@misc{5560, abstract = {This repository contains the data collected for the manuscript "Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity". The data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication. Data is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic "mother machine" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication.}, author = {Bergmiller, Tobias and Andersson, Anna M and Tomasek, Kathrin and Balleza, Enrique and Kiviet, Daniel and Hauschild, Robert and Tkacik, Gasper and Guet, Calin C}, keywords = {single cell microscopy, mother machine microfluidic device, AcrAB-TolC pump, multi-drug efflux, Escherichia coli}, publisher = {Institute of Science and Technology Austria}, title = {{Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity}}, doi = {10.15479/AT:ISTA:53}, year = {2017}, } @misc{5561, abstract = {Graph matching problems as described in "Active Graph Matching for Automatic Joint Segmentation and Annotation of C. Elegans." by Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Myers, Gene, MICCAI 2014. Problems are in OpenGM2 hdf5 format (see http://hciweb2.iwr.uni-heidelberg.de/opengm/) and a custom text format used by the feature matching solver described in "Feature Correspondence via Graph Matching: Models and Global Optimization." by Lorenzo Torresani, Vladimir Kolmogorov and Carsten Rother, ECCV 2008, code at http://pub.ist.ac.at/~vnk/software/GraphMatching-v1.02.src.zip. }, author = {Kainmueller, Dagmar and Jug, Florian and Rother, Carsten and Meyers, Gene}, keywords = {graph matching, feature matching, QAP, MAP-inference}, publisher = {Institute of Science and Technology Austria}, title = {{Graph matching problems for annotating C. Elegans}}, doi = {10.15479/AT:ISTA:57}, year = {2017}, } @misc{5562, abstract = {This data was collected as part of the study [1]. It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing: [1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408.}, author = {Marre, Olivier and Tkacik, Gasper and Amodei, Dario and Schneidman, Elad and Bialek, William and Berry, Michael}, keywords = {multi-electrode recording, retinal ganglion cells}, publisher = {Institute of Science and Technology Austria}, title = {{Multi-electrode array recording from salamander retinal ganglion cells}}, doi = {10.15479/AT:ISTA:61}, year = {2017}, } @misc{5563, abstract = {MATLAB code and processed datasets available for reproducing the results in: Lukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast. *equal contributions}, author = {Lukacisin, Martin}, publisher = {Institute of Science and Technology Austria}, title = {{MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'}}, doi = {10.15479/AT:ISTA:64}, year = {2017}, } @misc{5564, abstract = {Compressed Fastq files with whole-genome sequencing data of IS-wt strain D and clones from four evolved populations (A11, C08, C10, D08). Information on this data collection is available in the Methods Section of the primary publication.}, author = {Steinrück, Magdalena and Guet, Calin C}, publisher = {Institute of Science and Technology Austria}, title = {{Fastq files for "Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection"}}, doi = {10.15479/AT:ISTA:65}, year = {2017}, } @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{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{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}, } @article{558, abstract = {Immune specificity is the degree to which a host’s immune system discriminates among various pathogens or antigenic variants. Vertebrate immune memory is highly specific due to antibody responses. On the other hand, some invertebrates show immune priming, i.e. improved survival after secondary exposure to a previously encountered pathogen. Until now, specificity of priming has only been demonstrated via the septic infection route or when live pathogens were used for priming. Therefore, we tested for specificity in the oral priming route in the red flour beetle, Tribolium castaneum. For priming, we used pathogen-free supernatants derived from three different strains of the entomopathogen, Bacillus thuringiensis, which express different Cry toxin variants known for their toxicity against this beetle. Subsequent exposure to the infective spores showed that oral priming was specific for two naturally occurring strains, while a third engineered strain did not induce any priming effect. Our data demonstrate that oral immune priming with a non-infectious bacterial agent can be specific, but the priming effect is not universal across all bacterial strains.}, author = {Futo, Momir and Sell, Marie and Kutzer, Megan and Kurtz, Joachim}, issn = {1744-9561}, journal = {Biology Letters}, number = {12}, publisher = {The Royal Society}, title = {{Specificity of oral immune priming in the red flour beetle Tribolium castaneum}}, doi = {10.1098/rsbl.2017.0632}, volume = {13}, 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 = {1364-5021}, 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}, } @book{567, abstract = {This book is a concise and self-contained introduction of recent techniques to prove local spectral universality for large random matrices. Random matrix theory is a fast expanding research area, and this book mainly focuses on the methods that the authors participated in developing over the past few years. Many other interesting topics are not included, and neither are several new developments within the framework of these methods. The authors have chosen instead to present key concepts that they believe are the core of these methods and should be relevant for future applications. They keep technicalities to a minimum to make the book accessible to graduate students. With this in mind, they include in this book the basic notions and tools for high-dimensional analysis, such as large deviation, entropy, Dirichlet form, and the logarithmic Sobolev inequality. }, author = {Erdös, László and Yau, Horng}, isbn = {9-781-4704-3648-3}, pages = {226}, publisher = {American Mathematical Society}, title = {{A Dynamical Approach to Random Matrix Theory}}, doi = {10.1090/cln/028}, volume = {28}, 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 = {1532-0073}, 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 = {2050-084X}, 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 = {2050-084X}, 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{571, abstract = {Blood platelets are critical for hemostasis and thrombosis and play diverse roles during immune responses. Despite these versatile tasks in mammalian biology, their skills on a cellular level are deemed limited, mainly consisting in rolling, adhesion, and aggregate formation. Here, we identify an unappreciated asset of platelets and show that adherent platelets use adhesion receptors to mechanically probe the adhesive substrate in their local microenvironment. When actomyosin-dependent traction forces overcome substrate resistance, platelets migrate and pile up the adhesive substrate together with any bound particulate material. They use this ability to act as cellular scavengers, scanning the vascular surface for potential invaders and collecting deposited bacteria. Microbe collection by migrating platelets boosts the activity of professional phagocytes, exacerbating inflammatory tissue injury in sepsis. This assigns platelets a central role in innate immune responses and identifies them as potential targets to dampen inflammatory tissue damage in clinical scenarios of severe systemic infection. In addition to their role in thrombosis and hemostasis, platelets can also migrate to sites of infection to help trap bacteria and clear the vascular surface.}, author = {Gärtner, Florian R and Ahmad, Zerkah and Rosenberger, Gerhild and Fan, Shuxia and Nicolai, Leo and Busch, Benjamin and Yavuz, Gökce and Luckner, Manja and Ishikawa Ankerhold, Hellen and Hennel, Roman and Benechet, Alexandre and Lorenz, Michael and Chandraratne, Sue and Schubert, Irene and Helmer, Sebastian and Striednig, Bianca and Stark, Konstantin and Janko, Marek and Böttcher, Ralph and Verschoor, Admar and Leon, Catherine and Gachet, Christian and Gudermann, Thomas and Mederos Y Schnitzler, Michael and Pincus, Zachary and Iannacone, Matteo and Haas, Rainer and Wanner, Gerhard and Lauber, Kirsten and Sixt, Michael K and Massberg, Steffen}, issn = {0092-8674}, journal = {Cell Press}, number = {6}, pages = {1368 -- 1382}, publisher = {Cell Press}, title = {{Migrating platelets are mechano scavengers that collect and bundle bacteria}}, doi = {10.1016/j.cell.2017.11.001}, volume = {171}, 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}, } @inbook{5803, abstract = {Different distance metrics produce Voronoi diagrams with different properties. It is a well-known that on the (real) 2D plane or even on any 3D plane, a Voronoi diagram (VD) based on the Euclidean distance metric produces convex Voronoi regions. In this paper, we first show that this metric produces a persistent VD on the 2D digital plane, as it comprises digitally convex Voronoi regions and hence correctly approximates the corresponding VD on the 2D real plane. Next, we show that on a 3D digital plane D, the Euclidean metric spanning over its voxel set does not guarantee a digital VD which is persistent with the real-space VD. As a solution, we introduce a novel concept of functional-plane-convexity, which is ensured by the Euclidean metric spanning over the pedal set of D. Necessary proofs and some visual result have been provided to adjudge the merit and usefulness of the proposed concept.}, author = {Biswas, Ranita and Bhowmick, Partha}, booktitle = {Combinatorial image analysis}, isbn = {978-3-319-59107-0}, issn = {0302-9743}, location = {Plovdiv, Bulgaria}, pages = {93--104}, publisher = {Springer Nature}, title = {{Construction of persistent Voronoi diagram on 3D digital plane}}, doi = {10.1007/978-3-319-59108-7_8}, volume = {10256}, 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 = {2041-3181}, 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}, }