[{"month":"06","article_processing_charge":"No","article_number":"FTu4C.2","title":"Photonic Recurrent Ising Sampler","publication_identifier":{"eisbn":["9781943580576"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"first_name":"Charles","last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles"},{"full_name":"Shen, Yichen","first_name":"Yichen","last_name":"Shen"},{"first_name":"Cristian","last_name":"Zanoci","full_name":"Zanoci, Cristian"},{"first_name":"Mihika","last_name":"Prabhu","full_name":"Prabhu, Mihika"},{"last_name":"Atieh","first_name":"Fadi","full_name":"Atieh, Fadi"},{"last_name":"Jing","first_name":"Li","full_name":"Jing, Li"},{"full_name":"Dubček, Tena","first_name":"Tena","last_name":"Dubček"},{"last_name":"Čeperić","first_name":"Vladimir","full_name":"Čeperić, Vladimir"},{"full_name":"Joannopoulos, John D.","first_name":"John D.","last_name":"Joannopoulos"},{"last_name":"Englund","first_name":"Dirk","full_name":"Englund, Dirk"},{"full_name":"Soljačić, Marin","last_name":"Soljačić","first_name":"Marin"}],"year":"2019","publication_status":"published","OA_type":"closed access","publisher":"Optica Publishing Group","day":"01","publication":"Conference on Lasers and Electro-Optics","type":"conference","quality_controlled":"1","extern":"1","date_updated":"2026-05-05T06:51:29Z","date_created":"2026-03-30T12:22:48Z","date_published":"2019-06-01T00:00:00Z","language":[{"iso":"eng"}],"abstract":[{"text":"We present the Photonic Recurrent Ising Sampler (PRIS), an algorithm tailored for photonic parallel networks, that can sample distributions of arbitrary Ising problems. The PRIS finds the ground state of general Ising problems and probes critical exponents of universality classes.","lang":"eng"}],"_id":"21620","citation":{"ista":"Roques-Carmes C, Shen Y, Zanoci C, Prabhu M, Atieh F, Jing L, Dubček T, Čeperić V, Joannopoulos JD, Englund D, Soljačić M. 2019. Photonic Recurrent Ising Sampler. Conference on Lasers and Electro-Optics. CLEO: Fundamental Science, FTu4C.2.","apa":"Roques-Carmes, C., Shen, Y., Zanoci, C., Prabhu, M., Atieh, F., Jing, L., … Soljačić, M. (2019). Photonic Recurrent Ising Sampler. In <i>Conference on Lasers and Electro-Optics</i>. San Jose, CA, United States: Optica Publishing Group. <a href=\"https://doi.org/10.1364/cleo_qels.2019.ftu4c.2\">https://doi.org/10.1364/cleo_qels.2019.ftu4c.2</a>","short":"C. Roques-Carmes, Y. Shen, C. Zanoci, M. Prabhu, F. Atieh, L. Jing, T. Dubček, V. Čeperić, J.D. Joannopoulos, D. Englund, M. Soljačić, in:, Conference on Lasers and Electro-Optics, Optica Publishing Group, 2019.","mla":"Roques-Carmes, Charles, et al. “Photonic Recurrent Ising Sampler.” <i>Conference on Lasers and Electro-Optics</i>, FTu4C.2, Optica Publishing Group, 2019, doi:<a href=\"https://doi.org/10.1364/cleo_qels.2019.ftu4c.2\">10.1364/cleo_qels.2019.ftu4c.2</a>.","ieee":"C. Roques-Carmes <i>et al.</i>, “Photonic Recurrent Ising Sampler,” in <i>Conference on Lasers and Electro-Optics</i>, San Jose, CA, United States, 2019.","chicago":"Roques-Carmes, Charles, Yichen Shen, Cristian Zanoci, Mihika Prabhu, Fadi Atieh, Li Jing, Tena Dubček, et al. “Photonic Recurrent Ising Sampler.” In <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group, 2019. <a href=\"https://doi.org/10.1364/cleo_qels.2019.ftu4c.2\">https://doi.org/10.1364/cleo_qels.2019.ftu4c.2</a>.","ama":"Roques-Carmes C, Shen Y, Zanoci C, et al. Photonic Recurrent Ising Sampler. In: <i>Conference on Lasers and Electro-Optics</i>. Optica Publishing Group; 2019. doi:<a href=\"https://doi.org/10.1364/cleo_qels.2019.ftu4c.2\">10.1364/cleo_qels.2019.ftu4c.2</a>"},"conference":{"start_date":"2019-05-05","end_date":"2019-05-10","location":"San Jose, CA, United States","name":"CLEO: Fundamental Science"},"oa_version":"None","doi":"10.1364/cleo_qels.2019.ftu4c.2"},{"date_published":"2019-12-01T00:00:00Z","language":[{"iso":"eng"}],"_id":"21568","citation":{"ista":"Hamerly R, Sludds A, Bernstein L, Prabhu M, Roques-Carmes C, Carolan J, Yamamoto Y, Soljacic M, Englund D. 2019. Towards large-scale photonic neural-network accelerators. 2019 IEEE International Electron Devices Meeting. IEDM: International Electron Devices Meeting.","ama":"Hamerly R, Sludds A, Bernstein L, et al. Towards large-scale photonic neural-network accelerators. In: <i>2019 IEEE International Electron Devices Meeting</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/iedm19573.2019.8993624\">10.1109/iedm19573.2019.8993624</a>","chicago":"Hamerly, R., A. Sludds, L. Bernstein, M. Prabhu, Charles Roques-Carmes, J. Carolan, Y. Yamamoto, M. Soljacic, and D. Englund. “Towards Large-Scale Photonic Neural-Network Accelerators.” In <i>2019 IEEE International Electron Devices Meeting</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/iedm19573.2019.8993624\">https://doi.org/10.1109/iedm19573.2019.8993624</a>.","short":"R. Hamerly, A. Sludds, L. Bernstein, M. Prabhu, C. Roques-Carmes, J. Carolan, Y. Yamamoto, M. Soljacic, D. Englund, in:, 2019 IEEE International Electron Devices Meeting, IEEE, 2019.","ieee":"R. Hamerly <i>et al.</i>, “Towards large-scale photonic neural-network accelerators,” in <i>2019 IEEE International Electron Devices Meeting</i>, San Francisco, CA, United States, 2019.","mla":"Hamerly, R., et al. “Towards Large-Scale Photonic Neural-Network Accelerators.” <i>2019 IEEE International Electron Devices Meeting</i>, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/iedm19573.2019.8993624\">10.1109/iedm19573.2019.8993624</a>.","apa":"Hamerly, R., Sludds, A., Bernstein, L., Prabhu, M., Roques-Carmes, C., Carolan, J., … Englund, D. (2019). Towards large-scale photonic neural-network accelerators. In <i>2019 IEEE International Electron Devices Meeting</i>. San Francisco, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/iedm19573.2019.8993624\">https://doi.org/10.1109/iedm19573.2019.8993624</a>"},"abstract":[{"lang":"eng","text":"Optical approaches to AI acceleration have gained intense interest recently due to the potentially breakthrough advantages of photonics: high bandwidth, low power consumption, and efficient data movement. We overview leading photonic AI platforms based on beamsplitter mesh networks, weight banks, and photoelectric multiplication. While the theoretical performance can be orders of magnitude beyond current state of the art, practical issues of chip area, input / output, and crosstalk paint a more nuanced near-term picture of photonic AI acceleration. Both fundamental and near-term limitations to energy efficiency are addressed, and bandwidth limitations due to temporal crosstalk are analyzed."}],"oa_version":"None","conference":{"location":"San Francisco, CA, United States","name":"IEDM: International Electron Devices Meeting","start_date":"2019-12-07","end_date":"2019-12-11"},"scopus_import":"1","doi":"10.1109/iedm19573.2019.8993624","quality_controlled":"1","date_updated":"2026-05-05T07:39:32Z","extern":"1","date_created":"2026-03-30T12:22:47Z","status":"public","author":[{"full_name":"Hamerly, R.","last_name":"Hamerly","first_name":"R."},{"full_name":"Sludds, A.","last_name":"Sludds","first_name":"A."},{"full_name":"Bernstein, L.","last_name":"Bernstein","first_name":"L."},{"full_name":"Prabhu, M.","first_name":"M.","last_name":"Prabhu"},{"first_name":"Charles","last_name":"Roques-Carmes","id":"e2e68fc9-6505-11ef-a541-eb4e72cc3e82","full_name":"Roques-Carmes, Charles"},{"full_name":"Carolan, J.","last_name":"Carolan","first_name":"J."},{"first_name":"Y.","last_name":"Yamamoto","full_name":"Yamamoto, Y."},{"last_name":"Soljacic","first_name":"M.","full_name":"Soljacic, M."},{"last_name":"Englund","first_name":"D.","full_name":"Englund, D."}],"OA_type":"closed access","year":"2019","publication_status":"published","publisher":"IEEE","day":"01","publication":"2019 IEEE International Electron Devices Meeting","type":"conference","month":"12","article_processing_charge":"No","title":"Towards large-scale photonic neural-network accelerators","publication_identifier":{"eisbn":["9781728140322"],"eissn":["2156-017X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publication":"Macromolecules","issue":"16","author":[{"full_name":"Mostafavi, Seyed Hossein","first_name":"Seyed Hossein","last_name":"Mostafavi"},{"first_name":"Wangxiang","last_name":"Li","full_name":"Li, Wangxiang"},{"first_name":"Kyle D.","last_name":"Clark","full_name":"Clark, Kyle D."},{"full_name":"Stricker, Friedrich J","id":"7aca2cfc-46cf-11f0-abd3-8c96b5186745","first_name":"Friedrich J","last_name":"Stricker"},{"first_name":"Javier Read de","last_name":"Alaniz","full_name":"Alaniz, Javier Read de"},{"first_name":"Christopher J.","last_name":"Bardeen","full_name":"Bardeen, Christopher J."}],"status":"public","page":"6311-6317","ddc":["540"],"volume":52,"month":"08","citation":{"ista":"Mostafavi SH, Li W, Clark KD, Stricker FJ, Alaniz JR de, Bardeen CJ. 2019. Photoinduced deadhesion of a polymer film using a photochromic donor-acceptor Stenhouse adduct. Macromolecules. 52(16), 6311–6317.","apa":"Mostafavi, S. H., Li, W., Clark, K. D., Stricker, F. J., Alaniz, J. R. de, &#38; Bardeen, C. J. (2019). Photoinduced deadhesion of a polymer film using a photochromic donor-acceptor Stenhouse adduct. <i>Macromolecules</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.macromol.9b00882\">https://doi.org/10.1021/acs.macromol.9b00882</a>","short":"S.H. Mostafavi, W. Li, K.D. Clark, F.J. Stricker, J.R. de Alaniz, C.J. Bardeen, Macromolecules 52 (2019) 6311–6317.","ieee":"S. H. Mostafavi, W. Li, K. D. Clark, F. J. Stricker, J. R. de Alaniz, and C. J. Bardeen, “Photoinduced deadhesion of a polymer film using a photochromic donor-acceptor Stenhouse adduct,” <i>Macromolecules</i>, vol. 52, no. 16. American Chemical Society, pp. 6311–6317, 2019.","mla":"Mostafavi, Seyed Hossein, et al. “Photoinduced Deadhesion of a Polymer Film Using a Photochromic Donor-Acceptor Stenhouse Adduct.” <i>Macromolecules</i>, vol. 52, no. 16, American Chemical Society, 2019, pp. 6311–17, doi:<a href=\"https://doi.org/10.1021/acs.macromol.9b00882\">10.1021/acs.macromol.9b00882</a>.","chicago":"Mostafavi, Seyed Hossein, Wangxiang Li, Kyle D. Clark, Friedrich J Stricker, Javier Read de Alaniz, and Christopher J. Bardeen. “Photoinduced Deadhesion of a Polymer Film Using a Photochromic Donor-Acceptor Stenhouse Adduct.” <i>Macromolecules</i>. American Chemical Society, 2019. <a href=\"https://doi.org/10.1021/acs.macromol.9b00882\">https://doi.org/10.1021/acs.macromol.9b00882</a>.","ama":"Mostafavi SH, Li W, Clark KD, Stricker FJ, Alaniz JR de, Bardeen CJ. Photoinduced deadhesion of a polymer film using a photochromic donor-acceptor Stenhouse adduct. <i>Macromolecules</i>. 2019;52(16):6311-6317. doi:<a href=\"https://doi.org/10.1021/acs.macromol.9b00882\">10.1021/acs.macromol.9b00882</a>"},"abstract":[{"text":"Photoisomerization of molecules dissolved in a polymer film can modulate its properties. In a previous paper (Mostafavi, S. H.; Macromolecules 2018, 51, 2388−2394), it was found that the ultraviolet light-induced photoisomerization of spiropyran dopants could substantially increase adhesion to a glass surface. In this work, a different photochromic reaction, the visible-light-induced cyclization of a donor–acceptor Stenhouse adduct (DASA), leads to the opposite effect: the deadhesion of a polystyrene film from a clean glass surface. Measurements of the shear and pull-off adhesion strengths before and after visible irradiation show a light-induced decrease of 20–30%. The time required for delamination in water shows an even more dramatic decrease of 90%. Changes in the water contact angle and other measurements suggest that molecular-level noncovalent interactions between the polymer and glass are weakened after photoisomerization, possibly due to the molecular contraction of the DASA that disrupts the interaction between its amine groups and the surface silanols. The ability to reduce polymer adhesion using visible light enables the controlled release of dye molecules from a glass container, where these have been stored as a dry powder, into an aqueous solution. Embedding photochromic molecules in a polymer can lead to new effects that may have practical applications in stimuli-responsive materials.","lang":"eng"}],"date_published":"2019-08-16T00:00:00Z","extern":"1","date_updated":"2026-05-11T08:48:38Z","intvolume":"        52","type":"journal_article","day":"16","publisher":"American Chemical Society","year":"2019","OA_type":"closed access","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1520-5835"],"issn":["0024-9297"]},"title":"Photoinduced deadhesion of a polymer film using a photochromic donor-acceptor Stenhouse adduct","article_processing_charge":"No","doi":"10.1021/acs.macromol.9b00882","scopus_import":"1","oa_version":"None","_id":"21814","article_type":"original","language":[{"iso":"eng"}],"date_created":"2026-05-06T10:52:25Z","quality_controlled":"1"},{"has_accepted_license":"1","abstract":[{"text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes.  \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. ","lang":"eng"}],"citation":{"short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019.","mla":"Lukacisin, Martin. <i>Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory</i>. IST Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>.","ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019.","apa":"Lukacisin, M. (2019). <i>Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>","chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>.","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria."},"supervisor":[{"first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias"}],"related_material":{"record":[{"id":"1029","status":"public","relation":"part_of_dissertation"}]},"date_published":"2019-05-09T00:00:00Z","date_updated":"2025-07-10T11:49:51Z","extern":"1","alternative_title":["IST Austria Thesis"],"status":"public","author":[{"orcid":"0000-0001-6549-4177","last_name":"Lukacisin","first_name":"Martin","full_name":"Lukacisin, Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87"}],"page":"103","file":[{"relation":"hidden","checksum":"829bda074444857c7935171237bb7c0c","creator":"mlukacisin","date_updated":"2020-07-14T12:47:29Z","embargo_to":"open_access","access_level":"closed","date_created":"2019-05-10T13:51:49Z","file_size":43740796,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Draft_v3.4Final.docx","file_id":"6409"},{"relation":"main_file","checksum":"56cb5e97f5f8fc41692401b53832d8e0","date_updated":"2021-02-11T11:17:16Z","embargo":"2020-04-17","creator":"mlukacisin","access_level":"open_access","date_created":"2019-05-10T14:13:42Z","file_size":35228388,"content_type":"application/pdf","file_name":"Thesis_Draft_v3.4FinalA.pdf","file_id":"6410"}],"ddc":["570"],"month":"05","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"doi":"10.15479/AT:ISTA:6392","_id":"6392","oa_version":"Published Version","file_date_updated":"2021-02-11T11:17:16Z","language":[{"iso":"eng"}],"date_created":"2019-05-09T19:53:00Z","type":"dissertation","day":"09","oa":1,"year":"2019","publication_status":"published","publisher":"IST Austria","department":[{"_id":"ToBo"}],"publication_identifier":{"isbn":["978-3-99078-001-5"],"issn":["2663-337X"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory"},{"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"12897"}]},"date_published":"2019-11-06T00:00:00Z","has_accepted_license":"1","abstract":[{"text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models.","lang":"eng"}],"citation":{"short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 6, 157, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3355089.3356576\">10.1145/3355089.3356576</a>.","ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 6. ACM, 2019.","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., &#38; Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3355089.3356576\">https://doi.org/10.1145/3355089.3356576</a>","ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. <i>ACM Transactions on Graphics</i>. 2019;38(6). doi:<a href=\"https://doi.org/10.1145/3355089.3356576\">10.1145/3355089.3356576</a>","chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3355089.3356576\">https://doi.org/10.1145/3355089.3356576</a>.","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157."},"intvolume":"        38","date_updated":"2026-05-17T22:30:07Z","author":[{"first_name":"Christian","last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian"},{"last_name":"Schumacher","first_name":"Christian","full_name":"Schumacher, Christian"},{"last_name":"Knoop","first_name":"Espen","full_name":"Knoop, Espen"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","full_name":"Auzinger, Thomas","last_name":"Auzinger","orcid":"0000-0002-1546-3265","first_name":"Thomas"},{"orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bächer, Moritz","last_name":"Bächer","first_name":"Moritz"}],"status":"public","publication":"ACM Transactions on Graphics","issue":"6","article_number":"157","ddc":["000"],"ec_funded":1,"volume":38,"month":"11","file":[{"file_name":"xcad_sup_mat_siga19.pdf","file_id":"7119","file_size":1673176,"content_type":"application/pdf","date_updated":"2020-07-14T12:47:49Z","creator":"bbickel","access_level":"open_access","date_created":"2019-11-26T14:24:26Z","relation":"supplementary_material","title":"X-CAD Supplemental Material","checksum":"56a2fb019adcb556d2b022f5e5acb68c"},{"file_id":"7120","file_name":"XCAD_authors_version.pdf","content_type":"application/pdf","description":"This is the author's version of the work.","file_size":14563618,"access_level":"open_access","date_created":"2019-11-26T14:24:27Z","creator":"bbickel","date_updated":"2020-07-14T12:47:49Z","checksum":"5f29d76aceb5102e766cbab9b17d776e","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","relation":"main_file"},{"content_type":"video/mp4","file_size":259979129,"file_id":"7121","file_name":"XCAD_video.mp4","checksum":"0d31e123286cbec9e28b2001c2bb0d55","relation":"main_file","date_created":"2019-11-26T14:27:37Z","access_level":"open_access","creator":"bbickel","date_updated":"2020-07-14T12:47:49Z"}],"article_type":"original","file_date_updated":"2020-07-14T12:47:49Z","language":[{"iso":"eng"}],"doi":"10.1145/3355089.3356576","scopus_import":"1","oa_version":"Submitted Version","_id":"7117","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767"}],"quality_controlled":"1","date_created":"2019-11-26T14:22:09Z","isi":1,"publisher":"ACM","year":"2019","publication_status":"published","department":[{"_id":"BeBi"}],"type":"journal_article","oa":1,"external_id":{"isi":["000498397300007"]},"day":"06","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["0730-0301"]}},{"oa_version":"Published Version","scopus_import":"1","_id":"6508","doi":"10.1016/j.cell.2019.04.030","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"file_date_updated":"2020-10-21T07:22:34Z","article_type":"original","isi":1,"date_created":"2019-06-02T21:59:12Z","quality_controlled":"1","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020","grant_number":"742573"},{"grant_number":"P31639","call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton","_id":"268294B6-B435-11E9-9278-68D0E5697425"}],"oa":1,"day":"30","pmid":1,"external_id":{"pmid":["31080065"],"isi":["000469415100013"]},"type":"journal_article","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"BjHo"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2019.04.030"}],"publisher":"Elsevier","year":"2019","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"title":"Bulk actin dynamics drive phase segregation in zebrafish oocytes","article_processing_charge":"No","abstract":[{"text":"Segregation of maternal determinants within the oocyte constitutes the first step in embryo patterning. In zebrafish oocytes, extensive ooplasmic streaming leads to the segregation of ooplasm from yolk granules along the animal-vegetal axis of the oocyte. Here, we show that this process does not rely on cortical actin reorganization, as previously thought, but instead on a cell-cycle-dependent bulk actin polymerization wave traveling from the animal to the vegetal pole of the oocyte. This wave functions in segregation by both pulling ooplasm animally and pushing yolk granules vegetally. Using biophysical experimentation and theory, we show that ooplasm pulling is mediated by bulk actin network flows exerting friction forces on the ooplasm, while yolk granule pushing is achieved by a mechanism closely resembling actin comet formation on yolk granules. Our study defines a novel role of cell-cycle-controlled bulk actin polymerization waves in oocyte polarization via ooplasmic segregation.","lang":"eng"}],"citation":{"chicago":"Shamipour, Shayan, Roland Kardos, Shi-lei Xue, Björn Hof, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">https://doi.org/10.1016/j.cell.2019.04.030</a>.","ama":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. Bulk actin dynamics drive phase segregation in zebrafish oocytes. <i>Cell</i>. 2019;177(6):1463-1479.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">10.1016/j.cell.2019.04.030</a>","apa":"Shamipour, S., Kardos, R., Xue, S., Hof, B., Hannezo, E. B., &#38; Heisenberg, C.-P. J. (2019). Bulk actin dynamics drive phase segregation in zebrafish oocytes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">https://doi.org/10.1016/j.cell.2019.04.030</a>","short":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E.B. Hannezo, C.-P.J. Heisenberg, Cell 177 (2019) 1463–1479.e18.","mla":"Shamipour, Shayan, et al. “Bulk Actin Dynamics Drive Phase Segregation in Zebrafish Oocytes.” <i>Cell</i>, vol. 177, no. 6, Elsevier, 2019, p. 1463–1479.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.030\">10.1016/j.cell.2019.04.030</a>.","ieee":"S. Shamipour, R. Kardos, S. Xue, B. Hof, E. B. Hannezo, and C.-P. J. Heisenberg, “Bulk actin dynamics drive phase segregation in zebrafish oocytes,” <i>Cell</i>, vol. 177, no. 6. Elsevier, p. 1463–1479.e18, 2019.","ista":"Shamipour S, Kardos R, Xue S, Hof B, Hannezo EB, Heisenberg C-PJ. 2019. Bulk actin dynamics drive phase segregation in zebrafish oocytes. Cell. 177(6), 1463–1479.e18."},"has_accepted_license":"1","date_published":"2019-05-30T00:00:00Z","related_material":{"link":[{"url":"https://ist.ac.at/en/news/how-the-cytoplasm-separates-from-the-yolk/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"id":"8350","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-05-17T22:30:09Z","intvolume":"       177","publication":"Cell","issue":"6","author":[{"id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Shamipour, Shayan","first_name":"Shayan","last_name":"Shamipour"},{"id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland","first_name":"Roland","last_name":"Kardos"},{"full_name":"Xue, Shi-lei","id":"31D2C804-F248-11E8-B48F-1D18A9856A87","first_name":"Shi-lei","last_name":"Xue"},{"orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"status":"public","file":[{"file_id":"8686","file_name":"2019_Cell_Shamipour_accepted.pdf","success":1,"content_type":"application/pdf","file_size":3356292,"date_created":"2020-10-21T07:22:34Z","access_level":"open_access","date_updated":"2020-10-21T07:22:34Z","creator":"dernst","checksum":"aea43726d80e35ce3885073a5f05c3e3","relation":"main_file"}],"page":"1463-1479.e18","month":"05","ddc":["570"],"ec_funded":1,"volume":177,"acknowledgement":"We would like to thank Pierre Recho, Guillaume Salbreux, and Silvia Grigolon for advice on the theory, Lila Solnica-Krezel for kindly providing us with zebrafish dachsous mutants, members of the Heisenberg and Hannezo groups for fruitful discussions, and the Bioimaging and zebrafish facilities at IST Austria for their continuous support. This project has received funding from the European Union (European Research Council Advanced Grant 742573 to C.P.H.) and from the Austrian Science Fund (FWF) (P 31639 to E.H.)."},{"related_material":{"link":[{"relation":"press_release","description":"News auf IST Website","url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/"}],"record":[{"status":"public","relation":"dissertation_contains","id":"7186"},{"id":"8350","relation":"dissertation_contains","status":"public"}]},"date_published":"2019-10-31T00:00:00Z","has_accepted_license":"1","citation":{"ieee":"C. Schwayer <i>et al.</i>, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” <i>Cell</i>, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>.","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.","apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. 2019;179(4):937-952.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">10.1016/j.cell.2019.10.006</a>","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>. Cell Press, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.10.006\">https://doi.org/10.1016/j.cell.2019.10.006</a>.","ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18."},"intvolume":"       179","date_updated":"2026-05-17T22:30:09Z","author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","last_name":"Schwayer","first_name":"Cornelia"},{"full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","first_name":"Shayan"},{"first_name":"Kornelija","last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schauer, Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer","orcid":"0000-0001-7659-9142","first_name":"Alexandra"},{"first_name":"M","last_name":"Balda","full_name":"Balda, M"},{"full_name":"Tada, M","first_name":"M","last_name":"Tada"},{"first_name":"K","last_name":"Matter","full_name":"Matter, K"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"status":"public","issue":"4","publication":"Cell","ddc":["570"],"volume":179,"ec_funded":1,"month":"10","page":"937-952.e18","file":[{"relation":"main_file","checksum":"33dac4bb77ee630e2666e936b4d57980","date_updated":"2020-10-21T07:09:45Z","creator":"dernst","access_level":"open_access","date_created":"2020-10-21T07:09:45Z","file_size":8805878,"content_type":"application/pdf","file_name":"2019_Cell_Schwayer_accepted.pdf","success":1,"file_id":"8684"}],"article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2020-10-21T07:09:45Z","doi":"10.1016/j.cell.2019.10.006","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"scopus_import":"1","oa_version":"Submitted Version","_id":"7001","project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"}],"quality_controlled":"1","date_created":"2019-11-12T12:51:06Z","isi":1,"publisher":"Cell Press","year":"2019","publication_status":"published","department":[{"_id":"CaHe"},{"_id":"BjHo"}],"type":"journal_article","oa":1,"pmid":1,"external_id":{"isi":["000493898000012"],"pmid":["31675500"]},"day":"31","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]}},{"corr_author":"1","citation":{"ama":"Kim O, Borges Merjane C, Jonas PM. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In: <i>Intrinsic Activity</i>. Vol 7. Austrian Pharmacological Society; 2019. doi:<a href=\"https://doi.org/10.25006/ia.7.s1-a3.27\">10.25006/ia.7.s1-a3.27</a>","chicago":"Kim, Olena, Carolina Borges Merjane, and Peter M Jonas. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” In <i>Intrinsic Activity</i>, Vol. 7. Austrian Pharmacological Society, 2019. <a href=\"https://doi.org/10.25006/ia.7.s1-a3.27\">https://doi.org/10.25006/ia.7.s1-a3.27</a>.","mla":"Kim, Olena, et al. “Functional Analysis of the Docked Vesicle Pool in Hippocampal Mossy Fiber Terminals by Electron Microscopy.” <i>Intrinsic Activity</i>, vol. 7, no. Suppl. 1, A3.27, Austrian Pharmacological Society, 2019, doi:<a href=\"https://doi.org/10.25006/ia.7.s1-a3.27\">10.25006/ia.7.s1-a3.27</a>.","ieee":"O. Kim, C. Borges Merjane, and P. M. Jonas, “Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy,” in <i>Intrinsic Activity</i>, Innsbruck, Austria, 2019, vol. 7, no. Suppl. 1.","short":"O. Kim, C. Borges Merjane, P.M. Jonas, in:, Intrinsic Activity, Austrian Pharmacological Society, 2019.","apa":"Kim, O., Borges Merjane, C., &#38; Jonas, P. M. (2019). Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. In <i>Intrinsic Activity</i> (Vol. 7). Innsbruck, Austria: Austrian Pharmacological Society. <a href=\"https://doi.org/10.25006/ia.7.s1-a3.27\">https://doi.org/10.25006/ia.7.s1-a3.27</a>","ista":"Kim O, Borges Merjane C, Jonas PM. 2019. Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy. Intrinsic Activity. ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society vol. 7, A3.27."},"conference":{"start_date":"2019-09-25","end_date":"2019-09-27","location":"Innsbruck, Austria","name":"ANA: Austrian Neuroscience Association ; APHAR: Austrian Pharmacological Society"},"related_material":{"record":[{"id":"11196","relation":"dissertation_contains","status":"public"}]},"date_published":"2019-09-11T00:00:00Z","date_updated":"2026-05-17T22:30:34Z","keyword":["hippocampus","mossy fibers","readily releasable pool","electron microscopy"],"intvolume":"         7","publication":"Intrinsic Activity","issue":"Suppl. 1","status":"public","author":[{"id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Olena","orcid":"0000-0003-2344-1039","last_name":"Kim","first_name":"Olena"},{"first_name":"Carolina","orcid":"0000-0003-0005-401X","last_name":"Borges Merjane","full_name":"Borges Merjane, Carolina","id":"4305C450-F248-11E8-B48F-1D18A9856A87"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M"}],"ec_funded":1,"volume":7,"acknowledgement":"This work was supported by the ERC and EU Horizon 2020 (ERC 692692; MSC-IF 708497) and FWF Z 312-B27 Wittgenstein award; W 1205-B09).","article_number":"A3.27","month":"09","doi":"10.25006/ia.7.s1-a3.27","_id":"11222","oa_version":"Published Version","language":[{"iso":"eng"}],"date_created":"2022-04-20T15:06:05Z","project":[{"call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","grant_number":"692692"},{"name":"Presynaptic calcium channels distribution and impact on coupling at the hippocampal mossy fiber synapse","_id":"25BAF7B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"708497"},{"grant_number":"W01205","name":"Zellkommunikation in Gesundheit und Krankheit","_id":"25C3DBB6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312"}],"quality_controlled":"1","type":"conference_abstract","day":"11","oa":1,"publication_status":"published","year":"2019","publisher":"Austrian Pharmacological Society","department":[{"_id":"PeJo"}],"main_file_link":[{"open_access":"1","url":"https://www.intrinsicactivity.org/2019/7/S1/A3.27/"}],"publication_identifier":{"issn":["2309-8503"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","title":"Functional analysis of the docked vesicle pool in hippocampal mossy fiber terminals by electron microscopy"},{"abstract":[{"lang":"eng","text":"Electron microscopy (EM) is a technology that enables visualization of single proteins at a nanometer resolution. However, current protein analysis by EM mainly relies on immunolabeling with gold-particle-conjugated antibodies, which is compromised by large size of antibody, precluding precise detection of protein location in biological samples. Here, we develop a specific chemical labeling method for EM detection of proteins at single-molecular level. Rational design of α-helical peptide tag and probe structure provided a complementary reaction pair that enabled specific cysteine conjugation of the tag. The developed chemical labeling with gold-nanoparticle-conjugated probe showed significantly higher labeling efficiency and detectability of high-density clusters of tag-fused G protein-coupled receptors in freeze-fracture replicas compared with immunogold labeling. Furthermore, in ultrathin sections, the spatial resolution of the chemical labeling was significantly higher than that of antibody-mediated labeling. These results demonstrate substantial advantages of the chemical labeling approach for single protein visualization by EM."}],"citation":{"ama":"Tabata S, Jevtic M, Kurashige N, et al. Electron microscopic detection of single membrane proteins by a specific chemical labeling. <i>iScience</i>. 2019;22(12):256-268. doi:<a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">10.1016/j.isci.2019.11.025</a>","chicago":"Tabata, Shigekazu, Marijo Jevtic, Nobutaka Kurashige, Hirokazu Fuchida, Munetsugu Kido, Kazushi Tani, Naoki Zenmyo, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” <i>IScience</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">https://doi.org/10.1016/j.isci.2019.11.025</a>.","mla":"Tabata, Shigekazu, et al. “Electron Microscopic Detection of Single Membrane Proteins by a Specific Chemical Labeling.” <i>IScience</i>, vol. 22, no. 12, Elsevier, 2019, pp. 256–68, doi:<a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">10.1016/j.isci.2019.11.025</a>.","ieee":"S. Tabata <i>et al.</i>, “Electron microscopic detection of single membrane proteins by a specific chemical labeling,” <i>iScience</i>, vol. 22, no. 12. Elsevier, pp. 256–268, 2019.","short":"S. Tabata, M. Jevtic, N. Kurashige, H. Fuchida, M. Kido, K. Tani, N. Zenmyo, S. Uchinomiya, H. Harada, M. Itakura, I. Hamachi, R. Shigemoto, A. Ojida, IScience 22 (2019) 256–268.","apa":"Tabata, S., Jevtic, M., Kurashige, N., Fuchida, H., Kido, M., Tani, K., … Ojida, A. (2019). Electron microscopic detection of single membrane proteins by a specific chemical labeling. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2019.11.025\">https://doi.org/10.1016/j.isci.2019.11.025</a>","ista":"Tabata S, Jevtic M, Kurashige N, Fuchida H, Kido M, Tani K, Zenmyo N, Uchinomiya S, Harada H, Itakura M, Hamachi I, Shigemoto R, Ojida A. 2019. Electron microscopic detection of single membrane proteins by a specific chemical labeling. iScience. 22(12), 256–268."},"has_accepted_license":"1","corr_author":"1","date_published":"2019-12-20T00:00:00Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"id":"11393","status":"public","relation":"dissertation_contains"}]},"date_updated":"2026-05-17T22:30:39Z","intvolume":"        22","issue":"12","publication":"iScience","author":[{"full_name":"Tabata, Shigekazu","id":"4427179E-F248-11E8-B48F-1D18A9856A87","first_name":"Shigekazu","last_name":"Tabata"},{"last_name":"Jevtic","first_name":"Marijo","id":"4BE3BC94-F248-11E8-B48F-1D18A9856A87","full_name":"Jevtic, Marijo"},{"first_name":"Nobutaka","last_name":"Kurashige","full_name":"Kurashige, Nobutaka"},{"full_name":"Fuchida, Hirokazu","last_name":"Fuchida","first_name":"Hirokazu"},{"first_name":"Munetsugu","last_name":"Kido","full_name":"Kido, Munetsugu"},{"last_name":"Tani","first_name":"Kazushi","full_name":"Tani, Kazushi"},{"full_name":"Zenmyo, Naoki","first_name":"Naoki","last_name":"Zenmyo"},{"first_name":"Shohei","last_name":"Uchinomiya","full_name":"Uchinomiya, Shohei"},{"full_name":"Harada, Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Harumi","orcid":"0000-0001-7429-7896","last_name":"Harada"},{"full_name":"Itakura, Makoto","first_name":"Makoto","last_name":"Itakura"},{"full_name":"Hamachi, Itaru","last_name":"Hamachi","first_name":"Itaru"},{"first_name":"Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ojida","first_name":"Akio","full_name":"Ojida, Akio"}],"status":"public","file":[{"file_name":"2019_iScience_Tabata.pdf","file_id":"7448","file_size":7197776,"content_type":"application/pdf","date_updated":"2020-07-14T12:47:57Z","creator":"dernst","date_created":"2020-02-04T10:48:36Z","access_level":"open_access","relation":"main_file","checksum":"f3e90056a49f09b205b1c4f8c739ffd1"}],"page":"256-268","month":"12","ddc":["570"],"ec_funded":1,"volume":22,"oa_version":"Published Version","scopus_import":"1","_id":"7391","doi":"10.1016/j.isci.2019.11.025","file_date_updated":"2020-07-14T12:47:57Z","language":[{"iso":"eng"}],"article_type":"original","isi":1,"date_created":"2020-01-29T15:56:56Z","quality_controlled":"1","project":[{"grant_number":"694539","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"720270","call_identifier":"H2020","name":"Human Brain Project Specific Grant Agreement 1","_id":"25CBA828-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000504652000020"],"pmid":["31786521"]},"pmid":1,"day":"20","type":"journal_article","department":[{"_id":"RySh"}],"publisher":"Elsevier","year":"2019","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2589-0042"]},"title":"Electron microscopic detection of single membrane proteins by a specific chemical labeling","article_processing_charge":"No"},{"external_id":{"isi":["000462738000034"]},"day":"29","oa":1,"type":"journal_article","department":[{"_id":"JoCs"}],"publication_status":"published","year":"2019","publisher":"American Association for the Advancement of Science","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","title":"The entorhinal cognitive map is attracted to goals","_id":"6194","scopus_import":"1","oa_version":"Submitted Version","doi":"10.1126/science.aav4837","file_date_updated":"2020-07-14T12:47:23Z","language":[{"iso":"eng"}],"article_type":"original","isi":1,"date_created":"2019-04-04T08:39:30Z","quality_controlled":"1","project":[{"grant_number":"281511","call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"issue":"6434","publication":"Science","status":"public","author":[{"full_name":"Boccara, Charlotte N.","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","first_name":"Charlotte N.","orcid":"0000-0001-7237-5109","last_name":"Boccara"},{"orcid":"0000-0001-8849-6570","last_name":"Nardin","first_name":"Michele","full_name":"Nardin, Michele","id":"30BD0376-F248-11E8-B48F-1D18A9856A87"},{"id":"39AF1E74-F248-11E8-B48F-1D18A9856A87","full_name":"Stella, Federico","last_name":"Stella","orcid":"0000-0001-9439-3148","first_name":"Federico"},{"full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","last_name":"O'Neill"},{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L"}],"file":[{"file_id":"7826","file_name":"2019_Science_Boccara.pdf","content_type":"application/pdf","file_size":9045923,"date_created":"2020-05-14T09:11:10Z","access_level":"open_access","creator":"dernst","date_updated":"2020-07-14T12:47:23Z","checksum":"5e6b16742cde10a560cfaf2130764da1","relation":"main_file"}],"page":"1443-1447","month":"03","volume":363,"ec_funded":1,"ddc":["570"],"citation":{"chicago":"Boccara, Charlotte N., Michele Nardin, Federico Stella, Joseph O’Neill, and Jozsef L Csicsvari. “The Entorhinal Cognitive Map Is Attracted to Goals.” <i>Science</i>. American Association for the Advancement of Science, 2019. <a href=\"https://doi.org/10.1126/science.aav4837\">https://doi.org/10.1126/science.aav4837</a>.","ama":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. The entorhinal cognitive map is attracted to goals. <i>Science</i>. 2019;363(6434):1443-1447. doi:<a href=\"https://doi.org/10.1126/science.aav4837\">10.1126/science.aav4837</a>","apa":"Boccara, C. N., Nardin, M., Stella, F., O’Neill, J., &#38; Csicsvari, J. L. (2019). The entorhinal cognitive map is attracted to goals. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aav4837\">https://doi.org/10.1126/science.aav4837</a>","short":"C.N. Boccara, M. Nardin, F. Stella, J. O’Neill, J.L. Csicsvari, Science 363 (2019) 1443–1447.","ieee":"C. N. Boccara, M. Nardin, F. Stella, J. O’Neill, and J. L. Csicsvari, “The entorhinal cognitive map is attracted to goals,” <i>Science</i>, vol. 363, no. 6434. American Association for the Advancement of Science, pp. 1443–1447, 2019.","mla":"Boccara, Charlotte N., et al. “The Entorhinal Cognitive Map Is Attracted to Goals.” <i>Science</i>, vol. 363, no. 6434, American Association for the Advancement of Science, 2019, pp. 1443–47, doi:<a href=\"https://doi.org/10.1126/science.aav4837\">10.1126/science.aav4837</a>.","ista":"Boccara CN, Nardin M, Stella F, O’Neill J, Csicsvari JL. 2019. The entorhinal cognitive map is attracted to goals. Science. 363(6434), 1443–1447."},"abstract":[{"text":"Grid cells with their rigid hexagonal firing fields are thought to provide an invariant metric to the hippocampal cognitive map, yet environmental geometrical features have recently been shown to distort the grid structure. Given that the hippocampal role goes beyond space, we tested the influence of nonspatial information on the grid organization. We trained rats to daily learn three new reward locations on a cheeseboard maze while recording from the medial entorhinal cortex and the hippocampal CA1 region. Many grid fields moved toward goal location, leading to long-lasting deformations of the entorhinal map. Therefore, distortions in the grid structure contribute to goal representation during both learning and recall, which demonstrates that grid cells participate in mnemonic coding and do not merely provide a simple metric of space.","lang":"eng"}],"has_accepted_license":"1","date_published":"2019-03-29T00:00:00Z","related_material":{"record":[{"relation":"popular_science","status":"public","id":"6062"},{"id":"11932","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/grid-cells-create-treasure-map-in-rat-brain/"}]},"date_updated":"2026-05-17T22:30:42Z","intvolume":"       363"},{"ddc":["570"],"month":"07","page":"171","file":[{"file_size":74735267,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Kopf_PhD_Thesis.docx","file_id":"6950","relation":"source_file","checksum":"00d100d6468e31e583051e0a006b640c","creator":"akopf","date_updated":"2020-10-17T22:30:03Z","access_level":"closed","date_created":"2019-10-15T05:28:42Z","embargo_to":"open_access"},{"date_updated":"2020-10-17T22:30:03Z","embargo":"2020-10-16","creator":"akopf","date_created":"2019-10-15T05:28:47Z","access_level":"open_access","relation":"main_file","checksum":"5d1baa899993ae6ca81aebebe1797000","file_name":"Kopf_PhD_Thesis1.pdf","file_id":"6951","file_size":52787224,"content_type":"application/pdf"}],"author":[{"full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja","last_name":"Kopf","orcid":"0000-0002-2187-6656"}],"status":"public","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"date_updated":"2026-04-08T07:11:03Z","related_material":{"record":[{"id":"6877","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"15"},{"status":"public","relation":"part_of_dissertation","id":"6328"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/feeling-like-a-cell/"}]},"date_published":"2019-07-24T00:00:00Z","corr_author":"1","has_accepted_license":"1","supervisor":[{"first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria.","chicago":"Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6891\">https://doi.org/10.15479/AT:ISTA:6891</a>.","ama":"Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6891\">10.15479/AT:ISTA:6891</a>","apa":"Kopf, A. (2019). <i>The implication of cytoskeletal dynamics on leukocyte migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6891\">https://doi.org/10.15479/AT:ISTA:6891</a>","mla":"Kopf, Aglaja. <i>The Implication of Cytoskeletal Dynamics on Leukocyte Migration</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6891\">10.15479/AT:ISTA:6891</a>.","ieee":"A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,” Institute of Science and Technology Austria, 2019.","short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019."},"abstract":[{"lang":"eng","text":"While cells of mesenchymal or epithelial origin perform their effector functions in a purely anchorage dependent manner, cells derived from the hematopoietic lineage are not committed to operate only within a specific niche. Instead, these cells are able to function autonomously of the molecular composition in a broad range of tissue compartments. By this means, cells of the hematopoietic lineage retain the capacity to disseminate into connective tissue and recirculate between organs, building the foundation for essential processes such as tissue regeneration or immune surveillance. \r\nCells of the immune system, specifically leukocytes, are extraordinarily good at performing this task. These cells are able to flexibly shift their mode of migration between an adhesion-mediated and an adhesion-independent manner, instantaneously accommodating for any changes in molecular composition of the external scaffold. The key component driving directed leukocyte migration is the chemokine receptor 7, which guides the cell along gradients of chemokine ligand. Therefore, the physical destination of migrating leukocytes is purely deterministic, i.e. given by global directional cues such as chemokine gradients. \r\nNevertheless, these cells typically reside in three-dimensional scaffolds of inhomogeneous complexity, raising the question whether cells are able to locally discriminate between multiple optional migration routes. Current literature provides evidence that leukocytes, specifically dendritic cells, do indeed probe their surrounding by virtue of multiple explorative protrusions. However, it remains enigmatic how these cells decide which one is the more favorable route to follow and what are the key players involved in performing this task. Due to the heterogeneous environment of most tissues, and the vast adaptability of migrating leukocytes, at this time it is not clear to what extent leukocytes are able to optimize their migratory strategy by adapting their level of adhesiveness. And, given the fact that leukocyte migration is characterized by branched cell shapes in combination with high migration velocities, it is reasonable to assume that these cells require fine tuned shape maintenance mechanisms that tightly coordinate protrusion and adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed to elucidate how rapidly migrating leukocytes opt for an ideal migratory path while maintaining a continuous cell shape and balancing adhesive forces to efficiently navigate through complex microenvironments. \r\nThe results of this study unraveled a role for the microtubule cytoskeleton in promoting the decision making process during path finding and for the first time point towards a microtubule-mediated function in cell shape maintenance of highly ramified cells such as dendritic cells. Furthermore, we found that migrating low-adhesive leukocytes are able to instantaneously adapt to increased tensile load by engaging adhesion receptors. This response was only occurring tangential to the substrate while adhesive properties in the vertical direction were not increased. As leukocytes are primed for rapid migration velocities, these results demonstrate that leukocyte integrins are able to confer a high level of traction forces parallel to the cell membrane along the direction of migration without wasting energy in gluing the cell to the substrate. \r\nThus, the data in the here presented thesis provide new insights into the pivotal role of cytoskeletal dynamics and the mechanisms of force transduction during leukocyte migration. \r\nThereby the here presented results help to further define fundamental principles underlying leukocyte migration and open up potential therapeutic avenues of clinical relevance.\r\n"}],"title":"The implication of cytoskeletal dynamics on leukocyte migration","article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"isbn":["978-3-99078-002-2"],"eissn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","year":"2019","publication_status":"published","department":[{"_id":"MiSi"}],"type":"dissertation","oa":1,"day":"24","project":[{"grant_number":"W01250-B20","_id":"265E2996-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF"}],"date_created":"2019-09-19T08:19:44Z","file_date_updated":"2020-10-17T22:30:03Z","OA_place":"publisher","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:6891","oa_version":"Published Version","_id":"6891"},{"publication":"Nature","author":[{"id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","full_name":"Renkawitz, Jörg","first_name":"Jörg","last_name":"Renkawitz","orcid":"0000-0003-2856-3369"},{"id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","full_name":"Kopf, Aglaja","first_name":"Aglaja","orcid":"0000-0002-2187-6656","last_name":"Kopf"},{"full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","last_name":"Stopp","first_name":"Julian A"},{"first_name":"Ingrid","last_name":"de Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","full_name":"de Vries, Ingrid"},{"first_name":"Meghan K.","last_name":"Driscoll","full_name":"Driscoll, Meghan K."},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert"},{"full_name":"Welf, Erik S.","first_name":"Erik S.","last_name":"Welf"},{"full_name":"Danuser, Gaudenz","last_name":"Danuser","first_name":"Gaudenz"},{"last_name":"Fiolka","first_name":"Reto","full_name":"Fiolka, Reto"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"status":"public","page":"546-550","ec_funded":1,"volume":568,"month":"04","abstract":[{"lang":"eng","text":"During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion."}],"citation":{"ista":"Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 568, 546–550.","apa":"Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin, J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along the path of least resistance. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1087-5\">https://doi.org/10.1038/s41586-019-1087-5</a>","ieee":"J. Renkawitz <i>et al.</i>, “Nuclear positioning facilitates amoeboid migration along the path of least resistance,” <i>Nature</i>, vol. 568. Springer Nature, pp. 546–550, 2019.","mla":"Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” <i>Nature</i>, vol. 568, Springer Nature, 2019, pp. 546–50, doi:<a href=\"https://doi.org/10.1038/s41586-019-1087-5\">10.1038/s41586-019-1087-5</a>.","short":"J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin, R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.","chicago":"Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K. Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1087-5\">https://doi.org/10.1038/s41586-019-1087-5</a>.","ama":"Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. <i>Nature</i>. 2019;568:546-550. doi:<a href=\"https://doi.org/10.1038/s41586-019-1087-5\">10.1038/s41586-019-1087-5</a>"},"related_material":{"link":[{"url":"https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/","relation":"press_release","description":"News on IST Homepage"}],"record":[{"status":"public","relation":"dissertation_contains","id":"14697"},{"status":"public","relation":"dissertation_contains","id":"6891"}]},"date_published":"2019-04-25T00:00:00Z","date_updated":"2026-05-17T22:30:43Z","intvolume":"       568","type":"journal_article","oa":1,"pmid":1,"day":"25","external_id":{"pmid":["30944468"],"isi":["000465594200050"]},"publisher":"Springer Nature","year":"2019","publication_status":"published","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/","open_access":"1"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Nuclear positioning facilitates amoeboid migration along the path of least resistance","article_processing_charge":"No","doi":"10.1038/s41586-019-1087-5","acknowledged_ssus":[{"_id":"SSU"}],"scopus_import":"1","oa_version":"Submitted Version","_id":"6328","article_type":"letter_note","language":[{"iso":"eng"}],"date_created":"2019-04-17T06:52:28Z","isi":1,"project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","grant_number":"281556"},{"grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020"},{"grant_number":"W01250-B20","call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","_id":"265FAEBA-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"name":"Molecular and system level view of immune cell migration","_id":"25A48D24-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1396-2014"}],"quality_controlled":"1"},{"intvolume":"         8","date_updated":"2026-05-17T22:30:44Z","date_published":"2019-06-06T00:00:00Z","related_material":{"record":[{"id":"9804","relation":"research_data","status":"public"},{"relation":"dissertation_contains","status":"public","id":"11388"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Castro JP, Yancoskie MN, Marchini M, Belohlavy S, Hiramatsu L, Kučka M, Beluch WH, Naumann R, Skuplik I, Cobb J, Barton NH, Rolian C, Chan YF. 2019. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. eLife. 8, e42014.","apa":"Castro, J. P., Yancoskie, M. N., Marchini, M., Belohlavy, S., Hiramatsu, L., Kučka, M., … Chan, Y. F. (2019). An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.42014\">https://doi.org/10.7554/eLife.42014</a>","ieee":"J. P. Castro <i>et al.</i>, “An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","mla":"Castro, João Pl, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” <i>ELife</i>, vol. 8, e42014, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/eLife.42014\">10.7554/eLife.42014</a>.","short":"J.P. Castro, M.N. Yancoskie, M. Marchini, S. Belohlavy, L. Hiramatsu, M. Kučka, W.H. Beluch, R. Naumann, I. Skuplik, J. Cobb, N.H. Barton, C. Rolian, Y.F. Chan, ELife 8 (2019).","chicago":"Castro, João Pl, Michelle N. Yancoskie, Marta Marchini, Stefanie Belohlavy, Layla Hiramatsu, Marek Kučka, William H. Beluch, et al. “An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/eLife.42014\">https://doi.org/10.7554/eLife.42014</a>.","ama":"Castro JP, Yancoskie MN, Marchini M, et al. An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/eLife.42014\">10.7554/eLife.42014</a>"},"abstract":[{"text":"Evolutionary studies are often limited by missing data that are critical to understanding the history of selection. Selection experiments, which reproduce rapid evolution under controlled conditions, are excellent tools to study how genomes evolve under selection. Here we present a genomic dissection of the Longshanks selection experiment, in which mice were selectively bred over 20 generations for longer tibiae relative to body mass, resulting in 13% longer tibiae in two replicates. We synthesized evolutionary theory, genome sequences and molecular genetics to understand the selection response and found that it involved both polygenic adaptation and discrete loci of major effect, with the strongest loci tending to be selected in parallel between replicates. We show that selection may favor de-repression of bone growth through inactivating two limb enhancers of an inhibitor, Nkx3-2. Our integrative genomic analyses thus show that it is possible to connect individual base-pair changes to the overall selection response.","lang":"eng"}],"has_accepted_license":"1","month":"06","article_number":"e42014","ddc":["576"],"volume":8,"file":[{"checksum":"fa0936fe58f0d9e3f8e75038570e5a17","relation":"main_file","date_created":"2019-07-29T07:41:18Z","access_level":"open_access","date_updated":"2020-07-14T12:47:38Z","creator":"apreinsp","content_type":"application/pdf","file_size":6748249,"file_id":"6721","file_name":"2019_eLife_Castro.pdf"}],"author":[{"full_name":"Castro, João Pl","last_name":"Castro","first_name":"João Pl"},{"full_name":"Yancoskie, Michelle N.","first_name":"Michelle N.","last_name":"Yancoskie"},{"full_name":"Marchini, Marta","last_name":"Marchini","first_name":"Marta"},{"id":"43FE426A-F248-11E8-B48F-1D18A9856A87","full_name":"Belohlavy, Stefanie","last_name":"Belohlavy","orcid":"0000-0002-9849-498X","first_name":"Stefanie"},{"last_name":"Hiramatsu","first_name":"Layla","full_name":"Hiramatsu, Layla"},{"full_name":"Kučka, Marek","first_name":"Marek","last_name":"Kučka"},{"full_name":"Beluch, William H.","first_name":"William H.","last_name":"Beluch"},{"last_name":"Naumann","first_name":"Ronald","full_name":"Naumann, Ronald"},{"full_name":"Skuplik, Isabella","last_name":"Skuplik","first_name":"Isabella"},{"last_name":"Cobb","first_name":"John","full_name":"Cobb, John"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Rolian","first_name":"Campbell","full_name":"Rolian, Campbell"},{"full_name":"Chan, Yingguang Frank","last_name":"Chan","first_name":"Yingguang Frank"}],"status":"public","publication":"eLife","quality_controlled":"1","isi":1,"date_created":"2019-07-28T21:59:17Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:38Z","scopus_import":"1","oa_version":"Published Version","_id":"6713","doi":"10.7554/eLife.42014","title":"An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","publication_status":"published","year":"2019","oa":1,"external_id":{"pmid":["31169497"],"isi":["000473588700001"]},"pmid":1,"day":"06","type":"journal_article"},{"date_created":"2019-09-15T22:00:46Z","isi":1,"quality_controlled":"1","doi":"10.1016/j.cell.2019.08.047","scopus_import":"1","oa_version":"None","_id":"6877","article_type":"original","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"title":"The neural crest pitches in to remove apoptotic debris","article_processing_charge":"No","type":"journal_article","external_id":{"isi":["000486618500011"],"pmid":["31539498"]},"pmid":1,"day":"19","publisher":"Elsevier","publication_status":"published","year":"2019","department":[{"_id":"MiSi"}],"date_updated":"2026-05-17T22:30:43Z","intvolume":"       179","citation":{"ista":"Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris. Cell. 179(1), 51–53.","chicago":"Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">https://doi.org/10.1016/j.cell.2019.08.047</a>.","ama":"Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. <i>Cell</i>. 2019;179(1):51-53. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">10.1016/j.cell.2019.08.047</a>","apa":"Kopf, A., &#38; Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic debris. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">https://doi.org/10.1016/j.cell.2019.08.047</a>","ieee":"A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,” <i>Cell</i>, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.","mla":"Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic Debris.” <i>Cell</i>, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.08.047\">10.1016/j.cell.2019.08.047</a>.","short":"A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53."},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6891"}]},"date_published":"2019-09-19T00:00:00Z","page":"51-53","volume":179,"month":"09","issue":"1","publication":"Cell","author":[{"full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","orcid":"0000-0002-2187-6656","first_name":"Aglaja"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","first_name":"Michael K","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"status":"public"},{"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","title":"Re-activation of stem cell pathways for pattern restoration in plant wound healing","type":"journal_article","external_id":{"pmid":["31051107"],"isi":["000466843000015"]},"day":"02","pmid":1,"oa":1,"publication_status":"published","year":"2019","publisher":"Elsevier","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"date_created":"2019-04-28T21:59:14Z","isi":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"}],"quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"}],"doi":"10.1016/j.cell.2019.04.015","_id":"6351","scopus_import":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:28Z","page":"957-969.e13","file":[{"file_name":"2019_Cell_Marhava.pdf","file_id":"6411","file_size":10272032,"content_type":"application/pdf","date_updated":"2020-07-14T12:47:28Z","creator":"dernst","date_created":"2019-05-13T06:12:45Z","access_level":"open_access","relation":"main_file","checksum":"4ceba04a96a74f5092ec3ce2c579a0c7"}],"ec_funded":1,"volume":177,"ddc":["570"],"month":"05","issue":"4","publication":"Cell","status":"public","author":[{"first_name":"Petra","last_name":"Marhavá","full_name":"Marhavá, Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Lukas","orcid":"0000-0001-8295-2926","last_name":"Hörmayer","full_name":"Hörmayer, Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6111-9353","last_name":"Yoshida","first_name":"Saiko","id":"2E46069C-F248-11E8-B48F-1D18A9856A87","full_name":"Yoshida, Saiko"},{"id":"3F45B078-F248-11E8-B48F-1D18A9856A87","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741","last_name":"Marhavy","first_name":"Peter"},{"last_name":"Benková","orcid":"0000-0002-8510-9739","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"date_updated":"2026-05-17T22:30:46Z","intvolume":"       177","corr_author":"1","has_accepted_license":"1","abstract":[{"text":"A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing.","lang":"eng"}],"citation":{"ieee":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” <i>Cell</i>, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019.","short":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13.","mla":"Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>.","apa":"Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., &#38; Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>","ama":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. 2019;177(4):957-969.e13. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>","chicago":"Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>.","ista":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13."},"related_material":{"record":[{"id":"9992","status":"public","relation":"dissertation_contains"}],"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2019-05-02T00:00:00Z"},{"type":"journal_article","day":"01","pmid":1,"external_id":{"pmid":["31585333"],"isi":["000502890600017"]},"oa":1,"publication_status":"published","year":"2019","publisher":"Elsevier","department":[{"_id":"JiFr"}],"publication_identifier":{"issn":["1369-5266"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","title":"Targeted cell ablation-based insights into wound healing and restorative patterning","doi":"10.1016/j.pbi.2019.08.006","_id":"6943","oa_version":"Published Version","scopus_import":"1","article_type":"original","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:45Z","date_created":"2019-10-14T07:00:24Z","isi":1,"project":[{"grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"}],"quality_controlled":"1","publication":"Current Opinion in Plant Biology","status":"public","author":[{"last_name":"Hörmayer","orcid":"0000-0001-8295-2926","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","full_name":"Hörmayer, Lukas"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"page":"124-130","file":[{"file_name":"2019_CurrentOpinionPlant_Hoermayer.pdf","file_id":"6946","file_size":1659288,"content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:47:45Z","access_level":"open_access","date_created":"2019-10-14T14:48:21Z","relation":"main_file","checksum":"d6fd68a6e965f1efe3f0bf2d2070a616"}],"ec_funded":1,"volume":52,"ddc":["580"],"month":"12","corr_author":"1","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Plants as sessile organisms are constantly under attack by herbivores, rough environmental situations, or mechanical pressure. These challenges often lead to the induction of wounds or destruction of already specified and developed tissues. Additionally, wounding makes plants vulnerable to invasion by pathogens, which is why wound signalling often triggers specific defence responses. To stay competitive or, eventually, survive under these circumstances, plants need to regenerate efficiently, which in rigid, tissue migration-incompatible plant tissues requires post-embryonic patterning and organogenesis. Now, several studies used laser-assisted single cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we discuss their findings and put them into context of a broader spectrum of wound signalling, pathogen responses and tissue as well as organ regeneration."}],"citation":{"ista":"Hörmayer L, Friml J. 2019. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 52, 124–130.","ieee":"L. Hörmayer and J. Friml, “Targeted cell ablation-based insights into wound healing and restorative patterning,” <i>Current Opinion in Plant Biology</i>, vol. 52. Elsevier, pp. 124–130, 2019.","short":"L. Hörmayer, J. Friml, Current Opinion in Plant Biology 52 (2019) 124–130.","mla":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” <i>Current Opinion in Plant Biology</i>, vol. 52, Elsevier, 2019, pp. 124–30, doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">10.1016/j.pbi.2019.08.006</a>.","apa":"Hörmayer, L., &#38; Friml, J. (2019). Targeted cell ablation-based insights into wound healing and restorative patterning. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">https://doi.org/10.1016/j.pbi.2019.08.006</a>","ama":"Hörmayer L, Friml J. Targeted cell ablation-based insights into wound healing and restorative patterning. <i>Current Opinion in Plant Biology</i>. 2019;52:124-130. doi:<a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">10.1016/j.pbi.2019.08.006</a>","chicago":"Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.pbi.2019.08.006\">https://doi.org/10.1016/j.pbi.2019.08.006</a>."},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9992"}]},"date_published":"2019-12-01T00:00:00Z","date_updated":"2026-05-17T22:30:46Z","intvolume":"        52"},{"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10058"}]},"date_published":"2019-10-13T00:00:00Z","corr_author":"1","abstract":[{"text":"We study double quantum dots in a Ge/SiGe heterostructure and test their maturity towards singlet-triplet ($S-T_0$) qubits. We demonstrate a large range of tunability, from two single quantum dots to a double quantum dot. We measure Pauli spin blockade and study the anisotropy of the $g$-factor. We use an adjacent quantum dot for sensing charge transitions in the double quantum dot at interest. In conclusion, Ge/SiGe possesses all ingredients necessary for building a singlet-triplet qubit.","lang":"eng"}],"citation":{"mla":"Hofmann, Andrea C., et al. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” <i>ArXiv</i>, 1910.05841, doi:<a href=\"https://doi.org/10.48550/arXiv.1910.05841\">10.48550/arXiv.1910.05841</a>.","ieee":"A. C. Hofmann <i>et al.</i>, “Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits,” <i>arXiv</i>. .","short":"A.C. Hofmann, D. Jirovec, M. Borovkov, I. Prieto Gonzalez, A. Ballabio, J. Frigerio, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.).","apa":"Hofmann, A. C., Jirovec, D., Borovkov, M., Prieto Gonzalez, I., Ballabio, A., Frigerio, J., … Katsaros, G. (n.d.). Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.1910.05841\">https://doi.org/10.48550/arXiv.1910.05841</a>","ama":"Hofmann AC, Jirovec D, Borovkov M, et al. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.1910.05841\">10.48550/arXiv.1910.05841</a>","chicago":"Hofmann, Andrea C, Daniel Jirovec, Maxim Borovkov, Ivan Prieto Gonzalez, Andrea Ballabio, Jacopo Frigerio, Daniel Chrastina, Giovanni Isella, and Georgios Katsaros. “Assessing the Potential of Ge/SiGe Quantum Dots as Hosts for Singlet-Triplet Qubits.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.1910.05841\">https://doi.org/10.48550/arXiv.1910.05841</a>.","ista":"Hofmann AC, Jirovec D, Borovkov M, Prieto Gonzalez I, Ballabio A, Frigerio J, Chrastina D, Isella G, Katsaros G. Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits. arXiv, 1910.05841."},"date_updated":"2026-05-17T22:30:48Z","author":[{"first_name":"Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C"},{"first_name":"Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec","id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel"},{"full_name":"Borovkov, Maxim","first_name":"Maxim","last_name":"Borovkov"},{"first_name":"Ivan","last_name":"Prieto Gonzalez","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ballabio, Andrea","first_name":"Andrea","last_name":"Ballabio"},{"first_name":"Jacopo","last_name":"Frigerio","full_name":"Frigerio, Jacopo"},{"full_name":"Chrastina, Daniel","first_name":"Daniel","last_name":"Chrastina"},{"last_name":"Isella","first_name":"Giovanni","full_name":"Isella, Giovanni"},{"orcid":"0000-0001-8342-202X","last_name":"Katsaros","first_name":"Georgios","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"status":"public","publication":"arXiv","article_number":"1910.05841","ec_funded":1,"acknowledgement":"We thank Matthias Brauns for helpful discussions and careful proofreading of the manuscript. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 844511 and from the FWF project P30207. The research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA machine shop and the nanofabrication\r\nfacility.","month":"10","language":[{"iso":"eng"}],"doi":"10.48550/arXiv.1910.05841","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"oa_version":"Preprint","_id":"10065","project":[{"name":"Majorana bound states in Ge/SiGe heterostructures","_id":"26A151DA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"844511"},{"grant_number":"P30207","call_identifier":"FWF","_id":"2641CE5E-B435-11E9-9278-68D0E5697425","name":"Hole spin orbit qubits in Ge quantum wells"}],"date_created":"2021-10-01T12:14:51Z","year":"2019","publication_status":"draft","department":[{"_id":"GeKa"}],"main_file_link":[{"url":"https://arxiv.org/abs/1910.05841","open_access":"1"}],"type":"preprint","oa":1,"day":"13","external_id":{"arxiv":["1910.05841"]},"title":"Assessing the potential of Ge/SiGe quantum dots as hosts for singlet-triplet qubits","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1},{"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425","grant_number":"306589"}],"isi":1,"date_created":"2019-05-26T21:59:13Z","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","oa_version":"Preprint","_id":"6486","doi":"10.1115/1.4043494","acknowledged_ssus":[{"_id":"M-Shop"}],"title":"Relaminarization of pipe flow by means of 3D-printed shaped honeycombs","article_processing_charge":"No","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0098-2202"],"eissn":["1528-901X"]},"department":[{"_id":"BjHo"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.07625"}],"publisher":"ASME","publication_status":"published","year":"2019","oa":1,"external_id":{"isi":["000487748600005"],"arxiv":["1809.07625"]},"day":"01","type":"journal_article","intvolume":"       141","date_updated":"2026-05-17T22:30:53Z","date_published":"2019-11-01T00:00:00Z","related_material":{"record":[{"id":"7258","status":"public","relation":"dissertation_contains"}]},"citation":{"chicago":"Kühnen, Jakob, Davide Scarselli, and Björn Hof. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” <i>Journal of Fluids Engineering</i>. ASME, 2019. <a href=\"https://doi.org/10.1115/1.4043494\">https://doi.org/10.1115/1.4043494</a>.","ama":"Kühnen J, Scarselli D, Hof B. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. <i>Journal of Fluids Engineering</i>. 2019;141(11). doi:<a href=\"https://doi.org/10.1115/1.4043494\">10.1115/1.4043494</a>","apa":"Kühnen, J., Scarselli, D., &#38; Hof, B. (2019). Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. <i>Journal of Fluids Engineering</i>. ASME. <a href=\"https://doi.org/10.1115/1.4043494\">https://doi.org/10.1115/1.4043494</a>","short":"J. Kühnen, D. Scarselli, B. Hof, Journal of Fluids Engineering 141 (2019).","mla":"Kühnen, Jakob, et al. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” <i>Journal of Fluids Engineering</i>, vol. 141, no. 11, 111105, ASME, 2019, doi:<a href=\"https://doi.org/10.1115/1.4043494\">10.1115/1.4043494</a>.","ieee":"J. Kühnen, D. Scarselli, and B. Hof, “Relaminarization of pipe flow by means of 3D-printed shaped honeycombs,” <i>Journal of Fluids Engineering</i>, vol. 141, no. 11. ASME, 2019.","ista":"Kühnen J, Scarselli D, Hof B. 2019. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 141(11), 111105."},"abstract":[{"lang":"eng","text":"Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow."}],"month":"11","article_number":"111105","volume":141,"ec_funded":1,"author":[{"orcid":"0000-0003-4312-0179","last_name":"Kühnen","first_name":"Jakob","full_name":"Kühnen, Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Scarselli","orcid":"0000-0001-5227-4271","first_name":"Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","full_name":"Scarselli, Davide"},{"full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","orcid":"0000-0003-2057-2754","first_name":"Björn"}],"status":"public","issue":"11","publication":"Journal of Fluids Engineering"},{"doi":"10.1017/jfm.2019.191","_id":"6228","oa_version":"Preprint","scopus_import":"1","language":[{"iso":"eng"}],"date_created":"2019-04-07T21:59:14Z","isi":1,"project":[{"grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7"},{"grant_number":"737549","call_identifier":"H2020","name":"Eliminating turbulence in oil pipelines","_id":"25104D44-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","type":"journal_article","external_id":{"isi":["000462606100001"],"arxiv":["1807.05357"]},"day":"25","oa":1,"publication_status":"published","year":"2019","publisher":"Cambridge University Press","main_file_link":[{"url":"https://arxiv.org/abs/1807.05357","open_access":"1"}],"department":[{"_id":"BjHo"}],"publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"article_processing_charge":"No","title":"Relaminarising pipe flow by wall movement","abstract":[{"lang":"eng","text":"Following  the  recent  observation  that  turbulent  pipe  flow  can  be  relaminarised  bya  relatively  simple  modification  of  the  mean  velocity  profile,  we  here  carry  out  aquantitative  experimental  investigation  of  this  phenomenon.  Our  study  confirms  thata  flat  velocity  profile  leads  to  a  collapse  of  turbulence  and  in  order  to  achieve  theblunted  profile  shape,  we  employ  a  moving  pipe  segment  that  is  briefly  and  rapidlyshifted  in  the  streamwise  direction.  The  relaminarisation  threshold  and  the  minimumshift  length  and  speeds  are  determined  as  a  function  of  Reynolds  number.  Althoughturbulence  is  still  active  after  the  acceleration  phase,  the  modulated  profile  possessesa  severely  decreased  lift-up  potential  as  measured  by  transient  growth.  As  shown,this  results  in  an  exponential  decay  of  fluctuations  and  the  flow  relaminarises.  Whilethis  method  can  be  easily  applied  at  low  to  moderate  flow  speeds,  the  minimumstreamwise  length  over  which  the  acceleration  needs  to  act  increases  linearly  with  theReynolds  number."}],"citation":{"mla":"Scarselli, Davide, et al. “Relaminarising Pipe Flow by Wall Movement.” <i>Journal of Fluid Mechanics</i>, vol. 867, Cambridge University Press, 2019, pp. 934–48, doi:<a href=\"https://doi.org/10.1017/jfm.2019.191\">10.1017/jfm.2019.191</a>.","short":"D. Scarselli, J. Kühnen, B. Hof, Journal of Fluid Mechanics 867 (2019) 934–948.","ieee":"D. Scarselli, J. Kühnen, and B. Hof, “Relaminarising pipe flow by wall movement,” <i>Journal of Fluid Mechanics</i>, vol. 867. Cambridge University Press, pp. 934–948, 2019.","apa":"Scarselli, D., Kühnen, J., &#38; Hof, B. (2019). Relaminarising pipe flow by wall movement. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2019.191\">https://doi.org/10.1017/jfm.2019.191</a>","ama":"Scarselli D, Kühnen J, Hof B. Relaminarising pipe flow by wall movement. <i>Journal of Fluid Mechanics</i>. 2019;867:934-948. doi:<a href=\"https://doi.org/10.1017/jfm.2019.191\">10.1017/jfm.2019.191</a>","chicago":"Scarselli, Davide, Jakob Kühnen, and Björn Hof. “Relaminarising Pipe Flow by Wall Movement.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2019. <a href=\"https://doi.org/10.1017/jfm.2019.191\">https://doi.org/10.1017/jfm.2019.191</a>.","ista":"Scarselli D, Kühnen J, Hof B. 2019. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 867, 934–948."},"related_material":{"link":[{"url":"https://doi.org/10.1017/jfm.2019.191","relation":"supplementary_material"}],"record":[{"id":"7258","status":"public","relation":"dissertation_contains"}]},"date_published":"2019-05-25T00:00:00Z","date_updated":"2026-05-17T22:30:53Z","intvolume":"       867","publication":"Journal of Fluid Mechanics","status":"public","author":[{"full_name":"Scarselli, Davide","id":"40315C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-4271","last_name":"Scarselli","first_name":"Davide"},{"orcid":"0000-0003-4312-0179","last_name":"Kühnen","first_name":"Jakob","id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","full_name":"Kühnen, Jakob"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn"}],"page":"934-948","ec_funded":1,"volume":867,"month":"05"},{"page":"1152-1165","month":"06","acknowledgement":"We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis work was supported by the Ministry of Education, Culture, Sports, Science, and Technology (Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.), and the European Union’s Horizon2020 program (European Research Council grant agreement no. 742985 to J.F.).","ec_funded":1,"volume":180,"issue":"2","publication":"Plant Physiology","status":"public","author":[{"last_name":"Oochi","first_name":"A","full_name":"Oochi, A"},{"last_name":"Hajny","orcid":"0000-0003-2140-7195","first_name":"Jakub","full_name":"Hajny, Jakub","id":"4800CC20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fukui","first_name":"K","full_name":"Fukui, K"},{"full_name":"Nakao, Y","first_name":"Y","last_name":"Nakao"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","full_name":"Gallei, Michelle C","first_name":"Michelle C","orcid":"0000-0003-1286-7368","last_name":"Gallei"},{"full_name":"Quareshy, M","first_name":"M","last_name":"Quareshy"},{"last_name":"Takahashi","first_name":"K","full_name":"Takahashi, K"},{"full_name":"Kinoshita, T","first_name":"T","last_name":"Kinoshita"},{"full_name":"Harborough, SR","first_name":"SR","last_name":"Harborough"},{"full_name":"Kepinski, S","first_name":"S","last_name":"Kepinski"},{"full_name":"Kasahara, H","last_name":"Kasahara","first_name":"H"},{"first_name":"RM","last_name":"Napier","full_name":"Napier, RM"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"last_name":"Hayashi","first_name":"KI","full_name":"Hayashi, KI"}],"date_updated":"2026-05-17T22:30:55Z","intvolume":"       180","abstract":[{"text":"Polar auxin transport plays a pivotal role in plant growth and development. PIN auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport.","lang":"eng"}],"citation":{"chicago":"Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy, K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” <i>Plant Physiology</i>. ASPB, 2019. <a href=\"https://doi.org/10.1104/pp.19.00201\">https://doi.org/10.1104/pp.19.00201</a>.","ama":"Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. <i>Plant Physiology</i>. 2019;180(2):1152-1165. doi:<a href=\"https://doi.org/10.1104/pp.19.00201\">10.1104/pp.19.00201</a>","apa":"Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., … Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN internalization. <i>Plant Physiology</i>. ASPB. <a href=\"https://doi.org/10.1104/pp.19.00201\">https://doi.org/10.1104/pp.19.00201</a>","ieee":"A. Oochi <i>et al.</i>, “Pinstatic acid promotes auxin transport by inhibiting PIN internalization,” <i>Plant Physiology</i>, vol. 180, no. 2. ASPB, pp. 1152–1165, 2019.","mla":"Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” <i>Plant Physiology</i>, vol. 180, no. 2, ASPB, 2019, pp. 1152–65, doi:<a href=\"https://doi.org/10.1104/pp.19.00201\">10.1104/pp.19.00201</a>.","short":"A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi, T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K. Hayashi, Plant Physiology 180 (2019) 1152–1165.","ista":"Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 180(2), 1152–1165."},"date_published":"2019-06-01T00:00:00Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11626"},{"id":"8822","status":"public","relation":"dissertation_contains"}]},"publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","title":"Pinstatic acid promotes auxin transport by inhibiting PIN internalization","day":"01","pmid":1,"external_id":{"isi":["000470086100045"],"pmid":["30936248"]},"oa":1,"type":"journal_article","department":[{"_id":"JiFr"}],"main_file_link":[{"url":"https://doi.org/10.1104/pp.19.00201","open_access":"1"}],"year":"2019","publication_status":"published","publisher":"ASPB","isi":1,"date_created":"2019-04-09T08:38:20Z","quality_controlled":"1","project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"_id":"6260","oa_version":"Published Version","scopus_import":"1","doi":"10.1104/pp.19.00201","language":[{"iso":"eng"}],"article_type":"original"}]