TY - JOUR
AB - The differential distribution of the plant signaling molecule auxin is required for many aspects of plant development. Local auxin maxima and gradients arise as a result of local auxin metabolism and, predominantly, from directional cell-to-cell transport. In this primer, we discuss how the coordinated activity of several auxin influx and efflux systems, which transport auxin across the plasma membrane, mediates directional auxin flow. This activity crucially contributes to the correct setting of developmental cues in embryogenesis, organogenesis, vascular tissue formation and directional growth in response to environmental stimuli.
AU - Petrášek, Jan
AU - Friml, Jirí
ID - 3057
IS - 16
JF - Development
TI - Auxin transport routes in plant development
VL - 136
ER -
TY - JOUR
AB - The PIN-FORMED (PIN) proteins are secondary transporters acting in the efflux of the plant signal molecule auxin from cells. They are asymmetrically localized within cells and their polarity determines the directionality of intercellular auxin flow. PIN genes are found exclusively in the genomes of multicellular plants and play an important role in regulating asymmetric auxin distribution in multiple developmental processes, including embryogenesis, organogenesis, tissue differentiation and tropic responses. All PIN proteins have a similar structure with amino- and carboxy-terminal hydrophobic, membrane-spanning domains separated by a central hydrophilic domain. The structure of the hydrophobic domains is well conserved. The hydrophilic domain is more divergent and it determines eight groups within the protein family. The activity of PIN proteins is regulated at multiple levels, including transcription, protein stability, subcellular localization and transport activity. Different endogenous and environmental signals can modulate PIN activity and thus modulate auxin-distribution-dependent development. A large group of PIN proteins, including the most ancient members known from mosses, localize to the endoplasmic reticulum and they regulate the subcellular compartmentalization of auxin and thus auxin metabolism. Further work is needed to establish the physiological importance of this unexpected mode of auxin homeostasis regulation. Furthermore, the evolution of PIN-based transport, PIN protein structure and more detailed biochemical characterization of the transport function are important topics for further studies.
AU - Křeček, Pavel
AU - Skůpa, Petr
AU - Libus, Jiří
AU - Naramoto, Satoshi
AU - Tejos, Ricardo
AU - Friml, Jirí
AU - Zažímalová, Eva
ID - 3061
IS - 12
JF - Genome Biology
TI - The PIN-FORMED (PIN) protein family of auxin transporters
VL - 10
ER -
TY - JOUR
AB - The problem of obtaining the maximum a posteriori estimate of a general discrete Markov random field (i.e., a Markov random field defined using a discrete set of labels) is known to be NP-hard. However, due to its central importance in many applications, several approximation algorithms have been proposed in the literature. In this paper, we present an analysis of three such algorithms based on convex relaxations: (i) LP-S: the linear programming (LP) relaxation proposed by Schlesinger (1976) for a special case and independently in Chekuri et al. (2001), Koster et al. (1998), and Wainwright et al. (2005) for the general case; (ii) QP-RL: the quadratic programming (QP) relaxation of Ravikumar and Lafferty (2006); and (iii) SOCP-MS: the second order cone programming (SOCP) relaxation first proposed by Muramatsu and Suzuki (2003) for two label problems and later extended by Kumar et al. (2006) for a general label set.
We show that the SOCP-MS and the QP-RL relaxations are equivalent. Furthermore, we prove that despite the flexibility in the form of the constraints/objective function offered by QP and SOCP, the LP-S relaxation strictly dominates (i.e., provides a better approximation than) QP-RL and SOCP-MS. We generalize these results by defining a large class of SOCP (and equivalent QP) relaxations which is dominated by the LP-S relaxation. Based on these results we propose some novel SOCP relaxations which define constraints using random variables that form cycles or cliques in the graphical model representation of the random field. Using some examples we show that the new SOCP relaxations strictly dominate the previous approaches.
AU - Kumar, M Pawan
AU - Vladimir Kolmogorov
AU - Torr, Philip H
ID - 3197
JF - Journal of Machine Learning Research
TI - An analysis of convex relaxations for MAP estimation of discrete MRFs
VL - 10
ER -
TY - CONF
AB - We give polynomial-time algorithms for computing the values of Markov decision processes (MDPs) with limsup and liminf objectives. A real-valued reward is assigned to each state, and the value of an infinite path in the MDP is the limsup (resp. liminf) of all rewards along the path. The value of an MDP is the maximal expected value of an infinite path that can be achieved by resolving the decisions of the MDP. Using our result on MDPs, we show that turn-based stochastic games with limsup and liminf objectives can be solved in NP ∩ coNP.
AU - Krishnendu Chatterjee
AU - Thomas Henzinger
ID - 3503
TI - Probabilistic systems with limsup and liminf objectives
VL - 5489
ER -
TY - JOUR
AB - Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo.
AU - Hsieh, Tzung-Fu
AU - Ibarra, Christian A.
AU - Silva, Pedro
AU - Zemach, Assaf
AU - Eshed-Williams, Leor
AU - Fischer, Robert L.
AU - ZILBERMAN, Daniel
ID - 9453
IS - 5933
JF - Science
KW - Multidisciplinary
SN - 0036-8075
TI - Genome-wide demethylation of Arabidopsis endosperm
VL - 324
ER -
TY - CONF
AB - We present a review of recent work on the mathematical aspects of the BCS gap equation, covering our results of Ref. 9 as well our recent joint work with Hamza and Solovej and with Frank and Naboko, respectively. In addition, we mention some related new results.
AU - Hainzl, Christian
AU - Robert Seiringer
ID - 2331
TI - Spectral properties of the BCS gap equation of superfluidity
ER -
TY - CONF
AB - We present a rigorous proof of the appearance of quantized vortices in dilute trapped Bose gases with repulsive two-body interactions subject to rotation, which was obtained recently in joint work with Elliott Lieb.14 Starting from the many-body Schrödinger equation, we show that the ground state of such gases is, in a suitable limit, well described by the nonlinear Gross-Pitaevskii equation. In the case of axially symmetric traps, our results show that the appearance of quantized vortices causes spontaneous symmetry breaking in the ground state.
AU - Robert Seiringer
ID - 2332
TI - Vortices and Spontaneous Symmetry Breaking in Rotating Bose Gases
ER -
TY - JOUR
AB - A lower bound is derived on the free energy (per unit volume) of a homogeneous Bose gas at density Q and temperature T. In the dilute regime, i.e., when a3 1, where a denotes the scattering length of the pair-interaction potential, our bound differs to leading order from the expression for non-interacting particles by the term 4πa(2 2}-[ - c]2+). Here, c(T) denotes the critical density for Bose-Einstein condensation (for the non-interacting gas), and [ · ]+ = max{ ·, 0} denotes the positive part. Our bound is uniform in the temperature up to temperatures of the order of the critical temperature, i.e., T ~ 2/3 or smaller. One of the key ingredients in the proof is the use of coherent states to extend the method introduced in [17] for estimating correlations to temperatures below the critical one.
AU - Robert Seiringer
ID - 2374
IS - 3
JF - Communications in Mathematical Physics
TI - Free energy of a dilute Bose gas: Lower bound
VL - 279
ER -
TY - JOUR
AB - We derive upper and lower bounds on the critical temperature Tc and the energy gap Ξ (at zero temperature) for the BCS gap equation, describing spin- 1 2 fermions interacting via a local two-body interaction potential λV(x). At weak coupling λ 1 and under appropriate assumptions on V(x), our bounds show that Tc ∼A exp(-B/λ) and Ξ∼C exp(-B/λ) for some explicit coefficients A, B, and C depending on the interaction V(x) and the chemical potential μ. The ratio A/C turns out to be a universal constant, independent of both V(x) and μ. Our analysis is valid for any μ; for small μ, or low density, our formulas reduce to well-known expressions involving the scattering length of V(x).
AU - Hainzl, Christian
AU - Robert Seiringer
ID - 2376
IS - 18
JF - Physical Review B - Condensed Matter and Materials Physics
TI - Critical temperature and energy gap for the BCS equation
VL - 77
ER -
TY - JOUR
AB - We prove that the critical temperature for the BCS gap equation is given by T c = μ ( 8\π e γ-2+ o(1)) e π/(2μa) in the low density limit μ→ 0, with γ denoting Euler's constant. The formula holds for a suitable class of interaction potentials with negative scattering length a in the absence of bound states.
AU - Hainzl, Christian
AU - Robert Seiringer
ID - 2377
IS - 2-3
JF - Letters in Mathematical Physics
TI - The BCS critical temperature for potentials with negative scattering length
VL - 84
ER -