@phdthesis{14306, abstract = {Function and activity of biomolecules often depend on their spatial arrangement. The method introduced here allows genetically encoding the spatial arrangement of proteins and DNA. The approach relies on staple proteins that fold double-stranded DNA into user-defined shapes. This thesis describes the development of staple proteins based on the DNA recognition of TAL effectors and presents experimentally derived rules for designing a variety of self-assembling nanoscale shapes featuring structural motifs such as curvature, vertices, corners, and multilayer helix packing. }, author = {Praetorius, Florian M}, publisher = {Technische Universität München}, title = {{Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures}}, year = {2018}, } @unpublished{6183, abstract = {We study the unique solution $m$ of the Dyson equation \[ -m(z)^{-1} = z - a + S[m(z)] \] on a von Neumann algebra $\mathcal{A}$ with the constraint $\mathrm{Im}\,m\geq 0$. Here, $z$ lies in the complex upper half-plane, $a$ is a self-adjoint element of $\mathcal{A}$ and $S$ is a positivity-preserving linear operator on $\mathcal{A}$. We show that $m$ is the Stieltjes transform of a compactly supported $\mathcal{A}$-valued measure on $\mathbb{R}$. Under suitable assumptions, we establish that this measure has a uniformly $1/3$-H\"{o}lder continuous density with respect to the Lebesgue measure, which is supported on finitely many intervals, called bands. In fact, the density is analytic inside the bands with a square-root growth at the edges and internal cubic root cusps whenever the gap between two bands vanishes. The shape of these singularities is universal and no other singularity may occur. We give a precise asymptotic description of $m$ near the singular points. These asymptotics generalize the analysis at the regular edges given in the companion paper on the Tracy-Widom universality for the edge eigenvalue statistics for correlated random matrices [arXiv:1804.07744] and they play a key role in the proof of the Pearcey universality at the cusp for Wigner-type matrices [arXiv:1809.03971,arXiv:1811.04055]. We also extend the finite dimensional band mass formula from [arXiv:1804.07744] to the von Neumann algebra setting by showing that the spectral mass of the bands is topologically rigid under deformations and we conclude that these masses are quantized in some important cases.}, author = {Alt, Johannes and Erdös, László and Krüger, Torben H}, booktitle = {arXiv}, title = {{The Dyson equation with linear self-energy: Spectral bands, edges and cusps}}, year = {2018}, } @unpublished{75, abstract = {We prove that any convex body in the plane can be partitioned into m convex parts of equal areas and perimeters for any integer m≥2; this result was previously known for prime powers m=pk. We also give a higher-dimensional generalization.}, author = {Akopyan, Arseniy and Avvakumov, Sergey and Karasev, Roman}, publisher = {arXiv}, title = {{Convex fair partitions into arbitrary number of pieces}}, doi = {10.48550/arXiv.1804.03057}, year = {2018}, } @article{556, abstract = {We investigate the free boundary Schur process, a variant of the Schur process introduced by Okounkov and Reshetikhin, where we allow the first and the last partitions to be arbitrary (instead of empty in the original setting). The pfaffian Schur process, previously studied by several authors, is recovered when just one of the boundary partitions is left free. We compute the correlation functions of the process in all generality via the free fermion formalism, which we extend with the thorough treatment of “free boundary states.” For the case of one free boundary, our approach yields a new proof that the process is pfaffian. For the case of two free boundaries, we find that the process is not pfaffian, but a closely related process is. We also study three different applications of the Schur process with one free boundary: fluctuations of symmetrized last passage percolation models, limit shapes and processes for symmetric plane partitions and for plane overpartitions.}, author = {Betea, Dan and Bouttier, Jeremie and Nejjar, Peter and Vuletic, Mirjana}, issn = {1424-0637}, journal = {Annales Henri Poincare}, number = {12}, pages = {3663--3742}, publisher = {Springer Nature}, title = {{The free boundary Schur process and applications I}}, doi = {10.1007/s00023-018-0723-1}, volume = {19}, year = {2018}, } @misc{5573, abstract = {Graph matching problems for large displacement optical flow of RGB-D images.}, author = {Alhaija, Hassan and Sellent, Anita and Kondermann, Daniel and Rother, Carsten}, keywords = {graph matching, quadratic assignment problem<}, publisher = {Institute of Science and Technology Austria}, title = {{Graph matching problems for GraphFlow – 6D Large Displacement Scene Flow}}, doi = {10.15479/AT:ISTA:82}, year = {2018}, } @misc{5577, abstract = {Data on Austrian open access publication output at Emerald from 2013-2017 including data analysis.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{Emerald Austrian Publications 2013-2017}}, doi = {10.15479/AT:ISTA:89}, year = {2018}, } @misc{5578, abstract = {Data on Austrian open access publication output at IOP from 2012-2015 including data analysis.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{IOP Austrian Publications 2012-2015}}, doi = {10.15479/AT:ISTA:90}, year = {2018}, } @misc{5574, abstract = {Comparison of Scopus' and publisher's data on Austrian publication output at IOP. }, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{Data Check IOP Scopus vs. Publisher}}, doi = {10.15479/AT:ISTA:86}, year = {2018}, } @phdthesis{278, abstract = {Consortial subscription contracts regulate the digital access to publications between publishers and scientific libraries. However, since a couple of years the tendency towards a freely accessible publishing (Open Access) intensifies. As a consequence of this trend the contractual relationship between licensor and licensee is gradually changing as well: More and more contracts exercise influence on open access publishing. The present study attempts to compare Austrian examples of consortial licence contracts, which include components of open access. It describes the difference between pure subscription contracts and differing innovative deals including open access components. Thereby it becomes obvious that for the evaluation of this licence contracts new methods are needed. An essential new element of such analyses is the evaluation of the open access publication numbers. So this study tries to carry out such publication analyses for Austrian open access deals focusing on quantitative questions: How does the number of publications evolve? How does the open access share change? Publications reports of the publishers and database queries from Scopus form the data basis. The analysis of the data points out that differing approaches of contracts result in highly divergent results: Particular deals can prioritize a saving in costs or else the increase of the open access rate. It is to be assumed that within the following years further numerous open access deals will be negotiated. The finding of this study shall provide guidance.}, author = {Villányi, Márton}, pages = {94}, publisher = {Universität Wien}, title = {{Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken}}, year = {2018}, } @misc{5588, abstract = {Script to perform a simple exponential lifetime fit of a ROI on time stacks acquired with a FLIM X16 TCSPC detector (+example data)}, author = {Hauschild, Robert}, keywords = {FLIM, FRET, fluorescence lifetime imaging}, publisher = {Institute of Science and Technology Austria}, title = {{Fluorescence lifetime analysis of FLIM X16 TCSPC data}}, doi = {10.15479/AT:ISTA:0113}, year = {2018}, } @misc{5582, abstract = {Data on Austrian open access publication output at Taylor&Francis from 2013-2017 including data analysis.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{Taylor&Francis Austrian Publications 2013-2017}}, doi = {10.15479/AT:ISTA:94}, year = {2018}, } @misc{5581, abstract = {Data on Austrian open access publication output at Springer from 2013-2016 including data analysis.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{Springer Austrian Publications 2013-2016}}, doi = {10.15479/AT:ISTA:93}, year = {2018}, } @misc{5580, abstract = {Data on Austrian open access publication output at SAGE from 2013-2017 including data analysis.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{SAGE Austrian Publications 2013-2017}}, doi = {10.15479/AT:ISTA:92}, year = {2018}, } @misc{5579, abstract = {Data on Austrian open access publication output at RSC from 2013-2017 including data analysis.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{RSC Austrian Publications 2013-2017}}, doi = {10.15479/AT:ISTA:91}, year = {2018}, } @misc{5576, abstract = {Comparison of Scopus' and FWF's data on Austrian publication output at T&F.}, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{Data Check T&F Scopus vs. FWF}}, doi = {10.15479/AT:ISTA:88}, year = {2018}, } @misc{5575, abstract = {Comparison of Scopus' and FWF's data on Austrian publication output at RSC. }, author = {Villányi, Márton}, keywords = {Publication analysis, Bibliography, Open Access}, publisher = {Institute of Science and Technology Austria}, title = {{Data Check RSC Scopus vs. FWF}}, doi = {10.15479/AT:ISTA:87}, year = {2018}, } @article{292, abstract = {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.}, author = {Botella Soler, Vicent and Deny, Stephane and Martius, Georg S and Marre, Olivier and Tkacik, Gasper}, journal = {PLoS Computational Biology}, number = {5}, publisher = {Public Library of Science}, title = {{Nonlinear decoding of a complex movie from the mammalian retina}}, doi = {10.1371/journal.pcbi.1006057}, volume = {14}, year = {2018}, } @article{438, abstract = {The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin–antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress.}, author = {Nikolic, Nela and Bergmiller, Tobias and Vandervelde, Alexandra and Albanese, Tanino and Gelens, Lendert and Moll, Isabella}, journal = {Nucleic Acids Research}, number = {6}, pages = {2918--2931}, publisher = {Oxford University Press}, title = {{Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations}}, doi = {10.1093/nar/gky079}, volume = {46}, year = {2018}, } @article{131, abstract = {XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. }, author = {Picard, Marion A and Cosseau, Celine and Ferré, Sabrina and Quack, Thomas and Grevelding, Christoph and Couté, Yohann and Vicoso, Beatriz}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Evolution of gene dosage on the Z-chromosome of schistosome parasites}}, doi = {10.7554/eLife.35684}, volume = {7}, year = {2018}, } @misc{5584, abstract = {This package contains data for the publication "Nonlinear decoding of a complex movie from the mammalian retina" by Deny S. et al, PLOS Comput Biol (2018). The data consists of (i) 91 spike sorted, isolated rat retinal ganglion cells that pass stability and quality criteria, recorded on the multi-electrode array, in response to the presentation of the complex movie with many randomly moving dark discs. The responses are represented as 648000 x 91 binary matrix, where the first index indicates the timebin of duration 12.5 ms, and the second index the neural identity. The matrix entry is 0/1 if the neuron didn't/did spike in the particular time bin. (ii) README file and a graphical illustration of the structure of the experiment, specifying how the 648000 timebins are split into epochs where 1, 2, 4, or 10 discs were displayed, and which stimulus segments are exact repeats or unique ball trajectories. (iii) a 648000 x 400 matrix of luminance traces for each of the 20 x 20 positions ("sites") in the movie frame, with time that is locked to the recorded raster. The luminance traces are produced as described in the manuscript by filtering the raw disc movie with a small gaussian spatial kernel. }, author = {Deny, Stephane and Marre, Olivier and Botella-Soler, Vicente and Martius, Georg S and Tkacik, Gasper}, keywords = {retina, decoding, regression, neural networks, complex stimulus}, publisher = {Institute of Science and Technology Austria}, title = {{Nonlinear decoding of a complex movie from the mammalian retina}}, doi = {10.15479/AT:ISTA:98}, year = {2018}, }