@article{3014,
  abstract     = {Plant biology is currently confronted with an overflow of expression profile data provided by high-throughput microarray transcription analyses. However, the tissue and cellular resolution of these techniques is limited. Thus, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here we present an in situ mRNA hybridization method that is routinely used in the analysis of gene expression patterns. The protocol is optimized for mRNA localizations in sectioned tissue of Arabidopsis seedlings including embryos, roots, hypocotyls, young primary leaves and flowers. The detailed protocol, recommended controls and troubleshooting are presented along with examples of application. The total time for the process is 10 days.},
  author       = {Brewer, Philip B and Heisler, Marcus G and Hejátko, Jan and Jirí Friml and Eva Benková},
  journal      = {Nature Protocols},
  number       = {3},
  pages        = {1462 -- 1467},
  publisher    = {Nature Publishing Group},
  title        = {{In situ hybridization for mRNA detection in Arabidopsis tissue sections}},
  doi          = {10.1038/nprot.2006.226},
  volume       = {1},
  year         = {2006},
}

@article{3015,
  abstract     = {As the field of plant molecular biology is swiftly advancing, a need has been created for methods that allow rapid and reliable in situ localization of proteins in plant cells. Here we describe a whole-mount 'immunolocalization' technique for various plant tissues, including roots, hypocotyls, cotyledons, young primary leaves and embryos of Arabidopsis thaliana and other species. The detailed protocol, recommended controls and troubleshooting are presented, along with examples of applications. The protocol consists of five main procedures: tissue fixation, tissue permeation, blocking, primary and secondary antibody incubation. Notably, the first procedure (tissue fixation) includes several steps (4-12) that are absolutely necessary for protein localization in hypocotyls, cotyledons and young primary leaves but should be omitted for other tissues. The protocol is usually done in 3 days, but could also be completed in 2 days.},
  author       = {Sauer, Michael and Paciorek, Tomasz and Eva Benková and Jirí Friml},
  journal      = {Nature Protocols},
  number       = {1},
  pages        = {98 -- 103},
  publisher    = {Nature Publishing Group},
  title        = {{Immunocytochemical techniques for whole mount in situ protein localization in plants}},
  doi          = {10.1038/nprot.2006.15},
  volume       = {1},
  year         = {2006},
}

@article{3016,
  abstract     = {Plant development is characterized by a profound ability to regenerate and form tissues with new axes of polarity. An unsolved question concerns how the position within a tissue and cues from neighboring cells are integrated to specify the polarity of individual cells. The canalization hypothesis proposes a feedback effect of the phytohormone auxin on the directionality of intercellular auxin flow as a means to polarize tissues. Here we identify a cellular and molecular mechanism for canalization. Local auxin application, wounding, or auxin accumulation during de novo organ formation lead to rearrangements in the subcellular polar localization of PIN auxin transport components. This auxin effect on PIN polarity is cell-specific, does not depend on PIN transcription, and involves the Aux/IAA-ARF (indole-3-acetic acid-auxin response factor) signaling pathway. Our data suggest that auxin acts as polarizing cue, which links individual cell polarity with tissue and organ polarity through control of PIN polar targeting. This feedback regulation provides a conceptual framework for polarization during multiple regenerative and patterning processes in plants.},
  author       = {Sauer, Michael and Balla, Jozef and Luschnig, Christian and Wiśniewska, Justyna and Reinöhl, Vilém and Friml, Jirí and Benková, Eva},
  journal      = {Genes and Development},
  number       = {20},
  pages        = {2902 -- 2911},
  publisher    = {Cold Spring Harbor Laboratory Press},
  title        = {{Canalization of auxin flow by Aux/IAA-ARF-dependent feedback regulation of PIN polarity}},
  doi          = {10.1101/gad.390806},
  volume       = {20},
  year         = {2006},
}

@article{3017,
  abstract     = {The plant hormone auxin plays crucial roles in regulating plant growth development, including embryo and root patterning, organ formation, vascular tissue differentiation and growth responses to environmental stimuli. Asymmetric auxin distribution patterns have been observed within tissues, and these so-called auxin gradients change dynamically during different developmental processes. Most auxin is synthesized in the shoot and distributed directionally throughout the plant. This polar auxin transport is mediated by auxin influx and efflux facilitators, whose subcellular polar localizations guide the direction of auxin flow. The polar localization of PIN auxin efflux carriers changes in response to developmental and external cues in order to channel auxin flow in a regulated manner for organized growth. Auxin itself modulates the expression and subcellular localization of PIN proteins, contributing to a complex pattern of feedback regulation. Here we review the available information mainly from studies of a model plant, Arabidopsis thaliana, on the generation of auxin gradients, the regulation of polar auxin transport and further downstream cellular events.},
  author       = {Tanaka, Hirokazu and Dhonukshe, Pankaj and Brewer, Philip and Friml, Jirí},
  journal      = {Cellular and Molecular Life Sciences},
  number       = {23},
  pages        = {2738 -- 2754},
  publisher    = {Birkhäuser},
  title        = {{Spatiotemporal asymmetric auxin distribution: A means to coordinate plant development}},
  doi          = {10.1007/s00018-006-6116-5},
  volume       = {63},
  year         = {2006},
}

@article{3018,
  abstract     = {The directional flow of the plant hormone auxin mediates multiple developmental processes, including patterning and tropisms. Apical and basal plasma membrane localization of AUXIN-RESISTANT1 (AUX1) and PIN-FORMED1 (PIN1) auxin transport components underpins the directionality of intercellular auxin flow in Arabidopsis thaliana roots. Here, we examined the mechanism of polar trafficking of AUX1. Real-time live cell analysis along with subcellular markers revealed that AUX1 resides at the apical plasma membrane of protophloem cells and at highly dynamic subpopulations of Golgi apparatus and endosomes in all cell types. Plasma membrane and intracellular pools of AUX1 are interconnected by actin-dependent constitutive trafficking, which is not sensitive to the vesicle trafficking inhibitor brefeldin A. AUX1 subcellular dynamics are not influenced by the auxin influx inhibitor NOA but are blocked by the auxin efflux inhibitors TIBA and PBA. Furthermore, auxin transport inhibitors and interference with the sterol composition of membranes disrupt polar AUX1 distribution at the plasma membrane. Compared with PIN1 trafficking, AUX1 dynamics display different sensitivities to trafficking inhibitors and are independent of the endosomal trafficking regulator ARF GEF GNOM. Hence, AUX1 uses a novel trafficking pathway in plants that is distinct from PIN trafficking, providing an additional mechanism for the fine regulation of auxin transport.},
  author       = {Kleine-Vehn, Jürgen and Dhonukshe, Pankaj and Swarup, Ranjan and Bennett, Malcolm and Jirí Friml},
  journal      = {Plant Cell},
  number       = {11},
  pages        = {3171 -- 3181},
  publisher    = {American Society of Plant Biologists},
  title        = {{Subcellular trafficking of the Arabidopsis auxin influx carrier AUX1 uses a novel pathway distinct from PIN1}},
  doi          = {10.1105/tpc.106.042770},
  volume       = {18},
  year         = {2006},
}

@article{3020,
  abstract     = {High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular level. Here, we present an in situ mRNA hybridization method that is routinely used for the analysis of plant gene expression patterns. The protocol is optimized for whole mount mRNA localizations in Arabidopsis seedling tissues including embryos, roots, hypocotyls and young primary leaves. It can also be used for comparable tissues in other species. Part of the protocol can also be automated and performed by a liquid handling robot. Here we present a detailed protocol, recommended controls and troubleshooting, along with examples of several applications. The total time to carry out the entire procedure is ∼7 d, depending on the tissue used.},
  author       = {Hejátko, Jan and Blilou, Ikram and Brewer, Philip B and Jirí Friml and Scheres, Ben and Eva Benková},
  journal      = {Nature Protocols},
  number       = {4},
  pages        = {1939 -- 1946},
  publisher    = {Nature Publishing Group},
  title        = {{In situ hybridization technique for mRNA detection in whole mount Arabidopsis samples}},
  doi          = {10.1038/nprot.2006.333},
  volume       = {1},
  year         = {2006},
}

@inproceedings{2088,
  abstract     = {We have measured 3D face geometry, skin reflectance, and subsurface scattering using custom-built devices for 149 subjects of varying age, gender, and race. We developed a novel skin reflectance model whose parameters can be estimated from measurements. The model decomposes the large amount of measured skin data into a spatially-varying analytic BRDF, a diffuse albedo map, and diffuse subsurface scattering. Our model is intuitive, physically plausible, and - since we do not use the original measured data - easy to edit as well. High-quality renderings come close to reproducing real photographs. The analysis of the model parameters for our sample population reveals variations according to subject age, gender, skin type, and external factors (e.g., sweat, cold, or makeup). Using our statistics, a user can edit the overall appearance of a face (e.g., changing skin type and age) or change small-scale features using texture synthesis (e.g., adding moles and freckles). We are making the collected statistics publicly available to the research community for applications in face synthesis and analysis. },
  author       = {Weyrich, Tim and Matusik, Wojciech and Pfister, Hanspeter and Bernd Bickel and Donner, Craig and Tu, Chien and McAndless, Janet M and Lee, Jinho and Ngan, Addy and Jensen, Henrik W and Groß, Markus S},
  pages        = {1013 -- 1024},
  publisher    = {ACM},
  title        = {{Analysis of human faces using a measurement-based skin reflectance model}},
  doi          = {10.1145/1179352.1141987},
  year         = {2006},
}

@article{2089,
  abstract     = {We have measured 3D face geometry, skin reflectance, and subsurface scattering using custom-built devices for 149 subjects of varying age, gender, and race. We developed a novel skin reflectance model whose parameters can be estimated from measurements. The model decomposes the large amount of measured skin data into a spatially-varying analytic BRDF, a diffuse albedo map, and diffuse subsurface scattering. Our model is intuitive, physically plausible, and - since we do not use the original measured data - easy to edit as well. High-quality renderings come close to reproducing real photographs. The analysis of the model parameters for our sample population reveals variations according to subject age, gender, skin type, and external factors (e.g., sweat, cold, or makeup). Using our statistics, a user can edit the overall appearance of a face (e.g., changing skin type and age) or change small-scale features using texture synthesis (e.g., adding moles and freckles). We are making the collected statistics publicly available to the research community for applications in face synthesis and analysis.},
  author       = {Weyrich, Tim and Matusik, Wojciech and Pfister, Hanspeter and Bernd Bickel and Donner, Craig and Tu, Chien and McAndless, Janet M and Lee, Jinho and Ngan, Addy and Jensen, Henrik W and Groß, Markus S},
  journal      = {ACM Transactions on Graphics},
  number       = {3},
  pages        = {1013 -- 1024},
  publisher    = {ACM},
  title        = {{Analysis of human faces using a measurement-based skin reflectance model}},
  doi          = {10.1145/1141911.1141987},
  volume       = {25},
  year         = {2006},
}

@inproceedings{2090,
  author       = {Bernd Bickel and Weyrich, Tim and Matusik, Wojciech and Pfister, Hanspeter and Donner, Craig and Tu, Chien and McAndless, Janet M and Lee, Jinho and Ngan, Addy and Jensen, Henrik W and Groß, Markus S},
  publisher    = {ACM},
  title        = {{Processing and editing of faces using a measurement-based skin reflectance model}},
  doi          = {10.1145/1179849.1180059},
  year         = {2006},
}

@article{213,
  abstract     = {For any integers d,n ≥2, let X ⊂ Pn be a non‐singular hypersurface of degree d that is defined over the rational numbers. The main result in this paper is a proof that the number of rational points on X which have height at most B is O(Bn − 1 + ɛ), for any ɛ > 0. The implied constant in this estimate depends at most upon d, ɛ and n. 2000 Mathematics Subject Classification 11D45 (primary), 11G35, 14G05 (secondary).},
  author       = {Timothy Browning and Heath-Brown, Roger and Starr, Jason M},
  journal      = {Proceedings of the London Mathematical Society},
  number       = {2},
  pages        = {273 -- 303},
  publisher    = {John Wiley and Sons Ltd},
  title        = {{The density of rational points on non-singular hypersurfaces, II}},
  doi          = {https://doi.org/10.1112/S0024611506015784},
  volume       = {93},
  year         = {2006},
}

@article{2134,
  abstract     = {Predissociation of the N+2 C 2Σ+u(v') vibrational levels with v' ≥ 3 was observed via dispersed C 2Σ+u → X 2Σ+g fluorescence in the spectral range of 165–208 nm after resonant 1s−1π*(vr) excitation of N2 and its subsequent autoionization into the N+2 C state. This range is dominated by lines in atomic nitrogen, by overlapped C 2Σ+u(v') → X 2Σ+g(v'') vibrational band sequences with Δv = const and broad unresolved band systems (D, (2))2Πg(v') → A2Πu(v'') in the N+2 molecular ion. With very high fluorescence resolution of about 0.1 nm FWHM individual C 2Σ+u(v') → X 2Σ+g(v'') vibrational bands have been resolved. Calculation of the observed fluorescence spectra by taking into account predissociation and molecular rotation describes well the shape of both individual vibrational bands C 2Σ+u(v') → X 2Σ+g(v'') and the whole band system.},
  author       = {Ehresmann, Arno and Werner, Lutz and Klumpp, Stefan and Demekhin, Ph V and Mikhail Lemeshko and Sukhorukov, V. L and Schartner, Karl H and Schmoranzer, Hans P},
  journal      = {Journal of Physics B: Atomic, Molecular and Optical Physics},
  number       = {6},
  pages        = {L119 -- L126},
  publisher    = {IOP Publishing Ltd.},
  title        = {{Predissociation of the N+2(C 2Σ+u) state observed via C 2Σ+u → X 2Σ+g fluorescence after resonant 1s−1π* excitation of N2 molecule}},
  doi          = {10.1088/0953-4075/39/6/L03},
  volume       = {39},
  year         = {2006},
}

@article{2142,
  abstract     = {Fluorescence from fragments formed after the de-excitation of the N*2(1s−1π*) resonance has been measured in the spectral range of 135–190 nm. This range is dominated by lines in atomic nitrogen and lines formed by overlapping C2Σ+u(v') → X2Σ+g(v'') bands with Δv = const in the N+2 molecular ion which result from the spectator Auger decays of the N*2(1s−1π*(vr)) resonances. Ab initio calculations of the corresponding potential curves and transition probabilities showed that the observed irregular intensity dependence of the C2Σ+u(v') → X2Σ+g(v'')(Δv = const) fluorescence lines on the vibrational quantum number vr is due to transitions between vibrational levels during the reaction N2(v0 = 0)→ N*2(1s−1π*(vr)) Longrightarrow C2Σ+u(v') → X2Σ+g(v'').},
  author       = {Ehresmann, Arno and Werner, Lutz and Klumpp, Stefan and Lucht, S and Schmoranzer, Hans P and Mickat, Sascha and Schill, Rüdiger H and Schartner, Karl H and Demekhin, Philipp and Mikhail Lemeshko and Sukhorukov, Victor L},
  journal      = {Journal of Physics B: Atomic, Molecular and Optical Physics},
  number       = {2},
  pages        = {283 -- 304},
  publisher    = {IOP Publishing Ltd.},
  title        = {{Studying the N+2(C2Σ+u → X2Σ+g) fluorescence excited via the 1s−1π* resonance}},
  doi          = {10.1088/0953-4075/39/2/006},
  volume       = {39},
  year         = {2006},
}

@article{2144,
  abstract     = {Temperature dependent preedge and extended x-ray absorption fine structure measurements at the Zr K edge for the perovskite-type zirconates Pb Zr0.515 Ti0.485 O3 (PZT), PbZr O3 (PZ), and BaZr O3 are performed. To carry out a more accurate study of the weak reconstruction of the local atomic structure we employed a combination of two techniques: (i) analysis of the preedge fine structure, and (ii) analysis of the Fourier transform of the difference between χ (k) functions obtained at different temperatures. A detailed investigation of local atomic structure in the cubic phase for all the crystals is also performed. It is shown that neither the displacive nor the order-disorder model can describe correctly the changes of local atomic structure during phase transitions in PZ and PZT. A spherical model describing the local atomic structure of perovskite-type crystals suffering structural phase transitions is proposed.},
  author       = {Vedrinskiǐ, Rostislav V and Nazarenko, Elena S and Mikhail Lemeshko and Nassif, Vivian M and Proux, Olivier and Novakovich, Alexander A and Joly, Yves},
  journal      = {Physical Review B - Condensed Matter and Materials Physics},
  number       = {13},
  publisher    = {American Physical Society},
  title        = {{Temperature dependent XAFS studies of local atomic structure of the perovskite-type zirconates}},
  doi          = {10.1103/PhysRevB.73.134109},
  volume       = {73},
  year         = {2006},
}

@article{215,
  abstract     = {For any n≥3, let F ∈ Z[X0,...,Xn ] be a form of degree d *≥5 that defines a non-singular hypersurface X ⊂ Pn . The main result in this paper is a proof of the fact that the number N (F ; B) of Q-rational points on X which have height at most B satisfiesN (F ; B) = Od,ε,n (Bn −1+ε ), for any ε > 0. The implied constant in this estimate depends at most upon d, ε and n. New estimates are also obtained for the number of representations of a positive integer as the sum of three dth powers, and for the paucity of integer solutions to equal sums of like polynomials.*},
  author       = {Timothy Browning and Heath-Brown, Roger},
  journal      = {Bulletin of the London Mathematical Society},
  number       = {3},
  pages        = {401 -- 410},
  publisher    = {Wiley-Blackwell},
  title        = {{The density of rational points on non-singular hypersurfaces, I}},
  doi          = {10.1112/S0024609305018412},
  volume       = {38},
  year         = {2006},
}

@article{216,
  abstract     = {For any N ≥ 2, let Z ⊂ ℙN be a geometrically integral algebraic variety of degree d. This article is concerned with the number Nz(B) of ℚ-rational points on Z which have height at most B. For any ε > 0, we establish the estimate NZ(B) = O d,ε,N(Bdim Z+ε), provided that d ≥ 6. As indicated, the implied constant depends at most on d, ε, and N.},
  author       = {Timothy Browning and Heath-Brown, Roger and Salberger, Per},
  journal      = {Duke Mathematical Journal},
  number       = {3},
  pages        = {545 -- 578},
  publisher    = {Unknown},
  title        = {{Counting rational points on algebraic varieties}},
  doi          = {10.1215/S0012-7094-06-13236-2},
  volume       = {132},
  year         = {2006},
}

@article{218,
  abstract     = {This paper is concerned with the average order of certain arithmetic functions, as they range over the values taken by binary forms.},
  author       = {de la Bretèche, Régis and Timothy Browning},
  journal      = {Acta Arithmetica},
  number       = {3},
  pages        = {291 -- 304},
  publisher    = {Instytut Matematyczny},
  title        = {{Sums of arithmetic functions over values of binary forms}},
  doi          = {10.4064/aa125-3-6},
  volume       = {125},
  year         = {2006},
}

@article{13428,
  abstract     = {Mixtures of oppositely charged nanoparticles of various sizes and charge ratios precipitate only at the point of electroneutrality. This phenomenonspecific to the nanoscale and reminiscent of threshold precipitation of ionsis a consequence of the formation of core-and-shell nanoparticle aggregates, in which the shells are composed of like-charged particles and are stabilized by efficient electrostatic screening.},
  author       = {Kalsin, Alexander M. and Kowalczyk, Bartlomiej and Smoukov, Stoyan K. and Klajn, Rafal and Grzybowski, Bartosz A.},
  issn         = {1520-5126},
  journal      = {Journal of the American Chemical Society},
  keywords     = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis},
  number       = {47},
  pages        = {15046--15047},
  publisher    = {American Chemical Society},
  title        = {{Ionic-like behavior of oppositely charged nanoparticles}},
  doi          = {10.1021/ja0642966},
  volume       = {128},
  year         = {2006},
}

@article{13429,
  abstract     = {The fruitful core: Organic syntheses reported in the literature from 1850 to 2004 are analyzed with mathematical tools from network theory and statistical physics. There is a set of substances (the core) from which the majority of other organic compounds can be made (see picture; red: core, blue: periphery, green: islands). Search algorithms are used to identify small optimal sets of maximally useful chemicals.},
  author       = {Bishop, Kyle J. M. and Klajn, Rafal and Grzybowski, Bartosz A.},
  issn         = {1521-3773},
  journal      = {Angewandte Chemie International Edition},
  keywords     = {General Chemistry, Catalysis},
  number       = {32},
  pages        = {5348--5354},
  publisher    = {Wiley},
  title        = {{The core and most useful molecules in organic chemistry}},
  doi          = {10.1002/anie.200600881},
  volume       = {45},
  year         = {2006},
}

@article{13430,
  abstract     = {Dynamic self-assembly (DySA) processes occurring outside of thermodynamic equilibrium underlie many forms of adaptive and intellligent behaviors in natural systems. Relatively little, however, is known about the principles that govern DySA and the ways in which it can be extended to artificial ensembles. This article discusses recent advances in both the theory and the practice of nonequilibrium self-assembly. It is argued that a union of ideas from thermodynamics and dynamic systems' theory can provide a general description of DySA. In parallel, heuristic design rules can be used to construct DySA systems of increasing complexities based on a variety of suitable interactions/potentials on length scales from nanoscopic to macroscopic. Applications of these rules to magnetohydrodynamic DySA are also discussed.},
  author       = {Fialkowski, Marcin and Bishop, Kyle J. M. and Klajn, Rafal and Smoukov, Stoyan K. and Campbell, Christopher J. and Grzybowski, Bartosz A.},
  issn         = {1520-6106},
  journal      = {The Journal of Physical Chemistry B},
  keywords     = {Materials Chemistry, Surfaces, Coatings and Films, Physical and Theoretical Chemistry},
  number       = {6},
  pages        = {2482--2496},
  publisher    = {American Chemical Society},
  title        = {{Principles and implementations of dissipative (dynamic) self-assembly}},
  doi          = {10.1021/jp054153q},
  volume       = {110},
  year         = {2006},
}

@article{1461,
  abstract     = {This note proves combinatorially that the intersection pairing on the middle-dimensional compactly supported cohomology of a toric hyperkähler variety is always definite, providing a large number of non-trivial L 2 harmonic forms for toric hyperkähler metrics on these varieties. This is motivated by a result of Hitchin about the definiteness of the pairing of L 2 harmonic forms on complete hyperkähler manifolds of linear growth.},
  author       = {Tamas Hausel and Swartz, Edward},
  journal      = {Proceedings of the American Mathematical Society},
  number       = {8},
  pages        = {2403 -- 2409},
  publisher    = {American Mathematical Society},
  title        = {{Intersection forms of toric hyperkähler varieties}},
  doi          = {10.1090/S0002-9939-06-08248-7},
  volume       = {134},
  year         = {2006},
}