TY - CONF
AB - Clinical guidelines and decision support systems (DSS) play an important role in daily practices of medicine. Many text-based guidelines have been encoded for work-flow simulation of DSS to automate health care. During the collaboration with Carle hospital to develop a DSS, we identify that, for some complex and life-critical diseases, it is highly desirable to automatically rigorously verify some complex temporal properties in guidelines, which brings new challenges to current simulation based DSS with limited support of automatical formal verification and real-time data analysis. In this paper, we conduct the first study on applying runtime verification to cooperate with current DSS based on real-time data. Within the proposed technique, a user-friendly domain specific language, named DRTV, is designed to specify vital real-time data sampled by medical devices and temporal properties originated from clinical guidelines. Some interfaces are developed for data acquisition and communication. Then, for medical practice scenarios described in DRTV model, we will automatically generate event sequences and runtime property verifier automata. If a temporal property violates, real-time warnings will be produced by the formal verifier and passed to medical DSS. We have used DRTV to specify different kinds of medical care scenarios, and applied the proposed technique to assist existing DSS. As presented in experiment results, in terms of warning detection, it outperforms the only use of DSS or human inspection, and improves the quality of clinical health care of hospital
AU - Jiang, Yu
AU - Liu, Han
AU - Kong, Hui
AU - Wang, Rui
AU - Hosseini, Mohamad
AU - Sun, Jiaguang
AU - Sha, Lui
ID - 479
T2 - Proceedings of the 38th International Conference on Software Engineering Companion
TI - Use runtime verification to improve the quality of medical care practice
ER -
TY - CONF
AB - Graph games provide the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic reactive processes, the traditional model is perfect-information stochastic games, where some transitions of the game graph are controlled by two adversarial players, and the other transitions are executed probabilistically. We consider such games where the objective is the conjunction of several quantitative objectives (specified as mean-payoff conditions), which we refer to as generalized mean-payoff objectives. The basic decision problem asks for the existence of a finite-memory strategy for a player that ensures the generalized mean-payoff objective be satisfied with a desired probability against all strategies of the opponent. A special case of the decision problem is the almost-sure problem where the desired probability is 1. Previous results presented a semi-decision procedure for -approximations of the almost-sure problem. In this work, we show that both the almost-sure problem as well as the general basic decision problem are coNP-complete, significantly improving the previous results. Moreover, we show that in the case of 1-player stochastic games, randomized memoryless strategies are sufficient and the problem can be solved in polynomial time. In contrast, in two-player stochastic games, we show that even with randomized strategies exponential memory is required in general, and present a matching exponential upper bound. We also study the basic decision problem with infinite-memory strategies and present computational complexity results for the problem. Our results are relevant in the synthesis of stochastic reactive systems with multiple quantitative requirements.
AU - Chatterjee, Krishnendu
AU - Doyen, Laurent
ID - 480
TI - Perfect-information stochastic games with generalized mean-payoff objectives
VL - 05-08-July-2016
ER -
TY - CONF
AB - Nonlinear electro-optical conversion of microwave radiation into the optical telecommunication band is achieved within a crystalline whispering gallery mode resonator, reaching 0.1% photon number conversion efficiency with MHz bandwidth.
AU - Rueda, Alfredo
AU - Sedlmeir, Florian
AU - Collodo, Michele
AU - Vogl, Ulrich
AU - Stiller, Birgit
AU - Schunk, Gerhard
AU - Strekalov, Dmitry
AU - Marquardt, Christoph
AU - Fink, Johannes M
AU - Painter, Oskar
AU - Leuchs, Gerd
AU - Schwefel, Harald
ID - 482
TI - Nonlinear single sideband microwave to optical conversion using an electro-optic WGM-resonator
ER -
TY - JOUR
AB - The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa . The potential roles of PtCLE genes were studied by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These fi ndings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants.
AU - Liu, Zhijun
AU - Yang, Nan
AU - Lv, Yanting
AU - Pan, Lixia
AU - Lv, Shuo
AU - Han, Huibin
AU - Wang, Guodong
ID - 510
IS - 6
JF - Plant Signaling & Behavior
TI - The CLE gene family in Populus trichocarpa
VL - 11
ER -
TY - JOUR
AB - Plants form new organs with patterned tissue organization throughout their lifespan. It is unknown whether this robust post-embryonic organ formation results from stereotypic dynamic processes, in which the arrangement of cells follows rigid rules. Here, we combine modeling with empirical observations of whole-organ development to identify the principles governing lateral root formation in Arabidopsis. Lateral roots derive from a small pool of founder cells in which some take a dominant role as seen by lineage tracing. The first division of the founders is asymmetric, tightly regulated, and determines the formation of a layered structure. Whereas the pattern of subsequent cell divisions is not stereotypic between different samples, it is characterized by a regular switch in division plane orientation. This switch is also necessary for the appearance of patterned layers as a result of the apical growth of the primordium. Our data suggest that lateral root morphogenesis is based on a limited set of rules. They determine cell growth and division orientation. The organ-level coupling of the cell behavior ensures the emergence of the lateral root's characteristic features. We propose that self-organizing, non-deterministic modes of development account for the robustness of plant organ morphogenesis.
AU - Daniel von Wangenheim
AU - Fangerau, Jens
AU - Schmitz, Alexander
AU - Smith, Richard S
AU - Leitte, Heike
AU - Stelzer, Ernst H
AU - Maizel, Alexis
ID - 526
IS - 4
JF - Current Biology
TI - Rules and self-organizing properties of post-embryonic plant organ cell division patterns
VL - 26
ER -
TY - GEN
AB - We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs.
AU - Chatterjee, Krishnendu
AU - Pavlogiannis, Andreas
AU - Velner, Yaron
ID - 5445
SN - 2664-1690
TI - Quantitative interprocedural analysis
ER -
TY - GEN
AB - We study the problem of developing efficient approaches for proving termination of recursive programs with one-dimensional arrays. Ranking functions serve as a sound and complete approach for proving termination of non-recursive programs without array operations. First, we generalize ranking functions to the notion of measure functions, and prove that measure functions (i) provide a sound method to prove termination of recursive programs (with one-dimensional arrays), and (ii) is both sound and complete over recursive programs without array operations. Our second contribution is the synthesis of measure functions of specific forms in polynomial time. More precisely, we prove that (i) polynomial measure functions over recursive programs can be synthesized in polynomial time through Farkas’ Lemma and Handelman’s Theorem, and (ii) measure functions involving logarithm and exponentiation can be synthesized in polynomial time through abstraction of logarithmic or exponential terms and Handelman’s Theorem. A key application of our method is the worst-case analysis of recursive programs. While previous methods obtain worst-case polynomial bounds of the form O(n^k), where k is an integer, our polynomial time methods can synthesize bounds of the form O(n log n), as well as O(n^x), where x is not an integer. We show the applicability of our automated technique to obtain worst-case complexity of classical recursive algorithms such as (i) Merge-Sort, the divideand-
conquer algorithm for the Closest-Pair problem, where we obtain O(n log n) worst-case bound, and (ii) Karatsuba’s algorithm for polynomial multiplication and Strassen’s algorithm for matrix multiplication, where we obtain O(n^x) bound, where x is not an integer and close to the best-known bounds for the respective algorithms. Finally, we present experimental results to demonstrate the
effectiveness of our approach.
AU - Anonymous, 1
AU - Anonymous, 2
AU - Anonymous, 3
ID - 5446
SN - 2664-1690
TI - Termination and worst-case analysis of recursive programs
ER -
TY - GEN
AB - We consider the problem of developing automated techniques to aid the average-case complexity analysis of programs. Several classical textbook algorithms have quite efficient average-case complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., QUICK-SORT), or completely ineffective (e.g., COUPONCOLLECTOR). Since the main focus of average-case analysis is to obtain efficient bounds, we consider bounds that are either logarithmic,
linear, or almost-linear (O(log n), O(n), O(n · log n),
respectively, where n represents the size of the input). Our main contribution is a sound approach for deriving such average-case bounds for randomized recursive programs. Our approach is efficient (a simple linear-time algorithm), and it is based on (a) the analysis of recurrence relations induced by randomized algorithms, and (b) a guess-and-check technique. Our approach can infer the asymptotically optimal average-case bounds for classical randomized algorithms, including RANDOMIZED-SEARCH, QUICKSORT, QUICK-SELECT, COUPON-COLLECTOR, where the worstcase
bounds are either inefficient (such as linear as compared to logarithmic of average-case, or quadratic as compared to linear or almost-linear of average-case), or ineffective. We have implemented our approach, and the experimental results show that we obtain the bounds efficiently for various classical algorithms.
AU - Anonymous, 1
AU - Anonymous, 2
AU - Anonymous, 3
ID - 5447
SN - 2664-1690
TI - Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds
ER -
TY - GEN
AB - We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.
We introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.
1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.
2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence.
Finally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes.
AU - Anonymous, 1
AU - Anonymous, 2
AU - Anonymous, 3
AU - Anonymous, 4
ID - 5448
SN - 2664-1690
TI - Data-centric dynamic partial order reduction
ER -
TY - GEN
AB - The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population.
The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure.
Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade.
In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.
AU - Pavlogiannis, Andreas
AU - Tkadlec, Josef
AU - Chatterjee, Krishnendu
AU - Nowak, Martin
ID - 5449
SN - 2664-1690
TI - Amplification on undirected population structures: Comets beat stars
ER -
TY - GEN
AU - Pavlogiannis, Andreas
AU - Tkadlec, Josef
AU - Chatterjee, Krishnendu
AU - Nowak, Martin
ID - 5451
SN - 2664-1690
TI - Strong amplifiers of natural selection
ER -
TY - GEN
AU - Pavlogiannis, Andreas
AU - Tkadlec, Josef
AU - Chatterjee, Krishnendu
AU - Nowak, Martin
ID - 5452
SN - 2664-1690
TI - Arbitrarily strong amplifiers of natural selection
ER -
TY - GEN
AU - Pavlogiannis, Andreas
AU - Tkadlec, Josef
AU - Chatterjee, Krishnendu
AU - Nowak, Martin
ID - 5453
SN - 2664-1690
TI - Arbitrarily strong amplifiers of natural selection
ER -
TY - DATA
AB - We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.
For full details of the methods see:
Ellis TJ and Field DL "Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)
AU - Ellis, Thomas
AU - Field, David
ID - 5550
TI - Flower colour data and phylogeny (NEXUS) files
ER -
TY - DATA
AB - Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.
We placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.
After 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.
AU - Ellis, Thomas
ID - 5551
TI - Data on pollinator observations and offpsring phenotypes
ER -
TY - DATA
AB - Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).
Snapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.
Also included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation.
AU - Ellis, Thomas
ID - 5552
TI - Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.
ER -
TY - DATA
AB - Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).
Tissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.
Other data were retreived from an online database of this population at www.antspec.org.
AU - Field, David
AU - Ellis, Thomas
ID - 5553
KW - paternity assignment
KW - pedigree
KW - matting patterns
KW - assortative mating
KW - Antirrhinum majus
KW - frequency-dependent selection
KW - plant-pollinator interaction
TI - Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012
ER -
TY - DATA
AB - This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies.
AU - Hauschild, Robert
ID - 5555
KW - cell migration
KW - wide field microscopy
KW - FIJI
TI - Fiji script to determine average speed and direction of migration of cells
ER -
TY - DATA
AB - MATLAB code and processed datasets available for reproducing the results in:
Lukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.
*equal contributions
AU - Lukacisin, Martin
AU - Landon, Matthieu
AU - Jajoo, Rishi
ID - 5556
KW - transcription
KW - pausing
KW - backtracking
KW - polymerase
KW - RNA
KW - NET-seq
KW - nucleosome
KW - basepairing
TI - MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'
ER -
TY - DATA
AB - Small synthetic discrete tomography problems.
Sizes are 32x32, 64z64 and 256x256.
Projection angles are 2, 4, and 6.
Number of labels are 3 and 5.
AU - Swoboda, Paul
ID - 5557
KW - discrete tomography
TI - Synthetic discrete tomography problems
ER -
TY - DATA
AB - PhD thesis LaTeX source code
AU - Bojsen-Hansen, Morten
ID - 5558
TI - Tracking, Correcting and Absorbing Water Surface Waves
ER -
TY - JOUR
AB - Retroviruses such as HIV-1 assemble and bud from infected cells in an immature, non-infectious form. Subsequently, a series of proteolytic cleavages catalysed by the viral protease leads to a spectacular structural rearrangement of the viral particle into a mature form that is competent to fuse with and infect a new cell. Maturation involves changes in the structures of protein domains, in the interactions between protein domains, and in the architecture of the viral components that are assembled by the proteins. Tight control of proteolytic cleavages at different sites is required for successful maturation, and the process is a major target of antiretroviral drugs. Here we will describe what is known about the structures of immature and mature retrovirus particles, and about the maturation process by which one transitions into the other. Despite a wealth of available data, fundamental questions about retroviral maturation remain unanswered.
AU - Mattei, Simone
AU - Schur, Florian
AU - Briggs, John AG
ID - 5771
IS - 6
JF - Current Opinion in Virology
SN - 1879-6257
TI - Retrovirus maturation—an extraordinary structural transformation
VL - 18
ER -
TY - CHAP
AU - Sen, Nabhasmita
AU - Biswas, Ranita
AU - Bhowmick, Partha
ID - 5805
SN - 0302-9743
T2 - Computational Topology in Image Context
TI - On Some Local Topological Properties of Naive Discrete Sphere
VL - 9667
ER -
TY - CONF
AB - Although the concept of functional plane for naive plane is studied and reported in the literature in great detail, no similar study is yet found for naive sphere. This article exposes the first study in this line, opening up further prospects of analyzing the topological properties of sphere in the discrete space. We show that each quadraginta octant Q of a naive sphere forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as the functional plane of Q, and hence gives rise to merely mono-jumps during back projection. The other two coordinate planes serve as para-functional and dia-functional planes for Q, as the former is ‘mono-jumping’ but not bijective, whereas the latter holds neither of the two. Owing to this, the quadraginta octants form symmetry groups and subgroups with equivalent jump conditions. We also show a potential application in generating a special class of discrete 3D circles based on back projection and jump bridging by Steiner voxels. A circle in this class possesses 4-symmetry, uniqueness, and bounded distance from the underlying real sphere and real plane.
AU - Biswas, Ranita
AU - Bhowmick, Partha
ID - 5806
SN - 0302-9743
T2 - Discrete Geometry for Computer Imagery
TI - On Functionality of Quadraginta Octants of Naive Sphere with Application to Circle Drawing
VL - 9647
ER -
TY - CHAP
AB - A discrete spherical circle is a topologically well-connected 3D circle in the integer space, which belongs to a discrete sphere as well as a discrete plane. It is one of the most important 3D geometric primitives, but has not possibly yet been studied up to its merit. This paper is a maiden exposition of some of its elementary properties, which indicates a sense of its profound theoretical prospects in the framework of digital geometry. We have shown how different types of discretization can lead to forbidden and admissible classes, when one attempts to define the discretization of a spherical circle in terms of intersection between a discrete sphere and a discrete plane. Several fundamental theoretical results have been presented, the algorithm for construction of discrete spherical circles has been discussed, and some test results have been furnished to demonstrate its practicality and usefulness.
AU - Biswas, Ranita
AU - Bhowmick, Partha
AU - Brimkov, Valentin E.
ID - 5809
SN - 0302-9743
T2 - Combinatorial image analysis
TI - On the Connectivity and Smoothness of Discrete Spherical Circles
VL - 9448
ER -
TY - JOUR
AB - Quantum metrology exploits entangled states of particles to improve sensing precision beyond the limit achievable with uncorrelated particles. All previous methods required detection noise levels below this standard quantum limit to realize the benefits of the intrinsic sensitivity provided by these states.We experimentally demonstrate a widely applicable method for entanglement-enhanced measurements without low-noise detection. The method involves an intermediate quantum phase magnification step that eases implementation complexity. We used it to perform squeezed-state metrology 8 decibels below the standard quantum limit with a detection system that has a noise floor 10 decibels above the standard quantum limit.
AU - Onur Hosten
AU - Krishnakumar, Rajiv
AU - Engelsen, Nils J
AU - Kasevich, Mark A
ID - 587
IS - 6293
JF - Science
TI - Quantum phase magnification
VL - 352
ER -
TY - JOUR
AB - Quantum metrology uses quantum entanglement - correlations in the properties of microscopic systems - to improve the statistical precision of physical measurements. When measuring a signal, such as the phase shift of a light beam or an atomic state, a prominent limitation to achievable precision arises from the noise associated with the counting of uncorrelated probe particles. This noise, commonly referred to as shot noise or projection noise, gives rise to the standard quantum limit (SQL) to phase resolution. However, it can be mitigated down to the fundamental Heisenberg limit by entangling the probe particles. Despite considerable experimental progress in a variety of physical systems, a question that persists is whether these methods can achieve performance levels that compare favourably with optimized conventional (non-entangled) systems. Here we demonstrate an approach that achieves unprecedented levels of metrological improvement using half a million 87Rb atoms in their 'clock' states. The ensemble is 20.1 ± 0.3 decibels (100-fold) spin-squeezed via an optical-cavity-based measurement. We directly resolve small microwave-induced rotations 18.5 ± 0.3 decibels (70-fold) beyond the SQL. The single-shot phase resolution of 147 microradians achieved by the apparatus is better than that achieved by the best engineered cold atom sensors despite lower atom numbers. We infer entanglement of more than 680 ± 35 particles in the atomic ensemble. Applications include atomic clocks, inertial sensors, and fundamental physics experiments such as tests of general relativity or searches for electron electric dipole moment. To this end, we demonstrate an atomic clock measurement with a quantum enhancement of 10.5 ± 0.3 decibels (11-fold), limited by the phase noise of our microwave source.
AU - Onur Hosten
AU - Engelsen, Nils J
AU - Krishnakumar, Rajiv
AU - Kasevich, Mark A
ID - 588
IS - 7587
JF - Nature
TI - Measurement noise 100 times lower than the quantum-projection limit using entangled atoms
VL - 529
ER -
TY - CONF
AB - We create up to 20 dB spin-squeezed states of atomic ensembles using an optical cavity-based measurement. The prepared states are suitable for atomic sensors that require free space release of the atoms.
AU - Engelsen, Nils
AU - Hosten, Onur
AU - Krishnakumar, Rajiv
AU - Kasevich, Mark
ID - 592
TI - Engineering spin squeezed states for quantum-enhanced atom interferometry
ER -
TY - JOUR
AB - RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species1-3. Structural studies of mammalian Pol II, however, remain limited to low-resolution electron microscopy analysis of human Pol II and its complexes with various proteins4-10. Here we report the 3.4 Å resolution cryo-electron microscopy structure of mammalian Pol II in the form of a transcribing complex comprising DNA template and RNA transcript. We use bovine Pol II, which is identical to the human enzyme except for seven amino-acid residues. The obtained atomic model closely resembles its yeast counterpart, but also reveals unknown features. Binding of nucleic acids to the polymerase involves 'induced fit' of the mobile Pol II clamp and active centre region. DNA downstream of the transcription bubble contacts a conserved 'TPSA motif' in the jaw domain of the Pol II subunit RPB5, an interaction that is apparently already established during transcription initiation7. Upstream DNA emanates from the active centre cleft at an angle of approximately 105° with respect to downstream DNA. This position of upstream DNA allows for binding of the general transcription elongation factor DSIF (SPT4-SPT5) that we localize over the active centre cleft in a conserved position on the clamp domain of Pol II. Our results define the structure of mammalian Pol II in its functional state, indicate that previous crystallographic analysis of yeast Pol II is relevant for understanding gene transcription in all eukaryotes, and provide a starting point for a mechanistic analysis of human transcription.
AU - Bernecky, Carrie A
AU - Herzog, Franz
AU - Baumeister, Wolfgang
AU - Plitzko, Jürgen
AU - Cramer, Patrick
ID - 602
IS - 7587
JF - Nature
TI - Structure of transcribing mammalian RNA polymerase II
VL - 529
ER -
TY - JOUR
AB - Consider the transmission of a polar code of block length N and rate R over a binary memoryless symmetric channel W and let P e be the block error probability under successive cancellation decoding. In this paper, we develop new bounds that characterize the relationship of the parameters R, N, P e , and the quality of the channel W quantified by its capacity I(W) and its Bhattacharyya parameter Z(W). In previous work, two main regimes were studied. In the error exponent regime, the channel W and the rate R <; I(W) are fixed, and it was proved that the error probability Pe scales roughly as 2 -√N . In the scaling exponent approach, the channel W and the error probability Pe are fixed and it was proved that the gap to capacity I(W) - R scales as N -1/μ . Here, μ is called scaling exponent and this scaling exponent depends on the channel W. A heuristic computation for the binary erasure channel (BEC) gives μ = 3.627 and it was shown that, for any channel W, 3.579 ≤ μ ≤ 5.702. Our contributions are as follows. First, we provide the tighter upper bound μ <;≤ 4.714 valid for any W. With the same technique, we obtain the upper bound μ ≤ 3.639 for the case of the BEC; this upper bound approaches very closely the heuristically derived value for the scaling exponent of the erasure channel. Second, we develop a trade-off between the gap to capacity I(W)- R and the error probability Pe as the functions of the block length N. In other words, we neither fix the gap to capacity (error exponent regime) nor the error probability (scaling exponent regime), but we do consider a moderate deviations regime in which we study how fast both quantities, as the functions of the block length N, simultaneously go to 0. Third, we prove that polar codes are not affected by error floors. To do so, we fix a polar code of block length N and rate R. Then, we vary the channel W and study the impact of this variation on the error probability. We show that the error probability Pe scales as the Bhattacharyya parameter Z(W) raised to a power that scales roughly like VN. This agrees with the scaling in the error exponent regime.
AU - Mondelli, Marco
AU - Hassani, S. Hamed
AU - Urbanke, Rudiger L.
ID - 6732
IS - 12
JF - IEEE Transactions on Information Theory
SN - 0018-9448
TI - Unified scaling of polar codes: Error exponent, scaling exponent, moderate deviations, and error floors
VL - 62
ER -
TY - CONF
AB - The question whether RM codes are capacity-achieving is a long-standing open problem in coding theory that was recently answered in the affirmative for transmission over erasure channels [1], [2]. Remarkably, the proof does not rely on specific properties of RM codes, apart from their symmetry. Indeed, the main technical result consists in showing that any sequence of linear codes, with doubly-transitive permutation groups, achieves capacity on the memoryless erasure channel under bit-MAP decoding. Thus, a natural question is what happens under block-MAP decoding. In [1], [2], by exploiting further symmetries of the code, the bit-MAP threshold was shown to be sharp enough so that the block erasure probability also converges to 0. However, this technique relies heavily on the fact that the transmission is over an erasure channel. We present an alternative approach to strengthen results regarding the bit-MAP threshold to block-MAP thresholds. This approach is based on a careful analysis of the weight distribution of RM codes. In particular, the flavor of the main result is the following: assume that the bit-MAP error probability decays as N -δ , for some δ > 0. Then, the block-MAP error probability also converges to 0. This technique applies to transmission over any binary memoryless symmetric channel. Thus, it can be thought of as a first step in extending the proof that RM codes are capacity-achieving to the general case.
AU - Kudekar, Shrinivas
AU - Kumar, Santhosh
AU - Mondelli, Marco
AU - Pfister, Henry D.
AU - Urbankez, Rudiger
ID - 6733
T2 - 2016 IEEE International Symposium on Information Theory
TI - Comparing the bit-MAP and block-MAP decoding thresholds of Reed-Muller codes on BMS channels
ER -
TY - CONF
AB - We describe a new method to compare the bit-MAP and block-MAP decoding thresholds of Reed-Muller (RM) codes for transmission over a binary memoryless symmetric channel. The question whether RM codes are capacity-achieving is a long-standing open problem in coding theory and it has recently been answered in the affirmative for transmission over
erasure channels. Remarkably, the proof does not rely on specific properties of RM codes, apart from their symmetry. Indeed, the main technical result consists in showing that any sequence of linear codes, with doubly-transitive permutation groups, achieves capacity on the memoryless erasure channel under bit-MAP decoding. A natural question is what happens under block-MAP decoding. If the minimum distance of the code family is close to linear (e.g., of order N/ log(N)), then one can combine an upper bound on the bit-MAP error probability with a lower bound on the minimum distance to show that the code family is also capacity-achieving under block-MAP decoding. This strategy is successful for BCH codes. Unfortunately, the minimum distance of RM codes scales only as √N, which does not suffice to obtain the desired result. Then, one can exploit further symmetries of RM codes to show that the bit-MAP threshold is sharp enough so that the block erasure probability also tends to 0. However, this technique relies heavily on the fact that the transmission is over an erasure channel.
We present an alternative approach to strengthen results regarding the bit-MAP threshold to block-MAP thresholds. This approach is based on a careful analysis of the weight distribution of RM codes. In particular, the flavor of the main result is the following: assume that the bit-MAP error probability decays as N−δ, for some δ > 0. Then, the block-MAP
error probability also converges to 0. This technique applies to the transmission over any binary memoryless symmetric channel. Thus, it can be thought of as a first step in extending the proof that RM codes are capacity-achieving to the general case.
AU - Mondelli, Marco
AU - Kudekar, Shrinivas
AU - Kumar, Santosh
AU - Pfister, Henry D.
AU - Şaşoğlu, Eren
AU - Urbanke, Rüdiger
ID - 6770
T2 - 24th International Zurich Seminar on Communications
TI - Reed-Muller codes: Thresholds and weight distribution
ER -
TY - JOUR
AB - Electrons in materials with linear dispersion behave as massless Weyl- or Dirac-quasiparticles, and continue to intrigue due to their close resemblance to elusive ultra-relativistic particles as well as their potential for future electronics. Yet the experimental signatures of Weyl-fermions are often subtle and indirect, in particular if they coexist with conventional, massive quasiparticles. Here we show a pronounced anomaly in the magnetic torque of the Weyl semimetal NbAs upon entering the quantum limit state in high magnetic fields. The torque changes sign in the quantum limit, signalling a reversal of the magnetic anisotropy that can be directly attributed to the topological nature of the Weyl electrons. Our results establish that anomalous quantum limit torque measurements provide a direct experimental method to identify and distinguish Weyl and Dirac systems.
AU - Moll, Philip J. W.
AU - Potter, Andrew C.
AU - Nair, Nityan L.
AU - Ramshaw, B. J.
AU - Modic, Kimberly A
AU - Riggs, Scott
AU - Zeng, Bin
AU - Ghimire, Nirmal J.
AU - Bauer, Eric D.
AU - Kealhofer, Robert
AU - Ronning, Filip
AU - Analytis, James G.
ID - 7068
JF - Nature Communications
SN - 2041-1723
TI - Magnetic torque anomaly in the quantum limit of Weyl semimetals
VL - 7
ER -
TY - JOUR
AB - The observation of a reconstructed Fermi surface via quantum oscillations in hole-doped cuprates opened a path towards identifying broken symmetry states in the pseudogap regime. However, such an identification has remained inconclusive due to the multi-frequency quantum oscillation spectra and complications accounting for bilayer effects in most studies. We overcome these impediments with high-resolution measurements on the structurally simpler cuprate HgBa2CuO4+δ (Hg1201), which features one CuO2 plane per primitive unit cell. We find only a single oscillatory component with no signatures of magnetic breakdown tunnelling to additional orbits. Therefore, the Fermi surface comprises a single quasi-two-dimensional pocket. Quantitative modelling of these results indicates that a biaxial charge density wave within each CuO2 plane is responsible for the reconstruction and rules out criss-crossed charge stripes between layers as a viable alternative in Hg1201. Lastly, we determine that the characteristic gap between reconstructed pockets is a significant fraction of the pseudogap energy.
AU - Chan, M. K.
AU - Harrison, N.
AU - McDonald, R. D.
AU - Ramshaw, B. J.
AU - Modic, Kimberly A
AU - Barišić, N.
AU - Greven, M.
ID - 7069
JF - Nature Communications
SN - 2041-1723
TI - Single reconstructed Fermi surface pocket in an underdoped single-layer cuprate superconductor
VL - 7
ER -
TY - JOUR
AU - Rolando, Chiara
AU - Erni, Andrea
AU - Grison, Alice
AU - Beattie, Robert J
AU - Engler, Anna
AU - Gokhale, Paul J.
AU - Milo, Marta
AU - Wegleiter, Thomas
AU - Jessberger, Sebastian
AU - Taylor, Verdon
ID - 7141
IS - 5
JF - Cell Stem Cell
SN - 1934-5909
TI - Multipotency of adult hippocampal NSCs in vivo is restricted by Drosha/NFIB
VL - 19
ER -
TY - JOUR
AB - Background: High directional persistence is often assumed to enhance the efficiency of chemotactic migration. Yet, cells in vivo usually display meandering trajectories with relatively low directional persistence, and the control and function of directional persistence during cell migration in three-dimensional environments are poorly understood. Results: Here, we use mesendoderm progenitors migrating during zebrafish gastrulation as a model system to investigate the control of directional persistence during migration in vivo. We show that progenitor cells alternate persistent run phases with tumble phases that result in cell reorientation. Runs are characterized by the formation of directed actin-rich protrusions and tumbles by enhanced blebbing. Increasing the proportion of actin-rich protrusions or blebs leads to longer or shorter run phases, respectively. Importantly, both reducing and increasing run phases result in larger spatial dispersion of the cells, indicative of reduced migration precision. A physical model quantitatively recapitulating the migratory behavior of mesendoderm progenitors indicates that the ratio of tumbling to run times, and thus the specific degree of directional persistence of migration, are critical for optimizing migration precision. Conclusions: Together, our experiments and model provide mechanistic insight into the control of migration directionality for cells moving in three-dimensional environments that combine different protrusion types, whereby the proportion of blebs to actin-rich protrusions determines the directional persistence and precision of movement by regulating the ratio of tumbling to run times.
AU - Diz Muñoz, Alba
AU - Romanczuk, Pawel
AU - Yu, Weimiao
AU - Bergert, Martin
AU - Ivanovitch, Kenzo
AU - Salbreux, Guillame
AU - Heisenberg, Carl-Philipp J
AU - Paluch, Ewa
ID - 1271
IS - 1
JF - BMC Biology
TI - Steering cell migration by alternating blebs and actin-rich protrusions
VL - 14
ER -
TY - JOUR
AB - We study different means to extend offsetting based on skeletal structures beyond the well-known constant-radius and mitered offsets supported by Voronoi diagrams and straight skeletons, for which the orthogonal distance of offset elements to their respective input elements is constant and uniform over all input elements. Our main contribution is a new geometric structure, called variable-radius Voronoi diagram, which supports the computation of variable-radius offsets, i.e., offsets whose distance to the input is allowed to vary along the input. We discuss properties of this structure and sketch a prototype implementation that supports the computation of variable-radius offsets based on this new variant of Voronoi diagrams.
AU - Held, Martin
AU - Huber, Stefan
AU - Palfrader, Peter
ID - 1272
IS - 5
JF - Computer-Aided Design and Applications
TI - Generalized offsetting of planar structures using skeletons
VL - 13
ER -
TY - JOUR
AB - Lateral root primordia (LRP) originate from pericycle stem cells located deep within parental root tissues. LRP emerge through overlying root tissues by inducing auxin-dependent cell separation and hydraulic changes in adjacent cells. The auxin-inducible auxin influx carrier LAX3 plays a key role concentrating this signal in cells overlying LRP. Delimiting LAX3 expression to two adjacent cell files overlying new LRP is crucial to ensure that auxin-regulated cell separation occurs solely along their shared walls. Multiscale modeling has predicted that this highly focused pattern of expression requires auxin to sequentially induce auxin efflux and influx carriers PIN3 and LAX3, respectively. Consistent with model predictions, we report that auxin-inducible LAX3 expression is regulated indirectly by AUXIN RESPONSE FACTOR 7 (ARF7). Yeast one-hybrid screens revealed that the LAX3 promoter is bound by the transcription factor LBD29, which is a direct target for regulation by ARF7. Disrupting auxin-inducible LBD29 expression or expressing an LBD29-SRDX transcriptional repressor phenocopied the lax3 mutant, resulting in delayed lateral root emergence. We conclude that sequential LBD29 and LAX3 induction by auxin is required to coordinate cell separation and organ emergence.
AU - Porco, Silvana
AU - Larrieu, Antoine
AU - Du, Yujuan
AU - Gaudinier, Allison
AU - Goh, Tatsuaki
AU - Swarup, Kamal
AU - Swarup, Ranjan
AU - Kuempers, Britta
AU - Bishopp, Anthony
AU - Lavenus, Julien
AU - Casimiro, Ilda
AU - Hill, Kristine
AU - Benková, Eva
AU - Fukaki, Hidehiro
AU - Brady, Siobhan
AU - Scheres, Ben
AU - Peéet, Benjamin
AU - Bennett, Malcolm
ID - 1273
IS - 18
JF - Development
TI - Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3
VL - 143
ER -
TY - JOUR
AB - Synchronized tissue polarization during regeneration or de novo vascular tissue formation is a plant-specific example of intercellular communication and coordinated development. According to the canalization hypothesis, the plant hormone auxin serves as polarizing signal that mediates directional channel formation underlying the spatio-temporal vasculature patterning. A necessary part of canalization is a positive feedback between auxin signaling and polarity of the intercellular auxin flow. The cellular and molecular mechanisms of this process are still poorly understood, not the least, because of a lack of a suitable model system. We show that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used to study the canalization during vascular cambium regeneration and new vasculature formation. We monitored localized auxin responses, directional auxin-transport channels formation, and establishment of new vascular cambium polarity during regenerative processes after stem wounding. The increased auxin response above and around the wound preceded the formation of PIN1 auxin transporter-marked channels from the primarily homogenous tissue and the transient, gradual changes in PIN1 localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis is a useful model for studies of coordinated tissue polarization and vasculature formation after wounding allowing for genetic and mechanistic dissection of the canalization hypothesis.
AU - Mazur, Ewa
AU - Benková, Eva
AU - Friml, Jirí
ID - 1274
JF - Scientific Reports
TI - Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis
VL - 6
ER -
TY - JOUR
AU - Callan Jones, Andrew
AU - Ruprecht, Verena
AU - Wieser, Stefan
AU - Heisenberg, Carl-Philipp J
AU - Voituriez, Raphaël
ID - 1275
IS - 13
JF - Physical Review Letters
TI - Callan-Jones et al. Reply
VL - 117
ER -
TY - JOUR
AB - The cytochrome (cyt) bc 1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme's substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Q i-site of the cyt bc 1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Q i-site to facilitate binding of half-protonated semiquinone-a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Q i-site.
AU - Postila, Pekka
AU - Kaszuba, Karol
AU - Kuleta, Patryk
AU - Vattulainen, Ilpo
AU - Sarewicz, Marcin
AU - Osyczka, Artur
AU - Róg, Tomasz
ID - 1276
JF - Scientific Reports
TI - Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex
VL - 6
ER -
TY - JOUR
AB - The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released into the apoplast after cellular damage caused by pathogens or wounding to induce innate immunity by direct binding to the membrane-localized leucine-rich repeat receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated signaling components and responses have been studied extensively, the contributions of the subcellular localization and dynamics of the active PEPRs remain largely unknown. We used live-cell imaging of the fluorescently labeled and bioactive pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different TGN/EE markers colocalized only rarely, implying that the intracellular route of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization and compromised AtPep1-mediated responses. Our results show that clathrin function at the PM is required to induce plant defense responses, likely through CME of cell surface-located signaling components.
AU - Ortiz Morea, Fausto
AU - Savatin, Daniel
AU - Dejonghe, Wim
AU - Kumar, Rahul
AU - Luo, Yu
AU - Adamowski, Maciek
AU - Van Begin, Jos
AU - Dressano, Keini
AU - De Oliveira, Guilherme
AU - Zhao, Xiuyang
AU - Lu, Qing
AU - Madder, Annemieke
AU - Friml, Jirí
AU - De Moura, Daniel
AU - Russinova, Eugenia
ID - 1277
IS - 39
JF - PNAS
TI - Danger-associated peptide signaling in Arabidopsis requires clathrin
VL - 113
ER -
TY - JOUR
AB - Adaptations of vestibulo-ocular and optokinetic response eye movements have been studied as an experimental model of cerebellum-dependent motor learning. Several previous physiological and pharmacological studies have consistently suggested that the cerebellar flocculus (FL) Purkinje cells (P-cells) and the medial vestibular nucleus (MVN) neurons targeted by FL (FL-targeted MVN neurons) may respectively maintain the memory traces of short- and long-term adaptation. To study the basic structures of the FL-MVN synapses by light microscopy (LM) and electron microscopy (EM), we injected green florescence protein (GFP)-expressing lentivirus into FL to anterogradely label the FL P-cell axons in C57BL/6J mice. The FL P-cell axonal boutons were distributed in the magnocellular MVN and in the border region of parvocellular MVN and prepositus hypoglossi (PrH). In the magnocellular MVN, the FL-P cell axons mainly terminated on somata and proximal dendrites. On the other hand, in the parvocellular MVN/PrH, the FL P-cell axonal synaptic boutons mainly terminated on the relatively small-diameter (< 1 μm) distal dendrites of MVN neurons, forming symmetrical synapses. The majority of such parvocellular MVN/PrH neurons were determined to be glutamatergic by immunocytochemistry and in-situ hybridization of GFP expressing transgenic mice. To further examine the spatial relationship between the synapses of FL P-cells and those of vestibular nerve on the neurons of the parvocellular MVN/ PrH, we added injections of biotinylated dextran amine into the semicircular canal and anterogradely labeled vestibular nerve axons in some mice. The MVN dendrites receiving the FL P-cell axonal synaptic boutons often closely apposed vestibular nerve synaptic boutons in both LM and EM studies. Such a partial overlap of synaptic boutons of FL P-cell axons with those of vestibular nerve axons in the distal dendrites of MVN neurons suggests that inhibitory synapses of FL P-cells may influence the function of neighboring excitatory synapses of vestibular nerve in the parvocellular MVN/PrH neurons.
AU - Matsuno, Hitomi
AU - Kudoh, Moeko
AU - Watakabe, Akiya
AU - Yamamori, Tetsuo
AU - Shigemoto, Ryuichi
AU - Nagao, Soichi
ID - 1278
IS - 10
JF - PLoS One
TI - Distribution and structure of synapses on medial vestibular nuclear neurons targeted by cerebellar flocculus purkinje cells and vestibular nerve in mice: Light and electron microscopy studies
VL - 11
ER -
TY - JOUR
AB - During hippocampal sharp wave/ripple (SWR) events, previously occurring, sensory inputdriven neuronal firing patterns are replayed. Such replay is thought to be important for plasticity- related processes and consolidation of memory traces. It has previously been shown that the electrical stimulation-induced disruption of SWR events interferes with learning in rodents in different experimental paradigms. On the other hand, the cognitive map theory posits that the plastic changes of the firing of hippocampal place cells constitute the electrophysiological counterpart of the spatial learning, observable at the behavioral level. Therefore, we tested whether intact SWR events occurring during the sleep/rest session after the first exploration of a novel environment are needed for the stabilization of the CA1 code, which process requires plasticity. We found that the newly-formed representation in the CA1 has the same level of stability with optogenetic SWR blockade as with a control manipulation that delivered the same amount of light into the brain. Therefore our results suggest that at least in the case of passive exploratory behavior, SWR-related plasticity is dispensable for the stability of CA1 ensembles.
AU - Kovács, Krisztián
AU - O'Neill, Joseph
AU - Schönenberger, Philipp
AU - Penttonen, Markku
AU - Rangel Guerrero, Dámaris K
AU - Csicsvari, Jozsef L
ID - 1279
IS - 10
JF - PLoS One
TI - Optogenetically blocking sharp wave ripple events in sleep does not interfere with the formation of stable spatial representation in the CA1 area of the hippocampus
VL - 11
ER -
TY - JOUR
AB - We prove the Wigner-Dyson-Mehta conjecture at fixed energy in the bulk of the spectrum for generalized symmetric and Hermitian Wigner matrices. Previous results concerning the universality of random matrices either require an averaging in the energy parameter or they hold only for Hermitian matrices if the energy parameter is fixed. We develop a homogenization theory of the Dyson Brownian motion and show that microscopic universality follows from mesoscopic statistics.
AU - Bourgade, Paul
AU - Erdös, László
AU - Yau, Horngtzer
AU - Yin, Jun
ID - 1280
IS - 10
JF - Communications on Pure and Applied Mathematics
TI - Fixed energy universality for generalized wigner matrices
VL - 69
ER -
TY - JOUR
AB - Plants are able to modulate root growth and development to optimize their nitrogen nutrition. In Arabidopsis (Arabidopsis thaliana), the adaptive root response to nitrate (NO3 -) depends on the NRT1.1/NPF6.3 transporter/sensor. NRT1.1 represses emergence of lateral root primordia (LRPs) at low concentration or absence of NO3 - through its auxin transport activity that lowers auxin accumulation in LR. However, these functional data strongly contrast with the known transcriptional regulation of NRT1.1, which is markedly repressed in LRPs in the absence of NO3 -. To explain this discrepancy, we investigated in detail the spatiotemporal expression pattern of the NRT1.1 protein during LRP development and combined local transcript analysis with the use of transgenic lines expressing tagged NRT1.1 proteins. Our results show that although NO3 - stimulates NRT1.1 transcription and probably mRNA stability both in primary root tissues and in LRPs, it acts differentially on protein accumulation, depending on the tissues considered with stimulation in cortex and epidermis of the primary root and a strong repression in LRPs and to a lower extent at the primary root tip. This demonstrates that NRT1.1 is strongly regulated at the posttranscriptional level by tissue-specific mechanisms. These mechanisms are crucial for controlling the large palette of adaptive responses to NO3 - mediated by NRT1.1 as they ensure that the protein is present in the proper tissue under the specific conditions where it plays a signaling role in this particular tissue.
AU - Bouguyon, Eléonore
AU - Perrine Walker, Francine
AU - Pervent, Marjorie
AU - Rochette, Juliette
AU - Cuesta, Candela
AU - Benková, Eva
AU - Martinière, Alexandre
AU - Bach, Lien
AU - Krouk, Gabriel
AU - Gojon, Alain
AU - Nacry, Philippe
ID - 1281
IS - 2
JF - Plant Physiology
TI - Nitrate controls root development through posttranscriptional regulation of the NRT1.1/NPF6.3 transporter sensor
VL - 172
ER -
TY - JOUR
AB - We consider higher-dimensional generalizations of the normalized Laplacian and the adjacency matrix of graphs and study their eigenvalues for the Linial–Meshulam model Xk(n, p) of random k-dimensional simplicial complexes on n vertices. We show that for p = Ω(logn/n), the eigenvalues of each of the matrices are a.a.s. concentrated around two values. The main tool, which goes back to the work of Garland, are arguments that relate the eigenvalues of these matrices to those of graphs that arise as links of (k - 2)-dimensional faces. Garland’s result concerns the Laplacian; we develop an analogous result for the adjacency matrix. The same arguments apply to other models of random complexes which allow for dependencies between the choices of k-dimensional simplices. In the second part of the paper, we apply this to the question of possible higher-dimensional analogues of the discrete Cheeger inequality, which in the classical case of graphs relates the eigenvalues of a graph and its edge expansion. It is very natural to ask whether this generalizes to higher dimensions and, in particular, whether the eigenvalues of the higher-dimensional Laplacian capture the notion of coboundary expansion—a higher-dimensional generalization of edge expansion that arose in recent work of Linial and Meshulam and of Gromov; this question was raised, for instance, by Dotterrer and Kahle. We show that this most straightforward version of a higher-dimensional discrete Cheeger inequality fails, in quite a strong way: For every k ≥ 2 and n ∈ N, there is a k-dimensional complex Yn k on n vertices that has strong spectral expansion properties (all nontrivial eigenvalues of the normalised k-dimensional Laplacian lie in the interval [1−O(1/√1), 1+0(1/√1]) but whose coboundary expansion is bounded from above by O(log n/n) and so tends to zero as n → ∞; moreover, Yn k can be taken to have vanishing integer homology in dimension less than k.
AU - Gundert, Anna
AU - Wagner, Uli
ID - 1282
IS - 2
JF - Israel Journal of Mathematics
TI - On eigenvalues of random complexes
VL - 216
ER -
TY - JOUR
AB - The impact of the plant hormone ethylene on seedling development has long been recognized; however, its ecophysiological relevance is unexplored. Three recent studies demonstrate that ethylene is a critical endogenous integrator of various environmental signals including mechanical stress, light, and oxygen availability during seedling germination and growth through the soil.
AU - Zhu, Qiang
AU - Benková, Eva
ID - 1283
IS - 10
JF - Trends in Plant Science
TI - Seedlings’ strategy to overcome a soil barrier
VL - 21
ER -
TY - JOUR
AB - Brassinosteroids (BRs) are growth-promoting plant hormones that play a role in abiotic stress responses, but molecular modes that enable this activity remain largely unknown. Here we show that BRs participate in the regulation of freezing tolerance. BR signaling-defective mutants of Arabidopsis thaliana were hypersensitive to freezing before and after cold acclimation. The constitutive activation of BR signaling, in contrast, enhanced freezing resistance. Evidence is provided that the BR-controlled basic helix-loop-helix transcription factor CESTA (CES) can contribute to the constitutive expression of the C-REPEAT/DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR (CBF) transcriptional regulators that control cold responsive (COR) gene expression. In addition, CBF-independent classes of BR-regulated COR genes are identified that are regulated in a BR- and CES-dependent manner during cold acclimation. A model is presented in which BRs govern different cold-responsive transcriptional cascades through the post-translational modification of CES and redundantly acting factors. This contributes to the basal resistance against freezing stress, but also to the further improvement of this resistance through cold acclimation.
AU - Eremina, Marina
AU - Unterholzner, Simon
AU - Rathnayake, Ajith
AU - Castellanos, Marcos
AU - Khan-Djamei, Mamoona
AU - Kügler, Karl
AU - May, Sean
AU - Mayer, Klaus
AU - Rozhon, Wilfried
AU - Poppenberger, Brigitte
ID - 1284
IS - 40
JF - PNAS
TI - Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants
VL - 113
ER -
TY - JOUR
AB - Cell migration is central to a multitude of physiological processes, including embryonic development, immune surveillance, and wound healing, and deregulated migration is key to cancer dissemination. Decades of investigations have uncovered many of the molecular and physical mechanisms underlying cell migration. Together with protrusion extension and cell body retraction, adhesion to the substrate via specific focal adhesion points has long been considered an essential step in cell migration. Although this is true for cells moving on two-dimensional substrates, recent studies have demonstrated that focal adhesions are not required for cells moving in three dimensions, in which confinement is sufficient to maintain a cell in contact with its substrate. Here, we review the investigations that have led to challenging the requirement of specific adhesions for migration, discuss the physical mechanisms proposed for cell body translocation during focal adhesion-independent migration, and highlight the remaining open questions for the future.
AU - Paluch, Ewa
AU - Aspalter, Irene
AU - Sixt, Michael K
ID - 1285
JF - Annual Review of Cell and Developmental Biology
TI - Focal adhesion-independent cell migration
VL - 32
ER -