@article{1569, abstract = {Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development.}, author = {Doyle, Siamsa and Haegera, Ash and Vain, Thomas and Rigala, Adeline and Viotti, Corrado and Łangowskaa, Małgorzata and Maa, Qian and Friml, Jirí and Raikhel, Natasha and Hickse, Glenn and Robert, Stéphanie}, journal = {PNAS}, number = {7}, pages = {E806 -- E815}, publisher = {National Academy of Sciences}, title = {{An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana}}, doi = {10.1073/pnas.1424856112}, volume = {112}, year = {2015}, } @article{1570, abstract = {Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution.}, author = {Der, Ralf and Martius, Georg S}, journal = {PNAS}, number = {45}, pages = {E6224 -- E6232}, publisher = {National Academy of Sciences}, title = {{Novel plasticity rule can explain the development of sensorimotor intelligence}}, doi = {10.1073/pnas.1508400112}, volume = {112}, year = {2015}, } @article{1571, abstract = {Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype-environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor-operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that crossenvironmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance.}, author = {De Vos, Marjon and Dawid, Alexandre and Šunderlíková, Vanda and Tans, Sander}, journal = {PNAS}, number = {48}, pages = {14906 -- 14911}, publisher = {National Academy of Sciences}, title = {{Breaking evolutionary constraint with a tradeoff ratchet}}, doi = {10.1073/pnas.1510282112}, volume = {112}, year = {2015}, } @article{1572, abstract = {We consider the quantum ferromagnetic Heisenberg model in three dimensions, for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation for the excitation spectrum, at the level of the first non-trivial contribution to the free energy at low temperatures. Our proof comes with explicit, constructive upper and lower bounds on the error term. It uses in an essential way the bosonic formulation of the model in terms of the Holstein-Primakoff representation. In this language, the model describes interacting bosons with a hard-core on-site repulsion and a nearest-neighbor attraction. This attractive interaction makes the lower bound on the free energy particularly tricky: the key idea there is to prove a differential inequality for the two-particle density, which is thereby shown to be smaller than the probability density of a suitably weighted two-particle random process on the lattice. }, author = {Correggi, Michele and Giuliani, Alessandro and Seiringer, Robert}, journal = {Communications in Mathematical Physics}, number = {1}, pages = {279 -- 307}, publisher = {Springer}, title = {{Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet}}, doi = {10.1007/s00220-015-2402-0}, volume = {339}, year = {2015}, } @article{1573, abstract = {We present a new, simpler proof of the unconditional uniqueness of solutions to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis is the quantum de Finetti theorem. Our uniqueness result is equivalent to the one established in the celebrated works of Erdos, Schlein, and Yau.}, author = {Chen, Thomas and Hainzl, Christian and Pavlović, Nataša and Seiringer, Robert}, journal = {Communications on Pure and Applied Mathematics}, number = {10}, pages = {1845 -- 1884}, publisher = {Wiley}, title = {{Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti}}, doi = {10.1002/cpa.21552}, volume = {68}, year = {2015}, } @article{1580, abstract = {Synapsins (Syns) are an evolutionarily conserved family of presynaptic proteins crucial for the fine-tuning of synaptic function. A large amount of experimental evidences has shown that Syns are involved in the development of epileptic phenotypes and several mutations in Syn genes have been associated with epilepsy in humans and animal models. Syn mutations induce alterations in circuitry and neurotransmitter release, differentially affecting excitatory and inhibitory synapses, thus causing an excitation/inhibition imbalance in network excitability toward hyperexcitability that may be a determinant with regard to the development of epilepsy. Another approach to investigate epileptogenic mechanisms is to understand how silencing Syn affects the cellular behavior of single neurons and is associated with the hyperexcitable phenotypes observed in epilepsy. Here, we examined the functional effects of antisense-RNA inhibition of Syn expression on individually identified and isolated serotonergic cells of the Helix land snail. We found that Helix synapsin silencing increases cell excitability characterized by a slightly depolarized resting membrane potential, decreases the rheobase, reduces the threshold for action potential (AP) firing and increases the mean and instantaneous firing rates, with respect to control cells. The observed increase of Ca2+ and BK currents in Syn-silenced cells seems to be related to changes in the shape of the AP waveform. These currents sustain the faster spiking in Syn-deficient cells by increasing the after hyperpolarization and limiting the Na+ and Ca2+ channel inactivation during repetitive firing. This in turn speeds up the depolarization phase by reaching the AP threshold faster. Our results provide evidence that Syn silencing increases intrinsic cell excitability associated with increased Ca2+ and Ca2+-dependent BK currents in the absence of excitatory or inhibitory inputs.}, author = {Brenes, Oscar and Vandael, David H and Carbone, Emilio and Montarolo, Pier and Ghirardi, Mirella}, journal = {Neuroscience}, pages = {430 -- 443}, publisher = {Elsevier}, title = {{Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons}}, doi = {10.1016/j.neuroscience.2015.10.046}, volume = {311}, year = {2015}, } @article{1577, abstract = {Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes.}, author = {Carvalho, Antonio and Vicoso, Beatriz and Russo, Claudia and Swenor, Bonnielin and Clark, Andrew}, journal = {PNAS}, number = {40}, pages = {12450 -- 12455}, publisher = {National Academy of Sciences}, title = {{Birth of a new gene on the Y chromosome of Drosophila melanogaster}}, doi = {10.1073/pnas.1516543112}, volume = {112}, year = {2015}, } @article{1579, abstract = {We show that the Galois group of any Schubert problem involving lines in projective space contains the alternating group. This constitutes the largest family of enumerative problems whose Galois groups have been largely determined. Using a criterion of Vakil and a special position argument due to Schubert, our result follows from a particular inequality among Kostka numbers of two-rowed tableaux. In most cases, a combinatorial injection proves the inequality. For the remaining cases, we use the Weyl integral formulas to obtain an integral formula for these Kostka numbers. This rewrites the inequality as an integral, which we estimate to establish the inequality.}, author = {Brooks, Christopher and Martin Del Campo Sanchez, Abraham and Sottile, Frank}, journal = {Transactions of the American Mathematical Society}, number = {6}, pages = {4183 -- 4206}, publisher = {American Mathematical Society}, title = {{Galois groups of Schubert problems of lines are at least alternating}}, doi = {10.1090/S0002-9947-2014-06192-8}, volume = {367}, year = {2015}, } @article{1578, abstract = {We prove that the dual of the digital Voronoi diagram constructed by flooding the plane from the data points gives a geometrically and topologically correct dual triangulation. This provides the proof of correctness for recently developed GPU algorithms that outperform traditional CPU algorithms for constructing two-dimensional Delaunay triangulations.}, author = {Cao, Thanhtung and Edelsbrunner, Herbert and Tan, Tiowseng}, journal = {Computational Geometry}, number = {7}, pages = {507 -- 519}, publisher = {Elsevier}, title = {{Triangulations from topologically correct digital Voronoi diagrams}}, doi = {10.1016/j.comgeo.2015.04.001}, volume = {48}, year = {2015}, } @article{1581, abstract = {In animal embryos, morphogen gradients determine tissue patterning and morphogenesis. Shyer et al. provide evidence that, during vertebrate gut formation, tissue folding generates graded activity of signals required for subsequent steps of gut growth and differentiation, thereby revealing an intriguing link between tissue morphogenesis and morphogen gradient formation.}, author = {Bollenbach, Mark Tobias and Heisenberg, Carl-Philipp J}, journal = {Cell}, number = {3}, pages = {431 -- 432}, publisher = {Cell Press}, title = {{Gradients are shaping up}}, doi = {10.1016/j.cell.2015.04.009}, volume = {161}, year = {2015}, } @article{1589, abstract = {We investigate the dynamics of ferrofluidic wavy vortex flows in the counter-rotating Taylor-Couette system, with a focus on wavy flows with a mixture of the dominant azimuthal modes. Without external magnetic field flows are stable and pro-grade with respect to the rotation of the inner cylinder. More complex behaviors can arise when an axial or a transverse magnetic field is applied. Depending on the direction and strength of the field, multi-stable wavy states and bifurcations can occur. We uncover the phenomenon of flow pattern reversal as the strength of the magnetic field is increased through a critical value. In between the regimes of pro-grade and retrograde flow rotations, standing waves with zero angular velocities can emerge. A striking finding is that, under a transverse magnetic field, a second reversal in the flow pattern direction can occur, where the flow pattern evolves into pro-grade rotation again from a retrograde state. Flow reversal is relevant to intriguing phenomena in nature such as geomagnetic reversal. Our results suggest that, in ferrofluids, flow pattern reversal can be induced by varying a magnetic field in a controlled manner, which can be realized in laboratory experiments with potential applications in the development of modern fluid devices.}, author = {Altmeyer, Sebastian and Do, Younghae and Lai, Ying}, journal = {Scientific Reports}, publisher = {Nature Publishing Group}, title = {{Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system}}, doi = {10.1038/srep18589}, volume = {5}, year = {2015}, } @article{1584, abstract = {We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights.}, author = {Biedl, Therese and Held, Martin and Huber, Stefan and Kaaser, Dominik and Palfrader, Peter}, journal = {Computational Geometry: Theory and Applications}, number = {5}, pages = {429 -- 442}, publisher = {Elsevier}, title = {{Reprint of: Weighted straight skeletons in the plane}}, doi = {10.1016/j.comgeo.2015.01.004}, volume = {48}, year = {2015}, } @article{1582, abstract = {We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights.}, author = {Biedl, Therese and Held, Martin and Huber, Stefan and Kaaser, Dominik and Palfrader, Peter}, journal = {Computational Geometry: Theory and Applications}, number = {2}, pages = {120 -- 133}, publisher = {Elsevier}, title = {{Weighted straight skeletons in the plane}}, doi = {10.1016/j.comgeo.2014.08.006}, volume = {48}, year = {2015}, } @article{1583, abstract = {We study the characteristics of straight skeletons of monotone polygonal chains and use them to devise an algorithm for computing positively weighted straight skeletons of monotone polygons. Our algorithm runs in O(nlogn) time and O(n) space, where n denotes the number of vertices of the polygon.}, author = {Biedl, Therese and Held, Martin and Huber, Stefan and Kaaser, Dominik and Palfrader, Peter}, journal = {Information Processing Letters}, number = {2}, pages = {243 -- 247}, publisher = {Elsevier}, title = {{A simple algorithm for computing positively weighted straight skeletons of monotone polygons}}, doi = {10.1016/j.ipl.2014.09.021}, volume = {115}, year = {2015}, } @article{1587, abstract = {We investigate the quantum interference shifts between energetically close states, where the state structure is observed by laser spectroscopy. We report a compact and analytical expression that models the quantum interference induced shift for any admixture of circular polarization of the incident laser and angle of observation. An experimental scenario free of quantum interference can thus be predicted with this formula. Although this study is exemplified here for muonic deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme.}, author = {Amaro, Pedro and Fratini, Filippo and Safari, Laleh and Antognini, Aldo and Indelicato, Paul and Pohl, Randolf and Santos, José}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {6}, publisher = {American Physical Society}, title = {{Quantum interference shifts in laser spectroscopy with elliptical polarization}}, doi = {10.1103/PhysRevA.92.062506}, volume = {92}, year = {2015}, } @article{1588, abstract = {We investigate the Taylor-Couette system where the radius ratio is close to unity. Systematically increasing the Reynolds number, we observe a number of previously known transitions, such as one from the classical Taylor vortex flow (TVF) to wavy vortex flow (WVF) and the transition to fully developed turbulence. Prior to the onset of turbulence, we observe intermittent bursting patterns of localized turbulent patches, confirming the experimentally observed pattern of very short wavelength bursts (VSWBs). A striking finding is that, for a Reynolds number larger than that for the onset of VSWBs, a new type of intermittently bursting behavior emerges: patterns of azimuthally closed rings of various orders. We call them ring-bursting patterns, which surround the cylinder completely but remain localized and separated in the axial direction through nonturbulent wavy structures. We employ a number of quantitative measures including the cross-flow energy to characterize the ring-bursting patterns and to distinguish them from the background flow. These patterns are interesting because they do not occur in the wide-gap Taylor-Couette flow systems. The narrow-gap regime is less studied but certainly deserves further attention to gain deeper insights into complex flow dynamics in fluids.}, author = {Altmeyer, Sebastian and Do, Younghae and Lai, Ying}, journal = {Physical Review E}, number = {5}, publisher = {American Physical Society}, title = {{Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows}}, doi = {10.1103/PhysRevE.92.053018}, volume = {92}, year = {2015}, } @article{1586, abstract = {Through metabolic engineering cyanobacteria can be employed in biotechnology. Combining the capacity for oxygenic photosynthesis and carbon fixation with an engineered metabolic pathway allows carbon-based product formation from CO2, light, and water directly. Such cyanobacterial 'cell factories' are constructed to produce biofuels, bioplastics, and commodity chemicals. Efforts of metabolic engineers and synthetic biologists allow the modification of the intermediary metabolism at various branching points, expanding the product range. The new biosynthesis routes 'tap' the metabolism ever more efficiently, particularly through the engineering of driving forces and utilization of cofactors generated during the light reactions of photosynthesis, resulting in higher product titers. High rates of carbon rechanneling ultimately allow an almost-complete allocation of fixed carbon to product above biomass.}, author = {Angermayr, Andreas and Gorchs, Aleix and Hellingwerf, Klaas}, journal = {Trends in Biotechnology}, number = {6}, pages = {352 -- 361}, publisher = {Elsevier}, title = {{Metabolic engineering of cyanobacteria for the synthesis of commodity products}}, doi = {10.1016/j.tibtech.2015.03.009}, volume = {33}, year = {2015}, } @article{1585, abstract = {In this paper, we consider the fluctuation of mutual information statistics of a multiple input multiple output channel communication systems without assuming that the entries of the channel matrix have zero pseudovariance. To this end, we also establish a central limit theorem of the linear spectral statistics for sample covariance matrices under general moment conditions by removing the restrictions imposed on the second moment and fourth moment on the matrix entries in Bai and Silverstein (2004).}, author = {Bao, Zhigang and Pan, Guangming and Zhou, Wang}, journal = {IEEE Transactions on Information Theory}, number = {6}, pages = {3413 -- 3426}, publisher = {IEEE}, title = {{Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices}}, doi = {10.1109/TIT.2015.2421894}, volume = {61}, year = {2015}, } @article{1593, abstract = {Plants are sessile organisms that are permanently restricted to their site of germination. To compensate for their lack of mobility, plants evolved unique mechanisms enabling them to rapidly react to ever changing environmental conditions and flexibly adapt their postembryonic developmental program. A prominent demonstration of this developmental plasticity is their ability to bend organs in order to reach the position most optimal for growth and utilization of light, nutrients, and other resources. Shortly after germination, dicotyledonous seedlings form a bended structure, the so-called apical hook, to protect the delicate shoot meristem and cotyledons from damage when penetrating through the soil. Upon perception of a light stimulus, the apical hook rapidly opens and the photomorphogenic developmental program is activated. After germination, plant organs are able to align their growth with the light source and adopt the most favorable orientation through bending, in a process named phototropism. On the other hand, when roots and shoots are diverted from their upright orientation, they immediately detect a change in the gravity vector and bend to maintain a vertical growth direction. Noteworthy, despite the diversity of external stimuli perceived by different plant organs, all plant tropic movements share a common mechanistic basis: differential cell growth. In our review, we will discuss the molecular principles underlying various tropic responses with the focus on mechanisms mediating the perception of external signals, transduction cascades and downstream responses that regulate differential cell growth and consequently, organ bending. In particular, we highlight common and specific features of regulatory pathways in control of the bending of organs and a role for the plant hormone auxin as a key regulatory component.}, author = {Žádníková, Petra and Smet, Dajo and Zhu, Qiang and Van Der Straeten, Dominique and Benková, Eva}, journal = {Frontiers in Plant Science}, number = {4}, publisher = {Frontiers Research Foundation}, title = {{Strategies of seedlings to overcome their sessile nature: Auxin in mobility control}}, doi = {10.3389/fpls.2015.00218}, volume = {6}, year = {2015}, } @inproceedings{1595, abstract = {A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, . . . , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing- free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Tóth.}, author = {Fulek, Radoslav and Pelsmajer, Michael and Schaefer, Marcus}, location = {Los Angeles, CA, USA}, pages = {99 -- 110}, publisher = {Springer}, title = {{Hanani-Tutte for radial planarity}}, doi = {10.1007/978-3-319-27261-0_9}, volume = {9411}, year = {2015}, }