@inproceedings{1675,
abstract = {Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto’92) as protection to a shared resource. The basic idea is to ask the service requestor to dedicate some non-trivial amount of computational work to every request. The original applications included prevention of spam and protection against denial of service attacks. More recently, PoWs have been used to prevent double spending in the Bitcoin digital currency system. In this work, we put forward an alternative concept for PoWs - so-called proofs of space (PoS), where a service requestor must dedicate a significant amount of disk space as opposed to computation. We construct secure PoS schemes in the random oracle model (with one additional mild assumption required for the proof to go through), using graphs with high “pebbling complexity” and Merkle hash-trees. We discuss some applications, including follow-up work where a decentralized digital currency scheme called Spacecoin is constructed that uses PoS (instead of wasteful PoW like in Bitcoin) to prevent double spending. The main technical contribution of this work is the construction of (directed, loop-free) graphs on N vertices with in-degree O(log logN) such that even if one places Θ(N) pebbles on the nodes of the graph, there’s a constant fraction of nodes that needs Θ(N) steps to be pebbled (where in every step one can put a pebble on a node if all its parents have a pebble).},
author = {Dziembowski, Stefan and Faust, Sebastian and Kolmogorov, Vladimir and Pietrzak, Krzysztof Z},
location = {Santa Barbara, CA, United States},
pages = {585 -- 605},
publisher = {Springer},
title = {{Proofs of space}},
doi = {10.1007/978-3-662-48000-7_29},
volume = {9216},
year = {2015},
}
@article{1598,
abstract = {We consider Markov decision processes (MDPs) with specifications given as Büchi (liveness) objectives, and examine the problem of computing the set of almost-sure winning vertices such that the objective can be ensured with probability 1 from these vertices. We study for the first time the average-case complexity of the classical algorithm for computing the set of almost-sure winning vertices for MDPs with Büchi objectives. Our contributions are as follows: First, we show that for MDPs with constant out-degree the expected number of iterations is at most logarithmic and the average-case running time is linear (as compared to the worst-case linear number of iterations and quadratic time complexity). Second, for the average-case analysis over all MDPs we show that the expected number of iterations is constant and the average-case running time is linear (again as compared to the worst-case linear number of iterations and quadratic time complexity). Finally we also show that when all MDPs are equally likely, the probability that the classical algorithm requires more than a constant number of iterations is exponentially small.},
author = {Chatterjee, Krishnendu and Joglekar, Manas and Shah, Nisarg},
journal = {Theoretical Computer Science},
number = {3},
pages = {71 -- 89},
publisher = {Elsevier},
title = {{Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives}},
doi = {10.1016/j.tcs.2015.01.050},
volume = {573},
year = {2015},
}
@inbook{258,
abstract = {Given a number field k and a projective algebraic variety X defined over k, the question of whether X contains a k-rational point is both very natural and very difficult. In the event that the set X(k) of k-rational points is not empty, one can also ask how the points of X(k) are distributed. Are they dense in X under the Zariski topology? Are they dense in the set.},
author = {Browning, Timothy D},
booktitle = {Arithmetic and Geometry},
pages = {89 -- 113},
publisher = {Cambridge University Press},
title = {{A survey of applications of the circle method to rational points}},
doi = {10.1017/CBO9781316106877.009},
year = {2015},
}
@inproceedings{1512,
abstract = {We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b,d) such that the following holds. If F is a finite family of subsets of R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent interest.},
author = {Goaoc, Xavier and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli},
location = {Eindhoven, Netherlands},
pages = {507 -- 521},
publisher = {ACM},
title = {{Bounding Helly numbers via Betti numbers}},
doi = {10.4230/LIPIcs.SOCG.2015.507},
volume = {34},
year = {2015},
}
@article{532,
abstract = {Ethylene is a gaseous phytohormone that plays vital roles in plant growth and development. Previous studies uncovered EIN2 as an essential signal transducer linking ethylene perception on ER to transcriptional regulation in the nucleus through a “cleave and shuttle” model. In this study, we report another mechanism of EIN2-mediated ethylene signaling, whereby EIN2 imposes the translational repression of EBF1 and EBF2 mRNA. We find that the EBF1/2 3′ UTRs mediate EIN2-directed translational repression and identify multiple poly-uridylates (PolyU) motifs as functional cis elements of 3′ UTRs. Furthermore, we demonstrate that ethylene induces EIN2 to associate with 3′ UTRs and target EBF1/2 mRNA to cytoplasmic processing-body (P-body) through interacting with multiple P-body factors, including EIN5 and PABs. Our study illustrates translational regulation as a key step in ethylene signaling and presents mRNA 3′ UTR functioning as a “signal transducer” to sense and relay cellular signaling in plants.},
author = {Li, Wenyang and Ma, Mengdi and Feng, Ying and Li, Hongjiang and Wang, Yichuan and Ma, Yutong and Li, Mingzhe and An, Fengying and Guo, Hongwei},
journal = {Cell},
number = {3},
pages = {670 -- 683},
publisher = {Cell Press},
title = {{EIN2-directed translational regulation of ethylene signaling in arabidopsis}},
doi = {10.1016/j.cell.2015.09.037},
volume = {163},
year = {2015},
}
@inproceedings{1656,
abstract = {Recently there has been a significant effort to handle quantitative properties in formal verification and synthesis. While weighted automata over finite and infinite words provide a natural and flexible framework to express quantitative properties, perhaps surprisingly, some basic system properties such as average response time cannot be expressed using weighted automata, nor in any other know decidable formalism. In this work, we introduce nested weighted automata as a natural extension of weighted automata which makes it possible to express important quantitative properties such as average response time. In nested weighted automata, a master automaton spins off and collects results from weighted slave automata, each of which computes a quantity along a finite portion of an infinite word. Nested weighted automata can be viewed as the quantitative analogue of monitor automata, which are used in run-time verification. We establish an almost complete decidability picture for the basic decision problems about nested weighted automata, and illustrate their applicability in several domains. In particular, nested weighted automata can be used to decide average response time properties.},
author = {Chatterjee, Krishnendu and Henzinger, Thomas A and Otop, Jan},
booktitle = {Proceedings - Symposium on Logic in Computer Science},
location = {Kyoto, Japan},
publisher = {IEEE},
title = {{Nested weighted automata}},
doi = {10.1109/LICS.2015.72},
volume = {2015-July},
year = {2015},
}
@misc{5437,
abstract = {We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff property, the ratio property, and the minimum initial credit for energy property.
The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let $n$ denote the number of nodes of a graph, $m$ the number of edges (for constant treewidth graphs $m=O(n)$) and $W$ the largest absolute value of the weights.
Our main theoretical results are as follows.
First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of $\epsilon$ in time $O(n \cdot \log (n/\epsilon))$ and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time $O(n \cdot \log (|a\cdot b|))=O(n\cdot\log (n\cdot W))$, when the output is $\frac{a}{b}$, as compared to the previously best known algorithm with running time $O(n^2 \cdot \log (n\cdot W))$. Third, for the minimum initial credit problem we show that (i)~for general graphs the problem can be solved in $O(n^2\cdot m)$ time and the associated decision problem can be solved in $O(n\cdot m)$ time, improving the previous known $O(n^3\cdot m\cdot \log (n\cdot W))$ and $O(n^2 \cdot m)$ bounds, respectively; and (ii)~for constant treewidth graphs we present an algorithm that requires $O(n\cdot \log n)$ time, improving the previous known $O(n^4 \cdot \log (n \cdot W))$ bound.
We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks. },
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas},
issn = {2664-1690},
pages = {27},
publisher = {IST Austria},
title = {{Faster algorithms for quantitative verification in constant treewidth graphs}},
doi = {10.15479/AT:IST-2015-330-v2-1},
year = {2015},
}
@misc{5444,
abstract = {A comprehensive understanding of the clonal evolution of cancer is critical for understanding neoplasia. Genome-wide sequencing data enables evolutionary studies at unprecedented depth. However, classical phylogenetic methods often struggle with noisy sequencing data of impure DNA samples and fail to detect subclones that have different evolutionary trajectories. We have developed a tool, called Treeomics, that allows us to reconstruct the phylogeny of a cancer with commonly available sequencing technologies. Using Bayesian inference and Integer Linear Programming, robust phylogenies consistent with the biological processes underlying cancer evolution were obtained for pancreatic, ovarian, and prostate cancers. Furthermore, Treeomics correctly identified sequencing artifacts such as those resulting from low statistical power; nearly 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumor heterogeneity among distinct samples. Importantly, we show that the evolutionary trees generated with Treeomics are mathematically optimal.},
author = {Reiter, Johannes and Makohon-Moore, Alvin and Gerold, Jeffrey and Bozic, Ivana and Chatterjee, Krishnendu and Iacobuzio-Donahue, Christine and Vogelstein, Bert and Nowak, Martin},
issn = {2664-1690},
pages = {25},
publisher = {IST Austria},
title = {{Reconstructing robust phylogenies of metastatic cancers}},
doi = {10.15479/AT:IST-2015-399-v1-1},
year = {2015},
}
@misc{5432,
abstract = {Evolution occurs in populations of reproducing individuals. The structure of the population affects the outcome of the evolutionary process. Evolutionary graph theory is a powerful approach to study this phenomenon. There are two graphs. The interaction graph specifies who interacts with whom in the context of evolution.The replacement graph specifies who competes with whom for reproduction.
The vertices of the two graphs are the same, and each vertex corresponds to an individual of the population. A key quantity is the fixation probability of a new mutant. It is defined as the probability that a newly introduced mutant (on a single vertex) generates a lineage of offspring which eventually takes over the entire population of resident individuals. The basic computational questions are as follows: (i) the qualitative question asks whether the fixation probability is positive; and (ii) the quantitative approximation question asks for an approximation of the fixation probability.
Our main results are:
(1) We show that the qualitative question is NP-complete and the quantitative approximation question is #P-hard in the special case when the interaction and the replacement graphs coincide and even with the restriction that the resident individuals do not reproduce (which corresponds to an invading population taking over an empty structure).
(2) We show that in general the qualitative question is PSPACE-complete and the quantitative approximation question is PSPACE-hard and can be solved in exponential time.
},
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Nowak, Martin},
issn = {2664-1690},
pages = {29},
publisher = {IST Austria},
title = {{The complexity of evolutionary games on graphs}},
doi = {10.15479/AT:IST-2015-323-v1-1},
year = {2015},
}
@article{594,
abstract = {Transcription of eukaryotic protein-coding genes commences with the assembly of a conserved initiation complex, which consists of RNA polymerase II (Pol II) and the general transcription factors, at promoter DNA. After two decades of research, the structural basis of transcription initiation is emerging. Crystal structures of many components of the initiation complex have been resolved, and structural information on Pol II complexes with general transcription factors has recently been obtained. Although mechanistic details await elucidation, available data outline how Pol II cooperates with the general transcription factors to bind to and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the promoter.},
author = {Sainsbury, Sarah and Bernecky, Carrie A and Cramer, Patrick},
journal = {Nature Reviews Molecular Cell Biology},
number = {3},
pages = {129 -- 143},
publisher = {Nature Publishing Group},
title = {{Structural basis of transcription initiation by RNA polymerase II}},
doi = {10.1038/nrm3952},
volume = {16},
year = {2015},
}
@article{6118,
abstract = {Carbon dioxide (CO2) gradients are ubiquitous and provide animals with information about their environment, such as the potential presence of prey or predators. The nematode Caenorhabditis elegans avoids elevated CO2, and previous work identified three neuron pairs called “BAG,” “AFD,” and “ASE” that respond to CO2 stimuli. Using in vivo Ca2+ imaging and behavioral analysis, we show that C. elegans can detect CO2 independently of these sensory pathways. Many of the C. elegans sensory neurons we examined, including the AWC olfactory neurons, the ASJ and ASK gustatory neurons, and the ASH and ADL nociceptors, respond to a rise in CO2 with a rise in Ca2+. In contrast, glial sheath cells harboring the sensory endings of C. elegans’ major chemosensory neurons exhibit strong and sustained decreases in Ca2+ in response to high CO2. Some of these CO2 responses appear to be cell intrinsic. Worms therefore may couple detection of CO2 to that of other cues at the earliest stages of sensory processing. We show that C. elegans persistently suppresses oviposition at high CO2. Hermaphrodite-specific neurons (HSNs), the executive neurons driving egg-laying, are tonically inhibited when CO2 is elevated. CO2 modulates the egg-laying system partly through the AWC olfactory neurons: High CO2 tonically activates AWC by a cGMP-dependent mechanism, and AWC output inhibits the HSNs. Our work shows that CO2 is a more complex sensory cue for C. elegans than previously thought, both in terms of behavior and neural circuitry.},
author = {Fenk, Lorenz A. and de Bono, Mario},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {27},
pages = {E3525--E3534},
publisher = {National Academy of Sciences},
title = {{Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity}},
doi = {10.1073/pnas.1423808112},
volume = {112},
year = {2015},
}
@article{6120,
abstract = {Brains organize behavior and physiology to optimize the response to threats or opportunities. We dissect how 21% O2, an indicator of surface exposure, reprograms C. elegans' global state, inducing sustained locomotory arousal and altering expression of neuropeptides, metabolic enzymes, and other non-neural genes. The URX O2-sensing neurons drive arousal at 21% O2 by tonically activating the RMG interneurons. Stimulating RMG is sufficient to switch behavioral state. Ablating the ASH, ADL, or ASK sensory neurons connected to RMG by gap junctions does not disrupt arousal. However, disrupting cation currents in these neurons curtails RMG neurosecretion and arousal. RMG signals high O2 by peptidergic secretion. Neuropeptide reporters reveal neural circuit state, as neurosecretion stimulates neuropeptide expression. Neural imaging in unrestrained animals shows that URX and RMG encode O2 concentration rather than behavior, while the activity of downstream interneurons such as AVB and AIY reflect both O2 levels and the behavior being executed.},
author = {Laurent, Patrick and Soltesz, Zoltan and Nelson, Geoffrey M and Chen, Changchun and Arellano-Carbajal, Fausto and Levy, Emmanuel and de Bono, Mario},
issn = {2050-084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Decoding a neural circuit controlling global animal state in C. elegans}},
doi = {10.7554/elife.04241},
volume = {4},
year = {2015},
}
@inproceedings{1637,
abstract = {An instance of the Valued Constraint Satisfaction Problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P ≠ NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in {0, ∞} corresponds to ordinary CSPs, where one deals only with the feasibility issue and there is no optimization. This case is the subject of the Algebraic CSP Dichotomy Conjecture predicting for which constraint languages CSPs are tractable (i.e. solvable in polynomial time) and for which NP-hard. The case when all allowed functions take only finite values corresponds to finite-valued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Zivny. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e. the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs.},
author = {Kolmogorov, Vladimir and Krokhin, Andrei and Rolinek, Michal},
location = {Berkeley, CA, United States},
pages = {1246 -- 1258},
publisher = {IEEE},
title = {{The complexity of general-valued CSPs}},
doi = {10.1109/FOCS.2015.80},
year = {2015},
}
@inproceedings{784,
abstract = {We demonstrate an optical switch design that can scale up to a thousand ports with high per-port bandwidth (25 Gbps+) and low switching latency (40 ns). Our design uses a broadcast and select architecture, based on a passive star coupler and fast tunable transceivers. In addition we employ time division multiplexing to achieve very low switching latency. Our demo shows the feasibility of the switch data plane using a small testbed, comprising two transmitters and a receiver, connected through a star coupler.},
author = {Alistarh, Dan-Adrian and Ballani, Hitesh and Costa, Paolo and Funnell, Adam and Benjamin, Joshua and Watts, Philip and Thomsen, Benn},
isbn = {978-1-4503-3542-3},
location = {London, United Kindgdom},
pages = {367 -- 368},
publisher = {ACM},
title = {{A high-radix, low-latency optical switch for data centers}},
doi = {10.1145/2785956.2790035},
year = {2015},
}
@inproceedings{1714,
abstract = {We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm-deadline real-time tasks based on multi-objective graphs: Given a task set and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. A clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including Dover, that have been proposed in the past, for various task sets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are task sets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application.},
author = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Kößler, Alexander and Schmid, Ulrich},
booktitle = {Real-Time Systems Symposium},
location = {Rome, Italy},
number = {January},
pages = {118 -- 127},
publisher = {IEEE},
title = {{A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks}},
doi = {10.1109/RTSS.2014.9},
volume = {2015},
year = {2015},
}
@article{99,
abstract = {Quasiparticle excitations can compromise the performance of superconducting devices, causing high-frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we use a system comprising a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify bound states in the semiconductor by means of bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms.},
author = {Higginbotham, Andrew P and Albrecht, S M and Kiršanskas, Gediminas and Chang, W and Kuemmeth, Ferdinand and Krogstrup, Peter and Jespersen, Thomas and Nygård, Jesper and Flensberg, Karsten and Marcus, Charles},
journal = {Nature Physics},
number = {12},
pages = {1017 -- 1021},
publisher = {Nature Publishing Group},
title = {{Parity lifetime of bound states in a proximitized semiconductor nanowire}},
doi = {10.1038/nphys3461},
volume = {11},
year = {2015},
}
@article{1311,
abstract = {In this paper, we develop an energy method to study finite speed of propagation and waiting time phenomena for the stochastic porous media equation with linear multiplicative noise in up to three spatial dimensions. Based on a novel iteration technique and on stochastic counterparts of weighted integral estimates used in the deterministic setting, we formulate a sufficient criterion on the growth of initial data which locally guarantees a waiting time phenomenon to occur almost surely. Up to a logarithmic factor, this criterion coincides with the optimal criterion known from the deterministic setting. Our technique can be modified to prove finite speed of propagation as well.},
author = {Julian Fischer and Grün, Günther},
journal = {SIAM Journal on Mathematical Analysis},
number = {1},
pages = {825 -- 854},
publisher = {Society for Industrial and Applied Mathematics },
title = {{Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach}},
doi = {10.1137/140960578},
volume = {47},
year = {2015},
}
@article{1316,
abstract = {In the present work we introduce the notion of a renormalized solution for reaction–diffusion systems with entropy-dissipating reactions. We establish the global existence of renormalized solutions. In the case of integrable reaction terms our notion of a renormalized solution reduces to the usual notion of a weak solution. Our existence result in particular covers all reaction–diffusion systems involving a single reversible reaction with mass-action kinetics and (possibly species-dependent) Fick-law diffusion; more generally, it covers the case of systems of reversible reactions with mass-action kinetics which satisfy the detailed balance condition. For such equations the existence of any kind of solution in general was an open problem, thereby motivating the study of renormalized solutions.},
author = {Julian Fischer},
journal = {Archive for Rational Mechanics and Analysis},
number = {1},
pages = {553 -- 587},
publisher = {Springer},
title = {{Global existence of renormalized solutions to entropy-dissipating reaction–diffusion systems}},
doi = {10.1007/s00205-015-0866-x},
volume = {218},
year = {2015},
}
@article{259,
abstract = {The Hasse principle and weak approximation is established for non-singular cubic hypersurfaces X over the function field },
author = {Timothy Browning and Vishe, Pankaj},
journal = {Geometric and Functional Analysis},
number = {3},
pages = {671 -- 732},
publisher = {Birkhäuser},
title = {{Rational points on cubic hypersurfaces over F_q(t) }},
doi = {10.1007/s00039-015-0328-5},
volume = {25},
year = {2015},
}
@article{362,
abstract = {Monodisperse Pd2Sn nanorods with tuned size and aspect ratio were prepared by co-reduction of metal salts in the presence of trioctylphosphine, amine, and chloride ions. Asymmetric Pd2Sn nanostructures were achieved by the selective desorption of a surfactant mediated by chlorine ions. A preliminary evaluation of the geometry influence on catalytic properties evidenced Pd2Sn nanorods to have improved catalytic performance. In view of these results, Pd2Sn nanorods were also evaluated for water denitration. },
author = {Lu, ZhiShan and Ibanez, Maria and Antolín, Ana M and Genç, Aziz and Shavel, Alexey and Contreras, Sandra and Medina, Francesc and Arbiol, Jordi and Cabot, Andreu},
journal = {Langmuir},
number = {13},
pages = {3952 -- 3957},
publisher = {American Chemical Society},
title = {{Size and aspect ratio control of Pd inf 2 inf Sn nanorods and their water denitration properties}},
doi = {10.1021/la504906q},
volume = {31},
year = {2015},
}
@inproceedings{778,
abstract = {Several Hybrid Transactional Memory (HyTM) schemes have recently been proposed to complement the fast, but best-effort nature of Hardware Transactional Memory (HTM) with a slow, reliable software backup. However, the costs of providing concurrency between hardware and software transactions in HyTM are still not well understood. In this paper, we propose a general model for HyTM implementations, which captures the ability of hardware transactions to buffer memory accesses. The model allows us to formally quantify and analyze the amount of overhead (instrumentation) caused by the potential presence of software transactions.We prove that (1) it is impossible to build a strictly serializable HyTM implementation that has both uninstrumented reads and writes, even for very weak progress guarantees, and (2) the instrumentation cost incurred by a hardware transaction in any progressive opaque HyTM is linear in the size of the transaction’s data set.We further describe two implementations which exhibit optimal instrumentation costs for two different progress conditions. In sum, this paper proposes the first formal HyTM model and captures for the first time the trade-off between the degree of hardware-software TM concurrency and the amount of instrumentation overhead.},
author = {Alistarh, Dan and Kopinsky, Justin and Kuznetsov, Petr V and Ravi, Srivatsan and Shavit, Nir N},
pages = {185 -- 199},
publisher = {Springer},
title = {{Inherent limitations of hybrid transactional memory}},
doi = {10.1007/978-3-662-48653-5_13},
volume = {9363},
year = {2015},
}
@article{886,
abstract = {The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space.},
author = {Kondrashov, Dmitry A and Fyodor Kondrashov},
journal = {Trends in Genetics},
number = {1},
pages = {24 -- 33},
publisher = {Elsevier},
title = {{Topological features of rugged fitness landscapes in sequence space}},
doi = {10.1016/j.tig.2014.09.009},
volume = {31},
year = {2015},
}
@article{906,
abstract = {The origin and evolution of novel biochemical functions remains one of the key questions in molecular evolution. We study recently emerged methacrylate reductase function that is thought to have emerged in the last century and reported in Geobacter sulfurreducens strain AM-1. We report the sequence and study the evolution of the operon coding for the flavin-containing methacrylate reductase (Mrd) and tetraheme cytochrome (Mcc) in the genome of G. sulfurreducens AM-1. Different types of signal peptides in functionally interlinked proteins Mrd and Mcc suggest a possible complex mechanism of biogenesis for chromoproteids of the methacrylate redox system. The homologs of the Mrd and Mcc sequence found in δ-Proteobacteria and Deferribacteres are also organized into an operon and their phylogenetic distribution suggested that these two genes tend to be horizontally transferred together. Specifically, the mrd and mcc genes from G. sulfurreducens AM-1 are not monophyletic with any of the homologs found in other Geobacter genomes. The acquisition of methacrylate reductase function by G. sulfurreducens AM-1 appears linked to a horizontal gene transfer event. However, the new function of the products of mrd and mcc may have evolved either prior or subsequent to their acquisition by G. sulfurreducens AM-1.},
author = {Arkhipova, Oksana V and Meer, Margarita V and Mikoulinskaia, Galina V and Zakharova, Marina V and Galushko, Alexander S and Akimenko, Vasilii K and Fyodor Kondrashov},
journal = {PLoS One},
number = {5},
publisher = {Public Library of Science},
title = {{Recent origin of the methacrylate redox system in Geobacter sulfurreducens AM-1 through horizontal gene transfer}},
doi = {10.1371/journal.pone.0125888},
volume = {10},
year = {2015},
}
@article{982,
abstract = {We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions.},
author = {Maksym Serbyn and Papić, Zlatko and Abanin, Dmitry A},
journal = {Physical Review X},
number = {4},
publisher = {American Physical Society},
title = {{Criterion for many-body localization-delocalization phase transition}},
doi = {10.1103/PhysRevX.5.041047},
volume = {5},
year = {2015},
}
@inproceedings{1424,
abstract = {We consider the problem of statistical computations with persistence diagrams, a summary representation of topological features in data. These diagrams encode persistent homology, a widely used invariant in topological data analysis. While several avenues towards a statistical treatment of the diagrams have been explored recently, we follow an alternative route that is motivated by the success of methods based on the embedding of probability measures into reproducing kernel Hilbert spaces. In fact, a positive definite kernel on persistence diagrams has recently been proposed, connecting persistent homology to popular kernel-based learning techniques such as support vector machines. However, important properties of that kernel enabling a principled use in the context of probability measure embeddings remain to be explored. Our contribution is to close this gap by proving universality of a variant of the original kernel, and to demonstrate its effective use in twosample hypothesis testing on synthetic as well as real-world data.},
author = {Kwitt, Roland and Huber, Stefan and Niethammer, Marc and Lin, Weili and Bauer, Ulrich},
location = {Montreal, Canada},
pages = {3070 -- 3078},
publisher = {Neural Information Processing Systems},
title = {{Statistical topological data analysis-A kernel perspective}},
volume = {28},
year = {2015},
}
@inproceedings{1474,
abstract = {Cryptographic access control offers selective access to encrypted data via a combination of key management and functionality-rich cryptographic schemes, such as attribute-based encryption. Using this approach, publicly available meta-data may inadvertently leak information on the access policy that is enforced by cryptography, which renders cryptographic access control unusable in settings where this information is highly sensitive. We begin to address this problem by presenting rigorous definitions for policy privacy in cryptographic access control. For concreteness we set our results in the model of Role-Based Access Control (RBAC), where we identify and formalize several different flavors of privacy, however, our framework should serve as inspiration for other models of access control. Based on our insights we propose a new system which significantly improves on the privacy properties of state-of-the-art constructions. Our design is based on a novel type of privacy-preserving attribute-based encryption, which we introduce and show how to instantiate. We present our results in the context of a cryptographic RBAC system by Ferrara et al. (CSF'13), which uses cryptography to control read access to files, while write access is still delegated to trusted monitors. We give an extension of the construction that permits cryptographic control over write access. Our construction assumes that key management uses out-of-band channels between the policy enforcer and the users but eliminates completely the need for monitoring read/write access to the data.},
author = {Ferrara, Anna and Fuchsbauer, Georg and Liu, Bin and Warinschi, Bogdan},
location = {Verona, Italy},
pages = {46--60},
publisher = {IEEE},
title = {{Policy privacy in cryptographic access control}},
doi = {10.1109/CSF.2015.11},
year = {2015},
}
@article{1513,
abstract = {Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.
In this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. },
author = {Pal, Arka and Vicoso, Beatriz},
journal = {Genome Biology and Evolution},
number = {12},
pages = {3259 -- 3268},
publisher = {Oxford University Press},
title = {{The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression}},
doi = {10.1093/gbe/evv215 },
volume = {7},
year = {2015},
}
@inproceedings{1520,
abstract = {Creating mechanical automata that can walk in stable and pleasing manners is a challenging task that requires both skill and expertise. We propose to use computational design to offset the technical difficulties of this process. A simple drag-and-drop interface allows casual users to create personalized walking toys from a library of pre-defined template mechanisms. Provided with this input, our method leverages physical simulation and evolutionary optimization to refine the mechanical designs such that the resulting toys are able to walk. The optimization process is guided by an intuitive set of objectives that measure the quality of the walking motions. We demonstrate our approach on a set of simulated mechanical toys with different numbers of legs and various distinct gaits. Two fabricated prototypes showcase the feasibility of our designs.},
author = {Bharaj, Gaurav and Coros, Stelian and Thomaszewski, Bernhard and Tompkin, James and Bickel, Bernd and Pfister, Hanspeter},
isbn = {978-1-4503-3496-9},
location = {Los Angeles, CA, United States},
pages = {93 -- 100},
publisher = {ACM},
title = {{Computational design of walking automata}},
doi = {10.1145/2786784.2786803},
year = {2015},
}
@article{1525,
abstract = {Based on 16 recommendations, efforts should be made to achieve the following goal: By 2025, all scholarly publication activity in Austria should be Open Access. In other words, the final versions of all scholarly publications resulting from the support of public resources must be freely accessible on the Internet without delay (Gold Open Access). The resources required to meet this obligation shall be provided to the authors, or the cost of the publication venues shall be borne directly by the research organisations.},
author = {Bauer, Bruno and Blechl, Guido and Bock, Christoph and Patrick Danowski and Ferus, Andreas and Graschopf, Anton and König, Thomas and Mayer, Katja and Reckling, Falk and Rieck, Katharina and Seitz, Peter and Stöger, Herwig and Welzig, Elvira},
journal = {VÖB Mitteilungen},
number = {3},
pages = {580 -- 607},
publisher = {Verein Österreichischer Bibliothekare},
title = {{Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA}},
doi = {10.5281/zenodo.33178},
volume = {68},
year = {2015},
}
@inproceedings{1498,
abstract = {Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. Nonetheless there is surprisingly little language and verification support to build distributed systems based on fault-tolerant algorithms. In this paper, we present some of the challenges that a designer has to overcome to implement a fault-tolerant distributed system. Then we review different models that have been proposed to reason about distributed algorithms and sketch how such a model can form the basis for a domain-specific programming language. Adopting a high-level programming model can simplify the programmer's life and make the code amenable to automated verification, while still compiling to efficiently executable code. We conclude by summarizing the current status of an ongoing language design and implementation project that is based on this idea.},
author = {Dragoi, Cezara and Henzinger, Thomas A and Zufferey, Damien},
isbn = {978-3-939897-80-4 },
location = {Asilomar, CA, United States},
pages = {90 -- 102},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{The need for language support for fault-tolerant distributed systems}},
doi = {10.4230/LIPIcs.SNAPL.2015.90},
volume = {32},
year = {2015},
}
@article{1501,
abstract = {We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. },
author = {Chatterjee, Krishnendu and Chmelik, Martin and Daca, Przemyslaw},
journal = {Formal Methods in System Design},
number = {2},
pages = {230 -- 264},
publisher = {Springer},
title = {{CEGAR for compositional analysis of qualitative properties in Markov decision processes}},
doi = {10.1007/s10703-015-0235-2},
volume = {47},
year = {2015},
}
@article{1506,
abstract = {Consider the square random matrix An = (aij)n,n, where {aij:= a(n)ij , i, j = 1, . . . , n} is a collection of independent real random variables with means zero and variances one. Under the additional moment condition supn max1≤i,j ≤n Ea4ij <∞, we prove Girko's logarithmic law of det An in the sense that as n→∞ log | detAn| ? (1/2) log(n-1)! d/→√(1/2) log n N(0, 1).},
author = {Bao, Zhigang and Pan, Guangming and Zhou, Wang},
journal = {Bernoulli},
number = {3},
pages = {1600 -- 1628},
publisher = {Bernoulli Society for Mathematical Statistics and Probability},
title = {{The logarithmic law of random determinant}},
doi = {10.3150/14-BEJ615},
volume = {21},
year = {2015},
}
@inbook{1544,
abstract = {Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics of membrane-bound proteins is often difficult to achieve in vivo. Here, we present protocols for the use of supported lipid bilayers to rebuild the cytokinetic machineries of cells with greatly different dimensions: the bacterium Escherichia coli and eggs of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence microscopy, these experimental setups allow for precise quantitative analyses of membrane-bound proteins. The protocols described to obtain glass-supported membranes from bacterial and vertebrate lipids can be used as starting points for other reconstitution experiments. We believe that similar biochemical assays will be instrumental to study the biochemistry and biophysics underlying a variety of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility.},
author = {Nguyen, Phuong and Field, Christine and Groen, Aaron and Mitchison, Timothy and Loose, Martin},
booktitle = {Building a Cell from its Components Parts},
pages = {223 -- 241},
publisher = {Academic Press},
title = {{Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins}},
doi = {10.1016/bs.mcb.2015.01.007},
volume = {128},
year = {2015},
}
@inbook{1549,
abstract = {Nature has incorporated small photochromic molecules, colloquially termed 'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis and vision. While Nature's ability to employ light-responsive functionalities has long been recognized, it was not until recently that scientists designed, synthesized and applied synthetic photochromes to manipulate many of which open rapidly and locally in their native cell types, biological processes with the temporal and spatial resolution of light. Ion channels in particular have come to the forefront of proteins that can be put under the designer control of synthetic photochromes. Photochromic ion channel controllers are comprised of three classes, photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and photochromic crosslinkers (PXs), and in each class ion channel functionality is controlled through reversible changes in photochrome structure. By acting as light-dependent ion channel agonists, antagonist or modulators, photochromic controllers effectively converted a wide range of ion channels, including voltage-gated ion channels, 'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive ion channels, into man-made photoreceptors. Control by photochromes can be reversible, unlike in the case of 'caged' compounds, and non-invasive with high spatial precision, unlike pharmacology and electrical manipulation. Here, we introduce design principles of emerging photochromic molecules that act on ion channels and discuss the impact that these molecules are beginning to have on ion channel biophysics and neuronal physiology.},
author = {Mckenzie, Catherine and Sanchez Romero, Inmaculada and Janovjak, Harald L},
booktitle = {Novel chemical tools to study ion channel biology},
isbn = {978-1-4939-2844-6},
pages = {101 -- 117},
publisher = {Springer},
title = {{Flipping the photoswitch: Ion channels under light control}},
doi = {10.1007/978-1-4939-2845-3_6},
volume = {869},
year = {2015},
}
@article{1551,
abstract = {Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i) high virulence was specifically favoured during pathogen–host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii) the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins.We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen's genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host–pathogen interaction system.},
author = {El Masri, Leila and Branca, Antoine and Sheppard, Anna and Papkou, Andrei and Laehnemann, David and Guenther, Patrick and Prahl, Swantje and Saebelfeld, Manja and Hollensteiner, Jacqueline and Liesegang, Heiko and Brzuszkiewicz, Elzbieta and Daniel, Rolf and Michiels, Nico and Schulte, Rebecca and Kurtz, Joachim and Rosenstiel, Philip and Telschow, Arndt and Bornberg Bauer, Erich and Schulenburg, Hinrich},
journal = {PLoS Biology},
number = {6},
pages = {1 -- 30},
publisher = {Public Library of Science},
title = {{Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes}},
doi = {10.1371/journal.pbio.1002169},
volume = {13},
year = {2015},
}
@article{1556,
abstract = {The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators.},
author = {Jia, Yuebin and Tian, Huiyu and Li, Hongjiang and Yu, Qianqian and Wang, Lei and Friml, Jirí and Ding, Zhaojun},
journal = {Journal of Experimental Botany},
number = {15},
pages = {4631 -- 4642},
publisher = {Oxford University Press},
title = {{The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development}},
doi = {10.1093/jxb/erv230},
volume = {66},
year = {2015},
}
@article{1563,
abstract = {For a given self-map $f$ of $M$, a closed smooth connected and simply-connected manifold of dimension $m\geq 4$, we provide an algorithm for estimating the values of the topological invariant $D^m_r[f]$, which equals the minimal number of $r$-periodic points in the smooth homotopy class of $f$. Our results are based on the combinatorial scheme for computing $D^m_r[f]$ introduced by G. Graff and J. Jezierski [J. Fixed Point Theory Appl. 13 (2013), 63-84]. An open-source implementation of the algorithm programmed in C++ is publicly available at {\tt http://www.pawelpilarczyk.com/combtop/}.},
author = {Graff, Grzegorz and Pilarczyk, Pawel},
journal = {Topological Methods in Nonlinear Analysis},
number = {1},
pages = {273 -- 286},
publisher = {Juliusz Schauder Center for Nonlinear Studies},
title = {{An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds}},
doi = {10.12775/TMNA.2015.014},
volume = {45},
year = {2015},
}
@inproceedings{1568,
abstract = {Aiming at the automatic diagnosis of tumors from narrow band imaging (NBI) magnifying endoscopy (ME) images of the stomach, we combine methods from image processing, computational topology, and machine learning to classify patterns into normal, tubular, vessel. Training the algorithm on a small number of images of each type, we achieve a high rate of correct classifications. The analysis of the learning algorithm reveals that a handful of geometric and topological features are responsible for the overwhelming majority of decisions.},
author = {Dunaeva, Olga and Edelsbrunner, Herbert and Lukyanov, Anton and Machin, Michael and Malkova, Daria},
booktitle = {Proceedings - 16th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing},
location = {Timisoara, Romania},
pages = {7034731},
publisher = {IEEE},
title = {{The classification of endoscopy images with persistent homology}},
doi = {10.1109/SYNASC.2014.81},
year = {2015},
}
@article{1570,
abstract = {Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution.},
author = {Der, Ralf and Martius, Georg S},
journal = {PNAS},
number = {45},
pages = {E6224 -- E6232},
publisher = {National Academy of Sciences},
title = {{Novel plasticity rule can explain the development of sensorimotor intelligence}},
doi = {10.1073/pnas.1508400112},
volume = {112},
year = {2015},
}
@article{1575,
abstract = {The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space.},
author = {Chabaud, Mélanie and Heuzé, Mélina and Bretou, Marine and Vargas, Pablo and Maiuri, Paolo and Solanes, Paola and Maurin, Mathieu and Terriac, Emmanuel and Le Berre, Maël and Lankar, Danielle and Piolot, Tristan and Adelstein, Robert and Zhang, Yingfan and Sixt, Michael K and Jacobelli, Jordan and Bénichou, Olivier and Voituriez, Raphaël and Piel, Matthieu and Lennon Duménil, Ana},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells}},
doi = {10.1038/ncomms8526},
volume = {6},
year = {2015},
}
@article{1582,
abstract = {We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights.},
author = {Biedl, Therese and Held, Martin and Huber, Stefan and Kaaser, Dominik and Palfrader, Peter},
journal = {Computational Geometry: Theory and Applications},
number = {2},
pages = {120 -- 133},
publisher = {Elsevier},
title = {{Weighted straight skeletons in the plane}},
doi = {10.1016/j.comgeo.2014.08.006},
volume = {48},
year = {2015},
}
@article{1587,
abstract = {We investigate the quantum interference shifts between energetically close states, where the state structure is observed by laser spectroscopy. We report a compact and analytical expression that models the quantum interference induced shift for any admixture of circular polarization of the incident laser and angle of observation. An experimental scenario free of quantum interference can thus be predicted with this formula. Although this study is exemplified here for muonic deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme.},
author = {Amaro, Pedro and Fratini, Filippo and Safari, Laleh and Antognini, Aldo and Indelicato, Paul and Pohl, Randolf and Santos, José},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {6},
publisher = {American Physical Society},
title = {{Quantum interference shifts in laser spectroscopy with elliptical polarization}},
doi = {10.1103/PhysRevA.92.062506},
volume = {92},
year = {2015},
}
@inproceedings{1594,
abstract = {Quantitative extensions of temporal logics have recently attracted significant attention. In this work, we study frequency LTL (fLTL), an extension of LTL which allows to speak about frequencies of events along an execution. Such an extension is particularly useful for probabilistic systems that often cannot fulfil strict qualitative guarantees on the behaviour. It has been recently shown that controller synthesis for Markov decision processes and fLTL is decidable when all the bounds on frequencies are 1. As a step towards a complete quantitative solution, we show that the problem is decidable for the fragment fLTL\GU, where U does not occur in the scope of G (but still F can). Our solution is based on a novel translation of such quantitative formulae into equivalent deterministic automata.},
author = {Forejt, Vojtěch and Krčál, Jan and Kretinsky, Jan},
location = {Suva, Fiji},
pages = {162 -- 177},
publisher = {Springer},
title = {{Controller synthesis for MDPs and frequency LTL\GU}},
doi = {10.1007/978-3-662-48899-7_12},
volume = {9450},
year = {2015},
}
@inproceedings{1626,
abstract = {This paper introduces "OmniAD," a novel data-driven pipeline to model and acquire the aerodynamics of three-dimensional rigid objects. Traditionally, aerodynamics are examined through elaborate wind tunnel experiments or expensive fluid dynamics computations, and are only measured for a small number of discrete wind directions. OmniAD allows the evaluation of aerodynamic forces, such as drag and lift, for any incoming wind direction using a novel representation based on spherical harmonics. Our datadriven technique acquires the aerodynamic properties of an object simply by capturing its falling motion using a single camera. Once model parameters are estimated, OmniAD enables realistic realtime simulation of rigid bodies, such as the tumbling and gliding of leaves, without simulating the surrounding air. In addition, we propose an intuitive user interface based on OmniAD to interactively design three-dimensional kites that actually fly. Various nontraditional kites were designed to demonstrate the physical validity of our model.},
author = {Martin, Tobias and Umetani, Nobuyuki and Bickel, Bernd},
location = {Los Angeles, CA, United States},
number = {4},
publisher = {ACM},
title = {{OmniAD: Data-driven omni-directional aerodynamics}},
doi = {10.1145/2766919},
volume = {34},
year = {2015},
}
@article{1614,
abstract = {GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. },
author = {Strüber, Michael and Jonas, Peter M and Bartos, Marlene},
journal = {PNAS},
number = {4},
pages = {1220 -- 1225},
publisher = {National Academy of Sciences},
title = {{Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells}},
doi = {10.1073/pnas.1412996112},
volume = {112},
year = {2015},
}
@inproceedings{1690,
abstract = {A number of powerful and scalable hybrid systems model checkers have recently emerged. Although all of them honor roughly the same hybrid systems semantics, they have drastically different model description languages. This situation (a) makes it difficult to quickly evaluate a specific hybrid automaton model using the different tools, (b) obstructs comparisons of reachability approaches, and (c) impedes the widespread application of research results that perform model modification and could benefit many of the tools. In this paper, we present Hyst, a Hybrid Source Transformer. Hyst is a source-to-source translation tool, currently taking input in the SpaceEx model format, and translating to the formats of HyCreate, Flow∗, or dReach. Internally, the tool supports generic model-to-model transformation passes that serve to both ease the translation and potentially improve reachability results for the supported tools. Although these model transformation passes could be implemented within each tool, the Hyst approach provides a single place for model modification, generating modified input sources for the unmodified target tools. Our evaluation demonstrates Hyst is capable of automatically translating benchmarks in several classes (including affine and nonlinear hybrid automata) to the input formats of several tools. Additionally, we illustrate a general model transformation pass based on pseudo-invariants implemented in Hyst that illustrates the reachability improvement.},
author = {Bak, Stanley and Bogomolov, Sergiy and Johnson, Taylor},
location = {Seattle, WA, United States},
pages = {128 -- 133},
publisher = {Springer},
title = {{HYST: A source transformation and translation tool for hybrid automaton models}},
doi = {10.1145/2728606.2728630},
year = {2015},
}
@article{1695,
abstract = {We give a comprehensive introduction into a diagrammatic method that allows for the evaluation of Gutzwiller wave functions in finite spatial dimensions. We discuss in detail some numerical schemes that turned out to be useful in the real-space evaluation of the diagrams. The method is applied to the problem of d-wave superconductivity in a two-dimensional single-band Hubbard model. Here, we discuss in particular the role of long-range contributions in our diagrammatic expansion. We further reconsider our previous analysis on the kinetic energy gain in the superconducting state.},
author = {Kaczmarczyk, Jan and Schickling, Tobias and Bünemann, Jörg},
journal = {Physica Status Solidi (B): Basic Solid State Physics},
number = {9},
pages = {2059 -- 2071},
publisher = {Wiley},
title = {{Evaluation techniques for Gutzwiller wave functions in finite dimensions}},
doi = {10.1002/pssb.201552082},
volume = {252},
year = {2015},
}
@article{1703,
abstract = {Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs.},
author = {Broadhurst, Linda and Fifield, Graham and Vanzella, Bindi and Pickup, Melinda},
journal = {Australian Journal of Botany},
number = {5},
pages = {455 -- 466},
publisher = {CSIRO},
title = {{An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas}},
doi = {10.1071/BT15023},
volume = {63},
year = {2015},
}
@article{1638,
abstract = {The mitochondrial respiratory chain, also known as the electron transport chain (ETC), is crucial to life, and energy production in the form of ATP is the main mitochondrial function. Three proton-translocating enzymes of the ETC, namely complexes I, III and IV, generate proton motive force, which in turn drives ATP synthase (complex V). The atomic structures and basic mechanisms of most respiratory complexes have previously been established, with the exception of complex I, the largest complex in the ETC. Recently, the crystal structure of the entire complex I was solved using a bacterial enzyme. The structure provided novel insights into the core architecture of the complex, the electron transfer and proton translocation pathways, as well as the mechanism that couples these two processes.},
author = {Sazanov, Leonid A},
journal = {Nature Reviews Molecular Cell Biology},
number = {6},
pages = {375 -- 388},
publisher = {Nature Publishing Group},
title = {{A giant molecular proton pump: structure and mechanism of respiratory complex I}},
doi = {10.1038/nrm3997},
volume = {16},
year = {2015},
}
@article{1640,
abstract = {Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development.},
author = {Šimášková, Mária and O'Brien, José and Khan-Djamei, Mamoona and Van Noorden, Giel and Ötvös, Krisztina and Vieten, Anne and De Clercq, Inge and Van Haperen, Johanna and Cuesta, Candela and Hoyerová, Klára and Vanneste, Steffen and Marhavy, Peter and Wabnik, Krzysztof T and Van Breusegem, Frank and Nowack, Moritz and Murphy, Angus and Friml, Jiřĺ and Weijers, Dolf and Beeckman, Tom and Benková, Eva},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Cytokinin response factors regulate PIN-FORMED auxin transporters}},
doi = {10.1038/ncomms9717},
volume = {6},
year = {2015},
}