[{"scopus_import":"1","publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"page":"130-137","external_id":{"pmid":["29255257"]},"keyword":["Genetics"],"date_published":"2017-12-18T00:00:00Z","acknowledgement":"We thank Daniel Zilberman for intellectual contributions to this work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript, Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method, Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector, Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431) to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to J.W.","department":[{"_id":"XiFe"}],"doi":"10.1038/s41588-017-0008-5","language":[{"iso":"eng"}],"day":"18","oa_version":"None","date_updated":"2023-10-18T07:21:53Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","status":"public","month":"12","date_created":"2023-01-16T09:18:05Z","intvolume":"        50","publisher":"Nature Research","article_type":"original","volume":50,"issue":"1","abstract":[{"text":"DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed during animal development. However, whether developmental methylation reprogramming during the sporophytic life cycle of flowering plants regulates genes is presently unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation (RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific epigenetic signature that controls gene expression and contributes to cellular function in flowering plants.","lang":"eng"}],"publication_status":"published","_id":"12193","oa":1,"pmid":1,"publication":"Nature Genetics","title":"Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis","year":"2017","author":[{"first_name":"James","last_name":"Walker","full_name":"Walker, James"},{"last_name":"Gao","first_name":"Hongbo","full_name":"Gao, Hongbo"},{"full_name":"Zhang, Jingyi","first_name":"Jingyi","last_name":"Zhang"},{"full_name":"Aldridge, Billy","first_name":"Billy","last_name":"Aldridge"},{"full_name":"Vickers, Martin","first_name":"Martin","last_name":"Vickers"},{"last_name":"Higgins","first_name":"James D.","full_name":"Higgins, James D."},{"first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"}],"quality_controlled":"1","citation":{"apa":"Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D., &#38; Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. Nature Research. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>","mla":"Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>, vol. 50, no. 1, Nature Research, 2017, pp. 130–37, doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>.","short":"J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng, Nature Genetics 50 (2017) 130–137.","chicago":"Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers, James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis in Arabidopsis.” <i>Nature Genetics</i>. Nature Research, 2017. <a href=\"https://doi.org/10.1038/s41588-017-0008-5\">https://doi.org/10.1038/s41588-017-0008-5</a>.","ista":"Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature Genetics. 50(1), 130–137.","ama":"Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. <i>Nature Genetics</i>. 2017;50(1):130-137. doi:<a href=\"https://doi.org/10.1038/s41588-017-0008-5\">10.1038/s41588-017-0008-5</a>","ieee":"J. Walker <i>et al.</i>, “Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis,” <i>Nature Genetics</i>, vol. 50, no. 1. Nature Research, pp. 130–137, 2017."},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/"}]},{"pubrep_id":"738","issue":"1","volume":45,"file_date_updated":"2020-07-14T12:44:39Z","publisher":"Wiley-Blackwell","article_type":"review","intvolume":"        45","isi":1,"publist_id":"6106","month":"01","date_created":"2018-12-11T11:50:50Z","status":"public","citation":{"mla":"Sauerzopf, Ulrich, et al. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>, vol. 45, no. 1, Wiley-Blackwell, 2017, pp. 45–57, doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>.","apa":"Sauerzopf, U., Sacco, R., Novarino, G., Niello, M., Weidenauer, A., Praschak Rieder, N., … Willeit, M. (2017). Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>","ama":"Sauerzopf U, Sacco R, Novarino G, et al. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. <i>European Journal of Neuroscience</i>. 2017;45(1):45-57. doi:<a href=\"https://doi.org/10.1111/ejn.13418\">10.1111/ejn.13418</a>","ieee":"U. Sauerzopf <i>et al.</i>, “Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence,” <i>European Journal of Neuroscience</i>, vol. 45, no. 1. Wiley-Blackwell, pp. 45–57, 2017.","ista":"Sauerzopf U, Sacco R, Novarino G, Niello M, Weidenauer A, Praschak Rieder N, Sitte H, Willeit M. 2017. Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence. European Journal of Neuroscience. 45(1), 45–57.","short":"U. Sauerzopf, R. Sacco, G. Novarino, M. Niello, A. Weidenauer, N. Praschak Rieder, H. Sitte, M. Willeit, European Journal of Neuroscience 45 (2017) 45–57.","chicago":"Sauerzopf, Ulrich, Roberto Sacco, Gaia Novarino, Marco Niello, Ana Weidenauer, Nicole Praschak Rieder, Harald Sitte, and Matthaeus Willeit. “Are Reprogrammed Cells a Useful Tool for Studying Dopamine Dysfunction in Psychotic Disorders? A Review of the Current Evidence.” <i>European Journal of Neuroscience</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/ejn.13418\">https://doi.org/10.1111/ejn.13418</a>."},"quality_controlled":"1","author":[{"last_name":"Sauerzopf","first_name":"Ulrich","full_name":"Sauerzopf, Ulrich"},{"first_name":"Roberto","last_name":"Sacco","full_name":"Sacco, Roberto","id":"42C9F57E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","first_name":"Gaia"},{"full_name":"Niello, Marco","first_name":"Marco","last_name":"Niello"},{"full_name":"Weidenauer, Ana","last_name":"Weidenauer","first_name":"Ana"},{"last_name":"Praschak Rieder","first_name":"Nicole","full_name":"Praschak Rieder, Nicole"},{"full_name":"Sitte, Harald","first_name":"Harald","last_name":"Sitte"},{"last_name":"Willeit","first_name":"Matthaeus","full_name":"Willeit, Matthaeus"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2017","pmid":1,"publication":"European Journal of Neuroscience","title":"Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence","_id":"1228","ddc":["616"],"oa":1,"abstract":[{"text":"Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD.","lang":"eng"}],"publication_status":"published","file":[{"file_name":"IST-2017-738-v1+1_Sauerzopf_et_al-2017-European_Journal_of_Neuroscience.pdf","checksum":"c572cf02be8fbb7020cfcfb892182e4c","access_level":"open_access","file_id":"4838","date_updated":"2020-07-14T12:44:39Z","file_size":169145,"creator":"system","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:10:48Z"}],"external_id":{"isi":["000392487100005"],"pmid":["27690184"]},"date_published":"2017-01-01T00:00:00Z","page":"45 - 57","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","oa_version":"Published Version","type":"journal_article","date_updated":"2023-09-20T11:16:01Z","day":"01","has_accepted_license":"1","department":[{"_id":"GaNo"}],"language":[{"iso":"eng"}],"doi":"10.1111/ejn.13418","acknowledgement":"This work was supported by grants of the Austrian Science Fund (FWF) P23585B09 to M.W. and F3506 to H.H.S. and the “Wiener Wissenschafts-, Forschungs- und Technologiefonds” (Vienna Science and Technology Fund; WWTF) CS15-033 to M.W."},{"page":"1095 - 1099","date_published":"2017-07-24T00:00:00Z","external_id":{"arxiv":["1705.03530"]},"arxiv":1,"day":"24","type":"journal_article","date_updated":"2021-01-12T06:49:14Z","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"A.S. acknowledges funding from the Delta Institute for Theoretical Physics and the hospitality of the IBS Center for Theoretical Physics of Complex Systems, Daejeon, South Korea. We acknowledge funding from the Netherlands Organisation for Scientific Research through grants VICI No. NWO-680-47-609 (M.v.H. and S.R.W.), VENI No. NWO-680-47-445 (C.C.) and VENI No. NWO-680-47-453 (S.R.W.).","language":[{"iso":"eng"}],"doi":"10.1038/nphys4194","publisher":"Nature Publishing Group","volume":13,"issue":"11","status":"public","date_created":"2018-12-11T11:44:45Z","month":"07","publist_id":"7931","intvolume":"        13","year":"2017","quality_controlled":"1","author":[{"first_name":"Scott R","last_name":"Waitukaitis","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","full_name":"Waitukaitis, Scott R","orcid":"0000-0002-2299-3176"},{"first_name":"Antal","last_name":"Zuiderwijk","full_name":"Zuiderwijk, Antal"},{"first_name":"Anton","last_name":"Souslov","full_name":"Souslov, Anton"},{"full_name":"Coulais, Corentin","last_name":"Coulais","first_name":"Corentin"},{"last_name":"Van Hecke","first_name":"Martin","full_name":"Van Hecke, Martin"}],"extern":"1","main_file_link":[{"url":"https://arxiv.org/abs/1705.03530","open_access":"1"}],"citation":{"ieee":"S. R. Waitukaitis, A. Zuiderwijk, A. Souslov, C. Coulais, and M. Van Hecke, “Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing,” <i>Nature Physics</i>, vol. 13, no. 11. Nature Publishing Group, pp. 1095–1099, 2017.","ama":"Waitukaitis SR, Zuiderwijk A, Souslov A, Coulais C, Van Hecke M. Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. <i>Nature Physics</i>. 2017;13(11):1095-1099. doi:<a href=\"https://doi.org/10.1038/nphys4194\">10.1038/nphys4194</a>","short":"S.R. Waitukaitis, A. Zuiderwijk, A. Souslov, C. Coulais, M. Van Hecke, Nature Physics 13 (2017) 1095–1099.","chicago":"Waitukaitis, Scott R, Antal Zuiderwijk, Anton Souslov, Corentin Coulais, and Martin Van Hecke. “Coupling the Leidenfrost Effect and Elastic Deformations to Power Sustained Bouncing.” <i>Nature Physics</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/nphys4194\">https://doi.org/10.1038/nphys4194</a>.","ista":"Waitukaitis SR, Zuiderwijk A, Souslov A, Coulais C, Van Hecke M. 2017. Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. Nature Physics. 13(11), 1095–1099.","mla":"Waitukaitis, Scott R., et al. “Coupling the Leidenfrost Effect and Elastic Deformations to Power Sustained Bouncing.” <i>Nature Physics</i>, vol. 13, no. 11, Nature Publishing Group, 2017, pp. 1095–99, doi:<a href=\"https://doi.org/10.1038/nphys4194\">10.1038/nphys4194</a>.","apa":"Waitukaitis, S. R., Zuiderwijk, A., Souslov, A., Coulais, C., &#38; Van Hecke, M. (2017). Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphys4194\">https://doi.org/10.1038/nphys4194</a>"},"publication_status":"published","abstract":[{"text":"The Leidenfrost effect occurs when an object near a hot surface vaporizes rapidly enough to lift itself up and hover. Although well understood for liquids and stiff sublimable solids, nothing is known about the effect with materials whose stiffness lies between these extremes. Here we introduce a new phenomenon that occurs with vaporizable soft solids - the elastic Leidenfrost effect. By dropping hydrogel spheres onto hot surfaces we find that, rather than hovering, they energetically bounce several times their diameter for minutes at a time. With high-speed video during a single impact, we uncover high-frequency microscopic gap dynamics at the sphere/substrate interface. We show how these otherwise-hidden agitations constitute work cycles that harvest mechanical energy from the vapour and sustain the bouncing. Our findings suggest a new strategy for injecting mechanical energy into a widely used class of soft materials, with potential relevance to fields such as active matter, soft robotics and microfluidics.","lang":"eng"}],"oa":1,"_id":"123","title":"Coupling the Leidenfrost effect and elastic deformations to power sustained bouncing","publication":"Nature Physics"},{"date_created":"2023-02-20T07:52:31Z","conference":{"location":"Waterloo, ON, Canada","start_date":"2017-06-26","name":"IPCO: Integer Programming and Combinatorial Optimization","end_date":"2017-06-28"},"month":"05","status":"public","intvolume":"     10328","publisher":"Springer Nature","volume":10328,"publication_status":"published","abstract":[{"text":"We consider the problems of maintaining approximate maximum matching and minimum vertex cover in a dynamic graph. Starting with the seminal work of Onak and Rubinfeld [STOC 2010], this problem has received significant attention in recent years. Very recently, extending the framework of Baswana, Gupta and Sen [FOCS 2011], Solomon [FOCS 2016] gave a randomized 2-approximation dynamic algorithm for this problem that has amortized update time of O(1) with high probability. We consider the natural open question of derandomizing this result. We present a new deterministic fully dynamic algorithm that maintains a O(1)-approximate minimum vertex cover and maximum fractional matching, with an amortized update time of O(1). Previously, the best deterministic algorithm for this problem was due to Bhattacharya, Henzinger and Italiano [SODA 2015]; it had an approximation ratio of (2+ϵ) and an amortized update time of O(logn/ϵ2). Our result can be generalized to give a fully dynamic O(f3)-approximation algorithm with O(f2) amortized update time for the hypergraph vertex cover and fractional matching problems, where every hyperedge has at most f vertices.","lang":"eng"}],"title":"Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time","publication":"19th International Conference on Integer Programming and Combinatorial Optimization","oa":1,"_id":"12571","year":"2017","citation":{"apa":"Bhattacharya, S., Chakrabarty, D., &#38; Henzinger, M. H. (2017). Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. In <i>19th International Conference on Integer Programming and Combinatorial Optimization</i> (Vol. 10328, pp. 86–98). Waterloo, ON, Canada: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-59250-3_8\">https://doi.org/10.1007/978-3-319-59250-3_8</a>","mla":"Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Approximate Vertex Cover and Fractional Matching in O(1) Amortized Update Time.” <i>19th International Conference on Integer Programming and Combinatorial Optimization</i>, vol. 10328, Springer Nature, 2017, pp. 86–98, doi:<a href=\"https://doi.org/10.1007/978-3-319-59250-3_8\">10.1007/978-3-319-59250-3_8</a>.","ama":"Bhattacharya S, Chakrabarty D, Henzinger MH. Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. In: <i>19th International Conference on Integer Programming and Combinatorial Optimization</i>. Vol 10328. Springer Nature; 2017:86-98. doi:<a href=\"https://doi.org/10.1007/978-3-319-59250-3_8\">10.1007/978-3-319-59250-3_8</a>","ieee":"S. Bhattacharya, D. Chakrabarty, and M. H. Henzinger, “Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time,” in <i>19th International Conference on Integer Programming and Combinatorial Optimization</i>, Waterloo, ON, Canada, 2017, vol. 10328, pp. 86–98.","ista":"Bhattacharya S, Chakrabarty D, Henzinger MH. 2017. Deterministic fully dynamic approximate vertex cover and fractional matching in O(1) amortized update time. 19th International Conference on Integer Programming and Combinatorial Optimization. IPCO: Integer Programming and Combinatorial Optimization, LNCS, vol. 10328, 86–98.","short":"S. Bhattacharya, D. Chakrabarty, M.H. Henzinger, in:, 19th International Conference on Integer Programming and Combinatorial Optimization, Springer Nature, 2017, pp. 86–98.","chicago":"Bhattacharya, Sayan, Deeparnab Chakrabarty, and Monika H Henzinger. “Deterministic Fully Dynamic Approximate Vertex Cover and Fractional Matching in O(1) Amortized Update Time.” In <i>19th International Conference on Integer Programming and Combinatorial Optimization</i>, 10328:86–98. Springer Nature, 2017. <a href=\"https://doi.org/10.1007/978-3-319-59250-3_8\">https://doi.org/10.1007/978-3-319-59250-3_8</a>."},"main_file_link":[{"url":"https://arxiv.org/abs/1611.00198","open_access":"1"}],"quality_controlled":"1","author":[{"full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya","first_name":"Sayan"},{"last_name":"Chakrabarty","first_name":"Deeparnab","full_name":"Chakrabarty, Deeparnab"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"}],"extern":"1","arxiv":1,"alternative_title":["LNCS"],"publication_identifier":{"isbn":["9783319592497"],"eisbn":["9783319592503"],"issn":["0302-9743","1611-3349"]},"scopus_import":"1","date_published":"2017-05-24T00:00:00Z","external_id":{"arxiv":["1611.00198"]},"page":"86-98","language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-59250-3_8","date_updated":"2023-02-20T07:57:24Z","type":"conference","oa_version":"Preprint","day":"24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No"},{"_id":"12608","oa":1,"publication":"Journal of Glaciology","title":"Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations","abstract":[{"text":"The spatio-temporal distribution of air temperature over mountain glaciers can demonstrate complex patterns, yet it is often represented simplistically using linear vertical temperature gradients (VTGs) extrapolated from off-glacier locations. We analyse a network of centreline and lateral air temperature observations at Tsanteleina Glacier, Italy, during summer 2015. On average, VTGs are steep (&lt;−0.0065 °C m<jats:sup>−1</jats:sup>), but they are shallow under warm ambient conditions when the correlation between air temperature and elevation becomes weaker. Published along-flowline temperature distribution methods explain centreline observations well, including warming on the lower glacier tongue, but cannot estimate lateral temperature variability. Application of temperature distribution methods improves simulation of melt rates (RMSE) in an energy-balance model by up to 36% compared to the environmental lapse rate extrapolated from an off-glacier station. However, results suggest that model parameters are not easily transferable to glaciers with a small fetch without recalibration. Such methods have potential to improve estimates of temperature across a glacier, but their parameter transferability should be further linked to the glacier and atmospheric characteristics. Furthermore, ‘cold spots’, which can be &gt;2°C cooler than expected for their elevation, whose occurrence is not predicted by the temperature distribution models, are identified at one-quarter of the measurement sites.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","extern":"1","author":[{"first_name":"THOMAS E.","last_name":"SHAW","full_name":"SHAW, THOMAS E."},{"full_name":"BROCK, BEN W.","first_name":"BEN W.","last_name":"BROCK"},{"full_name":"AYALA, ÁLVARO","first_name":"ÁLVARO","last_name":"AYALA"},{"full_name":"RUTTER, NICK","first_name":"NICK","last_name":"RUTTER"},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca"}],"citation":{"chicago":"SHAW, THOMAS E., BEN W. BROCK, ÁLVARO AYALA, NICK RUTTER, and Francesca Pellicciotti. “Centreline and Cross-Glacier Air Temperature Variability on an Alpine Glacier: Assessing Temperature Distribution Methods and Their Influence on Melt Model Calculations.” <i>Journal of Glaciology</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jog.2017.65\">https://doi.org/10.1017/jog.2017.65</a>.","short":"T.E. SHAW, B.W. BROCK, Á. AYALA, N. RUTTER, F. Pellicciotti, Journal of Glaciology 63 (2017) 973–988.","ista":"SHAW TE, BROCK BW, AYALA Á, RUTTER N, Pellicciotti F. 2017. Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations. Journal of Glaciology. 63(242), 973–988.","ieee":"T. E. SHAW, B. W. BROCK, Á. AYALA, N. RUTTER, and F. Pellicciotti, “Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations,” <i>Journal of Glaciology</i>, vol. 63, no. 242. Cambridge University Press, pp. 973–988, 2017.","ama":"SHAW TE, BROCK BW, AYALA Á, RUTTER N, Pellicciotti F. Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations. <i>Journal of Glaciology</i>. 2017;63(242):973-988. doi:<a href=\"https://doi.org/10.1017/jog.2017.65\">10.1017/jog.2017.65</a>","apa":"SHAW, T. E., BROCK, B. W., AYALA, Á., RUTTER, N., &#38; Pellicciotti, F. (2017). Centreline and cross-glacier air temperature variability on an Alpine glacier: Assessing temperature distribution methods and their influence on melt model calculations. <i>Journal of Glaciology</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jog.2017.65\">https://doi.org/10.1017/jog.2017.65</a>","mla":"SHAW, THOMAS E., et al. “Centreline and Cross-Glacier Air Temperature Variability on an Alpine Glacier: Assessing Temperature Distribution Methods and Their Influence on Melt Model Calculations.” <i>Journal of Glaciology</i>, vol. 63, no. 242, Cambridge University Press, 2017, pp. 973–88, doi:<a href=\"https://doi.org/10.1017/jog.2017.65\">10.1017/jog.2017.65</a>."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/jog.2017.65"}],"year":"2017","intvolume":"        63","status":"public","month":"12","date_created":"2023-02-20T08:13:47Z","volume":63,"issue":"242","publisher":"Cambridge University Press","article_type":"original","language":[{"iso":"eng"}],"doi":"10.1017/jog.2017.65","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","oa_version":"Published Version","date_updated":"2023-02-28T11:30:34Z","type":"journal_article","scopus_import":"1","publication_identifier":{"eissn":["1727-5652"],"issn":["0022-1430"]},"page":"973-988","keyword":["Earth-Surface Processes"],"date_published":"2017-12-01T00:00:00Z"},{"abstract":[{"lang":"eng","text":"Previous estimates of melt and surface sublimation on glaciers of the subtropical semiarid Andes (29–34°S) have been obtained at few specific locations, but it is not clear how ablation components vary across the entire extent of a glacier in this dry environment. Here, we simulate the distributed energy and mass balance of Juncal Norte Glacier (33°S) during a 2-month summer period. Forcing fields of near-surface air temperature and wind speed are generated using two methods accounting for the main physical processes that shape their spatial variations. Simulated meteorological variables and ablation agree well with observations on the glacier tongue and reveal complex patterns of energy and mass fluxes. Ablation decreases from 70 mm w.e. d<jats:sup>−1</jats:sup> at the low-albedo glacier terminus (~3000 m), where almost 100% of total ablation corresponds to melt, to &lt;5 mm w.e. d<jats:sup>−1</jats:sup> at wind-exposed, strong-radiated sites above 5500 m, where surface sublimation represents &gt;75% of total ablation. Our simulations provide the first glacier-scale estimates of ablation components on a glacier in the study region and better reproduce the observed and expected spatial variations of melt and surface sublimation, in comparison with more simple assumptions, such as linear gradients and uniform wind speeds."}],"publication_status":"published","_id":"12609","oa":1,"title":"Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile","publication":"Journal of Glaciology","year":"2017","quality_controlled":"1","author":[{"last_name":"AYALA","first_name":"A.","full_name":"AYALA, A."},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti"},{"full_name":"PELEG, N.","first_name":"N.","last_name":"PELEG"},{"first_name":"P.","last_name":"BURLANDO","full_name":"BURLANDO, P."}],"extern":"1","citation":{"apa":"AYALA, A., Pellicciotti, F., PELEG, N., &#38; BURLANDO, P. (2017). Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile. <i>Journal of Glaciology</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jog.2017.46\">https://doi.org/10.1017/jog.2017.46</a>","mla":"AYALA, A., et al. “Melt and Surface Sublimation across a Glacier in a Dry Environment: Distributed Energy-Balance Modelling of Juncal Norte Glacier, Chile.” <i>Journal of Glaciology</i>, vol. 63, no. 241, Cambridge University Press, 2017, pp. 803–22, doi:<a href=\"https://doi.org/10.1017/jog.2017.46\">10.1017/jog.2017.46</a>.","short":"A. AYALA, F. Pellicciotti, N. PELEG, P. BURLANDO, Journal of Glaciology 63 (2017) 803–822.","chicago":"AYALA, A., Francesca Pellicciotti, N. PELEG, and P. BURLANDO. “Melt and Surface Sublimation across a Glacier in a Dry Environment: Distributed Energy-Balance Modelling of Juncal Norte Glacier, Chile.” <i>Journal of Glaciology</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jog.2017.46\">https://doi.org/10.1017/jog.2017.46</a>.","ista":"AYALA A, Pellicciotti F, PELEG N, BURLANDO P. 2017. Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile. Journal of Glaciology. 63(241), 803–822.","ama":"AYALA A, Pellicciotti F, PELEG N, BURLANDO P. Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile. <i>Journal of Glaciology</i>. 2017;63(241):803-822. doi:<a href=\"https://doi.org/10.1017/jog.2017.46\">10.1017/jog.2017.46</a>","ieee":"A. AYALA, F. Pellicciotti, N. PELEG, and P. BURLANDO, “Melt and surface sublimation across a glacier in a dry environment: distributed energy-balance modelling of Juncal Norte Glacier, Chile,” <i>Journal of Glaciology</i>, vol. 63, no. 241. Cambridge University Press, pp. 803–822, 2017."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/jog.2017.46"}],"status":"public","month":"10","date_created":"2023-02-20T08:13:53Z","intvolume":"        63","publisher":"Cambridge University Press","article_type":"original","issue":"241","volume":63,"doi":"10.1017/jog.2017.46","language":[{"iso":"eng"}],"day":"01","oa_version":"Published Version","type":"journal_article","date_updated":"2023-02-28T11:28:19Z","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","publication_identifier":{"issn":["0022-1430"],"eissn":["1727-5652"]},"page":"803-822","keyword":["Earth-Surface Processes"],"date_published":"2017-10-01T00:00:00Z"},{"volume":5,"publisher":"Frontiers Media","article_type":"original","intvolume":"         5","status":"public","article_number":"69","date_created":"2023-02-20T08:14:04Z","month":"09","extern":"1","quality_controlled":"1","author":[{"last_name":"Miles","first_name":"Evan S.","full_name":"Miles, Evan S."},{"full_name":"Steiner, Jakob","first_name":"Jakob","last_name":"Steiner"},{"full_name":"Willis, Ian","first_name":"Ian","last_name":"Willis"},{"last_name":"Buri","first_name":"Pascal","full_name":"Buri, Pascal"},{"last_name":"Immerzeel","first_name":"Walter W.","full_name":"Immerzeel, Walter W."},{"full_name":"Chesnokova, Anna","first_name":"Anna","last_name":"Chesnokova"},{"first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"}],"citation":{"apa":"Miles, E. S., Steiner, J., Willis, I., Buri, P., Immerzeel, W. W., Chesnokova, A., &#38; Pellicciotti, F. (2017). Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal. <i>Frontiers in Earth Science</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/feart.2017.00069\">https://doi.org/10.3389/feart.2017.00069</a>","mla":"Miles, Evan S., et al. “Pond Dynamics and Supraglacial-Englacial Connectivity on Debris-Covered Lirung Glacier, Nepal.” <i>Frontiers in Earth Science</i>, vol. 5, 69, Frontiers Media, 2017, doi:<a href=\"https://doi.org/10.3389/feart.2017.00069\">10.3389/feart.2017.00069</a>.","short":"E.S. Miles, J. Steiner, I. Willis, P. Buri, W.W. Immerzeel, A. Chesnokova, F. Pellicciotti, Frontiers in Earth Science 5 (2017).","chicago":"Miles, Evan S., Jakob Steiner, Ian Willis, Pascal Buri, Walter W. Immerzeel, Anna Chesnokova, and Francesca Pellicciotti. “Pond Dynamics and Supraglacial-Englacial Connectivity on Debris-Covered Lirung Glacier, Nepal.” <i>Frontiers in Earth Science</i>. Frontiers Media, 2017. <a href=\"https://doi.org/10.3389/feart.2017.00069\">https://doi.org/10.3389/feart.2017.00069</a>.","ista":"Miles ES, Steiner J, Willis I, Buri P, Immerzeel WW, Chesnokova A, Pellicciotti F. 2017. Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal. Frontiers in Earth Science. 5, 69.","ieee":"E. S. Miles <i>et al.</i>, “Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal,” <i>Frontiers in Earth Science</i>, vol. 5. Frontiers Media, 2017.","ama":"Miles ES, Steiner J, Willis I, et al. Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal. <i>Frontiers in Earth Science</i>. 2017;5. doi:<a href=\"https://doi.org/10.3389/feart.2017.00069\">10.3389/feart.2017.00069</a>"},"main_file_link":[{"url":"https://doi.org/10.3389/feart.2017.00069","open_access":"1"}],"year":"2017","oa":1,"_id":"12610","title":"Pond dynamics and supraglacial-englacial connectivity on debris-covered Lirung Glacier, Nepal","publication":"Frontiers in Earth Science","publication_status":"published","abstract":[{"text":"The hydrological systems of heavily-downwasted debris-covered glaciers differ from those of clean-ice glaciers due to the hummocky surface and debris mantle of such glaciers, leading to a relatively limited understanding of drainage pathways. Supraglacial ponds represent sinks within the discontinuous supraglacial drainage system, and occasionally drain englacially. To assess pond dynamics, we made pond water level measurements on Lirung Glacier, Nepal, during May and October of 2013 and 2014. Simultaneously, aerial, satellite, and terrestrial orthoimages and digital elevation models were obtained, providing snapshots of the ponds and their surroundings. We performed a DEM-based analysis of the glacier's closed surface catchments to identify surface drainage pathways and englacial drainage points, and compared this to field observations of surface and near-surface water flow. The total ponded area was higher in the pre-monsoon than post-monsoon, with individual ponds filling and draining seasonally associated with the surface exposure of englacial conduit segments. We recorded four pond drainage events, all of which occurred gradually (duration of weeks), observed diurnal fluctuations indicative of varying water supply and outflow discharge, and we documented instances of interaction between distant ponds. The DEM drainage analysis identified numerous sinks >3 m in depth across the glacier surface, few of which exhibited ponds (23%), while the field survey highlighted instances of surface water only explicable via englacial routes. Taken together, our observations provide evidence for widespread supraglacial-englacial connectivity of meltwater drainage paths. Results suggest that successive englacial conduit collapse events, themselves likely driven by supraglacial pond drainage, cause the glacier surface drainage system to evolve into a configuration following relict englacial conduit systems. Within this system, ponds form in depressions of reduced drainage efficiency and link the supraglacial and englacial drainage networks.","lang":"eng"}],"date_published":"2017-09-21T00:00:00Z","keyword":["General Earth and Planetary Sciences"],"publication_identifier":{"issn":["2296-6463"]},"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"21","date_updated":"2023-02-28T11:13:23Z","type":"journal_article","oa_version":"Published Version","doi":"10.3389/feart.2017.00069","language":[{"iso":"eng"}]},{"page":"5601-5625","date_published":"2017-07-10T00:00:00Z","keyword":["Water Science and Technology"],"publication_identifier":{"issn":["0043-1397"]},"scopus_import":"1","day":"10","date_updated":"2023-02-24T11:41:55Z","type":"journal_article","oa_version":"None","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1002/2016wr020126","language":[{"iso":"eng"}],"publisher":"American Geophysical Union","article_type":"original","volume":53,"issue":"7","status":"public","date_created":"2023-02-20T08:14:10Z","month":"07","intvolume":"        53","year":"2017","quality_controlled":"1","author":[{"full_name":"Ayala, A.","first_name":"A.","last_name":"Ayala"},{"full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca"},{"last_name":"MacDonell","first_name":"S.","full_name":"MacDonell, S."},{"full_name":"McPhee, J.","first_name":"J.","last_name":"McPhee"},{"first_name":"P.","last_name":"Burlando","full_name":"Burlando, P."}],"extern":"1","citation":{"apa":"Ayala, A., Pellicciotti, F., MacDonell, S., McPhee, J., &#38; Burlando, P. (2017). Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/2016wr020126\">https://doi.org/10.1002/2016wr020126</a>","mla":"Ayala, A., et al. “Patterns of Glacier Ablation across North-Central Chile: Identifying the Limits of Empirical Melt Models under Sublimation-Favorable Conditions.” <i>Water Resources Research</i>, vol. 53, no. 7, American Geophysical Union, 2017, pp. 5601–25, doi:<a href=\"https://doi.org/10.1002/2016wr020126\">10.1002/2016wr020126</a>.","short":"A. Ayala, F. Pellicciotti, S. MacDonell, J. McPhee, P. Burlando, Water Resources Research 53 (2017) 5601–5625.","chicago":"Ayala, A., Francesca Pellicciotti, S. MacDonell, J. McPhee, and P. Burlando. “Patterns of Glacier Ablation across North-Central Chile: Identifying the Limits of Empirical Melt Models under Sublimation-Favorable Conditions.” <i>Water Resources Research</i>. American Geophysical Union, 2017. <a href=\"https://doi.org/10.1002/2016wr020126\">https://doi.org/10.1002/2016wr020126</a>.","ista":"Ayala A, Pellicciotti F, MacDonell S, McPhee J, Burlando P. 2017. Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions. Water Resources Research. 53(7), 5601–5625.","ieee":"A. Ayala, F. Pellicciotti, S. MacDonell, J. McPhee, and P. Burlando, “Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions,” <i>Water Resources Research</i>, vol. 53, no. 7. American Geophysical Union, pp. 5601–5625, 2017.","ama":"Ayala A, Pellicciotti F, MacDonell S, McPhee J, Burlando P. Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions. <i>Water Resources Research</i>. 2017;53(7):5601-5625. doi:<a href=\"https://doi.org/10.1002/2016wr020126\">10.1002/2016wr020126</a>"},"publication_status":"published","abstract":[{"lang":"eng","text":"We investigate the energy balance and ablation regimes of glaciers in high-elevation, dry environments using glaciometeorological data collected on six glaciers in the semiarid Andes of North-Central Chile (29–34°S, 3127–5324 m). We use a point-scale physically based energy balance (EB) model and an enhanced Temperature-Index (ETI) model that calculates melt rates only as a function of air temperature and net shortwave radiation. At all sites, the largest energy inputs are net shortwave and incoming longwave radiation, which are controlled by surface albedo and elevation, respectively. Turbulent fluxes cancel each other out at the lower sites, but as elevation increases, cold, dry and wind-exposed conditions increase the magnitude of negative latent heat fluxes, associated with large surface sublimation rates. In midsummer (January), ablation rates vary from 67.9 mm w.e. d−1 at the lowest site (∼100% corresponding to melt), to 2.3 mm w.e. d−1 at the highest site (>85% corresponding to surface sublimation). At low-elevation, low-albedo, melt-dominated sites, the ETI model correctly reproduces melt using a large range of possible parameters, but both the performance and parameter transferability decrease with elevation for two main reasons: (i) the air temperature threshold approach for melt onset does not capture the diurnal variability of melt in cold and strong irradiated environments and (ii) energy losses decrease the correlation between melt and net shortwave radiation. We summarize our results by means of an elevation profile of ablation components that can be used as reference in future studies of glacier ablation in the semiarid Andes."}],"_id":"12611","title":"Patterns of glacier ablation across North-Central Chile: Identifying the limits of empirical melt models under sublimation-favorable conditions","publication":"Water Resources Research"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","type":"journal_article","date_updated":"2023-02-24T11:38:31Z","oa_version":"Published Version","day":"01","doi":"10.1017/jog.2016.120","language":[{"iso":"eng"}],"date_published":"2017-02-01T00:00:00Z","keyword":["Earth-Surface Processes"],"page":"88-105","publication_identifier":{"issn":["0022-1430"],"eissn":["1727-5652"]},"scopus_import":"1","citation":{"apa":"MILES, E. S., WILLIS, I. C., ARNOLD, N. S., STEINER, J., &#38; Pellicciotti, F. (2017). Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013. <i>Journal of Glaciology</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jog.2016.120\">https://doi.org/10.1017/jog.2016.120</a>","mla":"MILES, EVAN S., et al. “Spatial, Seasonal and Interannual Variability of Supraglacial Ponds in the Langtang Valley of Nepal, 1999–2013.” <i>Journal of Glaciology</i>, vol. 63, no. 237, Cambridge University Press, 2017, pp. 88–105, doi:<a href=\"https://doi.org/10.1017/jog.2016.120\">10.1017/jog.2016.120</a>.","short":"E.S. MILES, I.C. WILLIS, N.S. ARNOLD, J. STEINER, F. Pellicciotti, Journal of Glaciology 63 (2017) 88–105.","chicago":"MILES, EVAN S., IAN C. WILLIS, NEIL S. ARNOLD, JAKOB STEINER, and Francesca Pellicciotti. “Spatial, Seasonal and Interannual Variability of Supraglacial Ponds in the Langtang Valley of Nepal, 1999–2013.” <i>Journal of Glaciology</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jog.2016.120\">https://doi.org/10.1017/jog.2016.120</a>.","ista":"MILES ES, WILLIS IC, ARNOLD NS, STEINER J, Pellicciotti F. 2017. Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013. Journal of Glaciology. 63(237), 88–105.","ama":"MILES ES, WILLIS IC, ARNOLD NS, STEINER J, Pellicciotti F. Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013. <i>Journal of Glaciology</i>. 2017;63(237):88-105. doi:<a href=\"https://doi.org/10.1017/jog.2016.120\">10.1017/jog.2016.120</a>","ieee":"E. S. MILES, I. C. WILLIS, N. S. ARNOLD, J. STEINER, and F. Pellicciotti, “Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013,” <i>Journal of Glaciology</i>, vol. 63, no. 237. Cambridge University Press, pp. 88–105, 2017."},"main_file_link":[{"url":"https://doi.org/10.1017/jog.2016.120","open_access":"1"}],"quality_controlled":"1","author":[{"last_name":"MILES","first_name":"EVAN S.","full_name":"MILES, EVAN S."},{"full_name":"WILLIS, IAN C.","first_name":"IAN C.","last_name":"WILLIS"},{"full_name":"ARNOLD, NEIL S.","last_name":"ARNOLD","first_name":"NEIL S."},{"full_name":"STEINER, JAKOB","first_name":"JAKOB","last_name":"STEINER"},{"first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"}],"extern":"1","year":"2017","title":"Spatial, seasonal and interannual variability of supraglacial ponds in the Langtang Valley of Nepal, 1999–2013","publication":"Journal of Glaciology","oa":1,"_id":"12612","publication_status":"published","abstract":[{"text":"Supraglacial ponds play a key role in absorbing atmospheric energy and directing it to the ice of debris-covered glaciers, but the spatial and temporal distribution of these features is not well documented. We analyse 172 Landsat TM/ETM+ scenes for the period 1999–2013 to identify thawed supraglacial ponds for the debris-covered tongues of five glaciers in the Langtang Valley of Nepal. We apply an advanced atmospheric correction routine (Landcor/6S) and use band ratio and image morphological techniques to identify ponds and validate our results with 2.5 m Cartosat-1 observations. We then characterize the spatial, seasonal and interannual patterns of ponds. We find high variability in pond incidence between glaciers (May–October means of 0.08–1.69% of debris area), with ponds most frequent in zones of low surface gradient and velocity. The ponds show pronounced seasonality, appearing in the pre-monsoon as snow melts, peaking at the monsoon onset at 2% of debris-covered area, then declining in the post-monsoon as ponds drain or freeze. Ponds are highly recurrent and persistent, with 40.5% of pond locations occurring for multiple years. Rather than a trend in pond cover over the study period, we find high interannual variability for each glacier after controlling for seasonality.","lang":"eng"}],"issue":"237","volume":63,"publisher":"Cambridge University Press","article_type":"original","intvolume":"        63","date_created":"2023-02-20T08:14:16Z","month":"02","status":"public"},{"publisher":"FSP Scientific Computing","file_date_updated":"2023-05-16T07:20:50Z","page":"28","date_published":"2017-03-03T00:00:00Z","file":[{"file_id":"12969","date_updated":"2023-05-16T07:20:50Z","success":1,"access_level":"open_access","checksum":"7bcc499479d4f4c5ce6c0071c24ca6c6","file_name":"2017_AHPC_Schloegl.pdf","date_created":"2023-05-16T07:20:50Z","relation":"main_file","content_type":"application/pdf","creator":"dernst","file_size":1005486}],"status":"public","date_created":"2023-05-05T12:58:53Z","conference":{"name":"AHPC: Austrian HPC Meeting","end_date":"2017-03-03","location":"Grundlsee, Austria","start_date":"2017-03-01"},"month":"03","day":"03","year":"2017","date_updated":"2023-05-16T07:22:23Z","type":"conference_abstract","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","last_name":"Schlögl"},{"full_name":"Kiss, Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","last_name":"Kiss","first_name":"Janos"}],"article_processing_charge":"No","main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc17/BOOKLET_AHPC17.pdf","open_access":"1"}],"citation":{"ieee":"A. Schlögl and J. Kiss, “Scientific Computing at IST Austria,” in <i>AHPC17 – Austrian HPC Meeting 2017</i>, Grundlsee, Austria, 2017, p. 28.","ama":"Schlögl A, Kiss J. Scientific Computing at IST Austria. In: <i>AHPC17 – Austrian HPC Meeting 2017</i>. FSP Scientific Computing; 2017:28.","short":"A. Schlögl, J. Kiss, in:, AHPC17 – Austrian HPC Meeting 2017, FSP Scientific Computing, 2017, p. 28.","chicago":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” In <i>AHPC17 – Austrian HPC Meeting 2017</i>, 28. FSP Scientific Computing, 2017.","ista":"Schlögl A, Kiss J. 2017. Scientific Computing at IST Austria. AHPC17 – Austrian HPC Meeting 2017. AHPC: Austrian HPC Meeting, 28.","apa":"Schlögl, A., &#38; Kiss, J. (2017). Scientific Computing at IST Austria. In <i>AHPC17 – Austrian HPC Meeting 2017</i> (p. 28). Grundlsee, Austria: FSP Scientific Computing.","mla":"Schlögl, Alois, and Janos Kiss. “Scientific Computing at IST Austria.” <i>AHPC17 – Austrian HPC Meeting 2017</i>, FSP Scientific Computing, 2017, p. 28."},"publication_status":"published","ddc":["000"],"language":[{"iso":"eng"}],"oa":1,"_id":"12905","has_accepted_license":"1","department":[{"_id":"ScienComp"}],"publication":"AHPC17 – Austrian HPC Meeting 2017","title":"Scientific Computing at IST Austria"},{"oa_version":"Published Version","date_updated":"2023-09-20T11:15:31Z","type":"journal_article","day":"01","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"department":[{"_id":"KrCh"}],"has_accepted_license":"1","doi":"10.1016/j.jcss.2016.09.009","language":[{"iso":"eng"}],"external_id":{"isi":["000388430000011"]},"file":[{"date_updated":"2020-07-14T12:44:42Z","file_id":"4885","checksum":"91271b23cf884d7c06d33bef0cd623b1","file_name":"IST-2016-717-v1+1_1-s2.0-S0022000016300897-main.pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:11:30Z","file_size":708657,"content_type":"application/pdf","creator":"system"}],"date_published":"2017-03-01T00:00:00Z","page":"144 - 170","scopus_import":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2017","citation":{"apa":"Brázdil, T., Chatterjee, K., Forejt, V., &#38; Kučera, A. (2017). Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>","mla":"Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>, vol. 84, Elsevier, 2017, pp. 144–70, doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>.","ieee":"T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” <i>Journal of Computer and System Sciences</i>, vol. 84. Elsevier, pp. 144–170, 2017.","ama":"Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. <i>Journal of Computer and System Sciences</i>. 2017;84:144-170. doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">10.1016/j.jcss.2016.09.009</a>","ista":"Brázdil T, Chatterjee K, Forejt V, Kučera A. 2017. Trading performance for stability in Markov decision processes. Journal of Computer and System Sciences. 84, 144–170.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jcss.2016.09.009\">https://doi.org/10.1016/j.jcss.2016.09.009</a>.","short":"T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, Journal of Computer and System Sciences 84 (2017) 144–170."},"author":[{"full_name":"Brázdil, Tomáš","first_name":"Tomáš","last_name":"Brázdil"},{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Forejt","first_name":"Vojtěch","full_name":"Forejt, Vojtěch"},{"first_name":"Antonín","last_name":"Kučera","full_name":"Kučera, Antonín"}],"quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"abstract":[{"lang":"eng","text":"We study controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize the expected mean-payoff performance and stability (also known as variability in the literature). We argue that the basic notion of expressing the stability using the statistical variance of the mean payoff is sometimes insufficient, and propose an alternative definition. We show that a strategy ensuring both the expected mean payoff and the variance below given bounds requires randomization and memory, under both the above definitions. We then show that the problem of finding such a strategy can be expressed as a set of constraints."}],"publication_status":"published","publication":"Journal of Computer and System Sciences","title":"Trading performance for stability in Markov decision processes","_id":"1294","related_material":{"record":[{"id":"2305","status":"public","relation":"earlier_version"}]},"oa":1,"ddc":["004","006"],"file_date_updated":"2020-07-14T12:44:42Z","publisher":"Elsevier","pubrep_id":"717","volume":84,"month":"03","date_created":"2018-12-11T11:51:12Z","status":"public","intvolume":"        84","isi":1,"publist_id":"6009"},{"oa":1,"_id":"13160","title":"Index appearance record for transforming Rabin automata into parity automata","publication":"Tools and Algorithms for the Construction and Analysis of Systems","publication_status":"published","abstract":[{"lang":"eng","text":"Transforming deterministic ω\r\n-automata into deterministic parity automata is traditionally done using variants of appearance records. We present a more efficient variant of this approach, tailored to Rabin automata, and several optimizations applicable to all appearance records. We compare the methods experimentally and find out that our method produces smaller automata than previous approaches. Moreover, the experiments demonstrate the potential of our method for LTL synthesis, using LTL-to-Rabin translators. It leads to significantly smaller parity automata when compared to state-of-the-art approaches on complex formulae."}],"author":[{"last_name":"Kretinsky","first_name":"Jan","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","last_name":"Meggendorfer","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias"},{"first_name":"Clara","last_name":"Waldmann","full_name":"Waldmann, Clara"},{"first_name":"Maximilian","last_name":"Weininger","full_name":"Weininger, Maximilian"}],"quality_controlled":"1","citation":{"ista":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. 2017. Index appearance record for transforming Rabin automata into parity automata. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10205, 443–460.","short":"J. Kretinsky, T. Meggendorfer, C. Waldmann, M. Weininger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer, 2017, pp. 443–460.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Clara Waldmann, and Maximilian Weininger. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, 10205:443–60. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>.","ieee":"J. Kretinsky, T. Meggendorfer, C. Waldmann, and M. Weininger, “Index appearance record for transforming Rabin automata into parity automata,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Uppsala, Sweden, 2017, vol. 10205, pp. 443–460.","ama":"Kretinsky J, Meggendorfer T, Waldmann C, Weininger M. Index appearance record for transforming Rabin automata into parity automata. In: <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 10205. Springer; 2017:443-460. doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>","mla":"Kretinsky, Jan, et al. “Index Appearance Record for Transforming Rabin Automata into Parity Automata.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, vol. 10205, Springer, 2017, pp. 443–60, doi:<a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">10.1007/978-3-662-54577-5_26</a>.","apa":"Kretinsky, J., Meggendorfer, T., Waldmann, C., &#38; Weininger, M. (2017). Index appearance record for transforming Rabin automata into parity automata. In <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 10205, pp. 443–460). Uppsala, Sweden: Springer. <a href=\"https://doi.org/10.1007/978-3-662-54577-5_26\">https://doi.org/10.1007/978-3-662-54577-5_26</a>"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1701.05738"}],"year":"2017","intvolume":"     10205","status":"public","date_created":"2023-06-21T13:21:14Z","month":"03","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2017-04-29","location":"Uppsala, Sweden","start_date":"2017-04-22"},"volume":10205,"publisher":"Springer","language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-54577-5_26","department":[{"_id":"KrCh"}],"acknowledgement":"This work is partially funded by the DFG project “Verified Model Checkers” and by the Czech Science Foundation, grant No. P202/12/G061.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"31","date_updated":"2023-06-21T13:29:46Z","type":"conference","oa_version":"Preprint","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783662545775"],"isbn":["9783662545768"],"eissn":["1611-3349"]},"alternative_title":["LNCS"],"arxiv":1,"page":"443-460","date_published":"2017-03-31T00:00:00Z","external_id":{"arxiv":["1701.05738"]}},{"supervisor":[{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","last_name":"Bollback"}],"day":"25","oa_version":"Published Version","date_updated":"2023-09-07T12:01:21Z","type":"dissertation","article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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. ","has_accepted_license":"1","department":[{"_id":"JoBo"}],"doi":"10.15479/AT:ISTA:th_857","language":[{"iso":"eng"}],"ec_funded":1,"page":"87","file":[{"file_size":3417773,"content_type":"application/pdf","creator":"system","relation":"main_file","date_created":"2018-12-12T10:17:00Z","checksum":"c62257a7bff0c5f39e1abffc6bfcca5c","file_name":"IST-2017-857-v1+1_thesis_fabienne.pdf","access_level":"open_access","date_updated":"2020-07-14T12:48:10Z","file_id":"5252"},{"checksum":"fc87d7d72fce52824a3ae7dcad0413a8","file_name":"2017_thesis_Jesse_source.tex","access_level":"closed","date_updated":"2020-07-14T12:48:10Z","file_id":"6212","file_size":215899,"content_type":"application/x-tex","creator":"dernst","relation":"source_file","date_created":"2019-04-05T08:51:59Z"}],"date_published":"2017-08-25T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"alternative_title":["ISTA Thesis"],"year":"2017","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Jesse, Fabienne","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","last_name":"Jesse","first_name":"Fabienne"}],"citation":{"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>","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>.","ieee":"F. Jesse, “The lac operon in the wild,” Institute of Science and Technology Austria, 2017.","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>","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>.","short":"F. Jesse, The Lac Operon in the Wild, Institute of Science and Technology Austria, 2017.","ista":"Jesse F. 2017. The lac operon in the wild. Institute of Science and Technology Austria."},"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"}],"publication_status":"published","project":[{"name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"_id":"820","oa":1,"ddc":["576","577","579"],"title":"The lac operon in the wild","publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:48:10Z","pubrep_id":"857","status":"public","month":"08","date_created":"2018-12-11T11:48:41Z","degree_awarded":"PhD","publist_id":"6829"},{"alternative_title":["ISTA Thesis"],"publication_identifier":{"issn":["2663-337X"]},"date_published":"2017-08-09T00:00:00Z","file":[{"file_id":"4900","date_updated":"2020-07-14T12:48:10Z","access_level":"open_access","file_name":"IST-2017-854-v1+1_Pavlogiannis_Thesis_PubRep.pdf","checksum":"3a3ec003f6ee73f41f82a544d63dfc77","date_created":"2018-12-12T10:11:44Z","relation":"main_file","content_type":"application/pdf","creator":"system","file_size":4103115},{"creator":"dernst","content_type":"application/zip","file_size":14744374,"relation":"source_file","date_created":"2019-04-05T07:59:31Z","checksum":"bd2facc45ff8a2e20c5ed313c2ccaa83","file_name":"2017_thesis_Pavlogiannis.zip","access_level":"closed","file_id":"6201","date_updated":"2020-07-14T12:48:10Z"}],"page":"418","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:th_854","department":[{"_id":"KrCh"}],"has_accepted_license":"1","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.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","type":"dissertation","date_updated":"2023-09-07T12:01:59Z","oa_version":"Published Version","day":"09","supervisor":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"publist_id":"6828","degree_awarded":"PhD","date_created":"2018-12-11T11:48:41Z","month":"08","status":"public","pubrep_id":"854","file_date_updated":"2020-07-14T12:48:10Z","publisher":"Institute of Science and Technology Austria","title":"Algorithmic advances in program analysis and their applications","ddc":["000"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1071"},{"id":"1437","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1602"},{"status":"public","relation":"part_of_dissertation","id":"1604"},{"relation":"part_of_dissertation","status":"public","id":"1607"},{"relation":"part_of_dissertation","status":"public","id":"1714"}]},"oa":1,"_id":"821","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","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"}],"citation":{"ista":"Pavlogiannis A. 2017. Algorithmic advances in program analysis and their applications. Institute of Science and Technology Austria.","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>.","short":"A. Pavlogiannis, Algorithmic Advances in Program Analysis and Their Applications, Institute of Science and Technology Austria, 2017.","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>","ieee":"A. Pavlogiannis, “Algorithmic advances in program analysis and their applications,” Institute of Science and Technology Austria, 2017.","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>"},"author":[{"last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","orcid":"0000-0002-8943-0722"}],"tmp":{"name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)"},"year":"2017"},{"volume":114,"issue":"40","publisher":"National Academy of Sciences","intvolume":"       114","publist_id":"6827","isi":1,"date_created":"2018-12-11T11:48:41Z","month":"10","status":"public","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5635929/","open_access":"1"}],"citation":{"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>","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>.","short":"M. de Vos, M.P. Zagórski, A. Mcnally, M.T. Bollenbach, PNAS 114 (2017) 10666–10671.","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.","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>"},"author":[{"id":"3111FFAC-F248-11E8-B48F-1D18A9856A87","full_name":"De Vos, Marjon","first_name":"Marjon","last_name":"De Vos"},{"last_name":"Zagórski","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P"},{"last_name":"Mcnally","first_name":"Alan","full_name":"Mcnally, Alan"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","last_name":"Bollenbach"}],"quality_controlled":"1","year":"2017","publication":"PNAS","title":"Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections","pmid":1,"oa":1,"_id":"822","project":[{"grant_number":"303507","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"publication_status":"published","abstract":[{"lang":"eng","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. "}],"date_published":"2017-10-03T00:00:00Z","external_id":{"isi":["000412130500061"],"pmid":["28923953"]},"page":"10666 - 10671","publication_identifier":{"issn":["00278424"]},"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","type":"journal_article","date_updated":"2023-09-26T16:18:48Z","oa_version":"Submitted Version","day":"03","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1713372114","department":[{"_id":"ToBo"}]},{"issue":"9","volume":2017,"publisher":"IOPscience","isi":1,"publist_id":"6826","intvolume":"      2017","status":"public","article_number":"093404","month":"09","date_created":"2018-12-11T11:48:41Z","quality_controlled":"1","author":[{"full_name":"Colabrese, Simona","first_name":"Simona","last_name":"Colabrese"},{"first_name":"Daniele","last_name":"De Martino","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706"},{"first_name":"Luca","last_name":"Leuzzi","full_name":"Leuzzi, Luca"},{"full_name":"Marinari, Enzo","last_name":"Marinari","first_name":"Enzo"}],"citation":{"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>","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>.","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>","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.","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>.","short":"S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari,  Journal of Statistical Mechanics: Theory and Experiment 2017 (2017)."},"main_file_link":[{"url":"https://arxiv.org/abs/1705.06303","open_access":"1"}],"year":"2017","_id":"823","oa":1,"publication":" Journal of Statistical Mechanics: Theory and Experiment","title":"Phase transitions in integer linear problems","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."}],"publication_status":"published","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000411842900001"]},"date_published":"2017-09-26T00:00:00Z","scopus_import":"1","publication_identifier":{"issn":["17425468"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","day":"26","oa_version":"Submitted Version","type":"journal_article","date_updated":"2023-09-26T16:18:12Z","department":[{"_id":"GaTk"}],"doi":"10.1088/1742-5468/aa85c3","language":[{"iso":"eng"}],"ec_funded":1},{"volume":8,"page":"83128-83141","date_published":"2017-09-15T00:00:00Z","article_type":"original","publisher":"Impact Journals","publication_identifier":{"issn":["1949-2553"]},"intvolume":"         8","status":"public","month":"09","date_created":"2020-08-10T11:53:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","author":[{"full_name":"Fazekas-Singer, Judit","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87","first_name":"Judit","last_name":"Fazekas-Singer"},{"last_name":"Berroterán-Infante","first_name":"Neydher","full_name":"Berroterán-Infante, Neydher"},{"full_name":"Rami-Mark, Christina","last_name":"Rami-Mark","first_name":"Christina"},{"first_name":"Monika","last_name":"Dumanic","full_name":"Dumanic, Monika"},{"first_name":"Miroslawa","last_name":"Matz","full_name":"Matz, Miroslawa"},{"full_name":"Willmann, Michael","last_name":"Willmann","first_name":"Michael"},{"full_name":"Andreae, Fritz","last_name":"Andreae","first_name":"Fritz"},{"full_name":"Singer, Josef","last_name":"Singer","first_name":"Josef"},{"full_name":"Wadsak, Wolfgang","first_name":"Wolfgang","last_name":"Wadsak"},{"last_name":"Mitterhauser","first_name":"Markus","full_name":"Mitterhauser, Markus"},{"full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim","first_name":"Erika"}],"extern":"1","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.18632/oncotarget.20914"}],"citation":{"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>.","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>","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.","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>","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>.","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."},"year":"2017","day":"15","oa_version":"Published Version","type":"journal_article","date_updated":"2021-01-12T08:17:39Z","_id":"8235","doi":"10.18632/oncotarget.20914","language":[{"iso":"eng"}],"oa":1,"title":"Development of a radiolabeled caninized anti-EGFR antibody for comparative oncology trials","publication":"Oncotarget","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"}],"publication_status":"published"},{"citation":{"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>","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>.","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.","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>.","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.","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>","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."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/all.13119"}],"author":[{"full_name":"Jensen-Jarolim, E.","orcid":"0000-0003-4019-5765","last_name":"Jensen-Jarolim","first_name":"E."},{"full_name":"Bax, H. J.","first_name":"H. J.","last_name":"Bax"},{"full_name":"Bianchini, R.","first_name":"R.","last_name":"Bianchini"},{"full_name":"Capron, M.","last_name":"Capron","first_name":"M."},{"last_name":"Corrigan","first_name":"C.","full_name":"Corrigan, C."},{"first_name":"M.","last_name":"Castells","full_name":"Castells, M."},{"full_name":"Dombrowicz, D.","first_name":"D.","last_name":"Dombrowicz"},{"full_name":"Daniels-Wells, T. R.","last_name":"Daniels-Wells","first_name":"T. R."},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","full_name":"Fazekas, Judit","first_name":"Judit","last_name":"Fazekas"},{"full_name":"Fiebiger, E.","last_name":"Fiebiger","first_name":"E."},{"last_name":"Gatault","first_name":"S.","full_name":"Gatault, S."},{"last_name":"Gould","first_name":"H. J.","full_name":"Gould, H. J."},{"full_name":"Janda, J.","last_name":"Janda","first_name":"J."},{"full_name":"Josephs, D. H.","last_name":"Josephs","first_name":"D. H."},{"full_name":"Karagiannis, P.","last_name":"Karagiannis","first_name":"P."},{"full_name":"Levi-Schaffer, F.","first_name":"F.","last_name":"Levi-Schaffer"},{"first_name":"A.","last_name":"Meshcheryakova","full_name":"Meshcheryakova, A."},{"full_name":"Mechtcheriakova, D.","last_name":"Mechtcheriakova","first_name":"D."},{"full_name":"Mekori, Y.","first_name":"Y.","last_name":"Mekori"},{"first_name":"F.","last_name":"Mungenast","full_name":"Mungenast, F."},{"first_name":"E. A.","last_name":"Nigro","full_name":"Nigro, E. A."},{"full_name":"Penichet, M. L.","last_name":"Penichet","first_name":"M. L."},{"first_name":"F.","last_name":"Redegeld","full_name":"Redegeld, F."},{"first_name":"L.","last_name":"Saul","full_name":"Saul, L."},{"first_name":"J.","last_name":"Singer","full_name":"Singer, J."},{"full_name":"Spicer, J. F.","first_name":"J. F.","last_name":"Spicer"},{"full_name":"Siccardi, A. G.","last_name":"Siccardi","first_name":"A. G."},{"full_name":"Spillner, E.","first_name":"E.","last_name":"Spillner"},{"first_name":"M. C.","last_name":"Turner","full_name":"Turner, M. C."},{"last_name":"Untersmayr","first_name":"E.","full_name":"Untersmayr, E."},{"full_name":"Vangelista, L.","last_name":"Vangelista","first_name":"L."},{"full_name":"Karagiannis, S. N.","first_name":"S. N.","last_name":"Karagiannis"}],"extern":"1","quality_controlled":"1","year":"2017","title":"AllergoOncology - the impact of allergy in oncology: EAACI position paper","publication":"Allergy","oa":1,"_id":"8236","publication_status":"published","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"}],"volume":72,"issue":"6","article_type":"original","publisher":"Wiley","intvolume":"        72","date_created":"2020-08-10T11:53:26Z","month":"06","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2021-01-12T08:17:39Z","type":"journal_article","oa_version":"Published Version","day":"01","doi":"10.1111/all.13119","language":[{"iso":"eng"}],"date_published":"2017-06-01T00:00:00Z","page":"866-887","publication_identifier":{"issn":["0105-4538"]}},{"date_updated":"2021-01-12T08:17:39Z","type":"journal_article","oa_version":"Published Version","day":"11","year":"2017","main_file_link":[{"open_access":"1","url":"https://doi.org/10.3389/fimmu.2017.01112"}],"citation":{"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>.","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>","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).","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.","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>","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."},"article_processing_charge":"No","author":[{"last_name":"Ilieva","first_name":"Kristina M.","full_name":"Ilieva, Kristina M."},{"last_name":"Fazekas-Singer","first_name":"Judit","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniela Y.","last_name":"Achkova","full_name":"Achkova, Daniela Y."},{"last_name":"Dodev","first_name":"Tihomir S.","full_name":"Dodev, Tihomir S."},{"last_name":"Mele","first_name":"Silvia","full_name":"Mele, Silvia"},{"last_name":"Crescioli","first_name":"Silvia","full_name":"Crescioli, Silvia"},{"first_name":"Heather J.","last_name":"Bax","full_name":"Bax, Heather J."},{"last_name":"Cheung","first_name":"Anthony","full_name":"Cheung, Anthony"},{"last_name":"Karagiannis","first_name":"Panagiotis","full_name":"Karagiannis, Panagiotis"},{"first_name":"Isabel","last_name":"Correa","full_name":"Correa, Isabel"},{"full_name":"Figini, Mariangela","last_name":"Figini","first_name":"Mariangela"},{"last_name":"Marlow","first_name":"Rebecca","full_name":"Marlow, Rebecca"},{"full_name":"Josephs, Debra H.","last_name":"Josephs","first_name":"Debra H."},{"first_name":"Andrew J.","last_name":"Beavil","full_name":"Beavil, Andrew J."},{"full_name":"Maher, John","first_name":"John","last_name":"Maher"},{"last_name":"Spicer","first_name":"James F.","full_name":"Spicer, James F."},{"full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim","first_name":"Erika"},{"first_name":"Andrew N.","last_name":"Tutt","full_name":"Tutt, Andrew N."},{"full_name":"Karagiannis, Sophia N.","last_name":"Karagiannis","first_name":"Sophia N."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication_status":"published","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"}],"title":"Functionally active Fc mutant antibodies recognizing cancer antigens generated rapidly at high yields","publication":"Frontiers in Immunology","language":[{"iso":"eng"}],"oa":1,"doi":"10.3389/fimmu.2017.01112","_id":"8237","article_type":"original","publisher":"Frontiers","date_published":"2017-09-11T00:00:00Z","volume":8,"date_created":"2020-08-10T11:53:32Z","month":"09","article_number":"1112","status":"public","intvolume":"         8","publication_identifier":{"issn":["1664-3224"]}},{"date_published":"2017-03-23T00:00:00Z","volume":7,"article_type":"original","publisher":"Springer Nature","intvolume":"         7","publication_identifier":{"issn":["2045-2322"]},"date_created":"2020-08-10T11:53:46Z","month":"03","article_number":"45067","status":"public","citation":{"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.","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).","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>.","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.","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>","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>","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>."},"main_file_link":[{"url":"https://doi.org/10.1038/srep45067","open_access":"1"}],"author":[{"full_name":"Roth-Walter, Franziska","first_name":"Franziska","last_name":"Roth-Walter"},{"full_name":"Bergmayr, Cornelia","last_name":"Bergmayr","first_name":"Cornelia"},{"last_name":"Meitz","first_name":"Sarah","full_name":"Meitz, Sarah"},{"first_name":"Stefan","last_name":"Buchleitner","full_name":"Buchleitner, Stefan"},{"last_name":"Stremnitzer","first_name":"Caroline","full_name":"Stremnitzer, Caroline"},{"first_name":"Judit","last_name":"Fazekas","full_name":"Fazekas, Judit","orcid":"0000-0002-8777-3502","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna","last_name":"Moskovskich","full_name":"Moskovskich, Anna"},{"last_name":"Müller","first_name":"Mario A.","full_name":"Müller, Mario A."},{"full_name":"Roth, Georg A.","first_name":"Georg A.","last_name":"Roth"},{"full_name":"Manzano-Szalai, Krisztina","first_name":"Krisztina","last_name":"Manzano-Szalai"},{"first_name":"Zdenek","last_name":"Dvorak","full_name":"Dvorak, Zdenek"},{"last_name":"Neunkirchner","first_name":"Alina","full_name":"Neunkirchner, Alina"},{"full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim","first_name":"Erika"}],"article_processing_charge":"No","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","date_updated":"2021-01-12T08:17:40Z","type":"journal_article","oa_version":"Published Version","day":"23","year":"2017","title":"Janus-faced Acrolein prevents allergy but accelerates tumor growth by promoting immunoregulatory Foxp3+ cells: Mouse model for passive respiratory exposure","publication":"Scientific Reports","oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/srep45067","_id":"8239","publication_status":"published","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."}]}]