TY - THES
AB - Accumulation of interstitial fluid (IF) between embryonic cells is a common phenomenon in vertebrate embryogenesis. Unlike other model systems, where these accumulations coalesce into a large central cavity – the blastocoel, in zebrafish, IF is more uniformly distributed between the deep cells (DC) before the onset of gastrulation. This is likely due to the presence of a large extraembryonic structure – the yolk cell (YC) at the position where the blastocoel typically forms in other model organisms. IF has long been speculated to play a role in tissue morphogenesis during embryogenesis, but direct evidence supporting such function is still sparse. Here we show that the relocalization of IF to the interface between the YC and DC/epiblast is critical for axial mesendoderm (ME) cell protrusion formation and migration along this interface, a key process in embryonic axis formation. We further demonstrate that axial ME cell migration and IF relocalization engage in a positive feedback loop, where axial ME migration triggers IF accumulation ahead of the advancing axial ME tissue by mechanically compressing the overlying epiblast cell layer. Upon compression, locally induced flow relocalizes the IF through the porous epiblast tissue resulting in an IF accumulation ahead of the leading axial ME. This IF accumulation, in turn, promotes cell protrusion formation and migration of the leading axial ME cells, thereby facilitating axial ME extension. Our findings reveal a central role of dynamic IF relocalization in orchestrating germ layer morphogenesis during gastrulation.
AU - Huljev, Karla
ID - 9397
SN - 2663-337X
TI - Coordinated spatiotemporal reorganization of interstitial fluid is required for axial mesendoderm migration in zebrafish gastrulation
ER -
TY - THES
AB - In this thesis, we consider several of the most classical and fundamental problems in static analysis and formal verification, including invariant generation, reachability analysis, termination analysis of probabilistic programs, data-flow analysis, quantitative analysis of Markov chains and Markov decision processes, and the problem of data packing in cache management.
We use techniques from parameterized complexity theory, polyhedral geometry, and real algebraic geometry to significantly improve the state-of-the-art, in terms of both scalability and completeness guarantees, for the mentioned problems. In some cases, our results are the first theoretical improvements for the respective problems in two or three decades.
AU - Goharshady, Amir Kafshdar
ID - 8934
SN - 2663-337X
TI - Parameterized and algebro-geometric advances in static program analysis
ER -
TY - GEN
AB - 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.
AU - Mühlböck, Fabian
AU - Henzinger, Thomas A
ID - 9946
KW - Run-time verification
KW - Software engineering
KW - Implicit specification
SN - 2664-1690
TI - Differential monitoring
ER -
TY - GEN
AB - We comment on two formal proofs of Fermat's sum of two squares theorem, written using the Mathematical Components libraries of the Coq proof assistant. The first one follows Zagier's celebrated one-sentence proof; the second follows David Christopher's recent new proof relying on partition-theoretic arguments. Both formal proofs rely on a general property of involutions of finite sets, of independent interest. The proof technique consists for the most part of automating recurrent tasks (such as case distinctions and computations on natural numbers) via ad hoc tactics.
AU - Dubach, Guillaume
AU - Mühlböck, Fabian
ID - 9281
T2 - arXiv
TI - Formal verification of Zagier's one-sentence proof
ER -
TY - JOUR
AB - 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.
AU - Velasquez, Silvia Melina
AU - Guo, Xiaoyuan
AU - Gallemi, Marçal
AU - Aryal, Bibek
AU - Venhuizen, Peter
AU - Barbez, Elke
AU - Dünser, Kai Alexander
AU - Darino, Martin
AU - Pӗnčík, Aleš
AU - Novák, Ondřej
AU - Kalyna, Maria
AU - Mouille, Gregory
AU - Benková, Eva
AU - Bhalerao, Rishikesh P.
AU - Mravec, Jozef
AU - Kleine-Vehn, Jürgen
ID - 9986
IS - 17
JF - International Journal of Molecular Sciences
KW - auxin
KW - growth
KW - cell wall
KW - xyloglucans
KW - hypocotyls
KW - gravitropism
SN - 1661-6596
TI - Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants
VL - 22
ER -
TY - GEN
AB - 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.
AU - Prehal, Christian
AU - Talian, Sara Drvarič
AU - Vizintin, Alen
AU - Amenitsch, Heinz
AU - Dominko, Robert
AU - Freunberger, Stefan Alexander
AU - Wood, Vanessa
ID - 9980
KW - Li2S
KW - Lithium Sulphur Batteries
KW - SAXS
KW - WAXS
TI - Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries
ER -
TY - THES
AB - 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.
AU - Hansen, Andi H
ID - 9962
KW - Neuronal migration
KW - Non-cell-autonomous
KW - Cell-autonomous
KW - Neurodevelopmental disease
SN - 2663-337X
TI - Cell-autonomous gene function and non-cell-autonomous effects in radial projection neuron migration
ER -
TY - THES
AB - This work is concerned with two fascinating circuit quantum electrodynamics components, the Josephson junction and the geometric superinductor, and the interesting experiments that can be done by combining the two. The Josephson junction has revolutionized the field of superconducting circuits as a non-linear dissipation-less circuit element and is used in almost all superconducting qubit implementations since the 90s. On the other hand, the superinductor is a relatively new circuit element introduced as a key component of the fluxonium qubit in 2009. This is an inductor with characteristic impedance larger than the resistance quantum and self-resonance frequency in the GHz regime. The combination of these two elements can occur in two fundamental ways: in parallel and in series. When connected in parallel the two create the fluxonium qubit, a loop with large inductance and a rich energy spectrum reliant on quantum tunneling. On the other hand placing the two elements in series aids with the measurement of the IV curve of a single Josephson junction in a high impedance environment. In this limit theory predicts that the junction will behave as its dual element: the phase-slip junction. While the Josephson junction acts as a non-linear inductor the phase-slip junction has the behavior of a non-linear capacitance and can be used to measure new Josephson junction phenomena, namely Coulomb blockade of Cooper pairs and phase-locked Bloch oscillations. The latter experiment allows for a direct link between frequency and current which is an elusive connection in quantum metrology. This work introduces the geometric superinductor, a superconducting circuit element where the high inductance is due to the geometry rather than the material properties of the superconductor, realized from a highly miniaturized superconducting planar coil. These structures will be described and characterized as resonators and qubit inductors and progress towards the measurement of phase-locked Bloch oscillations will be presented.
AU - Peruzzo, Matilda
ID - 9920
KW - quantum computing
KW - superinductor
KW - quantum metrology
SN - 2663-337X
TI - Geometric superinductors and their applications in circuit quantum electrodynamics
ER -
TY - GEN
AB - There are two elementary superconducting qubit types that derive directly from the quantum harmonic oscillator. In one the inductor is replaced by a nonlinear Josephson junction to realize the widely used charge qubits with a compact phase variable and a discrete charge wavefunction. In the other the junction is added in parallel, which gives rise to an extended phase variable, continuous wavefunctions and a rich energy level structure due to the loop topology. While the corresponding rf-SQUID Hamiltonian was introduced as a quadratic, quasi-1D potential approximation to describe the fluxonium qubit implemented with long Josephson junction arrays, in this work we implement it directly using a linear superinductor formed by a single uninterrupted aluminum wire. We present a large variety of qubits all stemming from the same circuit but with drastically different characteristic energy scales. This includes flux and fluxonium qubits but also the recently introduced quasi-charge qubit with strongly enhanced zero point phase fluctuations and a heavily suppressed flux dispersion. The use of a geometric inductor results in high precision of the inductive and capacitive energy as guaranteed by top-down lithography - a key ingredient for intrinsically protected superconducting qubits. The geometric fluxonium also exhibits a large magnetic dipole, which renders it an interesting new candidate for quantum sensing applications.
AU - Peruzzo, Matilda
AU - Hassani, Farid
AU - Szep, Gregory
AU - Trioni, Andrea
AU - Redchenko, Elena
AU - Zemlicka, Martin
AU - Fink, Johannes M
ID - 9928
KW - Quantum physics
KW - Mesoscale and Nanoscale physics
T2 - arXiv
TI - Geometric superinductance qubits: controlling phase delocalization across a single Josephson junction
ER -
TY - JOUR
AB - 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.
AU - Watson, Jake
AU - Pinggera, Alexandra
AU - Ho, Hinze
AU - Greger, Ingo H.
ID - 9985
IS - 1
JF - Nature Communications
TI - AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions
VL - 12
ER -
TY - JOUR
AB - 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.
AU - Wirth, Melchior
AU - Zhang, Haonan
ID - 9973
JF - Communications in Mathematical Physics
KW - Mathematical Physics
KW - Statistical and Nonlinear Physics
SN - 0010-3616
TI - Complete gradient estimates of quantum Markov semigroups
ER -
TY - CHAP
AB - Tissue morphogenesis is driven by mechanical forces triggering cell movements and shape changes. Quantitatively measuring tension within tissues is of great importance for understanding the role of mechanical signals acting on the cell and tissue level during morphogenesis. Here we introduce laser ablation as a useful tool to probe tissue tension within the granulosa layer, an epithelial monolayer of somatic cells that surround the zebrafish female gamete during folliculogenesis. We describe in detail how to isolate follicles, mount samples, perform laser surgery, and analyze the data.
AU - Xia, Peng
AU - Heisenberg, Carl-Philipp J
ED - Dosch, Roland
ID - 9245
KW - Tissue tension
KW - Morphogenesis
KW - Laser ablation
KW - Zebrafish folliculogenesis
KW - Granulosa cells
SN - 1064-3745
T2 - Germline Development in the Zebrafish
TI - Quantifying tissue tension in the granulosa layer after laser surgery
VL - 2218
ER -
TY - GEN
AB - 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.
AU - B R, Mallikarjun
AU - Tewari, Ayush
AU - Oh, Tae-Hyun
AU - Weyrich, Tim
AU - Bickel, Bernd
AU - Seidel, Hans-Peter
AU - Pfister, Hanspeter
AU - Matusik, Wojciech
AU - Elgharib, Mohamed
AU - Theobalt, Christian
ID - 9957
T2 - Computer Vision Foundation
TI - Monocular reconstruction of neural face reflectance fields
ER -
TY - CONF
AB - 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.
AU - Agarwal, Pratyush
AU - Chatterjee, Krishnendu
AU - Pathak, Shreya
AU - Pavlogiannis, Andreas
AU - Toman, Viktor
ID - 9987
SN - 0302-9743
T2 - 33rd International Conference on Computer-Aided Verification
TI - Stateless model checking under a reads-value-from equivalence
VL - 12759
ER -
TY - JOUR
AB - 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.
AU - Schmid, Laura
AU - Shati, Pouya
AU - Hilbe, Christian
AU - Chatterjee, Krishnendu
ID - 9997
IS - 1
JF - Scientific Reports
KW - Multidisciplinary
TI - The evolution of indirect reciprocity under action and assessment generosity
VL - 11
ER -
TY - GEN
AB - We propose a new weak solution concept for (two-phase) mean curvature flow which enjoys both (unconditional) existence and (weak-strong) uniqueness properties. These solutions are evolving varifolds, just as in Brakke's formulation, but are coupled to the phase volumes by a simple transport equation. First, we show that, in the exact same setup as in Ilmanen's proof [J. Differential Geom. 38, 417-461, (1993)], any limit point of solutions to the Allen-Cahn equation is a varifold solution in our sense. Second, we prove that any calibrated flow in the sense of Fischer et al. [arXiv:2003.05478] - and hence any classical solution to mean curvature flow - is unique in the class of our new varifold solutions. This is in sharp contrast to the case of Brakke flows, which a priori may disappear at any given time and are therefore fatally non-unique. Finally, we propose an extension of the solution concept to the multi-phase case which is at least guaranteed to satisfy a weak-strong uniqueness principle.
AU - Hensel, Sebastian
AU - Laux, Tim
ID - 10011
KW - Mean curvature flow
KW - gradient flows
KW - varifolds
KW - weak solutions
KW - weak-strong uniqueness
KW - calibrated geometry
KW - gradient-flow calibrations
T2 - arXiv
TI - A new varifold solution concept for mean curvature flow: Convergence of the Allen-Cahn equation and weak-strong uniqueness
ER -
TY - JOUR
AB - Inhibition or targeted deletion of histone deacetylase 3 (HDAC3) is neuroprotective in a variety neurodegenerative conditions, including retinal ganglion cells (RGCs) after acute optic nerve damage. Consistent with this, induced HDAC3 expression in cultured cells shows selective toxicity to neurons. Despite an established role for HDAC3 in neuronal pathology, little is known regarding the mechanism of this pathology.
AU - Schmitt, Heather M.
AU - Fehrman, Rachel L.
AU - Maes, Margaret E
AU - Yang, Huan
AU - Guo, Lian Wang
AU - Schlamp, Cassandra L.
AU - Pelzel, Heather R.
AU - Nickells, Robert W.
ID - 10000
IS - 10
JF - Investigative Ophthalmology and Visual Science
SN - 0146-0404
TI - Increased susceptibility and intrinsic apoptotic signaling in neurons by induced HDAC3 expression
VL - 62
ER -
TY - JOUR
AB - 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.
AU - Koroteev, Peter
AU - Pushkar, Petr
AU - Smirnov, Andrey V.
AU - Zeitlin, Anton M.
ID - 9998
IS - 5
JF - Selecta Mathematica
SN - 1022-1824
TI - Quantum K-theory of quiver varieties and many-body systems
VL - 27
ER -
TY - JOUR
AB - We study systems of nonlinear partial differential equations of parabolic type, in which the elliptic operator is replaced by the first-order divergence operator acting on a flux function, which is related to the spatial gradient of the unknown through an additional implicit equation. This setting, broad enough in terms of applications, significantly expands the paradigm of nonlinear parabolic problems. Formulating four conditions concerning the form of the implicit equation, we first show that these conditions describe a maximal monotone p-coercive graph. We then establish the global-in-time and large-data existence of a (weak) solution and its uniqueness. To this end, we adopt and significantly generalize Minty’s method of monotone mappings. A unified theory, containing several novel tools, is developed in a way to be tractable from the point of view of numerical approximations.
AU - Bulíček, Miroslav
AU - Maringová, Erika
AU - Málek, Josef
ID - 10005
IS - 09
JF - Mathematical Models and Methods in Applied Sciences
KW - Nonlinear parabolic systems
KW - implicit constitutive theory
KW - weak solutions
KW - existence
KW - uniqueness
SN - 0218-2025
TI - On nonlinear problems of parabolic type with implicit constitutive equations involving flux
VL - 31
ER -
TY - JOUR
AB - Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research.
AU - Friml, Jiří
ID - 10016
JF - Cold Spring Harbor Perspectives in Biology
SN - 1943-0264
TI - Fourteen stations of auxin
ER -