--- _id: '9647' abstract: - lang: eng text: 'Gene expression is regulated by the set of transcription factors (TFs) that bind to the promoter. The ensuing regulating function is often represented as a combinational logic circuit, where output (gene expression) is determined by current input values (promoter bound TFs) only. However, the simultaneous arrival of TFs is a strong assumption, since transcription and translation of genes introduce intrinsic time delays and there is no global synchronisation among the arrival times of different molecular species at their targets. We present an experimentally implementable genetic circuit with two inputs and one output, which in the presence of small delays in input arrival, exhibits qualitatively distinct population-level phenotypes, over timescales that are longer than typical cell doubling times. From a dynamical systems point of view, these phenotypes represent long-lived transients: although they converge to the same value eventually, they do so after a very long time span. The key feature of this toy model genetic circuit is that, despite having only two inputs and one output, it is regulated by twenty-three distinct DNA-TF configurations, two of which are more stable than others (DNA looped states), one promoting and another blocking the expression of the output gene. Small delays in input arrival time result in a majority of cells in the population quickly reaching the stable state associated with the first input, while exiting of this stable state occurs at a slow timescale. In order to mechanistically model the behaviour of this genetic circuit, we used a rule-based modelling language, and implemented a grid-search to find parameter combinations giving rise to long-lived transients. Our analysis shows that in the absence of feedback, there exist path-dependent gene regulatory mechanisms based on the long timescale of transients. The behaviour of this toy model circuit suggests that gene regulatory networks can exploit event timing to create phenotypes, and it opens the possibility that they could use event timing to memorise events, without regulatory feedback. The model reveals the importance of (i) mechanistically modelling the transitions between the different DNA-TF states, and (ii) employing transient analysis thereof.' acknowledgement: 'Tatjana Petrov’s research was supported in part by SNSF Advanced Postdoctoral Mobility Fellowship grant number P300P2 161067, the Ministry of Science, Research and the Arts of the state of Baden-Wurttemberg, and the DFG Centre of Excellence 2117 ‘Centre for the Advanced Study of Collective Behaviour’ (ID: 422037984). Claudia Igler is the recipient of a DOC Fellowship of the Austrian Academy of Sciences. Thomas A. Henzinger’s research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).' article_processing_charge: No article_type: original author: - first_name: Tatjana full_name: Petrov, Tatjana last_name: Petrov - first_name: Claudia full_name: Igler, Claudia id: 46613666-F248-11E8-B48F-1D18A9856A87 last_name: Igler - first_name: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. Long lived transients in gene regulation. Theoretical Computer Science. 2021;893:1-16. doi:10.1016/j.tcs.2021.05.023 apa: Petrov, T., Igler, C., Sezgin, A., Henzinger, T. A., & Guet, C. C. (2021). Long lived transients in gene regulation. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2021.05.023 chicago: Petrov, Tatjana, Claudia Igler, Ali Sezgin, Thomas A Henzinger, and Calin C Guet. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.05.023. ieee: T. Petrov, C. Igler, A. Sezgin, T. A. Henzinger, and C. C. Guet, “Long lived transients in gene regulation,” Theoretical Computer Science, vol. 893. Elsevier, pp. 1–16, 2021. ista: Petrov T, Igler C, Sezgin A, Henzinger TA, Guet CC. 2021. Long lived transients in gene regulation. Theoretical Computer Science. 893, 1–16. mla: Petrov, Tatjana, et al. “Long Lived Transients in Gene Regulation.” Theoretical Computer Science, vol. 893, Elsevier, 2021, pp. 1–16, doi:10.1016/j.tcs.2021.05.023. short: T. Petrov, C. Igler, A. Sezgin, T.A. Henzinger, C.C. Guet, Theoretical Computer Science 893 (2021) 1–16. date_created: 2021-07-11T22:01:18Z date_published: 2021-06-04T00:00:00Z date_updated: 2023-08-10T14:11:19Z day: '04' ddc: - '004' department: - _id: ToHe - _id: CaGu doi: 10.1016/j.tcs.2021.05.023 external_id: isi: - '000710180500002' file: - access_level: open_access checksum: d3aef34cfb13e53bba4cf44d01680793 content_type: application/pdf creator: dernst date_created: 2022-05-12T12:13:27Z date_updated: 2022-05-12T12:13:27Z file_id: '11364' file_name: 2021_TheoreticalComputerScience_Petrov.pdf file_size: 2566504 relation: main_file success: 1 file_date_updated: 2022-05-12T12:13:27Z has_accepted_license: '1' intvolume: ' 893' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1-16 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Long lived transients in gene regulation tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 893 year: '2021' ... --- _id: '9761' abstract: - lang: eng text: 'The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. ' acknowledgement: The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript. article_number: '1593' article_processing_charge: Yes article_type: original author: - first_name: Nicole A. full_name: Muench, Nicole A. last_name: Muench - first_name: Sonia full_name: Patel, Sonia last_name: Patel - first_name: Margaret E full_name: Maes, Margaret E id: 3838F452-F248-11E8-B48F-1D18A9856A87 last_name: Maes orcid: 0000-0001-9642-1085 - first_name: Ryan J. full_name: Donahue, Ryan J. last_name: Donahue - first_name: Akihiro full_name: Ikeda, Akihiro last_name: Ikeda - first_name: Robert W. full_name: Nickells, Robert W. last_name: Nickells citation: ama: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 2021;10(7). doi:10.3390/cells10071593 apa: Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., & Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. MDPI. https://doi.org/10.3390/cells10071593 chicago: Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells. MDPI, 2021. https://doi.org/10.3390/cells10071593. ieee: N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” Cells, vol. 10, no. 7. MDPI, 2021. ista: Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593. mla: Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” Cells, vol. 10, no. 7, 1593, MDPI, 2021, doi:10.3390/cells10071593. short: N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021). date_created: 2021-08-01T22:01:22Z date_published: 2021-06-25T00:00:00Z date_updated: 2023-08-10T14:14:53Z day: '25' ddc: - '570' department: - _id: SaSi doi: 10.3390/cells10071593 external_id: isi: - '000678193300001' pmid: - '34201955' file: - access_level: open_access checksum: e0497ce5c77fa3b65a538c7d6e0f6c66 content_type: application/pdf creator: cziletti date_created: 2021-08-04T14:01:30Z date_updated: 2021-08-04T14:01:30Z file_id: '9768' file_name: 2021_Cells_Muench.pdf file_size: 4555611 relation: main_file success: 1 file_date_updated: 2021-08-04T14:01:30Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '7' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Cells publication_identifier: eissn: - '20734409' publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2021' ... --- _id: '9641' abstract: - lang: eng text: At the encounter with a novel environment, contextual memory formation is greatly enhanced, accompanied with increased arousal and active exploration. Although this phenomenon has been widely observed in animal and human daily life, how the novelty in the environment is detected and contributes to contextual memory formation has lately started to be unveiled. The hippocampus has been studied for many decades for its largely known roles in encoding spatial memory, and a growing body of evidence indicates a differential involvement of dorsal and ventral hippocampal divisions in novelty detection. In this brief review article, we discuss the recent findings of the role of mossy cells in the ventral hippocampal moiety in novelty detection and put them in perspective with other novelty-related pathways in the hippocampus. We propose a mechanism for novelty-driven memory acquisition in the dentate gyrus by the direct projection of ventral mossy cells to dorsal dentate granule cells. By this projection, the ventral hippocampus sends novelty signals to the dorsal hippocampus, opening a gate for memory encoding in dentate granule cells based on information coming from the entorhinal cortex. We conclude that, contrary to the presently accepted functional independence, the dorsal and ventral hippocampi cooperate to link the novelty and contextual information, and this dorso-ventral interaction is crucial for the novelty-dependent memory formation. acknowledgement: This work was supported by a European Research Council Advanced Grant 694539 to Ryuichi Shigemoto. article_number: '107486' article_processing_charge: No article_type: original author: - first_name: Felipe full_name: Fredes, Felipe last_name: Fredes - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Fredes F, Shigemoto R. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 2021;183. doi:10.1016/j.nlm.2021.107486 apa: Fredes, F., & Shigemoto, R. (2021). The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. Elsevier. https://doi.org/10.1016/j.nlm.2021.107486 chicago: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory. Elsevier, 2021. https://doi.org/10.1016/j.nlm.2021.107486. ieee: F. Fredes and R. Shigemoto, “The role of hippocampal mossy cells in novelty detection,” Neurobiology of Learning and Memory, vol. 183. Elsevier, 2021. ista: Fredes F, Shigemoto R. 2021. The role of hippocampal mossy cells in novelty detection. Neurobiology of Learning and Memory. 183, 107486. mla: Fredes, Felipe, and Ryuichi Shigemoto. “The Role of Hippocampal Mossy Cells in Novelty Detection.” Neurobiology of Learning and Memory, vol. 183, 107486, Elsevier, 2021, doi:10.1016/j.nlm.2021.107486. short: F. Fredes, R. Shigemoto, Neurobiology of Learning and Memory 183 (2021). date_created: 2021-07-11T22:01:16Z date_published: 2021-06-30T00:00:00Z date_updated: 2023-08-10T14:10:37Z day: '30' ddc: - '610' department: - _id: RySh doi: 10.1016/j.nlm.2021.107486 ec_funded: 1 external_id: isi: - '000677694900004' pmid: - '34214666' file: - access_level: open_access checksum: 8e8298a9e8c7df146ad23f32c2a63929 content_type: application/pdf creator: cziletti date_created: 2021-07-19T13:46:06Z date_updated: 2021-07-19T13:46:06Z file_id: '9694' file_name: 2021_NeurobLearnMemory_Fredes.pdf file_size: 1994793 relation: main_file success: 1 file_date_updated: 2021-07-19T13:46:06Z has_accepted_license: '1' intvolume: ' 183' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' publication: Neurobiology of Learning and Memory publication_identifier: eissn: - '10959564' issn: - '10747427' publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: The role of hippocampal mossy cells in novelty detection tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 183 year: '2021' ... --- _id: '9646' abstract: - lang: eng text: We consider the fundamental problem of deriving quantitative bounds on the probability that a given assertion is violated in a probabilistic program. We provide automated algorithms that obtain both lower and upper bounds on the assertion violation probability. The main novelty of our approach is that we prove new and dedicated fixed-point theorems which serve as the theoretical basis of our algorithms and enable us to reason about assertion violation bounds in terms of pre and post fixed-point functions. To synthesize such fixed-points, we devise algorithms that utilize a wide range of mathematical tools, including repulsing ranking supermartingales, Hoeffding's lemma, Minkowski decompositions, Jensen's inequality, and convex optimization. On the theoretical side, we provide (i) the first automated algorithm for lower-bounds on assertion violation probabilities, (ii) the first complete algorithm for upper-bounds of exponential form in affine programs, and (iii) provably and significantly tighter upper-bounds than the previous approaches. On the practical side, we show our algorithms can handle a wide variety of programs from the literature and synthesize bounds that are remarkably tighter than previous results, in some cases by thousands of orders of magnitude. acknowledgement: 'We are very thankful to the anonymous reviewers for the helpful and valuable comments. The work was partially supported by the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the ERC CoG 863818 (ForM-SMArt), the Facebook PhD Fellowship Program and DOC Fellowship #24956 of the Austrian Academy of Sciences (ÖAW).' article_processing_charge: No author: - first_name: Jinyi full_name: Wang, Jinyi last_name: Wang - first_name: Yican full_name: Sun, Yican last_name: Sun - first_name: Hongfei full_name: Fu, Hongfei id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87 last_name: Fu - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 citation: ama: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. Quantitative analysis of assertion violations in probabilistic programs. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:1171-1186. doi:10.1145/3453483.3454102' apa: 'Wang, J., Sun, Y., Fu, H., Chatterjee, K., & Goharshady, A. K. (2021). Quantitative analysis of assertion violations in probabilistic programs. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 1171–1186). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454102' chicago: Wang, Jinyi, Yican Sun, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 1171–86. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454102. ieee: J. Wang, Y. Sun, H. Fu, K. Chatterjee, and A. K. Goharshady, “Quantitative analysis of assertion violations in probabilistic programs,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 1171–1186. ista: 'Wang J, Sun Y, Fu H, Chatterjee K, Goharshady AK. 2021. Quantitative analysis of assertion violations in probabilistic programs. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 1171–1186.' mla: Wang, Jinyi, et al. “Quantitative Analysis of Assertion Violations in Probabilistic Programs.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–86, doi:10.1145/3453483.3454102. short: J. Wang, Y. Sun, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 1171–1186. conference: end_date: 2021-06-26 location: Online name: 'PLDI: Programming Language Design and Implementation' start_date: 2021-06-20 date_created: 2021-07-11T22:01:18Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-10T14:14:08Z day: '01' department: - _id: KrCh doi: 10.1145/3453483.3454102 ec_funded: 1 external_id: arxiv: - '2011.14617' isi: - '000723661700076' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2011.14617 month: '06' oa: 1 oa_version: Preprint page: 1171-1186 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 267066CE-B435-11E9-9278-68D0E5697425 name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation publication_identifier: isbn: - '9781450383912' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Quantitative analysis of assertion violations in probabilistic programs type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9645' abstract: - lang: eng text: "We consider the fundamental problem of reachability analysis over imperative programs with real variables. Previous works that tackle reachability are either unable to handle programs consisting of general loops (e.g. symbolic execution), or lack completeness guarantees (e.g. abstract interpretation), or are not automated (e.g. incorrectness logic). In contrast, we propose a novel approach for reachability analysis that can handle general and complex loops, is complete, and can be entirely automated for a wide family of programs. Through the notion of Inductive Reachability Witnesses (IRWs), our approach extends ideas from both invariant generation and termination to reachability analysis.\r\n\r\nWe first show that our IRW-based approach is sound and complete for reachability analysis of imperative programs. Then, we focus on linear and polynomial programs and develop automated methods for synthesizing linear and polynomial IRWs. In the linear case, we follow the well-known approaches using Farkas' Lemma. Our main contribution is in the polynomial case, where we present a push-button semi-complete algorithm. We achieve this using a novel combination of classical theorems in real algebraic geometry, such as Putinar's Positivstellensatz and Hilbert's Strong Nullstellensatz. Finally, our experimental results show we can prove complex reachability objectives over various benchmarks that were beyond the reach of previous methods." acknowledgement: This research was partially supported by the ERC CoG 863818 (ForM-SMArt), the National Natural Science Foundation of China (NSFC) Grant No. 61802254, the Huawei Innovation Research Program, the Facebook PhD Fellowship Program, and DOC Fellowship No. 24956 of the Austrian Academy of Sciences (ÖAW). article_processing_charge: No author: - first_name: Ali full_name: Asadi, Ali last_name: Asadi - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Hongfei full_name: Fu, Hongfei id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87 last_name: Fu - first_name: Amir Kafshdar full_name: Goharshady, Amir Kafshdar id: 391365CE-F248-11E8-B48F-1D18A9856A87 last_name: Goharshady orcid: 0000-0003-1702-6584 - first_name: Mohammad full_name: Mahdavi, Mohammad last_name: Mahdavi citation: ama: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. Polynomial reachability witnesses via Stellensätze. In: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. Association for Computing Machinery; 2021:772-787. doi:10.1145/3453483.3454076' apa: 'Asadi, A., Chatterjee, K., Fu, H., Goharshady, A. K., & Mahdavi, M. (2021). Polynomial reachability witnesses via Stellensätze. In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation (pp. 772–787). Online: Association for Computing Machinery. https://doi.org/10.1145/3453483.3454076' chicago: Asadi, Ali, Krishnendu Chatterjee, Hongfei Fu, Amir Kafshdar Goharshady, and Mohammad Mahdavi. “Polynomial Reachability Witnesses via Stellensätze.” In Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, 772–87. Association for Computing Machinery, 2021. https://doi.org/10.1145/3453483.3454076. ieee: A. Asadi, K. Chatterjee, H. Fu, A. K. Goharshady, and M. Mahdavi, “Polynomial reachability witnesses via Stellensätze,” in Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Online, 2021, pp. 772–787. ista: 'Asadi A, Chatterjee K, Fu H, Goharshady AK, Mahdavi M. 2021. Polynomial reachability witnesses via Stellensätze. Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation. PLDI: Programming Language Design and Implementation, 772–787.' mla: Asadi, Ali, et al. “Polynomial Reachability Witnesses via Stellensätze.” Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–87, doi:10.1145/3453483.3454076. short: A. Asadi, K. Chatterjee, H. Fu, A.K. Goharshady, M. Mahdavi, in:, Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2021, pp. 772–787. conference: end_date: 2021-06-26 location: Online name: ' PLDI: Programming Language Design and Implementation' start_date: 2021-06-20 date_created: 2021-07-11T22:01:17Z date_published: 2021-06-01T00:00:00Z date_updated: 2023-08-10T14:13:39Z day: '01' department: - _id: KrCh doi: 10.1145/3453483.3454076 ec_funded: 1 external_id: isi: - '000723661700050' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-03183862/ month: '06' oa: 1 oa_version: Submitted Version page: 772-787 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 267066CE-B435-11E9-9278-68D0E5697425 name: Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies publication: Proceedings of the 42nd ACM SIGPLAN International Conference on Programming Language Design and Implementation publication_identifier: isbn: - '9781450383912' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Polynomial reachability witnesses via Stellensätze type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '9759' acknowledgement: The authors thank Inez Lam of Johns Hopkins University for valuable comments on an earlier version of the manuscript. We also thank the facilitators of the 2019–2020 eLife Community Ambassador program. article_number: e1009124 article_processing_charge: Yes article_type: letter_note author: - first_name: Michael John full_name: Bartlett, Michael John last_name: Bartlett - first_name: Feyza N full_name: Arslan, Feyza N id: 49DA7910-F248-11E8-B48F-1D18A9856A87 last_name: Arslan orcid: 0000-0001-5809-9566 - first_name: Adriana full_name: Bankston, Adriana last_name: Bankston - first_name: Sarvenaz full_name: Sarabipour, Sarvenaz last_name: Sarabipour citation: ama: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 2021;17(7). doi:10.1371/journal.pcbi.1009124 apa: Bartlett, M. J., Arslan, F. N., Bankston, A., & Sarabipour, S. (2021). Ten simple rules to improve academic work- life balance. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009124 chicago: Bartlett, Michael John, Feyza N Arslan, Adriana Bankston, and Sarvenaz Sarabipour. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009124. ieee: M. J. Bartlett, F. N. Arslan, A. Bankston, and S. Sarabipour, “Ten simple rules to improve academic work- life balance,” PLoS Computational Biology, vol. 17, no. 7. Public Library of Science, 2021. ista: Bartlett MJ, Arslan FN, Bankston A, Sarabipour S. 2021. Ten simple rules to improve academic work- life balance. PLoS Computational Biology. 17(7), e1009124. mla: Bartlett, Michael John, et al. “Ten Simple Rules to Improve Academic Work- Life Balance.” PLoS Computational Biology, vol. 17, no. 7, e1009124, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009124. short: M.J. Bartlett, F.N. Arslan, A. Bankston, S. Sarabipour, PLoS Computational Biology 17 (2021). date_created: 2021-08-01T22:01:21Z date_published: 2021-07-15T00:00:00Z date_updated: 2023-08-10T14:16:46Z day: '15' ddc: - '613' department: - _id: CaHe doi: 10.1371/journal.pcbi.1009124 external_id: isi: - '000677713500008' pmid: - '34264932' file: - access_level: open_access checksum: e56d91f0eeadb36f143a90e2c1b3ab63 content_type: application/pdf creator: cchlebak date_created: 2021-08-05T12:06:49Z date_updated: 2021-08-05T12:06:49Z file_id: '9771' file_name: 2021_PlosCompBio_Bartlett.pdf file_size: 693633 relation: main_file file_date_updated: 2021-08-05T12:06:49Z has_accepted_license: '1' intvolume: ' 17' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Computational Biology publication_identifier: eissn: - '15537358' issn: - 1553734X publication_status: published publisher: Public Library of Science scopus_import: '1' status: public title: Ten simple rules to improve academic work- life balance tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 17 year: '2021' ... --- _id: '9822' abstract: - lang: eng text: Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science. acknowledgement: We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Themistoklis full_name: Zisis, Themistoklis last_name: Zisis - first_name: Jan full_name: Schwarz, Jan id: 346C1EC6-F248-11E8-B48F-1D18A9856A87 last_name: Schwarz - first_name: Miriam full_name: Balles, Miriam last_name: Balles - first_name: Maibritt full_name: Kretschmer, Maibritt last_name: Kretschmer - first_name: Maria full_name: Nemethova, Maria id: 34E27F1C-F248-11E8-B48F-1D18A9856A87 last_name: Nemethova - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Janina full_name: Lange, Janina last_name: Lange - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-4561-241X - first_name: Stefan full_name: Zahler, Stefan last_name: Zahler citation: ama: Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850 apa: Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.1c09850 chicago: Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850. ieee: T. Zisis et al., “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” ACS Applied Materials and Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021. ista: Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560. mla: Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:10.1021/acsami.1c09850. short: T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560. date_created: 2021-08-08T22:01:28Z date_published: 2021-08-04T00:00:00Z date_updated: 2023-08-10T14:22:48Z day: '04' ddc: - '620' - '570' department: - _id: MiSi - _id: GaTk - _id: Bio - _id: CaGu doi: 10.1021/acsami.1c09850 ec_funded: 1 external_id: isi: - '000683741400026' pmid: - '34283577' file: - access_level: open_access checksum: b043a91d9f9200e467b970b692687ed3 content_type: application/pdf creator: asandaue date_created: 2021-08-09T09:44:03Z date_updated: 2021-08-09T09:44:03Z file_id: '9833' file_name: 2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf file_size: 7123293 relation: main_file success: 1 file_date_updated: 2021-08-09T09:44:03Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '30' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 35545–35560 pmid: 1 project: - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular navigation along spatial gradients publication: ACS Applied Materials and Interfaces publication_identifier: eissn: - '19448252' issn: - '19448244' publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Sequential and switchable patterning for studying cellular processes under spatiotemporal control tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2021' ... --- _id: '9819' abstract: - lang: eng text: Photorealistic editing of head portraits is a challenging task as humans are very sensitive to inconsistencies in faces. We present an approach for high-quality intuitive editing of the camera viewpoint and scene illumination (parameterised with an environment map) in a portrait image. This requires our method to capture and control the full reflectance field of the person in the image. Most editing approaches rely on supervised learning using training data captured with setups such as light and camera stages. Such datasets are expensive to acquire, not readily available and do not capture all the rich variations of in-the-wild portrait images. In addition, most supervised approaches only focus on relighting, and do not allow camera viewpoint editing. Thus, they only capture and control a subset of the reflectance field. Recently, portrait editing has been demonstrated by operating in the generative model space of StyleGAN. While such approaches do not require direct supervision, there is a significant loss of quality when compared to the supervised approaches. In this paper, we present a method which learns from limited supervised training data. The training images only include people in a fixed neutral expression with eyes closed, without much hair or background variations. Each person is captured under 150 one-light-at-a-time conditions and under 8 camera poses. Instead of training directly in the image space, we design a supervised problem which learns transformations in the latent space of StyleGAN. This combines the best of supervised learning and generative adversarial modeling. We show that the StyleGAN prior allows for generalisation to different expressions, hairstyles and backgrounds. This produces high-quality photorealistic results for in-the-wild images and significantly outperforms existing methods. Our approach can edit the illumination and pose simultaneously, and runs at interactive rates. acknowledgement: This work was supported by the ERC Consolidator Grant 4DReply (770784). We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng Sun for kindly helping us with the comparisons with Sun et al. [2019]. article_number: '44' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: B. R. full_name: Mallikarjun, B. R. last_name: Mallikarjun - first_name: Ayush full_name: Tewari, Ayush last_name: Tewari - first_name: Abdallah full_name: Dib, Abdallah last_name: Dib - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Hans Peter full_name: Seidel, Hans Peter last_name: Seidel - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Louis full_name: Chevallier, Louis last_name: Chevallier - first_name: Mohamed A. full_name: Elgharib, Mohamed A. last_name: Elgharib - first_name: Christian full_name: Theobalt, Christian last_name: Theobalt citation: ama: 'Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459765' apa: 'Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel, H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459765' chicago: 'Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel, Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459765.' ieee: 'B. R. Mallikarjun et al., “PhotoApp: Photorealistic appearance editing of head portraits,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.' ista: 'Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.' mla: 'Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” ACM Transactions on Graphics, vol. 40, no. 4, 44, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459765.' short: B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel, H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions on Graphics 40 (2021). date_created: 2021-08-08T22:01:27Z date_published: 2021-08-01T00:00:00Z date_updated: 2023-08-10T14:25:08Z day: '01' ddc: - '000' department: - _id: BeBi doi: 10.1145/3450626.3459765 external_id: arxiv: - '2103.07658' isi: - '000674930900011' file: - access_level: open_access checksum: 51b61b7e5c175e2d7ed8fa3b35f7525a content_type: application/pdf creator: asandaue date_created: 2021-08-09T11:41:50Z date_updated: 2021-08-09T11:41:50Z file_id: '9834' file_name: 2021_ACMTransactionsOnGraphics_Mallikarjun.pdf file_size: 49840741 relation: main_file success: 1 file_date_updated: 2021-08-09T11:41:50Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: ACM Transactions on Graphics publication_identifier: eissn: - '15577368' issn: - '07300301' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'PhotoApp: Photorealistic appearance editing of head portraits' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '9816' abstract: - lang: eng text: "Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test." acknowledgement: We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used. article_number: e0255267 article_processing_charge: Yes article_type: original author: - first_name: Michal full_name: Hledik, Michal id: 4171253A-F248-11E8-B48F-1D18A9856A87 last_name: Hledik - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: Mathias full_name: Beiglböck, Mathias last_name: Beiglböck - first_name: Anna Nele full_name: Herdina, Anna Nele last_name: Herdina - first_name: Robert full_name: Strassl, Robert last_name: Strassl - first_name: Martin full_name: Posch, Martin last_name: Posch citation: ama: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0255267 apa: Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., & Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0255267 chicago: Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0255267. ieee: M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021. ista: Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267. mla: Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” PLoS ONE, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:10.1371/journal.pone.0255267. short: M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021). date_created: 2021-08-08T22:01:26Z date_published: 2021-07-29T00:00:00Z date_updated: 2023-08-10T14:26:32Z day: '29' ddc: - '610' department: - _id: NiBa doi: 10.1371/journal.pone.0255267 external_id: isi: - '000685248200095' pmid: - '34324553' file: - access_level: open_access checksum: ae4df60eb62f4491278588548d0c1f93 content_type: application/pdf creator: asandaue date_created: 2021-08-09T11:52:14Z date_updated: 2021-08-09T11:52:14Z file_id: '9835' file_name: 2021_PLoSONE_Hledík.pdf file_size: 773921 relation: main_file success: 1 file_date_updated: 2021-08-09T11:52:14Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS ONE publication_identifier: eissn: - 1932-6203 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2021' ... --- _id: '9821' abstract: - lang: eng text: Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode. acknowledgement: We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper. article_number: e0253851 article_processing_charge: Yes article_type: original author: - first_name: Grzegorz full_name: Graff, Grzegorz last_name: Graff - first_name: Beata full_name: Graff, Beata last_name: Graff - first_name: Pawel full_name: Pilarczyk, Pawel id: 3768D56A-F248-11E8-B48F-1D18A9856A87 last_name: Pilarczyk - first_name: Grzegorz full_name: Jablonski, Grzegorz id: 4483EF78-F248-11E8-B48F-1D18A9856A87 last_name: Jablonski orcid: 0000-0002-3536-9866 - first_name: Dariusz full_name: Gąsecki, Dariusz last_name: Gąsecki - first_name: Krzysztof full_name: Narkiewicz, Krzysztof last_name: Narkiewicz citation: ama: Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 2021;16(7). doi:10.1371/journal.pone.0253851 apa: Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., & Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0253851 chicago: Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0253851. ieee: G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz, “Persistent homology as a new method of the assessment of heart rate variability,” PLoS ONE, vol. 16, no. 7. Public Library of Science, 2021. ista: Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 16(7), e0253851. mla: Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” PLoS ONE, vol. 16, no. 7, e0253851, Public Library of Science, 2021, doi:10.1371/journal.pone.0253851. short: G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021). date_created: 2021-08-08T22:01:28Z date_published: 2021-07-01T00:00:00Z date_updated: 2023-08-10T14:21:42Z day: '01' ddc: - '006' department: - _id: HeEd doi: 10.1371/journal.pone.0253851 external_id: isi: - '000678124900050' pmid: - '34292957' file: - access_level: open_access checksum: 0277aa155d5db1febd2cb384768bba5f content_type: application/pdf creator: asandaue date_created: 2021-08-09T09:25:41Z date_updated: 2021-08-09T09:25:41Z file_id: '9832' file_name: 2021_PLoSONE_Graff.pdf file_size: 2706919 relation: main_file success: 1 file_date_updated: 2021-08-09T09:25:41Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS ONE publication_identifier: eissn: - '19326203' publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Persistent homology as a new method of the assessment of heart rate variability tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 16 year: '2021' ... --- _id: '9820' abstract: - lang: eng text: Material appearance hinges on material reflectance properties but also surface geometry and illumination. The unlimited number of potential combinations between these factors makes understanding and predicting material appearance a very challenging task. In this work, we collect a large-scale dataset of perceptual ratings of appearance attributes with more than 215,680 responses for 42,120 distinct combinations of material, shape, and illumination. The goal of this dataset is twofold. First, we analyze for the first time the effects of illumination and geometry in material perception across such a large collection of varied appearances. We connect our findings to those of the literature, discussing how previous knowledge generalizes across very diverse materials, shapes, and illuminations. Second, we use the collected dataset to train a deep learning architecture for predicting perceptual attributes that correlate with human judgments. We demonstrate the consistent and robust behavior of our predictor in various challenging scenarios, which, for the first time, enables estimating perceived material attributes from general 2D images. Since our predictor relies on the final appearance in an image, it can compare appearance properties across different geometries and illumination conditions. Finally, we demonstrate several applications that use our predictor, including appearance reproduction using 3D printing, BRDF editing by integrating our predictor in a differentiable renderer, illumination design, or material recommendations for scene design. acknowledgement: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie, grant agreement Nº 765911 (RealVision) and from the European Research Council (ERC), grant agreement Nº 804226 (PERDY). article_number: '125' article_processing_charge: No article_type: original author: - first_name: Ana full_name: Serrano, Ana last_name: Serrano - first_name: Bin full_name: Chen, Bin last_name: Chen - first_name: Chao full_name: Wang, Chao last_name: Wang - first_name: Michael full_name: Piovarci, Michael id: 62E473F4-5C99-11EA-A40E-AF823DDC885E last_name: Piovarci orcid: 0000-0002-5062-4474 - first_name: Hans Peter full_name: Seidel, Hans Peter last_name: Seidel - first_name: Piotr full_name: Didyk, Piotr last_name: Didyk - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski citation: ama: 'Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459813' apa: 'Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., & Myszkowski, K. (2021). The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459813' chicago: 'Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459813.' ieee: 'A. Serrano et al., “The effect of shape and illumination on material perception: Model and applications,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021.' ista: 'Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K. 2021. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 40(4), 125.' mla: 'Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” ACM Transactions on Graphics, vol. 40, no. 4, 125, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459813.' short: A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, ACM Transactions on Graphics 40 (2021). date_created: 2021-08-08T22:01:28Z date_published: 2021-08-01T00:00:00Z date_updated: 2023-08-10T14:20:10Z day: '01' department: - _id: BeBi doi: 10.1145/3450626.3459813 external_id: isi: - '000674930900090' intvolume: ' 40' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://zaguan.unizar.es/record/110704/files/texto_completo.pdf month: '08' oa: 1 oa_version: Submitted Version publication: ACM Transactions on Graphics publication_identifier: eissn: - '15577368' issn: - '07300301' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'The effect of shape and illumination on material perception: Model and applications' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '9818' abstract: - lang: eng text: Triangle mesh-based simulations are able to produce satisfying animations of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level simulations. Naive texturing approaches do not consider yarn-level physics, while full yarn-level simulations may become prohibitively expensive for large garments. We propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching. In combination with precomputed mesh animation or real-time mesh simulation, our method is able to animate yarn-level cloth in real-time at large scales. acknowledged_ssus: - _id: ScienComp acknowledgement: "We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank Seddi Labs for providing the garment model with fold-over seams.\r\nThis research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific\r\nComputing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc." article_number: '168' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Georg full_name: Sperl, Georg id: 4DD40360-F248-11E8-B48F-1D18A9856A87 last_name: Sperl - first_name: Rahul full_name: Narain, Rahul last_name: Narain - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 2021;40(4). doi:10.1145/3450626.3459816 apa: Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3450626.3459816 chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” ACM Transactions on Graphics. Association for Computing Machinery, 2021. https://doi.org/10.1145/3450626.3459816. ieee: G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern geometry,” ACM Transactions on Graphics, vol. 40, no. 4. Association for Computing Machinery, 2021. ista: Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 40(4), 168. mla: Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” ACM Transactions on Graphics, vol. 40, no. 4, 168, Association for Computing Machinery, 2021, doi:10.1145/3450626.3459816. short: G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021). date_created: 2021-08-08T22:01:27Z date_published: 2021-08-01T00:00:00Z date_updated: 2023-08-10T14:24:36Z day: '01' department: - _id: GradSch - _id: ChWo doi: 10.1145/3450626.3459816 ec_funded: 1 external_id: isi: - '000674930900132' intvolume: ' 40' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/3450626.3459816 month: '08' oa: 1 oa_version: Published Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication: ACM Transactions on Graphics publication_identifier: eissn: - '15577368' issn: - '07300301' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' related_material: link: - description: News on IST Webpage relation: press_release url: https://ist.ac.at/en/news/knitting-virtual-yarn/ record: - id: '12358' relation: dissertation_contains status: public - id: '9327' relation: software status: public scopus_import: '1' status: public title: Mechanics-aware deformation of yarn pattern geometry type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '9828' abstract: - lang: eng text: Amplitude demodulation is a classical operation used in signal processing. For a long time, its effective applications in practice have been limited to narrowband signals. In this work, we generalize amplitude demodulation to wideband signals. We pose demodulation as a recovery problem of an oversampled corrupted signal and introduce special iterative schemes belonging to the family of alternating projection algorithms to solve it. Sensibly chosen structural assumptions on the demodulation outputs allow us to reveal the high inferential accuracy of the method over a rich set of relevant signals. This new approach surpasses current state-of-the-art demodulation techniques apt to wideband signals in computational efficiency by up to many orders of magnitude with no sacrifice in quality. Such performance opens the door for applications of the amplitude demodulation procedure in new contexts. In particular, the new method makes online and large-scale offline data processing feasible, including the calculation of modulator-carrier pairs in higher dimensions and poor sampling conditions, independent of the signal bandwidth. We illustrate the utility and specifics of applications of the new method in practice by using natural speech and synthetic signals. acknowledgement: The author thanks his colleagues K. Huszár and G. Tkačik for valuable discussions and comments on the manuscript. article_processing_charge: No article_type: original author: - first_name: Mantas full_name: Gabrielaitis, Mantas id: 4D5B0CBC-F248-11E8-B48F-1D18A9856A87 last_name: Gabrielaitis orcid: 0000-0002-7758-2016 citation: ama: Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 2021;69:4039-4054. doi:10.1109/TSP.2021.3087899 apa: Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TSP.2021.3087899 chicago: Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/TSP.2021.3087899. ieee: M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,” IEEE Transactions on Signal Processing, vol. 69. Institute of Electrical and Electronics Engineers, pp. 4039–4054, 2021. ista: Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 69, 4039–4054. mla: Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing, vol. 69, Institute of Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:10.1109/TSP.2021.3087899. short: M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054. date_created: 2021-08-08T22:01:31Z date_published: 2021-06-09T00:00:00Z date_updated: 2023-08-10T14:19:33Z day: '09' department: - _id: GaTk doi: 10.1109/TSP.2021.3087899 external_id: arxiv: - '2102.04832' isi: - '000682123900002' intvolume: ' 69' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2102.04832 month: '06' oa: 1 oa_version: Preprint page: 4039 - 4054 publication: IEEE Transactions on Signal Processing publication_identifier: eissn: - 1941-0476 issn: - 1053-587X publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Fast and accurate amplitude demodulation of wideband signals type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 69 year: '2021' ... --- _id: '9327' abstract: - lang: eng text: "This archive contains the missing sweater mesh animations and displacement models for the code of \"Mechanics-Aware Deformation of Yarn Pattern Geometry\"\r\n\r\nCode Repository: https://git.ist.ac.at/gsperl/MADYPG" author: - first_name: Georg full_name: Sperl, Georg id: 4DD40360-F248-11E8-B48F-1D18A9856A87 last_name: Sperl - first_name: Rahul full_name: Narain, Rahul last_name: Narain - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Sperl G, Narain R, Wojtan C. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). 2021. doi:10.15479/AT:ISTA:9327 apa: Sperl, G., Narain, R., & Wojtan, C. (2021). Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria. https://doi.org/10.15479/AT:ISTA:9327 chicago: Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9327. ieee: G. Sperl, R. Narain, and C. Wojtan, “Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data).” IST Austria, 2021. ista: Sperl G, Narain R, Wojtan C. 2021. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data), IST Austria, 10.15479/AT:ISTA:9327. mla: Sperl, Georg, et al. Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data). IST Austria, 2021, doi:10.15479/AT:ISTA:9327. short: G. Sperl, R. Narain, C. Wojtan, (2021). date_created: 2021-04-16T14:26:19Z date_published: 2021-05-01T00:00:00Z date_updated: 2023-08-10T14:24:36Z ddc: - '005' department: - _id: GradSch - _id: ChWo doi: 10.15479/AT:ISTA:9327 file: - access_level: open_access checksum: 0324cb519273371708743f3282e7c081 content_type: application/zip creator: gsperl date_created: 2021-04-16T14:15:12Z date_updated: 2021-04-16T14:15:12Z file_id: '9328' file_name: MADYPG_extra_data.zip file_size: 802586232 relation: main_file success: 1 - access_level: open_access checksum: 4c224551adf852b136ec21a4e13f0c1b content_type: application/gzip creator: pub-gitlab-bot date_created: 2021-04-26T09:33:44Z date_updated: 2021-04-26T09:33:44Z file_id: '9353' file_name: MADYPG.zip file_size: 64962865 relation: main_file file_date_updated: 2021-04-26T09:33:44Z gitlab_commit_id: 6a77e7e22769230ae5f5edaa090fb4b828e57573 gitlab_url: https://git.ist.ac.at/gsperl/MADYPG has_accepted_license: '1' license: https://opensource.org/licenses/MIT month: '05' oa: 1 publisher: IST Austria related_material: record: - id: '9818' relation: used_for_analysis_in status: public status: public title: Mechanics-Aware Deformation of Yarn Pattern Geometry (Additional Animation/Model Data) tmp: legal_code_url: https://opensource.org/licenses/MIT name: The MIT License short: MIT type: software user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- _id: '9770' abstract: - lang: eng text: We study an effective one-dimensional quantum model that includes friction and spin-orbit coupling (SOC), and show that the model exhibits spin polarization when both terms are finite. Most important, strong spin polarization can be observed even for moderate SOC, provided that the friction is strong. Our findings might help to explain the pronounced effect of chirality on spin distribution and transport in chiral molecules. In particular, our model implies static magnetic properties of a chiral molecule, which lead to Shiba-like states when a molecule is placed on a superconductor, in accordance with recent experimental data. acknowledgement: "We thank Rafael Barfknecht for useful discussions. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.\r\nand A.G.V.). M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). Y.P. and O.M. acknowledge funding from the Nidersachsen Ministry of Science and Culture, and from the\r\nAcademia Sinica Research Program. O.M. is thankful for support through the Harry de Jur Chair in Applied Science." article_number: '024430' article_processing_charge: No article_type: original author: - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 - first_name: Hen full_name: Alpern, Hen last_name: Alpern - first_name: Yossi full_name: Paltiel, Yossi last_name: Paltiel - first_name: Oded full_name: Millo, Oded last_name: Millo - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 citation: ama: Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 2021;104(2). doi:10.1103/physrevb.104.024430 apa: Volosniev, A., Alpern, H., Paltiel, Y., Millo, O., Lemeshko, M., & Ghazaryan, A. (2021). Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.104.024430 chicago: Volosniev, Artem, Hen Alpern, Yossi Paltiel, Oded Millo, Mikhail Lemeshko, and Areg Ghazaryan. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” Physical Review B. American Physical Society, 2021. https://doi.org/10.1103/physrevb.104.024430. ieee: A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, and A. Ghazaryan, “Interplay between friction and spin-orbit coupling as a source of spin polarization,” Physical Review B, vol. 104, no. 2. American Physical Society, 2021. ista: Volosniev A, Alpern H, Paltiel Y, Millo O, Lemeshko M, Ghazaryan A. 2021. Interplay between friction and spin-orbit coupling as a source of spin polarization. Physical Review B. 104(2), 024430. mla: Volosniev, Artem, et al. “Interplay between Friction and Spin-Orbit Coupling as a Source of Spin Polarization.” Physical Review B, vol. 104, no. 2, 024430, American Physical Society, 2021, doi:10.1103/physrevb.104.024430. short: A. Volosniev, H. Alpern, Y. Paltiel, O. Millo, M. Lemeshko, A. Ghazaryan, Physical Review B 104 (2021). date_created: 2021-08-04T15:05:32Z date_published: 2021-07-01T00:00:00Z date_updated: 2023-08-10T14:27:07Z day: '01' department: - _id: MiLe doi: 10.1103/physrevb.104.024430 ec_funded: 1 external_id: arxiv: - '2101.05173' isi: - '000678780800003' intvolume: ' 104' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2101.05173 month: '07' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Interplay between friction and spin-orbit coupling as a source of spin polarization type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 104 year: '2021' ... --- _id: '9827' abstract: - lang: eng text: 'The Nearest neighbour search (NNS) is a fundamental problem in many application domains dealing with multidimensional data. In a concurrent setting, where dynamic modifications are allowed, a linearizable implementation of the NNS is highly desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free concurrent kD-tree, which implements an abstract data type (ADT) that provides the operations Add, Remove, Contains, and NNS. Our implementation is linearizable. The operations in the LFkD-tree use single-word read and compare-and-swap (Image 1 ) atomic primitives, which are readily supported on available multi-core processors. We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world and synthetic datasets. The experiments show that the presented design is scalable and achieves significant speed-up compared to the implementations of an existing sequential kD-tree and a recently proposed multidimensional indexing structure, PH-tree.' article_processing_charge: No article_type: original author: - first_name: Bapi full_name: Chatterjee, Bapi id: 3C41A08A-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-2742-4028 - first_name: Ivan full_name: Walulya, Ivan last_name: Walulya - first_name: Philippas full_name: Tsigas, Philippas last_name: Tsigas citation: ama: Chatterjee B, Walulya I, Tsigas P. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. 2021;886:27-48. doi:10.1016/j.tcs.2021.06.041 apa: Chatterjee, B., Walulya, I., & Tsigas, P. (2021). Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2021.06.041 chicago: Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science. Elsevier, 2021. https://doi.org/10.1016/j.tcs.2021.06.041. ieee: B. Chatterjee, I. Walulya, and P. Tsigas, “Concurrent linearizable nearest neighbour search in LockFree-kD-tree,” Theoretical Computer Science, vol. 886. Elsevier, pp. 27–48, 2021. ista: Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48. mla: Chatterjee, Bapi, et al. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” Theoretical Computer Science, vol. 886, Elsevier, 2021, pp. 27–48, doi:10.1016/j.tcs.2021.06.041. short: B. Chatterjee, I. Walulya, P. Tsigas, Theoretical Computer Science 886 (2021) 27–48. date_created: 2021-08-08T22:01:31Z date_published: 2021-09-13T00:00:00Z date_updated: 2023-08-10T14:27:43Z day: '13' department: - _id: DaAl doi: 10.1016/j.tcs.2021.06.041 external_id: isi: - '000694718900004' intvolume: ' 886' isi: 1 keyword: - Concurrent data structure - kD-tree - Nearest neighbor search - Similarity search - Lock-free - Linearizability language: - iso: eng main_file_link: - open_access: '1' url: https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf month: '09' oa: 1 oa_version: Submitted Version page: 27-48 publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Concurrent linearizable nearest neighbour search in LockFree-kD-tree type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 886 year: '2021' ... --- _id: '9877' abstract: - lang: eng text: 'Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution.' acknowledgement: We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing team for generating the IR64 genome sequence and initial analysis; L. Bartley and E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University of California (UC), Berkeley Sanger sequencing team for technical advice and service. This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174. article_number: e2104445118 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Jessica A. full_name: Rodrigues, Jessica A. last_name: Rodrigues - first_name: Ping-Hung full_name: Hsieh, Ping-Hung last_name: Hsieh - first_name: Deling full_name: Ruan, Deling last_name: Ruan - first_name: Toshiro full_name: Nishimura, Toshiro last_name: Nishimura - first_name: Manoj K. full_name: Sharma, Manoj K. last_name: Sharma - first_name: Rita full_name: Sharma, Rita last_name: Sharma - first_name: XinYi full_name: Ye, XinYi last_name: Ye - first_name: Nicholas D. full_name: Nguyen, Nicholas D. last_name: Nguyen - first_name: Sukhranjan full_name: Nijjar, Sukhranjan last_name: Nijjar - first_name: Pamela C. full_name: Ronald, Pamela C. last_name: Ronald - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 2021;118(29). doi:10.1073/pnas.2104445118 apa: Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma, R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2104445118 chicago: Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2104445118. ieee: J. A. Rodrigues et al., “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” Proceedings of the National Academy of Sciences, vol. 118, no. 29. National Academy of Sciences, 2021. ista: Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 118(29), e2104445118. mla: Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” Proceedings of the National Academy of Sciences, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:10.1073/pnas.2104445118. short: J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 118 (2021). date_created: 2021-08-10T19:30:41Z date_published: 2021-07-16T00:00:00Z date_updated: 2023-08-11T10:28:10Z day: '16' ddc: - '580' - '570' department: - _id: DaZi doi: 10.1073/pnas.2104445118 external_id: isi: - '000685037700012' pmid: - '34272287' file: - access_level: open_access checksum: 19e84ad8c03c60222744ee8e16cd6998 content_type: application/pdf creator: asandaue date_created: 2021-08-11T09:31:41Z date_updated: 2021-08-11T09:31:41Z file_id: '9879' file_name: 2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf file_size: 1898360 relation: main_file success: 1 file_date_updated: 2021-08-11T09:31:41Z has_accepted_license: '1' intvolume: ' 118' isi: 1 issue: '29' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 118 year: '2021' ... --- _id: '9874' abstract: - lang: eng text: Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse heart provokes cardiomyocyte proliferation by targeting a network of negative cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated remodeling to overload by derepression of the prohypertrophic transcription factors Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25 provokes nearly complete regeneration of the adult myocardium after ischemic injury. Our data demonstrate that exploitation of conserved molecular programs can enhance the regenerative capacity of the injured heart. acknowledgement: E.D. is supported by a VENI award 916-150-16 from the Netherlands Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship (EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number 627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência, Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART). article_number: '4808' article_processing_charge: Yes article_type: original author: - first_name: Andrea full_name: Raso, Andrea last_name: Raso - first_name: Ellen full_name: Dirkx, Ellen last_name: Dirkx - first_name: Vasco full_name: Sampaio-Pinto, Vasco last_name: Sampaio-Pinto - first_name: Hamid full_name: el Azzouzi, Hamid last_name: el Azzouzi - first_name: Ryan J full_name: Cubero, Ryan J id: 850B2E12-9CD4-11E9-837F-E719E6697425 last_name: Cubero orcid: 0000-0003-0002-1867 - first_name: Daniel W. full_name: Sorensen, Daniel W. last_name: Sorensen - first_name: Lara full_name: Ottaviani, Lara last_name: Ottaviani - first_name: Servé full_name: Olieslagers, Servé last_name: Olieslagers - first_name: Manon M. full_name: Huibers, Manon M. last_name: Huibers - first_name: Roel full_name: de Weger, Roel last_name: de Weger - first_name: Sailay full_name: Siddiqi, Sailay last_name: Siddiqi - first_name: Silvia full_name: Moimas, Silvia last_name: Moimas - first_name: Consuelo full_name: Torrini, Consuelo last_name: Torrini - first_name: Lorena full_name: Zentillin, Lorena last_name: Zentillin - first_name: Luca full_name: Braga, Luca last_name: Braga - first_name: Diana S. full_name: Nascimento, Diana S. last_name: Nascimento - first_name: Paula A. full_name: da Costa Martins, Paula A. last_name: da Costa Martins - first_name: Jop H. full_name: van Berlo, Jop H. last_name: van Berlo - first_name: Serena full_name: Zacchigna, Serena last_name: Zacchigna - first_name: Mauro full_name: Giacca, Mauro last_name: Giacca - first_name: Leon J. full_name: De Windt, Leon J. last_name: De Windt citation: ama: Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 2021;12. doi:10.1038/s41467-021-25211-4 apa: Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen, D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-25211-4 chicago: Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-25211-4. ieee: A. Raso et al., “A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration,” Nature Communications, vol. 12. Springer Nature, 2021. ista: Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 12, 4808. mla: Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” Nature Communications, vol. 12, 4808, Springer Nature, 2021, doi:10.1038/s41467-021-25211-4. short: A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen, L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas, C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H. van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021). date_created: 2021-08-10T11:49:20Z date_published: 2021-08-10T00:00:00Z date_updated: 2023-08-11T10:27:03Z day: '10' ddc: - '610' - '570' department: - _id: SaSi doi: 10.1038/s41467-021-25211-4 external_id: isi: - '000683910200042' pmid: - '34376683' file: - access_level: open_access checksum: 48d8562e8229e4282f3f354b329722c5 content_type: application/pdf creator: asandaue date_created: 2021-08-10T12:29:59Z date_updated: 2021-08-10T12:29:59Z file_id: '9876' file_name: 2021_NatureCommunications_Raso.pdf file_size: 4364333 relation: main_file success: 1 file_date_updated: 2021-08-10T12:29:59Z genbank: - GSE178867 has_accepted_license: '1' intvolume: ' 12' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-022-32785-0 scopus_import: '1' status: public title: A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '9769' abstract: - lang: eng text: A few years ago, flow equations were introduced as a technique for calculating the ground-state energies of cold Bose gases with and without impurities. In this paper, we extend this approach to compute observables other than the energy. As an example, we calculate the densities, and phase fluctuations of one-dimensional Bose gases with one and two impurities. For a single mobile impurity, we use flow equations to validate the mean-field results obtained upon the Lee-Low-Pines transformation. We show that the mean-field approximation is accurate for all values of the boson-impurity interaction strength as long as the phase coherence length is much larger than the healing length of the condensate. For two static impurities, we calculate impurity-impurity interactions induced by the Bose gas. We find that leading order perturbation theory fails when boson-impurity interactions are stronger than boson-boson interactions. The mean-field approximation reproduces the flow equation results for all values of the boson-impurity interaction strength as long as boson-boson interactions are weak. acknowledgement: We thank Matthias Heinz and Volker Karle for helpful comments on the manuscript; Zoran Ristivojevic for useful correspondence regarding mean-field calculations of induced impurity-impurity interactions; Fabian Grusdt for sharing with us the data for the densities presented in Ref. [14]. This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (F. B., H.-W. H., A. G. V.) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A. G. V.). M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). H.-W.H. thanks the ECT* for hospitality during the workshop “Universal physics in Many-Body Quantum Systems – From Atoms to Quarks". This infrastructure is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824093. H.-W.H. was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 279384907 - SFB 1245. article_number: '008' article_processing_charge: Yes article_type: original author: - first_name: Fabian full_name: Brauneis, Fabian last_name: Brauneis - first_name: Hans-Werner full_name: Hammer, Hans-Werner last_name: Hammer - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: 'Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 2021;11(1). doi:10.21468/scipostphys.11.1.008' apa: 'Brauneis, F., Hammer, H.-W., Lemeshko, M., & Volosniev, A. (2021). Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. SciPost. https://doi.org/10.21468/scipostphys.11.1.008' chicago: 'Brauneis, Fabian, Hans-Werner Hammer, Mikhail Lemeshko, and Artem Volosniev. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost Physics. SciPost, 2021. https://doi.org/10.21468/scipostphys.11.1.008.' ieee: 'F. Brauneis, H.-W. Hammer, M. Lemeshko, and A. Volosniev, “Impurities in a one-dimensional Bose gas: The flow equation approach,” SciPost Physics, vol. 11, no. 1. SciPost, 2021.' ista: 'Brauneis F, Hammer H-W, Lemeshko M, Volosniev A. 2021. Impurities in a one-dimensional Bose gas: The flow equation approach. SciPost Physics. 11(1), 008.' mla: 'Brauneis, Fabian, et al. “Impurities in a One-Dimensional Bose Gas: The Flow Equation Approach.” SciPost Physics, vol. 11, no. 1, 008, SciPost, 2021, doi:10.21468/scipostphys.11.1.008.' short: F. Brauneis, H.-W. Hammer, M. Lemeshko, A. Volosniev, SciPost Physics 11 (2021). date_created: 2021-08-04T15:00:55Z date_published: 2021-07-13T00:00:00Z date_updated: 2023-08-11T10:25:44Z day: '13' ddc: - '530' department: - _id: MiLe doi: 10.21468/scipostphys.11.1.008 ec_funded: 1 external_id: arxiv: - '2101.10958' isi: - '000680039500013' file: - access_level: open_access checksum: eaa847346b1a023d97bbb291779610ed content_type: application/pdf creator: asandaue date_created: 2021-08-10T11:44:59Z date_updated: 2021-08-10T11:44:59Z file_id: '9875' file_name: 2021_SciPostPhysics_Brauneis.pdf file_size: 1085300 relation: main_file success: 1 file_date_updated: 2021-08-10T11:44:59Z has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: SciPost Physics publication_identifier: eissn: - 2542-4653 publication_status: published publisher: SciPost quality_controlled: '1' scopus_import: '1' status: public title: 'Impurities in a one-dimensional Bose gas: The flow equation approach' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2021' ... --- _id: '9746' abstract: - lang: eng text: Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs. acknowledgement: We would like to thank Leif Tueffers and João Botelho for discussions and suggestions as well as Kira Haas and Julia Bunk for technical support. We acknowledge financial support from the German Science Foundation (grant SCHU 1415/12-2 to HS, and funding under Germany’s Excellence Strategy EXC 2167–390884018 as well as the Research Training Group 2501 TransEvo to HS and SN), the Max Planck Society (IMPRS scholarship to AB; Max-Planck fellowship to HS), and the Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG, to HS and SN). This work was further supported by the German Science Foundation Research Infrastructure NGS_CC (project 407495230) as part of the Next Generation Sequencing Competence Network (project 423957469). NGS analyses were carried out at the Competence Centre for Genomic Analysis Kiel (CCGA Kiel). article_number: e68876 article_processing_charge: No article_type: original author: - first_name: Aditi full_name: Batra, Aditi last_name: Batra - first_name: Roderich full_name: Römhild, Roderich id: 68E56E44-62B0-11EA-B963-444F3DDC885E last_name: Römhild orcid: 0000-0001-9480-5261 - first_name: Emilie full_name: Rousseau, Emilie last_name: Rousseau - first_name: Sören full_name: Franzenburg, Sören last_name: Franzenburg - first_name: Stefan full_name: Niemann, Stefan last_name: Niemann - first_name: Hinrich full_name: Schulenburg, Hinrich last_name: Schulenburg citation: ama: Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 2021;10. doi:10.7554/elife.68876 apa: Batra, A., Römhild, R., Rousseau, E., Franzenburg, S., Niemann, S., & Schulenburg, H. (2021). High potency of sequential therapy with only beta-lactam antibiotics. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68876 chicago: Batra, Aditi, Roderich Römhild, Emilie Rousseau, Sören Franzenburg, Stefan Niemann, and Hinrich Schulenburg. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.68876. ieee: A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, and H. Schulenburg, “High potency of sequential therapy with only beta-lactam antibiotics,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Batra A, Römhild R, Rousseau E, Franzenburg S, Niemann S, Schulenburg H. 2021. High potency of sequential therapy with only beta-lactam antibiotics. eLife. 10, e68876. mla: Batra, Aditi, et al. “High Potency of Sequential Therapy with Only Beta-Lactam Antibiotics.” ELife, vol. 10, e68876, eLife Sciences Publications, 2021, doi:10.7554/elife.68876. short: A. Batra, R. Römhild, E. Rousseau, S. Franzenburg, S. Niemann, H. Schulenburg, ELife 10 (2021). date_created: 2021-07-28T13:36:57Z date_published: 2021-07-28T00:00:00Z date_updated: 2023-08-11T10:26:29Z day: '28' department: - _id: CaGu doi: 10.7554/elife.68876 external_id: isi: - '000692027800001' pmid: - '34318749' intvolume: ' 10' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.7554/eLife.68876 month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: High potency of sequential therapy with only beta-lactam antibiotics type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2021' ...