[{"publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"Mathematical Sciences Publishers","year":"2021","acknowledgement":"N. L. and R. S. gratefully acknowledge financial support by the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (grant\r\nagreement No 694227). B. S. acknowledges support from the Swiss National Science Foundation (grant 200020_172623) and from the NCCR SwissMAP. N. L. would like to thank\r\nAndreas Deuchert and David Mitrouskas for interesting discussions. B. S. and R. S. would\r\nlike to thank Rupert Frank for stimulating discussions about the time-evolution of a polaron.\r\n","date_updated":"2023-10-17T11:26:45Z","date_created":"2022-02-06T23:01:33Z","volume":14,"author":[{"last_name":"Leopold","first_name":"Nikolai K","orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","full_name":"Leopold, Nikolai K"},{"last_name":"Rademacher","first_name":"Simone Anna Elvira","orcid":"0000-0001-5059-4466","id":"856966FE-A408-11E9-977E-802DE6697425","full_name":"Rademacher, Simone Anna Elvira"},{"first_name":"Benjamin","last_name":"Schlein","full_name":"Schlein, Benjamin"},{"first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"ec_funded":1,"quality_controlled":"1","isi":1,"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"oa":1,"external_id":{"isi":["000733976600004"],"arxiv":["1904.12532"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1904.12532"}],"language":[{"iso":"eng"}],"doi":"10.2140/APDE.2021.14.2079","month":"11","publication_identifier":{"issn":["2157-5045"],"eissn":["1948-206X"]},"status":"public","title":" The Landau–Pekar equations: Adiabatic theorem and accuracy","intvolume":" 14","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10738","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We prove an adiabatic theorem for the Landau–Pekar equations. This allows us to derive new results on the accuracy of their use as effective equations for the time evolution generated by the Fröhlich Hamiltonian with large coupling constant α. In particular, we show that the time evolution of Pekar product states with coherent phonon field and the electron being trapped by the phonons is well approximated by the Landau–Pekar equations until times short compared to α2."}],"issue":"7","article_type":"original","page":"2079-2100","publication":"Analysis and PDE","citation":{"mla":"Leopold, Nikolai K., et al. “ The Landau–Pekar Equations: Adiabatic Theorem and Accuracy.” Analysis and PDE, vol. 14, no. 7, Mathematical Sciences Publishers, 2021, pp. 2079–100, doi:10.2140/APDE.2021.14.2079.","short":"N.K. Leopold, S.A.E. Rademacher, B. Schlein, R. Seiringer, Analysis and PDE 14 (2021) 2079–2100.","chicago":"Leopold, Nikolai K, Simone Anna Elvira Rademacher, Benjamin Schlein, and Robert Seiringer. “ The Landau–Pekar Equations: Adiabatic Theorem and Accuracy.” Analysis and PDE. Mathematical Sciences Publishers, 2021. https://doi.org/10.2140/APDE.2021.14.2079.","ama":"Leopold NK, Rademacher SAE, Schlein B, Seiringer R. The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. 2021;14(7):2079-2100. doi:10.2140/APDE.2021.14.2079","ista":"Leopold NK, Rademacher SAE, Schlein B, Seiringer R. 2021. The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. 14(7), 2079–2100.","ieee":"N. K. Leopold, S. A. E. Rademacher, B. Schlein, and R. Seiringer, “ The Landau–Pekar equations: Adiabatic theorem and accuracy,” Analysis and PDE, vol. 14, no. 7. Mathematical Sciences Publishers, pp. 2079–2100, 2021.","apa":"Leopold, N. K., Rademacher, S. A. E., Schlein, B., & Seiringer, R. (2021). The Landau–Pekar equations: Adiabatic theorem and accuracy. Analysis and PDE. Mathematical Sciences Publishers. https://doi.org/10.2140/APDE.2021.14.2079"},"date_published":"2021-11-10T00:00:00Z","scopus_import":"1","day":"10","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"supervisor":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:10429","project":[{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"month":"12","date_updated":"2023-10-17T11:48:55Z","date_created":"2021-12-08T21:52:28Z","related_material":{"record":[{"id":"10432","status":"public","relation":"part_of_dissertation"},{"id":"6673","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"5965"},{"id":"10435","status":"public","relation":"part_of_dissertation"}]},"author":[{"first_name":"Giorgi","last_name":"Nadiradze","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5634-0731","full_name":"Nadiradze, Giorgi"}],"department":[{"_id":"GradSch"},{"_id":"DaAl"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","year":"2021","ec_funded":1,"file_date_updated":"2022-03-28T12:55:12Z","date_published":"2021-12-09T00:00:00Z","page":"132","citation":{"mla":"Nadiradze, Giorgi. On Achieving Scalability through Relaxation. Institute of Science and Technology Austria, 2021, doi:10.15479/at:ista:10429.","short":"G. Nadiradze, On Achieving Scalability through Relaxation, Institute of Science and Technology Austria, 2021.","chicago":"Nadiradze, Giorgi. “On Achieving Scalability through Relaxation.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/at:ista:10429.","ama":"Nadiradze G. On achieving scalability through relaxation. 2021. doi:10.15479/at:ista:10429","ista":"Nadiradze G. 2021. On achieving scalability through relaxation. Institute of Science and Technology Austria.","apa":"Nadiradze, G. (2021). On achieving scalability through relaxation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:10429","ieee":"G. Nadiradze, “On achieving scalability through relaxation,” Institute of Science and Technology Austria, 2021."},"article_processing_charge":"No","has_accepted_license":"1","day":"09","file":[{"file_name":"Thesis_Final_09_12_2021.pdf","access_level":"open_access","file_size":2370859,"content_type":"application/pdf","creator":"gnadirad","relation":"main_file","file_id":"10436","date_updated":"2021-12-09T17:47:49Z","date_created":"2021-12-09T17:47:49Z","checksum":"6bf14e9a523387328f016c0689f5e10e","success":1},{"checksum":"914d6c5ca86bd0add471971a8f4c4341","date_updated":"2022-03-28T12:55:12Z","date_created":"2021-12-09T17:47:49Z","relation":"source_file","file_id":"10437","content_type":"application/zip","file_size":2596924,"creator":"gnadirad","access_level":"closed","file_name":"Thesis_Final_09_12_2021.zip"}],"oa_version":"Published Version","title":"On achieving scalability through relaxation","status":"public","ddc":["000"],"_id":"10429","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"text":"The scalability of concurrent data structures and distributed algorithms strongly depends on\r\nreducing the contention for shared resources and the costs of synchronization and communication. We show how such cost reductions can be attained by relaxing the strict consistency conditions required by sequential implementations. In the first part of the thesis, we consider relaxation in the context of concurrent data structures. Specifically, in data structures \r\nsuch as priority queues, imposing strong semantics renders scalability impossible, since a correct implementation of the remove operation should return only the element with highest priority. Intuitively, attempting to invoke remove operations concurrently creates a race condition. This bottleneck can be circumvented by relaxing semantics of the affected data structure, thus allowing removal of the elements which are no longer required to have the highest priority. We prove that the randomized implementations of relaxed data structures provide provable guarantees on the priority of the removed elements even under concurrency. Additionally, we show that in some cases the relaxed data structures can be used to scale the classical algorithms which are usually implemented with the exact ones. In the second part, we study parallel variants of the stochastic gradient descent (SGD) algorithm, which distribute computation among the multiple processors, thus reducing the running time. Unfortunately, in order for standard parallel SGD to succeed, each processor has to maintain a local copy of the necessary model parameter, which is identical to the local copies of other processors; the overheads from this perfect consistency in terms of communication and synchronization can negate the speedup gained by distributing the computation. We show that the consistency conditions required by SGD can be relaxed, allowing the algorithm to be more flexible in terms of tolerating quantized communication, asynchrony, or even crash faults, while its convergence remains asymptotically the same.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation"},{"month":"12","day":"01","article_processing_charge":"No","quality_controlled":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425"}],"publication":"35th Conference on Neural Information Processing Systems","citation":{"chicago":"Nadiradze, Giorgi, Amirmojtaba Sabour, Peter Davies, Shigang Li, and Dan-Adrian Alistarh. “Asynchronous Decentralized SGD with Quantized and Local Updates.” In 35th Conference on Neural Information Processing Systems. Neural Information Processing Systems Foundation, 2021.","mla":"Nadiradze, Giorgi, et al. “Asynchronous Decentralized SGD with Quantized and Local Updates.” 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","short":"G. Nadiradze, A. Sabour, P. Davies, S. Li, D.-A. Alistarh, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","ista":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. 2021. Asynchronous decentralized SGD with quantized and local updates. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.","apa":"Nadiradze, G., Sabour, A., Davies, P., Li, S., & Alistarh, D.-A. (2021). Asynchronous decentralized SGD with quantized and local updates. In 35th Conference on Neural Information Processing Systems. Sydney, Australia: Neural Information Processing Systems Foundation.","ieee":"G. Nadiradze, A. Sabour, P. Davies, S. Li, and D.-A. Alistarh, “Asynchronous decentralized SGD with quantized and local updates,” in 35th Conference on Neural Information Processing Systems, Sydney, Australia, 2021.","ama":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. Asynchronous decentralized SGD with quantized and local updates. In: 35th Conference on Neural Information Processing Systems. Neural Information Processing Systems Foundation; 2021."},"oa":1,"main_file_link":[{"open_access":"1","url":"https://papers.nips.cc/paper/2021/hash/362c99307cdc3f2d8b410652386a9dd1-Abstract.html"}],"external_id":{"arxiv":["1910.12308"]},"language":[{"iso":"eng"}],"conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2021-12-14","location":"Sydney, Australia","start_date":"2021-12-06"},"date_published":"2021-12-01T00:00:00Z","type":"conference","abstract":[{"lang":"eng","text":"Decentralized optimization is emerging as a viable alternative for scalable distributed machine learning, but also introduces new challenges in terms of synchronization costs. To this end, several communication-reduction techniques, such as non-blocking communication, quantization, and local steps, have been explored in the decentralized setting. Due to the complexity of analyzing optimization in such a relaxed setting, this line of work often assumes \\emph{global} communication rounds, which require additional synchronization. In this paper, we consider decentralized optimization in the simpler, but harder to analyze, \\emph{asynchronous gossip} model, in which communication occurs in discrete, randomly chosen pairings among nodes. Perhaps surprisingly, we show that a variant of SGD called \\emph{SwarmSGD} still converges in this setting, even if \\emph{non-blocking communication}, \\emph{quantization}, and \\emph{local steps} are all applied \\emph{in conjunction}, and even if the node data distributions and underlying graph topology are both \\emph{heterogenous}. Our analysis is based on a new connection with multi-dimensional load-balancing processes. We implement this algorithm and deploy it in a super-computing environment, showing that it can outperform previous decentralized methods in terms of end-to-end training time, and that it can even rival carefully-tuned large-batch SGD for certain tasks."}],"ec_funded":1,"title":"Asynchronous decentralized SGD with quantized and local updates","publication_status":"published","status":"public","department":[{"_id":"DaAl"}],"publisher":"Neural Information Processing Systems Foundation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10435","year":"2021","acknowledgement":"We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). PD partly conducted this work while at IST Austria and was supported by the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No. 754411. SL was funded in part by European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement DAPP, No. 678880, and EPiGRAM-HS, No. 801039).\r\n","date_updated":"2023-10-17T11:48:56Z","date_created":"2021-12-09T10:59:12Z","oa_version":"Published Version","author":[{"full_name":"Nadiradze, Giorgi","orcid":"0000-0001-5634-0731","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","last_name":"Nadiradze","first_name":"Giorgi"},{"first_name":"Amirmojtaba","last_name":"Sabour","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","full_name":"Sabour, Amirmojtaba"},{"last_name":"Davies","first_name":"Peter","orcid":"0000-0002-5646-9524","id":"11396234-BB50-11E9-B24C-90FCE5697425","full_name":"Davies, Peter"},{"last_name":"Li","first_name":"Shigang","full_name":"Li, Shigang"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10429"}]}},{"date_published":"2021-12-01T00:00:00Z","page":"29616-29629","citation":{"chicago":"Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate Message Passing in Rotationally Invariant Models.” In 35th Conference on Neural Information Processing Systems, 35:29616–29. Neural Information Processing Systems Foundation, 2021.","mla":"Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate Message Passing in Rotationally Invariant Models.” 35th Conference on Neural Information Processing Systems, vol. 35, Neural Information Processing Systems Foundation, 2021, pp. 29616–29.","short":"M. Mondelli, R. Venkataramanan, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 29616–29629.","ista":"Mondelli M, Venkataramanan R. 2021. PCA initialization for approximate message passing in rotationally invariant models. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 35, 29616–29629.","ieee":"M. Mondelli and R. Venkataramanan, “PCA initialization for approximate message passing in rotationally invariant models,” in 35th Conference on Neural Information Processing Systems, Virtual, 2021, vol. 35, pp. 29616–29629.","apa":"Mondelli, M., & Venkataramanan, R. (2021). PCA initialization for approximate message passing in rotationally invariant models. In 35th Conference on Neural Information Processing Systems (Vol. 35, pp. 29616–29629). Virtual: Neural Information Processing Systems Foundation.","ama":"Mondelli M, Venkataramanan R. PCA initialization for approximate message passing in rotationally invariant models. In: 35th Conference on Neural Information Processing Systems. Vol 35. Neural Information Processing Systems Foundation; 2021:29616-29629."},"publication":"35th Conference on Neural Information Processing Systems","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"Preprint","intvolume":" 35","title":"PCA initialization for approximate message passing in rotationally invariant models","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10593","abstract":[{"lang":"eng","text":"We study the problem of estimating a rank-$1$ signal in the presence of rotationally invariant noise-a class of perturbations more general than Gaussian noise. Principal Component Analysis (PCA) provides a natural estimator, and sharp results on its performance have been obtained in the high-dimensional regime. Recently, an Approximate Message Passing (AMP) algorithm has been proposed as an alternative estimator with the potential to improve the accuracy of PCA. However, the existing analysis of AMP requires an initialization that is both correlated with the signal and independent of the noise, which is often unrealistic in practice. In this work, we combine the two methods, and propose to initialize AMP with PCA. Our main result is a rigorous asymptotic characterization of the performance of this estimator. Both the AMP algorithm and its analysis differ from those previously derived in the Gaussian setting: at every iteration, our AMP algorithm requires a specific term to account for PCA initialization, while in the Gaussian case, PCA initialization affects only the first iteration of AMP. The proof is based on a two-phase artificial AMP that first approximates the PCA estimator and then mimics the true AMP. Our numerical simulations show an excellent agreement between AMP results and theoretical predictions, and suggest an interesting open direction on achieving Bayes-optimal performance."}],"type":"conference","language":[{"iso":"eng"}],"conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2021-12-06","location":"Virtual","end_date":"2021-12-14"},"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.02356"}],"oa":1,"external_id":{"arxiv":["2106.02356"]},"publication_identifier":{"issn":["1049-5258"],"isbn":["9781713845393"]},"month":"12","volume":35,"date_created":"2022-01-03T10:50:02Z","date_updated":"2023-10-17T11:48:23Z","author":[{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco"},{"full_name":"Venkataramanan, Ramji","first_name":"Ramji","last_name":"Venkataramanan"}],"department":[{"_id":"MaMo"}],"publisher":"Neural Information Processing Systems Foundation","publication_status":"published","acknowledgement":"M. Mondelli would like to thank László Erdős for helpful discussions. M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1.\r\n","year":"2021"},{"date_published":"2021-12-01T00:00:00Z","citation":{"ieee":"Q. Nguyen, P. Bréchet, and M. Mondelli, “When are solutions connected in deep networks?,” in 35th Conference on Neural Information Processing Systems, Virtual, 2021, vol. 35.","apa":"Nguyen, Q., Bréchet, P., & Mondelli, M. (2021). When are solutions connected in deep networks? In 35th Conference on Neural Information Processing Systems (Vol. 35). Virtual: Neural Information Processing Systems Foundation.","ista":"Nguyen Q, Bréchet P, Mondelli M. 2021. When are solutions connected in deep networks? 35th Conference on Neural Information Processing Systems. 35th Conference on Neural Information Processing Systems vol. 35.","ama":"Nguyen Q, Bréchet P, Mondelli M. When are solutions connected in deep networks? In: 35th Conference on Neural Information Processing Systems. Vol 35. Neural Information Processing Systems Foundation; 2021.","chicago":"Nguyen, Quynh, Pierre Bréchet, and Marco Mondelli. “When Are Solutions Connected in Deep Networks?” In 35th Conference on Neural Information Processing Systems, Vol. 35. Neural Information Processing Systems Foundation, 2021.","short":"Q. Nguyen, P. Bréchet, M. Mondelli, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","mla":"Nguyen, Quynh, et al. “When Are Solutions Connected in Deep Networks?” 35th Conference on Neural Information Processing Systems, vol. 35, Neural Information Processing Systems Foundation, 2021."},"publication":"35th Conference on Neural Information Processing Systems","article_processing_charge":"No","day":"01","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10594","intvolume":" 35","status":"public","title":"When are solutions connected in deep networks?","abstract":[{"lang":"eng","text":"The question of how and why the phenomenon of mode connectivity occurs in training deep neural networks has gained remarkable attention in the research community. From a theoretical perspective, two possible explanations have been proposed: (i) the loss function has connected sublevel sets, and (ii) the solutions found by stochastic gradient descent are dropout stable. While these explanations provide insights into the phenomenon, their assumptions are not always satisfied in practice. In particular, the first approach requires the network to have one layer with order of N neurons (N being the number of training samples), while the second one requires the loss to be almost invariant after removing half of the neurons at each layer (up to some rescaling of the remaining ones). In this work, we improve both conditions by exploiting the quality of the features at every intermediate layer together with a milder over-parameterization condition. More specifically, we show that: (i) under generic assumptions on the features of intermediate layers, it suffices that the last two hidden layers have order of N−−√ neurons, and (ii) if subsets of features at each layer are linearly separable, then no over-parameterization is needed to show the connectivity. Our experiments confirm that the proposed condition ensures the connectivity of solutions found by stochastic gradient descent, even in settings where the previous requirements do not hold."}],"type":"conference","conference":{"start_date":"2021-12-06","location":"Virtual","end_date":"2021-12-14","name":"35th Conference on Neural Information Processing Systems"},"language":[{"iso":"eng"}],"external_id":{"arxiv":["2102.09671"]},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2102.09671","open_access":"1"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]},"month":"12","author":[{"full_name":"Nguyen, Quynh","last_name":"Nguyen","first_name":"Quynh"},{"last_name":"Bréchet","first_name":"Pierre","full_name":"Bréchet, Pierre"},{"full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","last_name":"Mondelli","first_name":"Marco"}],"volume":35,"date_updated":"2023-10-17T11:48:40Z","date_created":"2022-01-03T10:56:20Z","year":"2021","acknowledgement":"MM was partially supported by the 2019 Lopez-Loreta Prize. QN and PB acknowledge support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 757983).","department":[{"_id":"MaMo"}],"publisher":"Neural Information Processing Systems Foundation","publication_status":"published"},{"day":"15","has_accepted_license":"1","article_processing_charge":"Yes","scopus_import":"1","date_published":"2021-07-15T00:00:00Z","article_type":"original","publication":"Quantum Science and Technology","citation":{"ista":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. 2021. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. 6(4), 045005.","ieee":"S. Mobassem, N. J. Lambert, A. R. Rueda Sanchez, J. M. Fink, G. Leuchs, and H. G. L. Schwefel, “Thermal noise in electro-optic devices at cryogenic temperatures,” Quantum Science and Technology, vol. 6, no. 4. IOP Publishing, 2021.","apa":"Mobassem, S., Lambert, N. J., Rueda Sanchez, A. R., Fink, J. M., Leuchs, G., & Schwefel, H. G. L. (2021). Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. IOP Publishing. https://doi.org/10.1088/2058-9565/ac0f36","ama":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. 2021;6(4). doi:10.1088/2058-9565/ac0f36","chicago":"Mobassem, Sonia, Nicholas J. Lambert, Alfredo R Rueda Sanchez, Johannes M Fink, Gerd Leuchs, and Harald G.L. Schwefel. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” Quantum Science and Technology. IOP Publishing, 2021. https://doi.org/10.1088/2058-9565/ac0f36.","mla":"Mobassem, Sonia, et al. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” Quantum Science and Technology, vol. 6, no. 4, 045005, IOP Publishing, 2021, doi:10.1088/2058-9565/ac0f36.","short":"S. Mobassem, N.J. Lambert, A.R. Rueda Sanchez, J.M. Fink, G. Leuchs, H.G.L. Schwefel, Quantum Science and Technology 6 (2021)."},"abstract":[{"text":"The quantum bits (qubits) on which superconducting quantum computers are based have energy scales corresponding to photons with GHz frequencies. The energy of photons in the gigahertz domain is too low to allow transmission through the noisy room-temperature environment, where the signal would be lost in thermal noise. Optical photons, on the other hand, have much higher energies, and signals can be detected using highly efficient single-photon detectors. Transduction from microwave to optical frequencies is therefore a potential enabling technology for quantum devices. However, in such a device the optical pump can be a source of thermal noise and thus degrade the fidelity; the similarity of input microwave state to the output optical state. In order to investigate the magnitude of this effect we model the sub-Kelvin thermal behavior of an electro-optic transducer based on a lithium niobate whispering gallery mode resonator. We find that there is an optimum power level for a continuous pump, whilst pulsed operation of the pump increases the fidelity of the conversion.","lang":"eng"}],"issue":"4","type":"journal_article","file":[{"access_level":"open_access","file_name":"2021_QuantumScienceTechnology_Mobassem.pdf","creator":"cchlebak","file_size":2366118,"content_type":"application/pdf","file_id":"9836","relation":"main_file","checksum":"b15c2c228487a75002c3b52d56f23d5c","date_updated":"2021-08-09T12:23:13Z","date_created":"2021-08-09T12:23:13Z"}],"oa_version":"Published Version","ddc":["530"],"status":"public","title":"Thermal noise in electro-optic devices at cryogenic temperatures","intvolume":" 6","_id":"9815","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","publication_identifier":{"eissn":["2058-9565"]},"language":[{"iso":"eng"}],"doi":"10.1088/2058-9565/ac0f36","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2008.08764"],"isi":["000673081500001"]},"oa":1,"file_date_updated":"2021-08-09T12:23:13Z","article_number":"045005","date_created":"2021-08-08T22:01:25Z","date_updated":"2023-10-17T12:54:54Z","volume":6,"author":[{"first_name":"Sonia","last_name":"Mobassem","full_name":"Mobassem, Sonia"},{"full_name":"Lambert, Nicholas J.","last_name":"Lambert","first_name":"Nicholas J."},{"full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez","first_name":"Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."}],"publication_status":"published","publisher":"IOP Publishing","department":[{"_id":"JoFi"}],"year":"2021","acknowledgement":"NJL is supported by the MBIE Endeavour Fund (UOOX1805) and GL is by the Julius von Haast Fellowship of New Zealand. SM acknowledges stimulating discussions with T M Jensen."},{"date_published":"2021-08-18T00:00:00Z","publication":"Research Square","citation":{"ieee":"D. Cao et al., “Sharp kinetic acceleration potentials during mediated redox catalysis of insulators,” Research Square. Research Square.","apa":"Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (n.d.). Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square. Research Square. https://doi.org/10.21203/rs.3.rs-750965/v1","ista":"Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square, 10.21203/rs.3.rs-750965/v1.","ama":"Cao D, Shen X, Wang A, et al. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square. doi:10.21203/rs.3.rs-750965/v1","chicago":"Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi, Stefan Alexander Freunberger, and Yuhui Chen. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” Research Square. Research Square, n.d. https://doi.org/10.21203/rs.3.rs-750965/v1.","short":"D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen, Research Square (n.d.).","mla":"Cao, Deqing, et al. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” Research Square, Research Square, doi:10.21203/rs.3.rs-750965/v1."},"page":"21","day":"18","has_accepted_license":"1","article_processing_charge":"No","keyword":["Catalysis","Energy engineering","Materials theory and modeling"],"oa_version":"Preprint","file":[{"creator":"cchlebak","file_size":1019662,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_ResearchSquare_Cao.pdf","success":1,"checksum":"1878e91c29d5769ed5a827b0b7addf00","date_updated":"2021-08-31T14:02:19Z","date_created":"2021-08-31T14:02:19Z","file_id":"9979","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9978","status":"public","title":"Sharp kinetic acceleration potentials during mediated redox catalysis of insulators","ddc":["541"],"abstract":[{"lang":"eng","text":"Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics yet the lowest possible overpotential. Here, we found that when the redox potentials of mediators are tuned via, e.g., Li + concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediators and electrolyte. The acceleration originates from the overpotentials required to activate fast Li + /e – extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids requires therefore carefully considering the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents."}],"type":"preprint","doi":"10.21203/rs.3.rs-750965/v1","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"08","publication_identifier":{"eissn":["2693-5015"]},"author":[{"full_name":"Cao, Deqing","last_name":"Cao","first_name":"Deqing"},{"full_name":"Shen, Xiaoxiao","last_name":"Shen","first_name":"Xiaoxiao"},{"last_name":"Wang","first_name":"Aiping","full_name":"Wang, Aiping"},{"first_name":"Fengjiao","last_name":"Yu","full_name":"Yu, Fengjiao"},{"full_name":"Wu, Yuping","last_name":"Wu","first_name":"Yuping"},{"full_name":"Shi, Siqi","last_name":"Shi","first_name":"Siqi"},{"first_name":"Stefan Alexander","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander"},{"last_name":"Chen","first_name":"Yuhui","full_name":"Chen, Yuhui"}],"related_material":{"record":[{"id":"10813","relation":"later_version","status":"public"}]},"date_updated":"2023-10-17T13:06:29Z","date_created":"2021-08-31T12:54:16Z","year":"2021","acknowledgement":"This work was financially supported by the National Natural Science Foundation of China (51773092, 21975124, 11874254, 51802187, U2030206). S.A.F. is indebted to IST Austria for support. ","publication_status":"submitted","department":[{"_id":"StFr"}],"publisher":"Research Square","file_date_updated":"2021-08-31T14:02:19Z"},{"intvolume":" 41","status":"public","title":"Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib","_id":"8730","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"P-glycoprotein (ABCB1) and breast cancer resistance protein (ABCG2) restrict at the blood–brain barrier (BBB) the brain distribution of the majority of currently known molecularly targeted anticancer drugs. To improve brain delivery of dual ABCB1/ABCG2 substrates, both ABCB1 and ABCG2 need to be inhibited simultaneously at the BBB. We examined the feasibility of simultaneous ABCB1/ABCG2 inhibition with i.v. co-infusion of erlotinib and tariquidar by studying brain distribution of the model ABCB1/ABCG2 substrate [11C]erlotinib in mice and rhesus macaques with PET. Tolerability of the erlotinib/tariquidar combination was assessed in human embryonic stem cell-derived cerebral organoids. In mice and macaques, baseline brain distribution of [11C]erlotinib was low (brain distribution volume, VT,brain < 0.3 mL/cm3). Co-infusion of erlotinib and tariquidar increased VT,brain in mice by 3.0-fold and in macaques by 3.4- to 5.0-fold, while infusion of erlotinib alone or tariquidar alone led to less pronounced VT,brain increases in both species. Treatment of cerebral organoids with erlotinib/tariquidar led to an induction of Caspase-3-dependent apoptosis. Co-infusion of erlotinib/tariquidar may potentially allow for complete ABCB1/ABCG2 inhibition at the BBB, while simultaneously achieving brain-targeted EGFR inhibition. Our protocol may be applicable to enhance brain delivery of molecularly targeted anticancer drugs for a more effective treatment of brain tumors."}],"page":"1634-1646","article_type":"original","citation":{"chicago":"Tournier, N, S Goutal, S Mairinger, IH Lozano, T Filip, M Sauberer, F Caillé, et al. “Complete Inhibition of ABCB1 and ABCG2 at the Blood-Brain Barrier by Co-Infusion of Erlotinib and Tariquidar to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Journal of Cerebral Blood Flow and Metabolism. SAGE Publications, 2021. https://doi.org/10.1177/0271678X20965500.","mla":"Tournier, N., et al. “Complete Inhibition of ABCB1 and ABCG2 at the Blood-Brain Barrier by Co-Infusion of Erlotinib and Tariquidar to Improve Brain Delivery of the Model ABCB1/ABCG2 Substrate [11C]Erlotinib.” Journal of Cerebral Blood Flow and Metabolism, vol. 41, no. 7, SAGE Publications, 2021, pp. 1634–46, doi:10.1177/0271678X20965500.","short":"N. Tournier, S. Goutal, S. Mairinger, I. Lozano, T. Filip, M. Sauberer, F. Caillé, L. Breuil, J. Stanek, A. Freeman, G. Novarino, C. Truillet, T. Wanek, O. Langer, Journal of Cerebral Blood Flow and Metabolism 41 (2021) 1634–1646.","ista":"Tournier N, Goutal S, Mairinger S, Lozano I, Filip T, Sauberer M, Caillé F, Breuil L, Stanek J, Freeman A, Novarino G, Truillet C, Wanek T, Langer O. 2021. Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. 41(7), 1634–1646.","ieee":"N. Tournier et al., “Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib,” Journal of Cerebral Blood Flow and Metabolism, vol. 41, no. 7. SAGE Publications, pp. 1634–1646, 2021.","apa":"Tournier, N., Goutal, S., Mairinger, S., Lozano, I., Filip, T., Sauberer, M., … Langer, O. (2021). Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. SAGE Publications. https://doi.org/10.1177/0271678X20965500","ama":"Tournier N, Goutal S, Mairinger S, et al. Complete inhibition of ABCB1 and ABCG2 at the blood-brain barrier by co-infusion of erlotinib and tariquidar to improve brain delivery of the model ABCB1/ABCG2 substrate [11C]erlotinib. Journal of Cerebral Blood Flow and Metabolism. 2021;41(7):1634-1646. doi:10.1177/0271678X20965500"},"publication":"Journal of Cerebral Blood Flow and Metabolism","date_published":"2021-07-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"01","publisher":"SAGE Publications","department":[{"_id":"GaNo"}],"publication_status":"published","pmid":1,"year":"2021","volume":41,"date_created":"2020-11-06T08:39:01Z","date_updated":"2023-10-18T06:45:30Z","author":[{"first_name":"N","last_name":"Tournier","full_name":"Tournier, N"},{"first_name":"S","last_name":"Goutal","full_name":"Goutal, S"},{"full_name":"Mairinger, S","first_name":"S","last_name":"Mairinger"},{"last_name":"Lozano","first_name":"IH","full_name":"Lozano, IH"},{"full_name":"Filip, T","first_name":"T","last_name":"Filip"},{"first_name":"M","last_name":"Sauberer","full_name":"Sauberer, M"},{"full_name":"Caillé, F","first_name":"F","last_name":"Caillé"},{"full_name":"Breuil, L","first_name":"L","last_name":"Breuil"},{"last_name":"Stanek","first_name":"J","full_name":"Stanek, J"},{"first_name":"AF","last_name":"Freeman","full_name":"Freeman, AF"},{"full_name":"Novarino, Gaia","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Truillet, C","first_name":"C","last_name":"Truillet"},{"last_name":"Wanek","first_name":"T","full_name":"Wanek, T"},{"full_name":"Langer, O","first_name":"O","last_name":"Langer"}],"isi":1,"quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8221757/","open_access":"1"}],"external_id":{"isi":["000664214100012"],"pmid":["33081568"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1177/0271678X20965500","publication_identifier":{"eissn":["1559-7016"],"issn":["0271-678x"]},"month":"07"},{"publication":"Evolution","citation":{"ama":"Stankowski S, Ravinet M. Defining the speciation continuum. Evolution. 2021;75(6):1256-1273. doi:10.1111/evo.14215","ista":"Stankowski S, Ravinet M. 2021. Defining the speciation continuum. Evolution. 75(6), 1256–1273.","ieee":"S. Stankowski and M. Ravinet, “Defining the speciation continuum,” Evolution, vol. 75, no. 6. Oxford University Press, pp. 1256–1273, 2021.","apa":"Stankowski, S., & Ravinet, M. (2021). Defining the speciation continuum. Evolution. Oxford University Press. https://doi.org/10.1111/evo.14215","mla":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution, vol. 75, no. 6, Oxford University Press, 2021, pp. 1256–73, doi:10.1111/evo.14215.","short":"S. Stankowski, M. Ravinet, Evolution 75 (2021) 1256–1273.","chicago":"Stankowski, Sean, and Mark Ravinet. “Defining the Speciation Continuum.” Evolution. Oxford University Press, 2021. https://doi.org/10.1111/evo.14215."},"article_type":"original","page":"1256-1273","date_published":"2021-03-22T00:00:00Z","scopus_import":"1","day":"22","has_accepted_license":"1","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9383","status":"public","ddc":["570"],"title":"Defining the speciation continuum","intvolume":" 75","oa_version":"Published Version","file":[{"success":1,"checksum":"96f6ccf15d95a4e9f7c0b27eee570fa6","date_created":"2022-03-25T12:02:04Z","date_updated":"2022-03-25T12:02:04Z","file_id":"10921","relation":"main_file","creator":"kschuh","file_size":719991,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_Evolution_Stankowski.pdf"}],"type":"journal_article","abstract":[{"lang":"eng","text":"A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present‐day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us."}],"issue":"6","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"external_id":{"isi":["000647226400001"]},"isi":1,"quality_controlled":"1","doi":"10.1111/evo.14215","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"eissn":["1558-5646"],"issn":["0014-3820"]},"year":"2021","acknowledgement":"We thank M. Garlovsky, S. Martin, C. Cooney, C. Roux, J. Larson, and J. Mallet for critical feedback and for discussion. K. Lohse, M. de la Cámara, J. Cerca, M. A. Chase, C. Baskett, A. M. Westram, and N. H. Barton gave feedback on a draft of the manuscript. O. Seehausen, two anonymous reviewers, and the AE (Michael Kopp) provided comments that greatly improved the manuscript. V. Holzmann made many corrections to the proofs. G. Bisschop and K. Lohse kindly contributed the simulations and analyses presented in Box 3. We would also like to extend our thanks to everyone who took part in the speciation survey, which received ethical approval through the University of Sheffield Ethics Review Procedure (Application 029768). We are especially grateful to R. K. Butlin for stimulating discussion throughout the writing of the manuscript and for feedback on an earlier draft.","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Oxford University Press","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","first_name":"Sean","full_name":"Stankowski, Sean"},{"last_name":"Ravinet","first_name":"Mark","full_name":"Ravinet, Mark"}],"date_updated":"2023-10-18T08:16:01Z","date_created":"2021-05-09T22:01:39Z","volume":75,"file_date_updated":"2022-03-25T12:02:04Z"},{"article_type":"original","page":"273-277","publication":"Nature","citation":{"mla":"Li, Lanxin, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature, vol. 599, no. 7884, Springer Nature, 2021, pp. 273–77, doi:10.1038/s41586-021-04037-6.","short":"L. Li, I. Verstraeten, M. Roosjen, K. Takahashi, L. Rodriguez Solovey, J. Merrin, J. Chen, L. Shabala, W. Smet, H. Ren, S. Vanneste, S. Shabala, B. De Rybel, D. Weijers, T. Kinoshita, W.M. Gray, J. Friml, Nature 599 (2021) 273–277.","chicago":"Li, Lanxin, Inge Verstraeten, Mark Roosjen, Koji Takahashi, Lesia Rodriguez Solovey, Jack Merrin, Jian Chen, et al. “Cell Surface and Intracellular Auxin Signalling for H+ Fluxes in Root Growth.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-04037-6.","ama":"Li L, Verstraeten I, Roosjen M, et al. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 2021;599(7884):273-277. doi:10.1038/s41586-021-04037-6","ista":"Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez Solovey L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. 2021. Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. 599(7884), 273–277.","ieee":"L. Li et al., “Cell surface and intracellular auxin signalling for H+ fluxes in root growth,” Nature, vol. 599, no. 7884. Springer Nature, pp. 273–277, 2021.","apa":"Li, L., Verstraeten, I., Roosjen, M., Takahashi, K., Rodriguez Solovey, L., Merrin, J., … Friml, J. (2021). Cell surface and intracellular auxin signalling for H+ fluxes in root growth. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-04037-6"},"date_published":"2021-11-11T00:00:00Z","keyword":["Multidisciplinary"],"scopus_import":"1","day":"11","article_processing_charge":"No","title":"Cell surface and intracellular auxin signalling for H+ fluxes in root growth","status":"public","intvolume":" 599","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10223","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments."}],"issue":"7884","quality_controlled":"1","isi":1,"project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985"},{"_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","grant_number":"25351","_id":"26B4D67E-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.21203/rs.3.rs-266395/v3"}],"oa":1,"external_id":{"pmid":["34707283"],"isi":["000713338100006"]},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41586-021-04037-6","month":"11","publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JiFr"},{"_id":"NanoFab"}],"year":"2021","acknowledgement":"We thank N. Gnyliukh and L. Hörmayer for technical assistance and N. Paris for sharing PM-Cyto seeds. We gratefully acknowledge the Life Science, Machine Shop and Bioimaging Facilities of IST Austria. This project has received funding from the European Research Council Advanced Grant (ETAP-742985) and the Austrian Science Fund (FWF) under I 3630-B25 to J.F., the National Institutes of Health (GM067203) to W.M.G., the Netherlands Organization for Scientific Research (NWO; VIDI-864.13.001), Research Foundation-Flanders (FWO; Odysseus II G0D0515N) and a European Research Council Starting Grant (TORPEDO-714055) to W.S. and B.D.R., the VICI grant (865.14.001) from the Netherlands Organization for Scientific Research to M.R. and D.W., the Australian Research Council and China National Distinguished Expert Project (WQ20174400441) to S.S., the MEXT/JSPS KAKENHI to K.T. (20K06685) and T.K. (20H05687 and 20H05910), the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie grant agreement no. 665385 and the DOC Fellowship of the Austrian Academy of Sciences to L.L., and the China Scholarship Council to J.C.","pmid":1,"date_updated":"2023-10-18T08:30:53Z","date_created":"2021-11-07T23:01:25Z","volume":599,"author":[{"last_name":"Li","first_name":"Lanxin","orcid":"0000-0002-5607-272X","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Lanxin"},{"last_name":"Verstraeten","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge"},{"full_name":"Roosjen, Mark","last_name":"Roosjen","first_name":"Mark"},{"last_name":"Takahashi","first_name":"Koji","full_name":"Takahashi, Koji"},{"full_name":"Rodriguez Solovey, Lesia","last_name":"Rodriguez Solovey","first_name":"Lesia","orcid":"0000-0002-7244-7237","id":"3922B506-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Merrin, Jack","first_name":"Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"full_name":"Chen, Jian","last_name":"Chen","first_name":"Jian"},{"full_name":"Shabala, Lana","last_name":"Shabala","first_name":"Lana"},{"full_name":"Smet, Wouter","first_name":"Wouter","last_name":"Smet"},{"first_name":"Hong","last_name":"Ren","full_name":"Ren, Hong"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Shabala, Sergey","first_name":"Sergey","last_name":"Shabala"},{"last_name":"De Rybel","first_name":"Bert","full_name":"De Rybel, Bert"},{"last_name":"Weijers","first_name":"Dolf","full_name":"Weijers, Dolf"},{"first_name":"Toshinori","last_name":"Kinoshita","full_name":"Kinoshita, Toshinori"},{"full_name":"Gray, William M.","first_name":"William M.","last_name":"Gray"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/stop-and-grow/","description":"News on IST Webpage","relation":"press_release"}],"record":[{"id":"10095","relation":"earlier_version","status":"public"}]},"ec_funded":1},{"author":[{"orcid":"0000-0002-8176-4824","id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","last_name":"Bolger-Munro","first_name":"Madison","full_name":"Bolger-Munro, Madison"},{"last_name":"Choi","first_name":"Kate","full_name":"Choi, Kate"},{"full_name":"Cheung, Faith","last_name":"Cheung","first_name":"Faith"},{"full_name":"Liu, Yi Tian","last_name":"Liu","first_name":"Yi Tian"},{"last_name":"Dang-Lawson","first_name":"May","full_name":"Dang-Lawson, May"},{"full_name":"Deretic, Nikola","last_name":"Deretic","first_name":"Nikola"},{"full_name":"Keane, Connor","first_name":"Connor","last_name":"Keane"},{"first_name":"Michael R.","last_name":"Gold","full_name":"Gold, Michael R."}],"volume":9,"date_updated":"2023-10-18T08:19:49Z","date_created":"2021-05-09T22:01:37Z","pmid":1,"acknowledgement":"We thank the UBC Life Sciences Institute Imaging Facility andthe UBC Flow Cytometry Facility.","year":"2021","department":[{"_id":"CaHe"}],"publisher":"Frontiers Media","publication_status":"published","file_date_updated":"2021-05-11T15:09:23Z","article_number":"649433","doi":"10.3389/fcell.2021.649433","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000644419500001"],"pmid":["33928084"]},"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["2296-634X"]},"month":"04","oa_version":"Published Version","file":[{"file_size":4076024,"content_type":"application/pdf","creator":"kschuh","file_name":"2021_Frontiers_Cell_Bolger-Munro.pdf","access_level":"open_access","date_updated":"2021-05-11T15:09:23Z","date_created":"2021-05-11T15:09:23Z","checksum":"8c8a03575d2f7583f88dc3b658b0976b","success":1,"relation":"main_file","file_id":"9386"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9379","intvolume":" 9","ddc":["570"],"title":"The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse","status":"public","abstract":[{"text":"When B cells encounter membrane-bound antigens, the formation and coalescence of B cell antigen receptor (BCR) microclusters amplifies BCR signaling. The ability of B cells to probe the surface of antigen-presenting cells (APCs) and respond to APC-bound antigens requires remodeling of the actin cytoskeleton. Initial BCR signaling stimulates actin-related protein (Arp) 2/3 complex-dependent actin polymerization, which drives B cell spreading as well as the centripetal movement and coalescence of BCR microclusters at the B cell-APC synapse. Sustained actin polymerization depends on concomitant actin filament depolymerization, which enables the recycling of actin monomers and Arp2/3 complexes. Cofilin-mediated severing of actin filaments is a rate-limiting step in the morphological changes that occur during immune synapse formation. Hence, regulators of cofilin activity such as WD repeat-containing protein 1 (Wdr1), LIM domain kinase (LIMK), and coactosin-like 1 (Cotl1) may also be essential for actin-dependent processes in B cells. Wdr1 enhances cofilin-mediated actin disassembly. Conversely, Cotl1 competes with cofilin for binding to actin and LIMK phosphorylates cofilin and prevents it from binding to actin filaments. We now show that Wdr1 and LIMK have distinct roles in BCR-induced assembly of the peripheral actin structures that drive B cell spreading, and that cofilin, Wdr1, and LIMK all contribute to the actin-dependent amplification of BCR signaling at the immune synapse. Depleting Cotl1 had no effect on these processes. Thus, the Wdr1-LIMK-cofilin axis is critical for BCR-induced actin remodeling and for B cell responses to APC-bound antigens.","lang":"eng"}],"type":"journal_article","date_published":"2021-04-13T00:00:00Z","citation":{"ama":"Bolger-Munro M, Choi K, Cheung F, et al. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 2021;9. doi:10.3389/fcell.2021.649433","apa":"Bolger-Munro, M., Choi, K., Cheung, F., Liu, Y. T., Dang-Lawson, M., Deretic, N., … Gold, M. R. (2021). The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. Frontiers Media. https://doi.org/10.3389/fcell.2021.649433","ieee":"M. Bolger-Munro et al., “The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse,” Frontiers in Cell and Developmental Biology, vol. 9. Frontiers Media, 2021.","ista":"Bolger-Munro M, Choi K, Cheung F, Liu YT, Dang-Lawson M, Deretic N, Keane C, Gold MR. 2021. The Wdr1-LIMK-Cofilin axis controls B cell antigen receptor-induced actin remodeling and signaling at the immune synapse. Frontiers in Cell and Developmental Biology. 9, 649433.","short":"M. Bolger-Munro, K. Choi, F. Cheung, Y.T. Liu, M. Dang-Lawson, N. Deretic, C. Keane, M.R. Gold, Frontiers in Cell and Developmental Biology 9 (2021).","mla":"Bolger-Munro, Madison, et al. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers in Cell and Developmental Biology, vol. 9, 649433, Frontiers Media, 2021, doi:10.3389/fcell.2021.649433.","chicago":"Bolger-Munro, Madison, Kate Choi, Faith Cheung, Yi Tian Liu, May Dang-Lawson, Nikola Deretic, Connor Keane, and Michael R. Gold. “The Wdr1-LIMK-Cofilin Axis Controls B Cell Antigen Receptor-Induced Actin Remodeling and Signaling at the Immune Synapse.” Frontiers in Cell and Developmental Biology. Frontiers Media, 2021. https://doi.org/10.3389/fcell.2021.649433."},"publication":"Frontiers in Cell and Developmental Biology","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"13","scopus_import":"1","keyword":["B cell","actin","immune synapse","cell spreading","cofilin","WDR1 (AIP1)","LIM domain kinase","B cell receptor (BCR)"]},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9371","date_updated":"2021-05-04T13:22:19Z","date_created":"2021-05-04T13:22:19Z","checksum":"c52da133850307d2031f552d998f00e8","success":1,"file_name":"2021_pone_Chalk.pdf","access_level":"open_access","file_size":2768282,"content_type":"application/pdf","creator":"kschuh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9362","intvolume":" 16","ddc":["570"],"status":"public","title":"Inferring the function performed by a recurrent neural network","issue":"4","abstract":[{"lang":"eng","text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics."}],"type":"journal_article","date_published":"2021-04-15T00:00:00Z","citation":{"short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).","mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:10.1371/journal.pone.0248940.","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0248940.","ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940","ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of Science, 2021.","apa":"Chalk, M. J., Tkačik, G., & Marre, O. (2021). Inferring the function performed by a recurrent neural network. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0248940","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940."},"publication":"PLoS ONE","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"15","scopus_import":"1","author":[{"first_name":"Matthew J","last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"}],"volume":16,"date_created":"2021-05-02T22:01:28Z","date_updated":"2023-10-18T08:17:42Z","pmid":1,"year":"2021","acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","file_date_updated":"2021-05-04T13:22:19Z","article_number":"e0248940","doi":"10.1371/journal.pone.0248940","language":[{"iso":"eng"}],"external_id":{"isi":["000641474900072"],"pmid":["33857170"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["19326203"]},"month":"04"},{"oa_version":"Published Version","file":[{"creator":"cchlebak","file_size":2162247,"content_type":"application/pdf","access_level":"open_access","file_name":"2021_IntJMolecularSciences_Velasquez.pdf","checksum":"6b7055cf89f1b7ed8594c3fdf56f000b","date_updated":"2021-09-07T09:04:53Z","date_created":"2021-09-06T12:50:19Z","file_id":"9988","relation":"main_file"}],"_id":"9986","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 22","status":"public","ddc":["575"],"title":"Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants","issue":"17","abstract":[{"lang":"eng","text":"Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan’s molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth."}],"type":"journal_article","date_published":"2021-08-26T00:00:00Z","citation":{"short":"S.M. Velasquez, X. Guo, M. Gallemi, B. Aryal, P. Venhuizen, E. Barbez, K.A. Dünser, M. Darino, A. Pӗnčík, O. Novák, M. Kalyna, G. Mouille, E. Benková, R.P. Bhalerao, J. Mravec, J. Kleine-Vehn, International Journal of Molecular Sciences 22 (2021).","mla":"Velasquez, Silvia Melina, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal of Molecular Sciences, vol. 22, no. 17, 9222, MDPI, 2021, doi:10.3390/ijms22179222.","chicago":"Velasquez, Silvia Melina, Xiaoyuan Guo, Marçal Gallemi, Bibek Aryal, Peter Venhuizen, Elke Barbez, Kai Alexander Dünser, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” International Journal of Molecular Sciences. MDPI, 2021. https://doi.org/10.3390/ijms22179222.","ama":"Velasquez SM, Guo X, Gallemi M, et al. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 2021;22(17). doi:10.3390/ijms22179222","apa":"Velasquez, S. M., Guo, X., Gallemi, M., Aryal, B., Venhuizen, P., Barbez, E., … Kleine-Vehn, J. (2021). Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms22179222","ieee":"S. M. Velasquez et al., “Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants,” International Journal of Molecular Sciences, vol. 22, no. 17. MDPI, 2021.","ista":"Velasquez SM, Guo X, Gallemi M, Aryal B, Venhuizen P, Barbez E, Dünser KA, Darino M, Pӗnčík A, Novák O, Kalyna M, Mouille G, Benková E, Bhalerao RP, Mravec J, Kleine-Vehn J. 2021. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 22(17), 9222."},"publication":"International Journal of Molecular Sciences","article_type":"original","article_processing_charge":"Yes","has_accepted_license":"1","day":"26","scopus_import":"1","keyword":["auxin","growth","cell wall","xyloglucans","hypocotyls","gravitropism"],"author":[{"full_name":"Velasquez, Silvia Melina","last_name":"Velasquez","first_name":"Silvia Melina"},{"first_name":"Xiaoyuan","last_name":"Guo","full_name":"Guo, Xiaoyuan"},{"id":"460C6802-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4675-6893","first_name":"Marçal","last_name":"Gallemi","full_name":"Gallemi, Marçal"},{"full_name":"Aryal, Bibek","last_name":"Aryal","first_name":"Bibek"},{"full_name":"Venhuizen, Peter","first_name":"Peter","last_name":"Venhuizen"},{"full_name":"Barbez, Elke","last_name":"Barbez","first_name":"Elke"},{"last_name":"Dünser","first_name":"Kai Alexander","full_name":"Dünser, Kai Alexander"},{"full_name":"Darino, Martin","first_name":"Martin","last_name":"Darino"},{"full_name":"Pӗnčík, Aleš","first_name":"Aleš","last_name":"Pӗnčík"},{"first_name":"Ondřej","last_name":"Novák","full_name":"Novák, Ondřej"},{"last_name":"Kalyna","first_name":"Maria","full_name":"Kalyna, Maria"},{"last_name":"Mouille","first_name":"Gregory","full_name":"Mouille, Gregory"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"},{"first_name":"Rishikesh P.","last_name":"Bhalerao","full_name":"Bhalerao, Rishikesh P."},{"first_name":"Jozef","last_name":"Mravec","full_name":"Mravec, Jozef"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine-Vehn","first_name":"Jürgen"}],"volume":22,"date_created":"2021-09-05T22:01:24Z","date_updated":"2023-10-31T19:29:38Z","pmid":1,"year":"2021","acknowledgement":"We are grateful to Paul Knox, Markus Pauly, Malcom O’Neill, and Ignacio Zarra for providing published material; the BOKU-VIBT Imaging Center for access and M. Debreczeny for expertise; J.I. Thaker and Georg Seifert for critical reading.\r\n","publisher":"MDPI","department":[{"_id":"EvBe"}],"publication_status":"published","file_date_updated":"2021-09-07T09:04:53Z","article_number":"9222","doi":"10.3390/ijms22179222","language":[{"iso":"eng"}],"external_id":{"pmid":["34502129"],"isi":["000694347100001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"publication_identifier":{"eissn":["1422-0067"],"issn":["1661-6596"]},"month":"08"},{"oa":1,"external_id":{"pmid":["33576018"],"isi":["000625398600001"]},"quality_controlled":"1","isi":1,"doi":"10.1111/pce.14029","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1365-3040"],"issn":["0140-7791"]},"month":"06","pmid":1,"year":"2021","publisher":"Wiley","department":[{"_id":"JiFr"}],"publication_status":"published","author":[{"full_name":"Zhao, Y","last_name":"Zhao","first_name":"Y"},{"full_name":"Wu, L","first_name":"L","last_name":"Wu"},{"last_name":"Fu","first_name":"Q","full_name":"Fu, Q"},{"last_name":"Wang","first_name":"D","full_name":"Wang, D"},{"full_name":"Li, J","last_name":"Li","first_name":"J"},{"full_name":"Yao, B","first_name":"B","last_name":"Yao"},{"full_name":"Yu, S","last_name":"Yu","first_name":"S"},{"full_name":"Jiang, L","first_name":"L","last_name":"Jiang"},{"last_name":"Qian","first_name":"J","full_name":"Qian, J"},{"full_name":"Zhou, X","last_name":"Zhou","first_name":"X"},{"last_name":"Han","first_name":"L","full_name":"Han, L"},{"last_name":"Zhao","first_name":"S","full_name":"Zhao, S"},{"last_name":"Ma","first_name":"C","full_name":"Ma, C"},{"first_name":"Y","last_name":"Zhang","full_name":"Zhang, Y"},{"full_name":"Luo, C","first_name":"C","last_name":"Luo"},{"full_name":"Dong, Q","last_name":"Dong","first_name":"Q"},{"first_name":"S","last_name":"Li","full_name":"Li, S"},{"last_name":"Zhang","first_name":"L","full_name":"Zhang, L"},{"last_name":"Jiang","first_name":"X","full_name":"Jiang, X"},{"last_name":"Li","first_name":"Y","full_name":"Li, Y"},{"full_name":"Luo, H","first_name":"H","last_name":"Luo"},{"full_name":"Li, K","first_name":"K","last_name":"Li"},{"full_name":"Yang, J","last_name":"Yang","first_name":"J"},{"full_name":"Luo, Q","first_name":"Q","last_name":"Luo"},{"full_name":"Li, L","last_name":"Li","first_name":"L"},{"full_name":"Peng, S","last_name":"Peng","first_name":"S"},{"first_name":"H","last_name":"Huang","full_name":"Huang, H"},{"full_name":"Zuo, Z","first_name":"Z","last_name":"Zuo"},{"first_name":"C","last_name":"Liu","full_name":"Liu, C"},{"full_name":"Wang, L","last_name":"Wang","first_name":"L"},{"last_name":"Li","first_name":"C","full_name":"Li, C"},{"last_name":"He","first_name":"X","full_name":"He, X"},{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří"},{"first_name":"Y","last_name":"Du","full_name":"Du, Y"}],"volume":44,"date_updated":"2023-11-07T08:18:36Z","date_created":"2021-02-24T10:07:21Z","file_date_updated":"2023-11-02T17:02:11Z","citation":{"mla":"Zhao, Y., et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant, Cell & Environment, vol. 44, no. 6, Wiley, 2021, pp. 1846–57, doi:10.1111/pce.14029.","short":"Y. Zhao, L. Wu, Q. Fu, D. Wang, J. Li, B. Yao, S. Yu, L. Jiang, J. Qian, X. Zhou, L. Han, S. Zhao, C. Ma, Y. Zhang, C. Luo, Q. Dong, S. Li, L. Zhang, X. Jiang, Y. Li, H. Luo, K. Li, J. Yang, Q. Luo, L. Li, S. Peng, H. Huang, Z. Zuo, C. Liu, L. Wang, C. Li, X. He, J. Friml, Y. Du, Plant, Cell & Environment 44 (2021) 1846–1857.","chicago":"Zhao, Y, L Wu, Q Fu, D Wang, J Li, B Yao, S Yu, et al. “INDITTO2 Transposon Conveys Auxin-Mediated DRO1 Transcription for Rice Drought Avoidance.” Plant, Cell & Environment. Wiley, 2021. https://doi.org/10.1111/pce.14029.","ama":"Zhao Y, Wu L, Fu Q, et al. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. 2021;44(6):1846-1857. doi:10.1111/pce.14029","ista":"Zhao Y, Wu L, Fu Q, Wang D, Li J, Yao B, Yu S, Jiang L, Qian J, Zhou X, Han L, Zhao S, Ma C, Zhang Y, Luo C, Dong Q, Li S, Zhang L, Jiang X, Li Y, Luo H, Li K, Yang J, Luo Q, Li L, Peng S, Huang H, Zuo Z, Liu C, Wang L, Li C, He X, Friml J, Du Y. 2021. INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. 44(6), 1846–1857.","apa":"Zhao, Y., Wu, L., Fu, Q., Wang, D., Li, J., Yao, B., … Du, Y. (2021). INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance. Plant, Cell & Environment. Wiley. https://doi.org/10.1111/pce.14029","ieee":"Y. Zhao et al., “INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance,” Plant, Cell & Environment, vol. 44, no. 6. Wiley, pp. 1846–1857, 2021."},"publication":"Plant, Cell & Environment","page":"1846-1857","article_type":"original","date_published":"2021-06-01T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"9189","intvolume":" 44","ddc":["580"],"status":"public","title":"INDITTO2 transposon conveys auxin-mediated DRO1 transcription for rice drought avoidance","oa_version":"Submitted Version","file":[{"content_type":"application/pdf","file_size":8437528,"creator":"amally","access_level":"open_access","file_name":"Zhao PlantCellEnv 2021_accepted.pdf","checksum":"a812418fede076741c9c4dc07f317068","success":1,"date_updated":"2023-11-02T17:02:11Z","date_created":"2023-11-02T17:02:11Z","relation":"main_file","file_id":"14481"}],"type":"journal_article","issue":"6","abstract":[{"text":"Transposable elements exist widely throughout plant genomes and play important roles in plant evolution. Auxin is an important regulator that is traditionally associated with root development and drought stress adaptation. The DEEPER ROOTING 1 (DRO1) gene is a key component of rice drought avoidance. Here, we identified a transposon that acts as an autonomous auxin‐responsive promoter and its presence at specific genome positions conveys physiological adaptations related to drought avoidance. Rice varieties with high and auxin‐mediated transcription of DRO1 in the root tip show deeper and longer root phenotypes and are thus better adapted to drought. The INDITTO2 transposon contains an auxin response element and displays auxin‐responsive promoter activity; it is thus able to convey auxin regulation of transcription to genes in its proximity. In the rice Acuce, which displays DRO1‐mediated drought adaptation, the INDITTO2 transposon was found to be inserted at the promoter region of the DRO1 locus. Transgenesis‐based insertion of the INDITTO2 transposon into the DRO1 promoter of the non‐adapted rice variety Nipponbare was sufficient to promote its drought avoidance. Our data identify an example of how transposons can act as promoters and convey hormonal regulation to nearby loci, improving plant fitness in response to different abiotic stresses.","lang":"eng"}]},{"ec_funded":1,"article_number":"2106.11217","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9733"},{"relation":"dissertation_contains","status":"public","id":"10030"},{"id":"12911","status":"public","relation":"later_version"}]},"author":[{"full_name":"Feliciangeli, Dario","first_name":"Dario","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0754-8530"},{"full_name":"Gerolin, Augusto","last_name":"Gerolin","first_name":"Augusto"},{"id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","first_name":"Lorenzo","last_name":"Portinale","full_name":"Portinale, Lorenzo"}],"date_updated":"2023-11-14T13:21:01Z","date_created":"2021-08-06T09:07:12Z","year":"2021","acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thanks the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. Finally, the authors also thanks J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article. L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and NoF65. D.F acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942].","department":[{"_id":"RoSe"},{"_id":"JaMa"}],"publication_status":"submitted","month":"07","doi":"10.48550/arXiv.2106.11217","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2106.11217"}],"external_id":{"arxiv":["2106.11217"]},"oa":1,"project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","grant_number":"716117","call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics"},{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"}],"abstract":[{"text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on careful a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.","lang":"eng"}],"type":"preprint","oa_version":"Preprint","_id":"9792","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","status":"public","ddc":["510"],"article_processing_charge":"No","has_accepted_license":"1","day":"21","date_published":"2021-07-21T00:00:00Z","citation":{"chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2106.11217.","short":"D. Feliciangeli, A. Gerolin, L. Portinale, ArXiv (n.d.).","mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” ArXiv, 2106.11217, doi:10.48550/arXiv.2106.11217.","apa":"Feliciangeli, D., Gerolin, A., & Portinale, L. (n.d.). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv. https://doi.org/10.48550/arXiv.2106.11217","ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” arXiv. .","ista":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv, 2106.11217.","ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv. doi:10.48550/arXiv.2106.11217"},"publication":"arXiv"},{"quality_controlled":"1","isi":1,"project":[{"name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000748748500019"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.omtm.2021.09.006","month":"12","publication_identifier":{"eissn":["2329-0501"]},"publication_status":"published","department":[{"_id":"SaSi"},{"_id":"SiHi"}],"publisher":"Elsevier","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 715571). The research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility, the Life Science Facility, and the Pre-Clinical Facility, namely Sonja Haslinger and Michael Schunn for their animal colony management and support. We would also like to thank Chakrabarty Lab for sharing the plasmids for AAV2/6 production. Finally, we would like to thank the Siegert team members for discussion about the manuscript.","year":"2021","date_created":"2022-01-23T23:01:28Z","date_updated":"2023-11-16T13:12:03Z","volume":23,"author":[{"last_name":"Maes","first_name":"Margaret E","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","full_name":"Maes, Margaret E"},{"full_name":"Wögenstein, Gabriele M.","last_name":"Wögenstein","first_name":"Gabriele M."},{"full_name":"Colombo, Gloria","first_name":"Gloria","last_name":"Colombo","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9434-8902"},{"full_name":"Casado Polanco, Raquel","id":"15240fc1-dbcd-11ea-9d1d-ac5a786425fd","orcid":"0000-0001-8293-4568","first_name":"Raquel","last_name":"Casado Polanco"},{"first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"file_date_updated":"2022-01-24T07:43:09Z","ec_funded":1,"article_type":"original","page":"210-224","publication":"Molecular Therapy - Methods and Clinical Development","citation":{"apa":"Maes, M. E., Wögenstein, G. M., Colombo, G., Casado Polanco, R., & Siegert, S. (2021). Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. Elsevier. https://doi.org/10.1016/j.omtm.2021.09.006","ieee":"M. E. Maes, G. M. Wögenstein, G. Colombo, R. Casado Polanco, and S. Siegert, “Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment,” Molecular Therapy - Methods and Clinical Development, vol. 23. Elsevier, pp. 210–224, 2021.","ista":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. 2021. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 23, 210–224.","ama":"Maes ME, Wögenstein GM, Colombo G, Casado Polanco R, Siegert S. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. Molecular Therapy - Methods and Clinical Development. 2021;23:210-224. doi:10.1016/j.omtm.2021.09.006","chicago":"Maes, Margaret E, Gabriele M. Wögenstein, Gloria Colombo, Raquel Casado Polanco, and Sandra Siegert. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular Therapy - Methods and Clinical Development. Elsevier, 2021. https://doi.org/10.1016/j.omtm.2021.09.006.","short":"M.E. Maes, G.M. Wögenstein, G. Colombo, R. Casado Polanco, S. Siegert, Molecular Therapy - Methods and Clinical Development 23 (2021) 210–224.","mla":"Maes, Margaret E., et al. “Optimizing AAV2/6 Microglial Targeting Identified Enhanced Efficiency in the Photoreceptor Degenerative Environment.” Molecular Therapy - Methods and Clinical Development, vol. 23, Elsevier, 2021, pp. 210–24, doi:10.1016/j.omtm.2021.09.006."},"date_published":"2021-12-10T00:00:00Z","scopus_import":"1","day":"10","article_processing_charge":"Yes","has_accepted_license":"1","ddc":["570"],"title":"Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment","status":"public","intvolume":" 23","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10655","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":4794147,"access_level":"open_access","file_name":"2021_MolTherMethodsClinDev_Maes.pdf","success":1,"checksum":"77dc540e8011c5475031bdf6ccef20a6","date_created":"2022-01-24T07:43:09Z","date_updated":"2022-01-24T07:43:09Z","file_id":"10657","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Adeno-associated viruses (AAVs) are widely used to deliver genetic material in vivo to distinct cell types such as neurons or glial cells, allowing for targeted manipulation. Transduction of microglia is mostly excluded from this strategy, likely due to the cells’ heterogeneous state upon environmental changes, which makes AAV design challenging. Here, we established the retina as a model system for microglial AAV validation and optimization. First, we show that AAV2/6 transduced microglia in both synaptic layers, where layer preference corresponds to the intravitreal or subretinal delivery method. Surprisingly, we observed significantly enhanced microglial transduction during photoreceptor degeneration. Thus, we modified the AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E, R576Q, K493S, and K459S), resulting in increased microglial transduction in the outer plexiform layer. Finally, to improve microglial-specific transduction, we validated a Cre-dependent transgene delivery cassette for use in combination with the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future studies optimizing AAV-mediated microglia transduction and highlight that environmental conditions influence microglial transduction efficiency.\r\n","lang":"eng"}]},{"day":"17","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2021-12-17T00:00:00Z","publication":"STAR Protocols","citation":{"chicago":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols. Elsevier ; Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.101012.","mla":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” STAR Protocols, vol. 2, no. 4, 101012, Elsevier ; Cell Press, 2021, doi:10.1016/j.xpro.2021.101012.","short":"A. Venturino, S. Siegert, STAR Protocols 2 (2021).","ista":"Venturino A, Siegert S. 2021. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2(4), 101012.","ieee":"A. Venturino and S. Siegert, “Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain,” STAR Protocols, vol. 2, no. 4. Elsevier ; Cell Press, 2021.","apa":"Venturino, A., & Siegert, S. (2021). Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. Elsevier ; Cell Press. https://doi.org/10.1016/j.xpro.2021.101012","ama":"Venturino A, Siegert S. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.101012"},"article_type":"original","abstract":[{"lang":"eng","text":"Enzymatic digestion of the extracellular matrix with chondroitinase-ABC reinstates juvenile-like plasticity in the adult cortex as it also disassembles the perineuronal nets (PNNs). The disadvantage of the enzyme is that it must be applied intracerebrally and it degrades the ECM for several weeks. Here, we provide two minimally invasive and transient protocols for microglia-enabled PNN disassembly in mouse cortex: repeated treatment with ketamine-xylazine-acepromazine (KXA) anesthesia and 60-Hz light entrainment. We also discuss how to analyze PNNs within microglial endosomes-lysosomes. For complete details on the use and execution of this protocol, please refer to Venturino et al. (2021)."}],"issue":"4","type":"journal_article","oa_version":"Published Version","file":[{"file_id":"10570","relation":"main_file","success":1,"checksum":"9ea2501056c5df99e84726b845e9b976","date_updated":"2021-12-20T08:58:40Z","date_created":"2021-12-20T08:58:40Z","access_level":"open_access","file_name":"2021_STARProt_Venturino.pdf","creator":"cchlebak","file_size":6207060,"content_type":"application/pdf"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"10565","ddc":["573"],"title":"Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain","status":"public","intvolume":" 2","month":"12","publication_identifier":{"eissn":["2666-1667"]},"doi":"10.1016/j.xpro.2021.101012","acknowledged_ssus":[{"_id":"Bio"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","name":"Microglia action towards neuronal circuit formation and function in health and disease","call_identifier":"H2020"}],"file_date_updated":"2021-12-20T08:58:40Z","ec_funded":1,"article_number":"101012","author":[{"full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","last_name":"Venturino","first_name":"Alessandro"},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8635-0877","first_name":"Sandra","last_name":"Siegert","full_name":"Siegert, Sandra"}],"date_created":"2021-12-19T23:01:32Z","date_updated":"2023-11-16T13:11:04Z","volume":2,"year":"2021","acknowledgement":"This research was supported by the European Research Council (grant 715571 to S.S.). We thank Rouven Schulz, Michael Schunn, Claudia Gold, Gabriel Krens, Sarah Gorkiewicz, Margaret Maes, Jürgen Siegert, Marco Benevento, and Sara Oakeley for comments on the manuscript and the IST Austria Bioimaging Facility for the technical support.","publication_status":"published","department":[{"_id":"SaSi"}],"publisher":"Elsevier ; Cell Press"},{"month":"11","publication_identifier":{"eissn":["2666-1667"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.xpro.2021.100939","quality_controlled":"1","project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031","call_identifier":"FWF","name":"Role of Eed in neural stem cell lineage progression"},{"_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2021-11-22T08:23:58Z","ec_funded":1,"article_number":"100939","date_updated":"2023-11-16T13:08:03Z","date_created":"2021-11-21T23:01:28Z","volume":2,"author":[{"full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","last_name":"Amberg","first_name":"Nicole"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"publication_status":"published","department":[{"_id":"SiHi"}],"publisher":"Cell Press","year":"2021","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). We particularly thank Mohammad Goudarzi for assistance with photography of mouse perfusion and dissection. N.A. received support from FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","day":"10","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2021-11-10T00:00:00Z","article_type":"original","publication":"STAR Protocols","citation":{"ieee":"N. Amberg and S. Hippenmeyer, “Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers,” STAR Protocols, vol. 2, no. 4. Cell Press, 2021.","apa":"Amberg, N., & Hippenmeyer, S. (2021). Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. Cell Press. https://doi.org/10.1016/j.xpro.2021.100939","ista":"Amberg N, Hippenmeyer S. 2021. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2(4), 100939.","ama":"Amberg N, Hippenmeyer S. Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers. STAR Protocols. 2021;2(4). doi:10.1016/j.xpro.2021.100939","chicago":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols. Cell Press, 2021. https://doi.org/10.1016/j.xpro.2021.100939.","short":"N. Amberg, S. Hippenmeyer, STAR Protocols 2 (2021).","mla":"Amberg, Nicole, and Simon Hippenmeyer. “Genetic Mosaic Dissection of Candidate Genes in Mice Using Mosaic Analysis with Double Markers.” STAR Protocols, vol. 2, no. 4, 100939, Cell Press, 2021, doi:10.1016/j.xpro.2021.100939."},"abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling and introduction of a mutation of a gene of interest with single-cell resolution. This protocol highlights major steps for the generation of genetic mosaic tissue and the isolation and processing of respective tissues for downstream histological analysis. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021)."}],"issue":"4","type":"journal_article","file":[{"date_created":"2021-11-22T08:23:58Z","date_updated":"2021-11-22T08:23:58Z","success":1,"checksum":"9e3f6d06bf583e7a8b6a9e9a60500a28","file_id":"10329","relation":"main_file","creator":"cchlebak","content_type":"application/pdf","file_size":7309464,"file_name":"2021_STARProtocols_Amberg.pdf","access_level":"open_access"}],"oa_version":"Published Version","title":"Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers","ddc":["573"],"status":"public","intvolume":" 2","_id":"10321","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"article_number":"107808","file_date_updated":"2021-11-15T13:11:27Z","publication_status":"published","publisher":"Elsevier ","department":[{"_id":"FlSc"}],"year":"2021","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.","date_created":"2021-11-15T12:21:42Z","date_updated":"2023-11-21T08:36:02Z","volume":213,"author":[{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","first_name":"Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Amiri, Behnam","first_name":"Behnam","last_name":"Amiri"},{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian","full_name":"Fäßler, Florian"},{"full_name":"Falcke, Martin","last_name":"Falcke","first_name":"Martin"},{"full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"related_material":{"record":[{"id":"14502","status":"public","relation":"software"}]},"month":"11","publication_identifier":{"issn":["1047-8477"]},"isi":1,"quality_controlled":"1","project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367"},{"grant_number":"M02495","_id":"2674F658-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Protein structure and function in filopodia across scales"}],"external_id":{"isi":["000720259500002"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.jsb.2021.107808","type":"journal_article","abstract":[{"text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner.","lang":"eng"}],"issue":"4","status":"public","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","ddc":["572"],"intvolume":" 213","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10290","oa_version":"Published Version","file":[{"file_name":"2021_JournalStructBiol_Dimchev.pdf","access_level":"open_access","file_size":16818304,"content_type":"application/pdf","creator":"cchlebak","relation":"main_file","file_id":"10291","date_updated":"2021-11-15T13:11:27Z","date_created":"2021-11-15T13:11:27Z","checksum":"6b209e4d44775d4e02b50f78982c15fa","success":1}],"keyword":["Structural Biology"],"scopus_import":"1","day":"03","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","article_type":"original","publication":"Journal of Structural Biology","citation":{"short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology, vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808.","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier , 2021. https://doi.org/10.1016/j.jsb.2021.107808.","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021.","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808."},"date_published":"2021-11-03T00:00:00Z"},{"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14506"}]},"author":[{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"},{"full_name":"Salem, Iosif","first_name":"Iosif","last_name":"Salem"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"},{"first_name":"Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X"}],"date_updated":"2023-11-30T10:54:50Z","date_created":"2021-08-29T22:01:16Z","year":"2021","publisher":"IEEE","department":[{"_id":"KrPi"}],"publication_status":"published","ec_funded":1,"doi":"10.23919/IFIPNetworking52078.2021.9472205","conference":{"name":"2021 IFIP Networking Conference (IFIP Networking)","end_date":"2021-06-24","location":"Espoo and Helsinki, Finland","start_date":"2021-06-21"},"language":[{"iso":"eng"}],"external_id":{"isi":["000853016800008"],"arxiv":["2104.04293"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.04293"}],"project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eisbn":["978-3-9031-7639-3"],"eissn":["1861-2288"],"isbn":["978-1-6654-4501-6"]},"month":"06","oa_version":"Submitted Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9969","status":"public","title":"LightPIR: Privacy-preserving route discovery for payment channel networks","abstract":[{"lang":"eng","text":"Payment channel networks are a promising approach to improve the scalability of cryptocurrencies: they allow to perform transactions in a peer-to-peer fashion, along multihop routes in the network, without requiring consensus on the blockchain. However, during the discovery of cost-efficient routes for the transaction, critical information may be revealed about the transacting entities. This paper initiates the study of privacy-preserving route discovery mechanisms for payment channel networks. In particular, we present LightPIR, an approach which allows a client to learn the shortest (or cheapest in terms of fees) path between two nodes without revealing any information about the endpoints of the transaction to the servers. The two main observations which allow for an efficient solution in LightPIR are that: (1) surprisingly, hub labelling algorithms – which were developed to preprocess “street network like” graphs so one can later efficiently compute shortest paths – also perform well for the graphs underlying payment channel networks, and that (2) hub labelling algorithms can be conveniently combined with private information retrieval. LightPIR relies on a simple hub labeling heuristic on top of existing hub labeling algorithms which leverages the specific topological features of cryptocurrency networks to further minimize storage and bandwidth overheads. In a case study considering the Lightning network, we show that our approach is an order of magnitude more efficient compared to a privacy-preserving baseline based on using private information retrieval on a database that stores all pairs shortest paths."}],"type":"conference","date_published":"2021-06-21T00:00:00Z","citation":{"mla":"Pietrzak, Krzysztof Z., et al. LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks. IEEE, 2021, doi:10.23919/IFIPNetworking52078.2021.9472205.","short":"K.Z. Pietrzak, I. Salem, S. Schmid, M.X. Yeo, in:, IEEE, 2021.","chicago":"Pietrzak, Krzysztof Z, Iosif Salem, Stefan Schmid, and Michelle X Yeo. “LightPIR: Privacy-Preserving Route Discovery for Payment Channel Networks.” IEEE, 2021. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205.","ama":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. LightPIR: Privacy-preserving route discovery for payment channel networks. In: IEEE; 2021. doi:10.23919/IFIPNetworking52078.2021.9472205","ista":"Pietrzak KZ, Salem I, Schmid S, Yeo MX. 2021. LightPIR: Privacy-preserving route discovery for payment channel networks. 2021 IFIP Networking Conference (IFIP Networking).","ieee":"K. Z. Pietrzak, I. Salem, S. Schmid, and M. X. Yeo, “LightPIR: Privacy-preserving route discovery for payment channel networks,” presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland, 2021.","apa":"Pietrzak, K. Z., Salem, I., Schmid, S., & Yeo, M. X. (2021). LightPIR: Privacy-preserving route discovery for payment channel networks. Presented at the 2021 IFIP Networking Conference (IFIP Networking), Espoo and Helsinki, Finland: IEEE. https://doi.org/10.23919/IFIPNetworking52078.2021.9472205"},"article_processing_charge":"No","day":"21","scopus_import":"1"}]