--- _id: '9308' acknowledgement: This research was carried out with the support of the Russian Foundation for Basic Research(grant no. 19-01-00169) article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 - first_name: Isaac full_name: Mabillard, Isaac id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87 last_name: Mabillard - first_name: A. B. full_name: Skopenkov, A. B. last_name: Skopenkov citation: ama: Avvakumov S, Wagner U, Mabillard I, Skopenkov AB. Eliminating higher-multiplicity intersections, III. Codimension 2. Russian Mathematical Surveys. 2020;75(6):1156-1158. doi:10.1070/RM9943 apa: Avvakumov, S., Wagner, U., Mabillard, I., & Skopenkov, A. B. (2020). Eliminating higher-multiplicity intersections, III. Codimension 2. Russian Mathematical Surveys. IOP Publishing. https://doi.org/10.1070/RM9943 chicago: Avvakumov, Sergey, Uli Wagner, Isaac Mabillard, and A. B. Skopenkov. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” Russian Mathematical Surveys. IOP Publishing, 2020. https://doi.org/10.1070/RM9943. ieee: S. Avvakumov, U. Wagner, I. Mabillard, and A. B. Skopenkov, “Eliminating higher-multiplicity intersections, III. Codimension 2,” Russian Mathematical Surveys, vol. 75, no. 6. IOP Publishing, pp. 1156–1158, 2020. ista: Avvakumov S, Wagner U, Mabillard I, Skopenkov AB. 2020. Eliminating higher-multiplicity intersections, III. Codimension 2. Russian Mathematical Surveys. 75(6), 1156–1158. mla: Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” Russian Mathematical Surveys, vol. 75, no. 6, IOP Publishing, 2020, pp. 1156–58, doi:10.1070/RM9943. short: S. Avvakumov, U. Wagner, I. Mabillard, A.B. Skopenkov, Russian Mathematical Surveys 75 (2020) 1156–1158. date_created: 2021-04-04T22:01:22Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-08-14T11:43:54Z day: '01' department: - _id: UlWa doi: 10.1070/RM9943 external_id: arxiv: - '1511.03501' isi: - '000625983100001' intvolume: ' 75' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.03501 month: '12' oa: 1 oa_version: Preprint page: 1156-1158 publication: Russian Mathematical Surveys publication_identifier: issn: - 0036-0279 publication_status: published publisher: IOP Publishing quality_controlled: '1' related_material: record: - id: '8183' relation: earlier_version status: public - id: '10220' relation: later_version status: public scopus_import: '1' status: public title: Eliminating higher-multiplicity intersections, III. Codimension 2 type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 75 year: '2020' ... --- _id: '9326' abstract: - lang: eng text: The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I. article_processing_charge: No author: - first_name: Chitrak full_name: Gupta, Chitrak last_name: Gupta - first_name: Umesh full_name: Khaniya, Umesh last_name: Khaniya - first_name: Chun full_name: Chan, Chun last_name: Chan - first_name: Francois full_name: Dehez, Francois last_name: Dehez - first_name: Mrinal full_name: Shekhar, Mrinal last_name: Shekhar - first_name: M. R. full_name: Gunner, M. R. last_name: Gunner - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: Abhishek full_name: Singharoy, Abhishek last_name: Singharoy citation: ama: Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002 apa: Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002 chicago: Gupta, Chitrak, Umesh Khaniya, Chun Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002. ieee: C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I.” American Chemical Society, 2020. ista: Gupta C, Khaniya U, Chan C, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I, American Chemical Society, 10.1021/jacs.9b13450.s002. mla: Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002. short: C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020). date_created: 2021-04-14T12:05:20Z date_published: 2020-05-20T00:00:00Z date_updated: 2023-08-22T07:49:37Z day: '20' department: - _id: LeSa doi: 10.1021/jacs.9b13450.s002 main_file_link: - open_access: '1' month: '05' oa: 1 oa_version: Published Version publisher: American Chemical Society related_material: record: - id: '8040' relation: used_in_publication status: public status: public title: Charge transfer and chemo-mechanical coupling in respiratory complex I tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '6918' abstract: - lang: eng text: "We consider the classic problem of Network Reliability. A network is given together with a source vertex, one or more target vertices, and probabilities assigned to each of the edges. Each edge of the network is operable with its associated probability and the problem is to determine the probability of having at least one source-to-target path that is entirely composed of operable edges. This problem is known to be NP-hard.\r\n\r\nWe provide a novel scalable algorithm to solve the Network Reliability problem when the treewidth of the underlying network is small. We also show our algorithm’s applicability for real-world transit networks that have small treewidth, including the metro networks of major cities, such as London and Tokyo. Our algorithm leverages tree decompositions to shrink the original graph into much smaller graphs, for which reliability can be efficiently and exactly computed using a brute force method. To the best of our knowledge, this is the first exact algorithm for Network Reliability that can scale to handle real-world instances of the problem." acknowledgement: We are grateful to the anonymous reviewers for their comments, which significantly improved the present work. The research was partially supported by the EPSRC Early Career Fellowship EP/R023379/1, grant no. SC7-1718-01 of the London Mathematical Society, an IBM PhD Fellowship, and a DOC Fellowship of the Austrian Academy of Sciences (ÖAW). article_number: '106665' article_processing_charge: No article_type: original arxiv: 1 author: - 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: Fatemeh full_name: Mohammadi, Fatemeh last_name: Mohammadi citation: ama: Goharshady AK, Mohammadi F. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 2020;193. doi:10.1016/j.ress.2019.106665 apa: Goharshady, A. K., & Mohammadi, F. (2020). An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. Elsevier. https://doi.org/10.1016/j.ress.2019.106665 chicago: Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety. Elsevier, 2020. https://doi.org/10.1016/j.ress.2019.106665. ieee: A. K. Goharshady and F. Mohammadi, “An efficient algorithm for computing network reliability in small treewidth,” Reliability Engineering and System Safety, vol. 193. Elsevier, 2020. ista: Goharshady AK, Mohammadi F. 2020. An efficient algorithm for computing network reliability in small treewidth. Reliability Engineering and System Safety. 193, 106665. mla: Goharshady, Amir Kafshdar, and Fatemeh Mohammadi. “An Efficient Algorithm for Computing Network Reliability in Small Treewidth.” Reliability Engineering and System Safety, vol. 193, 106665, Elsevier, 2020, doi:10.1016/j.ress.2019.106665. short: A.K. Goharshady, F. Mohammadi, Reliability Engineering and System Safety 193 (2020). date_created: 2019-09-29T22:00:44Z date_published: 2020-01-01T00:00:00Z date_updated: 2024-03-25T23:30:18Z day: '01' department: - _id: KrCh doi: 10.1016/j.ress.2019.106665 external_id: arxiv: - '1712.09692' isi: - '000501641400050' intvolume: ' 193' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.09692 month: '01' oa: 1 oa_version: Preprint project: - _id: 266EEEC0-B435-11E9-9278-68D0E5697425 name: Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts publication: Reliability Engineering and System Safety publication_identifier: issn: - '09518320' publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '8934' relation: dissertation_contains status: public scopus_import: '1' status: public title: An efficient algorithm for computing network reliability in small treewidth type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 193 year: '2020' ... --- _id: '6944' abstract: - lang: eng text: 'We study the problem of automatically detecting if a given multi-class classifier operates outside of its specifications (out-of-specs), i.e. on input data from a different distribution than what it was trained for. This is an important problem to solve on the road towards creating reliable computer vision systems for real-world applications, because the quality of a classifier’s predictions cannot be guaranteed if it operates out-of-specs. Previously proposed methods for out-of-specs detection make decisions on the level of single inputs. This, however, is insufficient to achieve low false positive rate and high false negative rates at the same time. In this work, we describe a new procedure named KS(conf), based on statistical reasoning. Its main component is a classical Kolmogorov–Smirnov test that is applied to the set of predicted confidence values for batches of samples. Working with batches instead of single samples allows increasing the true positive rate without negatively affecting the false positive rate, thereby overcoming a crucial limitation of single sample tests. We show by extensive experiments using a variety of convolutional network architectures and datasets that KS(conf) reliably detects out-of-specs situations even under conditions where other tests fail. It furthermore has a number of properties that make it an excellent candidate for practical deployment: it is easy to implement, adds almost no overhead to the system, works with any classifier that outputs confidence scores, and requires no a priori knowledge about how the data distribution could change.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Rémy full_name: Sun, Rémy last_name: Sun - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Sun R, Lampert C. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 2020;128(4):970-995. doi:10.1007/s11263-019-01232-x' apa: 'Sun, R., & Lampert, C. (2020). KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-019-01232-x' chicago: 'Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” International Journal of Computer Vision. Springer Nature, 2020. https://doi.org/10.1007/s11263-019-01232-x.' ieee: 'R. Sun and C. Lampert, “KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications,” International Journal of Computer Vision, vol. 128, no. 4. Springer Nature, pp. 970–995, 2020.' ista: 'Sun R, Lampert C. 2020. KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications. International Journal of Computer Vision. 128(4), 970–995.' mla: 'Sun, Rémy, and Christoph Lampert. “KS(Conf): A Light-Weight Test If a Multiclass Classifier Operates Outside of Its Specifications.” International Journal of Computer Vision, vol. 128, no. 4, Springer Nature, 2020, pp. 970–95, doi:10.1007/s11263-019-01232-x.' short: R. Sun, C. Lampert, International Journal of Computer Vision 128 (2020) 970–995. date_created: 2019-10-14T09:14:28Z date_published: 2020-04-01T00:00:00Z date_updated: 2024-02-22T14:57:30Z day: '01' ddc: - '004' department: - _id: ChLa doi: 10.1007/s11263-019-01232-x ec_funded: 1 external_id: isi: - '000494406800001' file: - access_level: open_access checksum: 155e63edf664dcacb3bdc1c2223e606f content_type: application/pdf creator: dernst date_created: 2019-11-26T10:30:02Z date_updated: 2020-07-14T12:47:45Z file_id: '7110' file_name: 2019_IJCV_Sun.pdf file_size: 1715072 relation: main_file file_date_updated: 2020-07-14T12:47:45Z has_accepted_license: '1' intvolume: ' 128' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 970-995 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: International Journal of Computer Vision publication_identifier: eissn: - 1573-1405 issn: - 0920-5691 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1007/s11263-019-01262-5 record: - id: '6482' relation: earlier_version status: public scopus_import: '1' status: public title: 'KS(conf): A light-weight test if a multiclass classifier operates outside of its specifications' 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 128 year: '2020' ... --- _id: '6952' abstract: - lang: eng text: 'We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, most existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to existing approaches, while also supporting weaker supervision. Importantly, it can be trained purely from 2D images, without pose annotations, and with only a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to reason over lighting parameters and exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach in various settings, showing that: (i) it learns to disentangle shape from pose and lighting; (ii) using shading in the loss improves performance compared to just silhouettes; (iii) when using a standard single white light, our model outperforms state-of-the-art 2D-supervised methods, both with and without pose supervision, thanks to exploiting shading cues; (iv) performance improves further when using multiple coloured lights, even approaching that of state-of-the-art 3D-supervised methods; (v) shapes produced by our model capture smooth surfaces and fine details better than voxel-based approaches; and (vi) our approach supports concave classes such as bathtubs and sofas, which methods based on silhouettes cannot learn.' acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Paul M full_name: Henderson, Paul M id: 13C09E74-18D9-11E9-8878-32CFE5697425 last_name: Henderson orcid: 0000-0002-5198-7445 - first_name: Vittorio full_name: Ferrari, Vittorio last_name: Ferrari citation: ama: Henderson PM, Ferrari V. Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. International Journal of Computer Vision. 2020;128:835-854. doi:10.1007/s11263-019-01219-8 apa: Henderson, P. M., & Ferrari, V. (2020). Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. International Journal of Computer Vision. Springer Nature. https://doi.org/10.1007/s11263-019-01219-8 chicago: Henderson, Paul M, and Vittorio Ferrari. “Learning Single-Image 3D Reconstruction by Generative Modelling of Shape, Pose and Shading.” International Journal of Computer Vision. Springer Nature, 2020. https://doi.org/10.1007/s11263-019-01219-8. ieee: P. M. Henderson and V. Ferrari, “Learning single-image 3D reconstruction by generative modelling of shape, pose and shading,” International Journal of Computer Vision, vol. 128. Springer Nature, pp. 835–854, 2020. ista: Henderson PM, Ferrari V. 2020. Learning single-image 3D reconstruction by generative modelling of shape, pose and shading. International Journal of Computer Vision. 128, 835–854. mla: Henderson, Paul M., and Vittorio Ferrari. “Learning Single-Image 3D Reconstruction by Generative Modelling of Shape, Pose and Shading.” International Journal of Computer Vision, vol. 128, Springer Nature, 2020, pp. 835–54, doi:10.1007/s11263-019-01219-8. short: P.M. Henderson, V. Ferrari, International Journal of Computer Vision 128 (2020) 835–854. date_created: 2019-10-17T13:38:20Z date_published: 2020-04-01T00:00:00Z date_updated: 2023-08-17T14:01:16Z day: '01' ddc: - '004' department: - _id: ChLa doi: 10.1007/s11263-019-01219-8 external_id: arxiv: - '1901.06447' isi: - '000491042100002' file: - access_level: open_access checksum: a0f05dd4f5f64e4f713d8d9d4b5b1e3f content_type: application/pdf creator: dernst date_created: 2019-10-25T10:28:29Z date_updated: 2020-07-14T12:47:46Z file_id: '6973' file_name: 2019_CompVision_Henderson.pdf file_size: 2243134 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 128' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 835-854 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: International Journal of Computer Vision publication_identifier: eissn: - 1573-1405 issn: - 0920-5691 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Learning single-image 3D reconstruction by generative modelling of shape, pose and shading 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: 128 year: '2020' ... --- _id: '6997' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Zhang Y, Friml J. Auxin guides roots to avoid obstacles during gravitropic growth. New Phytologist. 2020;225(3):1049-1052. doi:10.1111/nph.16203 apa: Zhang, Y., & Friml, J. (2020). Auxin guides roots to avoid obstacles during gravitropic growth. New Phytologist. Wiley. https://doi.org/10.1111/nph.16203 chicago: Zhang, Yuzhou, and Jiří Friml. “Auxin Guides Roots to Avoid Obstacles during Gravitropic Growth.” New Phytologist. Wiley, 2020. https://doi.org/10.1111/nph.16203. ieee: Y. Zhang and J. Friml, “Auxin guides roots to avoid obstacles during gravitropic growth,” New Phytologist, vol. 225, no. 3. Wiley, pp. 1049–1052, 2020. ista: Zhang Y, Friml J. 2020. Auxin guides roots to avoid obstacles during gravitropic growth. New Phytologist. 225(3), 1049–1052. mla: Zhang, Yuzhou, and Jiří Friml. “Auxin Guides Roots to Avoid Obstacles during Gravitropic Growth.” New Phytologist, vol. 225, no. 3, Wiley, 2020, pp. 1049–52, doi:10.1111/nph.16203. short: Y. Zhang, J. Friml, New Phytologist 225 (2020) 1049–1052. date_created: 2019-11-12T11:41:32Z date_published: 2020-02-01T00:00:00Z date_updated: 2023-08-17T14:01:49Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1111/nph.16203 ec_funded: 1 external_id: isi: - '000489638800001' pmid: - '31603260' file: - access_level: open_access checksum: cd42ffdb381fd52812b9583d4d407139 content_type: application/pdf creator: dernst date_created: 2020-11-18T16:42:48Z date_updated: 2020-11-18T16:42:48Z file_id: '8772' file_name: 2020_NewPhytologist_Zhang.pdf file_size: 717345 relation: main_file success: 1 file_date_updated: 2020-11-18T16:42:48Z has_accepted_license: '1' intvolume: ' 225' isi: 1 issue: '3' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 1049-1052 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646x publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Auxin guides roots to avoid obstacles during gravitropic growth 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: 225 year: '2020' ... --- _id: '7004' abstract: - lang: eng text: We define an action of the (double of) Cohomological Hall algebra of Kontsevich and Soibelman on the cohomology of the moduli space of spiked instantons of Nekrasov. We identify this action with the one of the affine Yangian of gl(1). Based on that we derive the vertex algebra at the corner Wr1,r2,r3 of Gaiotto and Rapčák. We conjecture that our approach works for a big class of Calabi–Yau categories, including those associated with toric Calabi–Yau 3-folds. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Miroslav full_name: Rapcak, Miroslav last_name: Rapcak - first_name: Yan full_name: Soibelman, Yan last_name: Soibelman - first_name: Yaping full_name: Yang, Yaping last_name: Yang - first_name: Gufang full_name: Zhao, Gufang id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87 last_name: Zhao citation: ama: Rapcak M, Soibelman Y, Yang Y, Zhao G. Cohomological Hall algebras, vertex algebras and instantons. Communications in Mathematical Physics. 2020;376:1803-1873. doi:10.1007/s00220-019-03575-5 apa: Rapcak, M., Soibelman, Y., Yang, Y., & Zhao, G. (2020). Cohomological Hall algebras, vertex algebras and instantons. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03575-5 chicago: Rapcak, Miroslav, Yan Soibelman, Yaping Yang, and Gufang Zhao. “Cohomological Hall Algebras, Vertex Algebras and Instantons.” Communications in Mathematical Physics. Springer Nature, 2020. https://doi.org/10.1007/s00220-019-03575-5. ieee: M. Rapcak, Y. Soibelman, Y. Yang, and G. Zhao, “Cohomological Hall algebras, vertex algebras and instantons,” Communications in Mathematical Physics, vol. 376. Springer Nature, pp. 1803–1873, 2020. ista: Rapcak M, Soibelman Y, Yang Y, Zhao G. 2020. Cohomological Hall algebras, vertex algebras and instantons. Communications in Mathematical Physics. 376, 1803–1873. mla: Rapcak, Miroslav, et al. “Cohomological Hall Algebras, Vertex Algebras and Instantons.” Communications in Mathematical Physics, vol. 376, Springer Nature, 2020, pp. 1803–73, doi:10.1007/s00220-019-03575-5. short: M. Rapcak, Y. Soibelman, Y. Yang, G. Zhao, Communications in Mathematical Physics 376 (2020) 1803–1873. date_created: 2019-11-12T14:01:27Z date_published: 2020-06-01T00:00:00Z date_updated: 2023-08-17T14:02:59Z day: '01' department: - _id: TaHa doi: 10.1007/s00220-019-03575-5 ec_funded: 1 external_id: arxiv: - '1810.10402' isi: - '000536255500004' intvolume: ' 376' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1810.10402 month: '06' oa: 1 oa_version: Preprint page: 1803-1873 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces publication: Communications in Mathematical Physics publication_identifier: eissn: - 1432-0916 issn: - 0010-3616 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Cohomological Hall algebras, vertex algebras and instantons type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 376 year: '2020' ... --- _id: '7033' abstract: - lang: eng text: Removal of the Bax gene from mice completely protects the somas of retinal ganglion cells (RGCs) from apoptosis following optic nerve injury. This makes BAX a promising therapeutic target to prevent neurodegeneration. In this study, Bax+/− mice were used to test the hypothesis that lowering the quantity of BAX in RGCs would delay apoptosis following optic nerve injury. RGCs were damaged by performing optic nerve crush (ONC) and then immunostaining for phospho-cJUN, and quantitative PCR were used to monitor the status of the BAX activation mechanism in the months following injury. The apoptotic susceptibility of injured cells was directly tested by virally introducing GFP-BAX into Bax−/− RGCs after injury. The competency of quiescent RGCs to reactivate their BAX activation mechanism was tested by intravitreal injection of the JNK pathway agonist, anisomycin. Twenty-four weeks after ONC, Bax+/− mice had significantly less cell loss in their RGC layer than Bax+/+ mice 3 weeks after ONC. Bax+/− and Bax+/+ RGCs exhibited similar patterns of nuclear phospho-cJUN accumulation immediately after ONC, which persisted in Bax+/− RGCs for up to 7 weeks before abating. The transcriptional activation of BAX-activating genes was similar in Bax+/− and Bax+/+ RGCs following ONC. Intriguingly, cells deactivated their BAX activation mechanism between 7 and 12 weeks after crush. Introduction of GFP-BAX into Bax−/− cells at 4 weeks after ONC showed that these cells had a nearly normal capacity to activate this protein, but this capacity was lost 8 weeks after crush. Collectively, these data suggest that 8–12 weeks after crush, damaged cells no longer displayed increased susceptibility to BAX activation relative to their naïve counterparts. In this same timeframe, retinal glial activation and the signaling of the pro-apoptotic JNK pathway also abated. Quiescent RGCs did not show a timely reactivation of their JNK pathway following intravitreal injection with anisomycin. These findings demonstrate that lowering the quantity of BAX in RGCs is neuroprotective after acute injury. Damaged RGCs enter a quiescent state months after injury and are no longer responsive to an apoptotic stimulus. Quiescent RGCs will require rejuvenation to reacquire functionality. acknowledgement: This work was supported by National Eye Institute grants R01 EY012223 (RWN), R01 EY030123 (RWN), T32 EY027721 (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), and a Vision Science Core grant P30 EY016665 (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), an unrestricted funding grant from Research to Prevent Blindness (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), the Frederick A. Davis Endowment (RWN), and the Mr. and Mrs. George Taylor Foundation (RWN). article_processing_charge: No article_type: original author: - first_name: RJ full_name: Donahue, RJ last_name: Donahue - 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: JA full_name: Grosser, JA last_name: Grosser - first_name: RW full_name: Nickells, RW last_name: Nickells citation: ama: Donahue R, Maes ME, Grosser J, Nickells R. BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. Molecular Neurobiology. 2020;57(2):1070–1084. doi:10.1007/s12035-019-01783-7 apa: Donahue, R., Maes, M. E., Grosser, J., & Nickells, R. (2020). BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. Molecular Neurobiology. Springer Nature. https://doi.org/10.1007/s12035-019-01783-7 chicago: Donahue, RJ, Margaret E Maes, JA Grosser, and RW Nickells. “BAX-Depleted Retinal Ganglion Cells Survive and Become Quiescent Following Optic Nerve Damage.” Molecular Neurobiology. Springer Nature, 2020. https://doi.org/10.1007/s12035-019-01783-7. ieee: R. Donahue, M. E. Maes, J. Grosser, and R. Nickells, “BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage,” Molecular Neurobiology, vol. 57, no. 2. Springer Nature, pp. 1070–1084, 2020. ista: Donahue R, Maes ME, Grosser J, Nickells R. 2020. BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage. Molecular Neurobiology. 57(2), 1070–1084. mla: Donahue, RJ, et al. “BAX-Depleted Retinal Ganglion Cells Survive and Become Quiescent Following Optic Nerve Damage.” Molecular Neurobiology, vol. 57, no. 2, Springer Nature, 2020, pp. 1070–1084, doi:10.1007/s12035-019-01783-7. short: R. Donahue, M.E. Maes, J. Grosser, R. Nickells, Molecular Neurobiology 57 (2020) 1070–1084. date_created: 2019-11-18T14:18:39Z date_published: 2020-02-01T00:00:00Z date_updated: 2023-08-17T14:05:48Z day: '01' department: - _id: SaSi doi: 10.1007/s12035-019-01783-7 external_id: isi: - '000493754200001' pmid: - '31673950' intvolume: ' 57' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035206/ month: '02' oa: 1 oa_version: Submitted Version page: 1070–1084 pmid: 1 publication: Molecular Neurobiology publication_identifier: eissn: - 1559-1182 issn: - 0893-7648 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: BAX-depleted retinal ganglion cells survive and become quiescent following optic nerve damage type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 57 year: '2020' ... --- _id: '7084' abstract: - lang: eng text: The unusual correlated state that emerges in URu2Si2 below THO = 17.5 K is known as “hidden order” because even basic characteristics of the order parameter, such as its dimensionality (whether it has one component or two), are “hidden.” We use resonant ultrasound spectroscopy to measure the symmetry-resolved elastic anomalies across THO. We observe no anomalies in the shear elastic moduli, providing strong thermodynamic evidence for a one-component order parameter. We develop a machine learning framework that reaches this conclusion directly from the raw data, even in a crystal that is too small for traditional resonant ultrasound. Our result rules out a broad class of theories of hidden order based on two-component order parameters, and constrains the nature of the fluctuations from which unconventional superconductivity emerges at lower temperature. Our machine learning framework is a powerful new tool for classifying the ubiquitous competing orders in correlated electron systems. article_number: eaaz4074 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Sayak full_name: Ghosh, Sayak last_name: Ghosh - first_name: Michael full_name: Matty, Michael last_name: Matty - first_name: Ryan full_name: Baumbach, Ryan last_name: Baumbach - first_name: Eric D. full_name: Bauer, Eric D. last_name: Bauer - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Arkady full_name: Shekhter, Arkady last_name: Shekhter - first_name: J. A. full_name: Mydosh, J. A. last_name: Mydosh - first_name: Eun-Ah full_name: Kim, Eun-Ah last_name: Kim - first_name: B. J. full_name: Ramshaw, B. J. last_name: Ramshaw citation: ama: Ghosh S, Matty M, Baumbach R, et al. One-component order parameter in URu2Si2 uncovered by resonant  ultrasound spectroscopy and machine learning. Science Advances. 2020;6(10). doi:10.1126/sciadv.aaz4074 apa: Ghosh, S., Matty, M., Baumbach, R., Bauer, E. D., Modic, K. A., Shekhter, A., … Ramshaw, B. J. (2020). One-component order parameter in URu2Si2 uncovered by resonant  ultrasound spectroscopy and machine learning. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaz4074 chicago: Ghosh, Sayak, Michael Matty, Ryan Baumbach, Eric D. Bauer, Kimberly A Modic, Arkady Shekhter, J. A. Mydosh, Eun-Ah Kim, and B. J. Ramshaw. “One-Component Order Parameter in URu2Si2 Uncovered by Resonant  Ultrasound Spectroscopy and Machine Learning.” Science Advances. American Association for the Advancement of Science, 2020. https://doi.org/10.1126/sciadv.aaz4074. ieee: S. Ghosh et al., “One-component order parameter in URu2Si2 uncovered by resonant  ultrasound spectroscopy and machine learning,” Science Advances, vol. 6, no. 10. American Association for the Advancement of Science, 2020. ista: Ghosh S, Matty M, Baumbach R, Bauer ED, Modic KA, Shekhter A, Mydosh JA, Kim E-A, Ramshaw BJ. 2020. One-component order parameter in URu2Si2 uncovered by resonant  ultrasound spectroscopy and machine learning. Science Advances. 6(10), eaaz4074. mla: Ghosh, Sayak, et al. “One-Component Order Parameter in URu2Si2 Uncovered by Resonant  Ultrasound Spectroscopy and Machine Learning.” Science Advances, vol. 6, no. 10, eaaz4074, American Association for the Advancement of Science, 2020, doi:10.1126/sciadv.aaz4074. short: S. Ghosh, M. Matty, R. Baumbach, E.D. Bauer, K.A. Modic, A. Shekhter, J.A. Mydosh, E.-A. Kim, B.J. Ramshaw, Science Advances 6 (2020). date_created: 2019-11-19T14:01:10Z date_published: 2020-03-06T00:00:00Z date_updated: 2022-08-25T15:08:41Z day: '06' doi: 10.1126/sciadv.aaz4074 extern: '1' external_id: arxiv: - '1903.00552' pmid: - '32181367' intvolume: ' 6' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1903.00552 month: '03' oa: 1 oa_version: Preprint pmid: 1 publication: Science Advances publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' status: public title: One-component order parameter in URu2Si2 uncovered by resonant ultrasound spectroscopy and machine learning type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2020' ... --- _id: '71' abstract: - lang: eng text: "We consider dynamical transport metrics for probability measures on discretisations of a bounded convex domain in ℝd. These metrics are natural discrete counterparts to the Kantorovich metric \U0001D54E2, defined using a Benamou-Brenier type formula. Under mild assumptions we prove an asymptotic upper bound for the discrete transport metric Wt in terms of \U0001D54E2, as the size of the mesh T tends to 0. However, we show that the corresponding lower bound may fail in general, even on certain one-dimensional and symmetric two-dimensional meshes. In addition, we show that the asymptotic lower bound holds under an isotropy assumption on the mesh, which turns out to be essentially necessary. This assumption is satisfied, e.g., for tilings by convex regular polygons, and it implies Gromov-Hausdorff convergence of the transport metric." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Peter full_name: Gladbach, Peter last_name: Gladbach - first_name: Eva full_name: Kopfer, Eva last_name: Kopfer - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: Gladbach P, Kopfer E, Maas J. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 2020;52(3):2759-2802. doi:10.1137/19M1243440 apa: Gladbach, P., Kopfer, E., & Maas, J. (2020). Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/19M1243440 chicago: Gladbach, Peter, Eva Kopfer, and Jan Maas. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics, 2020. https://doi.org/10.1137/19M1243440. ieee: P. Gladbach, E. Kopfer, and J. Maas, “Scaling limits of discrete optimal transport,” SIAM Journal on Mathematical Analysis, vol. 52, no. 3. Society for Industrial and Applied Mathematics, pp. 2759–2802, 2020. ista: Gladbach P, Kopfer E, Maas J. 2020. Scaling limits of discrete optimal transport. SIAM Journal on Mathematical Analysis. 52(3), 2759–2802. mla: Gladbach, Peter, et al. “Scaling Limits of Discrete Optimal Transport.” SIAM Journal on Mathematical Analysis, vol. 52, no. 3, Society for Industrial and Applied Mathematics, 2020, pp. 2759–802, doi:10.1137/19M1243440. short: P. Gladbach, E. Kopfer, J. Maas, SIAM Journal on Mathematical Analysis 52 (2020) 2759–2802. date_created: 2018-12-11T11:44:28Z date_published: 2020-10-01T00:00:00Z date_updated: 2023-09-18T08:13:15Z day: '01' department: - _id: JaMa doi: 10.1137/19M1243440 external_id: arxiv: - '1809.01092' isi: - '000546975100017' intvolume: ' 52' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.01092 month: '10' oa: 1 oa_version: Preprint page: 2759-2802 publication: SIAM Journal on Mathematical Analysis publication_identifier: eissn: - '10957154' issn: - '00361410' publication_status: published publisher: Society for Industrial and Applied Mathematics publist_id: '7983' quality_controlled: '1' scopus_import: '1' status: public title: Scaling limits of discrete optimal transport type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 52 year: '2020' ... --- _id: '7161' abstract: - lang: eng text: In this paper, we introduce an inertial projection-type method with different updating strategies for solving quasi-variational inequalities with strongly monotone and Lipschitz continuous operators in real Hilbert spaces. Under standard assumptions, we establish different strong convergence results for the proposed algorithm. Primary numerical experiments demonstrate the potential applicability of our scheme compared with some related methods in the literature. acknowledgement: We are grateful to the anonymous referees and editor whose insightful comments helped to considerably improve an earlier version of this paper. The research of the first author is supported by an ERC Grant from the Institute of Science and Technology (IST). article_processing_charge: No article_type: original author: - first_name: Yekini full_name: Shehu, Yekini id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87 last_name: Shehu orcid: 0000-0001-9224-7139 - first_name: Aviv full_name: Gibali, Aviv last_name: Gibali - first_name: Simone full_name: Sagratella, Simone last_name: Sagratella citation: ama: Shehu Y, Gibali A, Sagratella S. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 2020;184:877–894. doi:10.1007/s10957-019-01616-6 apa: Shehu, Y., Gibali, A., & Sagratella, S. (2020). Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. Springer Nature. https://doi.org/10.1007/s10957-019-01616-6 chicago: Shehu, Yekini, Aviv Gibali, and Simone Sagratella. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications. Springer Nature, 2020. https://doi.org/10.1007/s10957-019-01616-6. ieee: Y. Shehu, A. Gibali, and S. Sagratella, “Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces,” Journal of Optimization Theory and Applications, vol. 184. Springer Nature, pp. 877–894, 2020. ista: Shehu Y, Gibali A, Sagratella S. 2020. Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces. Journal of Optimization Theory and Applications. 184, 877–894. mla: Shehu, Yekini, et al. “Inertial Projection-Type Methods for Solving Quasi-Variational Inequalities in Real Hilbert Spaces.” Journal of Optimization Theory and Applications, vol. 184, Springer Nature, 2020, pp. 877–894, doi:10.1007/s10957-019-01616-6. short: Y. Shehu, A. Gibali, S. Sagratella, Journal of Optimization Theory and Applications 184 (2020) 877–894. date_created: 2019-12-09T21:33:44Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-09-06T11:27:15Z day: '01' ddc: - '518' - '510' - '515' department: - _id: VlKo doi: 10.1007/s10957-019-01616-6 ec_funded: 1 external_id: isi: - '000511805200009' file: - access_level: open_access checksum: 9f6dc6c6bf2b48cb3a2091a9ed5feaf2 content_type: application/pdf creator: dernst date_created: 2020-10-12T10:40:27Z date_updated: 2021-03-16T23:30:04Z embargo: 2021-03-15 file_id: '8647' file_name: 2020_JourOptimizationTheoryApplic_Shehu.pdf file_size: 332641 relation: main_file file_date_updated: 2021-03-16T23:30:04Z has_accepted_license: '1' intvolume: ' 184' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 877–894 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Journal of Optimization Theory and Applications publication_identifier: eissn: - 1573-2878 issn: - 0022-3239 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Inertial projection-type methods for solving quasi-variational inequalities in real Hilbert spaces type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 184 year: '2020' ... --- _id: '7166' abstract: - lang: eng text: In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors. article_processing_charge: No article_type: letter_note author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Reinhard full_name: Lipowsky, Reinhard last_name: Lipowsky citation: ama: Ucar MC, Lipowsky R. Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. 2020;20(1):669-676. doi:10.1021/acs.nanolett.9b04445 apa: Ucar, M. C., & Lipowsky, R. (2020). Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.9b04445 chicago: Ucar, Mehmet C, and Reinhard Lipowsky. “Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” Nano Letters. American Chemical Society, 2020. https://doi.org/10.1021/acs.nanolett.9b04445. ieee: M. C. Ucar and R. Lipowsky, “Collective force generation by molecular motors is determined by strain-induced unbinding,” Nano Letters, vol. 20, no. 1. American Chemical Society, pp. 669–676, 2020. ista: Ucar MC, Lipowsky R. 2020. Collective force generation by molecular motors is determined by strain-induced unbinding. Nano Letters. 20(1), 669–676. mla: Ucar, Mehmet C., and Reinhard Lipowsky. “Collective Force Generation by Molecular Motors Is Determined by Strain-Induced Unbinding.” Nano Letters, vol. 20, no. 1, American Chemical Society, 2020, pp. 669–76, doi:10.1021/acs.nanolett.9b04445. short: M.C. Ucar, R. Lipowsky, Nano Letters 20 (2020) 669–676. date_created: 2019-12-10T15:36:05Z date_published: 2020-01-08T00:00:00Z date_updated: 2023-08-17T14:07:52Z day: '08' department: - _id: EdHa doi: 10.1021/acs.nanolett.9b04445 external_id: isi: - '000507151600087' pmid: - '31797672' intvolume: ' 20' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1021/acs.nanolett.9b04445 month: '01' oa: 1 oa_version: Published Version page: 669-676 pmid: 1 publication: Nano Letters publication_identifier: eissn: - 1530-6992 issn: - 1530-6984 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: record: - id: '9726' relation: research_data status: public - id: '9885' relation: research_data status: public scopus_import: '1' status: public title: Collective force generation by molecular motors is determined by strain-induced unbinding type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2020' ... --- _id: '7196' abstract: - lang: eng text: 'In this thesis we study certain mathematical aspects of evolution. The two primary forces that drive an evolutionary process are mutation and selection. Mutation generates new variants in a population. Selection chooses among the variants depending on the reproductive rates of individuals. Evolutionary processes are intrinsically random – a new mutation that is initially present in the population at low frequency can go extinct, even if it confers a reproductive advantage. The overall rate of evolution is largely determined by two quantities: the probability that an invading advantageous mutation spreads through the population (called fixation probability) and the time until it does so (called fixation time). Both those quantities crucially depend not only on the strength of the invading mutation but also on the population structure. In this thesis, we aim to understand how the underlying population structure affects the overall rate of evolution. Specifically, we study population structures that increase the fixation probability of advantageous mutants (called amplifiers of selection). Broadly speaking, our results are of three different types: We present various strong amplifiers, we identify regimes under which only limited amplification is feasible, and we propose population structures that provide different tradeoffs between high fixation probability and short fixation time.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 citation: ama: Tkadlec J. A role of graphs in evolutionary processes. 2020. doi:10.15479/AT:ISTA:7196 apa: Tkadlec, J. (2020). A role of graphs in evolutionary processes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7196 chicago: Tkadlec, Josef. “A Role of Graphs in Evolutionary Processes.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7196. ieee: J. Tkadlec, “A role of graphs in evolutionary processes,” Institute of Science and Technology Austria, 2020. ista: Tkadlec J. 2020. A role of graphs in evolutionary processes. Institute of Science and Technology Austria. mla: Tkadlec, Josef. A Role of Graphs in Evolutionary Processes. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7196. short: J. Tkadlec, A Role of Graphs in Evolutionary Processes, Institute of Science and Technology Austria, 2020. date_created: 2019-12-20T12:26:36Z date_published: 2020-01-12T00:00:00Z date_updated: 2023-10-17T12:29:46Z day: '12' ddc: - '519' degree_awarded: PhD department: - _id: KrCh - _id: GradSch doi: 10.15479/AT:ISTA:7196 file: - access_level: closed checksum: 451f8e64b0eb26bf297644ac72bfcbe9 content_type: application/zip creator: jtkadlec date_created: 2020-01-12T11:49:49Z date_updated: 2020-07-14T12:47:52Z file_id: '7255' file_name: thesis.zip file_size: 21100497 relation: source_file - access_level: open_access checksum: d8c44cbc4f939c49a8efc9d4b8bb3985 content_type: application/pdf creator: dernst date_created: 2020-01-28T07:32:42Z date_updated: 2020-07-14T12:47:52Z file_id: '7367' file_name: 2020_Tkadlec_Thesis.pdf file_size: 11670983 relation: main_file file_date_updated: 2020-07-14T12:47:52Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '144' publication_identifier: eissn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7210' relation: dissertation_contains status: public - id: '5751' relation: dissertation_contains status: public - id: '7212' relation: dissertation_contains status: public status: public supervisor: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X title: A role of graphs in evolutionary processes type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '7204' abstract: - lang: eng text: Plant root architecture dynamically adapts to various environmental conditions, such as salt‐containing soil. The phytohormone abscisic acid (ABA) is involved among others also in these developmental adaptations, but the underlying molecular mechanism remains elusive. Here, a novel branch of the ABA signaling pathway in Arabidopsis involving PYR/PYL/RCAR (abbreviated as PYLs) receptor‐protein phosphatase 2A (PP2A) complex that acts in parallel to the canonical PYLs‐protein phosphatase 2C (PP2C) mechanism is identified. The PYLs‐PP2A signaling modulates root gravitropism and lateral root formation through regulating phytohormone auxin transport. In optimal conditions, PYLs ABA receptor interacts with the catalytic subunits of PP2A, increasing their phosphatase activity and thus counteracting PINOID (PID) kinase‐mediated phosphorylation of PIN‐FORMED (PIN) auxin transporters. By contrast, in salt and osmotic stress conditions, ABA binds to PYLs, inhibiting the PP2A activity, which leads to increased PIN phosphorylation and consequently modulated directional auxin transport leading to adapted root architecture. This work reveals an adaptive mechanism that may flexibly adjust plant root growth to withstand saline and osmotic stresses. It occurs via the cross‐talk between the stress hormone ABA and the versatile developmental regulator auxin. article_number: '1901455' article_processing_charge: No article_type: original author: - first_name: Yang full_name: Li, Yang last_name: Li - first_name: Yaping full_name: Wang, Yaping last_name: Wang - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Zhen full_name: Li, Zhen last_name: Li - first_name: Zhi full_name: Yuan, Zhi last_name: Yuan - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 - first_name: David full_name: Domjan, David id: C684CD7A-257E-11EA-9B6F-D8588B4F947F last_name: Domjan orcid: 0000-0003-2267-106X - first_name: Kai full_name: Wang, Kai last_name: Wang - first_name: Wei full_name: Xuan, Wei last_name: Xuan - first_name: Yan full_name: Guo, Yan last_name: Guo - first_name: Zhizhong full_name: Gong, Zhizhong last_name: Gong - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jing full_name: Zhang, Jing last_name: Zhang citation: ama: Li Y, Wang Y, Tan S, et al. Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex. Advanced Science. 2020;7(3). doi:10.1002/advs.201901455 apa: Li, Y., Wang, Y., Tan, S., Li, Z., Yuan, Z., Glanc, M., … Zhang, J. (2020). Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex. Advanced Science. Wiley. https://doi.org/10.1002/advs.201901455 chicago: Li, Yang, Yaping Wang, Shutang Tan, Zhen Li, Zhi Yuan, Matous Glanc, David Domjan, et al. “Root Growth Adaptation Is Mediated by PYLs ABA Receptor-PP2A Protein Phosphatase Complex.” Advanced Science. Wiley, 2020. https://doi.org/10.1002/advs.201901455. ieee: Y. Li et al., “Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex,” Advanced Science, vol. 7, no. 3. Wiley, 2020. ista: Li Y, Wang Y, Tan S, Li Z, Yuan Z, Glanc M, Domjan D, Wang K, Xuan W, Guo Y, Gong Z, Friml J, Zhang J. 2020. Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex. Advanced Science. 7(3), 1901455. mla: Li, Yang, et al. “Root Growth Adaptation Is Mediated by PYLs ABA Receptor-PP2A Protein Phosphatase Complex.” Advanced Science, vol. 7, no. 3, 1901455, Wiley, 2020, doi:10.1002/advs.201901455. short: Y. Li, Y. Wang, S. Tan, Z. Li, Z. Yuan, M. Glanc, D. Domjan, K. Wang, W. Xuan, Y. Guo, Z. Gong, J. Friml, J. Zhang, Advanced Science 7 (2020). date_created: 2019-12-22T23:00:43Z date_published: 2020-02-05T00:00:00Z date_updated: 2023-08-17T14:13:17Z day: '05' ddc: - '580' department: - _id: JiFr doi: 10.1002/advs.201901455 external_id: isi: - '000501912800001' pmid: - '32042554' file: - access_level: open_access checksum: 016eeab5860860af038e2da95ffe75c3 content_type: application/pdf creator: dernst date_created: 2020-02-24T14:29:54Z date_updated: 2020-07-14T12:47:53Z file_id: '7519' file_name: 2020_AdvScience_Li.pdf file_size: 3586924 relation: main_file file_date_updated: 2020-07-14T12:47:53Z has_accepted_license: '1' intvolume: ' 7' isi: 1 issue: '3' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 publication: Advanced Science publication_identifier: eissn: - 2198-3844 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Root growth adaptation is mediated by PYLs ABA receptor-PP2A protein phosphatase complex 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: 7 year: '2020' ... --- _id: '7205' abstract: - lang: eng text: Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the "Crab" and "Wave" ecotypes of the snail Littorina saxatilis, divergent selection forms strong barriers to gene flow, while the role of post‐zygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Post‐zygotic barriers might include genetic incompatibilities (e.g. Dobzhansky–Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1,011 embryos (mean 130 ± 123), and abortion rates varied between 0% and 100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterized female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index, and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant post‐zygotic barriers contributing to ecotype divergence, and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females. article_processing_charge: No article_type: original author: - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Zuzanna full_name: Zagrodzka, Zuzanna last_name: Zagrodzka - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 2020;33(3):342-351. doi:10.1111/jeb.13570 apa: Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. K. (2020). Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13570 chicago: Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger K. Butlin. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology. Wiley, 2020. https://doi.org/10.1111/jeb.13570. ieee: K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. K. Butlin, “Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes?,” Journal of Evolutionary Biology, vol. 33, no. 3. Wiley, pp. 342–351, 2020. ista: Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin RK. 2020. Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? Journal of Evolutionary Biology. 33(3), 342–351. mla: Johannesson, Kerstin, et al. “Is Embryo Abortion a Post-Zygotic Barrier to Gene Flow between Littorina Ecotypes?” Journal of Evolutionary Biology, vol. 33, no. 3, Wiley, 2020, pp. 342–51, doi:10.1111/jeb.13570. short: K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R.K. Butlin, Journal of Evolutionary Biology 33 (2020) 342–351. date_created: 2019-12-22T23:00:43Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-09-06T14:48:57Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1111/jeb.13570 external_id: isi: - '000500954800001' pmid: - '31724256' file: - access_level: open_access checksum: 7534ff0839709c0c5265c12d29432f03 content_type: application/pdf creator: dernst date_created: 2020-09-22T09:42:18Z date_updated: 2020-09-22T09:42:18Z file_id: '8553' file_name: 2020_EvolBiology_Johannesson.pdf file_size: 885611 relation: main_file success: 1 file_date_updated: 2020-09-22T09:42:18Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 342-351 pmid: 1 publication: Journal of Evolutionary Biology publication_identifier: eissn: - '14209101' issn: - 1010061X publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '13067' relation: research_data status: public scopus_import: '1' status: public title: Is embryo abortion a post-zygotic barrier to gene flow between Littorina ecotypes? 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 33 year: '2020' ... --- _id: '7207' abstract: - lang: eng text: The hippocampus plays key roles in learning and memory and is a main target of Alzheimer's disease (AD), which causes progressive memory impairments. Despite numerous investigations about the processes required for the normal hippocampal functions, the neurotransmitter receptors involved in the synaptic deficits by which AD disables the hippocampus are not yet characterized. By combining histoblots, western blots, immunohistochemistry and high‐resolution immunoelectron microscopic methods for GABAB receptors, this study provides a quantitative description of the expression and the subcellular localization of GABAB1 in the hippocampus in a mouse model of AD at 1, 6 and 12 months of age. Western blots and histoblots showed that the total amount of protein and the laminar expression pattern of GABAB1 were similar in APP/PS1 mice and in age‐matched wild‐type mice. In contrast, immunoelectron microscopic techniques showed that the subcellular localization of GABAB1 subunit did not change significantly in APP/PS1 mice at 1 month of age, was significantly reduced in the stratum lacunosum‐moleculare of CA1 pyramidal cells at 6 months of age and significantly reduced at the membrane surface of CA1 pyramidal cells at 12 months of age. This reduction of plasma membrane GABAB1 was paralleled by a significant increase of the subunit at the intracellular sites. We further observed a decrease of membrane‐targeted GABAB receptors in axon terminals contacting CA1 pyramidal cells. Our data demonstrate compartment‐ and age‐dependent reduction of plasma membrane‐targeted GABAB receptors in the CA1 region of the hippocampus, suggesting that this decrease might be enough to alter the GABAB‐mediated synaptic transmission taking place in AD. article_processing_charge: No article_type: original author: - first_name: Alejandro full_name: Martín-Belmonte, Alejandro last_name: Martín-Belmonte - first_name: Carolina full_name: Aguado, Carolina last_name: Aguado - first_name: Rocío full_name: Alfaro-Ruíz, Rocío last_name: Alfaro-Ruíz - first_name: Ana Esther full_name: Moreno-Martínez, Ana Esther last_name: Moreno-Martínez - first_name: Luis full_name: De La Ossa, Luis last_name: De La Ossa - first_name: José full_name: Martínez-Hernández, José last_name: Martínez-Hernández - first_name: Alain full_name: Buisson, Alain last_name: Buisson - first_name: Simon full_name: Früh, Simon last_name: Früh - first_name: Bernhard full_name: Bettler, Bernhard last_name: Bettler - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Rafael full_name: Luján, Rafael last_name: Luján citation: ama: Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, et al. Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 2020;30(3):554-575. doi:10.1111/bpa.12802 apa: Martín-Belmonte, A., Aguado, C., Alfaro-Ruíz, R., Moreno-Martínez, A. E., De La Ossa, L., Martínez-Hernández, J., … Luján, R. (2020). Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. Wiley. https://doi.org/10.1111/bpa.12802 chicago: Martín-Belmonte, Alejandro, Carolina Aguado, Rocío Alfaro-Ruíz, Ana Esther Moreno-Martínez, Luis De La Ossa, José Martínez-Hernández, Alain Buisson, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA>B< Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” Brain Pathology. Wiley, 2020. https://doi.org/10.1111/bpa.12802. ieee: A. Martín-Belmonte et al., “Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease,” Brain Pathology, vol. 30, no. 3. Wiley, pp. 554–575, 2020. ista: Martín-Belmonte A, Aguado C, Alfaro-Ruíz R, Moreno-Martínez AE, De La Ossa L, Martínez-Hernández J, Buisson A, Früh S, Bettler B, Shigemoto R, Fukazawa Y, Luján R. 2020. Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer’s disease. Brain Pathology. 30(3), 554–575. mla: Martín-Belmonte, Alejandro, et al. “Reduction in the Neuronal Surface of Post and Presynaptic GABA>B< Receptors in the Hippocampus in a Mouse Model of Alzheimer’s Disease.” Brain Pathology, vol. 30, no. 3, Wiley, 2020, pp. 554–75, doi:10.1111/bpa.12802. short: A. Martín-Belmonte, C. Aguado, R. Alfaro-Ruíz, A.E. Moreno-Martínez, L. De La Ossa, J. Martínez-Hernández, A. Buisson, S. Früh, B. Bettler, R. Shigemoto, Y. Fukazawa, R. Luján, Brain Pathology 30 (2020) 554–575. date_created: 2019-12-22T23:00:43Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-09-06T14:48:01Z day: '01' ddc: - '570' department: - _id: RySh doi: 10.1111/bpa.12802 ec_funded: 1 external_id: isi: - '000502270900001' pmid: - '31729777' file: - access_level: open_access checksum: 549cc1b18f638a21d17a939ba5563fa9 content_type: application/pdf creator: dernst date_created: 2020-09-22T09:47:19Z date_updated: 2020-09-22T09:47:19Z file_id: '8554' file_name: 2020_BrainPathology_MartinBelmonte.pdf file_size: 4220935 relation: main_file success: 1 file_date_updated: 2020-09-22T09:47:19Z has_accepted_license: '1' intvolume: ' 30' isi: 1 issue: '3' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 554-575 pmid: 1 project: - _id: 25CBA828-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '720270' name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1) - _id: 26436750-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '785907' name: Human Brain Project Specific Grant Agreement 2 (HBP SGA 2) publication: Brain Pathology publication_identifier: eissn: - '17503639' issn: - '10156305' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Reduction in the neuronal surface of post and presynaptic GABA>B< receptors in the hippocampus in a mouse model of Alzheimer's 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 30 year: '2020' ... --- _id: '7212' abstract: - lang: eng text: The fixation probability of a single mutant invading a population of residents is among the most widely-studied quantities in evolutionary dynamics. Amplifiers of natural selection are population structures that increase the fixation probability of advantageous mutants, compared to well-mixed populations. Extensive studies have shown that many amplifiers exist for the Birth-death Moran process, some of them substantially increasing the fixation probability or even guaranteeing fixation in the limit of large population size. On the other hand, no amplifiers are known for the death-Birth Moran process, and computer-assisted exhaustive searches have failed to discover amplification. In this work we resolve this disparity, by showing that any amplification under death-Birth updating is necessarily bounded and transient. Our boundedness result states that even if a population structure does amplify selection, the resulting fixation probability is close to that of the well-mixed population. Our transience result states that for any population structure there exists a threshold r⋆ such that the population structure ceases to amplify selection if the mutant fitness advantage r is larger than r⋆. Finally, we also extend the above results to δ-death-Birth updating, which is a combination of Birth-death and death-Birth updating. On the positive side, we identify population structures that maintain amplification for a wide range of values r and δ. These results demonstrate that amplification of natural selection depends on the specific mechanisms of the evolutionary process. article_number: e1007494 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin A. full_name: Nowak, Martin A. last_name: Nowak citation: ama: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 2020;16. doi:10.1371/journal.pcbi.1007494 apa: Tkadlec, J., Pavlogiannis, A., Chatterjee, K., & Nowak, M. A. (2020). Limits on amplifiers of natural selection under death-Birth updating. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007494 chicago: Tkadlec, Josef, Andreas Pavlogiannis, Krishnendu Chatterjee, and Martin A. Nowak. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology. Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007494. ieee: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, and M. A. Nowak, “Limits on amplifiers of natural selection under death-Birth updating,” PLoS computational biology, vol. 16. Public Library of Science, 2020. ista: Tkadlec J, Pavlogiannis A, Chatterjee K, Nowak MA. 2020. Limits on amplifiers of natural selection under death-Birth updating. PLoS computational biology. 16, e1007494. mla: Tkadlec, Josef, et al. “Limits on Amplifiers of Natural Selection under Death-Birth Updating.” PLoS Computational Biology, vol. 16, e1007494, Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007494. short: J. Tkadlec, A. Pavlogiannis, K. Chatterjee, M.A. Nowak, PLoS Computational Biology 16 (2020). date_created: 2019-12-23T13:45:11Z date_published: 2020-01-17T00:00:00Z date_updated: 2023-10-17T12:29:47Z day: '17' ddc: - '000' department: - _id: KrCh doi: 10.1371/journal.pcbi.1007494 ec_funded: 1 external_id: arxiv: - '1906.02785' isi: - '000510916500025' file: - access_level: open_access checksum: ce32ee2d2f53aed832f78bbd47e882df content_type: application/pdf creator: dernst date_created: 2020-02-03T07:32:42Z date_updated: 2020-07-14T12:47:53Z file_id: '7441' file_name: 2020_PlosCompBio_Tkadlec.pdf file_size: 1817531 relation: main_file file_date_updated: 2020-07-14T12:47:53Z has_accepted_license: '1' intvolume: ' 16' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: PLoS computational biology publication_identifier: eissn: - '15537358' publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '7196' relation: part_of_dissertation status: public scopus_import: '1' status: public title: Limits on amplifiers of natural selection under death-Birth updating 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2020' ... --- _id: '7213' abstract: - lang: eng text: Persistent homology is a powerful tool in Topological Data Analysis (TDA) to capture the topological properties of data succinctly at different spatial resolutions. For graphical data, the shape, and structure of the neighborhood of individual data items (nodes) are an essential means of characterizing their properties. We propose the use of persistent homology methods to capture structural and topological properties of graphs and use it to address the problem of link prediction. We achieve encouraging results on nine different real-world datasets that attest to the potential of persistent homology-based methods for network analysis. alternative_title: - SCI article_processing_charge: No author: - first_name: Sumit full_name: Bhatia, Sumit last_name: Bhatia - first_name: Bapi full_name: Chatterjee, Bapi id: 3C41A08A-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-2742-4028 - first_name: Deepak full_name: Nathani, Deepak last_name: Nathani - first_name: Manohar full_name: Kaul, Manohar last_name: Kaul citation: ama: 'Bhatia S, Chatterjee B, Nathani D, Kaul M. A persistent homology perspective to the link prediction problem. In: Complex Networks and Their Applications VIII. Vol 881. Springer Nature; 2020:27-39. doi:10.1007/978-3-030-36687-2_3' apa: 'Bhatia, S., Chatterjee, B., Nathani, D., & Kaul, M. (2020). A persistent homology perspective to the link prediction problem. In Complex Networks and their applications VIII (Vol. 881, pp. 27–39). Lisbon, Portugal: Springer Nature. https://doi.org/10.1007/978-3-030-36687-2_3' chicago: Bhatia, Sumit, Bapi Chatterjee, Deepak Nathani, and Manohar Kaul. “A Persistent Homology Perspective to the Link Prediction Problem.” In Complex Networks and Their Applications VIII, 881:27–39. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-36687-2_3. ieee: S. Bhatia, B. Chatterjee, D. Nathani, and M. Kaul, “A persistent homology perspective to the link prediction problem,” in Complex Networks and their applications VIII, Lisbon, Portugal, 2020, vol. 881, pp. 27–39. ista: 'Bhatia S, Chatterjee B, Nathani D, Kaul M. 2020. A persistent homology perspective to the link prediction problem. Complex Networks and their applications VIII. COMPLEX: International Conference on Complex Networks and their Applications, SCI, vol. 881, 27–39.' mla: Bhatia, Sumit, et al. “A Persistent Homology Perspective to the Link Prediction Problem.” Complex Networks and Their Applications VIII, vol. 881, Springer Nature, 2020, pp. 27–39, doi:10.1007/978-3-030-36687-2_3. short: S. Bhatia, B. Chatterjee, D. Nathani, M. Kaul, in:, Complex Networks and Their Applications VIII, Springer Nature, 2020, pp. 27–39. conference: end_date: 2019-12-12 location: Lisbon, Portugal name: 'COMPLEX: International Conference on Complex Networks and their Applications' start_date: 2019-12-10 date_created: 2019-12-29T23:00:45Z date_published: 2020-01-01T00:00:00Z date_updated: 2024-02-22T13:16:06Z day: '01' ddc: - '004' department: - _id: DaAl doi: 10.1007/978-3-030-36687-2_3 ec_funded: 1 external_id: isi: - '000843927300003' file: - access_level: open_access checksum: 8951f094c8c7dae9ff8db885199bc296 content_type: application/pdf creator: bchatter date_created: 2020-10-08T08:16:48Z date_updated: 2020-10-08T08:16:48Z file_id: '8625' file_name: main.pdf file_size: 310598 relation: main_file success: 1 file_date_updated: 2020-10-08T08:16:48Z has_accepted_license: '1' intvolume: ' 881' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 27-39 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Complex Networks and their applications VIII publication_identifier: eissn: - '18609503' isbn: - '9783030366865' issn: - 1860949X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A persistent homology perspective to the link prediction problem type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 881 year: '2020' ... --- _id: '7224' abstract: - lang: eng text: 'Habitat loss is one of the key drivers of the ongoing decline of biodiversity. However, ecologists still argue about how fragmentation of habitat (independent of habitat loss) affects species richness. The recently proposed habitat amount hypothesis posits that species richness only depends on the total amount of habitat in a local landscape. In contrast, empirical studies report contrasting patterns: some find positive and others negative effects of fragmentation per se on species richness. To explain this apparent disparity, we devise a stochastic, spatially explicit model of competitive species communities in heterogeneous habitats. The model shows that habitat loss and fragmentation have complex effects on species diversity in competitive communities. When the total amount of habitat is large, fragmentation per se tends to increase species diversity, but if the total amount of habitat is small, the situation is reversed: fragmentation per se decreases species diversity.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 - first_name: Nerea full_name: Abrego, Nerea last_name: Abrego - first_name: Otso full_name: Ovaskainen, Otso last_name: Ovaskainen citation: ama: Rybicki J, Abrego N, Ovaskainen O. Habitat fragmentation and species diversity in competitive communities. Ecology Letters. 2020;23(3):506-517. doi:10.1111/ele.13450 apa: Rybicki, J., Abrego, N., & Ovaskainen, O. (2020). Habitat fragmentation and species diversity in competitive communities. Ecology Letters. Wiley. https://doi.org/10.1111/ele.13450 chicago: Rybicki, Joel, Nerea Abrego, and Otso Ovaskainen. “Habitat Fragmentation and Species Diversity in Competitive Communities.” Ecology Letters. Wiley, 2020. https://doi.org/10.1111/ele.13450. ieee: J. Rybicki, N. Abrego, and O. Ovaskainen, “Habitat fragmentation and species diversity in competitive communities,” Ecology Letters, vol. 23, no. 3. Wiley, pp. 506–517, 2020. ista: Rybicki J, Abrego N, Ovaskainen O. 2020. Habitat fragmentation and species diversity in competitive communities. Ecology Letters. 23(3), 506–517. mla: Rybicki, Joel, et al. “Habitat Fragmentation and Species Diversity in Competitive Communities.” Ecology Letters, vol. 23, no. 3, Wiley, 2020, pp. 506–17, doi:10.1111/ele.13450. short: J. Rybicki, N. Abrego, O. Ovaskainen, Ecology Letters 23 (2020) 506–517. date_created: 2020-01-04T11:04:30Z date_published: 2020-03-01T00:00:00Z date_updated: 2023-09-05T16:04:30Z day: '01' ddc: - '000' department: - _id: DaAl doi: 10.1111/ele.13450 ec_funded: 1 external_id: isi: - '000503625200001' file: - access_level: open_access checksum: 372f67f2744f4b6049e9778364766c22 content_type: application/pdf creator: dernst date_created: 2020-02-14T12:02:50Z date_updated: 2020-07-14T12:47:54Z file_id: '7486' file_name: 2020_EcologyLetters_Rybicki.pdf file_size: 3005474 relation: main_file file_date_updated: 2020-07-14T12:47:54Z has_accepted_license: '1' intvolume: ' 23' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 506-517 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 26A5D39A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '840605' name: Coordination in constrained and natural distributed systems publication: Ecology Letters publication_identifier: eissn: - 1461-0248 issn: - 1461-023X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Habitat fragmentation and species diversity in competitive communities 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 23 year: '2020' ... --- _id: '7234' abstract: - lang: eng text: T lymphocytes utilize amoeboid migration to navigate effectively within complex microenvironments. The precise rearrangement of the actin cytoskeleton required for cellular forward propulsion is mediated by actin regulators, including the actin‐related protein 2/3 (Arp2/3) complex, a macromolecular machine that nucleates branched actin filaments at the leading edge. The consequences of modulating Arp2/3 activity on the biophysical properties of the actomyosin cortex and downstream T cell function are incompletely understood. We report that even a moderate decrease of Arp3 levels in T cells profoundly affects actin cortex integrity. Reduction in total F‐actin content leads to reduced cortical tension and disrupted lamellipodia formation. Instead, in Arp3‐knockdown cells, the motility mode is dominated by blebbing migration characterized by transient, balloon‐like protrusions at the leading edge. Although this migration mode seems to be compatible with interstitial migration in three‐dimensional environments, diminished locomotion kinetics and impaired cytotoxicity interfere with optimal T cell function. These findings define the importance of finely tuned, Arp2/3‐dependent mechanophysical membrane integrity in cytotoxic effector T lymphocyte activities. article_processing_charge: No article_type: original author: - first_name: Peyman full_name: Obeidy, Peyman last_name: Obeidy - first_name: Lining A. full_name: Ju, Lining A. last_name: Ju - first_name: Stefan H. full_name: Oehlers, Stefan H. last_name: Oehlers - first_name: Nursafwana S. full_name: Zulkhernain, Nursafwana S. last_name: Zulkhernain - first_name: Quintin full_name: Lee, Quintin last_name: Lee - first_name: Jorge L. full_name: Galeano Niño, Jorge L. last_name: Galeano Niño - first_name: Rain Y.Q. full_name: Kwan, Rain Y.Q. last_name: Kwan - first_name: Shweta full_name: Tikoo, Shweta last_name: Tikoo - first_name: Lois L. full_name: Cavanagh, Lois L. last_name: Cavanagh - first_name: Paulus full_name: Mrass, Paulus last_name: Mrass - first_name: Adam J.L. full_name: Cook, Adam J.L. last_name: Cook - first_name: Shaun P. full_name: Jackson, Shaun P. last_name: Jackson - first_name: Maté full_name: Biro, Maté last_name: Biro - first_name: Ben full_name: Roediger, Ben last_name: Roediger - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Wolfgang full_name: Weninger, Wolfgang last_name: Weninger citation: ama: Obeidy P, Ju LA, Oehlers SH, et al. Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes. Immunology and Cell Biology. 2020;98(2):93-113. doi:10.1111/imcb.12304 apa: Obeidy, P., Ju, L. A., Oehlers, S. H., Zulkhernain, N. S., Lee, Q., Galeano Niño, J. L., … Weninger, W. (2020). Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes. Immunology and Cell Biology. Wiley. https://doi.org/10.1111/imcb.12304 chicago: Obeidy, Peyman, Lining A. Ju, Stefan H. Oehlers, Nursafwana S. Zulkhernain, Quintin Lee, Jorge L. Galeano Niño, Rain Y.Q. Kwan, et al. “Partial Loss of Actin Nucleator Actin-Related Protein 2/3 Activity Triggers Blebbing in Primary T Lymphocytes.” Immunology and Cell Biology. Wiley, 2020. https://doi.org/10.1111/imcb.12304. ieee: P. Obeidy et al., “Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes,” Immunology and Cell Biology, vol. 98, no. 2. Wiley, pp. 93–113, 2020. ista: Obeidy P, Ju LA, Oehlers SH, Zulkhernain NS, Lee Q, Galeano Niño JL, Kwan RYQ, Tikoo S, Cavanagh LL, Mrass P, Cook AJL, Jackson SP, Biro M, Roediger B, Sixt MK, Weninger W. 2020. Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes. Immunology and Cell Biology. 98(2), 93–113. mla: Obeidy, Peyman, et al. “Partial Loss of Actin Nucleator Actin-Related Protein 2/3 Activity Triggers Blebbing in Primary T Lymphocytes.” Immunology and Cell Biology, vol. 98, no. 2, Wiley, 2020, pp. 93–113, doi:10.1111/imcb.12304. short: P. Obeidy, L.A. Ju, S.H. Oehlers, N.S. Zulkhernain, Q. Lee, J.L. Galeano Niño, R.Y.Q. Kwan, S. Tikoo, L.L. Cavanagh, P. Mrass, A.J.L. Cook, S.P. Jackson, M. Biro, B. Roediger, M.K. Sixt, W. Weninger, Immunology and Cell Biology 98 (2020) 93–113. date_created: 2020-01-05T23:00:48Z date_published: 2020-02-01T00:00:00Z date_updated: 2023-08-17T14:21:12Z day: '01' ddc: - '570' department: - _id: MiSi doi: 10.1111/imcb.12304 external_id: isi: - '000503885600001' pmid: - '31698518' file: - access_level: open_access checksum: c389477b4b52172ef76afff8a06c6775 content_type: application/pdf creator: dernst date_created: 2020-11-19T11:22:33Z date_updated: 2020-11-19T11:22:33Z file_id: '8775' file_name: 2020_ImmunologyCellBio_Obeidy.pdf file_size: 8569945 relation: main_file success: 1 file_date_updated: 2020-11-19T11:22:33Z has_accepted_license: '1' intvolume: ' 98' isi: 1 issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 93-113 pmid: 1 publication: Immunology and Cell Biology publication_identifier: eissn: - '14401711' issn: - '08189641' publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Partial loss of actin nucleator actin-related protein 2/3 activity triggers blebbing in primary T lymphocytes 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: 98 year: '2020' ...