ε-core in a Markov chain. Our contributions include both negative and positive results: (i) We show that the decision problem on the existence of an ε-core of a given size is NP-complete. This solves an open problem posed in [Jan Kretínský and Tobias Meggendorfer, 2020]. We additionally show that the problem remains NP-complete even when limited to acyclic Markov chains with bounded maximal vertex degree; (ii) We provide a polynomial time algorithm for computing a minimal ε-core on Markov chains over control-flow graphs of structured programs. A straightforward combination of our algorithm with standard branch prediction techniques allows one to apply the idea of cores to find a subset of program lines that are left with low probability and then focus any desired static analysis on this core subset.}, author = {Ahmadi, Ali and Chatterjee, Krishnendu and Goharshady, Amir Kafshdar and Meggendorfer, Tobias and Safavi Hemami, Roodabeh and Zikelic, Dorde}, booktitle = {42nd IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science}, isbn = {9783959772617}, issn = {1868-8969}, location = {Madras, India}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Algorithms and hardness results for computing cores of Markov chains}}, doi = {10.4230/LIPIcs.FSTTCS.2022.29}, volume = {250}, year = {2022}, } @article{12117, abstract = {To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia. For complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1}, author = {Hübschmann, Verena and Korkut, Medina and Siegert, Sandra}, issn = {2666-1667}, journal = {STAR Protocols}, keywords = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Neuroscience}, number = {4}, publisher = {Elsevier}, title = {{Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay}}, doi = {10.1016/j.xpro.2022.101866}, volume = {3}, year = {2022}, } @article{8909, abstract = {Spin qubits are considered to be among the most promising candidates for building a quantum processor. Group IV hole spin qubits have moved into the focus of interest due to the ease of operation and compatibility with Si technology. In addition, Ge offers the option for monolithic superconductor-semiconductor integration. Here we demonstrate a hole spin qubit operating at fields below 10 mT, the critical field of Al, by exploiting the large out-of-plane hole g-factors in planar Ge and by encoding the qubit into the singlet-triplet states of a double quantum dot. We observe electrically controlled X and Z-rotations with tunable frequencies exceeding 100 MHz and dephasing times of 1μs which we extend beyond 15μs with echo techniques. These results show that Ge hole singlet triplet qubits outperform their electronic Si and GaAs based counterparts in speed and coherence, respectively. In addition, they are on par with Ge single spin qubits, but can be operated at much lower fields underlining their potential for on chip integration with superconducting technologies.}, author = {Jirovec, Daniel and Hofmann, Andrea C and Ballabio, Andrea and Mutter, Philipp M. and Tavani, Giulio and Botifoll, Marc and Crippa, Alessandro and Kukucka, Josip and Sagi, Oliver and Martins, Frederico and Saez Mollejo, Jaime and Prieto Gonzalez, Ivan and Borovkov, Maksim and Arbiol, Jordi and Chrastina, Daniel and Isella, Giovanni and Katsaros, Georgios}, issn = {1476-4660}, journal = {Nature Materials}, number = {8}, pages = {1106–1112}, publisher = {Springer Nature}, title = {{A singlet triplet hole spin qubit in planar Ge}}, doi = {10.1038/s41563-021-01022-2}, volume = {20}, year = {2021}, } @phdthesis{8934, abstract = {In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management. We use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.}, author = {Goharshady, Amir Kafshdar}, issn = {2663-337X}, pages = {278}, publisher = {Institute of Science and Technology Austria}, title = {{Parameterized and algebro-geometric advances in static program analysis}}, doi = {10.15479/AT:ISTA:8934}, year = {2021}, } @phdthesis{9022, abstract = {In the first part of the thesis we consider Hermitian random matrices. Firstly, we consider sample covariance matrices XX∗ with X having independent identically distributed (i.i.d.) centred entries. We prove a Central Limit Theorem for differences of linear statistics of XX∗ and its minor after removing the first column of X. Secondly, we consider Wigner-type matrices and prove that the eigenvalue statistics near cusp singularities of the limiting density of states are universal and that they form a Pearcey process. Since the limiting eigenvalue distribution admits only square root (edge) and cubic root (cusp) singularities, this concludes the third and last remaining case of the Wigner-Dyson-Mehta universality conjecture. The main technical ingredients are an optimal local law at the cusp, and the proof of the fast relaxation to equilibrium of the Dyson Brownian motion in the cusp regime. In the second part we consider non-Hermitian matrices X with centred i.i.d. entries. We normalise the entries of X to have variance N −1. It is well known that the empirical eigenvalue density converges to the uniform distribution on the unit disk (circular law). In the first project, we prove universality of the local eigenvalue statistics close to the edge of the spectrum. This is the non-Hermitian analogue of the TracyWidom universality at the Hermitian edge. Technically we analyse the evolution of the spectral distribution of X along the Ornstein-Uhlenbeck flow for very long time (up to t = +∞). In the second project, we consider linear statistics of eigenvalues for macroscopic test functions f in the Sobolev space H2+ϵ and prove their convergence to the projection of the Gaussian Free Field on the unit disk. We prove this result for non-Hermitian matrices with real or complex entries. The main technical ingredients are: (i) local law for products of two resolvents at different spectral parameters, (ii) analysis of correlated Dyson Brownian motions. In the third and final part we discuss the mathematically rigorous application of supersymmetric techniques (SUSY ) to give a lower tail estimate of the lowest singular value of X − z, with z ∈ C. More precisely, we use superbosonisation formula to give an integral representation of the resolvent of (X − z)(X − z)∗ which reduces to two and three contour integrals in the complex and real case, respectively. The rigorous analysis of these integrals is quite challenging since simple saddle point analysis cannot be applied (the main contribution comes from a non-trivial manifold). Our result improves classical smoothing inequalities in the regime |z| ≈ 1; this result is essential to prove edge universality for i.i.d. non-Hermitian matrices.}, author = {Cipolloni, Giorgio}, issn = {2663-337X}, pages = {380}, publisher = {Institute of Science and Technology Austria}, title = {{Fluctuations in the spectrum of random matrices}}, doi = {10.15479/AT:ISTA:9022}, year = {2021}, }