@inbook{411, abstract = {Immunolocalization is a valuable tool for cell biology research that allows to rapidly determine the localization and expression levels of endogenous proteins. In plants, whole-mount in situ immunolocalization remains a challenging method, especially in tissues protected by waxy layers and complex cell wall carbohydrates. Here, we present a robust method for whole-mount in situ immunolocalization in primary root meristems and lateral root primordia in Arabidopsis thaliana. For good epitope preservation, fixation is done in an alkaline paraformaldehyde/glutaraldehyde mixture. This fixative is suitable for detecting a wide range of proteins, including integral transmembrane proteins and proteins peripherally attached to the plasma membrane. From initiation until emergence from the primary root, lateral root primordia are surrounded by several layers of differentiated tissues with a complex cell wall composition that interferes with the efficient penetration of all buffers. Therefore, immunolocalization in early lateral root primordia requires a modified method, including a strong solvent treatment for removal of hydrophobic barriers and a specific cocktail of cell wall-degrading enzymes. The presented method allows for easy, reliable, and high-quality in situ detection of the subcellular localization of endogenous proteins in primary and lateral root meristems without the need of time-consuming crosses or making translational fusions to fluorescent proteins.}, author = {Karampelias, Michael and Tejos, Ricardo and Friml, Jirí and Vanneste, Steffen}, booktitle = {Root Development. Methods and Protocols}, editor = {Ristova, Daniela and Barbez, Elke}, pages = {131 -- 143}, publisher = {Springer}, title = {{Optimized whole mount in situ immunolocalization for Arabidopsis thaliana root meristems and lateral root primordia}}, doi = {10.1007/978-1-4939-7747-5_10}, volume = {1761}, year = {2018}, } @article{456, abstract = {Inhibition of the endoplasmic reticulum stress pathway may hold the key to Zika virus-associated microcephaly treatment. }, author = {Novarino, Gaia}, journal = {Science Translational Medicine}, number = {423}, publisher = {American Association for the Advancement of Science}, title = {{Zika-associated microcephaly: Reduce the stress and race for the treatment}}, doi = {10.1126/scitranslmed.aar7514}, volume = {10}, year = {2018}, } @article{53, abstract = {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.}, author = {Petritsch, Barbara and Porsche, Jana}, journal = {VÖB Mitteilungen}, number = {1}, pages = {199 -- 206}, publisher = {Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare}, title = {{IST PubRep and IST DataRep: the institutional repositories at IST Austria}}, doi = {10.31263/voebm.v71i1.1993}, volume = {71}, year = {2018}, } @article{536, abstract = {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.}, author = {Alistarh, Dan-Adrian and Aspnes, James and King, Valerie and Saia, Jared}, issn = {01782770}, journal = {Distributed Computing}, number = {6}, pages = {489--501}, publisher = {Springer}, title = {{Communication-efficient randomized consensus}}, doi = {10.1007/s00446-017-0315-1}, volume = {31}, year = {2018}, } @article{554, abstract = {We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a 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.).}, author = {Napiórkowski, Marcin M and Reuvers, Robin and Solovej, Jan}, issn = {00103616}, journal = {Communications in Mathematical Physics}, number = {1}, pages = {347--403}, publisher = {Springer}, title = {{The Bogoliubov free energy functional II: The dilute Limit}}, doi = {10.1007/s00220-017-3064-x}, volume = {360}, year = {2018}, } @inbook{562, abstract = {Primary neuronal cell culture preparations are widely used to investigate synaptic functions. This chapter describes a detailed protocol for the preparation of a neuronal cell culture in which giant calyx-type synaptic terminals are formed. This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals.}, author = {Dimitrov, Dimitar and Guillaud, Laurent and Eguchi, Kohgaku and Takahashi, Tomoyuki}, booktitle = {Neurotrophic Factors}, editor = {Skaper, Stephen D.}, pages = {201 -- 215}, publisher = {Springer}, title = {{Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses}}, doi = {10.1007/978-1-4939-7571-6_15}, volume = {1727}, year = {2018}, } @inbook{59, abstract = {Graph-based games are an important tool in computer science. They have applications in synthesis, verification, refinement, and far beyond. We review graphbased games with objectives on infinite plays. We give definitions and algorithms to solve the games and to give a winning strategy. The objectives we consider are mostly Boolean, but we also look at quantitative graph-based games and their objectives. Synthesis aims to turn temporal logic specifications into correct reactive systems. We explain the reduction of synthesis to graph-based games (or equivalently tree automata) using synthesis of LTL specifications as an example. We treat the classical approach that uses determinization of parity automata and more modern approaches.}, author = {Bloem, Roderick and Chatterjee, Krishnendu and Jobstmann, Barbara}, booktitle = {Handbook of Model Checking}, editor = {Henzinger, Thomas A and Clarke, Edmund M. and Veith, Helmut and Bloem, Roderick}, isbn = {978-3-319-10574-1}, pages = {921 -- 962}, publisher = {Springer}, title = {{Graph games and reactive synthesis}}, doi = {10.1007/978-3-319-10575-8_27}, year = {2018}, } @inbook{60, abstract = {Model checking is a computer-assisted method for the analysis of dynamical systems that can be modeled by state-transition systems. Drawing from research traditions in mathematical logic, programming languages, hardware design, and theoretical computer science, model checking is now widely used for the verification of hardware and software in industry. This chapter is an introduction and short survey of model checking. The chapter aims to motivate and link the individual chapters of the handbook, and to provide context for readers who are not familiar with model checking.}, author = {Clarke, Edmund and Henzinger, Thomas A and Veith, Helmut}, booktitle = {Handbook of Model Checking}, editor = {Henzinger, Thomas A}, pages = {1 -- 26}, publisher = {Springer}, title = {{Introduction to model checking}}, doi = {10.1007/978-3-319-10575-8_1}, year = {2018}, } @inbook{61, abstract = {We prove that there is no strongly regular graph (SRG) with parameters (460; 153; 32; 60). The proof is based on a recent lower bound on the number of 4-cliques in a SRG and some applications of Euclidean representation of SRGs. }, author = {Bondarenko, Andriy and Mellit, Anton and Prymak, Andriy and Radchenko, Danylo and Viazovska, Maryna}, booktitle = {Contemporary Computational Mathematics}, pages = {131 -- 134}, publisher = {Springer}, title = {{There is no strongly regular graph with parameters (460; 153; 32; 60)}}, doi = {10.1007/978-3-319-72456-0_7}, year = {2018}, } @article{6111, abstract = {Neurons develop elaborate morphologies that provide a model for understanding cellular architecture. By studying C. elegans sensory dendrites, we previously identified genes that act to promote the extension of ciliated sensory dendrites during embryogenesis. Interestingly, the nonciliated dendrite of the oxygen-sensing neuron URX is not affected by these genes, suggesting it develops through a distinct mechanism. Here, we use a visual forward genetic screen to identify mutants that affect URX dendrite morphogenesis. We find that disruption of the MAP kinase MAPK-15 or the βH-spectrin SMA-1 causes a phenotype opposite to what we had seen before: dendrites extend normally during embryogenesis but begin to overgrow as the animals reach adulthood, ultimately extending up to 150% of their normal length. SMA-1 is broadly expressed and acts non-cell-autonomously, while MAPK-15 is expressed in many sensory neurons including URX and acts cell-autonomously. MAPK-15 acts at the time of overgrowth, localizes at the dendrite ending, and requires its kinase activity, suggesting it acts locally in time and space to constrain dendrite growth. Finally, we find that the oxygen-sensing guanylate cyclase GCY-35, which normally localizes at the dendrite ending, is localized throughout the overgrown region, and that overgrowth can be suppressed by overexpressing GCY-35 or by genetically mimicking elevated cGMP signaling. These results suggest that overgrowth may correspond to expansion of a sensory compartment at the dendrite ending, reminiscent of the remodeling of sensory cilia or dendritic spines. Thus, in contrast to established pathways that promote dendrite growth during early development, our results reveal a distinct mechanism that constrains dendrite growth throughout the life of the animal, possibly by controlling the size of a sensory compartment at the dendrite ending.}, author = {McLachlan, Ian G. and Beets, Isabel and de Bono, Mario and Heiman, Maxwell G.}, issn = {1553-7404}, journal = {PLOS Genetics}, number = {6}, publisher = {Public Library of Science}, title = {{A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism}}, doi = {10.1371/journal.pgen.1007435}, volume = {14}, year = {2018}, } @article{6109, abstract = {Neuropeptides are ubiquitous modulators of behavior and physiology. They are packaged in specialized secretory organelles called dense core vesicles (DCVs) that are released upon neural stimulation. Unlike synaptic vesicles, which can be recycled and refilled close to release sites, DCVs must be replenished by de novo synthesis in the cell body. Here, we dissect DCV cell biology in vivo in a Caenorhabditis elegans sensory neuron whose tonic activity we can control using a natural stimulus. We express fluorescently tagged neuropeptides in the neuron and define parameters that describe their subcellular distribution. We measure these parameters at high and low neural activity in 187 mutants defective in proteins implicated in membrane traffic, neuroendocrine secretion, and neuronal or synaptic activity. Using unsupervised hierarchical clustering methods, we analyze these data and identify 62 groups of genes with similar mutant phenotypes. We explore the function of a subset of these groups. We recapitulate many previous findings, validating our paradigm. We uncover a large battery of proteins involved in recycling DCV membrane proteins, something hitherto poorly explored. We show that the unfolded protein response promotes DCV production, which may contribute to intertissue communication of stress. We also find evidence that different mechanisms of priming and exocytosis may operate at high and low neural activity. Our work provides a defined framework to study DCV biology at different neural activity levels.}, author = {Laurent, Patrick and Ch’ng, QueeLim and Jospin, Maëlle and Chen, Changchun and Lorenzo, Ramiro and de Bono, Mario}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {29}, pages = {E6890--E6899}, publisher = {National Academy of Sciences}, title = {{Genetic dissection of neuropeptide cell biology at high and low activity in a defined sensory neuron}}, doi = {10.1073/pnas.1714610115}, volume = {115}, year = {2018}, } @inproceedings{6164, abstract = {In this paper, we propose an algorithm to build discrete spherical shell having integer center and real-valued inner and outer radii on the face-centered cubic (FCC) grid. We address the problem by mapping it to a 2D scenario and building the shell layer by layer on hexagonal grids with additive manufacturing in mind. The layered hexagonal grids get shifted according to need as we move from one layer to another and forms the FCC grid in 3D. However, we restrict our computation strictly to 2D in order to utilize symmetry and simplicity.}, author = {Koshti, Girish and Biswas, Ranita and Largeteau-Skapin, Gaëlle and Zrour, Rita and Andres, Eric and Bhowmick, Partha}, booktitle = {19th International Workshop}, isbn = {978-3-030-05287-4}, issn = {1611-3349}, location = {Porto, Portugal}, pages = {82--96}, publisher = {Springer}, title = {{Sphere construction on the FCC grid interpreted as layered hexagonal grids in 3D}}, doi = {10.1007/978-3-030-05288-1_7}, volume = {11255}, year = {2018}, } @article{6354, abstract = {Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow.}, author = {Fan, Shuxia and Lorenz, Michael and Massberg, Steffen and Gärtner, Florian R}, issn = {2331-8325}, journal = {Bio-Protocol}, keywords = {Platelets, Cell migration, Bacteria, Shear flow, Fibrinogen, E. coli}, number = {18}, publisher = {Bio-Protocol}, title = {{Platelet migration and bacterial trapping assay under flow}}, doi = {10.21769/bioprotoc.3018}, volume = {8}, year = {2018}, } @article{6368, abstract = {An optical network of superconducting quantum bits (qubits) is an appealing platform for quantum communication and distributed quantum computing, but developing a quantum-compatible link between the microwave and optical domains remains an outstanding challenge. Operating at T < 100 mK temperatures, as required for quantum electrical circuits, we demonstrate a mechanically mediated microwave–optical converter with 47% conversion efficiency, and use a classical feed-forward protocol to reduce added noise to 38 photons. The feed-forward protocol harnesses our discovery that noise emitted from the two converter output ports is strongly correlated because both outputs record thermal motion of the same mechanical mode. We also discuss a quantum feed-forward protocol that, given high system efficiencies, would allow quantum information to be transferred even when thermal phonons enter the mechanical element faster than the electro-optic conversion rate.}, author = {Higginbotham, Andrew P and Burns, P. S. and Urmey, M. D. and Peterson, R. W. and Kampel, N. S. and Brubaker, B. M. and Smith, G. and Lehnert, K. W. and Regal, C. A.}, issn = {1745-2473}, journal = {Nature Physics}, number = {10}, pages = {1038--1042}, publisher = {Springer Nature}, title = {{Harnessing electro-optic correlations in an efficient mechanical converter}}, doi = {10.1038/s41567-018-0210-0}, volume = {14}, year = {2018}, } @article{6369, abstract = {We construct a metamaterial from radio-frequency harmonic oscillators, and find two topologically distinct phases resulting from dissipation engineered into the system. These phases are distinguished by a quantized value of bulk energy transport. The impulse response of our circuit is measured and used to reconstruct the band structure and winding number of circuit eigenfunctions around a dark mode. Our results demonstrate that dissipative topological transport can occur in a wider class of physical systems than considered before.}, author = {Rosenthal, Eric I. and Ehrlich, Nicole K. and Rudner, Mark S. and Higginbotham, Andrew P and Lehnert, K. W.}, issn = {2469-9950}, journal = {Physical Review B}, number = {22}, publisher = {American Physical Society (APS)}, title = {{Topological phase transition measured in a dissipative metamaterial}}, doi = {10.1103/physrevb.97.220301}, volume = {97}, year = {2018}, } @misc{6459, author = {Petritsch, Barbara}, keywords = {Open Access, Publication Analysis}, location = {Graz, Austria}, publisher = {IST Austria}, title = {{Open Access at IST Austria 2009-2017}}, doi = {10.5281/zenodo.1410279}, year = {2018}, } @inbook{6525, abstract = {This chapter finds an agreement of equivariant indices of semi-classical homomorphisms between pairwise mirror branes in the GL2 Higgs moduli space on a Riemann surface. On one side of the agreement, components of the Lagrangian brane of U(1,1) Higgs bundles, whose mirror was proposed by Hitchin to be certain even exterior powers of the hyperholomorphic Dirac bundle on the SL2 Higgs moduli space, are present. The agreement arises from a mysterious functional equation. This gives strong computational evidence for Hitchin’s proposal.}, author = {Hausel, Tamás and Mellit, Anton and Pei, Du}, booktitle = {Geometry and Physics: Volume I}, isbn = {9780198802013}, pages = {189--218}, publisher = {Oxford University Press}, title = {{Mirror symmetry with branes by equivariant verlinde formulas}}, doi = {10.1093/oso/9780198802013.003.0009}, year = {2018}, } @inproceedings{6664, abstract = {Reed-Muller (RM) and polar codes are a class of capacity-achieving channel coding schemes with the same factor graph representation. Low-complexity decoding algorithms fall short in providing a good error-correction performance for RM and polar codes. Using the symmetric group of RM and polar codes, the specific decoding algorithm can be carried out on multiple permutations of the factor graph to boost the error-correction performance. However, this approach results in high decoding complexity. In this paper, we first derive the total number of factor graph permutations on which the decoding can be performed. We further propose a successive permutation (SP) scheme which finds the permutations on the fly, thus the decoding always progresses on a single factor graph permutation. We show that SP can be used to improve the error-correction performance of RM and polar codes under successive-cancellation (SC) and SC list (SCL) decoding, while keeping the memory requirements of the decoders unaltered. Our results for RM and polar codes of length 128 and rate 0.5 show that when SP is used and at a target frame error rate of 10 -4 , up to 0.5 dB and 0.1 dB improvement can be achieved for RM and polar codes respectively.}, author = {Hashemi, Seyyed Ali and Doan, Nghia and Mondelli, Marco and Gross, Warren }, booktitle = {2018 IEEE 10th International Symposium on Turbo Codes & Iterative Information Processing}, location = {Hong Kong, China}, pages = {1--5}, publisher = {IEEE}, title = {{Decoding Reed-Muller and polar codes by successive factor graph permutations}}, doi = {10.1109/istc.2018.8625281}, year = {2018}, } @article{6674, abstract = {Polar codes represent one of the major recent breakthroughs in coding theory and, because of their attractive features, they have been selected for the incoming 5G standard. As such, a lot of attention has been devoted to the development of decoding algorithms with good error performance and efficient hardware implementation. One of the leading candidates in this regard is represented by successive-cancellation list (SCL) decoding. However, its hardware implementation requires a large amount of memory. Recently, a partitioned SCL (PSCL) decoder has been proposed to significantly reduce the memory consumption. In this paper, we consider the paradigm of PSCL decoding from a practical standpoint, and we provide several improvements. First, by changing the target signal-to-noise ratio and consequently modifying the construction of the code, we are able to improve the performance at no additional computational, latency, or memory cost. Second, we bridge the performance gap between SCL and PSCL decoding by introducing a generalized PSCL decoder and a layered PSCL decoder. In this way, we obtain almost the same performance of the SCL decoder with a significantly lower memory requirement, as testified by hardware implementation results. Third, we present an optimal scheme to allocate cyclic redundancy checks. Finally, we provide a lower bound on the list size that guarantees optimal maximum a posteriori performance for the binary erasure channel.}, author = {Hashemi, Seyyed Ali and Mondelli, Marco and Hassani, S. Hamed and Condo, Carlo and Urbanke, Rudiger L. and Gross, Warren J.}, issn = {1558-0857}, journal = {IEEE Transactions on Communications}, number = {9}, pages = {3749--3759}, publisher = {IEEE}, title = {{Decoder partitioning: Towards practical list decoding of polar codes}}, doi = {10.1109/tcomm.2018.2832207}, volume = {66}, year = {2018}, } @inproceedings{6728, abstract = {Polar codes are a channel coding scheme for the next generation of wireless communications standard (5G). The belief propagation (BP) decoder allows for parallel decoding of polar codes, making it suitable for high throughput applications. However, the error-correction performance of polar codes under BP decoding is far from the requirements of 5G. It has been shown that the error-correction performance of BP can be improved if the decoding is performed on multiple permuted factor graphs of polar codes. However, a different BP decoding scheduling is required for each factor graph permutation which results in the design of a different decoder for each permutation. Moreover, the selection of the different factor graph permutations is at random, which prevents the decoder to achieve a desirable error correction performance with a small number of permutations. In this paper, we first show that the permutations on the factor graph can be mapped into suitable permutations on the codeword positions. As a result, we can make use of a single decoder for all the permutations. In addition, we introduce a method to construct a set of predetermined permutations which can provide the correct codeword if the decoding fails on the original permutation. We show that for the 5G polar code of length 1024, the error-correction performance of the proposed decoder is more than 0.25 dB better than that of the BP decoder with the same number of random permutations at the frame error rate of 10 -4 .}, author = {Doan, Nghia and Hashemi, Seyyed Ali and Mondelli, Marco and Gross, Warren J.}, booktitle = {2018 IEEE Global Communications Conference }, isbn = {9781538647271}, location = {Abu Dhabi, United Arab Emirates}, publisher = {IEEE}, title = {{On the decoding of polar codes on permuted factor graphs}}, doi = {10.1109/glocom.2018.8647308}, year = {2018}, }