@article{2290, abstract = {The plant hormone indole-acetic acid (auxin) is essential for many aspects of plant development. Auxin-mediated growth regulation typically involves the establishment of an auxin concentration gradient mediated by polarly localized auxin transporters. The localization of auxin carriers and their amount at the plasma membrane are controlled by membrane trafficking processes such as secretion, endocytosis, and recycling. In contrast to endocytosis or recycling, how the secretory pathway mediates the localization of auxin carriers is not well understood. In this study we have used the differential cell elongation process during apical hook development to elucidate the mechanisms underlying the post-Golgi trafficking of auxin carriers in Arabidopsis. We show that differential cell elongation during apical hook development is defective in Arabidopsis mutant echidna (ech). ECH protein is required for the trans-Golgi network (TGN)-mediated trafficking of the auxin influx carrier AUX1 to the plasma membrane. In contrast, ech mutation only marginally perturbs the trafficking of the highly related auxin influx carrier LIKE-AUX1-3 or the auxin efflux carrier PIN-FORMED-3, both also involved in hook development. Electron tomography reveals that the trafficking defects in ech mutant are associated with the perturbation of secretory vesicle genesis from the TGN. Our results identify differential mechanisms for the post-Golgi trafficking of de novo-synthesized auxin carriers to plasma membrane from the TGN and reveal how trafficking of auxin influx carriers mediates the control of differential cell elongation in apical hook development.}, author = {Boutté, Yohann and Jonsson, Kristoffer and Mcfarlane, Heather and Johnson, Errin and Gendre, Delphine and Swarup, Ranjan and Friml, Jirí and Samuels, Lacey and Robert, Stéphanie and Bhalerao, Rishikesh}, journal = {PNAS}, number = {40}, pages = {16259 -- 16264}, publisher = {National Academy of Sciences}, title = {{ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation}}, doi = {10.1073/pnas.1309057110}, volume = {110}, year = {2013}, } @inproceedings{2294, abstract = {In this work we propose a system for automatic classification of Drosophila embryos into developmental stages. While the system is designed to solve an actual problem in biological research, we believe that the principle underly- ing it is interesting not only for biologists, but also for researchers in computer vision. The main idea is to combine two orthogonal sources of information: one is a classifier trained on strongly invariant features, which makes it applicable to images of very different conditions, but also leads to rather noisy predictions. The other is a label propagation step based on a more powerful similarity measure that however is only consistent within specific subsets of the data at a time. In our biological setup, the information sources are the shape and the staining patterns of embryo images. We show experimentally that while neither of the methods can be used by itself to achieve satisfactory results, their combina- tion achieves prediction quality comparable to human performance.}, author = {Kazmar, Tomas and Kvon, Evgeny and Stark, Alexander and Lampert, Christoph}, location = {Sydney, Australia}, publisher = {IEEE}, title = {{Drosophila Embryo Stage Annotation using Label Propagation}}, doi = {10.1109/ICCV.2013.139}, year = {2013}, } @proceedings{2292, abstract = {This book constitutes the thoroughly refereed conference proceedings of the 38th International Symposium on Mathematical Foundations of Computer Science, MFCS 2013, held in Klosterneuburg, Austria, in August 2013. The 67 revised full papers presented together with six invited talks were carefully selected from 191 submissions. Topics covered include algorithmic game theory, algorithmic learning theory, algorithms and data structures, automata, formal languages, bioinformatics, complexity, computational geometry, computer-assisted reasoning, concurrency theory, databases and knowledge-based systems, foundations of computing, logic in computer science, models of computation, semantics and verification of programs, and theoretical issues in artificial intelligence.}, editor = {Chatterjee, Krishnendu and Sgall, Jiri}, isbn = {978-3-642-40312-5}, location = {Klosterneuburg, Austria}, pages = {VI -- 854}, publisher = {Springer}, title = {{Mathematical Foundations of Computer Science 2013}}, doi = {10.1007/978-3-642-40313-2}, volume = {8087}, year = {2013}, } @inproceedings{2293, abstract = {Many computer vision problems have an asymmetric distribution of information between training and test time. In this work, we study the case where we are given additional information about the training data, which however will not be available at test time. This situation is called learning using privileged information (LUPI). We introduce two maximum-margin techniques that are able to make use of this additional source of information, and we show that the framework is applicable to several scenarios that have been studied in computer vision before. Experiments with attributes, bounding boxes, image tags and rationales as additional information in object classification show promising results.}, author = {Sharmanska, Viktoriia and Quadrianto, Novi and Lampert, Christoph}, location = {Sydney, Australia}, pages = {825 -- 832}, publisher = {IEEE}, title = {{Learning to rank using privileged information}}, doi = {10.1109/ICCV.2013.107}, year = {2013}, } @inproceedings{2291, abstract = {Cryptographic access control promises to offer easily distributed trust and broader applicability, while reducing reliance on low-level online monitors. Traditional implementations of cryptographic access control rely on simple cryptographic primitives whereas recent endeavors employ primitives with richer functionality and security guarantees. Worryingly, few of the existing cryptographic access-control schemes come with precise guarantees, the gap between the policy specification and the implementation being analyzed only informally, if at all. In this paper we begin addressing this shortcoming. Unlike prior work that targeted ad-hoc policy specification, we look at the well-established Role-Based Access Control (RBAC) model, as used in a typical file system. In short, we provide a precise syntax for a computational version of RBAC, offer rigorous definitions for cryptographic policy enforcement of a large class of RBAC security policies, and demonstrate that an implementation based on attribute-based encryption meets our security notions. We view our main contribution as being at the conceptual level. Although we work with RBAC for concreteness, our general methodology could guide future research for uses of cryptography in other access-control models. }, author = {Ferrara, Anna and Fuchsbauer, Georg and Warinschi, Bogdan}, location = {New Orleans, LA, United States}, pages = {115 -- 129}, publisher = {IEEE}, title = {{Cryptographically enforced RBAC}}, doi = {10.1109/CSF.2013.15}, year = {2013}, } @proceedings{2288, abstract = {This book constitutes the proceedings of the 11th International Conference on Computational Methods in Systems Biology, CMSB 2013, held in Klosterneuburg, Austria, in September 2013. The 15 regular papers included in this volume were carefully reviewed and selected from 27 submissions. They deal with computational models for all levels, from molecular and cellular, to organs and entire organisms.}, editor = {Gupta, Ashutosh and Henzinger, Thomas A}, isbn = {978-3-642-40707-9}, location = {Klosterneuburg, Austria}, publisher = {Springer}, title = {{Computational Methods in Systems Biology}}, doi = {10.1007/978-3-642-40708-6}, volume = {8130}, year = {2013}, } @inproceedings{2298, abstract = {We present a shape analysis for programs that manipulate overlaid data structures which share sets of objects. The abstract domain contains Separation Logic formulas that (1) combine a per-object separating conjunction with a per-field separating conjunction and (2) constrain a set of variables interpreted as sets of objects. The definition of the abstract domain operators is based on a notion of homomorphism between formulas, viewed as graphs, used recently to define optimal decision procedures for fragments of the Separation Logic. Based on a Frame Rule that supports the two versions of the separating conjunction, the analysis is able to reason in a modular manner about non-overlaid data structures and then, compose information only at a few program points, e.g., procedure returns. We have implemented this analysis in a prototype tool and applied it on several interesting case studies that manipulate overlaid and nested linked lists. }, author = {Dragoi, Cezara and Enea, Constantin and Sighireanu, Mihaela}, location = {Seattle, WA, United States}, pages = {150 -- 171}, publisher = {Springer}, title = {{Local shape analysis for overlaid data structures}}, doi = {10.1007/978-3-642-38856-9_10}, volume = {7935}, year = {2013}, } @article{2299, abstract = {The standard hardware design flow involves: (a) design of an integrated circuit using a hardware description language, (b) extensive functional and formal verification, and (c) logical synthesis. However, the above-mentioned processes consume significant effort and time. An alternative approach is to use a formal specification language as a high-level hardware description language and synthesize hardware from formal specifications. Our work is a case study of the synthesis of the widely and industrially used AMBA AHB protocol from formal specifications. Bloem et al. presented the first formal specifications for the AMBA AHB Arbiter and synthesized the AHB Arbiter circuit. However, in the first formal specification some important assumptions were missing. Our contributions are as follows: (a) We present detailed formal specifications for the AHB Arbiter incorporating the missing details, and obtain significant improvements in the synthesis results (both with respect to the number of gates in the synthesized circuit and with respect to the time taken to synthesize the circuit), and (b) we present formal specifications to generate compact circuits for the remaining two main components of AMBA AHB, namely, AHB Master and AHB Slave. Thus with systematic description we are able to automatically and completely synthesize an important and widely used industrial protocol.}, author = {Godhal, Yashdeep and Chatterjee, Krishnendu and Henzinger, Thomas A}, journal = {International Journal on Software Tools for Technology Transfer}, number = {5-6}, pages = {585 -- 601}, publisher = {Springer}, title = {{Synthesis of AMBA AHB from formal specification: A case study}}, doi = {10.1007/s10009-011-0207-9}, volume = {15}, year = {2013}, } @article{2297, abstract = {We present an overview of mathematical results on the low temperature properties of dilute quantum gases, which have been obtained in the past few years. The presentation includes a discussion of Bose-Einstein condensation, the excitation spectrum for trapped gases and its relation to superfluidity, as well as the appearance of quantized vortices in rotating systems. All these properties are intensely being studied in current experiments on cold atomic gases. We will give a description of the mathematics involved in understanding these phenomena, starting from the underlying many-body Schrödinger equation.}, author = {Seiringer, Robert}, journal = {Japanese Journal of Mathematics}, number = {2}, pages = {185 -- 232}, publisher = {Springer}, title = {{Hot topics in cold gases: A mathematical physics perspective}}, doi = {10.1007/s11537-013-1264-5}, volume = {8}, year = {2013}, } @book{2306, abstract = {Das Buch ist sowohl eine Einführung in die Themen Linked Data, Open Data und Open Linked Data als es auch den konkreten Bezug auf Bibliotheken behandelt. Hierzu werden konkrete Anwendungsprojekte beschrieben. Der Band wendet sich dabei sowohl an Personen aus der Bibliothekspraxis als auch an Personen aus dem Bibliotheksmanagement, die noch nicht mit dem Thema vertraut sind.}, author = {Danowski, Patrick and Pohl, Adrian}, isbn = { 978-3-11-027634-3}, issn = {2191-3587}, publisher = {De Gruyter}, title = {{(Open) Linked Data in Bibliotheken}}, doi = {10.1515/9783110278736}, volume = {50}, year = {2013}, } @inproceedings{2301, abstract = {We describe the design and implementation of P, a domain-specific language to write asynchronous event driven code. P allows the programmer to specify the system as a collection of interacting state machines, which communicate with each other using events. P unifies modeling and programming into one activity for the programmer. Not only can a P program be compiled into executable code, but it can also be tested using model checking techniques. P allows the programmer to specify the environment, used to "close" the system during testing, as nondeterministic ghost machines. Ghost machines are erased during compilation to executable code; a type system ensures that the erasure is semantics preserving. The P language is designed so that a P program can be checked for responsiveness-the ability to handle every event in a timely manner. By default, a machine needs to handle every event that arrives in every state. But handling every event in every state is impractical. The language provides a notion of deferred events where the programmer can annotate when she wants to delay processing an event. The default safety checker looks for presence of unhan-dled events. The language also provides default liveness checks that an event cannot be potentially deferred forever. P was used to implement and verify the core of the USB device driver stack that ships with Microsoft Windows 8. The resulting driver is more reliable and performs better than its prior incarnation (which did not use P); we have more confidence in the robustness of its design due to the language abstractions and verification provided by P.}, author = {Desai, Ankush and Gupta, Vivek and Jackson, Ethan and Qadeer, Shaz and Rajamani, Sriram and Zufferey, Damien}, booktitle = {Proceedings of the 34th ACM SIGPLAN Conference on Programming Language Design and Implementation}, location = {Seattle, WA, United States}, pages = {321 -- 331}, publisher = {ACM}, title = {{P: Safe asynchronous event-driven programming}}, doi = {10.1145/2491956.2462184}, year = {2013}, } @article{2300, abstract = {We consider Ising models in two and three dimensions with nearest neighbor ferromagnetic interactions and long-range, power law decaying, antiferromagnetic interactions. If the strength of the ferromagnetic coupling J is larger than a critical value Jc, then the ground state is homogeneous and ferromagnetic. As the critical value is approached from smaller values of J, it is believed that the ground state consists of a periodic array of stripes (d=2) or slabs (d=3), all of the same size and alternating magnetization. Here we prove rigorously that the ground state energy per site converges to that of the optimal periodic striped or slabbed state, in the limit that J tends to the ferromagnetic transition point. While this theorem does not prove rigorously that the ground state is precisely striped or slabbed, it does prove that in any suitably large box the ground state is striped or slabbed with high probability.}, author = {Giuliani, Alessandro and Lieb, Élliott and Seiringer, Robert}, journal = {Physical Review B}, number = {6}, publisher = {American Physical Society}, title = {{Realization of stripes and slabs in two and three dimensions}}, doi = {10.1103/PhysRevB.88.064401}, volume = {88}, year = {2013}, } @article{2303, abstract = {MADM (Mosaic Analysis with Double Markers) technology offers a genetic approach in mice to visualize and concomitantly manipulate genetically defined cells at clonal level and single cell resolution. MADM employs Cre recombinase/loxP-dependent interchromosomal mitotic recombination to reconstitute two split marker genes—green GFP and red tdTomato—and can label sparse clones of homozygous mutant cells in one color and wild-type cells in the other color in an otherwise unlabeled background. At present, major MADM applications include lineage tracing, single cell labeling, conditional knockouts in small populations of cells and induction of uniparental chromosome disomy to assess effects of genomic imprinting. MADM can be applied universally in the mouse with the sole limitation being the specificity of the promoter controlling Cre recombinase expression. Here I review recent developments and extensions of the MADM technique and give an overview of the major discoveries and progresses enabled by the implementation of the novel genetic MADM tools.}, author = {Hippenmeyer, Simon}, journal = {Frontiers in Biology}, number = {6}, pages = {557 -- 568}, publisher = {Springer}, title = {{Dissection of gene function at clonal level using mosaic analysis with double markers}}, doi = {10.1007/s11515-013-1279-6}, volume = {8}, year = {2013}, } @article{2304, abstract = {This extended abstract is concerned with the irregularities of distribution of one-dimensional permuted van der Corput sequences that are generated from linear permutations. We show how to obtain upper bounds for the discrepancy and diaphony of these sequences, by relating them to Kronecker sequences and applying earlier results of Faure and Niederreiter.}, author = {Pausinger, Florian}, journal = {Electronic Notes in Discrete Mathematics}, pages = {43 -- 50}, publisher = {Elsevier}, title = {{Van der Corput sequences and linear permutations}}, doi = {10.1016/j.endm.2013.07.008}, volume = {43}, year = {2013}, } @inproceedings{2315, abstract = { We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval in the Gross-Pitaevskii regime. We prove that Bose Einstein condensation survives even a strong random potential with a high density of scatterers. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the interval. }, author = {Seiringer, Robert and Yngvason, Jakob and Zagrebnov, Valentin}, pages = {610--619}, publisher = {World Scientific Publishing}, title = {{Disordered Bose-Einstein condensates with interaction}}, doi = {10.1142/9789814449243_0063}, year = {2013}, } @inproceedings{2319, abstract = {In a recent paper [7] we give the first rigorous derivation of the celebrated Ginzburg-Landau (GL)theory, starting from the microscopic Bardeen- Cooper-Schrieffer (BCS)model. Here we present our results in the simplified case of a one-dimensional system of particles interacting via a δ-potential.}, author = {Frank, Rupert L and Hainzl, Christian and Robert Seiringer and Solovej, Jan P}, pages = {57 -- 88}, publisher = {Springer}, title = {{ Derivation of Ginzburg-Landau theory for a one-dimensional system with contact interaction}}, doi = {10.1007/978-3-0348-0531-5_3}, year = {2013}, } @inproceedings{2328, abstract = {Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on identifying the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates. In response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof.}, author = {Henzinger, Thomas A and Sezgin, Ali and Vafeiadis, Viktor}, location = {Buenos Aires, Argentina}, pages = {242 -- 256}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Aspect-oriented linearizability proofs}}, doi = {10.1007/978-3-642-40184-8_18}, volume = {8052}, year = {2013}, } @article{2404, abstract = {The Lieb-Thirring inequalities give a bound on the negative eigenvalues of a Schrödinger operator in terms of an Lp-norm of the potential. These are dual to bounds on the H1-norms of a system of orthonormal functions. Here we extend these bounds to analogous inequalities for perturbations of the Fermi sea of noninteracting particles (i.e., for perturbations of the continuous spectrum of the Laplacian by local potentials).}, author = {Frank, Rupert L and Lewin, Mathieu and Lieb, Élliott H and Robert Seiringer}, journal = {Duke Mathematical Journal}, number = {3}, pages = {435 -- 495}, publisher = {Duke University Press}, title = {{A positive density analogue of the Lieb-Thirring inequality}}, doi = {10.1215/00127094-2019477}, volume = {162}, year = {2013}, } @article{2406, abstract = {We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval. We prove that, in the Gross-Pitaevskii limit, Bose Einstein condensation takes place in the whole parameter range considered. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the unit interval.}, author = {Robert Seiringer and Yngvason, Jakob and Zagrebnov, Valentin A}, journal = {European Physical Journal: Special Topics}, number = {1}, pages = {103 -- 107}, publisher = {Springer}, title = {{Condensation of interacting bosons in a random potential}}, doi = {10.1140/epjst/e2013-01759-5}, volume = {217}, year = {2013}, } @article{2405, abstract = {We consider the bipolaron in the Pekar-Tomasevich approximation and address the question whether the ground state is spherically symmetric or not. Numerical analysis has, so far, not completely settled the question. Our contribution is to prove rigorously that the ground state remains spherical for small values of the electron-electron Coulomb repulsion.}, author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer}, journal = {Communications in Mathematical Physics}, number = {2}, pages = {557 -- 573}, publisher = {Springer}, title = {{Symmetry of bipolaron bound states for small Coulomb repulsion}}, doi = {10.1007/s00220-012-1604-y}, volume = {319}, year = {2013}, }