@misc{9946, abstract = {We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs.}, author = {Mühlböck, Fabian and Henzinger, Thomas A}, issn = {2664-1690}, keywords = {run-time verification, software engineering, implicit specification}, pages = {17}, publisher = {IST Austria}, title = {{Differential monitoring}}, doi = {10.15479/AT:ISTA:9946}, year = {2021}, } @misc{9949, author = {Vicoso, Beatriz}, publisher = {Institute of Science and Technology Austria}, title = {{Data from Hyulmans et al 2021, "Transitions to asexuality and evolution of gene expression in Artemia brine shrimp"}}, doi = {10.15479/AT:ISTA:9949}, year = {2021}, } @inproceedings{9951, abstract = {There has recently been a surge of interest in the computational and complexity properties of the population model, which assumes n anonymous, computationally-bounded nodes, interacting at random, with the goal of jointly computing global predicates. Significant work has gone towards investigating majority or consensus dynamics in this model: that is, assuming that every node is initially in one of two states X or Y, determine which state had higher initial count. In this paper, we consider a natural generalization of majority/consensus, which we call comparison : in its simplest formulation, we are given two baseline states, X and Y, present in any initial configuration in fixed, but possibly small counts. One of these states has higher count than the other: we will assume |X_0| > C |Y_0| for some constant C > 1. The challenge is to design a protocol by which nodes can quickly and reliably decide on which of the baseline states X_0 and Y_0 has higher initial count. We begin by analyzing a simple and general dynamics solving the above comparison problem, which uses O( log n ) states per node, and converges in O(log n) (parallel) time, with high probability, to a state where the whole population votes on opinions X or Y at rates proportional to the initial concentrations of |X_0| vs. |Y_0|. We then describe how this procedure can be bootstrapped to solve comparison, i.e. have every node in the population reach the "correct'' decision, with probability 1 - o(1), at the cost of O (log log n) additional states. Further, we prove that this dynamics is self-stabilizing, in the sense that it converges to the correct decision from arbitrary initial states, and leak-robust, in the sense that it can withstand spurious faulty reactions, which are known to occur in practical implementations of population protocols. Our analysis is based on a new martingale concentration result relating the discrete-time evolution of a population protocol to its expected (steady-state) analysis, which should be a useful tool when analyzing opinion dynamics and epidemic dissemination in the population model.}, author = {Alistarh, Dan-Adrian and Töpfer, Martin and Uznański, Przemysław}, booktitle = {Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing}, isbn = {9781450385480}, location = {Virtual, Italy}, pages = {55--65}, publisher = {Association for Computing Machinery}, title = {{Comparison dynamics in population protocols}}, doi = {10.1145/3465084.3467915}, year = {2021}, } @article{9952, abstract = {Proper control of division orientation and symmetry, largely determined by spindle positioning, is essential to development and homeostasis. Spindle positioning has been extensively studied in cells dividing in two-dimensional (2D) environments and in epithelial tissues, where proteins such as NuMA (also known as NUMA1) orient division along the interphase long axis of the cell. However, little is known about how cells control spindle positioning in three-dimensional (3D) environments, such as early mammalian embryos and a variety of adult tissues. Here, we use mouse embryonic stem cells (ESCs), which grow in 3D colonies, as a model to investigate division in 3D. We observe that, at the periphery of 3D colonies, ESCs display high spindle mobility and divide asymmetrically. Our data suggest that enhanced spindle movements are due to unequal distribution of the cell–cell junction protein E-cadherin between future daughter cells. Interestingly, when cells progress towards differentiation, division becomes more symmetric, with more elongated shapes in metaphase and enhanced cortical NuMA recruitment in anaphase. Altogether, this study suggests that in 3D contexts, the geometry of the cell and its contacts with neighbors control division orientation and symmetry.}, author = {Chaigne, Agathe and Smith, Matthew B. and Cavestany, R. L. and Hannezo, Edouard B and Chalut, Kevin J. and Paluch, Ewa K.}, issn = {14779137}, journal = {Journal of Cell Science}, number = {14}, publisher = {The Company of Biologists}, title = {{Three-dimensional geometry controls division symmetry in stem cell colonies}}, doi = {10.1242/jcs.255018}, volume = {134}, year = {2021}, } @article{9953, abstract = {Chronic psychological stress is one of the most important triggers and environmental risk factors for neuropsychiatric disorders. Chronic stress can influence all organs via the secretion of stress hormones, including glucocorticoids by the adrenal glands, which coordinate the stress response across the body. In the brain, glucocorticoid receptors (GR) are expressed by various cell types including microglia, which are its resident immune cells regulating stress-induced inflammatory processes. To study the roles of microglial GR under normal homeostatic conditions and following chronic stress, we generated a mouse model in which the GR gene is depleted in microglia specifically at adulthood to prevent developmental confounds. We first confirmed that microglia were depleted in GR in our model in males and females among the cingulate cortex and the hippocampus, both stress-sensitive brain regions. Then, cohorts of microglial-GR depleted and wild-type (WT) adult female mice were housed for 3 weeks in a standard or stressful condition, using a chronic unpredictable mild stress (CUMS) paradigm. CUMS induced stress-related behavior in both microglial-GR depleted and WT animals as demonstrated by a decrease of both saccharine preference and progressive ratio breakpoint. Nevertheless, the hippocampal microglial and neural mechanisms underlying the adaptation to stress occurred differently between the two genotypes. Upon CUMS exposure, microglial morphology was altered in the WT controls, without any apparent effect in microglial-GR depleted mice. Furthermore, in the standard environment condition, GR depleted-microglia showed increased expression of pro-inflammatory genes, and genes involved in microglial homeostatic functions (such as Trem2, Cx3cr1 and Mertk). On the contrary, in CUMS condition, GR depleted-microglia showed reduced expression levels of pro-inflammatory genes and increased neuroprotective as well as anti-inflammatory genes compared to WT-microglia. Moreover, in microglial-GR depleted mice, but not in WT mice, CUMS led to a significant reduction of CA1 long-term potentiation and paired-pulse ratio. Lastly, differences in adult hippocampal neurogenesis were observed between the genotypes during normal homeostatic conditions, with microglial-GR deficiency increasing the formation of newborn neurons in the dentate gyrus subgranular zone independently from stress exposure. Together, these findings indicate that, although the deletion of microglial GR did not prevent the animal’s ability to respond to stress, it contributed to modulating hippocampal functions in both standard and stressful conditions, notably by shaping the microglial response to chronic stress.}, author = {Picard, Katherine and Bisht, Kanchan and Poggini, Silvia and Garofalo, Stefano and Golia, Maria Teresa and Basilico, Bernadette and Abdallah, Fatima and Ciano Albanese, Naomi and Amrein, Irmgard and Vernoux, Nathalie and Sharma, Kaushik and Hui, Chin Wai and C. Savage, Julie and Limatola, Cristina and Ragozzino, Davide and Maggi, Laura and Branchi, Igor and Tremblay, Marie Ève}, issn = {0889-1591}, journal = {Brain, Behavior, and Immunity}, pages = {423--439}, publisher = {Elsevier}, title = {{Microglial-glucocorticoid receptor depletion alters the response of hippocampal microglia and neurons in a chronic unpredictable mild stress paradigm in female mice}}, doi = {10.1016/j.bbi.2021.07.022}, volume = {97}, year = {2021}, } @inproceedings{9957, abstract = {The reflectance field of a face describes the reflectance properties responsible for complex lighting effects including diffuse, specular, inter-reflection and self shadowing. Most existing methods for estimating the face reflectance from a monocular image assume faces to be diffuse with very few approaches adding a specular component. This still leaves out important perceptual aspects of reflectance as higher-order global illumination effects and self-shadowing are not modeled. We present a new neural representation for face reflectance where we can estimate all components of the reflectance responsible for the final appearance from a single monocular image. Instead of modeling each component of the reflectance separately using parametric models, our neural representation allows us to generate a basis set of faces in a geometric deformation-invariant space, parameterized by the input light direction, viewpoint and face geometry. We learn to reconstruct this reflectance field of a face just from a monocular image, which can be used to render the face from any viewpoint in any light condition. Our method is trained on a light-stage training dataset, which captures 300 people illuminated with 150 light conditions from 8 viewpoints. We show that our method outperforms existing monocular reflectance reconstruction methods, in terms of photorealism due to better capturing of physical premitives, such as sub-surface scattering, specularities, self-shadows and other higher-order effects.}, author = {B R, Mallikarjun and Tewari, Ayush and Oh, Tae-Hyun and Weyrich, Tim and Bickel, Bernd and Seidel, Hans-Peter and Pfister, Hanspeter and Matusik, Wojciech and Elgharib, Mohamed and Theobalt, Christian}, booktitle = {Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition}, isbn = {978-166544509-2}, issn = {1063-6919}, location = {Nashville, TN, United States; Virtual}, pages = {4791--4800}, publisher = {IEEE}, title = {{Monocular reconstruction of neural face reflectance fields}}, doi = {10.1109/CVPR46437.2021.00476}, year = {2021}, } @article{9960, abstract = {The control of many-body quantum dynamics in complex systems is a key challenge in the quest to reliably produce and manipulate large-scale quantum entangled states. Recently, quench experiments in Rydberg atom arrays [Bluvstein et al. Science 371, 1355 (2021)] demonstrated that coherent revivals associated with quantum many-body scars can be stabilized by periodic driving, generating stable subharmonic responses over a wide parameter regime. We analyze a simple, related model where these phenomena originate from spatiotemporal ordering in an effective Floquet unitary, corresponding to discrete time-crystalline behavior in a prethermal regime. Unlike conventional discrete time crystals, the subharmonic response exists only for Néel-like initial states, associated with quantum scars. We predict robustness to perturbations and identify emergent timescales that could be observed in future experiments. Our results suggest a route to controlling entanglement in interacting quantum systems by combining periodic driving with many-body scars.}, author = {Maskara, N. and Michailidis, Alexios and Ho, W. W. and Bluvstein, D. and Choi, S. and Lukin, M. D. and Serbyn, Maksym}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {9}, publisher = {American Physical Society}, title = {{Discrete time-crystalline order enabled by quantum many-body scars: Entanglement steering via periodic driving}}, doi = {10.1103/PhysRevLett.127.090602}, volume = {127}, year = {2021}, } @article{9961, abstract = {The notion of Thouless energy plays a central role in the theory of Anderson localization. We investigate and compare the scaling of Thouless energy across the many-body localization (MBL) transition in a Floquet model. We use a combination of methods that are reliable on the ergodic side of the transition (e.g., spectral form factor) and methods that work on the MBL side (e.g., typical matrix elements of local operators) to obtain a complete picture of the Thouless energy behavior across the transition. On the ergodic side, Thouless energy decreases slowly with the system size, while at the transition it becomes comparable to the level spacing. Different probes yield consistent estimates of Thouless energy in their overlapping regime of applicability, giving the location of the transition point nearly free of finite-size drift. This work establishes a connection between different definitions of Thouless energy in a many-body setting and yields insights into the MBL transition in Floquet systems.}, author = {Sonner, Michael and Serbyn, Maksym and Papić, Zlatko and Abanin, Dmitry A.}, issn = {2469-9969}, journal = {Physical Review B}, number = {8}, publisher = {American Physical Society}, title = {{Thouless energy across the many-body localization transition in Floquet systems}}, doi = {10.1103/PhysRevB.104.L081112}, volume = {104}, year = {2021}, } @phdthesis{9962, abstract = {The brain is one of the largest and most complex organs and it is composed of billions of neurons that communicate together enabling e.g. consciousness. The cerebral cortex is the largest site of neural integration in the central nervous system. Concerted radial migration of newly born cortical projection neurons, from their birthplace to their final position, is a key step in the assembly of the cerebral cortex. The cellular and molecular mechanisms regulating radial neuronal migration in vivo are however still unclear. Recent evidence suggests that distinct signaling cues act cell-autonomously but differentially at certain steps during the overall migration process. Moreover, functional analysis of genetic mosaics (mutant neurons present in wild-type/heterozygote environment) using the MADM (Mosaic Analysis with Double Markers) analyses in comparison to global knockout also indicate a significant degree of non-cell-autonomous and/or community effects in the control of cortical neuron migration. The interactions of cell-intrinsic (cell-autonomous) and cell-extrinsic (non-cell-autonomous) components are largely unknown. In part of this thesis work we established a MADM-based experimental strategy for the quantitative analysis of cell-autonomous gene function versus non-cell-autonomous and/or community effects. The direct comparison of mutant neurons from the genetic mosaic (cell-autonomous) to mutant neurons in the conditional and/or global knockout (cell-autonomous + non-cell-autonomous) allows to quantitatively analyze non-cell-autonomous effects. Such analysis enable the high-resolution analysis of projection neuron migration dynamics in distinct environments with concomitant isolation of genomic and proteomic profiles. Using these experimental paradigms and in combination with computational modeling we show and characterize the nature of non-cell-autonomous effects to coordinate radial neuron migration. Furthermore, this thesis discusses recent developments in neurodevelopment with focus on neuronal polarization and non-cell-autonomous mechanisms in neuronal migration.}, author = {Hansen, Andi H}, issn = {2663-337X}, keywords = {Neuronal migration, Non-cell-autonomous, Cell-autonomous, Neurodevelopmental disease}, pages = {182}, publisher = {Institute of Science and Technology Austria}, title = {{Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration}}, doi = {10.15479/at:ista:9962}, year = {2021}, } @inproceedings{9969, abstract = {Payment channel networks are a promising approach to improve the scalability of cryptocurrencies: they allow to perform transactions in a peer-to-peer fashion, along multihop routes in the network, without requiring consensus on the blockchain. However, during the discovery of cost-efficient routes for the transaction, critical information may be revealed about the transacting entities. This paper initiates the study of privacy-preserving route discovery mechanisms for payment channel networks. In particular, we present LightPIR, an approach which allows a client to learn the shortest (or cheapest in terms of fees) path between two nodes without revealing any information about the endpoints of the transaction to the servers. The two main observations which allow for an efficient solution in LightPIR are that: (1) surprisingly, hub labelling algorithms – which were developed to preprocess “street network like” graphs so one can later efficiently compute shortest paths – also perform well for the graphs underlying payment channel networks, and that (2) hub labelling algorithms can be conveniently combined with private information retrieval. LightPIR relies on a simple hub labeling heuristic on top of existing hub labeling algorithms which leverages the specific topological features of cryptocurrency networks to further minimize storage and bandwidth overheads. In a case study considering the Lightning network, we show that our approach is an order of magnitude more efficient compared to a privacy-preserving baseline based on using private information retrieval on a database that stores all pairs shortest paths.}, author = {Pietrzak, Krzysztof Z and Salem, Iosif and Schmid, Stefan and Yeo, Michelle X}, isbn = {978-1-6654-4501-6}, issn = {1861-2288}, location = {Espoo and Helsinki, Finland}, publisher = {IEEE}, title = {{LightPIR: Privacy-preserving route discovery for payment channel networks}}, doi = {10.23919/IFIPNetworking52078.2021.9472205}, year = {2021}, } @article{9973, abstract = {In this article we introduce a complete gradient estimate for symmetric quantum Markov semigroups on von Neumann algebras equipped with a normal faithful tracial state, which implies semi-convexity of the entropy with respect to the recently introduced noncommutative 2-Wasserstein distance. We show that this complete gradient estimate is stable under tensor products and free products and establish its validity for a number of examples. As an application we prove a complete modified logarithmic Sobolev inequality with optimal constant for Poisson-type semigroups on free group factors.}, author = {Wirth, Melchior and Zhang, Haonan}, issn = {1432-0916}, journal = {Communications in Mathematical Physics}, keywords = {Mathematical Physics, Statistical and Nonlinear Physics}, pages = {761–791}, publisher = {Springer Nature}, title = {{Complete gradient estimates of quantum Markov semigroups}}, doi = {10.1007/s00220-021-04199-4}, volume = {387}, year = {2021}, } @unpublished{9978, abstract = {Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics yet the lowest possible overpotential. Here, we found that when the redox potentials of mediators are tuned via, e.g., Li + concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediators and electrolyte. The acceleration originates from the overpotentials required to activate fast Li + /e – extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids requires therefore carefully considering the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents.}, author = {Cao, Deqing and Shen, Xiaoxiao and Wang, Aiping and Yu, Fengjiao and Wu, Yuping and Shi, Siqi and Freunberger, Stefan Alexander and Chen, Yuhui}, booktitle = {Research Square}, issn = {2693-5015}, keywords = {Catalysis, Energy engineering, Materials theory and modeling}, pages = {21}, publisher = {Research Square}, title = {{Sharp kinetic acceleration potentials during mediated redox catalysis of insulators}}, doi = {10.21203/rs.3.rs-750965/v1}, year = {2021}, } @unpublished{9980, abstract = {Insufficient understanding of the mechanism that reversibly converts sulphur into lithium sulphide (Li2S) via soluble polysulphides (PS) hampers the realization of high performance lithium-sulphur cells. Typically Li2S formation is explained by direct electroreduction of a PS to Li2S; however, this is not consistent with the size of the insulating Li2S deposits. Here, we use in situ small and wide angle X-ray scattering (SAXS/WAXS) to track the growth and dissolution of crystalline and amorphous deposits from atomic to sub-micron scales during charge and discharge. Stochastic modelling based on the SAXS data allows quantification of the chemical phase evolution during discharge and charge. We show that Li2S deposits predominantly via disproportionation of transient, solid Li2S2 to form primary Li2S crystallites and solid Li2S4 particles. We further demonstrate that this process happens in reverse during charge. These findings show that the discharge capacity and rate capability in Li-S battery cathodes are therefore limited by mass transport through the increasingly tortuous network of Li2S / Li2S4 / carbon pores rather than electron transport through a passivating surface film.}, author = {Prehal, Christian and Talian, Sara Drvarič and Vizintin, Alen and Amenitsch, Heinz and Dominko, Robert and Freunberger, Stefan Alexander and Wood, Vanessa}, booktitle = {Research Square}, keywords = {Li2S, Lithium Sulphur Batteries, SAXS, WAXS}, pages = {21}, title = {{Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries}}, doi = {10.21203/rs.3.rs-818607/v1}, year = {2021}, } @article{9981, abstract = {The numerical simulation of dynamical phenomena in interacting quantum systems is a notoriously hard problem. Although a number of promising numerical methods exist, they often have limited applicability due to the growth of entanglement or the presence of the so-called sign problem. In this work, we develop an importance sampling scheme for the simulation of quantum spin dynamics, building on a recent approach mapping quantum spin systems to classical stochastic processes. The importance sampling scheme is based on identifying the classical trajectory that yields the largest contribution to a given quantum observable. An exact transformation is then carried out to preferentially sample trajectories that are close to the dominant one. We demonstrate that this approach is capable of reducing the temporal growth of fluctuations in the stochastic quantities, thus extending the range of accessible times and system sizes compared to direct sampling. We discuss advantages and limitations of the proposed approach, outlining directions for further developments.}, author = {De Nicola, Stefano}, issn = {2666-9366}, journal = {SciPost Physics}, keywords = {General Physics and Astronomy}, number = {3}, publisher = {SciPost}, title = {{Importance sampling scheme for the stochastic simulation of quantum spin dynamics}}, doi = {10.21468/scipostphys.11.3.048}, volume = {11}, year = {2021}, } @article{9985, abstract = {AMPA receptor (AMPAR) abundance and positioning at excitatory synapses regulates the strength of transmission. Changes in AMPAR localisation can enact synaptic plasticity, allowing long-term information storage, and is therefore tightly controlled. Multiple mechanisms regulating AMPAR synaptic anchoring have been described, but with limited coherence or comparison between reports, our understanding of this process is unclear. Here, combining synaptic recordings from mouse hippocampal slices and super-resolution imaging in dissociated cultures, we compare the contributions of three AMPAR interaction domains controlling transmission at hippocampal CA1 synapses. We show that the AMPAR C-termini play only a modulatory role, whereas the extracellular N-terminal domain (NTD) and PDZ interactions of the auxiliary subunit TARP γ8 are both crucial, and each is sufficient to maintain transmission. Our data support a model in which γ8 accumulates AMPARs at the postsynaptic density, where the NTD further tunes their positioning. This interplay between cytosolic (TARP γ8) and synaptic cleft (NTD) interactions provides versatility to regulate synaptic transmission and plasticity.}, author = {Watson, Jake and Pinggera, Alexandra and Ho, Hinze and Greger, Ingo H.}, issn = {2041-1723}, journal = {Nature Communications}, number = {1}, publisher = {Nature Publishing Group}, title = {{AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions}}, doi = {10.1038/s41467-021-25281-4}, volume = {12}, year = {2021}, } @article{9986, abstract = {Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan’s molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth.}, author = {Velasquez, Silvia Melina and Guo, Xiaoyuan and Gallemi, Marçal and Aryal, Bibek and Venhuizen, Peter and Barbez, Elke and Dünser, Kai Alexander and Darino, Martin and Pӗnčík, Aleš and Novák, Ondřej and Kalyna, Maria and Mouille, Gregory and Benková, Eva and Bhalerao, Rishikesh P. and Mravec, Jozef and Kleine-Vehn, Jürgen}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, keywords = {auxin, growth, cell wall, xyloglucans, hypocotyls, gravitropism}, number = {17}, publisher = {MDPI}, title = {{Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants}}, doi = {10.3390/ijms22179222}, volume = {22}, year = {2021}, } @inproceedings{9987, abstract = {Stateless model checking (SMC) is one of the standard approaches to the verification of concurrent programs. As scheduling non-determinism creates exponentially large spaces of thread interleavings, SMC attempts to partition this space into equivalence classes and explore only a few representatives from each class. The efficiency of this approach depends on two factors: (a) the coarseness of the partitioning, and (b) the time to generate representatives in each class. For this reason, the search for coarse partitionings that are efficiently explorable is an active research challenge. In this work we present RVF-SMC , a new SMC algorithm that uses a novel reads-value-from (RVF) partitioning. Intuitively, two interleavings are deemed equivalent if they agree on the value obtained in each read event, and read events induce consistent causal orderings between them. The RVF partitioning is provably coarser than recent approaches based on Mazurkiewicz and “reads-from” partitionings. Our experimental evaluation reveals that RVF is quite often a very effective equivalence, as the underlying partitioning is exponentially coarser than other approaches. Moreover, RVF-SMC generates representatives very efficiently, as the reduction in the partitioning is often met with significant speed-ups in the model checking task.}, author = {Agarwal, Pratyush and Chatterjee, Krishnendu and Pathak, Shreya and Pavlogiannis, Andreas and Toman, Viktor}, booktitle = {33rd International Conference on Computer-Aided Verification }, isbn = {978-3-030-81684-1}, issn = {1611-3349}, location = {Virtual}, pages = {341--366}, publisher = {Springer Nature}, title = {{Stateless model checking under a reads-value-from equivalence}}, doi = {10.1007/978-3-030-81685-8_16}, volume = {12759 }, year = {2021}, } @phdthesis{9992, abstract = {Blood – this is what animals use to heal wounds fast and efficient. Plants do not have blood circulation and their cells cannot move. However, plants have evolved remarkable capacities to regenerate tissues and organs preventing further damage. In my PhD research, I studied the wound healing in the Arabidopsis root. I used a UV laser to ablate single cells in the root tip and observed the consequent wound healing. Interestingly, the inner adjacent cells induced a division plane switch and subsequently adopted the cell type of the killed cell to replace it. We termed this form of wound healing “restorative divisions”. This initial observation triggered the questions of my PhD studies: How and why do cells orient their division planes, how do they feel the wound and why does this happen only in inner adjacent cells. For answering these questions, I used a quite simple experimental setup: 5 day - old seedlings were stained with propidium iodide to visualize cell walls and dead cells; ablation was carried out using a special laser cutter and a confocal microscope. Adaptation of the novel vertical microscope system made it possible to observe wounds in real time. This revealed that restorative divisions occur at increased frequency compared to normal divisions. Additionally, the major plant hormone auxin accumulates in wound adjacent cells and drives the expression of the wound-stress responsive transcription factor ERF115. Using this as a marker gene for wound responses, we found that an important part of wound signalling is the sensing of the collapse of the ablated cell. The collapse causes a radical pressure drop, which results in strong tissue deformations. These deformations manifest in an invasion of the now free spot specifically by the inner adjacent cells within seconds, probably because of higher pressure of the inner tissues. Long-term imaging revealed that those deformed cells continuously expand towards the wound hole and that this is crucial for the restorative division. These wound-expanding cells exhibit an abnormal, biphasic polarity of microtubule arrays before the division. Experiments inhibiting cell expansion suggest that it is the biphasic stretching that induces those MT arrays. Adapting the micromanipulator aspiration system from animal scientists at our institute confirmed the hypothesis that stretching influences microtubule stability. In conclusion, this shows that microtubules react to tissue deformation and this facilitates the observed division plane switch. This puts mechanical cues and tensions at the most prominent position for explaining the growth and wound healing properties of plants. Hence, it shines light onto the importance of understanding mechanical signal transduction. }, author = {Hörmayer, Lukas}, issn = {2663-337X}, pages = {168}, publisher = {Institute of Science and Technology Austria}, title = {{Wound healing in the Arabidopsis root meristem}}, doi = {10.15479/at:ista:9992}, year = {2021}, } @article{9997, abstract = {Indirect reciprocity is a mechanism for the evolution of cooperation based on social norms. This mechanism requires that individuals in a population observe and judge each other’s behaviors. Individuals with a good reputation are more likely to receive help from others. Previous work suggests that indirect reciprocity is only effective when all relevant information is reliable and publicly available. Otherwise, individuals may disagree on how to assess others, even if they all apply the same social norm. Such disagreements can lead to a breakdown of cooperation. Here we explore whether the predominantly studied ‘leading eight’ social norms of indirect reciprocity can be made more robust by equipping them with an element of generosity. To this end, we distinguish between two kinds of generosity. According to assessment generosity, individuals occasionally assign a good reputation to group members who would usually be regarded as bad. According to action generosity, individuals occasionally cooperate with group members with whom they would usually defect. Using individual-based simulations, we show that the two kinds of generosity have a very different effect on the resulting reputation dynamics. Assessment generosity tends to add to the overall noise and allows defectors to invade. In contrast, a limited amount of action generosity can be beneficial in a few cases. However, even when action generosity is beneficial, the respective simulations do not result in full cooperation. Our results suggest that while generosity can favor cooperation when individuals use the most simple strategies of reciprocity, it is disadvantageous when individuals use more complex social norms.}, author = {Schmid, Laura and Shati, Pouya and Hilbe, Christian and Chatterjee, Krishnendu}, issn = {2045-2322}, journal = {Scientific Reports}, keywords = {Multidisciplinary}, number = {1}, publisher = {Springer Nature}, title = {{The evolution of indirect reciprocity under action and assessment generosity}}, doi = {10.1038/s41598-021-96932-1}, volume = {11}, year = {2021}, } @article{9998, abstract = {We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss type A in detail as well as its connections with quantum XXZ spin chains and trigonometric Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic version of results of Givental and Kim, connecting quantum geometry of flag varieties and Toda lattice.}, author = {Koroteev, Peter and Pushkar, Petr and Smirnov, Andrey V. and Zeitlin, Anton M.}, issn = {1420-9020}, journal = {Selecta Mathematica}, number = {5}, publisher = {Springer Nature}, title = {{Quantum K-theory of quiver varieties and many-body systems}}, doi = {10.1007/s00029-021-00698-3}, volume = {27}, year = {2021}, }