TY - CONF
AB - We consider the problem of expected cost analysis over nondeterministic probabilistic programs,
which aims at automated methods for analyzing the resource-usage of such programs.
Previous approaches for this problem could only handle nonnegative bounded costs.
However, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols,
both positive and negative costs are necessary and the costs are unbounded as well.
In this work, we present a sound and efficient approach to obtain polynomial bounds on the
expected accumulated cost of nondeterministic probabilistic programs.
Our approach can handle (a) general positive and negative costs with bounded updates in
variables; and (b) nonnegative costs with general updates to variables.
We show that several natural examples which could not be
handled by previous approaches are captured in our framework.
Moreover, our approach leads to an efficient polynomial-time algorithm, while no
previous approach for cost analysis of probabilistic programs could guarantee polynomial runtime.
Finally, we show the effectiveness of our approach using experimental results on a variety of programs for which we efficiently synthesize tight resource-usage bounds.
AU - Wang, Peixin
AU - Fu, Hongfei
AU - Goharshady, Amir Kafshdar
AU - Chatterjee, Krishnendu
AU - Qin, Xudong
AU - Shi, Wenjun
ID - 6175
KW - Program Cost Analysis
KW - Program Termination
KW - Probabilistic Programs
KW - Martingales
T2 - PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation
TI - Cost analysis of nondeterministic probabilistic programs
ER -
TY - JOUR
AB - There is a huge gap between the speeds of modern caches and main memories, and therefore cache misses account for a considerable loss of efficiency in programs. The predominant technique to address this issue has been Data Packing: data elements that are frequently accessed within time proximity are packed into the same cache block, thereby minimizing accesses to the main memory. We consider the algorithmic problem of Data Packing on a two-level memory system. Given a reference sequence R of accesses to data elements, the task is to partition the elements into cache blocks such that the number of cache misses on R is minimized. The problem is notoriously difficult: it is NP-hard even when the cache has size 1, and is hard to approximate for any cache size larger than 4. Therefore, all existing techniques for Data Packing are based on heuristics and lack theoretical guarantees. In this work, we present the first positive theoretical results for Data Packing, along with new and stronger negative results. We consider the problem under the lens of the underlying access hypergraphs, which are hypergraphs of affinities between the data elements, where the order of an access hypergraph corresponds to the size of the affinity group. We study the problem parameterized by the treewidth of access hypergraphs, which is a standard notion in graph theory to measure the closeness of a graph to a tree. Our main results are as follows: We show there is a number q* depending on the cache parameters such that (a) if the access hypergraph of order q* has constant treewidth, then there is a linear-time algorithm for Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy depending on a single parameter, namely, the highest order among access hypegraphs that have constant treewidth; and establish the optimal value q* of this parameter. Finally, we present an experimental evaluation of a prototype implementation of our algorithm. Our results demonstrate that, in practice, access hypergraphs of many commonly-used algorithms have small treewidth. We compare our approach with several state-of-the-art heuristic-based algorithms and show that our algorithm leads to significantly fewer cache-misses.
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
AU - Okati, Nastaran
AU - Pavlogiannis, Andreas
ID - 6380
IS - POPL
JF - Proceedings of the ACM on Programming Languages
SN - 2475-1421
TI - Efficient parameterized algorithms for data packing
VL - 3
ER -
TY - CONF
AB - Smart contracts are programs that are stored and executed on the Blockchain and can receive, manage and transfer money (cryptocurrency units). Two important problems regarding smart contracts are formal analysis and compiler optimization. Formal analysis is extremely important, because smart contracts hold funds worth billions of dollars and their code is immutable after deployment. Hence, an undetected bug can cause significant financial losses. Compiler optimization is also crucial, because every action of a smart contract has to be executed by every node in the Blockchain network. Therefore, optimizations in compiling smart contracts can lead to significant savings in computation, time and energy.
Two classical approaches in program analysis and compiler optimization are intraprocedural and interprocedural analysis. In intraprocedural analysis, each function is analyzed separately, while interprocedural analysis considers the entire program. In both cases, the analyses are usually reduced to graph problems over the control flow graph (CFG) of the program. These graph problems are often computationally expensive. Hence, there has been ample research on exploiting structural properties of CFGs for efficient algorithms. One such well-studied property is the treewidth, which is a measure of tree-likeness of graphs. It is known that intraprocedural CFGs of structured programs have treewidth at most 6, whereas the interprocedural treewidth cannot be bounded. This result has been used as a basis for many efficient intraprocedural analyses.
In this paper, we explore the idea of exploiting the treewidth of smart contracts for formal analysis and compiler optimization. First, similar to classical programs, we show that the intraprocedural treewidth of structured Solidity and Vyper smart contracts is at most 9. Second, for global analysis, we prove that the interprocedural treewidth of structured smart contracts is bounded by 10 and, in sharp contrast with classical programs, treewidth-based algorithms can be easily applied for interprocedural analysis. Finally, we supplement our theoretical results with experiments using a tool we implemented for computing treewidth of smart contracts and show that the treewidth is much lower in practice. We use 36,764 real-world Ethereum smart contracts as benchmarks and find that they have an average treewidth of at most 3.35 for the intraprocedural case and 3.65 for the interprocedural case.
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
AU - Goharshady, Ehsan Kafshdar
ID - 6490
SN - 9781450359337
T2 - Proceedings of the 34th ACM Symposium on Applied Computing
TI - The treewidth of smart contracts
VL - Part F147772
ER -
TY - JOUR
AB -
Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, and so on. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, and so on. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in an important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect we consider is that the control flow graphs for most programs have constant treewidth.
Our main contributions are simple and implementable algorithms that support multiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing but can answer subsequent queries significantly faster as compared to the current algorithmic solutions for interprocedural dataflow analysis. We have also implemented our algorithms and evaluated their performance for performing on-demand interprocedural dataflow analysis on various domains, such as for live variable analysis and reaching definitions, on a standard benchmark set. Our experimental results align with our theoretical statements and show that after a lightweight preprocessing, on-demand queries are answered much faster than the standard existing algorithmic approaches.
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
AU - Goyal, Prateesh
AU - Ibsen-Jensen, Rasmus
AU - Pavlogiannis, Andreas
ID - 7158
IS - 4
JF - ACM Transactions on Programming Languages and Systems
SN - 0164-0925
TI - Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth
VL - 41
ER -
TY - CONF
AB - In today's programmable blockchains, smart contracts are limited to being deterministic and non-probabilistic. This lack of randomness is a consequential limitation, given that a wide variety of real-world financial contracts, such as casino games and lotteries, depend entirely on randomness. As a result, several ad-hoc random number generation approaches have been developed to be used in smart contracts. These include ideas such as using an oracle or relying on the block hash. However, these approaches are manipulatable, i.e. their output can be tampered with by parties who might not be neutral, such as the owner of the oracle or the miners.We propose a novel game-theoretic approach for generating provably unmanipulatable pseudorandom numbers on the blockchain. Our approach allows smart contracts to access a trustworthy source of randomness that does not rely on potentially compromised miners or oracles, hence enabling the creation of a new generation of smart contracts that are not limited to being non-probabilistic and can be drawn from the much more general class of probabilistic programs.
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
AU - Pourdamghani, Arash
ID - 6056
T2 - IEEE International Conference on Blockchain and Cryptocurrency
TI - Probabilistic smart contracts: Secure randomness on the blockchain
ER -
TY - JOUR
AB - We study the problem of developing efficient approaches for proving
worst-case bounds of non-deterministic recursive programs. Ranking functions
are sound and complete for proving termination and worst-case bounds of
nonrecursive programs. First, we apply ranking functions to recursion,
resulting in measure functions. We show that measure functions provide a sound
and complete approach to prove worst-case bounds of non-deterministic recursive
programs. Our second contribution is the synthesis of measure functions in
nonpolynomial forms. We show that non-polynomial measure functions with
logarithm and exponentiation can be synthesized through abstraction of
logarithmic or exponentiation terms, Farkas' Lemma, and Handelman's Theorem
using linear programming. While previous methods obtain worst-case polynomial
bounds, our approach can synthesize bounds of the form $\mathcal{O}(n\log n)$
as well as $\mathcal{O}(n^r)$ where $r$ is not an integer. We present
experimental results to demonstrate that our approach can obtain efficiently
worst-case bounds of classical recursive algorithms such as (i) Merge-Sort, the
divide-and-conquer algorithm for the Closest-Pair problem, where we obtain
$\mathcal{O}(n \log n)$ worst-case bound, and (ii) Karatsuba's algorithm for
polynomial multiplication and Strassen's algorithm for matrix multiplication,
where we obtain $\mathcal{O}(n^r)$ bound such that $r$ is not an integer and
close to the best-known bounds for the respective algorithms.
AU - Chatterjee, Krishnendu
AU - Fu, Hongfei
AU - Goharshady, Amir Kafshdar
ID - 7014
IS - 4
JF - ACM Transactions on Programming Languages and Systems
TI - Non-polynomial worst-case analysis of recursive programs
VL - 41
ER -
TY - CONF
AB - In this work, we consider the almost-sure termination problem for probabilistic programs that asks whether a
given probabilistic program terminates with probability 1. Scalable approaches for program analysis often
rely on modularity as their theoretical basis. In non-probabilistic programs, the classical variant rule (V-rule)
of Floyd-Hoare logic provides the foundation for modular analysis. Extension of this rule to almost-sure
termination of probabilistic programs is quite tricky, and a probabilistic variant was proposed in [16]. While the
proposed probabilistic variant cautiously addresses the key issue of integrability, we show that the proposed
modular rule is still not sound for almost-sure termination of probabilistic programs.
Besides establishing unsoundness of the previous rule, our contributions are as follows: First, we present a
sound modular rule for almost-sure termination of probabilistic programs. Our approach is based on a novel
notion of descent supermartingales. Second, for algorithmic approaches, we consider descent supermartingales
that are linear and show that they can be synthesized in polynomial time. Finally, we present experimental
results on a variety of benchmarks and several natural examples that model various types of nested while
loops in probabilistic programs and demonstrate that our approach is able to efficiently prove their almost-sure
termination property
AU - Huang, Mingzhang
AU - Fu, Hongfei
AU - Chatterjee, Krishnendu
AU - Goharshady, Amir Kafshdar
ID - 6780
T2 - Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications
TI - Modular verification for almost-sure termination of probabilistic programs
VL - 3
ER -
TY - JOUR
AB - Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.
AU - Granados, Alejandro
AU - Pietsch, Julian
AU - Cepeda Humerez, Sarah A
AU - Farquhar, Isebail
AU - Tkacik, Gasper
AU - Swain, Peter
ID - 281
IS - 23
JF - PNAS
TI - Distributed and dynamic intracellular organization of extracellular information
VL - 115
ER -
TY - JOUR
AB - Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci.
AU - Sachdeva, Himani
AU - Barton, Nicholas H
ID - 282
IS - 4
JF - Genetics
TI - Introgression of a block of genome under infinitesimal selection
VL - 209
ER -
TY - JOUR
AB - Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors.
AU - Ceinos, Rosa Maria
AU - Frigato, Elena
AU - Pagano, Cristina
AU - Frohlich, Nadine
AU - Negrini, Pietro
AU - Cavallari, Nicola
AU - Vallone, Daniela
AU - Fuselli, Silvia
AU - Bertolucci, Cristiano
AU - Foulkes, Nicholas S
ID - 283
IS - 1
JF - Scientific Reports
TI - Mutations in blind cavefish target the light regulated circadian clock gene period 2
VL - 8
ER -
TY - JOUR
AB - Borel probability measures living on metric spaces are fundamental
mathematical objects. There are several meaningful distance functions that make the collection of the probability measures living on a certain space a metric space. We are interested in the description of the structure of the isometries of such metric spaces. We overview some of the recent results of the topic and we also provide some new ones concerning the Wasserstein distance. More specifically, we consider the space of all Borel probability measures on the unit sphere of a Euclidean space endowed with the Wasserstein metric W_p for arbitrary p >= 1, and we show that the action of a Wasserstein isometry on the set of Dirac measures is induced by an isometry of the underlying unit sphere.
AU - Virosztek, Daniel
ID - 284
IS - 1-2
JF - Acta Scientiarum Mathematicarum (Szeged)
TI - Maps on probability measures preserving certain distances - a survey and some new results
VL - 84
ER -
TY - CONF
AB - In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how "simple" or "thin" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1)).
AU - Huszár, Kristóf
AU - Spreer, Jonathan
AU - Wagner, Uli
ID - 285
SN - 18688969
TI - On the treewidth of triangulated 3-manifolds
VL - 99
ER -
TY - JOUR
AB - In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer therapy. We propose an investigation on the coupling of electromagnetic radiation to mechanical vibrations of MTs as an important basis for biological and medical applications. In our opinion, optomechanical methods can accurately monitor and control the mechanical properties of isolated MTs in a liquid environment. Consequently, studying nanomechanical properties of MTs may give useful information for future applications to diagnostic and therapeutic technologies involving non-invasive externally applied physical fields. For example, electromagnetic fields or high intensity ultrasound can be used therapeutically avoiding harmful side effects of chemotherapeutic agents or classical radiation therapy.
AU - Salari, Vahid
AU - Barzanjeh, Shabir
AU - Cifra, Michal
AU - Simon, Christoph
AU - Scholkmann, Felix
AU - Alirezaei, Zahra
AU - Tuszynski, Jack
ID - 287
IS - 8
JF - Frontiers in Bioscience - Landmark
TI - Electromagnetic fields and optomechanics In cancer diagnostics and treatment
VL - 23
ER -
TY - JOUR
AB - Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer.
AU - Lilja, Anna
AU - Rodilla, Veronica
AU - Huyghe, Mathilde
AU - Hannezo, Edouard B
AU - Landragin, Camille
AU - Renaud, Olivier
AU - Leroy, Olivier
AU - Rulands, Steffen
AU - Simons, Benjamin
AU - Fré, Silvia
ID - 288
IS - 6
JF - Nature Cell Biology
TI - Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland
VL - 20
ER -
TY - JOUR
AB - We report on quantum capacitance measurements of high quality, graphite- and hexagonal boron nitride encapsulated Bernal stacked trilayer graphene devices. At zero applied magnetic field, we observe a number of electron density- and electrical displacement-tuned features in the electronic compressibility associated with changes in Fermi surface topology. At high displacement field and low density, strong trigonal warping gives rise to emergent Dirac gullies centered near the corners of the hexagonal Brillouin and related by three fold rotation symmetry. At low magnetic fields of B=1.25~T, the gullies manifest as a change in the degeneracy of the Landau levels from two to three. Weak incompressible states are also observed at integer filling within these triplets Landau levels, which a Hartree-Fock analysis indicates are associated with Coulomb-driven nematic phases that spontaneously break rotation symmetry.
AU - Zibrov, Alexander
AU - Peng, Rao
AU - Kometter, Carlos
AU - Li, Jia
AU - Dean, Cory
AU - Taniguchi, Takashi
AU - Watanabe, Kenji
AU - Serbyn, Maksym
AU - Young, Andrea
ID - 289
IS - 16
JF - Physical Review Letters
TI - Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene
VL - 121
ER -
TY - JOUR
AB - Social insects have evolved enormous capacities to collectively build nests and defend their colonies against both predators and pathogens. The latter is achieved by a combination of individual immune responses and sophisticated collective behavioral and organizational disease defenses, that is, social immunity. We investigated how the presence or absence of these social defense lines affects individual-level immunity in ant queens after bacterial infection. To this end, we injected queens of the ant Linepithema humile with a mix of gram+ and gram− bacteria or a control solution, reared them either with workers or alone and analyzed their gene expression patterns at 2, 4, 8, and 12 hr post-injection, using RNA-seq. This allowed us to test for the effect of bacterial infection, social context, as well as the interaction between the two over the course of infection and raising of an immune response. We found that social isolation per se affected queen gene expression for metabolism genes, but not for immune genes. When infected, queens reared with and without workers up-regulated similar numbers of innate immune genes revealing activation of Toll and Imd signaling pathways and melanization. Interestingly, however, they mostly regulated different genes along the pathways and showed a different pattern of overall gene up-regulation or down-regulation. Hence, we can conclude that the absence of workers does not compromise the onset of an individual immune response by the queens, but that the social environment impacts the route of the individual innate immune responses.
AU - Viljakainen, Lumi
AU - Jurvansuu, Jaana
AU - Holmberg, Ida
AU - Pamminger, Tobias
AU - Erler, Silvio
AU - Cremer, Sylvia
ID - 29
IS - 22
JF - Ecology and Evolution
SN - 20457758
TI - Social environment affects the transcriptomic response to bacteria in ant queens
VL - 8
ER -
TY - JOUR
AB - Over the past decade, the edge of chaos has proven to be a fruitful starting point for investigations of shear flows when the laminar base flow is linearly stable. Numerous computational studies of shear flows demonstrated the existence of states that separate laminar and turbulent regions of the state space. In addition, some studies determined invariant solutions that reside on this edge. In this paper, we study the unstable manifold of one such solution with the aid of continuous symmetry reduction, which we formulate here for the simultaneous quotiening of axial and azimuthal symmetries. Upon our investigation of the unstable manifold, we discover a previously unknown traveling-wave solution on the laminar-turbulent boundary with a relatively complex structure. By means of low-dimensional projections, we visualize different dynamical paths that connect these solutions to the turbulence. Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits qualitatively different regions whose properties are influenced by the nearby invariant solutions.
AU - Budanur, Nazmi B
AU - Hof, Björn
ID - 291
IS - 5
JF - Physical Review Fluids
TI - Complexity of the laminar-turbulent boundary in pipe flow
VL - 3
ER -
TY - JOUR
AB - Retina is a paradigmatic system for studying sensory encoding: the transformation of light into spiking activity of ganglion cells. The inverse problem, where stimulus is reconstructed from spikes, has received less attention, especially for complex stimuli that should be reconstructed “pixel-by-pixel”. We recorded around a hundred neurons from a dense patch in a rat retina and decoded movies of multiple small randomly-moving discs. We constructed nonlinear (kernelized and neural network) decoders that improved significantly over linear results. An important contribution to this was the ability of nonlinear decoders to reliably separate between neural responses driven by locally fluctuating light signals, and responses at locally constant light driven by spontaneous-like activity. This improvement crucially depended on the precise, non-Poisson temporal structure of individual spike trains, which originated in the spike-history dependence of neural responses. We propose a general principle by which downstream circuitry could discriminate between spontaneous and stimulus-driven activity based solely on higher-order statistical structure in the incoming spike trains.
AU - Botella Soler, Vicent
AU - Deny, Stephane
AU - Martius, Georg S
AU - Marre, Olivier
AU - Tkacik, Gasper
ID - 292
IS - 5
JF - PLoS Computational Biology
TI - Nonlinear decoding of a complex movie from the mammalian retina
VL - 14
ER -
TY - JOUR
AB - People sometimes make their admirable deeds and accomplishments hard to spot, such as by giving anonymously or avoiding bragging. Such ‘buried’ signals are hard to reconcile with standard models of signalling or indirect reciprocity, which motivate costly pro-social behaviour by reputational gains. To explain these phenomena, we design a simple game theory model, which we call the signal-burying game. This game has the feature that senders can bury their signal by deliberately reducing the probability of the signal being observed. If the signal is observed, however, it is identified as having been buried. We show under which conditions buried signals can be maintained, using static equilibrium concepts and calculations of the evolutionary dynamics. We apply our analysis to shed light on a number of otherwise puzzling social phenomena, including modesty, anonymous donations, subtlety in art and fashion, and overeagerness.
AU - Hoffman, Moshe
AU - Hilbe, Christian
AU - Nowak, Martin
ID - 293
JF - Nature Human Behaviour
TI - The signal-burying game can explain why we obscure positive traits and good deeds
VL - 2
ER -
TY - JOUR
AB - We developed a method to calculate two-photon processes in quantum mechanics that replaces the infinite summation over the intermediate states by a perturbation expansion. This latter consists of a series of commutators that involve position, momentum, and Hamiltonian quantum operators. We analyzed several single- and many-particle cases for which a closed-form solution to the perturbation expansion exists, as well as more complicated cases for which a solution is found by convergence. Throughout the article, Rayleigh and Raman scattering are taken as examples of two-photon processes. The present method provides a clear distinction between the Thomson scattering, regarded as classical scattering, and quantum contributions. Such a distinction lets us derive general results concerning light scattering. Finally, possible extensions to the developed formalism are discussed.
AU - Fratini, Filippo
AU - Safari, Laleh
AU - Amaro, Pedro
AU - Santos, José
ID - 294
IS - 4
JF - Physical Review A - Atomic, Molecular, and Optical Physics
TI - Two-photon processes based on quantum commutators
VL - 97
ER -
TY - JOUR
AB - We prove upper and lower bounds on the ground-state energy of the ideal two-dimensional anyon gas. Our bounds are extensive in the particle number, as for fermions, and linear in the statistics parameter (Formula presented.). The lower bounds extend to Lieb–Thirring inequalities for all anyons except bosons.
AU - Lundholm, Douglas
AU - Seiringer, Robert
ID - 295
IS - 11
JF - Letters in Mathematical Physics
TI - Fermionic behavior of ideal anyons
VL - 108
ER -
TY - JOUR
AB - The thermodynamic description of many-particle systems rests on the assumption of ergodicity, the ability of a system to explore all allowed configurations in the phase space. Recent studies on many-body localization have revealed the existence of systems that strongly violate ergodicity in the presence of quenched disorder. Here, we demonstrate that ergodicity can be weakly broken by a different mechanism, arising from the presence of special eigenstates in the many-body spectrum that are reminiscent of quantum scars in chaotic non-interacting systems. In the single-particle case, quantum scars correspond to wavefunctions that concentrate in the vicinity of unstable periodic classical trajectories. We show that many-body scars appear in the Fibonacci chain, a model with a constrained local Hilbert space that has recently been experimentally realized in a Rydberg-atom quantum simulator. The quantum scarred eigenstates are embedded throughout the otherwise thermalizing many-body spectrum but lead to direct experimental signatures, as we show for periodic recurrences that reproduce those observed in the experiment. Our results suggest that scarred many-body bands give rise to a new universality class of quantum dynamics, opening up opportunities for the creation of novel states with long-lived coherence in systems that are now experimentally realizable.
AU - Turner, Christopher
AU - Michailidis, Alexios
AU - Abanin, Dmitry
AU - Serbyn, Maksym
AU - Papić, Zlatko
ID - 296
JF - Nature Physics
TI - Weak ergodicity breaking from quantum many-body scars
VL - 14
ER -
TY - CONF
AB - Graph games played by two players over finite-state graphs are central in many problems in computer science. In particular, graph games with ω -regular winning conditions, specified as parity objectives, which can express properties such as safety, liveness, fairness, are the basic framework for verification and synthesis of reactive systems. The decisions for a player at various states of the graph game are represented as strategies. While the algorithmic problem for solving graph games with parity objectives has been widely studied, the most prominent data-structure for strategy representation in graph games has been binary decision diagrams (BDDs). However, due to the bit-level representation, BDDs do not retain the inherent flavor of the decisions of strategies, and are notoriously hard to minimize to obtain succinct representation. In this work we propose decision trees for strategy representation in graph games. Decision trees retain the flavor of decisions of strategies and allow entropy-based minimization to obtain succinct trees. However, decision trees work in settings (e.g., probabilistic models) where errors are allowed, and overfitting of data is typically avoided. In contrast, for strategies in graph games no error is allowed, and the decision tree must represent the entire strategy. We develop new techniques to extend decision trees to overcome the above obstacles, while retaining the entropy-based techniques to obtain succinct trees. We have implemented our techniques to extend the existing decision tree solvers. We present experimental results for problems in reactive synthesis to show that decision trees provide a much more efficient data-structure for strategy representation as compared to BDDs.
AU - Brázdil, Tomáš
AU - Chatterjee, Krishnendu
AU - Kretinsky, Jan
AU - Toman, Viktor
ID - 297
TI - Strategy representation by decision trees in reactive synthesis
VL - 10805
ER -
TY - CONF
AB - Memory-hard functions (MHF) are functions whose evaluation cost is dominated by memory cost. MHFs are egalitarian, in the sense that evaluating them on dedicated hardware (like FPGAs or ASICs) is not much cheaper than on off-the-shelf hardware (like x86 CPUs). MHFs have interesting cryptographic applications, most notably to password hashing and securing blockchains.
Alwen and Serbinenko [STOC’15] define the cumulative memory complexity (cmc) of a function as the sum (over all time-steps) of the amount of memory required to compute the function. They advocate that a good MHF must have high cmc. Unlike previous notions, cmc takes into account that dedicated hardware might exploit amortization and parallelism. Still, cmc has been critizised as insufficient, as it fails to capture possible time-memory trade-offs; as memory cost doesn’t scale linearly, functions with the same cmc could still have very different actual hardware cost.
In this work we address this problem, and introduce the notion of sustained-memory complexity, which requires that any algorithm evaluating the function must use a large amount of memory for many steps. We construct functions (in the parallel random oracle model) whose sustained-memory complexity is almost optimal: our function can be evaluated using n steps and O(n/log(n)) memory, in each step making one query to the (fixed-input length) random oracle, while any algorithm that can make arbitrary many parallel queries to the random oracle, still needs Ω(n/log(n)) memory for Ω(n) steps.
As has been done for various notions (including cmc) before, we reduce the task of constructing an MHFs with high sustained-memory complexity to proving pebbling lower bounds on DAGs. Our main technical contribution is the construction is a family of DAGs on n nodes with constant indegree with high “sustained-space complexity”, meaning that any parallel black-pebbling strategy requires Ω(n/log(n)) pebbles for at least Ω(n) steps.
Along the way we construct a family of maximally “depth-robust” DAGs with maximum indegree O(logn) , improving upon the construction of Mahmoody et al. [ITCS’13] which had maximum indegree O(log2n⋅
AU - Alwen, Joel F
AU - Blocki, Jeremiah
AU - Pietrzak, Krzysztof Z
ID - 298
TI - Sustained space complexity
VL - 10821
ER -
TY - CONF
AB - We introduce in this paper AMT 2.0 , a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended Signal Temporal Logic (xSTL), which integrates Timed Regular Expressions (TRE) within Signal Temporal Logic (STL). The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal.
AU - Nickovic, Dejan
AU - Lebeltel, Olivier
AU - Maler, Oded
AU - Ferrere, Thomas
AU - Ulus, Dogan
ED - Beyer, Dirk
ED - Huisman, Marieke
ID - 299
TI - AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic
VL - 10806
ER -
TY - JOUR
AB - SETD5 gene mutations have been identified as a frequent cause of idiopathic intellectual disability. Here we show that Setd5-haploinsufficient mice present developmental defects such as abnormal brain-to-body weight ratios and neural crest defect-associated phenotypes. Furthermore, Setd5-mutant mice show impairments in cognitive tasks, enhanced long-term potentiation, delayed ontogenetic profile of ultrasonic vocalization, and behavioral inflexibility. Behavioral issues are accompanied by abnormal expression of postsynaptic density proteins previously associated with cognition. Our data additionally indicate that Setd5 regulates RNA polymerase II dynamics and gene transcription via its interaction with the Hdac3 and Paf1 complexes, findings potentially explaining the gene expression defects observed in Setd5-haploinsufficient mice. Our results emphasize the decisive role of Setd5 in a biological pathway found to be disrupted in humans with intellectual disability and autism spectrum disorder.
AU - Deliu, Elena
AU - Arecco, Niccoló
AU - Morandell, Jasmin
AU - Dotter, Christoph
AU - Contreras, Ximena
AU - Girardot, Charles
AU - Käsper, Eva
AU - Kozlova, Alena
AU - Kishi, Kasumi
AU - Chiaradia, Ilaria
AU - Noh, Kyung
AU - Novarino, Gaia
ID - 3
IS - 12
JF - Nature Neuroscience
TI - Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition
VL - 21
ER -
TY - CONF
AB - We introduce a formal quantitative notion of “bit security” for a general type of cryptographic games (capturing both decision and search problems), aimed at capturing the intuition that a cryptographic primitive with k-bit security is as hard to break as an ideal cryptographic function requiring a brute force attack on a k-bit key space. Our new definition matches the notion of bit security commonly used by cryptographers and cryptanalysts when studying search (e.g., key recovery) problems, where the use of the traditional definition is well established. However, it produces a quantitatively different metric in the case of decision (indistinguishability) problems, where the use of (a straightforward generalization of) the traditional definition is more problematic and leads to a number of paradoxical situations or mismatches between theoretical/provable security and practical/common sense intuition. Key to our new definition is to consider adversaries that may explicitly declare failure of the attack. We support and justify the new definition by proving a number of technical results, including tight reductions between several standard cryptographic problems, a new hybrid theorem that preserves bit security, and an application to the security analysis of indistinguishability primitives making use of (approximate) floating point numbers. This is the first result showing that (standard precision) 53-bit floating point numbers can be used to achieve 100-bit security in the context of cryptographic primitives with general indistinguishability-based security definitions. Previous results of this type applied only to search problems, or special types of decision problems.
AU - Micciancio, Daniele
AU - Walter, Michael
ID - 300
TI - On the bit security of cryptographic primitives
VL - 10820
ER -
TY - CONF
AB - At ITCS 2013, Mahmoody, Moran and Vadhan [MMV13] introduce and construct publicly verifiable proofs of sequential work, which is a protocol for proving that one spent sequential computational work related to some statement. The original motivation for such proofs included non-interactive time-stamping and universally verifiable CPU benchmarks. A more recent application, and our main motivation, are blockchain designs, where proofs of sequential work can be used – in combination with proofs of space – as a more ecological and economical substitute for proofs of work which are currently used to secure Bitcoin and other cryptocurrencies. The construction proposed by [MMV13] is based on a hash function and can be proven secure in the random oracle model, or assuming inherently sequential hash-functions, which is a new standard model assumption introduced in their work. In a proof of sequential work, a prover gets a “statement” χ, a time parameter N and access to a hash-function H, which for the security proof is modelled as a random oracle. Correctness requires that an honest prover can make a verifier accept making only N queries to H, while soundness requires that any prover who makes the verifier accept must have made (almost) N sequential queries to H. Thus a solution constitutes a proof that N time passed since χ was received. Solutions must be publicly verifiable in time at most polylogarithmic in N. The construction of [MMV13] is based on “depth-robust” graphs, and as a consequence has rather poor concrete parameters. But the major drawback is that the prover needs not just N time, but also N space to compute a proof. In this work we propose a proof of sequential work which is much simpler, more efficient and achieves much better concrete bounds. Most importantly, the space required can be as small as log (N) (but we get better soundness using slightly more memory than that). An open problem stated by [MMV13] that our construction does not solve either is achieving a “unique” proof, where even a cheating prover can only generate a single accepting proof. This property would be extremely useful for applications to blockchains.
AU - Cohen, Bram
AU - Pietrzak, Krzysztof Z
ID - 302
TI - Simple proofs of sequential work
VL - 10821
ER -
TY - JOUR
AB - The theory of tropical series, that we develop here, firstly appeared in the study of the growth of pluriharmonic functions. Motivated by waves in sandpile models we introduce a dynamic on the set of tropical series, and it is experimentally observed that this dynamic obeys a power law. So, this paper serves as a compilation of results we need for other articles and also introduces several objects interesting by themselves.
AU - Kalinin, Nikita
AU - Shkolnikov, Mikhail
ID - 303
IS - 6
JF - Discrete and Continuous Dynamical Systems- Series A
TI - Introduction to tropical series and wave dynamic on them
VL - 38
ER -
TY - JOUR
AB - Additive manufacturing has recently seen drastic improvements in resolution, making it now possible to fabricate features at scales of hundreds or even dozens of nanometers, which previously required very expensive lithographic methods.
As a result, additive manufacturing now seems poised for optical applications, including those relevant to computer graphics, such as material design, as well as display and imaging applications.
In this work, we explore the use of additive manufacturing for generating structural colors, where the structures are designed using a fabrication-aware optimization process.
This requires a combination of full-wave simulation, a feasible parameterization of the design space, and a tailored optimization procedure.
Many of these components should be re-usable for the design of other optical structures at this scale.
We show initial results of material samples fabricated based on our designs.
While these suffer from the prototype character of state-of-the-art fabrication hardware, we believe they clearly demonstrate the potential of additive nanofabrication for structural colors and other graphics applications.
AU - Auzinger, Thomas
AU - Heidrich, Wolfgang
AU - Bickel, Bernd
ID - 304
IS - 4
JF - ACM Transactions on Graphics
TI - Computational design of nanostructural color for additive manufacturing
VL - 37
ER -
TY - JOUR
AB - A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data.
AU - De Martino, Andrea
AU - De Martino, Daniele
ID - 306
IS - 4
JF - Heliyon
TI - An introduction to the maximum entropy approach and its application to inference problems in biology
VL - 4
ER -
TY - JOUR
AB - Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system.
AU - Redchenko, Elena
AU - Makarov, Alexander
AU - Yudson, Vladimir
ID - 307
IS - 4
JF - Physical Review A - Atomic, Molecular, and Optical Physics
TI - Nanoscopy of pairs of atoms by fluorescence in a magnetic field
VL - 97
ER -
TY - JOUR
AB - Migrating cells penetrate tissue barriers during development, inflammatory responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally confined environments requires changes in the mechanical properties of the surrounding cells using embryonic Drosophila melanogaster hemocytes, also called macrophages, as a model. We find that macrophage invasion into the germband through transient separation of the apposing ectoderm and mesoderm requires cell deformations and reductions in apical tension in the ectoderm. Interestingly, the genetic pathway governing these mechanical shifts acts downstream of the only known tumor necrosis factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald. Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated tight junction protein). We therefore elucidate a distinct molecular pathway that controls tissue tension and demonstrate the importance of such regulation for invasive migration in vivo.
AU - Ratheesh, Aparna
AU - Biebl, Julia
AU - Smutny, Michael
AU - Veselá, Jana
AU - Papusheva, Ekaterina
AU - Krens, Gabriel
AU - Kaufmann, Walter
AU - György, Attila
AU - Casano, Alessandra M
AU - Siekhaus, Daria E
ID - 308
IS - 3
JF - Developmental Cell
TI - Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration
VL - 45
ER -
TY - CONF
AB - We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ' : G ! M of a graph G into a 2manifold M maps the vertices in V (G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to a common node or arc, due to data compression or low resolution. This raises the computational problem of deciding whether a given map ' : G ! M comes from an embedding. A map ' : G ! M is a weak embedding if it can be perturbed into an embedding ψ: G ! M with k' "k < " for every " > 0. A polynomial-time algorithm for recognizing weak embeddings was recently found by Fulek and Kyncl [14], which reduces to solving a system of linear equations over Z2. It runs in O(n2!) O(n4:75) time, where 2:373 is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler than [14]: We perform a sequence of local operations that gradually "untangles" the image '(G) into an embedding (G), or reports that ' is not a weak embedding. It generalizes a recent technique developed for the case that G is a cycle and the embedding is a simple polygon [1], and combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.
AU - Akitaya, Hugo
AU - Fulek, Radoslav
AU - Tóth, Csaba
ID - 309
TI - Recognizing weak embeddings of graphs
ER -
TY - JOUR
AB - Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expected to be robust to changes in the stimulus ensemble. Despite the importance of this distinction for understanding how sensory networks encode information collectively, no method exists to reliably separate intrinsic interactions from extrinsic correlations in neural activity data, limiting our ability to build predictive models of the network response. In this paper we introduce a general strategy to infer population models of interacting neurons that collectively encode stimulus information. The key to disentangling intrinsic from extrinsic correlations is to infer the couplings between neurons separately from the encoding model and to combine the two using corrections calculated in a mean-field approximation. We demonstrate the effectiveness of this approach in retinal recordings. The same coupling network is inferred from responses to radically different stimulus ensembles, showing that these couplings indeed reflect stimulus-independent interactions between neurons. The inferred model predicts accurately the collective response of retinal ganglion cell populations as a function of the stimulus.
AU - Ferrari, Ulisse
AU - Deny, Stephane
AU - Chalk, Matthew J
AU - Tkacik, Gasper
AU - Marre, Olivier
AU - Mora, Thierry
ID - 31
IS - 4
JF - Physical Review E
SN - 24700045
TI - Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons
VL - 98
ER -
TY - JOUR
AB - Motivated by biological questions, we study configurations of equal spheres that neither pack nor cover. Placing their centers on a lattice, we define the soft density of the configuration by penalizing multiple overlaps. Considering the 1-parameter family of diagonally distorted 3-dimensional integer lattices, we show that the soft density is maximized at the FCC lattice.
AU - Edelsbrunner, Herbert
AU - Iglesias Ham, Mabel
ID - 312
IS - 1
JF - SIAM J Discrete Math
SN - 08954801
TI - On the optimality of the FCC lattice for soft sphere packing
VL - 32
ER -
TY - JOUR
AB - The interface of physics and biology pro-vides a fruitful environment for generatingnew concepts and exciting ways forwardto understanding living matter. Examplesof successful studies include the estab-lishment and readout of morphogen gra-dients during development, signal pro-cessing in protein and genetic networks,the role of ﬂuctuations in determining thefates of cells and tissues, and collectiveeffects in proteins and in tissues. It is nothard to envision that signiﬁcant further ad-vances will translate to societal beneﬁtsby initiating the development of new de-vices and strategies for curing disease.However, research at the interface posesvarious challenges, in particular for youngscientists, and current institutions arerarely designed to facilitate such scientiﬁcprograms. In this Letter, we propose aninternational initiative that addressesthese challenges through the establish-ment of a worldwide network of platformsfor cross-disciplinary training and incuba-tors for starting new collaborations.
AU - Bauer, Guntram
AU - Fakhri, Nikta
AU - Kicheva, Anna
AU - Kondev, Jané
AU - Kruse, Karsten
AU - Noji, Hiroyuki
AU - Riveline, Daniel
AU - Saunders, Timothy
AU - Thatta, Mukund
AU - Wieschaus, Eric
ID - 314
IS - 4
JF - Cell Systems
TI - The science of living matter for tomorrow
VL - 6
ER -
TY - JOUR
AB - More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.
AU - Polechova, Jitka
ID - 315
IS - 6
JF - PLoS Biology
SN - 15449173
TI - Is the sky the limit? On the expansion threshold of a species’ range
VL - 16
ER -
TY - JOUR
AB - We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack.
AU - Brauns, Matthias
AU - Amitonov, Sergey
AU - Spruijtenburg, Paul
AU - Zwanenburg, Floris
ID - 317
IS - 1
JF - Scientific Reports
TI - Palladium gates for reproducible quantum dots in silicon
VL - 8
ER -
TY - JOUR
AB - The insect’s fat body combines metabolic and immunological functions. In this issue of Developmental Cell, Franz et al. (2018) show that in Drosophila, cells of the fat body are not static, but can actively “swim” toward sites of epithelial injury, where they physically clog the wound and locally secrete antimicrobial peptides.
AU - Casano, Alessandra M
AU - Sixt, Michael K
ID - 318
IS - 4
JF - Developmental Cell
TI - A fat lot of good for wound healing
VL - 44
ER -
TY - JOUR
AB - The functional role of AMPA receptor (AMPAR)-mediated synaptic signaling between neurons and oligodendrocyte precursor cells (OPCs) remains enigmatic. We modified the properties of AMPARs at axon-OPC synapses in the mouse corpus callosum in vivo during the peak of myelination by targeting the GluA2 subunit. Expression of the unedited (Ca2+ permeable) or the pore-dead GluA2 subunit of AMPARs triggered proliferation of OPCs and reduced their differentiation into oligodendrocytes. Expression of the cytoplasmic C-terminal (GluA2(813-862)) of the GluA2 subunit (C-tail), a modification designed to affect the interaction between GluA2 and AMPAR-binding proteins and to perturb trafficking of GluA2-containing AMPARs, decreased the differentiation of OPCs without affecting their proliferation. These findings suggest that ionotropic and non-ionotropic properties of AMPARs in OPCs, as well as specific aspects of AMPAR-mediated signaling at axon-OPC synapses in the mouse corpus callosum, are important for balancing the response of OPCs to proliferation and differentiation cues. In the brain, oligodendrocyte precursor cells (OPCs) receive glutamatergic AMPA-receptor-mediated synaptic input from neurons. Chen et al. show that modifying AMPA-receptor properties at axon-OPC synapses alters proliferation and differentiation of OPCs. This expands the traditional view of synaptic transmission by suggesting neurons also use synapses to modulate behavior of glia.
AU - Chen, Ting
AU - Kula, Bartosz
AU - Nagy, Balint
AU - Barzan, Ruxandra
AU - Gall, Andrea
AU - Ehrlich, Ingrid
AU - Kukley, Maria
ID - 32
IS - 4
JF - Cell Reports
TI - In Vivo regulation of Oligodendrocyte processor cell proliferation and differentiation by the AMPA-receptor Subunit GluA2
VL - 25
ER -
TY - JOUR
AB - Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express a complex machinery of rapid signaling mechanisms, including specialized voltage-gated ion channels to generate brief action potentials (APs). However, short APs are associated with overlapping Na+ and K+ fluxes and are therefore energetically expensive. How the potentially vicious combination of high AP frequency and inefficient spike generation can be reconciled with limited energy supply is presently unclear. To address this question, we performed direct recordings from the PV+-BC axon, the subcellular structure where active conductances for AP initiation and propagation are located. Surprisingly, the energy required for the AP was, on average, only ∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels, which minimized ion flux overlap during APs. Thus, the complementary tuning of axonal Na+ and K+ channel gating optimizes both fast signaling properties and metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing GABAergic interneuron axons are energetically efficient, which is highly unexpected given their brief duration. High energy efficiency emerges from the combination of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3 channels in the axon.
AU - Hu, Hua
AU - Roth, Fabian
AU - Vandael, David H
AU - Jonas, Peter M
ID - 320
IS - 1
JF - Neuron
TI - Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons
VL - 98
ER -
TY - JOUR
AB - The twelve papers in this special section focus on learning systems with shared information for computer vision and multimedia communication analysis. In the real world, a realistic setting for computer vision or multimedia recognition problems is that we have some classes containing lots of training data and many classes containing a small amount of training data. Therefore, how to use frequent classes to help learning rare classes for which it is harder to collect the training data is an open question. Learning with shared information is an emerging topic in machine learning, computer vision and multimedia analysis. There are different levels of components that can be shared during concept modeling and machine learning stages, such as sharing generic object parts, sharing attributes, sharing transformations, sharing regularization parameters and sharing training examples, etc. Regarding the specific methods, multi-task learning, transfer learning and deep learning can be seen as using different strategies to share information. These learning with shared information methods are very effective in solving real-world large-scale problems.
AU - Darrell, Trevor
AU - Lampert, Christoph
AU - Sebe, Nico
AU - Wu, Ying
AU - Yan, Yan
ID - 321
IS - 5
JF - IEEE Transactions on Pattern Analysis and Machine Intelligence
TI - Guest editors' introduction to the special section on learning with Shared information for computer vision and multimedia analysis
VL - 40
ER -
TY - JOUR
AB - We construct quantizations of multiplicative hypertoric varieties using an algebra of q-difference operators on affine space, where q is a root of unity in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the multiplicative hypertoric variety and admits an explicit finite étale splitting. The global sections of this Azumaya algebra is a hypertoric quantum group, and we prove a localization theorem. We introduce a general framework of Frobenius quantum moment maps and their Hamiltonian reductions; our results shed light on an instance of this framework.
AU - Ganev, Iordan V
ID - 322
JF - Journal of Algebra
TI - Quantizations of multiplicative hypertoric varieties at a root of unity
VL - 506
ER -
TY - THES
AB - Neuronal networks in the brain consist of two main types of neuron, glutamatergic principal neurons and GABAergic interneurons. Although these interneurons only represent 10–20% of the whole population, they mediate feedback and feedforward inhibition and are involved in the generation of high-frequency network oscillations. A hallmark functional property of GABAergic interneurons, especially of the parvalbumin‑expressing (PV+) subtypes, is the speed of signaling at their output synapse across species and brain regions. Several molecular and subcellular factors may underlie the submillisecond signaling at GABAergic synapses. Such as the selective use of P/Q type Ca2+ channels and the tight coupling between Ca2+ channels and Ca2+ sensors of exocytosis. However, whether the molecular identity of the release sensor contributes to these signaling properties remains unclear. Besides, these interneurons are mainly show depression in response to train of stimuli. How could they keep sufficient release to control the activity of postsynaptic principal neurons during high network activity, is largely elusive. For my Ph.D. work, we firstly examined the Ca2+ sensor of exocytosis at the GABAergic basket cell (BC) to Purkinje cell (PC) synapse in the cerebellum. Immunolabeling suggested that BC terminals selectively expressed synaptotagmin 2 (Syt2), whereas synaptotagmin 1 (Syt1) was enriched in excitatory terminals. Genetic elimination of Syt2 reduced action potential-evoked release to ~10% compared to the wild-type control, identifying Syt2 as the major Ca2+ sensor at BC‑PC synapses. Differential adenovirus-mediated rescue revealed Syt2 triggered release with shorter latency and higher temporal precision, and mediated faster vesicle pool replenishment than Syt1. Furthermore, deletion of Syt2 severely reduced and delayed disynaptic inhibition following parallel fiber stimulation. Thus, the selective use of Syt2 as the release sensor at BC–PC synapse ensures fast feedforward inhibition in cerebellar microcircuits. Additionally, we tested the function of another synaptotagmin member, Syt7, for inhibitory synaptic transmission at the BC–PC synapse. Syt7 is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, it is strongly expressed in fast-spiking, PV+ GABAergic interneurons and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. How could Syt7, a facilitation sensor, contribute to the depressed inhibitory synaptic transmission needs to be further investigated and understood. Our results indicated that at the BC–PC synapse, Syt7 contributes to asynchronous release, pool replenishment and facilitation. In combination, these three effects ensure efficient transmitter release during high‑frequency activity and guarantee frequency independence of inhibition. Taken together, our results confirmed that Syt2, which has the fastest kinetic properties among all synaptotagmin members, is mainly used by the inhibitory BC‑PC synapse for synaptic transmission, contributing to the speed and temporal precision of transmitter release. Furthermore, we showed that Syt7, another highly expressed synaptotagmin member in the output synapses of cerebellar BCs, is used for ensuring efficient inhibitor synaptic transmission during high activity.
AU - Chen, Chong
ID - 324
TI - Synaptotagmins ensure speed and efficiency of inhibitory neurotransmitter release
ER -
TY - CONF
AB - Probabilistic programs extend classical imperative programs with real-valued random variables and random branching. The most basic liveness property for such programs is the termination property. The qualitative (aka almost-sure) termination problem asks whether a given program program terminates with probability 1. While ranking functions provide a sound and complete method for non-probabilistic programs, the extension of them to probabilistic programs is achieved via ranking supermartingales (RSMs). Although deep theoretical results have been established about RSMs, their application to probabilistic programs with nondeterminism has been limited only to programs of restricted control-flow structure. For non-probabilistic programs, lexicographic ranking functions provide a compositional and practical approach for termination analysis of real-world programs. In this work we introduce lexicographic RSMs and show that they present a sound method for almost-sure termination of probabilistic programs with nondeterminism. We show that lexicographic RSMs provide a tool for compositional reasoning about almost-sure termination, and for probabilistic programs with linear arithmetic they can be synthesized efficiently (in polynomial time). We also show that with additional restrictions even asymptotic bounds on expected termination time can be obtained through lexicographic RSMs. Finally, we present experimental results on benchmarks adapted from previous work to demonstrate the effectiveness of our approach.
AU - Agrawal, Sheshansh
AU - Chatterjee, Krishnendu
AU - Novotny, Petr
ID - 325
IS - POPL
TI - Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs
VL - 2
ER -
TY - JOUR
AB - Three-dimensional (3D) super-resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID-treated slices, and 160-nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)-treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high-NA confocal imaging. Thus, super-resolution SIM imaging represents a promising high-throughput method for revealing spine morphologies in single dendrites.
AU - Sawada, Kazuaki
AU - Kawakami, Ryosuke
AU - Shigemoto, Ryuichi
AU - Nemoto, Tomomi
ID - 326
IS - 9
JF - European Journal of Neuroscience
TI - Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices
VL - 47
ER -
TY - JOUR
AB - Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations.
AU - Michailidis, Alexios
AU - Žnidarič, Marko
AU - Medvedyeva, Mariya
AU - Abanin, Dmitry
AU - Prosen, Tomaž
AU - Papić, Zlatko
ID - 327
IS - 10
JF - Physical Review B
TI - Slow dynamics in translation-invariant quantum lattice models
VL - 97
ER -
TY - JOUR
AB - The drag of turbulent flows can be drastically decreased by adding small amounts of high molecular weight polymers. While drag reduction initially increases with polymer concentration, it eventually saturates to what is known as the maximum drag reduction (MDR) asymptote; this asymptote is generally attributed to the dynamics being reduced to a marginal yet persistent state of subdued turbulent motion. Contrary to this accepted view, we show that, for an appropriate choice of parameters, polymers can reduce the drag beyond the suggested asymptotic limit, eliminating turbulence and giving way to laminar flow. At higher polymer concentrations, however, the laminar state becomes unstable, resulting in a fluctuating flow with the characteristic drag of the MDR asymptote. Our findings indicate that the asymptotic state is hence dynamically disconnected from ordinary turbulence. © 2018 American Physical Society.
AU - Choueiri, George H
AU - Lopez Alonso, Jose M
AU - Hof, Björn
ID - 328
IS - 12
JF - Physical Review Letters
TI - Exceeding the asymptotic limit of polymer drag reduction
VL - 120
ER -
TY - JOUR
AB - Secondary contact is the reestablishment of gene flow between sister populations that have diverged. For instance, at the end of the Quaternary glaciations in Europe, secondary contact occurred during the northward expansion of the populations which had found refugia in the southern peninsulas. With the advent of multi-locus markers, secondary contact can be investigated using various molecular signatures including gradients of allele frequency, admixture clines, and local increase of genetic differentiation. We use coalescent simulations to investigate if molecular data provide enough information to distinguish between secondary contact following range expansion and an alternative evolutionary scenario consisting of a barrier to gene flow in an isolation-by-distance model. We find that an excess of linkage disequilibrium and of genetic diversity at the suture zone is a unique signature of secondary contact. We also find that the directionality index ψ, which was proposed to study range expansion, is informative to distinguish between the two hypotheses. However, although evidence for secondary contact is usually conveyed by statistics related to admixture coefficients, we find that they can be confounded by isolation-by-distance. We recommend to account for the spatial repartition of individuals when investigating secondary contact in order to better reflect the complex spatio-temporal evolution of populations and species.
AU - Bertl, Johanna
AU - Ringbauer, Harald
AU - Blum, Michaël
ID - 33
IS - 10
JF - PeerJ
TI - Can secondary contact following range expansion be distinguished from barriers to gene flow?
VL - 2018
ER -
TY - CONF
AB - Partially observable Markov decision processes (POMDPs) are widely used in probabilistic planning problems in which an agent interacts with an environment using noisy and imprecise sensors. We study a setting in which the sensors are only partially defined and the goal is to synthesize “weakest” additional sensors, such that in the resulting POMDP, there is a small-memory policy for the agent that almost-surely (with probability 1) satisfies a reachability objective. We show that the problem is NP-complete, and present a symbolic algorithm by encoding the problem into SAT instances. We illustrate trade-offs between the amount of memory of the policy and the number of additional sensors on a simple example. We have implemented our approach and consider three classical POMDP examples from the literature, and show that in all the examples the number of sensors can be significantly decreased (as compared to the existing solutions in the literature) without increasing the complexity of the policies.
AU - Chatterjee, Krishnendu
AU - Chemlík, Martin
AU - Topcu, Ufuk
ID - 34
TI - Sensor synthesis for POMDPs with reachability objectives
VL - 2018
ER -
TY - GEN
AB - The Drosophila Genetic Reference Panel (DGRP) serves as a valuable resource to better understand the genetic landscapes underlying quantitative traits. However, such DGRP studies have so far only focused on nuclear genetic variants. To address this, we sequenced the mitochondrial genomes of >170 DGRP lines, identifying 229 variants including 21 indels and 7 frameshifts. We used our mitochondrial variation data to identify 12 genetically distinct mitochondrial haplotypes, thus revealing important population structure at the mitochondrial level. We further examined whether this population structure was reflected on the nuclear genome by screening for the presence of potential mito-nuclear genetic incompatibilities in the form of significant genotype ratio distortions (GRDs) between mitochondrial and nuclear variants. In total, we detected a remarkable 1,845 mito-nuclear GRDs, with the highest enrichment observed in a 40 kb region around the gene Sex-lethal (Sxl). Intriguingly, downstream phenotypic analyses did not uncover major fitness effects associated with these GRDs, suggesting that a large number of mito-nuclear GRDs may reflect population structure at the mitochondrial level rather than actual genomic incompatibilities. This is further supported by the GRD landscape showing particular large genomic regions associated with a single mitochondrial haplotype. Next, we explored the functional relevance of the detected mitochondrial haplotypes through an association analysis on a set of 259 assembled, non-correlating DGRP phenotypes. We found multiple significant associations with stress- and metabolism-related phenotypes, including food intake in males. We validated the latter observation by reciprocal swapping of mitochondrial genomes from high food intake DGRP lines to low food intake ones. In conclusion, our study uncovered important mitochondrial population structure and haplotype-specific metabolic variation in the DGRP, thus demonstrating the significance of incorporating mitochondrial haplotypes in geno-phenotype relationship studies.
AU - Bevers, Roel P.J.
AU - Litovchenko, Maria
AU - Kapopoulou, Adamandia
AU - Braman, Virginie S.
AU - Robinson, Matthew Richard
AU - Auwerx, Johan
AU - Hollis, Brian
AU - Deplancke, Bart
ID - 7783
T2 - bioRxiv
TI - Extensive mitochondrial population structure and haplotype-specific phenotypic variation in the Drosophila Genetic Reference Panel
ER -
TY - CONF
AB - We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated.
AU - Bakhirkin, Alexey
AU - Ferrere, Thomas
AU - Nickovic, Dejan
AU - Maler, Oded
AU - Asarin, Eugene
ID - 78
SN - 978-3-030-00150-6
TI - Online timed pattern matching using automata
VL - 11022
ER -
TY - CONF
AB - Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices.
AU - Polino, Antonio
AU - Pascanu, Razvan
AU - Alistarh, Dan-Adrian
ID - 7812
T2 - 6th International Conference on Learning Representations
TI - Model compression via distillation and quantization
ER -
TY - CONF
AB - Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol.
AU - Arming, Sebastian
AU - Bartocci, Ezio
AU - Chatterjee, Krishnendu
AU - Katoen, Joost P
AU - Sokolova, Ana
ID - 79
TI - Parameter-independent strategies for pMDPs via POMDPs
VL - 11024
ER -
TY - JOUR
AB - Feste Alkalicarbonate sind universelle Bestandteile von Passivierungsschichten an Materialien für Interkalationsbatterien, übliche Nebenprodukte in Metall‐O2‐Batterien, und es wird angenommen, dass sie sich reversibel in Metall‐O2 /CO2‐Zellen bilden und zersetzen. In all diesen Kathoden zersetzt sich Li2CO3 zu CO2, sobald es Spannungen >3.8 V vs. Li/Li+ ausgesetzt wird. Beachtenswert ist, dass keine O2‐Entwicklung detektiert wird, wie gemäß der Zersetzungsreaktion 2 Li2CO3 → 4 Li+ + 4 e− + 2 CO2 + O2 zu erwarten wäre. Deswegen war der Verbleib eines der O‐Atome ungeklärt und wurde nicht identifizierten parasitären Reaktionen zugerechnet. Hier zeigen wir, dass hochreaktiver Singulett‐Sauerstoff (1O2) bei der Oxidation von Li2CO3 in einem aprotischen Elektrolyten gebildet und daher nicht als O2 freigesetzt wird. Diese Ergebnisse haben weitreichende Auswirkungen auf die langfristige Zyklisierbarkeit von Batterien: sie untermauern die Wichtigkeit, 1O2 in Metall‐O2‐Batterien zu verhindern, stellen die Möglichkeit einer reversiblen Metall‐O2 /CO2‐Batterie basierend auf einem Carbonat‐Entladeprodukt in Frage und helfen, Grenzflächenreaktivität von Übergangsmetallkathoden mit Li2CO3‐Resten zu erklären.
AU - Mahne, Nika
AU - Renfrew, Sara E.
AU - McCloskey, Bryan D.
AU - Freunberger, Stefan Alexander
ID - 7983
IS - 19
JF - Angewandte Chemie
SN - 0044-8249
TI - Elektrochemische Oxidation von Lithiumcarbonat generiert Singulett-Sauerstoff
VL - 130
ER -
TY - JOUR
AB - The neural code of cortical processing remains uncracked; however, it must necessarily rely on faithful signal propagation between cortical areas. In this issue of Neuron, Joglekar et al. (2018) show that strong inter-areal excitation balanced by local inhibition can enable reliable signal propagation in data-constrained network models of macaque cortex.
AU - Stroud, Jake P.
AU - Vogels, Tim P
ID - 8015
IS - 1
JF - Neuron
SN - 0896-6273
TI - Cortical signal propagation: Balance, amplify, transmit
VL - 98
ER -
TY - JOUR
AB - Motor cortex (M1) exhibits a rich repertoire of neuronal activities to support the generation of complex movements. Although recent neuronal-network models capture many qualitative aspects of M1 dynamics, they can generate only a few distinct movements. Additionally, it is unclear how M1 efficiently controls movements over a wide range of shapes and speeds. We demonstrate that modulation of neuronal input–output gains in recurrent neuronal-network models with a fixed architecture can dramatically reorganize neuronal activity and thus downstream muscle outputs. Consistent with the observation of diffuse neuromodulatory projections to M1, a relatively small number of modulatory control units provide sufficient flexibility to adjust high-dimensional network activity using a simple reward-based learning rule. Furthermore, it is possible to assemble novel movements from previously learned primitives, and one can separately change movement speed while preserving movement shape. Our results provide a new perspective on the role of modulatory systems in controlling recurrent cortical activity.
AU - Stroud, Jake P.
AU - Porter, Mason A.
AU - Hennequin, Guillaume
AU - Vogels, Tim P
ID - 8073
IS - 12
JF - Nature Neuroscience
SN - 1097-6256
TI - Motor primitives in space and time via targeted gain modulation in cortical networks
VL - 21
ER -
TY - CONF
AB - We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring,
AU - Elgyütt, Adrian
AU - Ferrere, Thomas
AU - Henzinger, Thomas A
ID - 81
TI - Monitoring temporal logic with clock variables
VL - 11022
ER -
TY - JOUR
AB - In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”.
AU - Chaudhry, Waqas
AU - Pleska, Maros
AU - Shah, Nilang
AU - Weiss, Howard
AU - Mccall, Ingrid
AU - Meyer, Justin
AU - Gupta, Animesh
AU - Guet, Calin C
AU - Levin, Bruce
ID - 82
IS - 8
JF - PLoS Biology
TI - Leaky resistance and the conditions for the existence of lytic bacteriophage
VL - 16
ER -
TY - JOUR
AU - Fazekas-Singer, Judit
AU - Singer, Josef
AU - Ilieva, Kristina M.
AU - Matz, Miroslawa
AU - Herrmann, Ina
AU - Spillner, Edzard
AU - Karagiannis, Sophia N.
AU - Jensen-Jarolim, Erika
ID - 8231
IS - 3
JF - Journal of Allergy and Clinical Immunology
SN - 0091-6749
TI - AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor
VL - 142
ER -
TY - JOUR
AB - Anti-epidermal growth factor receptor (EGFR) antibody therapy is used in EGFR expressing cancers including lung, colon, head and neck, and bladder cancers, however results have been modest. Near infrared photoimmunotherapy (NIR-PIT) is a highly selective tumor treatment that employs an antibody-photo-absorber conjugate which is activated by NIR light. NIR-PIT is in clinical trials in patients with recurrent head and neck cancers using cetuximab-IR700 as the conjugate. However, its use has otherwise been restricted to mouse models. This is an effort to explore larger animal models with NIR-PIT. We describe the use of a recombinant canine anti-EGFR monoclonal antibody (mAb), can225IgG, conjugated to the photo-absorber, IR700DX, in three EGFR expressing canine transitional cell carcinoma (TCC) cell lines as a prelude to possible canine clinical studies. Can225-IR700 conjugate showed specific binding and cell-specific killing after NIR-PIT on EGFR expressing cells in vitro. In the in vivo study, can225-IR700 conjugate demonstrated accumulation of the fluorescent conjugate with high tumor-to-background ratio. Tumor-bearing mice were separated into 4 groups: (1) no treatment; (2) 100 μg of can225-IR700 i.v. only; (3) NIR light exposure only; (4) 100 μg of can225-IR700 i.v., NIR light exposure. Tumor growth was significantly inhibited by NIR-PIT treatment compared with the other groups (p < 0.001), and significantly prolonged survival was achieved (p < 0.001 vs. other groups) in the treatment groups. In conclusion, NIR-PIT with can225-IR700 is a promising treatment for canine EGFR-expressing cancers, including invasive transitional cell carcinoma in pet dogs, that could provide a pathway to translation to humans.
AU - Nagaya, Tadanobu
AU - Okuyama, Shuhei
AU - Ogata, Fusa
AU - Maruoka, Yasuhiro
AU - Knapp, Deborah W.
AU - Karagiannis, Sophia N.
AU - Fazekas-Singer, Judit
AU - Choyke, Peter L.
AU - LeBlanc, Amy K.
AU - Jensen-Jarolim, Erika
AU - Kobayashi, Hisataka
ID - 8232
JF - Oncotarget
TI - Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody
VL - 9
ER -
TY - JOUR
AB - The M2a subtype of macrophages plays an important role in human immunoglobulin E (IgE-mediated allergies) and other Th2 type immune reactions. In contrast, very little is known about these cells in the dog. Here we describe an in vitro method to activate canine histiocytic DH82 cells and primary canine monocyte-derived macrophages (MDMs) toward the M2a macrophages using human cytokines. For a side-by-side comparison, we compared the canine cells to human MDMs, and the human monocytic cell line U937 activated towards M1 and M2a cells on the cellular and molecular level. In analogy to activated human M2a cells, canine M2a, differentiated from both DH82 and MDMs, showed an increase in CD206 surface receptor expression compared to M1. Interestingly, canine M2a, but not M1 derived from MDM, upregulated the high-affinity IgE receptor (FcεRI). Transcription levels of M2a-associated genes (IL10, CCL22, TGFβ, CD163) showed a diverse pattern between the human and dog species, whereas M1 genes (IDO1, CXCL11, IL6, TNF-α) were similarly upregulated in canine and human M1 cells (cell lines and MDMs). We suggest that our novel in vitro method will be suitable in comparative allergology studies focussing on macrophages.
AU - Herrmann, Ina
AU - Gotovina, Jelena
AU - Fazekas-Singer, Judit
AU - Fischer, Michael B.
AU - Hufnagl, Karin
AU - Bianchini, Rodolfo
AU - Jensen-Jarolim, Erika
ID - 8233
IS - 5
JF - Developmental & Comparative Immunology
SN - 0145-305X
TI - Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy
VL - 82
ER -
TY - JOUR
AB - Molecular imaging probes such as PET-tracers have the potential to improve the accuracy of tumor characterization by directly visualizing the biochemical situation. Thus, molecular changes can be detected early before morphological manifestation. The A3 adenosine receptor (A3AR) is described to be highly expressed in colon cancer cell lines and human colorectal cancer (CRC), suggesting this receptor as a tumor marker. The aim of this preclinical study was the evaluation of FE@SUPPY as a PET-tracer for CRC using in vitro imaging and in vivo PET imaging. First, affinity and selectivity of FE@SUPPY and its metabolites were determined, proving the favorable binding profile of FE@SUPPY. The human adenocarcinoma cell line HT-29 was characterized regarding its hA3AR expression and was subsequently chosen as tumor graft. Promising results regarding the potential of FE@SUPPY as a PET-tracer for CRC imaging were obtained by autoradiography as ≥2.3-fold higher accumulation of FE@SUPPY was found in CRC tissue compared to adjacent healthy colon tissue from the same patient. Nevertheless, first in vivo studies using HT-29 xenografts showed insufficient tumor uptake due to (1) poor conservation of target expression in xenografts and (2) unfavorable pharmacokinetics of FE@SUPPY in mice. We therefore conclude that HT-29 xenografts are not adequate to visualize hA3ARs using FE@SUPPY.
AU - Balber, T.
AU - Singer, Judit
AU - Berroterán-Infante, N.
AU - Dumanic, M.
AU - Fetty, L.
AU - Fazekas-Singer, J.
AU - Vraka, C.
AU - Nics, L.
AU - Bergmann, M.
AU - Pallitsch, K.
AU - Spreitzer, H.
AU - Wadsak, W.
AU - Hacker, M.
AU - Jensen-Jarolim, E.
AU - Viernstein, H.
AU - Mitterhauser, M.
ID - 8234
JF - Contrast Media & Molecular Imaging
SN - 1555-4309
TI - Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer
VL - 2018
ER -
TY - JOUR
AB - Background: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.
Results: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.
Conclusions: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.
AU - Bochkareva, Olga
AU - Moroz, Elena V.
AU - Davydov, Iakov I.
AU - Gelfand, Mikhail S.
ID - 8262
JF - BMC Genomics
SN - 1471-2164
TI - Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.
VL - 19
ER -
TY - JOUR
AB - Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content.
AU - Bochkareva, Olga
AU - Dranenko, Natalia O.
AU - Ocheredko, Elena S.
AU - Kanevsky, German M.
AU - Lozinsky, Yaroslav N.
AU - Khalaycheva, Vera A.
AU - Artamonova, Irena I.
AU - Gelfand, Mikhail S.
ID - 8265
JF - PeerJ
SN - 2167-8359
TI - Genome rearrangements and phylogeny reconstruction in Yersinia pestis
VL - 6
ER -
TY - CONF
AB - Designing a secure permissionless distributed ledger (blockchain) that performs on par with centralized payment
processors, such as Visa, is a challenging task. Most existing distributed ledgers are unable to scale-out, i.e., to grow their totalprocessing capacity with the number of validators; and those that do, compromise security or decentralization. We present OmniLedger, a novel scale-out distributed ledger that preserves longterm security under permissionless operation. It ensures security and correctness by using a bias-resistant public-randomness protocol for choosing large, statistically representative shards that process transactions, and by introducing an efficient crossshard commit protocol that atomically handles transactions affecting multiple shards. OmniLedger also optimizes performance via parallel intra-shard transaction processing, ledger pruning via collectively-signed state blocks, and low-latency “trust-butverify”
validation for low-value transactions. An evaluation ofour experimental prototype shows that OmniLedger’s throughput
scales linearly in the number of active validators, supporting Visa-level workloads and beyond, while confirming typical transactions in under two seconds.
AU - Kokoris Kogias, Eleftherios
AU - Jovanovic, Philipp
AU - Gasser, Linus
AU - Gailly, Nicolas
AU - Syta, Ewa
AU - Ford, Bryan
ID - 8297
SN - 2375-1207
T2 - 2018 IEEE Symposium on Security and Privacy
TI - OmniLedger: A secure, scale-out, decentralized ledger via sharding
ER -
TY - THES
AB - A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.
Proofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds.
AU - Abusalah, Hamza M
ID - 83
TI - Proof systems for sustainable decentralized cryptocurrencies
ER -
TY - JOUR
AB - We show that in the space of all convex billiard boundaries, the set of boundaries with rational caustics is dense. More precisely, the set of billiard boundaries with caustics of rotation number 1/q is polynomially sense in the smooth case, and exponentially dense in the analytic case.
AU - Kaloshin, Vadim
AU - Zhang, Ke
ID - 8420
IS - 11
JF - Nonlinearity
KW - Mathematical Physics
KW - General Physics and Astronomy
KW - Applied Mathematics
KW - Statistical and Nonlinear Physics
SN - 0951-7715
TI - Density of convex billiards with rational caustics
VL - 31
ER -
TY - JOUR
AB - The classical Birkhoff conjecture claims that the boundary of a strictly convex integrable billiard table is necessarily an ellipse (or a circle as a special case). In this article we prove a complete local version of this conjecture: a small integrable perturbation of an ellipse must be an ellipse. This extends and completes the result in Avila-De Simoi-Kaloshin, where nearly circular domains were considered. One of the crucial ideas in the proof is to extend action-angle coordinates for elliptic billiards into complex domains (with respect to the angle), and to thoroughly analyze the nature of their complex singularities. As an application, we are able to prove some spectral rigidity results for elliptic domains.
AU - Kaloshin, Vadim
AU - Sorrentino, Alfonso
ID - 8421
IS - 1
JF - Annals of Mathematics
KW - Statistics
KW - Probability and Uncertainty
KW - Statistics and Probability
SN - 0003-486X
TI - On the local Birkhoff conjecture for convex billiards
VL - 188
ER -
TY - JOUR
AB - The Birkhoff conjecture says that the boundary of a strictly convex integrable billiard table is necessarily an ellipse. In this article, we consider a stronger notion of integrability, namely integrability close to the boundary, and prove a local version of this conjecture: a small perturbation of an ellipse of small eccentricity which preserves integrability near the boundary, is itself an ellipse. This extends the result in Avila et al. (Ann Math 184:527–558, ADK16), where integrability was assumed on a larger set. In particular, it shows that (local) integrability near the boundary implies global integrability. One of the crucial ideas in the proof consists in analyzing Taylor expansion of the corresponding action-angle coordinates with respect to the eccentricity parameter, deriving and studying higher order conditions for the preservation of integrable rational caustics.
AU - Huang, Guan
AU - Kaloshin, Vadim
AU - Sorrentino, Alfonso
ID - 8422
IS - 2
JF - Geometric and Functional Analysis
KW - Geometry and Topology
KW - Analysis
SN - 1016-443X
TI - Nearly circular domains which are integrable close to the boundary are ellipses
VL - 28
ER -
TY - JOUR
AB - For any strictly convex planar domain Ω ⊂ R2 with a C∞ boundary one can associate an infinite sequence of spectral invariants introduced by Marvizi–Merlose [5]. These invariants can generically be determined using the spectrum of the Dirichlet problem of the Laplace operator. A natural question asks if this collection is sufficient to determine Ω up to isometry. In this paper we give a counterexample, namely, we present two nonisometric domains Ω and Ω¯ with the same collection of Marvizi–Melrose invariants. Moreover, each domain has countably many periodic orbits {Sn}n≥1 (resp. {S¯n}n⩾1) of period going to infinity such that Sn and S¯n have the same period and perimeter for each n.
AU - Buhovsky, Lev
AU - Kaloshin, Vadim
ID - 8426
JF - Regular and Chaotic Dynamics
SN - 1560-3547
TI - Nonisometric domains with the same Marvizi-Melrose invariants
VL - 23
ER -
TY - CONF
AB - Concurrent accesses to shared data structures must be synchronized to avoid data races. Coarse-grained synchronization, which locks the entire data structure, is easy to implement but does not scale. Fine-grained synchronization can scale well, but can be hard to reason about. Hand-over-hand locking, in which operations are pipelined as they traverse the data structure, combines fine-grained synchronization with ease of use. However, the traditional implementation suffers from inherent overheads. This paper introduces snapshot-based synchronization (SBS), a novel hand-over-hand locking mechanism. SBS decouples the synchronization state from the data, significantly improving cache utilization. Further, it relies on guarantees provided by pipelining to minimize synchronization that requires cross-thread communication. Snapshot-based synchronization thus scales much better than traditional hand-over-hand locking, while maintaining the same ease of use.
AU - Gilad, Eran
AU - Brown, Trevor A
AU - Oskin, Mark
AU - Etsion, Yoav
ID - 85
SN - 03029743
TI - Snapshot based synchronization: A fast replacement for Hand-over-Hand locking
VL - 11014
ER -
TY - GEN
AB - The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex.
AU - Llorca, Alfredo
AU - Ciceri, Gabriele
AU - Beattie, Robert J
AU - Wong, Fong K.
AU - Diana, Giovanni
AU - Serafeimidou, Eleni
AU - Fernández-Otero, Marian
AU - Streicher, Carmen
AU - Arnold, Sebastian J.
AU - Meyer, Martin
AU - Hippenmeyer, Simon
AU - Maravall, Miguel
AU - Marín, Oscar
ID - 8547
T2 - bioRxiv
TI - Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture
ER -
TY - CHAP
AB - Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms.
AU - Chatterjee, Krishnendu
AU - Henzinger, Thomas A
AU - Otop, Jan
ED - Lohstroh, Marten
ED - Derler, Patricia
ED - Sirjani, Marjan
ID - 86
T2 - Principles of Modeling
TI - Computing average response time
VL - 10760
ER -
TY - JOUR
AB - The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting.
AU - Gregor, Carola
AU - Sidenstein, Sven C.
AU - Andresen, Martin
AU - Sahl, Steffen J.
AU - Danzl, Johann G
AU - Hell, Stefan W.
ID - 8618
JF - Scientific Reports
KW - Multidisciplinary
SN - 2045-2322
TI - Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA
VL - 8
ER -
TY - JOUR
AB - The rapid auxin-triggered growth of the Arabidopsis hypocotyls involves the nuclear TIR1/AFB-Aux/IAA signaling and is accompanied by acidification of the apoplast and cell walls (Fendrych et al., 2016). Here, we describe in detail the method for analysis of the elongation and the TIR1/AFB-Aux/IAA-dependent auxin response in hypocotyl segments as well as the determination of relative values of the cell wall pH.
AU - Li, Lanxin
AU - Krens, Gabriel
AU - Fendrych, Matyas
AU - Friml, Jirí
ID - 442
IS - 1
JF - Bio-protocol
TI - Real-time analysis of auxin response, cell wall pH and elongation in Arabidopsis thaliana Hypocotyls
VL - 8
ER -
TY - JOUR
AB - We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z > 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential.
AU - Frank, Rupert
AU - Phan Thanh, Nam
AU - Van Den Bosch, Hanne
ID - 446
IS - 3
JF - Communications on Pure and Applied Mathematics
TI - The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory
VL - 71
ER -
TY - JOUR
AB - Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.
AU - Harrison, Mark
AU - Jongepier, Evelien
AU - Robertson, Hugh
AU - Arning, Nicolas
AU - Bitard Feildel, Tristan
AU - Chao, Hsu
AU - Childers, Christopher
AU - Dinh, Huyen
AU - Doddapaneni, Harshavardhan
AU - Dugan, Shannon
AU - Gowin, Johannes
AU - Greiner, Carolin
AU - Han, Yi
AU - Hu, Haofu
AU - Hughes, Daniel
AU - Huylmans, Ann K
AU - Kemena, Karsten
AU - Kremer, Lukas
AU - Lee, Sandra
AU - López Ezquerra, Alberto
AU - Mallet, Ludovic
AU - Monroy Kuhn, Jose
AU - Moser, Annabell
AU - Murali, Shwetha
AU - Muzny, Donna
AU - Otani, Saria
AU - Piulachs, Maria
AU - Poelchau, Monica
AU - Qu, Jiaxin
AU - Schaub, Florentine
AU - Wada Katsumata, Ayako
AU - Worley, Kim
AU - Xie, Qiaolin
AU - Ylla, Guillem
AU - Poulsen, Michael
AU - Gibbs, Richard
AU - Schal, Coby
AU - Richards, Stephen
AU - Belles, Xavier
AU - Korb, Judith
AU - Bornberg Bauer, Erich
ID - 448
IS - 3
JF - Nature Ecology and Evolution
TI - Hemimetabolous genomes reveal molecular basis of termite eusociality
VL - 2
ER -
TY - JOUR
AB - Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games.
AU - Reiter, Johannes
AU - Hilbe, Christian
AU - Rand, David
AU - Chatterjee, Krishnendu
AU - Nowak, Martin
ID - 454
IS - 1
JF - Nature Communications
TI - Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness
VL - 9
ER -
TY - JOUR
AB - The derivation of effective evolution equations is central to the study of non-stationary quantum many-body systems, and widely used in contexts such as superconductivity, nuclear physics, Bose–Einstein condensation and quantum chemistry. We reformulate the Dirac–Frenkel approximation principle in terms of reduced density matrices and apply it to fermionic and bosonic many-body systems. We obtain the Bogoliubov–de Gennes and Hartree–Fock–Bogoliubov equations, respectively. While we do not prove quantitative error estimates, our formulation does show that the approximation is optimal within the class of quasifree states. Furthermore, we prove well-posedness of the Bogoliubov–de Gennes equations in energy space and discuss conserved quantities
AU - Benedikter, Niels P
AU - Sok, Jérémy
AU - Solovej, Jan
ID - 455
IS - 4
JF - Annales Henri Poincare
TI - The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations
VL - 19
ER -
TY - JOUR
AB - We consider congruences of straight lines in a plane with the combinatorics of the square grid, with all elementary quadrilaterals possessing an incircle. It is shown that all the vertices of such nets (we call them incircular or IC-nets) lie on confocal conics. Our main new results are on checkerboard IC-nets in the plane. These are congruences of straight lines in the plane with the combinatorics of the square grid, combinatorially colored as a checkerboard, such that all black coordinate quadrilaterals possess inscribed circles. We show how this larger class of IC-nets appears quite naturally in Laguerre geometry of oriented planes and spheres and leads to new remarkable incidence theorems. Most of our results are valid in hyperbolic and spherical geometries as well. We present also generalizations in spaces of higher dimension, called checkerboard IS-nets. The construction of these nets is based on a new 9 inspheres incidence theorem.
AU - Akopyan, Arseniy
AU - Bobenko, Alexander
ID - 458
IS - 4
JF - Transactions of the American Mathematical Society
TI - Incircular nets and confocal conics
VL - 370
ER -
TY - JOUR
AB - We analyze a disordered central spin model, where a central spin interacts equally with each spin in a periodic one-dimensional (1D) random-field Heisenberg chain. If the Heisenberg chain is initially in the many-body localized (MBL) phase, we find that the coupling to the central spin suffices to delocalize the chain for a substantial range of coupling strengths. We calculate the phase diagram of the model and identify the phase boundary between the MBL and ergodic phase. Within the localized phase, the central spin significantly enhances the rate of the logarithmic entanglement growth and its saturation value. We attribute the increase in entanglement entropy to a nonextensive enhancement of magnetization fluctuations induced by the central spin. Finally, we demonstrate that correlation functions of the central spin can be utilized to distinguish between MBL and ergodic phases of the 1D chain. Hence, we propose the use of a central spin as a possible experimental probe to identify the MBL phase.
AU - Hetterich, Daniel
AU - Yao, Norman
AU - Serbyn, Maksym
AU - Pollmann, Frank
AU - Trauzettel, Björn
ID - 46
IS - 16
JF - Physical Review B
TI - Detection and characterization of many-body localization in central spin models
VL - 98
ER -
TY - JOUR
AB - AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes.
AU - Fan, Ligang
AU - Zhao, Lei
AU - Hu, Wei
AU - Li, Weina
AU - Novák, Ondřej
AU - Strnad, Miroslav
AU - Simon, Sibu
AU - Friml, Jirí
AU - Shen, Jinbo
AU - Jiang, Liwen
AU - Qiu, Quan
ID - 462
JF - Plant, Cell and Environment
TI - NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development
VL - 41
ER -
TY - THES
AB - Nowadays, quantum computation is receiving more and more attention as an alternative to the classical way of computing. For realizing a quantum computer, different devices are investigated as potential quantum bits. In this thesis, the focus is on Ge hut wires, which turned out to be promising candidates for implementing hole spin quantum bits. The advantages of Ge as a material system are the low hyperfine interaction for holes and the strong spin orbit coupling, as well as the compatibility with the highly developed CMOS processes in industry. In addition, Ge can also be isotopically purified which is expected to boost the spin coherence times. The strong spin orbit interaction for holes in Ge on the one hand enables the full electrical control of the quantum bit and on the other hand should allow short spin manipulation times. Starting with a bare Si wafer, this work covers the entire process reaching from growth over the fabrication and characterization of hut wire devices up to the demonstration of hole spin resonance. From experiments with single quantum dots, a large g-factor anisotropy between the in-plane and the out-of-plane direction was found. A comparison to a theoretical model unveiled the heavy-hole character of the lowest energy states. The second part of the thesis addresses double quantum dot devices, which were realized by adding two gate electrodes to a hut wire. In such devices, Pauli spin blockade was observed, which can serve as a read-out mechanism for spin quantum bits. Applying oscillating electric fields in spin blockade allowed the demonstration of continuous spin rotations and the extraction of a lower bound for the spin dephasing time. Despite the strong spin orbit coupling in Ge, the obtained value for the dephasing time is comparable to what has been recently reported for holes in Si. All in all, the presented results point out the high potential of Ge hut wires as a platform for long-lived, fast and fully electrically tunable hole spin quantum bits.
AU - Watzinger, Hannes
ID - 49
TI - Ge hut wires - from growth to hole spin resonance
ER -
TY - JOUR
AB - This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion.
AU - Altmeyer, Sebastian
ID - 519
JF - Journal of Magnetism and Magnetic Materials
TI - Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow
VL - 452
ER -
TY - THES
AB - In this thesis we will discuss systems of point interacting fermions, their stability and other spectral properties. Whereas for bosons a point interacting system is always unstable this ques- tion is more subtle for a gas of two species of fermions. In particular the answer depends on the mass ratio between these two species. Most of this work will be focused on the N + M model which consists of two species of fermions with N, M particles respectively which interact via point interactions. We will introduce this model using a formal limit and discuss the N + 1 system in more detail. In particular, we will show that for mass ratios above a critical one, which does not depend on the particle number, the N + 1 system is stable. In the context of this model we will prove rigorous versions of Tan relations which relate various quantities of the point-interacting model. By restricting the N + 1 system to a box we define a finite density model with point in- teractions. In the context of this system we will discuss the energy change when introducing a point-interacting impurity into a system of non-interacting fermions. We will see that this change in energy is bounded independently of the particle number and in particular the bound only depends on the density and the scattering length. As another special case of the N + M model we will show stability of the 2 + 2 model for mass ratios in an interval around one. Further we will investigate a different model of point interactions which was discussed before in the literature and which is, contrary to the N + M model, not given by a limiting procedure but is based on a Dirichlet form. We will show that this system behaves trivially in the thermodynamic limit, i.e. the free energy per particle is the same as the one of the non-interacting system.
AU - Moser, Thomas
ID - 52
TI - Point interactions in systems of fermions
ER -
TY - JOUR
AB - In 2013, a publication repository was implemented at IST Austria and 2015 after a thorough preparation phase a data repository was implemented - both based on the Open Source Software EPrints. In this text, designed as field report, we will reflect on our experiences with Open Source Software in general and specifically with EPrints regarding technical aspects but also regarding their characteristics of the user community. The second part is a pleading for including the end users in the process of implementation, adaption and evaluation.
AU - Petritsch, Barbara
AU - Porsche, Jana
ID - 53
IS - 1
JF - VÖB Mitteilungen
TI - IST PubRep and IST DataRep: the institutional repositories at IST Austria
VL - 71
ER -
TY - JOUR
AB - Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software.
AU - Edelsbrunner, Herbert
AU - Iglesias Ham, Mabel
ID - 530
JF - Computational Geometry: Theory and Applications
TI - Multiple covers with balls I: Inclusion–exclusion
VL - 68
ER -
TY - JOUR
AB - We consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary. We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(nlog3n) messages in expectation, which is again within logarithmic factors of optimal. We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model.
AU - Alistarh, Dan-Adrian
AU - Aspnes, James
AU - King, Valerie
AU - Saia, Jared
ID - 536
IS - 6
JF - Distributed Computing
SN - 01782770
TI - Communication-efficient randomized consensus
VL - 31
ER -
TY - JOUR
AB - The t-haplotype, a mouse meiotic driver found on chromosome 17, has been a model for autosomal segregation distortion for close to a century, but several questions remain regarding its biology and evolutionary history. A recently published set of population genomics resources for wild mice includes several individuals heterozygous for the t-haplotype, which we use to characterize this selfish element at the genomic and transcriptomic level. Our results show that large sections of the t-haplotype have been replaced by standard homologous sequences, possibly due to occasional events of recombination, and that this complicates the inference of its history. As expected for a long genomic segment of very low recombination, the t-haplotype carries an excess of fixed nonsynonymous mutations compared to the standard chromosome. This excess is stronger for regions that have not undergone recent recombination, suggesting that occasional gene flow between the t and the standard chromosome may provide a mechanism to regenerate coding sequences that have accumulated deleterious mutations. Finally, we find that t-complex genes with altered expression largely overlap with deleted or amplified regions, and that carrying a t-haplotype alters the testis expression of genes outside of the t-complex, providing new leads into the pathways involved in the biology of this segregation distorter.
AU - Kelemen, Réka K
AU - Vicoso, Beatriz
ID - 542
IS - 1
JF - Genetics
TI - Complex history and differentiation patterns of the t-haplotype, a mouse meiotic driver
VL - 208
ER -
TY - JOUR
AB - A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits.
AU - Chalk, Matthew J
AU - Marre, Olivier
AU - Tkacik, Gasper
ID - 543
IS - 1
JF - PNAS
TI - Toward a unified theory of efficient, predictive, and sparse coding
VL - 115
ER -
TY - GEN
AB - We consider the problem of expected cost analysis over nondeterministic probabilistic programs, which aims at automated methods for analyzing the resource-usage of such programs. Previous approaches for this problem could only handle nonnegative bounded costs. However, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols, both positive and negative costs are necessary and the costs are unbounded as well.
In this work, we present a sound and efficient approach to obtain polynomial bounds on the expected accumulated cost of nondeterministic probabilistic programs. Our approach can handle (a) general positive and negative costs with bounded updates in variables; and (b) nonnegative costs with general updates to variables. We show that several natural examples which could not be handled by previous approaches are captured in our framework.
Moreover, our approach leads to an efficient polynomial-time algorithm, while no previous approach for cost analysis of probabilistic programs could guarantee polynomial runtime. Finally, we show the effectiveness of our approach by presenting experimental results on a variety of programs, motivated by real-world applications, for which we efficiently synthesize tight resource-usage bounds.
AU - Anonymous, 1
AU - Anonymous, 2
AU - Anonymous, 3
AU - Anonymous, 4
AU - Anonymous, 5
AU - Anonymous, 6
ID - 5457
SN - 2664-1690
TI - Cost analysis of nondeterministic probabilistic programs
ER -
TY - JOUR
AB - 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 self-medicate 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.
AU - Pull, Christopher
AU - Metzler, Sina
AU - Naderlinger, Elisabeth
AU - Cremer, Sylvia
ID - 55
IS - 19
JF - Current Biology
TI - Protection against the lethal side effects of social immunity in ants
VL - 28
ER -
TY - JOUR
AB - We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order 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 pair-interaction 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.).
AU - Napiórkowski, Marcin M
AU - Reuvers, Robin
AU - Solovej, Jan
ID - 554
IS - 1
JF - Communications in Mathematical Physics
SN - 00103616
TI - The Bogoliubov free energy functional II: The dilute Limit
VL - 360
ER -
TY - JOUR
AB - 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 semi-flexibility — underpin the overall properties of GAG-rich 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 GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions.
AU - Richter, Ralf
AU - Baranova, Natalia
AU - Day, Anthony
AU - Kwok, Jessica
ID - 555
JF - Current Opinion in Structural Biology
TI - Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?
VL - 50
ER -
TY - JOUR
AB - 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.
AU - Betea, Dan
AU - Bouttier, Jeremie
AU - Nejjar, Peter
AU - Vuletic, Mirjana
ID - 556
IS - 12
JF - Annales Henri Poincare
SN - 14240637
TI - The free boundary Schur process and applications I
VL - 19
ER -
TY - DATA
AB - 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.
AU - Bergmiller, Tobias
AU - Nikolic, Nela
ID - 5569
KW - microscopy
KW - microfluidics
TI - Time-lapse microscopy data
ER -
TY - DATA
AB - Graph matching problems for large displacement optical flow of RGB-D images.
AU - Alhaija, Hassan
AU - Sellent, Anita
AU - Kondermann, Daniel
AU - Rother, Carsten
ID - 5573
KW - graph matching
KW - quadratic assignment problem<
TI - Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow
ER -
TY - DATA
AB - Comparison of Scopus' and publisher's data on Austrian publication output at IOP.
AU - Villányi, Márton
ID - 5574
KW - Publication analysis
KW - Bibliography
KW - Open Access
TI - Data Check IOP Scopus vs. Publisher
ER -