[{"page":"174","ec_funded":1,"file_date_updated":"2021-01-13T23:30:05Z","publisher":"Institute of Science and Technology Austria","_id":"7258","author":[{"last_name":"Scarselli","first_name":"Davide","full_name":"Scarselli, Davide","orcid":"0000-0001-5227-4271","id":"40315C30-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","article_processing_charge":"No","department":[{"_id":"BjHo"}],"date_created":"2020-01-12T16:07:26Z","title":"New approaches to reduce friction in turbulent pipe flow","alternative_title":["ISTA Thesis"],"ddc":["532"],"date_updated":"2023-09-15T12:20:08Z","citation":{"ista":"Scarselli D. 2020. New approaches to reduce friction in turbulent pipe flow. Institute of Science and Technology Austria.","mla":"Scarselli, Davide. <i>New Approaches to Reduce Friction in Turbulent Pipe Flow</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7258\">10.15479/AT:ISTA:7258</a>.","short":"D. Scarselli, New Approaches to Reduce Friction in Turbulent Pipe Flow, Institute of Science and Technology Austria, 2020.","ieee":"D. Scarselli, “New approaches to reduce friction in turbulent pipe flow,” Institute of Science and Technology Austria, 2020.","chicago":"Scarselli, Davide. “New Approaches to Reduce Friction in Turbulent Pipe Flow.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7258\">https://doi.org/10.15479/AT:ISTA:7258</a>.","ama":"Scarselli D. New approaches to reduce friction in turbulent pipe flow. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7258\">10.15479/AT:ISTA:7258</a>","apa":"Scarselli, D. (2020). <i>New approaches to reduce friction in turbulent pipe flow</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7258\">https://doi.org/10.15479/AT:ISTA:7258</a>"},"year":"2020","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7258","day":"13","abstract":[{"lang":"eng","text":"Many flows encountered in nature and applications are characterized by a chaotic motion known as turbulence. Turbulent flows generate intense friction with pipe walls and are responsible for considerable amounts of energy losses at world scale. The nature of turbulent friction and techniques aimed at reducing it have been subject of extensive research over the last century, but no definite answer has been found yet. In this thesis we show that in pipes at moderate turbulent Reynolds numbers friction is better described by the power law first introduced by Blasius and not by the Prandtl–von Kármán formula. At higher Reynolds numbers, large scale motions gradually become more important in the flow and can be related to the change in scaling of friction. Next, we present a series of new techniques that can relaminarize turbulence by suppressing a key mechanism that regenerates it at walls, the lift–up effect. In addition, we investigate the process of turbulence decay in several experiments and discuss the drag reduction potential. Finally, we examine the behavior of friction under pulsating conditions inspired by the human heart cycle and we show that under such circumstances turbulent friction can be reduced to produce energy savings."}],"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"None","project":[{"call_identifier":"FP7","_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","grant_number":"306589"},{"_id":"25104D44-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"737549","name":"Eliminating turbulence in oil pipelines"},{"name":"Experimental studies of the turbulence transition and transport processes in turbulent Taylor-Couette currents","grant_number":"HO 4393/1-2","_id":"25136C54-B435-11E9-9278-68D0E5697425"}],"month":"01","file":[{"checksum":"4df1ab24e9896635106adde5a54615bf","file_size":26640830,"embargo_to":"open_access","date_created":"2020-01-12T15:57:14Z","content_type":"application/zip","file_name":"2020_Scarselli_Thesis.zip","date_updated":"2021-01-13T23:30:05Z","relation":"source_file","access_level":"closed","creator":"dscarsel","file_id":"7259"},{"access_level":"open_access","relation":"main_file","creator":"dscarsel","file_id":"7260","file_size":8515844,"checksum":"48659ab98e3414293c7a721385c2fd1c","embargo":"2021-01-12","date_created":"2020-01-12T15:56:14Z","file_name":"2020_Scarselli_Thesis.pdf","content_type":"application/pdf","date_updated":"2021-01-13T23:30:05Z"}],"status":"public","related_material":{"record":[{"relation":"part_of_dissertation","id":"6228","status":"public"},{"status":"public","id":"6486","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"461"},{"status":"public","id":"422","relation":"part_of_dissertation"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2020-01-13T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","first_name":"Björn"}],"oa":1},{"file":[{"checksum":"1df9f8c530b443c0e63a3f2e4fde412e","file_size":76195184,"date_created":"2020-02-06T14:43:54Z","content_type":"application/pdf","file_name":"thesis_ist-final_noack.pdf","date_updated":"2020-07-14T12:47:58Z","relation":"main_file","access_level":"open_access","creator":"koelsboe","file_id":"7461"},{"file_name":"latex-files.zip","content_type":"application/x-zip-compressed","date_updated":"2020-07-14T12:47:58Z","file_size":122103715,"checksum":"7a52383c812b0be64d3826546509e5a4","date_created":"2020-02-06T14:52:45Z","creator":"koelsboe","file_id":"7462","description":"latex source files, figures","relation":"source_file","access_level":"closed"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"id":"6608","relation":"part_of_dissertation","status":"public"}]},"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert"}],"oa":1,"tmp":{"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)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"date_published":"2020-02-10T00:00:00Z","type":"dissertation","language":[{"iso":"eng"}],"keyword":["shape reconstruction","hole manipulation","ordered complexes","Alpha complex","Wrap complex","computational topology","Bregman geometry"],"oa_version":"Published Version","month":"02","has_accepted_license":"1","ddc":["514"],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7460","day":"10","abstract":[{"lang":"eng","text":"Many methods for the reconstruction of shapes from sets of points produce ordered simplicial complexes, which are collections of vertices, edges, triangles, and their higher-dimensional analogues, called simplices, in which every simplex gets assigned a real value measuring its size. This thesis studies ordered simplicial complexes, with a focus on their topology, which reflects the connectedness of the represented shapes and the presence of holes. We are interested both in understanding better the structure of these complexes, as well as in developing algorithms for applications.\r\n\r\nFor the Delaunay triangulation, the most popular measure for a simplex is the radius of the smallest empty circumsphere. Based on it, we revisit Alpha and Wrap complexes and experimentally determine their probabilistic properties for random data. Also, we prove the existence of tri-partitions, propose algorithms to open and close holes, and extend the concepts from Euclidean to Bregman geometries."}],"date_updated":"2023-09-07T13:15:30Z","citation":{"apa":"Ölsböck, K. (2020). <i>The hole system of triangulated shapes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>","ama":"Ölsböck K. The hole system of triangulated shapes. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>","chicago":"Ölsböck, Katharina. “The Hole System of Triangulated Shapes.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7460\">https://doi.org/10.15479/AT:ISTA:7460</a>.","ieee":"K. Ölsböck, “The hole system of triangulated shapes,” Institute of Science and Technology Austria, 2020.","short":"K. Ölsböck, The Hole System of Triangulated Shapes, Institute of Science and Technology Austria, 2020.","mla":"Ölsböck, Katharina. <i>The Hole System of Triangulated Shapes</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7460\">10.15479/AT:ISTA:7460</a>.","ista":"Ölsböck K. 2020. The hole system of triangulated shapes. Institute of Science and Technology Austria."},"year":"2020","publisher":"Institute of Science and Technology Austria","page":"155","file_date_updated":"2020-07-14T12:47:58Z","publication_status":"published","article_processing_charge":"No","department":[{"_id":"HeEd"},{"_id":"GradSch"}],"date_created":"2020-02-06T14:56:53Z","alternative_title":["ISTA Thesis"],"title":"The hole system of triangulated shapes","_id":"7460","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","author":[{"full_name":"Ölsböck, Katharina","orcid":"0000-0002-4672-8297","last_name":"Ölsböck","first_name":"Katharina","id":"4D4AA390-F248-11E8-B48F-1D18A9856A87"}]},{"author":[{"id":"30C4630A-F248-11E8-B48F-1D18A9856A87","full_name":"Mayer, Simon","first_name":"Simon","last_name":"Mayer"}],"_id":"7514","alternative_title":["ISTA Thesis"],"title":"The free energy of a dilute two-dimensional Bose gas","publication_status":"published","date_created":"2020-02-24T09:17:27Z","department":[{"_id":"RoSe"},{"_id":"GradSch"}],"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:59Z","page":"148","ec_funded":1,"publisher":"Institute of Science and Technology Austria","date_updated":"2023-09-07T13:12:42Z","citation":{"apa":"Mayer, S. (2020). <i>The free energy of a dilute two-dimensional Bose gas</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7514\">https://doi.org/10.15479/AT:ISTA:7514</a>","ama":"Mayer S. The free energy of a dilute two-dimensional Bose gas. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7514\">10.15479/AT:ISTA:7514</a>","ieee":"S. Mayer, “The free energy of a dilute two-dimensional Bose gas,” Institute of Science and Technology Austria, 2020.","chicago":"Mayer, Simon. “The Free Energy of a Dilute Two-Dimensional Bose Gas.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7514\">https://doi.org/10.15479/AT:ISTA:7514</a>.","mla":"Mayer, Simon. <i>The Free Energy of a Dilute Two-Dimensional Bose Gas</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7514\">10.15479/AT:ISTA:7514</a>.","short":"S. Mayer, The Free Energy of a Dilute Two-Dimensional Bose Gas, Institute of Science and Technology Austria, 2020.","ista":"Mayer S. 2020. The free energy of a dilute two-dimensional Bose gas. Institute of Science and Technology Austria."},"year":"2020","abstract":[{"text":"We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.\r\nWe motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks.","lang":"eng"}],"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7514","day":"24","ddc":["510"],"has_accepted_license":"1","month":"02","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"language":[{"iso":"eng"}],"date_published":"2020-02-24T00:00:00Z","type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"supervisor":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"id":"7524","relation":"part_of_dissertation","status":"public"}]},"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_created":"2020-02-24T09:15:06Z","checksum":"b4de7579ddc1dbdd44ff3f17c48395f6","file_size":1563429,"date_updated":"2020-07-14T12:47:59Z","file_name":"thesis.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"7515","creator":"dernst"},{"relation":"source_file","access_level":"closed","creator":"dernst","file_id":"7516","checksum":"ad7425867b52d7d9e72296e87bc9cb67","file_size":2028038,"date_created":"2020-02-24T09:15:16Z","file_name":"thesis_source.zip","content_type":"application/x-zip-compressed","date_updated":"2020-07-14T12:47:59Z"}]},{"publisher":"Institute of Science and Technology Austria","page":"79","file_date_updated":"2021-03-01T23:30:04Z","department":[{"_id":"RySh"}],"date_created":"2020-02-26T10:56:37Z","article_processing_charge":"No","publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","_id":"7525","author":[{"id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep","first_name":"Pradeep","last_name":"Bhandari"}],"ddc":["570"],"day":"28","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7525","abstract":[{"lang":"eng","text":"The medial habenula (MHb) is an evolutionary conserved epithalamic structure important for the modulation of emotional memory. It is involved in regulation of anxiety, compulsive behavior, addiction (nicotinic and opioid), sexual and feeding behavior. MHb receives inputs from septal regions and projects exclusively to the interpeduncular nucleus (IPN). Distinct sub-regions of the septum project to different subnuclei of MHb: the bed nucleus of anterior commissure projects to dorsal MHb and the triangular septum projects to ventral MHb. Furthermore, the dorsal and ventral MHb project to the lateral and rostral/central IPN, respectively. Importantly, these projections have unique features of prominent co-release of different neurotransmitters and requirement of a peculiar type of calcium channel for release. In general, synaptic neurotransmission requires an activity-dependent influx of Ca2+ into the presynaptic terminal through voltage-gated calcium channels. The calcium channel family most commonly involved in neurotransmitter release comprises three members, P/Q-, N- and R-type with Cav2.1, Cav2.2 and Cav2.3 subunits, respectively. In contrast to most CNS synapses that mainly express Cav2.1 and/or Cav2.2, MHb terminals in the IPN exclusively express Cav2.3. In other parts of the brain, such as the hippocampus, Cav2.3 is mostly located to postsynaptic elements. This unusual presynaptic location of Cav2.3 in the MHb-IPN pathway implies unique mechanisms of glutamate release in this pathway. One potential example of such uniqueness is the facilitation of release by GABAB receptor (GBR) activation. Presynaptic GBRs usually inhibit the release of neurotransmitters by inhibiting presynaptic calcium channels. MHb shows the highest expression levels of GBR in the brain. GBRs comprise two subunits, GABAB1 (GB1) and GABAB2 (GB2), and are associated with auxiliary subunits, called potassium channel tetramerization domain containing proteins (KCTD) 8, 12, 12b and 16. Among these four subunits, KCTD12b is exclusively expressed in ventral MHb, and KCTD8 shows the strongest expression in the whole MHb among other brain regions, indicating that KCTD8 and KCTD12b may be involved in the unique mechanisms of neurotransmitter release mediated by Cav2.3 and regulated by GBRs in this pathway. \r\nIn the present study, we first verified that neurotransmission in both dorsal and ventral MHb-IPN pathways is mainly mediated by Cav2.3 using a selective blocker of R-type channels, SNX-482. We next found that baclofen, a GBR agonist, has facilitatory effects on release from ventral MHb terminal in rostral IPN, whereas it has inhibitory effects on release from dorsal MHb terminals in lateral IPN, indicating that KCTD12b expressed exclusively in ventral MHb may have a role in the facilitatory effects of GBR activation. In a heterologous expression system using HEK cells, we found that KCTD8 and KCTD12b but not KCTD12 directly bind with Cav2.3. Pre-embedding immunogold electron microscopy data show that Cav2.3 and KCTD12b are distributed most densely in presynaptic active zone in IPN with KCTD12b being present only in rostral/central but not lateral IPN, whereas GABAB, KCTD8 and KCTD12 are distributed most densely in perisynaptic sites with KCTD12 present more frequently in postsynaptic elements and only in rostral/central IPN. In freeze-fracture replica labelling, Cav2.3, KCTD8 and KCTD12b are co-localized with each other in the same active zone indicating that they may form complexes regulating vesicle release in rostral IPN. \r\nOn electrophysiological studies of wild type (WT) mice, we found that paired-pulse ratio in rostral IPN of KCTD12b knock-out (KO) mice is lower than those of WT and KCTD8 KO mice. Consistent with this finding, in mean variance analysis, release probability in rostral IPN of KCTD12b KO mice is higher than that of WT and KCTD8 KO mice. Although paired-pulse ratios are not different between WT and KCTD8 KO mice, the mean variance analysis revealed significantly lower release probability in rostral IPN of KCTD8 KO than WT mice. These results demonstrate bidirectional regulation of Cav2.3-mediated release by KCTD8 and KCTD12b without GBR activation in rostral IPN. Finally, we examined the baclofen effects in rostral IPN of KCTD8 and KCTD12b KO mice, and found the facilitation of release remained in both KO mice, indicating that the peculiar effects of the GBR activation in this pathway do not depend on the selective expression of these KCTD subunits in ventral MHb. However, we found that presynaptic potentiation of evoked EPSC amplitude by baclofen falls to baseline after washout faster in KCTD12b KO mice than WT, KCTD8 KO and KCTD8/12b double KO mice. This result indicates that KCTD12b is involved in sustained potentiation of vesicle release by GBR activation, whereas KCTD8 is involved in its termination in the absence of KCTD12b. Consistent with these functional findings, replica labelling revealed an increase in density of KCTD8, but not Cav2.3 or GBR at active zone in rostral IPN of KCTD12b KO mice compared with that of WT mice, suggesting that increased association of KCTD8 with Cav2.3 facilitates the release probability and termination of the GBR effect in the absence of KCTD12b.\r\nIn summary, our study provided new insights into the physiological roles of presynaptic Cav2.3, GBRs and their auxiliary subunits KCTDs at an evolutionary conserved neuronal circuit. Future studies will be required to identify the exact molecular mechanism underlying the GBR-mediated presynaptic potentiation on ventral MHb terminals. It remains to be determined whether the prominent presence of presynaptic KCTDs at active zone could exert similar neuromodulatory functions in different pathways of the brain.\r\n"}],"citation":{"chicago":"Bhandari, Pradeep. “Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7525\">https://doi.org/10.15479/AT:ISTA:7525</a>.","ieee":"P. Bhandari, “Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway,” Institute of Science and Technology Austria, 2020.","ama":"Bhandari P. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7525\">10.15479/AT:ISTA:7525</a>","apa":"Bhandari, P. (2020). <i>Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7525\">https://doi.org/10.15479/AT:ISTA:7525</a>","ista":"Bhandari P. 2020. Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway. Institute of Science and Technology Austria.","mla":"Bhandari, Pradeep. <i>Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7525\">10.15479/AT:ISTA:7525</a>.","short":"P. Bhandari, Localization and Functional Role of Cav2.3 in the Medial Habenula to Interpeduncular Nucleus Pathway, Institute of Science and Technology Austria, 2020."},"year":"2020","date_updated":"2023-09-07T13:20:03Z","keyword":["Cav2.3","medial habenula (MHb)","interpeduncular nucleus (IPN)"],"language":[{"iso":"eng"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"02","has_accepted_license":"1","file":[{"creator":"pbhandari","file_id":"7538","access_level":"open_access","relation":"main_file","file_name":"Pradeep Bhandari Thesis.pdf","content_type":"application/pdf","date_updated":"2021-03-01T23:30:04Z","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","file_size":9646346,"checksum":"4589234fdb12b4ad72273b311723a7b4","date_created":"2020-02-28T08:37:53Z","embargo":"2021-02-28"},{"date_created":"2020-02-28T08:47:14Z","file_size":35252164,"checksum":"aa79490553ca0a5c9b6fbcd152e93928","title":"Localization and functional role of Cav2.3 in the medial habenula to interpeduncular nucleus pathway","embargo_to":"open_access","date_updated":"2021-03-01T23:30:04Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Pradeep Bhandari Thesis.docx","relation":"source_file","access_level":"closed","file_id":"7539","creator":"pbhandari"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto"}],"type":"dissertation","date_published":"2020-02-28T00:00:00Z"},{"_id":"7629","author":[{"id":"35C79D68-F248-11E8-B48F-1D18A9856A87","last_name":"Forkert","first_name":"Dominik L","full_name":"Forkert, Dominik L"}],"publication_status":"published","article_processing_charge":"No","date_created":"2020-04-02T06:40:23Z","department":[{"_id":"JaMa"}],"alternative_title":["ISTA Thesis"],"title":"Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains","page":"154","ec_funded":1,"file_date_updated":"2020-07-14T12:48:01Z","publisher":"Institute of Science and Technology Austria","date_updated":"2023-09-07T13:03:12Z","year":"2020","citation":{"ista":"Forkert DL. 2020. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. Institute of Science and Technology Austria.","short":"D.L. Forkert, Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains, Institute of Science and Technology Austria, 2020.","mla":"Forkert, Dominik L. <i>Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7629\">10.15479/AT:ISTA:7629</a>.","chicago":"Forkert, Dominik L. “Gradient Flows in Spaces of Probability Measures for Finite-Volume Schemes, Metric Graphs and Non-Reversible Markov Chains.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7629\">https://doi.org/10.15479/AT:ISTA:7629</a>.","ieee":"D. L. Forkert, “Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains,” Institute of Science and Technology Austria, 2020.","apa":"Forkert, D. L. (2020). <i>Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7629\">https://doi.org/10.15479/AT:ISTA:7629</a>","ama":"Forkert DL. Gradient flows in spaces of probability measures for finite-volume schemes, metric graphs and non-reversible Markov chains. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7629\">10.15479/AT:ISTA:7629</a>"},"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7629","day":"31","abstract":[{"text":"This thesis is based on three main topics: In the first part, we study convergence of discrete gradient flow structures associated with regular finite-volume discretisations of Fokker-Planck equations. We show evolutionary I convergence of the discrete gradient flows to the L2-Wasserstein gradient flow corresponding to the solution of a Fokker-Planck\r\nequation in arbitrary dimension d >= 1. Along the argument, we prove Mosco- and I-convergence results for discrete energy functionals, which are of independent interest for convergence of equivalent gradient flow structures in Hilbert spaces.\r\nThe second part investigates L2-Wasserstein flows on metric graph. The starting point is a Benamou-Brenier formula for the L2-Wasserstein distance, which is proved via a regularisation scheme for solutions of the continuity equation, adapted to the peculiar geometric structure of metric graphs. Based on those results, we show that the L2-Wasserstein space over a metric graph admits a gradient flow which may be identified as a solution of a Fokker-Planck equation.\r\nIn the third part, we focus again on the discrete gradient flows, already encountered in the first part. We propose a variational structure which extends the gradient flow structure to Markov chains violating the detailed-balance conditions. Using this structure, we characterise contraction estimates for the discrete heat flow in terms of convexity of\r\ncorresponding path-dependent energy functionals. In addition, we use this approach to derive several functional inequalities for said functionals.","lang":"eng"}],"ddc":["510"],"has_accepted_license":"1","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117"}],"month":"03","language":[{"iso":"eng"}],"date_published":"2020-03-31T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"file":[{"access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"7657","checksum":"c814a1a6195269ca6fe48b0dca45ae8a","file_size":3297129,"date_created":"2020-04-14T10:47:59Z","file_name":"Thesis_Forkert_PDFA.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:48:01Z"},{"file_id":"7658","creator":"dernst","relation":"source_file","access_level":"closed","date_updated":"2020-07-14T12:48:01Z","content_type":"application/x-zip-compressed","file_name":"Thesis_Forkert_source.zip","date_created":"2020-04-14T10:47:59Z","file_size":1063908,"checksum":"ceafb53f923d1b5bdf14b2b0f22e4a81"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"language":[{"iso":"eng"}],"oa_version":"Published Version","month":"08","has_accepted_license":"1","file":[{"creator":"szhechev","file_id":"6771","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Stephan_Zhechev_thesis.pdf","date_updated":"2020-07-14T12:47:37Z","file_size":1464227,"checksum":"3231e7cbfca3b5687366f84f0a57a0c0","date_created":"2019-08-07T13:02:50Z"},{"date_updated":"2020-07-14T12:47:37Z","file_name":"Stephan_Zhechev_thesis.tex","content_type":"application/octet-stream","date_created":"2019-08-07T13:03:22Z","file_size":303988,"checksum":"85d65eb27b4377a9e332ee37a70f08b6","file_id":"6772","creator":"szhechev","access_level":"closed","relation":"source_file"},{"file_name":"supplementary_material.zip","content_type":"application/zip","date_updated":"2020-07-14T12:47:37Z","file_size":1087004,"checksum":"86b374d264ca2dd53e712728e253ee75","date_created":"2019-08-07T13:03:34Z","creator":"szhechev","file_id":"6773","relation":"supplementary_material","access_level":"closed"}],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6774"}]},"publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","first_name":"Uli","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"dissertation","date_published":"2019-08-08T00:00:00Z","publisher":"Institute of Science and Technology Austria","page":"104","file_date_updated":"2020-07-14T12:47:37Z","department":[{"_id":"UlWa"}],"article_processing_charge":"No","date_created":"2019-07-26T11:14:34Z","publication_status":"published","title":"Algorithmic aspects of homotopy theory and embeddability","alternative_title":["ISTA Thesis"],"_id":"6681","author":[{"last_name":"Zhechev","first_name":"Stephan Y","full_name":"Zhechev, Stephan Y","id":"3AA52972-F248-11E8-B48F-1D18A9856A87"}],"ddc":["514"],"day":"08","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:6681","abstract":[{"lang":"eng","text":"The first part of the thesis considers the computational aspects of the homotopy groups πd(X) of a topological space X. It is well known that there is no algorithm to decide whether the fundamental group π1(X) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with π1(X) trivial), compute the higher homotopy group πd(X) for any given d ≥ 2.\r\nHowever, these algorithms come with a caveat: They compute the isomorphism type of πd(X), d ≥ 2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of πd(X). We present an algorithm that, given a simply connected space X, computes πd(X) and represents its elements as simplicial maps from suitable triangulations of the d-sphere Sd to X. For fixed d, the algorithm runs in time exponential in size(X), the number of simplices of X. Moreover, we prove that this is optimal: For every fixed d ≥ 2,\r\nwe construct a family of simply connected spaces X such that for any simplicial map representing a generator of πd(X), the size of the triangulation of S d on which the map is defined, is exponential in size(X).\r\nIn the second part of the thesis, we prove that the following question is algorithmically undecidable for d < ⌊3(k+1)/2⌋, k ≥ 5 and (k, d) ̸= (5, 7), which covers essentially everything outside the meta-stable range: Given a finite simplicial complex K of dimension k, decide whether there exists a piecewise-linear (i.e., linear on an arbitrarily fine subdivision of K) embedding f : K ↪→ Rd of K into a d-dimensional Euclidean space."}],"year":"2019","citation":{"chicago":"Zhechev, Stephan Y. “Algorithmic Aspects of Homotopy Theory and Embeddability.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6681\">https://doi.org/10.15479/AT:ISTA:6681</a>.","ieee":"S. Y. Zhechev, “Algorithmic aspects of homotopy theory and embeddability,” Institute of Science and Technology Austria, 2019.","ama":"Zhechev SY. Algorithmic aspects of homotopy theory and embeddability. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6681\">10.15479/AT:ISTA:6681</a>","apa":"Zhechev, S. Y. (2019). <i>Algorithmic aspects of homotopy theory and embeddability</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6681\">https://doi.org/10.15479/AT:ISTA:6681</a>","ista":"Zhechev SY. 2019. Algorithmic aspects of homotopy theory and embeddability. Institute of Science and Technology Austria.","mla":"Zhechev, Stephan Y. <i>Algorithmic Aspects of Homotopy Theory and Embeddability</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6681\">10.15479/AT:ISTA:6681</a>.","short":"S.Y. Zhechev, Algorithmic Aspects of Homotopy Theory and Embeddability, Institute of Science and Technology Austria, 2019."},"date_updated":"2023-09-07T13:10:36Z"},{"file_date_updated":"2020-09-15T22:30:05Z","page":"89","publisher":"Institute of Science and Technology Austria","author":[{"full_name":"Käfer, Karola","last_name":"Käfer","first_name":"Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"}],"_id":"6825","title":"The hippocampus and medial prefrontal cortex during flexible behavior","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","date_created":"2019-08-21T15:00:57Z","department":[{"_id":"JoCs"}],"publication_status":"published","ddc":["570"],"citation":{"mla":"Käfer, Karola. <i>The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6825\">10.15479/AT:ISTA:6825</a>.","short":"K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior, Institute of Science and Technology Austria, 2019.","ista":"Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria.","apa":"Käfer, K. (2019). <i>The hippocampus and medial prefrontal cortex during flexible behavior</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6825\">https://doi.org/10.15479/AT:ISTA:6825</a>","ama":"Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6825\">10.15479/AT:ISTA:6825</a>","chicago":"Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6825\">https://doi.org/10.15479/AT:ISTA:6825</a>.","ieee":"K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,” Institute of Science and Technology Austria, 2019."},"year":"2019","date_updated":"2023-09-07T13:01:42Z","abstract":[{"text":"The solving of complex tasks requires the functions of more than one brain area and their interaction. Whilst spatial navigation and memory is dependent on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC). To further examine the roles of the hippocampus and mPFC, we recorded their neural activity during a task that depends on both of these brain regions.\r\nWith tetrodes, we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC neurons in Long-Evans rats performing a rule-switching task on the plus-maze. The plus-maze task had a spatial component since it required navigation along one of the two start arms and at the maze center a choice between one of the two goal arms. Which goal contained a reward depended on the rule currently in place. After an uncued rule change the animal had to abandon the old strategy and switch to the new rule, testing cognitive flexibility. Investigating the coordination of activity between the HPC and mPFC allows determination during which task stages their interaction is required. Additionally, comparing neural activity patterns in these two brain regions allows delineation of the specialized functions of the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC in terms of oscillatory interactions, rule coding and replay.\r\nWe found that theta coherence between the HPC and mPFC is increased at the center and goals of the maze, both when the rule was stable or has changed. Similar results were found for locking of HPC and mPFC neurons to HPC theta oscillations. However, no differences in HPC-mPFC theta coordination were observed between the spatially- and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations was not modulated by\r\nmaze position or rule type. We found that the HPC coded for the two different rules with cofiring relationships between\r\ncell pairs. However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective firing in the mPFC generalized between the two start and two goal arms. With Bayesian positional decoding, we found that the mPFC reactivated non-local positions during awake immobility periods. Replay of these non-local positions could represent entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore, mPFC\r\ntrajectory-replay at the goal positively correlated with rule-switching performance. \r\nFinally, HPC and mPFC trajectory replay occurred independently of each other. These results show that the mPFC can replay ordered patterns of activity during awake immobility, possibly underlying its role in flexible behavior. ","lang":"eng"}],"day":"24","doi":"10.15479/AT:ISTA:6825","degree_awarded":"PhD","language":[{"iso":"eng"}],"has_accepted_license":"1","month":"08","oa_version":"Published Version","status":"public","related_material":{"record":[{"status":"public","id":"5949","relation":"part_of_dissertation"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"date_updated":"2020-09-06T22:30:03Z","file_name":"Thesis_Kaefer_PDFA.pdf","content_type":"application/pdf","date_created":"2019-09-03T08:07:13Z","embargo":"2020-09-05","checksum":"2664420e332a33338568f4f3bfc59287","file_size":3205202,"file_id":"6846","creator":"kkaefer","request_a_copy":0,"relation":"main_file","access_level":"open_access"},{"date_created":"2019-09-03T08:07:17Z","checksum":"9a154eab6f07aa590a3d2651dc0d926a","file_size":2506835,"embargo_to":"open_access","date_updated":"2020-09-15T22:30:05Z","file_name":"Thesis_Kaefer.zip","content_type":"application/zip","access_level":"closed","relation":"main_file","file_id":"6847","creator":"kkaefer"}],"type":"dissertation","date_published":"2019-08-24T00:00:00Z","oa":1,"supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"publication_identifier":{"issn":["2663-337X"]}},{"language":[{"iso":"eng"}],"month":"09","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"M-Shop"}],"oa_version":"Published Version","has_accepted_license":"1","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","id":"5914","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file":[{"file_id":"6865","creator":"drangel","relation":"source_file","access_level":"closed","date_updated":"2021-02-10T23:30:09Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Damaris_Rangel_source.docx","date_created":"2019-09-09T13:09:45Z","embargo_to":"open_access","file_size":18253100,"checksum":"244dc4f74dbfc94f414156092298831f"},{"content_type":"application/pdf","file_name":"Thesis_Damaris_Rangel_pdfa.pdf","date_updated":"2020-09-11T22:30:04Z","file_size":2160109,"checksum":"59c73be40eeaa1c4db24067270151555","embargo":"2020-09-10","date_created":"2019-09-09T13:09:52Z","creator":"drangel","file_id":"6866","access_level":"open_access","relation":"main_file","request_a_copy":0}],"oa":1,"supervisor":[{"last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["9783990780039"]},"type":"dissertation","date_published":"2019-09-09T00:00:00Z","publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-02-10T23:30:09Z","page":"97","title":"The role of CCK-interneurons in regulating hippocampal network dynamics","alternative_title":["ISTA Thesis"],"date_created":"2019-09-06T06:54:16Z","department":[{"_id":"JoCs"}],"article_processing_charge":"No","publication_status":"published","author":[{"id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","full_name":"Rangel Guerrero, Dámaris K","orcid":"0000-0002-8602-4374","last_name":"Rangel Guerrero","first_name":"Dámaris K"}],"_id":"6849","ddc":["570"],"abstract":[{"lang":"eng","text":"Brain function is mediated by complex dynamical interactions between excitatory and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons) are one of the least studied types, despite being suspected to play important roles in cognitive processes. We studied the network effects of optogenetic silencing of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states. The cell firing pattern in response to light pulses allowed us to classify the recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal cell and interneurons, and the inhibited interneurons corresponding to the CCK group. The light application, which inhibited the activity of CCK interneurons triggered wider changes in the firing dynamics of cells. We observed rate changes (i.e. remapping) of pyramidal cells during the exploration session in which the light was applied relative to the previous control session that was not restricted neither in time nor space to the light delivery. Also, the disinhibited pyramidal cells had higher increase in bursting than in single spike firing rate as a result of CCK silencing. In addition, the firing activity patterns during exploratory periods were more weakly reactivated in sleep for those periods in which CCK-interneuron were silenced than in the unaffected periods. Furthermore, light pulses during sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK neurons during exploration suppressed the reactivation of waking firing patterns in sleep and CCK interneuron activity was also required during sleep for the normal reactivation of waking patterns. These findings demonstrate the involvement of CCK cells in reactivation-related memory consolidation. An important part of our analysis was to test the relationship of the identified CCKinterneurons to brain oscillations. Our findings showed that these cells exhibited different oscillatory behaviour during anaesthesia and natural waking and sleep conditions. We showed that: 1) Contrary to the past studies performed under anaesthesia, the identified CCKinterneurons fired on the descending portion of the theta phase in waking exploration. 2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3) Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons increased around the peak activity of the sharp-wave ripple (SWR) events in natural sleep, which is congruent with new reports about their functional connectivity. We also found that light driven CCK-interneuron silencing altered the dynamics on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted their preferred theta phases when the light was applied, while interneurons responses were less consistent. 2) As a population, pyramidal cells negatively shifted their preferred activity during gamma oscillations, albeit we did not find gamma modulation differences related to the light application when pyramidal cells were subdivided into the disinhibited and unaffected groups. 3) During the peak of SWR events, all but the CCK-interneurons had a reduction in their relative firing rate change during the light application as compared to the change observed at SWR initiation. Finally, regarding to the place field activity of the recorded pyramidal neurons, we showed that the disinhibited pyramidal cells had reduced place field similarity, coherence and spatial information, but only during the light application. The mechanisms behind such observed behaviours might involve eCB signalling and plastic changes in CCK-interneuron synapses. In conclusion, the observed changes related to the light-mediated silencing of CCKinterneurons have unravelled characteristics of this interneuron subpopulation that might change the understanding not only of their particular network interactions, but also of the current theories about the emergence of certain cognitive processes such as place coding needed for navigation or hippocampus-dependent memory consolidation. "}],"day":"09","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:6849","citation":{"ama":"Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal network dynamics. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6849\">10.15479/AT:ISTA:6849</a>","apa":"Rangel Guerrero, D. K. (2019). <i>The role of CCK-interneurons in regulating hippocampal network dynamics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6849\">https://doi.org/10.15479/AT:ISTA:6849</a>","chicago":"Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6849\">https://doi.org/10.15479/AT:ISTA:6849</a>.","ieee":"D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal network dynamics,” Institute of Science and Technology Austria, 2019.","short":"D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics, Institute of Science and Technology Austria, 2019.","mla":"Rangel Guerrero, Dámaris K. <i>The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6849\">10.15479/AT:ISTA:6849</a>.","ista":"Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria."},"year":"2019","date_updated":"2023-09-19T10:01:12Z"},{"date_updated":"2023-09-13T08:50:57Z","citation":{"short":"F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019.","mla":"Assen, Frank P. <i>Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6947\">10.15479/AT:ISTA:6947</a>.","ista":"Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria.","apa":"Assen, F. P. (2019). <i>Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6947\">https://doi.org/10.15479/AT:ISTA:6947</a>","ama":"Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6947\">10.15479/AT:ISTA:6947</a>","ieee":"F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019.","chicago":"Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6947\">https://doi.org/10.15479/AT:ISTA:6947</a>."},"year":"2019","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:6947","day":"9","abstract":[{"text":"Lymph nodes  are es s ential organs  of the immune  s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular  cells (FRCs) are  the  main  stromal  cells and  form  a sponge-like extracellular matrix network,   called  conduits ,  which  they   thems elves   enwrap   and  contract.  Lymph,  containing  s oluble  antigens ,  arrive in  lymph  nodes  via afferent lymphatic  vessels that  connect  to  the  s ubcaps ular  s inus   and  conduit  network.  According  to  the  current  paradigm,  the  conduit  network   dis tributes   afferent  lymph  through   lymph  nodes   and  thus   provides   acces s   for  immune  cells to lymph-borne  antigens. An  elas tic  caps ule  s urrounds   the  organ  and  confines   the immune  cells and  FRC  network.   Lymph   nodes   are  completely  packed  with  lymphocytes   and  lymphocyte  numbers  directly  dictates  the size  of  the  organ.  Although  lymphocytes   cons tantly  enter  and  leave  the  lymph  node,  its   s ize  remains   remarkedly   s table  under  homeostatic conditions. It is only partly known  how the cellularity and s ize of the lymph node is regulated and  how  the  lymph  node  is able to swell in inflammation.  The role of the FRC network   in  lymph  node   s welling  and  trans fer  of  fluids   are  inves tigated in  this   thes is.  Furthermore,   we  s tudied  what  trafficking  routes   are  us ed  by  cancer  cells   in  lymph  nodes   to  form  distal metastases.We examined the role of a mechanical feedback in regulation of lymph  node swelling. Using parallel plate compression  and UV-las er  cutting  experiments   we  dis s ected  the  mechanical  force dynamics  of the whole lymph  node, and individually for FRCs  and the  caps ule. Physical forces   generated  by  packed  lymphocytes   directly  affect  the  tens ion  on  the  FRC  network  and  capsule,  which  increases  its  resistance  to   swelling.  This  implies  a  feedback  mechanism  between   tis s ue   pres s ure   and   ability   of   lymphocytes    to   enter   the   organ.   Following   inflammation,  the  lymph  node  swells ∼10 fold in two weeks . Yet, what  is  the role  for tens ion on  the  FRC  network   and  caps ule,  and  how  are  lymphocytes   able  to  enter  in  conditions  that resist swelling remain open ques tions . We s how that tens ion on the FRC network is  important to  limit  the  swelling  rate  of  the  organ  so  that  the  FRC  network  can  grow  in  a  coordinated  fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates  and a dis organized FRC network  in the inflamed lymph  node. Growth  of the FRC network  in  turn  is   expected  to  releas e  tens ion  on  thes e  s tructures   and  lowers   the  res is tance  to  swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of  swelling coincides   with  a  thickening  of  the  caps ule,  which  forms   a  thick  res is tant  band  around  the organ and lowers  tens ion on the FRC network  to form a new force equilibrium.The  FRC  and  conduit   network   are  further   believed  to  be  a  privileged  s ite  of  s oluble  information  within  the  lymph  node,  although  many  details   remain  uns olved.  We  s how  by  3D  ultra-recons truction   that  FRCs   and  antigen  pres enting  cells   cover  the  s urface  of  conduit  s ys tem for more  than 99% and we dis cus s  the implications  for s oluble information  exchangeat the conduit level.Finally, there  is an ongoing debate in the cancer field whether and how cancer cells  in lymph nodes   s eed  dis tal  metas tas es .  We  s how  that  cancer  cells   infus ed  into  the  lymph  node  can  utilize trafficking routes of immune  cells and  rapidly  migrate  to  blood  vessels. Once  in  the  blood circulation,  these cells are able to form  metastases in distal tissues.","lang":"eng"}],"ddc":["570"],"_id":"6947","author":[{"last_name":"Assen","first_name":"Frank P","full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","article_processing_charge":"No","department":[{"_id":"MiSi"}],"date_created":"2019-10-14T16:54:52Z","alternative_title":["ISTA Thesis"],"title":"Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking","page":"142","file_date_updated":"2020-11-07T23:30:03Z","publisher":"Institute of Science and Technology Austria","date_published":"2019-10-09T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"file":[{"creator":"fassen","file_id":"6990","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"PhDthesis_FrankAssen_revised2.docx","date_updated":"2020-11-07T23:30:03Z","embargo_to":"open_access","file_size":214172667,"checksum":"53a739752a500f84d0f8ec953cbbd0b6","date_created":"2019-11-06T12:30:02Z"},{"creator":"fassen","file_id":"6991","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"PhDthesis_FrankAssen_revised2.pdf","date_updated":"2020-11-07T23:30:03Z","file_size":83637532,"checksum":"8c156b65d9347bb599623a4b09f15d15","embargo":"2020-11-06","date_created":"2019-11-06T12:30:57Z"}],"status":"public","related_material":{"record":[{"status":"public","id":"664","relation":"part_of_dissertation"},{"status":"public","id":"402","relation":"part_of_dissertation"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"oa_version":"Published Version","month":"10","language":[{"iso":"eng"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","id":"6266","relation":"old_edition"}]},"status":"public","file":[{"creator":"dernst","file_id":"7133","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.docx","date_updated":"2020-07-14T12:47:50Z","file_size":5054633,"checksum":"34d0fe0f6e0af97b5937205a3e350423","date_created":"2019-11-27T09:06:10Z"},{"date_created":"2019-11-27T09:06:10Z","file_size":3231837,"checksum":"140dfb5e3df7edca34f4b6fcc55d876f","date_updated":"2020-07-14T12:47:50Z","content_type":"application/pdf","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.pdf","access_level":"open_access","relation":"main_file","file_id":"7134","creator":"dernst"}],"supervisor":[{"last_name":"Janovjak","first_name":"Harald L","full_name":"Janovjak, Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"date_published":"2019-06-27T00:00:00Z","type":"dissertation","language":[{"iso":"eng"}],"month":"06","oa_version":"Published Version","has_accepted_license":"1","ddc":["571","573"],"abstract":[{"lang":"eng","text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta.\r\nSynthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing."}],"doi":"10.15479/at:ista:7132","degree_awarded":"PhD","day":"27","date_updated":"2024-03-25T23:30:11Z","citation":{"apa":"Mckenzie, C. (2019). <i>Design and characterization of methods and biological components to realize synthetic neurotransmission</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:7132\">https://doi.org/10.15479/at:ista:7132</a>","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission. 2019. doi:<a href=\"https://doi.org/10.15479/at:ista:7132\">10.15479/at:ista:7132</a>","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/at:ista:7132\">https://doi.org/10.15479/at:ista:7132</a>.","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission,” Institute of Science and Technology Austria, 2019.","mla":"Mckenzie, Catherine. <i>Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/at:ista:7132\">10.15479/at:ista:7132</a>.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission, Institute of Science and Technology Austria, 2019.","ista":"Mckenzie C. 2019. Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria."},"year":"2019","publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:47:50Z","page":"95","alternative_title":["ISTA Thesis"],"title":"Design and characterization of methods and biological components to realize synthetic neurotransmission","publication_status":"published","department":[{"_id":"HaJa"}],"article_processing_charge":"No","date_created":"2019-11-27T09:07:14Z","author":[{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","first_name":"Catherine","last_name":"Mckenzie","full_name":"Mckenzie, Catherine"}],"_id":"7132"},{"page":"107","file_date_updated":"2020-07-14T12:47:52Z","publisher":"Institute of Science and Technology Austria","_id":"7186","author":[{"full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226","last_name":"Schwayer","first_name":"Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2019-12-16T14:26:14Z","article_processing_charge":"No","department":[{"_id":"CaHe"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow","ddc":["570"],"citation":{"apa":"Schwayer, C. (2019). <i>Mechanosensation of tight junctions depends on ZO-1 phase separation and flow</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7186\">https://doi.org/10.15479/AT:ISTA:7186</a>","ama":"Schwayer C. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7186\">10.15479/AT:ISTA:7186</a>","ieee":"C. Schwayer, “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Institute of Science and Technology Austria, 2019.","chicago":"Schwayer, Cornelia. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:7186\">https://doi.org/10.15479/AT:ISTA:7186</a>.","mla":"Schwayer, Cornelia. <i>Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7186\">10.15479/AT:ISTA:7186</a>.","short":"C. Schwayer, Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow, Institute of Science and Technology Austria, 2019.","ista":"Schwayer C. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Institute of Science and Technology Austria."},"year":"2019","date_updated":"2023-09-07T12:56:42Z","day":"16","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:7186","abstract":[{"text":"Tissue morphogenesis in developmental or physiological processes is regulated by molecular\r\nand mechanical signals. While the molecular signaling cascades are increasingly well\r\ndescribed, the mechanical signals affecting tissue shape changes have only recently been\r\nstudied in greater detail. To gain more insight into the mechanochemical and biophysical\r\nbasis of an epithelial spreading process (epiboly) in early zebrafish development, we studied\r\ncell-cell junction formation and actomyosin network dynamics at the boundary between\r\nsurface layer epithelial cells (EVL) and the yolk syncytial layer (YSL). During zebrafish epiboly,\r\nthe cell mass sitting on top of the yolk cell spreads to engulf the yolk cell by the end of\r\ngastrulation. It has been previously shown that an actomyosin ring residing within the YSL\r\npulls on the EVL tissue through a cable-constriction and a flow-friction motor, thereby\r\ndragging the tissue vegetal wards. Pulling forces are likely transmitted from the YSL\r\nactomyosin ring to EVL cells; however, the nature and formation of the junctional structure\r\nmediating this process has not been well described so far. Therefore, our main aim was to\r\ndetermine the nature, dynamics and potential function of the EVL-YSL junction during this\r\nepithelial tissue spreading. Specifically, we show that the EVL-YSL junction is a\r\nmechanosensitive structure, predominantly made of tight junction (TJ) proteins. The process\r\nof TJ mechanosensation depends on the retrograde flow of non-junctional, phase-separated\r\nZonula Occludens-1 (ZO-1) protein clusters towards the EVL-YSL boundary. Interestingly, we\r\ncould demonstrate that ZO-1 is present in a non-junctional pool on the surface of the yolk\r\ncell, and ZO-1 undergoes a phase separation process that likely renders the protein\r\nresponsive to flows. These flows are directed towards the junction and mediate proper\r\ntension-dependent recruitment of ZO-1. Upon reaching the EVL-YSL junction ZO-1 gets\r\nincorporated into the junctional pool mediated through its direct actin-binding domain.\r\nWhen the non-junctional pool and/or ZO-1 direct actin binding is absent, TJs fail in their\r\nproper mechanosensitive responses resulting in slower tissue spreading. We could further\r\ndemonstrate that depletion of ZO proteins within the YSL results in diminished actomyosin\r\nring formation. This suggests that a mechanochemical feedback loop is at work during\r\nzebrafish epiboly: ZO proteins help in proper actomyosin ring formation and actomyosin\r\ncontractility and flows positively influence ZO-1 junctional recruitment. Finally, such a\r\nmesoscale polarization process mediated through the flow of phase-separated protein\r\nclusters might have implications for other processes such as immunological synapse\r\nformation, C. elegans zygote polarization and wound healing.","lang":"eng"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"SSU"}],"oa_version":"Published Version","month":"12","file":[{"creator":"cschwayer","file_id":"7194","relation":"source_file","access_level":"closed","file_name":"DocumentSourceFiles.zip","content_type":"application/zip","date_updated":"2020-07-14T12:47:52Z","checksum":"585583c1c875c5d9525703a539668a7c","file_size":19431292,"date_created":"2019-12-19T15:18:11Z"},{"date_updated":"2020-07-14T12:47:52Z","file_name":"Thesis_CS_final.pdf","content_type":"application/pdf","date_created":"2019-12-19T15:19:21Z","file_size":19226428,"checksum":"9b9b24351514948d27cec659e632e2cd","file_id":"7195","creator":"cschwayer","access_level":"open_access","relation":"main_file"}],"related_material":{"record":[{"status":"public","id":"1096","relation":"dissertation_contains"},{"status":"public","id":"7001","relation":"part_of_dissertation"}]},"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","date_published":"2019-12-16T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}]},{"date_updated":"2025-05-28T11:57:05Z","year":"2019","citation":{"ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","mla":"Prizak, Roshan. <i>Coevolution of Transcription Factors and Their Binding Sites in Sequence Space</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/at:ista:th6071\">10.15479/at:ista:th6071</a>.","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019.","chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/at:ista:th6071\">https://doi.org/10.15479/at:ista:th6071</a>.","apa":"Prizak, R. (2019). <i>Coevolution of transcription factors and their binding sites in sequence space</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:th6071\">https://doi.org/10.15479/at:ista:th6071</a>","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:<a href=\"https://doi.org/10.15479/at:ista:th6071\">10.15479/at:ista:th6071</a>"},"abstract":[{"text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. ","lang":"eng"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:th6071","day":"11","ddc":["576"],"author":[{"full_name":"Prizak, Roshan","last_name":"Prizak","first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87"}],"_id":"6071","title":"Coevolution of transcription factors and their binding sites in sequence space","alternative_title":["ISTA Thesis"],"publication_status":"published","article_processing_charge":"No","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"date_created":"2019-03-06T16:16:10Z","file_date_updated":"2020-07-14T12:47:18Z","page":"189","publisher":"Institute of Science and Technology Austria","date_published":"2019-03-11T00:00:00Z","type":"dissertation","supervisor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"oa":1,"publication_identifier":{"issn":["2663-337X"]},"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"relation":"part_of_dissertation","id":"1358","status":"public"},{"id":"955","relation":"part_of_dissertation","status":"public"}]},"file":[{"checksum":"e60a72de35d270b31f1a23d50f224ec0","file_size":20995465,"date_created":"2019-03-06T16:05:07Z","content_type":"application/pdf","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","date_updated":"2020-07-14T12:47:18Z","relation":"main_file","access_level":"open_access","creator":"rprizak","file_id":"6072"},{"file_name":"thesis_v2_merge.zip","content_type":"application/zip","date_updated":"2020-07-14T12:47:18Z","title":"Latex files","file_size":85705272,"checksum":"67c2630333d05ebafef5f018863a8465","date_created":"2019-03-06T16:09:39Z","creator":"rprizak","file_id":"6073","access_level":"closed","relation":"source_file"}],"has_accepted_license":"1","month":"03","oa_version":"Published Version","project":[{"call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"}],"type":"dissertation","date_published":"2019-03-18T00:00:00Z","file":[{"relation":"source_file","access_level":"closed","creator":"dernst","file_id":"6180","file_size":7104482,"checksum":"6926f66f28079a81c4937e3764be00fc","date_created":"2019-03-28T08:53:52Z","file_name":"2019_Schroeder_Thesis.tar.gz","content_type":"application/x-gzip","date_updated":"2020-07-14T12:47:21Z"},{"date_updated":"2020-07-14T12:47:21Z","content_type":"application/pdf","file_name":"2019_Schroeder_Thesis.pdf","date_created":"2019-03-28T08:53:52Z","file_size":4228794,"checksum":"7d0ebb8d1207e89768cdd497a5bf80fb","file_id":"6181","creator":"dernst","relation":"main_file","access_level":"open_access"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"relation":"part_of_dissertation","id":"1144","status":"public"},{"relation":"part_of_dissertation","id":"6186","status":"public"},{"status":"public","id":"6185","relation":"part_of_dissertation"},{"id":"6182","relation":"part_of_dissertation","status":"public"},{"id":"1012","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6184"}]},"status":"public","project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"oa_version":"Published Version","month":"03","has_accepted_license":"1","language":[{"iso":"eng"}],"day":"18","doi":"10.15479/AT:ISTA:th6179","degree_awarded":"PhD","abstract":[{"lang":"eng","text":"In the first part of this thesis we consider large random matrices with arbitrary expectation and a general slowly decaying correlation among its entries. We prove universality of the local eigenvalue statistics and optimal local laws for the resolvent in the bulk and edge regime. The main novel tool is a systematic diagrammatic control of a multivariate cumulant expansion.\r\nIn the second part we consider Wigner-type matrices and show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are uni- versal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner- Dyson-Mehta universality conjecture for the last remaining universality type. Our analysis holds not only for exact cusps, but approximate cusps as well, where an ex- tended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp, and extend the fast relaxation to equilibrium of the Dyson Brow- nian motion to the cusp regime.\r\nIn the third and final part we explore the entrywise linear statistics of Wigner ma- trices and identify the fluctuations for a large class of test functions with little regularity. This enables us to study the rectangular Young diagram obtained from the interlacing eigenvalues of the random matrix and its minor, and we find that, despite having the same limit, the fluctuations differ from those of the algebraic Young tableaux equipped with the Plancharel measure."}],"citation":{"ama":"Schröder DJ. From Dyson to Pearcey: Universal statistics in random matrix theory. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th6179\">10.15479/AT:ISTA:th6179</a>","apa":"Schröder, D. J. (2019). <i>From Dyson to Pearcey: Universal statistics in random matrix theory</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th6179\">https://doi.org/10.15479/AT:ISTA:th6179</a>","chicago":"Schröder, Dominik J. “From Dyson to Pearcey: Universal Statistics in Random Matrix Theory.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:th6179\">https://doi.org/10.15479/AT:ISTA:th6179</a>.","ieee":"D. J. Schröder, “From Dyson to Pearcey: Universal statistics in random matrix theory,” Institute of Science and Technology Austria, 2019.","mla":"Schröder, Dominik J. <i>From Dyson to Pearcey: Universal Statistics in Random Matrix Theory</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th6179\">10.15479/AT:ISTA:th6179</a>.","short":"D.J. Schröder, From Dyson to Pearcey: Universal Statistics in Random Matrix Theory, Institute of Science and Technology Austria, 2019.","ista":"Schröder DJ. 2019. From Dyson to Pearcey: Universal statistics in random matrix theory. Institute of Science and Technology Austria."},"year":"2019","date_updated":"2024-02-22T14:34:33Z","ddc":["515","519"],"department":[{"_id":"LaEr"}],"article_processing_charge":"No","date_created":"2019-03-28T08:58:59Z","publication_status":"published","title":"From Dyson to Pearcey: Universal statistics in random matrix theory","alternative_title":["ISTA Thesis"],"_id":"6179","author":[{"id":"408ED176-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","first_name":"Dominik J","last_name":"Schröder"}],"publisher":"Institute of Science and Technology Austria","ec_funded":1,"page":"375","file_date_updated":"2020-07-14T12:47:21Z"},{"publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-02-11T23:30:15Z","page":"138","title":"Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ","alternative_title":["ISTA Thesis"],"department":[{"_id":"JiFr"}],"article_processing_charge":"No","date_created":"2019-04-09T14:37:06Z","publication_status":"published","author":[{"last_name":"Narasimhan","first_name":"Madhumitha","full_name":"Narasimhan, Madhumitha","orcid":"0000-0002-8600-0671","id":"44BF24D0-F248-11E8-B48F-1D18A9856A87"}],"_id":"6269","ddc":["575"],"abstract":[{"text":"Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking that is constantly regulated for mediating developmental and physiological responses. The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic trafficking in the whole multicellular organ systems of Arabidopsis. The first chapter of my thesis describes the search for new components involved in CME. Tandem affinity purification was conducted using CLC and its interacting partners were identified. Amongst the identified proteins were the Auxilin-likes1 and 2 (Axl1/2), putative uncoating factors, for which we made a full functional analysis. Over-expression of Axl1/2 causes extreme modifications in the dynamics of the machinery proteins and inhibition of endocytosis altogether. However the loss of function of the axl1/2 did not present any cellular or physiological phenotype, meaning Auxilin-likes do not form the major uncoating machinery. The second chapter of my thesis describes the establishment/utilisation of techniques to capture the dynamicity and the complexity of CME and post-endocytic trafficking. We have studied the development of endocytic pits at the PM – specifically, the mode of membrane remodeling during pit development and the role of actin in it, given plant cells possess high turgor pressure. Utilizing the improved z-resolution of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events at the plasma membrane; and using particle detection software, we quantitatively analysed all the endocytic trajectories in an unbiased way to obtain the endocytic rate of the system. This together with the direct analysis of cargo internalisation from the PM provided an estimate on the endocytic potential of the cell. We also developed a methodology for ultrastructural analysis of different populations of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed protoplasts. Structural analysis, together with the intensity profile of CCSs at the PM show that the mode of CCP development at the PM follows ‘Constant curvature model’; meaning that clathrin polymerisation energy is a major contributing factor of membrane remodeling. In addition, other analyses clearly show that actin is not required for membrane remodeling during invagination or any other step of CCP development, despite the prevalent high turgor pressure. However, actin is essential in orchestrating the post-endocytic trafficking of CCVs facilitating the EE formation. We also observed that the uncoating process post-endocytosis is not immediate; an alternative mechanism of uncoating – Sequential multi-step process – functions in the cell. Finally we also looked at one of the important physiological stimuli modulating the process – hormone, auxin. auxin has been known to influence CME before. We have made a detailed study on the concentration-time based effect of auxin on the machinery proteins, CCP development, and the specificity of cargoes endocytosed. To this end, we saw no general effect of auxin on CME at earlier time points. However, very low concentration of IAA, such as 50nM, accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory control with high specificity to PIN2 could be essential in modulating its polarity. ","lang":"eng"}],"day":"04","degree_awarded":"PhD","doi":"10.15479/at:ista:th1075","citation":{"ista":"Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria.","short":"M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants , Institute of Science and Technology Austria, 2019.","mla":"Narasimhan, Madhumitha. <i>Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants </i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/at:ista:th1075\">10.15479/at:ista:th1075</a>.","chicago":"Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants .” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/at:ista:th1075\">https://doi.org/10.15479/at:ista:th1075</a>.","ieee":"M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ,” Institute of Science and Technology Austria, 2019.","ama":"Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . 2019. doi:<a href=\"https://doi.org/10.15479/at:ista:th1075\">10.15479/at:ista:th1075</a>","apa":"Narasimhan, M. (2019). <i>Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:th1075\">https://doi.org/10.15479/at:ista:th1075</a>"},"year":"2019","date_updated":"2025-05-07T11:12:27Z","language":[{"iso":"eng"}],"month":"02","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"oa_version":"Published 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Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","date_published":"2019-02-04T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"ddc":["570"],"day":"30","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:6363","abstract":[{"lang":"eng","text":"Distinguishing  between  similar  experiences  is  achieved  by  the  brain  in  a  process called  pattern  separation.  In  the  hippocampus,  pattern  separation  reduces  the interference of memories and increases the storage capacity by decorrelating similar inputs  patterns  of  neuronal  activity  into  non-overlapping output  firing  patterns. Winners-take-all  (WTA)  mechanism  is  a  theoretical  model  for  pattern  separation  in which  a  \"winner\"  cell  suppresses  the  activity  of  the  neighboring  neurons  through feedback inhibition. However, if the network properties of the dentate gyrus support WTA as a biologically conceivable model remains unknown. Here, we showed that the connectivity rules of PV+interneurons and their synaptic properties are optimizedfor efficient pattern separation. We found using multiple whole-cell in vitrorecordings that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition, a form of  feedback  inhibition  in  which  a  GC  inhibits  other  GCs  but  not  itself  through  the activation of PV+interneurons. Thus, lateral inhibition between GC–PV+interneurons was ~10 times more abundant than recurrent connections. Furthermore, the GC–PV+interneuron  connectivity  was  more  spatially  confined  but  less  abundant  than  PV+interneurons–GC  connectivity,  leading  to  an  asymmetrical  distribution  of  excitatory and inhibitory connectivity. Our network model of the dentate gyrus with incorporated real connectivity rules efficiently decorrelates neuronal activity patterns using WTA as the  primary  mechanism.  This  process  relied  on  lateral  inhibition,  fast-signaling properties  of  PV+interneurons  and  the  asymmetrical  distribution  of  excitatory  and inhibitory connectivity. Finally, we found that silencing the activity of PV+interneurons in  vivoleads  to  acute  deficits  in  discrimination  between  similar  environments, suggesting  that  PV+interneuron  networks  are  necessary  for  behavioral  relevant computations.  Our   results   demonstrate   that   PV+interneurons  possess  unique connectivity  and  fast  signaling  properties  that confer  to  the  dentate  gyrus  network properties that allow the emergence of pattern separation. Thus, our results contribute to the knowledge of how specific forms of network organization underlie sophisticated types of information processing. \r\n"}],"citation":{"chicago":"Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6363\">https://doi.org/10.15479/AT:ISTA:6363</a>.","ieee":"C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits,” Institute of Science and Technology Austria, 2019.","ama":"Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6363\">10.15479/AT:ISTA:6363</a>","apa":"Espinoza Martinez, C. (2019). <i>Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6363\">https://doi.org/10.15479/AT:ISTA:6363</a>","ista":"Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria.","mla":"Espinoza Martinez, Claudia. <i>Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6363\">10.15479/AT:ISTA:6363</a>.","short":"C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria, 2019."},"year":"2019","date_updated":"2023-09-15T12:03:48Z","publisher":"Institute of Science and Technology Austria","page":"140","file_date_updated":"2021-02-11T11:17:15Z","article_processing_charge":"No","department":[{"_id":"PeJo"}],"date_created":"2019-04-30T11:56:10Z","publication_status":"published","title":"Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits","alternative_title":["ISTA Thesis"],"_id":"6363","author":[{"id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87","full_name":"Espinoza Martinez, Claudia ","orcid":"0000-0003-4710-2082","last_name":"Espinoza Martinez","first_name":"Claudia "}],"file":[{"file_id":"6389","creator":"cespinoza","access_level":"open_access","relation":"main_file","date_updated":"2021-02-11T11:17:15Z","content_type":"application/pdf","file_name":"Espinozathesis_all2.pdf","embargo":"2020-05-09","date_created":"2019-05-07T16:00:39Z","file_size":13966891,"checksum":"77c6c05cfe8b58c8abcf1b854375d084"},{"relation":"source_file","access_level":"closed","file_id":"6390","creator":"cespinoza","date_created":"2019-05-07T16:00:48Z","checksum":"f6aa819f127691a2b0fc21c76eb09746","file_size":11159900,"embargo_to":"open_access","date_updated":"2020-07-14T12:47:28Z","file_name":"Espinoza_Thesis.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","id":"21","relation":"part_of_dissertation"}]},"status":"public","publication_identifier":{"isbn":["978-3-99078-000-8"],"issn":["2663-337X"]},"oa":1,"supervisor":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M"}],"type":"dissertation","date_published":"2019-04-30T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"Published Version","month":"04","has_accepted_license":"1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","id":"67","status":"public"},{"id":"5585","relation":"popular_science","status":"public"}]},"file":[{"checksum":"c0085d47c58c9cbcab1b0a783480f6da","file_size":12597663,"embargo":"2020-05-02","date_created":"2019-05-03T11:54:52Z","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","content_type":"application/pdf","date_updated":"2021-02-11T11:17:13Z","relation":"main_file","access_level":"open_access","creator":"cigler","file_id":"6373"},{"file_id":"6374","creator":"cigler","relation":"source_file","access_level":"closed","date_updated":"2020-07-14T12:47:28Z","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-05-03T11:54:54Z","embargo_to":"open_access","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","file_size":34644426}],"oa":1,"supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","date_published":"2019-05-03T00:00:00Z","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"language":[{"iso":"eng"}],"month":"05","project":[{"name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","has_accepted_license":"1","ddc":["576","579"],"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"}],"day":"03","doi":"10.15479/AT:ISTA:6371","degree_awarded":"PhD","year":"2019","citation":{"apa":"Igler, C. (2019). <i>On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6371\">https://doi.org/10.15479/AT:ISTA:6371</a>","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6371\">10.15479/AT:ISTA:6371</a>","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. <a href=\"https://doi.org/10.15479/AT:ISTA:6371\">https://doi.org/10.15479/AT:ISTA:6371</a>.","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.","mla":"Igler, Claudia. <i>On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6371\">10.15479/AT:ISTA:6371</a>.","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.","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."},"date_updated":"2024-02-21T13:45:52Z","publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-02-11T11:17:13Z","page":"152","alternative_title":["ISTA Thesis"],"title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","date_created":"2019-05-03T11:55:51Z","department":[{"_id":"CaGu"}],"article_processing_charge":"No","publication_status":"published","author":[{"last_name":"Igler","first_name":"Claudia","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"}],"_id":"6371"},{"date_updated":"2023-09-22T09:19:41Z","citation":{"ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019.","chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>.","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>","apa":"Lukacisin, M. (2019). <i>Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria.","mla":"Lukacisin, Martin. <i>Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory</i>. IST Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>.","short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019."},"year":"2019","doi":"10.15479/AT:ISTA:6392","day":"09","abstract":[{"lang":"eng","text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes.  \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. "}],"extern":"1","ddc":["570"],"_id":"6392","author":[{"full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177","last_name":"Lukacisin","first_name":"Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"ToBo"}],"date_created":"2019-05-09T19:53:00Z","title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory","alternative_title":["IST Austria Thesis"],"page":"103","file_date_updated":"2021-02-11T11:17:16Z","publisher":"IST Austria","date_published":"2019-05-09T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-001-5"]},"supervisor":[{"first_name":"Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"file":[{"checksum":"829bda074444857c7935171237bb7c0c","file_size":43740796,"embargo_to":"open_access","date_created":"2019-05-10T13:51:49Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Draft_v3.4Final.docx","date_updated":"2020-07-14T12:47:29Z","relation":"hidden","access_level":"closed","creator":"mlukacisin","file_id":"6409"},{"access_level":"open_access","relation":"main_file","creator":"mlukacisin","file_id":"6410","checksum":"56cb5e97f5f8fc41692401b53832d8e0","file_size":35228388,"date_created":"2019-05-10T14:13:42Z","embargo":"2020-04-17","content_type":"application/pdf","file_name":"Thesis_Draft_v3.4FinalA.pdf","date_updated":"2021-02-11T11:17:16Z"}],"status":"public","related_material":{"record":[{"status":"public","id":"1029","relation":"part_of_dissertation"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"month":"05","language":[{"iso":"eng"}]},{"type":"dissertation","date_published":"2019-05-07T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"oa":1,"supervisor":[{"last_name":"Cremer","first_name":"Sylvia M","full_name":"Cremer, Sylvia M","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"file":[{"checksum":"6daf2d2086111aa8fd3fbc919a3e2833","file_size":3895187,"embargo":"2020-05-08","date_created":"2019-05-13T09:16:20Z","content_type":"application/pdf","file_name":"tesisDoctoradoBC.pdf","date_updated":"2021-02-11T11:17:15Z","relation":"main_file","access_level":"open_access","creator":"casillas","file_id":"6438"},{"creator":"casillas","file_id":"6439","access_level":"closed","relation":"source_file","content_type":"application/zip","file_name":"tesisDoctoradoBC.zip","date_updated":"2020-07-14T12:47:30Z","embargo_to":"open_access","file_size":7365118,"checksum":"3d221aaff7559a7060230a1ff610594f","date_created":"2019-05-13T09:16:20Z"}],"status":"public","related_material":{"record":[{"id":"1999","relation":"part_of_dissertation","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","project":[{"name":"Epidemics in ant societies on a chip","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"oa_version":"Published Version","month":"05","keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"language":[{"iso":"eng"}],"citation":{"apa":"Casillas Perez, B. E. (2019). <i>Collective defenses of garden ants against a fungal pathogen</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>","ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>.","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","mla":"Casillas Perez, Barbara E. <i>Collective Defenses of Garden Ants against a Fungal Pathogen</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>.","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria."},"year":"2019","date_updated":"2023-09-07T12:57:04Z","day":"07","doi":"10.15479/AT:ISTA:6435","degree_awarded":"PhD","abstract":[{"text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour.","lang":"eng"}],"ddc":["570","006","578","592"],"_id":"6435","author":[{"full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez","first_name":"Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"SyCr"}],"article_processing_charge":"No","date_created":"2019-05-13T08:58:35Z","publication_status":"published","title":"Collective defenses of garden ants against a fungal pathogen","alternative_title":["ISTA Thesis"],"ec_funded":1,"page":"183","file_date_updated":"2021-02-11T11:17:15Z","publisher":"Institute of Science and Technology Austria"},{"has_accepted_license":"1","oa_version":"Published Version","month":"05","language":[{"iso":"eng"}],"keyword":["Information estimation","Time-series","data analysis"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2019-05-23T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"file":[{"date_created":"2019-05-23T11:18:16Z","checksum":"75f9184c1346e10a5de5f9cc7338309a","file_size":23937464,"date_updated":"2020-07-14T12:47:31Z","file_name":"Thesis_Cepeda.zip","content_type":"application/zip","access_level":"closed","relation":"source_file","file_id":"6480","creator":"scepeda"},{"creator":"scepeda","file_id":"6481","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"CepedaThesis.pdf","date_updated":"2020-07-14T12:47:31Z","checksum":"afdc0633ddbd71d5b13550d7fb4f4454","file_size":16646985,"date_created":"2019-05-23T11:18:13Z"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","related_material":{"record":[{"id":"6900","relation":"dissertation_contains","status":"public"},{"status":"public","relation":"dissertation_contains","id":"281"},{"relation":"dissertation_contains","id":"2016","status":"public"},{"relation":"dissertation_contains","id":"1576","status":"public"}]},"_id":"6473","author":[{"first_name":"Sarah A","last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"GaTk"}],"article_processing_charge":"No","date_created":"2019-05-21T00:11:23Z","title":"Estimating information flow in single cells","alternative_title":["ISTA Thesis"],"page":"135","file_date_updated":"2020-07-14T12:47:31Z","publisher":"Institute of Science and Technology Austria","date_updated":"2025-05-28T11:57:00Z","citation":{"chicago":"Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6473\">https://doi.org/10.15479/AT:ISTA:6473</a>.","ieee":"S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute of Science and Technology Austria, 2019.","apa":"Cepeda Humerez, S. A. (2019). <i>Estimating information flow in single cells</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6473\">https://doi.org/10.15479/AT:ISTA:6473</a>","ama":"Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6473\">10.15479/AT:ISTA:6473</a>","ista":"Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute of Science and Technology Austria.","short":"S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019.","mla":"Cepeda Humerez, Sarah A. <i>Estimating Information Flow in Single Cells</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6473\">10.15479/AT:ISTA:6473</a>."},"year":"2019","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:6473","day":"23","abstract":[{"lang":"eng","text":"Single cells are constantly interacting with their environment and each other, more importantly, the accurate perception of environmental cues is crucial for growth, survival, and reproduction. This communication between cells and their environment can be formalized in mathematical terms and be quantified as the information flow between them, as prescribed by information theory. \r\nThe recent availability of real–time dynamical patterns of signaling molecules in single cells has allowed us to identify encoding about the identity of the environment in the time–series. However, efficient estimation of the information transmitted by these signals has been a data–analysis challenge due to the high dimensionality of the trajectories and the limited number of samples. In the first part of this thesis, we develop and evaluate decoding–based estimation methods to lower bound the mutual information and derive model–based precise information estimates for biological reaction networks governed by the chemical master equation. This is followed by applying the decoding-based methods to study the intracellular representation of extracellular changes in budding yeast, by observing the transient dynamics of nuclear translocation of 10 transcription factors in response to 3 stress conditions. Additionally, we apply these estimators to previously published data on ERK and Ca2+ signaling and yeast stress response. We argue that this single cell decoding-based measure of information provides an unbiased, quantitative and interpretable measure for the fidelity of biological signaling processes. \r\nFinally, in the last section, we deal with gene regulation which is primarily controlled by transcription factors (TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate TFs activate transcription diminishes the accuracy of regulation with potentially disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored source of noise in biochemical networks and puts a strong constraint on their performance. To mitigate erroneous initiation we propose an out of equilibrium scheme that implements kinetic proofreading. We show that such architectures are favored  over their equilibrium counterparts for complex organisms despite introducing noise in gene expression. "}],"ddc":["004"]},{"abstract":[{"lang":"eng","text":"Invasive migration plays a crucial role not only during development and homeostasis but also in pathological states, such as tumor metastasis. Drosophila macrophage migration into the extended germband is an interesting system to study invasive migration. It carries similarities to immune cell transmigration and cancer cell invasion, therefore studying this process could also bring new understanding of invasion in higher organisms. In our work, we uncover a highly conserved member of the major facilitator family that plays a role in tissue invasion through regulation of glycosylation on a subgroup of proteins and/or by aiding the precise timing of DN-Cadherin downregulation. \r\n\r\nAberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify \r\na key conserved regulator that orchestrates O-glycosylation on a protein subset to activate \r\na program governing migration steps important for both development and cancer metastasis. \r\n"}],"day":"07","degree_awarded":"PhD","doi":"10.15479/AT:ISTA:6546","citation":{"apa":"Valosková, K. (2019). <i>The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6546\">https://doi.org/10.15479/AT:ISTA:6546</a>","ama":"Valosková K. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6546\">10.15479/AT:ISTA:6546</a>","ieee":"K. Valosková, “The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration,” Institute of Science and Technology Austria, 2019.","chicago":"Valosková, Katarina. “The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6546\">https://doi.org/10.15479/AT:ISTA:6546</a>.","short":"K. Valosková, The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration, Institute of Science and Technology Austria, 2019.","mla":"Valosková, Katarina. <i>The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6546\">10.15479/AT:ISTA:6546</a>.","ista":"Valosková K. 2019. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria."},"year":"2019","date_updated":"2023-09-19T10:15:54Z","ddc":["570"],"title":"The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","department":[{"_id":"DaSi"}],"date_created":"2019-06-07T12:49:19Z","publication_status":"published","author":[{"id":"46F146FC-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Valosková","full_name":"Valosková, Katarina"}],"_id":"6546","publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-02-11T11:17:14Z","page":"141","oa":1,"supervisor":[{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","date_published":"2019-06-07T00:00:00Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"6187"},{"relation":"part_of_dissertation","id":"544","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","file":[{"date_created":"2019-06-07T13:00:04Z","checksum":"68949c2d96210b45b981a23e9c9cd93c","file_size":14110626,"embargo_to":"open_access","date_updated":"2020-07-14T12:47:33Z","file_name":"Katarina Valoskova_PhD thesis_final version.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_id":"6549","creator":"khribikova"},{"file_name":"Katarina Valoskova_PhD thesis_final version.pdf","content_type":"application/pdf","date_updated":"2021-02-11T11:17:14Z","checksum":"555329cd76e196c96f5278c480ee2e6e","file_size":10054156,"embargo":"2020-06-07","date_created":"2019-06-07T13:00:08Z","creator":"khribikova","file_id":"6550","access_level":"open_access","relation":"main_file"}],"month":"06","project":[{"_id":"253CDE40-B435-11E9-9278-68D0E5697425","grant_number":"24283","name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"}],"has_accepted_license":"1","language":[{"iso":"eng"}]}]