--- _id: '6371' abstract: - lang: eng text: "Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \ \r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Claudia full_name: Igler, Claudia id: 46613666-F248-11E8-B48F-1D18A9856A87 last_name: Igler citation: ama: Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371 apa: Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371 chicago: Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371. ieee: C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019. ista: Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. mla: Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371. short: C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019. date_created: 2019-05-03T11:55:51Z date_published: 2019-05-03T00:00:00Z date_updated: 2024-02-21T13:45:52Z day: '03' ddc: - '576' - '579' degree_awarded: PhD department: - _id: CaGu doi: 10.15479/AT:ISTA:6371 file: - access_level: open_access checksum: c0085d47c58c9cbcab1b0a783480f6da content_type: application/pdf creator: cigler date_created: 2019-05-03T11:54:52Z date_updated: 2021-02-11T11:17:13Z embargo: 2020-05-02 file_id: '6373' file_name: IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf file_size: 12597663 relation: main_file - access_level: closed checksum: 2eac954de1c8bbf7e6fb35ed0221ae8c content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cigler date_created: 2019-05-03T11:54:54Z date_updated: 2020-07-14T12:47:28Z embargo_to: open_access file_id: '6374' file_name: IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx file_size: 34644426 relation: source_file file_date_updated: 2021-02-11T11:17:13Z has_accepted_license: '1' keyword: - gene regulation - biophysics - transcription factor binding - bacteria language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '152' project: - _id: 251EE76E-B435-11E9-9278-68D0E5697425 grant_number: '24573' name: Design principles underlying genetic switch architecture (DOC Fellowship) publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '67' relation: part_of_dissertation status: public - id: '5585' relation: popular_science status: public status: public supervisor: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 title: On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '49' abstract: - lang: eng text: Nowadays, quantum computation is receiving more and more attention as an alternative to the classical way of computing. For realizing a quantum computer, different devices are investigated as potential quantum bits. In this thesis, the focus is on Ge hut wires, which turned out to be promising candidates for implementing hole spin quantum bits. The advantages of Ge as a material system are the low hyperfine interaction for holes and the strong spin orbit coupling, as well as the compatibility with the highly developed CMOS processes in industry. In addition, Ge can also be isotopically purified which is expected to boost the spin coherence times. The strong spin orbit interaction for holes in Ge on the one hand enables the full electrical control of the quantum bit and on the other hand should allow short spin manipulation times. Starting with a bare Si wafer, this work covers the entire process reaching from growth over the fabrication and characterization of hut wire devices up to the demonstration of hole spin resonance. From experiments with single quantum dots, a large g-factor anisotropy between the in-plane and the out-of-plane direction was found. A comparison to a theoretical model unveiled the heavy-hole character of the lowest energy states. The second part of the thesis addresses double quantum dot devices, which were realized by adding two gate electrodes to a hut wire. In such devices, Pauli spin blockade was observed, which can serve as a read-out mechanism for spin quantum bits. Applying oscillating electric fields in spin blockade allowed the demonstration of continuous spin rotations and the extraction of a lower bound for the spin dephasing time. Despite the strong spin orbit coupling in Ge, the obtained value for the dephasing time is comparable to what has been recently reported for holes in Si. All in all, the presented results point out the high potential of Ge hut wires as a platform for long-lived, fast and fully electrically tunable hole spin quantum bits. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hannes full_name: Watzinger, Hannes id: 35DF8E50-F248-11E8-B48F-1D18A9856A87 last_name: Watzinger citation: ama: Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:10.15479/AT:ISTA:th_1033 apa: Watzinger, H. (2018). Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1033 chicago: Watzinger, Hannes. “Ge Hut Wires - from Growth to Hole Spin Resonance.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1033. ieee: H. Watzinger, “Ge hut wires - from growth to hole spin resonance,” Institute of Science and Technology Austria, 2018. ista: Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria. mla: Watzinger, Hannes. Ge Hut Wires - from Growth to Hole Spin Resonance. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1033. short: H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:21Z date_published: 2018-07-30T00:00:00Z date_updated: 2023-09-07T12:27:43Z day: '30' ddc: - '530' degree_awarded: PhD department: - _id: GeKa doi: 10.15479/AT:ISTA:th_1033 file: - access_level: open_access checksum: b653b5216251f938ddbeafd1de88667c content_type: application/pdf creator: dernst date_created: 2019-04-09T07:13:28Z date_updated: 2020-07-14T12:46:35Z file_id: '6249' file_name: 2018_Thesis_Watzinger.pdf file_size: 85539748 relation: main_file - access_level: closed checksum: 39bcf8de7ac5b1bb516b11ce2f966785 content_type: application/zip creator: dernst date_created: 2019-04-09T07:13:27Z date_updated: 2020-07-14T12:46:35Z file_id: '6250' file_name: 2018_Thesis_Watzinger_source.zip file_size: 21830697 relation: source_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '07' oa: 1 oa_version: Published Version page: '77' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '8005' pubrep_id: '1033' status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: Ge hut wires - from growth to hole spin resonance 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '201' abstract: - lang: eng text: 'We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mabel full_name: Iglesias Ham, Mabel id: 41B58C0C-F248-11E8-B48F-1D18A9856A87 last_name: Iglesias Ham citation: ama: Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026 apa: Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1026 chicago: Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026. ieee: M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018. ista: Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria. mla: Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026. short: M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:45:10Z date_published: 2018-06-11T00:00:00Z date_updated: 2023-09-07T12:25:32Z day: '11' ddc: - '514' - '516' degree_awarded: PhD department: - _id: HeEd doi: 10.15479/AT:ISTA:th_1026 file: - access_level: closed checksum: dd699303623e96d1478a6ae07210dd05 content_type: application/zip creator: kschuh date_created: 2019-02-05T07:43:31Z date_updated: 2020-07-14T12:45:24Z file_id: '5918' file_name: IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip file_size: 11827713 relation: source_file - access_level: open_access checksum: ba163849a190d2b41d66fef0e4983294 content_type: application/pdf creator: kschuh date_created: 2019-02-05T07:43:45Z date_updated: 2020-07-14T12:45:24Z file_id: '5919' file_name: IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf file_size: 4783846 relation: main_file file_date_updated: 2020-07-14T12:45:24Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '171' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7712' pubrep_id: '1026' status: public supervisor: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 title: Multiple covers with balls type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '68' abstract: - lang: eng text: The most common assumption made in statistical learning theory is the assumption of the independent and identically distributed (i.i.d.) data. While being very convenient mathematically, it is often very clearly violated in practice. This disparity between the machine learning theory and applications underlies a growing demand in the development of algorithms that learn from dependent data and theory that can provide generalization guarantees similar to the independent situations. This thesis is dedicated to two variants of dependencies that can arise in practice. One is a dependence on the level of samples in a single learning task. Another dependency type arises in the multi-task setting when the tasks are dependent on each other even though the data for them can be i.i.d. In both cases we model the data (samples or tasks) as stochastic processes and introduce new algorithms for both settings that take into account and exploit the resulting dependencies. We prove the theoretical guarantees on the performance of the introduced algorithms under different evaluation criteria and, in addition, we compliment the theoretical study by the empirical one, where we evaluate some of the algorithms on two real world datasets to highlight their practical applicability. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Alexander full_name: Zimin, Alexander id: 37099E9C-F248-11E8-B48F-1D18A9856A87 last_name: Zimin citation: ama: Zimin A. Learning from dependent data. 2018. doi:10.15479/AT:ISTA:TH1048 apa: Zimin, A. (2018). Learning from dependent data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH1048 chicago: Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH1048. ieee: A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018. ista: Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria. mla: Zimin, Alexander. Learning from Dependent Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH1048. short: A. Zimin, Learning from Dependent Data, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:27Z date_published: 2018-09-01T00:00:00Z date_updated: 2023-09-07T12:29:07Z day: '01' ddc: - '004' - '519' degree_awarded: PhD department: - _id: ChLa doi: 10.15479/AT:ISTA:TH1048 ec_funded: 1 file: - access_level: open_access checksum: e849dd40a915e4d6c5572b51b517f098 content_type: application/pdf creator: dernst date_created: 2019-04-09T07:32:47Z date_updated: 2020-07-14T12:47:40Z file_id: '6253' file_name: 2018_Thesis_Zimin.pdf file_size: 1036137 relation: main_file - access_level: closed checksum: da092153cec55c97461bd53c45c5d139 content_type: application/zip creator: dernst date_created: 2019-04-09T07:32:47Z date_updated: 2020-07-14T12:47:40Z file_id: '6254' file_name: 2018_Thesis_Zimin_Source.zip file_size: 637490 relation: source_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '92' project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7986' pubrep_id: '1048' 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: Learning from dependent data type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '83' abstract: - lang: eng text: "A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Hamza M full_name: Abusalah, Hamza M id: 40297222-F248-11E8-B48F-1D18A9856A87 last_name: Abusalah citation: ama: Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:10.15479/AT:ISTA:TH_1046 apa: Abusalah, H. M. (2018). Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1046 chicago: Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1046. ieee: H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018. ista: Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria. mla: Abusalah, Hamza M. Proof Systems for Sustainable Decentralized Cryptocurrencies. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1046. short: H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:32Z date_published: 2018-09-05T00:00:00Z date_updated: 2023-09-07T12:30:23Z day: '05' ddc: - '004' degree_awarded: PhD department: - _id: KrPi doi: 10.15479/AT:ISTA:TH_1046 ec_funded: 1 file: - access_level: open_access checksum: c4b5f7d111755d1396787f41886fc674 content_type: application/pdf creator: dernst date_created: 2019-04-09T06:43:41Z date_updated: 2020-07-14T12:48:11Z file_id: '6245' file_name: 2018_Thesis_Abusalah.pdf file_size: 876241 relation: main_file - access_level: closed checksum: 0f382ac56b471c48fd907d63eb87dafe content_type: application/x-gzip creator: dernst date_created: 2019-04-09T06:43:41Z date_updated: 2020-07-14T12:48:11Z file_id: '6246' file_name: 2018_Thesis_Abusalah_source.tar.gz file_size: 2029190 relation: source_file file_date_updated: 2020-07-14T12:48:11Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '59' project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7971' pubrep_id: '1046' related_material: record: - id: '1229' relation: part_of_dissertation status: public - id: '1235' relation: part_of_dissertation status: public - id: '1236' relation: part_of_dissertation status: public - id: '559' relation: part_of_dissertation status: public status: public supervisor: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 title: Proof systems for sustainable decentralized cryptocurrencies type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '197' abstract: - lang: eng text: Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task. acknowledgement: I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Alexander full_name: Kolesnikov, Alexander id: 2D157DB6-F248-11E8-B48F-1D18A9856A87 last_name: Kolesnikov citation: ama: Kolesnikov A. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. 2018. doi:10.15479/AT:ISTA:th_1021 apa: Kolesnikov, A. (2018). Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1021 chicago: Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1021. ieee: A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images,” Institute of Science and Technology Austria, 2018. ista: Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria. mla: Kolesnikov, Alexander. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1021. short: A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:45:09Z date_published: 2018-05-25T00:00:00Z date_updated: 2023-09-07T12:51:46Z day: '25' ddc: - '004' degree_awarded: PhD department: - _id: ChLa doi: 10.15479/AT:ISTA:th_1021 ec_funded: 1 file: - access_level: open_access checksum: bc678e02468d8ebc39dc7267dfb0a1c4 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:57Z date_updated: 2020-07-14T12:45:22Z file_id: '5113' file_name: IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf file_size: 12918758 relation: main_file - access_level: closed checksum: bc66973b086da5a043f1162dcfb1fde4 content_type: application/zip creator: dernst date_created: 2019-04-05T09:34:49Z date_updated: 2020-07-14T12:45:22Z file_id: '6225' file_name: 2018_Thesis_Kolesnikov_source.zip file_size: 55973760 relation: source_file file_date_updated: 2020-07-14T12:45:22Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '113' project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7718' pubrep_id: '1021' 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: Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '200' abstract: - lang: eng text: This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Harald full_name: Ringbauer, Harald id: 417FCFF4-F248-11E8-B48F-1D18A9856A87 last_name: Ringbauer orcid: 0000-0002-4884-9682 citation: ama: Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:10.15479/AT:ISTA:th_963 apa: Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963 chicago: Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963. ieee: H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018. ista: Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria. mla: Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963. short: H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:45:10Z date_published: 2018-02-21T00:00:00Z date_updated: 2023-09-20T12:00:56Z day: '21' ddc: - '576' degree_awarded: PhD department: - _id: NiBa doi: 10.15479/AT:ISTA:th_963 file: - access_level: open_access checksum: 8cc534d2b528ae017acf80874cce48c9 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:55Z date_updated: 2020-07-14T12:45:23Z file_id: '5111' file_name: IST-2018-963-v1+1_thesis.pdf file_size: 5792935 relation: main_file - access_level: closed checksum: 6af18d7e5a7e2728ceda2f41ee24f628 content_type: application/zip creator: dernst date_created: 2019-04-05T09:30:12Z date_updated: 2020-07-14T12:45:23Z file_id: '6224' file_name: 2018_thesis_ringbauer_source.zip file_size: 113365 relation: source_file file_date_updated: 2020-07-14T12:45:23Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '02' oa: 1 oa_version: Published Version page: '146' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7713' pubrep_id: '963' related_material: record: - id: '563' relation: part_of_dissertation status: public - id: '1074' relation: part_of_dissertation status: public status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Inferring recent demography from spatial genetic structure 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: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '418' abstract: - lang: eng text: "The aim of this thesis was the development of new strategies for optical and optogenetic control of proliferative and pro-survival signaling, and characterizing them from the molecular mechanism up to cellular effects. These new light-based methods have unique features, such as red light as an activator, or the avoidance of gene delivery, which enable to overcome current limitations, such as light delivery to target tissues and feasibility as therapeutic approach. A special focus was placed on implementing these new light-based approaches in pancreatic β-cells, as β-cells are the key players in diabetes and especially their loss in number negatively affects disease progression. Currently no treatment options are available to compensate the lack of functional β-cells in diabetic patients.\r\nIn a first approach, red-light-activated growth factor receptors, in particular receptor tyrosine kinases were engineered and characterized. Receptor activation with light allows spatio-temporal control compared to ligand-based activation, and especially red light exhibits deeper tissue penetration than other wavelengths of the visible spectrum. Red-light-activated receptor tyrosine kinases robustly activated major growth factor related signaling pathways with a high temporal resolution. Moreover, the remote activation of the proliferative MAPK/Erk pathway by red-light-activated receptor tyrosine kinases in a pancreatic β-cell line was also achieved, through one centimeter thick mouse tissue. Although red-light-activated receptor tyrosine kinases are particularly attractive for applications in animal models due to the deep tissue penetration of red light, a drawback, especially with regard to translation into humans, is the requirement of gene therapy.\r\nIn a second approach an endogenous light-sensitive mechanism was identified and its potential to promote proliferative and pro-survival signals was explored, towards light-based tissue regeneration without the need for gene transfer. Blue-green light illumination was found to be sufficient for the activation of proliferation and survival promoting signaling pathways in primary pancreatic murine and human islets. Blue-green light also led to an increase in proliferation of primary islet cells, an effect which was shown to be mostly β-cell specific in human islets. Moreover, it was demonstrated that this approach of pancreatic β-cell expansion did not have any negative effect on the β-cell function, in particular on their insulin secretion capacity. In contrast, a trend for enhanced insulin secretion under high glucose conditions after illumination was detected. In order to unravel the detailed characteristics of this endogenous light-sensitive mechanism, the precise light requirements were determined. In addition, the expression of light sensing proteins, OPN3 and rhodopsin, was detected. The observed effects were found to be independent of handling effects such as temperature differences and cytochrome c oxidase dependent ATP increase, but they were found to be enhanced through the knockout of OPN3. The exact mechanism of how islets cells sense light and the identity of the photoreceptor remains unknown.\r\nSummarized two new light-based systems with unique features were established that enable the activation of proliferative and pro-survival signaling pathways. While red-light-activated receptor tyrosine kinases open a new avenue for optogenetics research, by allowing non-invasive control of signaling in vivo, the identified endogenous light-sensitive mechanism has the potential to be the basis of a gene therapy-free therapeutical approach for light-based β-cell expansion." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Eva full_name: Gschaider-Reichhart, Eva id: 3FEE232A-F248-11E8-B48F-1D18A9856A87 last_name: Gschaider-Reichhart orcid: 0000-0002-7218-7738 citation: ama: Gschaider-Reichhart E. Optical and optogenetic control of proliferation and survival . 2018. doi:10.15479/AT:ISTA:th_913 apa: Gschaider-Reichhart, E. (2018). Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_913 chicago: Gschaider-Reichhart, Eva. “Optical and Optogenetic Control of Proliferation and Survival .” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_913. ieee: E. Gschaider-Reichhart, “Optical and optogenetic control of proliferation and survival ,” Institute of Science and Technology Austria, 2018. ista: Gschaider-Reichhart E. 2018. Optical and optogenetic control of proliferation and survival . Institute of Science and Technology Austria. mla: Gschaider-Reichhart, Eva. Optical and Optogenetic Control of Proliferation and Survival . Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_913. short: E. Gschaider-Reichhart, Optical and Optogenetic Control of Proliferation and Survival , Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:46:22Z date_published: 2018-01-08T00:00:00Z date_updated: 2023-09-22T09:20:10Z day: '08' ddc: - '571' - '570' degree_awarded: PhD department: - _id: HaJa doi: 10.15479/AT:ISTA:th_913 file: - access_level: closed checksum: 697fa72ca36fb1b8ceabc133d58a73e5 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dernst date_created: 2019-04-05T09:28:03Z date_updated: 2020-07-14T12:46:24Z file_id: '6222' file_name: 2018_THESIS_Gschaider-Reichhart_source.docx file_size: 7012495 relation: source_file - access_level: open_access checksum: 58d7d1e9e58aeb7f061ab686b1d8a48c content_type: application/pdf creator: dernst date_created: 2019-04-05T09:28:03Z date_updated: 2020-07-14T12:46:24Z file_id: '6223' file_name: 2018_THESIS_Gschaider-Reichhart.pdf file_size: 6355280 relation: main_file file_date_updated: 2020-07-14T12:46:24Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '107' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7405' pubrep_id: '913' related_material: record: - id: '1441' relation: part_of_dissertation status: public - id: '1678' relation: part_of_dissertation status: public - id: '2084' relation: part_of_dissertation status: public - id: '1028' relation: part_of_dissertation status: public status: public supervisor: - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 title: 'Optical and optogenetic control of proliferation and survival ' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '52' abstract: - lang: eng text: In this thesis we will discuss systems of point interacting fermions, their stability and other spectral properties. Whereas for bosons a point interacting system is always unstable this ques- tion is more subtle for a gas of two species of fermions. In particular the answer depends on the mass ratio between these two species. Most of this work will be focused on the N + M model which consists of two species of fermions with N, M particles respectively which interact via point interactions. We will introduce this model using a formal limit and discuss the N + 1 system in more detail. In particular, we will show that for mass ratios above a critical one, which does not depend on the particle number, the N + 1 system is stable. In the context of this model we will prove rigorous versions of Tan relations which relate various quantities of the point-interacting model. By restricting the N + 1 system to a box we define a finite density model with point in- teractions. In the context of this system we will discuss the energy change when introducing a point-interacting impurity into a system of non-interacting fermions. We will see that this change in energy is bounded independently of the particle number and in particular the bound only depends on the density and the scattering length. As another special case of the N + M model we will show stability of the 2 + 2 model for mass ratios in an interval around one. Further we will investigate a different model of point interactions which was discussed before in the literature and which is, contrary to the N + M model, not given by a limiting procedure but is based on a Dirichlet form. We will show that this system behaves trivially in the thermodynamic limit, i.e. the free energy per particle is the same as the one of the non-interacting system. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Thomas full_name: Moser, Thomas id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87 last_name: Moser citation: ama: Moser T. Point interactions in systems of fermions. 2018. doi:10.15479/AT:ISTA:th_1043 apa: Moser, T. (2018). Point interactions in systems of fermions. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1043 chicago: Moser, Thomas. “Point Interactions in Systems of Fermions.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1043. ieee: T. Moser, “Point interactions in systems of fermions,” Institute of Science and Technology Austria, 2018. ista: Moser T. 2018. Point interactions in systems of fermions. Institute of Science and Technology Austria. mla: Moser, Thomas. Point Interactions in Systems of Fermions. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1043. short: T. Moser, Point Interactions in Systems of Fermions, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:22Z date_published: 2018-09-04T00:00:00Z date_updated: 2023-09-27T12:34:14Z day: '04' ddc: - '515' - '530' - '519' degree_awarded: PhD department: - _id: RoSe doi: 10.15479/AT:ISTA:th_1043 file: - access_level: open_access checksum: fbd8c747d148b468a21213b7cf175225 content_type: application/pdf creator: dernst date_created: 2019-04-09T07:45:38Z date_updated: 2020-07-14T12:46:37Z file_id: '6256' file_name: 2018_Thesis_Moser.pdf file_size: 851164 relation: main_file - access_level: closed checksum: c28e16ecfc1126d3ce324ec96493c01e content_type: application/zip creator: dernst date_created: 2019-04-09T07:45:38Z date_updated: 2020-07-14T12:46:37Z file_id: '6257' file_name: 2018_Thesis_Moser_Source.zip file_size: 1531516 relation: source_file file_date_updated: 2020-07-14T12:46:37Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '115' project: - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '8002' pubrep_id: '1043' related_material: record: - id: '5856' relation: part_of_dissertation status: public - id: '154' relation: part_of_dissertation status: public - id: '1198' relation: part_of_dissertation status: public - id: '741' relation: part_of_dissertation status: public status: public supervisor: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 title: Point interactions in systems of fermions type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '69' abstract: - lang: eng text: 'A qubit, a unit of quantum information, is essentially any quantum mechanical two-level system which can be coherently controlled. Still, to be used for computation, it has to fulfill criteria. Qubits, regardless of the system in which they are realized, suffer from decoherence. This leads to loss of the information stored in the qubit. The upper bound of the time scale on which decoherence happens is set by the spin relaxation time. In this thesis I studied a two-level system consisting of a Zeeman-split hole spin confined in a quantum dot formed in a Ge hut wire. Such Ge hut wires have emerged as a promising material system for the realization of spin qubits, due to the combination of two significant properties: long spin coherence time as expected for group IV semiconductors due to the low hyperfine interaction and a strong valence band spin-orbit coupling. Here, I present how to fabricate quantum dot devices suitable for electrical transport measurements. Coupled quantum dot devices allowed the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot. By integrating the charge sensor into a radio-frequency reflectometry setup, I performed for the first time single-shot readout measurements of hole spins and extracted the hole spin relaxation times in Ge hut wires.' alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lada full_name: Vukušić, Lada id: 31E9F056-F248-11E8-B48F-1D18A9856A87 last_name: Vukušić orcid: 0000-0003-2424-8636 citation: ama: Vukušić L. Charge sensing and spin relaxation times of holes in Ge hut wires. 2018. doi:10.15479/AT:ISTA:TH_1047 apa: Vukušić, L. (2018). Charge sensing and spin relaxation times of holes in Ge hut wires. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1047 chicago: Vukušić, Lada. “Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1047. ieee: L. Vukušić, “Charge sensing and spin relaxation times of holes in Ge hut wires,” Institute of Science and Technology Austria, 2018. ista: Vukušić L. 2018. Charge sensing and spin relaxation times of holes in Ge hut wires. Institute of Science and Technology Austria. mla: Vukušić, Lada. Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1047. short: L. Vukušić, Charge Sensing and Spin Relaxation Times of Holes in Ge Hut Wires, Institute of Science and Technology Austria, 2018. date_created: 2018-12-11T11:44:28Z date_published: 2018-09-01T00:00:00Z date_updated: 2023-09-26T15:50:22Z day: '01' ddc: - '530' - '600' degree_awarded: PhD department: - _id: GeKa - _id: GradSch doi: 10.15479/AT:ISTA:TH_1047 file: - access_level: open_access checksum: c570b656e30749cd65b1c7e13a9ce0a8 content_type: application/pdf creator: dernst date_created: 2019-04-09T07:00:40Z date_updated: 2020-07-14T12:47:44Z file_id: '6247' file_name: 2018_Thesis_Vukusic.pdf file_size: 28452385 relation: main_file - access_level: closed checksum: 7856771d9cd401fe0b311191076db6e1 content_type: application/zip creator: dernst date_created: 2019-04-09T07:00:40Z date_updated: 2020-07-14T12:47:44Z file_id: '6248' file_name: 2018_Thesis_Vukusic_source.zip file_size: 53058704 relation: source_file file_date_updated: 2020-07-14T12:47:44Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '103' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '7985' pubrep_id: '1047' related_material: record: - id: '23' relation: part_of_dissertation status: public - id: '840' relation: part_of_dissertation status: public status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: Charge sensing and spin relaxation times of holes in Ge hut wires 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ...