@techreport{5450,
abstract = {In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.},
author = {Barbara Petritsch},
publisher = {IST Austria},
title = {{Implementing the institutional data repository IST DataRep}},
year = {2017},
}
@misc{5456,
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 = {Chalupa, Marek and Chatterjee, Krishnendu and Pavlogiannis, Andreas and Sinha, Nishant and Vaidya, Kapil},
issn = {2664-1690},
pages = {36},
publisher = {IST Austria},
title = {{Data-centric dynamic partial order reduction}},
doi = {10.15479/AT:IST-2017-872-v1-1},
year = {2017},
}
@article{548,
abstract = {In this work maximum entropy distributions in the space of steady states of metabolic networks are considered upon constraining the first and second moments of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux distributions, emerges upon considering control on the average growth (optimization) and its fluctuations (heterogeneity). This is applied to the carbon catabolic core of Escherichia coli where it quantifies the metabolic activity of slow growing phenotypes and it provides a quantitative map with metabolic fluxes, opening the possibility to detect coexistence from flux data. A preliminary analysis on data for E. coli cultures in standard conditions shows degeneracy for the inferred parameters that extend in the coexistence region.},
author = {De Martino, Daniele},
issn = {24700045},
journal = {Physical Review E},
number = {6},
publisher = {American Physiological Society},
title = {{Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes}},
doi = {10.1103/PhysRevE.96.060401},
volume = {96},
year = {2017},
}
@inproceedings{549,
abstract = {Model checking is usually based on a comprehensive traversal of the state space. Causality-based model checking is a radically different approach that instead analyzes the cause-effect relationships in a program. We give an overview on a new class of model checking algorithms that capture the causal relationships in a special data structure called concurrent traces. Concurrent traces identify key events in an execution history and link them through their cause-effect relationships. The model checker builds a tableau of concurrent traces, where the case splits represent different causal explanations of a hypothetical error. Causality-based model checking has been implemented in the ARCTOR tool, and applied to previously intractable multi-threaded benchmarks.},
author = {Finkbeiner, Bernd and Kupriyanov, Andrey},
booktitle = {Electronic Proceedings in Theoretical Computer Science},
issn = {20752180},
location = {Uppsala, Sweden},
pages = {31 -- 38},
publisher = {Open Publishing Association},
title = {{Causality-based model checking}},
doi = {10.4204/EPTCS.259.3},
volume = {259},
year = {2017},
}
@article{550,
abstract = {For large random matrices X with independent, centered entries but not necessarily identical variances, the eigenvalue density of XX* is well-approximated by a deterministic measure on ℝ. We show that the density of this measure has only square and cubic-root singularities away from zero. We also extend the bulk local law in [5] to the vicinity of these singularities.},
author = {Alt, Johannes},
issn = {1083589X},
journal = {Electronic Communications in Probability},
publisher = {Institute of Mathematical Statistics},
title = {{Singularities of the density of states of random Gram matrices}},
doi = {10.1214/17-ECP97},
volume = {22},
year = {2017},
}
@inproceedings{551,
abstract = {Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider the classical birth-death Moran process where there are two types of individuals, namely, the residents with fitness 1 and mutants with fitness r. The fitness indicates the reproductive strength. The evolutionary dynamics happens as follows: in the initial step, in a population of all resident individuals a mutant is introduced, and then at each step, an individual is chosen proportional to the fitness of its type to reproduce, and the offspring replaces a neighbor uniformly at random. The process stops when all individuals are either residents or mutants. The probability that all individuals in the end are mutants is called the fixation probability, which is a key factor in the rate of evolution. We consider the problem of approximating the fixation probability. The class of algorithms that is extremely relevant for approximation of the fixation probabilities is the Monte-Carlo simulation of the process. Previous results present a polynomial-time Monte-Carlo algorithm for undirected graphs when r is given in unary. First, we present a simple modification: instead of simulating each step, we discard ineffective steps, where no node changes type (i.e., either residents replace residents, or mutants replace mutants). Using the above simple modification and our result that the number of effective steps is concentrated around the expected number of effective steps, we present faster polynomial-time Monte-Carlo algorithms for undirected graphs. Our algorithms are always at least a factor O(n2/ log n) faster as compared to the previous algorithms, where n is the number of nodes, and is polynomial even if r is given in binary. We also present lower bounds showing that the upper bound on the expected number of effective steps we present is asymptotically tight for undirected graphs. },
author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Nowak, Martin},
booktitle = {Leibniz International Proceedings in Informatics},
isbn = {978-395977046-0},
location = {Aalborg, Denmark},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Faster Monte Carlo algorithms for fixation probability of the Moran process on undirected graphs}},
doi = {10.4230/LIPIcs.MFCS.2017.61},
volume = {83},
year = {2017},
}
@inproceedings{552,
abstract = {Graph games provide the foundation for modeling and synthesis of reactive processes. Such games are played over graphs where the vertices are controlled by two adversarial players. We consider graph games where the objective of the first player is the conjunction of a qualitative objective (specified as a parity condition) and a quantitative objective (specified as a meanpayoff condition). There are two variants of the problem, namely, the threshold problem where the quantitative goal is to ensure that the mean-payoff value is above a threshold, and the value problem where the quantitative goal is to ensure the optimal mean-payoff value; in both cases ensuring the qualitative parity objective. The previous best-known algorithms for game graphs with n vertices, m edges, parity objectives with d priorities, and maximal absolute reward value W for mean-payoff objectives, are as follows: O(nd+1 . m . w) for the threshold problem, and O(nd+2 · m · W) for the value problem. Our main contributions are faster algorithms, and the running times of our algorithms are as follows: O(nd-1 · m ·W) for the threshold problem, and O(nd · m · W · log(n · W)) for the value problem. For mean-payoff parity objectives with two priorities, our algorithms match the best-known bounds of the algorithms for mean-payoff games (without conjunction with parity objectives). Our results are relevant in synthesis of reactive systems with both functional requirement (given as a qualitative objective) and performance requirement (given as a quantitative objective).},
author = {Chatterjee, Krishnendu and Henzinger, Monika and Svozil, Alexander},
booktitle = {Leibniz International Proceedings in Informatics},
isbn = {978-395977046-0},
location = {Aalborg, Denmark},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Faster algorithms for mean payoff parity games}},
doi = {10.4230/LIPIcs.MFCS.2017.39},
volume = {83},
year = {2017},
}
@inproceedings{553,
abstract = {We consider two player, zero-sum, finite-state concurrent reachability games, played for an infinite number of rounds, where in every round, each player simultaneously and independently of the other players chooses an action, whereafter the successor state is determined by a probability distribution given by the current state and the chosen actions. Player 1 wins iff a designated goal state is eventually visited. We are interested in the complexity of stationary strategies measured by their patience, which is defined as the inverse of the smallest non-zero probability employed. Our main results are as follows: We show that: (i) the optimal bound on the patience of optimal and -optimal strategies, for both players is doubly exponential; and (ii) even in games with a single non-absorbing state exponential (in the number of actions) patience is necessary. },
author = {Chatterjee, Krishnendu and Hansen, Kristofer and Ibsen-Jensen, Rasmus},
booktitle = {Leibniz International Proceedings in Informatics},
isbn = {978-395977046-0},
location = {Aalborg, Denmark},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Strategy complexity of concurrent safety games}},
doi = {10.4230/LIPIcs.MFCS.2017.55},
volume = {83},
year = {2017},
}
@misc{5559,
abstract = {Strong amplifiers of natural selection},
author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak , Martin},
keywords = {natural selection},
publisher = {IST Austria},
title = {{Strong amplifiers of natural selection}},
doi = {10.15479/AT:ISTA:51},
year = {2017},
}
@misc{5560,
abstract = {This repository contains the data collected for the manuscript "Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity".
The data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication.
Data is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic "mother machine" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication.},
author = {Bergmiller, Tobias and Andersson, Anna M and Tomasek, Kathrin and Balleza, Enrique and Kiviet, Daniel and Hauschild, Robert and Tkacik, Gasper and Guet, Calin C},
keywords = {single cell microscopy, mother machine microfluidic device, AcrAB-TolC pump, multi-drug efflux, Escherichia coli},
publisher = {IST Austria},
title = {{Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity}},
doi = {doi:10.15479/AT:ISTA:53},
year = {2017},
}
@misc{5561,
abstract = {Graph matching problems as described in "Active Graph Matching for Automatic Joint Segmentation and Annotation of C. Elegans." by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in "Feature Correspondence via Graph Matching: Models and Global Optimization." by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. },
author = {Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Meyers, Gene},
keywords = {graph matching, feature matching, QAP, MAP-inference},
publisher = {IST Austria},
title = {{Graph matching problems for annotating C. Elegans}},
doi = {10.15479/AT:ISTA:57},
year = {2017},
}
@misc{5562,
abstract = {This data was collected as part of the study [1]. It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:
[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408.},
author = {Marre, Olivier and Tkacik, Gasper and Amodei, Dario and Schneidman, Elad and Bialek, William and Berry, Michael},
keywords = {multi-electrode recording, retinal ganglion cells},
publisher = {IST Austria},
title = {{Multi-electrode array recording from salamander retinal ganglion cells}},
doi = {10.15479/AT:ISTA:61},
year = {2017},
}
@misc{5563,
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},
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:64},
year = {2017},
}
@misc{5564,
abstract = {Compressed Fastq files with whole-genome sequencing data of IS-wt strain D and clones from four evolved populations (A11, C08, C10, D08). Information on this data collection is available in the Methods Section of the primary publication.},
author = {Steinrück, Magdalena and Guet, Calin C},
publisher = {IST Austria},
title = {{Fastq files for "Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection"}},
doi = {10.15479/AT:ISTA:65},
year = {2017},
}
@misc{5565,
abstract = {One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions.
The Video is licensed under a CC BY NC ND license. },
author = {Von Wangenheim, Daniel and Hauschild, Robert and Friml, Jirí},
publisher = {IST Austria},
title = {{Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel}},
doi = {10.15479/AT:ISTA:66},
year = {2017},
}
@misc{5566,
abstract = {Current minimal version of TipTracker},
author = {Hauschild, Robert},
keywords = {tool, tracking, confocal microscopy},
publisher = {IST Austria},
title = {{Live tracking of moving samples in confocal microscopy for vertically grown roots}},
doi = {10.15479/AT:ISTA:69},
year = {2017},
}
@misc{5567,
abstract = {Immunological synapse DC-Tcells},
author = {Leithner, Alexander F},
keywords = {Immunological synapse},
publisher = {IST Austria},
title = {{Immunological synapse DC-Tcells}},
doi = {10.15479/AT:ISTA:71},
year = {2017},
}
@misc{5568,
abstract = {Includes source codes, test cases, and example data used in the thesis Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Also includes pre-built binaries of the HyENA library, but not sources - please contact the HyENA authors to obtain these sources if required (https://mech.tugraz.at/hyena)},
author = {Hahn, David},
keywords = {Boundary elements, brittle fracture, computer graphics, fracture simulation},
publisher = {IST Austria},
title = {{Source codes: Brittle fracture simulation with boundary elements for computer graphics}},
doi = {10.15479/AT:ISTA:73},
year = {2017},
}
@article{557,
abstract = {PURPOSE. Gene therapy of retinal ganglion cells (RGCs) has promise as a powerful therapeutic for the rescue and regeneration of these cells after optic nerve damage. However, early after damage, RGCs undergo atrophic changes, including gene silencing. It is not known if these changes will deleteriously affect transduction and transgene expression, or if the therapeutic protein can influence reactivation of the endogenous genome. METHODS. Double-transgenic mice carrying a Rosa26-(LoxP)-tdTomato reporter, and a mutant allele for the proapoptotic Bax gene were reared. The Bax mutant blocks apoptosis, but RGCs still exhibit nuclear atrophy and gene silencing. At times ranging from 1 hour to 4 weeks after optic nerve crush (ONC), eyes received an intravitreal injection of AAV2 virus carrying the Cre recombinase. Successful transduction was monitored by expression of the tdTomato reporter. Immunostaining was used to localize tdTomato expression in select cell types. RESULTS. Successful transduction of RGCs was achieved at all time points after ONC using AAV2 expressing Cre from the phosphoglycerate kinase (Pgk) promoter, but not the CMV promoter. ONC promoted an increase in the transduction of cell types in the inner nuclear layer, including Müller cells and rod bipolar neurons. There was minimal evidence of transduction of amacrine cells and astrocytes in the inner retina or optic nerve. CONCLUSIONS. Damaged RGCs can be transduced and at least some endogenous genes can be subsequently activated. Optic nerve damage may change retinal architecture to allow greater penetration of an AAV2 virus to transduce several additional cell types in the inner nuclear layer.},
author = {Nickells, Robert and Schmitt, Heather and Maes, Margaret E and Schlamp, Cassandra},
issn = {01460404},
journal = {Investigative Ophthalmology and Visual Science},
number = {14},
pages = {6091 -- 6104},
publisher = {Association for Research in Vision and Ophthalmology Inc.},
title = {{AAV2 mediated transduction of the mouse retina after optic nerve injury}},
doi = {10.1167/iovs.17-22634},
volume = {58},
year = {2017},
}
@misc{5570,
abstract = {Matlab script to calculate the forward migration indexes (/) from TrackMate spot-statistics files.},
author = {Hauschild, Robert},
keywords = {Cell migration, tracking, forward migration index, FMI},
publisher = {IST Austria},
title = {{Forward migration indexes}},
doi = {10.15479/AT:ISTA:75},
year = {2017},
}
@misc{5571,
abstract = {This folder contains all the data used in each of the main figures of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.), as well as in the supplementary figures.
},
author = {Vicoso, Beatriz},
publisher = {IST Austria},
title = {{Data for "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology"}},
doi = {10.15479/AT:ISTA:78},
year = {2017},
}
@misc{5572,
abstract = {Code described in the Supplementary Methods of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.)},
author = {Vicoso, Beatriz},
publisher = {IST Austria},
title = {{Code for "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology"}},
doi = {10.15479/AT:ISTA:79 },
year = {2017},
}
@article{558,
abstract = {Immune specificity is the degree to which a host’s immune system discriminates among various pathogens or antigenic variants. Vertebrate immune memory is highly specific due to antibody responses. On the other hand, some invertebrates show immune priming, i.e. improved survival after secondary exposure to a previously encountered pathogen. Until now, specificity of priming has only been demonstrated via the septic infection route or when live pathogens were used for priming. Therefore, we tested for specificity in the oral priming route in the red flour beetle, Tribolium castaneum. For priming, we used pathogen-free supernatants derived from three different strains of the entomopathogen, Bacillus thuringiensis, which express different Cry toxin variants known for their toxicity against this beetle. Subsequent exposure to the infective spores showed that oral priming was specific for two naturally occurring strains, while a third engineered strain did not induce any priming effect. Our data demonstrate that oral immune priming with a non-infectious bacterial agent can be specific, but the priming effect is not universal across all bacterial strains.},
author = {Futo, Momir and Sell, Marie and Kutzer, Megan and Kurtz, Joachim},
issn = {17449561},
journal = {Biology Letters},
number = {12},
publisher = {Royal Society, The},
title = {{Specificity of oral immune priming in the red flour beetle Tribolium castaneum}},
doi = {10.1098/rsbl.2017.0632},
volume = {13},
year = {2017},
}
@inproceedings{559,
abstract = {Proofs of space (PoS) were suggested as more ecological and economical alternative to proofs of work, which are currently used in blockchain designs like Bitcoin. The existing PoS are based on rather sophisticated graph pebbling lower bounds. Much simpler and in several aspects more efficient schemes based on inverting random functions have been suggested, but they don’t give meaningful security guarantees due to existing time-memory trade-offs. In particular, Hellman showed that any permutation over a domain of size N can be inverted in time T by an algorithm that is given S bits of auxiliary information whenever (Formula presented). For functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To prove lower bounds, one considers an adversary who has access to an oracle f: [ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈ Ω(N) and holds for random functions and permutations. We construct functions that provably require more time and/or space to invert. Specifically, for any constant k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk) (in particular, S= T≈ (Formula presented). Our construction does not contradict Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in forward direction. However, its entire function table can be computed in time quasilinear in N, which is sufficient for the PoS application. Our simplest construction is built from a random function oracle g: [N] × [N] → [ N] and a random permutation oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with π being any involution without a fixed point, e.g. flipping all the bits. For this function we prove that any adversary who gets S bits of auxiliary information, makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must satisfy S2· T∈ Ω(ϵ2N2).},
author = {Abusalah, Hamza M and Alwen, Joel F and Cohen, Bram and Khilko, Danylo and Pietrzak, Krzysztof Z and Reyzin, Leonid},
isbn = {978-331970696-2},
location = {Hong Kong, China},
pages = {357 -- 379},
publisher = {Springer},
title = {{Beyond Hellman’s time-memory trade-offs with applications to proofs of space}},
doi = {10.1007/978-3-319-70697-9_13},
volume = {10625},
year = {2017},
}
@article{560,
abstract = {In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions.},
author = {Gerencser, Mate and Jentzen, Arnulf and Salimova, Diyora},
issn = {13645021},
journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},
number = {2207},
publisher = {Royal Society of London},
title = {{On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions}},
doi = {10.1098/rspa.2017.0104},
volume = {473},
year = {2017},
}
@book{567,
abstract = {This book is a concise and self-contained introduction of recent techniques to prove local spectral universality for large random matrices. Random matrix theory is a fast expanding research area, and this book mainly focuses on the methods that the authors participated in developing over the past few years. Many other interesting topics are not included, and neither are several new developments within the framework of these methods. The authors have chosen instead to present key concepts that they believe are the core of these methods and should be relevant for future applications. They keep technicalities to a minimum to make the book accessible to graduate students. With this in mind, they include in this book the basic notions and tools for high-dimensional analysis, such as large deviation, entropy, Dirichlet form, and the logarithmic Sobolev inequality.
},
author = {Erdös, László and Yau, Horng},
isbn = {9781470436483},
pages = {226},
publisher = {American Mathematical Society},
title = {{A dynamical approach to random matrix theory}},
volume = {28},
year = {2017},
}
@article{568,
abstract = {We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r > 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C).},
author = {Franek, Peter and Krcál, Marek},
issn = {15320073},
journal = {Homology, Homotopy and Applications},
number = {2},
pages = {313 -- 342},
publisher = {International Press},
title = {{Persistence of zero sets}},
doi = {10.4310/HHA.2017.v19.n2.a16},
volume = {19},
year = {2017},
}
@article{569,
abstract = {The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings.},
author = {Spira, Felix and Cuylen Haering, Sara and Mehta, Shalin and Samwer, Matthias and Reversat, Anne and Verma, Amitabh and Oldenbourg, Rudolf and Sixt, Michael K and Gerlich, Daniel},
issn = {2050084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments}},
doi = {10.7554/eLife.30867},
volume = {6},
year = {2017},
}
@article{570,
abstract = {Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. },
author = {Lagator, Mato and Sarikas, Srdjan and Acar, Hande and Bollback, Jonathan P and Guet, Calin C},
issn = {2050084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Regulatory network structure determines patterns of intermolecular epistasis}},
doi = {10.7554/eLife.28921},
volume = {6},
year = {2017},
}
@article{571,
abstract = {Blood platelets are critical for hemostasis and thrombosis and play diverse roles during immune responses. Despite these versatile tasks in mammalian biology, their skills on a cellular level are deemed limited, mainly consisting in rolling, adhesion, and aggregate formation. Here, we identify an unappreciated asset of platelets and show that adherent platelets use adhesion receptors to mechanically probe the adhesive substrate in their local microenvironment. When actomyosin-dependent traction forces overcome substrate resistance, platelets migrate and pile up the adhesive substrate together with any bound particulate material. They use this ability to act as cellular scavengers, scanning the vascular surface for potential invaders and collecting deposited bacteria. Microbe collection by migrating platelets boosts the activity of professional phagocytes, exacerbating inflammatory tissue injury in sepsis. This assigns platelets a central role in innate immune responses and identifies them as potential targets to dampen inflammatory tissue damage in clinical scenarios of severe systemic infection. In addition to their role in thrombosis and hemostasis, platelets can also migrate to sites of infection to help trap bacteria and clear the vascular surface.},
author = {Gärtner, Florian R and Ahmad, Zerkah and Rosenberger, Gerhild and Fan, Shuxia and Nicolai, Leo and Busch, Benjamin and Yavuz, Gökce and Luckner, Manja and Ishikawa Ankerhold, Hellen and Hennel, Roman and Benechet, Alexandre and Lorenz, Michael and Chandraratne, Sue and Schubert, Irene and Helmer, Sebastian and Striednig, Bianca and Stark, Konstantin and Janko, Marek and Böttcher, Ralph and Verschoor, Admar and Leon, Catherine and Gachet, Christian and Gudermann, Thomas and Mederos Y Schnitzler, Michael and Pincus, Zachary and Iannacone, Matteo and Haas, Rainer and Wanner, Gerhard and Lauber, Kirsten and Sixt, Michael K and Massberg, Steffen},
issn = {00928674},
journal = {Cell Press},
number = {6},
pages = {1368 -- 1382},
publisher = {Cell Press},
title = {{Migrating platelets are mechano scavengers that collect and bundle bacteria}},
doi = {10.1016/j.cell.2017.11.001},
volume = {171},
year = {2017},
}
@article{572,
abstract = {In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.},
author = {Olatunji, Damilola and Geelen, Danny and Verstraeten, Inge},
journal = {International Journal of Molecular Sciences},
number = {12},
publisher = {MDPI},
title = {{Control of endogenous auxin levels in plant root development}},
doi = {10.3390/ijms18122587},
volume = {18},
year = {2017},
}
@article{5799,
abstract = {We construct a polyhedral surface called a graceful surface, which provides best possible approximation to a given sphere regarding certain criteria. In digital geometry terms, the graceful surface is uniquely characterized by its minimality while guaranteeing the connectivity of certain discrete (polyhedral) curves defined on it. The notion of “gracefulness” was first proposed in Brimkov and Barneva (1999) and shown to be useful for triangular mesh discretization through graceful planes and graceful lines. In this paper we extend the considerations to a nonlinear object such as a sphere. In particular, we investigate the properties of a discrete geodesic path between two voxels and show that discrete 3D circles, circular arcs, and Mobius triangles are all constructible on a graceful sphere, with guaranteed minimum thickness and the desired connectivity in the discrete topological space.},
author = {Biswas, Ranita and Bhowmick, Partha and Brimkov, Valentin E.},
issn = {0166-218X},
journal = {Discrete Applied Mathematics},
pages = {362--375},
publisher = {Elsevier},
title = {{On the polyhedra of graceful spheres and circular geodesics}},
doi = {10.1016/j.dam.2015.11.017},
volume = {216},
year = {2017},
}
@article{5800,
abstract = {This paper presents a novel study on the functional gradation of coordinate planes in connection with the thinnest and tunnel-free (i.e., naive) discretization of sphere in the integer space. For each of the 48-symmetric quadraginta octants of naive sphere with integer radius and integer center, we show that the corresponding voxel set forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as its functional plane. We use this fundamental property to prove several other theoretical results for naive sphere. First, the quadraginta octants form symmetry groups and subgroups with certain equivalent topological properties. Second, a naive sphere is always unique and consists of fewest voxels. Third, it is efficiently constructible from its functional-plane projection. And finally, a special class of 4-symmetric discrete 3D circles can be constructed on a naive sphere based on back projection from the functional plane.},
author = {Biswas, Ranita and Bhowmick, Partha},
issn = {09249907},
journal = {Journal of Mathematical Imaging and Vision},
number = {1},
pages = {69--83},
publisher = {Springer Nature},
title = {{On the functionality and usefulness of Quadraginta octants of naive sphere}},
doi = {10.1007/s10851-017-0718-4},
volume = {59},
year = {2017},
}
@inproceedings{5801,
abstract = {Space filling circles and spheres have various applications in mathematical imaging and physical modeling. In this paper, we first show how the thinnest (i.e., 2-minimal) model of digital sphere can be augmented to a space filling model by fixing certain “simple voxels” and “filler voxels” associated with it. Based on elementary number-theoretic properties of such voxels, we design an efficient incremental algorithm for generation of these space filling spheres with successively increasing radius. The novelty of the proposed technique is established further through circular space filling on 3D digital plane. As evident from a preliminary set of experimental result, this can particularly be useful for parallel computing of 3D Voronoi diagrams in the digital space.},
author = {Dwivedi, Shivam and Gupta, Aniket and Roy, Siddhant and Biswas, Ranita and Bhowmick, Partha},
isbn = {9783319662718},
issn = {0302-9743},
location = {Vienna, Austria},
pages = {347--359},
publisher = {Springer International Publishing},
title = {{Fast and Efficient Incremental Algorithms for Circular and Spherical Propagation in Integer Space}},
doi = {10.1007/978-3-319-66272-5_28},
volume = {10502},
year = {2017},
}
@inproceedings{5802,
abstract = {This papers introduces a definition of digital primitives based on focal points and weighted distances (with positive weights). The proposed definition is applicable to general dimensions and covers in its gamut various regular curves and surfaces like circles, ellipses, digital spheres and hyperspheres, ellipsoids and k-ellipsoids, Cartesian k-ovals, etc. Several interesting properties are presented for this class of digital primitives such as space partitioning, topological separation, and connectivity properties. To demonstrate further the potential of this new way of defining digital primitives, we propose, as extension, another class of digital conics defined by focus-directrix combination.},
author = {Andres, Eric and Biswas, Ranita and Bhowmick, Partha},
isbn = {9783319662718},
issn = {0302-9743},
location = {Vienna, Austria},
pages = {388--398},
publisher = {Springer International Publishing},
title = {{Digital Primitives Defined by Weighted Focal Set}},
doi = {10.1007/978-3-319-66272-5_31},
volume = {10502},
year = {2017},
}
@inbook{5803,
abstract = {Different distance metrics produce Voronoi diagrams with different properties. It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions. In this paper, we first show that this metric produces a persistent VD on the 2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly approximates the corresponding VD on the 2D real plane. Next, we show that on a 3D digital plane D, the Euclidean metric spanning over its voxel set does not guarantee a digital VD which is persistent with the real-space VD. As a solution, we introduce a novel concept of functional-plane-convexity, which is ensured by the Euclidean metric spanning over the pedal set of D. Necessary proofs and some visual result have been provided to adjudge the merit and usefulness of the proposed concept.},
author = {Biswas, Ranita and Bhowmick, Partha},
booktitle = {Combinatorial image analysis},
isbn = {9783319591070},
issn = {0302-9743},
location = {Plovdiv, Bulgaria},
pages = {93--104},
publisher = {Springer International Publishing},
title = {{Construction of Persistent Voronoi Diagram on 3D Digital Plane}},
doi = {10.1007/978-3-319-59108-7_8},
volume = {10256},
year = {2017},
}
@article{593,
abstract = {Bell correlations, indicating nonlocality in composite quantum systems, were until recently only seen in small systems. Here, we demonstrate Bell correlations in squeezed states of 5×105 Rb87 atoms. The correlations are inferred using collective measurements as witnesses and are statistically significant to 124 standard deviations. The states are both generated and characterized using optical-cavity aided measurements.},
author = {Engelsen, Nils and Krishnakumar, Rajiv and Hosten, Onur and Kasevich, Mark},
journal = {Physical Review Letters},
number = {14},
publisher = {American Physical Society},
title = {{Bell correlations in spin-squeezed states of 500 000 atoms}},
doi = {10.1103/PhysRevLett.118.140401},
volume = {118},
year = {2017},
}
@article{600,
abstract = {Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis. Comparison with the Pol II system suggests that promoter specificity relies on a distinct “bendability” and “meltability” of the promoter sequence that enables contacts between initiation factors, DNA, and polymerase.},
author = {Engel, Christoph and Gubbey, Tobias and Neyer, Simon and Sainsbury, Sarah and Oberthuer, Christiane and Baejen, Carlo and Bernecky, Carrie A and Cramer, Patrick},
issn = {00928674},
journal = {Cell},
number = {1},
pages = {120 -- 131.e22},
publisher = {Cell Press},
title = {{Structural basis of RNA polymerase I transcription initiation}},
doi = {10.1016/j.cell.2017.03.003},
volume = {169},
year = {2017},
}
@article{601,
abstract = {The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple roles in chromatin transcription and genomic regulation. Paf1C comprises the five subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II (Pol II) transcription elongation complex (EC). Here we report the reconstitution of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent with the structural observations, the initiation factor TFIIF impairs Paf1C binding to Pol II, whereas the elongation factor TFIIS enhances it. We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin. },
author = {Xu, Youwei and Bernecky, Carrie A and Lee, Chung and Maier, Kerstin and Schwalb, Björn and Tegunov, Dimitri and Plitzko, Jürgen and Urlaub, Henning and Cramer, Patrick},
issn = {20411723},
journal = {Nature Communications},
publisher = {Nature Publishing Group},
title = {{Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex}},
doi = {10.1038/ncomms15741},
volume = {8},
year = {2017},
}
@article{6013,
abstract = {The first hundred attoseconds of the electron dynamics during strong field tunneling ionization are investigated. We quantify theoretically how the electron’s classical trajectories in the continuum emerge from the tunneling process and test the results with those achieved in parallel from attoclock measurements. An especially high sensitivity on the tunneling barrier is accomplished here by comparing the momentum distributions of two atomic species of slightly deviating atomic potentials (argon and krypton) being ionized under absolutely identical conditions with near-infrared laser pulses (1300 nm). The agreement between experiment and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing longitudinal momentum of the electron at the “tunnel exit.”},
author = {Camus, Nicolas and Yakaboylu, Enderalp and Fechner, Lutz and Klaiber, Michael and Laux, Martin and Mi, Yonghao and Hatsagortsyan, Karen Z. and Pfeifer, Thomas and Keitel, Christoph H. and Moshammer, Robert},
issn = {1079-7114},
journal = {Physical Review Letters},
number = {2},
publisher = {American Physical Society},
title = {{Experimental evidence for quantum tunneling time}},
doi = {10.1103/PhysRevLett.119.023201},
volume = {119},
year = {2017},
}
@article{603,
abstract = {During transcription, RNA polymerase II (Pol II) associates with the conserved elongation factor DSIF. DSIF renders the elongation complex stable and functions during Pol II pausing and RNA processing. We combined cryo-EM and X-ray crystallography to determine the structure of the mammalian Pol II-DSIF elongation complex at a nominal resolution of 3.4. Human DSIF has a modular structure with two domains forming a DNA clamp, two domains forming an RNA clamp, and one domain buttressing the RNA clamp. The clamps maintain the transcription bubble, position upstream DNA, and retain the RNA transcript in the exit tunnel. The mobile C-terminal region of DSIF is located near exiting RNA, where it can recruit factors for RNA processing. The structure provides insight into the roles of DSIF during mRNA synthesis.},
author = {Bernecky, Carrie A and Plitzko, Jürgen and Cramer, Patrick},
issn = {15459993},
journal = {Nature Structural and Molecular Biology},
number = {10},
pages = {809 -- 815},
publisher = {Nature Publishing Group},
title = {{Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp}},
doi = {10.1038/nsmb.3465},
volume = {24},
year = {2017},
}
@inbook{604,
abstract = {In several settings of physics and chemistry one has to deal with molecules interacting with some kind of an external environment, be it a gas, a solution, or a crystal surface. Understanding molecular processes in the presence of such a many-particle bath is inherently challenging, and usually requires large-scale numerical computations. Here, we present an alternative approach to the problem, based on the notion of the angulon quasiparticle. We show that molecules rotating inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons, and therefore can be described by straightforward solutions of a simple microscopic Hamiltonian. Casting the problem in the language of angulons allows us not only to greatly simplify it, but also to gain insights into the origins of the observed phenomena and to make predictions for future experimental studies.},
author = {Lemeshko, Mikhail and Schmidt, Richard},
booktitle = {Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero },
editor = {Dulieu, Oliver and Osterwalder, Andreas},
issn = {20413181},
pages = {444 -- 495},
publisher = {The Royal Society of Chemistry},
title = {{Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets}},
doi = {10.1039/9781782626800-00444},
volume = {11},
year = {2017},
}
@inproceedings{605,
abstract = {Position based cryptography (PBC), proposed in the seminal work of Chandran, Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing cryptographic schemes in which the identity of the user is his geographic position. Chandran et al. construct PBC schemes for secure positioning and position-based key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart from bounded memory, their security proofs need a strong additional restriction on the power of the adversary: he cannot compute joint functions of his inputs. Removing this assumption is left as an open problem. We show that an answer to this question would resolve a long standing open problem in multiparty communication complexity: finding a function that is hard to compute with low communication complexity in the simultaneous message model, but easy to compute in the fully adaptive model. On a more positive side: we also show some implications in the other direction, i.e.: we prove that lower bounds on the communication complexity of certain multiparty problems imply existence of PBC primitives. Using this result we then show two attractive ways to “bypass” our hardness result: the first uses the random oracle model, the second weakens the locality requirement in the bounded-storage model to online computability. The random oracle construction is arguably one of the simplest proposed so far in this area. Our results indicate that constructing improved provably secure protocols for PBC requires a better understanding of multiparty communication complexity. This is yet another example where negative results in one area (in our case: lower bounds in multiparty communication complexity) can be used to construct secure cryptographic schemes.},
author = {Brody, Joshua and Dziembowski, Stefan and Faust, Sebastian and Pietrzak, Krzysztof Z},
editor = {Kalai, Yael and Reyzin, Leonid},
isbn = {978-331970499-9},
location = {Baltimore, MD, United States},
pages = {56 -- 81},
publisher = {Springer},
title = {{Position based cryptography and multiparty communication complexity}},
doi = {10.1007/978-3-319-70500-2_3},
volume = {10677},
year = {2017},
}
@article{6059,
abstract = {Neutrophils or polymorphonuclear cells (PMN) eliminate bacteria via phagocytosis and/or NETosis. Apartfrom these conventional roles, PMN also have immune-regulatory functions. They can transdifferentiateand upregulate MHCII as well as ligands for costimulatory receptors which enables them to behave asantigen presenting cells (APC). The initial step for activating T-cells is the formation of an immunesynapse between T-cells and antigen-presenting cells. However, the immune synapse that develops atthe PMN/T-cell contact zone is as yet hardly investigated due to the non-availability of methods foranalysis of large number of PMN interactions. In order to overcome these obstacles, we introduce herea workflow to analyse the immune synapse of primary human PMN and T-cells using multispectral imag-ing flow cytometry (InFlow microscopy) and super-resolution microscopy. For that purpose, we used CD3and CD66b as the lineage markers for T-cells and PMN, respectively. Thereafter, we applied and criticallydiscussed various ‘‘masks” for identification of T-cell PMN interactions. Using this approach, we foundthat a small fraction of transdifferentiated PMN (CD66b+CD86high) formed stable PMN/T-cell conjugates.Interestingly, while both CD3 and CD66b accumulation in the immune synapse was dependent on thematuration state of the PMN, only CD3 accumulation was greatly enhanced by the presence of superanti-gen. The actin cytoskeleton was weakly rearranged at the PMN side on the immune synapse upon contactwith a T-cell in the presence of superantigen. A more detailed analysis using super-resolution microscopy(structured-illumination microscopy, SIM) confirmed this finding. Together, we present an InFlow micro-scopy based approach for the large scale analysis of PMN/T-cell interactions and – combined with SIM – apossibility for an in-depth analysis of protein translocation at the site of interactions.},
author = {Balta, Emre and Stopp, Julian A and Castelletti, Laura and Kirchgessner, Henning and Samstag, Yvonne and Wabnitz, Guido H.},
issn = {1046-2023},
journal = {Methods},
number = {1},
pages = {25--38},
publisher = {Elsevier},
title = {{Qualitative and quantitative analysis of PMN/T-cell interactions by InFlow and super-resolution microscopy}},
doi = {10.1016/j.ymeth.2016.09.013},
volume = {112},
year = {2017},
}
@inproceedings{609,
abstract = {Several cryptographic schemes and applications are based on functions that are both reasonably efficient to compute and moderately hard to invert, including client puzzles for Denial-of-Service protection, password protection via salted hashes, or recent proof-of-work blockchain systems. Despite their wide use, a definition of this concept has not yet been distilled and formalized explicitly. Instead, either the applications are proven directly based on the assumptions underlying the function, or some property of the function is proven, but the security of the application is argued only informally. The goal of this work is to provide a (universal) definition that decouples the efforts of designing new moderately hard functions and of building protocols based on them, serving as an interface between the two. On a technical level, beyond the mentioned definitions, we instantiate the model for four different notions of hardness. We extend the work of Alwen and Serbinenko (STOC 2015) by providing a general tool for proving security for the first notion of memory-hard functions that allows for provably secure applications. The tool allows us to recover all of the graph-theoretic techniques developed for proving security under the older, non-composable, notion of security used by Alwen and Serbinenko. As an application of our definition of moderately hard functions, we prove the security of two different schemes for proofs of effort (PoE). We also formalize and instantiate the concept of a non-interactive proof of effort (niPoE), in which the proof is not bound to a particular communication context but rather any bit-string chosen by the prover.},
author = {Alwen, Joel F and Tackmann, Björn},
editor = {Kalai, Yael and Reyzin, Leonid},
isbn = {978-331970499-9},
location = {Baltimore, MD, United States},
pages = {493 -- 526},
publisher = {Springer},
title = {{Moderately hard functions: Definition, instantiations, and applications}},
doi = {10.1007/978-3-319-70500-2_17},
volume = {10677},
year = {2017},
}
@article{610,
abstract = {The fact that the complete graph K5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph Kn embeds in a closed surface M (other than the Klein bottle) if and only if (n−3)(n−4) ≤ 6b1(M), where b1(M) is the first Z2-Betti number of M. On the other hand, van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of Kn+1) embeds in R2k if and only if n ≤ 2k + 1. Two decades ago, Kühnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k − 1)-connected 2k-manifold with kth Z2-Betti number bk only if the following generalized Heawood inequality holds: (k+1 n−k−1) ≤ (k+1 2k+1)bk. This is a common generalization of the case of graphs on surfaces as well as the van Kampen–Flores theorem. In the spirit of Kühnel’s conjecture, we prove that if the k-skeleton of the n-simplex embeds in a compact 2k-manifold with kth Z2-Betti number bk, then n ≤ 2bk(k 2k+2)+2k+4. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k−1)-connected. Our results generalize to maps without q-covered points, in the spirit of Tverberg’s theorem, for q a prime power. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.},
author = {Goaoc, Xavier and Mabillard, Isaac and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli},
journal = {Israel Journal of Mathematics},
number = {2},
pages = {841 -- 866},
publisher = {Springer},
title = {{On generalized Heawood inequalities for manifolds: A van Kampen–Flores type nonembeddability result}},
doi = {10.1007/s11856-017-1607-7},
volume = {222},
year = {2017},
}
@article{611,
abstract = {Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity.},
author = {Bradley, Desmond and Xu, Ping and Mohorianu, Irina and Whibley, Annabel and Field, David and Tavares, Hugo and Couchman, Matthew and Copsey, Lucy and Carpenter, Rosemary and Li, Miaomiao and Li, Qun and Xue, Yongbiao and Dalmay, Tamas and Coen, Enrico},
issn = {00368075},
journal = {Science},
number = {6365},
pages = {925 -- 928},
publisher = {American Association for the Advancement of Science},
title = {{Evolution of flower color pattern through selection on regulatory small RNAs}},
doi = {10.1126/science.aao3526},
volume = {358},
year = {2017},
}
@article{6113,
author = {Oda, Shigekazu and Toyoshima, Yu and de Bono, Mario},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {23},
pages = {E4658--E4665},
publisher = {National Academy of Sciences},
title = {{Modulation of sensory information processing by a neuroglobin in Caenorhabditis elegans}},
doi = {10.1073/pnas.1614596114},
volume = {114},
year = {2017},
}
@article{6115,
abstract = {Animals adjust their behavioral priorities according to momentary needs and prior experience. We show that Caenorhabditis elegans changes how it processes sensory information according to the oxygen environment it experienced recently. C. elegans acclimated to 7% O2 are aroused by CO2 and repelled by pheromones that attract animals acclimated to 21% O2. This behavioral plasticity arises from prolonged activity differences in a circuit that continuously signals O2 levels. A sustained change in the activity of O2-sensing neurons reprograms the properties of their postsynaptic partners, the RMG hub interneurons. RMG is gap-junctionally coupled to the ASK and ADL pheromone sensors that respectively drive pheromone attraction and repulsion. Prior O2 experience has opposite effects on the pheromone responsiveness of these neurons. These circuit changes provide a physiological correlate of altered pheromone valence. Our results suggest C. elegans stores a memory of recent O2 experience in the RMG circuit and illustrate how a circuit is flexibly sculpted to guide behavioral decisions in a context-dependent manner.},
author = {Fenk, Lorenz A. and de Bono, Mario},
issn = {0027-8424},
journal = {Proceedings of the National Academy of Sciences},
number = {16},
pages = {4195--4200},
publisher = {National Academy of Sciences},
title = {{Memory of recent oxygen experience switches pheromone valence inCaenorhabditis elegans}},
doi = {10.1073/pnas.1618934114},
volume = {114},
year = {2017},
}
@article{6117,
abstract = {Interleukin-17 (IL-17) is a major pro-inflammatory cytokine: it mediates responses to pathogens or tissue damage, and drives autoimmune diseases. Little is known about its role in the nervous system. Here we show that IL-17 has neuromodulator-like properties in Caenorhabditis elegans. IL-17 can act directly on neurons to alter their response properties and contribution to behaviour. Using unbiased genetic screens, we delineate an IL-17 signalling pathway and show that it acts in the RMG hub interneurons. Disrupting IL-17 signalling reduces RMG responsiveness to input from oxygen sensors, and renders sustained escape from 21% oxygen transient and contingent on additional stimuli. Over-activating IL-17 receptors abnormally heightens responses to 21% oxygen in RMG neurons and whole animals. IL-17 deficiency can be bypassed by optogenetic stimulation of RMG. Inducing IL-17 expression in adults can rescue mutant defects within 6 h. These findings reveal a non-immunological role of IL-17 modulating circuit function and behaviour.},
author = {Chen, Changchun and Itakura, Eisuke and Nelson, Geoffrey M. and Sheng, Ming and Laurent, Patrick and Fenk, Lorenz A. and Butcher, Rebecca A. and Hegde, Ramanujan S. and de Bono, Mario},
issn = {0028-0836},
journal = {Nature},
number = {7639},
pages = {43--48},
publisher = {Springer Nature},
title = {{IL-17 is a neuromodulator of Caenorhabditis elegans sensory responses}},
doi = {10.1038/nature20818},
volume = {542},
year = {2017},
}