@techreport{5450,
  abstract     = {In this report the implementation of the institutional data repository IST DataRep at IST Austria will be covered: Starting with the research phase when requirements for a repository were established, the procedure of choosing a repository-software and its customization based on the results of user-testings will be discussed. Followed by reflections on the marketing strategies in regard of impact, and at the end sharing some experiences of one year operating IST DataRep.},
  author       = {Barbara Petritsch},
  publisher    = {IST Austria},
  title        = {{Implementing the institutional data repository IST DataRep}},
  year         = {2017},
}

@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{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{5570,
  abstract     = {Matlab script to calculate the forward migration indexes (<d_y>/<L>) 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},
}

@inproceedings{630,
  abstract     = {Background: Standards have become available to share semantically encoded vital parameters from medical devices, as required for example by personal healthcare records. Standardised sharing of biosignal data largely remains open. Objectives: The goal of this work is to explore available biosignal file format and data exchange standards and profiles, and to conceptualise end-To-end solutions. Methods: The authors reviewed and discussed available biosignal file format standards with other members of international standards development organisations (SDOs). Results: A raw concept for standards based acquisition, storage, archiving and sharing of biosignals was developed. The GDF format may serve for storing biosignals. Signals can then be shared using FHIR resources and may be stored on FHIR servers or in DICOM archives, with DICOM waveforms as one possible format. Conclusion: Currently a group of international SDOs (e.g. HL7, IHE, DICOM, IEEE) is engaged in intensive discussions. This discussion extends existing work that already was adopted by large implementer communities. The concept presented here only reports the current status of the discussion in Austria. The discussion will continue internationally, with results to be expected over the coming years.},
  author       = {Sauermann, Stefan and David, Veronika and Schlögl, Alois and Egelkraut, Reinhard and Frohner, Matthias and Pohn, Birgit and Urbauer, Philipp and Mense, Alexander},
  isbn         = {978-161499758-0},
  location     = {Vienna, Austria},
  pages        = {356 -- 362},
  publisher    = {IOS Press},
  title        = {{Biosignals standards and FHIR: The way to go}},
  doi          = {10.3233/978-1-61499-759-7-356},
  volume       = {236},
  year         = {2017},
}

@article{661,
  abstract     = {During embryonic development, mechanical forces are essential for cellular rearrangements driving tissue morphogenesis. Here, we show that in the early zebrafish embryo, friction forces are generated at the interface between anterior axial mesoderm (prechordal plate, ppl) progenitors migrating towards the animal pole and neurectoderm progenitors moving in the opposite direction towards the vegetal pole of the embryo. These friction forces lead to global rearrangement of cells within the neurectoderm and determine the position of the neural anlage. Using a combination of experiments and simulations, we show that this process depends on hydrodynamic coupling between neurectoderm and ppl as a result of E-cadherin-mediated adhesion between those tissues. Our data thus establish the emergence of friction forces at the interface between moving tissues as a critical force-generating process shaping the embryo.},
  author       = {Smutny, Michael and Ákos, Zsuzsa and Grigolon, Silvia and Shamipour, Shayan and Ruprecht, Verena and Capek, Daniel and Behrndt, Martin and Papusheva, Ekaterina and Tada, Masazumi and Hof, Björn and Vicsek, Tamás and Salbreux, Guillaume and Heisenberg, Carl-Philipp J},
  issn         = {14657392},
  journal      = {Nature Cell Biology},
  pages        = {306 -- 317},
  publisher    = {Nature Publishing Group},
  title        = {{Friction forces position the neural anlage}},
  doi          = {10.1038/ncb3492},
  volume       = {19},
  year         = {2017},
}

@article{665,
  abstract     = {The molecular mechanisms underlying phenotypic variation in isogenic bacterial populations remain poorly understood.We report that AcrAB-TolC, the main multidrug efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex formation. Mother cells inheriting old poles are phenotypically distinct and display increased drug efflux activity relative to daughters. Consequently, we find systematic and long-lived growth differences between mother and daughter cells in the presence of subinhibitory drug concentrations. A simple model for biased partitioning predicts a population structure of long-lived and highly heterogeneous phenotypes. This straightforward mechanism of generating sustained growth rate differences at subinhibitory antibiotic concentrations has implications for understanding the emergence of multidrug resistance in bacteria.},
  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},
  issn         = {00368075},
  journal      = {Science},
  number       = {6335},
  pages        = {311 -- 315},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity}},
  doi          = {10.1126/science.aaf4762},
  volume       = {356},
  year         = {2017},
}

@article{672,
  abstract     = {Trafficking cells frequently transmigrate through epithelial and endothelial monolayers. How monolayers cooperate with the penetrating cells to support their transit is poorly understood. We studied dendritic cell (DC) entry into lymphatic capillaries as a model system for transendothelial migration. We find that the chemokine CCL21, which is the decisive guidance cue for intravasation, mainly localizes in the trans-Golgi network and intracellular vesicles of lymphatic endothelial cells. Upon DC transmigration, these Golgi deposits disperse and CCL21 becomes extracellularly enriched at the sites of endothelial cell-cell junctions. When we reconstitute the transmigration process in vitro, we find that secretion of CCL21-positive vesicles is triggered by a DC contact-induced calcium signal, and selective calcium chelation in lymphatic endothelium attenuates transmigration. Altogether, our data demonstrate a chemokine-mediated feedback between DCs and lymphatic endothelium, which facilitates transendothelial migration.},
  author       = {Vaahtomeri, Kari and Brown, Markus and Hauschild, Robert and De Vries, Ingrid and Leithner, Alexander F and Mehling, Matthias and Kaufmann, Walter and Sixt, Michael K},
  issn         = {22111247},
  journal      = {Cell Reports},
  number       = {5},
  pages        = {902 -- 909},
  publisher    = {Cell Press},
  title        = {{Locally triggered release of the chemokine CCL21 promotes dendritic cell transmigration across lymphatic endothelia}},
  doi          = {10.1016/j.celrep.2017.04.027},
  volume       = {19},
  year         = {2017},
}

@article{674,
  abstract     = {Navigation of cells along gradients of guidance cues is a determining step in many developmental and immunological processes. Gradients can either be soluble or immobilized to tissues as demonstrated for the haptotactic migration of dendritic cells (DCs) toward higher concentrations of immobilized chemokine CCL21. To elucidate how gradient characteristics govern cellular response patterns, we here introduce an in vitro system allowing to track migratory responses of DCs to precisely controlled immobilized gradients of CCL21. We find that haptotactic sensing depends on the absolute CCL21 concentration and local steepness of the gradient, consistent with a scenario where DC directionality is governed by the signal-to-noise ratio of CCL21 binding to the receptor CCR7. We find that the conditions for optimal DC guidance are perfectly provided by the CCL21 gradients we measure in vivo. Furthermore, we find that CCR7 signal termination by the G-protein-coupled receptor kinase 6 (GRK6) is crucial for haptotactic but dispensable for chemotactic CCL21 gradient sensing in vitro and confirm those observations in vivo. These findings suggest that stable, tissue-bound CCL21 gradients as sustainable “roads” ensure optimal guidance in vivo.},
  author       = {Schwarz, Jan and Bierbaum, Veronika and Vaahtomeri, Kari and Hauschild, Robert and Brown, Markus and De Vries, Ingrid and Leithner, Alexander F and Reversat, Anne and Merrin, Jack and Tarrant, Teresa and Bollenbach, Tobias and Sixt, Michael K},
  issn         = {09609822},
  journal      = {Current Biology},
  number       = {9},
  pages        = {1314 -- 1325},
  publisher    = {Cell Press},
  title        = {{Dendritic cells interpret haptotactic chemokine gradients in a manner governed by signal to noise ratio and dependent on GRK6}},
  doi          = {10.1016/j.cub.2017.04.004},
  volume       = {27},
  year         = {2017},
}

@article{675,
  abstract     = {We report the enhancement of infrared absorption of chemisorbed carbon monoxide on platinum in the gap of plasmonic nanoantennas. Our method is based on the self-assembled formation of platinum nanoislands on nanoscopic dipole antenna arrays manufactured via electron beam lithography. We employ systematic variations of the plasmonic antenna resonance to precisely couple to the molecular stretch vibration of carbon monoxide adsorbed on the platinum nanoislands. Ultimately, we reach more than 1500-fold infrared absorption enhancements, allowing for an ultrasensitive detection of a monolayer of chemisorbed carbon monoxide. The developed procedure can be adapted to other metal adsorbents and molecular species and could be utilized for coverage sensing in surface catalytic reactions. },
  author       = {Haase, Johannes and Bagiante, Salvatore and Sigg, Hans and Van Bokhoven, Jeroen},
  journal      = {Optics Letters},
  number       = {10},
  pages        = {1931 -- 1934},
  publisher    = {Optica Publishing Group},
  title        = {{Surface enhanced infrared absorption of chemisorbed carbon monoxide using plasmonic nanoantennas}},
  doi          = {10.1364/OL.42.001931},
  volume       = {42},
  year         = {2017},
}

@article{676,
  abstract     = {The segregation of different cell types into distinct tissues is a fundamental process in metazoan development. Differences in cell adhesion and cortex tension are commonly thought to drive cell sorting by regulating tissue surface tension (TST). However, the role that differential TST plays in cell segregation within the developing embryo is as yet unclear. Here, we have analyzed the role of differential TST for germ layer progenitor cell segregation during zebrafish gastrulation. Contrary to previous observations that differential TST drives germ layer progenitor cell segregation in vitro, we show that germ layers display indistinguishable TST within the gastrulating embryo, arguing against differential TST driving germ layer progenitor cell segregation in vivo. We further show that the osmolarity of the interstitial fluid (IF) is an important factor that influences germ layer TST in vivo, and that lower osmolarity of the IF compared with standard cell culture medium can explain why germ layers display differential TST in culture but not in vivo. Finally, we show that directed migration of mesendoderm progenitors is required for germ layer progenitor cell segregation and germ layer formation.},
  author       = {Krens, Gabriel and Veldhuis, Jim and Barone, Vanessa and Capek, Daniel and Maître, Jean-Léon and Brodland, Wayne and Heisenberg, Carl-Philipp J},
  issn         = {09501991},
  journal      = {Development},
  number       = {10},
  pages        = {1798 -- 1806},
  publisher    = {Company of Biologists},
  title        = {{Interstitial fluid osmolarity modulates the action of differential tissue surface tension in progenitor cell segregation during gastrulation}},
  doi          = {10.1242/dev.144964},
  volume       = {144},
  year         = {2017},
}

@article{1030,
  abstract     = {Auf der Suche nach einem Bibliothekssystem entschied sich die Forschungseinrichtung IST Austria im Jahr 2014 für das Open-Source-Produkt Koha. In einem ersten Schritt wurden zunächst Grundfunktionen aktiviert um im Anschluss diverse zusätzliche Tools zum Einsatz zu bringen. Die große Flexibilität des Systems erlaubt maßgeschneiderte Lösungen für unterschiedlichste Institutionen. Trotz Herausforderungen kann die Bibliothek auf eine erfolgreiche Implementierung zurückblicken.},
  author       = {Villányi, Márton},
  issn         = {2297-3249},
  journal      = {Informationspraxis},
  number       = {1},
  publisher    = {Verein Informationspraxis },
  title        = {{Ein freies Bibliothekssystem für wissenschaftliche Bibliotheken – Werkstattbericht der IST Austria Library}},
  doi          = {10.11588/ip.2017.1.35227},
  volume       = {3},
  year         = {2017},
}

@article{1078,
  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. },
  author       = {Von Wangenheim, Daniel and Hauschild, Robert and Friml, Jirí},
  journal      = {Journal of visualized experiments JoVE},
  number       = {119},
  publisher    = {Journal of Visualized Experiments},
  title        = {{Light sheet fluorescence microscopy of plant roots growing on the surface of a gel}},
  doi          = {10.3791/55044},
  volume       = {2017},
  year         = {2017},
}

@article{946,
  abstract     = {Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes.},
  author       = {Von Wangenheim, Daniel and Hauschild, Robert and Fendrych, Matyas and Barone, Vanessa and Benková, Eva and Friml, Jirí},
  journal      = {eLife},
  publisher    = {eLife Sciences Publications},
  title        = {{Live tracking of moving samples in confocal microscopy for vertically grown roots}},
  doi          = {10.7554/eLife.26792},
  volume       = {6},
  year         = {2017},
}

@article{988,
  abstract     = {The current-phase relation (CPR) of a Josephson junction (JJ) determines how the supercurrent evolves with the superconducting phase difference across the junction. Knowledge of the CPR is essential in order to understand the response of a JJ to various external parameters. Despite the rising interest in ultraclean encapsulated graphene JJs, the CPR of such junctions remains unknown. Here, we use a fully gate-tunable graphene superconducting quantum intereference device (SQUID) to determine the CPR of ballistic graphene JJs. Each of the two JJs in the SQUID is made with graphene encapsulated in hexagonal boron nitride. By independently controlling the critical current of the JJs, we can operate the SQUID either in a symmetric or asymmetric configuration. The highly asymmetric SQUID allows us to phase-bias one of the JJs and thereby directly obtain its CPR. The CPR is found to be skewed, deviating significantly from a sinusoidal form. The skewness can be tuned with the gate voltage and oscillates in antiphase with Fabry-Pérot resistance oscillations of the ballistic graphene cavity. We compare our experiments with tight-binding calculations that include realistic graphene-superconductor interfaces and find a good qualitative agreement.},
  author       = {Nanda, Gaurav and Aguilera Servin, Juan L and Rakyta, Péter and Kormányos, Andor and Kleiner, Reinhold and Koelle, Dieter and Watanabe, Kazuo and Taniguchi, Takashi and Vandersypen, Lieven and Goswami, Srijit},
  issn         = {15306984},
  journal      = {Nano Letters},
  number       = {6},
  pages        = {3396 -- 3401},
  publisher    = {American Chemical Society},
  title        = {{Current-phase relation of ballistic graphene Josephson junctions}},
  doi          = {10.1021/acs.nanolett.7b00097},
  volume       = {17},
  year         = {2017},
}

@inproceedings{12903,
  author       = {Schlögl, Alois and Stadlbauer, Stephan},
  booktitle    = {AHPC16 - Austrian HPC Meeting 2016},
  location     = {Grundlsee, Austria},
  pages        = {37},
  publisher    = {VSC - Vienna Scientific Cluster},
  title        = {{High performance computing at IST Austria: Modelling the human hippocampus}},
  year         = {2016},
}

@article{1321,
  abstract     = {Most migrating cells extrude their front by the force of actin polymerization. Polymerization requires an initial nucleation step, which is mediated by factors establishing either parallel filaments in the case of filopodia or branched filaments that form the branched lamellipodial network. Branches are considered essential for regular cell motility and are initiated by the Arp2/3 complex, which in turn is activated by nucleation-promoting factors of the WASP and WAVE families. Here we employed rapid amoeboid crawling leukocytes and found that deletion of the WAVE complex eliminated actin branching and thus lamellipodia formation. The cells were left with parallel filaments at the leading edge, which translated, depending on the differentiation status of the cell, into a unipolar pointed cell shape or cells with multiple filopodia. Remarkably, unipolar cells migrated with increased speed and enormous directional persistence, while they were unable to turn towards chemotactic gradients. Cells with multiple filopodia retained chemotactic activity but their migration was progressively impaired with increasing geometrical complexity of the extracellular environment. These findings establish that diversified leading edge protrusions serve as explorative structures while they slow down actual locomotion.},
  author       = {Leithner, Alexander F and Eichner, Alexander and Müller, Jan and Reversat, Anne and Brown, Markus and Schwarz, Jan and Merrin, Jack and De Gorter, David and Schur, Florian and Bayerl, Jonathan and De Vries, Ingrid and Wieser, Stefan and Hauschild, Robert and Lai, Frank and Moser, Markus and Kerjaschki, Dontscho and Rottner, Klemens and Small, Victor and Stradal, Theresia and Sixt, Michael K},
  journal      = {Nature Cell Biology},
  pages        = {1253 -- 1259},
  publisher    = {Nature Publishing Group},
  title        = {{Diversified actin protrusions promote environmental exploration but are dispensable for locomotion of leukocytes}},
  doi          = {10.1038/ncb3426},
  volume       = {18},
  year         = {2016},
}

@article{1350,
  abstract     = {The hippocampal CA3 region plays a key role in learning and memory. Recurrent CA3–CA3
synapses are thought to be the subcellular substrate of pattern completion. However, the
synaptic mechanisms of this network computation remain enigmatic. To investigate these mechanisms, we combined functional connectivity analysis with network modeling.
Simultaneous recording fromup to eight CA3 pyramidal neurons revealed that connectivity was sparse, spatially uniform, and highly enriched in disynaptic motifs (reciprocal, convergence,divergence, and chain motifs). Unitary connections were composed of one or two synaptic contacts, suggesting efficient use of postsynaptic space. Real-size modeling indicated that CA3 networks with sparse connectivity, disynaptic motifs, and single-contact connections robustly generated pattern completion.Thus, macro- and microconnectivity contribute to efficient
memory storage and retrieval in hippocampal networks.},
  author       = {Guzmán, José and Schlögl, Alois and Frotscher, Michael and Jonas, Peter M},
  journal      = {Science},
  number       = {6304},
  pages        = {1117 -- 1123},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Synaptic mechanisms of pattern completion in the hippocampal CA3 network}},
  doi          = {10.1126/science.aaf1836},
  volume       = {353},
  year         = {2016},
}

@misc{5555,
  abstract     = {This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies.},
  author       = {Hauschild, Robert},
  keywords     = {cell migration, wide field microscopy, FIJI},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Fiji script to determine average speed and direction of migration of cells}},
  doi          = {10.15479/AT:ISTA:44},
  year         = {2016},
}