TY - JOUR
AB - It is well known that special Kubo-Ando operator means admit divergence center interpretations, moreover, they are also mean squared error estimators for certain metrics on positive definite operators. In this paper we give a divergence center interpretation for every symmetric Kubo-Ando mean. This characterization of the symmetric means naturally leads to a definition of weighted and multivariate versions of a large class of symmetric Kubo-Ando means. We study elementary properties of these weighted multivariate means, and note in particular that in the special case of the geometric mean we recover the weighted A#H-mean introduced by Kim, Lawson, and Lim.
AU - Pitrik, József
AU - Virosztek, Daniel
ID - 8373
JF - Linear Algebra and its Applications
KW - Kubo-Ando mean
KW - weighted multivariate mean
KW - barycenter
SN - 0024-3795
TI - A divergence center interpretation of general symmetric Kubo-Ando means, and related weighted multivariate operator means
VL - 609
ER -
TY - JOUR
AB - The phytohormone auxin plays a central role in shaping plant growth and development. With decades of genetic and biochemical studies, numerous core molecular components and their networks, underlying auxin biosynthesis, transport, and signaling, have been identified. Notably, protein phosphorylation, catalyzed by kinases and oppositely hydrolyzed by phosphatases, has been emerging to be a crucial type of post-translational modification, regulating physiological and developmental auxin output at all levels. In this review, we comprehensively discuss earlier and recent advances in our understanding of genetics, biochemistry, and cell biology of the kinases and phosphatases participating in auxin action. We provide insights into the mechanisms by which reversible protein phosphorylation defines developmental auxin responses, discuss current challenges, and provide our perspectives on future directions involving the integration of the control of protein phosphorylation into the molecular auxin network.
AU - Tan, Shutang
AU - Luschnig, Christian
AU - Friml, Jiří
ID - 8992
IS - 1
JF - Molecular Plant
SN - 16742052
TI - Pho-view of auxin: Reversible protein phosphorylation in auxin biosynthesis, transport and signaling
VL - 14
ER -
TY - JOUR
AB - Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.
AU - Kavcic, Bor
AU - Tkačik, Gašper
AU - Bollenbach, Tobias
ID - 8997
IS - 1
JF - PLOS Computational Biology
KW - Modelling and Simulation
KW - Genetics
KW - Molecular Biology
KW - Antibiotics
KW - Drug interactions
SN - 1553-7358
TI - Minimal biophysical model of combined antibiotic action
VL - 17
ER -
TY - JOUR
AB - In many basic shear flows, such as pipe, Couette, and channel flow, turbulence does not
arise from an instability of the laminar state, and both dynamical states co-exist. With decreasing flow speed (i.e., decreasing Reynolds number) the fraction of fluid in laminar motion increases while turbulence recedes and eventually the entire flow relaminarizes. The first step towards understanding the nature of this transition is to determine if the phase change is of either first or second order. In the former case, the turbulent fraction would drop discontinuously to zero as the Reynolds number decreases while in the latter the process would be continuous. For Couette flow, the flow between two parallel plates, earlier studies suggest a discontinuous scenario. In the present study we realize a Couette flow between two concentric cylinders which allows studies to be carried out in large aspect ratios and for extensive observation times. The presented measurements show that the transition in this circular Couette geometry is continuous suggesting that former studies were limited by finite size effects. A further characterization of this transition, in particular its relation to the directed percolation universality class, requires even larger system sizes than presently available.
AU - Avila, Kerstin
AU - Hof, Björn
ID - 8999
IS - 1
JF - Entropy
TI - Second-order phase transition in counter-rotating taylor-couette flow experiment
VL - 23
ER -
TY - JOUR
AB - Studies on the experimental realization of two-dimensional anyons in terms of quasiparticles have been restricted, so far, to only anyons on the plane. It is known, however, that the geometry and topology of space can have significant effects on quantum statistics for particles moving on it. Here, we have undertaken the first step toward realizing the emerging fractional statistics for particles restricted to move on the sphere instead of on the plane. We show that such a model arises naturally in the context of quantum impurity problems. In particular, we demonstrate a setup in which the lowest-energy spectrum of two linear bosonic or fermionic molecules immersed in a quantum many-particle environment can coincide with the anyonic spectrum on the sphere. This paves the way toward the experimental realization of anyons on the sphere using molecular impurities. Furthermore, since a change in the alignment of the molecules corresponds to the exchange of the particles on the sphere, such a realization reveals a novel type of exclusion principle for molecular impurities, which could also be of use as a powerful technique to measure the statistics parameter. Finally, our approach opens up a simple numerical route to investigate the spectra of many anyons on the sphere. Accordingly, we present the spectrum of two anyons on the sphere in the presence of a Dirac monopole field.
AU - Brooks, Morris
AU - Lemeshko, Mikhail
AU - Lundholm, D.
AU - Yakaboylu, Enderalp
ID - 9005
IS - 1
JF - Physical Review Letters
SN - 00319007
TI - Molecular impurities as a realization of anyons on the two-sphere
VL - 126
ER -
TY - JOUR
AB - We study dynamics and thermodynamics of ion transport in narrow, water-filled channels, considered as effective 1D Coulomb systems. The long range nature of the inter-ion interactions comes about due to the dielectric constants mismatch between the water and the surrounding medium, confining the electric filed to stay mostly within the water-filled channel. Statistical mechanics of such Coulomb systems is dominated by entropic effects which may be accurately accounted for by mapping onto an effective quantum mechanics. In presence of multivalent ions the corresponding quantum mechanics appears to be non-Hermitian. In this review we discuss a framework for semiclassical calculations for the effective non-Hermitian Hamiltonians. Non-Hermiticity elevates WKB action integrals from the real line to closed cycles on a complex Riemann surfaces where direct calculations are not attainable. We circumvent this issue by applying tools from algebraic topology, such as the Picard-Fuchs equation. We discuss how its solutions relate to the thermodynamics and correlation functions of multivalent solutions within narrow, water-filled channels.
AU - Gulden, Tobias
AU - Kamenev, Alex
ID - 9020
IS - 1
JF - Entropy
TI - Dynamics of ion channels via non-hermitian quantum mechanics
VL - 23
ER -
TY - JOUR
AB - We develop a geometric version of the circle method and use it to compute the compactly supported cohomology of the space of rational curves through a point on a smooth affine hypersurface of sufficiently low degree.
AU - Browning, Timothy D
AU - Sawin, Will
ID - 177
IS - 3
JF - Annals of Mathematics
TI - A geometric version of the circle method
VL - 191
ER -
TY - JOUR
AB - An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed.
AU - Browning, Timothy D
AU - Heath Brown, Roger
ID - 179
IS - 16
JF - Duke Mathematical Journal
TI - Density of rational points on a quadric bundle in ℙ3×ℙ3
VL - 169
ER -
TY - JOUR
AB - We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms.
AU - Hikaru, Ibayashi
AU - Wojtan, Christopher J
AU - Thuerey, Nils
AU - Igarashi, Takeo
AU - Ando, Ryoichi
ID - 5681
IS - 6
JF - IEEE Transactions on Visualization and Computer Graphics
SN - 10772626
TI - Simulating liquids on dynamically warping grids
VL - 26
ER -
TY - JOUR
AB - For complex Wigner-type matrices, i.e. Hermitian random matrices with independent, not necessarily identically distributed entries above the diagonal, we show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are universal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner–Dyson–Mehta universality conjecture for the last remaining universality type in the complex Hermitian class. Our analysis holds not only for exact cusps, but approximate cusps as well, where an extended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp for both symmetry classes. This result is also the key input in the companion paper (Cipolloni et al. in Pure Appl Anal, 2018. arXiv:1811.04055) where the cusp universality for real symmetric Wigner-type matrices is proven. The novel cusp fluctuation mechanism is also essential for the recent results on the spectral radius of non-Hermitian random matrices (Alt et al. in Spectral radius of random matrices with independent entries, 2019. arXiv:1907.13631), and the non-Hermitian edge universality (Cipolloni et al. in Edge universality for non-Hermitian random matrices, 2019. arXiv:1908.00969).
AU - Erdös, László
AU - Krüger, Torben H
AU - Schröder, Dominik J
ID - 6185
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - Cusp universality for random matrices I: Local law and the complex Hermitian case
VL - 378
ER -
TY - JOUR
AB - We prove edge universality for a general class of correlated real symmetric or complex Hermitian Wigner matrices with arbitrary expectation. Our theorem also applies to internal edges of the self-consistent density of states. In particular, we establish a strong form of band rigidity which excludes mismatches between location and label of eigenvalues close to internal edges in these general models.
AU - Alt, Johannes
AU - Erdös, László
AU - Krüger, Torben H
AU - Schröder, Dominik J
ID - 6184
IS - 2
JF - Annals of Probability
TI - Correlated random matrices: Band rigidity and edge universality
VL - 48
ER -
TY - JOUR
AB - We study dynamical optimal transport metrics between density matricesassociated to symmetric Dirichlet forms on finite-dimensional C∗-algebras. Our settingcovers arbitrary skew-derivations and it provides a unified framework that simultaneously generalizes recently constructed transport metrics for Markov chains, Lindblad equations, and the Fermi Ornstein–Uhlenbeck semigroup. We develop a non-nommutative differential calculus that allows us to obtain non-commutative Ricci curvature bounds, logarithmic Sobolev inequalities, transport-entropy inequalities, andspectral gap estimates.
AU - Carlen, Eric A.
AU - Maas, Jan
ID - 6358
IS - 2
JF - Journal of Statistical Physics
SN - 00224715
TI - Non-commutative calculus, optimal transport and functional inequalities in dissipative quantum systems
VL - 178
ER -
TY - JOUR
AB - The strong rate of convergence of the Euler-Maruyama scheme for nondegenerate SDEs with irregular drift coefficients is considered. In the case of α-Hölder drift in the recent literature the rate α/2 was proved in many related situations. By exploiting the regularising effect of the noise more efficiently, we show that the rate is in fact arbitrarily close to 1/2 for all α>0. The result extends to Dini continuous coefficients, while in d=1 also to all bounded measurable coefficients.
AU - Dareiotis, Konstantinos
AU - Gerencser, Mate
ID - 6359
JF - Electronic Journal of Probability
TI - On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift
VL - 25
ER -
TY - JOUR
AB - We prove a central limit theorem for the difference of linear eigenvalue statistics of a sample covariance matrix W˜ and its minor W. We find that the fluctuation of this difference is much smaller than those of the individual linear statistics, as a consequence of the strong correlation between the eigenvalues of W˜ and W. Our result identifies the fluctuation of the spatial derivative of the approximate Gaussian field in the recent paper by Dumitru and Paquette. Unlike in a similar result for Wigner matrices, for sample covariance matrices, the fluctuation may entirely vanish.
AU - Cipolloni, Giorgio
AU - Erdös, László
ID - 6488
IS - 3
JF - Random Matrices: Theory and Application
SN - 20103263
TI - Fluctuations for differences of linear eigenvalue statistics for sample covariance matrices
VL - 9
ER -
TY - JOUR
AB - This paper presents two algorithms. The first decides the existence of a pointed homotopy between given simplicial maps 𝑓,𝑔:𝑋→𝑌, and the second computes the group [𝛴𝑋,𝑌]∗ of pointed homotopy classes of maps from a suspension; in both cases, the target Y is assumed simply connected. More generally, these algorithms work relative to 𝐴⊆𝑋.
AU - Filakovský, Marek
AU - Vokřínek, Lukas
ID - 6563
JF - Foundations of Computational Mathematics
SN - 16153375
TI - Are two given maps homotopic? An algorithmic viewpoint
VL - 20
ER -
TY - JOUR
AB - We consider the monotone variational inequality problem in a Hilbert space and describe a projection-type method with inertial terms under the following properties: (a) The method generates a strongly convergent iteration sequence; (b) The method requires, at each iteration, only one projection onto the feasible set and two evaluations of the operator; (c) The method is designed for variational inequality for which the underline operator is monotone and uniformly continuous; (d) The method includes an inertial term. The latter is also shown to speed up the convergence in our numerical results. A comparison with some related methods is given and indicates that the new method is promising.
AU - Shehu, Yekini
AU - Li, Xiao-Huan
AU - Dong, Qiao-Li
ID - 6593
JF - Numerical Algorithms
SN - 1017-1398
TI - An efficient projection-type method for monotone variational inequalities in Hilbert spaces
VL - 84
ER -
TY - JOUR
AB - While Hartree–Fock theory is well established as a fundamental approximation for interacting fermions, it has been unclear how to describe corrections to it due to many-body correlations. In this paper we start from the Hartree–Fock state given by plane waves and introduce collective particle–hole pair excitations. These pairs can be approximately described by a bosonic quadratic Hamiltonian. We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type upper bound to the ground state energy. Our result justifies the random-phase approximation in the mean-field scaling regime, for repulsive, regular interaction potentials.
AU - Benedikter, Niels P
AU - Nam, Phan Thành
AU - Porta, Marcello
AU - Schlein, Benjamin
AU - Seiringer, Robert
ID - 6649
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime
VL - 374
ER -
TY - JOUR
AB - Fitting a function by using linear combinations of a large number N of `simple' components is one of the most fruitful ideas in statistical learning. This idea lies at the core of a variety of methods, from two-layer neural networks to kernel regression, to boosting. In general, the resulting risk minimization problem is non-convex and is solved by gradient descent or its variants. Unfortunately, little is known about global convergence properties of these approaches.
Here we consider the problem of learning a concave function f on a compact convex domain Ω⊆ℝd, using linear combinations of `bump-like' components (neurons). The parameters to be fitted are the centers of N bumps, and the resulting empirical risk minimization problem is highly non-convex. We prove that, in the limit in which the number of neurons diverges, the evolution of gradient descent converges to a Wasserstein gradient flow in the space of probability distributions over Ω. Further, when the bump width δ tends to 0, this gradient flow has a limit which is a viscous porous medium equation. Remarkably, the cost function optimized by this gradient flow exhibits a special property known as displacement convexity, which implies exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory appears to capture well the behavior for moderate values of δ,N. Explaining this phenomenon, and understanding the dependence on δ,N in a quantitative manner remains an outstanding challenge.
AU - Javanmard, Adel
AU - Mondelli, Marco
AU - Montanari, Andrea
ID - 6748
IS - 6
JF - Annals of Statistics
TI - Analysis of a two-layer neural network via displacement convexity
VL - 48
ER -
TY - JOUR
AB - Nearby grid cells have been observed to express a remarkable degree of long-rangeorder, which is often idealized as extending potentially to infinity. Yet their strict peri-odic firing and ensemble coherence are theoretically possible only in flat environments, much unlike the burrows which rodents usually live in. Are the symmetrical, coherent grid maps inferred in the lab relevant to chart their way in their natural habitat? We consider spheres as simple models of curved environments and waiting for the appropriate experiments to be performed, we use our adaptation model to predict what grid maps would emerge in a network with the same type of recurrent connections, which on the plane produce coherence among the units. We find that on the sphere such connections distort the maps that single grid units would express on their own, and aggregate them into clusters. When remapping to a different spherical environment, units in each cluster maintain only partial coherence, similar to what is observed in disordered materials, such as spin glasses.
AU - Stella, Federico
AU - Urdapilleta, Eugenio
AU - Luo, Yifan
AU - Treves, Alessandro
ID - 6796
IS - 4
JF - Hippocampus
SN - 10509631
TI - Partial coherence and frustration in self-organizing spherical grids
VL - 30
ER -
TY - JOUR
AB - Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions.
AU - Jahr, Wiebke
AU - Velicky, Philipp
AU - Danzl, Johann G
ID - 6808
IS - 3
JF - Methods
SN - 1046-2023
TI - Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens
VL - 174
ER -
TY - JOUR
AB - In resource allocation games, selfish players share resources that are needed in order to fulfill their objectives. The cost of using a resource depends on the load on it. In the traditional setting, the players make their choices concurrently and in one-shot. That is, a strategy for a player is a subset of the resources. We introduce and study dynamic resource allocation games. In this setting, the game proceeds in phases. In each phase each player chooses one resource. A scheduler dictates the order in which the players proceed in a phase, possibly scheduling several players to proceed concurrently. The game ends when each player has collected a set of resources that fulfills his objective. The cost for each player then depends on this set as well as on the load on the resources in it – we consider both congestion and cost-sharing games. We argue that the dynamic setting is the suitable setting for many applications in practice. We study the stability of dynamic resource allocation games, where the appropriate notion of stability is that of subgame perfect equilibrium, study the inefficiency incurred due to selfish behavior, and also study problems that are particular to the dynamic setting, like constraints on the order in which resources can be chosen or the problem of finding a scheduler that achieves stability.
AU - Avni, Guy
AU - Henzinger, Thomas A
AU - Kupferman, Orna
ID - 6761
JF - Theoretical Computer Science
SN - 03043975
TI - Dynamic resource allocation games
VL - 807
ER -
TY - JOUR
AB - We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, most existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to existing approaches, while also supporting weaker supervision. Importantly, it can be trained purely from 2D images, without pose annotations, and with only a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to reason over lighting parameters and exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach in various settings, showing that: (i) it learns to disentangle shape from pose and lighting; (ii) using shading in the loss improves performance compared to just silhouettes; (iii) when using a standard single white light, our model outperforms state-of-the-art 2D-supervised methods, both with and without pose supervision, thanks to exploiting shading cues; (iv) performance improves further when using multiple coloured lights, even approaching that of state-of-the-art 3D-supervised methods; (v) shapes produced by our model capture smooth surfaces and fine details better than voxel-based approaches; and (vi) our approach supports concave classes such as bathtubs and sofas, which methods based on silhouettes cannot learn.
AU - Henderson, Paul M
AU - Ferrari, Vittorio
ID - 6952
JF - International Journal of Computer Vision
SN - 0920-5691
TI - Learning single-image 3D reconstruction by generative modelling of shape, pose and shading
VL - 128
ER -
TY - JOUR
AU - Zhang, Yuzhou
AU - Friml, Jiří
ID - 6997
IS - 3
JF - New Phytologist
SN - 0028-646x
TI - Auxin guides roots to avoid obstacles during gravitropic growth
VL - 225
ER -
TY - JOUR
AB - The central object of investigation of this paper is the Hirzebruch class, a deformation of the Todd class, given by Hirzebruch (for smooth varieties). The generalization for singular varieties is due to Brasselet–Schürmann–Yokura. Following the work of Weber, we investigate its equivariant version for (possibly singular) toric varieties. The local decomposition of the Hirzebruch class to the fixed points of the torus action and a formula for the local class in terms of the defining fan are recalled. After this review part, we prove the positivity of local Hirzebruch classes for all toric varieties, thus proving false the alleged counterexample given by Weber.
AU - Rychlewicz, Kamil P
ID - 6965
JF - Bulletin of the London Mathematical Society
SN - 0024-6093
TI - The positivity of local equivariant Hirzebruch class for toric varieties
ER -
TY - JOUR
AB - We define an action of the (double of) Cohomological Hall algebra of Kontsevich and Soibelman on the cohomology of the moduli space of spiked instantons of Nekrasov. We identify this action with the one of the affine Yangian of gl(1). Based on that we derive the vertex algebra at the corner Wr1,r2,r3 of Gaiotto and Rapčák. We conjecture that our approach works for a big class of Calabi–Yau categories, including those associated with toric Calabi–Yau 3-folds.
AU - Rapcak, Miroslav
AU - Soibelman, Yan
AU - Yang, Yaping
AU - Zhao, Gufang
ID - 7004
JF - Communications in Mathematical Physics
SN - 0010-3616
TI - Cohomological Hall algebras, vertex algebras and instantons
VL - 376
ER -
TY - JOUR
AB - The unusual correlated state that emerges in URu2Si2 below THO = 17.5 K is known as “hidden order” because even basic characteristics of the order parameter, such as its dimensionality (whether it has one component or two), are “hidden.” We use resonant ultrasound spectroscopy to measure the symmetry-resolved elastic anomalies across THO. We observe no anomalies in the shear elastic moduli, providing strong thermodynamic evidence for a one-component order parameter. We develop a machine learning framework that reaches this conclusion directly from the raw data, even in a crystal that is too small for traditional resonant ultrasound. Our result rules out a broad class of theories of hidden order based on two-component order parameters, and constrains the nature of the fluctuations from which unconventional superconductivity emerges at lower temperature. Our machine learning framework is a powerful new tool for classifying the ubiquitous competing orders in correlated electron systems.
AU - Ghosh, Sayak
AU - Matty, Michael
AU - Baumbach, Ryan
AU - Bauer, Eric D.
AU - Modic, Kimberly A
AU - Shekhter, Arkady
AU - Mydosh, J. A.
AU - Kim, Eun-Ah
AU - Ramshaw, B. J.
ID - 7084
IS - 10
JF - Science Advances
TI - One-component order parameter in URu2Si2 uncovered by resonant ultrasound spectroscopy and machine learning
VL - 6
ER -
TY - JOUR
AB - Removal of the Bax gene from mice completely protects the somas of retinal ganglion cells (RGCs) from apoptosis following optic nerve injury. This makes BAX a promising therapeutic target to prevent neurodegeneration. In this study, Bax+/− mice were used to test the hypothesis that lowering the quantity of BAX in RGCs would delay apoptosis following optic nerve injury. RGCs were damaged by performing optic nerve crush (ONC) and then immunostaining for phospho-cJUN, and quantitative PCR were used to monitor the status of the BAX activation mechanism in the months following injury. The apoptotic susceptibility of injured cells was directly tested by virally introducing GFP-BAX into Bax−/− RGCs after injury. The competency of quiescent RGCs to reactivate their BAX activation mechanism was tested by intravitreal injection of the JNK pathway agonist, anisomycin. Twenty-four weeks after ONC, Bax+/− mice had significantly less cell loss in their RGC layer than Bax+/+ mice 3 weeks after ONC. Bax+/− and Bax+/+ RGCs exhibited similar patterns of nuclear phospho-cJUN accumulation immediately after ONC, which persisted in Bax+/− RGCs for up to 7 weeks before abating. The transcriptional activation of BAX-activating genes was similar in Bax+/− and Bax+/+ RGCs following ONC. Intriguingly, cells deactivated their BAX activation mechanism between 7 and 12 weeks after crush. Introduction of GFP-BAX into Bax−/− cells at 4 weeks after ONC showed that these cells had a nearly normal capacity to activate this protein, but this capacity was lost 8 weeks after crush. Collectively, these data suggest that 8–12 weeks after crush, damaged cells no longer displayed increased susceptibility to BAX activation relative to their naïve counterparts. In this same timeframe, retinal glial activation and the signaling of the pro-apoptotic JNK pathway also abated. Quiescent RGCs did not show a timely reactivation of their JNK pathway following intravitreal injection with anisomycin. These findings demonstrate that lowering the quantity of BAX in RGCs is neuroprotective after acute injury. Damaged RGCs enter a quiescent state months after injury and are no longer responsive to an apoptotic stimulus. Quiescent RGCs will require rejuvenation to reacquire functionality.
AU - Donahue, RJ
AU - Maes, Margaret E
AU - Grosser, JA
AU - Nickells, RW
ID - 7033
IS - 2
JF - Molecular Neurobiology
SN - 0893-7648
TI - BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage
VL - 57
ER -
TY - JOUR
AB - The phytohormone auxin acts as an amazingly versatile coordinator of plant growth and development. With its morphogen-like properties, auxin controls sites and timing of differentiation and/or growth responses both, in quantitative and qualitative terms. Specificity in the auxin response depends largely on distinct modes of signal transmission, by which individual cells perceive and convert auxin signals into a remarkable diversity of responses. The best understood, or so-called canonical mechanism of auxin perception ultimately results in variable adjustments of the cellular transcriptome, via a short, nuclear signal transduction pathway. Additional findings that accumulated over decades implied that an additional, presumably, cell surface-based auxin perception mechanism mediates very rapid cellular responses and decisively contributes to the cell's overall hormonal response. Recent investigations into both, nuclear and cell surface auxin signalling challenged this assumed partition of roles for different auxin signalling pathways and revealed an unexpected complexity in transcriptional and non-transcriptional cellular responses mediated by auxin.
AU - Gallei, Michelle C
AU - Luschnig, C
AU - Friml, Jiří
ID - 7142
IS - 2
JF - Current Opinion in Plant Biology
SN - 1369-5266
TI - Auxin signalling in growth: Schrödinger's cat out of the bag
VL - 53
ER -
TY - JOUR
AB - In recent years, many genes have been associated with chromatinopathies classified as “Cornelia de Lange Syndrome‐like.” It is known that the phenotype of these patients becomes less recognizable, overlapping to features characteristic of other syndromes caused by genetic variants affecting different regulators of chromatin structure and function. Therefore, Cornelia de Lange syndrome diagnosis might be arduous due to the seldom discordance between unexpected molecular diagnosis and clinical evaluation. Here, we review the molecular features of Cornelia de Lange syndrome, supporting the hypothesis that “CdLS‐like syndromes” are part of a larger “rare disease family” sharing multiple clinical features and common disrupted molecular pathways.
AU - Avagliano, Laura
AU - Parenti, Ilaria
AU - Grazioli, Paolo
AU - Di Fede, Elisabetta
AU - Parodi, Chiara
AU - Mariani, Milena
AU - Kaiser, Frank J.
AU - Selicorni, Angelo
AU - Gervasini, Cristina
AU - Massa, Valentina
ID - 7149
IS - 1
JF - Clinical Genetics
SN - 0009-9163
TI - Chromatinopathies: A focus on Cornelia de Lange syndrome
VL - 97
ER -
TY - JOUR
AB - We consider dynamical transport metrics for probability measures on discretisations of a bounded convex domain in ℝd. These metrics are natural discrete counterparts to the Kantorovich metric 𝕎2, defined using a Benamou-Brenier type formula. Under mild assumptions we prove an asymptotic upper bound for the discrete transport metric Wt in terms of 𝕎2, as the size of the mesh T tends to 0. However, we show that the corresponding lower bound may fail in general, even on certain one-dimensional and symmetric two-dimensional meshes. In addition, we show that the asymptotic lower bound holds under an isotropy assumption on the mesh, which turns out to be essentially necessary. This assumption is satisfied, e.g., for tilings by convex regular polygons, and it implies Gromov-Hausdorff convergence of the transport metric.
AU - Gladbach, Peter
AU - Kopfer, Eva
AU - Maas, Jan
ID - 71
IS - 3
JF - SIAM Journal on Mathematical Analysis
SN - 00361410
TI - Scaling limits of discrete optimal transport
VL - 52
ER -
TY - JOUR
AB - In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors.
AU - Ucar, Mehmet C
AU - Lipowsky, Reinhard
ID - 7166
IS - 1
JF - Nano Letters
SN - 1530-6984
TI - Collective force generation by molecular motors is determined by strain-induced unbinding
VL - 20
ER -
TY - JOUR
AB - Plant root architecture dynamically adapts to various environmental conditions, such as salt‐containing soil. The phytohormone abscisic acid (ABA) is involved among others also in these developmental adaptations, but the underlying molecular mechanism remains elusive. Here, a novel branch of the ABA signaling pathway in Arabidopsis involving PYR/PYL/RCAR (abbreviated as PYLs) receptor‐protein phosphatase 2A (PP2A) complex that acts in parallel to the canonical PYLs‐protein phosphatase 2C (PP2C) mechanism is identified. The PYLs‐PP2A signaling modulates root gravitropism and lateral root formation through regulating phytohormone auxin transport. In optimal conditions, PYLs ABA receptor interacts with the catalytic subunits of PP2A, increasing their phosphatase activity and thus counteracting PINOID (PID) kinase‐mediated phosphorylation of PIN‐FORMED (PIN) auxin transporters. By contrast, in salt and osmotic stress conditions, ABA binds to PYLs, inhibiting the PP2A activity, which leads to increased PIN phosphorylation and consequently modulated directional auxin transport leading to adapted root architecture. This work reveals an adaptive mechanism that may flexibly adjust plant root growth to withstand saline and osmotic stresses. It occurs via the cross‐talk between the stress hormone ABA and the versatile developmental regulator auxin.
AU - Li, Yang
AU - Wang, Yaping
AU - Tan, Shutang
AU - Li, Zhen
AU - Yuan, Zhi
AU - Glanc, Matous
AU - Domjan, David
AU - Wang, Kai
AU - Xuan, Wei
AU - Guo, Yan
AU - Gong, Zhizhong
AU - Friml, Jiří
AU - Zhang, Jing
ID - 7204
IS - 3
JF - Advanced Science
TI - Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex
VL - 7
ER -
TY - JOUR
AB - Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.
AU - Johannesson, Kerstin
AU - Zagrodzka, Zuzanna
AU - Faria, Rui
AU - Westram, Anja M
AU - Butlin, Roger K.
ID - 7205
IS - 3
JF - Journal of Evolutionary Biology
SN - 1010061X
TI - Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?
VL - 33
ER -
TY - JOUR
AB - The hippocampus plays key roles in learning and memory and is a main target of Alzheimer's disease (AD), which causes progressive memory impairments. Despite numerous investigations about the processes required for the normal hippocampal functions, the neurotransmitter receptors involved in the synaptic deficits by which AD disables the hippocampus are not yet characterized. By combining histoblots, western blots, immunohistochemistry and high‐resolution immunoelectron microscopic methods for GABAB receptors, this study provides a quantitative description of the expression and the subcellular localization of GABAB1 in the hippocampus in a mouse model of AD at 1, 6 and 12 months of age. Western blots and histoblots showed that the total amount of protein and the laminar expression pattern of GABAB1 were similar in APP/PS1 mice and in age‐matched wild‐type mice. In contrast, immunoelectron microscopic techniques showed that the subcellular localization of GABAB1 subunit did not change significantly in APP/PS1 mice at 1 month of age, was significantly reduced in the stratum lacunosum‐moleculare of CA1 pyramidal cells at 6 months of age and significantly reduced at the membrane surface of CA1 pyramidal cells at 12 months of age. This reduction of plasma membrane GABAB1 was paralleled by a significant increase of the subunit at the intracellular sites. We further observed a decrease of membrane‐targeted GABAB receptors in axon terminals contacting CA1 pyramidal cells. Our data demonstrate compartment‐ and age‐dependent reduction of plasma membrane‐targeted GABAB receptors in the CA1 region of the hippocampus, suggesting that this decrease might be enough to alter the GABAB‐mediated synaptic transmission taking place in AD.
AU - Martín-Belmonte, Alejandro
AU - Aguado, Carolina
AU - Alfaro-Ruíz, Rocío
AU - Moreno-Martínez, Ana Esther
AU - De La Ossa, Luis
AU - Martínez-Hernández, José
AU - Buisson, Alain
AU - Früh, Simon
AU - Bettler, Bernhard
AU - Shigemoto, Ryuichi
AU - Fukazawa, Yugo
AU - Luján, Rafael
ID - 7207
IS - 3
JF - Brain Pathology
SN - 10156305
TI - Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer's disease
VL - 30
ER -
TY - THES
AB - In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time.
AU - Tkadlec, Josef
ID - 7196
TI - A role of graphs in evolutionary processes
ER -
TY - CONF
AB - Many systems rely on optimistic concurrent search trees for multi-core scalability. In principle, optimistic trees have a simple performance story: searches are read-only and so run in parallel, with writes to shared memory occurring only when modifying the data structure. However, this paper shows that in practice, obtaining the full performance benefits of optimistic search trees is not so simple.
We focus on optimistic binary search trees (BSTs) and perform a detailed performance analysis of 10 state-of-the-art BSTs on large scale x86-64 hardware, using both microbenchmarks and an in-memory database system. We find and explain significant unexpected performance differences between BSTs with similar tree structure and search implementations, which we trace to subtle performance-degrading interactions of BSTs with systems software and hardware subsystems. We further derive a prescriptive approach to avoid this performance degradation, as well as algorithmic insights on optimistic BST design. Our work underlines the gap between the theory and practice of multi-core performance, and calls for further research to help bridge this gap.
AU - Arbel-Raviv, Maya
AU - Brown, Trevor A
AU - Morrison, Adam
ID - 7272
SN - 9781939133021
T2 - Proceedings of the 2018 USENIX Annual Technical Conference
TI - Getting to the root of concurrent binary search tree performance
ER -
TY - JOUR
AB - The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process.
AU - Tkadlec, Josef
AU - Pavlogiannis, Andreas
AU - Chatterjee, Krishnendu
AU - Nowak, Martin A.
ID - 7212
JF - PLoS computational biology
TI - Limits on amplifiers of natural selection under death-Birth updating
VL - 16
ER -
TY - JOUR
AB - Habitat loss is one of the key drivers of the ongoing decline of biodiversity. However, ecologists still argue about how fragmentation of habitat (independent of habitat loss) affects species richness. The recently proposed habitat amount hypothesis posits that species richness only depends on the total amount of habitat in a local landscape. In contrast, empirical studies report contrasting patterns: some find positive and others negative effects of fragmentation per se on species richness. To explain this apparent disparity, we devise a stochastic, spatially explicit model of competitive species communities in heterogeneous habitats. The model shows that habitat loss and fragmentation have complex effects on species diversity in competitive communities. When the total amount of habitat is large, fragmentation per se tends to increase species diversity, but if the total amount of habitat is small, the situation is reversed: fragmentation per se decreases species diversity.
AU - Rybicki, Joel
AU - Abrego, Nerea
AU - Ovaskainen, Otso
ID - 7224
IS - 3
JF - Ecology Letters
SN - 1461-023X
TI - Habitat fragmentation and species diversity in competitive communities
VL - 23
ER -
TY - JOUR
AB - T lymphocytes utilize amoeboid migration to navigate effectively within complex microenvironments. The precise rearrangement of the actin cytoskeleton required for cellular forward propulsion is mediated by actin regulators, including the actin‐related protein 2/3 (Arp2/3) complex, a macromolecular machine that nucleates branched actin filaments at the leading edge. The consequences of modulating Arp2/3 activity on the biophysical properties of the actomyosin cortex and downstream T cell function are incompletely understood. We report that even a moderate decrease of Arp3 levels in T cells profoundly affects actin cortex integrity. Reduction in total F‐actin content leads to reduced cortical tension and disrupted lamellipodia formation. Instead, in Arp3‐knockdown cells, the motility mode is dominated by blebbing migration characterized by transient, balloon‐like protrusions at the leading edge. Although this migration mode seems to be compatible with interstitial migration in three‐dimensional environments, diminished locomotion kinetics and impaired cytotoxicity interfere with optimal T cell function. These findings define the importance of finely tuned, Arp2/3‐dependent mechanophysical membrane integrity in cytotoxic effector T lymphocyte activities.
AU - Obeidy, Peyman
AU - Ju, Lining A.
AU - Oehlers, Stefan H.
AU - Zulkhernain, Nursafwana S.
AU - Lee, Quintin
AU - Galeano Niño, Jorge L.
AU - Kwan, Rain Y.Q.
AU - Tikoo, Shweta
AU - Cavanagh, Lois L.
AU - Mrass, Paulus
AU - Cook, Adam J.L.
AU - Jackson, Shaun P.
AU - Biro, Maté
AU - Roediger, Ben
AU - Sixt, Michael K
AU - Weninger, Wolfgang
ID - 7234
IS - 2
JF - Immunology and Cell Biology
SN - 08189641
TI - Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes
VL - 98
ER -
TY - JOUR
AB - We consider the Fröhlich model of a polaron, and show that its effective mass diverges in thestrong coupling limit.
AU - Lieb, Elliott H.
AU - Seiringer, Robert
ID - 7235
JF - Journal of Statistical Physics
SN - 0022-4715
TI - Divergence of the effective mass of a polaron in the strong coupling limit
VL - 180
ER -
TY - JOUR
AB - The biotic interactions hypothesis posits that biotic interactions are more important drivers of adaptation closer to the equator, evidenced by “stronger” contemporary interactions (e.g. greater interaction rates) and/or patterns of trait evolution consistent with a history of stronger interactions. Support for the hypothesis is mixed, but few studies span tropical and temperate regions while experimentally controlling for evolutionary history. Here, we integrate field observations and common garden experiments to quantify the relative importance of pollination and herbivory in a pair of tropical‐temperate congeneric perennial herbs. Phytolacca rivinoides and P. americana are pioneer species native to the Neotropics and the eastern USA, respectively. We compared plant‐pollinator and plant‐herbivore interactions between three tropical populations of P. rivinoides from Costa Rica and three temperate populations of P. americana from its northern range edge in Michigan and Ohio. For some metrics of interaction importance, we also included three subtropical populations of P. americana from its southern range edge in Florida. This approach confounds species and region but allows us, uniquely, to measure complementary proxies of interaction importance across a tropical‐temperate range in one system. To test the prediction that lower‐latitude plants are more reliant on insect pollinators, we quantified floral display and reward, insect visitation rates, and self‐pollination ability (autogamy). To test the prediction that lower‐latitude plants experience more herbivore pressure, we quantified herbivory rates, herbivore abundance, and leaf palatability. We found evidence supporting the biotic interactions hypothesis for most comparisons between P. rivinoides and north‐temperate P. americana (floral display, insect visitation, autogamy, herbivory, herbivore abundance, and young‐leaf palatability). Results for subtropical P. americana populations, however, were typically not intermediate between P. rivinoides and north‐temperate P. americana, as would be predicted by a linear latitudinal gradient in interaction importance. Subtropical young‐leaf palatability was intermediate, but subtropical mature leaves were the least palatable, and pollination‐related traits did not differ between temperate and subtropical regions. These nonlinear patterns of interaction importance suggest future work to relate interaction importance to climatic or biotic thresholds. In sum, we found that the biotic interactions hypothesis was more consistently supported at the larger spatial scale of our study.
AU - Baskett, Carina
AU - Schroeder, Lucy
AU - Weber, Marjorie G.
AU - Schemske, Douglas W.
ID - 7236
IS - 1
JF - Ecological Monographs
SN - 0012-9615
TI - Multiple metrics of latitudinal patterns in insect pollination and herbivory for a tropical‐temperate congener pair
VL - 90
ER -
TY - JOUR
AB - The cyclin-dependent kinase inhibitor p57KIP2 is encoded by the imprinted Cdkn1c locus, exhibits maternal expression, and is essential for cerebral cortex development. How Cdkn1c regulates corticogenesis is however not clear. To this end we employ Mosaic Analysis with Double Markers (MADM) technology to genetically dissect Cdkn1c gene function in corticogenesis at single cell resolution. We find that the previously described growth-inhibitory Cdkn1c function is a non-cell-autonomous one, acting on the whole organism. In contrast we reveal a growth-promoting cell-autonomous Cdkn1c function which at the mechanistic level mediates radial glial progenitor cell and nascent projection neuron survival. Strikingly, the growth-promoting function of Cdkn1c is highly dosage sensitive but not subject to genomic imprinting. Collectively, our results suggest that the Cdkn1c locus regulates cortical development through distinct cell-autonomous and non-cell-autonomous mechanisms. More generally, our study highlights the importance to probe the relative contributions of cell intrinsic gene function and tissue-wide mechanisms to the overall phenotype.
AU - Laukoter, Susanne
AU - Beattie, Robert J
AU - Pauler, Florian
AU - Amberg, Nicole
AU - Nakayama, Keiichi I.
AU - Hippenmeyer, Simon
ID - 7253
JF - Nature Communications
SN - 2041-1723
TI - Imprinted Cdkn1c genomic locus cell-autonomously promotes cell survival in cerebral cortex development
VL - 11
ER -
TY - JOUR
AB - Cytoskeletal filaments such as microtubules (MTs) and filamentous actin (F-actin) dynamically support cell structure and functions. In central presynaptic terminals, F-actin is expressed along the release edge and reportedly plays diverse functional roles, but whether axonal MTs extend deep into terminals and play any physiological role remains controversial. At the calyx of Held in rats of either sex, confocal and high-resolution microscopy revealed that MTs enter deep into presynaptic terminal swellings and partially colocalize with a subset of synaptic vesicles (SVs). Electrophysiological analysis demonstrated that depolymerization of MTs specifically prolonged the slow-recovery time component of EPSCs from short-term depression induced by a train of high-frequency stimulation, whereas depolymerization of F-actin specifically prolonged the fast-recovery component. In simultaneous presynaptic and postsynaptic action potential recordings, depolymerization of MTs or F-actin significantly impaired the fidelity of high-frequency neurotransmission. We conclude that MTs and F-actin differentially contribute to slow and fast SV replenishment, thereby maintaining high-frequency neurotransmission.
AU - Piriya Ananda Babu, Lashmi
AU - Wang, Han Ying
AU - Eguchi, Kohgaku
AU - Guillaud, Laurent
AU - Takahashi, Tomoyuki
ID - 7339
IS - 1
JF - Journal of neuroscience
TI - Microtubule and actin differentially regulate synaptic vesicle cycling to maintain high-frequency neurotransmission
VL - 40
ER -
TY - JOUR
AB - We propose that correlations among neurons are generically strong enough to organize neural activity patterns into a discrete set of clusters, which can each be viewed as a population codeword. Our reasoning starts with the analysis of retinal ganglion cell data using maximum entropy models, showing that the population is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads to an argument that neural populations in many other brain areas might share this structure. Next, we use latent variable models to show that this glassy state possesses well-defined clusters of neural activity. Clusters have three appealing properties: (i) clusters exhibit error correction, i.e., they are reproducibly elicited by the same stimulus despite variability at the level of constituent neurons; (ii) clusters encode qualitatively different visual features than their constituent neurons; and (iii) clusters can be learned by downstream neural circuits in an unsupervised fashion. We hypothesize that these properties give rise to a “learnable” neural code which the cortical hierarchy uses to extract increasingly complex features without supervision or reinforcement.
AU - Berry, Michael J.
AU - Tkačik, Gašper
ID - 7656
JF - Frontiers in Computational Neuroscience
TI - Clustering of neural activity: A design principle for population codes
VL - 14
ER -
TY - JOUR
AB - Wood, as the most abundant carbon dioxide storing bioresource, is currently driven beyond its traditional use through creative innovations and nanotechnology. For many properties the micro- and nanostructure plays a crucial role and one key challenge is control and detection of chemical and physical processes in the confined microstructure and nanopores of the wooden cell wall. In this study, correlative Raman and atomic force microscopy show high potential for tracking in situ molecular rearrangement of wood polymers during compression. More water molecules (interpreted as wider cellulose microfibril distances) and disentangling of hemicellulose chains are detected in the opened cell wall regions, whereas an increase of lignin is revealed in the compressed areas. These results support a new more “loose” cell wall model based on flexible lignin nanodomains and advance our knowledge of the molecular reorganization during deformation of wood for optimized processing and utilization.
AU - Felhofer, Martin
AU - Bock, Peter
AU - Singh, Adya
AU - Prats Mateu, Batirtze
AU - Zirbs, Ronald
AU - Gierlinger, Notburga
ID - 7663
IS - 4
JF - Nano Letters
TI - Wood deformation leads to rearrangement of molecules at the nanoscale
VL - 20
ER -
TY - JOUR
AB - Metabotropic γ-aminobutyric acid (GABAB) receptors contribute to the control of network activity and information processing in hippocampal circuits by regulating neuronal excitability and synaptic transmission. The dysfunction in the dentate gyrus (DG) has been implicated in Alzheimer´s disease (AD). Given the involvement of GABAB receptors in AD, to determine their subcellular localisation and possible alteration in granule cells of the DG in a mouse model of AD at 12 months of age, we used high-resolution immunoelectron microscopic analysis. Immunohistochemistry at the light microscopic level showed that the regional and cellular expression pattern of GABAB1 was similar in an AD model mouse expressing mutated human amyloid precursor protein and presenilin1 (APP/PS1) and in age-matched wild type mice. High-resolution immunoelectron microscopy revealed a distance-dependent gradient of immunolabelling for GABAB receptors, increasing from proximal to distal dendrites in both wild type and APP/PS1 mice. However, the overall density of GABAB receptors at the neuronal surface of these postsynaptic compartments of granule cells was significantly reduced in APP/PS1 mice. Parallel to this reduction in surface receptors, we found a significant increase in GABAB1 at cytoplasmic sites. GABAB receptors were also detected at presynaptic sites in the molecular layer of the DG. We also found a decrease in plasma membrane GABAB receptors in axon terminals contacting dendritic spines of granule cells, which was more pronounced in the outer than in the inner molecular layer. Altogether, our data showing post- and presynaptic reduction in surface GABAB receptors in the DG suggest the alteration of the GABAB-mediated modulation of excitability and synaptic transmission in granule cells, which may contribute to the cognitive dysfunctions in the APP/PS1 model of AD
AU - Martín-Belmonte, Alejandro
AU - Aguado, Carolina
AU - Alfaro-Ruíz, Rocío
AU - Moreno-Martínez, Ana Esther
AU - De La Ossa, Luis
AU - Martínez-Hernández, José
AU - Buisson, Alain
AU - Shigemoto, Ryuichi
AU - Fukazawa, Yugo
AU - Luján, Rafael
ID - 7664
IS - 7
JF - International journal of molecular sciences
TI - Density of GABAB receptors is reduced in granule cells of the hippocampus in a mouse model of Alzheimer's disease
VL - 21
ER -
TY - JOUR
AB - Acute brain slice preparation is a powerful experimental model for investigating the characteristics of synaptic function in the brain. Although brain tissue is usually cut at ice-cold temperature (CT) to facilitate slicing and avoid neuronal damage, exposure to CT causes molecular and architectural changes of synapses. To address these issues, we investigated ultrastructural and electrophysiological features of synapses in mouse acute cerebellar slices prepared at ice-cold and physiological temperature (PT). In the slices prepared at CT, we found significant spine loss and reconstruction, synaptic vesicle rearrangement and decrease in synaptic proteins, all of which were not detected in slices prepared at PT. Consistent with these structural findings, slices prepared at PT showed higher release probability. Furthermore, preparation at PT allows electrophysiological recording immediately after slicing resulting in higher detectability of long-term depression (LTD) after motor learning compared with that at CT. These results indicate substantial advantages of the slice preparation at PT for investigating synaptic functions in different physiological conditions.
AU - Eguchi, Kohgaku
AU - Velicky, Philipp
AU - Hollergschwandtner, Elena
AU - Itakura, Makoto
AU - Fukazawa, Yugo
AU - Danzl, Johann G
AU - Shigemoto, Ryuichi
ID - 7665
JF - Frontiers in Cellular Neuroscience
SN - 16625102
TI - Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions
VL - 14
ER -
TY - JOUR
AB - Generalizing the decomposition of a connected planar graph into a tree and a dual tree, we prove a combinatorial analog of the classic Helmholtz–Hodge decomposition of a smooth vector field. Specifically, we show that for every polyhedral complex, K, and every dimension, p, there is a partition of the set of p-cells into a maximal p-tree, a maximal p-cotree, and a collection of p-cells whose cardinality is the p-th reduced Betti number of K. Given an ordering of the p-cells, this tri-partition is unique, and it can be computed by a matrix reduction algorithm that also constructs canonical bases of cycle and boundary groups.
AU - Edelsbrunner, Herbert
AU - Ölsböck, Katharina
ID - 7666
JF - Discrete and Computational Geometry
SN - 01795376
TI - Tri-partitions and bases of an ordered complex
VL - 64
ER -
TY - JOUR
AB - Large overpotentials upon discharge and charge of Li-O2 cells have motivated extensive research into heterogeneous solid electrocatalysts or non-carbon electrodes with the aim to improve rate capability, round-trip efficiency and cycle life. These features are equally governed by parasitic reactions, which are now recognized to be caused by the highly reactive singlet oxygen (1O2). However, the link between the presence of electrocatalysts and 1O2 formation in metal-O2 cells is unknown. Here, we show that, compared to pristine carbon black electrodes, a representative selection of electrocatalysts or non-carbon electrodes (noble metal, transition metal compounds) may both slightly reduce or severely increase the 1O2 formation. The individual reaction steps, where the surfaces impact the 1O2 yield are deciphered, showing that 1O2 yield from superoxide disproportionation as well as the decomposition of trace H2O2 are sensitive to catalysts. Transition metal compounds in general are prone to increase 1O2.
AU - Samojlov, Aleksej
AU - Schuster, David
AU - Kahr, Jürgen
AU - Freunberger, Stefan Alexander
ID - 7672
IS - 12
JF - Electrochimica Acta
TI - Surface and catalyst driven singlet oxygen formation in Li-O2 cells
VL - 362
ER -
TY - DATA
AB - Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.
AU - Grah, Rok
ID - 7383
KW - Matlab scripts
KW - analysis of microfluidics
KW - mathematical model
TI - Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation
ER -
TY - JOUR
AB - The growing sample size of genome-wide association studies has facilitated the discovery of gene-environment interactions (GxE). Here we propose a maximum likelihood method to estimate the contribution of GxE to continuous traits taking into account all interacting environmental variables, without the need to measure any. Extensive simulations demonstrate that our method provides unbiased interaction estimates and excellent coverage. We also offer strategies to distinguish specific GxE from general scale effects. Applying our method to 32 traits in the UK Biobank reveals that while the genetic risk score (GRS) of 376 variants explains 5.2% of body mass index (BMI) variance, GRSxE explains an additional 1.9%. Nevertheless, this interaction holds for any variable with identical correlation to BMI as the GRS, hence may not be GRS-specific. Still, we observe that the global contribution of specific GRSxE to complex traits is substantial for nine obesity-related measures (including leg impedance and trunk fat-free mass).
AU - Sulc, Jonathan
AU - Mounier, Ninon
AU - Günther, Felix
AU - Winkler, Thomas
AU - Wood, Andrew R.
AU - Frayling, Timothy M.
AU - Heid, Iris M.
AU - Robinson, Matthew Richard
AU - Kutalik, Zoltán
ID - 7707
JF - Nature Communications
SN - 2041-1723
TI - Quantification of the overall contribution of gene-environment interaction for obesity-related traits
VL - 11
ER -
TY - JOUR
AB - We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor.
AU - Nabais, Marta F.
AU - Lin, Tian
AU - Benyamin, Beben
AU - Williams, Kelly L.
AU - Garton, Fleur C.
AU - Vinkhuyzen, Anna A. E.
AU - Zhang, Futao
AU - Vallerga, Costanza L.
AU - Restuadi, Restuadi
AU - Freydenzon, Anna
AU - Zwamborn, Ramona A. J.
AU - Hop, Paul J.
AU - Robinson, Matthew Richard
AU - Gratten, Jacob
AU - Visscher, Peter M.
AU - Hannon, Eilis
AU - Mill, Jonathan
AU - Brown, Matthew A.
AU - Laing, Nigel G.
AU - Mather, Karen A.
AU - Sachdev, Perminder S.
AU - Ngo, Shyuan T.
AU - Steyn, Frederik J.
AU - Wallace, Leanne
AU - Henders, Anjali K.
AU - Needham, Merrilee
AU - Veldink, Jan H.
AU - Mathers, Susan
AU - Nicholson, Garth
AU - Rowe, Dominic B.
AU - Henderson, Robert D.
AU - McCombe, Pamela A.
AU - Pamphlett, Roger
AU - Yang, Jian
AU - Blair, Ian P.
AU - McRae, Allan F.
AU - Wray, Naomi R.
ID - 7708
JF - npj Genomic Medicine
SN - 2056-7944
TI - Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis
VL - 5
ER -
TY - GEN
AB - Recent advances in synthetic post-translational protein circuits are significantly impacting the landscape of biomimicry engineering. However, designing sustained dynamic phenomena in these circuits remains an outstanding challenge. Inspired by the KaiABC system regulating the circadian clock in cyanobacteria, we develop two experimentally realizable post-translational oscillators. The oscillators rely on a small number of components interacting only through reversible binding and phosphorylation/dephosphorylation reactions.
AU - Kimchi, Ofer
AU - Goodrich, Carl Peter
AU - Courbet, Alexis
AU - Curatolo, Agnese I.
AU - Woodall, Nicholas B.
AU - Baker, David
AU - Brenner, Michael P.
ID - 7778
T2 - bioRxiv
TI - Self-assembly based post-translational protein oscillators
ER -
TY - JOUR
AB - Mutations in NDUFS4, which encodes an accessory subunit of mitochondrial oxidative phosphorylation (OXPHOS) complex I (CI), induce Leigh syndrome (LS). LS is a poorly understood pediatric disorder featuring brain-specific anomalies and early death. To study the LS pathomechanism, we here compared OXPHOS proteomes between various Ndufs4−/− mouse tissues. Ndufs4−/− animals displayed significantly lower CI subunit levels in brain/diaphragm relative to other tissues (liver/heart/kidney/skeletal muscle), whereas other OXPHOS subunit levels were not reduced. Absence of NDUFS4 induced near complete absence of the NDUFA12 accessory subunit, a 50% reduction in other CI subunit levels, and an increase in specific CI assembly factors. Among the latter, NDUFAF2 was most highly increased. Regarding NDUFS4, NDUFA12 and NDUFAF2, identical results were obtained in Ndufs4−/− mouse embryonic fibroblasts (MEFs) and NDUFS4-mutated LS patient cells. Ndufs4−/− MEFs contained active CI in situ but blue-native-PAGE highlighted that NDUFAF2 attached to an inactive CI subcomplex (CI-830) and inactive assemblies of higher MW. In NDUFA12-mutated LS patient cells, NDUFA12 absence did not reduce NDUFS4 levels but triggered NDUFAF2 association to active CI. BN-PAGE revealed no such association in LS patient fibroblasts with mutations in other CI subunit-encoding genes where NDUFAF2 was attached to CI-830 (NDUFS1, NDUFV1 mutation) or not detected (NDUFS7 mutation). Supported by enzymological and CI in silico structural analysis, we conclude that absence of NDUFS4 induces near complete absence of NDUFA12 but not vice versa, and that NDUFAF2 stabilizes active CI in Ndufs4−/− mice and LS patient cells, perhaps in concert with mitochondrial inner membrane lipids.
AU - Adjobo-Hermans, Merel J.W.
AU - De Haas, Ria
AU - Willems, Peter H.G.M.
AU - Wojtala, Aleksandra
AU - Van Emst-De Vries, Sjenet E.
AU - Wagenaars, Jori A.
AU - Van Den Brand, Mariel
AU - Rodenburg, Richard J.
AU - Smeitink, Jan A.M.
AU - Nijtmans, Leo G.
AU - Sazanov, Leonid A
AU - Wieckowski, Mariusz R.
AU - Koopman, Werner J.H.
ID - 7788
IS - 8
JF - Biochimica et Biophysica Acta - Bioenergetics
SN - 00052728
TI - NDUFS4 deletion triggers loss of NDUFA12 in Ndufs4−/− mice and Leigh syndrome patients: A stabilizing role for NDUFAF2
VL - 1861
ER -
TY - JOUR
AB - During embryonic and postnatal development, organs and tissues grow steadily to achieve their final size at the end of puberty. However, little is known about the cellular dynamics that mediate postnatal growth. By combining in vivo clonal lineage tracing, proliferation kinetics, single-cell transcriptomics, andin vitro micro-pattern experiments, we resolved the cellular dynamics taking place during postnatal skin epidermis expansion. Our data revealed that harmonious growth is engineered by a single population of developmental progenitors presenting a fixed fate imbalance of self-renewing divisions with an ever-decreasing proliferation rate. Single-cell RNA sequencing revealed that epidermal developmental progenitors form a more uniform population compared with adult stem and progenitor cells. Finally, we found that the spatial pattern of cell division orientation is dictated locally by the underlying collagen fiber orientation. Our results uncover a simple design principle of organ growth where progenitors and differentiated cells expand in harmony with their surrounding tissues.
AU - Dekoninck, Sophie
AU - Hannezo, Edouard B
AU - Sifrim, Alejandro
AU - Miroshnikova, Yekaterina A.
AU - Aragona, Mariaceleste
AU - Malfait, Milan
AU - Gargouri, Souhir
AU - De Neunheuser, Charlotte
AU - Dubois, Christine
AU - Voet, Thierry
AU - Wickström, Sara A.
AU - Simons, Benjamin D.
AU - Blanpain, Cédric
ID - 7789
IS - 3
JF - Cell
SN - 00928674
TI - Defining the design principles of skin epidermis postnatal growth
VL - 181
ER -
TY - JOUR
AB - The TPLATE complex (TPC) is a key endocytic adaptor protein complex in plants. TPC in Arabidopsis (Arabidopsis thaliana) contains six evolutionarily conserved subunits and two plant-specific subunits, AtEH1/Pan1 and AtEH2/Pan1, although cytoplasmic proteins are not associated with the hexameric subcomplex in the cytoplasm. To investigate the dynamic assembly of the octameric TPC at the plasma membrane (PM), we performed state-of-the-art dual-color live cell imaging at physiological and lowered temperatures. Lowering the temperature slowed down endocytosis, thereby enhancing the temporal resolution of the differential recruitment of endocytic components. Under both normal and lowered temperature conditions, the core TPC subunit TPLATE and the AtEH/Pan1 proteins exhibited simultaneous recruitment at the PM. These results, together with co-localization analysis of different TPC subunits, allow us to conclude that TPC in plant cells is not recruited to the PM sequentially but as an octameric complex.
AU - Wang, J
AU - Mylle, E
AU - Johnson, Alexander J
AU - Besbrugge, N
AU - De Jaeger, G
AU - Friml, Jiří
AU - Pleskot, R
AU - van Damme, D
ID - 7695
IS - 3
JF - Plant Physiology
SN - 0032-0889
TI - High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits
VL - 183
ER -
TY - JOUR
AB - * Morphogenesis and adaptive tropic growth in plants depend on gradients of the phytohormone auxin, mediated by the membrane‐based PIN‐FORMED (PIN) auxin transporters. PINs localize to a particular side of the plasma membrane (PM) or to the endoplasmic reticulum (ER) to directionally transport auxin and maintain intercellular and intracellular auxin homeostasis, respectively. However, the molecular cues that confer their diverse cellular localizations remain largely unknown.
* In this study, we systematically swapped the domains between ER‐ and PM‐localized PIN proteins, as well as between apical and basal PM‐localized PINs from Arabidopsis thaliana , to shed light on why PIN family members with similar topological structures reside at different membrane compartments within cells.
* Our results show that not only do the N‐ and C‐terminal transmembrane domains (TMDs) and central hydrophilic loop contribute to their differential subcellular localizations and cellular polarity, but that the pairwise‐matched N‐ and C‐terminal TMDs resulting from intramolecular domain–domain coevolution are also crucial for their divergent patterns of localization.
* These findings illustrate the complexity of the evolutionary path of PIN proteins in acquiring their plethora of developmental functions and adaptive growth in plants.
AU - Zhang, Yuzhou
AU - Hartinger, Corinna
AU - Wang, Xiaojuan
AU - Friml, Jiří
ID - 7697
IS - 5
JF - New Phytologist
SN - 0028-646X
TI - Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters
VL - 227
ER -
TY - JOUR
AB - For any free oriented Borel–Moore homology theory A, we construct an associative product on the A-theory of the stack of Higgs torsion sheaves over a projective curve C. We show that the resulting algebra AHa0C admits a natural shuffle presentation, and prove it is faithful when A is replaced with usual Borel–Moore homology groups. We also introduce moduli spaces of stable triples, heavily inspired by Nakajima quiver varieties, whose A-theory admits an AHa0C-action. These triples can be interpreted as certain sheaves on PC(ωC⊕OC). In particular, we obtain an action of AHa0C on the cohomology of Hilbert schemes of points on T∗C.
AU - Minets, Sasha
ID - 7683
IS - 2
JF - Selecta Mathematica, New Series
SN - 10221824
TI - Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces
VL - 26
ER -
TY - JOUR
AU - Gridchyn, Igor
AU - Schönenberger, Philipp
AU - O'Neill, Joseph
AU - Csicsvari, Jozsef L
ID - 7684
IS - 2
JF - Neuron
SN - 08966273
TI - Assembly-specific disruption of hippocampal replay leads to selective memory deficit
VL - 106
ER -
TY - JOUR
AB - We consider a gas of interacting bosons trapped in a box of side length one in the Gross–Pitaevskii limit. We review the proof of the validity of Bogoliubov’s prediction for the ground state energy and the low-energy excitation spectrum. This note is based on joint work with C. Brennecke, S. Cenatiempo and B. Schlein.
AU - Boccato, Chiara
ID - 7685
JF - Reviews in Mathematical Physics
SN - 0129055X
TI - The excitation spectrum of the Bose gas in the Gross-Pitaevskii regime
ER -
TY - JOUR
AB - A working group, which was established within the Network of Repository Managers (RepManNet), has dealt with common certifications for repositories. In addition, current requirements of the research funding agencies FWF and EU were also taken into account. The Core Trust Seal was examined in more detail. For this purpose, a questionnaire was sent to those organizations that are already certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested.
AU - Ernst, Doris
AU - Novotny, Gertraud
AU - Schönher, Eva Maria
ID - 7687
IS - 1
JF - Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare
SN - 1022-2588
TI - (Core Trust) Seal your repository!
VL - 73
ER -
TY - CONF
AB - Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e. manifolds defined as the zero set of some multivariate vector-valued smooth function f: ℝ^d → ℝ^(d-n). A natural (and efficient) way to approximate an isomanifold is to consider its Piecewise-Linear (PL) approximation based on a triangulation 𝒯 of the ambient space ℝ^d. In this paper, we give conditions under which the PL-approximation of an isomanifold is topologically equivalent to the isomanifold. The conditions are easy to satisfy in the sense that they can always be met by taking a sufficiently fine triangulation 𝒯. This contrasts with previous results on the triangulation of manifolds where, in arbitrary dimensions, delicate perturbations are needed to guarantee topological correctness, which leads to strong limitations in practice. We further give a bound on the Fréchet distance between the original isomanifold and its PL-approximation. Finally we show analogous results for the PL-approximation of an isomanifold with boundary.
AU - Boissonnat, Jean-Daniel
AU - Wintraecken, Mathijs
ID - 7952
SN - 1868-8969
T2 - 36th International Symposium on Computational Geometry
TI - The topological correctness of PL-approximations of isomanifolds
VL - 164
ER -
TY - CONF
AB - Simple stochastic games are turn-based 2½-player games with a reachability objective. The basic question asks whether one player can ensure reaching a given target with at least a given probability. A natural extension is games with a conjunction of such conditions as objective. Despite a plethora of recent results on the analysis of systems with multiple objectives, the decidability of this basic problem remains open. In this paper, we present an algorithm approximating the Pareto frontier of the achievable values to a given precision. Moreover, it is an anytime algorithm, meaning it can be stopped at any time returning the current approximation and its error bound.
AU - Ashok, Pranav
AU - Chatterjee, Krishnendu
AU - Kretinsky, Jan
AU - Weininger, Maximilian
AU - Winkler, Tobias
ID - 7955
SN - 9781450371049
T2 - Proceedings of the 35th Annual ACM/IEEE Symposium on Logic in Computer Science
TI - Approximating values of generalized-reachability stochastic games
ER -
TY - JOUR
AB - When short-range attractions are combined with long-range repulsions in colloidal particle systems, complex microphases can emerge. Here, we study a system of isotropic particles, which can form lamellar structures or a disordered fluid phase when temperature is varied. We show that, at equilibrium, the lamellar structure crystallizes, while out of equilibrium, the system forms a variety of structures at different shear rates and temperatures above melting. The shear-induced ordering is analyzed by means of principal component analysis and artificial neural networks, which are applied to data of reduced dimensionality. Our results reveal the possibility of inducing ordering by shear, potentially providing a feasible route to the fabrication of ordered lamellar structures from isotropic particles.
AU - Pȩkalski, J.
AU - Rzadkowski, Wojciech
AU - Panagiotopoulos, A. Z.
ID - 7956
IS - 20
JF - The Journal of chemical physics
TI - Shear-induced ordering in systems with competing interactions: A machine learning study
VL - 152
ER -
TY - JOUR
AB - Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of
mutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches.
AU - Parenti, Ilaria
AU - Garcia Rabaneda, Luis E
AU - Schön, Hanna
AU - Novarino, Gaia
ID - 7957
IS - 8
JF - Trends in Neurosciences
SN - 01662236
TI - Neurodevelopmental disorders: From genetics to functional pathways
VL - 43
ER -
TY - JOUR
AB - Let A={A1,…,An} be a family of sets in the plane. For 0≤i2b be integers. We prove that if each k-wise or (k+1)-wise intersection of sets from A has at most b path-connected components, which all are open, then fk+1=0 implies fk≤cfk−1 for some positive constant c depending only on b and k. These results also extend to two-dimensional compact surfaces.
AU - Kalai, Gil
AU - Patakova, Zuzana
ID - 7960
JF - Discrete and Computational Geometry
SN - 01795376
TI - Intersection patterns of planar sets
VL - 64
ER -
TY - JOUR
AB - A string graph is the intersection graph of a family of continuous arcs in the plane. The intersection graph of a family of plane convex sets is a string graph, but not all string graphs can be obtained in this way. We prove the following structure theorem conjectured by Janson and Uzzell: The vertex set of almost all string graphs on n vertices can be partitioned into five cliques such that some pair of them is not connected by any edge (n→∞). We also show that every graph with the above property is an intersection graph of plane convex sets. As a corollary, we obtain that almost all string graphs on n vertices are intersection graphs of plane convex sets.
AU - Pach, János
AU - Reed, Bruce
AU - Yuditsky, Yelena
ID - 7962
IS - 4
JF - Discrete and Computational Geometry
SN - 01795376
TI - Almost all string graphs are intersection graphs of plane convex sets
VL - 63
ER -
TY - CONF
AB - For 1≤m≤n, we consider a natural m-out-of-n multi-instance scenario for a public-key encryption (PKE) scheme. An adversary, given n independent instances of PKE, wins if he breaks at least m out of the n instances. In this work, we are interested in the scaling factor of PKE schemes, SF, which measures how well the difficulty of breaking m out of the n instances scales in m. That is, a scaling factor SF=ℓ indicates that breaking m out of n instances is at least ℓ times more difficult than breaking one single instance. A PKE scheme with small scaling factor hence provides an ideal target for mass surveillance. In fact, the Logjam attack (CCS 2015) implicitly exploited, among other things, an almost constant scaling factor of ElGamal over finite fields (with shared group parameters).
For Hashed ElGamal over elliptic curves, we use the generic group model to argue that the scaling factor depends on the scheme's granularity. In low granularity, meaning each public key contains its independent group parameter, the scheme has optimal scaling factor SF=m; In medium and high granularity, meaning all public keys share the same group parameter, the scheme still has a reasonable scaling factor SF=√m. Our findings underline that instantiating ElGamal over elliptic curves should be preferred to finite fields in a multi-instance scenario.
As our main technical contribution, we derive new generic-group lower bounds of Ω(√(mp)) on the difficulty of solving both the m-out-of-n Gap Discrete Logarithm and the m-out-of-n Gap Computational Diffie-Hellman problem over groups of prime order p, extending a recent result by Yun (EUROCRYPT 2015). We establish the lower bound by studying the hardness of a related computational problem which we call the search-by-hypersurface problem.
AU - Auerbach, Benedikt
AU - Giacon, Federico
AU - Kiltz, Eike
ID - 7966
SN - 0302-9743
T2 - Advances in Cryptology – EUROCRYPT 2020
TI - Everybody’s a target: Scalability in public-key encryption
VL - 12107
ER -
TY - JOUR
AB - Organic materials are known to feature long spin-diffusion times, originating in a generally small spin–orbit coupling observed in these systems. From that perspective, chiral molecules acting as efficient spin selectors pose a puzzle that attracted a lot of attention in recent years. Here, we revisit the physical origins of chiral-induced spin selectivity (CISS) and propose a simple analytic minimal model to describe it. The model treats a chiral molecule as an anisotropic wire with molecular dipole moments aligned arbitrarily with respect to the wire’s axes and is therefore quite general. Importantly, it shows that the helical structure of the molecule is not necessary to observe CISS and other chiral nonhelical molecules can also be considered as potential candidates for the CISS effect. We also show that the suggested simple model captures the main characteristics of CISS observed in the experiment, without the need for additional constraints employed in the previous studies. The results pave the way for understanding other related physical phenomena where the CISS effect plays an essential role.
AU - Ghazaryan, Areg
AU - Paltiel, Yossi
AU - Lemeshko, Mikhail
ID - 7968
IS - 21
JF - The Journal of Physical Chemistry C
SN - 1932-7447
TI - Analytic model of chiral-induced spin selectivity
VL - 124
ER -
TY - JOUR
AB - Multilayer graphene lattices allow for an additional tunability of the band structure by the strong perpendicular electric field. In particular, the emergence of the new multiple Dirac points in ABA stacked trilayer graphene subject to strong transverse electric fields was proposed theoretically and confirmed experimentally. These new Dirac points dubbed “gullies” emerge from the interplay between strong electric field and trigonal warping. In this work, we first characterize the properties of new emergent Dirac points and show that the electric field can be used to tune the distance between gullies in the momentum space. We demonstrate that the band structure has multiple Lifshitz transitions and higher-order singularity of “monkey saddle” type. Following the characterization of the band structure, we consider the spectrum of Landau levels and structure of their wave functions. In the limit of strong electric fields when gullies are well separated in momentum space, they give rise to triply degenerate Landau levels. In the second part of this work, we investigate how degeneracy between three gully Landau levels is lifted in the presence of interactions. Within the Hartree-Fock approximation we show that the symmetry breaking state interpolates between the fully gully polarized state that breaks C3 symmetry at high displacement field and the gully symmetric state when the electric field is decreased. The discontinuous transition between these two states is driven by enhanced intergully tunneling and exchange. We conclude by outlining specific experimental predictions for the existence of such a symmetry-breaking state.
AU - Rao, Peng
AU - Serbyn, Maksym
ID - 7971
IS - 24
JF - Physical Review B
SN - 2469-9950
TI - Gully quantum Hall ferromagnetism in biased trilayer graphene
VL - 101
ER -
TY - JOUR
AB - The goal of limiting global warming to 1.5 °C requires a drastic reduction in CO2 emissions across many sectors of the world economy. Batteries are vital to this endeavor, whether used in electric vehicles, to store renewable electricity, or in aviation. Present lithium-ion technologies are preparing the public for this inevitable change, but their maximum theoretical specific capacity presents a limitation. Their high cost is another concern for commercial viability. Metal–air batteries have the highest theoretical energy density of all possible secondary battery technologies and could yield step changes in energy storage, if their practical difficulties could be overcome. The scope of this review is to provide an objective, comprehensive, and authoritative assessment of the intensive work invested in nonaqueous rechargeable metal–air batteries over the past few years, which identified the key problems and guides directions to solve them. We focus primarily on the challenges and outlook for Li–O2 cells but include Na–O2, K–O2, and Mg–O2 cells for comparison. Our review highlights the interdisciplinary nature of this field that involves a combination of materials chemistry, electrochemistry, computation, microscopy, spectroscopy, and surface science. The mechanisms of O2 reduction and evolution are considered in the light of recent findings, along with developments in positive and negative electrodes, electrolytes, electrocatalysis on surfaces and in solution, and the degradative effect of singlet oxygen, which is typically formed in Li–O2 cells.
AU - Kwak, WJ
AU - Sharon, D
AU - Xia, C
AU - Kim, H
AU - Johnson, LR
AU - Bruce, PG
AU - Nazar, LF
AU - Sun, YK
AU - Frimer, AA
AU - Noked, M
AU - Freunberger, Stefan Alexander
AU - Aurbach, D
ID - 7985
IS - 14
JF - Chemical Reviews
SN - 0009-2665
TI - Lithium-oxygen batteries and related systems: Potential, status, and future
VL - 120
ER -
TY - CONF
AB - We prove general topological Radon-type theorems for sets in ℝ^d, smooth real manifolds or finite dimensional simplicial complexes. Combined with a recent result of Holmsen and Lee, it gives fractional Helly theorem, and consequently the existence of weak ε-nets as well as a (p,q)-theorem. More precisely: Let X be either ℝ^d, smooth real d-manifold, or a finite d-dimensional simplicial complex. Then if F is a finite, intersection-closed family of sets in X such that the ith reduced Betti number (with ℤ₂ coefficients) of any set in F is at most b for every non-negative integer i less or equal to k, then the Radon number of F is bounded in terms of b and X. Here k is the smallest integer larger or equal to d/2 - 1 if X = ℝ^d; k=d-1 if X is a smooth real d-manifold and not a surface, k=0 if X is a surface and k=d if X is a d-dimensional simplicial complex. Using the recent result of the author and Kalai, we manage to prove the following optimal bound on fractional Helly number for families of open sets in a surface: Let F be a finite family of open sets in a surface S such that the intersection of any subfamily of F is either empty, or path-connected. Then the fractional Helly number of F is at most three. This also settles a conjecture of Holmsen, Kim, and Lee about an existence of a (p,q)-theorem for open subsets of a surface.
AU - Patakova, Zuzana
ID - 7989
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Bounding radon number via Betti numbers
VL - 164
ER -
TY - CONF
AB - Given a finite point set P in general position in the plane, a full triangulation is a maximal straight-line embedded plane graph on P. A partial triangulation on P is a full triangulation of some subset P' of P containing all extreme points in P. A bistellar flip on a partial triangulation either flips an edge, removes a non-extreme point of degree 3, or adds a point in P ⧵ P' as vertex of degree 3. The bistellar flip graph has all partial triangulations as vertices, and a pair of partial triangulations is adjacent if they can be obtained from one another by a bistellar flip. The goal of this paper is to investigate the structure of this graph, with emphasis on its connectivity. For sets P of n points in general position, we show that the bistellar flip graph is (n-3)-connected, thereby answering, for sets in general position, an open questions raised in a book (by De Loera, Rambau, and Santos) and a survey (by Lee and Santos) on triangulations. This matches the situation for the subfamily of regular triangulations (i.e., partial triangulations obtained by lifting the points and projecting the lower convex hull), where (n-3)-connectivity has been known since the late 1980s through the secondary polytope (Gelfand, Kapranov, Zelevinsky) and Balinski’s Theorem. Our methods also yield the following results (see the full version [Wagner and Welzl, 2020]): (i) The bistellar flip graph can be covered by graphs of polytopes of dimension n-3 (products of secondary polytopes). (ii) A partial triangulation is regular, if it has distance n-3 in the Hasse diagram of the partial order of partial subdivisions from the trivial subdivision. (iii) All partial triangulations are regular iff the trivial subdivision has height n-3 in the partial order of partial subdivisions. (iv) There are arbitrarily large sets P with non-regular partial triangulations, while every proper subset has only regular triangulations, i.e., there are no small certificates for the existence of non-regular partial triangulations (answering a question by F. Santos in the unexpected direction).
AU - Wagner, Uli
AU - Welzl, Emo
ID - 7990
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Connectivity of triangulation flip graphs in the plane (Part II: Bistellar flips)
VL - 164
ER -
TY - CONF
AB - We define and study a discrete process that generalizes the convex-layer decomposition of a planar point set. Our process, which we call homotopic curve shortening (HCS), starts with a closed curve (which might self-intersect) in the presence of a set P⊂ ℝ² of point obstacles, and evolves in discrete steps, where each step consists of (1) taking shortcuts around the obstacles, and (2) reducing the curve to its shortest homotopic equivalent. We find experimentally that, if the initial curve is held fixed and P is chosen to be either a very fine regular grid or a uniformly random point set, then HCS behaves at the limit like the affine curve-shortening flow (ACSF). This connection between HCS and ACSF generalizes the link between "grid peeling" and the ACSF observed by Eppstein et al. (2017), which applied only to convex curves, and which was studied only for regular grids. We prove that HCS satisfies some properties analogous to those of ACSF: HCS is invariant under affine transformations, preserves convexity, and does not increase the total absolute curvature. Furthermore, the number of self-intersections of a curve, or intersections between two curves (appropriately defined), does not increase. Finally, if the initial curve is simple, then the number of inflection points (appropriately defined) does not increase.
AU - Avvakumov, Sergey
AU - Nivasch, Gabriel
ID - 7991
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Homotopic curve shortening and the affine curve-shortening flow
VL - 164
ER -
TY - CONF
AB - Let K be a convex body in ℝⁿ (i.e., a compact convex set with nonempty interior). Given a point p in the interior of K, a hyperplane h passing through p is called barycentric if p is the barycenter of K ∩ h. In 1961, Grünbaum raised the question whether, for every K, there exists an interior point p through which there are at least n+1 distinct barycentric hyperplanes. Two years later, this was seemingly resolved affirmatively by showing that this is the case if p=p₀ is the point of maximal depth in K. However, while working on a related question, we noticed that one of the auxiliary claims in the proof is incorrect. Here, we provide a counterexample; this re-opens Grünbaum’s question. It follows from known results that for n ≥ 2, there are always at least three distinct barycentric cuts through the point p₀ ∈ K of maximal depth. Using tools related to Morse theory we are able to improve this bound: four distinct barycentric cuts through p₀ are guaranteed if n ≥ 3.
AU - Patakova, Zuzana
AU - Tancer, Martin
AU - Wagner, Uli
ID - 7992
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Barycentric cuts through a convex body
VL - 164
ER -
TY - CONF
AB - In the recent study of crossing numbers, drawings of graphs that can be extended to an arrangement of pseudolines (pseudolinear drawings) have played an important role as they are a natural combinatorial extension of rectilinear (or straight-line) drawings. A characterization of the pseudolinear drawings of K_n was found recently. We extend this characterization to all graphs, by describing the set of minimal forbidden subdrawings for pseudolinear drawings. Our characterization also leads to a polynomial-time algorithm to recognize pseudolinear drawings and construct the pseudolines when it is possible.
AU - Arroyo Guevara, Alan M
AU - Bensmail, Julien
AU - Bruce Richter, R.
ID - 7994
SN - 18688969
T2 - 36th International Symposium on Computational Geometry
TI - Extending drawings of graphs to arrangements of pseudolines
VL - 164
ER -
TY - JOUR
AB - We prove that the Yangian associated to an untwisted symmetric affine Kac–Moody Lie algebra is isomorphic to the Drinfeld double of a shuffle algebra. The latter is constructed in [YZ14] as an algebraic formalism of cohomological Hall algebras. As a consequence, we obtain the Poincare–Birkhoff–Witt (PBW) theorem for this class of affine Yangians. Another independent proof of the PBW theorem is given recently by Guay, Regelskis, and Wendlandt [GRW18].
AU - Yang, Yaping
AU - Zhao, Gufang
ID - 7940
JF - Transformation Groups
SN - 10834362
TI - The PBW theorem for affine Yangians
VL - 25
ER -
TY - JOUR
AB - An understanding of the missing antinodal electronic excitations in the pseudogap state is essential for uncovering the physics of the underdoped cuprate high-temperature superconductors1,2,3,4,5,6. The majority of high-temperature experiments performed thus far, however, have been unable to discern whether the antinodal states are rendered unobservable due to their damping or whether they vanish due to their gapping7,8,9,10,11,12,13,14,15,16,17,18. Here, we distinguish between these two scenarios by using quantum oscillations to examine whether the small Fermi surface pocket, found to occupy only 2% of the Brillouin zone in the underdoped cuprates19,20,21,22,23,24, exists in isolation against a majority of completely gapped density of states spanning the antinodes, or whether it is thermodynamically coupled to a background of ungapped antinodal states. We find that quantum oscillations associated with the small Fermi surface pocket exhibit a signature sawtooth waveform characteristic of an isolated two-dimensional Fermi surface pocket25,26,27,28,29,30,31,32. This finding reveals that the antinodal states are destroyed by a hard gap that extends over the majority of the Brillouin zone, placing strong constraints on a drastic underlying origin of quasiparticle disappearance over almost the entire Brillouin zone in the pseudogap regime7,8,9,10,11,12,13,14,15,16,17,18.
AU - Hartstein, Máté
AU - Hsu, Yu Te
AU - Modic, Kimberly A
AU - Porras, Juan
AU - Loew, Toshinao
AU - Tacon, Matthieu Le
AU - Zuo, Huakun
AU - Wang, Jinhua
AU - Zhu, Zengwei
AU - Chan, Mun K.
AU - Mcdonald, Ross D.
AU - Lonzarich, Gilbert G.
AU - Keimer, Bernhard
AU - Sebastian, Suchitra E.
AU - Harrison, Neil
ID - 7942
JF - Nature Physics
SN - 17452473
TI - Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors
VL - 16
ER -
TY - JOUR
AB - In agricultural systems, nitrate is the main source of nitrogen available for plants. Besides its role as a nutrient, nitrate has been shown to act as a signal molecule for plant growth, development and stress responses. In Arabidopsis, the NRT1.1 nitrate transceptor represses lateral root (LR) development at low nitrate availability by promoting auxin basipetal transport out of the LR primordia (LRPs). In addition, our present study shows that NRT1.1 acts as a negative regulator of the TAR2 auxin biosynthetic gene expression in the root stele. This is expected to repress local auxin biosynthesis and thus to reduce acropetal auxin supply to the LRPs. Moreover, NRT1.1 also negatively affects expression of the LAX3 auxin influx carrier, thus preventing cell wall remodeling required for overlying tissues separation during LRP emergence. Both NRT1.1-mediated repression of TAR2 and LAX3 are suppressed at high nitrate availability, resulting in the nitrate induction of TAR2 and LAX3 expression that is required for optimal stimulation of LR development by nitrate. Altogether, our results indicate that the NRT1.1 transceptor coordinately controls several crucial auxin-associated processes required for LRP development, and as a consequence that NRT1.1 plays a much more integrated role than previously anticipated in regulating the nitrate response of root system architecture.
AU - Maghiaoui, A
AU - Bouguyon, E
AU - Cuesta, Candela
AU - Perrine-Walker, F
AU - Alcon, C
AU - Krouk, G
AU - Benková, Eva
AU - Nacry, P
AU - Gojon, A
AU - Bach, L
ID - 7948
IS - 15
JF - Journal of Experimental Botany
SN - 0022-0957
TI - The Arabidopsis NRT1.1 transceptor coordinately controls auxin biosynthesis and transport to regulate root branching in response to nitrate
VL - 71
ER -
TY - JOUR
AB - Peptides derived from non-functional precursors play important roles in various developmental processes, but also in (a)biotic stress signaling. Our (phospho)proteome-wide analyses of C-terminally encoded peptide 5 (CEP5)-mediated changes revealed an impact on abiotic stress-related processes. Drought has a dramatic impact on plant growth, development and reproduction, and the plant hormone auxin plays a role in drought responses. Our genetic, physiological, biochemical and pharmacological results demonstrated that CEP5-mediated signaling is relevant for osmotic and drought stress tolerance in Arabidopsis, and that CEP5 specifically counteracts auxin effects. Specifically, we found that CEP5 signaling stabilizes AUX/IAA transcriptional repressors, suggesting the existence of a novel peptide-dependent control mechanism that tunes auxin signaling. These observations align with the recently described role of AUX/IAAs in stress tolerance and provide a novel role for CEP5 in osmotic and drought stress tolerance.
AU - Smith, S
AU - Zhu, S
AU - Joos, L
AU - Roberts, I
AU - Nikonorova, N
AU - Vu, LD
AU - Stes, E
AU - Cho, H
AU - Larrieu, A
AU - Xuan, W
AU - Goodall, B
AU - van de Cotte, B
AU - Waite, JM
AU - Rigal, A
AU - R Harborough, SR
AU - Persiau, G
AU - Vanneste, S
AU - Kirschner, GK
AU - Vandermarliere, E
AU - Martens, L
AU - Stahl, Y
AU - Audenaert, D
AU - Friml, Jiří
AU - Felix, G
AU - Simon, R
AU - Bennett, M
AU - Bishopp, A
AU - De Jaeger, G
AU - Ljung, K
AU - Kepinski, S
AU - Robert, S
AU - Nemhauser, J
AU - Hwang, I
AU - Gevaert, K
AU - Beeckman, T
AU - De Smet, I
ID - 7949
IS - 8
JF - Molecular & Cellular Proteomics
SN - 1535-9476
TI - The CEP5 peptide promotes abiotic stress tolerance, as revealed by quantitative proteomics, and attenuates the AUX/IAA equilibrium in Arabidopsis
VL - 19
ER -
TY - THES
AB - This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.
For triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.
In the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars.
AU - Masárová, Zuzana
ID - 7944
KW - reconfiguration
KW - reconfiguration graph
KW - triangulations
KW - flip
KW - constrained triangulations
KW - shellability
KW - piecewise-linear balls
KW - token swapping
KW - trees
KW - coloured weighted token swapping
SN - 978-3-99078-005-3
TI - Reconfiguration problems
ER -
TY - JOUR
AB - We design fast deterministic algorithms for distance computation in the Congested Clique model. Our key contributions include:
A (2+ϵ)-approximation for all-pairs shortest paths in O(log2n/ϵ) rounds on unweighted undirected graphs. With a small additional additive factor, this also applies for weighted graphs. This is the first sub-polynomial constant-factor approximation for APSP in this model.
A (1+ϵ)-approximation for multi-source shortest paths from O(n−−√) sources in O(log2n/ϵ) rounds on weighted undirected graphs. This is the first sub-polynomial algorithm obtaining this approximation for a set of sources of polynomial size.
Our main techniques are new distance tools that are obtained via improved algorithms for sparse matrix multiplication, which we leverage to construct efficient hopsets and shortest paths. Furthermore, our techniques extend to additional distance problems for which we improve upon the state-of-the-art, including diameter approximation, and an exact single-source shortest paths algorithm for weighted undirected graphs in O~(n1/6) rounds.
AU - Censor-Hillel, Keren
AU - Dory, Michal
AU - Korhonen, Janne
AU - Leitersdorf, Dean
ID - 7939
JF - Distributed Computing
SN - 01782770
TI - Fast approximate shortest paths in the congested clique
ER -
TY - THES
AB - Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”
In this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus.
AU - Huszár, Kristóf
ID - 8032
SN - 2663-337X
TI - Combinatorial width parameters for 3-dimensional manifolds
ER -
TY - JOUR
AB - When tiny soft ferromagnetic particles are placed along a liquid interface and exposed to a vertical magnetic field, the balance between capillary attraction and magnetic repulsion leads to self-organization into well-defined patterns. Here, we demonstrate experimentally that precessing magnetic fields induce metachronal waves on the periphery of these assemblies, similar to the ones observed in ciliates and some arthropods. The outermost layer of particles behaves like an array of cilia or legs whose sequential movement causes a net and controllable locomotion. This bioinspired many-particle swimming strategy is effective even at low Reynolds number, using only spatially uniform fields to generate the waves.
AU - Collard, Ylona
AU - Grosjean, Galien M
AU - Vandewalle, Nicolas
ID - 8036
JF - Communications Physics
TI - Magnetically powered metachronal waves induce locomotion in self-assemblies
VL - 3
ER -
TY - JOUR
AB - Genetic perturbations that affect bacterial resistance to antibiotics have been characterized genome-wide, but how do such perturbations interact with subsequent evolutionary adaptation to the drug? Here, we show that strong epistasis between resistance mutations and systematically identified genes can be exploited to control spontaneous resistance evolution. We evolved hundreds of Escherichia coli K-12 mutant populations in parallel, using a robotic platform that tightly controls population size and selection pressure. We find a global diminishing-returns epistasis pattern: strains that are initially more sensitive generally undergo larger resistance gains. However, some gene deletion strains deviate from this general trend and curtail the evolvability of resistance, including deletions of genes for membrane transport, LPS biosynthesis, and chaperones. Deletions of efflux pump genes force evolution on inferior mutational paths, not explored in the wild type, and some of these essentially block resistance evolution. This effect is due to strong negative epistasis with resistance mutations. The identified genes and cellular functions provide potential targets for development of adjuvants that may block spontaneous resistance evolution when combined with antibiotics.
AU - Lukacisinova, Marta
AU - Fernando, Booshini
AU - Bollenbach, Mark Tobias
ID - 8037
JF - Nature Communications
TI - Highly parallel lab evolution reveals that epistasis can curb the evolution of antibiotic resistance
VL - 11
ER -
TY - JOUR
AB - Microelectromechanical systems and integrated photonics provide the basis for many reliable and compact circuit elements in modern communication systems. Electro-opto-mechanical devices are currently one of the leading approaches to realize ultra-sensitive, low-loss transducers for an emerging quantum information technology. Here we present an on-chip microwave frequency converter based on a planar aluminum on silicon nitride platform that is compatible with slot-mode coupled photonic crystal cavities. We show efficient frequency conversion between two propagating microwave modes mediated by the radiation pressure interaction with a metalized dielectric nanobeam oscillator. We achieve bidirectional coherent conversion with a total device efficiency of up to ~60%, a dynamic range of 2 × 10^9 photons/s and an instantaneous bandwidth of up to 1.7 kHz. A high fidelity quantum state transfer would be possible if the drive dependent output noise of currently ~14 photons s^−1 Hz^−1 is further reduced. Such a silicon nitride based transducer is in situ reconfigurable and could be used for on-chip classical and quantum signal routing and filtering, both for microwave and hybrid microwave-optical applications.
AU - Fink, Johannes M
AU - Kalaee, M.
AU - Norte, R.
AU - Pitanti, A.
AU - Painter, O.
ID - 8038
IS - 3
JF - Quantum Science and Technology
TI - Efficient microwave frequency conversion mediated by a photonics compatible silicon nitride nanobeam oscillator
VL - 5
ER -
TY - JOUR
AB - We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N.
AU - Boccato, Chiara
AU - Brennecke, Christian
AU - Cenatiempo, Serena
AU - Schlein, Benjamin
ID - 8042
IS - 7
JF - Journal of the European Mathematical Society
SN - 14359855
TI - The excitation spectrum of Bose gases interacting through singular potentials
VL - 22
ER -
TY - JOUR
AB - With decreasing Reynolds number, Re, turbulence in channel flow becomes spatio-temporally intermittent and self-organises into solitary stripes oblique to the mean flow direction. We report here the existence of localised nonlinear travelling wave solutions of the Navier–Stokes equations possessing this obliqueness property. Such solutions are identified numerically using edge tracking coupled with arclength continuation. All solutions emerge in saddle-node bifurcations at values of Re lower than the non-localised solutions. Relative periodic orbit solutions bifurcating from branches of travelling waves have also been computed. A complete parametric study is performed, including their stability, the investigation of their large-scale flow, and the robustness to changes of the numerical domain.
AU - Paranjape, Chaitanya S
AU - Duguet, Yohann
AU - Hof, Björn
ID - 8043
JF - Journal of Fluid Mechanics
SN - 00221120
TI - Oblique stripe solutions of channel flow
VL - 897
ER -
TY - JOUR
AB - Water-in-salt electrolytes based on highly concentrated bis(trifluoromethyl)sulfonimide (TFSI) promise aqueous electrolytes with stabilities approaching 3 V. However, especially with an electrode approaching the cathodic (reductive) stability, cycling stability is insufficient. While stability critically relies on a solid electrolyte interphase (SEI), the mechanism behind the cathodic stability limit remains unclear. Here, we reveal two distinct reduction potentials for the chemical environments of ‘free’ and ‘bound’ water and that both contribute to SEI formation. Free-water is reduced ~1V above bound water in a hydrogen evolution reaction (HER) and responsible for SEI formation via reactive intermediates of the HER; concurrent LiTFSI precipitation/dissolution establishes a dynamic interface. The free-water population emerges, therefore, as the handle to extend the cathodic limit of aqueous electrolytes and the battery cycling stability.
AU - Bouchal, Roza
AU - Li, Zhujie
AU - Bongu, Chandra
AU - Le Vot, Steven
AU - Berthelot, Romain
AU - Rotenberg, Benjamin
AU - Favier, Frederic
AU - Freunberger, Stefan Alexander
AU - Salanne, Mathieu
AU - Fontaine, Olivier
ID - 8057
IS - 37
JF - Angewandte Chemie
SN - 0044-8249
TI - Competitive salt precipitation/dissolution during free‐water reduction in water‐in‐salt electrolyte
VL - 132
ER -
TY - JOUR
AB - The projection methods with vanilla inertial extrapolation step for variational inequalities have been of interest to many authors recently due to the improved convergence speed contributed by the presence of inertial extrapolation step. However, it is discovered that these projection methods with inertial steps lose the Fejér monotonicity of the iterates with respect to the solution, which is being enjoyed by their corresponding non-inertial projection methods for variational inequalities. This lack of Fejér monotonicity makes projection methods with vanilla inertial extrapolation step for variational inequalities not to converge faster than their corresponding non-inertial projection methods at times. Also, it has recently been proved that the projection methods with vanilla inertial extrapolation step may provide convergence rates that are worse than the classical projected gradient methods for strongly convex functions. In this paper, we introduce projection methods with alternated inertial extrapolation step for solving variational inequalities. We show that the sequence of iterates generated by our methods converges weakly to a solution of the variational inequality under some appropriate conditions. The Fejér monotonicity of even subsequence is recovered in these methods and linear rate of convergence is obtained. The numerical implementations of our methods compared with some other inertial projection methods show that our method is more efficient and outperforms some of these inertial projection methods.
AU - Shehu, Yekini
AU - Iyiola, Olaniyi S.
ID - 8077
JF - Applied Numerical Mathematics
SN - 0168-9274
TI - Projection methods with alternating inertial steps for variational inequalities: Weak and linear convergence
VL - 157
ER -
TY - GEN
AB - Here, we employ micro- and nanosized cellulose particles, namely paper fines and cellulose
nanocrystals, to induce hierarchical organization over a wide length scale. After processing
them into carbonaceous materials, we demonstrate that these hierarchically organized materials
outperform the best materials for supercapacitors operating with organic electrolytes reported
in literature in terms of specific energy/power (Ragone plot) while showing hardly any capacity
fade over 4,000 cycles. The highly porous materials feature a specific surface area as high as
2500 m2ˑg-1 and exhibit pore sizes in the range of 0.5 to 200 nm as proven by scanning electron
microscopy and N2 physisorption. The carbonaceous materials have been further investigated
by X-ray photoelectron spectroscopy and RAMAN spectroscopy. Since paper fines are an
underutilized side stream in any paper production process, they are a cheap and highly available
feedstock to prepare carbonaceous materials with outstanding performance in electrochemical
applications.
AU - Hobisch, Mathias A.
AU - Mourad, Eléonore
AU - Fischer, Wolfgang J.
AU - Prehal, Christian
AU - Eyley, Samuel
AU - Childress, Anthony
AU - Zankel, Armin
AU - Mautner, Andreas
AU - Breitenbach, Stefan
AU - Rao, Apparao M.
AU - Thielemans, Wim
AU - Freunberger, Stefan Alexander
AU - Eckhart, Rene
AU - Bauer, Wolfgang
AU - Spirk, Stefan
ID - 8081
TI - High specific capacitance supercapacitors from hierarchically organized all-cellulose composites
ER -
TY - JOUR
AB - Origin and functions of intermittent transitions among sleep stages, including brief awakenings and arousals, constitute a challenge to the current homeostatic framework for sleep regulation, focusing on factors modulating sleep over large time scales. Here we propose that the complex micro-architecture characterizing sleep on scales of seconds and minutes results from intrinsic non-equilibrium critical dynamics. We investigate θ- and δ-wave dynamics in control rats and in rats where the sleep-promoting ventrolateral preoptic nucleus (VLPO) is lesioned (male Sprague-Dawley rats). We demonstrate that bursts in θ and δ cortical rhythms exhibit complex temporal organization, with long-range correlations and robust duality of power-law (θ-bursts, active phase) and exponential-like (δ-bursts, quiescent phase) duration distributions, features typical of non-equilibrium systems self-organizing at criticality. We show that such non-equilibrium behavior relates to anti-correlated coupling between θ- and δ-bursts, persists across a range of time scales, and is independent of the dominant physiologic state; indications of a basic principle in sleep regulation. Further, we find that VLPO lesions lead to a modulation of cortical dynamics resulting in altered dynamical parameters of θ- and δ-bursts and significant reduction in θ–δ coupling. Our empirical findings and model simulations demonstrate that θ–δ coupling is essential for the emerging non-equilibrium critical dynamics observed across the sleep–wake cycle, and indicate that VLPO neurons may have dual role for both sleep and arousal/brief wake activation. The uncovered critical behavior in sleep- and wake-related cortical rhythms indicates a mechanism essential for the micro-architecture of spontaneous sleep-stage and arousal transitions within a novel, non-homeostatic paradigm of sleep regulation.
AU - Lombardi, Fabrizio
AU - Gómez-Extremera, Manuel
AU - Bernaola-Galván, Pedro
AU - Vetrivelan, Ramalingam
AU - Saper, Clifford B.
AU - Scammell, Thomas E.
AU - Ivanov, Plamen Ch.
ID - 8084
IS - 1
JF - Journal of Neuroscience
SN - 0270-6474
TI - Critical dynamics and coupling in bursts of cortical rhythms indicate non-homeostatic mechanism for sleep-stage transitions and dual role of VLPO neurons in both sleep and wake
VL - 40
ER -
TY - JOUR
AB - In the setting of the fractional quantum Hall effect we study the effects of strong, repulsive two-body interaction potentials of short range. We prove that Haldane’s pseudo-potential operators, including their pre-factors, emerge as mathematically rigorous limits of such interactions when the range of the potential tends to zero while its strength tends to infinity. In a common approach the interaction potential is expanded in angular momentum eigenstates in the lowest Landau level, which amounts to taking the pre-factors to be the moments of the potential. Such a procedure is not appropriate for very strong interactions, however, in particular not in the case of hard spheres. We derive the formulas valid in the short-range case, which involve the scattering lengths of the interaction potential in different angular momentum channels rather than its moments. Our results hold for bosons and fermions alike and generalize previous results in [6], which apply to bosons in the lowest angular momentum channel. Our main theorem asserts the convergence in a norm-resolvent sense of the Hamiltonian on the whole Hilbert space, after appropriate energy scalings, to Hamiltonians with contact interactions in the lowest Landau level.
AU - Seiringer, Robert
AU - Yngvason, Jakob
ID - 8091
JF - Journal of Statistical Physics
SN - 00224715
TI - Emergence of Haldane pseudo-potentials in systems with short-range interactions
VL - 181
ER -
TY - GEN
AB - We present a generative model of images that explicitly reasons over the set
of objects they show. Our model learns a structured latent representation that
separates objects from each other and from the background; unlike prior works,
it explicitly represents the 2D position and depth of each object, as well as
an embedding of its segmentation mask and appearance. The model can be trained
from images alone in a purely unsupervised fashion without the need for object
masks or depth information. Moreover, it always generates complete objects,
even though a significant fraction of training images contain occlusions.
Finally, we show that our model can infer decompositions of novel images into
their constituent objects, including accurate prediction of depth ordering and
segmentation of occluded parts.
AU - Anciukevicius, Titas
AU - Lampert, Christoph
AU - Henderson, Paul M
ID - 8063
T2 - arXiv
TI - Object-centric image generation with factored depths, locations, and appearances
ER -
TY - JOUR
AB - In mammalian genomes, a subset of genes is regulated by genomic imprinting, resulting in silencing of one parental allele. Imprinting is essential for cerebral cortex development, but prevalence and functional impact in individual cells is unclear. Here, we determined allelic expression in cortical cell types and established a quantitative platform to interrogate imprinting in single cells. We created cells with uniparental chromosome disomy (UPD) containing two copies of either the maternal or the paternal chromosome; hence, imprinted genes will be 2-fold overexpressed or not expressed. By genetic labeling of UPD, we determined cellular phenotypes and transcriptional responses to deregulated imprinted gene expression at unprecedented single-cell resolution. We discovered an unexpected degree of cell-type specificity and a novel function of imprinting in the regulation of cortical astrocyte survival. More generally, our results suggest functional relevance of imprinted gene expression in glial astrocyte lineage and thus for generating cortical cell-type diversity.
AU - Laukoter, Susanne
AU - Pauler, Florian
AU - Beattie, Robert J
AU - Amberg, Nicole
AU - Hansen, Andi H
AU - Streicher, Carmen
AU - Penz, Thomas
AU - Bock, Christoph
AU - Hippenmeyer, Simon
ID - 8162
IS - 6
JF - Neuron
SN - 0896-6273
TI - Cell-type specificity of genomic imprinting in cerebral cortex
VL - 107
ER -
TY - JOUR
AB - Fejes Tóth [3] studied approximations of smooth surfaces in three-space by piecewise flat triangular meshes with a given number of vertices on the surface that are optimal with respect to Hausdorff distance. He proves that this Hausdorff distance decreases inversely proportional with the number of vertices of the approximating mesh if the surface is convex. He also claims that this Hausdorff distance is inversely proportional to the square of the number of vertices for a specific non-convex surface, namely a one-sheeted hyperboloid of revolution bounded by two congruent circles. We refute this claim, and show that the asymptotic behavior of the Hausdorff distance is linear, that is the same as for convex surfaces.
AU - Vegter, Gert
AU - Wintraecken, Mathijs
ID - 8163
IS - 2
JF - Studia Scientiarum Mathematicarum Hungarica
SN - 0081-6906
TI - Refutation of a claim made by Fejes Tóth on the accuracy of surface meshes
VL - 57
ER -
TY - JOUR
AB - The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions.
AU - Stankowski, Sean
AU - Westram, Anja M
AU - Zagrodzka, Zuzanna B.
AU - Eyres, Isobel
AU - Broquet, Thomas
AU - Johannesson, Kerstin
AU - Butlin, Roger K.
ID - 8167
IS - 1806
JF - Philosophical Transactions of the Royal Society. Series B: Biological Sciences
TI - The evolution of strong reproductive isolation between sympatric intertidal snails
VL - 375
ER -
TY - JOUR
AB - Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed.
AU - Kulmuni, Jonna
AU - Butlin, Roger K.
AU - Lucek, Kay
AU - Savolainen, Vincent
AU - Westram, Anja M
ID - 8168
IS - 1806
JF - Philosophical Transactions of the Royal Society. Series B: Biological sciences
SN - 0962-8436
TI - Towards the completion of speciation: The evolution of reproductive isolation beyond the first barriers
VL - 375
ER -
TY - JOUR
AB - Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the ‘escape’ of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation.
AU - Shang, Huiying
AU - Hess, Jaqueline
AU - Pickup, Melinda
AU - Field, David
AU - Ingvarsson, Pär K.
AU - Liu, Jianquan
AU - Lexer, Christian
ID - 8169
IS - 1806
JF - Philosophical Transactions of the Royal Society. Series B: Biological Sciences
TI - Evolution of strong reproductive isolation in plants: Broad-scale patterns and lessons from a perennial model group
VL - 375
ER -
TY - JOUR
AB - Alignment of OCS, CS2, and I2 molecules embedded in helium nanodroplets is measured as a function
of time following rotational excitation by a nonresonant, comparatively weak ps laser pulse. The distinct
peaks in the power spectra, obtained by Fourier analysis, are used to determine the rotational, B, and
centrifugal distortion, D, constants. For OCS, B and D match the values known from IR spectroscopy. For
CS2 and I2, they are the first experimental results reported. The alignment dynamics calculated from the
gas-phase rotational Schrödinger equation, using the experimental in-droplet B and D values, agree in
detail with the measurement for all three molecules. The rotational spectroscopy technique for molecules in
helium droplets introduced here should apply to a range of molecules and complexes.
AU - Chatterley, Adam S.
AU - Christiansen, Lars
AU - Schouder, Constant A.
AU - Jørgensen, Anders V.
AU - Shepperson, Benjamin
AU - Cherepanov, Igor
AU - Bighin, Giacomo
AU - Zillich, Robert E.
AU - Lemeshko, Mikhail
AU - Stapelfeldt, Henrik
ID - 8170
IS - 1
JF - Physical Review Letters
SN - 00319007
TI - Rotational coherence spectroscopy of molecules in Helium nanodroplets: Reconciling the time and the frequency domains
VL - 125
ER -