@article{6563,
abstract = {This paper presents two algorithms. The first decides the existence of a pointed homotopy between given simplicial maps đ,đ:đâđ, and the second computes the group [đŽđ,đ]â 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 đŽâđ.},
author = {FilakovskĂœ, Marek and VokĆĂnek, Lukas},
issn = {16153383},
journal = {Foundations of Computational Mathematics},
pages = {311--330},
publisher = {Springer Nature},
title = {{Are two given maps homotopic? An algorithmic viewpoint}},
doi = {10.1007/s10208-019-09419-x},
volume = {20},
year = {2020},
}
@article{7142,
abstract = {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.},
author = {Gallei, Michelle C and Luschnig, C and Friml, JiĆĂ},
issn = {1879-0356},
journal = {Current Opinion in Plant Biology},
pages = {43--49},
publisher = {Elsevier},
title = {{Auxin signalling in growth: SchrĂ¶dinger's cat out of the bag}},
doi = {10.1016/j.pbi.2019.10.003},
volume = {53},
year = {2020},
}
@article{7149,
abstract = {In recent years, many genes have been associated with chromatinopathies classified as âCornelia de Lange Syndromeâlike.â 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 âCdLSâlike syndromesâ are part of a larger ârare disease familyâ sharing multiple clinical features and common disrupted molecular pathways.},
author = {Avagliano, Laura and Parenti, Ilaria and Grazioli, Paolo and Di Fede, Elisabetta and Parodi, Chiara and Mariani, Milena and Kaiser, Frank J. and Selicorni, Angelo and Gervasini, Cristina and Massa, Valentina},
issn = {1399-0004},
journal = {Clinical Genetics},
number = {1},
pages = {3--11},
publisher = {Wiley},
title = {{Chromatinopathies: A focus on Cornelia de Lange syndrome}},
doi = {10.1111/cge.13674},
volume = {97},
year = {2020},
}
@article{7166,
abstract = {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.},
author = {Ucar, Mehmet C and Lipowsky, Reinhard},
issn = {1530-6992},
journal = {Nano Letters},
number = {1},
pages = {669--676},
publisher = {ACS},
title = {{Collective force generation by molecular motors is determined by strain-induced unbinding}},
doi = {10.1021/acs.nanolett.9b04445},
volume = {20},
year = {2020},
}
@article{6808,
abstract = {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.},
author = {Jahr, Wiebke and Velicky, Philipp and Danzl, Johann G},
issn = {1046-2023},
journal = {Methods},
number = {3},
pages = {27--41},
publisher = {Elsevier},
title = {{Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens}},
doi = {10.1016/j.ymeth.2019.07.019},
volume = {174},
year = {2020},
}
@article{6918,
abstract = {We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge of the network is operable with its associated probability and the problem is to determine the probability of having at least one source-to-target path that is entirely composed of operable edges. This problem is known to be NP-hard.
We provide a novel scalable algorithm to solve the Network Reliability problem when the treewidth of the underlying network is small. We also show our algorithmâs applicability for real-world transit networks that have small treewidth, including the metro networks of major cities, such as London and Tokyo. Our algorithm leverages tree decompositions to shrink the original graph into much smaller graphs, for which reliability can be efficiently and exactly computed using a brute force method. To the best of our knowledge, this is the first exact algorithm for Network Reliability that can scale to handle real-world instances of the problem.},
author = {Goharshady, Amir Kafshdar and Mohammadi, Fatemeh},
issn = {09518320},
journal = {Reliability Engineering and System Safety},
publisher = {Elsevier},
title = {{An efficient algorithm for computing network reliability in small treewidth}},
doi = {10.1016/j.ress.2019.106665},
volume = {193},
year = {2020},
}
@inproceedings{7272,
abstract = {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.},
author = {Arbel-Raviv, Maya and Brown, Trevor A and Morrison, Adam},
booktitle = {Proceedings of the 2018 USENIX Annual Technical Conference, USENIX ATC 2018},
isbn = {9781939133021},
location = {Boston, MA, United States},
pages = {295--306},
publisher = {USENIX Association},
title = {{Getting to the root of concurrent binary search tree performance}},
year = {2020},
}
@article{7219,
abstract = {Root system architecture (RSA), governed by the phytohormone auxin, endows plants with an adaptive advantage in particular environments. Using geographically representative arabidopsis (Arabidopsis thaliana) accessions as a resource for GWA mapping, Waidmann et al. and Ogura et al. recently identified two novel components involved in modulating auxin-mediated RSA and conferring plant fitness in particular habitats.},
author = {Xiao, Guanghui and Zhang, Yuzhou},
issn = {13601385},
journal = {Trends in Plant Science},
number = {2},
pages = {121--123},
publisher = {Elsevier},
title = {{Adaptive growth: Shaping auxin-mediated root system architecture}},
doi = {10.1016/j.tplants.2019.12.001},
volume = {25},
year = {2020},
}
@article{7426,
abstract = {This paper presents a novel abstraction technique for analyzing Lyapunov and asymptotic stability of polyhedral switched systems. A polyhedral switched system is a hybrid system in which the continuous dynamics is specified by polyhedral differential inclusions, the invariants and guards are specified by polyhedral sets and the switching between the modes do not involve reset of variables. A finite state weighted graph abstracting the polyhedral switched system is constructed from a finite partition of the stateâspace, such that the satisfaction of certain graph conditions, such as the absence of cycles with product of weights on the edges greater than (or equal) to 1, implies the stability of the system. However, the graph is in general conservative and hence, the violation of the graph conditions does not imply instability. If the analysis fails to establish stability due to the conservativeness in the approximation, a counterexample (cycle with product of edge weights greater than or equal to 1) indicating a potential reason for the failure is returned. Further, a more precise approximation of the switched system can be constructed by considering a finer partition of the stateâspace in the construction of the finite weighted graph. We present experimental results on analyzing stability of switched systems using the above method.},
author = {Garcia Soto, Miriam and Prabhakar, Pavithra},
issn = {1751570X},
journal = {Nonlinear Analysis: Hybrid Systems},
number = {5},
publisher = {Elsevier},
title = {{Abstraction based verification of stability of polyhedral switched systems}},
doi = {10.1016/j.nahs.2020.100856},
volume = {36},
year = {2020},
}
@article{7427,
author = {Tan, Shutang and Abas, Melinda F and Verstraeten, Inge and Glanc, Matous and Molnar, Gergely and Hajny, Jakub and LasĂĄk, Pavel and PetĆĂk, Ivan and Russinova, Eugenia and PetrĂĄĆĄek, Jan and NovĂĄk, OndĆej and PospĂĆĄil, JiĆĂ and Friml, JiĆĂ},
issn = {09609822},
journal = {Current Biology},
number = {3},
pages = {381--395.e8},
publisher = {Cell Press},
title = {{Salicylic acid targets protein phosphatase 2A to attenuate growth in plants}},
doi = {10.1016/j.cub.2019.11.058},
volume = {30},
year = {2020},
}
@article{7428,
abstract = {In the superconducting regime of FeTe(1âx)Sex, there exist two types of vortices which are distinguished by the presence or absence of zero-energy states in their core. To understand their origin, we examine the interplay of Zeeman coupling and superconducting pairings in three-dimensional metals with band inversion. Weak Zeeman fields are found to suppress intraorbital spin-singlet pairing, known to localize the states at the ends of the vortices on the surface. On the other hand, an orbital-triplet pairing is shown to be stable against Zeeman interactions, but leads to delocalized zero-energy Majorana modes which extend through the vortex. In contrast, the finite-energy vortex modes remain localized at the vortex ends even when the pairing is of orbital-triplet form. Phenomenologically, this manifests as an observed disappearance of zero-bias peaks within the cores of topological vortices upon an increase of the applied magnetic field. The presence of magnetic impurities in FeTe(1âx)Sex, which are attracted to the vortices, would lead to such Zeeman-induced delocalization of Majorana modes in a fraction of vortices that capture a large enough number of magnetic impurities. Our results provide an explanation for the dichotomy between topological and nontopological vortices recently observed in FeTe(1âx)Sex.},
author = {Ghazaryan, Areg and Lopes, P. L.S. and Hosur, Pavan and Gilbert, Matthew J. and Ghaemi, Pouyan},
issn = {24699969},
journal = {Physical Review B},
number = {2},
publisher = {APS},
title = {{Effect of Zeeman coupling on the Majorana vortex modes in iron-based topological superconductors}},
doi = {10.1103/PhysRevB.101.020504},
volume = {101},
year = {2020},
}
@article{7431,
abstract = {In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g. when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g. when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance.},
author = {Kolchinsky, Artemy and Corominas-Murtra, Bernat},
issn = {17425662},
journal = {Journal of the Royal Society Interface},
number = {162},
pages = {20190623},
publisher = {Royal Society},
title = {{Decomposing information into copying versus transformation}},
doi = {10.1098/rsif.2019.0623},
volume = {17},
year = {2020},
}
@article{7387,
abstract = {Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZâFtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site.},
author = {Baranova, Natalia S. and Radler, Philipp and HernĂĄndez-Rocamora, VĂctor M. and Alfonso, Carlos and Lopez Pelegrin, Maria D and Rivas, GermĂĄn and Vollmer, Waldemar and Loose, Martin},
issn = {2058-5276},
journal = {Nature Microbiology},
publisher = {Springer Nature},
title = {{Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins}},
doi = {10.1038/s41564-019-0657-5},
year = {2020},
}
@article{7388,
abstract = {We give a Wong-Zakai type characterisation of the solutions of quasilinear heat equations driven by space-time white noise in 1 + 1 dimensions. In order to show that the renormalisation counterterms are local in the solution, a careful arrangement of a few hundred terms is required. The main tool in this computation is a general âintegration by partsâ formula that provides a number of linear identities for the renormalisation constants.},
author = {Gerencser, Mate},
issn = {0294-1449},
journal = {Annales de l'Institut Henri PoincarĂ© C, Analyse non linĂ©aire},
publisher = {Elsevier},
title = {{Nondivergence form quasilinear heat equations driven by space-time white noise}},
doi = {10.1016/j.anihpc.2020.01.003},
year = {2020},
}
@article{7389,
abstract = {Recently Kloeckner described the structure of the isometry group of the quadratic Wasserstein space W_2(R^n). It turned out that the case of the real line is exceptional in the sense that there exists an exotic isometry flow. Following this line of investigation, we compute Isom(W_p(R)), the isometry group of the Wasserstein space
W_p(R) for all p \in [1,\infty) \setminus {2}. We show that W_2(R) is also exceptional regarding the
parameter p: W_p(R) is isometrically rigid if and only if p is not equal to 2. Regarding the underlying
space, we prove that the exceptionality of p = 2 disappears if we replace R by the compact
interval [0,1]. Surprisingly, in that case, W_p([0,1]) is isometrically rigid if and only if
p is not equal to 1. Moreover, W_1([0,1]) admits isometries that split mass, and Isom(W_1([0,1]))
cannot be embedded into Isom(W_1(R)).},
author = {Geher, Gyorgy Pal and Titkos, Tamas and Virosztek, Daniel},
issn = {10886850},
journal = {Transactions of the American Mathematical Society},
keywords = {Wasserstein space, isometric embeddings, isometric rigidity, exotic isometry flow},
pages = {32},
publisher = {American Mathematical Society},
title = {{Isometric study of Wasserstein spaces - the real line}},
doi = {10.1090/tran/8113},
year = {2020},
}
@inbook{74,
abstract = {We study the Gromov waist in the sense of t-neighborhoods for measures in the Euclidean space, motivated by the famous theorem of Gromov about the waist of radially symmetric Gaussian measures. In particular, it turns our possible to extend Gromovâs original result to the case of not necessarily radially symmetric Gaussian measure. We also provide examples of measures having no t-neighborhood waist property, including a rather wide class
of compactly supported radially symmetric measures and their maps into the Euclidean space of dimension at least 2.
We use a simpler form of Gromovâs pancake argument to produce some estimates of t-neighborhoods of (weighted) volume-critical submanifolds in the spirit of the waist theorems, including neighborhoods of algebraic manifolds in the complex projective space. In the appendix of this paper we provide for readerâs convenience a more detailed explanation of the Caffarelli theorem that we use to handle not necessarily radially symmetric Gaussian
measures.},
author = {Akopyan, Arseniy and Karasev, Roman},
booktitle = {Geometric Aspects of Functional Analysis},
editor = {Klartag, Bo'az and Milman, Emanuel},
isbn = {9783030360191},
issn = {16179692},
pages = {1--27},
publisher = {Springer Nature},
title = {{Gromov's waist of non-radial Gaussian measures and radial non-Gaussian measures}},
doi = {10.1007/978-3-030-36020-7_1},
volume = {2256},
year = {2020},
}
@unpublished{7553,
abstract = {Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy âoptimization priors.â This family defines a smooth interpolation between a data-rich inference regime (characteristic of âbottom-upâ statistical models), and a data-limited ab inito prediction regime (characteristic of âtop-downâ normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems.},
author = {Mlynarski, Wiktor F and Hledik, Michal and Sokolowski, Thomas R and TkaÄik, GaĆĄper},
booktitle = {bioRxiv},
pages = {13},
publisher = {Cold Spring Harbor Laboratory},
title = {{Statistical analysis and optimality of biological systems}},
year = {2020},
}
@article{7554,
abstract = {Slicing a Voronoi tessellation in ${R}^n$ with a $k$-plane gives a $k$-dimensional weighted Voronoi tessellation, also known as a power diagram or Laguerre tessellation. Mapping every simplex of the dual weighted Delaunay mosaic to the radius of the smallest empty circumscribed sphere whose center lies in the $k$-plane gives a generalized discrete Morse function. Assuming the Voronoi tessellation is generated by a Poisson point process in ${R}^n$, we study the expected number of simplices in the $k$-dimensional weighted Delaunay mosaic as well as the expected number of intervals of the Morse function, both as functions of a radius threshold. As a by-product, we obtain a new proof for the expected number of connected components (clumps) in a line section of a circular Boolean model in ${R}^n$.},
author = {Edelsbrunner, Herbert and Nikitenko, Anton},
issn = {10957219},
journal = {Theory of Probability and its Applications},
number = {4},
pages = {595--614},
publisher = {SIAM},
title = {{Weighted PoissonâDelaunay mosaics}},
doi = {10.1137/S0040585X97T989726},
volume = {64},
year = {2020},
}
@article{7563,
abstract = {We introduce âstate space persistence analysisâ for deducing the symbolic dynamics of time series data obtained from high-dimensional chaotic attractors. To this end, we adapt a topological data analysis technique known as persistent homology for the characterization of state space projections of chaotic trajectories and periodic orbits. By comparing the shapes along a chaotic trajectory to those of the periodic orbits, state space persistence analysis quantifies the shape similarity of chaotic trajectory segments and periodic orbits. We demonstrate the method by applying it to the three-dimensional RĂ¶ssler system and a 30-dimensional discretization of the KuramotoâSivashinsky partial differential equation in (1+1) dimensions.
One way of studying chaotic attractors systematically is through their symbolic dynamics, in which one partitions the state space into qualitatively different regions and assigns a symbol to each such region.1â3 This yields a âcoarse-grainedâ state space of the system, which can then be reduced to a Markov chain encoding all possible transitions between the states of the system. While it is possible to obtain the symbolic dynamics of low-dimensional chaotic systems with standard tools such as PoincarĂ© maps, when applied to high-dimensional systems such as turbulent flows, these tools alone are not sufficient to determine symbolic dynamics.4,5 In this paper, we develop âstate space persistence analysisâ and demonstrate that it can be utilized to infer the symbolic dynamics in very high-dimensional settings.},
author = {Yalniz, GĂ¶khan and Budanur, Nazmi B},
issn = {1089-7682},
journal = {Chaos},
number = {3},
publisher = {AIP Publishing},
title = {{Inferring symbolic dynamics of chaotic flows from persistence}},
doi = {10.1063/1.5122969},
volume = {30},
year = {2020},
}
@unpublished{7568,
abstract = {Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e.manifolds defined as the zero set of some multivariate multivalued functionf:RdâRdân.A natural (and efficient) way to approximate an isomanifold is to consider its Piecewise-Linear(PL) approximation based on a triangulationTof the ambient spaceRd. In this paper, we giveconditions under which the PL-approximation of an isomanifold is topologically equivalent to theisomanifold. The conditions can always be met by taking a sufficiently fine triangulationT.},
author = {Boissonnat, Jean-Daniel and Wintraecken, Mathijs},
booktitle = {EUROCG 2020},
pages = {8},
title = {{The topological correctness of the PL-approximation of isomanifolds}},
year = {2020},
}