--- OA_place: publisher _id: '22255' abstract: - lang: eng text: "This thesis studies spectral rigidity and nonrigidity phenomena in dynamical systems. The central question is whether a dynamical system can be determined, up to a natural conjugacy, from its spectrum. We consider three related spectra: the length spectrum, the action spectrum, and the Lyapunov spectrum.\r\n\r\nThe first part of the thesis concerns Liouville metrics on the two-dimensional torus. It is a long-standing folklore conjecture that Liouville metrics are the only integrable metrics on the torus. We prove a length-spectral rigidity result for linear conformal deformations of Liouville metrics by exploiting the dynamical properties of the rational tori -- analogues of the resonant convex caustics in billiards. We also establish a complementary classification result showing that marked-length-isospectral Liouville metrics are characterized by rearrangements of the one-dimensional functions appearing in their conformal factors, generalizing a theorem of Abbondandolo-Mazzucchelli. In particular, the second result gives nonrigidity examples within the class of Liouville metrics.\r\n\r\nThe second part of the thesis studies the standard map from the viewpoint of action and Lyapunov spectra. We construct nontrivial deformations of the standard map which preserve the symplectic actions (respectively, the Lyapunov exponents) of infinitely many periodic orbits accumulating on an invariant curve. The proof combines a resonant normal form construction with Picard iteration schemes to obtain a sequence of periodic orbits accumulating on an invariant curve with a Liouville rotation number. Within the resonant normal forms we capture the dependence of these periodic orbits on the resonant Fourier coefficients of the dynamics on the invariant curve and, using the contraction mapping principle, obtain a suitable deformation achieving the prescribed spectral data associated with this sequence of orbits. The result can be viewed as a symplectic twist-map analogue of a length-spectral nonrigidity phenomenon for Riemannian manifolds and convex billiards, and it motivates the existence problem for similar 'partially length-isospectral' deformations of strictly convex billiard tables.\r\n" acknowledged_ssus: - _id: E-Lib - _id: CampIT acknowledgement: "The financial support of the ERC grant SPERIG #885707 is gratefully acknowledged.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Yunzhe full_name: Li, Yunzhe id: 41cb05d3-f128-11eb-9611-e4e2b3cfba31 last_name: Li citation: ama: Li Y. Spectral rigidity and nonrigidity of dynamical systems. 2026. doi:10.15479/AT-ISTA-22255 apa: Li, Y. (2026). Spectral rigidity and nonrigidity of dynamical systems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22255 chicago: Li, Yunzhe. “Spectral Rigidity and Nonrigidity of Dynamical Systems.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22255. ieee: Y. Li, “Spectral rigidity and nonrigidity of dynamical systems,” Institute of Science and Technology Austria, 2026. ista: Li Y. 2026. Spectral rigidity and nonrigidity of dynamical systems. Institute of Science and Technology Austria. mla: Li, Yunzhe. Spectral Rigidity and Nonrigidity of Dynamical Systems. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22255. short: Y. Li, Spectral Rigidity and Nonrigidity of Dynamical Systems, Institute of Science and Technology Austria, 2026. corr_author: '1' date_created: 2026-07-08T12:44:31Z date_published: 2026-07-11T00:00:00Z date_updated: 2026-07-20T14:58:23Z day: '11' ddc: - '515' degree_awarded: PhD department: - _id: GradSch - _id: VaKa doi: 10.15479/AT-ISTA-22255 doi_confirm: '1' ec_funded: 1 file: - access_level: open_access checksum: 8201cb5a427656a41828ecde8a85c04b content_type: application/pdf creator: yli date_created: 2026-07-14T10:48:45Z date_updated: 2026-07-14T10:48:45Z file_id: '22337' file_name: 2026_Li_Yunzhe_Thesis.pdf file_size: 1260717 relation: main_file - access_level: closed checksum: 19ee8461ed77f5b7980fc9461f778b6f content_type: application/x-zip-compressed creator: yli date_created: 2026-07-14T11:07:18Z date_updated: 2026-07-20T14:00:33Z file_id: '22339' file_name: 2026_Li_Yunzhe_Thesis.zip file_size: 418752 relation: source_file file_date_updated: 2026-07-20T14:00:33Z fulldoi: https://doi.org/10.15479/AT-ISTA-22255 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '07' oa: 1 oa_version: Published Version page: '131' project: - _id: 9B8B92DE-BA93-11EA-9121-9846C619BF3A call_identifier: H2020 grant_number: '885707' name: Spectral rigidity and integrability for billiards and geodesic flows publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '22340' relation: part_of_dissertation status: public - id: '22341' relation: part_of_dissertation status: public status: public supervisor: - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 title: Spectral rigidity and nonrigidity of dynamical systems 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: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '22873' acknowledged_ssus: - _id: ScienComp - _id: CampIT acknowledgement: I acknowledge funding by the Austrian Science Fund (FWF) [10.55776/PAT8537123]. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andreas full_name: Ehrmann, Andreas id: eaa689ed-f6e0-11ea-865d-bd98cbcf83c2 last_name: Ehrmann orcid: 0000-0002-0997-5678 citation: ama: 'Ehrmann A. Biological functionality without biochemistry: Designing nanomachines for target behavior. 2026. doi:10.15479/AT-ISTA-22873' apa: 'Ehrmann, A. (2026). Biological functionality without biochemistry: Designing nanomachines for target behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-22873' chicago: 'Ehrmann, Andreas. “Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior.” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-22873.' ieee: 'A. Ehrmann, “Biological functionality without biochemistry: Designing nanomachines for target behavior,” Institute of Science and Technology Austria, 2026.' ista: 'Ehrmann A. 2026. Biological functionality without biochemistry: Designing nanomachines for target behavior. Institute of Science and Technology Austria.' mla: 'Ehrmann, Andreas. Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior. Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-22873.' short: 'A. Ehrmann, Biological Functionality without Biochemistry: Designing Nanomachines for Target Behavior, Institute of Science and Technology Austria, 2026.' corr_author: '1' das_tickbox: '0' date_created: 2026-09-09T12:18:24Z date_published: 2026-09-04T00:00:00Z date_updated: 2026-09-18T11:28:29Z day: '04' ddc: - '530' - '600' - '621' - '004' - '005' degree_awarded: PhD department: - _id: GradSch - _id: CaGo - _id: EdHa doi: 10.15479/AT-ISTA-22873 doi_confirm: '1' file: - access_level: closed checksum: a5e3d79e0e5f3f4fb3c414e48116dc9e content_type: application/pdf creator: aehrmann date_created: 2026-09-11T07:23:57Z date_updated: 2026-09-17T08:59:39Z embargo: 2027-01-15 embargo_to: open_access file_id: '22901' file_name: 2026_Ehrmann_Andreas_Thesis.pdf file_size: 14782662 relation: main_file - access_level: closed checksum: 0235b9c52fee0c97f402f1c3d4efc1eb content_type: application/zip creator: aehrmann date_created: 2026-09-11T07:24:14Z date_updated: 2026-09-11T07:24:14Z description: All LaTeX files to compile my PhD Thesis. file_id: '22902' file_name: thesis_latex_files.zip file_size: 155228 relation: source_file file_date_updated: 2026-09-17T08:59:39Z fulldoi: https://doi.org/10.15479/AT-ISTA-22873 has_accepted_license: '1' keyword: - PhD Thesis - functional nanomachines - biological functionality - nanotechnology - energy delivery - target behavior - dynamics - design principles - optimization - differentiable statistical physics - machine learning language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '09' oa_version: Published Version page: '168' project: - _id: 90a98bb5-16d5-11f0-9cad-9675f3f8015d grant_number: PAT 8537123 name: Functional bio-inspired nanomachines from sticky colloids publication_identifier: isbn: - 978-3-99078-092-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '22893' relation: part_of_dissertation status: public - id: '22892' relation: part_of_dissertation status: public researchdata_availability: upon request status: public supervisor: - first_name: Carl Peter full_name: Goodrich, Carl Peter id: EB352CD2-F68A-11E9-89C5-A432E6697425 last_name: Goodrich orcid: 0000-0002-1307-5074 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 supplementarymaterial: not applicable title: 'Biological functionality without biochemistry: Designing nanomachines for target behavior' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '23145' acknowledged_ssus: - _id: LifeSc - _id: M-Shop - _id: CampIT - _id: Bio acknowledgement: "European Research Council (101142681 CYNIPS), Cyclic nucleotides as second messengers \r\nin plants, DOI: https://doi.org/10.3030/101142681 \r\nAustrian Science Fund (P 37051-B), Guanylate cyclase activity of TIR1/AFBs auxin receptors, \r\nDOI: https://doi.org/10.55776/P37051 " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marek full_name: Randuch, Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch citation: ama: 'Randuch M. Fast growth responses in plants: Growth regulation and phospho-proteomic . 2026. doi:10.15479/AT-ISTA-23145' apa: 'Randuch, M. (2026). Fast growth responses in plants: Growth regulation and phospho-proteomic . Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-23145' chicago: 'Randuch, Marek. “Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic .” Institute of Science and Technology Austria, 2026. https://doi.org/10.15479/AT-ISTA-23145.' ieee: 'M. Randuch, “Fast growth responses in plants: Growth regulation and phospho-proteomic ,” Institute of Science and Technology Austria, 2026.' ista: 'Randuch M. 2026. Fast growth responses in plants: Growth regulation and phospho-proteomic . Institute of Science and Technology Austria.' mla: 'Randuch, Marek. Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic . Institute of Science and Technology Austria, 2026, doi:10.15479/AT-ISTA-23145.' short: 'M. Randuch, Fast Growth Responses in Plants: Growth Regulation and Phospho-Proteomic , Institute of Science and Technology Austria, 2026.' corr_author: '1' date_created: 2026-10-16T17:14:40Z date_published: 2026-10-18T00:00:00Z date_updated: 2026-10-22T09:15:44Z day: '18' ddc: - '580' degree_awarded: PhD department: - _id: GradSch - _id: JiFr doi: 10.15479/AT-ISTA-23145 doi_confirm: '1' file: - access_level: closed checksum: 4ace20ba4f1bb0f8dcc3f8eb45eb68fa content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mranduch date_created: 2026-10-20T09:17:28Z date_updated: 2026-10-20T11:48:37Z file_id: '23176' file_name: 2026_Marek_Randuch_Thesis.docx file_size: 89544771 relation: source_file - access_level: closed checksum: fc630c7e8d795e7f13000cbb428424b3 content_type: application/pdf creator: mranduch date_created: 2026-10-20T09:17:20Z date_updated: 2026-10-20T11:48:37Z embargo: 2027-10-20 embargo_to: open_access file_id: '23177' file_name: 2026_Marek_Randuch_Thesis.pdf file_size: 28321059 relation: main_file file_date_updated: 2026-10-20T11:48:37Z fulldoi: https://doi.org/10.15479/AT-ISTA-23145 has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ month: '10' oa_version: Published Version page: '289' project: - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors - _id: 8f347782-16d5-11f0-9cad-8c19706ee739 grant_number: '101142681' name: Cyclic nucleotides as second messengers in plants publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12291' relation: part_of_dissertation status: public - id: '21763' relation: part_of_dissertation status: public - id: '23175' relation: part_of_dissertation status: public - id: '23174' relation: part_of_dissertation status: public - id: '20656' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 title: 'Fast growth responses in plants: Growth regulation and phospho-proteomic ' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2026' ... --- OA_place: publisher _id: '20551' abstract: - lang: eng text: "The space of codimension-2 shapes, such as curves in 3D and surfaces in 4D, is an infinite-dimensional manifold. This thesis explores geometric structures and dynamics on this space, with emphasis on their implications for physics, particularly hydrodynamics.\r\n\r\nOur investigation ranges from theoretical studies of infinite-dimensional symplectic and prequantum geometry to numerical computation of the time evolution of shapes. The thesis presents four main contributions.\r\n\r\nIn the first part, we introduce implicit representations of codimension-2 shapes using a class of complex-valued functions, and prove that the space of these implicit representations forms a prequantum bundle over the codimension-2 shape space. This reveals a new geometric interpretation of the canonical symplectic structure on the codimension-2 shape space.\r\n\r\nIn the second part, we use implicit representations to develop a simulation method for the dynamics of space curves. To handle chaotic systems such as vortex filaments in hydrodynamics, we exploit the infinite degrees of freedom, hidden in both the configuration and dynamics of implicit representations.\r\n\r\nIn the third part, we introduce new symplectic structures on the space of space curves, which generalize the only previously known symplectic structure on this space, allowing for new Hamiltonian dynamics of space curves.\r\n\r\nIn the fourth part, we apply a symplectic viewpoint to a differential geometric problem with practical applications. We derive a new area formula for spherical polygons via prequantization. " acknowledged_ssus: - _id: CampIT acknowledgement: "Projects contained in this thesis were financially supported in part by the\r\nEuropean Research Council with grants 1. ERC Consolidator Grant 101045083 CoDiNA,\r\nand 2. the European Union’s Horizon 2020 research and innovation programme under grant\r\nagreement No. 638176." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Sadashige full_name: Ishida, Sadashige id: 6F7C4B96-A8E9-11E9-A7CA-09ECE5697425 last_name: Ishida orcid: 0000-0002-3121-3100 citation: ama: Ishida S. Symplectic-prequantum structures and dynamics on the codimension-2 shape space. 2025. doi:10.15479/AT-ISTA-20551 apa: Ishida, S. (2025). Symplectic-prequantum structures and dynamics on the codimension-2 shape space. Institute of Science and Technology Austria. https://doi.org/10.15479/AT-ISTA-20551 chicago: Ishida, Sadashige. “Symplectic-Prequantum Structures and Dynamics on the Codimension-2 Shape Space.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT-ISTA-20551. ieee: S. Ishida, “Symplectic-prequantum structures and dynamics on the codimension-2 shape space,” Institute of Science and Technology Austria, 2025. ista: Ishida S. 2025. Symplectic-prequantum structures and dynamics on the codimension-2 shape space. Institute of Science and Technology Austria. mla: Ishida, Sadashige. Symplectic-Prequantum Structures and Dynamics on the Codimension-2 Shape Space. Institute of Science and Technology Austria, 2025, doi:10.15479/AT-ISTA-20551. short: S. Ishida, Symplectic-Prequantum Structures and Dynamics on the Codimension-2 Shape Space, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-10-27T10:28:52Z date_published: 2025-10-31T00:00:00Z date_updated: 2026-10-02T11:17:04Z day: '31' ddc: - '516' degree_awarded: PhD department: - _id: GradSch - _id: ChWo doi: 10.15479/AT-ISTA-20551 ec_funded: 1 file: - access_level: open_access checksum: 4eef80afcb67691cbb6549c4756fa534 content_type: application/zip creator: sishida date_created: 2025-11-01T18:26:14Z date_updated: 2025-11-01T18:26:14Z file_id: '20583' file_name: Thesis_tex.zip file_size: 72487812 relation: source_file - access_level: open_access checksum: 1e5a557900bf2dce01966b211b15d0fe content_type: application/pdf creator: sishida date_created: 2025-11-10T08:45:05Z date_updated: 2025-11-10T08:45:05Z file_id: '20623' file_name: Thesis_Sadashige_Ishida_PDFA.pdf file_size: 8945141 relation: main_file success: 1 file_date_updated: 2025-11-10T08:45:05Z fulldoi: https://doi.org/10.15479/AT-ISTA-20551 has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '141' project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: 'Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales' - _id: 34bc2376-11ca-11ed-8bc3-9a3b3961a088 grant_number: '101045083' name: Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena publication_identifier: isbn: - 978-3-99078-070-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12431' relation: part_of_dissertation status: public - id: '20580' relation: part_of_dissertation status: public - id: '17361' relation: part_of_dissertation status: public - id: '12846' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Albert full_name: Chern, Albert last_name: Chern title: Symplectic-prequantum structures and dynamics on the codimension-2 shape space 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: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: publisher _id: '19048' abstract: - lang: eng text: 'Rotations are found in physics problems at all scales: from spatial motion of celestial bodies, to transitions between quantum states of atoms and molecules. Mathematically, they represent a fundamental class of transformations and symmetries. Unlike spatial displacements, rotational transformations in three-dimensional space are non-commutative: the result of applying a sequence of rotations depends on the order of these operations. This feature makes the emergent physics that involves rotations rather intricate, but instrumental for studies of highly-interconnected many-body systems. In the presence of an environment, rotational properties of an object change, due to the interaction with particles of the environment. Owing to the complexity of this interaction, it can be engineered to exhibit certain properties of interest. In this Thesis, we examine several scenarios of how the rotational behavior of an impurity can be modified by interactions with its environment.' acknowledged_ssus: - _id: CampIT - _id: E-Lib - _id: SSU acknowledgement: "I am grateful to the European Research Council (ERC) [10.3030/801770] and Austrian\r\nScience Fund (FWF) [10.55776/F1004] for funding my research and to the Physical\r\nReview journals for publishing it. I also want to thank the VCQ (previously CoQuS) and\r\nIQOQI for organizing wonderful networking events for the physics community in Vienna\r\nand Innsbruck, respectively. Moreover, I thank Austrian Science Fund (FWF) for the\r\ncontinuous support for quantum research." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mikhail full_name: Maslov, Mikhail id: 2E65BB0E-F248-11E8-B48F-1D18A9856A87 last_name: Maslov orcid: 0000-0003-4074-2570 citation: ama: Maslov M. Emergent physics of rotating quantum impurities in many-body environments. 2025. doi:10.15479/at:ista:19048 apa: Maslov, M. (2025). Emergent physics of rotating quantum impurities in many-body environments. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:19048 chicago: Maslov, Mikhail. “Emergent Physics of Rotating Quantum Impurities in Many-Body Environments.” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/at:ista:19048. ieee: M. Maslov, “Emergent physics of rotating quantum impurities in many-body environments,” Institute of Science and Technology Austria, 2025. ista: Maslov M. 2025. Emergent physics of rotating quantum impurities in many-body environments. Institute of Science and Technology Austria. mla: Maslov, Mikhail. Emergent Physics of Rotating Quantum Impurities in Many-Body Environments. Institute of Science and Technology Austria, 2025, doi:10.15479/at:ista:19048. short: M. Maslov, Emergent Physics of Rotating Quantum Impurities in Many-Body Environments, Institute of Science and Technology Austria, 2025. corr_author: '1' date_created: 2025-02-18T01:41:27Z date_published: 2025-02-18T00:00:00Z date_updated: 2026-10-02T11:36:24Z day: '18' ddc: - '539' - '535' - '541' degree_awarded: PhD department: - _id: GradSch - _id: MiLe doi: 10.15479/at:ista:19048 ec_funded: 1 file: - access_level: open_access checksum: 5822a4dd31724c512b37c658af1787ab content_type: application/pdf creator: mmaslov date_created: 2025-02-18T14:25:59Z date_updated: 2025-02-18T14:25:59Z file_id: '19061' file_name: thesis_Maslov.pdf file_size: 7779825 relation: main_file - access_level: open_access checksum: 89bdce4774406d26ceca88a8bbcd6a9a content_type: application/zip creator: mmaslov date_created: 2025-02-18T14:25:59Z date_updated: 2025-02-18T14:25:59Z file_id: '19062' file_name: thesis_Maslov_source.zip file_size: 14453726 relation: source_file file_date_updated: 2025-02-18T14:25:59Z fulldoi: https://doi.org/10.15479/at:ista:19048 has_accepted_license: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: '86' project: - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' - _id: 7c040762-9f16-11ee-852c-dd79eeee4ab3 grant_number: F100403 name: Coherent Optical Metrology Beyond Electric-Dipole-Allowed Transitions publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '10845' relation: part_of_dissertation status: public - id: '7933' relation: part_of_dissertation status: public - id: '18087' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 title: Emergent physics of rotating quantum impurities in many-body environments tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2025' ... --- OA_place: repository OA_type: green _id: '19518' abstract: - lang: eng text: "The rising footprint of machine learning has led to a focus on imposing model\r\nsparsity as a means of reducing computational and memory costs. For deep neural\r\nnetworks (DNNs), the state-of-the-art accuracy-vs-sparsity is achieved by heuristics\r\ninspired by the classical Optimal Brain Surgeon (OBS) framework [LeCun et al.,\r\n1989, Hassibi and Stork, 1992, Hassibi et al., 1993], which leverages loss curvature\r\ninformation to make better pruning decisions. Yet, these results still lack a solid\r\ntheoretical understanding, and it is unclear whether they can be improved by\r\nleveraging connections to the wealth of work on sparse recovery algorithms. In this\r\npaper, we draw new connections between these two areas and present new sparse\r\nrecovery algorithms inspired by the OBS framework that comes with theoretical\r\nguarantees under reasonable assumptions and have strong practical performance.\r\nSpecifically, our work starts from the observation that we can leverage curvature\r\ninformation in OBS-like fashion upon the projection step of classic iterative sparse\r\nrecovery algorithms such as IHT. We show for the first time that this leads both\r\nto improved convergence bounds under standard assumptions. Furthermore, we\r\npresent extensions of this approach to the practical task of obtaining accurate sparse\r\nDNNs, and validate it experimentally at scale for Transformer-based models on\r\nvision and language tasks." acknowledged_ssus: - _id: CampIT acknowledgement: The authors thank the anonymous NeurIPS reviewers for their useful comments and feedback, the IT department from the Institute of Science and Technology Austria for the hardware support, and Weights and Biases for the infrastructure to track all our experiments. Mher Safaryan has received funding from the European Union’s Horizon 2020 research and innovation program under the Maria Skłodowska-Curie grant agreement No 101034413. alternative_title: - Advances in Neural Information Processing Systems article_processing_charge: No arxiv: 1 author: - first_name: Diyuan full_name: Wu, Diyuan id: 1a5914c2-896a-11ed-bdf8-fb80621a0635 last_name: Wu - first_name: Ionut-Vlad full_name: Modoranu, Ionut-Vlad id: 449f7a18-f128-11eb-9611-9b430c0c6333 last_name: Modoranu - first_name: Mher full_name: Safaryan, Mher id: dd546b39-0804-11ed-9c55-ef075c39778d last_name: Safaryan - first_name: Denis full_name: Kuznedelev, Denis last_name: Kuznedelev - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Wu D, Modoranu I-V, Safaryan M, Kuznedelev D, Alistarh D-A. The iterative optimal brain surgeon: Faster sparse recovery by leveraging second-order information. In: 38th Conference on Neural Information Processing Systems. Vol 37. Neural Information Processing Systems Foundation; 2024.' apa: 'Wu, D., Modoranu, I.-V., Safaryan, M., Kuznedelev, D., & Alistarh, D.-A. (2024). The iterative optimal brain surgeon: Faster sparse recovery by leveraging second-order information. In 38th Conference on Neural Information Processing Systems (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.' chicago: 'Wu, Diyuan, Ionut-Vlad Modoranu, Mher Safaryan, Denis Kuznedelev, and Dan-Adrian Alistarh. “The Iterative Optimal Brain Surgeon: Faster Sparse Recovery by Leveraging Second-Order Information.” In 38th Conference on Neural Information Processing Systems, Vol. 37. Neural Information Processing Systems Foundation, 2024.' ieee: 'D. Wu, I.-V. Modoranu, M. Safaryan, D. Kuznedelev, and D.-A. Alistarh, “The iterative optimal brain surgeon: Faster sparse recovery by leveraging second-order information,” in 38th Conference on Neural Information Processing Systems, Vancouver, Canada, 2024, vol. 37.' ista: 'Wu D, Modoranu I-V, Safaryan M, Kuznedelev D, Alistarh D-A. 2024. The iterative optimal brain surgeon: Faster sparse recovery by leveraging second-order information. 38th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.' mla: 'Wu, Diyuan, et al. “The Iterative Optimal Brain Surgeon: Faster Sparse Recovery by Leveraging Second-Order Information.” 38th Conference on Neural Information Processing Systems, vol. 37, Neural Information Processing Systems Foundation, 2024.' short: D. Wu, I.-V. Modoranu, M. Safaryan, D. Kuznedelev, D.-A. Alistarh, in:, 38th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024. conference: end_date: 2024-12-15 location: Vancouver, Canada name: 'NeurIPS: Neural Information Processing Systems' start_date: 2024-12-09 corr_author: '1' date_created: 2025-04-06T22:01:32Z date_published: 2024-12-20T00:00:00Z date_updated: 2025-05-14T11:37:10Z day: '20' department: - _id: DaAl - _id: MaMo ec_funded: 1 external_id: arxiv: - '2408.17163' intvolume: ' 37' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2408.17163 month: '12' oa: 1 oa_version: Preprint project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: 38th Conference on Neural Information Processing Systems publication_identifier: issn: - 1049-5258 publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' scopus_import: '1' status: public title: 'The iterative optimal brain surgeon: Faster sparse recovery by leveraging second-order information' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2024' ... --- OA_place: repository OA_type: green _id: '18975' abstract: - lang: eng text: Leveraging second-order information about the loss at the scale of deep networks is one of the main lines of approach for improving the performance of current optimizers for deep learning. Yet, existing approaches for accurate full-matrix preconditioning, such as Full-Matrix Adagrad (GGT) or Matrix-Free Approximate Curvature (M-FAC) suffer from massive storage costs when applied even to small-scale models, as they must store a sliding window of gradients, whose memory requirements are multiplicative in the model dimension. In this paper, we address this issue via a novel and efficient error-feedback technique that can be applied to compress preconditioners by up to two orders of magnitude in practice, without loss of convergence. Specifically, our approach compresses the gradient information via sparsification or low-rank compression before it is fed into the preconditioner, feeding the compression error back into future iterations. Extensive experiments on deep neural networks show that this approach can compress full-matrix preconditioners to up to 99% sparsity without accuracy loss, effectively removing the memory overhead of fullmatrix preconditioners such as GGT and M-FAC. acknowledged_ssus: - _id: CampIT acknowledgement: The authors thank Adrian Vladu, Razvan Pascanu, Alexandra Peste, Mher Safaryan for their valuable feedback, the IT department from Institute of Science and Technology Austria for the hardware support and Weights and Biases for the infrastructure to track all our experiments. alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Ionut-Vlad full_name: Modoranu, Ionut-Vlad id: 449f7a18-f128-11eb-9611-9b430c0c6333 last_name: Modoranu - first_name: Aleksei full_name: Kalinov, Aleksei id: 44b7120e-eb97-11eb-a6c2-e1557aa81d02 last_name: Kalinov orcid: 0000-0003-2189-3904 - first_name: Eldar full_name: Kurtic, Eldar id: 47beb3a5-07b5-11eb-9b87-b108ec578218 last_name: Kurtic - first_name: Elias full_name: Frantar, Elias id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f last_name: Frantar - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Modoranu I-V, Kalinov A, Kurtic E, Frantar E, Alistarh D-A. Error feedback can accurately compress preconditioners. In: 41st International Conference on Machine Learning. Vol 235. ML Research Press; 2024:35910-35933.' apa: 'Modoranu, I.-V., Kalinov, A., Kurtic, E., Frantar, E., & Alistarh, D.-A. (2024). Error feedback can accurately compress preconditioners. In 41st International Conference on Machine Learning (Vol. 235, pp. 35910–35933). Vienna, Austria: ML Research Press.' chicago: Modoranu, Ionut-Vlad, Aleksei Kalinov, Eldar Kurtic, Elias Frantar, and Dan-Adrian Alistarh. “Error Feedback Can Accurately Compress Preconditioners.” In 41st International Conference on Machine Learning, 235:35910–33. ML Research Press, 2024. ieee: I.-V. Modoranu, A. Kalinov, E. Kurtic, E. Frantar, and D.-A. Alistarh, “Error feedback can accurately compress preconditioners,” in 41st International Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 35910–35933. ista: 'Modoranu I-V, Kalinov A, Kurtic E, Frantar E, Alistarh D-A. 2024. Error feedback can accurately compress preconditioners. 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 35910–35933.' mla: Modoranu, Ionut-Vlad, et al. “Error Feedback Can Accurately Compress Preconditioners.” 41st International Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 35910–33. short: I.-V. Modoranu, A. Kalinov, E. Kurtic, E. Frantar, D.-A. Alistarh, in:, 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 35910–35933. conference: end_date: 2024-07-27 location: Vienna, Austria name: 'ICML: International Conference on Machine Learning' start_date: 2024-07-21 corr_author: '1' das_tickbox: '0' date_created: 2025-01-30T07:53:22Z date_published: 2024-07-30T00:00:00Z date_updated: 2026-10-01T09:33:07Z day: '30' department: - _id: DaAl external_id: arxiv: - '2306.06098' intvolume: ' 235' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2306.06098 month: '07' oa: 1 oa_version: Preprint page: 35910-35933 publication: 41st International Conference on Machine Learning publication_identifier: eissn: - 2640-3498 publication_status: published publisher: ML Research Press quality_controlled: '1' researchdata_availability: yes scopus_import: '1' status: public supplementarymaterial: no title: Error feedback can accurately compress preconditioners type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 235 year: '2024' ... --- OA_place: repository OA_type: green _id: '19510' abstract: - lang: eng text: "We propose a new variant of the Adam optimizer [Kingma and Ba, 2014] called\r\nMICROADAM that specifically minimizes memory overheads, while maintaining\r\ntheoretical convergence guarantees. We achieve this by compressing the gradient\r\ninformation before it is fed into the optimizer state, thereby reducing its memory\r\nfootprint significantly. We control the resulting compression error via a novel\r\ninstance of the classical error feedback mechanism from distributed optimization [Seide et al., 2014, Alistarh et al., 2018, Karimireddy et al., 2019] in which\r\nthe error correction information is itself compressed to allow for practical memory\r\ngains. We prove that the resulting approach maintains theoretical convergence\r\nguarantees competitive to those of AMSGrad, while providing good practical performance. Specifically, we show that MICROADAM can be implemented efficiently\r\non GPUs: on both million-scale (BERT) and billion-scale (LLaMA) models, MICROADAM provides practical convergence competitive to that of the uncompressed\r\nAdam baseline, with lower memory usage and similar running time. Our code is\r\navailable at https://github.com/IST-DASLab/MicroAdam." acknowledged_ssus: - _id: CampIT acknowledgement: The authors thank Razvan Pascanu, Mahdi Nikdan and Soroush Tabesh for their valuable feedback, the IT department from Institute of Science and Technology Austria for the hardware support and Weights and Biases for the infrastructure to track all our experiments. Mher Safaryan has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 101034413. alternative_title: - Advances in Neural Information Processing Systems article_processing_charge: No arxiv: 1 author: - first_name: Ionut-Vlad full_name: Modoranu, Ionut-Vlad id: 449f7a18-f128-11eb-9611-9b430c0c6333 last_name: Modoranu - first_name: Mher full_name: Safaryan, Mher id: dd546b39-0804-11ed-9c55-ef075c39778d last_name: Safaryan - first_name: Grigory full_name: Malinovsky, Grigory last_name: Malinovsky - first_name: Eldar full_name: Kurtic, Eldar id: 47beb3a5-07b5-11eb-9b87-b108ec578218 last_name: Kurtic - first_name: Thomas full_name: Robert, Thomas id: de632733-1457-11f0-ae22-b5914b8c1c41 last_name: Robert - first_name: Peter full_name: Richtárik, Peter last_name: Richtárik - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Modoranu I-V, Safaryan M, Malinovsky G, et al. MICROADAM: Accurate adaptive optimization with low space overhead and provable convergence. In: 38th Conference on Neural Information Processing Systems. Vol 37. Neural Information Processing Systems Foundation; 2024. doi:10.52202/079017-0001' apa: 'Modoranu, I.-V., Safaryan, M., Malinovsky, G., Kurtic, E., Robert, T., Richtárik, P., & Alistarh, D.-A. (2024). MICROADAM: Accurate adaptive optimization with low space overhead and provable convergence. In 38th Conference on Neural Information Processing Systems (Vol. 37). Neural Information Processing Systems Foundation. https://doi.org/10.52202/079017-0001' chicago: 'Modoranu, Ionut-Vlad, Mher Safaryan, Grigory Malinovsky, Eldar Kurtic, Thomas Robert, Peter Richtárik, and Dan-Adrian Alistarh. “MICROADAM: Accurate Adaptive Optimization with Low Space Overhead and Provable Convergence.” In 38th Conference on Neural Information Processing Systems, Vol. 37. Neural Information Processing Systems Foundation, 2024. https://doi.org/10.52202/079017-0001.' ieee: 'I.-V. Modoranu et al., “MICROADAM: Accurate adaptive optimization with low space overhead and provable convergence,” in 38th Conference on Neural Information Processing Systems, 2024, vol. 37.' ista: 'Modoranu I-V, Safaryan M, Malinovsky G, Kurtic E, Robert T, Richtárik P, Alistarh D-A. 2024. MICROADAM: Accurate adaptive optimization with low space overhead and provable convergence. 38th Conference on Neural Information Processing Systems. , Advances in Neural Information Processing Systems, vol. 37.' mla: 'Modoranu, Ionut-Vlad, et al. “MICROADAM: Accurate Adaptive Optimization with Low Space Overhead and Provable Convergence.” 38th Conference on Neural Information Processing Systems, vol. 37, Neural Information Processing Systems Foundation, 2024, doi:10.52202/079017-0001.' short: I.-V. Modoranu, M. Safaryan, G. Malinovsky, E. Kurtic, T. Robert, P. Richtárik, D.-A. Alistarh, in:, 38th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024. corr_author: '1' date_created: 2025-04-06T22:01:32Z date_published: 2024-12-20T00:00:00Z date_updated: 2026-10-15T09:49:27Z day: '20' department: - _id: DaAl doi: 10.52202/079017-0001 ec_funded: 1 external_id: arxiv: - '2405.15593' fulldoi: https://doi.org/10.52202/079017-0001 intvolume: ' 37' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2405.15593 month: '12' oa: 1 oa_version: Preprint project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: 38th Conference on Neural Information Processing Systems publication_identifier: issn: - 1049-5258 publication_status: published publisher: Neural Information Processing Systems Foundation quality_controlled: '1' related_material: link: - relation: software url: https://github.com/IST-DASLab/MicroAdam scopus_import: '1' status: public title: 'MICROADAM: Accurate adaptive optimization with low space overhead and provable convergence' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 37 year: '2024' ... --- OA_embargo: '6' OA_place: publisher _id: '18531' abstract: - lang: eng text: "Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. " acknowledged_ssus: - _id: ScienComp - _id: CampIT alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Andrea full_name: Mrnjavac, Andrea id: 353FAC84-AE61-11E9-8BFC-00D3E5697425 last_name: Mrnjavac citation: ama: Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:10.15479/at:ista:18531 apa: Mrnjavac, A. (2024). Early stages of sex chromosome evolution. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18531 chicago: Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18531. ieee: A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024. ista: Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria. mla: Mrnjavac, Andrea. Early Stages of Sex Chromosome Evolution. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18531. short: A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-11-11T08:40:45Z date_published: 2024-11-11T00:00:00Z date_updated: 2026-10-02T11:14:08Z day: '11' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/at:ista:18531 doi_confirm: '1' file: - access_level: closed checksum: 3e48b163c22114ef5d5371f758668289 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: amrnjava date_created: 2024-11-13T12:15:28Z date_updated: 2025-05-11T22:30:04Z embargo_to: open_access file_id: '18551' file_name: AMrnjavac_thesis_library.docx file_size: 26870629 relation: source_file title: Early stages of sex chromosome evolution - access_level: open_access checksum: 3ead60c1b678e7dcf018043aef3b5db2 content_type: application/pdf creator: amrnjava date_created: 2024-11-13T12:15:54Z date_updated: 2025-05-11T22:30:04Z embargo: 2025-05-11 file_id: '18552' file_name: AMrnjavac_thesis_library.pdf file_size: 4228766 relation: main_file title: Early stages of sex chromosome evolution file_date_updated: 2025-05-11T22:30:04Z fulldoi: https://doi.org/10.15479/at:ista:18531 has_accepted_license: '1' keyword: - Sex chromosomes - evolution - selection - sheltering language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '11' oa: 1 oa_version: Published Version page: '181' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12521' relation: part_of_dissertation status: public - id: '18549' relation: part_of_dissertation status: public researchdata_availability: unclear status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 supplementarymaterial: unclear title: Early stages of sex chromosome evolution 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: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: publisher _id: '12716' abstract: - lang: eng text: "The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism." acknowledged_ssus: - _id: PreCl - _id: Bio - _id: LifeSc - _id: M-Shop - _id: CampIT alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Laura full_name: Burnett, Laura id: 3B717F68-F248-11E8-B48F-1D18A9856A87 last_name: Burnett orcid: 0000-0002-8937-410X citation: ama: Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:10.15479/at:ista:12716 apa: Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716 chicago: Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716. ieee: L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023. ista: Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. mla: Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716. short: L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023. corr_author: '1' date_created: 2023-03-08T15:19:45Z date_published: 2023-03-10T00:00:00Z date_updated: 2026-04-07T13:25:15Z day: '10' ddc: - '599' - '573' degree_awarded: PhD department: - _id: GradSch - _id: MaJö doi: 10.15479/at:ista:12716 ec_funded: 1 file: - access_level: closed checksum: 6c6d9cc2c4cdacb74e6b1047a34d7332 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lburnett date_created: 2023-03-08T15:08:46Z date_updated: 2023-03-08T15:08:46Z file_id: '12717' file_name: Burnett_Thesis_2023.docx file_size: 23029260 relation: source_file - access_level: open_access checksum: cebc77705288bf4382db9b3541483cd0 content_type: application/pdf creator: lburnett date_created: 2023-03-08T15:08:46Z date_updated: 2023-03-08T15:08:46Z file_id: '12718' file_name: Burnett_Thesis_2023_pdfA.pdf file_size: 11959869 relation: main_file success: 1 file_date_updated: 2023-03-08T15:08:46Z fulldoi: https://doi.org/10.15479/at:ista:12716 has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '178' project: - _id: 2634E9D2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '756502' name: Circuits of Visual Attention publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 title: To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2023' ... --- OA_place: publisher _id: '14641' abstract: - lang: eng text: "Mutation rates represent the net result of complex interactions among various\r\ncellular processes and can dramatically influence the evolutionary fate of\r\nmicrobial populations. However, many popular techniques used to study\r\nmutations are subject to the confounding effects of heredity and the subtleties\r\nof adaptation to selection, all of which make it difficult to observe any dynamic\r\nresponses of mutation rates to fitness challenges. Furthermore, in spite of the\r\nubiquity of quorum sensing systems across the bacterial domain and relevance\r\nfor many physiological behaviors, the effects of such mechanisms on mutation\r\nrate and adaptation remain poorly understood. In the following work, I\r\npresent the development of a microfluidic droplet-based method to measure\r\nsingle base-pair mutation rates in growing populations of the bacterium\r\nEscherichia coli. I use this method to observe a stress-induced increase in\r\nmutation rate that is mediated by luxS, a highly conserved bacterial quorum\r\nsensing component. I also show that the aforementioned increase in mutation\r\nrate, and its associated control by luxS, corresponds to a higher degree of\r\nadaptability under competitive environments." acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: CampIT alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mike full_name: Hennessey-Wesen, Mike id: 3F338C72-F248-11E8-B48F-1D18A9856A87 last_name: Hennessey-Wesen citation: ama: Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:10.15479/at:ista:14641 apa: Hennessey-Wesen, M. (2023). Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14641 chicago: Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14641. ieee: M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023. ista: Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria. mla: Hennessey-Wesen, Mike. Adaptive Mutation in E. Coli Modulated by LuxS. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14641. short: M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023. corr_author: '1' das_tickbox: '1' date_created: 2023-12-04T13:17:37Z date_published: 2023-11-30T00:00:00Z date_updated: 2026-07-13T10:55:56Z day: '30' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: BjHo doi: 10.15479/at:ista:14641 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: 4127c285b34f4bf7fb31ef24f9d14c25 content_type: application/vnd.oasis.opendocument.text creator: mhenness date_created: 2023-12-06T13:13:26Z date_updated: 2024-11-30T23:30:05Z embargo_to: open_access file_id: '14648' file_name: mike_thesis_v06-12-2023.odt file_size: 46405919 relation: source_file - access_level: closed checksum: f5203a61eddaf35235bbc51904d73982 content_type: application/pdf creator: mhenness date_created: 2023-12-06T13:14:15Z date_updated: 2026-07-13T10:55:56Z embargo: 2026-11-18 embargo_to: open_access file_id: '14649' file_name: mike_thesis_v06-12-2023.pdf file_size: 21282155 relation: main_file - access_level: closed checksum: 902102d26d30e74dbd6cdd70a65820c3 content_type: application/pdf creator: cchlebak date_created: 2025-05-20T12:59:12Z date_updated: 2025-05-20T22:31:34Z description: for printing purposes only embargo_to: open_access file_id: '19720' file_name: 2023_Hennessey_Michael_Thesis_print.pdf file_size: 45847968 relation: other title: Print version file_date_updated: 2026-07-13T10:55:56Z fulldoi: https://doi.org/10.15479/at:ista:14641 has_accepted_license: '1' keyword: - microfluidics - miceobiology - mutations - quorum sensing language: - iso: eng month: '11' oa_version: Published Version page: '104' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 title: Adaptive mutation in E. coli modulated by luxS type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- OA_place: publisher _id: '9418' abstract: - lang: eng text: "Deep learning is best known for its empirical success across a wide range of applications\r\nspanning computer vision, natural language processing and speech. Of equal significance,\r\nthough perhaps less known, are its ramifications for learning theory: deep networks have\r\nbeen observed to perform surprisingly well in the high-capacity regime, aka the overfitting\r\nor underspecified regime. Classically, this regime on the far right of the bias-variance curve\r\nis associated with poor generalisation; however, recent experiments with deep networks\r\nchallenge this view.\r\n\r\nThis thesis is devoted to investigating various aspects of underspecification in deep learning.\r\nFirst, we argue that deep learning models are underspecified on two levels: a) any given\r\ntraining dataset can be fit by many different functions, and b) any given function can be\r\nexpressed by many different parameter configurations. We refer to the second kind of\r\nunderspecification as parameterisation redundancy and we precisely characterise its extent.\r\nSecond, we characterise the implicit criteria (the inductive bias) that guide learning in the\r\nunderspecified regime. Specifically, we consider a nonlinear but tractable classification\r\nsetting, and show that given the choice, neural networks learn classifiers with a large margin.\r\nThird, we consider learning scenarios where the inductive bias is not by itself sufficient to\r\ndeal with underspecification. We then study different ways of ‘tightening the specification’: i)\r\nIn the setting of representation learning with variational autoencoders, we propose a hand-\r\ncrafted regulariser based on mutual information. ii) In the setting of binary classification, we\r\nconsider soft-label (real-valued) supervision. We derive a generalisation bound for linear\r\nnetworks supervised in this way and verify that soft labels facilitate fast learning. Finally, we\r\nexplore an application of soft-label supervision to the training of multi-exit models." acknowledged_ssus: - _id: ScienComp - _id: CampIT - _id: E-Lib alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Phuong full_name: Bui Thi Mai, Phuong id: 3EC6EE64-F248-11E8-B48F-1D18A9856A87 last_name: Bui Thi Mai citation: ama: Phuong M. Underspecification in deep learning. 2021. doi:10.15479/AT:ISTA:9418 apa: Phuong, M. (2021). Underspecification in deep learning. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9418 chicago: Phuong, Mary. “Underspecification in Deep Learning.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9418. ieee: M. Phuong, “Underspecification in deep learning,” Institute of Science and Technology Austria, 2021. ista: Phuong M. 2021. Underspecification in deep learning. Institute of Science and Technology Austria. mla: Phuong, Mary. Underspecification in Deep Learning. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9418. short: M. Phuong, Underspecification in Deep Learning, Institute of Science and Technology Austria, 2021. corr_author: '1' date_created: 2021-05-24T13:06:23Z date_published: 2021-05-30T00:00:00Z date_updated: 2026-07-30T05:33:52Z day: '30' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: ChLa doi: 10.15479/AT:ISTA:9418 doi_confirm: '1' file: - access_level: open_access checksum: 4f0abe64114cfed264f9d36e8d1197e3 content_type: application/pdf creator: bphuong date_created: 2021-05-24T11:22:29Z date_updated: 2021-05-24T11:22:29Z file_id: '9419' file_name: mph-thesis-v519-pdfimages.pdf file_size: 2673905 relation: main_file success: 1 - access_level: closed checksum: f5699e876bc770a9b0df8345a77720a2 content_type: application/zip creator: bphuong date_created: 2021-05-24T11:56:02Z date_updated: 2021-05-24T11:56:02Z file_id: '9420' file_name: thesis.zip file_size: 92995100 relation: source_file file_date_updated: 2021-05-24T11:56:02Z fulldoi: https://doi.org/10.15479/AT:ISTA:9418 has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '125' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7435' relation: part_of_dissertation status: deleted - id: '7481' relation: part_of_dissertation status: public - id: '9416' relation: part_of_dissertation status: public - id: '7479' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: Underspecification in deep learning type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- OA_place: publisher _id: '8032' abstract: - lang: eng text: "Algorithms in computational 3-manifold topology typically take a triangulation as an input and return topological information about the underlying 3-manifold. However, extracting the desired information from a triangulation (e.g., evaluating an invariant) is often computationally very expensive. In recent years this complexity barrier has been successfully tackled in some cases by importing ideas from the theory of parameterized algorithms into the realm of 3-manifolds. Various computationally hard problems were shown to be efficiently solvable for input triangulations that are sufficiently “tree-like.”\r\nIn this thesis we focus on the key combinatorial parameter in the above context: we consider the treewidth of a compact, orientable 3-manifold, i.e., the smallest treewidth of the dual graph of any triangulation thereof. By building on the work of Scharlemann–Thompson and Scharlemann–Schultens–Saito on generalized Heegaard splittings, and on the work of Jaco–Rubinstein on layered triangulations, we establish quantitative relations between the treewidth and classical topological invariants of a 3-manifold. In particular, among other results, we show that the treewidth of a closed, orientable, irreducible, non-Haken 3-manifold is always within a constant factor of its Heegaard genus." acknowledged_ssus: - _id: E-Lib - _id: CampIT alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kristóf full_name: Huszár, Kristóf id: 33C26278-F248-11E8-B48F-1D18A9856A87 last_name: Huszár orcid: 0000-0002-5445-5057 citation: ama: Huszár K. Combinatorial width parameters for 3-dimensional manifolds. 2020. doi:10.15479/AT:ISTA:8032 apa: Huszár, K. (2020). Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8032 chicago: Huszár, Kristóf. “Combinatorial Width Parameters for 3-Dimensional Manifolds.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8032. ieee: K. Huszár, “Combinatorial width parameters for 3-dimensional manifolds,” Institute of Science and Technology Austria, 2020. ista: Huszár K. 2020. Combinatorial width parameters for 3-dimensional manifolds. Institute of Science and Technology Austria. mla: Huszár, Kristóf. Combinatorial Width Parameters for 3-Dimensional Manifolds. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8032. short: K. Huszár, Combinatorial Width Parameters for 3-Dimensional Manifolds, Institute of Science and Technology Austria, 2020. corr_author: '1' date_created: 2020-06-26T10:00:36Z date_published: 2020-06-26T00:00:00Z date_updated: 2026-04-08T07:21:28Z day: '26' ddc: - '514' degree_awarded: PhD department: - _id: UlWa doi: 10.15479/AT:ISTA:8032 file: - access_level: open_access checksum: bd8be6e4f1addc863dfcc0fad29ee9c3 content_type: application/pdf creator: khuszar date_created: 2020-06-26T10:03:58Z date_updated: 2020-07-14T12:48:08Z file_id: '8034' file_name: Kristof_Huszar-Thesis.pdf file_size: 2637562 relation: main_file - access_level: closed checksum: d5f8456202b32f4a77552ef47a2837d1 content_type: application/x-zip-compressed creator: khuszar date_created: 2020-06-26T10:10:06Z date_updated: 2020-07-14T12:48:08Z file_id: '8035' file_name: Kristof_Huszar-Thesis-source.zip file_size: 7163491 relation: source_file file_date_updated: 2020-07-14T12:48:08Z fulldoi: https://doi.org/10.15479/AT:ISTA:8032 has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: xviii+120 publication_identifier: isbn: - 978-3-99078-006-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '6556' relation: dissertation_contains status: public - id: '7093' relation: dissertation_contains status: public status: public supervisor: - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 - first_name: Jonathan full_name: Spreer, Jonathan last_name: Spreer title: Combinatorial width parameters for 3-dimensional manifolds 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: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2020' ... --- OA_place: publisher _id: '8390' abstract: - lang: eng text: "Deep neural networks have established a new standard for data-dependent feature extraction pipelines in the Computer Vision literature. Despite their remarkable performance in the standard supervised learning scenario, i.e. when models are trained with labeled data and tested on samples that follow a similar distribution, neural networks have been shown to struggle with more advanced generalization abilities, such as transferring knowledge across visually different domains, or generalizing to new unseen combinations of known concepts. In this thesis we argue that, in contrast to the usual black-box behavior of neural networks, leveraging more structured internal representations is a promising direction\r\nfor tackling such problems. In particular, we focus on two forms of structure. First, we tackle modularity: We show that (i) compositional architectures are a natural tool for modeling reasoning tasks, in that they efficiently capture their combinatorial nature, which is key for generalizing beyond the compositions seen during training. We investigate how to to learn such models, both formally and experimentally, for the task of abstract visual reasoning. Then, we show that (ii) in some settings, modularity allows us to efficiently break down complex tasks into smaller, easier, modules, thereby improving computational efficiency; We study this behavior in the context of generative models for colorization, as well as for small objects detection. Secondly, we investigate the inherently layered structure of representations learned by neural networks, and analyze its role in the context of transfer learning and domain adaptation across visually\r\ndissimilar domains. " acknowledged_ssus: - _id: CampIT - _id: ScienComp acknowledgement: Last but not least, I would like to acknowledge the support of the IST IT and scientific computing team for helping provide a great work environment. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Amélie full_name: Royer, Amélie id: 3811D890-F248-11E8-B48F-1D18A9856A87 last_name: Royer orcid: 0000-0002-8407-0705 citation: ama: Royer A. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. 2020. doi:10.15479/AT:ISTA:8390 apa: Royer, A. (2020). Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8390 chicago: Royer, Amélie. “Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8390. ieee: A. Royer, “Leveraging structure in Computer Vision tasks for flexible Deep Learning models,” Institute of Science and Technology Austria, 2020. ista: Royer A. 2020. Leveraging structure in Computer Vision tasks for flexible Deep Learning models. Institute of Science and Technology Austria. mla: Royer, Amélie. Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8390. short: A. Royer, Leveraging Structure in Computer Vision Tasks for Flexible Deep Learning Models, Institute of Science and Technology Austria, 2020. corr_author: '1' date_created: 2020-09-14T13:42:09Z date_published: 2020-09-14T00:00:00Z date_updated: 2026-04-08T07:26:44Z day: '14' ddc: - '000' degree_awarded: PhD department: - _id: ChLa doi: 10.15479/AT:ISTA:8390 file: - access_level: open_access checksum: c914d2f88846032f3d8507734861b6ee content_type: application/pdf creator: dernst date_created: 2020-09-14T13:39:14Z date_updated: 2020-09-14T13:39:14Z file_id: '8391' file_name: 2020_Thesis_Royer.pdf file_size: 30224591 relation: main_file success: 1 - access_level: closed checksum: ae98fb35d912cff84a89035ae5794d3c content_type: application/x-zip-compressed creator: dernst date_created: 2020-09-14T13:39:17Z date_updated: 2020-09-14T13:39:17Z file_id: '8392' file_name: thesis_sources.zip file_size: 74227627 relation: main_file file_date_updated: 2020-09-14T13:39:17Z fulldoi: https://doi.org/10.15479/AT:ISTA:8390 has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '197' publication_identifier: isbn: - 978-3-99078-007-7 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '7936' relation: part_of_dissertation status: public - id: '8092' relation: part_of_dissertation status: public - id: '911' relation: part_of_dissertation status: public - id: '8193' relation: part_of_dissertation status: public - id: '7937' relation: part_of_dissertation status: public status: public supervisor: - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 title: Leveraging structure in Computer Vision tasks for flexible Deep Learning models tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2020' ... --- OA_place: publisher _id: '8983' abstract: - lang: eng text: Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: E-Lib - _id: CampIT acknowledgement: Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Shamsi full_name: Emtenani, Shamsi id: 49D32318-F248-11E8-B48F-1D18A9856A87 last_name: Emtenani orcid: 0000-0001-6981-6938 citation: ama: Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:10.15479/AT:ISTA:8983 apa: Emtenani, S. (2020). Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8983 chicago: Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8983. ieee: S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020. ista: Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria. mla: Emtenani, Shamsi. Metabolic Regulation of Drosophila Macrophage Tissue Invasion. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8983. short: S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020. corr_author: '1' date_created: 2020-12-30T15:41:26Z date_published: 2020-12-30T00:00:00Z date_updated: 2026-04-08T07:28:54Z day: '30' ddc: - '570' degree_awarded: PhD department: - _id: DaSi doi: 10.15479/AT:ISTA:8983 file: - access_level: open_access checksum: ec2797ab7a6f253b35df0572b36d1b43 content_type: application/pdf creator: semtenan date_created: 2020-12-30T15:34:01Z date_updated: 2021-12-31T23:30:04Z embargo: 2021-12-30 file_id: '8984' file_name: Thesis_Shamsi_Emtenani_pdfA.pdf file_size: 10848175 relation: main_file - access_level: closed checksum: cc30e6608a9815414024cf548dff3b3a content_type: application/pdf creator: semtenan date_created: 2020-12-30T15:37:36Z date_updated: 2021-12-31T23:30:04Z embargo_to: open_access file_id: '8985' file_name: Thesis_Shamsi_Emtenani_source file.pdf file_size: 10073648 relation: source_file file_date_updated: 2021-12-31T23:30:04Z fulldoi: https://doi.org/10.15479/AT:ISTA:8983 has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '141' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8557' relation: part_of_dissertation status: public - id: '6187' relation: part_of_dissertation status: public status: public supervisor: - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 title: Metabolic regulation of Drosophila macrophage tissue invasion type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2020' ... --- _id: '6755' abstract: - lang: eng text: 'Differentiated sex chromosomes are accompanied by a difference in gene dose between X/Z-specific and autosomal genes. At the transcriptomic level, these sex-linked genes can lead to expression imbalance, or gene dosage can be compensated by epigenetic mechanisms and results into expression level equalization. Schistosoma mansoni has been previously described as a ZW species (i.e., female heterogamety, in opposition to XY male heterogametic species) with a partial dosage compensation, but underlying mechanisms are still unexplored. Here, we combine transcriptomic (RNA-Seq) and epigenetic data (ChIP-Seq against H3K4me3, H3K27me3,andH4K20me1histonemarks) in free larval cercariae and intravertebrate parasitic stages. For the first time, we describe differences in dosage compensation status in ZW females, depending on the parasitic status: free cercariae display global dosage compensation, whereas intravertebrate stages show a partial dosage compensation. We also highlight regional differences of gene expression along the Z chromosome in cercariae, but not in the intravertebrate stages. Finally, we feature a consistent permissive chromatin landscape of the Z chromosome in both sexes and stages. We argue that dosage compensation in schistosomes is characterized by chromatin remodeling mechanisms in the Z-specific region.' acknowledged_ssus: - _id: CampIT article_processing_charge: No article_type: original author: - first_name: Marion A L full_name: Picard, Marion A L id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: David full_name: Roquis, David last_name: Roquis - first_name: Ingo full_name: Bulla, Ingo last_name: Bulla - first_name: Ronaldo C. full_name: Augusto, Ronaldo C. last_name: Augusto - first_name: Nathalie full_name: Arancibia, Nathalie last_name: Arancibia - first_name: Christoph full_name: Grunau, Christoph last_name: Grunau - first_name: Jérôme full_name: Boissier, Jérôme last_name: Boissier - first_name: Céline full_name: Cosseau, Céline last_name: Cosseau citation: ama: 'Picard MAL, Vicoso B, Roquis D, et al. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 2019;11(7):1909-1922. doi:10.1093/gbe/evz133' apa: 'Picard, M. A. L., Vicoso, B., Roquis, D., Bulla, I., Augusto, R. C., Arancibia, N., … Cosseau, C. (2019). Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evz133' chicago: 'Picard, Marion A L, Beatriz Vicoso, David Roquis, Ingo Bulla, Ronaldo C. Augusto, Nathalie Arancibia, Christoph Grunau, Jérôme Boissier, and Céline Cosseau. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution. Oxford University Press, 2019. https://doi.org/10.1093/gbe/evz133.' ieee: 'M. A. L. Picard et al., “Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome,” Genome biology and evolution, vol. 11, no. 7. Oxford University Press, pp. 1909–1922, 2019.' ista: 'Picard MAL, Vicoso B, Roquis D, Bulla I, Augusto RC, Arancibia N, Grunau C, Boissier J, Cosseau C. 2019. Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome. Genome biology and evolution. 11(7), 1909–1922.' mla: 'Picard, Marion A. L., et al. “Dosage Compensation throughout the Schistosoma Mansoni Lifecycle: Specific Chromatin Landscape of the Z Chromosome.” Genome Biology and Evolution, vol. 11, no. 7, Oxford University Press, 2019, pp. 1909–22, doi:10.1093/gbe/evz133.' short: M.A.L. Picard, B. Vicoso, D. Roquis, I. Bulla, R.C. Augusto, N. Arancibia, C. Grunau, J. Boissier, C. Cosseau, Genome Biology and Evolution 11 (2019) 1909–1922. date_created: 2019-08-04T21:59:18Z date_published: 2019-07-01T00:00:00Z date_updated: 2025-05-14T11:08:50Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/gbe/evz133 external_id: isi: - '000484039500018' pmid: - '31273378' file: - access_level: open_access checksum: f9e8f6863a406dcc5a36b2be001c138c content_type: application/pdf creator: dernst date_created: 2019-08-05T07:55:02Z date_updated: 2020-07-14T12:47:39Z file_id: '6765' file_name: 2019_GenomeBiology_Picard.pdf file_size: 580205 relation: main_file file_date_updated: 2020-07-14T12:47:39Z fulldoi: https://doi.org/10.1093/gbe/evz133 has_accepted_license: '1' intvolume: ' 11' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1909-1922 pmid: 1 publication: Genome biology and evolution publication_identifier: eissn: - 1759-6653 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Dosage compensation throughout the Schistosoma mansoni lifecycle: Specific chromatin landscape of the Z chromosome' 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: 11 year: '2019' ... --- _id: '131' abstract: - lang: eng text: 'XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. ' acknowledged_ssus: - _id: CampIT acknowledgement: We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript. article_number: e35684 article_processing_charge: No article_type: original author: - first_name: Marion A full_name: Picard, Marion A id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 - first_name: Celine full_name: Cosseau, Celine last_name: Cosseau - first_name: Sabrina full_name: Ferré, Sabrina last_name: Ferré - first_name: Thomas full_name: Quack, Thomas last_name: Quack - first_name: Christoph full_name: Grevelding, Christoph last_name: Grevelding - first_name: Yohann full_name: Couté, Yohann last_name: Couté - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 2018;7. doi:10.7554/eLife.35684 apa: Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., & Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.35684 chicago: Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.35684. ieee: M. A. L. Picard et al., “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” eLife, vol. 7. eLife Sciences Publications, 2018. ista: Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684. mla: Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” ELife, vol. 7, e35684, eLife Sciences Publications, 2018, doi:10.7554/eLife.35684. short: M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018). das_tickbox: '1' date_created: 2018-12-11T11:44:47Z date_published: 2018-08-13T00:00:00Z date_updated: 2026-07-28T09:45:56Z day: '13' ddc: - '570' department: - _id: BeVi doi: 10.7554/eLife.35684 external_id: isi: - '000441388200001' file: - access_level: open_access checksum: d6331d4385b1fffd6b47b45d5949d841 content_type: application/pdf creator: dernst date_created: 2018-12-17T11:55:05Z date_updated: 2020-07-14T12:44:43Z file_id: '5695' file_name: 2018_eLife_Picard.pdf file_size: 3158125 relation: main_file file_date_updated: 2020-07-14T12:44:43Z fulldoi: https://doi.org/10.7554/eLife.35684 has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '7792' quality_controlled: '1' related_material: record: - id: '5586' relation: popular_science status: public scopus_import: '1' status: public title: Evolution of gene dosage on the Z-chromosome of schistosome parasites 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: 7 year: '2018' ...