@article{2251, abstract = {Sharp wave/ripple (SWR, 150–250 Hz) hippocampal events have long been postulated to be involved in memory consolidation. However, more recent work has investigated SWRs that occur during active waking behaviour: findings that suggest that SWRs may also play a role in cell assembly strengthening or spatial working memory. Do such theories of SWR function apply to animal learning? This review discusses how general theories linking SWRs to memory-related function may explain circuit mechanisms related to rodent spatial learning and to the associated stabilization of new cognitive maps.}, author = {Csicsvari, Jozsef L and Dupret, David}, issn = {09628436}, journal = {Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences}, number = {1635}, publisher = {Royal Society, The}, title = {{Sharp wave/ripple network oscillations and learning-associated hippocampal maps}}, doi = {10.1098/rstb.2012.0528}, volume = {369}, year = {2014}, } @article{2252, abstract = {The pattern of inheritance and mechanism of sex determination can have important evolutionary consequences. We studied probabilistic sex determination in the ciliate Tetrahymena thermophila, which was previously shown to cause evolution of skewed sex ratios. We find that the genetic background alters the sex determination patterns of mat alleles in heterozygotes and that allelic interaction can differentially influence the expression probability of the 7 sexes. We quantify the dominance relationships between several mat alleles and find that A-type alleles, which specify sex I, are indeed recessive to B-type alleles, which are unable to specify that sex. Our results provide additional support for the presence of modifier loci and raise implications for the dynamics of sex ratios in populations of T. thermophila.}, author = {Phadke, Sujal and Paixao, Tiago and Pham, Tuan and Pham, Stephanie and Zufall, Rebecca}, issn = {00221503}, journal = {Journal of Heredity}, number = {1}, pages = {130 -- 135}, publisher = {Oxford University Press}, title = {{Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena Thermophila}}, doi = {10.1093/jhered/est063}, volume = {105}, year = {2014}, } @article{2253, abstract = {Plant growth is achieved predominantly by cellular elongation, which is thought to be controlled on several levels by apoplastic auxin. Auxin export into the apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN) and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP) classes; the latter were shown to depend on interaction with the FKBP42, TWISTED DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical, biochemical and cell biological analyses we demonstrate the importance of a putative C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1 gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct) show hypermorphic plant architecture, characterized by enhanced stem length and leaf surface but reduced shoot branching. Greater hypocotyl length is the result of enhanced cell elongation that correlates with reduced polar auxin transport capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl auxin accumulation, which is shown to result in elevated auxin-induced cell elongation rates. Our data highlight the importance of C-terminal membrane anchoring for TWD1 action, which is required for specific regulation of ABCB-mediated auxin transport. These data support a model in which TWD1 controls lateral ABCB1-mediated export into the apoplast, which is required for auxin-mediated cell elongation.}, author = {Bailly, Aurélien and Wang, Bangjun and Zwiewka, Marta and Pollmann, Stephan and Schenck, Daniel and Lüthen, Hartwig and Schulz, Alexander and Friml, Jirí and Geisler, Markus}, issn = {09607412}, journal = {Plant Journal}, number = {1}, pages = {108 -- 118}, publisher = {Wiley-Blackwell}, title = {{Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth}}, doi = {10.1111/tpj.12369}, volume = {77}, year = {2014}, } @article{2254, abstract = {Theta-gamma network oscillations are thought to represent key reference signals for information processing in neuronal ensembles, but the underlying synaptic mechanisms remain unclear. To address this question, we performed whole-cell (WC) patch-clamp recordings from mature hippocampal granule cells (GCs) in vivo in the dentate gyrus of anesthetized and awake rats. GCs in vivo fired action potentials at low frequency, consistent with sparse coding in the dentate gyrus. GCs were exposed to barrages of fast AMPAR-mediated excitatory postsynaptic currents (EPSCs), primarily relayed from the entorhinal cortex, and inhibitory postsynaptic currents (IPSCs), presumably generated by local interneurons. EPSCs exhibited coherence with the field potential predominantly in the theta frequency band, whereas IPSCs showed coherence primarily in the gamma range. Action potentials in GCs were phase locked to network oscillations. Thus, theta-gamma-modulated synaptic currents may provide a framework for sparse temporal coding of information in the dentate gyrus.}, author = {Pernia-Andrade, Alejandro and Jonas, Peter M}, issn = {08966273}, journal = {Neuron}, number = {1}, pages = {140 -- 152}, publisher = {Elsevier}, title = {{Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations}}, doi = {10.1016/j.neuron.2013.09.046}, volume = {81}, year = {2014}, } @article{2255, abstract = {Motivated by applications in biology, we present an algorithm for estimating the length of tube-like shapes in 3-dimensional Euclidean space. In a first step, we combine the tube formula of Weyl with integral geometric methods to obtain an integral representation of the length, which we approximate using a variant of the Koksma-Hlawka Theorem. In a second step, we use tools from computational topology to decrease the dependence on small perturbations of the shape. We present computational experiments that shed light on the stability and the convergence rate of our algorithm.}, author = {Edelsbrunner, Herbert and Pausinger, Florian}, issn = {09249907}, journal = {Journal of Mathematical Imaging and Vision}, number = {1}, pages = {164 -- 177}, publisher = {Springer}, title = {{Stable length estimates of tube-like shapes}}, doi = {10.1007/s10851-013-0468-x}, volume = {50}, year = {2014}, } @article{2257, abstract = {Maximum entropy models are the least structured probability distributions that exactly reproduce a chosen set of statistics measured in an interacting network. Here we use this principle to construct probabilistic models which describe the correlated spiking activity of populations of up to 120 neurons in the salamander retina as it responds to natural movies. Already in groups as small as 10 neurons, interactions between spikes can no longer be regarded as small perturbations in an otherwise independent system; for 40 or more neurons pairwise interactions need to be supplemented by a global interaction that controls the distribution of synchrony in the population. Here we show that such “K-pairwise” models—being systematic extensions of the previously used pairwise Ising models—provide an excellent account of the data. We explore the properties of the neural vocabulary by: 1) estimating its entropy, which constrains the population's capacity to represent visual information; 2) classifying activity patterns into a small set of metastable collective modes; 3) showing that the neural codeword ensembles are extremely inhomogenous; 4) demonstrating that the state of individual neurons is highly predictable from the rest of the population, allowing the capacity for error correction.}, author = {Tkacik, Gasper and Marre, Olivier and Amodei, Dario and Schneidman, Elad and Bialek, William and Berry, Michael}, issn = {1553734X}, journal = {PLoS Computational Biology}, number = {1}, publisher = {Public Library of Science}, title = {{Searching for collective behavior in a large network of sensory neurons}}, doi = {10.1371/journal.pcbi.1003408}, volume = {10}, year = {2014}, } @article{2261, abstract = {To reveal the full potential of human pluripotent stem cells, new methods for rapid, site-specific genomic engineering are needed. Here, we describe a system for precise genetic modification of human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). We identified a novel human locus, H11, located in a safe, intergenic, transcriptionally active region of chromosome 22, as the recipient site, to provide robust, ubiquitous expression of inserted genes. Recipient cell lines were established by site-specific placement of a ‘landing pad’ cassette carrying attP sites for phiC31 and Bxb1 integrases at the H11 locus by spontaneous or TALEN-assisted homologous recombination. Dual integrase cassette exchange (DICE) mediated by phiC31 and Bxb1 integrases was used to insert genes of interest flanked by phiC31 and Bxb1 attB sites at the H11 locus, replacing the landing pad. This system provided complete control over content, direction and copy number of inserted genes, with a specificity of 100%. A series of genes, including mCherry and various combinations of the neural transcription factors LMX1a, FOXA2 and OTX2, were inserted in recipient cell lines derived from H9 ESC, as well as iPSC lines derived from a Parkinson’s disease patient and a normal sibling control. The DICE system offers rapid, efficient and precise gene insertion in ESC and iPSC and is particularly well suited for repeated modifications of the same locus.}, author = {Zhu, Fangfang and Gamboa, Matthew and Farruggio, Alfonso and Hippenmeyer, Simon and Tasic, Bosiljka and Schüle, Birgitt and Chen Tsai, Yanru and Calos, Michele}, journal = {Nucleic Acids Research}, number = {5}, publisher = {Oxford University Press}, title = {{DICE, an efficient system for iterative genomic editing in human pluripotent stem cells}}, doi = {10.1093/nar/gkt1290}, volume = {42}, year = {2014}, } @inbook{2265, abstract = {Coordinated migration of newly-born neurons to their target territories is essential for correct neuronal circuit assembly in the developing brain. Although a cohort of signaling pathways has been implicated in the regulation of cortical projection neuron migration, the precise molecular mechanisms and how a balanced interplay of cell-autonomous and non-autonomous functions of candidate signaling molecules controls the discrete steps in the migration process, are just being revealed. In this chapter, I will focally review recent advances that improved our understanding of the cell-autonomous and possible cell-nonautonomous functions of the evolutionarily conserved LIS1/NDEL1-complex in regulating the sequential steps of cortical projection neuron migration. I will then elaborate on the emerging concept that the Reelin signaling pathway, acts exactly at precise stages in the course of cortical projection neuron migration. Lastly, I will discuss how finely tuned transcriptional programs and downstream effectors govern particular aspects in driving radial migration at discrete stages and how they regulate the precise positioning of cortical projection neurons in the developing cerebral cortex.}, author = {Hippenmeyer, Simon}, booktitle = { Cellular and Molecular Control of Neuronal Migration}, editor = {Nguyen, Laurent}, pages = {1 -- 24}, publisher = {Springer}, title = {{Molecular pathways controlling the sequential steps of cortical projection neuron migration}}, doi = {10.1007/978-94-007-7687-6_1}, volume = {800}, year = {2014}, } @inproceedings{2275, abstract = {Energies with high-order non-submodular interactions have been shown to be very useful in vision due to their high modeling power. Optimization of such energies, however, is generally NP-hard. A naive approach that works for small problem instances is exhaustive search, that is, enumeration of all possible labelings of the underlying graph. We propose a general minimization approach for large graphs based on enumeration of labelings of certain small patches. This partial enumeration technique reduces complex high-order energy formulations to pairwise Constraint Satisfaction Problems with unary costs (uCSP), which can be efficiently solved using standard methods like TRW-S. Our approach outperforms a number of existing state-of-the-art algorithms on well known difficult problems (e.g. curvature regularization, stereo, deconvolution); it gives near global minimum and better speed. Our main application of interest is curvature regularization. In the context of segmentation, our partial enumeration technique allows to evaluate curvature directly on small patches using a novel integral geometry approach. }, author = {Olsson, Carl and Ulen, Johannes and Boykov, Yuri and Kolmogorov, Vladimir}, location = {Sydney, Australia}, pages = {2936 -- 2943}, publisher = {IEEE}, title = {{Partial enumeration and curvature regularization}}, doi = {10.1109/ICCV.2013.365}, year = {2014}, } @article{2281, abstract = {We consider two-dimensional Bose-Einstein condensates with attractive interaction, described by the Gross-Pitaevskii functional. Minimizers of this functional exist only if the interaction strength a satisfies {Mathematical expression}, where Q is the unique positive radial solution of {Mathematical expression} in {Mathematical expression}. We present a detailed analysis of the behavior of minimizers as a approaches a*, where all the mass concentrates at a global minimum of the trapping potential.}, author = {Guo, Yujin and Seiringer, Robert}, journal = {Letters in Mathematical Physics}, number = {2}, pages = {141 -- 156}, publisher = {Springer}, title = {{On the mass concentration for Bose-Einstein condensates with attractive interactions}}, doi = {10.1007/s11005-013-0667-9}, volume = {104}, year = {2014}, } @article{2285, abstract = {GABAergic inhibitory interneurons control fundamental aspects of neuronal network function. Their functional roles are assumed to be defined by the identity of their input synapses, the architecture of their dendritic tree, the passive and active membrane properties and finally the nature of their postsynaptic targets. Indeed, interneurons display a high degree of morphological and physiological heterogeneity. However, whether their morphological and physiological characteristics are correlated and whether interneuron diversity can be described by a continuum of GABAergic cell types or by distinct classes has remained unclear. Here we perform a detailed morphological and physiological characterization of GABAergic cells in the dentate gyrus, the input region of the hippocampus. To achieve an unbiased and efficient sampling and classification we used knock-in mice expressing the enhanced green fluorescent protein (eGFP) in glutamate decarboxylase 67 (GAD67)-positive neurons and performed cluster analysis. We identified five interneuron classes, each of them characterized by a distinct set of anatomical and physiological parameters. Cross-correlation analysis further revealed a direct relation between morphological and physiological properties indicating that dentate gyrus interneurons fall into functionally distinct classes which may differentially control neuronal network activity.}, author = {Hosp, Jonas and Strüber, Michael and Yanagawa, Yuchio and Obata, Kunihiko and Vida, Imre and Jonas, Peter M and Bartos, Marlene}, journal = {Hippocampus}, number = {2}, pages = {189 -- 203}, publisher = {Wiley-Blackwell}, title = {{Morpho-physiological criteria divide dentate gyrus interneurons into classes}}, doi = {10.1002/hipo.22214}, volume = {23}, year = {2014}, } @article{2407, abstract = {Two definitions of the effective mass of a particle interacting with a quantum field, such as a polaron, are considered and shown to be equal in models similar to the Fröhlich polaron model. These are: 1. the mass defined by the low momentum energy E(P)≈E(0)+P2/2 M of the translation invariant system constrained to have momentum P and 2. the mass M of a simple particle in an arbitrary slowly varying external potential, V, described by the nonrelativistic Schrödinger equation, whose ground state energy equals that of the combined particle/field system in a bound state in the same V.}, author = {Lieb, Élliott and Seiringer, Robert}, journal = {Journal of Statistical Physics}, number = {1-2}, pages = {51 -- 57}, publisher = {Springer}, title = {{Equivalence of two definitions of the effective mass of a polaron}}, doi = {10.1007/s10955-013-0791-z}, volume = {154}, year = {2014}, } @article{6739, abstract = {We explore the relationship between polar and RM codes and we describe a coding scheme which improves upon the performance of the standard polar code at practical block lengths. Our starting point is the experimental observation that RM codes have a smaller error probability than polar codes under MAP decoding. This motivates us to introduce a family of codes that “interpolates” between RM and polar codes, call this family C inter = {C α : α ∈ [0, 1j}, where C α|α=1 is the original polar code, and C α|α=0 is an RM code. Based on numerical observations, we remark that the error probability under MAP decoding is an increasing function of α. MAP decoding has in general exponential complexity, but empirically the performance of polar codes at finite block lengths is boosted by moving along the family Cinter even under low-complexity decoding schemes such as, for instance, belief propagation or successive cancellation list decoder. We demonstrate the performance gain via numerical simulations for transmission over the erasure channel as well as the Gaussian channel.}, author = {Mondelli, Marco and Hassani, Hamed and Urbanke, Rudiger}, issn = {0090-6778}, journal = {IEEE Transactions on Communications}, number = {9}, pages = {3084--3091}, publisher = {IEEE}, title = {{From polar to Reed-Muller codes: A technique to improve the finite-length performance}}, doi = {10.1109/tcomm.2014.2345069}, volume = {62}, year = {2014}, } @inproceedings{6740, abstract = {We describe coding techniques that achieve the capacity of a discrete memoryless asymmetric channel. To do so, we discuss how recent advances in coding for symmetric channels yield more efficient solutions also for the asymmetric case. In more detail, we consider three basic approaches. The first one is Gallager's scheme that concatenates a linear code with a non-linear mapper, in order to bias the input distribution. We explicitly show that both polar codes and spatially coupled codes can be employed in this scenario. Further, we derive a scaling law between the gap to capacity, the cardinality of channel input and output alphabets, and the required size of the mapper. The second one is an integrated approach in which the coding scheme is used both for source coding, in order to create codewords with the capacity-achieving distribution, and for channel coding, in order to provide error protection. Such a technique has been recently introduced by Honda and Yamamoto in the context of polar codes, and we show how to apply it also to the design of sparse graph codes. The third approach is based on an idea due to Böcherer and Mathar and separates completely the two tasks of source coding and channel coding by “chaining” together several codewords. We prove that we can combine any suitable source code with any suitable channel code in order to provide optimal schemes for asymmetric channels. In particular, polar codes and spatially coupled codes fulfill the required conditions.}, author = {Mondelli, Marco and Urbanke, Rudiger and Hassani, Hamed}, booktitle = {52nd Annual Allerton Conference on Communication, Control, and Computing}, location = {Monticello, IL, United States}, pages = {789--796}, publisher = {IEEE}, title = {{How to achieve the capacity of asymmetric channels}}, doi = {10.1109/allerton.2014.7028535}, year = {2014}, } @article{6744, abstract = {With the aim of extending the coverage and improving the performance of impulse radio ultra-wideband (UWB) systems, this paper focuses on developing a novel single differential encoded decode and forward (DF) non-cooperative relaying scheme (NCR). To favor simple receiver structures, differential noncoherent detection is employed which enables effective energy capture without any channel estimation. Putting emphasis on the general case of multi-hop relaying, we illustrate an original algorithm for the joint power allocation and path selection (JPAPS), minimizing an approximate expression of the overall bit error rate (BER). In particular, after deriving a closed-form power allocation strategy, the optimal path selection is reduced to a shortest path problem on a connected graph, which can be solved without any topology information with complexity O(N 3 ), N being the number of available relays of the network. An approximate scheme is also presented, which reduces the complexity to O(N 2 ) while showing a negligible performance loss, and for benchmarking purposes, an exhaustive-search based multi-hop DF cooperative strategy is derived. Simulation results for various network setups corroborate the effectiveness of the proposed low-complexity JPAPS algorithm, which favorably compares to existing AF and DF relaying methods.}, author = {Mondelli, Marco and Zhou, Qi and Lottici, Vincenzo and Ma, Xiaoli}, journal = {IEEE Transactions on Wireless Communications}, number = {3}, pages = {1397--1409}, publisher = {IEEE}, title = {{Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications}}, doi = {10.1109/twc.2014.020914.130669}, volume = {13}, year = {2014}, } @book{6853, abstract = {This monograph presents a short course in computational geometry and topology. In the first part the book covers Voronoi diagrams and Delaunay triangulations, then it presents the theory of alpha complexes which play a crucial role in biology. The central part of the book is the homology theory and their computation, including the theory of persistence which is indispensable for applications, e.g. shape reconstruction. The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields.}, author = {Edelsbrunner, Herbert}, isbn = {9-783-3190-5956-3}, issn = {2191-5318}, pages = {IX, 110}, publisher = {Springer Nature}, title = {{A Short Course in Computational Geometry and Topology}}, doi = {10.1007/978-3-319-05957-0}, year = {2014}, } @techreport{7038, author = {Huszár, Kristóf and Rolinek, Michal}, pages = {5}, publisher = {IST Austria}, title = {{Playful Math - An introduction to mathematical games}}, year = {2014}, } @article{7071, abstract = {Spin and orbital quantum numbers play a key role in the physics of Mott insulators, but in most systems they are connected only indirectly—via the Pauli exclusion principle and the Coulomb interaction. Iridium-based oxides (iridates) introduce strong spin–orbit coupling directly, such that these numbers become entwined together and the Mott physics attains a strong orbital character. In the layered honeycomb iridates this is thought to generate highly spin–anisotropic magnetic interactions, coupling the spin to a given spatial direction of exchange and leading to strongly frustrated magnetism. Here we report a new iridate structure that has the same local connectivity as the layered honeycomb and exhibits striking evidence for highly spin–anisotropic exchange. The basic structural units of this material suggest that a new family of three-dimensional structures could exist, the ‘harmonic honeycomb’ iridates, of which the present compound is the first example.}, author = {Modic, Kimberly A and Smidt, Tess E. and Kimchi, Itamar and Breznay, Nicholas P. and Biffin, Alun and Choi, Sungkyun and Johnson, Roger D. and Coldea, Radu and Watkins-Curry, Pilanda and McCandless, Gregory T. and Chan, Julia Y. and Gandara, Felipe and Islam, Z. and Vishwanath, Ashvin and Shekhter, Arkady and McDonald, Ross D. and Analytis, James G.}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Science and Business Media LLC}, title = {{Realization of a three-dimensional spin–anisotropic harmonic honeycomb iridate}}, doi = {10.1038/ncomms5203}, volume = {5}, year = {2014}, } @article{7072, abstract = {We investigate the structural and magnetic properties of two molecule-based magnets synthesized from the same starting components. Their different structural motifs promote contrasting exchange pathways and consequently lead to markedly different magnetic ground states. Through examination of their structural and magnetic properties we show that [Cu(pyz)(H2O)(gly)2](ClO4)2 may be considered a quasi-one-dimensional quantum Heisenberg antiferromagnet whereas the related compound [Cu(pyz)(gly)](ClO4), which is formed from dimers of antiferromagnetically interacting Cu2+ spins, remains disordered down to at least 0.03 K in zero field but shows a field-temperature phase diagram reminiscent of that seen in materials showing a Bose-Einstein condensation of magnons.}, author = {Lancaster, T. and Goddard, P. A. and Blundell, S. J. and Foronda, F. R. and Ghannadzadeh, S. and Möller, J. S. and Baker, P. J. and Pratt, F. L. and Baines, C. and Huang, L. and Wosnitza, J. and McDonald, R. D. and Modic, Kimberly A and Singleton, J. and Topping, C. V. and Beale, T. A. W. and Xiao, F. and Schlueter, J. A. and Barton, A. M. and Cabrera, R. D. and Carreiro, K. E. and Tran, H. E. and Manson, J. L.}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {20}, publisher = {APS}, title = {{Controlling magnetic order and quantum disorder in molecule-based magnets}}, doi = {10.1103/physrevlett.112.207201}, volume = {112}, year = {2014}, } @article{7300, abstract = {Photoinduced electron transfer (PET), which causes pH-dependent quenching of fluorescent dyes, is more effectively introduced by phenolic groups than by amino groups which have been much more commonly used so far. That is demonstrated by fluorescence measurements involving several classes of fluorophores. Electrochemical measurements show that PET in several amino-modified dyes is thermodynamically favorable, even though it was not experimentally found, underlining the importance of kinetic aspects to the process. Consequently, the attachment of phenolic groups allows for fast and simple preparation of a wide selection of fluorescent pH-probes with tailor-made spectral properties, sensitive ranges, and individual advantages, so that a large number of applications can be realized. Fluorophores carrying phenolic groups may also be used for sensing analytes other than pH or molecular switching and signaling.}, author = {Aigner, Daniel and Freunberger, Stefan Alexander and Wilkening, Martin and Saf, Robert and Borisov, Sergey M. and Klimant, Ingo}, issn = {0003-2700}, journal = {Analytical Chemistry}, number = {18}, pages = {9293--9300}, publisher = {ACS}, title = {{Enhancing photoinduced electron transfer efficiency of fluorescent pH-probes with halogenated phenols}}, doi = {10.1021/ac502513g}, volume = {86}, year = {2014}, }