@article{55,
abstract = {Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to selfmedicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation.},
author = {Pull, Christopher and Metzler, Sina and Naderlinger, Elisabeth and Cremer, Sylvia},
journal = {Current Biology},
number = {19},
pages = {R1139  R1140},
publisher = {Cell Press},
title = {{Protection against the lethal side effects of social immunity in ants}},
doi = {10.1016/j.cub.2018.08.063},
volume = {28},
year = {2018},
}
@article{554,
abstract = {We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a firstorder phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pairinteraction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.).},
author = {Napiórkowski, Marcin M and Reuvers, Robin and Solovej, Jan},
issn = {00103616},
journal = {Communications in Mathematical Physics},
number = {1},
pages = {347403},
publisher = {Springer},
title = {{The Bogoliubov free energy functional II: The dilute Limit}},
doi = {10.1007/s002200173064x},
volume = {360},
year = {2018},
}
@article{555,
abstract = {Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semiflexibility — underpin the overall properties of GAGrich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAGrich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAGrich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions.},
author = {Richter, Ralf and Baranova, Natalia and Day, Anthony and Kwok, Jessica},
journal = {Current Opinion in Structural Biology},
pages = {65  74},
publisher = {Elsevier},
title = {{Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?}},
doi = {10.1016/j.sbi.2017.12.002},
volume = {50},
year = {2018},
}
@article{556,
abstract = {We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions.},
author = {Betea, Dan and Bouttier, Jeremie and Nejjar, Peter and Vuletic, Mirjana},
issn = {14240637},
journal = {Annales Henri Poincare},
number = {12},
pages = {36633742},
publisher = {Fakultät für Mathematik Universität Wien},
title = {{The free boundary Schur process and applications I}},
doi = {10.1007/s0002301807231},
volume = {19},
year = {2018},
}
@misc{5569,
abstract = {Nela Nikolic, Tobias Bergmiller, Alexandra Vandervelde, Tanino G. Albanese, Lendert Gelens, and Isabella Moll (2018)
“Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations” Nucleic Acids Research, doi: 10.15479/AT:ISTA:74;
microscopy experiments by Tobias Bergmiller; image and data analysis by Nela Nikolic.},
author = {Bergmiller, Tobias and Nikolic, Nela},
keywords = {microscopy, microfluidics},
publisher = {IST Austria},
title = {{Timelapse microscopy data}},
doi = {10.15479/AT:ISTA:74},
year = {2018},
}
@misc{5573,
abstract = {Graph matching problems for large displacement optical flow of RGBD images.},
author = {Alhaija, Hassan and Sellent, Anita and Kondermann, Daniel and Rother, Carsten},
keywords = {graph matching, quadratic assignment problem<},
publisher = {IST Austria},
title = {{Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow}},
doi = {10.15479/AT:ISTA:82},
year = {2018},
}
@misc{5574,
abstract = {Comparison of Scopus' and publisher's data on Austrian publication output at IOP. },
author = {Villányi, Márton},
keywords = {Publication analysis, Bibliography, Open Access},
publisher = {IST Austria},
title = {{Data Check IOP Scopus vs. Publisher}},
doi = {10.15479/AT:ISTA:86},
year = {2018},
}
@misc{5575,
abstract = {Comparison of Scopus' and FWF's data on Austrian publication output at RSC. },
author = {Villányi, Márton},
keywords = {Publication analysis, Bibliography, Open Access},
publisher = {IST Austria},
title = {{Data Check RSC Scopus vs. FWF}},
doi = {10.15479/AT:ISTA:87},
year = {2018},
}
@misc{5576,
abstract = {Comparison of Scopus' and FWF's data on Austrian publication output at T&F.},
author = {Villányi, Márton},
keywords = {Publication analysis, Bibliography, Open Access},
publisher = {IST Austria},
title = {{Data Check T&F Scopus vs. FWF}},
doi = {10.15479/AT:ISTA:88},
year = {2018},
}
@misc{5577,
abstract = {Data on Austrian open access publication output at Emerald from 20132017 including data analysis.},
author = {Villányi, Márton},
keywords = {Publication analysis, Bibliography, Open Access},
publisher = {IST Austria},
title = {{Emerald Austrian Publications 20132017}},
doi = {10.15479/AT:ISTA:89},
year = {2018},
}
@misc{5578,
abstract = {Data on Austrian open access publication output at IOP from 20122015 including data analysis.},
author = {Villányi, Márton},
keywords = {Publication analysis, Bibliography, Open Access},
publisher = {IST Austria},
title = {{IOP Austrian Publications 20122015}},
doi = {10.15479/AT:ISTA:90},
year = {2018},
}
@misc{5579,
abstract = {Data on Austrian open access publication output at RSC from 20132017 including data analysis.},
author = {Villányi, Márton},
keywords = {Publication analysis, Bibliography, Open Access},
publisher = {IST Austria},
title = {{RSC Austrian Publications 20132017}},
doi = {10.15479/AT:ISTA:91},
year = {2018},
}
@misc{5580,
abstract = {Data on Austrian open access publication output at SAGE from 20132017 including data analysis.},
author = {Villányi, Márton},
keywords = {Publication analysis, Bibliography, Open Access},
publisher = {IST Austria},
title = {{SAGE Austrian Publications 20132017}},
doi = {10.15479/AT:ISTA:92},
year = {2018},
}
@misc{5581,
abstract = {Data on Austrian open access publication output at Springer from 20132016 including data analysis.},
author = {Villányi, Márton},
keywords = {Publication analysis, Bibliography, Open Access},
publisher = {IST Austria},
title = {{Springer Austrian Publications 20132016}},
doi = {10.15479/AT:ISTA:93},
year = {2018},
}
@misc{5582,
abstract = {Data on Austrian open access publication output at Taylor&Francis from 20132017 including data analysis.},
author = {Villányi, Márton},
keywords = {Publication analysis, Bibliography, Open Access},
publisher = {IST Austria},
title = {{Taylor&Francis Austrian Publications 20132017}},
doi = {10.15479/AT:ISTA:94},
year = {2018},
}
@misc{5583,
abstract = {Data and scripts are provided in support of the manuscript "Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering", and the associated Python package FAPS, available from www.github.com/ellisztamas/faps.
Simulation scripts cover:
1. Performance under different mating scenarios.
2. Comparison with Colony2.
3. Effect of changing the number of Monte Carlo draws
The final script covers the analysis of halfsib arrays from wildpollinated seed in an Antirrhinum majus hybrid zone.},
author = {Ellis, Thomas},
publisher = {IST Austria},
title = {{Data and Python scripts supporting Python package FAPS}},
doi = {10.15479/AT:ISTA:95},
year = {2018},
}
@misc{5584,
abstract = {This package contains data for the publication "Nonlinear decoding of a complex movie from the mammalian retina" by Deny S. et al, PLOS Comput Biol (2018).
The data consists of
(i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multielectrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin.
(ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments are exact repeats or unique ball trajectories.
(iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions ("sites") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. },
author = {Deny, Stephane and Marre, Olivier and BotellaSoler, Vicente and Martius, Georg S and Tkacik, Gasper},
keywords = {retina, decoding, regression, neural networks, complex stimulus},
publisher = {IST Austria},
title = {{Nonlinear decoding of a complex movie from the mammalian retina}},
doi = {10.15479/AT:ISTA:98},
year = {2018},
}
@misc{5586,
abstract = {Input files and scripts from "Evolution of gene dosage on the Zchromosome of schistosome parasites" by Picard M.A.L., et al (2018).},
author = {Vicoso, Beatriz},
keywords = {schistosoma, Zchromosome, gene expression},
publisher = {IST Austria},
title = {{Input files and scripts from "Evolution of gene dosage on the Zchromosome of schistosome parasites" by Picard M.A.L., et al (2018)}},
doi = {10.15479/AT:ISTA:109},
year = {2018},
}
@misc{5587,
abstract = {Supporting material to the article
STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADYSTATE GROWTH
boundscoli.dat
Flux Bounds of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium.
polcoli.dat
Matrix enconding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium,
obtained from the soichiometric matrix by standard linear algebra (reduced row echelon form).
ellis.dat
Approximate LownerJohn ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium
obtained with the Lovasz method.
point0.dat
Center of the approximate LownerJohn ellipsoid rounding the polytope of the E. coli catabolic core model iAF1260 in a glucose limited minimal medium
obtained with the Lovasz method.
lovasz.cpp
This c++ code file receives in input the polytope of the feasible steady states of a metabolic network,
(matrix and bounds), and it gives in output an approximate LownerJohn ellipsoid rounding the polytope
with the Lovasz method
NB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260.
For further details we refer to PLoS ONE 10.4 e0122670 (2015).
sampleHRnew.cpp
This c++ code file receives in input the polytope of the feasible steady states of a metabolic network,
(matrix and bounds), the ellipsoid rounding the polytope, a point inside and
it gives in output a max entropy sampling at fixed average growth rate
of the steady states by performing an HitandRun Monte Carlo Markov chain.
NB inputs are referred by defaults to the catabolic core of the E.Coli network iAF1260.
For further details we refer to PLoS ONE 10.4 e0122670 (2015).},
author = {De Martino, Daniele and Tkacik, Gasper},
keywords = {metabolic networks, e.coli core, maximum entropy, monte carlo markov chain sampling, ellipsoidal rounding},
publisher = {IST Austria},
title = {{Supporting materials "STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADYSTATE GROWTH"}},
doi = {10.15479/AT:ISTA:62},
year = {2018},
}
@misc{5588,
abstract = {Script to perform a simple exponential lifetime fit of a ROI on time stacks acquired with a FLIM X16 TCSPC detector (+example data)},
author = {Hauschild, Robert},
keywords = {FLIM, FRET, fluorescence lifetime imaging},
publisher = {IST Austria},
title = {{Fluorescence lifetime analysis of FLIM X16 TCSPC data}},
doi = {10.15479/AT:ISTA:0113},
year = {2018},
}
@inbook{562,
abstract = {Primary neuronal cell culture preparations are widely used to investigate synaptic functions. This chapter describes a detailed protocol for the preparation of a neuronal cell culture in which giant calyxtype synaptic terminals are formed. This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals.},
author = {Dimitrov, Dimitar and Guillaud, Laurent and Eguchi, Kohgaku and Takahashi, Tomoyuki},
booktitle = {Neurotrophic Factors},
editor = {Skaper, Stephen D.},
pages = {201  215},
publisher = {Springer},
title = {{Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses}},
doi = {10.1007/9781493975716_15},
volume = {1727},
year = {2018},
}
@article{563,
abstract = {In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes
than geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in twodimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.},
author = {Ringbauer, Harald and Kolesnikov, Alexander and Field, David and Barton, Nicholas H},
journal = {Genetics},
number = {3},
pages = {12311245},
publisher = {Genetics Society of America},
title = {{Estimating barriers to gene flow from distorted isolationbydistance patterns}},
doi = {10.1534/genetics.117.300638},
volume = {208},
year = {2018},
}
@article{564,
abstract = {Maladapted individuals can only colonise a new habitat if they can evolve a
positive growth rate fast enough to avoid extinction, a process known as evolutionary
rescue. We treat log fitness at low density in the new habitat as a
single polygenic trait and thus use the infinitesimal model to follow the evolution
of the growth rate; this assumes that the trait values of offspring of a
sexual union are normally distributed around the mean of the parents’ trait
values, with variance that depends only on the parents’ relatedness. The
probability that a single migrant can establish depends on just two parameters:
the mean and genetic variance of the trait in the source population.
The chance of success becomes small if migrants come from a population
with mean growth rate in the new habitat more than a few standard deviations
below zero; this chance depends roughly equally on the probability
that the initial founder is unusually fit, and on the subsequent increase in
growth rate of its offspring as a result of selection. The loss of genetic variation
during the founding event is substantial, but highly variable. With
continued migration at rate M, establishment is inevitable; when migration
is rare, the expected time to establishment decreases inversely with M.
However, above a threshold migration rate, the population may be trapped
in a ‘sink’ state, in which adaptation is held back by gene flow; above this
threshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,
which assumes a Gaussian distribution of the trait in the founder population
with mean and variance evolving deterministically. By assuming a constant
genetic variance, we also develop a diffusion approximation for the joint distribution
of population size and trait mean, which extends to include stabilising
selection and density regulation. Divergence of the population from its
ancestors causes partial reproductive isolation, which we measure through
the reproductive value of migrants into the newly established population.},
author = {Barton, Nicholas H and Etheridge, Alison},
journal = {Theoretical Population Biology},
number = {7},
pages = {110127},
publisher = {Academic Press},
title = {{Establishment in a new habitat by polygenic adaptation}},
doi = {10.1016/j.tpb.2017.11.007},
volume = {122},
year = {2018},
}
@article{565,
abstract = {We reexamine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. },
author = {Charlesworth, Brian and Barton, Nicholas H},
journal = {Genetics},
number = {1},
pages = {377  382},
publisher = {Genetics },
title = {{The spread of an inversion with migration and selection}},
doi = {10.1534/genetics.117.300426},
volume = {208},
year = {2018},
}
@article{566,
abstract = {We consider large random matrices X with centered, independent entries which have comparable but not necessarily identical variances. Girko's circular law asserts that the spectrum is supported in a disk and in case of identical variances, the limiting density is uniform. In this special case, the local circular law by Bourgade et. al. [11,12] shows that the empirical density converges even locally on scales slightly above the typical eigenvalue spacing. In the general case, the limiting density is typically inhomogeneous and it is obtained via solving a system of deterministic equations. Our main result is the local inhomogeneous circular law in the bulk spectrum on the optimal scale for a general variance profile of the entries of X.
},
author = {Alt, Johannes and Erdös, László and Krüger, Torben H},
journal = {Annals Applied Probability },
number = {1},
pages = {148203},
publisher = {Institute of Mathematical Statistics},
title = {{Local inhomogeneous circular law}},
doi = {10.1214/17AAP1302},
volume = {28},
year = {2018},
}
@article{5672,
abstract = {The release of IgM is the first line of an antibody response and precedes the generation of high affinity IgG in germinal centers. Once secreted by freshly activated plasmablasts, IgM is released into the efferent lymph of reactive lymph nodes as early as 3 d after immunization. As pentameric IgM has an enormous size of 1,000 kD, its diffusibility is low, and one might wonder how it can pass through the densely lymphocytepacked environment of a lymph node parenchyma in order to reach its exit. In this issue of JEM, Thierry et al. show that, in order to reach the blood stream, IgM molecules take a specific microanatomical route via lymph node conduits.},
author = {Reversat, Anne and Sixt, Michael K},
issn = {00221007},
journal = {Journal of Experimental Medicine},
number = {12},
pages = {29592961},
publisher = {Rockefeller University Press},
title = {{IgM's exit route}},
doi = {10.1084/jem.20181934},
volume = {215},
year = {2018},
}
@article{5673,
abstract = {Cell polarity, manifested by the localization of proteins to distinct polar plasma membrane domains, is a key prerequisite of multicellular life. In plants, PIN auxin transporters are prominent polarity markers crucial for a plethora of developmental processes. Cell polarity mechanisms in plants are distinct from other eukaryotes and still largely elusive. In particular, how the cell polarities are propagated and maintained following cell division remains unknown. Plant cytokinesis is orchestrated by the cell plate—a transient centrifugally growing endomembrane compartment ultimately forming the cross wall1. Trafficking of polar membrane proteins is typically redirected to the cell plate, and these will consequently have opposite polarity in at least one of the daughter cells2–5. Here, we provide mechanistic insights into postcytokinetic reestablishment of cell polarity as manifested by the apical, polar localization of PIN2. We show that the apical domain is defined in a cellintrinsic manner and that reestablishment of PIN2 localization to this domain requires de novo protein secretion and endocytosis, but not basaltoapical transcytosis. Furthermore, we identify a PINOIDrelated kinase WAG1, which phosphorylates PIN2 in vitro6 and is transcriptionally upregulated specifically in dividing cells, as a crucial regulator of postcytokinetic PIN2 polarity reestablishment.},
author = {Glanc, Matous and Fendrych, Matyas and Friml, Jirí},
issn = {20550278},
journal = {Nature Plants},
number = {12},
pages = {10821088},
publisher = {Palgrave Macmillan Ltd.},
title = {{Mechanistic framework for cellintrinsic reestablishment of PIN2 polarity after cell division}},
doi = {10.1038/s4147701803183},
volume = {4},
year = {2018},
}
@article{5676,
abstract = {In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in woundclosure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge.},
author = {Carvalho, Lara and Patricio, Pedro and Ponte, Susana and Heisenberg, CarlPhilipp J and Almeida, Luis and Nunes, André S. and Araújo, Nuno A.M. and Jacinto, Antonio},
issn = {00219525},
journal = {Journal of Cell Biology},
number = {12},
pages = {42674283},
publisher = {Rockefeller University Press},
title = {{Occluding junctions as novel regulators of tissue mechanics during wound repair}},
doi = {10.1083/jcb.201804048},
volume = {217},
year = {2018},
}
@article{5677,
abstract = {Recently, contractbased design has been proposed as an “orthogonal” approach that complements system design methodologies proposed so far to cope with the complexity of system design. Contractbased design provides a rigorous scaffolding for verification, analysis, abstraction/refinement, and even synthesis. A number of results have been obtained in this domain but a unified treatment of the topic that can help put contractbased design in perspective was missing. This monograph intends to provide such a treatment where contracts are precisely defined and characterized so that they can be used in design methodologies with no ambiguity. In particular, this monograph identifies the essence of complex system design using contracts through a mathematical “metatheory”, where all the properties of the methodology are derived from a very abstract and generic notion of contract. We show that the metatheory provides deep and illuminating links with existing contract and interface theories, as well as guidelines for designing new theories. Our study encompasses contracts for both software and systems, with emphasis on the latter. We illustrate the use of contracts with two examples: requirement engineering for a parking garage management, and the development of contracts for timing and scheduling in the context of the Autosar methodology in use in the automotive sector.},
author = {Benveniste, Albert and Nickovic, Dejan and Caillaud, Benoît and Passerone, Roberto and Raclet, Jean Baptiste and Reinkemeier, Philipp and SangiovanniVincentelli, Alberto and Damm, Werner and Henzinger, Thomas A and Larsen, Kim G.},
issn = {15513939},
journal = {Foundations and Trends in Electronic Design Automation},
number = {23},
pages = {124400},
publisher = {Now Publishers Inc},
title = {{Contracts for system design}},
doi = {10.1561/1000000053},
volume = {12},
year = {2018},
}
@inproceedings{5679,
abstract = {We study the almostsure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almostsure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of nontermination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almostsure termination problem, and show that this approach can establish almostsure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almostsure termination of probabilistic programs.},
author = {Huang, Mingzhang and Fu, Hongfei and Chatterjee, Krishnendu},
editor = {Ryu, Sukyoung},
isbn = {9783030027674},
issn = {03029743},
location = {Wellington, New Zealand},
pages = {181201},
publisher = {Springer},
title = {{New approaches for almostsure termination of probabilistic programs}},
doi = {10.1007/9783030027681_11},
volume = {11275},
year = {2018},
}
@techreport{5686,
author = {Danowski, Patrick},
pages = {5},
title = {{An Austrian proposal for the Classification of Open Access Tuples (COAT)  Distinguish different Open Access types beyond colors}},
doi = {10.5281/zenodo.1244154},
year = {2018},
}
@article{5751,
abstract = {Because of the intrinsic randomness of the evolutionary process, a mutant with a fitness advantage has some chance to be selected but no certainty. Any experiment that searches for advantageous mutants will lose many of them due to random drift. It is therefore of great interest to find population structures that improve the odds of advantageous mutants. Such structures are called amplifiers of natural selection: they increase the probability that advantageous mutants are selected. Arbitrarily strong amplifiers guarantee the selection of advantageous mutants, even for very small fitness advantage. Despite intensive research over the past decade, arbitrarily strong amplifiers have remained rare. Here we show how to construct a large variety of them. Our amplifiers are so simple that they could be useful in biotechnology, when optimizing biological molecules, or as a diagnostic tool, when searching for faster dividing cells or viruses. They could also occur in natural population structures.},
author = {Pavlogiannis, Andreas and Tkadlec, Josef and Chatterjee, Krishnendu and Nowak, Martin A.},
issn = {23993642},
journal = {Communications Biology},
number = {1},
publisher = {Springer Nature},
title = {{Construction of arbitrarily strong amplifiers of natural selection using evolutionary graph theory}},
doi = {10.1038/s4200301800787},
volume = {1},
year = {2018},
}
@misc{5757,
abstract = {File S1. Variant Calling Format file of the ingroup: 197 haploid sequences of D. melanogaster from Zambia (Africa) aligned to the D. melanogaster 5.57 reference genome.
File S2. Variant Calling Format file of the outgroup: 1 haploid sequence of D. simulans aligned to the D. melanogaster 5.57 reference genome.
File S3. Annotations of each transcript in coding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pn (# of nonsynonymous polymorphic sites); Ds (# of synonymous divergent sites); Dn (# of nonsynonymous divergent sites); DoS; ⍺ MK . All variants were included.
File S4. Annotations of each transcript in noncoding regions with SNPeff: Ps (# of synonymous polymorphic sites); Pu (# of UTR polymorphic sites); Ds (# of synonymous divergent sites); Du (# of UTR divergent sites); DoS; ⍺ MK . All variants were included.
File S5. Annotations of each transcript in coding regions with SNPGenie: Ps (# of synonymous polymorphic sites); πs (synonymous diversity); Ss_p (total # of synonymous sites in the polymorphism data); Pn (# of nonsynonymous polymorphic sites); πn (nonsynonymous diversity); Sn_p (total # of nonsynonymous sites in the polymorphism data); Ds (# of synonymous divergent sites); ks (synonymous evolutionary rate); Ss_d (total # of synonymous sites in the divergence data); Dn (# of nonsynonymous divergent sites); kn (nonsynonymous evolutionary rate); Sn_d (total # of non
synonymous sites in the divergence data); DoS; ⍺ MK . All variants were included.
File S6. Gene expression values (RPKM summed over all transcripts) for each sample. Values were quantilenormalized across all samples.
File S7. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for coding sites, excluding variants below 5% frequency.
File S8. Final dataset with all covariates, ⍺ MK , ωA MK and DoS for noncoding sites, excluding variants below 5%
frequency.
File S9. Final dataset with all covariates, ⍺ EWK , ωA EWK and deleterious SFS for coding sites obtained with the EyreWalker and Keightley method on binned data and using all variants.},
author = {Fraisse, Christelle},
keywords = {(mal)adaptation, pleiotropy, selective constraint, evodevo, gene expression, Drosophila melanogaster},
publisher = {IST Austria},
title = {{Supplementary Files for "Pleiotropy modulates the efficacy of selection in Drosophila melanogaster"}},
doi = {10.15479/at:ista:/5757},
year = {2018},
}
@article{5767,
abstract = {Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spinorbit coupling. Using spin and angleresolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spinmomentum locking that circles the Brillouin zone center and a spinlayer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spinorbit interaction has been mostly neglected, and open the intriguing question of how the hightemperature superconducting state emerges in the presence of this nontrivial spin texture. },
author = {Gotlieb, Kenneth and Lin, ChiuYun and Serbyn, Maksym and Zhang, Wentao and Smallwood, Christopher L. and Jozwiak, Christopher and Eisaki, Hiroshi and Hussain, Zahid and Vishwanath, Ashvin and Lanzara, Alessandra},
issn = {00368075},
journal = {Science},
number = {6420},
pages = {12711275},
publisher = {American Association for the Advancement of Science},
title = {{Revealing hidden spinmomentum locking in a hightemperature cuprate superconductor}},
doi = {10.1126/science.aao0980},
volume = {362},
year = {2018},
}
@article{5770,
abstract = {Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γretrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined Xray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV1, uncovers conserved and variable features. In contrast to HIV1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.},
author = {Qu, Kun and Glass, Bärbel and Doležal, Michal and Schur, Florian and Murciano, Brice and Rein, Alan and Rumlová, Michaela and Ruml, Tomáš and Kräusslich, HansGeorg and Briggs, John A. G.},
issn = {00278424},
journal = {Proceedings of the National Academy of Sciences},
number = {50},
pages = {E11751E11760},
publisher = {Proceedings of the National Academy of Sciences},
title = {{Structure and architecture of immature and mature murine leukemia virus capsids}},
doi = {10.1073/pnas.1811580115},
volume = {115},
year = {2018},
}
@article{5780,
abstract = {Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering.},
author = {Kotlobay, Alexey A. and Sarkisyan, Karen and Mokrushina, Yuliana A. and MarcetHouben, Marina and Serebrovskaya, Ekaterina O. and Markina, Nadezhda M. and Gonzalez Somermeyer, Louisa and Gorokhovatsky, Andrey Y. and Vvedensky, Andrey and Purtov, Konstantin V. and Petushkov, Valentin N. and Rodionova, Natalja S. and Chepurnyh, Tatiana V. and Fakhranurova, Liliia and Guglya, Elena B. and Ziganshin, Rustam and Tsarkova, Aleksandra S. and Kaskova, Zinaida M. and Shender, Victoria and Abakumov, Maxim and Abakumova, Tatiana O. and Povolotskaya, Inna S. and Eroshkin, Fedor M. and Zaraisky, Andrey G. and Mishin, Alexander S. and Dolgov, Sergey V. and Mitiouchkina, Tatiana Y. and Kopantzev, Eugene P. and Waldenmaier, Hans E. and Oliveira, Anderson G. and Oba, Yuichi and Barsova, Ekaterina and Bogdanova, Ekaterina A. and Gabaldón, Toni and Stevani, Cassius V. and Lukyanov, Sergey and Smirnov, Ivan V. and Gitelson, Josef I. and Kondrashov, Fyodor and Yampolsky, Ilia V.},
issn = {00278424},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {50},
pages = {1272812732},
publisher = {National Academy of Sciences},
title = {{Genetically encodable bioluminescent system from fungi}},
doi = {10.1073/pnas.1803615115},
volume = {115},
year = {2018},
}
@article{5787,
abstract = {Branching morphogenesis remains a subject of abiding interest. Although much is
known about the gene regulatory programs and signaling pathways that operate at
the cellular scale, it has remained unclear how the macroscopic features of branched
organs, including their size, network topology and spatial patterning, are encoded.
Lately, it has been proposed that, these features can be explained quantitatively in
several organs within a single unifying framework. Based on large
scale organ recon

structions and cell lineage tracing, it has been argued that morphogenesis follows
from the collective dynamics of sublineage
restricted self
renewing progenitor cells,
localized at ductal tips, that act cooperatively to drive a serial process of ductal elon

gation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit
with proximity to maturing ducts, this dynamic results in the specification of a com
plex network of defined density and statistical organization. These results suggest
that, for several mammalian tissues, branched epithelial structures develop as a self
organized process, reliant upon a strikingly simple, but generic, set of local rules,
without recourse to a rigid and deterministic sequence of genetically programmed
events. Here, we review the basis of these findings and discuss their implications.},
author = {Hannezo, Edouard B and Simons, Benjamin D.},
issn = {00121592},
journal = {Development Growth and Differentiation},
number = {9},
pages = {512521},
publisher = {Wiley},
title = {{Statistical theory of branching morphogenesis}},
doi = {10.1111/dgd.12570},
volume = {60},
year = {2018},
}
@inproceedings{5788,
abstract = {In twoplayer games on graphs, the players move a token through a graph to produce an infinite path, which determines the winner or payoff of the game. Such games are central in formal verification since they model the interaction between a nonterminating system and its environment. We study bidding games in which the players bid for the right to move the token. Two bidding rules have been defined. In Richman bidding, in each round, the players simultaneously submit bids, and the higher bidder moves the token and pays the other player. Poorman bidding is similar except that the winner of the bidding pays the “bank” rather than the other player. While poorman reachability games have been studied before, we present, for the first time, results on infiniteduration poorman games. A central quantity in these games is the ratio between the two players’ initial budgets. The questions we study concern a necessary and sufficient ratio with which a player can achieve a goal. For reachability objectives, such threshold ratios are known to exist for both bidding rules. We show that the properties of poorman reachability games extend to complex qualitative objectives such as parity, similarly to the Richman case. Our most interesting results concern quantitative poorman games, namely poorman meanpayoff games, where we construct optimal strategies depending on the initial ratio, by showing a connection with randomturn based games. The connection in itself is interesting, because it does not hold for reachability poorman games. We also solve the complexity problems that arise in poorman bidding games.},
author = {Avni, Guy and Henzinger, Thomas A and IbsenJensen, Rasmus},
isbn = {9783030046118},
issn = {03029743},
location = {Oxford, UK},
pages = {2136},
publisher = {Springer},
title = {{Infiniteduration poormanbidding games}},
doi = {10.1007/9783030046125_2},
volume = {11316},
year = {2018},
}
@inproceedings{5791,
abstract = {Due to data compression or low resolution, nearby vertices and edges of a graph drawing may be bundled to a common node or arc. We model such a “compromised” drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily small ε>0 into a proper drawing (in which the vertices are distinct points, any two edges intersect in finitely many points, and no three edges have a common interior point) that minimizes the number of crossings. An εperturbation, for every ε>0, is given by a piecewise linear map (Formula Presented), where with · is the uniform norm (i.e., sup norm). We present a polynomialtime solution for this optimization problem when G is a cycle and the map φ has no spurs (i.e., no two adjacent edges are mapped to overlapping arcs). We also show that the problem becomes NPcomplete (i) when G is an arbitrary graph and φ has no spurs, and (ii) when φ may have spurs and G is a cycle or a union of disjoint paths.},
author = {Fulek, Radoslav and Tóth, Csaba D.},
isbn = {9783030044138},
location = {Barcelona, Spain},
pages = {229241},
publisher = {Springer},
title = {{Crossing minimization in perturbed drawings}},
doi = {10.1007/9783030044145_16},
volume = {11282 },
year = {2018},
}
@article{5794,
abstract = {We present an approach to interacting quantum manybody systems based on the notion of quantum groups, also known as qdeformed Lie algebras. In particular, we show that, if the symmetry of a free quantum particle corresponds to a Lie group G, in the presence of a manybody environment this particle can be described by a deformed group, Gq. Crucially, the single deformation parameter, q, contains all the information about the manyparticle interactions in the system. We exemplify our approach by considering a quantum rotor interacting with a bath of bosons, and demonstrate that extracting the value of q from closedform solutions in the perturbative regime allows one to predict the behavior of the system for arbitrary values of the impuritybath coupling strength, in good agreement with nonperturbative calculations. Furthermore, the value of the deformation parameter allows one to predict at which coupling strengths rotorbath interactions result in a formation of a stable quasiparticle. The approach based on quantum groups does not only allow for a drastic simplification of impurity problems, but also provides valuable insights into hidden symmetries of interacting manyparticle systems.},
author = {Yakaboylu, Enderalp and Shkolnikov, Mikhail and Lemeshko, Mikhail},
issn = {00319007},
journal = {Physical Review Letters},
number = {25},
publisher = {American Physical Society},
title = {{Quantum groups as hidden symmetries of quantum impurities}},
doi = {10.1103/PhysRevLett.121.255302},
volume = {121},
year = {2018},
}
@article{58,
abstract = {Inside a twodimensional region (``cake""), there are m nonoverlapping tiles of a certain kind (``toppings""). We want to expand the toppings while keeping them nonoverlapping, and possibly add some blank pieces of the same ``certain kind,"" such that the entire cake is covered. How many blanks must we add? We study this question in several cases: (1) The cake and toppings are general polygons. (2) The cake and toppings are convex figures. (3) The cake and toppings are axisparallel rectangles. (4) The cake is an axisparallel rectilinear polygon and the toppings are axisparallel rectangles. In all four cases, we provide tight bounds on the number of blanks.},
author = {Akopyan, Arseniy and Segal Halevi, Erel},
journal = {SIAM Journal on Discrete Mathematics},
number = {3},
pages = {2242  2257},
publisher = {Society for Industrial and Applied Mathematics },
title = {{Counting blanks in polygonal arrangements}},
doi = {10.1137/16M110407X},
volume = {32},
year = {2018},
}
@article{5816,
abstract = {Solidstate qubit manipulation and readout fidelities are reaching faulttolerance, but quantum error correction requires millions of physical qubits and therefore a scalable quantum computer architecture. To solve signalline bandwidth and fanout problems, microwave sources required for qubit manipulation might be embedded close to the qubit chip, typically operating at temperatures below 4 K. Here, we perform the first low temperature measurements of a 130 nm BiCMOS based SiGe voltage controlled oscillator at cryogenic temperature. We determined the frequency and output power dependence on temperature and magnetic field up to 5 T and measured the temperature influence on its noise performance. The device maintains its full functionality from 300 K to 4 K. The carrier frequency at 4 K increases by 3% with respect to the carrier frequency at 300 K, and the output power at 4 K increases by 10 dB relative to the output power at 300 K. The frequency tuning range of approximately 20% remains unchanged between 300 K and 4 K. In an inplane magnetic field of 5 T, the carrier frequency shifts by only 0.02% compared to the frequency at zero magnetic field.},
author = {Hollmann, Arne and Jirovec, Daniel and Kucharski, Maciej and Kissinger, Dietmar and Fischer, Gunter and Schreiber, Lars R.},
issn = {00346748},
journal = {Review of Scientific Instruments},
number = {11},
publisher = {AIP Publishing},
title = {{30 GHzvoltage controlled oscillator operating at 4 K}},
doi = {10.1063/1.5038258},
volume = {89},
year = {2018},
}
@article{5830,
abstract = {CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 lossoffunction mutants were sensitivity to drought stress. CLE9induced stomatal closure was impaired in abscisic acid (ABA)deficient mutants, indicating that ABA is required for CLE9medaited guard cell signalling. We further deciphered that two guard cell ABAsignalling components, OST1 and SLAC1, were responsible for CLE9induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidasedeficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABAdependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants.},
author = {Zhang, Luosha and Shi, Xiong and Zhang, Yutao and Wang, Jiajing and Yang, Jingwei and Ishida, Takashi and Jiang, Wenqian and Han, Xiangyu and Kang, Jingke and Wang, Xuening and Pan, Lixia and Lv, Shuo and Cao, Bing and Zhang, Yonghong and Wu, Jinbin and Han, Huibin and Hu, Zhubing and Cui, Langjun and Sawa, Shinichiro and He, Junmin and Wang, Guodong},
issn = {01407791},
journal = {Plant Cell and Environment},
publisher = {Wiley},
title = {{CLE9 peptideinduced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana}},
doi = {10.1111/pce.13475},
year = {2018},
}
@article{5858,
abstract = {Spatial patterns are ubiquitous on the subcellular, cellular and tissue level, and can be studied using imaging techniques such as light and fluorescence microscopy. Imaging data provide quantitative information about biological systems; however, mechanisms causing spatial patterning often remain elusive. In recent years, spatiotemporal mathematical modelling has helped to overcome this problem. Yet, outliers and structured noise limit modelling of whole imaging data, and models often consider spatial summary statistics. Here, we introduce an integrated datadriven modelling approach that can cope with measurement artefacts and whole imaging data. Our approach combines mechanistic models of the biological processes with robust statistical models of the measurement process. The parameters of the integrated model are calibrated using a maximumlikelihood approach. We used this integrated modelling approach to study in vivo gradients of the chemokine (CC motif) ligand 21 (CCL21). CCL21 gradients guide dendritic cells and are important in the adaptive immune response. Using artificial data, we verified that the integrated modelling approach provides reliable parameter estimates in the presence of measurement noise and that bias and variance of these estimates are reduced compared to conventional approaches. The application to experimental data allowed the parametrization and subsequent refinement of the model using additional mechanisms. Among other results, modelbased hypothesis testing predicted lymphatic vesseldependent concentration of heparan sulfate, the binding partner of CCL21. The selected model provided an accurate description of the experimental data and was partially validated using published data. Our findings demonstrate that integrated statistical modelling of whole imaging data is computationally feasible and can provide novel biological insights.},
author = {Hross, Sabrina and Theis, Fabian J. and Sixt, Michael K and Hasenauer, Jan},
issn = {17425689},
journal = {Journal of the Royal Society Interface},
number = {149},
publisher = {Royal Society Publishing},
title = {{Mechanistic description of spatial processes using integrative modelling of noisecorrupted imaging data}},
doi = {10.1098/rsif.2018.0600},
volume = {15},
year = {2018},
}
@article{5859,
abstract = {The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a twoword, treelike network of syntactic relations among words from the scalefree graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display nontrivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.},
author = {CorominasMurtra, Bernat and Fibla, Martí Sànchez and Valverde, Sergi and Solé, Ricard},
issn = {20545703},
journal = {Royal Society Open Science},
number = {12},
publisher = {Royal Society Publishing},
title = {{Chromatic transitions in the emergence of syntax networks}},
doi = {10.1098/rsos.181286},
volume = {5},
year = {2018},
}
@article{5860,
abstract = {A major problem for evolutionary theory is understanding the socalled openended nature of evolutionary change, from its definition to its origins. Openended evolution (OEE) refers to the unbounded increase in complexity that seems to characterize evolution on multiple scales. This property seems to be a characteristic feature of biological and technological evolution and is strongly tied to the generative potential associated with combinatorics, which allows the system to grow and expand their available state spaces. Interestingly, many complex systems presumably displaying OEE, from language to proteins, share a common statistical property: the presence of Zipf's Law. Given an inventory of basic items (such as words or protein domains) required to build more complex structures (sentences or proteins) Zipf's Law tells us that most of these elements are rare whereas a few of them are extremely common. Using algorithmic information theory, in this paper we provide a fundamental definition for openendedness, which can be understood as postulates. Its statistical counterpart, based on standard Shannon information theory, has the structure of a variational problem which is shown to lead to Zipf's Law as the expected consequence of an evolutionary process displaying OEE. We further explore the problem of information conservation through an OEE process and we conclude that statistical information (standard Shannon information) is not conserved, resulting in the paradoxical situation in which the increase of information content has the effect of erasing itself. We prove that this paradox is solved if we consider nonstatistical forms of information. This last result implies that standard information theory may not be a suitable theoretical framework to explore the persistence and increase of the information content in OEE systems.},
author = {CorominasMurtra, Bernat and Seoane, Luís F. and Solé, Ricard},
issn = {17425689},
journal = {Journal of the Royal Society Interface},
number = {149},
publisher = {Royal Society Publishing},
title = {{Zipf's Law, unbounded complexity and openended evolution}},
doi = {10.1098/rsif.2018.0395},
volume = {15},
year = {2018},
}
@article{5861,
abstract = {In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal.},
author = {Alanko, Jonna H and Sixt, Michael K},
issn = {2050084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{The cell sets the tone}},
doi = {10.7554/eLife.37888},
volume = {7},
year = {2018},
}
@article{5888,
abstract = {Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental
disorders (e.g., autism spectrum disorder, intellectual disability) remains a great challenge. Recent advancements in
genomics, such as wholeexome or wholegenome sequencing, have enabled scientists to identify numerous
mutations underlying neurodevelopmental disorders. Given the few hundred risk genes that have been discovered,
the etiological variability and the heterogeneous clinical presentation, the need for genotype — along with phenotype
based diagnosis of individual patients has become a requisite. In this review we look at recent advancements in
genomic analysis and their translation into clinical practice.},
author = {Tarlungeanu, DoraClara and Novarino, Gaia},
issn = {20926413},
journal = {Experimental & Molecular Medicine},
number = {8},
publisher = {Springer Nature},
title = {{Genomics in neurodevelopmental disorders: an avenue to personalized medicine}},
doi = {10.1038/s1227601801297},
volume = {50},
year = {2018},
}
@inproceedings{5959,
abstract = {Formalizing properties of systems with continuous dynamics is a challenging task. In this paper, we propose a formal framework for specifying and monitoring rich temporal properties of realvalued signals. We introduce signal firstorder logic (SFO) as a specification language that combines firstorder logic with linearreal arithmetic and unary function symbols interpreted as piecewiselinear signals. We first show that while the satisfiability problem for SFO is undecidable, its membership and monitoring problems are decidable. We develop an offline monitoring procedure for SFO that has polynomial complexity in the size of the input trace and the specification, for a fixed number of quantifiers and function symbols. We show that the algorithm has computation time linear in the size of the input trace for the important fragment of boundedresponse specifications interpreted over input traces with finite variability. We can use our results to extend signal temporal logic with firstorder quantifiers over time and value parameters, while preserving its efficient monitoring. We finally demonstrate the practical appeal of our logic through a case study in the microelectronics domain.},
author = {Bakhirkin, Alexey and Ferrere, Thomas and Henzinger, Thomas A and Nickovicl, Deian},
booktitle = {2018 International Conference on Embedded Software},
isbn = {9781538655603},
location = {Turin, Italy},
pages = {110},
publisher = {IEEE},
title = {{Keynote: The firstorder logic of signals}},
doi = {10.1109/emsoft.2018.8537203},
year = {2018},
}
@article{5960,
abstract = {In this paper we present a reliable method to verify the existence of loops along the uncertain trajectory of a robot, based on proprioceptive measurements only, within a boundederror context. The loop closure detection is one of the key points in simultaneous localization and mapping (SLAM) methods, especially in homogeneous environments with difficult scenes recognitions. The proposed approach is generic and could be coupled with conventional SLAM algorithms to reliably reduce their computing burden, thus improving the localization and mapping processes in the most challenging environments such as unexplored underwater extents. To prove that a robot performed a loop whatever the uncertainties in its evolution, we employ the notion of topological degree that originates in the field of differential topology. We show that a verification tool based on the topological degree is an optimal method for proving robot loops. This is demonstrated both on datasets from real missions involving autonomous underwater vehicles and by a mathematical discussion.},
author = {Rohou, Simon and Franek, Peter and Aubry, Clément and Jaulin, Luc},
issn = {02783649},
journal = {The International Journal of Robotics Research},
number = {12},
pages = {15001516},
publisher = {SAGE Publications},
title = {{Proving the existence of loops in robot trajectories}},
doi = {10.1177/0278364918808367},
volume = {37},
year = {2018},
}
@inproceedings{5962,
abstract = {Stochastic Gradient Descent (SGD) is a fundamental algorithm in machine learning, representing the optimization backbone for training several classic models, from regression to neural networks. Given the recent practical focus on distributed machine learning, significant work has been dedicated to the convergence properties of this algorithm under the inconsistent and noisy updates arising from execution in a distributed environment. However, surprisingly, the convergence properties of this classic algorithm in the standard sharedmemory model are still not wellunderstood. In this work, we address this gap, and provide new convergence bounds for lockfree concurrent stochastic gradient descent, executing in the classic asynchronous shared memory model, against a strong adaptive adversary. Our results give improved upper and lower bounds on the "price of asynchrony'' when executing the fundamental SGD algorithm in a concurrent setting. They show that this classic optimization tool can converge faster and with a wider range of parameters than previously known under asynchronous iterations. At the same time, we exhibit a fundamental tradeoff between the maximum delay in the system and the rate at which SGD can converge, which governs the set of parameters under which this algorithm can still work efficiently.},
author = {Alistarh, DanAdrian and De Sa, Christopher and Konstantinov, Nikola H},
booktitle = {Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  PODC '18},
isbn = {9781450357951},
location = {Egham, United Kingdom},
pages = {169178},
publisher = {ACM Press},
title = {{The convergence of stochastic gradient descent in asynchronous shared memory}},
doi = {10.1145/3212734.3212763},
year = {2018},
}
@inproceedings{5963,
abstract = {There has been significant progress in understanding the parallelism inherent to iterative sequential algorithms: for many classic algorithms, the depth of the dependence structure is now well understood, and scheduling techniques have been developed to exploit this shallow dependence structure for efficient parallel implementations. A related, applied research strand has studied methods by which certain iterative taskbased algorithms can be efficiently parallelized via relaxed concurrent priority schedulers. These allow for high concurrency when inserting and removing tasks, at the cost of executing superfluous work due to the relaxed semantics of the scheduler. In this work, we take a step towards unifying these two research directions, by showing that there exists a family of relaxed priority schedulers that can efficiently and deterministically execute classic iterative algorithms such as greedy maximal independent set (MIS) and matching. Our primary result shows that, given a randomized scheduler with an expected relaxation factor of k in terms of the maximum allowed priority inversions on a task, and any graph on n vertices, the scheduler is able to execute greedy MIS with only an additive factor of \poly(k) expected additional iterations compared to an exact (but not scalable) scheduler. This counterintuitive result demonstrates that the overhead of relaxation when computing MIS is not dependent on the input size or structure of the input graph. Experimental results show that this overhead can be clearly offset by the gain in performance due to the highly scalable scheduler. In sum, we present an efficient method to deterministically parallelize iterative sequential algorithms, with provable runtime guarantees in terms of the number of executed tasks to completion.},
author = {Alistarh, DanAdrian and Brown, Trevor A and Kopinsky, Justin and Nadiradze, Giorgi},
booktitle = {Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  PODC '18},
isbn = {9781450357951},
location = {Egham, United Kingdom},
pages = {377386},
publisher = {ACM Press},
title = {{Relaxed schedulers can efficiently parallelize iterative algorithms}},
doi = {10.1145/3212734.3212756},
year = {2018},
}
@inproceedings{5964,
abstract = {A standard design pattern found in many concurrent data structures, such as hash tables or ordered containers, is an alternation of parallelizable sections that incur no data conflicts and critical sections that must run sequentially and are protected with locks. A lock can be viewed as a queue that arbitrates the order in which the critical sections are executed, and a natural question is whether we can use stochastic analysis to predict the resulting throughput. As a preliminary evidence to the affirmative, we describe a simple model that can be used to predict the throughput of coarsegrained lockbased algorithms. We show that our model works well for CLH lock, and we expect it to work for other popular lock designs such as TTAS, MCS, etc.},
author = {Aksenov, Vitaly and Alistarh, DanAdrian and Kuznetsov, Petr},
booktitle = {Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  PODC '18},
isbn = {9781450357951},
location = {Egham, United Kingdom},
pages = {411413},
publisher = {ACM Press},
title = {{Brief Announcement: Performance prediction for coarsegrained locking}},
doi = {10.1145/3212734.3212785},
year = {2018},
}
@inproceedings{5965,
abstract = {Relaxed concurrent data structures have become increasingly popular, due to their scalability in graph processing and machine learning applications (\citeNguyen13, gonzalez2012powergraph ). Despite considerable interest, there exist families of natural, high performing randomized relaxed concurrent data structures, such as the popular MultiQueue~\citeMQ pattern for implementing relaxed priority queue data structures, for which no guarantees are known in the concurrent setting~\citeAKLN17. Our main contribution is in showing for the first time that, under a set of analytic assumptions, a family of relaxed concurrent data structures, including variants of MultiQueues, but also a new approximate counting algorithm we call the MultiCounter, provides strong probabilistic guarantees on the degree of relaxation with respect to the sequential specification, in arbitrary concurrent executions. We formalize these guarantees via a new correctness condition called distributional linearizability, tailored to concurrent implementations with randomized relaxations. Our result is based on a new analysis of an asynchronous variant of the classic poweroftwochoices load balancing algorithm, in which placement choices can be based on inconsistent, outdated information (this result may be of independent interest). We validate our results empirically, showing that the MultiCounter algorithm can implement scalable relaxed timestamps.},
author = {Alistarh, DanAdrian and Brown, Trevor A and Kopinsky, Justin and Li, Jerry Z. and Nadiradze, Giorgi},
booktitle = {Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  SPAA '18},
isbn = {9781450357999},
location = {Vienna, Austria},
pages = {133142},
publisher = {ACM Press},
title = {{Distributionally linearizable data structures}},
doi = {10.1145/3210377.3210411},
year = {2018},
}
@inproceedings{5966,
abstract = {The transactional conflict problem arises in transactional systems whenever two or more concurrent transactions clash on a data item. While the standard solution to such conflicts is to immediately abort one of the transactions, some practical systems consider the alternative of delaying conflict resolution for a short interval, which may allow one of the transactions to commit. The challenge in the transactional conflict problem is to choose the optimal length of this delay interval so as to minimize the overall running time penalty for the conflicting transactions. In this paper, we propose a family of optimal online algorithms for the transactional conflict problem. Specifically, we consider variants of this problem which arise in different implementations of transactional systems, namely "requestor wins'' and "requestor aborts'' implementations: in the former, the recipient of a coherence request is aborted, whereas in the latter, it is the requestor which has to abort. Both strategies are implemented by real systems. We show that the requestor aborts case can be reduced to a classic instance of the ski rental problem, while the requestor wins case leads to a new version of this classical problem, for which we derive optimal deterministic and randomized algorithms. Moreover, we prove that, under a simplified adversarial model, our algorithms are constantcompetitive with the offline optimum in terms of throughput. We validate our algorithmic results empirically through a hardware simulation of hardware transactional memory (HTM), showing that our algorithms can lead to nontrivial performance improvements for classic concurrent data structures.},
author = {Alistarh, DanAdrian and Haider, Syed Kamran and Kübler, Raphael and Nadiradze, Giorgi},
booktitle = {Proceedings of the 30th on Symposium on Parallelism in Algorithms and Architectures  SPAA '18},
isbn = {9781450357999},
location = {Vienna, Austria},
pages = {383392},
publisher = {ACM Press},
title = {{The transactional conflict problem}},
doi = {10.1145/3210377.3210406},
year = {2018},
}
@inproceedings{5967,
abstract = {The Big Match is a multistage twoplayer game. In each stage Player 1 hides one or two pebbles in his hand, and his opponent has to guess that number; Player 1 loses a point if Player 2 is correct, and otherwise he wins a point. As soon as Player 1 hides one pebble, the players cannot change their choices in any future stage.
Blackwell and Ferguson (1968) give an εoptimal strategy for Player 1 that hides, in each stage, one pebble with a probability that depends on the entire past history. Any strategy that depends just on the clock or on a finite memory is worthless. The longstanding natural open problem has been whether every strategy that depends just on the clock and a finite memory is worthless. We prove that there is such a strategy that is εoptimal. In fact, we show that just two states of memory are sufficient.
},
author = {Hansen, Kristoffer Arnsfelt and IbsenJensen, Rasmus and Neyman, Abraham},
booktitle = {Proceedings of the 2018 ACM Conference on Economics and Computation  EC '18},
isbn = {9781450358293},
location = {Ithaca, NY, United States},
pages = {149150},
publisher = {ACM Press},
title = {{The Big Match with a clock and a bit of memory}},
doi = {10.1145/3219166.3219198},
year = {2018},
}
@article{5971,
abstract = {We consider a Wignertype ensemble, i.e. large hermitian N×N random matrices H=H∗ with centered independent entries and with a general matrix of variances Sxy=𝔼∣∣Hxy∣∣2. The norm of H is asymptotically given by the maximum of the support of the selfconsistent density of states. We establish a bound on this maximum in terms of norms of powers of S that substantially improves the earlier bound 2∥S∥1/2∞ given in [O. Ajanki, L. Erdős and T. Krüger, Universality for general Wignertype matrices, Prob. Theor. Rel. Fields169 (2017) 667–727]. The key element of the proof is an effective Markov chain approximation for the contributions of the weighted Dyck paths appearing in the iterative solution of the corresponding Dyson equation.},
author = {Erdös, László and Mühlbacher, Peter},
issn = {20103263},
journal = {Random matrices: Theory and applications},
publisher = {World Scientific Publishing},
title = {{Bounds on the norm of Wignertype random matrices}},
doi = {10.1142/s2010326319500096},
year = {2018},
}
@article{5975,
abstract = {We consider the recent formulation of the algorithmic Lov ́asz Local Lemma [N. Harvey and J. Vondr ́ak, inProceedings of FOCS, 2015, pp. 1327–1345; D. Achlioptas and F. Iliopoulos,inProceedings of SODA, 2016, pp. 2024–2038; D. Achlioptas, F. Iliopoulos, and V. Kolmogorov,ALocal Lemma for Focused Stochastic Algorithms, arXiv preprint, 2018] for finding objects that avoid“bad features,” or “flaws.” It extends the Moser–Tardos resampling algorithm [R. A. Moser andG. Tardos,J. ACM, 57 (2010), 11] to more general discrete spaces. At each step the method picks aflaw present in the current state and goes to a new state according to some prespecified probabilitydistribution (which depends on the current state and the selected flaw). However, the recent formulation is less flexible than the Moser–Tardos method since it requires a specific flaw selection rule,whereas the algorithm of Moser and Tardos allows an arbitrary rule (and thus can potentially beimplemented more efficiently). We formulate a new “commutativity” condition and prove that it issufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additionalassumption. We then show that existing resampling oracles for perfect matchings and permutationsdo satisfy this condition.},
author = {Kolmogorov, Vladimir},
issn = {00975397},
journal = {SIAM Journal on Computing},
number = {6},
pages = {20292056},
publisher = {Society for Industrial & Applied Mathematics (SIAM)},
title = {{Commutativity in the algorithmic Lovász local lemma}},
doi = {10.1137/16m1093306},
volume = {47},
year = {2018},
}
@article{5976,
abstract = {We propose FlexMaps, a novel framework for fabricating smooth shapes out of flat, flexible panels with tailored mechanical properties. We start by mapping the 3D surface onto a 2D domain as in traditional UV mapping to design a set of deformable flat panels called FlexMaps. For these panels, we design and obtain specific mechanical properties such that, once they are assembled, the static equilibrium configuration matches the desired 3D shape. FlexMaps can be fabricated from an almost rigid material, such as wood or plastic, and are made flexible in a controlled way by using computationally designed spiraling microstructures.},
author = {Malomo, Luigi and Perez Rodriguez, Jesus and Iarussi, Emmanuel and Pietroni, Nico and Miguel, Eder and Cignoni, Paolo and Bickel, Bernd},
issn = {07300301},
journal = {ACM Transactions on Graphics},
number = {6},
publisher = {Association for Computing Machinery (ACM)},
title = {{FlexMaps: Computational design of flat flexible shells for shaping 3D objects}},
doi = {10.1145/3272127.3275076},
volume = {37},
year = {2018},
}
@inproceedings{5978,
abstract = {We consider the MAPinference problem for graphical models,which is a valued constraint satisfaction problem defined onreal numbers with a natural summation operation. We proposea family of relaxations (different from the famous SheraliAdams hierarchy), which naturally define lower bounds for itsoptimum. This family always contains a tight relaxation andwe give an algorithm able to find it and therefore, solve theinitial nonrelaxed NPhard problem.The relaxations we consider decompose the original probleminto two nonoverlapping parts: an easy LPtight part and adifficult one. For the latter part a combinatorial solver must beused. As we show in our experiments, in a number of applications the second, difficult part constitutes only a small fractionof the whole problem. This property allows to significantlyreduce the computational time of the combinatorial solver andtherefore solve problems which were out of reach before.},
author = {Haller, Stefan and Swoboda, Paul and Savchynskyy, Bogdan},
booktitle = {Proceedings of the 32st AAAI Conference on Artificial Intelligence},
location = {New Orleans, LU, United States},
pages = {65816588},
publisher = {AAAI Press},
title = {{Exact MAPinference by confining combinatorial search with LP relaxation}},
year = {2018},
}
@article{5982,
abstract = {In the present work, we detail a fast and simple solutionbased method to synthesize hexagonal SnSe2 nanoplates (NPLs) and their use to produce crystallographically textured SnSe2 nanomaterials. We also demonstrate that the same strategy can be used to produce orthorhombic SnSe nanostructures and nanomaterials. NPLs are grown through a screw dislocationdriven mechanism. This mechanism typically results in pyramidal structures, but we demonstrate here that the growth from multiple dislocations results in flowerlike structures. Crystallographically textured SnSe2 bulk nanomaterials obtained from the hot pressing of these SnSe2 structures display highly anisotropic charge and heat transport properties and thermoelectric (TE) figures of merit limited by relatively low electrical conductivities. To improve this parameter, SnSe2 NPLs are blended here with metal nanoparticles. The electrical conductivities of the blends are significantly improved with respect to bare SnSe2 NPLs, what translates into a threefold increase of the TE Figure of merit, reaching unprecedented ZT values up to 0.65.},
author = {Zhang, Yu and Liu, Yu and Lim, Khak Ho and Xing, Congcong and Li, Mengyao and Zhang, Ting and Tang, Pengyi and Arbiol, Jordi and Llorca, Jordi and Ng, Ka Ming and Ibáñez, Maria and Guardia, Pablo and Prato, Mirko and Cadavid, Doris and Cabot, Andreu},
issn = {14337851},
journal = {Angewandte Chemie International Edition},
number = {52},
pages = {1706317068},
publisher = {Wiley},
title = {{Tin diselenide molecular precursor for solutionprocessable thermoelectric materials}},
doi = {10.1002/anie.201809847},
volume = {57},
year = {2018},
}
@article{5983,
abstract = {We study a quantum impurity possessing both translational and internal rotational degrees of freedom interacting with a bosonic bath. Such a system corresponds to a “rotating polaron,” which can be used to model, e.g., a rotating molecule immersed in an ultracold Bose gas or superfluid helium. We derive the Hamiltonian of the rotating polaron and study its spectrum in the weak and strongcoupling regimes using a combination of variational, diagrammatic, and meanfield approaches. We reveal how the coupling between linear and angular momenta affects stable quasiparticle states, and demonstrate that internal rotation leads to an enhanced selflocalization in the translational degrees of freedom.},
author = {Yakaboylu, Enderalp and Midya, Bikashkali and Deuchert, Andreas and Leopold, Nikolai K and Lemeshko, Mikhail},
issn = {24699950},
journal = {Physical Review B},
number = {22},
publisher = {American Physical Society},
title = {{Theory of the rotating polaron: Spectrum and selflocalization}},
doi = {10.1103/physrevb.98.224506},
volume = {98},
year = {2018},
}
@article{5984,
abstract = {Gproteincoupled receptors (GPCRs) form the largest receptor family, relay environmental stimuli to changes in cell behavior and represent prime drug targets. Many GPCRs are classified as orphan receptors because of the limited knowledge on their ligands and coupling to cellular signaling machineries. Here, we engineer a library of 63 chimeric receptors that contain the signaling domains of human orphan and understudied GPCRs functionally linked to the lightsensing domain of rhodopsin. Upon stimulation with visible light, we identify activation of canonical cell signaling pathways, including cAMP, Ca2+, MAPK/ERK, and Rhodependent pathways, downstream of the engineered receptors. For the human pseudogene GPR33, we resurrect a signaling function that supports its hypothesized role as a pathogen entry site. These results demonstrate that substituting unknown chemical activators with a light switch can reveal information about protein function and provide an optically controlled protein library for exploring the physiology and therapeutic potential of understudied GPCRs.},
author = {Morri, Maurizio and SanchezRomero, Inmaculada and Tichy, AlexandraMadelaine and Kainrath, Stephanie and Gerrard, Elliot J. and Hirschfeld, Priscila and Schwarz, Jan and Janovjak, Harald L},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Springer Nature},
title = {{Optical functionalization of human class A orphan Gproteincoupled receptors}},
doi = {10.1038/s41467018043421},
volume = {9},
year = {2018},
}
@article{5989,
abstract = {Schistosomes are the causative agents of schistosomiasis, a neglected tropical disease affecting over 230 million people worldwide.Additionally to their major impact on human health, they are also models of choice in evolutionary biology. These parasitic flatwormsare unique among the common hermaphroditic trematodes as they have separate sexes. This socalled “evolutionary scandal”displays a female heterogametic genetic sexdetermination system (ZZ males and ZW females), as well as a pronounced adult sexualdimorphism. These phenotypic differences are determined by a shared set of genes in both sexes, potentially leading to intralocussexual conflicts. To resolve these conflicts in sexually selected traits, molecular mechanisms such as sexbiased gene expression couldoccur, but parentoforigin gene expression also provides an alternative. In this work we investigated the latter mechanism, that is,genes expressed preferentially from either the maternal or the paternal allele, inSchistosoma mansonispecies. To this end, transcriptomes from male and female hybrid adults obtained by strain crosses were sequenced. Strainspecific single nucleotide polymorphism (SNP) markers allowed us to discriminate the parental origin, while reciprocal crosses helped to differentiate parentalexpression from strainspecific expression. We identified genes containing SNPs expressed in a parentoforigin manner consistentwith paternal and maternal imprints. Although the majority of the SNPs was identified in mitochondrial and Zspecific loci, theremaining SNPs found in male and female transcriptomes were situated in genes that have the potential to explain sexual differencesin schistosome parasites. Furthermore, we identified and validated four new Zspecific scaffolds.},
author = {KincaidSmith, Julien and Picard, Marion A L and Cosseau, Céline and Boissier, Jérôme and Severac, Dany and Grunau, Christoph and Toulza, Eve},
issn = {17596653},
journal = {Genome Biology and Evolution},
number = {3},
pages = {840856},
publisher = {Oxford University Press},
title = {{ParentofOriginDependent Gene Expression in Male and Female Schistosome Parasites}},
doi = {10.1093/gbe/evy037},
volume = {10},
year = {2018},
}
@article{5990,
abstract = {A Ge–Si core–shell nanowire is used to realize a Josephson field‐effect transistor with highly transparent contacts to superconducting leads. By changing the electric field, access to two distinct regimes, not combined before in a single device, is gained: in the accumulation mode the device is highly transparent and the supercurrent is carried by multiple subbands, while near depletion, the supercurrent is carried by single‐particle levels of a strongly coupled quantum dot operating in the few‐hole regime. These results establish Ge–Si nanowires as an important platform for hybrid superconductor–semiconductor physics and Majorana fermions.},
author = {Ridderbos, Joost and Brauns, Matthias and Shen, Jie and de Vries, Folkert K. and Li, Ang and Bakkers, Erik P. A. M. and Brinkman, Alexander and Zwanenburg, Floris A.},
issn = {09359648},
journal = {Advanced Materials},
number = {44},
publisher = {Wiley},
title = {{Josephson effect in a fewhole quantum dot}},
doi = {10.1002/adma.201802257},
volume = {30},
year = {2018},
}
@article{5992,
abstract = {Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the Factin density in lamellipodia of B16F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the Factin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive Factin network retrograde flow.},
author = {Dolati, Setareh and Kage, Frieda and Mueller, Jan and Müsken, Mathias and Kirchner, Marieluise and Dittmar, Gunnar and Sixt, Michael K and Rottner, Klemens and Falcke, Martin},
issn = {10591524},
journal = {Molecular Biology of the Cell},
number = {22},
pages = {26742686},
publisher = {American Society for Cell Biology },
title = {{On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility}},
doi = {10.1091/mbc.e18020082},
volume = {29},
year = {2018},
}
@article{5993,
abstract = {In this article, we consider the termination problem of probabilistic programs with realvalued variables. Thequestions concerned are: qualitative ones that ask (i) whether the program terminates with probability 1(almostsure termination) and (ii) whether the expected termination time is finite (finite termination); andquantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) tocompute a boundBsuch that the probability not to terminate afterBsteps decreases exponentially (concentration problem). To solve these questions, we utilize the notion of ranking supermartingales, which isa powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmicsynthesis of linear rankingsupermartingales over affine probabilistic programs (Apps) with both angelic anddemonic nondeterminism. An important subclass of Apps is LRApp which is defined as the class of all Appsover which a linear rankingsupermartingale exists.Our main contributions are as follows. Firstly, we show that the membership problem of LRApp (i) canbe decided in polynomial time for Apps with at most demonic nondeterminism, and (ii) isNPhard and inPSPACEfor Apps with angelic nondeterminism. Moreover, theNPhardness result holds already for Appswithout probability and demonic nondeterminism. Secondly, we show that the concentration problem overLRApp can be solved in the same complexity as for the membership problem of LRApp. Finally, we show thatthe expectation problem over LRApp can be solved in2EXPTIMEand isPSPACEhard even for Apps withoutprobability and nondeterminism (i.e., deterministic programs). Our experimental results demonstrate theeffectiveness of our approach to answer the qualitative and quantitative questions over Apps with at mostdemonic nondeterminism.},
author = {Chatterjee, Krishnendu and Fu, Hongfei and Novotný, Petr and Hasheminezhad, Rouzbeh},
issn = {01640925},
journal = {ACM Transactions on Programming Languages and Systems},
number = {2},
publisher = {Association for Computing Machinery (ACM)},
title = {{Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs}},
doi = {10.1145/3174800},
volume = {40},
year = {2018},
}
@article{5995,
abstract = {Motivation
Computational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.
Results
Here we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a selfconsistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and IMutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here.},
author = {Usmanova, Dinara R and Bogatyreva, Natalya S and Ariño Bernad, Joan and Eremina, Aleksandra A and Gorshkova, Anastasiya A and Kanevskiy, German M and Lonishin, Lyubov R and Meister, Alexander V and Yakupova, Alisa G and Kondrashov, Fyodor and Ivankov, Dmitry},
issn = {13674803},
journal = {Bioinformatics},
number = {21},
pages = {36533658},
publisher = {Oxford University Press },
title = {{Selfconsistency test reveals systematic bias in programs for prediction change of stability upon mutation}},
doi = {10.1093/bioinformatics/bty340},
volume = {34},
year = {2018},
}
@article{5996,
abstract = {In pipes, turbulence sets in despite the linear stability of the laminar Hagen–Poiseuille flow. The Reynolds number ( ) for which turbulence first appears in a given experiment – the ‘natural transition point’ – depends on imperfections of the setup, or, more precisely, on the magnitude of finite amplitude perturbations. At onset, turbulence typically only occupies a certain fraction of the flow, and this fraction equally is found to differ from experiment to experiment. Despite these findings, Reynolds proposed that after sufficiently long times, flows may settle to steady conditions: below a critical velocity, flows should (regardless of initial conditions) always return to laminar, while above this velocity, eddying motion should persist. As will be shown, even in pipes several thousand diameters long, the spatiotemporal intermittent flow patterns observed at the end of the pipe strongly depend on the initial conditions, and there is no indication that different flow patterns would eventually settle to a (statistical) steady state. Exploiting the fact that turbulent puffs do not age (i.e. they are memoryless), we continuously recreate the puff sequence exiting the pipe at the pipe entrance, and in doing so introduce periodic boundary conditions for the puff pattern. This procedure allows us to study the evolution of the flow patterns for arbitrary long times, and we find that after times in excess of advective time units, indeed a statistical steady state is reached. Although the resulting flows remain spatiotemporally intermittent, puff splitting and decay rates eventually reach a balance, so that the turbulent fraction fluctuates around a welldefined level which only depends on . In accordance with Reynolds’ proposition, we find that at lower (here 2020), flows eventually always resume to laminar, while for higher ( ), turbulence persists. The critical point for pipe flow hence falls in the interval of $2020 , which is in very good agreement with the recently proposed value of . The latter estimate was based on singlepuff statistics and entirely neglected puff interactions. Unlike in typical contact processes where such interactions strongly affect the percolation threshold, in pipe flow, the critical point is only marginally influenced. Interactions, on the other hand, are responsible for the approach to the statistical steady state. As shown, they strongly affect the resulting flow patterns, where they cause ‘puff clustering’, and these regions of large puff densities are observed to travel across the puff pattern in a wavelike fashion.},
author = {Vasudevan, Mukund and Hof, Björn},
issn = {00221120},
journal = {Journal of Fluid Mechanics},
pages = {7694},
publisher = {Cambridge University Press},
title = {{The critical point of the transition to turbulence in pipe flow}},
doi = {10.1017/jfm.2017.923},
volume = {839},
year = {2018},
}
@article{5998,
abstract = {Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genomewide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cellcycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescenceassociated (SA) βgalactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycledependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHMEVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidylimiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM.},
author = {Velicky, Philipp and Meinhardt, Gudrun and Plessl, Kerstin and Vondra, Sigrid and Weiss, Tamara and Haslinger, Peter and Lendl, Thomas and Aumayr, Karin and Mairhofer, Mario and Zhu, Xiaowei and Schütz, Birgit and Hannibal, Roberta L. and Lindau, Robert and Weil, Beatrix and Ernerudh, Jan and Neesen, Jürgen and Egger, Gerda and Mikula, Mario and Röhrl, Clemens and Urban, Alexander E. and Baker, Julie and Knöfler, Martin and Pollheimer, Jürgen},
issn = {15537404},
journal = {PLOS Genetics},
number = {10},
publisher = {Public Library of Science},
title = {{Genome amplification and cellular senescence are hallmarks of human placenta development}},
doi = {10.1371/journal.pgen.1007698},
volume = {14},
year = {2018},
}
@article{5999,
abstract = {We introduce for each quiver Q and each algebraic oriented cohomology theory A, the cohomological Hall algebra (CoHA) of Q, as the Ahomology of the moduli of representations of the preprojective algebra of Q. This generalizes the Ktheoretic Hall algebra of commuting varieties defined by SchiffmannVasserot. When A is the Morava Ktheory, we show evidence that this algebra is a candidate for Lusztig's reformulated conjecture on modular representations of algebraic groups.
We construct an action of the preprojective CoHA on the Ahomology of Nakajima quiver varieties. We compare this with the action of the Borel subalgebra of Yangian when A is the intersection theory. We also give a shuffle algebra description of this CoHA in terms of the underlying formal group law of A. As applications, we obtain a shuffle description of the Yangian. },
author = {Yang, Yaping and Zhao, Gufang},
issn = {00246115},
journal = {Proceedings of the London Mathematical Society},
number = {5},
pages = {10291074},
publisher = {Oxford University Press},
title = {{The cohomological Hall algebra of a preprojective algebra}},
doi = {10.1112/plms.12111},
volume = {116},
year = {2018},
}
@article{6002,
abstract = {The Bogoliubov free energy functional is analysed. The functional serves as a model of a translationinvariant Bose gas at positive temperature. We prove the existence of minimizers in the case of repulsive interactions given by a sufficiently regular twobody potential. Furthermore, we prove the existence of a phase transition in this model and provide its phase diagram.},
author = {Napiórkowski, Marcin M and Reuvers, Robin and Solovej, Jan Philip},
issn = {00039527},
journal = {Archive for Rational Mechanics and Analysis},
number = {3},
pages = {10371090},
publisher = {Springer Nature},
title = {{The Bogoliubov free energy functional I: Existence of minimizers and phase diagram}},
doi = {10.1007/s0020501812326},
volume = {229},
year = {2018},
}
@article{6003,
abstract = {Digital fabrication devices are powerful tools for creating tangible reproductions of 3D digital models. Most available printing technologies aim at producing an accurate copy of a tridimensional shape. However, fabrication technologies can also be used to create a stylistic representation of a digital shape. We refer to this class of methods as ‘stylized fabrication methods’. These methods abstract geometric and physical features of a given shape to create an unconventional representation, to produce an optical illusion or to devise a particular interaction with the fabricated model. In this state‐of‐the‐art report, we classify and overview this broad and emerging class of approaches and also propose possible directions for future research.},
author = {Bickel, Bernd and Cignoni, Paolo and Malomo, Luigi and Pietroni, Nico},
issn = {01677055},
journal = {Computer Graphics Forum},
number = {6},
pages = {325342},
publisher = {Wiley},
title = {{State of the art on stylized fabrication}},
doi = {10.1111/cgf.13327},
volume = {37},
year = {2018},
}
@inproceedings{6005,
abstract = {Network games are widely used as a model for selfish resourceallocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting.},
author = {Avni, Guy and Guha, Shibashis and Kupferman, Orna},
issn = {18688969},
location = {Liverpool, United Kingdom},
publisher = {Schloss Dagstuhl  LeibnizZentrum für Informatik},
title = {{Timed network games with clocks}},
doi = {10.4230/LIPICS.MFCS.2018.23},
volume = {117},
year = {2018},
}
@article{6006,
abstract = {Network games (NGs) are played on directed graphs and are extensively used in network design and analysis. Search problems for NGs include finding special strategy profiles such as a Nash equilibrium and a globallyoptimal solution. The networks modeled by NGs may be huge. In formal verification, abstraction has proven to be an extremely effective technique for reasoning about systems with big and even infinite state spaces. We describe an abstractionrefinement methodology for reasoning about NGs. Our methodology is based on an abstraction function that maps the state space of an NG to a much smaller state space. We search for a global optimum and a Nash equilibrium by reasoning on an under and an overapproximation defined on top of this smaller state space. When the approximations are too coarse to find such profiles, we refine the abstraction function. We extend the abstractionrefinement methodology to labeled networks, where the objectives of the players are regular languages. Our experimental results demonstrate the effectiveness of the methodology. },
author = {Avni, Guy and Guha, Shibashis and Kupferman, Orna},
issn = {20734336},
journal = {Games},
number = {3},
publisher = {MDPI AG},
title = {{An abstractionrefinement methodology for reasoning about network games}},
doi = {10.3390/g9030039},
volume = {9},
year = {2018},
}
@article{6010,
abstract = {The optic tectum (TeO), or superior colliculus, is a multisensory midbrain center that organizes spatially orienting responses to relevant stimuli. To define the stimulus with the highest priority at each moment, a network of reciprocal connections between the TeO and the isthmi promotes competition between concurrent tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression of tectal inputs are located in separate isthmic nuclei, facilitating the analysis of the neural processes that mediate competition. A specific subset of radial neurons in the intermediate tectal layers relay retinal inputs to the isthmi, but at present it is unclear whether separate neurons innervate individual nuclei or a single neural type sends a common input to several of them. In this study, we used in vitro neural tracing and cellfilling experiments in chickens to show that single neurons innervate, via axon collaterals, the three nuclei that comprise the isthmotectal network. This demonstrates that the input signals representing the strength of the incoming stimuli are simultaneously relayed to the mechanisms promoting both enhancement and suppression of the input signals. By performing in vivo recordings in anesthetized chicks, we also show that this common input generates synchrony between both antagonistic mechanisms, demonstrating that activity enhancement and suppression are closely coordinated. From a computational point of view, these results suggest that these tectal neurons constitute integrative nodes that combine inputs from different sources to drive in parallel several concurrent neural processes, each performing complementary functions within the network through different firing patterns and connectivity.},
author = {GarridoCharad, Florencia and Vega Zuniga, Tomas A and GutiérrezIbáñez, Cristián and Fernandez, Pedro and LópezJury, Luciana and GonzálezCabrera, Cristian and Karten, Harvey J. and Luksch, Harald and Marín, Gonzalo J.},
issn = {00278424},
journal = {Proceedings of the National Academy of Sciences},
number = {32},
pages = {E7615E7623},
publisher = {National Academy of Sciences},
title = {{“Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network}},
doi = {10.1073/pnas.1804517115},
volume = {115},
year = {2018},
}
@inproceedings{6011,
abstract = {We establish a datadependent notion of algorithmic stability for Stochastic Gradient Descent (SGD), and employ it to develop novel generalization bounds. This is in contrast to previous distributionfree algorithmic stability results for SGD which depend on the worstcase constants. By virtue of the datadependent argument, our bounds provide new insights into learning with SGD on convex and nonconvex problems. In the convex case, we show that the bound on the generalization error depends on the risk at the initialization point. In the nonconvex case, we prove that the expected curvature of the objective function around the initialization point has crucial influence on the generalization error. In both cases, our results suggest a simple datadriven strategy to stabilize SGD by prescreening its initialization. As a corollary, our results allow us to show optimistic generalization bounds that exhibit fast convergence rates for SGD subject to a vanishing empirical risk and low noise of stochastic gradient. },
author = {Kuzborskij, Ilja and Lampert, Christoph},
booktitle = {Proceedings of the 35 th International Conference on Machine Learning},
location = {Stockholm, Sweden},
pages = {28152824},
publisher = {International Machine Learning Society},
title = {{Datadependent stability of stochastic gradient descent}},
volume = {80},
year = {2018},
}
@inproceedings{6012,
abstract = {We present an approach to identify concise equations from data using a shallow neural network approach. In contrast to ordinary blackbox regression, this approach allows understanding functional relations and generalizing them from observed data to unseen parts of the parameter space. We show how to extend the class of learnable equations for a recently proposed equation learning network to include divisions, and we improve the learning and model selection strategy to be useful for challenging realworld data. For systems governed by analytical expressions, our method can in many cases identify the true underlying equation and extrapolate to unseen domains. We demonstrate its effectiveness by experiments on a cartpendulum system, where only 2 random rollouts are required to learn the forward dynamics and successfully achieve the swingup task.},
author = {Sahoo, Subham and Lampert, Christoph and Martius, Georg S},
booktitle = {Proceedings of the 35th International Conference on Machine Learning},
location = {Stockholm, Sweden},
pages = {44424450},
publisher = {International Machine Learning Society},
title = {{Learning equations for extrapolation and control}},
volume = {80},
year = {2018},
}
@article{6032,
abstract = {The main result of this article is a generalization of the classical blossom algorithm for finding perfect matchings. Our algorithm can efficiently solve Boolean CSPs where each variable appears in exactly two constraints (we call it edge CSP) and all constraints are even Δmatroid relations (represented by lists of tuples). As a consequence of this, we settle the complexity classification of planar Boolean CSPs started by Dvorak and Kupec. Using a reduction to even Δmatroids, we then extend the tractability result to larger classes of Δmatroids that we call efficiently coverable. It properly includes classes that were known to be tractable before, namely, coindependent, compact, local, linear, and binary, with the following caveat:We represent Δmatroids by lists of tuples, while the last two use a representation by matrices. Since an n ×n matrix can represent exponentially many tuples, our tractability result is not strictly stronger than the known algorithm for linear and binary Δmatroids.},
author = {Kazda, Alexandr and Kolmogorov, Vladimir and Rolinek, Michal},
journal = {ACM Transactions on Algorithms},
number = {2},
publisher = {ACM},
title = {{Even deltamatroids and the complexity of planar boolean CSPs}},
doi = {10.1145/3230649},
volume = {15},
year = {2018},
}
@article{606,
abstract = {We establish the existence of a global solution for a new family of fluidlike equations, which are obtained in certain regimes in as the meanfield evolution of the supercurrent density in a (2D section of a) typeII superconductor with pinning and with imposed electric current. We also consider general vortexsheet initial data, and investigate the uniqueness and regularity properties of the solution. For some choice of parameters, the equation under investigation coincides with the socalled lake equation from 2D shallow water fluid dynamics, and our analysis then leads to a new existence result for rough initial data.},
author = {Duerinckx, Mitia and Fischer, Julian L},
journal = {Annales de l'Institut Henri Poincare (C) Non Linear Analysis},
number = {5},
pages = {12671319},
publisher = {Elsevier},
title = {{Wellposedness for meanfield evolutions arising in superconductivity}},
doi = {10.1016/j.anihpc.2017.11.004},
volume = {35},
year = {2018},
}
@article{7,
abstract = {Animal social networks are shaped by multiple selection pressures, including the need to ensure efficient communication and functioning while simultaneously limiting disease transmission. Social animals could potentially further reduce epidemic risk by altering their social networks in the presence of pathogens, yet there is currently no evidence for such pathogentriggered responses. We tested this hypothesis experimentally in the ant Lasius niger using a combination of automated tracking, controlled pathogen exposure, transmission quantification, and temporally explicit simulations. Pathogen exposure induced behavioral changes in both exposed ants and their nestmates, which helped contain the disease by reinforcing key transmissioninhibitory properties of the colony's contact network. This suggests that social network plasticity in response to pathogens is an effective strategy for mitigating the effects of disease in social groups.},
author = {Stroeymeyt, Nathalie and Grasse, Anna V and Crespi, Alessandro and Mersch, Danielle and Cremer, Sylvia and Keller, Laurent},
issn = {10959203},
journal = {Science},
number = {6417},
pages = {941  945},
publisher = {NLM },
title = {{Social network plasticity decreases disease transmission in a eusocial insect}},
doi = {10.1126/science.aat4793},
volume = {362},
year = {2018},
}
@article{70,
abstract = {We consider the totally asymmetric simple exclusion process in a critical scaling parametrized by a≥0, which creates a shock in the particle density of order aT−1/3, T the observation time. When starting from step initial data, we provide bounds on the limiting law which in particular imply that in the double limit lima→∞limT→∞ one recovers the product limit law and the degeneration of the correlation length observed at shocks of order 1. This result is shown to apply to a general lastpassage percolation model. We also obtain bounds on the twopoint functions of several airy processes.},
author = {Nejjar, Peter},
issn = {19800436},
journal = {Latin American Journal of Probability and Mathematical Statistics},
number = {2},
pages = {13111334},
publisher = {ALEA},
title = {{Transition to shocks in TASEP and decoupling of last passage times}},
doi = {10.30757/ALEA.v1549},
volume = {15},
year = {2018},
}
@article{703,
abstract = {We consider the NPhard problem of MAPinference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) nonoptimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAPinference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is wellscalable and shows stateoftheart results on computational benchmarks from machine learning and computer vision.},
author = {Shekhovtsov, Alexander and Swoboda, Paul and Savchynskyy, Bogdan},
issn = {01628828},
journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
number = {7},
pages = {16681682},
publisher = {IEEE},
title = {{Maximum persistency via iterative relaxed inference with graphical models}},
doi = {10.1109/TPAMI.2017.2730884},
volume = {40},
year = {2018},
}
@article{7058,
abstract = {We examine recent magnetic torque measurements in two compounds, γ−Li2IrO3 and RuCl3, which have been discussed as possible realizations of the Kitaev model. The analysis of the reported discontinuity in torque, as an external magnetic field is rotated across the c axis in both crystals, suggests that they have a translationally invariant chiral spin order of the form ⟨Si⋅(Sj×Sk)⟩≠0 in the ground state and persisting over a very wide range of magnetic field and temperature. An extraordinary BB2 dependence of the torque for small fields, beside the usual B2 part, is predicted by the chiral spin order. Data for small fields are available for γ−Li2IrO3 and are found to be consistent with the prediction upon further analysis. Other experiments such as inelastic scattering and thermal Hall effect and several questions raised by the discovery of chiral spin order, including its topological consequences, are discussed.},
author = {Modic, Kimberly A and Ramshaw, B. J. and Shekhter, A. and Varma, C. M.},
issn = {24699969},
journal = {Physical Review B},
number = {20},
publisher = {APS},
title = {{Chiral spin order in some purported Kitaev spinliquid compounds}},
doi = {10.1103/physrevb.98.205110},
volume = {98},
year = {2018},
}
@article{7059,
abstract = {Unusual behavior in quantum materials commonly arises from their effective lowdimensional physics, reflecting the underlying anisotropy in the spin and charge degrees of freedom. Here we introduce the magnetotropic coefficient k = ∂2F/∂θ2, the second derivative of the free energy F with respect to the magnetic field orientation θ in the crystal. We show that the magnetotropic coefficient can be quantitatively determined from a shift in the resonant frequency of a commercially available atomic force microscopy cantilever under magnetic field. This detection method enables part per 100 million sensitivity and the ability to measure magnetic anisotropy in nanogramscale samples, as demonstrated on the Weyl semimetal NbP. Measurement of the magnetotropic coefficient in the spinliquid candidate RuCl3 highlights its sensitivity to anisotropic phase transitions and allows a quantitative comparison to other thermodynamic coefficients via the Ehrenfest relations.},
author = {Modic, Kimberly A and Bachmann, Maja D. and Ramshaw, B. J. and Arnold, F. and Shirer, K. R. and Estry, Amelia and Betts, J. B. and Ghimire, Nirmal J. and Bauer, E. D. and Schmidt, Marcus and Baenitz, Michael and Svanidze, E. and McDonald, Ross D. and Shekhter, Arkady and Moll, Philip J. W.},
issn = {20411723},
journal = {Nature Communications},
number = {1},
pages = {3975},
publisher = {Springer Nature},
title = {{Resonant torsion magnetometry in anisotropic quantum materials}},
doi = {10.1038/s4146701806412w},
volume = {9},
year = {2018},
}
@article{7062,
abstract = {Weyl fermions are a recently discovered ingredient for correlated states of electronic matter. A key difficulty has been that real materials also contain nonWeyl quasiparticles, and disentangling the experimental signatures has proven challenging. Here we use magnetic fields up to 95 T to drive the Weyl semimetal TaAs far into its quantum limit, where only the purely chiral 0th Landau levels of the Weyl fermions are occupied. We find the electrical resistivity to be nearly independent of magnetic field up to 50 T: unusual for conventional metals but consistent with the chiral anomaly for Weyl fermions. Above 50 T we observe a twoorderofmagnitude increase in resistivity, indicating that a gap opens in the chiral Landau levels. Above 80 T we observe strong ultrasonic attenuation below 2 K, suggesting a mesoscopically textured state of matter. These results point the way to inducing new correlated states of matter in the quantum limit of Weyl semimetals.},
author = {Ramshaw, B. J. and Modic, Kimberly A and Shekhter, Arkady and Zhang, Yi and Kim, EunAh and Moll, Philip J. W. and Bachmann, Maja D. and Chan, M. K. and Betts, J. B. and Balakirev, F. and Migliori, A. and Ghimire, N. J. and Bauer, E. D. and Ronning, F. and McDonald, R. D.},
issn = {20411723},
journal = {Nature Communications},
number = {1},
publisher = {Springer Nature},
title = {{Quantum limit transport and destruction of the Weyl nodes in TaAs}},
doi = {10.1038/s41467018045429},
volume = {9},
year = {2018},
}
@article{7063,
abstract = {The highpressure synthesis and incommensurately modulated structure are reported for the new compound Sr2Pt8−xAs, with x = 0.715 (5). The structure consists of Sr2Pt3As layers alternating with Ptonly corrugated grids. Ab initio calculations predict a metallic character with a dominant role of the Pt d electrons. The electrical resistivity (ρ) and Seebeck coefficient confirm the metallic character, but surprisingly, ρ showed a nearflat temperature dependence. This observation fits the description of the Mooij correlation for electrical resistivity in disordered metals, originally developed for statistically distributed point defects. The discussed material has a longrange crystallographic order, but the high concentration of Pt vacancies, incommensurately ordered, strongly influences the electronic conduction properties. This result extends the range of validity of the Mooij correlation to longrange ordered incommensurately modulated vacancies. Motivated by the layered structure, the resistivity anisotropy was measured in a focusedionbeam microfabricated well oriented single crystal. A low resistivity anisotropy indicates that the layers are electrically coupled and conduction channels along different directions are intermixed.},
author = {Martino, Edoardo and Arakcheeva, Alla and Autès, Gabriel and Pisoni, Andrea and Bachmann, Maja D. and Modic, Kimberly A and Helm, Toni and Yazyev, Oleg V. and Moll, Philip J. W. and Forró, László and Katrych, Sergiy},
issn = {20522525},
journal = {IUCrJ},
number = {4},
pages = {470477},
publisher = {International Union of Crystallography (IUCr)},
title = {{Sr2Pt8−xAs: A layered incommensurately modulated metal with saturated resistivity}},
doi = {10.1107/s2052252518007303},
volume = {5},
year = {2018},
}
@inproceedings{7116,
abstract = {Training deep learning models has received tremendous research interest recently. In particular, there has been intensive research on reducing the communication cost of training when using multiple computational devices, through reducing the precision of the underlying data representation. Naturally, such methods induce system tradeoffs—lowering communication precision could decrease communication overheads and improve scalability; but, on the other hand, it can also reduce the accuracy of training. In this paper, we study this tradeoff space, and ask:Can lowprecision communication consistently improve the endtoend performance of training modern neural networks, with no accuracy loss?From the performance point of view, the answer to this question may appear deceptively easy: compressing communication through low precision should help when the ratio between communication and computation is high. However, this answer is less straightforward when we try to generalize this principle across various neural network architectures (e.g., AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g., EC2 instances vs. NVIDIA DGX1), communication primitives (e.g., MPI vs. NCCL), and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is not clear how a realistic realization of all these factors maps to the speed up provided by lowprecision communication. In this paper, we conduct an empirical study to answer this question and report the insights.},
author = {Grubic, Demjan and Tam, Leo and Alistarh, DanAdrian and Zhang, Ce},
booktitle = {Proceedings of the 21st International Conference on Extending Database Technology},
isbn = {9783893180783},
issn = {23672005},
location = {Vienna, Austria},
pages = {145156},
publisher = {OpenProceedings},
title = {{Synchronous multiGPU training for deep learning with lowprecision communications: An empirical study}},
doi = {10.5441/002/EDBT.2018.14},
year = {2018},
}
@inproceedings{7123,
abstract = {Population protocols are a popular model of distributed computing, in which n agents with limited local state interact randomly, and cooperate to collectively compute global predicates. Inspired by recent developments in DNA programming, an extensive series of papers, across different communities, has examined the computability and complexity characteristics of this model. Majority, or consensus, is a central task in this model, in which agents need to collectively reach a decision as to which one of two states A or B had a higher initial count. Two metrics are important: the time that a protocol requires to stabilize to an output decision, and the state space size that each agent requires to do so. It is known that majority requires Ω(log log n) states per agent to allow for fast (polylogarithmic time) stabilization, and that O(log2 n) states are sufficient. Thus, there is an exponential gap between the space upper and lower bounds for this problem. This paper addresses this question.
On the negative side, we provide a new lower bound of Ω(log n) states for any protocol which stabilizes in O(n1–c) expected time, for any constant c > 0. This result is conditional on monotonicity and output assumptions, satisfied by all known protocols. Technically, it represents a departure from previous lower bounds, in that it does not rely on the existence of dense configurations. Instead, we introduce a new generalized surgery technique to prove the existence of incorrect executions for any algorithm which would contradict the lower bound. Subsequently, our lower bound also applies to general initial configurations, including ones with a leader. On the positive side, we give a new algorithm for majority which uses O(log n) states, and stabilizes in O(log2 n) expected time. Central to the algorithm is a new leaderless phase clock technique, which allows agents to synchronize in phases of Θ(n log n) consecutive interactions using O(log n) states per agent, exploiting a new connection between population protocols and poweroftwochoices load balancing mechanisms. We also employ our phase clock to build a leader election algorithm with a state space of size O(log n), which stabilizes in O(log2 n) expected time.},
author = {Alistarh, DanAdrian and Aspnes, James and Gelashvili, Rati},
booktitle = {Proceedings of the 29th Annual ACMSIAM Symposium on Discrete Algorithms},
isbn = {9781611975031},
location = {New Orleans, LA, United States},
pages = {22212239},
publisher = {ACM},
title = {{Spaceoptimal majority in population protocols}},
doi = {10.1137/1.9781611975031.144},
year = {2018},
}
@article{7126,
abstract = {In the Minimum Description Length (MDL) principle, learning from the data is equivalent to an optimal coding problem. We show that the codes that achieve optimal compression in MDL are critical in a very precise sense. First, when they are taken as generative models of samples, they generate samples with broad empirical distributions and with a high value of the relevance, defined as the entropy of the empirical frequencies. These results are derived for different statistical models (Dirichlet model, independent and pairwise dependent spin models, and restricted Boltzmann machines). Second, MDL codes sit precisely at a second order phase transition point where the symmetry between the sampled outcomes is spontaneously broken. The order parameter controlling the phase transition is the coding cost of the samples. The phase transition is a manifestation of the optimality of MDL codes, and it arises because codes that achieve a higher compression do not exist. These results suggest a clear interpretation of the widespread occurrence of statistical criticality as a characterization of samples which are maximally informative on the underlying generative process.},
author = {Cubero, Ryan J and Marsili, Matteo and Roudi, Yasser},
issn = {10994300},
journal = {Entropy},
keywords = {Minimum Description Length, normalized maximum likelihood, statistical criticality, phase transitions, large deviations},
number = {10},
publisher = {MDPI},
title = {{Minimum description length codes are critical}},
doi = {10.3390/e20100755},
volume = {20},
year = {2018},
}
@article{723,
abstract = {Escaping local optima is one of the major obstacles to function optimisation. Using the metaphor of a fitness landscape, local optima correspond to hills separated by fitness valleys that have to be overcome. We define a class of fitness valleys of tunable difficulty by considering their length, representing the Hamming path between the two optima and their depth, the drop in fitness. For this function class we present a runtime comparison between stochastic search algorithms using different search strategies. The (1+1) EA is a simple and wellstudied evolutionary algorithm that has to jump across the valley to a point of higher fitness because it does not accept worsening moves (elitism). In contrast, the Metropolis algorithm and the Strong Selection Weak Mutation (SSWM) algorithm, a famous process in population genetics, are both able to cross the fitness valley by accepting worsening moves. We show that the runtime of the (1+1) EA depends critically on the length of the valley while the runtimes of the nonelitist algorithms depend crucially on the depth of the valley. Moreover, we show that both SSWM and Metropolis can also efficiently optimise a rugged function consisting of consecutive valleys.},
author = {Oliveto, Pietro and Paixao, Tiago and Pérez Heredia, Jorge and Sudholt, Dirk and Trubenova, Barbora},
journal = {Algorithmica},
number = {5},
pages = {1604  1633},
publisher = {Springer},
title = {{How to escape local optima in black box optimisation when non elitism outperforms elitism}},
doi = {10.1007/s0045301703692},
volume = {80},
year = {2018},
}
@article{7277,
abstract = {Solid alkali metal carbonates are universal passivation layer components of intercalation battery materials and common side products in metal‐O2 batteries, and are believed to form and decompose reversibly in metal‐O2/CO2 cells. In these cathodes, Li2CO3 decomposes to CO2 when exposed to potentials above 3.8 V vs. Li/Li+. However, O2 evolution, as would be expected according to the decomposition reaction 2 Li2CO3→4 Li++4 e−+2 CO2+O2, is not detected. O atoms are thus unaccounted for, which was previously ascribed to unidentified parasitic reactions. Here, we show that highly reactive singlet oxygen (1O2) forms upon oxidizing Li2CO3 in an aprotic electrolyte and therefore does not evolve as O2. These results have substantial implications for the long‐term cyclability of batteries: they underpin the importance of avoiding 1O2 in metal‐O2 batteries, question the possibility of a reversible metal‐O2/CO2 battery based on a carbonate discharge product, and help explain the interfacial reactivity of transition‐metal cathodes with residual Li2CO3.},
author = {Mahne, Nika and Renfrew, Sara E. and McCloskey, Bryan D. and Freunberger, Stefan Alexander},
issn = {14337851},
journal = {Angewandte Chemie International Edition},
number = {19},
pages = {55295533},
publisher = {Wiley},
title = {{Electrochemical oxidation of Lithium Carbonate generates singlet oxygen}},
doi = {10.1002/anie.201802277},
volume = {57},
year = {2018},
}
@article{7285,
abstract = {Hydrogelation, the selfassembly of molecules into soft, waterloaded networks, is one way to bridge the structural gap between single molecules and functional materials. The potential of hydrogels, such as those based on perylene bisimides, lies in their chemical, physical, optical, and electronic properties, which are governed by the supramolecular structure of the gel. However, the structural motifs and their precise role for longrange conductivity are yet to be explored. Here, we present a comprehensive structural picture of a perylene bisimide hydrogel, suggesting that its longrange conductivity is limited by charge transfer between electronic backbones. We reveal nanocrystalline ribbonlike structures as the electronic and structural backbone units between which charge transfer is mediated by polar solvent bridges. We exemplify this effect with sensing, where exposure to polar vapor enhances conductivity by 5 orders of magnitude, emphasizing the crucial role of the interplay between structural motif and surrounding medium for the rational design of devices based on nanocrystalline hydrogels.},
author = {Burian, Max and Rigodanza, Francesco and Demitri, Nicola and D̵ord̵ević, Luka and Marchesan, Silvia and Steinhartova, Tereza and LetofskyPapst, Ilse and Khalakhan, Ivan and Mourad, Eléonore and Freunberger, Stefan Alexander and Amenitsch, Heinz and Prato, Maurizio and Syrgiannis, Zois},
issn = {19360851},
journal = {ACS Nano},
number = {6},
pages = {58005806},
publisher = {ACS},
title = {{Interbackbone charge transfer as prerequisite for longrange conductivity in perylene bisimide hydrogels}},
doi = {10.1021/acsnano.8b01689},
volume = {12},
year = {2018},
}
@article{7287,
abstract = {Passivation layers on electrode materials are ubiquitous in nonaqueous battery chemistries and strongly govern performance and lifetime. They comprise breakdown products of the electrolyte including carbonate, alkyl carbonates, alkoxides, carboxylates, and polymers. Parasitic chemistry in metal–O2 batteries forms similar products and is tied to the deviation of the O2 balance from the ideal stoichiometry during formation/decomposition of alkaline peroxides or superoxides. Accurate and integral quantification of carbonaceous species and peroxides or superoxides in battery electrodes remains, however, elusive. We present a refined procedure to quantify them accurately and sensitively by pointing out and rectifying pitfalls of previous procedures. Carbonaceous compounds are differentiated into inorganic and organic ones. We combine mass and UV–vis spectrometry to quantify evolved O2 and complexed peroxide and CO2 evolved from carbonaceous compounds by acid treatment and Fenton’s reaction. The capabilities of the method are exemplified by means of Li–O2 and Na–O2 cathodes, graphite anodes, and LiNi0.8Co0.15Al0.05O2 cathodes.},
author = {Schafzahl, Bettina and Mourad, Eléonore and Schafzahl, Lukas and Petit, Yann K. and Raju, Anjana R. and Thotiyl, Musthafa Ottakam and Wilkening, Martin and Slugovc, Christian and Freunberger, Stefan Alexander},
issn = {23808195},
journal = {ACS Energy Letters},
number = {1},
pages = {170176},
publisher = {ACS},
title = {{Quantifying total superoxide, peroxide, and carbonaceous compounds in metal–O2 batteries and the solid electrolyte interphase}},
doi = {10.1021/acsenergylett.7b01111},
volume = {3},
year = {2018},
}
@article{738,
abstract = {This paper is devoted to automatic competitive analysis of realtime scheduling algorithms for firmdeadline tasksets, where only completed tasks con tribute some utility to the system. Given such a taskset T , the competitive ratio of an online scheduling algorithm A for T is the worstcase utility ratio of A over the utility achieved by a clairvoyant algorithm. We leverage the theory of quantitative graph games to address the competitive analysis and competitive synthesis problems. For the competitive analysis case, given any taskset T and any finitememory on line scheduling algorithm A , we show that the competitive ratio of A in T can be computed in polynomial time in the size of the state space of A . Our approach is flexible as it also provides ways to model meaningful constraints on the released task sequences that determine the competitive ratio. We provide an experimental study of many wellknown online scheduling algorithms, which demonstrates the feasibility of our competitive analysis approach that effectively replaces human ingenuity (required Preliminary versions of this paper have appeared in Chatterjee et al. ( 2013 , 2014 ). B Andreas Pavlogiannis pavlogiannis@ist.ac.at Krishnendu Chatterjee krish.chat@ist.ac.at Alexander Kößler koe@ecs.tuwien.ac.at Ulrich Schmid s@ecs.tuwien.ac.at 1 IST Austria (Institute of Science and Technology Austria), Am Campus 1, 3400 Klosterneuburg, Austria 2 Embedded Computing Systems Group, Vienna University of Technology, Treitlstrasse 3, 1040 Vienna, Austria 123 RealTime Syst for finding worstcase scenarios) by computing power. For the competitive synthesis case, we are just given a taskset T , and the goal is to automatically synthesize an opti mal online scheduling algorithm A , i.e., one that guarantees the largest competitive ratio possible for T . We show how the competitive synthesis problem can be reduced to a twoplayer graph game with partial information, and establish that the compu tational complexity of solving this game is Np complete. The competitive synthesis problem is hence in Np in the size of the state space of the nondeterministic labeled transition system encoding the taskset. Overall, the proposed framework assists in the selection of suitable scheduling algorithms for a given taskset, which is in fact the most common situation in realtime systems design. },
author = {Chatterjee, Krishnendu and Pavlogiannis, Andreas and Kößler, Alexander and Schmid, Ulrich},
journal = {RealTime Systems},
number = {1},
pages = {166  207},
publisher = {Springer},
title = {{Automated competitive analysis of real time scheduling with graph games}},
doi = {10.1007/s1124101792934},
volume = {54},
year = {2018},
}
@inproceedings{7407,
abstract = {Proofs of space (PoS) [Dziembowski et al., CRYPTO'15] are proof systems where a prover can convince a verifier that he "wastes" disk space. PoS were introduced as a more ecological and economical replacement for proofs of work which are currently used to secure blockchains like Bitcoin. In this work we investigate extensions of PoS which allow the prover to embed useful data into the dedicated space, which later can be recovered. Our first contribution is a security proof for the original PoS from CRYPTO'15 in the random oracle model (the original proof only applied to a restricted class of adversaries which can store a subset of the data an honest prover would store). When this PoS is instantiated with recent constructions of maximally depth robust graphs, our proof implies basically optimal security. As a second contribution we show three different extensions of this PoS where useful data can be embedded into the space required by the prover. Our security proof for the PoS extends (nontrivially) to these constructions. We discuss how some of these variants can be used as proofs of catalytic space (PoCS), a notion we put forward in this work, and which basically is a PoS where most of the space required by the prover can be used to backup useful data. Finally we discuss how one of the extensions is a candidate construction for a proof of replication (PoR), a proof system recently suggested in the Filecoin whitepaper. },
author = {Pietrzak, Krzysztof Z},
booktitle = {10th Innovations in Theoretical Computer Science Conference (ITCS 2019)},
isbn = {9783959770958},
issn = {18688969},
location = {San Diego, CA, United States},
pages = {59:159:25},
publisher = {Schloss Dagstuhl  LeibnizZentrum für Informatik},
title = {{Proofs of catalytic space}},
doi = {10.4230/LIPICS.ITCS.2019.59},
volume = {124},
year = {2018},
}
@article{742,
abstract = {We give a detailed and easily accessible proof of Gromov’s Topological Overlap Theorem. Let X be a finite simplicial complex or, more generally, a finite polyhedral cell complex of dimension d. Informally, the theorem states that if X has sufficiently strong higherdimensional expansion properties (which generalize edge expansion of graphs and are defined in terms of cellular cochains of X) then X has the following topological overlap property: for every continuous map (Formula presented.) there exists a point (Formula presented.) that is contained in the images of a positive fraction (Formula presented.) of the dcells of X. More generally, the conclusion holds if (Formula presented.) is replaced by any ddimensional piecewiselinear manifold M, with a constant (Formula presented.) that depends only on d and on the expansion properties of X, but not on M.},
author = {Dotterrer, Dominic and Kaufman, Tali and Wagner, Uli},
journal = {Geometriae Dedicata},
number = {1},
pages = {307–317},
publisher = {Springer},
title = {{On expansion and topological overlap}},
doi = {10.1007/s1071101702914},
volume = {195},
year = {2018},
}
@unpublished{75,
abstract = {We prove that any convex body in the plane can be partitioned into m convex parts of equal areas and perimeters for any integer m≥2; this result was previously known for prime powers m=pk. We also give a higherdimensional generalization.},
author = {Akopyan, Arseniy and Avvakumov, Sergey and Karasev, Roman},
pages = {11},
publisher = {arXiv},
title = {{Convex fair partitions into arbitrary number of pieces}},
year = {2018},
}
@article{76,
abstract = {Consider a fullyconnected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous Ccounting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the selfstabilising firing squad problem, the task is to eventually guarantee that all nonfaulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the nottoodistant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for selfstabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions.},
author = {Lenzen, Christoph and Rybicki, Joel},
journal = {Distributed Computing},
publisher = {Springer},
title = {{Nearoptimal selfstabilising counting and firing squads}},
doi = {10.1007/s0044601803426},
year = {2018},
}
@article{77,
abstract = {Holes confined in quantum dots have gained considerable interest in the past few years due to their potential as spin qubits. Here we demonstrate twoaxis control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double quantum dot device. The Pauli spin blockade principle allowed us to demonstrate electric dipole spin resonance by applying a radio frequency electric field to one of the electrodes defining the double quantum dot. Coherent hole spin oscillations with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of 130 ns are measured. The reported results emphasize the potential of Ge as a platform for fast and electrically tunable hole spin qubit devices.},
author = {Watzinger, Hannes and Kukucka, Josip and Vukusic, Lada and Gao, Fei and Wang, Ting and Schäffler, Friedrich and Zhang, Jian and Katsaros, Georgios},
journal = {Nature Communications},
number = {3902 },
publisher = {Nature Publishing Group},
title = {{A germanium hole spin qubit}},
doi = {10.1038/s41467018064184},
volume = {9},
year = {2018},
}