@misc{5565, abstract = {One of the key questions in understanding plant development is how single cells behave in a larger context of the tissue. Therefore, it requires the observation of the whole organ with a high spatial- as well as temporal resolution over prolonged periods of time, which may cause photo-toxic effects. This protocol shows a plant sample preparation method for light-sheet microscopy, which is characterized by mounting the plant vertically on the surface of a gel. The plant is mounted in such a way that the roots are submerged in a liquid medium while the leaves remain in the air. In order to ensure photosynthetic activity of the plant, a custom-made lighting system illuminates the leaves. To keep the roots in darkness the water surface is covered with sheets of black plastic foil. This method allows long-term imaging of plant organ development in standardized conditions. The Video is licensed under a CC BY NC ND license. }, author = {Von Wangenheim, Daniel and Hauschild, Robert and Friml, Jirí}, publisher = {Institute of Science and Technology Austria}, title = {{Light Sheet Fluorescence microscopy of plant roots growing on the surface of a gel}}, doi = {10.15479/AT:ISTA:66}, year = {2017}, } @misc{5566, abstract = {Current minimal version of TipTracker}, author = {Hauschild, Robert}, keywords = {tool, tracking, confocal microscopy}, publisher = {Institute of Science and Technology Austria}, title = {{Live tracking of moving samples in confocal microscopy for vertically grown roots}}, doi = {10.15479/AT:ISTA:69}, year = {2017}, } @misc{5567, abstract = {Immunological synapse DC-Tcells}, author = {Leithner, Alexander F}, keywords = {Immunological synapse}, publisher = {Institute of Science and Technology Austria}, title = {{Immunological synapse DC-Tcells}}, doi = {10.15479/AT:ISTA:71}, year = {2017}, } @misc{5568, abstract = {Includes source codes, test cases, and example data used in the thesis Brittle Fracture Simulation with Boundary Elements for Computer Graphics. Also includes pre-built binaries of the HyENA library, but not sources - please contact the HyENA authors to obtain these sources if required (https://mech.tugraz.at/hyena)}, author = {Hahn, David}, keywords = {Boundary elements, brittle fracture, computer graphics, fracture simulation}, publisher = {Institute of Science and Technology Austria}, title = {{Source codes: Brittle fracture simulation with boundary elements for computer graphics}}, doi = {10.15479/AT:ISTA:73}, year = {2017}, } @article{557, abstract = {PURPOSE. Gene therapy of retinal ganglion cells (RGCs) has promise as a powerful therapeutic for the rescue and regeneration of these cells after optic nerve damage. However, early after damage, RGCs undergo atrophic changes, including gene silencing. It is not known if these changes will deleteriously affect transduction and transgene expression, or if the therapeutic protein can influence reactivation of the endogenous genome. METHODS. Double-transgenic mice carrying a Rosa26-(LoxP)-tdTomato reporter, and a mutant allele for the proapoptotic Bax gene were reared. The Bax mutant blocks apoptosis, but RGCs still exhibit nuclear atrophy and gene silencing. At times ranging from 1 hour to 4 weeks after optic nerve crush (ONC), eyes received an intravitreal injection of AAV2 virus carrying the Cre recombinase. Successful transduction was monitored by expression of the tdTomato reporter. Immunostaining was used to localize tdTomato expression in select cell types. RESULTS. Successful transduction of RGCs was achieved at all time points after ONC using AAV2 expressing Cre from the phosphoglycerate kinase (Pgk) promoter, but not the CMV promoter. ONC promoted an increase in the transduction of cell types in the inner nuclear layer, including Müller cells and rod bipolar neurons. There was minimal evidence of transduction of amacrine cells and astrocytes in the inner retina or optic nerve. CONCLUSIONS. Damaged RGCs can be transduced and at least some endogenous genes can be subsequently activated. Optic nerve damage may change retinal architecture to allow greater penetration of an AAV2 virus to transduce several additional cell types in the inner nuclear layer.}, author = {Nickells, Robert and Schmitt, Heather and Maes, Margaret E and Schlamp, Cassandra}, issn = {01460404}, journal = {Investigative Ophthalmology and Visual Science}, number = {14}, pages = {6091 -- 6104}, publisher = {Association for Research in Vision and Ophthalmology}, title = {{AAV2 mediated transduction of the mouse retina after optic nerve injury}}, doi = {10.1167/iovs.17-22634}, volume = {58}, year = {2017}, } @misc{5570, abstract = {Matlab script to calculate the forward migration indexes (/) from TrackMate spot-statistics files.}, author = {Hauschild, Robert}, keywords = {Cell migration, tracking, forward migration index, FMI}, publisher = {Institute of Science and Technology Austria}, title = {{Forward migration indexes}}, doi = {10.15479/AT:ISTA:75}, year = {2017}, } @misc{5571, abstract = {This folder contains all the data used in each of the main figures of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.), as well as in the supplementary figures. }, author = {Vicoso, Beatriz}, publisher = {Institute of Science and Technology Austria}, title = {{Data for "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology"}}, doi = {10.15479/AT:ISTA:78}, year = {2017}, } @misc{5572, abstract = {Code described in the Supplementary Methods of "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology" (Kelemen, R., Vicoso, B.)}, author = {Vicoso, Beatriz}, publisher = {Institute of Science and Technology Austria}, title = {{Code for "The genomic characterization of the t-haplotype, a mouse meiotic driver, highlights its complex history and specialized biology"}}, doi = {10.15479/AT:ISTA:79 }, year = {2017}, } @inproceedings{559, abstract = {Proofs of space (PoS) were suggested as more ecological and economical alternative to proofs of work, which are currently used in blockchain designs like Bitcoin. The existing PoS are based on rather sophisticated graph pebbling lower bounds. Much simpler and in several aspects more efficient schemes based on inverting random functions have been suggested, but they don’t give meaningful security guarantees due to existing time-memory trade-offs. In particular, Hellman showed that any permutation over a domain of size N can be inverted in time T by an algorithm that is given S bits of auxiliary information whenever (Formula presented). For functions Hellman gives a weaker attack with S2· T≈ N2 (e.g., S= T≈ N2/3). To prove lower bounds, one considers an adversary who has access to an oracle f: [ N] → [N] and can make T oracle queries. The best known lower bound is S· T∈ Ω(N) and holds for random functions and permutations. We construct functions that provably require more time and/or space to invert. Specifically, for any constant k we construct a function [N] → [N] that cannot be inverted unless Sk· T∈ Ω(Nk) (in particular, S= T≈ (Formula presented). Our construction does not contradict Hellman’s time-memory trade-off, because it cannot be efficiently evaluated in forward direction. However, its entire function table can be computed in time quasilinear in N, which is sufficient for the PoS application. Our simplest construction is built from a random function oracle g: [N] × [N] → [ N] and a random permutation oracle f: [N] → N] and is defined as h(x) = g(x, x′) where f(x) = π(f(x′)) with π being any involution without a fixed point, e.g. flipping all the bits. For this function we prove that any adversary who gets S bits of auxiliary information, makes at most T oracle queries, and inverts h on an ϵ fraction of outputs must satisfy S2· T∈ Ω(ϵ2N2).}, author = {Abusalah, Hamza M and Alwen, Joel F and Cohen, Bram and Khilko, Danylo and Pietrzak, Krzysztof Z and Reyzin, Leonid}, isbn = {978-331970696-2}, location = {Hong Kong, China}, pages = {357 -- 379}, publisher = {Springer}, title = {{Beyond Hellman’s time-memory trade-offs with applications to proofs of space}}, doi = {10.1007/978-3-319-70697-9_13}, volume = {10625}, year = {2017}, } @article{560, abstract = {In a recent article (Jentzen et al. 2016 Commun. Math. Sci. 14, 1477–1500 (doi:10.4310/CMS.2016.v14. n6.a1)), it has been established that, for every arbitrarily slow convergence speed and every natural number d ? {4, 5, . . .}, there exist d-dimensional stochastic differential equations with infinitely often differentiable and globally bounded coefficients such that no approximation method based on finitely many observations of the driving Brownian motion can converge in absolute mean to the solution faster than the given speed of convergence. In this paper, we strengthen the above result by proving that this slow convergence phenomenon also arises in two (d = 2) and three (d = 3) space dimensions.}, author = {Gerencser, Mate and Jentzen, Arnulf and Salimova, Diyora}, issn = {13645021}, journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences}, number = {2207}, publisher = {Royal Society of London}, title = {{On stochastic differential equations with arbitrarily slow convergence rates for strong approximation in two space dimensions}}, doi = {10.1098/rspa.2017.0104}, volume = {473}, year = {2017}, } @article{561, abstract = {Restriction–modification systems are widespread genetic elements that protect bacteria from bacteriophage infections by recognizing and cleaving heterologous DNA at short, well-defined sequences called restriction sites. Bioinformatic evidence shows that restriction sites are significantly underrepresented in bacteriophage genomes, presumably because bacteriophages with fewer restriction sites are more likely to escape cleavage by restriction–modification systems. However, how mutations in restriction sites affect the likelihood of bacteriophage escape is unknown. Using the bacteriophage l and the restriction–modification system EcoRI, we show that while mutation effects at different restriction sites are unequal, they are independent. As a result, the probability of bacteriophage escape increases with each mutated restriction site. Our results experimentally support the role of restriction site avoidance as a response to selection imposed by restriction–modification systems and offer an insight into the events underlying the process of bacteriophage escape.}, author = {Pleska, Maros and Guet, Calin C}, issn = {1744-9561}, journal = {Biology Letters}, number = {12}, publisher = {The Royal Society}, title = {{Effects of mutations in phage restriction sites during escape from restriction–modification}}, doi = {10.1098/rsbl.2017.0646}, volume = {13}, year = {2017}, } @article{568, abstract = {We study robust properties of zero sets of continuous maps f: X → ℝn. Formally, we analyze the family Z< r(f) := (g-1(0): ||g - f|| < r) of all zero sets of all continuous maps g closer to f than r in the max-norm. All of these sets are outside A := (x: |f(x)| ≥ r) and we claim that Z< r(f) is fully determined by A and an element of a certain cohomotopy group which (by a recent result) is computable whenever the dimension of X is at most 2n - 3. By considering all r > 0 simultaneously, the pointed cohomotopy groups form a persistence module-a structure leading to persistence diagrams as in the case of persistent homology or well groups. Eventually, we get a descriptor of persistent robust properties of zero sets that has better descriptive power (Theorem A) and better computability status (Theorem B) than the established well diagrams. Moreover, if we endow every point of each zero set with gradients of the perturbation, the robust description of the zero sets by elements of cohomotopy groups is in some sense the best possible (Theorem C).}, author = {Franek, Peter and Krcál, Marek}, issn = {15320073}, journal = {Homology, Homotopy and Applications}, number = {2}, pages = {313 -- 342}, publisher = {International Press}, title = {{Persistence of zero sets}}, doi = {10.4310/HHA.2017.v19.n2.a16}, volume = {19}, year = {2017}, } @article{569, abstract = {The actomyosin ring generates force to ingress the cytokinetic cleavage furrow in animal cells, yet its filament organization and the mechanism of contractility is not well understood. We quantified actin filament order in human cells using fluorescence polarization microscopy and found that cleavage furrow ingression initiates by contraction of an equatorial actin network with randomly oriented filaments. The network subsequently gradually reoriented actin filaments along the cell equator. This strictly depended on myosin II activity, suggesting local network reorganization by mechanical forces. Cortical laser microsurgery revealed that during cytokinesis progression, mechanical tension increased substantially along the direction of the cell equator, while the network contracted laterally along the pole-to-pole axis without a detectable increase in tension. Our data suggest that an asymmetric increase in cortical tension promotes filament reorientation along the cytokinetic cleavage furrow, which might have implications for diverse other biological processes involving actomyosin rings.}, author = {Spira, Felix and Cuylen Haering, Sara and Mehta, Shalin and Samwer, Matthias and Reversat, Anne and Verma, Amitabh and Oldenbourg, Rudolf and Sixt, Michael K and Gerlich, Daniel}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Cytokinesis in vertebrate cells initiates by contraction of an equatorial actomyosin network composed of randomly oriented filaments}}, doi = {10.7554/eLife.30867}, volume = {6}, year = {2017}, } @article{570, abstract = {Most phenotypes are determined by molecular systems composed of specifically interacting molecules. However, unlike for individual components, little is known about the distributions of mutational effects of molecular systems as a whole. We ask how the distribution of mutational effects of a transcriptional regulatory system differs from the distributions of its components, by first independently, and then simultaneously, mutating a transcription factor and the associated promoter it represses. We find that the system distribution exhibits increased phenotypic variation compared to individual component distributions - an effect arising from intermolecular epistasis between the transcription factor and its DNA-binding site. In large part, this epistasis can be qualitatively attributed to the structure of the transcriptional regulatory system and could therefore be a common feature in prokaryotes. Counter-intuitively, intermolecular epistasis can alleviate the constraints of individual components, thereby increasing phenotypic variation that selection could act on and facilitating adaptive evolution. }, author = {Lagator, Mato and Sarikas, Srdjan and Acar, Hande and Bollback, Jonathan P and Guet, Calin C}, issn = {2050084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Regulatory network structure determines patterns of intermolecular epistasis}}, doi = {10.7554/eLife.28921}, volume = {6}, year = {2017}, } @article{572, abstract = {In this review, we summarize the different biosynthesis-related pathways that contribute to the regulation of endogenous auxin in plants. We demonstrate that all known genes involved in auxin biosynthesis also have a role in root formation, from the initiation of a root meristem during embryogenesis to the generation of a functional root system with a primary root, secondary lateral root branches and adventitious roots. Furthermore, the versatile adaptation of root development in response to environmental challenges is mediated by both local and distant control of auxin biosynthesis. In conclusion, auxin homeostasis mediated by spatial and temporal regulation of auxin biosynthesis plays a central role in determining root architecture.}, author = {Olatunji, Damilola and Geelen, Danny and Verstraeten, Inge}, journal = {International Journal of Molecular Sciences}, number = {12}, publisher = {MDPI}, title = {{Control of endogenous auxin levels in plant root development}}, doi = {10.3390/ijms18122587}, volume = {18}, year = {2017}, } @article{601, abstract = {The conserved polymerase-Associated factor 1 complex (Paf1C) plays multiple roles in chromatin transcription and genomic regulation. Paf1C comprises the five subunits Paf1, Leo1, Ctr9, Cdc73 and Rtf1, and binds to the RNA polymerase II (Pol II) transcription elongation complex (EC). Here we report the reconstitution of Paf1C from Saccharomyces cerevisiae, and a structural analysis of Paf1C bound to a Pol II EC containing the elongation factor TFIIS. Cryo-electron microscopy and crosslinking data reveal that Paf1C is highly mobile and extends over the outer Pol II surface from the Rpb2 to the Rpb3 subunit. The Paf1-Leo1 heterodimer and Cdc73 form opposite ends of Paf1C, whereas Ctr9 bridges between them. Consistent with the structural observations, the initiation factor TFIIF impairs Paf1C binding to Pol II, whereas the elongation factor TFIIS enhances it. We further show that Paf1C is globally required for normal mRNA transcription in yeast. These results provide a three-dimensional framework for further analysis of Paf1C function in transcription through chromatin. }, author = {Xu, Youwei and Bernecky, Carrie A and Lee, Chung and Maier, Kerstin and Schwalb, Björn and Tegunov, Dimitri and Plitzko, Jürgen and Urlaub, Henning and Cramer, Patrick}, issn = {20411723}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex}}, doi = {10.1038/ncomms15741}, volume = {8}, year = {2017}, } @article{6013, abstract = {The first hundred attoseconds of the electron dynamics during strong field tunneling ionization are investigated. We quantify theoretically how the electron’s classical trajectories in the continuum emerge from the tunneling process and test the results with those achieved in parallel from attoclock measurements. An especially high sensitivity on the tunneling barrier is accomplished here by comparing the momentum distributions of two atomic species of slightly deviating atomic potentials (argon and krypton) being ionized under absolutely identical conditions with near-infrared laser pulses (1300 nm). The agreement between experiment and theory provides clear evidence for a nonzero tunneling time delay and a nonvanishing longitudinal momentum of the electron at the “tunnel exit.”}, author = {Camus, Nicolas and Yakaboylu, Enderalp and Fechner, Lutz and Klaiber, Michael and Laux, Martin and Mi, Yonghao and Hatsagortsyan, Karen Z. and Pfeifer, Thomas and Keitel, Christoph H. and Moshammer, Robert}, issn = {1079-7114}, journal = {Physical Review Letters}, number = {2}, publisher = {American Physical Society}, title = {{Experimental evidence for quantum tunneling time}}, doi = {10.1103/PhysRevLett.119.023201}, volume = {119}, year = {2017}, } @inbook{604, abstract = {In several settings of physics and chemistry one has to deal with molecules interacting with some kind of an external environment, be it a gas, a solution, or a crystal surface. Understanding molecular processes in the presence of such a many-particle bath is inherently challenging, and usually requires large-scale numerical computations. Here, we present an alternative approach to the problem, based on the notion of the angulon quasiparticle. We show that molecules rotating inside superfluid helium nanodroplets and Bose–Einstein condensates form angulons, and therefore can be described by straightforward solutions of a simple microscopic Hamiltonian. Casting the problem in the language of angulons allows us not only to greatly simplify it, but also to gain insights into the origins of the observed phenomena and to make predictions for future experimental studies.}, author = {Lemeshko, Mikhail and Schmidt, Richard}, booktitle = {Cold Chemistry: Molecular Scattering and Reactivity Near Absolute Zero }, editor = {Dulieu, Oliver and Osterwalder, Andreas}, issn = {20413181}, pages = {444 -- 495}, publisher = {The Royal Society of Chemistry}, title = {{Molecular impurities interacting with a many-particle environment: From ultracold gases to helium nanodroplets}}, doi = {10.1039/9781782626800-00444}, volume = {11}, year = {2017}, } @inproceedings{605, abstract = {Position based cryptography (PBC), proposed in the seminal work of Chandran, Goyal, Moriarty, and Ostrovsky (SIAM J. Computing, 2014), aims at constructing cryptographic schemes in which the identity of the user is his geographic position. Chandran et al. construct PBC schemes for secure positioning and position-based key agreement in the bounded-storage model (Maurer, J. Cryptology, 1992). Apart from bounded memory, their security proofs need a strong additional restriction on the power of the adversary: he cannot compute joint functions of his inputs. Removing this assumption is left as an open problem. We show that an answer to this question would resolve a long standing open problem in multiparty communication complexity: finding a function that is hard to compute with low communication complexity in the simultaneous message model, but easy to compute in the fully adaptive model. On a more positive side: we also show some implications in the other direction, i.e.: we prove that lower bounds on the communication complexity of certain multiparty problems imply existence of PBC primitives. Using this result we then show two attractive ways to “bypass” our hardness result: the first uses the random oracle model, the second weakens the locality requirement in the bounded-storage model to online computability. The random oracle construction is arguably one of the simplest proposed so far in this area. Our results indicate that constructing improved provably secure protocols for PBC requires a better understanding of multiparty communication complexity. This is yet another example where negative results in one area (in our case: lower bounds in multiparty communication complexity) can be used to construct secure cryptographic schemes.}, author = {Brody, Joshua and Dziembowski, Stefan and Faust, Sebastian and Pietrzak, Krzysztof Z}, editor = {Kalai, Yael and Reyzin, Leonid}, isbn = {978-331970499-9}, location = {Baltimore, MD, United States}, pages = {56 -- 81}, publisher = {Springer}, title = {{Position based cryptography and multiparty communication complexity}}, doi = {10.1007/978-3-319-70500-2_3}, volume = {10677}, year = {2017}, } @inproceedings{609, abstract = {Several cryptographic schemes and applications are based on functions that are both reasonably efficient to compute and moderately hard to invert, including client puzzles for Denial-of-Service protection, password protection via salted hashes, or recent proof-of-work blockchain systems. Despite their wide use, a definition of this concept has not yet been distilled and formalized explicitly. Instead, either the applications are proven directly based on the assumptions underlying the function, or some property of the function is proven, but the security of the application is argued only informally. The goal of this work is to provide a (universal) definition that decouples the efforts of designing new moderately hard functions and of building protocols based on them, serving as an interface between the two. On a technical level, beyond the mentioned definitions, we instantiate the model for four different notions of hardness. We extend the work of Alwen and Serbinenko (STOC 2015) by providing a general tool for proving security for the first notion of memory-hard functions that allows for provably secure applications. The tool allows us to recover all of the graph-theoretic techniques developed for proving security under the older, non-composable, notion of security used by Alwen and Serbinenko. As an application of our definition of moderately hard functions, we prove the security of two different schemes for proofs of effort (PoE). We also formalize and instantiate the concept of a non-interactive proof of effort (niPoE), in which the proof is not bound to a particular communication context but rather any bit-string chosen by the prover.}, author = {Alwen, Joel F and Tackmann, Björn}, editor = {Kalai, Yael and Reyzin, Leonid}, isbn = {978-331970499-9}, location = {Baltimore, MD, United States}, pages = {493 -- 526}, publisher = {Springer}, title = {{Moderately hard functions: Definition, instantiations, and applications}}, doi = {10.1007/978-3-319-70500-2_17}, volume = {10677}, year = {2017}, }