@article{1015,
abstract = {Vortices are commonly observed in the context of classical hydrodynamics: from whirlpools after stirring the coffee in a cup to a violent atmospheric phenomenon such as a tornado, all classical vortices are characterized by an arbitrary circulation value of the local velocity field. On the other hand the appearance of vortices with quantized circulation represents one of the fundamental signatures of macroscopic quantum phenomena. In two-dimensional superfluids quantized vortices play a key role in determining finite-temperature properties, as the superfluid phase and the normal state are separated by a vortex unbinding transition, the Berezinskii-Kosterlitz-Thouless transition. Very recent experiments with two-dimensional superfluid fermions motivate the present work: we present theoretical results based on the renormalization group showing that the universal jump of the superfluid density and the critical temperature crucially depend on the interaction strength, providing a strong benchmark for forthcoming investigations.},
author = {Bighin, Giacomo and Salasnich, Luca},
issn = {20452322},
journal = {Scientific Reports},
publisher = {Nature Publishing Group},
title = {{Vortices and antivortices in two-dimensional ultracold Fermi gases}},
doi = {10.1038/srep45702},
volume = {7},
year = {2017},
}
@article{1022,
abstract = {We introduce a multiscale topological description of the Megaparsec web-like cosmic matter distribution. Betti numbers and topological persistence offer a powerful means of describing the rich connectivity structure of the cosmic web and of its multiscale arrangement of matter and galaxies. Emanating from algebraic topology and Morse theory, Betti numbers and persistence diagrams represent an extension and deepening of the cosmologically familiar topological genus measure and the related geometric Minkowski functionals. In addition to a description of the mathematical background, this study presents the computational procedure for computing Betti numbers and persistence diagrams for density field filtrations. The field may be computed starting from a discrete spatial distribution of galaxies or simulation particles. The main emphasis of this study concerns an extensive and systematic exploration of the imprint of different web-like morphologies and different levels of multiscale clustering in the corresponding computed Betti numbers and persistence diagrams. To this end, we use Voronoi clustering models as templates for a rich variety of web-like configurations and the fractal-like Soneira-Peebles models exemplify a range of multiscale configurations. We have identified the clear imprint of cluster nodes, filaments, walls, and voids in persistence diagrams, along with that of the nested hierarchy of structures in multiscale point distributions. We conclude by outlining the potential of persistent topology for understanding the connectivity structure of the cosmic web, in large simulations of cosmic structure formation and in the challenging context of the observed galaxy distribution in large galaxy surveys.},
author = {Pranav, Pratyush and Edelsbrunner, Herbert and Van De Weygaert, Rien and Vegter, Gert and Kerber, Michael and Jones, Bernard and Wintraecken, Mathijs},
issn = {00358711},
journal = {Monthly Notices of the Royal Astronomical Society},
number = {4},
pages = {4281 -- 4310},
publisher = {Oxford University Press},
title = {{The topology of the cosmic web in terms of persistent Betti numbers}},
doi = {10.1093/mnras/stw2862},
volume = {465},
year = {2017},
}
@article{1111,
abstract = {Adaptation depends critically on the effects of new mutations and their dependency on the genetic background in which they occur. These two factors can be summarized by the fitness landscape. However, it would require testing all mutations in all backgrounds, making the definition and analysis of fitness landscapes mostly inaccessible. Instead of postulating a particular fitness landscape, we address this problem by considering general classes of landscapes and calculating an upper limit for the time it takes for a population to reach a fitness peak, circumventing the need to have full knowledge about the fitness landscape. We analyze populations in the weak-mutation regime and characterize the conditions that enable them to quickly reach the fitness peak as a function of the number of sites under selection. We show that for additive landscapes there is a critical selection strength enabling populations to reach high-fitness genotypes, regardless of the distribution of effects. This threshold scales with the number of sites under selection, effectively setting a limit to adaptation, and results from the inevitable increase in deleterious mutational pressure as the population adapts in a space of discrete genotypes. Furthermore, we show that for the class of all unimodal landscapes this condition is sufficient but not necessary for rapid adaptation, as in some highly epistatic landscapes the critical strength does not depend on the number of sites under selection; effectively removing this barrier to adaptation.},
author = {Heredia, Jorge and Trubenova, Barbora and Sudholt, Dirk and Paixao, Tiago},
issn = {00166731},
journal = {Genetics},
number = {2},
pages = {803 -- 825},
publisher = {Genetics Society of America},
title = {{Selection limits to adaptive walks on correlated landscapes}},
doi = {10.1534/genetics.116.189340},
volume = {205},
year = {2017},
}
@article{1084,
abstract = {BceRS and PsdRS are paralogous two-component systems in Bacillus subtilis controlling the response to antimicrobial peptides. In the presence of extracellular bacitracin and nisin, respectively, the two response regulators (RRs) bind their target promoters, PbceA or PpsdA, resulting in a strong up-regulation of target gene expression and ultimately antibiotic resistance. Despite high sequence similarity between the RRs BceR and PsdR and their known binding sites, no cross-regulation has been observed between them. We therefore investigated the specificity determinants of PbceA and PpsdA that ensure the insulation of these two paralogous pathways at the RR–promoter interface. In vivo and in vitro analyses demonstrate that the regulatory regions within these two promoters contain three important elements: in addition to the known (main) binding site, we identified a linker region and a secondary binding site that are crucial for functionality. Initial binding to the high-affinity, low-specificity main binding site is a prerequisite for the subsequent highly specific binding of a second RR dimer to the low-affinity secondary binding site. In addition to this hierarchical cooperative binding, discrimination requires a competition of the two RRs for their respective binding site mediated by only slight differences in binding affinities.},
author = {Fang, Chong and Nagy-Staron, Anna A and Grafe, Martin and Heermann, Ralf and Jung, Kirsten and Gebhard, Susanne and Mascher, Thorsten},
issn = { 0950382X},
journal = {Molecular Microbiology},
number = {1},
pages = {16 -- 31},
publisher = {Wiley-Blackwell},
title = {{Insulation and wiring specificity of BceR like response regulators and their target promoters in Bacillus subtilis}},
doi = {10.1111/mmi.13597},
volume = {104},
year = {2017},
}
@article{1077,
abstract = {Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.},
author = {Fernandes Redondo, Rodrigo A and Vladar, Harold and Włodarski, Tomasz and Bollback, Jonathan P},
issn = {17425689},
journal = {Journal of the Royal Society Interface},
number = {126},
publisher = {Royal Society of London},
title = {{Evolutionary interplay between structure, energy and epistasis in the coat protein of the fX174 phage family}},
doi = {10.1098/rsif.2016.0139},
volume = {14},
year = {2017},
}
@article{1072,
abstract = {Given a finite set of points in Rn and a radius parameter, we study the Čech, Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel sets of generalized discrete Morse functions, we prove that the four complexes are simple-homotopy equivalent by a sequence of simplicial collapses, which are explicitly described by a single discrete gradient field.},
author = {Bauer, Ulrich and Edelsbrunner, Herbert},
journal = {Transactions of the American Mathematical Society},
number = {5},
pages = {3741 -- 3762},
publisher = {American Mathematical Society},
title = {{The Morse theory of Čech and delaunay complexes}},
volume = {369},
year = {2017},
}
@article{1159,
abstract = {Auxin steers numerous physiological processes in plants, making the tight control of its endogenous levels and spatiotemporal distribution a necessity. This regulation is achieved by different mechanisms, including auxin biosynthesis, metabolic conversions, degradation, and transport. Here, we introduce cis-cinnamic acid (c-CA) as a novel and unique addition to a small group of endogenous molecules affecting in planta auxin concentrations. c-CA is the photo-isomerization product of the phenylpropanoid pathway intermediate trans-CA (t-CA). When grown on c-CA-containing medium, an evolutionary diverse set of plant species were shown to exhibit phenotypes characteristic for high auxin levels, including inhibition of primary root growth, induction of root hairs, and promotion of adventitious and lateral rooting. By molecular docking and receptor binding assays, we showed that c-CA itself is neither an auxin nor an anti-auxin, and auxin profiling data revealed that c-CA does not significantly interfere with auxin biosynthesis. Single cell-based auxin accumulation assays showed that c-CA, and not t-CA, is a potent inhibitor of auxin efflux. Auxin signaling reporters detected changes in spatiotemporal distribution of the auxin response along the root of c-CA-treated plants, and long-distance auxin transport assays showed no inhibition of rootward auxin transport. Overall, these results suggest that the phenotypes of c-CA-treated plants are the consequence of a local change in auxin accumulation, induced by the inhibition of auxin efflux. This work reveals a novel mechanism how plants may regulate auxin levels and adds a novel, naturally occurring molecule to the chemical toolbox for the studies of auxin homeostasis.},
author = {Steenackers, Ward and Klíma, Petr and Quareshy, Mussa and Cesarino, Igor and Kumpf, Robert and Corneillie, Sander and Araújo, Pedro and Viaene, Tom and Goeminne, Geert and Nowack, Moritz and Ljung, Karin and Friml, Jirí and Blakeslee, Joshua and Novák, Ondřej and Zažímalová, Eva and Napier, Richard and Boerjan, Wout and Vanholme, Bartel},
issn = {00320889},
journal = {Plant Physiology},
number = {1},
pages = {552 -- 565},
publisher = {American Society of Plant Biologists},
title = {{Cis-cinnamic acid is a novel natural auxin efflux inhibitor that promotes lateral root formation}},
doi = {10.1104/pp.16.00943},
volume = {173},
year = {2017},
}
@article{1161,
abstract = {Coordinated changes of cell shape are often the result of the excitable, wave-like dynamics of the actin cytoskeleton. New work shows that, in migrating cells, protrusion waves arise from mechanochemical crosstalk between adhesion sites, membrane tension and the actin protrusive machinery.},
author = {Müller, Jan and Sixt, Michael K},
issn = {09609822},
journal = {Current Biology},
number = {1},
pages = {R24 -- R25},
publisher = {Cell Press},
title = {{Cell migration: Making the waves}},
doi = {10.1016/j.cub.2016.11.035},
volume = {27},
year = {2017},
}
@article{1173,
abstract = {We introduce the Voronoi functional of a triangulation of a finite set of points in the Euclidean plane and prove that among all geometric triangulations of the point set, the Delaunay triangulation maximizes the functional. This result neither extends to topological triangulations in the plane nor to geometric triangulations in three and higher dimensions.},
author = {Edelsbrunner, Herbert and Glazyrin, Alexey and Musin, Oleg and Nikitenko, Anton},
issn = {02099683},
journal = {Combinatorica},
number = {5},
pages = {887 -- 910},
publisher = {Springer},
title = {{The Voronoi functional is maximized by the Delaunay triangulation in the plane}},
doi = {10.1007/s00493-016-3308-y},
volume = {37},
year = {2017},
}
@inproceedings{1178,
abstract = {For any pair (X, Z) of correlated random variables we can think of Z as a randomized function of X. If the domain of Z is small, one can make this function computationally efficient by allowing it to be only approximately correct. In folklore this problem is known as simulating auxiliary inputs. This idea of simulating auxiliary information turns out to be a very usefull tool, finding applications in complexity theory, cryptography, pseudorandomness and zero-knowledge. In this paper we revisit this problem, achieving the following results: (a) We present a novel boosting algorithm for constructing the simulator. This boosting proof is of independent interest, as it shows how to handle “negative mass” issues when constructing probability measures by shifting distinguishers in descent algorithms. Our technique essentially fixes the flaw in the TCC’14 paper “How to Fake Auxiliary Inputs”. (b) The complexity of our simulator is better than in previous works, including results derived from the uniform min-max theorem due to Vadhan and Zheng. To achieve (s,ϵ) -indistinguishability we need the complexity O(s⋅25ℓϵ−2) in time/circuit size, which improve previous bounds by a factor of ϵ−2. In particular, with we get meaningful provable security for the EUROCRYPT’09 leakage-resilient stream cipher instantiated with a standard 256-bit block cipher, like },
author = {Skórski, Maciej},
pages = {159 -- 179},
publisher = {Springer},
title = {{Simulating auxiliary inputs, revisited}},
doi = {10.1007/978-3-662-53641-4_7},
volume = {9985},
year = {2017},
}
@article{1180,
abstract = {In this article we define an algebraic vertex of a generalized polyhedron and show that the set of algebraic vertices is the smallest set of points needed to define the polyhedron. We prove that the indicator function of a generalized polytope P is a linear combination of indicator functions of simplices whose vertices are algebraic vertices of P. We also show that the indicator function of any generalized polyhedron is a linear combination, with integer coefficients, of indicator functions of cones with apices at algebraic vertices and line-cones. The concept of an algebraic vertex is closely related to the Fourier–Laplace transform. We show that a point v is an algebraic vertex of a generalized polyhedron P if and only if the tangent cone of P, at v, has non-zero Fourier–Laplace transform.},
author = {Akopyan, Arseniy and Bárány, Imre and Robins, Sinai},
issn = {00018708},
journal = {Advances in Mathematics},
pages = {627 -- 644},
publisher = {Academic Press},
title = {{Algebraic vertices of non-convex polyhedra}},
doi = {10.1016/j.aim.2016.12.026},
volume = {308},
year = {2017},
}
@article{1337,
abstract = {We consider the local eigenvalue distribution of large self-adjoint N×N random matrices H=H∗ with centered independent entries. In contrast to previous works the matrix of variances sij=\mathbbmE|hij|2 is not assumed to be stochastic. Hence the density of states is not the Wigner semicircle law. Its possible shapes are described in the companion paper (Ajanki et al. in Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We show that as N grows, the resolvent, G(z)=(H−z)−1, converges to a diagonal matrix, diag(m(z)), where m(z)=(m1(z),…,mN(z)) solves the vector equation −1/mi(z)=z+∑jsijmj(z) that has been analyzed in Ajanki et al. (Quadratic Vector Equations on the Complex Upper Half Plane. arXiv:1506.05095). We prove a local law down to the smallest spectral resolution scale, and bulk universality for both real symmetric and complex hermitian symmetry classes.},
author = {Ajanki, Oskari H and Erdös, László and Krüger, Torben H},
issn = {01788051},
journal = {Probability Theory and Related Fields},
number = {3-4},
pages = {667 -- 727},
publisher = {Springer},
title = {{Universality for general Wigner-type matrices}},
doi = {10.1007/s00440-016-0740-2},
volume = {169},
year = {2017},
}
@article{1433,
abstract = {Phat is an open-source C. ++ library for the computation of persistent homology by matrix reduction, targeted towards developers of software for topological data analysis. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. We provide numerous different reduction strategies as well as data types to store and manipulate the boundary matrix. We compare the different combinations through extensive experimental evaluation and identify optimization techniques that work well in practical situations. We also compare our software with various other publicly available libraries for persistent homology.},
author = {Bauer, Ulrich and Kerber, Michael and Reininghaus, Jan and Wagner, Hubert},
issn = { 07477171},
journal = {Journal of Symbolic Computation},
pages = {76 -- 90},
publisher = {Academic Press},
title = {{Phat - Persistent homology algorithms toolbox}},
doi = {10.1016/j.jsc.2016.03.008},
volume = {78},
year = {2017},
}
@article{1010,
abstract = {We prove a local law in the bulk of the spectrum for random Gram matrices XX∗, a generalization of sample covariance matrices, where X is a large matrix with independent, centered entries with arbitrary variances. The limiting eigenvalue density that generalizes the Marchenko-Pastur law is determined by solving a system of nonlinear equations. Our entrywise and averaged local laws are on the optimal scale with the optimal error bounds. They hold both in the square case (hard edge) and in the properly rectangular case (soft edge). In the latter case we also establish a macroscopic gap away from zero in the spectrum of XX∗. },
author = {Alt, Johannes and Erdös, László and Krüger, Torben H},
issn = {10836489},
journal = {Electronic Journal of Probability},
publisher = {Institute of Mathematical Statistics},
title = {{Local law for random Gram matrices}},
doi = {10.1214/17-EJP42},
volume = {22},
year = {2017},
}
@article{268,
abstract = {We show that any subset of the squares of positive relative upper density contains nontrivial solutions to a translation-invariant linear equation in five or more variables, with explicit quantitative bounds. As a consequence, we establish the partition regularity of any diagonal quadric in five or more variables whose coefficients sum to zero. Unlike previous approaches, which are limited to equations in seven or more variables, we employ transference technology of Green to import bounds from the linear setting.},
author = {Timothy Browning and Prendiville, Sean M},
journal = {International Mathematics Research Notices},
number = {7},
pages = {2219 -- 2248},
publisher = {Oxford University Press},
title = {{A transference approach to a Roth-type theorem in the squares}},
doi = {10.1093/imrn/rnw096},
volume = {2017},
year = {2017},
}
@article{270,
abstract = {Given a symmetric variety Y defined over Q and a non-zero polynomial with integer coefficients, we use techniques from homogeneous dynamics to establish conditions under which the polynomial can be made r-free for a Zariski dense set of integral points on Y . We also establish an asymptotic counting formula for this set. In the special case that Y is a quadric hypersurface, we give explicit bounds on the size of r by combining the argument with a uniform upper bound for the density of integral points on general affine quadrics defined over Q.},
author = {Timothy Browning and Gorodnik, Alexander},
journal = {Proceedings of the London Mathematical Society},
number = {6},
pages = {1044 -- 1080},
publisher = {Wiley Blackwell},
title = {{Power-free values of polynomials on symmetric varieties}},
doi = {10.1112/plms.12030},
volume = {114},
year = {2017},
}
@article{453,
abstract = {Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor.},
author = {Fallesen, Todd and Roostalu, Johanna and Duellberg, Cristian and Pruessner, Gunnar and Surrey, Thomas},
journal = {Biophysical Journal},
number = {9},
pages = {2055 -- 2067},
publisher = {Biophysical Society},
title = {{Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement}},
doi = {10.1016/j.bpj.2017.09.006},
volume = {113},
year = {2017},
}
@article{472,
abstract = {α-Synuclein is a presynaptic protein the function of which has yet to be identified, but its neuronal content increases in patients of synucleinopa-thies including Parkinson’s disease. Chronic overexpression of α-synuclein reportedly expresses various phenotypes of synaptic dysfunction, but the primary target of its toxicity has not been determined. To investigate this, we acutely loaded human recombinant α-synuclein or its pathological mutants in their monomeric forms into the calyces of Held presynaptic terminals in slices from auditorily mature and immature rats of either sex. Membrane capacitance measurements revealed significant and specific inhibitory effects of WT monomeric α-synuclein on vesicle endocytosis throughout development. However, the α-synuclein A53T mutant affected vesicle endocytosis only at immature calyces, where as the A30P mutant had no effect throughout. The endocytic impairment by WTα-synuclein was rescued by intraterminal coloading of the microtubule (MT) polymerization blocker nocodazole. Furthermore, it was reversibly rescued by presynaptically loaded photostatin-1, a pho-toswitcheable inhibitor of MT polymerization, inalight-wavelength-dependent manner. Incontrast, endocyticinhibition by the A53T mutant at immature calyces was not rescued by nocodazole. Functionally, presynaptically loaded WT α-synuclein had no effect on basal synaptic transmission evoked at a low frequency, but significantly attenuated exocytosis and impaired the fidelity of neurotransmission during prolonged high-frequency stimulation. We conclude that monomeric WTα-synuclein primarily inhibits vesicle endocytosis via MT overassembly, thereby impairing high-frequency neurotransmission.},
author = {Eguchi, Kohgaku and Taoufiq, Zachari and Thorn Seshold, Oliver and Trauner, Dirk and Hasegawa, Masato and Takahashi, Tomoyuki},
issn = {02706474},
journal = {European Journal of Neuroscience},
number = {25},
pages = {6043 -- 6052},
publisher = {Wiley-Blackwell},
title = {{Wild-type monomeric α-synuclein can impair vesicle endocytosis and synaptic fidelity via tubulin polymerization at the calyx of held}},
doi = {10.1523/JNEUROSCI.0179-17.2017},
volume = {37},
year = {2017},
}
@misc{5562,
abstract = {This data was collected as part of the study [1]. It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:
[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408.},
author = {Marre, Olivier and Tkacik, Gasper and Amodei, Dario and Schneidman, Elad and Bialek, William and Berry, Michael},
keyword = {multi-electrode recording, retinal ganglion cells},
publisher = {IST Austria},
title = {{Multi-electrode array recording from salamander retinal ganglion cells}},
doi = {10.15479/AT:ISTA:61},
year = {2017},
}
@misc{5567,
abstract = {Immunological synapse DC-Tcells},
author = {Leithner, Alexander F},
keyword = {Immunological synapse},
publisher = {IST Austria},
title = {{Immunological synapse DC-Tcells}},
doi = {10.15479/AT:ISTA:71},
year = {2017},
}