TY - CONF AB - In classical machine learning, regression is treated as a black box process of identifying a suitable function from a hypothesis set without attempting to gain insight into the mechanism connecting inputs and outputs. In the natural sciences, however, finding an interpretable function for a phenomenon is the prime goal as it allows to understand and generalize results. This paper proposes a novel type of function learning network, called equation learner (EQL), that can learn analytical expressions and is able to extrapolate to unseen domains. It is implemented as an end-to-end differentiable feed-forward network and allows for efficient gradient based training. Due to sparsity regularization concise interpretable expressions can be obtained. Often the true underlying source expression is identified. AU - Martius, Georg S AU - Lampert, Christoph ID - 6841 T2 - 5th International Conference on Learning Representations, ICLR 2017 - Workshop Track Proceedings TI - Extrapolation and learning equations ER - TY - JOUR AB - We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic. AU - Chatterjee, Krishnendu AU - Piterman, Nir ID - 684 IS - 2 JF - Journal of Symbolic Logic SN - 0022-4812 TI - Obligation blackwell games and p-automata VL - 82 ER - TY - JOUR AB - By applying methods and principles from the physical sciences to biological problems, D'Arcy Thompson's On Growth and Form demonstrated how mathematical reasoning reveals elegant, simple explanations for seemingly complex processes. This has had a profound influence on subsequent generations of developmental biologists. We discuss how this influence can be traced through twentieth century morphologists, embryologists and theoreticians to current research that explores the molecular and cellular mechanisms of tissue growth and patterning, including our own studies of the vertebrate neural tube. AU - Briscoe, James AU - Kicheva, Anna ID - 685 JF - Mechanisms of Development SN - 09254773 TI - The physics of development 100 years after D'Arcy Thompson's “on growth and form” VL - 145 ER - TY - CONF AB - We show that the framework of topological data analysis can be extended from metrics to general Bregman divergences, widening the scope of possible applications. Examples are the Kullback - Leibler divergence, which is commonly used for comparing text and images, and the Itakura - Saito divergence, popular for speech and sound. In particular, we prove that appropriately generalized čech and Delaunay (alpha) complexes capture the correct homotopy type, namely that of the corresponding union of Bregman balls. Consequently, their filtrations give the correct persistence diagram, namely the one generated by the uniformly growing Bregman balls. Moreover, we show that unlike the metric setting, the filtration of Vietoris-Rips complexes may fail to approximate the persistence diagram. We propose algorithms to compute the thus generalized čech, Vietoris-Rips and Delaunay complexes and experimentally test their efficiency. Lastly, we explain their surprisingly good performance by making a connection with discrete Morse theory. AU - Edelsbrunner, Herbert AU - Wagner, Hubert ID - 688 SN - 18688969 TI - Topological data analysis with Bregman divergences VL - 77 ER - TY - JOUR AB - Pursuing the similarity between the Kontsevich-Soibelman construction of the cohomological Hall algebra (CoHA) of BPS states and Lusztig's construction of canonical bases for quantum enveloping algebras, and the similarity between the integrality conjecture for motivic Donaldson-Thomas invariants and the PBW theorem for quantum enveloping algebras, we build a coproduct on the CoHA associated to a quiver with potential. We also prove a cohomological dimensional reduction theorem, further linking a special class of CoHAs with Yangians, and explaining how to connect the study of character varieties with the study of CoHAs. AU - Davison, Ben ID - 687 IS - 2 JF - Quarterly Journal of Mathematics SN - 00335606 TI - The critical CoHA of a quiver with potential VL - 68 ER - TY - JOUR AB - Tissues are thought to behave like fluids with a given surface tension. Differences in tissue surface tension (TST) have been proposed to trigger cell sorting and tissue envelopment. D'Arcy Thompson in his seminal book ‘On Growth and Form’ has introduced this concept of differential TST as a key physical mechanism dictating tissue formation and organization within the developing organism. Over the past century, many studies have picked up the concept of differential TST and analyzed the role and cell biological basis of TST in development, underlining the importance and influence of this concept in developmental biology. AU - Heisenberg, Carl-Philipp J ID - 686 JF - Mechanisms of Development SN - 09254773 TI - D'Arcy Thompson's ‘on growth and form’: From soap bubbles to tissue self organization VL - 145 ER - TY - JOUR AB - Rett syndrome modeling in monkey mirrors the human disorder. AU - Novarino, Gaia ID - 689 IS - 393 JF - Science Translational Medicine SN - 19466234 TI - Rett syndrome modeling goes simian VL - 9 ER - TY - JOUR AB - Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. AU - Miki, Takafumi AU - Kaufmann, Walter AU - Malagon, Gerardo AU - Gomez, Laura AU - Tabuchi, Katsuhiko AU - Watanabe, Masahiko AU - Shigemoto, Ryuichi AU - Marty, Alain ID - 693 IS - 26 JF - PNAS SN - 00278424 TI - Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses VL - 114 ER - TY - CONF AB - LCLs or locally checkable labelling problems (e.g. maximal independent set, maximal matching, and vertex colouring) in the LOCAL model of computation are very well-understood in cycles (toroidal 1-dimensional grids): every problem has a complexity of O(1), Θ(log* n), or Θ(n), and the design of optimal algorithms can be fully automated. This work develops the complexity theory of LCL problems for toroidal 2-dimensional grids. The complexity classes are the same as in the 1-dimensional case: O(1), Θ(log* n), and Θ(n). However, given an LCL problem it is undecidable whether its complexity is Θ(log* n) or Θ(n) in 2-dimensional grids. Nevertheless, if we correctly guess that the complexity of a problem is Θ(log* n), we can completely automate the design of optimal algorithms. For any problem we can find an algorithm that is of a normal form A' o Sk, where A' is a finite function, Sk is an algorithm for finding a maximal independent set in kth power of the grid, and k is a constant. Finally, partially with the help of automated design tools, we classify the complexity of several concrete LCL problems related to colourings and orientations. AU - Brandt, Sebastian AU - Hirvonen, Juho AU - Korhonen, Janne H. AU - Lempiäinen, Tuomo AU - Östergård, Patric R.J. AU - Purcell, Christopher AU - Rybicki, Joel AU - Suomela, Jukka AU - Uznański, Przemysław ID - 6932 SN - 9781450349925 TI - LCL problems on grids ER - TY - JOUR AB - A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells. AU - Veß, Astrid AU - Blache, Ulrich AU - Leitner, Laura AU - Kurz, Angela AU - Ehrenpfordt, Anja AU - Sixt, Michael K AU - Posern, Guido ID - 694 IS - 13 JF - Journal of Cell Science SN - 00219533 TI - A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity VL - 130 ER - TY - JOUR AB - It has been known since Stefan Vogel's observations in 1969 that solitary female oil bees collect fatty floral oils from specialized oil-secreting plants with the aid of hairy patches on either their legs or abdomen, a reward used as food for their larvae and/or to line their brood cells. Similar adaptations are also known from male oil bees, although the purpose of their oil-collecting behavior has not yet been clarified. Here, we describe a novel pollination system involving male Paratetrapedia oil bees and the tropical herb Anthurium acutifolium. We present ultrastructural morphological details of bee and plant structures involved in this interaction and the composition of floral scents likely mediating pollinator attraction. Inflorescences of A. acutifolium were visited almost exclusively by male P. chocoensis oil bees. The bees mopped with a hairy patch of their abdominal sterna 3 across the inflorescence surface. During this activity on both staminate and pistillate stage inflorescences, bees’ abdomens and legs became loaded with pollen and contacted receptive stigmas. In contrast to what has been observed in other angiosperms visited for the collection of fatty floral oils, the inflorescences/flowers of A. acutifolium do not have structures specialized in oil secretion, i.e., elaiophores. These inflorescences, nonetheless, were strongly scented during the time interval they were visited by the bees. Gas chromatography/mass spectrometry (GC/MS) analyses of dynamic headspace floral samples revealed that inflorescences of both anthetic phases emitted scent bouquets consisting mainly of aliphatic esters, indole and uncommmon terpenoids (megastigmanes). Interestingly enough, our data suggest that the unusual floral scent of A. acutifolium is a perfume reward collected by male P. chocoensis oil bees. This pollination system thus bears a remarkable resemblence with the interactions between perfume-collecting male euglossine bees and their preferred flowers, discovered by Stefan Vogel half a century ago. AU - Etl, Florian AU - Franschitz, Anna AU - Aguiar, Antonio AU - Schönenberger, Jürg AU - Dötterl, Stefan ID - 695 JF - Flora: Morphology, Distribution, Functional Ecology of Plants SN - 03672530 TI - A perfume collecting male oil bee? Evidences of a novel pollination system involving Anthurium acutifolium Araceae and Paratetrapedia chocoensis Apidae Tapinotaspidini VL - 232 ER - TY - CONF AB - De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. AU - Pietrzak, Krzysztof Z AU - Skórski, Maciej ID - 697 SN - 18688969 TI - Non uniform attacks against pseudoentropy VL - 80 ER - TY - JOUR AB - Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. AU - Wang, Yejun AU - Nagarajan, Mallika AU - Uhler, Caroline AU - Shivashankar, Gv ID - 698 IS - 14 JF - Molecular Biology of the Cell SN - 10591524 TI - Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression VL - 28 ER - TY - JOUR AB - In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. AU - Veller, Carl AU - Hayward, Laura AU - Nowak, Martin AU - Hilbe, Christian ID - 699 IS - 27 JF - PNAS SN - 00278424 TI - The red queen and king in finite populations VL - 114 ER - TY - JOUR AB - Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs. AU - Barzanjeh, Shabir AU - Salari, Vahid AU - Tuszynski, Jack AU - Cifra, Michal AU - Simon, Christoph ID - 700 IS - 1 JF - Physical Review E Statistical Nonlinear and Soft Matter Physics SN - 24700045 TI - Optomechanical proposal for monitoring microtubule mechanical vibrations VL - 96 ER - TY - JOUR AB - A d-dimensional simplex S is called a k-reptile (or a k-reptile simplex) if it can be tiled by k simplices with disjoint interiors that are all mutually congruent and similar to S. For d = 2, triangular k-reptiles exist for all k of the form a^2, 3a^2 or a^2+b^2 and they have been completely characterized by Snover, Waiveris, and Williams. On the other hand, the only k-reptile simplices that are known for d ≥ 3, have k = m^d, where m is a positive integer. We substantially simplify the proof by Matoušek and the second author that for d = 3, k-reptile tetrahedra can exist only for k = m^3. We then prove a weaker analogue of this result for d = 4 by showing that four-dimensional k-reptile simplices can exist only for k = m^2. AU - Kynčl, Jan AU - Patakova, Zuzana ID - 701 IS - 3 JF - The Electronic Journal of Combinatorics SN - 10778926 TI - On the nonexistence of k reptile simplices in ℝ^3 and ℝ^4 VL - 24 ER - TY - JOUR AB - Leading autism-associated mutation in mouse partially mimics human disorder. AU - Novarino, Gaia ID - 702 IS - 399 JF - Science Translational Medicine SN - 19466234 TI - The riddle of CHD8 haploinsufficiency in autism spectrum disorder VL - 9 ER - TY - JOUR AB - A hippocampal mossy fiber synapse has a complex structure and is implicated in learning and memory. In this synapse, the mossy fiber boutons attach to the dendritic shaft by puncta adherentia junctions and wrap around a multiply-branched spine, forming synaptic junctions. We have recently shown using transmission electron microscopy, immunoelectron microscopy and serial block face-scanning electron microscopy that atypical puncta adherentia junctions are formed in the afadin-deficient mossy fiber synapse and that the complexity of postsynaptic spines and mossy fiber boutons, the number of spine heads, the area of postsynaptic densities and the density of synaptic vesicles docked to active zones are decreased in the afadin-deficient synapse. We investigated here the roles of afadin in the functional differentiations of the mossy fiber synapse using the afadin-deficient mice. The electrophysiological studies showed that both the release probability of glutamate and the postsynaptic responsiveness to glutamate were markedly reduced, but not completely lost, in the afadin-deficient mossy fiber synapse, whereas neither long-term potentiation nor long-term depression was affected. These results indicate that afadin plays roles in the functional differentiations of the presynapse and the postsynapse of the hippocampal mossy fiber synapse. AU - Geng, Xiaoqi AU - Maruo, Tomohiko AU - Mandai, Kenji AU - Supriyanto, Irwan AU - Miyata, Muneaki AU - Sakakibara, Shotaro AU - Mizoguchi, Akira AU - Takai, Yoshimi AU - Mori, Masahiro ID - 706 IS - 8 JF - Genes to Cells SN - 13569597 TI - Roles of afadin in functional differentiations of hippocampal mossy fiber synapse VL - 22 ER - TY - JOUR AB - The complex antiferromagnetic orders observed in the honeycomb iridates are a double-edged sword in the search for a quantum spin-liquid: both attesting that the magnetic interactions provide many of the necessary ingredients, while simultaneously impeding access. Focus has naturally been drawn to the unusual magnetic orders that hint at the underlying spin correlations. However, the study of any particular broken symmetry state generally provides little clue about the possibility of other nearby ground states. Here we use magnetic fields approaching 100 Tesla to reveal the extent of the spin correlations in γ-lithium iridate. We find that a small component of field along the magnetic easy-axis melts long-range order, revealing a bistable, strongly correlated spin state. Far from the usual destruction of antiferromagnetism via spin polarization, the high-field state possesses only a small fraction of the total iridium moment, without evidence for long-range order up to the highest attainable magnetic fields. AU - Modic, Kimberly A AU - Ramshaw, B. J. AU - Betts, J. B. AU - Breznay, Nicholas P. AU - Analytis, James G. AU - McDonald, Ross D. AU - Shekhter, Arkady ID - 7064 IS - 1 JF - Nature Communications SN - 2041-1723 TI - Robust spin correlations at high magnetic fields in the harmonic honeycomb iridates VL - 8 ER - TY - JOUR AB - Broken fourfold rotational (C4) symmetry is observed in the experimental properties of several classes of unconventional superconductors. It has been proposed that this symmetry breaking is important for superconducting pairing in these materials, but in the high-Tc cuprates this broken symmetry has never been observed on the Fermi surface. Here we report a pronounced anisotropy in the angle dependence of the interlayer magnetoresistance of the underdoped high transition temperature (high-Tc) superconductor YBa2Cu3O6.58, directly revealing broken C4 symmetry on the Fermi surface. Moreover, we demonstrate that this Fermi surface has C2 symmetry of the type produced by a uniaxial or anisotropic density-wave phase. This establishes the central role of C4 symmetry breaking in the Fermi surface reconstruction of YBa2Cu3O6+δ , and suggests a striking degree of universality among unconventional superconductors. AU - Ramshaw, B. J. AU - Harrison, N. AU - Sebastian, S. E. AU - Ghannadzadeh, S. AU - Modic, Kimberly A AU - Bonn, D. A. AU - Hardy, W. N. AU - Liang, Ruixing AU - Goddard, P. A. ID - 7067 IS - 1 JF - npj Quantum Materials SN - 2397-4648 TI - Broken rotational symmetry on the Fermi surface of a high-Tc superconductor VL - 2 ER -