@inproceedings{639,
abstract = {We study the problem of developing efficient approaches for proving worst-case bounds of non-deterministic recursive programs. Ranking functions are sound and complete for proving termination and worst-case bounds of non-recursive programs. First, we apply ranking functions to recursion, resulting in measure functions, and show that they provide a sound and complete approach to prove worst-case bounds of non-deterministic recursive programs. Our second contribution is the synthesis of measure functions in non-polynomial forms. We show that non-polynomial measure functions with logarithm and exponentiation can be synthesized through abstraction of logarithmic or exponentiation terms, Farkas’ Lemma, and Handelman’s Theorem using linear programming. While previous methods obtain worst-case polynomial bounds, our approach can synthesize bounds of the form O(n log n) as well as O(nr) where r is not an integer. We present experimental results to demonstrate that our approach can efficiently obtain worst-case bounds of classical recursive algorithms such as Merge-Sort, Closest-Pair, Karatsuba’s algorithm and Strassen’s algorithm.},
author = {Chatterjee, Krishnendu and Fu, Hongfei and Goharshady, Amir},
editor = {Majumdar, Rupak and Kunčak, Viktor},
isbn = {978-331963389-3},
location = {Heidelberg, Germany},
pages = {41 -- 63},
publisher = {Springer},
title = {{Non-polynomial worst case analysis of recursive programs}},
doi = {10.1007/978-3-319-63390-9_3},
volume = {10427},
year = {2017},
}
@article{704,
abstract = {How the organization of genes on a chromosome shapes adaptation is essential for understanding evolutionary paths. Here, we investigate how adaptation to rapidly increasing levels of antibiotic depends on the chromosomal neighborhood of a drug-resistance gene inserted at different positions of the Escherichia coli chromosome. Using a dual-fluorescence reporter that allows us to distinguish gene amplifications from other up-mutations, we track in real-time adaptive changes in expression of the drug-resistance gene. We find that the relative contribution of several mutation types differs systematically between loci due to properties of neighboring genes: essentiality, expression, orientation, termination, and presence of duplicates. These properties determine rate and fitness effects of gene amplification, deletions, and mutations compromising transcriptional termination. Thus, the adaptive potential of a gene under selection is a system-property with a complex genetic basis that is specific for each chromosomal locus, and it can be inferred from detailed functional and genomic data.},
author = {Steinrück, Magdalena and Guet, Calin C},
issn = {2050084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection}},
doi = {10.7554/eLife.25100},
volume = {6},
year = {2017},
}
@article{676,
abstract = {The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation.},
author = {Krens, Gabriel and Veldhuis, Jim and Barone, Vanessa and Capek, Daniel and Maître, Jean-Léon and Brodland, Wayne and Heisenberg, Carl-Philipp J},
issn = {09501991},
journal = {Development},
number = {10},
pages = {1798 -- 1806},
publisher = {Company of Biologists},
title = {{Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation}},
doi = {10.1242/dev.144964},
volume = {144},
year = {2017},
}
@article{661,
abstract = {During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo.},
author = {Smutny, Michael and Ákos, Zsuzsa and Grigolon, Silvia and Shamipour, Shayan and Ruprecht, Verena and Capek, Daniel and Behrndt, Martin and Papusheva, Ekaterina and Tada, Masazumi and Hof, Björn and Vicsek, Tamás and Salbreux, Guillaume and Heisenberg, Carl-Philipp J},
issn = {14657392},
journal = {Nature Cell Biology},
pages = {306 -- 317},
publisher = {Nature Publishing Group},
title = {{Friction forces position the neural anlage}},
doi = {10.1038/ncb3492},
volume = {19},
year = {2017},
}
@article{684,
abstract = {We generalize winning conditions in two-player games by adding a structural acceptance condition called obligations. Obligations are orthogonal to the linear winning conditions that define whether a play is winning. Obligations are a declaration that player 0 can achieve a certain value from a configuration. If the obligation is met, the value of that configuration for player 0 is 1. We define the value in such games and show that obligation games are determined. For Markov chains with Borel objectives and obligations, and finite turn-based stochastic parity games with obligations we give an alternative and simpler characterization of the value function. Based on this simpler definition we show that the decision problem of winning finite turn-based stochastic parity games with obligations is in NP∩co-NP. We also show that obligation games provide a game framework for reasoning about p-automata. © 2017 The Association for Symbolic Logic.},
author = {Chatterjee, Krishnendu and Piterman, Nir},
issn = {1943-5886},
journal = {Journal of Symbolic Logic},
number = {2},
pages = {420 -- 452},
publisher = {Cambridge University Press},
title = {{Obligation blackwell games and p-automata}},
doi = {10.1017/jsl.2016.71},
volume = {82},
year = {2017},
}
@inproceedings{999,
abstract = {In multi-task learning, a learner is given a collection of prediction tasks and needs to solve all of them. In contrast to previous work, which required that annotated training data must be available for all tasks, we consider a new setting, in which for some tasks, potentially most of them, only unlabeled training data is provided. Consequently, to solve all tasks, information must be transferred between tasks with labels and tasks without labels. Focusing on an instance-based transfer method we analyze two variants of this setting: when the set of labeled tasks is fixed, and when it can be actively selected by the learner. We state and prove a generalization bound that covers both scenarios and derive from it an algorithm for making the choice of labeled tasks (in the active case) and for transferring information between the tasks in a principled way. We also illustrate the effectiveness of the algorithm on synthetic and real data. },
author = {Pentina, Anastasia and Lampert, Christoph},
isbn = {9781510855144},
location = {Sydney, Australia},
pages = {2807 -- 2816},
publisher = {Omnipress},
title = {{Multi-task learning with labeled and unlabeled tasks}},
volume = {70},
year = {2017},
}
@article{262,
abstract = {For any number field we calculate the exact proportion of rational numbers which are everywhere locally a norm but not globally a norm from the number field.},
author = {Timothy Browning and Newton, Rachel},
journal = {Mathematika},
number = {2},
pages = {337 -- 347},
publisher = {Cambridge University Press},
title = {{The proportion of failures of the Hasse norm principle}},
doi = {10.1112/S0025579315000261},
volume = {62},
year = {2016},
}
@article{263,
abstract = {We count rational points of bounded height on the Cayley ruled cubic surface and interpret the result in the context of general conjectures due to Batyrev and Tschinkel.},
author = {de la Bretèche, Régis and Timothy Browning and Salberger, Per},
journal = {European Journal of Mathematics},
number = {1},
pages = {55 -- 72},
publisher = {Springer Nature},
title = {{Counting rational points on the Cayley ruled cubic}},
doi = {10.1007/s40879-015-0049-1},
volume = {2},
year = {2016},
}
@article{264,
abstract = {Given a family of varieties over a number field, we determine conditions under which there is a Brauer-Manin obstruction to weak approximation for 100% of the fibres which are everywhere locally soluble.},
author = {Bright, Maritn J and Timothy Browning and Loughran, Daniel},
journal = {Compositio Mathematica},
number = {7},
pages = {1435 -- 1475},
publisher = {Cambridge University Press},
title = {{Failures of weak approximation in families}},
doi = {10.1112/S0010437X16007405},
volume = {152},
year = {2016},
}
@article{8020,
abstract = {Balance of cortical excitation and inhibition (EI) is thought to be disrupted in several neuropsychiatric conditions, yet it is not clear how it is maintained in the healthy human brain. When EI balance is disturbed during learning and memory in animal models, it can be restabilized via formation of inhibitory replicas of newly formed excitatory connections. Here we assess evidence for such selective inhibitory rebalancing in humans. Using fMRI repetition suppression we measure newly formed cortical associations in the human brain. We show that expression of these associations reduces over time despite persistence in behavior, consistent with inhibitory rebalancing. To test this, we modulated excitation/inhibition balance with transcranial direct current stimulation (tDCS). Using ultra-high-field (7T) MRI and spectroscopy, we show that reducing GABA allows cortical associations to be re-expressed. This suggests that in humans associative memories are stored in balanced excitatory-inhibitory ensembles that lie dormant unless latent inhibitory connections are unmasked.},
author = {Barron, H.C. and Vogels, Tim P and Emir, U.E. and Makin, T.R. and O’Shea, J. and Clare, S. and Jbabdi, S. and Dolan, R.J. and Behrens, T.E.J.},
issn = {0896-6273},
journal = {Neuron},
number = {1},
pages = {191--203},
publisher = {Elsevier},
title = {{Unmasking latent inhibitory connections in human cortex to reveal dormant cortical memories}},
doi = {10.1016/j.neuron.2016.02.031},
volume = {90},
year = {2016},
}
@inproceedings{8094,
abstract = {With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.},
author = {Martius, Georg S and Hostettler, Rafael and Knoll, Alois and Der, Ralf},
booktitle = {Proceedings of the Artificial Life Conference 2016},
isbn = {9780262339360},
location = {Cancun, Mexico},
pages = {142--143},
publisher = {MIT Press},
title = {{Self-organized control of an tendon driven arm by differential extrinsic plasticity}},
doi = {10.7551/978-0-262-33936-0-ch029},
volume = {28},
year = {2016},
}
@unpublished{8128,
abstract = {The stimulus selectivity of synaptic currents in cortical neurons often shows a co-tuning of excitation and inhibition, but the mechanisms that underlie the emergence and plasticity of this co-tuning are not fully understood. Using a computational model, we show that an interaction of excitatory and inhibitory synaptic plasticity reproduces both the developmental and – when combined with a disinhibitory gate – the adult plasticity of excitatory and inhibitory receptive fields in auditory cortex. The co-tuning arises from inhibitory plasticity that balances excitation and inhibition, while excitatory stimulus selectivity can result from two different mechanisms. Inhibitory inputs with a broad stimulus tuning introduce a sliding threshold as in Bienenstock-Cooper-Munro rules, introducing an excitatory stimulus selectivity at the cost of a broader inhibitory receptive field. Alternatively, input asymmetries can be amplified by synaptic competition. The latter leaves any receptive field plasticity transient, a prediction we verify in recordings in auditory cortex.},
author = {Clopath, Claudia and Vogels, Tim P and Froemke, Robert C. and Sprekeler, Henning},
booktitle = {bioRxiv},
pages = {43},
publisher = {Cold Spring Harbor Laboratory},
title = {{Receptive field formation by interacting excitatory and inhibitory synaptic plasticity}},
year = {2016},
}
@article{8241,
abstract = {Background: Anticancer vaccines could represent a valuable complementary strategy to established therapies, especially in settings of early stage and minimal residual disease. HER-2 is an important target for immunotherapy and addressed by the monoclonal antibody trastuzumab. We have previously generated HER-2 mimotope peptides from phage display libraries. The synthesized peptides were coupled to carriers and applied for epitope-specific induction of trastuzumab-like IgG. For simplification and to avoid methodological limitations of synthesis and coupling chemistry, we herewith present a novel and optimized approach by using adeno-associated viruses (AAV) as effective and high-density mimotope-display system, which can be directly used for vaccination. Methods: An AAV capsid display library was constructed by genetically incorporating random peptides in a plasmid encoding the wild-type AAV2 capsid protein. AAV clones, expressing peptides specifically reactive to trastuzumab, were employed to immunize BALB/c mice. Antibody titers against human HER-2 were determined, and the isotype composition and functional properties of these were tested. Finally, prophylactically immunized mice were challenged with human HER-2 transfected mouse D2F2/E2 cells. Results: HER-2 mimotope AAV-vaccines induced antibodies specific to human HER-2. Two clones were selected for immunization of mice, which were subsequently grafted D2F2/E2 cells. Both mimotope AAV clones delayed the growth of tumors significantly, as compared to controls. Conclusion: In this study, a novel mimotope AAV-based platform was created allowing the isolation of mimotopes, which can be directly used as anticancer vaccines. The example of trastuzumab AAV-mimotopes demonstrates that this vaccine strategy could help to establish active immunotherapy for breast-cancer patients.},
author = {Singer, Josef and Manzano-Szalai, Krisztina and Fazekas, Judit and Thell, Kathrin and Bentley-Lukschal, Anna and Stremnitzer, Caroline and Roth-Walter, Franziska and Weghofer, Margit and Ritter, Mirko and Pino Tossi, Kerstin and Hörer, Markus and Michaelis, Uwe and Jensen-Jarolim, Erika},
issn = {2162-402X},
journal = {OncoImmunology},
number = {7},
publisher = {Taylor & Francis},
title = {{Proof of concept study with an HER-2 mimotope anticancer vaccine deduced from a novel AAV-mimotope library platform}},
doi = {10.1080/2162402x.2016.1171446},
volume = {5},
year = {2016},
}
@inproceedings{8302,
abstract = {While showing great promise, Bitcoin requires users to wait tens of minutes for transactions to commit, and even then, offering only probabilistic guarantees. This paper introduces ByzCoin, a novel Byzantine consensus protocol that leverages scalable collective signing to commit Bitcoin transactions irreversibly within seconds. ByzCoin achieves Byzantine consensus while preserving Bitcoin’s open membership by dynamically forming hash power-proportionate consensus groups that represent recently-successful block miners. ByzCoin employs communication trees to optimize transaction commitment and verification under normal operation while guaranteeing safety and liveness under Byzantine faults, up to a near-optimal tolerance of f faulty group members among 3f + 2 total. ByzCoin mitigates double spending and selfish mining attacks by producing collectively signed transaction blocks within one minute of transaction submission. Tree-structured communication further reduces this latency to less than 30 seconds. Due to these optimizations, ByzCoin achieves a throughput higher than Paypal currently handles, with a confirmation latency of 15-20 seconds.},
author = {Kokoris Kogias, Eleftherios and Jovanovic, Philipp and Gailly, Nicolas and Khoffi, Ismail and Gasser, Linus and Ford, Bryan},
booktitle = {Proceedings of the 25th USENIX Conference on Security Symposium},
isbn = {9781931971324},
location = {Austin, TX, United States},
pages = {279–296},
publisher = {USENIX Association},
title = {{Enhancing bitcoin security and performance with strong consistency via collective signing}},
year = {2016},
}
@article{1705,
abstract = {Hybrid systems represent an important and powerful formalism for modeling real-world applications such as embedded systems. A verification tool like SpaceEx is based on the exploration of a symbolic search space (the region space). As a verification tool, it is typically optimized towards proving the absence of errors. In some settings, e.g., when the verification tool is employed in a feedback-directed design cycle, one would like to have the option to call a version that is optimized towards finding an error trajectory in the region space. A recent approach in this direction is based on guided search. Guided search relies on a cost function that indicates which states are promising to be explored, and preferably explores more promising states first. In this paper, we propose an abstraction-based cost function based on coarse-grained space abstractions for guiding the reachability analysis. For this purpose, a suitable abstraction technique that exploits the flexible granularity of modern reachability analysis algorithms is introduced. The new cost function is an effective extension of pattern database approaches that have been successfully applied in other areas. The approach has been implemented in the SpaceEx model checker. The evaluation shows its practical potential.},
author = {Bogomolov, Sergiy and Donzé, Alexandre and Frehse, Goran and Grosu, Radu and Johnson, Taylor and Ladan, Hamed and Podelski, Andreas and Wehrle, Martin},
journal = {International Journal on Software Tools for Technology Transfer},
number = {4},
pages = {449 -- 467},
publisher = {Springer},
title = {{Guided search for hybrid systems based on coarse-grained space abstractions}},
doi = {10.1007/s10009-015-0393-y},
volume = {18},
year = {2016},
}
@article{173,
abstract = {We calculate admissible values of r such that a square-free polynomial with integer coefficients, no fixed prime divisor and irreducible factors of degree at most 3 takes infinitely many values that are a product of at most r distinct primes.},
author = {Browning, Timothy D and Booker, Andrew},
journal = {Discrete Analysis},
pages = {1 -- 18},
title = {{Square-free values of reducible polynomials}},
doi = {10.19086/da.732},
volume = {8},
year = {2016},
}
@article{1794,
abstract = {We consider Conditional random fields (CRFs) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) (Formula presented.) is the sum of terms over intervals [i, j] where each term is non-zero only if the substring (Formula presented.) equals a prespecified pattern w. Such CRFs can be naturally applied to many sequence tagging problems. We present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.) where L is the combined length of input patterns, (Formula presented.) is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of Ye et al. (NIPS, 2009) whose complexities are respectively (Formula presented.), (Formula presented.) and (Formula presented.), where (Formula presented.) is the number of input patterns. In addition, we give an efficient algorithm for sampling, and revisit the case of MAP with non-positive weights.},
author = {Kolmogorov, Vladimir and Takhanov, Rustem},
journal = {Algorithmica},
number = {1},
pages = {17 -- 46},
publisher = {Springer},
title = {{Inference algorithms for pattern-based CRFs on sequence data}},
doi = {10.1007/s00453-015-0017-7},
volume = {76},
year = {2016},
}
@article{1833,
abstract = {Relational models for contingency tables are generalizations of log-linear models, allowing effects associated with arbitrary subsets of cells in the table, and not necessarily containing the overall effect, that is, a common parameter in every cell. Similarly to log-linear models, relational models can be extended to non-negative distributions, but the extension requires more complex methods. An extended relational model is defined as an algebraic variety, and it turns out to be the closure of the original model with respect to the Bregman divergence. In the extended relational model, the MLE of the cell parameters always exists and is unique, but some of its properties may be different from those of the MLE under log-linear models. The MLE can be computed using a generalized iterative scaling procedure based on Bregman projections. },
author = {Klimova, Anna and Rudas, Tamás},
journal = {Journal of Multivariate Analysis},
pages = {440 -- 452},
publisher = {Elsevier},
title = {{On the closure of relational models}},
doi = {10.1016/j.jmva.2015.10.005},
volume = {143},
year = {2016},
}
@article{1881,
abstract = {We consider random matrices of the form H=W+λV, λ∈ℝ+, where W is a real symmetric or complex Hermitian Wigner matrix of size N and V is a real bounded diagonal random matrix of size N with i.i.d.\ entries that are independent of W. We assume subexponential decay for the matrix entries of W and we choose λ∼1, so that the eigenvalues of W and λV are typically of the same order. Further, we assume that the density of the entries of V is supported on a single interval and is convex near the edges of its support. In this paper we prove that there is λ+∈ℝ+ such that the largest eigenvalues of H are in the limit of large N determined by the order statistics of V for λ>λ+. In particular, the largest eigenvalue of H has a Weibull distribution in the limit N→∞ if λ>λ+. Moreover, for N sufficiently large, we show that the eigenvectors associated to the largest eigenvalues are partially localized for λ>λ+, while they are completely delocalized for λ<λ+. Similar results hold for the lowest eigenvalues. },
author = {Lee, Jioon and Schnelli, Kevin},
journal = {Probability Theory and Related Fields},
number = {1-2},
pages = {165 -- 241},
publisher = {Springer},
title = {{Extremal eigenvalues and eigenvectors of deformed Wigner matrices}},
doi = {10.1007/s00440-014-0610-8},
volume = {164},
year = {2016},
}
@article{7279,
abstract = {Kinetics of electrochemical reactions are several orders of magnitude slower in solids than in liquids as a result of the much lower ion diffusivity. Yet, the solid state maximizes the density of redox species, which is at least two orders of magnitude lower in liquids because of solubility limitations. With regard to electrochemical energy storage devices, this leads to high-energy batteries with limited power and high-power supercapacitors with a well-known energy deficiency. For such devices the ideal system should endow the liquid state with a density of redox species close to the solid state. Here we report an approach based on biredox ionic liquids to achieve bulk-like redox density at liquid-like fast kinetics. The cation and anion of these biredox ionic liquids bear moieties that undergo very fast reversible redox reactions. As a first demonstration of their potential for high-capacity/high-rate charge storage, we used them in redox supercapacitors. These ionic liquids are able to decouple charge storage from an ion-accessible electrode surface, by storing significant charge in the pores of the electrodes, to minimize self-discharge and leakage current as a result of retaining the redox species in the pores, and to raise working voltage due to their wide electrochemical window.},
author = {Mourad, Eléonore and Coustan, Laura and Lannelongue, Pierre and Zigah, Dodzi and Mehdi, Ahmad and Vioux, André and Freunberger, Stefan Alexander and Favier, Frédéric and Fontaine, Olivier},
issn = {1476-1122},
journal = {Nature Materials},
number = {4},
pages = {446--453},
publisher = {Springer Nature},
title = {{Biredox ionic liquids with solid-like redox density in the liquid state for high-energy supercapacitors}},
doi = {10.1038/nmat4808},
volume = {16},
year = {2016},
}
@article{7297,
abstract = {Redox mediators facilitate the oxidation of the highly insulating discharge product in metal–oxygen batteries during recharge and offer opportunities to achieve high reversible capacities. Now a design principle for selecting redox mediators that can recharge the batteries more efficiently is suggested.},
author = {Freunberger, Stefan Alexander},
issn = {2058-7546},
journal = {Nature Energy},
number = {6},
publisher = {Springer Nature},
title = {{Batteries: Charging ahead rationally}},
doi = {10.1038/nenergy.2016.74},
volume = {1},
year = {2016},
}
@article{7599,
abstract = {Normal leaf margin development is important for leaf morphogenesis and contributes to diverse leaf shapes in higher plants. We here show the crucial roles of an atypical type II phosphatidylinositol 4-kinase, PI4Kγ5, in Arabidopsis leaf margin development. PI4Kγ5 presents a dynamics expression pattern along with leaf development and a T-DNA mutant lacking PI4Kγ5, pi4kγ5–1, presents serrated leaves, which is resulted from the accelerated cell division and increased auxin concentration at serration tips. Studies revealed that PI4Kγ5 interacts with and phosphorylates a membrane-bound NAC transcription factor, ANAC078. Previous studies demonstrated that membrane-bound transcription factors regulate gene transcription by undergoing proteolytic process to translocate into nucleus, and ANAC078 undergoes proteolysis by cleaving off the transmembrane region and carboxyl terminal. Western blot analysis indeed showed that ANAC078 deleting of carboxyl terminal is significantly reduced in pi4kγ5–1, indicating that PI4Kγ5 is important for the cleavage of ANAC078. This is consistent with the subcellular localization observation showing that fluorescence by GFP-ANAC078 is detected at plasma membrane but not nucleus in pi4kγ5–1 mutant and that expression of ANAC078 deleting of carboxyl terminal, driven by PI4Kγ5 promoter, could rescue the leaf serration defects of pi4kγ5–1. Further analysis showed that ANAC078 suppresses the auxin synthesis by directly binding and regulating the expression of auxin synthesis-related genes. These results indicate that PI4Kγ5 interacts with ANAC078 to negatively regulate auxin synthesis and hence influences cell proliferation and leaf development, providing informative clues for the regulation of in situ auxin synthesis and cell division, as well as the cleavage and functional mechanism of membrane-bound transcription factors.},
author = {Tang, Yong and Zhao, Chun-Yan and Tan, Shutang and Xue, Hong-Wei},
issn = {1553-7404},
journal = {PLOS Genetics},
number = {8},
publisher = {Public Library of Science},
title = {{Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078}},
doi = {10.1371/journal.pgen.1006252},
volume = {12},
year = {2016},
}
@article{7737,
abstract = {Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with human complex traits. However, the genes or functional DNA elements through which these variants exert their effects on the traits are often unknown. We propose a method (called SMR) that integrates summary-level data from GWAS with data from expression quantitative trait locus (eQTL) studies to identify genes whose expression levels are associated with a complex trait because of pleiotropy. We apply the method to five human complex traits using GWAS data on up to 339,224 individuals and eQTL data on 5,311 individuals, and we prioritize 126 genes (for example, TRAF1 and ANKRD55 for rheumatoid arthritis and SNX19 and NMRAL1 for schizophrenia), of which 25 genes are new candidates; 77 genes are not the nearest annotated gene to the top associated GWAS SNP. These genes provide important leads to design future functional studies to understand the mechanism whereby DNA variation leads to complex trait variation.},
author = {Zhu, Zhihong and Zhang, Futao and Hu, Han and Bakshi, Andrew and Robinson, Matthew Richard and Powell, Joseph E and Montgomery, Grant W and Goddard, Michael E and Wray, Naomi R and Visscher, Peter M and Yang, Jian},
issn = {1061-4036},
journal = {Nature Genetics},
number = {5},
pages = {481--487},
publisher = {Springer Nature},
title = {{Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets}},
doi = {10.1038/ng.3538},
volume = {48},
year = {2016},
}
@article{786,
abstract = {Lock-free concurrent algorithms guarantee that some concurrent operation will always make progress in a finite number of steps. Yet programmers prefer to treat concurrent code as if it were wait-free, guaranteeing that all operations always make progress. Unfortunately, designing wait-free algorithms is generally a very complex task, and the resulting algorithms are not always efficient. Although obtaining efficient wait-free algorithms has been a long-time goal for the theory community, most nonblocking commercial code is only lock-free. This article suggests a simple solution to this problem.We show that for a large class of lock-free algorithms, under scheduling conditions that approximate those found in commercial hardware architectures, lock-free algorithms behave as if they are wait-free. In other words, programmers can continue to design simple lock-free algorithms instead of complex wait-free ones, and in practice, they will get wait-free progress. Our main contribution is a new way of analyzing a general class of lock-free algorithms under a stochastic scheduler. Our analysis relates the individual performance of processes to the global performance of the system using Markov chain lifting between a complex per-process chain and a simpler system progress chain. We show that lock-free algorithms are not only wait-free with probability 1 but that in fact a general subset of lock-free algorithms can be closely bounded in terms of the average number of steps required until an operation completes. To the best of our knowledge, this is the first attempt to analyze progress conditions, typically stated in relation to a worst-case adversary, in a stochastic model capturing their expected asymptotic behavior.},
author = {Alistarh, Dan-Adrian and Censor Hillel, Keren and Shavit, Nir},
journal = {Journal of the ACM},
number = {4},
publisher = {ACM},
title = {{Are lock free concurrent algorithms practically wait free }},
doi = {10.1145/2903136},
volume = {63},
year = {2016},
}
@article{460,
abstract = {NF-κB signaling is a central pathway of immunity and integrates signal transduction upon a wide array of inflammatory stimuli. Noncanonical NF-κB signaling is activated by a small subset of TNF family receptors and characterized by NF-κB2/p52 transcriptional activity. The medical relevance of this pathway has recently re-emerged from the discovery of primary immunodeficiency patients that have loss-of-function mutations in the MAP3K14 gene encoding NIK. Nevertheless, knowledge of protein interactions that regulate noncanonical NF-κB signaling is sparse. Here we report a detailed state-of-the-art mass spectrometry-based protein–protein interaction network including the noncanonical NF-κB signaling nodes TRAF2, TRAF3, IKKα, NIK, and NF-κB2/p100. The value of the data set was confirmed by the identification of interactions already known to regulate this pathway. In addition, a remarkable number of novel interactors were identified. We provide validation of the novel NIK and IKKα interactor FKBP8, which may regulate processes downstream of noncanonical NF-κB signaling. To understand perturbed noncanonical NF-κB signaling in the context of misregulated NIK in disease, we also provide a differential interactome of NIK mutants that cause immunodeficiency. Altogether, this data set not only provides critical insight into how protein–protein interactions can regulate immune signaling but also offers a novel resource on noncanonical NF-κB signaling.},
author = {Willmann, Katharina L and Roberto Sacco and Martins, Rui and Garncarz, Wojciech and Krolo, Ana and Knapp, Sylvia and Bennett, Keiryn L and Boztug, Kaan},
journal = {Journal of Proteome Research},
number = {9},
pages = {2900 -- 2909},
publisher = {American Chemical Society},
title = {{Expanding the interactome of the noncanonical NF-κB signaling pathway}},
doi = {10.1021/acs.jproteome.5b01004},
volume = {15},
year = {2016},
}
@inproceedings{478,
abstract = {Magic: the Gathering is a game about magical combat for any number of players. Formally it is a zero-sum, imperfect information stochastic game that consists of a potentially unbounded number of steps. We consider the problem of deciding if a move is legal in a given single step of Magic. We show that the problem is (a) coNP-complete in general; and (b) in P if either of two small sets of cards are not used. Our lower bound holds even for single-player Magic games. The significant aspects of our results are as follows: First, in most real-life game problems, the task of deciding whether a given move is legal in a single step is trivial, and the computationally hard task is to find the best sequence of legal moves in the presence of multiple players. In contrast, quite uniquely our hardness result holds for single step and with only one-player. Second, we establish efficient algorithms for important special cases of Magic.},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus},
location = {The Hague, Netherlands},
pages = {1432 -- 1439},
publisher = {IOS Press},
title = {{The complexity of deciding legality of a single step of magic: The gathering}},
doi = {10.3233/978-1-61499-672-9-1432},
volume = {285},
year = {2016},
}
@inproceedings{480,
abstract = {Graph games provide the foundation for modeling and synthesizing reactive processes. In the synthesis of stochastic reactive processes, the traditional model is perfect-information stochastic games, where some transitions of the game graph are controlled by two adversarial players, and the other transitions are executed probabilistically. We consider such games where the objective is the conjunction of several quantitative objectives (specified as mean-payoff conditions), which we refer to as generalized mean-payoff objectives. The basic decision problem asks for the existence of a finite-memory strategy for a player that ensures the generalized mean-payoff objective be satisfied with a desired probability against all strategies of the opponent. A special case of the decision problem is the almost-sure problem where the desired probability is 1. Previous results presented a semi-decision procedure for -approximations of the almost-sure problem. In this work, we show that both the almost-sure problem as well as the general basic decision problem are coNP-complete, significantly improving the previous results. Moreover, we show that in the case of 1-player stochastic games, randomized memoryless strategies are sufficient and the problem can be solved in polynomial time. In contrast, in two-player stochastic games, we show that even with randomized strategies exponential memory is required in general, and present a matching exponential upper bound. We also study the basic decision problem with infinite-memory strategies and present computational complexity results for the problem. Our results are relevant in the synthesis of stochastic reactive systems with multiple quantitative requirements.},
author = {Chatterjee, Krishnendu and Doyen, Laurent},
location = {New York, NY, USA},
pages = {247 -- 256},
publisher = {IEEE},
title = {{Perfect-information stochastic games with generalized mean-payoff objectives}},
doi = {10.1145/2933575.2934513},
volume = {05-08-July-2016},
year = {2016},
}
@article{510,
abstract = {The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa . The potential roles of PtCLE genes were studied by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These fi ndings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants. },
author = {Liu, Zhijun and Yang, Nan and Lv, Yanting and Pan, Lixia and Lv, Shuo and Han, Huibin and Wang, Guodong},
journal = {Plant Signaling & Behavior},
number = {6},
publisher = {Landes Bioscience},
title = {{The CLE gene family in Populus trichocarpa}},
doi = {10.1080/15592324.2016.1191734},
volume = {11},
year = {2016},
}
@misc{5445,
abstract = {We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs. },
author = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Velner, Yaron},
issn = {2664-1690},
pages = {33},
publisher = {IST Austria},
title = {{Quantitative interprocedural analysis}},
doi = {10.15479/AT:IST-2016-523-v1-1},
year = {2016},
}
@misc{5446,
abstract = {We study the problem of developing efficient approaches for proving termination of recursive programs with one-dimensional arrays. Ranking functions serve as a sound and complete approach for proving termination of non-recursive programs without array operations. First, we generalize ranking functions to the notion of measure functions, and prove that measure functions (i) provide a sound method to prove termination of recursive programs (with one-dimensional arrays), and (ii) is both sound and complete over recursive programs without array operations. Our second contribution is the synthesis of measure functions of specific forms in polynomial time. More precisely, we prove that (i) polynomial measure functions over recursive programs can be synthesized in polynomial time through Farkas’ Lemma and Handelman’s Theorem, and (ii) measure functions involving logarithm and exponentiation can be synthesized in polynomial time through abstraction of logarithmic or exponential terms and Handelman’s Theorem. A key application of our method is the worst-case analysis of recursive programs. While previous methods obtain worst-case polynomial bounds of the form O(n^k), where k is an integer, our polynomial time methods can synthesize bounds of the form O(n log n), as well as O(n^x), where x is not an integer. We show the applicability of our automated technique to obtain worst-case complexity of classical recursive algorithms such as (i) Merge-Sort, the divideand-
conquer algorithm for the Closest-Pair problem, where we obtain O(n log n) worst-case bound, and (ii) Karatsuba’s algorithm for polynomial multiplication and Strassen’s algorithm for matrix multiplication, where we obtain O(n^x) bound, where x is not an integer and close to the best-known bounds for the respective algorithms. Finally, we present experimental results to demonstrate the
effectiveness of our approach.},
author = {Anonymous, 1 and Anonymous, 2 and Anonymous, 3},
issn = {2664-1690},
pages = {26},
publisher = {IST Austria},
title = {{Termination and worst-case analysis of recursive programs}},
year = {2016},
}
@misc{5447,
abstract = {We consider the problem of developing automated techniques to aid the average-case complexity analysis of programs. Several classical textbook algorithms have quite efficient average-case complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., QUICK-SORT), or completely ineffective (e.g., COUPONCOLLECTOR). Since the main focus of average-case analysis is to obtain efficient bounds, we consider bounds that are either logarithmic,
linear, or almost-linear (O(log n), O(n), O(n · log n),
respectively, where n represents the size of the input). Our main contribution is a sound approach for deriving such average-case bounds for randomized recursive programs. Our approach is efficient (a simple linear-time algorithm), and it is based on (a) the analysis of recurrence relations induced by randomized algorithms, and (b) a guess-and-check technique. Our approach can infer the asymptotically optimal average-case bounds for classical randomized algorithms, including RANDOMIZED-SEARCH, QUICKSORT, QUICK-SELECT, COUPON-COLLECTOR, where the worstcase
bounds are either inefficient (such as linear as compared to logarithmic of average-case, or quadratic as compared to linear or almost-linear of average-case), or ineffective. We have implemented our approach, and the experimental results show that we obtain the bounds efficiently for various classical algorithms.},
author = {Anonymous, 1 and Anonymous, 2 and Anonymous, 3},
issn = {2664-1690},
pages = {20},
publisher = {IST Austria},
title = {{Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds}},
year = {2016},
}
@misc{5448,
abstract = {We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.
We introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.
1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.
2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence.
Finally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes.},
author = {Anonymous, 1 and Anonymous, 2 and Anonymous, 3 and Anonymous, 4},
issn = {2664-1690},
pages = {20},
publisher = {IST Austria},
title = {{Data-centric dynamic partial order reduction}},
year = {2016},
}
@misc{5449,
abstract = {The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population.
The fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure.
Amplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade.
In this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.},
author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak, Martin},
issn = {2664-1690},
pages = {22},
publisher = {IST Austria},
title = {{Amplification on undirected population structures: Comets beat stars}},
doi = {10.15479/AT:IST-2016-648-v1-1},
year = {2016},
}
@misc{5451,
author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak, Martin},
issn = {2664-1690},
pages = {34},
publisher = {IST Austria},
title = {{Strong amplifiers of natural selection}},
doi = {10.15479/AT:IST-2016-728-v1-1},
year = {2016},
}
@misc{5452,
author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak, Martin},
issn = {2664-1690},
pages = {32},
publisher = {IST Austria},
title = {{Arbitrarily strong amplifiers of natural selection}},
doi = {10.15479/AT:IST-2017-728-v2-1},
year = {2016},
}
@misc{5453,
author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak, Martin},
issn = {2664-1690},
pages = {34},
publisher = {IST Austria},
title = {{Arbitrarily strong amplifiers of natural selection}},
doi = {10.15479/AT:IST-2017-749-v3-1},
year = {2016},
}
@misc{5550,
abstract = {We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.
For full details of the methods see:
Ellis TJ and Field DL "Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)},
author = {Ellis, Thomas and Field, David},
publisher = {IST Austria},
title = {{Flower colour data and phylogeny (NEXUS) files}},
doi = {10.15479/AT:ISTA:34},
year = {2016},
}
@misc{5551,
abstract = {Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.
We placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.
After 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid.},
author = {Ellis, Thomas},
publisher = {IST Austria},
title = {{Data on pollinator observations and offpsring phenotypes}},
doi = {10.15479/AT:ISTA:35},
year = {2016},
}
@misc{5552,
abstract = {Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).
Snapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.
Also included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation.},
author = {Ellis, Thomas},
publisher = {IST Austria},
title = {{Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.}},
doi = {10.15479/AT:ISTA:36},
year = {2016},
}
@misc{5553,
abstract = {Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).
Tissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.
Other data were retreived from an online database of this population at www.antspec.org.},
author = {Field, David and Ellis, Thomas},
keywords = {paternity assignment, pedigree, matting patterns, assortative mating, Antirrhinum majus, frequency-dependent selection, plant-pollinator interaction},
publisher = {IST Austria},
title = {{Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012}},
doi = {10.15479/AT:ISTA:37},
year = {2016},
}
@misc{5555,
abstract = {This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies.},
author = {Hauschild, Robert},
keywords = {cell migration, wide field microscopy, FIJI},
publisher = {IST Austria},
title = {{Fiji script to determine average speed and direction of migration of cells}},
doi = {10.15479/AT:ISTA:44},
year = {2016},
}
@misc{5556,
abstract = {MATLAB code and processed datasets available for reproducing the results in:
Lukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.
*equal contributions},
author = {Lukacisin, Martin and Landon, Matthieu and Jajoo, Rishi},
keywords = {transcription, pausing, backtracking, polymerase, RNA, NET-seq, nucleosome, basepairing},
publisher = {IST Austria},
title = {{MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'}},
doi = {10.15479/AT:ISTA:45},
year = {2016},
}
@misc{5557,
abstract = {Small synthetic discrete tomography problems.
Sizes are 32x32, 64z64 and 256x256.
Projection angles are 2, 4, and 6.
Number of labels are 3 and 5.},
author = {Swoboda, Paul},
keywords = {discrete tomography},
publisher = {IST Austria},
title = {{Synthetic discrete tomography problems}},
doi = {10.15479/AT:ISTA:46},
year = {2016},
}
@misc{5558,
abstract = {PhD thesis LaTeX source code},
author = {Bojsen-Hansen, Morten},
publisher = {IST Austria},
title = {{Tracking, Correcting and Absorbing Water Surface Waves}},
doi = {10.15479/AT:ISTA:48},
year = {2016},
}
@article{5771,
abstract = {Retroviruses such as HIV-1 assemble and bud from infected cells in an immature, non-infectious form. Subsequently, a series of proteolytic cleavages catalysed by the viral protease leads to a spectacular structural rearrangement of the viral particle into a mature form that is competent to fuse with and infect a new cell. Maturation involves changes in the structures of protein domains, in the interactions between protein domains, and in the architecture of the viral components that are assembled by the proteins. Tight control of proteolytic cleavages at different sites is required for successful maturation, and the process is a major target of antiretroviral drugs. Here we will describe what is known about the structures of immature and mature retrovirus particles, and about the maturation process by which one transitions into the other. Despite a wealth of available data, fundamental questions about retroviral maturation remain unanswered.},
author = {Mattei, Simone and Schur, Florian and Briggs, John AG},
issn = {1879-6257},
journal = {Current Opinion in Virology},
number = {6},
pages = {27--35},
publisher = {Elsevier},
title = {{Retrovirus maturation—an extraordinary structural transformation}},
doi = {10.1016/j.coviro.2016.02.008},
volume = {18},
year = {2016},
}
@article{587,
abstract = {Quantum metrology exploits entangled states of particles to improve sensing precision beyond the limit achievable with uncorrelated particles. All previous methods required detection noise levels below this standard quantum limit to realize the benefits of the intrinsic sensitivity provided by these states.We experimentally demonstrate a widely applicable method for entanglement-enhanced measurements without low-noise detection. The method involves an intermediate quantum phase magnification step that eases implementation complexity. We used it to perform squeezed-state metrology 8 decibels below the standard quantum limit with a detection system that has a noise floor 10 decibels above the standard quantum limit.},
author = {Onur Hosten and Krishnakumar, Rajiv and Engelsen, Nils J and Kasevich, Mark A},
journal = {Science},
number = {6293},
pages = {1552 -- 1555},
publisher = {American Association for the Advancement of Science},
title = {{Quantum phase magnification}},
doi = {10.1126/science.aaf3397},
volume = {352},
year = {2016},
}
@article{6732,
abstract = {Consider the transmission of a polar code of block length N and rate R over a binary memoryless symmetric channel W and let P e be the block error probability under successive cancellation decoding. In this paper, we develop new bounds that characterize the relationship of the parameters R, N, P e , and the quality of the channel W quantified by its capacity I(W) and its Bhattacharyya parameter Z(W). In previous work, two main regimes were studied. In the error exponent regime, the channel W and the rate R <; I(W) are fixed, and it was proved that the error probability Pe scales roughly as 2 -√N . In the scaling exponent approach, the channel W and the error probability Pe are fixed and it was proved that the gap to capacity I(W) - R scales as N -1/μ . Here, μ is called scaling exponent and this scaling exponent depends on the channel W. A heuristic computation for the binary erasure channel (BEC) gives μ = 3.627 and it was shown that, for any channel W, 3.579 ≤ μ ≤ 5.702. Our contributions are as follows. First, we provide the tighter upper bound μ <;≤ 4.714 valid for any W. With the same technique, we obtain the upper bound μ ≤ 3.639 for the case of the BEC; this upper bound approaches very closely the heuristically derived value for the scaling exponent of the erasure channel. Second, we develop a trade-off between the gap to capacity I(W)- R and the error probability Pe as the functions of the block length N. In other words, we neither fix the gap to capacity (error exponent regime) nor the error probability (scaling exponent regime), but we do consider a moderate deviations regime in which we study how fast both quantities, as the functions of the block length N, simultaneously go to 0. Third, we prove that polar codes are not affected by error floors. To do so, we fix a polar code of block length N and rate R. Then, we vary the channel W and study the impact of this variation on the error probability. We show that the error probability Pe scales as the Bhattacharyya parameter Z(W) raised to a power that scales roughly like VN. This agrees with the scaling in the error exponent regime.},
author = {Mondelli, Marco and Hassani, S. Hamed and Urbanke, Rudiger L.},
issn = {1557-9654},
journal = {IEEE Transactions on Information Theory},
number = {12},
pages = {6698--6712},
publisher = {IEEE},
title = {{Unified scaling of polar codes: Error exponent, scaling exponent, moderate deviations, and error floors}},
doi = {10.1109/tit.2016.2616117},
volume = {62},
year = {2016},
}
@inproceedings{6733,
abstract = {The question whether RM codes are capacity-achieving is a long-standing open problem in coding theory that was recently answered in the affirmative for transmission over erasure channels [1], [2]. Remarkably, the proof does not rely on specific properties of RM codes, apart from their symmetry. Indeed, the main technical result consists in showing that any sequence of linear codes, with doubly-transitive permutation groups, achieves capacity on the memoryless erasure channel under bit-MAP decoding. Thus, a natural question is what happens under block-MAP decoding. In [1], [2], by exploiting further symmetries of the code, the bit-MAP threshold was shown to be sharp enough so that the block erasure probability also converges to 0. However, this technique relies heavily on the fact that the transmission is over an erasure channel. We present an alternative approach to strengthen results regarding the bit-MAP threshold to block-MAP thresholds. This approach is based on a careful analysis of the weight distribution of RM codes. In particular, the flavor of the main result is the following: assume that the bit-MAP error probability decays as N -δ , for some δ > 0. Then, the block-MAP error probability also converges to 0. This technique applies to transmission over any binary memoryless symmetric channel. Thus, it can be thought of as a first step in extending the proof that RM codes are capacity-achieving to the general case.},
author = {Kudekar, Shrinivas and Kumar, Santhosh and Mondelli, Marco and Pfister, Henry D. and Urbankez, Rudiger},
booktitle = {2016 IEEE International Symposium on Information Theory },
location = {Barcelona, Spain},
pages = {1755--1759},
publisher = {IEEE},
title = {{Comparing the bit-MAP and block-MAP decoding thresholds of Reed-Muller codes on BMS channels}},
doi = {10.1109/isit.2016.7541600},
year = {2016},
}
@article{7068,
abstract = {Electrons in materials with linear dispersion behave as massless Weyl- or Dirac-quasiparticles, and continue to intrigue due to their close resemblance to elusive ultra-relativistic particles as well as their potential for future electronics. Yet the experimental signatures of Weyl-fermions are often subtle and indirect, in particular if they coexist with conventional, massive quasiparticles. Here we show a pronounced anomaly in the magnetic torque of the Weyl semimetal NbAs upon entering the quantum limit state in high magnetic fields. The torque changes sign in the quantum limit, signalling a reversal of the magnetic anisotropy that can be directly attributed to the topological nature of the Weyl electrons. Our results establish that anomalous quantum limit torque measurements provide a direct experimental method to identify and distinguish Weyl and Dirac systems.},
author = {Moll, Philip J. W. and Potter, Andrew C. and Nair, Nityan L. and Ramshaw, B. J. and Modic, Kimberly A and Riggs, Scott and Zeng, Bin and Ghimire, Nirmal J. and Bauer, Eric D. and Kealhofer, Robert and Ronning, Filip and Analytis, James G.},
issn = {2041-1723},
journal = {Nature Communications},
publisher = {Springer Nature},
title = {{Magnetic torque anomaly in the quantum limit of Weyl semimetals}},
doi = {10.1038/ncomms12492},
volume = {7},
year = {2016},
}
@article{1270,
abstract = {A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of Wolpert's paradigmatic "French Flag" model, to patterning by several interacting, spatially coupled genes subject to intrinsic and extrinsic noise. Our model, a variant of an Ising spin system, allows us to systematically explore expression patterns that optimally encode positional information. We find that optimal patterning systems use positional cues, as in the French Flag model, together with gene-gene interactions to generate combinatorial codes for position which we call "Counter" patterns. Counter patterns can also be stabilized against noise and variations in system size or morphogen dosage by longer-range spatial interactions of the type invoked in the Turing model. The simple setup proposed here qualitatively captures many of the experimentally observed properties of biological patterning systems and allows them to be studied in a single, theoretically consistent framework.},
author = {Hillenbrand, Patrick and Gerland, Ulrich and Tkacik, Gasper},
journal = {PLoS One},
number = {9},
publisher = {Public Library of Science},
title = {{Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information}},
doi = {10.1371/journal.pone.0163628},
volume = {11},
year = {2016},
}