[{"pmid":1,"date_published":"2017-03-06T00:00:00Z","extern":"1","publication":"eLife","status":"public","year":"2017","external_id":{"pmid":["28267430"]},"quality_controlled":"1","ddc":["570"],"date_updated":"2021-01-12T08:16:46Z","_id":"8075","type":"journal_article","doi":"10.7554/elife.22152","article_processing_charge":"No","publisher":"eLife Sciences Publications, Ltd","citation":{"short":"W.F. Podlaski, A. Seeholzer, L.N. Groschner, G. Miesenböck, R. Ranjan, T.P. Vogels, ELife 6 (2017).","ieee":"W. F. Podlaski, A. Seeholzer, L. N. Groschner, G. Miesenböck, R. Ranjan, and T. P. Vogels, “Mapping the function of neuronal ion channels in model and experiment,” <i>eLife</i>, vol. 6. eLife Sciences Publications, Ltd, 2017.","ama":"Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP. Mapping the function of neuronal ion channels in model and experiment. <i>eLife</i>. 2017;6. doi:<a href=\"https://doi.org/10.7554/elife.22152\">10.7554/elife.22152</a>","mla":"Podlaski, William F., et al. “Mapping the Function of Neuronal Ion Channels in Model and Experiment.” <i>ELife</i>, vol. 6, e22152, eLife Sciences Publications, Ltd, 2017, doi:<a href=\"https://doi.org/10.7554/elife.22152\">10.7554/elife.22152</a>.","apa":"Podlaski, W. F., Seeholzer, A., Groschner, L. N., Miesenböck, G., Ranjan, R., &#38; Vogels, T. P. (2017). Mapping the function of neuronal ion channels in model and experiment. <i>ELife</i>. eLife Sciences Publications, Ltd. <a href=\"https://doi.org/10.7554/elife.22152\">https://doi.org/10.7554/elife.22152</a>","ista":"Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP. 2017. Mapping the function of neuronal ion channels in model and experiment. eLife. 6, e22152.","chicago":"Podlaski, William F, Alexander Seeholzer, Lukas N Groschner, Gero Miesenböck, Rajnish Ranjan, and Tim P Vogels. “Mapping the Function of Neuronal Ion Channels in Model and Experiment.” <i>ELife</i>. eLife Sciences Publications, Ltd, 2017. <a href=\"https://doi.org/10.7554/elife.22152\">https://doi.org/10.7554/elife.22152</a>."},"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","oa":1,"language":[{"iso":"eng"}],"article_number":"e22152","file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"2017_elife_Podlaski.pdf","success":1,"checksum":"e5c5a33bcb3ac38ad62df1010ab29040","relation":"main_file","creator":"cziletti","date_updated":"2020-07-16T12:08:40Z","file_size":16034505,"date_created":"2020-07-16T12:08:40Z","file_id":"8124"}],"month":"03","publication_status":"published","publication_identifier":{"issn":["2050-084X"]},"file_date_updated":"2020-07-16T12:08:40Z","has_accepted_license":"1","intvolume":"         6","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Ion channel models are the building blocks of computational neuron models. Their biological fidelity is therefore crucial for the interpretation of simulations. However, the number of published models, and the lack of standardization, make the comparison of ion channel models with one another and with experimental data difficult. Here, we present a framework for the automated large-scale classification of ion channel models. Using annotated metadata and responses to a set of voltage-clamp protocols, we assigned 2378 models of voltage- and calcium-gated ion channels coded in NEURON to 211 clusters. The IonChannelGenealogy (ICGenealogy) web interface provides an interactive resource for the categorization of new and existing models and experimental recordings. It enables quantitative comparisons of simulated and/or measured ion channel kinetics, and facilitates field-wide standardization of experimentally-constrained modeling.","lang":"eng"}],"volume":6,"article_type":"original","date_created":"2020-06-30T13:32:18Z","author":[{"first_name":"William F","last_name":"Podlaski","full_name":"Podlaski, William F"},{"full_name":"Seeholzer, Alexander","last_name":"Seeholzer","first_name":"Alexander"},{"first_name":"Lukas N","last_name":"Groschner","full_name":"Groschner, Lukas N"},{"full_name":"Miesenböck, Gero","last_name":"Miesenböck","first_name":"Gero"},{"full_name":"Ranjan, Rajnish","last_name":"Ranjan","first_name":"Rajnish"},{"full_name":"Vogels, Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","first_name":"Tim P","orcid":"0000-0003-3295-6181"}],"day":"06","oa_version":"Published Version","title":"Mapping the function of neuronal ion channels in model and experiment"},{"external_id":{"arxiv":["1711.02448"]},"year":"2017","conference":{"location":"Long Beach, CA, United States","name":"NIPS: Neural Information Processing System","start_date":"2017-12-04","end_date":"2017-12-09"},"date_published":"2017-12-01T00:00:00Z","extern":"1","publication":"Advances in Neural Information Processing Systems","status":"public","type":"conference","_id":"8129","date_updated":"2021-01-12T08:17:03Z","publisher":"Neural Information Processing Systems Foundation","article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.02448"}],"page":"272-283","arxiv":1,"month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. Cortical microcircuits as gated-recurrent neural networks. In: <i>Advances in Neural Information Processing Systems</i>. Vol 30. Neural Information Processing Systems Foundation; 2017:272-283.","short":"R.P. Costa, Y.M. Assael, B. Shillingford, N. de Freitas, T.P. Vogels, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2017, pp. 272–283.","ieee":"R. P. Costa, Y. M. Assael, B. Shillingford, N. de Freitas, and T. P. Vogels, “Cortical microcircuits as gated-recurrent neural networks,” in <i>Advances in Neural Information Processing Systems</i>, Long Beach, CA, United States, 2017, vol. 30, pp. 272–283.","ista":"Costa RP, Assael YM, Shillingford B, Freitas N de, Vogels TP. 2017. Cortical microcircuits as gated-recurrent neural networks. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing System vol. 30, 272–283.","chicago":"Costa, Rui Ponte, Yannis M. Assael, Brendan Shillingford, Nando de Freitas, and Tim P Vogels. “Cortical Microcircuits as Gated-Recurrent Neural Networks.” In <i>Advances in Neural Information Processing Systems</i>, 30:272–83. Neural Information Processing Systems Foundation, 2017.","mla":"Costa, Rui Ponte, et al. “Cortical Microcircuits as Gated-Recurrent Neural Networks.” <i>Advances in Neural Information Processing Systems</i>, vol. 30, Neural Information Processing Systems Foundation, 2017, pp. 272–83.","apa":"Costa, R. P., Assael, Y. M., Shillingford, B., Freitas, N. de, &#38; Vogels, T. P. (2017). Cortical microcircuits as gated-recurrent neural networks. In <i>Advances in Neural Information Processing Systems</i> (Vol. 30, pp. 272–283). Long Beach, CA, United States: Neural Information Processing Systems Foundation."},"language":[{"iso":"eng"}],"oa":1,"date_created":"2020-07-16T19:13:10Z","volume":30,"oa_version":"Preprint","title":"Cortical microcircuits as gated-recurrent neural networks","day":"01","author":[{"full_name":"Costa, Rui Ponte","last_name":"Costa","first_name":"Rui Ponte"},{"full_name":"Assael, Yannis M.","last_name":"Assael","first_name":"Yannis M."},{"last_name":"Shillingford","full_name":"Shillingford, Brendan","first_name":"Brendan"},{"full_name":"Freitas, Nando de","last_name":"Freitas","first_name":"Nando de"},{"orcid":"0000-0003-3295-6181","first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P","last_name":"Vogels"}],"publication_identifier":{"issn":["10495258"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Cortical circuits exhibit intricate recurrent architectures that are remarkably similar across different brain areas. Such stereotyped structure suggests the existence of common computational principles. However, such principles have remained largely elusive. Inspired by gated-memory networks, namely long short-term memory networks (LSTMs), we introduce a recurrent neural network in which information is gated through inhibitory cells that are subtractive (subLSTM). We propose a natural mapping of subLSTMs onto known canonical excitatory-inhibitory cortical microcircuits. Our empirical evaluation across sequential image classification and language modelling tasks shows that subLSTM units can achieve similar performance to LSTM units. These results suggest that cortical circuits can be optimised to solve complex contextual problems and proposes a novel view on their computational function.\r\nOverall our work provides a step towards unifying recurrent networks as used in machine learning with their biological counterparts."}],"intvolume":"        30"},{"file":[{"relation":"main_file","checksum":"7f2d4bbac767f9acc254d1a4114d181a","file_name":"2017_Elsevier_Turonova.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"6168","file_size":1310009,"date_created":"2019-03-22T09:29:44Z","date_updated":"2020-07-14T12:48:09Z","creator":"kschuh"}],"month":"09","issue":"3","citation":{"chicago":"Turoňová, Beata, Florian KM Schur, William Wan, and John Briggs. “Efficient 3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” <i>Journal of Structural Biology</i>. Academic Press, 2017. <a href=\"https://doi.org/10.1016/j.jsb.2017.07.007\">https://doi.org/10.1016/j.jsb.2017.07.007</a>.","ista":"Turoňová B, Schur FK, Wan W, Briggs J. 2017. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. Journal of Structural Biology. 199(3), 187–195.","apa":"Turoňová, B., Schur, F. K., Wan, W., &#38; Briggs, J. (2017). Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. <i>Journal of Structural Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jsb.2017.07.007\">https://doi.org/10.1016/j.jsb.2017.07.007</a>","mla":"Turoňová, Beata, et al. “Efficient 3D-CTF Correction for Cryo-Electron Tomography Using NovaCTF Improves Subtomogram Averaging Resolution to 3.4Å.” <i>Journal of Structural Biology</i>, vol. 199, no. 3, Academic Press, 2017, pp. 187–95, doi:<a href=\"https://doi.org/10.1016/j.jsb.2017.07.007\">10.1016/j.jsb.2017.07.007</a>.","ama":"Turoňová B, Schur FK, Wan W, Briggs J. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å. <i>Journal of Structural Biology</i>. 2017;199(3):187-195. doi:<a href=\"https://doi.org/10.1016/j.jsb.2017.07.007\">10.1016/j.jsb.2017.07.007</a>","ieee":"B. Turoňová, F. K. Schur, W. Wan, and J. Briggs, “Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å,” <i>Journal of Structural Biology</i>, vol. 199, no. 3. Academic Press, pp. 187–195, 2017.","short":"B. Turoňová, F.K. Schur, W. Wan, J. Briggs, Journal of Structural Biology 199 (2017) 187–195."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"volume":199,"date_created":"2018-12-11T11:48:40Z","author":[{"first_name":"Beata","last_name":"Turoňová","full_name":"Turoňová, Beata"},{"first_name":"Florian","orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wan","full_name":"Wan, William","first_name":"William"},{"last_name":"Briggs","full_name":"Briggs, John","first_name":"John"}],"day":"01","title":"Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å","oa_version":"Published Version","publication_status":"published","file_date_updated":"2020-07-14T12:48:09Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       199","abstract":[{"lang":"eng","text":"Cryo-electron tomography (cryo-ET) allows cellular ultrastructures and macromolecular complexes to be imaged in three-dimensions in their native environments. Cryo-electron tomograms are reconstructed from projection images taken at defined tilt-angles. In order to recover high-resolution information from cryo-electron tomograms, it is necessary to measure and correct for the contrast transfer function (CTF) of the microscope. Most commonly, this is performed using protocols that approximate the sample as a two-dimensional (2D) plane. This approximation accounts for differences in defocus and therefore CTF across the tilted sample. It does not account for differences in defocus of objects at different heights within the sample; instead, a 3D approach is required. Currently available approaches for 3D-CTF correction are computationally expensive and have not been widely implemented. Here we simulate the benefits of 3D-CTF correction for high-resolution subtomogram averaging, and present a user-friendly, computationally-efficient 3D-CTF correction tool, NovaCTF, that is compatible with standard tomogram reconstruction workflows in IMOD. We validate the approach on synthetic data and test it using subtomogram averaging of real data. Consistent with our simulations, we find that 3D-CTF correction allows high-resolution structures to be obtained with much smaller subtomogram averaging datasets than are required using 2D-CTF. We also show that using equivalent dataset sizes, 3D-CTF correction can be used to obtain higher-resolution structures. We present a 3.4. Å resolution structure determined by subtomogram averaging."}],"publist_id":"6832","year":"2017","date_published":"2017-09-01T00:00:00Z","extern":"1","publication":"Journal of Structural Biology","status":"public","date_updated":"2021-01-12T08:17:16Z","_id":"817","type":"journal_article","doi":"10.1016/j.jsb.2017.07.007","publisher":"Academic Press","quality_controlled":"1","page":"187-195","ddc":["570"]},{"day":"27","author":[{"last_name":"Mitosch","full_name":"Mitosch, Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin"}],"title":"Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics","oa_version":"Published Version","date_created":"2018-12-11T11:48:40Z","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Antibiotics have diverse effects on bacteria, including massive changes in bacterial gene expression. Whereas the gene expression changes under many antibiotics have been measured, the temporal organization of these responses and their dependence on the bacterial growth rate are unclear. As described in Chapter 1, we quantified the temporal gene expression changes in the bacterium Escherichia coli in response to the sudden exposure to antibiotics using a fluorescent reporter library and a robotic system. Our data show temporally structured gene expression responses, with response times for individual genes ranging from tens of minutes to several hours. We observed that many stress response genes were activated in response to antibiotics. As certain stress responses cross-protect bacteria from other stressors, we then asked whether cellular responses to antibiotics have a similar protective role in Chapter 2. Indeed, we found that the trimethoprim-induced acid stress response protects bacteria from subsequent acid stress. We combined microfluidics with time-lapse imaging to monitor survival, intracellular pH, and acid stress response in single cells. This approach revealed that the variable expression of the acid resistance operon gadBC strongly correlates with single-cell survival time. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. Overall, we provide a way to identify single-cell cross-protection between antibiotics and environmental stressors from temporal gene expression data, and show how antibiotics can increase bacterial fitness in changing environments. While gene expression changes to antibiotics show a clear temporal structure at the population-level, it is unclear whether this clear temporal order is followed by every single cell. Using dual-reporter strains described in Chapter 3, we measured gene expression dynamics of promoter pairs in the same cells using microfluidics and microscopy. Chapter 4 shows that the oxidative stress response and the DNA stress response showed little timing variability and a clear temporal order under the antibiotic nitrofurantoin. In contrast, the acid stress response under trimethoprim ran independently from all other activated response programs including the DNA stress response, which showed particularly high timing variability in this stress condition. In summary, this approach provides insight into the temporal organization of gene expression programs at the single-cell level and suggests dependencies between response programs and the underlying variability-introducing mechanisms. Altogether, this work advances our understanding of the diverse effects that antibiotics have on bacteria. These results were obtained by taking into account gene expression dynamics, which allowed us to identify general principles, molecular mechanisms, and dependencies between genes. Our findings may have implications for infectious disease treatments, and microbial communities in the human body and in nature. "}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2020-07-14T12:48:09Z","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias"}],"month":"09","department":[{"_id":"ToBo"}],"file":[{"file_id":"6210","creator":"dernst","date_updated":"2020-07-14T12:48:09Z","date_created":"2019-04-05T08:48:51Z","file_size":6331071,"checksum":"da3993c5f90f59a8e8623cc31ad501dd","relation":"source_file","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_KarinMitosch.docx"},{"date_updated":"2020-07-14T12:48:09Z","creator":"dernst","date_created":"2019-04-05T08:48:51Z","file_size":9289852,"file_id":"6211","access_level":"open_access","content_type":"application/pdf","file_name":"Thesis_KarinMitosch.pdf","checksum":"24c3d9e51992f1b721f3df55aa13fcb8","relation":"main_file"}],"oa":1,"language":[{"iso":"eng"}],"pubrep_id":"862","citation":{"apa":"Mitosch, K. (2017). <i>Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">https://doi.org/10.15479/AT:ISTA:th_862</a>","mla":"Mitosch, Karin. <i>Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">10.15479/AT:ISTA:th_862</a>.","chicago":"Mitosch, Karin. “Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">https://doi.org/10.15479/AT:ISTA:th_862</a>.","ista":"Mitosch K. 2017. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. Institute of Science and Technology Austria.","ieee":"K. Mitosch, “Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics,” Institute of Science and Technology Austria, 2017.","short":"K. Mitosch, Timing, Variability and Cross-Protection in Bacteria – Insights from Dynamic Gene Expression Responses to Antibiotics, Institute of Science and Technology Austria, 2017.","ama":"Mitosch K. Timing, variability and cross-protection in bacteria – insights from dynamic gene expression responses to antibiotics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_862\">10.15479/AT:ISTA:th_862</a>"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:th_862","publisher":"Institute of Science and Technology Austria","_id":"818","date_updated":"2023-09-07T12:00:26Z","type":"dissertation","page":"113","ddc":["571","579"],"year":"2017","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"2001"},{"status":"public","relation":"part_of_dissertation","id":"666"}]},"publist_id":"6831","degree_awarded":"PhD","status":"public","acknowledgement":"First of all, I would like to express great gratitude to my PhD supervisor Tobias Bollenbach. Through his open and trusting attitude I had the freedom to explore different scientific directions during this project, and follow the research lines of my interest. I am thankful for constructive and often extensive discussions and his support and commitment during the different stages of my PhD. I want to thank my committee members, Călin Guet, Terry Hwa and Nassos Typas for their interest and their valuable input to this project. Special thanks to Nassos for career guidance, and for accepting me in his lab. A big thank you goes to the past, present and affiliated members of the Bollenbach group: Guillaume Chevereau, Marjon de Vos, Marta Lukačišinová, Veronika Bierbaum, Qi Qin, Marcin Zagórski, Martin Lukačišin, Andreas Angermayr, Bor Kavčič, Julia Tischler, Dilay Ayhan, Jaroslav Ferenc, and Georg Rieckh. I enjoyed working and discussing with you very much and I will miss our lengthy group meetings, our inspiring journal clubs, and our common lunches. Special thanks to Bor for great mental and professional support during the hard months of thesis writing, and to Marta for very creative times during the beginning of our PhDs. May the ‘Bacterial Survival Guide’ decorate the walls of IST forever! A great thanks to my friend and collaborator Georg Rieckh for his enthusiasm and for getting so involved in these projects, for his endurance and for his company throughout the years. Thanks to the FriSBi crowd at IST Austria for interesting meetings and discussions. In particular I want to thank Magdalena Steinrück, and Anna Andersson for inspiring exchange, and enjoyable time together. Thanks to everybody who contributed to the cover for Cell Systems: The constructive input from Tobias Bollenbach, Bor Kavčič, Georg Rieckh, Marta Lukačišinová, and Sebastian Nozzi, and the professional implementation by the graphic designer Martina Markus from the University of Cologne. Thanks to all my office mates in the first floor Bertalanffy building throughout the years: for ensuring a pleasant working atmosphere, and for your company! In general, I want to thank all the people that make IST such a great environment, with the many possibilities to shape our own social and research environment. I want to thank my family for all kind of practical support during the years, and my second family in Argentina for their enthusiasm. Thanks to my brother Bernhard and my sister Martina for being great siblings, and to Helena and Valentin for the joy you brought to my life. My deep gratitude goes to Sebastian Nozzi, for constant support, patience, love and for believing in me. ","date_published":"2017-09-27T00:00:00Z"},{"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","doi":"10.15479/AT:ISTA:th_861","type":"dissertation","_id":"819","date_updated":"2023-09-28T11:31:32Z","ddc":["576","577","578","579","590","592"],"page":"122","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"616"},{"relation":"part_of_dissertation","status":"public","id":"806"},{"relation":"part_of_dissertation","status":"public","id":"734"},{"id":"732","status":"public","relation":"part_of_dissertation"}]},"year":"2017","publist_id":"6830","status":"public","degree_awarded":"PhD","date_published":"2017-09-26T00:00:00Z","acknowledgement":"ERC FP7 programme (grant agreement no. 240371)\r\nI have been supremely spoilt to work in a lab with such good resources and I must thank the wonderful Cremer group technicians, Anna, Barbara, Eva and Florian, for all of their help and keeping the lab up and running. You guys will probably be the most missed once I realise just how much work you have been saving me! For the same reason, I must say a big Dzi ę kuj ę Ci to Wonder Woman Wanda, for her tireless efforts feeding my colonies and cranking out thousands of petri dishes and sugar tubes. Again, you will be sorely missed now that I will have to take this task on myself. Of course, I will be eternally indebted to Prof. Sylvia Cremer for taking me under her wing and being a constant source of guidance and inspiration. You have given me the perfect balance of independence and supervision. I cannot thank you enough for creating such a great working environment and allowing me the freedom to follow my own research questions. I have had so many exceptional opportunities – attending and presenting at conferences all over the world, inviting me to write the ARE with you, going to workshops in Panama and Switzerland, and even organising our own PhD course – that I often think I must have had the best PhD in the world. You have taught me so much and made me a scientist. I sincerely hope we get the chance to work together again in the future. Thank you for everything. I must also thank my PhD Committee, Daria Siekhaus and Jacobus “Koos” Boomsma, for being very supportive throughout the duration of my PhD. ","title":"Disease defence in garden ants","oa_version":"Published Version","day":"26","author":[{"full_name":"Pull, Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","last_name":"Pull","orcid":"0000-0003-1122-3982","first_name":"Christopher"}],"date_created":"2018-12-11T11:48:40Z","abstract":[{"lang":"eng","text":"Contagious diseases must transmit from infectious to susceptible hosts in order to reproduce. Whilst vectored pathogens can rely on intermediaries to find new hosts for them, many infectious pathogens require close contact or direct interaction between hosts for transmission. Hence, this means that conspecifics are often the main source of infection for most animals and so, in theory, animals should avoid conspecifics to reduce their risk of infection. Of course, in reality animals must interact with one another, as a bare minimum, to mate. However, being social provides many additional benefits and group living has become a taxonomically diverse and widespread trait. How then do social animals overcome the issue of increased disease? Over the last few decades, the social insects (ants, termites and some bees and wasps) have become a model system for studying disease in social animals. On paper, a social insect colony should be particularly susceptible to disease, given that they often contain thousands of potential hosts that are closely related and frequently interact, as well as exhibiting stable environmental conditions that encourage microbial growth. Yet, disease outbreaks appear to be rare and attempts to eradicate pest species using pathogens have failed time and again. Evolutionary biologists investigating this observation have discovered that the reduced disease susceptibility in social insects is, in part, due to collectively performed disease defences of the workers. These defences act like a “social immune system” for the colony, resulting in a per capita decrease in disease, termed social immunity. Our understanding of social immunity, and its importance in relation to the immunological defences of each insect, continues to grow, but there remain many open questions. In this thesis I have studied disease defence in garden ants. In the first data chapter, I use the invasive garden ant, Lasius neglectus, to investigate how colonies mitigate lethal infections and prevent them from spreading systemically. I find that ants have evolved ‘destructive disinfection’ – a behaviour that uses endogenously produced acidic poison to kill diseased brood and to prevent the pathogen from replicating. In the second experimental chapter, I continue to study the use of poison in invasive garden ant colonies, finding that it is sprayed prophylactically within the nest. However, this spraying has negative effects on developing pupae when they have had their cocoons artificially removed. Hence, I suggest that acidic nest sanitation may be maintaining larval cocoon spinning in this species. In the next experimental chapter, I investigated how colony founding black garden ant queens (Lasius niger) prevent disease when a co-foundress dies. I show that ant queens prophylactically perform undertaking behaviours, similar to those performed by the workers in mature nests. When a co-foundress was infected, these undertaking behaviours improved the survival of the healthy queen. In the final data chapter, I explored how immunocompetence (measured as antifungal activity) changes as incipient black garden ant colonies grow and mature, from the solitary queen phase to colonies with several hundred workers. Queen and worker antifungal activity varied throughout this time period, but despite social immunity, did not decrease as colonies matured. In addition to the above data chapters, this thesis includes two co-authored reviews. In the first, we examine the state of the art in the field of social immunity and how it might develop in the future. In the second, we identify several challenges and open questions in the study of disease defence in animals. We highlight how social insects offer a unique model to tackle some of these problems, as disease defence can be studied from the cell to the society. "}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","file_date_updated":"2020-07-14T12:48:09Z","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","month":"09","supervisor":[{"full_name":"Cremer, Sylvia M","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia M","orcid":"0000-0002-2193-3868"}],"file":[{"date_created":"2019-04-05T07:53:04Z","file_size":18580400,"creator":"dernst","date_updated":"2020-07-14T12:48:09Z","file_id":"6199","file_name":"2017_Thesis_Pull.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"4993cdd5382295758ecc3ecbd2a9aaff"},{"content_type":"application/pdf","access_level":"open_access","file_name":"2017_Thesis_Pull.pdf","checksum":"ee2e3ebb5b53c154c866f5b052b25153","relation":"main_file","date_updated":"2020-07-14T12:48:09Z","creator":"dernst","file_size":14400681,"date_created":"2019-04-05T07:53:04Z","file_id":"6200"}],"department":[{"_id":"SyCr"}],"language":[{"iso":"eng"}],"pubrep_id":"861","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Pull C. Disease defence in garden ants. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">10.15479/AT:ISTA:th_861</a>","ieee":"C. Pull, “Disease defence in garden ants,” Institute of Science and Technology Austria, 2017.","short":"C. Pull, Disease Defence in Garden Ants, Institute of Science and Technology Austria, 2017.","ista":"Pull C. 2017. Disease defence in garden ants. Institute of Science and Technology Austria.","chicago":"Pull, Christopher. “Disease Defence in Garden Ants.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">https://doi.org/10.15479/AT:ISTA:th_861</a>.","apa":"Pull, C. (2017). <i>Disease defence in garden ants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">https://doi.org/10.15479/AT:ISTA:th_861</a>","mla":"Pull, Christopher. <i>Disease Defence in Garden Ants</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_861\">10.15479/AT:ISTA:th_861</a>."}},{"ddc":["576","577","579"],"page":"87","type":"dissertation","_id":"820","date_updated":"2023-09-07T12:01:21Z","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"doi":"10.15479/AT:ISTA:th_857","acknowledgement":"ERC H2020 programme (grant agreement no. 648440)\r\nThanks to Jon Bollback for giving me the chance to do this work, for sharing the ideas that lay at the basis of this work, for his honesty and openness, showing himself to me as a person and not just as a boss. Thanks to Nick Barton for his guidance at the last stage, reading and commenting extensively on several versions of this manuscript, and for his encouragement; thanks to both Jon and Nick for their kindness and patience. Thanks to Erik van Nimwegen and Calin Guet for their time and willingness to be in my thesis committee, and to Erik van Nimwegen especially for agreeing to enter my thesis committee at the last moment, and for his very sharp, helpful and relevant comments during and after the defense. Thanks to my collaborators and discussion partners: Anne Kupczok, for her guidance, ideas and discussions during the construction of the manuscript of Chapter Two, and her comments on the manuscript; Georg Rieckh for making me aware of the issue of parameter identifiability, suggesting how to solve it, and for his unfortunate idea to start the plasmid enterprise in the first place; Murat Tugrul for sharing his model, for his enthusiasm, and his comments on Chapter Three; Srdjan Sarikas for his collaboration on the Monod model fitting, fast forwarding the analysis to turbo speed and making beautiful figures, and making the discussion fun on top of it all; Vanessa Barone for her last minute comments, especially on Chapter Three, providing a sharp and very helpful experimentalist perspective at the last moment; Maros Pleska and Marjon de Vos for their comments on the manuscript of Chapter Two; Gasper Tkacik for his crucial input on the relation between growth rate and lactose concentration; Bor Kavcic for his input on growth rate modeling and error propagation. Thanks to the Bollback, Bollenbach, Barton, Guet and Tkacik group members for both pro- viding an inspiring and supportive scientific environment to work in, as well as a lot of warmth and colour to everyday life. And thanks to the friends I found here, to the people who were there for me and to the people who changed my life, making it stranger and more beautiful than I could have imagined, Maros, Vanessa, Tade, Suzi, Andrej, Peter, Tiago, Kristof, Karin, Irene, Misha, Mato, Guillaume and Zanin. ","date_published":"2017-08-25T00:00:00Z","ec_funded":1,"status":"public","project":[{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"degree_awarded":"PhD","publist_id":"6829","year":"2017","file_date_updated":"2020-07-14T12:48:10Z","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"abstract":[{"text":"The lac operon is a classic model system for bacterial gene regulation, and has been studied extensively in E. coli, a classic model organism. However, not much is known about E. coli’s ecology and life outside the laboratory, in particular in soil and water environments. The natural diversity of the lac operon outside the laboratory, its role in the ecology of E. coli and the selection pressures it is exposed to, are similarly unknown.\r\nIn Chapter Two of this thesis, I explore the genetic diversity, phylogenetic history and signatures of selection of the lac operon across 20 natural isolates of E. coli and divergent clades of Escherichia. I found that complete lac operons were present in all isolates examined, which in all but one case were functional. The lac operon phylogeny conformed to the whole-genome phylogeny of the divergent Escherichia clades, which excludes horizontal gene transfer as an explanation for the presence of functional lac operons in these clades. All lac operon genes showed a signature of purifying selection; this signature was strongest for the lacY gene. Lac operon genes of human and environmental isolates showed similar signatures of selection, except the lacZ gene, which showed a stronger signature of selection in environmental isolates.\r\nIn Chapter Three, I try to identify the natural genetic variation relevant for phenotype and fitness in the lac operon, comparing growth rate on lactose and LacZ activity of the lac operons of these wild isolates in a common genetic background. Sequence variation in the lac promoter region, upstream of the -10 and -35 RNA polymerase binding motif, predicted variation in LacZ activity at full induction, using a thermodynamic model of polymerase binding (Tugrul, 2016). However, neither variation in LacZ activity, nor RNA polymerase binding predicted by the model correlated with variation in growth rate. Lac operons of human and environmental isolates did not differ systematically in either growth rate on lactose or LacZ protein activity, suggesting that these lac operons have been exposed to similar selection pressures. We thus have no evidence that the phenotypic variation we measured is relevant for fitness.\r\nTo start assessing the effect of genomic background on the growth phenotype conferred by the lac operon, I compared growth on minimal medium with lactose between lac operon constructs and the corresponding original isolates, I found that maximal growth rate was determined by genomic background, with almost all backgrounds conferring higher growth rates than lab strain K12 MG1655. However, I found no evidence that the lactose concentration at which growth was half maximal depended on genomic background.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"has_accepted_license":"1","date_created":"2018-12-11T11:48:41Z","title":"The lac operon in the wild","oa_version":"Published Version","day":"25","author":[{"last_name":"Jesse","full_name":"Jesse, Fabienne","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","first_name":"Fabienne"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Jesse, Fabienne. “The Lac Operon in the Wild.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">https://doi.org/10.15479/AT:ISTA:th_857</a>.","ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria.","mla":"Jesse, Fabienne. <i>The Lac Operon in the Wild</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">10.15479/AT:ISTA:th_857</a>.","apa":"Jesse, F. (2017). <i>The lac operon in the wild</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">https://doi.org/10.15479/AT:ISTA:th_857</a>","ama":"Jesse F. The lac operon in the wild. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_857\">10.15479/AT:ISTA:th_857</a>","short":"F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017.","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017."},"language":[{"iso":"eng"}],"pubrep_id":"857","oa":1,"file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","relation":"main_file","date_updated":"2020-07-14T12:48:10Z","creator":"system","date_created":"2018-12-12T10:17:00Z","file_size":3417773,"file_id":"5252"},{"relation":"source_file","checksum":"fc87d7d72fce52824a3ae7dcad0413a8","file_name":"2017_thesis_Jesse_source.tex","content_type":"application/x-tex","access_level":"closed","file_id":"6212","file_size":215899,"date_created":"2019-04-05T08:51:59Z","creator":"dernst","date_updated":"2020-07-14T12:48:10Z"}],"department":[{"_id":"JoBo"}],"month":"08","supervisor":[{"last_name":"Bollback","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","orcid":"0000-0002-4624-4612"}]},{"type":"dissertation","date_updated":"2023-09-07T12:01:59Z","_id":"821","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:th_854","article_processing_charge":"No","alternative_title":["ISTA Thesis"],"ddc":["000"],"page":"418","publist_id":"6828","related_material":{"record":[{"id":"1071","relation":"part_of_dissertation","status":"public"},{"id":"1437","status":"public","relation":"part_of_dissertation"},{"id":"1602","status":"public","relation":"part_of_dissertation"},{"id":"1604","relation":"part_of_dissertation","status":"public"},{"id":"1607","status":"public","relation":"part_of_dissertation"},{"id":"1714","status":"public","relation":"part_of_dissertation"}]},"year":"2017","acknowledgement":"First, I am thankful to my advisor, Krishnendu Chatterjee, for offering me the opportunity to\r\nmaterialize my scientific curiosity in a remarkably wide range of interesting topics, as well as for his constant availability and continuous support throughout my doctoral studies. I have had the privilege of collaborating with, discussing and getting inspired by all members of my committee: Thomas A. Henzinger, Ulrich Schmid and Martin A. Nowak. The role of the above four people has been very instrumental both to the research carried out for this dissertation, and to the researcher I evolved to in the process.\r\nI have greatly enjoyed my numerous brainstorming sessions with Rasmus Ibsen-Jensen, many\r\nof which led to results on low-treewidth graphs presented here.  I thank Alex Kößler for our\r\ndiscussions on modeling and analyzing real-time scheduling algorithms, Yaron Velner for our\r\ncollaboration on the Quantitative Interprocedural Analysis framework, and Nishant Sinha for our initial discussions on partial order reduction techniques in stateless model checking. I also thank Jan Otop, Ben Adlam, Bernhard Kragl and Josef Tkadlec for our fruitful collaborations on\r\ntopics outside the scope of this dissertation, as well as the interns Prateesh Goyal, Amir Kafshdar Goharshady, Samarth Mishra, Bhavya Choudhary and Marek Chalupa, with whom I have shared my excitement on various research topics. Together with my collaborators, I thank officemates and members of the Chatterjee and Henzinger groups throughout the years, Thorsten Tarrach, Ventsi Chonev, Roopsha Samanta, Przemek Daca, Mirco Giacobbe, Tanja Petrov, Ashutosh\r\nGupta,  Arjun Radhakrishna,  Petr Novontý,  Christian Hilbe,  Jakob Ruess,  Martin Chmelik,\r\nCezara Dragoi, Johannes Reiter, Andrey Kupriyanov, Guy Avni, Sasha Rubin, Jessica Davies, Hongfei Fu, Thomas Ferrère, Pavol Cerný, Ali Sezgin, Jan Kretínský, Sergiy Bogomolov, Hui\r\nKong, Benjamin Aminof, Duc-Hiep Chu, and Damien Zufferey.  Besides collaborations and office spaces, with many of the above people I have been fortunate to share numerous whiteboard\r\ndiscussions, as well as memorable long walks and amicable meals accompanied by stimulating\r\nconversations. I am highly indebted to Elisabeth Hacker for her continuous assistance in matters\r\nthat often exceeded her official duties, and who made my integration in Austria a smooth process.","date_published":"2017-08-09T00:00:00Z","ec_funded":1,"project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"status":"public","degree_awarded":"PhD","date_created":"2018-12-11T11:48:41Z","oa_version":"Published Version","title":"Algorithmic advances in program analysis and their applications","author":[{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","first_name":"Andreas"}],"day":"09","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","file_date_updated":"2020-07-14T12:48:10Z","abstract":[{"text":"This dissertation focuses on algorithmic aspects of program verification, and presents modeling and complexity advances on several problems related to the\r\nstatic analysis of programs, the stateless model checking of concurrent programs, and the competitive analysis of real-time scheduling algorithms.\r\nOur contributions can be broadly grouped into five categories.\r\n\r\nOur first contribution is a set of new algorithms and data structures for the quantitative and data-flow analysis of programs, based on the graph-theoretic notion of treewidth.\r\nIt has been observed that the control-flow graphs of typical programs have special structure, and are characterized as graphs of small treewidth.\r\nWe utilize this structural property to provide faster algorithms for the quantitative and data-flow analysis of recursive and concurrent programs.\r\nIn most cases we make an algebraic treatment of the considered problem,\r\nwhere several interesting analyses, such as the reachability, shortest path, and certain kind of data-flow analysis problems follow as special cases. \r\nWe exploit the constant-treewidth property to obtain algorithmic improvements for on-demand versions of the problems, \r\nand provide data structures with various tradeoffs between the resources spent in the preprocessing and querying phase.\r\nWe also improve on the algorithmic complexity of quantitative problems outside the algebraic path framework,\r\nnamely of the minimum mean-payoff, minimum ratio, and minimum initial credit for energy problems.\r\n\r\n\r\nOur second contribution is a set of algorithms for Dyck reachability with applications to data-dependence analysis and alias analysis.\r\nIn particular, we develop an optimal algorithm for Dyck reachability on bidirected graphs, which are ubiquitous in context-insensitive, field-sensitive points-to analysis.\r\nAdditionally, we develop an efficient algorithm for context-sensitive data-dependence analysis via Dyck reachability,\r\nwhere the task is to obtain analysis summaries of library code in the presence of callbacks.\r\nOur algorithm preprocesses libraries in almost linear time, after which the contribution of the library in the complexity of the client analysis is (i)~linear in the number of call sites and (ii)~only logarithmic in the size of the whole library, as opposed to linear in the size of the whole library.\r\nFinally, we prove that Dyck reachability is Boolean Matrix Multiplication-hard in general, and the hardness also holds for graphs of constant treewidth.\r\nThis hardness result strongly indicates that there exist no combinatorial algorithms for Dyck reachability with truly subcubic complexity.\r\n\r\n\r\nOur third contribution is the formalization and algorithmic treatment of the Quantitative Interprocedural Analysis framework.\r\nIn this framework, the transitions of a recursive program are annotated as good, bad or neutral, and receive a weight which measures\r\nthe magnitude of their respective effect.\r\nThe Quantitative Interprocedural Analysis problem asks to determine whether there exists an infinite run of the program where the long-run ratio of the bad weights over the good weights is above a given threshold.\r\nWe illustrate how several quantitative problems related to static analysis of recursive programs can be instantiated in this framework,\r\nand present some case studies to this direction.\r\n\r\n\r\nOur fourth contribution is a new dynamic partial-order reduction for the stateless model checking of concurrent programs. Traditional approaches rely on the standard Mazurkiewicz equivalence between  traces, by means of partitioning the trace space into equivalence classes, and attempting to explore a few representatives from each class.\r\nWe present a new dynamic partial-order reduction method  called the Data-centric Partial Order Reduction (DC-DPOR).\r\nOur algorithm is based on a new equivalence between traces, called the observation equivalence.\r\nDC-DPOR explores a coarser partitioning of the trace space than any exploration method based on the standard Mazurkiewicz equivalence.\r\nDepending on the program, the new partitioning can be even exponentially coarser.\r\nAdditionally, DC-DPOR spends only polynomial time in each explored class.\r\n\r\n\r\nOur fifth contribution is the use of automata and game-theoretic verification techniques in the competitive analysis and synthesis of real-time scheduling algorithms for firm-deadline tasks.\r\nOn the analysis side, we leverage automata on infinite words to compute the competitive ratio of real-time schedulers subject to various environmental constraints.\r\nOn the synthesis side, we introduce a new instance of two-player mean-payoff partial-information games, and show\r\nhow the synthesis of an optimal real-time scheduler can be reduced to computing winning strategies in this new type of games.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nd/4.0/","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","short":"CC BY-ND (4.0)"},"has_accepted_license":"1","file":[{"file_id":"4900","date_updated":"2020-07-14T12:48:10Z","creator":"system","date_created":"2018-12-12T10:11:44Z","file_size":4103115,"checksum":"3a3ec003f6ee73f41f82a544d63dfc77","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf"},{"content_type":"application/zip","access_level":"closed","file_name":"2017_thesis_Pavlogiannis.zip","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","relation":"source_file","creator":"dernst","date_updated":"2020-07-14T12:48:10Z","date_created":"2019-04-05T07:59:31Z","file_size":14744374,"file_id":"6201"}],"department":[{"_id":"KrCh"}],"month":"08","supervisor":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Pavlogiannis, Andreas. “Algorithmic Advances in Program Analysis and Their Applications.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">https://doi.org/10.15479/AT:ISTA:th_854</a>.","ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria.","mla":"Pavlogiannis, Andreas. <i>Algorithmic Advances in Program Analysis and Their Applications</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">10.15479/AT:ISTA:th_854</a>.","apa":"Pavlogiannis, A. (2017). <i>Algorithmic advances in program analysis and their applications</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">https://doi.org/10.15479/AT:ISTA:th_854</a>","ama":"Pavlogiannis A. Algorithmic advances in program analysis and their applications. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_854\">10.15479/AT:ISTA:th_854</a>","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017.","ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017."},"pubrep_id":"854","language":[{"iso":"eng"}],"oa":1},{"external_id":{"isi":["000412130500061"],"pmid":["28923953"]},"isi":1,"year":"2017","publist_id":"6827","publication":"PNAS","status":"public","project":[{"name":"Optimality principles in responses to antibiotics","grant_number":"303507","call_identifier":"FP7","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","call_identifier":"FWF"}],"date_published":"2017-10-03T00:00:00Z","ec_funded":1,"pmid":1,"publisher":"National Academy of Sciences","article_processing_charge":"No","doi":"10.1073/pnas.1713372114","type":"journal_article","_id":"822","date_updated":"2023-09-26T16:18:48Z","page":"10666 - 10671","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/"}],"month":"10","department":[{"_id":"ToBo"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"de Vos, Marjon, et al. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” <i>PNAS</i>, vol. 114, no. 40, National Academy of Sciences, 2017, pp. 10666–71, doi:<a href=\"https://doi.org/10.1073/pnas.1713372114\">10.1073/pnas.1713372114</a>.","apa":"de Vos, M., Zagórski, M. P., Mcnally, A., &#38; Bollenbach, M. T. (2017). Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713372114\">https://doi.org/10.1073/pnas.1713372114</a>","chicago":"Vos, Marjon de, Marcin P Zagórski, Alan Mcnally, and Mark Tobias Bollenbach. “Interaction Networks, Ecological Stability, and Collective Antibiotic Tolerance in Polymicrobial Infections.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1713372114\">https://doi.org/10.1073/pnas.1713372114</a>.","ista":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. 2017. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. PNAS. 114(40), 10666–10671.","short":"M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.","ieee":"M. de Vos, M. P. Zagórski, A. Mcnally, and M. T. Bollenbach, “Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections,” <i>PNAS</i>, vol. 114, no. 40. National Academy of Sciences, pp. 10666–10671, 2017.","ama":"de Vos M, Zagórski MP, Mcnally A, Bollenbach MT. Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections. <i>PNAS</i>. 2017;114(40):10666-10671. doi:<a href=\"https://doi.org/10.1073/pnas.1713372114\">10.1073/pnas.1713372114</a>"},"issue":"40","title":"Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections","oa_version":"Submitted Version","day":"03","scopus_import":"1","author":[{"first_name":"Marjon","id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","full_name":"De Vos, Marjon","last_name":"De Vos"},{"last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P","first_name":"Marcin P","orcid":"0000-0001-7896-7762"},{"last_name":"Mcnally","full_name":"Mcnally, Alan","first_name":"Alan"},{"orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:48:41Z","volume":114,"abstract":[{"text":"Polymicrobial infections constitute small ecosystems that accommodate several bacterial species. Commonly, these bacteria are investigated in isolation. However, it is unknown to what extent the isolates interact and whether their interactions alter bacterial growth and ecosystem resilience in the presence and absence of antibiotics. We quantified the complete ecological interaction network for 72 bacterial isolates collected from 23 individuals diagnosed with polymicrobial urinary tract infections and found that most interactions cluster based on evolutionary relatedness. Statistical network analysis revealed that competitive and cooperative reciprocal interactions are enriched in the global network, while cooperative interactions are depleted in the individual host community networks. A population dynamics model parameterized by our measurements suggests that interactions restrict community stability, explaining the observed species diversity of these communities. We further show that the clinical isolates frequently protect each other from clinically relevant antibiotics. Together, these results highlight that ecological interactions are crucial for the growth and survival of bacteria in polymicrobial infection communities and affect their assembly and resilience. ","lang":"eng"}],"intvolume":"       114","publication_status":"published","publication_identifier":{"issn":["00278424"]}},{"department":[{"_id":"GaTk"}],"article_number":"093404","month":"09","issue":"9","citation":{"ista":"Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions in integer linear problems.  Journal of Statistical Mechanics: Theory and Experiment. 2017(9), 093404.","chicago":"Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOPscience, 2017. <a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">https://doi.org/10.1088/1742-5468/aa85c3</a>.","mla":"Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2017, no. 9, 093404, IOPscience, 2017, doi:<a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">10.1088/1742-5468/aa85c3</a>.","apa":"Colabrese, S., De Martino, D., Leuzzi, L., &#38; Marinari, E. (2017). Phase transitions in integer linear problems. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. IOPscience. <a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">https://doi.org/10.1088/1742-5468/aa85c3</a>","ama":"Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. <i> Journal of Statistical Mechanics: Theory and Experiment</i>. 2017;2017(9). doi:<a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">10.1088/1742-5468/aa85c3</a>","short":"S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari,  Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).","ieee":"S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,” <i> Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2017, no. 9. IOPscience, 2017."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"language":[{"iso":"eng"}],"volume":2017,"date_created":"2018-12-11T11:48:41Z","author":[{"full_name":"Colabrese, Simona","last_name":"Colabrese","first_name":"Simona"},{"first_name":"Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele"},{"first_name":"Luca","full_name":"Leuzzi, Luca","last_name":"Leuzzi"},{"full_name":"Marinari, Enzo","last_name":"Marinari","first_name":"Enzo"}],"scopus_import":"1","day":"26","title":"Phase transitions in integer linear problems","oa_version":"Submitted Version","publication_status":"published","publication_identifier":{"issn":["17425468"]},"abstract":[{"lang":"eng","text":"The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region."}],"intvolume":"      2017","publist_id":"6826","isi":1,"year":"2017","external_id":{"isi":["000411842900001"]},"ec_funded":1,"date_published":"2017-09-26T00:00:00Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"publication":" Journal of Statistical Mechanics: Theory and Experiment","status":"public","date_updated":"2023-09-26T16:18:12Z","_id":"823","type":"journal_article","doi":"10.1088/1742-5468/aa85c3","article_processing_charge":"No","publisher":"IOPscience","main_file_link":[{"url":"https://arxiv.org/abs/1705.06303","open_access":"1"}],"quality_controlled":"1"},{"month":"09","year":"2017","status":"public","language":[{"iso":"eng"}],"extern":"1","publication":"Oncotarget","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2017-09-15T00:00:00Z","citation":{"ieee":"J. Singer <i>et al.</i>, “Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials,” <i>Oncotarget</i>, vol. 8. Impact Journals, pp. 83128–83141, 2017.","short":"J. Singer, N. Berroterán-Infante, C. Rami-Mark, M. Dumanic, M. Matz, M. Willmann, F. Andreae, J. Singer, W. Wadsak, M. Mitterhauser, E. Jensen-Jarolim, Oncotarget 8 (2017) 83128–83141.","ama":"Singer J, Berroterán-Infante N, Rami-Mark C, et al. Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials. <i>Oncotarget</i>. 2017;8:83128-83141. doi:<a href=\"https://doi.org/10.18632/oncotarget.20914\">10.18632/oncotarget.20914</a>","apa":"Singer, J., Berroterán-Infante, N., Rami-Mark, C., Dumanic, M., Matz, M., Willmann, M., … Jensen-Jarolim, E. (2017). Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials. <i>Oncotarget</i>. Impact Journals. <a href=\"https://doi.org/10.18632/oncotarget.20914\">https://doi.org/10.18632/oncotarget.20914</a>","mla":"Singer, Judit, et al. “Development of a Radiolabeled Caninized Anti-EGFR Antibody for Comparative Oncology Trials.” <i>Oncotarget</i>, vol. 8, Impact Journals, 2017, pp. 83128–41, doi:<a href=\"https://doi.org/10.18632/oncotarget.20914\">10.18632/oncotarget.20914</a>.","ista":"Singer J, Berroterán-Infante N, Rami-Mark C, Dumanic M, Matz M, Willmann M, Andreae F, Singer J, Wadsak W, Mitterhauser M, Jensen-Jarolim E. 2017. Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials. Oncotarget. 8, 83128–83141.","chicago":"Singer, Judit, Neydher Berroterán-Infante, Christina Rami-Mark, Monika Dumanic, Miroslawa Matz, Michael Willmann, Fritz Andreae, et al. “Development of a Radiolabeled Caninized Anti-EGFR Antibody for Comparative Oncology Trials.” <i>Oncotarget</i>. Impact Journals, 2017. <a href=\"https://doi.org/10.18632/oncotarget.20914\">https://doi.org/10.18632/oncotarget.20914</a>."},"oa_version":"Published Version","title":"Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials","publisher":"Impact Journals","day":"15","article_processing_charge":"No","author":[{"last_name":"Fazekas-Singer","full_name":"Fazekas-Singer, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","first_name":"Judit"},{"first_name":"Neydher","full_name":"Berroterán-Infante, Neydher","last_name":"Berroterán-Infante"},{"first_name":"Christina","last_name":"Rami-Mark","full_name":"Rami-Mark, Christina"},{"last_name":"Dumanic","full_name":"Dumanic, Monika","first_name":"Monika"},{"first_name":"Miroslawa","full_name":"Matz, Miroslawa","last_name":"Matz"},{"full_name":"Willmann, Michael","last_name":"Willmann","first_name":"Michael"},{"first_name":"Fritz","full_name":"Andreae, Fritz","last_name":"Andreae"},{"full_name":"Singer, Josef","last_name":"Singer","first_name":"Josef"},{"first_name":"Wolfgang","last_name":"Wadsak","full_name":"Wadsak, Wolfgang"},{"first_name":"Markus","last_name":"Mitterhauser","full_name":"Mitterhauser, Markus"},{"first_name":"Erika","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika"}],"doi":"10.18632/oncotarget.20914","date_created":"2020-08-10T11:53:18Z","article_type":"original","type":"journal_article","volume":8,"_id":"8235","date_updated":"2021-01-12T08:17:39Z","intvolume":"         8","abstract":[{"text":"Due to large homology of human and canine EGFR, dogs suffering from spontaneous EGFR+ cancer can be considered as ideal translational models. Thereby, novel immunotherapeutic compounds can be developed for both human and veterinary patients. This study describes the radiolabeling of a canine anti-EGFR IgG antibody (can225IgG) with potential diagnostic and therapeutic value in comparative clinical settings. Can225IgG was functionalized with DTPA for subsequent chelation with the radionuclide 99mTc. Successful coupling of 10 DTPA molecules per antibody on average was proven by significant mass increase in MALDI-TOF spectroscopy, gel electrophoresis and immunoblots. Following functionalization and radiolabeling, 99mTc-DTPA-can225IgG fully retained its binding capacity towards human and canine EGFR in flow cytometry, immuno- and radioblots, and autoradiography. The affinity of radiolabeled can225IgG was determined to KD 0.8 ±0.0031 nM in a real-time kinetics assay on canine carcinoma cells by a competition binding technique. Stability tests of the radiolabeled compound identified TRIS buffered saline as the ideal formulation for short-term storage with 87.11 ±6.04% intact compound being still detected 60 minutes post radiolabeling. High stability, specificity and EGFR binding affinity pinpoint towards 99mTc-radiolabeled can225IgG antibody as an ideal lead compound for the first proof-of-concept diagnostic and therapeutic applications in canine cancer patients.","lang":"eng"}],"page":"83128-83141","quality_controlled":"1","publication_identifier":{"issn":["1949-2553"]},"publication_status":"published","main_file_link":[{"url":"https://doi.org/10.18632/oncotarget.20914","open_access":"1"}]},{"article_type":"original","date_created":"2020-08-10T11:53:26Z","volume":72,"title":"AllergoOncology - the impact of allergy in oncology: EAACI position paper","oa_version":"Published Version","author":[{"orcid":"0000-0003-4019-5765","first_name":"E.","last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, E."},{"last_name":"Bax","full_name":"Bax, H. J.","first_name":"H. J."},{"first_name":"R.","full_name":"Bianchini, R.","last_name":"Bianchini"},{"full_name":"Capron, M.","last_name":"Capron","first_name":"M."},{"first_name":"C.","last_name":"Corrigan","full_name":"Corrigan, C."},{"last_name":"Castells","full_name":"Castells, M.","first_name":"M."},{"last_name":"Dombrowicz","full_name":"Dombrowicz, D.","first_name":"D."},{"first_name":"T. R.","full_name":"Daniels-Wells, T. R.","last_name":"Daniels-Wells"},{"orcid":"0000-0002-8777-3502","first_name":"Judit","last_name":"Fazekas","full_name":"Fazekas, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"first_name":"E.","last_name":"Fiebiger","full_name":"Fiebiger, E."},{"last_name":"Gatault","full_name":"Gatault, S.","first_name":"S."},{"full_name":"Gould, H. J.","last_name":"Gould","first_name":"H. J."},{"full_name":"Janda, J.","last_name":"Janda","first_name":"J."},{"first_name":"D. H.","full_name":"Josephs, D. H.","last_name":"Josephs"},{"first_name":"P.","full_name":"Karagiannis, P.","last_name":"Karagiannis"},{"full_name":"Levi-Schaffer, F.","last_name":"Levi-Schaffer","first_name":"F."},{"last_name":"Meshcheryakova","full_name":"Meshcheryakova, A.","first_name":"A."},{"first_name":"D.","full_name":"Mechtcheriakova, D.","last_name":"Mechtcheriakova"},{"first_name":"Y.","last_name":"Mekori","full_name":"Mekori, Y."},{"first_name":"F.","full_name":"Mungenast, F.","last_name":"Mungenast"},{"full_name":"Nigro, E. A.","last_name":"Nigro","first_name":"E. A."},{"last_name":"Penichet","full_name":"Penichet, M. L.","first_name":"M. L."},{"last_name":"Redegeld","full_name":"Redegeld, F.","first_name":"F."},{"first_name":"L.","full_name":"Saul, L.","last_name":"Saul"},{"first_name":"J.","full_name":"Singer, J.","last_name":"Singer"},{"first_name":"J. F.","last_name":"Spicer","full_name":"Spicer, J. F."},{"full_name":"Siccardi, A. G.","last_name":"Siccardi","first_name":"A. G."},{"first_name":"E.","full_name":"Spillner, E.","last_name":"Spillner"},{"last_name":"Turner","full_name":"Turner, M. C.","first_name":"M. C."},{"full_name":"Untersmayr, E.","last_name":"Untersmayr","first_name":"E."},{"first_name":"L.","full_name":"Vangelista, L.","last_name":"Vangelista"},{"full_name":"Karagiannis, S. N.","last_name":"Karagiannis","first_name":"S. N."}],"day":"01","publication_status":"published","publication_identifier":{"issn":["0105-4538"]},"abstract":[{"text":"Th2 immunity and allergic immune surveillance play critical roles in host responses to pathogens, parasites and allergens. Numerous studies have reported significant links between Th2 responses and cancer, including insights into the functions of IgE antibodies and associated effector cells in both antitumour immune surveillance and therapy. The interdisciplinary field of AllergoOncology was given Task Force status by the European Academy of Allergy and Clinical Immunology in 2014. Affiliated expert groups focus on the interface between allergic responses and cancer, applied to immune surveillance, immunomodulation and the functions of IgE‐mediated immune responses against cancer, to derive novel insights into more effective treatments. Coincident with rapid expansion in clinical application of cancer immunotherapies, here we review the current state‐of‐the‐art and future translational opportunities, as well as challenges in this relatively new field. Recent developments include improved understanding of Th2 antibodies, intratumoral innate allergy effector cells and mediators, IgE‐mediated tumour antigen cross‐presentation by dendritic cells, as well as immunotherapeutic strategies such as vaccines and recombinant antibodies, and finally, the management of allergy in daily clinical oncology. Shedding light on the crosstalk between allergic response and cancer is paving the way for new avenues of treatment.","lang":"eng"}],"intvolume":"        72","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","citation":{"chicago":"Jensen-Jarolim, E., H. J. Bax, R. Bianchini, M. Capron, C. Corrigan, M. Castells, D. Dombrowicz, et al. “AllergoOncology - the Impact of Allergy in Oncology: EAACI Position Paper.” <i>Allergy</i>. Wiley, 2017. <a href=\"https://doi.org/10.1111/all.13119\">https://doi.org/10.1111/all.13119</a>.","ista":"Jensen-Jarolim E, Bax HJ, Bianchini R, Capron M, Corrigan C, Castells M, Dombrowicz D, Daniels-Wells TR, Singer J, Fiebiger E, Gatault S, Gould HJ, Janda J, Josephs DH, Karagiannis P, Levi-Schaffer F, Meshcheryakova A, Mechtcheriakova D, Mekori Y, Mungenast F, Nigro EA, Penichet ML, Redegeld F, Saul L, Singer J, Spicer JF, Siccardi AG, Spillner E, Turner MC, Untersmayr E, Vangelista L, Karagiannis SN. 2017. AllergoOncology - the impact of allergy in oncology: EAACI position paper. Allergy. 72(6), 866–887.","mla":"Jensen-Jarolim, E., et al. “AllergoOncology - the Impact of Allergy in Oncology: EAACI Position Paper.” <i>Allergy</i>, vol. 72, no. 6, Wiley, 2017, pp. 866–87, doi:<a href=\"https://doi.org/10.1111/all.13119\">10.1111/all.13119</a>.","apa":"Jensen-Jarolim, E., Bax, H. J., Bianchini, R., Capron, M., Corrigan, C., Castells, M., … Karagiannis, S. N. (2017). AllergoOncology - the impact of allergy in oncology: EAACI position paper. <i>Allergy</i>. Wiley. <a href=\"https://doi.org/10.1111/all.13119\">https://doi.org/10.1111/all.13119</a>","ama":"Jensen-Jarolim E, Bax HJ, Bianchini R, et al. AllergoOncology - the impact of allergy in oncology: EAACI position paper. <i>Allergy</i>. 2017;72(6):866-887. doi:<a href=\"https://doi.org/10.1111/all.13119\">10.1111/all.13119</a>","short":"E. Jensen-Jarolim, H.J. Bax, R. Bianchini, M. Capron, C. Corrigan, M. Castells, D. Dombrowicz, T.R. Daniels-Wells, J. Singer, E. Fiebiger, S. Gatault, H.J. Gould, J. Janda, D.H. Josephs, P. Karagiannis, F. Levi-Schaffer, A. Meshcheryakova, D. Mechtcheriakova, Y. Mekori, F. Mungenast, E.A. Nigro, M.L. Penichet, F. Redegeld, L. Saul, J. Singer, J.F. Spicer, A.G. Siccardi, E. Spillner, M.C. Turner, E. Untersmayr, L. Vangelista, S.N. Karagiannis, Allergy 72 (2017) 866–887.","ieee":"E. Jensen-Jarolim <i>et al.</i>, “AllergoOncology - the impact of allergy in oncology: EAACI position paper,” <i>Allergy</i>, vol. 72, no. 6. Wiley, pp. 866–887, 2017."},"language":[{"iso":"eng"}],"oa":1,"type":"journal_article","date_updated":"2021-01-12T08:17:39Z","_id":"8236","publisher":"Wiley","doi":"10.1111/all.13119","article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1111/all.13119","open_access":"1"}],"page":"866-887","year":"2017","date_published":"2017-06-01T00:00:00Z","extern":"1","publication":"Allergy","status":"public"},{"year":"2017","month":"09","article_number":"1112","oa":1,"language":[{"iso":"eng"}],"extern":"1","status":"public","publication":"Frontiers in Immunology","citation":{"apa":"Ilieva, K. M., Singer, J., Achkova, D. Y., Dodev, T. S., Mele, S., Crescioli, S., … Karagiannis, S. N. (2017). Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields. <i>Frontiers in Immunology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fimmu.2017.01112\">https://doi.org/10.3389/fimmu.2017.01112</a>","mla":"Ilieva, Kristina M., et al. “Functionally Active Fc Mutant Antibodies Recognizing Cancer Antigens Generated Rapidly at High Yields.” <i>Frontiers in Immunology</i>, vol. 8, 1112, Frontiers, 2017, doi:<a href=\"https://doi.org/10.3389/fimmu.2017.01112\">10.3389/fimmu.2017.01112</a>.","chicago":"Ilieva, Kristina M., Judit Singer, Daniela Y. Achkova, Tihomir S. Dodev, Silvia Mele, Silvia Crescioli, Heather J. Bax, et al. “Functionally Active Fc Mutant Antibodies Recognizing Cancer Antigens Generated Rapidly at High Yields.” <i>Frontiers in Immunology</i>. Frontiers, 2017. <a href=\"https://doi.org/10.3389/fimmu.2017.01112\">https://doi.org/10.3389/fimmu.2017.01112</a>.","ista":"Ilieva KM, Singer J, Achkova DY, Dodev TS, Mele S, Crescioli S, Bax HJ, Cheung A, Karagiannis P, Correa I, Figini M, Marlow R, Josephs DH, Beavil AJ, Maher J, Spicer JF, Jensen-Jarolim E, Tutt AN, Karagiannis SN. 2017. Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields. Frontiers in Immunology. 8, 1112.","ieee":"K. M. Ilieva <i>et al.</i>, “Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields,” <i>Frontiers in Immunology</i>, vol. 8. Frontiers, 2017.","short":"K.M. Ilieva, J. Singer, D.Y. Achkova, T.S. Dodev, S. Mele, S. Crescioli, H.J. Bax, A. Cheung, P. Karagiannis, I. Correa, M. Figini, R. Marlow, D.H. Josephs, A.J. Beavil, J. Maher, J.F. Spicer, E. Jensen-Jarolim, A.N. Tutt, S.N. Karagiannis, Frontiers in Immunology 8 (2017).","ama":"Ilieva KM, Singer J, Achkova DY, et al. Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields. <i>Frontiers in Immunology</i>. 2017;8. doi:<a href=\"https://doi.org/10.3389/fimmu.2017.01112\">10.3389/fimmu.2017.01112</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2017-09-11T00:00:00Z","day":"11","article_processing_charge":"No","author":[{"first_name":"Kristina M.","last_name":"Ilieva","full_name":"Ilieva, Kristina M."},{"orcid":"0000-0002-8777-3502","first_name":"Judit","last_name":"Fazekas-Singer","full_name":"Fazekas-Singer, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Achkova, Daniela Y.","last_name":"Achkova","first_name":"Daniela Y."},{"first_name":"Tihomir S.","full_name":"Dodev, Tihomir S.","last_name":"Dodev"},{"first_name":"Silvia","last_name":"Mele","full_name":"Mele, Silvia"},{"first_name":"Silvia","last_name":"Crescioli","full_name":"Crescioli, Silvia"},{"full_name":"Bax, Heather J.","last_name":"Bax","first_name":"Heather J."},{"last_name":"Cheung","full_name":"Cheung, Anthony","first_name":"Anthony"},{"full_name":"Karagiannis, Panagiotis","last_name":"Karagiannis","first_name":"Panagiotis"},{"first_name":"Isabel","last_name":"Correa","full_name":"Correa, Isabel"},{"first_name":"Mariangela","full_name":"Figini, Mariangela","last_name":"Figini"},{"first_name":"Rebecca","last_name":"Marlow","full_name":"Marlow, Rebecca"},{"last_name":"Josephs","full_name":"Josephs, Debra H.","first_name":"Debra H."},{"first_name":"Andrew J.","last_name":"Beavil","full_name":"Beavil, Andrew J."},{"full_name":"Maher, John","last_name":"Maher","first_name":"John"},{"first_name":"James F.","last_name":"Spicer","full_name":"Spicer, James F."},{"full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim","first_name":"Erika"},{"last_name":"Tutt","full_name":"Tutt, Andrew N.","first_name":"Andrew N."},{"first_name":"Sophia N.","full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis"}],"doi":"10.3389/fimmu.2017.01112","publisher":"Frontiers","title":"Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields","oa_version":"Published Version","volume":8,"_id":"8237","date_updated":"2021-01-12T08:17:39Z","date_created":"2020-08-10T11:53:32Z","article_type":"original","type":"journal_article","intvolume":"         8","abstract":[{"text":"Monoclonal antibodies find broad application as therapy for various types of cancer by employing multiple mechanisms of action against tumors. Manipulating the Fc-mediated functions of antibodies that engage immune effector cells, such as NK cells, represents a strategy to influence effector cell activation and to enhance antibody potency and potentially efficacy. We developed a novel approach to generate and ascertain the functional attributes of Fc mutant monoclonal antibodies. This entailed coupling single expression vector (pVitro1) antibody cloning, using polymerase incomplete primer extension (PIPE) polymerase chain reaction, together with simultaneous Fc region point mutagenesis and high yield transient expression in human mammalian cells. Employing this, we engineered wild type, low (N297Q, NQ), and high (S239D/I332E, DE) FcR-binding Fc mutant monoclonal antibody panels recognizing two cancer antigens, HER2/neu and chondroitin sulfate proteoglycan 4. Antibodies were generated with universal mutagenic primers applicable to any IgG1 pVitro1 constructs, with high mutagenesis and transfection efficiency, in small culture volumes, at high yields and within 12 days from design to purified material. Antibody variants conserved their Fab-mediated recognition of target antigens and their direct anti-proliferative effects against cancer cells. Fc mutations had a significant impact on antibody interactions with Fc receptors (FcRs) on human NK cells, and consequently on the potency of NK cell activation, quantified by immune complex-mediated calcium mobilization and by antibody-dependent cellular cytotoxicity (ADCC) of tumor cells. This strategy for manipulation and testing of Fc region engagement with cognate FcRs can facilitate the design of antibodies with defined effector functions and potentially enhanced efficacy against tumor cells.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.3389/fimmu.2017.01112","open_access":"1"}],"publication_status":"published","publication_identifier":{"issn":["1664-3224"]},"quality_controlled":"1"},{"abstract":[{"lang":"eng","text":"Acrolein, a highly reactive unsaturated aldehyde, is generated in large amounts during smoking and is best known for its genotoxic capacity. Here, we aimed to assess whether acrolein at concentrations relevant for smokers may also exert immunomodulatory effects that could be relevant in allergy or cancer. In a BALB/c allergy model repeated nasal exposure to acrolein abrogated allergen-specific antibody and cytokine formation, and led to a relative accumulation of regulatory T cells in the lungs. Only the acrolein-treated mice were protected from bronchial hyperreactivity as well as from anaphylactic reactions upon challenge with the specific allergen. Moreover, grafted D2F2 tumor cells grew faster and intratumoral Foxp3+ cell accumulation was observed in these mice compared to sham-treated controls. Results from reporter cell lines suggested that acrolein acts via the aryl-hydrocarbon receptor which could be inhibited by resveratrol and 3′-methoxy-4′-nitroflavone Acrolein- stimulation of human PBMCs increased Foxp3+ expression by T cells which could be antagonized by resveratrol. Our mouse and human data thus revealed that acrolein exerts systemic immunosuppression by promoting Foxp3+ regulatory cells. This provides a novel explanation why smokers have a lower allergy, but higher cancer risk."}],"intvolume":"         7","publication_identifier":{"issn":["2045-2322"]},"quality_controlled":"1","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/srep45067"}],"title":"Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure","publisher":"Springer Nature","oa_version":"Published Version","doi":"10.1038/srep45067","author":[{"last_name":"Roth-Walter","full_name":"Roth-Walter, Franziska","first_name":"Franziska"},{"first_name":"Cornelia","full_name":"Bergmayr, Cornelia","last_name":"Bergmayr"},{"last_name":"Meitz","full_name":"Meitz, Sarah","first_name":"Sarah"},{"first_name":"Stefan","full_name":"Buchleitner, Stefan","last_name":"Buchleitner"},{"first_name":"Caroline","full_name":"Stremnitzer, Caroline","last_name":"Stremnitzer"},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","full_name":"Fazekas, Judit","last_name":"Fazekas","first_name":"Judit","orcid":"0000-0002-8777-3502"},{"first_name":"Anna","full_name":"Moskovskich, Anna","last_name":"Moskovskich"},{"first_name":"Mario A.","last_name":"Müller","full_name":"Müller, Mario A."},{"first_name":"Georg A.","full_name":"Roth, Georg A.","last_name":"Roth"},{"first_name":"Krisztina","full_name":"Manzano-Szalai, Krisztina","last_name":"Manzano-Szalai"},{"full_name":"Dvorak, Zdenek","last_name":"Dvorak","first_name":"Zdenek"},{"first_name":"Alina","last_name":"Neunkirchner","full_name":"Neunkirchner, Alina"},{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika","first_name":"Erika"}],"article_processing_charge":"No","day":"23","article_type":"original","type":"journal_article","date_created":"2020-08-10T11:53:46Z","date_updated":"2021-01-12T08:17:40Z","volume":7,"_id":"8239","language":[{"iso":"eng"}],"extern":"1","publication":"Scientific Reports","status":"public","oa":1,"date_published":"2017-03-23T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Roth-Walter F, Bergmayr C, Meitz S, et al. Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure. <i>Scientific Reports</i>. 2017;7. doi:<a href=\"https://doi.org/10.1038/srep45067\">10.1038/srep45067</a>","short":"F. Roth-Walter, C. Bergmayr, S. Meitz, S. Buchleitner, C. Stremnitzer, J. Singer, A. Moskovskich, M.A. Müller, G.A. Roth, K. Manzano-Szalai, Z. Dvorak, A. Neunkirchner, E. Jensen-Jarolim, Scientific Reports 7 (2017).","ieee":"F. Roth-Walter <i>et al.</i>, “Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure,” <i>Scientific Reports</i>, vol. 7. Springer Nature, 2017.","ista":"Roth-Walter F, Bergmayr C, Meitz S, Buchleitner S, Stremnitzer C, Singer J, Moskovskich A, Müller MA, Roth GA, Manzano-Szalai K, Dvorak Z, Neunkirchner A, Jensen-Jarolim E. 2017. Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure. Scientific Reports. 7, 45067.","chicago":"Roth-Walter, Franziska, Cornelia Bergmayr, Sarah Meitz, Stefan Buchleitner, Caroline Stremnitzer, Judit Singer, Anna Moskovskich, et al. “Janus-Faced Acrolein Prevents Allergy but Accelerates Tumor Growth by Promoting Immunoregulatory Foxp3+ Cells: Mouse Model for Passive Respiratory Exposure.” <i>Scientific Reports</i>. Springer Nature, 2017. <a href=\"https://doi.org/10.1038/srep45067\">https://doi.org/10.1038/srep45067</a>.","mla":"Roth-Walter, Franziska, et al. “Janus-Faced Acrolein Prevents Allergy but Accelerates Tumor Growth by Promoting Immunoregulatory Foxp3+ Cells: Mouse Model for Passive Respiratory Exposure.” <i>Scientific Reports</i>, vol. 7, 45067, Springer Nature, 2017, doi:<a href=\"https://doi.org/10.1038/srep45067\">10.1038/srep45067</a>.","apa":"Roth-Walter, F., Bergmayr, C., Meitz, S., Buchleitner, S., Stremnitzer, C., Singer, J., … Jensen-Jarolim, E. (2017). Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/srep45067\">https://doi.org/10.1038/srep45067</a>"},"month":"03","year":"2017","article_number":"45067"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Budanur NB, Hof B. Heteroclinic path to spatially localized chaos in pipe flow. <i>Journal of Fluid Mechanics</i>. 2017;827. doi:<a href=\"https://doi.org/10.1017/jfm.2017.516\">10.1017/jfm.2017.516</a>","ieee":"N. B. Budanur and B. Hof, “Heteroclinic path to spatially localized chaos in pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 827. Cambridge University Press, 2017.","short":"N.B. Budanur, B. Hof, Journal of Fluid Mechanics 827 (2017).","chicago":"Budanur, Nazmi B, and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jfm.2017.516\">https://doi.org/10.1017/jfm.2017.516</a>.","ista":"Budanur NB, Hof B. 2017. Heteroclinic path to spatially localized chaos in pipe flow. Journal of Fluid Mechanics. 827, R1.","apa":"Budanur, N. B., &#38; Hof, B. (2017). Heteroclinic path to spatially localized chaos in pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2017.516\">https://doi.org/10.1017/jfm.2017.516</a>","mla":"Budanur, Nazmi B., and Björn Hof. “Heteroclinic Path to Spatially Localized Chaos in Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 827, R1, Cambridge University Press, 2017, doi:<a href=\"https://doi.org/10.1017/jfm.2017.516\">10.1017/jfm.2017.516</a>."},"language":[{"iso":"eng"}],"oa":1,"article_number":"R1","department":[{"_id":"BjHo"}],"month":"08","publication_status":"published","publication_identifier":{"issn":["00221120"]},"intvolume":"       827","abstract":[{"text":"In shear flows at transitional Reynolds numbers, localized patches of turbulence, known as puffs, coexist with the laminar flow. Recently, Avila et al. (Phys. Rev. Lett., vol. 110, 2013, 224502) discovered two spatially localized relative periodic solutions for pipe flow, which appeared in a saddle-node bifurcation at low Reynolds number. Combining slicing methods for continuous symmetry reduction with Poincaré sections for the first time in a shear flow setting, we compute and visualize the unstable manifold of the lower-branch solution and show that it extends towards the neighbourhood of the upper-branch solution. Surprisingly, this connection even persists far above the bifurcation point and appears to mediate the first stage of the puff generation: amplification of streamwise localized fluctuations. When the state-space trajectories on the unstable manifold reach the vicinity of the upper branch, corresponding fluctuations expand in space and eventually take the usual shape of a puff.","lang":"eng"}],"date_created":"2018-12-11T11:48:42Z","volume":827,"title":"Heteroclinic path to spatially localized chaos in pipe flow","oa_version":"Submitted Version","day":"18","scopus_import":"1","author":[{"first_name":"Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","full_name":"Budanur, Nazmi B"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn"}],"date_published":"2017-08-18T00:00:00Z","publication":"Journal of Fluid Mechanics","status":"public","publist_id":"6824","external_id":{"isi":["000408326300001"]},"isi":1,"year":"2017","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.10484"}],"type":"journal_article","_id":"824","date_updated":"2023-09-26T16:17:43Z","publisher":"Cambridge University Press","article_processing_charge":"No","doi":"10.1017/jfm.2017.516"},{"citation":{"ieee":"J. Singer, T. W. Grunt, E. Jensen-Jarolim, and J. Singer, “Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474,” <i>Oncotarget</i>, vol. 8. Impact Journals, pp. 35076–35087, 2017.","short":"J. Singer, T.W. Grunt, E. Jensen-Jarolim, J. Singer, Oncotarget 8 (2017) 35076–35087.","ama":"Singer J, Grunt TW, Jensen-Jarolim E, Singer J. Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474. <i>Oncotarget</i>. 2017;8:35076-35087. doi:<a href=\"https://doi.org/10.18632/oncotarget.16623\">10.18632/oncotarget.16623</a>","apa":"Singer, J., Grunt, T. W., Jensen-Jarolim, E., &#38; Singer, J. (2017). Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474. <i>Oncotarget</i>. Impact Journals. <a href=\"https://doi.org/10.18632/oncotarget.16623\">https://doi.org/10.18632/oncotarget.16623</a>","mla":"Singer, Judit, et al. “Long Term Storage in Liquid Nitrogen Leads to Only Minor Phenotypic and Gene Expression Changes in the Mammary Carcinoma Model Cell Line BT474.” <i>Oncotarget</i>, vol. 8, Impact Journals, 2017, pp. 35076–87, doi:<a href=\"https://doi.org/10.18632/oncotarget.16623\">10.18632/oncotarget.16623</a>.","chicago":"Singer, Judit, Thomas W. Grunt, Erika Jensen-Jarolim, and Josef Singer. “Long Term Storage in Liquid Nitrogen Leads to Only Minor Phenotypic and Gene Expression Changes in the Mammary Carcinoma Model Cell Line BT474.” <i>Oncotarget</i>. Impact Journals, 2017. <a href=\"https://doi.org/10.18632/oncotarget.16623\">https://doi.org/10.18632/oncotarget.16623</a>.","ista":"Singer J, Grunt TW, Jensen-Jarolim E, Singer J. 2017. Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474. Oncotarget. 8, 35076–35087."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2017-03-28T00:00:00Z","oa":1,"status":"public","publication":"Oncotarget","extern":"1","language":[{"iso":"eng"}],"year":"2017","month":"03","main_file_link":[{"url":"https://doi.org/10.18632/oncotarget.16623","open_access":"1"}],"publication_identifier":{"issn":["1949-2553"]},"publication_status":"published","quality_controlled":"1","page":"35076-35087","intvolume":"         8","abstract":[{"lang":"eng","text":"Background/Aim: Cancer cell lines are indispensible surrogate models in cancer research, as they can be used off-the-shelf, expanded to the desired extent, easily modified and exchanged between research groups for affirmation, reproduction or follow-up experiments.\r\nAs malignant cells are prone to genomic instability, phenotypical changes may occur after certain passages in culture. Thus, cell lines have to be regularly authenticated to ensure data quality. In between experiments these cell lines are often stored in liquid nitrogen for extended time periods.\r\nAlthough freezing of cells is a necessary evil, little research is performed on how long-term storage affects cancer cell lines. Therefore, this study investigated the effects of a 28-year long liquid nitrogen storage period on BT474 cells with regard to phenotypical changes, differences in cell-surface receptor expression as well as cytokine and gene expressional variations.\r\nMethods: Two batches of BT474 cells, one frozen in 1986, the other directly purchased from ATCC were investigated by light microscopy, cell growth analysis, flow cytometry and cytokine as well as whole-transcriptome expression profiling.\r\nResults: The cell lines were morphologically indifferent and showed similar growth rates and similar cell-surface receptor expression. Transcriptome analysis revealed significant differences in only 26 of 40,716 investigated RefSeq transcripts with 4 of them being up-regulated and 22 down-regulated.\r\nConclusion: This study demonstrates that even after very long periods of storage in liquid nitrogen, cancer cell lines display only minimal changes in their gene expression profiles. However, also such minor changes should be carefully assessed before continuation of experiments, especially if phenotypic alterations can be additionally observed."}],"_id":"8240","volume":8,"date_updated":"2021-01-12T08:17:41Z","date_created":"2020-08-10T11:53:53Z","article_type":"original","type":"journal_article","day":"28","article_processing_charge":"No","author":[{"last_name":"Fazekas","full_name":"Fazekas, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","orcid":"0000-0002-8777-3502"},{"first_name":"Thomas W.","full_name":"Grunt, Thomas W.","last_name":"Grunt"},{"first_name":"Erika","full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim"},{"first_name":"Josef","full_name":"Singer, Josef","last_name":"Singer"}],"doi":"10.18632/oncotarget.16623","oa_version":"Published Version","title":"Long term storage in liquid nitrogen leads to only minor phenotypic and gene expression changes in the mammary carcinoma model cell line BT474","publisher":"Impact Journals"},{"page":"200 - 207","ddc":["020"],"doi":"10.31263/voebm.v70i2.1678","publisher":"VÖB","_id":"825","date_updated":"2021-01-12T08:17:44Z","type":"journal_article","status":"public","publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","date_published":"2017-08-01T00:00:00Z","year":"2017","publist_id":"6823","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        70","abstract":[{"text":"What data is needed about data? Describing the process to answer this question for the institutional data repository IST DataRep.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:11Z","publication_status":"published","publication_identifier":{"issn":["10222588"]},"scopus_import":1,"day":"01","author":[{"full_name":"Petritsch, Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87","last_name":"Petritsch","first_name":"Barbara","orcid":"0000-0003-2724-4614"}],"oa_version":"Published Version","title":"Metadata for research data in practice","volume":70,"date_created":"2018-12-11T11:48:42Z","oa":1,"language":[{"iso":"eng"}],"citation":{"ista":"Petritsch B. 2017. Metadata for research data in practice. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare. 70(2), 200–207.","chicago":"Petritsch, Barbara. “Metadata for Research Data in Practice.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>. VÖB, 2017. <a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">https://doi.org/10.31263/voebm.v70i2.1678</a>.","apa":"Petritsch, B. (2017). Metadata for research data in practice. <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>. VÖB. <a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">https://doi.org/10.31263/voebm.v70i2.1678</a>","mla":"Petritsch, Barbara. “Metadata for Research Data in Practice.” <i>Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>, vol. 70, no. 2, VÖB, 2017, pp. 200–07, doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">10.31263/voebm.v70i2.1678</a>.","ama":"Petritsch B. Metadata for research data in practice. <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>. 2017;70(2):200-207. doi:<a href=\"https://doi.org/10.31263/voebm.v70i2.1678\">10.31263/voebm.v70i2.1678</a>","ieee":"B. Petritsch, “Metadata for research data in practice,” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare</i>, vol. 70, no. 2. VÖB, pp. 200–207, 2017.","short":"B. Petritsch, Mitteilungen Der Vereinigung Österreichischer Bibliothekarinnen &#38; Bibliothekare 70 (2017) 200–207."},"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","department":[{"_id":"E-Lib"}],"file":[{"relation":"main_file","checksum":"7c4544d07efa2c2add8612b489abb4e2","file_name":"2017_VOEB_Petritsch.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"5850","file_size":7843975,"date_created":"2019-01-18T13:32:17Z","date_updated":"2020-07-14T12:48:11Z","creator":"dernst"}]},{"year":"2017","month":"06","article_number":"7966966","language":[{"iso":"eng"}],"publication":"2017 IEEE European Symposium on Security and Privacy Workshops","extern":"1","status":"public","citation":{"ama":"Borge M, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Ford B. Proof-of-personhood: Redemocratizing permissionless cryptocurrencies. In: <i>2017 IEEE European Symposium on Security and Privacy Workshops</i>. IEEE; 2017. doi:<a href=\"https://doi.org/10.1109/eurospw.2017.46\">10.1109/eurospw.2017.46</a>","short":"M. Borge, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, B. Ford, in:, 2017 IEEE European Symposium on Security and Privacy Workshops, IEEE, 2017.","ieee":"M. Borge, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, and B. Ford, “Proof-of-personhood: Redemocratizing permissionless cryptocurrencies,” in <i>2017 IEEE European Symposium on Security and Privacy Workshops</i>, Paris, France, 2017.","ista":"Borge M, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Ford B. 2017. Proof-of-personhood: Redemocratizing permissionless cryptocurrencies. 2017 IEEE European Symposium on Security and Privacy Workshops. EuroS&#38;PW: European Symposium on Security and Privacy Workshops, 7966966.","chicago":"Borge, Maria, Eleftherios Kokoris Kogias, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, and Bryan Ford. “Proof-of-Personhood: Redemocratizing Permissionless Cryptocurrencies.” In <i>2017 IEEE European Symposium on Security and Privacy Workshops</i>. IEEE, 2017. <a href=\"https://doi.org/10.1109/eurospw.2017.46\">https://doi.org/10.1109/eurospw.2017.46</a>.","mla":"Borge, Maria, et al. “Proof-of-Personhood: Redemocratizing Permissionless Cryptocurrencies.” <i>2017 IEEE European Symposium on Security and Privacy Workshops</i>, 7966966, IEEE, 2017, doi:<a href=\"https://doi.org/10.1109/eurospw.2017.46\">10.1109/eurospw.2017.46</a>.","apa":"Borge, M., Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., &#38; Ford, B. (2017). Proof-of-personhood: Redemocratizing permissionless cryptocurrencies. In <i>2017 IEEE European Symposium on Security and Privacy Workshops</i>. Paris, France: IEEE. <a href=\"https://doi.org/10.1109/eurospw.2017.46\">https://doi.org/10.1109/eurospw.2017.46</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"EuroS&PW: European Symposium on Security and Privacy Workshops","end_date":"2017-04-28","start_date":"2017-04-26","location":"Paris, France"},"date_published":"2017-06-30T00:00:00Z","day":"30","article_processing_charge":"No","author":[{"last_name":"Borge","full_name":"Borge, Maria","first_name":"Maria"},{"first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias"},{"full_name":"Jovanovic, Philipp","last_name":"Jovanovic","first_name":"Philipp"},{"full_name":"Gasser, Linus","last_name":"Gasser","first_name":"Linus"},{"first_name":"Nicolas","full_name":"Gailly, Nicolas","last_name":"Gailly"},{"first_name":"Bryan","full_name":"Ford, Bryan","last_name":"Ford"}],"doi":"10.1109/eurospw.2017.46","publisher":"IEEE","title":"Proof-of-personhood: Redemocratizing permissionless cryptocurrencies","oa_version":"None","_id":"8299","date_updated":"2021-01-12T08:17:57Z","date_created":"2020-08-26T11:48:11Z","type":"conference","abstract":[{"lang":"eng","text":"Permissionless blockchain-based cryptocurrencies commonly use proof-of-work (PoW) or proof-of-stake (PoS) to ensure their security, e.g. to prevent double spending attacks. However, both approaches have disadvantages: PoW leads to massive amounts of wasted electricity and re-centralization, whereas major stakeholders in PoS might be able to create a monopoly. In this work, we propose proof-of-personhood (PoP), a mechanism that binds physical entities to virtual identities in a way that enables accountability while preserving anonymity. Afterwards we introduce PoPCoin, a new cryptocurrency, whose consensus mechanism leverages PoP to eliminate the dis-advantages of PoW and PoS while ensuring security. PoPCoin leads to a continuously fair and democratic wealth creation process which paves the way for an experimental basic income infrastructure."}],"publication_identifier":{"eisbn":["9781538622445"]},"quality_controlled":"1","publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2017-09-01T00:00:00Z","conference":{"end_date":"2017-08-18","start_date":"2017-08-16","name":"SEC: Security Symposium","location":"Vancouver, Canada"},"citation":{"apa":"Nikitin, K., Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Khoffi, I., … Ford, B. (2017). CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds. In <i>Proceedings of the 26th USENIX Conference on Security Symposium</i> (pp. 1271–1287). Vancouver, Canada: USENIX Association.","mla":"Nikitin, Kirill, et al. “CHAINIAC: Proactive Software-Update Transparency via Collectively Signed Skipchains and Verified Builds.” <i>Proceedings of the 26th USENIX Conference on Security Symposium</i>, USENIX Association, 2017, pp. 1271–1287.","ista":"Nikitin K, Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Khoffi I, Cappos J, Ford B. 2017. CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds. Proceedings of the 26th USENIX Conference on Security Symposium. SEC: Security Symposium, 1271–1287.","chicago":"Nikitin, Kirill, Eleftherios Kokoris Kogias, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, Ismail Khoffi, Justin Cappos, and Bryan Ford. “CHAINIAC: Proactive Software-Update Transparency via Collectively Signed Skipchains and Verified Builds.” In <i>Proceedings of the 26th USENIX Conference on Security Symposium</i>, 1271–1287. USENIX Association, 2017.","ieee":"K. Nikitin <i>et al.</i>, “CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds,” in <i>Proceedings of the 26th USENIX Conference on Security Symposium</i>, Vancouver, Canada, 2017, pp. 1271–1287.","short":"K. Nikitin, E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, I. Khoffi, J. Cappos, B. Ford, in:, Proceedings of the 26th USENIX Conference on Security Symposium, USENIX Association, 2017, pp. 1271–1287.","ama":"Nikitin K, Kokoris Kogias E, Jovanovic P, et al. CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds. In: <i>Proceedings of the 26th USENIX Conference on Security Symposium</i>. USENIX Association; 2017:1271–1287."},"language":[{"iso":"eng"}],"extern":"1","status":"public","publication":"Proceedings of the 26th USENIX Conference on Security Symposium","oa":1,"month":"09","year":"2017","publication_status":"published","publication_identifier":{"isbn":["9781931971409"]},"quality_controlled":"1","main_file_link":[{"url":"https://www.usenix.org/system/files/conference/usenixsecurity17/sec17-nikitin.pdf","open_access":"1"}],"abstract":[{"text":"Software-update mechanisms are critical to the security of modern systems, but their typically centralized design presents a lucrative and frequently attacked target. In this work, we propose CHAINIAC, a decentralized software-update framework that eliminates single points of failure, enforces transparency, and provides efficient verifiability of integrity and authenticity for software-release processes. Independent witness servers collectively verify conformance of software updates to release policies, build verifiers validate the source-to-binary correspondence, and a tamper-proof release log stores collectively signed updates, thus ensuring that no release is accepted by clients before being widely disclosed and validated. The release log embodies a skipchain, a novel data structure, enabling arbitrarily out-of-date clients to efficiently validate updates and signing keys. Evaluation of our CHAINIAC prototype on reproducible Debian packages shows that the automated update process takes the average of 5 minutes per release for individual packages, and only 20 seconds for the aggregate timeline. We further evaluate the framework using real-world data from the PyPI package repository and show that it offers clients security comparable to verifying every single update themselves while consuming only one-fifth of the bandwidth and having a minimal computational overhead.","lang":"eng"}],"page":"1271–1287","date_created":"2020-08-26T12:04:44Z","type":"conference","_id":"8301","date_updated":"2021-01-12T08:18:00Z","title":"CHAINIAC: Proactive software-update transparency via collectively signed skipchains and verified builds","oa_version":"Published Version","publisher":"USENIX Association","day":"01","article_processing_charge":"No","author":[{"first_name":"Kirill","last_name":"Nikitin","full_name":"Nikitin, Kirill"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"first_name":"Philipp","full_name":"Jovanovic, Philipp","last_name":"Jovanovic"},{"full_name":"Gasser, Linus","last_name":"Gasser","first_name":"Linus"},{"full_name":"Gailly, Nicolas","last_name":"Gailly","first_name":"Nicolas"},{"first_name":"Ismail","full_name":"Khoffi, Ismail","last_name":"Khoffi"},{"first_name":"Justin","full_name":"Cappos, Justin","last_name":"Cappos"},{"first_name":"Bryan","last_name":"Ford","full_name":"Ford, Bryan"}]},{"page":"444-460","abstract":[{"lang":"eng","text":"Bias-resistant public randomness is a critical component in many (distributed) protocols. Generating public randomness is hard, however, because active adversaries may behave dishonestly to bias public random choices toward their advantage. Existing solutions do not scale to hundreds or thousands of participants, as is needed in many decentralized systems. We propose two large-scale distributed protocols, RandHound and RandHerd, which provide publicly-verifiable, unpredictable, and unbiasable randomness against Byzantine adversaries. RandHound relies on an untrusted client to divide a set of randomness servers into groups for scalability, and it depends on the pigeonhole principle to ensure output integrity, even for non-random, adversarial group choices. RandHerd implements an efficient, decentralized randomness beacon. RandHerd is structurally similar to a BFT protocol, but uses RandHound in a one-time setup to arrange participants into verifiably unbiased random secret-sharing groups, which then repeatedly produce random output at predefined intervals. Our prototype demonstrates that RandHound and RandHerd achieve good performance across hundreds of participants while retaining a low failure probability by properly selecting protocol parameters, such as a group size and secret-sharing threshold. For example, when sharding 512 nodes into groups of 32, our experiments show that RandHound can produce fresh random output after 240 seconds. RandHerd, after a setup phase of 260 seconds, is able to generate fresh random output in intervals of approximately 6 seconds. For this configuration, both protocols operate at a failure probability of at most 0.08% against a Byzantine adversary."}],"main_file_link":[{"url":"https://eprint.iacr.org/2016/1067","open_access":"1"}],"publication_identifier":{"isbn":["9781509055340"],"issn":["2375-1207"]},"quality_controlled":"1","publication_status":"published","day":"01","article_processing_charge":"No","doi":"10.1109/SP.2017.45","author":[{"first_name":"E.","full_name":"Syta, E.","last_name":"Syta"},{"full_name":"Jovanovic, P.","last_name":"Jovanovic","first_name":"P."},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"full_name":"Gailly, N.","last_name":"Gailly","first_name":"N."},{"first_name":"L.","full_name":"Gasser, L.","last_name":"Gasser"},{"full_name":"Khoffi, I.","last_name":"Khoffi","first_name":"I."},{"last_name":"Fischer","full_name":"Fischer, M. J.","first_name":"M. J."},{"full_name":"Ford, B.","last_name":"Ford","first_name":"B."}],"publisher":"IEEE","title":"Scalable bias-resistant distributed randomness","oa_version":"Preprint","_id":"8306","date_updated":"2021-01-12T08:18:02Z","date_created":"2020-08-26T12:26:08Z","type":"conference","oa":1,"language":[{"iso":"eng"}],"status":"public","extern":"1","publication":"2017 IEEE Symposium on Security and Privacy","citation":{"ieee":"E. Syta <i>et al.</i>, “Scalable bias-resistant distributed randomness,” in <i>2017 IEEE Symposium on Security and Privacy</i>, San Jose, CA, United States, 2017, pp. 444–460.","short":"E. Syta, P. Jovanovic, E. Kokoris Kogias, N. Gailly, L. Gasser, I. Khoffi, M.J. Fischer, B. Ford, in:, 2017 IEEE Symposium on Security and Privacy, IEEE, 2017, pp. 444–460.","ama":"Syta E, Jovanovic P, Kokoris Kogias E, et al. Scalable bias-resistant distributed randomness. In: <i>2017 IEEE Symposium on Security and Privacy</i>. IEEE; 2017:444-460. doi:<a href=\"https://doi.org/10.1109/SP.2017.45\">10.1109/SP.2017.45</a>","apa":"Syta, E., Jovanovic, P., Kokoris Kogias, E., Gailly, N., Gasser, L., Khoffi, I., … Ford, B. (2017). Scalable bias-resistant distributed randomness. In <i>2017 IEEE Symposium on Security and Privacy</i> (pp. 444–460). San Jose, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/SP.2017.45\">https://doi.org/10.1109/SP.2017.45</a>","mla":"Syta, E., et al. “Scalable Bias-Resistant Distributed Randomness.” <i>2017 IEEE Symposium on Security and Privacy</i>, IEEE, 2017, pp. 444–60, doi:<a href=\"https://doi.org/10.1109/SP.2017.45\">10.1109/SP.2017.45</a>.","chicago":"Syta, E., P. Jovanovic, Eleftherios Kokoris Kogias, N. Gailly, L. Gasser, I. Khoffi, M. J. Fischer, and B. Ford. “Scalable Bias-Resistant Distributed Randomness.” In <i>2017 IEEE Symposium on Security and Privacy</i>, 444–60. IEEE, 2017. <a href=\"https://doi.org/10.1109/SP.2017.45\">https://doi.org/10.1109/SP.2017.45</a>.","ista":"Syta E, Jovanovic P, Kokoris Kogias E, Gailly N, Gasser L, Khoffi I, Fischer MJ, Ford B. 2017. Scalable bias-resistant distributed randomness. 2017 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 444–460."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"location":"San Jose, CA, United States","name":"SP: Symposium on Security and Privacy","end_date":"2017-05-26","start_date":"2017-05-22"},"date_published":"2017-06-01T00:00:00Z","year":"2017","month":"06"},{"month":"07","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Heiss, Teresa, and Hubert Wagner. <i>Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images</i>. Edited by Michael Felsberg et al., vol. 10424, Springer, 2017, pp. 397–409, doi:<a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">10.1007/978-3-319-64689-3_32</a>.","apa":"Heiss, T., &#38; Wagner, H. (2017). Streaming algorithm for Euler characteristic curves of multidimensional images. In M. Felsberg, A. Heyden, &#38; N. Krüger (Eds.) (Vol. 10424, pp. 397–409). Presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">https://doi.org/10.1007/978-3-319-64689-3_32</a>","ista":"Heiss T, Wagner H. 2017. Streaming algorithm for Euler characteristic curves of multidimensional images. CAIP: Computer Analysis of Images and Patterns, LNCS, vol. 10424, 397–409.","chicago":"Heiss, Teresa, and Hubert Wagner. “Streaming Algorithm for Euler Characteristic Curves of Multidimensional Images.” edited by Michael Felsberg, Anders Heyden, and Norbert Krüger, 10424:397–409. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">https://doi.org/10.1007/978-3-319-64689-3_32</a>.","short":"T. Heiss, H. Wagner, in:, M. Felsberg, A. Heyden, N. Krüger (Eds.), Springer, 2017, pp. 397–409.","ieee":"T. Heiss and H. Wagner, “Streaming algorithm for Euler characteristic curves of multidimensional images,” presented at the CAIP: Computer Analysis of Images and Patterns, Ystad, Sweden, 2017, vol. 10424, pp. 397–409.","ama":"Heiss T, Wagner H. Streaming algorithm for Euler characteristic curves of multidimensional images. In: Felsberg M, Heyden A, Krüger N, eds. Vol 10424. Springer; 2017:397-409. doi:<a href=\"https://doi.org/10.1007/978-3-319-64689-3_32\">10.1007/978-3-319-64689-3_32</a>"},"title":"Streaming algorithm for Euler characteristic curves of multidimensional images","oa_version":"Submitted Version","author":[{"last_name":"Heiss","full_name":"Heiss, Teresa","id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","first_name":"Teresa","orcid":"0000-0002-1780-2689"},{"last_name":"Wagner","full_name":"Wagner, Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","first_name":"Hubert"}],"day":"28","scopus_import":"1","date_created":"2018-12-11T11:48:45Z","volume":10424,"intvolume":"     10424","abstract":[{"lang":"eng","text":"We present an efficient algorithm to compute Euler characteristic curves of gray scale images of arbitrary dimension. In various applications the Euler characteristic curve is used as a descriptor of an image. Our algorithm is the first streaming algorithm for Euler characteristic curves. The usage of streaming removes the necessity to store the entire image in RAM. Experiments show that our implementation handles terabyte scale images on commodity hardware. Due to lock-free parallelism, it scales well with the number of processor cores. Additionally, we put the concept of the Euler characteristic curve in the wider context of computational topology. In particular, we explain the connection with persistence diagrams."}],"publication_identifier":{"issn":["03029743"]},"publication_status":"published","external_id":{"isi":["000432085900032"]},"year":"2017","isi":1,"publist_id":"6815","status":"public","conference":{"location":"Ystad, Sweden","name":"CAIP: Computer Analysis of Images and Patterns","end_date":"2017-08-24","start_date":"2017-08-22"},"date_published":"2017-07-28T00:00:00Z","editor":[{"last_name":"Felsberg","full_name":"Felsberg, Michael","first_name":"Michael"},{"full_name":"Heyden, Anders","last_name":"Heyden","first_name":"Anders"},{"first_name":"Norbert","full_name":"Krüger, Norbert","last_name":"Krüger"}],"publisher":"Springer","doi":"10.1007/978-3-319-64689-3_32","alternative_title":["LNCS"],"article_processing_charge":"No","type":"conference","date_updated":"2023-09-26T16:10:03Z","_id":"833","page":"397 - 409","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02045"}]}]