@article{2871, abstract = {Despite their relatively simple appearance, roots are incredibly complex organs that are highly adapted to differing environments. Many aspects of root development are co-ordinated by subtle spatial differences in the concentrations of the phytohormones auxin and cytokinin. Events from the formation of a root during embryogenesis to the determination of the network of lateral roots are controlled by interactions between these hormones. Recently, interactions have been defined where auxin signaling promotes the expression of cytokinin signaling inhibitors, cytokinin signaling promotes the expression of auxin signaling inhibitors and finally where cytokinin signaling regulates the complex network of auxin transport proteins to position zones of high auxin signaling. We are witnessing a period of discovery in which we are beginning to understand how these hormonal pathways communicate to regulate root formation.}, author = {Bishopp, Anthony and Eva Benková and Helariutta, Ykä}, journal = {Current Opinion in Plant Biology}, number = {1}, pages = {10 -- 16}, publisher = {Elsevier}, title = {{Sending mixed messages: Auxin-cytokinin crosstalk in roots}}, doi = {10.1016/j.pbi.2010.08.014}, volume = {14}, year = {2011}, } @article{2874, abstract = {The apical hook develops in the upper part of the hypocotyl when seeds buried in the soil germinate, and serves to protect cotyledons and the shoot apical meristem from possible damage caused by pushing through the soil. The curvature is formed through differential cell growth that occurs at the two opposite sides of the hypocotyl, and it is established by a gradient of auxin activity and refined by the coordinated action of auxin and ethylene. Here we show that gibberellins (GAs) promote hook development through the transcriptional regulation of several genes of the ethylene and auxin pathways in Arabidopsis. The level of GA activity determines the speed of hook formation and the extent of the curvature during the formation phase independently of ethylene, probably by modulating auxin transport and response through HLS1, PIN3, and PIN7. Moreover, GAs cooperate with ethylene in preventing hook opening, in part through the induction of ethylene production mediated by ACS5/ETO2 and ACS8.}, author = {Gallego-Bartolomé, Javier and Arana, María V and Vandenbussche, Filip and Žádníková, Petra and Minguet, Eugenio G and Guardiola, Vicente and Van Der Straeten, Dominique and Eva Benková and Alabadí, David and Blázquez, Miguel A}, journal = {Plant Journal}, number = {4}, pages = {622 -- 634}, publisher = {Wiley-Blackwell}, title = {{Hierarchy of hormone action controlling apical hook development in Arabidopsis}}, doi = {10.1111/j.1365-313X.2011.04621.x}, volume = {67}, year = {2011}, } @article{2897, author = {Tiago Paixao and Azevedo, Ricardo B}, journal = {PLoS Computational Biology}, number = {7}, publisher = {Public Library of Science}, title = {{Redundancy and the Evolution of Cis Regulatory Element Multiplicity}}, doi = {10.1371/journal.pcbi.1000848}, volume = {6}, year = {2011}, } @article{2898, abstract = {Sex allocation theory has been remarkably successful at explaining the prevalence of even sex ratios in natural populations and at identifying specific conditions that can result in biased sex ratios. Much of this theory focuses on parental sex determination (SD) strategies. Here, we consider instead the evolutionary causes and consequences of mixed offspring SD strategies, in which the genotype of an individual determines not its sex, but the probability of developing one of multiple sexes. We find that alleles specifying mixed offspring SD strategies can generally outcompete alleles that specify pure strategies, but generate constraints that may prevent a population from reaching an even sex ratio. We use our model to analyze sex ratios in natural populations of Tetrahymena thermophila, a ciliate with seven sexes determined by mixed SD alleles. We show that probabilistic SD is sufficient to account for the occurrence of skewed sex ratios in natural populations of T. thermophila, provided that their effective population sizes are small. Our results highlight the importance of genetic drift in sex ratio evolution and suggest that mixed offspring SD strategies should be more common than currently thought.}, author = {Tiago Paixao and Phadke, Sujal S and Azevedo, Ricardo B and Zufall, Rebecca A}, journal = {Evolution; International Journal of Organic Evolution}, number = {7}, pages = {2050 -- 2060}, publisher = {Wiley-Blackwell}, title = {{Sex ratio evolution under probabilistic sex determination}}, doi = {10.1111/j.1558-5646.2011.01266.x}, volume = {65}, year = {2011}, } @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{12649, abstract = {Physically based hydrological models describe natural processes more accurately than conceptual models but require extensive data sets to produce accurate results. To identify the value of different data sets for improving the performance of the distributed hydrological model TOPKAPI we combine a multivariable validation technique with Monte Carlo simulations. The study is carried out in the snow and ice-dominated Rhonegletscher basin, as these types of mountainous basins are generally the most critical with respect to data availability and sensitivity to climate fluctuations. Each observational data set is used individually and in combination with the other data sets to determine a subset of best parameter combinations out of 10,000 Monte Carlos runs performed with randomly generated parameter sets. We validate model results against discharge, glacier mass balance, and satellite snow cover images for a 14 year time period (1994–2007). While the use of all data sets combined provides the best overall model performance (defined by the concurrent best agreement of simulated discharge, snow cover and mass balance with their respective measurements), the use of one or two variables for constraining the model results in poorer performance. Using only one data set for constraining the model glacier mass balance proved to be the most efficient observation leading to the best overall model performance. Our main result is that a combination of discharge and satellite snow cover images is best for improving model performance, since the volumetric information of discharge data and the spatial information of snow cover images are complementary.}, author = {Finger, David and Pellicciotti, Francesca and Konz, Markus and Rimkus, Stefan and Burlando, Paolo}, issn = {0043-1397}, journal = {Water Resources Research}, number = {7}, publisher = {American Geophysical Union}, title = {{The value of glacier mass balance, satellite snow cover images, and hourly discharge for improving the performance of a physically based distributed hydrological model}}, doi = {10.1029/2010wr009824}, volume = {47}, year = {2011}, } @inbook{12650, abstract = {Streamflow is a hydrological variable measured at a defined river cross-section; it spatially integrates the runoff generating processes in the contributing watershed, including precipitation and air temperature. Trends in streamflow are progressive changes in the time series of streamflow that can be detected with statistical methods and their statistical significance can be assessed. Mountainous regions are particularly vulnerable to streamflow change because of their high specific runoff and the sensitivity to the distribution of precipitation and air temperature, and the processes of snow accumulation and melt.}, author = {Molnar, Peter and Burlando, Paolo and Pellicciotti, Francesca}, booktitle = {Encyclopedia of Snow, Ice and Glaciers}, editor = {Singh, Vijay and Singh, Pratap and Haritashya, Umesh}, isbn = {978-90-481-2641-5}, issn = {1871-756X}, pages = {1084--1089}, publisher = {Springer Nature}, title = {{Streamflow Trends in Mountainous Regions}}, doi = {10.1007/978-90-481-2642-2_543}, year = {2011}, }