@article{12290,
  abstract     = {We prove local laws, i.e. optimal concentration estimates for arbitrary products of resolvents of a Wigner random matrix with deterministic matrices in between. We find that the size of such products heavily depends on whether some of the deterministic matrices are traceless. Our estimates correctly account for this dependence and they hold optimally down to the smallest possible spectral scale.},
  author       = {Cipolloni, Giorgio and Erdös, László and Schröder, Dominik J},
  issn         = {1083-6489},
  journal      = {Electronic Journal of Probability},
  keywords     = {Statistics, Probability and Uncertainty, Statistics and Probability},
  pages        = {1--38},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Optimal multi-resolvent local laws for Wigner matrices}},
  doi          = {10.1214/22-ejp838},
  volume       = {27},
  year         = {2022},
}

@article{12291,
  abstract     = {The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1,2,3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.},
  author       = {Friml, Jiří and Gallei, Michelle C and Gelová, Zuzana and Johnson, Alexander J and Mazur, Ewa and Monzer, Aline and Rodriguez Solovey, Lesia and Roosjen, Mark and Verstraeten, Inge and Živanović, Branka D. and Zou, Minxia and Fiedler, Lukas and Giannini, Caterina and Grones, Peter and Hrtyan, Mónika and Kaufmann, Walter and Kuhn, Andre and Narasimhan, Madhumitha and Randuch, Marek and Rýdza, Nikola and Takahashi, Koji and Tan, Shutang and Teplova, Anastasiia and Kinoshita, Toshinori and Weijers, Dolf and Rakusová, Hana},
  issn         = {1476-4687},
  journal      = {Nature},
  number       = {7927},
  pages        = {575--581},
  publisher    = {Springer Nature},
  title        = {{ABP1–TMK auxin perception for global phosphorylation and auxin canalization}},
  doi          = {10.1038/s41586-022-05187-x},
  volume       = {609},
  year         = {2022},
}

@inbook{12294,
  abstract     = {Brassicaceae are blessed with specialized metabolites called glucosinolates (GSLs), which along with their degradation products, are beneficial in agriculture and human health. To date, more than 130 GSL structures have been identified, mostly derived from the amino acid methionine. The biosynthesis of methionine-derived aliphatic GSLs starts with a side-chain elongation step involving a recursive three-step cyclic process that incorporates a new methylene group into the 2-oxo acid to form a series of elongated 2-oxo acids. Methylthioalkylmalate synthase (MAMS) catalyzes the first committed step in the side-chain elongation of methionine-derived GSLs. The substrate specificity of MAMS with different 2-oxo acids determines whether reaction products of a given cycle enter for an additional round of chain elongation or enter into core GSLs structure formation. Multiple MAMS encoding genes are present in the Brassicaceae species and are known to play a central role in shaping the diverse profile of aliphatic GSLs. We recently established a highly sensitive LC-MS/MS-based methodology that quantifies the MAMS activity by estimating the amount of the next intermediate of the pathway, the 2-malate derivatives. Overall, this chapter describes the protocol for the expression, purification, and steady-state kinetic analysis of the recombinant MAMS protein.},
  author       = {Kumar, Roshan and Reichelt, Michael and Bisht, Naveen C.},
  booktitle    = {Biochemical Pathways and Environmental Responses in Plants: Part A},
  editor       = {Jez, Joseph},
  isbn         = {9780323955614},
  issn         = {0076-6879},
  pages        = {49--69},
  publisher    = {Elsevier},
  title        = {{An LC-MS/MS Assay for Enzymatic Characterization of Methylthioalkylmalate Synthase (MAMS) Involved in Glucosinolate Biosynthesis}},
  doi          = {10.1016/bs.mie.2022.07.019},
  volume       = {676},
  year         = {2022},
}

@inproceedings{12298,
  abstract     = {Existing committee-based Byzantine state machine replication (SMR) protocols, typically deployed in production blockchains, face a clear trade-off: (1) they either achieve linear communication cost in the steady state, but sacrifice liveness during periods of asynchrony, or (2) they are robust (progress with probability one) but pay quadratic communication cost. We believe this trade-off is unwarranted since existing linear protocols still have asymptotic quadratic cost in the worst case. We design Ditto, a Byzantine SMR protocol that enjoys the best of both worlds: optimal communication on and off the steady state (linear and quadratic, respectively) and progress guarantee under asynchrony and DDoS attacks. We achieve this by replacing the view-synchronization of partially synchronous protocols with an asynchronous fallback mechanism at no extra asymptotic cost. Specifically, we start from HotStuff, a state-of-the-art linear protocol, and gradually build Ditto. As a separate contribution and an intermediate step, we design a 2-chain version of HotStuff, Jolteon, which leverages a quadratic view-change mechanism to reduce the latency of the standard 3-chain HotStuff. We implement and experimentally evaluate all our systems to prove that breaking the robustness-efficiency trade-off is in the realm of practicality.},
  author       = {Gelashvili, Rati and Kokoris Kogias, Eleftherios and Sonnino, Alberto and Spiegelman, Alexander and Xiang, Zhuolun},
  booktitle    = {Financial Cryptography and Data Security},
  isbn         = {9783031182822},
  issn         = {1611-3349},
  location     = {Radisson Grenada Beach Resort, Grenada},
  pages        = {296--315},
  publisher    = {Springer Nature},
  title        = {{Jolteon and ditto: Network-adaptive efficient consensus with asynchronous fallback}},
  doi          = {10.1007/978-3-031-18283-9_14},
  volume       = {13411},
  year         = {2022},
}

@inproceedings{12299,
  abstract     = {Transfer learning is a classic paradigm by which models pretrained on large “upstream” datasets are adapted to yield good results on “downstream” specialized datasets. Generally, more accurate models on the “upstream” dataset tend to provide better transfer accuracy “downstream”. In this work, we perform an in-depth investigation of this phenomenon in the context of convolutional neural networks (CNNs) trained on the ImageNet dataset, which have been pruned-that is, compressed by sparsifiying their connections. We consider transfer using unstructured pruned models obtained by applying several state-of-the-art pruning methods, including magnitude-based, second-order, regrowth, lottery-ticket, and regularization approaches, in the context of twelve standard transfer tasks. In a nutshell, our study shows that sparse models can match or even outperform the transfer performance of dense models, even at high sparsities, and, while doing so, can lead to significant inference and even training speedups. At the same time, we observe and analyze significant differences in the behaviour of different pruning methods. The code is available at: https://github.com/IST-DASLab/sparse-imagenet-transfer.},
  author       = {Iofinova, Eugenia B and Peste, Elena-Alexandra and Kurtz, Mark and Alistarh, Dan-Adrian},
  booktitle    = {2022 IEEE/CVF Conference on Computer Vision and Pattern Recognition},
  issn         = {2575-7075},
  location     = {New Orleans, LA, United States},
  pages        = {12256--12266},
  publisher    = {Institute of Electrical and Electronics Engineers},
  title        = {{How well do sparse ImageNet models transfer?}},
  doi          = {10.1109/cvpr52688.2022.01195},
  year         = {2022},
}

@inproceedings{12300,
  abstract     = {Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted third party and is a building block to decentralized protocols such as randomness beacons, threshold signatures, and general multiparty computation. Until recently, DKG protocols have assumed the synchronous model and thus are vulnerable when their underlying network assumptions do not hold. The recent advancements in asynchronous DKG protocols are insufficient as they either have poor efficiency or limited functionality, resulting in a lack of concrete implementations. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol. In a network of n nodes, our ADKG protocol can tolerate up to t<n/3 malicious nodes and have an expected O(κn3) communication cost, where κ is the security parameter. Our ADKG protocol produces a field element as the secret and is thus compatible with off-the-shelf threshold cryptosystems. We implement our ADKG protocol and evaluate it using a network of up to 128 nodes in geographically distributed AWS instances. Our evaluation shows that our protocol takes as low as 3 and 9.5 seconds to terminate for 32 and 64 nodes, respectively. Also, each node sends only 0.7 Megabytes and 2.9 Megabytes of data during the two experiments, respectively.},
  author       = {Das, Sourav and Yurek, Thomas and Xiang, Zhuolun and Miller, Andrew and Kokoris Kogias, Eleftherios and Ren, Ling},
  booktitle    = {2022 IEEE Symposium on Security and Privacy},
  issn         = {2375-1207},
  location     = {San Francisco, CA, United States},
  pages        = {2518--2534},
  publisher    = {Institute of Electrical and Electronics Engineers},
  title        = {{Practical asynchronous distributed key generation}},
  doi          = {10.1109/sp46214.2022.9833584},
  year         = {2022},
}

@inproceedings{12302,
  abstract     = {We propose a novel algorithm to decide the language inclusion between (nondeterministic) Büchi automata, a PSPACE-complete problem. Our approach, like others before, leverage a notion of quasiorder to prune the search for a counterexample by discarding candidates which are subsumed by others for the quasiorder. Discarded candidates are guaranteed to not compromise the completeness of the algorithm. The novelty of our work lies in the quasiorder used to discard candidates. We introduce FORQs (family of right quasiorders) that we obtain by adapting the notion of family of right congruences put forward by Maler and Staiger in 1993. We define a FORQ-based inclusion algorithm which we prove correct and instantiate it for a specific FORQ, called the structural FORQ, induced by the Büchi automaton to the right of the inclusion sign. The resulting implementation, called FORKLIFT, scales up better than the state-of-the-art on a variety of benchmarks including benchmarks from program verification and theorem proving for word combinatorics. Artifact: https://doi.org/10.5281/zenodo.6552870},
  author       = {Doveri, Kyveli and Ganty, Pierre and Mazzocchi, Nicolas Adrien},
  booktitle    = {Computer Aided Verification},
  isbn         = {9783031131875},
  issn         = {1611-3349},
  location     = {Haifa, Israel},
  pages        = {109--129},
  publisher    = {Springer Nature},
  title        = {{FORQ-based language inclusion formal testing}},
  doi          = {10.1007/978-3-031-13188-2_6},
  volume       = {13372},
  year         = {2022},
}

@inbook{12303,
  abstract     = {We construct for each choice of a quiver Q, a cohomology theory A, and a poset P a “loop Grassmannian” GP(Q,A). This generalizes loop Grassmannians of semisimple groups and the loop Grassmannians of based quadratic forms. The addition of a “dilation” torus D⊆G2m gives a quantization GPD(Q,A). This construction is motivated by the program of introducing an inner cohomology theory in algebraic geometry adequate for the Geometric Langlands program (Mirković, Some extensions of the notion of loop Grassmannians. Rad Hrvat. Akad. Znan. Umjet. Mat. Znan., the Mardešić issue. No. 532, 53–74, 2017) and on the construction of affine quantum groups from generalized cohomology theories (Yang and Zhao, Quiver varieties and elliptic quantum groups, preprint. arxiv1708.01418).},
  author       = {Mirković, Ivan and Yang, Yaping and Zhao, Gufang},
  booktitle    = {Representation Theory and Algebraic Geometry},
  editor       = {Baranovskky, Vladimir and Guay, Nicolas and Schedler, Travis},
  isbn         = {9783030820060},
  issn         = {2297-024X},
  pages        = {347--392},
  publisher    = {Springer Nature; Birkhäuser},
  title        = {{Loop Grassmannians of Quivers and Affine Quantum Groups}},
  doi          = {10.1007/978-3-030-82007-7_8},
  year         = {2022},
}

@article{12304,
  abstract     = {We establish sharp criteria for the instantaneous propagation of free boundaries in solutions to the thin-film equation. The criteria are formulated in terms of the initial distribution of mass (as opposed to previous almost-optimal results), reflecting the fact that mass is a locally conserved quantity for the thin-film equation. In the regime of weak slippage, our criteria are at the same time necessary and sufficient. The proof of our upper bounds on free boundary propagation is based on a strategy of “propagation of degeneracy” down to arbitrarily small spatial scales: We combine estimates on the local mass and estimates on energies to show that “degeneracy” on a certain space-time cylinder entails “degeneracy” on a spatially smaller space-time cylinder with the same time horizon. The derivation of our lower bounds on free boundary propagation is based on a combination of a monotone quantity and almost optimal estimates established previously by the second author with a new estimate connecting motion of mass to entropy production.},
  author       = {De Nitti, Nicola and Fischer, Julian L},
  issn         = {1532-4133},
  journal      = {Communications in Partial Differential Equations},
  keywords     = {Applied Mathematics, Analysis},
  number       = {7},
  pages        = {1394--1434},
  publisher    = {Taylor & Francis},
  title        = {{Sharp criteria for the waiting time phenomenon in solutions to the thin-film equation}},
  doi          = {10.1080/03605302.2022.2056702},
  volume       = {47},
  year         = {2022},
}

@article{12305,
  abstract     = {This paper is concerned with the sharp interface limit for the Allen--Cahn equation with a nonlinear Robin boundary condition in a bounded smooth domain Ω⊂\R2. We assume that a diffuse interface already has developed and that it is in contact with the boundary ∂Ω. The boundary condition is designed in such a way that the limit problem is given by the mean curvature flow with constant α-contact angle. For α close to 90° we prove a local in time convergence result for well-prepared initial data for times when a smooth solution to the limit problem exists. Based on the latter we construct a suitable curvilinear coordinate system and carry out a rigorous asymptotic expansion for the Allen--Cahn equation with the nonlinear Robin boundary condition. Moreover, we show a spectral estimate for the corresponding linearized Allen--Cahn operator and with its aid we derive strong norm estimates for the difference of the exact and approximate solutions using a Gronwall-type argument.},
  author       = {Abels, Helmut and Moser, Maximilian},
  issn         = {1095-7154},
  journal      = {SIAM Journal on Mathematical Analysis},
  keywords     = {Applied Mathematics, Computational Mathematics, Analysis},
  number       = {1},
  pages        = {114--172},
  publisher    = {Society for Industrial and Applied Mathematics},
  title        = {{Convergence of the Allen--Cahn equation with a nonlinear Robin boundary condition to mean curvature flow with contact angle close to 90°}},
  doi          = {10.1137/21m1424925},
  volume       = {54},
  year         = {2022},
}

@article{12307,
  abstract     = {Point-set topology is among the most abstract branches of mathematics in that it lacks tangible notions of distance, length, magnitude, order, and size. There is no shape, no geometry, no algebra, and no direction. Everything we are used to visualizing is gone. In the teaching and learning of mathematics, this can present a conundrum. Yet, this very property makes point set topology perfect for teaching and learning abstract mathematical concepts. It clears our minds of preconceived intuitions and expectations and forces us to think in new and creative ways. In this paper, we present guided investigations into topology through questions and thinking strategies that open up fascinating problems. They are intended for faculty who already teach or are thinking about teaching a class in topology or abstract mathematical reasoning for undergraduates. They can be used to build simple to challenging projects in topology, proofs, honors programs, and research experiences.},
  author       = {Shipman, Barbara A. and Stephenson, Elizabeth R},
  issn         = {1935-4053},
  journal      = {PRIMUS},
  keywords     = {Education, General Mathematics},
  number       = {5},
  pages        = {593--609},
  publisher    = {Taylor & Francis},
  title        = {{Tangible topology through the lens of limits}},
  doi          = {10.1080/10511970.2021.1872750},
  volume       = {32},
  year         = {2022},
}

@unpublished{12311,
  abstract     = {In this note we prove a formula for the cancellation exponent $k_{v,n}$ between division polynomials $\psi_n$ and $\phi_n$ associated with a sequence $\{nP\}_{n\in\mathbb{N}}$ of points on an elliptic curve $E$ defined over a discrete valuation field $K$. The formula is identical with the result of Yabuta-Voutier for the case of finite extension of $\mathbb{Q}_{p}$ and
generalizes to the case of non-standard Kodaira types for non-perfect residue fields.},
  author       = {Naskręcki, Bartosz and Verzobio, Matteo},
  booktitle    = {arXiv},
  title        = {{Common valuations of division polynomials}},
  doi          = {10.48550/arXiv.2203.02015},
  year         = {2022},
}

@article{12332,
  abstract     = {Activity of sensory neurons is driven not only by external stimuli but also by feedback signals from higher brain areas. Attention is one particularly important internal signal whose presumed role is to modulate sensory representations such that they only encode information currently relevant to the organism at minimal cost. This hypothesis has, however, not yet been expressed in a normative computational framework. Here, by building on normative principles of probabilistic inference and efficient coding, we developed a model of dynamic population coding in the visual cortex. By continuously adapting the sensory code to changing demands of the perceptual observer, an attention-like modulation emerges. This modulation can dramatically reduce the amount of neural activity without deteriorating the accuracy of task-specific inferences. Our results suggest that a range of seemingly disparate cortical phenomena such as intrinsic gain modulation, attention-related tuning modulation, and response variability could be manifestations of the same underlying principles, which combine efficient sensory coding with optimal probabilistic inference in dynamic environments.},
  author       = {Mlynarski, Wiktor F and Tkačik, Gašper},
  issn         = {1545-7885},
  journal      = {PLoS Biology},
  number       = {12},
  pages        = {e3001889},
  publisher    = {Public Library of Science},
  title        = {{Efficient coding theory of dynamic attentional modulation}},
  doi          = {10.1371/journal.pbio.3001889},
  volume       = {20},
  year         = {2022},
}

@article{12333,
  abstract     = {Together, copy-number and point mutations form the basis for most evolutionary novelty, through the process of gene duplication and divergence. While a plethora of genomic data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic reporter system that can distinguish between copy-number and point mutations, we study their early and transient adaptive dynamics in real time in Escherichia coli. We find two qualitatively different routes of adaptation, depending on the level of functional improvement needed. In conditions of high gene expression demand, the two mutation types occur as a combination. However, under low gene expression demand, copy-number and point mutations are mutually exclusive; here, owing to their higher frequency, adaptation is dominated by copy-number mutations, in a process we term amplification hindrance. Ultimately, due to high reversal rates and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation, but also constrain sequence divergence over evolutionary time scales.},
  author       = {Tomanek, Isabella and Guet, Calin C},
  issn         = {2050-084X},
  journal      = {eLife},
  publisher    = {eLife Sciences Publications},
  title        = {{Adaptation dynamics between copynumber and point mutations}},
  doi          = {10.7554/ELIFE.82240},
  volume       = {11},
  year         = {2022},
}

@misc{12339,
  abstract     = {Copy-number and point mutations form the basis for most evolutionary novelty through the process of gene duplication and divergence. While a plethora of genomic sequence data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic system that allows us to distinguish copy-number and point mutations, we study their early and transient adaptive dynamics in real-time in Escherichia coli. We find two qualitatively different routes of adaptation depending on the level of functional improvement selected for: In conditions of high gene expression demand, the two types of mutations occur as a combination. Under low gene expression demand, negative epistasis between the two types of mutations renders them mutually exclusive. Thus, owing to their higher frequency, adaptation is dominated by copy-number mutations. Ultimately, due to high rates of reversal and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation but also constrain sequence divergence over evolutionary time scales.},
  author       = {Tomanek, Isabella and Guet, Calin C},
  publisher    = {Dryad},
  title        = {{Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose}},
  doi          = {10.5061/dryad.rfj6q57ds},
  year         = {2022},
}

@phdthesis{12358,
  abstract     = {The complex yarn structure of knitted and woven fabrics gives rise to both a mechanical and
visual complexity. The small-scale interactions of yarns colliding with and pulling on each
other result in drastically different large-scale stretching and bending behavior, introducing
anisotropy, curling, and more. While simulating cloth as individual yarns can reproduce this
complexity and match the quality of real fabric, it may be too computationally expensive for
large fabrics. On the other hand, continuum-based approaches do not need to discretize the
cloth at a stitch-level, but it is non-trivial to find a material model that would replicate the
large-scale behavior of yarn fabrics, and they discard the intricate visual detail. In this thesis,
we discuss three methods to try and bridge the gap between small-scale and large-scale yarn
mechanics using numerical homogenization: fitting a continuum model to periodic yarn simulations, adding mechanics-aware yarn detail onto thin-shell simulations, and quantitatively
fitting yarn parameters to physical measurements of real fabric.
To start, we present a method for animating yarn-level cloth effects using a thin-shell solver.
We first use a large number of periodic yarn-level simulations to build a model of the potential
energy density of the cloth, and then use it to compute forces in a thin-shell simulator. The
resulting simulations faithfully reproduce expected effects like the stiffening of woven fabrics
and the highly deformable nature and anisotropy of knitted fabrics at a fraction of the cost of
full yarn-level simulation.
While our thin-shell simulations are able to capture large-scale yarn mechanics, they lack
the rich visual detail of yarn-level simulations. Therefore, we propose a method to animate
yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware
fashion in real time. Using triangle strains to interpolate precomputed yarn geometry, we are
able to reproduce effects such as knit loops tightening under stretching at negligible cost.
Finally, we introduce a methodology for inverse-modeling of yarn-level mechanics of cloth,
based on the mechanical response of fabrics in the real world. We compile a database from
physical tests of several knitted fabrics used in the textile industry spanning diverse physical
properties like stiffness, nonlinearity, and anisotropy. We then develop a system for approximating these mechanical responses with yarn-level cloth simulation, using homogenized
shell models to speed up computation and adding some small-but-necessary extensions to
yarn-level models used in computer graphics.
},
  author       = {Sperl, Georg},
  isbn         = {978-3-99078-020-6},
  issn         = {2663-337X},
  pages        = {138},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Homogenizing yarn simulations: Large-scale mechanics, small-scale detail, and quantitative fitting}},
  doi          = {10.15479/at:ista:12103},
  year         = {2022},
}

@phdthesis{12364,
  abstract     = {Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders characterized by behavioral symptoms such as problems in social communication and interaction, as
well as repetitive, restricted behaviors and interests. These disorders show a high degree
of heritability and hundreds of risk genes have been identifed using high throughput
sequencing technologies. This genetic heterogeneity has hampered eforts in understanding
the pathogenesis of ASD but at the same time given rise to the concept of convergent
mechanisms. Previous studies have identifed that risk genes for ASD broadly converge
onto specifc functional categories with transcriptional regulation being one of the biggest
groups. In this thesis, I focus on this subgroup of genes and investigate the gene regulatory
consequences of some of them in the context of neurodevelopment.
First, we showed that mutations in the ASD and intellectual disability risk gene Setd5 lead
to perturbations of gene regulatory programs in early cell fate specifcation. In addition,
adult animals display abnormal learning behavior which is mirrored at the transcriptional
level by altered activity dependent regulation of postsynaptic gene expression. Lastly,
we link the regulatory function of Setd5 to its interaction with the Paf1 and the NCoR
complex.
Second, by modeling the heterozygous loss of the top ASD gene CHD8 in human cerebral
organoids we demonstrate profound changes in the developmental trajectories of both
inhibitory and excitatory neurons using single cell RNA-sequencing. While the former
were generated earlier in CHD8+/- organoids, the generation of the latter was shifted to
later times in favor of a prolonged progenitor expansion phase and ultimately increased
organoid size.
Finally, by modeling heterozygous mutations for four ASD associated chromatin modifers,
ASH1L, KDM6B, KMT5B, and SETD5 in human cortical spheroids we show evidence of
regulatory convergence across three of those genes. We observe a shift from dorsal cortical
excitatory neuron fates towards partially ventralized cell types resembling cells from the
lateral ganglionic eminence. As this project is still ongoing at the time of writing, future
experiments will aim at elucidating the regulatory mechanisms underlying this shift with
the aim of linking these three ASD risk genes through biological convergence.},
  author       = {Dotter, Christoph},
  issn         = {2663-337X},
  pages        = {152},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Transcriptional consequences of mutations in genes associated with Autism Spectrum Disorder}},
  doi          = {10.15479/at:ista:12094},
  year         = {2022},
}

@phdthesis{12366,
  abstract     = {Recent substantial advances in the feld of superconducting circuits have shown its
potential as a leading platform for future quantum computing. In contrast to classical
computers based on bits that are represented by a single binary value, 0 or 1, quantum
bits (or qubits) can be in a superposition of both. Thus, quantum computers can store
and handle more information at the same time and a quantum advantage has already
been demonstrated for two types of computational tasks. Rapid progress in academic
and industry labs accelerates the development of superconducting processors which may
soon fnd applications in complex computations, chemical simulations, cryptography, and
optimization. Now that these machines are scaled up to tackle such problems the questions
of qubit interconnects and networks becomes very relevant. How to route signals on-chip
between diferent processor components? What is the most efcient way to entangle
qubits? And how to then send and process entangled signals between distant cryostats
hosting superconducting processors?
In this thesis, we are looking for solutions to these problems by studying the collective
behavior of superconducting qubit ensembles. We frst demonstrate on-demand tunable
directional scattering of microwave photons from a pair of qubits in a waveguide. Such a
device can route microwave photons on-chip with a high diode efciency. Then we focus
on studying ultra-strong coupling regimes between light (microwave photons) and matter
(superconducting qubits), a regime that could be promising for extremely fast multi-qubit
entanglement generation. Finally, we show coherent pulse storage and periodic revivals
in a fve qubit ensemble strongly coupled to a resonator. Such a reconfgurable storage
device could be used as part of a quantum repeater that is needed for longer-distance
quantum communication.
The achieved high degree of control over multi-qubit ensembles highlights not only the
beautiful physics of circuit quantum electrodynamics, it also represents the frst step
toward new quantum simulation and communication methods, and certain techniques
may also fnd applications in future superconducting quantum computing hardware.
},
  author       = {Redchenko, Elena},
  isbn         = {978-3-99078-024-4},
  issn         = {2663-337X},
  pages        = {168},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Controllable states of superconducting Qubit ensembles}},
  doi          = {10.15479/at:ista:12132},
  year         = {2022},
}

@phdthesis{12368,
  abstract     = {Metazoan development relies on the formation and remodeling of cell-cell contacts. The 
binding of adhesion receptors and remodeling of the actomyosin cell cortex at cell-cell 
interaction sites have been implicated in cell-cell contact formation. Yet, how these two 
processes functionally interact to drive cell-cell contact expansion and strengthening 
remains unclear. Here, we study how primary germ layer progenitor cells from zebrafish 
bind to supported lipid bilayers (SLB) functionalized with E-cadherin ectodomains as an 
assay system for monitoring cell-cell contact formation at high spatiotemporal resolution. 
We show that cell-cell contact formation represents a two-tiered process: E-cadherinmediated downregulation of the small GTPase RhoA at the forming contact leads to both 
depletion of Myosin-2 and decrease of F-actin. This is followed by centrifugal actin 
network flows at the contact triggered by a sharp gradient of Myosin-2 at the rim of the 
contact zone, with Myosin-2 displaying higher cortical localization outside than inside of 
the contact. These centrifugal cortical actin flows, in turn, not only further dilute the actin 
network at the contact disc, but also lead to an accumulation of both F-actin and Ecadherin at the contact rim. Eventually, this combination of actomyosin downregulation 
and flows at the contact contribute to the characteristic molecular organization implicated 
in contact formation and maintenance: depletion of cortical actomyosin at the contact disc, 
driving contact expansion by lowering interfacial tension at the contact, and accumulation 
of both E-cadherin and F-actin at the contact rim, mechanically linking the contractile 
cortices of the adhering cells. Thus, using a biomimetic assay, we exemplify how 
adhesion signaling and cell mechanics function together to modulate the spatial 
organization of cell-cell contacts.},
  author       = {Arslan, Feyza N},
  isbn         = { 978-3-99078-025-1 },
  issn         = {2663-337X},
  pages        = {113},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Remodeling of E-cadherin-mediated contacts via cortical  flows}},
  doi          = {10.15479/at:ista:12153},
  year         = {2022},
}

@phdthesis{12378,
  abstract     = {Environmental cues influence the highly dynamic morphology of microglia. Strategies to 
characterize these changes usually involve user-selected morphometric features, which 
preclude the identification of a spectrum of context-dependent morphological phenotypes. 
Here, we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes,
overcomes feature-selection bias and minimizes biological variability. 
First, with MorphOMICs we derive the morphological spectrum of microglia across seven 
brain regions during postnatal development and in two distinct Alzheimer’s disease 
degeneration mouse models. We uncover region-specific and sexually dimorphic
morphological trajectories, with females showing an earlier morphological shift than males in 
the degenerating brain. Overall, we demonstrate that both long primary- and short terminal 
processes provide distinct insights to morphological phenotypes. Moreover, using machine 
learning to map novel condition on the spectrum, we observe that microglia morphologies 
reflect a dose-dependent adaptation upon ketamine anesthesia and do not recover to control 
morphologies.
Next, we took advantage of MorphOMICs to build a high-resolution and layer-specific map of 
microglial morphological spectrum in the retina, covering postnatal development and rd10 
degeneration. Here, following photoreceptor death, microglia assume an early developmentlike morphology. Finally, we map microglial morphology following optic nerve crush on the 
retinal spectrum and observe a layer- and sex-dependent response. 
Overall, MorphOMICs opens a new perspective to analyze microglial morphology across 
multiple conditions, and provides a novel tool to characterize microglial morphology beyond 
the traditionally dichotomized view of microglia.},
  author       = {Colombo, Gloria},
  issn         = {2663-337X},
  pages        = {142},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{MorphOMICs, a tool for mapping microglial morphology, reveals brain region- and sex-dependent phenotypes}},
  doi          = {10.15479/at:ista:12378},
  year         = {2022},
}