@article{11739,
  abstract     = {We consider finite-volume approximations of Fokker--Planck equations on bounded convex domains in $\mathbb{R}^d$ and study the corresponding gradient flow structures. We reprove the convergence of the discrete to continuous Fokker--Planck equation via the method of evolutionary $\Gamma$-convergence, i.e., we pass to the limit at the level of the gradient flow structures, generalizing the one-dimensional result obtained by Disser and Liero. The proof is of variational nature and relies on a Mosco convergence result for functionals in the discrete-to-continuum limit that is of independent interest. Our results apply to arbitrary regular meshes, even though the associated discrete transport distances may fail to converge to the Wasserstein distance in this generality.},
  author       = {Forkert, Dominik L and Maas, Jan and Portinale, Lorenzo},
  issn         = {1095-7154},
  journal      = {SIAM Journal on Mathematical Analysis},
  keywords     = {Fokker--Planck equation, gradient flow, evolutionary $\Gamma$-convergence},
  number       = {4},
  pages        = {4297--4333},
  publisher    = {Society for Industrial and Applied Mathematics},
  title        = {{Evolutionary $\Gamma$-convergence of entropic gradient flow structures for Fokker-Planck equations in multiple dimensions}},
  doi          = {10.1137/21M1410968},
  volume       = {54},
  year         = {2022},
}

@article{11740,
  abstract     = {We consider a generalised model of a random simplicial complex, which arises from a random hypergraph. Our model is generated by taking the downward-closure of a non-uniform binomial random hypergraph, in which for each k, each set of k+1 vertices forms an edge with some probability pk independently. As a special case, this contains an extensively studied model of a (uniform) random simplicial complex, introduced by Meshulam and Wallach [Random Structures & Algorithms 34 (2009), no. 3, pp. 408–417].
We consider a higher-dimensional notion of connectedness on this new model according to the vanishing of cohomology groups over an arbitrary abelian group R. We prove that this notion of connectedness displays a phase transition and determine the threshold. We also prove a hitting time result for a natural process interpretation, in which simplices and their downward-closure are added one by one. In addition, we determine the asymptotic behaviour of cohomology groups inside the critical window around the time of the phase transition.},
  author       = {Cooley, Oliver and Del Giudice, Nicola and Kang, Mihyun and Sprüssel, Philipp},
  issn         = {1077-8926},
  journal      = {Electronic Journal of Combinatorics},
  number       = {3},
  publisher    = {Electronic Journal of Combinatorics},
  title        = {{Phase transition in cohomology groups of non-uniform random simplicial complexes}},
  doi          = {10.37236/10607},
  volume       = {29},
  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},
}

@article{11783,
  abstract     = {We consider a gas of N bosons with interactions in the mean-field scaling regime. We review the proof of an asymptotic expansion of its low-energy spectrum, eigenstates, and dynamics, which provides corrections to Bogoliubov theory to all orders in 1/ N. This is based on joint works with Petrat, Pickl, Seiringer, and Soffer. In addition, we derive a full asymptotic expansion of the ground state one-body reduced density matrix.},
  author       = {Bossmann, Lea},
  issn         = {1089-7658},
  journal      = {Journal of Mathematical Physics},
  keywords     = {Mathematical Physics, Statistical and Nonlinear Physics},
  number       = {6},
  publisher    = {AIP Publishing},
  title        = {{Low-energy spectrum and dynamics of the weakly interacting Bose gas}},
  doi          = {10.1063/5.0089983},
  volume       = {63},
  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},
}

@article{11841,
  abstract     = {Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process.},
  author       = {Toprakcioglu, Zenon and Kamada, Ayaka and Michaels, Thomas C.T. and Xie, Mengqi and Krausser, Johannes and Wei, Jiapeng and Šarić, Anđela and Vendruscolo, Michele and Knowles, Tuomas P.J.},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  number       = {31},
  publisher    = {Proceedings of the National Academy of Sciences},
  title        = {{Adsorption free energy predicts amyloid protein nucleation rates}},
  doi          = {10.1073/pnas.2109718119},
  volume       = {119},
  year         = {2022},
}

@article{11842,
  abstract     = {We consider the flow of two viscous and incompressible fluids within a bounded domain modeled by means of a two-phase Navier–Stokes system. The two fluids are assumed to be immiscible, meaning that they are separated by an interface. With respect to the motion of the interface, we consider pure transport by the fluid flow. Along the boundary of the domain, a complete slip boundary condition for the fluid velocities and a constant ninety degree contact angle condition for the interface are assumed. In the present work, we devise for the resulting evolution problem a suitable weak solution concept based on the framework of varifolds and establish as the main result a weak-strong uniqueness principle in 2D. The proof is based on a relative entropy argument and requires a non-trivial further development of ideas from the recent work of Fischer and the first author (Arch. Ration. Mech. Anal. 236, 2020) to incorporate the contact angle condition. To focus on the effects of the necessarily singular geometry of the evolving fluid domains, we work for simplicity in the regime of same viscosities for the two fluids.},
  author       = {Hensel, Sebastian and Marveggio, Alice},
  issn         = {1422-6952},
  journal      = {Journal of Mathematical Fluid Mechanics},
  number       = {3},
  publisher    = {Springer Nature},
  title        = {{Weak-strong uniqueness for the Navier–Stokes equation for two fluids with ninety degree contact angle and same viscosities}},
  doi          = {10.1007/s00021-022-00722-2},
  volume       = {24},
  year         = {2022},
}

@article{11843,
  abstract     = {A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on mouse dendritic cells (DCs) as a binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of the pathogenic strain CFT073 to CD14 reduced DC migration by overactivation of integrins and blunted expression of co-stimulatory molecules by overactivating the NFAT (nuclear factor of activated T-cells) pathway, both rate-limiting factors of T cell activation. This response was binary at the single-cell level, but averaged in larger populations exposed to both piliated and non-piliated pathogens, presumably via the exchange of immunomodulatory cytokines. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease.},
  author       = {Tomasek, Kathrin and Leithner, Alexander F and Glatzová, Ivana and Lukesch, Michael S. and Guet, Calin C and Sixt, Michael K},
  issn         = {2050-084X},
  journal      = {eLife},
  publisher    = {eLife Sciences Publications},
  title        = {{Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14}},
  doi          = {10.7554/eLife.78995},
  volume       = {11},
  year         = {2022},
}

@inproceedings{11844,
  abstract     = {In the stochastic population protocol model, we are given a connected graph with n nodes, and in every time step, a scheduler samples an edge of the graph uniformly at random and the nodes connected by this edge interact. A fundamental task in this model is stable leader election, in which all nodes start in an identical state and the aim is to reach a configuration in which (1) exactly one node is elected as leader and (2) this node remains as the unique leader no matter what sequence of interactions follows. On cliques, the complexity of this problem has recently been settled: time-optimal protocols stabilize in Θ(n log n) expected steps using Θ(log log n) states, whereas protocols that use O(1) states require Θ(n2) expected steps.

In this work, we investigate the complexity of stable leader election on general graphs. We provide the first non-trivial time lower bounds for leader election on general graphs, showing that, when moving beyond cliques, the complexity landscape of leader election becomes very diverse: the time required to elect a leader can range from O(1) to Θ(n3) expected steps. On the upper bound side, we first observe that there exists a protocol that is time-optimal on many graph families, but uses polynomially-many states. In contrast, we give a near-time-optimal protocol that uses only O(log2n) states that is at most a factor log n slower. Finally, we show that the constant-state protocol of Beauquier et al. [OPODIS 2013] is at most a factor n log n slower than the fast polynomial-state protocol. Moreover, among constant-state protocols, this protocol has near-optimal average case complexity on dense random graphs.},
  author       = {Alistarh, Dan-Adrian and Rybicki, Joel and Voitovych, Sasha},
  booktitle    = {Proceedings of the Annual ACM Symposium on Principles of Distributed Computing},
  isbn         = {9781450392624},
  location     = {Salerno, Italy},
  pages        = {246--256},
  publisher    = {Association for Computing Machinery},
  title        = {{Near-optimal leader election in population protocols on graphs}},
  doi          = {10.1145/3519270.3538435},
  year         = {2022},
}

@article{11858,
  abstract     = {This paper is a continuation of Part I of this project, where we developed a new local well-posedness theory for nonlinear stochastic PDEs with Gaussian noise. In the current Part II we consider blow-up criteria and regularization phenomena. As in Part I we can allow nonlinearities with polynomial growth and rough initial values from critical spaces. In the first main result we obtain several new blow-up criteria for quasi- and semilinear stochastic evolution equations. In particular, for semilinear equations we obtain a Serrin type blow-up criterium, which extends a recent result of Prüss–Simonett–Wilke (J Differ Equ 264(3):2028–2074, 2018) to the stochastic setting. Blow-up criteria can be used to prove global well-posedness for SPDEs. As in Part I, maximal regularity techniques and weights in time play a central role in the proofs. Our second contribution is a new method to bootstrap Sobolev and Hölder regularity in time and space, which does not require smoothness of the initial data. The blow-up criteria are at the basis of these new methods. Moreover, in applications the bootstrap results can be combined with our blow-up criteria, to obtain efficient ways to prove global existence. This gives new results even in classical 𝐿2-settings, which we illustrate for a concrete SPDE. In future works in preparation we apply the results of the current paper to obtain global well-posedness results and regularity for several concrete SPDEs. These include stochastic Navier–Stokes equations, reaction– diffusion equations and the Allen–Cahn equation. Our setting allows to put these SPDEs into a more flexible framework, where less restrictions on the nonlinearities are needed, and we are able to treat rough initial values from critical spaces. Moreover, we will obtain higher-order regularity results.},
  author       = {Agresti, Antonio and Veraar, Mark},
  issn         = {1424-3202},
  journal      = {Journal of Evolution Equations},
  keywords     = {Mathematics (miscellaneous)},
  number       = {2},
  publisher    = {Springer Nature},
  title        = {{Nonlinear parabolic stochastic evolution equations in critical spaces part II}},
  doi          = {10.1007/s00028-022-00786-7},
  volume       = {22},
  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},
}

@article{11916,
  abstract     = {A domain is called Kac regular for a quadratic form on L2 if every functions vanishing almost everywhere outside the domain can be approximated in form norm by functions with compact support in the domain. It is shown that this notion is stable under domination of quadratic forms. As applications measure perturbations of quasi-regular Dirichlet forms, Cheeger energies on metric measure spaces and Schrödinger operators on manifolds are studied. Along the way a characterization of the Sobolev space with Dirichlet boundary conditions on domains in infinitesimally Riemannian metric measure spaces is obtained.},
  author       = {Wirth, Melchior},
  issn         = {2538-225X},
  journal      = {Advances in Operator Theory},
  keywords     = {Algebra and Number Theory, Analysis},
  number       = {3},
  publisher    = {Springer Nature},
  title        = {{Kac regularity and domination of quadratic forms}},
  doi          = {10.1007/s43036-022-00199-w},
  volume       = {7},
  year         = {2022},
}

@article{11917,
  abstract     = {We study the many-body dynamics of an initially factorized bosonic wave function in the mean-field regime. We prove large deviation estimates for the fluctuations around the condensate. We derive an upper bound extending a recent result to more general interactions. Furthermore, we derive a new lower bound which agrees with the upper bound in leading order.},
  author       = {Rademacher, Simone Anna Elvira and Seiringer, Robert},
  issn         = {1572-9613},
  journal      = {Journal of Statistical Physics},
  keywords     = {Mathematical Physics, Statistical and Nonlinear Physics},
  publisher    = {Springer Nature},
  title        = {{Large deviation estimates for weakly interacting bosons}},
  doi          = {10.1007/s10955-022-02940-4},
  volume       = {188},
  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},
}

@article{11937,
  abstract     = {Most experimentally known high-pressure ice phases have a body-centred cubic (bcc) oxygen lattice. Our large-scale molecular-dynamics simulations with a machine-learning potential indicate that, amongst these bcc ice phases, ices VII, VII′ and X are the same thermodynamic phase under different conditions, whereas superionic ice VII″ has a first-order phase boundary with ice VII′. Moreover, at about 300 GPa, the transformation between ice X and the Pbcm phase has a sharp structural change but no apparent activation barrier, whilst at higher pressures the barrier gradually increases. Our study thus clarifies the phase behaviour of the high-pressure ices and reveals peculiar solid–solid transition mechanisms not known in other systems.},
  author       = {Reinhardt, Aleks and Bethkenhagen, Mandy and Coppari, Federica and Millot, Marius and Hamel, Sebastien and Cheng, Bingqing},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Thermodynamics of high-pressure ice phases explored with atomistic simulations}},
  doi          = {10.1038/s41467-022-32374-1},
  volume       = {13},
  year         = {2022},
}

@article{11938,
  abstract     = {A matching is compatible to two or more labeled point sets of size n with labels {1, . . . , n} if its straight-line drawing on each of these point sets is crossing-free. We study the maximum number of edges in a matching compatible to two or more labeled point sets in general position in the plane. We show that for any two labeled sets of n points in convex position there exists a compatible matching with ⌊√2n + 1 − 1⌋ edges. More generally, for any ℓ labeled point sets we construct compatible matchings of size Ω(n1/ℓ). As a corresponding upper bound, we use probabilistic arguments to show that for any ℓ given sets of n points there exists a labeling of each set such that the largest compatible matching has O(n2/(ℓ+1)) edges. Finally, we show that Θ(log n) copies of any set of n points are necessary and sufficient for the existence of labelings of these point sets such that any compatible matching consists only of a single edge.},
  author       = {Aichholzer, Oswin and Arroyo Guevara, Alan M and Masárová, Zuzana and Parada, Irene and Perz, Daniel and Pilz, Alexander and Tkadlec, Josef and Vogtenhuber, Birgit},
  issn         = {1526-1719},
  journal      = {Journal of Graph Algorithms and Applications},
  number       = {2},
  pages        = {225--240},
  publisher    = {Brown University},
  title        = {{On compatible matchings}},
  doi          = {10.7155/jgaa.00591},
  volume       = {26},
  year         = {2022},
}

@unpublished{11943,
  abstract     = {Complex wiring between neurons underlies the information-processing network enabling all brain functions, including cognition and memory. For understanding how the network is structured, processes information, and changes over time, comprehensive visualization of the architecture of living brain tissue with its cellular and molecular components would open up major opportunities. However, electron microscopy (EM) provides nanometre-scale resolution required for full <jats:italic>in-silico</jats:italic> reconstruction<jats:sup>1–5</jats:sup>, yet is limited to fixed specimens and static representations. Light microscopy allows live observation, with super-resolution approaches<jats:sup>6–12</jats:sup> facilitating nanoscale visualization, but comprehensive 3D-reconstruction of living brain tissue has been hindered by tissue photo-burden, photobleaching, insufficient 3D-resolution, and inadequate signal-to-noise ratio (SNR). Here we demonstrate saturated reconstruction of living brain tissue. We developed an integrated imaging and analysis technology, adapting stimulated emission depletion (STED) microscopy<jats:sup>6,13</jats:sup> in extracellularly labelled tissue<jats:sup>14</jats:sup> for high SNR and near-isotropic resolution. Centrally, a two-stage deep-learning approach leveraged previously obtained information on sample structure to drastically reduce photo-burden and enable automated volumetric reconstruction down to single synapse level. Live reconstruction provides unbiased analysis of tissue architecture across time in relation to functional activity and targeted activation, and contextual understanding of molecular labelling. This adoptable technology will facilitate novel insights into the dynamic functional architecture of living brain tissue.},
  author       = {Velicky, Philipp and Miguel Villalba, Eder and Michalska, Julia M and Wei, Donglai and Lin, Zudi and Watson, Jake and Troidl, Jakob and Beyer, Johanna and Ben Simon, Yoav and Sommer, Christoph M and Jahr, Wiebke and Cenameri, Alban and Broichhagen, Johannes and Grant, Seth G. N. and Jonas, Peter M and Novarino, Gaia and Pfister, Hanspeter and Bickel, Bernd and Danzl, Johann G},
  booktitle    = {bioRxiv},
  publisher    = {Cold Spring Harbor Laboratory},
  title        = {{Saturated reconstruction of living brain tissue}},
  doi          = {10.1101/2022.03.16.484431},
  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},
}

@unpublished{11950,
  abstract     = {Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanoscopic synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS leverages fixation-compatible extracellular labeling and advanced optical readout, in particular stimulated-emission depletion and expansion microscopy, to comprehensively delineate cellular structures. It enables 3D-reconstructing single synapses and mapping synaptic connectivity by identification and tailored analysis of putative synaptic cleft regions. Applying CATS to the hippocampal mossy fiber circuitry, we demonstrate its power to reveal the system’s molecularly informed ultrastructure across spatial scales and assess local connectivity by reconstructing and quantifying the synaptic input and output structure of identified neurons.},
  author       = {Michalska, Julia M and Lyudchik, Julia and Velicky, Philipp and Korinkova, Hana and Watson, Jake and Cenameri, Alban and Sommer, Christoph M and Venturino, Alessandro and Roessler, Karl and Czech, Thomas and Siegert, Sandra and Novarino, Gaia and Jonas, Peter M and Danzl, Johann G},
  booktitle    = {bioRxiv},
  publisher    = {Cold Spring Harbor Laboratory},
  title        = {{Uncovering brain tissue architecture across scales with super-resolution light microscopy}},
  doi          = {10.1101/2022.08.17.504272},
  year         = {2022},
}