@inbook{2922, author = {Vicente, Sara and Vladimir Kolmogorov and Rother, Carsten}, booktitle = {Markov Random Fields for Vision and Image Processing}, editor = {Blake, Andrew and Kohli, Pushmeet and Rother, Carsten}, publisher = {Massachusetts Institute of Technology Press}, title = {{Graph-cut Based Image Segmentation with Connectivity Priors}}, year = {2011}, } @inbook{2923, author = {Kumar, M Pawan and Vladimir Kolmogorov and Torr, Philip H}, booktitle = {Markov Random Fields for Vision and Image Processing}, editor = {Blake, Andrew and Kohli, Pushmeet and Rother, Carsten}, publisher = {Massachusetts Institute of Technology Press}, title = {{Analyzing Convex Relaxations for MAP Estimation}}, year = {2011}, } @inbook{2924, author = {Criminisi, Antonio and Cross, Geoffrey and Blake, Andrew and Vladimir Kolmogorov}, booktitle = {Markov Random Fields for Vision and Image Processing}, editor = {Blake, Andrew and Kohli, Pushmeet and Rother, Carsten}, publisher = {Massachusetts Institute of Technology Press}, title = {{Bilayer Segmentation of Video}}, year = {2011}, } @inbook{2925, author = {Rother, Carsten and Vladimir Kolmogorov and Boykov, Yuri and Blake, Andrew}, booktitle = {Markov Random Fields for Vision and Image Processing}, editor = {Blake, Andrew and Kohli, Pushmeet and Rother, Carsten}, publisher = {Massachusetts Institute of Technology Press}, title = {{Interactive Foreground Extraction using graph cut}}, year = {2011}, } @inbook{2935, author = {Boykov, Yuri and Vladimir Kolmogorov}, booktitle = {Markov Random Fields for Vision and Image Processing}, editor = {Blake, Andrew and Kohli, Pushmeet and Rother, Carsten}, pages = {31 -- 50}, publisher = {Massachusetts Institute of Technology Press}, title = {{Basic graph cut algorithms}}, year = {2011}, } @inproceedings{2960, abstract = {Traditional statistical methods for the confidentiality protection for statistical databases do not scale well to deal with GWAS (genome-wide association studies) databases and external information on them. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual's privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially private approach to penalized logistic regression.}, author = {Fienberg, Stephen E and Slavkovic, Aleksandra and Caroline Uhler}, publisher = {IEEE}, title = {{Privacy Preserving GWAS Data Sharing}}, doi = {10.1109/ICDMW.2011.140}, year = {2011}, } @article{2961, abstract = {Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specic phenotype. However, a particular phenotype is usually the result of complex relationships between multiple loci and the environment. In this paper, we describe a two-stage method for detecting epistasis by combining the traditionally used single-locus search with a search for multiway interactions. Our method is based on an extended version of Fisher's exact test. To perform this test, a Markov chain is constructed on the space of multidimensional contingency tables using the elements of a Markov basis as moves. We test our method on simulated data and compare it to a two-stage logistic regression method and to a fully Bayesian method, showing that we are able to detect the interacting loci when other methods fail to do so. Finally, we apply our method to a genome-wide data set consisting of 685 dogs and identify epistasis associated with canine hair length for four pairs of single nucleotide polymorphisms (SNPs).}, author = {Malaspinas, Anna-Sapfo and Caroline Uhler}, journal = {Journal of Algebraic Statistics}, number = {1}, pages = {36 -- 53}, publisher = {Public Knowledge Project}, title = {{Detecting epistasis via Markov bases}}, doi = {http://dx.doi.org/10.18409/jas.v2i1.27}, volume = {2}, year = {2011}, } @inproceedings{2975, abstract = {Zero-knowledge proofs of knowledge (ZK-PoK) for discrete logarithms and related problems are indispensable for practical cryptographic protocols. Recently, Camenisch, Kiayias, and Yung provided a specification language (the CKY-language) for such protocols which allows for a modular design and protocol analysis: for every zero-knowledge proof specified in this language, protocol designers are ensured that there exists an efficient protocol which indeed proves the specified statement. However, the protocols resulting from their compilation techniques only satisfy the classical notion of ZK-PoK, which is not retained are when they used as building blocks for higher-level applications or composed with other protocols. This problem can be tackled by moving to the Universal Composability (UC) framework, which guarantees retention of security when composing protocols in arbitrary ways. While there exist generic transformations from $\Sigma$-protocols to UC-secure protocols, these transformation are often too inefficient for practice. In this paper we introduce a specification language akin to the CKY-language and a compiler such that the resulting protocols are UC-secure and efficient. To this end, we propose an extension of the UC-framework addressing the issue that UC-secure zero-knowledge proofs are by definition proofs of knowledge, and state a special composition theorem which allows one to use the weaker -- but more efficient and often sufficient -- notion of proofs of membership in the UC-framework. We believe that our contributions enable the design of practically efficient protocols that are UC-secure and thus themselves can be used as building blocks.}, author = {Camenisch, Jan and Stephan Krenn and Shoup, Victor}, editor = {Lee, Dong Hoon and Wang, Xiaoyun}, pages = {449 -- 467}, publisher = {Springer}, title = {{A Framework for Practical Universally Composable Zero-Knowledge Protocols}}, doi = {10.1007/978-3-642-25385-0}, volume = {7073}, year = {2011}, } @inproceedings{2976, abstract = {Side channel attacks on cryptographic systems exploit information gained from physical implementations rather than theoretical weaknesses of a scheme. In recent years, major achievements were made for the class of so called access-driven cache attacks. Such attacks exploit the leakage of the memory locations accessed by a victim process. In this paper we consider the AES block cipher and present an attack which is capable of recovering the full secret key in almost realtime for AES-128, requiring only a very limited number of observed encryptions. Unlike previous attacks, we do not require any information about the plaintext (such as its distribution, etc.). Moreover, for the first time, we also show how the plaintext can be recovered without having access to the ciphertext at all. It is the first working attack on AES implementations using compressed tables. There, no efficient techniques to identify the beginning of AES rounds is known, which is the fundamental assumption underlying previous attacks. We have a fully working implementation of our attack which is able to recover AES keys after observing as little as 100 encryptions. It works against the OpenSSL 0.9.8n implementation of AES on Linux systems. Our spy process does not require any special privileges beyond those of a standard Linux user. A contribution of probably independent interest is a denial of service attack on the task scheduler of current Linux systems (CFS), which allows one to observe (on average) every single memory access of a victim process.}, author = {Gullasch, David and Bangerter, Endre and Stephan Krenn}, pages = {490 -- 505}, publisher = {IEEE}, title = {{Cache Games - Bringing Access-Based Cache Attacks on AES to Practice}}, doi = {10.1109/SP.2011.22}, year = {2011}, } @inproceedings{2977, abstract = {Cryptographic two-party protocols are used ubiquitously in everyday life. While some of these protocols are easy to understand and implement (e.g., key exchange or transmission of encrypted data), many of them are much more complex (e.g., e-banking and e-voting applications, or anonymous authentication and credential systems). For a software engineer without appropriate cryptographic skills the implementation of such protocols is often difficult, time consuming and error-prone. For this reason, a number of compilers supporting programmers have been published in recent years. However, they are either designed for very specific cryptographic primitives (e.g., zero-knowledge proofs of knowledge), or they only offer a very low level of abstraction and thus again demand substantial mathematical and cryptographic skills from the programmer. Finally, some of the existing compilers do not produce executable code, but only metacode which has to be instantiated with mathematical libraries, encryption routines, etc. before it can actually be used. In this paper we present a cryptographically aware compiler which is equally useful to cryptographers who want to benchmark protocols designed on paper, and to programmers who want to implement complex security sensitive protocols without having to understand all subtleties. Our tool offers a high level of abstraction and outputs well-structured and documented Java code. We believe that our compiler can contribute to shortening the development cycles of cryptographic applications and to reducing their error-proneness.}, author = {Bangerter, Endre and Stephan Krenn and Seifriz, Martial and Ultes-Nitsche, Ulrich}, editor = {Venter, Hein S. and Coetzee, Marijke and Loock, Marianne}, publisher = {IEEE}, title = {{cPLC - A Cryptographic Programming Language and Compiler}}, doi = {10.1109/ISSA.2011.6027533}, year = {2011}, } @article{3082, abstract = {Shoot branching is one of the major determinants of plant architecture. Polar auxin transport in stems is necessary for the control of bud outgrowth by a dominant apex. Here, we show that following decapitation in pea (Pisum sativum L.), the axillary buds establish directional auxin export by subcellular polarization of PIN auxin transporters. Apical auxin application on the decapitated stem prevents this PIN polarization and canalization of laterally applied auxin. These results support a model in which the apical and lateral auxin sources compete for primary channels of auxin transport in the stem to control the outgrowth of axillary buds.}, author = {Balla, Jozef and Kalousek, Petr and Reinöhl, Vilém and Jirí Friml and Procházka, Stanislav}, journal = {Plant Journal}, number = {4}, pages = {571 -- 577}, publisher = {Wiley-Blackwell}, title = {{Competitive canalization of PIN dependent auxin flow from axillary buds controls pea bud outgrowth}}, doi = {10.1111/j.1365-313X.2010.04443.x}, volume = {65}, year = {2011}, } @article{3083, author = {Robinson, David G and Scheuring, David and Naramoto, Satoshi and Jirí Friml}, journal = {Plant Cell}, number = {3}, pages = {846 -- 849}, publisher = {American Society of Plant Biologists}, title = {{ARF1 localizes to the golgi and the trans Golgi network}}, doi = {10.1105/tpc.110.082099}, volume = {23}, year = {2011}, } @article{3084, abstract = { A central question in developmental biology concerns the mechanism of generation and maintenance of cell polarity, because these processes are essential for many cellular functions and multicellular development [1]. In plants, cell polarity has an additional role in mediating directional transport of the plant hormone auxin that is crucial for multiple developmental processes [2-4]. In addition, plant cells have a complex extracellular matrix, the cell wall [5, 6], whose role in regulating cellular processes, including cell polarity, is unexplored. We have found that polar distribution of PIN auxin transporters [7] in plant cells is maintained by connections between polar domains at the plasma membrane and the cell wall. Genetic and pharmacological interference with cellulose, the major component of the cell wall, or mechanical interference with the cell wall disrupts these connections and leads to increased lateral diffusion and loss of polar distribution of PIN transporters for the phytohormone auxin. Our results reveal a plant-specific mechanism for cell polarity maintenance and provide a conceptual framework for modulating cell polarity and plant development via endogenous and environmental manipulations of the cellulose-based extracellular matrix.}, author = {Feraru, Elena and Feraru, Mugurel I and Kleine-Vehn, Jürgen and Martinière, Alexandre and Mouille, Grégory and Vanneste, Steffen and Vernhettes, Samantha and Runions, John and Jirí Friml}, journal = {Current Biology}, number = {4}, pages = {338 -- 343}, publisher = {Cell Press}, title = {{PIN polarity maintenance by the cell wall in Arabidopsis}}, doi = {10.1016/j.cub.2011.01.036}, volume = {21}, year = {2011}, } @article{3085, abstract = {Phototropism is an adaptation response, through which plants grow towards the light. It involves light perception and asymmetric distribution of the plant hormone auxin. Here we identify a crucial part of the mechanism for phototropism, revealing how light perception initiates auxin redistribution that leads to directional growth. We show that light polarizes the cellular localization of the auxin efflux carrier PIN3 in hypocotyl endodermis cells, resulting in changes in auxin distribution and differential growth. In the dark, high expression and activity of the PINOID (PID) kinase correlates with apolar targeting of PIN3 to all cell sides. Following illumination, light represses PINOID transcription and PIN3 is polarized specifically to the inner cell sides by GNOM ARF GTPase GEF (guanine nucleotide exchange factor)-dependent trafficking. Thus, differential trafficking at the shaded and illuminated hypocotyl side aligns PIN3 polarity with the light direction, and presumably redirects auxin flow towards the shaded side, where auxin promotes growth, causing hypocotyls to bend towards the light. Our results imply that PID phosphorylation-dependent recruitment of PIN proteins into distinct trafficking pathways is a mechanism to polarize auxin fluxes in response to different environmental and endogenous cues.}, author = {Ding, Zhaojun and Galván-Ampudia, Carlos S and Demarsy, Emilie and Łangowski, Łukasz and Kleine-Vehn, Jürgen and Fan, Yuanwei and Morita, Miyo T and Tasaka, Masao and Fankhauser, Christian and Offringa, Remko and Jirí Friml}, journal = {Nature Cell Biology}, number = {4}, pages = {447 -- 453}, publisher = {Nature Publishing Group}, title = {{Light-mediated polarization of the PIN3 auxin transporter for the phototropic response in Arabidopsis}}, doi = {10.1038/ncb2208}, volume = {13}, year = {2011}, } @article{3086, abstract = {PIN-FORMED (PIN)-dependent auxin transport is essential for plant development and its modulation in response to the environment or endogenous signals. A NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3)-like protein, MACCHI-BOU 4 (MAB4), has been shown to control PIN1 localization during organ formation, but its contribution is limited. The Arabidopsis genome contains four genes, MAB4/ENP/NPY1-LIKE1 (MEL1), MEL2, MEL3 and MEL4, highly homologous to MAB4. Genetic analysis disclosed functional redundancy between MAB4 and MEL genes in regulation of not only organ formation but also of root gravitropism, revealing that NPH3 family proteins have a wider range of functions than previously suspected. Multiple mutants showed severe reduction in PIN abundance and PIN polar localization, leading to defective expression of an auxin responsive marker DR5rev::GFP. Pharmacological analyses and fluorescence recovery after photo-bleaching experiments showed that mel mutations increase PIN2 internalization from the plasma membrane, but affect neither intracellular PIN2 trafficking nor PIN2 lateral diffusion at the plasma membrane. Notably, all MAB4 subfamily proteins show polar localization at the cell periphery in plants. The MAB4 polarity was almost identical to PIN polarity. Our results suggest that the MAB4 subfamily proteins specifically retain PIN proteins in a polarized manner at the plasma membrane, thus controlling directional auxin transport and plant development.}, author = {Furutani, Masahiko and Sakamoto, Norihito and Yoshida, Shuhei and Kajiwara, Takahito and Robert, Hélène S and Jirí Friml and Tasaka, Masao}, journal = {Development}, number = {10}, pages = {2069 -- 2078}, publisher = {Company of Biologists}, title = {{Polar localized NPH3-like proteins regulate polarity and endocytosis of PIN-FORMED auxin efflux carriers}}, doi = {10.1242/dev.057745}, volume = {138}, year = {2011}, } @article{3087, abstract = {Endocytosis is a crucial mechanism by which eukaryotic cells internalize extracellular and plasma membrane material, and it is required for a multitude of cellular and developmental processes in unicellular and multicellular organisms. In animals and yeast, the best characterized pathway for endocytosis depends on the function of the vesicle coat protein clathrin. Clathrinmediated endocytosis has recently been demonstrated also in plant cells, but its physiological and developmental roles remain unclear. Here, we assessed the roles of the clathrin-mediated mechanism of endocytosis in plants by genetic means. We interfered with clathrin heavy chain (CHC) function through mutants and dominant-negative approaches in Arabidopsis thaliana and established tools to manipulate clathrin function in a cell type-specific manner. The chc2 single mutants and dominant-negative CHC1 (HUB) transgenic lines were defective in bulk endocytosis as well as in internalization of prominent plasma membrane proteins. Interference with clathrin-mediated endocytosis led to defects in constitutive endocytic recycling of PIN auxin transporters and their polar distribution in embryos and roots. Consistent with this, these lines had altered auxin distribution patterns and associated auxin transport-related phenotypes, such as aberrant embryo patterning, imperfect cotyledon specification, agravitropic growth, and impaired lateral root organogenesis. Together, these data demonstrate a fundamental role for clathrin function in cell polarity, growth, patterning, and organogenesis in plants.}, author = {Kitakura, Saeko and Vanneste, Steffen and Robert, Stéphanie and Löfke, Christian and Teichmann, Thomas and Tanaka, Hirokazu and Jirí Friml}, journal = {Plant Cell}, number = {5}, pages = {1920 -- 1931}, publisher = {American Society of Plant Biologists}, title = {{Clathrin mediates endocytosis and polar distribution of PIN auxin transporters in Arabidopsis}}, doi = {10.1105/tpc.111.083030}, volume = {23}, year = {2011}, } @article{3088, abstract = {Background: Whereas the majority of animals develop toward a predetermined body plan, plants show iterative growth and continually produce new organs and structures from actively dividing meristems. This raises an intriguing question: How are these newly developed organs patterned? In Arabidopsis embryos, radial symmetry is broken by the bisymmetric specification of the cotyledons in the apical domain. Subsequently, this bisymmetry is propagated to the root promeristem. Results: Here we present a mutually inhibitory feedback loop between auxin and cytokinin that sets distinct boundaries of hormonal output. Cytokinins promote the bisymmetric distribution of the PIN-FORMED (PIN) auxin efflux proteins, which channel auxin toward a central domain. High auxin promotes transcription of the cytokinin signaling inhibitor AHP6, which closes the interaction loop. This bisymmetric auxin response domain specifies the differentiation of protoxylem in a bisymmetric pattern. In embryonic roots, cytokinin is required to translate a bisymmetric auxin response in the cotyledons to a bisymmetric vascular pattern in the root promeristem. Conclusions: Our results present an interactive feedback loop between hormonal signaling and transport by which small biases in hormonal input are propagated into distinct signaling domains to specify the vascular pattern in the root meristem. It is an intriguing possibility that such a mechanism could transform radial patterns and allow continuous vascular connections between other newly emerging organs.}, author = {Bishopp, Anthony and Help, Hanna and El-Showk, Sedeer and Weijers, Dolf and Scheres, Ben and Jirí Friml and Eva Benková and Mähönen, Ari Pekka and Helariutta, Ykä}, journal = {Current Biology}, number = {11}, pages = {917 -- 926}, publisher = {Cell Press}, title = {{A mutually inhibitory interaction between auxin and cytokinin specifies vascular pattern in roots}}, doi = {10.1016/j.cub.2011.04.017}, volume = {21}, year = {2011}, } @article{3089, abstract = {The phytohormone auxin is an important determinant of plant development. Directional auxin flow within tissues depends on polar localization of PIN auxin transporters. To explore regulation of PIN-mediated auxin transport, we screened for suppressors of PIN1 overexpression (supo) and identified an inositol polyphosphate 1-phosphatase mutant (supo1), with elevated inositol trisphosphate (InsP 3) and cytosolic Ca 2+ levels. Pharmacological and genetic increases in InsP 3 or Ca 2+ levels also suppressed the PIN1 gain-of-function phenotypes and caused defects in basal PIN localization, auxin transport and auxin-mediated development. In contrast, the reductions in InsP 3 levels and Ca 2+ signaling antagonized the effects of the supo1 mutation and disrupted preferentially apical PIN localization. InsP 3 and Ca 2+ are evolutionarily conserved second messengers involved in various cellular functions, particularly stress responses. Our findings implicate them as modifiers of cell polarity and polar auxin transport, and highlight a potential integration point through which Ca 2+ signaling-related stimuli could influence auxin-mediated development.}, author = {Zhang, Jing and Vanneste, Steffen and Brewer, Philip B and Michniewicz, Marta and Peter Grones and Kleine-Vehn, Jürgen and Löfke, Christian and Teichmann, Thomas and Bielach, Agnieszka and Cannoot, Bernard and Hoyerová, Klára and Xu Chen and Xue, Hong-Wei and Eva Benková and Zažímalová, Eva and Jirí Friml}, journal = {Developmental Cell}, number = {6}, pages = {855 -- 866}, publisher = {Cell Press}, title = {{Inositol trisphosphate-induced ca^2+ signaling modulates auxin transport and pin polarity}}, doi = {10.1016/j.devcel.2011.05.013}, volume = {20}, year = {2011}, } @article{3090, abstract = {The polarized transport of the phytohormone auxin [1], which is crucial for the regulation of different stages of plant development [2, 3], depends on the asymmetric plasma membrane distribution of the PIN-FORMED (PIN) auxin efflux carriers [4, 5]. The PIN polar localization results from clathrin-mediated endocytosis (CME) from the plasma membrane and subsequent polar recycling [6]. The Arabidopsis genome encodes two groups of dynamin-related proteins (DRPs) that show homology to mammalian dynamin - a protein required for fission of endocytic vesicles during CME [7, 8]. Here we show by coimmunoprecipitation (coIP), bimolecular fluorescence complementation (BiFC), and Förster resonance energy transfer (FRET) that members of the DRP1 group closely associate with PIN proteins at the cell plate. Localization and phenotypic analysis of novel drp1 mutants revealed a requirement for DRP1 function in correct PIN distribution and in auxin-mediated development. We propose that rapid and specific internalization of PIN proteins mediated by the DRP1 proteins and the associated CME machinery from the cell plate membranes during cytokinesis is an important mechanism for proper polar PIN positioning in interphase cells.}, author = {Mravec, Jozef and Petrášek, Jan and Li, Na and Boeren, Sjef and Karlova, Rumyana and Kitakura, Saeko and Pařezová, Markéta and Naramoto, Satoshi and Nodzyński, Thomasz and Dhonukshe, Pankaj and Bednarek, Sebastian Y and Zažímalová, Eva and De Vries, Sacco and Jirí Friml}, journal = {Current Biology}, number = {12}, pages = {1055 -- 1060}, publisher = {Cell Press}, title = {{Cell plate restricted association of DRP1A and PIN proteins is required for cell polarity establishment in arabidopsis}}, doi = {10.1016/j.cub.2011.05.018}, volume = {21}, year = {2011}, } @article{3091, author = {Sauer, Michael and Friml, Jirí}, journal = {Molecular Systems Biology}, publisher = {Nature Publishing Group}, title = {{Fleeting hormone cues get stabilized for plant organogenesis}}, doi = {10.1038/msb.2011.45}, volume = {7}, year = {2011}, }