[{"doi":"10.1080/07900627.2015.1020417","intvolume":"        31","scopus_import":"1","publication":"International Journal of Water Resources Development","year":"2015","volume":31,"date_published":"2015-04-18T00:00:00Z","article_type":"original","author":[{"last_name":"Shea","full_name":"Shea, J.M.","first_name":"J.M."},{"last_name":"Wagnon","first_name":"P.","full_name":"Wagnon, P."},{"first_name":"W.W.","full_name":"Immerzeel, W.W.","last_name":"Immerzeel"},{"first_name":"R.","full_name":"Biron, R.","last_name":"Biron"},{"full_name":"Brun, F.","first_name":"F.","last_name":"Brun"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","first_name":"Francesca"}],"date_created":"2023-02-20T08:16:17Z","title":"A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya","issue":"2","day":"18","publication_identifier":{"eissn":["1360-0648"],"issn":["0790-0627"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/07900627.2015.1020417"}],"status":"public","extern":"1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","keyword":["Water Science and Technology","Development"],"_id":"12629","abstract":[{"lang":"eng","text":"Meteorological studies in high-mountain environments form the basis of our understanding of catchment hydrology and glacier accumulation and melt processes, yet high-altitude (>4000 m above sea level, asl) observatories are rare. This research presents meteorological data recorded between December 2012 and November 2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl. Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation are compared between sites. Solar radiation strongly affects diurnal temperature and vapour pressure cycles, but local topography and valley-scale circulations alter wind speed and precipitation cycles. The observed diurnal variability in vertical temperature gradients in all seasons highlights the importance of in situ measurements for melt modelling. The monsoon signal (progressive onset and sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon Phailin in mid-October 2013 provides an interesting case study on the possible effects of such storms on glaciers in the region."}],"page":"174-200","oa":1,"month":"04","type":"journal_article","citation":{"short":"J.M. Shea, P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, F. Pellicciotti, International Journal of Water Resources Development 31 (2015) 174–200.","apa":"Shea, J. M., Wagnon, P., Immerzeel, W. W., Biron, R., Brun, F., &#38; Pellicciotti, F. (2015). A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. <i>International Journal of Water Resources Development</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/07900627.2015.1020417\">https://doi.org/10.1080/07900627.2015.1020417</a>","ama":"Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. <i>International Journal of Water Resources Development</i>. 2015;31(2):174-200. doi:<a href=\"https://doi.org/10.1080/07900627.2015.1020417\">10.1080/07900627.2015.1020417</a>","chicago":"Shea, J.M., P. Wagnon, W.W. Immerzeel, R. Biron, F. Brun, and Francesca Pellicciotti. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” <i>International Journal of Water Resources Development</i>. Taylor &#38; Francis, 2015. <a href=\"https://doi.org/10.1080/07900627.2015.1020417\">https://doi.org/10.1080/07900627.2015.1020417</a>.","ista":"Shea JM, Wagnon P, Immerzeel WW, Biron R, Brun F, Pellicciotti F. 2015. A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya. International Journal of Water Resources Development. 31(2), 174–200.","mla":"Shea, J. M., et al. “A Comparative High-Altitude Meteorological Analysis from Three Catchments in the Nepalese Himalaya.” <i>International Journal of Water Resources Development</i>, vol. 31, no. 2, Taylor &#38; Francis, 2015, pp. 174–200, doi:<a href=\"https://doi.org/10.1080/07900627.2015.1020417\">10.1080/07900627.2015.1020417</a>.","ieee":"J. M. Shea, P. Wagnon, W. W. Immerzeel, R. Biron, F. Brun, and F. Pellicciotti, “A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya,” <i>International Journal of Water Resources Development</i>, vol. 31, no. 2. Taylor &#38; Francis, pp. 174–200, 2015."},"publisher":"Taylor & Francis","quality_controlled":"1","oa_version":"Published Version","date_updated":"2023-02-24T09:30:42Z","language":[{"iso":"eng"}]},{"article_type":"original","date_published":"2015-04-01T00:00:00Z","issue":"4","date_created":"2023-02-20T08:16:21Z","author":[{"full_name":"Ragettli, S.","first_name":"S.","last_name":"Ragettli"},{"last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca","first_name":"Francesca"},{"last_name":"Immerzeel","full_name":"Immerzeel, W.W.","first_name":"W.W."},{"last_name":"Miles","first_name":"E.S.","full_name":"Miles, E.S."},{"first_name":"L.","full_name":"Petersen, L.","last_name":"Petersen"},{"first_name":"M.","full_name":"Heynen, M.","last_name":"Heynen"},{"first_name":"J.M.","full_name":"Shea, J.M.","last_name":"Shea"},{"last_name":"Stumm","first_name":"D.","full_name":"Stumm, D."},{"last_name":"Joshi","full_name":"Joshi, S.","first_name":"S."},{"full_name":"Shrestha, A.","first_name":"A.","last_name":"Shrestha"}],"title":"Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model","intvolume":"        78","doi":"10.1016/j.advwatres.2015.01.013","volume":78,"scopus_import":"1","year":"2015","publication":"Advances in Water Resources","status":"public","day":"01","publication_identifier":{"issn":["0309-1708"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","extern":"1","abstract":[{"lang":"eng","text":"The hydrology of high-elevation watersheds of the Hindu Kush-Himalaya region (HKH) is poorly known. The correct representation of internal states and process dynamics in glacio-hydrological models can often not be verified due to missing in situ measurements. We use a new set of detailed ground data from the upper Langtang valley in Nepal to systematically guide a state-of-the art glacio-hydrological model through a parameter assigning process with the aim to understand the hydrology of the catchment and contribution of snow and ice processes to runoff. 14 parameters are directly calculated on the basis of local data, and 13 parameters are calibrated against 5 different datasets of in situ or remote sensing data. Spatial fields of debris thickness are reconstructed through a novel approach that employs data from an Unmanned Aerial Vehicle (UAV), energy balance modeling and statistical techniques. The model is validated against measured catchment runoff (Nash–Sutcliffe efficiency 0.87) and modeled snow cover is compared to Landsat snow cover. The advanced representation of processes allowed assessing the role played by avalanching for runoff for the first time for a Himalayan catchment (5% of annual water inputs to the hydrological system are due to snow redistribution) and to quantify the hydrological significance of sub-debris ice melt (9% of annual water inputs). Snowmelt is the most important contributor to total runoff during the hydrological year 2012/2013 (representing 40% of all sources), followed by rainfall (34%) and ice melt (26%). A sensitivity analysis is used to assess the efficiency of the monitoring network and identify the timing and location of field measurements that constrain model uncertainty. The methodology to set up a glacio-hydrological model in high-elevation regions presented in this study can be regarded as a benchmark for modelers in the HKH seeking to evaluate their calibration approach, their experimental setup and thus to reduce the predictive model uncertainty.\r\n\r\n"}],"keyword":["Water Science and Technology"],"_id":"12630","type":"journal_article","citation":{"ieee":"S. Ragettli <i>et al.</i>, “Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model,” <i>Advances in Water Resources</i>, vol. 78, no. 4. Elsevier, pp. 94–111, 2015.","mla":"Ragettli, S., et al. “Unraveling the Hydrology of a Himalayan Catchment through Integration of High Resolution in Situ Data and Remote Sensing with an Advanced Simulation Model.” <i>Advances in Water Resources</i>, vol. 78, no. 4, Elsevier, 2015, pp. 94–111, doi:<a href=\"https://doi.org/10.1016/j.advwatres.2015.01.013\">10.1016/j.advwatres.2015.01.013</a>.","ama":"Ragettli S, Pellicciotti F, Immerzeel WW, et al. Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. <i>Advances in Water Resources</i>. 2015;78(4):94-111. doi:<a href=\"https://doi.org/10.1016/j.advwatres.2015.01.013\">10.1016/j.advwatres.2015.01.013</a>","chicago":"Ragettli, S., Francesca Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M. Heynen, J.M. Shea, D. Stumm, S. Joshi, and A. Shrestha. “Unraveling the Hydrology of a Himalayan Catchment through Integration of High Resolution in Situ Data and Remote Sensing with an Advanced Simulation Model.” <i>Advances in Water Resources</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.advwatres.2015.01.013\">https://doi.org/10.1016/j.advwatres.2015.01.013</a>.","ista":"Ragettli S, Pellicciotti F, Immerzeel WW, Miles ES, Petersen L, Heynen M, Shea JM, Stumm D, Joshi S, Shrestha A. 2015. Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. Advances in Water Resources. 78(4), 94–111.","apa":"Ragettli, S., Pellicciotti, F., Immerzeel, W. W., Miles, E. S., Petersen, L., Heynen, M., … Shrestha, A. (2015). Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model. <i>Advances in Water Resources</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.advwatres.2015.01.013\">https://doi.org/10.1016/j.advwatres.2015.01.013</a>","short":"S. Ragettli, F. Pellicciotti, W.W. Immerzeel, E.S. Miles, L. Petersen, M. Heynen, J.M. Shea, D. Stumm, S. Joshi, A. Shrestha, Advances in Water Resources 78 (2015) 94–111."},"month":"04","page":"94-111","oa_version":"None","publisher":"Elsevier","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2023-02-24T09:28:04Z"},{"publication":"Journal of Geophysical Research: Atmospheres","year":"2015","scopus_import":"1","volume":120,"doi":"10.1002/2015jd023137","intvolume":"       120","date_created":"2023-02-20T08:16:28Z","author":[{"last_name":"Ayala","full_name":"Ayala, A.","first_name":"A."},{"full_name":"Pellicciotti, Francesca","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti"},{"first_name":"J. M.","full_name":"Shea, J. M.","last_name":"Shea"}],"title":"Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming","issue":"8","date_published":"2015-04-18T00:00:00Z","article_type":"original","extern":"1","publication_status":"published","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"18","publication_identifier":{"eissn":["2169-8996"],"issn":["2169-897X"]},"status":"public","page":"3139-3157","month":"04","type":"journal_article","citation":{"apa":"Ayala, A., Pellicciotti, F., &#38; Shea, J. M. (2015). Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union. <a href=\"https://doi.org/10.1002/2015jd023137\">https://doi.org/10.1002/2015jd023137</a>","short":"A. Ayala, F. Pellicciotti, J.M. Shea, Journal of Geophysical Research: Atmospheres 120 (2015) 3139–3157.","ama":"Ayala A, Pellicciotti F, Shea JM. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. <i>Journal of Geophysical Research: Atmospheres</i>. 2015;120(8):3139-3157. doi:<a href=\"https://doi.org/10.1002/2015jd023137\">10.1002/2015jd023137</a>","chicago":"Ayala, A., Francesca Pellicciotti, and J. M. Shea. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” <i>Journal of Geophysical Research: Atmospheres</i>. American Geophysical Union, 2015. <a href=\"https://doi.org/10.1002/2015jd023137\">https://doi.org/10.1002/2015jd023137</a>.","ista":"Ayala A, Pellicciotti F, Shea JM. 2015. Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming. Journal of Geophysical Research: Atmospheres. 120(8), 3139–3157.","mla":"Ayala, A., et al. “Modeling 2 m Air Temperatures over Mountain Glaciers: Exploring the Influence of Katabatic Cooling and External Warming.” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 120, no. 8, American Geophysical Union, 2015, pp. 3139–57, doi:<a href=\"https://doi.org/10.1002/2015jd023137\">10.1002/2015jd023137</a>.","ieee":"A. Ayala, F. Pellicciotti, and J. M. Shea, “Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming,” <i>Journal of Geophysical Research: Atmospheres</i>, vol. 120, no. 8. American Geophysical Union, pp. 3139–3157, 2015."},"keyword":["Space and Planetary Science","Earth and Planetary Sciences (miscellaneous)","Atmospheric Science","Geophysics"],"_id":"12631","abstract":[{"lang":"eng","text":"Air temperature is one of the most relevant input variables for snow and ice melt calculations. However, local meteorological conditions, complex topography, and logistical concerns in glacierized regions make the measuring and modeling of air temperature a difficult task. In this study, we investigate the spatial distribution of 2 m air temperature over mountain glaciers and propose a modification to an existing model to improve its representation. Spatially distributed meteorological data from Haut Glacier d'Arolla (Switzerland), Place (Canada), and Juncal Norte (Chile) Glaciers are used to examine approximate flow line temperatures during their respective ablation seasons. During warm conditions (off-glacier temperatures well above 0°C), observed air temperatures in the upper reaches of Place Glacier and Haut Glacier d'Arolla decrease down glacier along the approximate flow line. At Juncal Norte and Haut Glacier d'Arolla, an increase in air temperature is observed over the glacier tongue. While the temperature behavior over the upper part can be explained by the cooling effect of the glacier surface, the temperature increase over the glacier tongue may be caused by several processes induced by the surrounding warm atmosphere. In order to capture the latter effect, we add an additional term to the Greuell and Böhm (GB) thermodynamic glacier wind model. For high off-glacier temperatures, the modified GB model reduces root-mean-square error up to 32% and provides a new approach for distributing air temperature over mountain glaciers as a function of off-glacier temperatures and approximate glacier flow lines."}],"language":[{"iso":"eng"}],"date_updated":"2023-02-24T09:16:26Z","quality_controlled":"1","publisher":"American Geophysical Union","oa_version":"Published Version"},{"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"date_updated":"2025-09-29T11:08:17Z","oa_version":"Published Version","corr_author":"1","publisher":"MIT Press","quality_controlled":"1","month":"07","citation":{"mla":"Martius, Georg S., and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” <i>Proceedings of the 13th European Conference on Artificial Life</i>, MIT Press, 2015, p. 78, doi:<a href=\"https://doi.org/10.7551/978-0-262-33027-5-ch018\">10.7551/978-0-262-33027-5-ch018</a>.","ieee":"G. S. Martius and E. Olbrich, “Quantifying self-organizing behavior of autonomous robots,” in <i>Proceedings of the 13th European Conference on Artificial Life</i>, York, United Kingdom, 2015, p. 78.","ama":"Martius GS, Olbrich E. Quantifying self-organizing behavior of autonomous robots. In: <i>Proceedings of the 13th European Conference on Artificial Life</i>. MIT Press; 2015:78. doi:<a href=\"https://doi.org/10.7551/978-0-262-33027-5-ch018\">10.7551/978-0-262-33027-5-ch018</a>","chicago":"Martius, Georg S, and Eckehard Olbrich. “Quantifying Self-Organizing Behavior of Autonomous Robots.” In <i>Proceedings of the 13th European Conference on Artificial Life</i>, 78. MIT Press, 2015. <a href=\"https://doi.org/10.7551/978-0-262-33027-5-ch018\">https://doi.org/10.7551/978-0-262-33027-5-ch018</a>.","ista":"Martius GS, Olbrich E. 2015. Quantifying self-organizing behavior of autonomous robots. Proceedings of the 13th European Conference on Artificial Life. ECAL: European Conference on Artificial Life, 78.","short":"G.S. Martius, E. Olbrich, in:, Proceedings of the 13th European Conference on Artificial Life, MIT Press, 2015, p. 78.","apa":"Martius, G. S., &#38; Olbrich, E. (2015). Quantifying self-organizing behavior of autonomous robots. In <i>Proceedings of the 13th European Conference on Artificial Life</i> (p. 78). York, United Kingdom: MIT Press. <a href=\"https://doi.org/10.7551/978-0-262-33027-5-ch018\">https://doi.org/10.7551/978-0-262-33027-5-ch018</a>"},"type":"conference","page":"78","conference":{"location":"York, United Kingdom","end_date":"2015-07-24","start_date":"2015-07-20","name":"ECAL: European Conference on Artificial Life"},"oa":1,"_id":"12881","license":"https://creativecommons.org/licenses/by/4.0/","department":[{"_id":"ChLa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","publication_status":"published","external_id":{"isi":["000510147800018"]},"has_accepted_license":"1","isi":1,"status":"public","day":"01","publication_identifier":{"isbn":["9780262330275"]},"file_date_updated":"2023-05-02T07:02:59Z","file":[{"date_updated":"2023-05-02T07:02:59Z","relation":"main_file","checksum":"880eabe59c9df12f06a882aa1bc4e600","content_type":"application/pdf","file_id":"12882","success":1,"access_level":"open_access","file_name":"2015_ECAL_Martius.pdf","creator":"dernst","date_created":"2023-05-02T07:02:59Z","file_size":1674241}],"title":"Quantifying self-organizing behavior of autonomous robots","author":[{"first_name":"Georg S","full_name":"Martius, Georg S","last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eckehard","full_name":"Olbrich, Eckehard","last_name":"Olbrich"}],"date_created":"2023-04-30T22:01:07Z","ec_funded":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"date_published":"2015-07-01T00:00:00Z","scopus_import":"1","year":"2015","publication":"Proceedings of the 13th European Conference on Artificial Life","acknowledgement":"This work was supported by the DFG (SPP 1527) and the EU (FP7, REA grant no 291734).","doi":"10.7551/978-0-262-33027-5-ch018","ddc":["000"]},{"title":"Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach","page":"825 - 854","date_created":"2018-12-11T11:51:18Z","author":[{"full_name":"Julian Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Günther","full_name":"Grün, Günther","last_name":"Grün"}],"month":"01","citation":{"apa":"Fischer, J. L., &#38; Grün, G. (2015). Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/140960578\">https://doi.org/10.1137/140960578</a>","short":"J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 47 (2015) 825–854.","chicago":"Fischer, Julian L, and Günther Grün. “Finite Speed of Propagation and Waiting Times for the Stochastic Porous Medium Equation: A Unifying Approach.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics , 2015. <a href=\"https://doi.org/10.1137/140960578\">https://doi.org/10.1137/140960578</a>.","ista":"Fischer JL, Grün G. 2015. Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach. SIAM Journal on Mathematical Analysis. 47(1), 825–854.","ama":"Fischer JL, Grün G. Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach. <i>SIAM Journal on Mathematical Analysis</i>. 2015;47(1):825-854. doi:<a href=\"https://doi.org/10.1137/140960578\">10.1137/140960578</a>","mla":"Fischer, Julian L., and Günther Grün. “Finite Speed of Propagation and Waiting Times for the Stochastic Porous Medium Equation: A Unifying Approach.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 47, no. 1, Society for Industrial and Applied Mathematics , 2015, pp. 825–54, doi:<a href=\"https://doi.org/10.1137/140960578\">10.1137/140960578</a>.","ieee":"J. L. Fischer and G. Grün, “Finite speed of propagation and waiting times for the stochastic porous medium equation: A unifying approach,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 47, no. 1. Society for Industrial and Applied Mathematics , pp. 825–854, 2015."},"type":"journal_article","issue":"1","publist_id":"5958","date_published":"2015-01-01T00:00:00Z","_id":"1311","abstract":[{"text":"In this paper, we develop an energy method to study finite speed of propagation and waiting time phenomena for the stochastic porous media equation with linear multiplicative noise in up to three spatial dimensions. Based on a novel iteration technique and on stochastic counterparts of weighted integral estimates used in the deterministic setting, we formulate a sufficient criterion on the growth of initial data which locally guarantees a waiting time phenomenon to occur almost surely. Up to a logarithmic factor, this criterion coincides with the optimal criterion known from the deterministic setting. Our technique can be modified to prove finite speed of propagation as well.","lang":"eng"}],"year":"2015","publication":"SIAM Journal on Mathematical Analysis","volume":47,"doi":"10.1137/140960578","acknowledgement":"The first author has been supported by the Lithuanian-Swiss co- operation program under the project agreement No. CH-SMM-01/0.","intvolume":"        47","extern":1,"publication_status":"published","day":"01","status":"public","date_updated":"2021-01-12T06:49:48Z","quality_controlled":0,"publisher":"Society for Industrial and Applied Mathematics "},{"page":"1 - 20","date_created":"2018-12-11T11:51:19Z","author":[{"orcid":"0000-0002-0479-558X","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Julian Fischer","first_name":"Julian L"}],"title":"Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach","citation":{"mla":"Fischer, Julian L. “Estimates on Front Propagation for Nonlinear Higher-Order Parabolic Equations: An Algorithmic Approach.” <i>Interfaces and Free Boundaries</i>, vol. 17, no. 1, European Mathematical Society Publishing House, 2015, pp. 1–20, doi:<a href=\"https://doi.org/10.4171/IFB/331\">10.4171/IFB/331</a>.","ieee":"J. L. Fischer, “Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach,” <i>Interfaces and Free Boundaries</i>, vol. 17, no. 1. European Mathematical Society Publishing House, pp. 1–20, 2015.","ama":"Fischer JL. Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach. <i>Interfaces and Free Boundaries</i>. 2015;17(1):1-20. doi:<a href=\"https://doi.org/10.4171/IFB/331\">10.4171/IFB/331</a>","ista":"Fischer JL. 2015. Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach. Interfaces and Free Boundaries. 17(1), 1–20.","chicago":"Fischer, Julian L. “Estimates on Front Propagation for Nonlinear Higher-Order Parabolic Equations: An Algorithmic Approach.” <i>Interfaces and Free Boundaries</i>. European Mathematical Society Publishing House, 2015. <a href=\"https://doi.org/10.4171/IFB/331\">https://doi.org/10.4171/IFB/331</a>.","apa":"Fischer, J. L. (2015). Estimates on front propagation for nonlinear higher-order parabolic equations: An algorithmic approach. <i>Interfaces and Free Boundaries</i>. European Mathematical Society Publishing House. <a href=\"https://doi.org/10.4171/IFB/331\">https://doi.org/10.4171/IFB/331</a>","short":"J.L. Fischer, Interfaces and Free Boundaries 17 (2015) 1–20."},"month":"01","type":"journal_article","issue":"1","publist_id":"5956","date_published":"2015-01-01T00:00:00Z","_id":"1313","abstract":[{"lang":"eng","text":"We present an algorithm for the derivation of lower bounds on support propagation for a certain class of nonlinear parabolic equations. We proceed by combining the ideas in some recent papers by the author with the algorithmic construction of entropies due to Jüngel and Matthes, reducing the problem to a quantifier elimination problem. Due to its complexity, the quantifier elimination problem cannot be solved by present exact algorithms. However, by tackling the quantifier elimination problem numerically, in the case of the thin-film equation we are able to improve recent results by the author in the regime of strong slippage n ∈ (1, 2). For certain second-order doubly nonlinear parabolic equations, we are able to extend the known lower bounds on free boundary propagation to the case of irregular oscillatory initial data. Finally, we apply our method to a sixth-order quantum drift-diffusion equation, resulting in an upper bound on the time which it takes for the support to reach every point in the domain."}],"year":"2015","publication":"Interfaces and Free Boundaries","volume":17,"doi":"10.4171/IFB/331","acknowledgement":"This research was supported by the Lithuanian-Swiss cooperation program under the project agreement No.  CH-SMM-01/0.","intvolume":"        17","publication_status":"published","extern":1,"day":"01","status":"public","date_updated":"2021-01-12T06:49:48Z","quality_controlled":0,"publisher":"European Mathematical Society Publishing House"},{"_id":"1314","publist_id":"5957","abstract":[{"text":"We derive a posteriori estimates for the modeling error caused by the assumption of perfect incompressibility in the incompressible Navier-Stokes equation: Real fluids are never perfectly incompressible but always feature at least some low amount of compressibility. Thus, their behavior is described by the compressible Navier-Stokes equation, the pressure being a steep function of the density. We rigorously estimate the difference between an approximate solution to the incompressible Navier-Stokes equation and any weak solution to the compressible Navier-Stokes equation in the sense of Lions (without assuming any additional regularity of solutions). Heuristics and numerical results suggest that our error estimates are of optimal order in the case of &quot;well-behaved&quot; flows and divergence-free approximations of the velocity field. Thus, we expect our estimates to justify the idealization of fluids as perfectly incompressible also in practical situations.","lang":"eng"}],"page":"2178 - 2205","citation":{"ama":"Fischer JL. A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation. <i>SIAM Journal on Numerical Analysis</i>. 2015;53(5):2178-2205. doi:<a href=\"https://doi.org/10.1137/140966654\">10.1137/140966654</a>","chicago":"Fischer, Julian L. “A Posteriori Modeling Error Estimates for the Assumption of Perfect Incompressibility in the Navier-Stokes Equation.” <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics , 2015. <a href=\"https://doi.org/10.1137/140966654\">https://doi.org/10.1137/140966654</a>.","ista":"Fischer JL. 2015. A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation. SIAM Journal on Numerical Analysis. 53(5), 2178–2205.","apa":"Fischer, J. L. (2015). A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation. <i>SIAM Journal on Numerical Analysis</i>. Society for Industrial and Applied Mathematics . <a href=\"https://doi.org/10.1137/140966654\">https://doi.org/10.1137/140966654</a>","short":"J.L. Fischer, SIAM Journal on Numerical Analysis 53 (2015) 2178–2205.","ieee":"J. L. Fischer, “A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation,” <i>SIAM Journal on Numerical Analysis</i>, vol. 53, no. 5. Society for Industrial and Applied Mathematics , pp. 2178–2205, 2015.","mla":"Fischer, Julian L. “A Posteriori Modeling Error Estimates for the Assumption of Perfect Incompressibility in the Navier-Stokes Equation.” <i>SIAM Journal on Numerical Analysis</i>, vol. 53, no. 5, Society for Industrial and Applied Mathematics , 2015, pp. 2178–205, doi:<a href=\"https://doi.org/10.1137/140966654\">10.1137/140966654</a>."},"month":"01","type":"journal_article","publisher":"Society for Industrial and Applied Mathematics ","quality_controlled":"1","oa_version":"None","language":[{"iso":"eng"}],"date_updated":"2025-09-22T14:34:15Z","doi":"10.1137/140966654","acknowledgement":"The research of the author was supported by the Lithuanian-Swiss cooperation program under the project agreement CH-SMM-01/0.","intvolume":"        53","publication":"SIAM Journal on Numerical Analysis","year":"2015","volume":53,"date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:51:19Z","author":[{"full_name":"Fischer, Julian L","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","last_name":"Fischer"}],"title":"A posteriori modeling error estimates for the assumption of perfect incompressibility in the Navier-Stokes equation","issue":"5","day":"01","status":"public","isi":1,"publication_status":"published","extern":"1","external_id":{"isi":["000364456100004"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No"},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","OA_place":"publisher","DOAJ_listed":"1","oa":1,"month":"10","citation":{"ieee":"P. Kushwaha <i>et al.</i>, “Nearly free electrons in a 5d delafossite oxide metal,” <i>Science Advances</i>, vol. 1, no. 9. American Association for the Advancement of Science, 2015.","mla":"Kushwaha, Pallavi, et al. “Nearly Free Electrons in a 5d Delafossite Oxide Metal.” <i>Science Advances</i>, vol. 1, no. 9, 1500692, American Association for the Advancement of Science, 2015, doi:<a href=\"https://doi.org/10.1126/sciadv.1500692\">10.1126/sciadv.1500692</a>.","apa":"Kushwaha, P., Sunko, V., Moll, P. J. W., Bawden, L., Riley, J. M., Nandi, N., … King, P. D. C. (2015). Nearly free electrons in a 5d delafossite oxide metal. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.1500692\">https://doi.org/10.1126/sciadv.1500692</a>","short":"P. Kushwaha, V. Sunko, P.J.W. Moll, L. Bawden, J.M. Riley, N. Nandi, H. Rosner, M.P. Schmidt, F. Arnold, E. Hassinger, T.K. Kim, M. Hoesch, A.P. Mackenzie, P.D.C. King, Science Advances 1 (2015).","ama":"Kushwaha P, Sunko V, Moll PJW, et al. Nearly free electrons in a 5d delafossite oxide metal. <i>Science Advances</i>. 2015;1(9). doi:<a href=\"https://doi.org/10.1126/sciadv.1500692\">10.1126/sciadv.1500692</a>","ista":"Kushwaha P, Sunko V, Moll PJW, Bawden L, Riley JM, Nandi N, Rosner H, Schmidt MP, Arnold F, Hassinger E, Kim TK, Hoesch M, Mackenzie AP, King PDC. 2015. Nearly free electrons in a 5d delafossite oxide metal. Science Advances. 1(9), 1500692.","chicago":"Kushwaha, Pallavi, Veronika Sunko, Philip J. W. Moll, Lewis Bawden, Jonathon M. Riley, Nabhanila Nandi, Helge Rosner, et al. “Nearly Free Electrons in a 5d Delafossite Oxide Metal.” <i>Science Advances</i>. American Association for the Advancement of Science, 2015. <a href=\"https://doi.org/10.1126/sciadv.1500692\">https://doi.org/10.1126/sciadv.1500692</a>."},"type":"journal_article","_id":"19805","abstract":[{"text":"Understanding the role of electron correlations in strong spin-orbit transition-metal oxides is key to the realization of numerous exotic phases including spin-orbit–assisted Mott insulators, correlated topological solids, and prospective new high-temperature superconductors. To date, most attention has been focused on the 5d iridium-based oxides. We instead consider the Pt-based delafossite oxide PtCoO2. Our transport measurements, performed on single-crystal samples etched to well-defined geometries using focused ion beam techniques, yield a room temperature resistivity of only 2.1 microhm·cm (μΩ-cm), establishing PtCoO2 as the most conductive oxide known. From angle-resolved photoemission and density functional theory, we show that the underlying Fermi surface is a single cylinder of nearly hexagonal cross-section, with very weak dispersion along kz. Despite being predominantly composed of d-orbital character, the conduction band is remarkably steep, with an average effective mass of only 1.14me. Moreover, the sharp spectral features observed in photoemission remain well defined with little additional broadening for more than 500 meV below EF, pointing to suppressed electron-electron scattering. Together, our findings establish PtCoO2 as a model nearly-free–electron system in a 5d delafossite transition-metal oxide.","lang":"eng"}],"tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"language":[{"iso":"eng"}],"date_updated":"2025-06-10T13:09:49Z","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa_version":"Published Version","scopus_import":"1","year":"2015","publication":"Science Advances","volume":1,"doi":"10.1126/sciadv.1500692","ddc":["530"],"intvolume":"         1","article_number":"1500692","author":[{"first_name":"Pallavi","full_name":"Kushwaha, Pallavi","last_name":"Kushwaha"},{"full_name":"Sunko, Veronika","first_name":"Veronika","orcid":"0000-0003-2724-3523","last_name":"Sunko","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3"},{"first_name":"Philip J. W.","full_name":"Moll, Philip J. W.","last_name":"Moll"},{"last_name":"Bawden","first_name":"Lewis","full_name":"Bawden, Lewis"},{"last_name":"Riley","full_name":"Riley, Jonathon M.","first_name":"Jonathon M."},{"full_name":"Nandi, Nabhanila","first_name":"Nabhanila","last_name":"Nandi"},{"full_name":"Rosner, Helge","first_name":"Helge","last_name":"Rosner"},{"last_name":"Schmidt","full_name":"Schmidt, Marcus P.","first_name":"Marcus P."},{"first_name":"Frank","full_name":"Arnold, Frank","last_name":"Arnold"},{"last_name":"Hassinger","first_name":"Elena","full_name":"Hassinger, Elena"},{"full_name":"Kim, Timur K.","first_name":"Timur K.","last_name":"Kim"},{"full_name":"Hoesch, Moritz","first_name":"Moritz","last_name":"Hoesch"},{"first_name":"Andrew P.","full_name":"Mackenzie, Andrew P.","last_name":"Mackenzie"},{"last_name":"King","first_name":"Phil D. C.","full_name":"King, Phil D. C."}],"date_created":"2025-06-10T09:09:54Z","title":"Nearly free electrons in a 5d delafossite oxide metal","issue":"9","date_published":"2015-10-01T00:00:00Z","article_type":"original","OA_type":"gold","publication_status":"published","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","publication_identifier":{"issn":["2375-2548"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/sciadv.1500692"}],"status":"public"},{"language":[{"iso":"eng"}],"date_updated":"2025-08-05T14:47:50Z","oa_version":"None","publisher":"Wiley","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","extern":"1","status":"public","day":"01","volume":53,"publication":"Journal of Zoological Systematics and Evolutionary Research","year":"2015","intvolume":"        53","doi":"10.1111/jzs.12079","acknowledgement":"Funded by      University of Alaska Center for Global Change Student Research     Cooperative Institute for Alaska Research and the Rasmuson Foundation","type":"journal_article","citation":{"ama":"Garvin M, Bielawski J, Sazanov LA, Gharrett A. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. <i>Journal of Zoological Systematics and Evolutionary Research</i>. 2015;53(1):1-17. doi:<a href=\"https://doi.org/10.1111/jzs.12079\">10.1111/jzs.12079</a>","chicago":"Garvin, Michael, Joseph Bielawski, Leonid A Sazanov, and Anthony Gharrett. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” <i>Journal of Zoological Systematics and Evolutionary Research</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/jzs.12079\">https://doi.org/10.1111/jzs.12079</a>.","ista":"Garvin M, Bielawski J, Sazanov LA, Gharrett A. 2015. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. Journal of Zoological Systematics and Evolutionary Research. 53(1), 1–17.","short":"M. Garvin, J. Bielawski, L.A. Sazanov, A. Gharrett, Journal of Zoological Systematics and Evolutionary Research 53 (2015) 1–17.","apa":"Garvin, M., Bielawski, J., Sazanov, L. A., &#38; Gharrett, A. (2015). Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. <i>Journal of Zoological Systematics and Evolutionary Research</i>. Wiley. <a href=\"https://doi.org/10.1111/jzs.12079\">https://doi.org/10.1111/jzs.12079</a>","mla":"Garvin, Michael, et al. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” <i>Journal of Zoological Systematics and Evolutionary Research</i>, vol. 53, no. 1, Wiley, 2015, pp. 1–17, doi:<a href=\"https://doi.org/10.1111/jzs.12079\">10.1111/jzs.12079</a>.","ieee":"M. Garvin, J. Bielawski, L. A. Sazanov, and A. Gharrett, “Review and meta-analysis of natural selection in mitochondrial complex I in metazoans,” <i>Journal of Zoological Systematics and Evolutionary Research</i>, vol. 53, no. 1. Wiley, pp. 1–17, 2015."},"month":"02","issue":"1","author":[{"full_name":"Garvin, Michael","first_name":"Michael","last_name":"Garvin"},{"last_name":"Bielawski","first_name":"Joseph","full_name":"Bielawski, Joseph"},{"first_name":"Leonid A","full_name":"Sazanov, Leonid A","last_name":"Sazanov","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989"},{"full_name":"Gharrett, Anthony","first_name":"Anthony","last_name":"Gharrett"}],"page":"1 - 17","title":"Review and meta-analysis of natural selection in mitochondrial complex I in metazoans","date_created":"2018-12-11T11:55:02Z","article_type":"review","abstract":[{"text":"Variation in mitochondrial DNA is often assumed to be neutral and is used to construct the genealogical relationships among populations and species. However, if extant variation is the result of episodes of positive selection, these genealogies may be incorrect, although this information itself may pro-vide biologically and evolutionary meaningful information. In fact, positive Darwinian selection has been detected in the mitochondrial-encoded subunits that comprise complex I from diverse taxa with seemingly dissimilar bioenergetic life histories, but the functional implications of the selected sites are unknown. Complex I produces roughly 40% of the proton flux that is used to synthesize ATP from ADP, and a functional model based on the high-resolution structure of complex I described a unique biomechanical apparatus for proton translocation. We reported positive selection at sites in this apparatus during the evolution of Pacific salmon, and it appeared this was also the case in published reports from other taxa, but a comparison among studies was difficult because different statistical tests were used to detect selection and oftentimes, specific sites were not reported. Here we review the literature of positive selection in mitochondrial genomes, the statistical tests used to detect selection, and the structural and functional models that are currently available to study the physiological implications of selection. We then search for signatures of positive selection among the coding mitochondrial genomes of 237 species with a common set of tests and verify that the ND5 subunit of complex I is a repeated target of positive Darwinian selection in diverse taxa. We propose a novel hypothesis to explain the results based on their bioenergetic life histories and provide a guide for laboratory and field studies to test this hypothesis.","lang":"eng"}],"date_published":"2015-02-01T00:00:00Z","publist_id":"5102","_id":"1981"},{"date_updated":"2025-03-07T08:44:29Z","language":[{"iso":"eng"}],"oa_version":"Submitted Version","quality_controlled":"1","publisher":"ACM","citation":{"short":"A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM, 2015, pp. 433–444.","apa":"Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., &#38; Tarrach, T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented at the POPL: Principles of Programming Languages, Mumbai, India: ACM. <a href=\"https://doi.org/10.1145/2676726.2677008\">https://doi.org/10.1145/2676726.2677008</a>","chicago":"Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta, and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44. ACM, 2015. <a href=\"https://doi.org/10.1145/2676726.2677008\">https://doi.org/10.1145/2676726.2677008</a>.","ista":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct representation of concurrent trace sets. POPL: Principles of Programming Languages, 433–444.","ama":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation of concurrent trace sets. In: ACM; 2015:433-444. doi:<a href=\"https://doi.org/10.1145/2676726.2677008\">10.1145/2676726.2677008</a>","ieee":"A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct representation of concurrent trace sets,” presented at the POPL: Principles of Programming Languages, Mumbai, India, 2015, pp. 433–444.","mla":"Gupta, Ashutosh, et al. <i>Succinct Representation of Concurrent Trace Sets</i>. ACM, 2015, pp. 433–44, doi:<a href=\"https://doi.org/10.1145/2676726.2677008\">10.1145/2676726.2677008</a>."},"type":"conference","month":"01","oa":1,"conference":{"end_date":"2015-01-17","start_date":"2015-01-15","name":"POPL: Principles of Programming Languages","location":"Mumbai, India"},"page":"433 - 444","abstract":[{"lang":"eng","text":"We present a method and a tool for generating succinct representations of sets of concurrent traces. We focus on trace sets that contain all correct or all incorrect permutations of events from a given trace. We represent trace sets as HB-Formulas that are Boolean combinations of happens-before constraints between events. To generate a representation of incorrect interleavings, our method iteratively explores interleavings that violate the specification and gathers generalizations of the discovered interleavings into an HB-Formula; its complement yields a representation of correct interleavings.\r\n\r\nWe claim that our trace set representations can drive diverse verification, fault localization, repair, and synthesis techniques for concurrent programs. We demonstrate this by using our tool in three case studies involving synchronization synthesis, bug summarization, and abstraction refinement based verification. In each case study, our initial experimental results have been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring missing synchronization from an HB-Formula representing correct interleavings of a given trace. The algorithm applies rules to rewrite specific patterns in the HB-Formula into locks, barriers, and wait-notify constructs. In the second case study, we use an HB-Formula representing incorrect interleavings for bug summarization. While the HB-Formula itself is a concise counterexample summary, we present additional inference rules to help identify specific concurrency bugs such as data races, define-use order violations, and two-stage access bugs. In the final case study, we present a novel predicate learning procedure that uses HB-Formulas representing abstract counterexamples to accelerate counterexample-guided abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure refines the abstraction to eliminate multiple spurious abstract counterexamples drawn from the HB-Formula."}],"publist_id":"5091","_id":"1992","file_date_updated":"2020-07-14T12:45:22Z","article_processing_charge":"No","department":[{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","has_accepted_license":"1","status":"public","publication_identifier":{"isbn":["978-1-4503-3300-9"]},"day":"15","year":"2015","scopus_import":"1","ddc":["005"],"doi":"10.1145/2676726.2677008","file":[{"date_created":"2018-12-12T10:17:56Z","creator":"system","file_size":399462,"content_type":"application/pdf","checksum":"f0d4395b600f410a191256ac0b73af32","access_level":"open_access","file_id":"5314","relation":"main_file","date_updated":"2020-07-14T12:45:22Z","file_name":"IST-2015-317-v1+1_author_version.pdf"}],"author":[{"first_name":"Ashutosh","full_name":"Gupta, Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"full_name":"Radhakrishna, Arjun","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna"},{"first_name":"Roopsha","full_name":"Samanta, Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","last_name":"Samanta"},{"orcid":"0000-0003-4409-8487","last_name":"Tarrach","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tarrach, Thorsten","first_name":"Thorsten"}],"date_created":"2018-12-11T11:55:05Z","title":"Succinct representation of concurrent trace sets","date_published":"2015-01-15T00:00:00Z","pubrep_id":"317"},{"oa_version":"Submitted Version","corr_author":"1","publisher":"The Royal Society","quality_controlled":"1","date_updated":"2025-09-23T07:55:03Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens. "}],"_id":"1993","publist_id":"5090","citation":{"ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1799. The Royal Society, 2015.","mla":"Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1799, 20141976, The Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rspb.2014.1976\">10.1098/rspb.2014.1976</a>.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2015). Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2014.1976\">https://doi.org/10.1098/rspb.2014.1976</a>","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2015;282(1799). doi:<a href=\"https://doi.org/10.1098/rspb.2014.1976\">10.1098/rspb.2014.1976</a>","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1799), 20141976.","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society, 2015. <a href=\"https://doi.org/10.1098/rspb.2014.1976\">https://doi.org/10.1098/rspb.2014.1976</a>."},"type":"journal_article","month":"01","related_material":{"record":[{"relation":"research_data","status":"public","id":"9740"}]},"oa":1,"isi":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/"}],"status":"public","day":"22","publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"SyCr"}],"article_processing_charge":"No","publication_status":"published","external_id":{"isi":["000345624600008"],"pmid":["25473011"]},"intvolume":"       282","doi":"10.1098/rspb.2014.1976","acknowledgement":"Funding was obtained by the German Research Foundation (CR 118–2) and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank Line V. Ugelvig for help with ant collection and statistical discussion, Xavier Espadaler for detailed information on the ant collection site, Birgit Lautenschläger for the electron microscopy images and Eva Sixt for ant drawings. We further thank Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization and immune gene primer development, Paul Schmid-Hempel for discussion, and Line V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript. S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments; M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with intense contributions of A.V.G. and S.T.; all authors approved the manuscript.","volume":282,"scopus_import":"1","pmid":1,"year":"2015","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","project":[{"name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071"},{"grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution"}],"article_type":"original","date_published":"2015-01-22T00:00:00Z","issue":"1799","date_created":"2018-12-11T11:55:06Z","author":[{"full_name":"Konrad, Matthias","first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad"},{"first_name":"Anna V","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse"},{"full_name":"Tragust, Simon","first_name":"Simon","last_name":"Tragust","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sylvia","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"title":"Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","article_number":"20141976","ec_funded":1},{"volume":"68/Part 2","year":"2015","publication":"Journal of Symbolic Computation","scopus_import":"1","doi":"10.1016/j.jsc.2014.09.014","issue":"May-June","author":[{"full_name":"Noren, Patrik","first_name":"Patrik","id":"46870C74-F248-11E8-B48F-1D18A9856A87","last_name":"Noren"}],"date_created":"2018-12-11T11:55:07Z","title":"The three-state toric homogeneous Markov chain model has Markov degree two","date_published":"2015-05-01T00:00:00Z","article_processing_charge":"No","department":[{"_id":"CaUh"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"arxiv":["1207.0077"],"isi":["000347767600016"]},"publication_status":"published","isi":1,"status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1207.0077"}],"day":"01","arxiv":1,"type":"journal_article","citation":{"ieee":"P. Noren, “The three-state toric homogeneous Markov chain model has Markov degree two,” <i>Journal of Symbolic Computation</i>, vol. 68/Part 2, no. May-June. Elsevier, pp. 285–296, 2015.","mla":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” <i>Journal of Symbolic Computation</i>, vol. 68/Part 2, no. May-June, Elsevier, 2015, pp. 285–96, doi:<a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">10.1016/j.jsc.2014.09.014</a>.","chicago":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” <i>Journal of Symbolic Computation</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">https://doi.org/10.1016/j.jsc.2014.09.014</a>.","ista":"Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296.","ama":"Noren P. The three-state toric homogeneous Markov chain model has Markov degree two. <i>Journal of Symbolic Computation</i>. 2015;68/Part 2(May-June):285-296. doi:<a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">10.1016/j.jsc.2014.09.014</a>","apa":"Noren, P. (2015). The three-state toric homogeneous Markov chain model has Markov degree two. <i>Journal of Symbolic Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">https://doi.org/10.1016/j.jsc.2014.09.014</a>","short":"P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296."},"month":"05","oa":1,"page":"285 - 296","abstract":[{"text":"We prove that the three-state toric homogeneous Markov chain model has Markov degree two. In algebraic terminology this means, that a certain class of toric ideals is generated by quadratic binomials. This was conjectured by Haws, Martin del Campo, Takemura and Yoshida, who proved that they are generated by degree six binomials.","lang":"eng"}],"publist_id":"5082","_id":"1997","language":[{"iso":"eng"}],"date_updated":"2025-09-23T14:17:34Z","corr_author":"1","oa_version":"Preprint","quality_controlled":"1","publisher":"Elsevier"},{"date_updated":"2025-09-23T14:07:49Z","language":[{"iso":"eng"}],"publisher":"Taylor & Francis","quality_controlled":"1","oa_version":"Preprint","page":"261 - 269","oa":1,"type":"journal_article","month":"06","citation":{"ama":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone secant conjecture in the real Schubert calculus. <i>Experimental Mathematics</i>. 2015;24(3):261-269. doi:<a href=\"https://doi.org/10.1080/10586458.2014.980044\">10.1080/10586458.2014.980044</a>","ista":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 24(3), 261–269.","chicago":"Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert Calculus.” <i>Experimental Mathematics</i>. Taylor &#38; Francis, 2015. <a href=\"https://doi.org/10.1080/10586458.2014.980044\">https://doi.org/10.1080/10586458.2014.980044</a>.","apa":"Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., &#38; Teitler, Z. (2015). The monotone secant conjecture in the real Schubert calculus. <i>Experimental Mathematics</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10586458.2014.980044\">https://doi.org/10.1080/10586458.2014.980044</a>","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269.","ieee":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler, “The monotone secant conjecture in the real Schubert calculus,” <i>Experimental Mathematics</i>, vol. 24, no. 3. Taylor &#38; Francis, pp. 261–269, 2015.","mla":"Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert Calculus.” <i>Experimental Mathematics</i>, vol. 24, no. 3, Taylor &#38; Francis, 2015, pp. 261–69, doi:<a href=\"https://doi.org/10.1080/10586458.2014.980044\">10.1080/10586458.2014.980044</a>."},"_id":"2006","publist_id":"5070","abstract":[{"text":"The monotone secant conjecture posits a rich class of polynomial systems, all of whose solutions are real. These systems come from the Schubert calculus on flag manifolds, and the monotone secant conjecture is a compelling generalization of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko). We present some theoretical evidence for this conjecture, as well as computational evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of the phenomena we observed in our data. ","lang":"eng"}],"arxiv":1,"publication_status":"published","external_id":{"isi":["000356873900001"],"arxiv":["1109.3436"]},"article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"CaUh"}],"day":"23","isi":1,"status":"public","main_file_link":[{"url":"http://arxiv.org/abs/1109.3436","open_access":"1"}],"date_created":"2018-12-11T11:55:10Z","title":"The monotone secant conjecture in the real Schubert calculus","author":[{"first_name":"Nicolas","full_name":"Hein, Nicolas","last_name":"Hein"},{"last_name":"Hillar","first_name":"Christopher","full_name":"Hillar, Christopher"},{"first_name":"Abraham","full_name":"Martin Del Campo Sanchez, Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","last_name":"Martin Del Campo Sanchez"},{"full_name":"Sottile, Frank","first_name":"Frank","last_name":"Sottile"},{"last_name":"Teitler","first_name":"Zach","full_name":"Teitler, Zach"}],"issue":"3","date_published":"2015-06-23T00:00:00Z","scopus_import":"1","year":"2015","publication":"Experimental Mathematics","volume":24,"doi":"10.1080/10586458.2014.980044","intvolume":"        24"},{"external_id":{"arxiv":["1307.3282"],"isi":["000360077100012"]},"publication_status":"published","department":[{"_id":"CaUh"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","day":"01","isi":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3282"}],"status":"public","author":[{"id":"31934120-F248-11E8-B48F-1D18A9856A87","last_name":"Klimova","full_name":"Klimova, Anna","first_name":"Anna"},{"full_name":"Rudas, Tamás","first_name":"Tamás","last_name":"Rudas"}],"date_created":"2018-12-11T11:55:11Z","title":"Iterative scaling in curved exponential families","issue":"3","date_published":"2015-09-01T00:00:00Z","year":"2015","publication":"Scandinavian Journal of Statistics","scopus_import":"1","volume":42,"doi":"10.1111/sjos.12139","acknowledgement":"Part of the material presented here was contained in the PhD thesis of the first author to which the second author and Thomas Richardson were advisers. The authors wish to thank him for several comments and suggestions. We also thank the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1 uses the idea of Olga Klimova, to whom the authors are also indebted. The second author was supported in part by Grant K-106154 from the Hungarian National Scientific Research Fund (OTKA).","intvolume":"        42","language":[{"iso":"eng"}],"date_updated":"2025-09-23T09:25:01Z","quality_controlled":"1","publisher":"Wiley","oa_version":"Preprint","oa":1,"page":"832 - 847","type":"journal_article","citation":{"short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.","apa":"Klimova, A., &#38; Rudas, T. (2015). Iterative scaling in curved exponential families. <i>Scandinavian Journal of Statistics</i>. Wiley. <a href=\"https://doi.org/10.1111/sjos.12139\">https://doi.org/10.1111/sjos.12139</a>","ama":"Klimova A, Rudas T. Iterative scaling in curved exponential families. <i>Scandinavian Journal of Statistics</i>. 2015;42(3):832-847. doi:<a href=\"https://doi.org/10.1111/sjos.12139\">10.1111/sjos.12139</a>","chicago":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” <i>Scandinavian Journal of Statistics</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/sjos.12139\">https://doi.org/10.1111/sjos.12139</a>.","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","ieee":"A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,” <i>Scandinavian Journal of Statistics</i>, vol. 42, no. 3. Wiley, pp. 832–847, 2015.","mla":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” <i>Scandinavian Journal of Statistics</i>, vol. 42, no. 3, Wiley, 2015, pp. 832–47, doi:<a href=\"https://doi.org/10.1111/sjos.12139\">10.1111/sjos.12139</a>."},"month":"09","publist_id":"5068","_id":"2008","abstract":[{"lang":"eng","text":"The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package."}],"arxiv":1},{"arxiv":1,"oa":1,"page":"57 - 72","type":"journal_article","month":"07","citation":{"ieee":"A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs from discrete distributions,” <i>Computational Statistics &#38; Data Analysis</i>, vol. 87, no. 7. Elsevier, pp. 57–72, 2015.","mla":"Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” <i>Computational Statistics &#38; Data Analysis</i>, vol. 87, no. 7, Elsevier, 2015, pp. 57–72, doi:<a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">10.1016/j.csda.2015.01.017</a>.","apa":"Klimova, A., Uhler, C., &#38; Rudas, T. (2015). Faithfulness and learning hypergraphs from discrete distributions. <i>Computational Statistics &#38; Data Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">https://doi.org/10.1016/j.csda.2015.01.017</a>","short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics &#38; Data Analysis 87 (2015) 57–72.","chicago":"Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” <i>Computational Statistics &#38; Data Analysis</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">https://doi.org/10.1016/j.csda.2015.01.017</a>.","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics &#38; Data Analysis. 87(7), 57–72.","ama":"Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete distributions. <i>Computational Statistics &#38; Data Analysis</i>. 2015;87(7):57-72. doi:<a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">10.1016/j.csda.2015.01.017</a>"},"publist_id":"5062","_id":"2014","abstract":[{"lang":"eng","text":"The concepts of faithfulness and strong-faithfulness are important for statistical learning of graphical models. Graphs are not sufficient for describing the association structure of a discrete distribution. Hypergraphs representing hierarchical log-linear models are considered instead, and the concept of parametric (strong-) faithfulness with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence of uniformly consistent parameter estimators and enables building uniformly consistent procedures for a hypergraph search. The strength of association in a discrete distribution can be quantified with various measures, leading to different concepts of strong-faithfulness. Lower and upper bounds for the proportions of distributions that do not satisfy strong-faithfulness are computed for different parameterizations and measures of association."}],"date_updated":"2025-09-23T08:45:54Z","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Elsevier","corr_author":"1","oa_version":"Preprint","year":"2015","publication":"Computational Statistics & Data Analysis","scopus_import":"1","volume":87,"doi":"10.1016/j.csda.2015.01.017","intvolume":"        87","author":[{"full_name":"Klimova, Anna","first_name":"Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","last_name":"Klimova"},{"last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline","full_name":"Uhler, Caroline"},{"first_name":"Tamás","full_name":"Rudas, Tamás","last_name":"Rudas"}],"title":"Faithfulness and learning hypergraphs from discrete distributions","date_created":"2018-12-11T11:55:13Z","issue":"7","date_published":"2015-07-01T00:00:00Z","external_id":{"arxiv":["1404.6617"],"isi":["000352661000005"]},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"CaUh"}],"article_processing_charge":"No","day":"01","isi":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.6617"}],"status":"public"},{"day":"01","status":"public","isi":1,"has_accepted_license":"1","publication_status":"published","external_id":{"isi":["000347598100014"]},"article_processing_charge":"No","department":[{"_id":"DaSi"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2020-07-14T12:45:25Z","pubrep_id":"615","date_published":"2015-01-01T00:00:00Z","title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","date_created":"2018-12-11T11:55:17Z","author":[{"last_name":"Kawada","full_name":"Kawada, Daiki","first_name":"Daiki"},{"last_name":"Kobayashi","first_name":"Hiromu","full_name":"Kobayashi, Hiromu"},{"full_name":"Tomita, Tsuyoshi","first_name":"Tsuyoshi","last_name":"Tomita"},{"last_name":"Nakata","first_name":"Eisuke","full_name":"Nakata, Eisuke"},{"last_name":"Nagano","first_name":"Makoto","full_name":"Nagano, Makoto"},{"orcid":"0000-0001-8323-8353","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","first_name":"Daria E"},{"full_name":"Toshima, Junko","first_name":"Junko","last_name":"Toshima"},{"last_name":"Toshimaa","full_name":"Toshimaa, Jiro","first_name":"Jiro"}],"issue":"1","file":[{"relation":"main_file","date_updated":"2020-07-14T12:45:25Z","file_id":"4936","access_level":"open_access","checksum":"5bb328edebb6a91337cadd7d63f961b7","content_type":"application/pdf","file_name":"IST-2016-615-v1+1_BBAMCR.pdf","creator":"system","date_created":"2018-12-12T10:12:18Z","file_size":926685}],"doi":"10.1016/j.bbamcr.2014.10.009","ddc":["570"],"intvolume":"      1853","scopus_import":"1","year":"2015","publication":"Biochimica et Biophysica Acta - Molecular Cell Research","volume":1853,"publisher":"Elsevier","quality_controlled":"1","oa_version":"Submitted Version","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"date_updated":"2025-09-23T14:51:55Z","language":[{"iso":"eng"}],"_id":"2025","publist_id":"5047","abstract":[{"text":"Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins.","lang":"eng"}],"page":"144 - 156","oa":1,"month":"01","type":"journal_article","citation":{"ama":"Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. 2015;1853(1):144-156. doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">10.1016/j.bbamcr.2014.10.009</a>","chicago":"Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">https://doi.org/10.1016/j.bbamcr.2014.10.009</a>.","ista":"Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(1), 144–156.","short":"D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus, J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 144–156.","apa":"Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D. E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">https://doi.org/10.1016/j.bbamcr.2014.10.009</a>","ieee":"D. Kawada <i>et al.</i>, “The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins,” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.","mla":"Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">10.1016/j.bbamcr.2014.10.009</a>."},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"date_published":"2015-01-01T00:00:00Z","issue":"1","title":"A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow","date_created":"2018-12-11T11:55:18Z","author":[{"id":"374A3F1A-F248-11E8-B48F-1D18A9856A87","last_name":"Shi","first_name":"Liang","full_name":"Shi, Liang"},{"last_name":"Rampp","first_name":"Markus","full_name":"Rampp, Markus"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn"},{"first_name":"Marc","full_name":"Avila, Marc","last_name":"Avila"}],"intvolume":"       106","doi":"10.1016/j.compfluid.2014.09.021","volume":106,"publication":"Computers and Fluids","year":"2015","scopus_import":"1","isi":1,"main_file_link":[{"url":"http://arxiv.org/abs/1311.2481","open_access":"1"}],"status":"public","day":"01","article_processing_charge":"No","department":[{"_id":"BjHo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"arxiv":["1311.2481"],"isi":["000346213200001"]},"publication_status":"published","abstract":[{"lang":"eng","text":"A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes."}],"publist_id":"5042","_id":"2030","type":"journal_article","month":"01","citation":{"ieee":"L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow,” <i>Computers and Fluids</i>, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.","mla":"Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” <i>Computers and Fluids</i>, vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:<a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">10.1016/j.compfluid.2014.09.021</a>.","apa":"Shi, L., Rampp, M., Hof, B., &#38; Avila, M. (2015). A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. <i>Computers and Fluids</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">https://doi.org/10.1016/j.compfluid.2014.09.021</a>","short":"L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11.","chicago":"Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” <i>Computers and Fluids</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">https://doi.org/10.1016/j.compfluid.2014.09.021</a>.","ista":"Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 106(1), 1–11.","ama":"Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. <i>Computers and Fluids</i>. 2015;106(1):1-11. doi:<a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">10.1016/j.compfluid.2014.09.021</a>"},"oa":1,"page":"1 - 11","arxiv":1,"oa_version":"Preprint","quality_controlled":"1","publisher":"Elsevier","date_updated":"2025-09-22T14:31:33Z","language":[{"iso":"eng"}]},{"external_id":{"arxiv":["1407.4225"],"isi":["000345478700010"]},"publication_status":"published","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"KrCh"}],"day":"01","main_file_link":[{"url":"http://arxiv.org/abs/1407.4225","open_access":"1"}],"isi":1,"status":"public","ec_funded":1,"date_created":"2018-12-11T11:55:20Z","author":[{"first_name":"Béatrice","full_name":"Bérard, Béatrice","last_name":"Bérard"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"first_name":"Nathalie","full_name":"Sznajder, Nathalie","last_name":"Sznajder"}],"title":"Probabilistic opacity for Markov decision processes","issue":"1","date_published":"2015-01-01T00:00:00Z","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publication":" Information Processing Letters","year":"2015","scopus_import":"1","volume":115,"doi":"10.1016/j.ipl.2014.09.001","intvolume":"       115","date_updated":"2025-09-23T09:54:42Z","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Elsevier","oa_version":"Preprint","oa":1,"page":"52 - 59","month":"01","citation":{"ama":"Bérard B, Chatterjee K, Sznajder N. Probabilistic opacity for Markov decision processes. <i> Information Processing Letters</i>. 2015;115(1):52-59. doi:<a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">10.1016/j.ipl.2014.09.001</a>","ista":"Bérard B, Chatterjee K, Sznajder N. 2015. Probabilistic opacity for Markov decision processes.  Information Processing Letters. 115(1), 52–59.","chicago":"Bérard, Béatrice, Krishnendu Chatterjee, and Nathalie Sznajder. “Probabilistic Opacity for Markov Decision Processes.” <i> Information Processing Letters</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">https://doi.org/10.1016/j.ipl.2014.09.001</a>.","short":"B. Bérard, K. Chatterjee, N. Sznajder,  Information Processing Letters 115 (2015) 52–59.","apa":"Bérard, B., Chatterjee, K., &#38; Sznajder, N. (2015). Probabilistic opacity for Markov decision processes. <i> Information Processing Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">https://doi.org/10.1016/j.ipl.2014.09.001</a>","mla":"Bérard, Béatrice, et al. “Probabilistic Opacity for Markov Decision Processes.” <i> Information Processing Letters</i>, vol. 115, no. 1, Elsevier, 2015, pp. 52–59, doi:<a href=\"https://doi.org/10.1016/j.ipl.2014.09.001\">10.1016/j.ipl.2014.09.001</a>.","ieee":"B. Bérard, K. Chatterjee, and N. Sznajder, “Probabilistic opacity for Markov decision processes,” <i> Information Processing Letters</i>, vol. 115, no. 1. Elsevier, pp. 52–59, 2015."},"type":"journal_article","publist_id":"5025","_id":"2034","abstract":[{"lang":"eng","text":"Opacity is a generic security property, that has been defined on (non-probabilistic) transition systems and later on Markov chains with labels. For a secret predicate, given as a subset of runs, and a function describing the view of an external observer, the value of interest for opacity is a measure of the set of runs disclosing the secret. We extend this definition to the richer framework of Markov decision processes, where non-deterministicchoice is combined with probabilistic transitions, and we study related decidability problems with partial or complete observation hypotheses for the schedulers. We prove that all questions are decidable with complete observation and ω-regular secrets. With partial observation, we prove that all quantitative questions are undecidable but the question whether a system is almost surely non-opaquebecomes decidable for a restricted class of ω-regular secrets, as well as for all ω-regular secrets under finite-memory schedulers."}],"arxiv":1},{"day":"01","has_accepted_license":"1","status":"public","isi":1,"external_id":{"isi":["000360862900004"]},"publication_status":"published","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:45:26Z","date_published":"2015-10-01T00:00:00Z","pubrep_id":"486","project":[{"grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Topological Complex Systems"}],"ec_funded":1,"author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"full_name":"Jablonski, Grzegorz","first_name":"Grzegorz","orcid":"0000-0002-3536-9866","last_name":"Jablonski","id":"4483EF78-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mrozek","first_name":"Marian","full_name":"Mrozek, Marian"}],"title":"The persistent homology of a self-map","date_created":"2018-12-11T11:55:20Z","file":[{"date_updated":"2020-07-14T12:45:26Z","relation":"main_file","access_level":"open_access","file_id":"4670","checksum":"3566f3a8b0c1bc550e62914a88c584ff","content_type":"application/pdf","file_name":"IST-2016-486-v1+1_s10208-014-9223-y.pdf","creator":"system","date_created":"2018-12-12T10:08:10Z","file_size":1317546}],"issue":"5","ddc":["000"],"acknowledgement":"This research is partially supported by the Toposys project FP7-ICT-318493-STREP, by ESF under the ACAT Research Network Programme, by the Russian Government under mega project 11.G34.31.0053, and by the Polish National Science Center under Grant No. N201 419639.","doi":"10.1007/s10208-014-9223-y","intvolume":"        15","year":"2015","publication":"Foundations of Computational Mathematics","scopus_import":"1","volume":15,"quality_controlled":"1","publisher":"Springer","oa_version":"Published Version","date_updated":"2025-09-23T14:08:54Z","language":[{"iso":"eng"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publist_id":"5022","_id":"2035","abstract":[{"text":"Considering a continuous self-map and the induced endomorphism on homology, we study the eigenvalues and eigenspaces of the latter. Taking a filtration of representations, we define the persistence of the eigenspaces, effectively introducing a hierarchical organization of the map. The algorithm that computes this information for a finite sample is proved to be stable, and to give the correct answer for a sufficiently dense sample. Results computed with an implementation of the algorithm provide evidence of its practical utility.\r\n","lang":"eng"}],"oa":1,"page":"1213 - 1244","month":"10","citation":{"ieee":"H. Edelsbrunner, G. Jablonski, and M. Mrozek, “The persistent homology of a self-map,” <i>Foundations of Computational Mathematics</i>, vol. 15, no. 5. Springer, pp. 1213–1244, 2015.","mla":"Edelsbrunner, Herbert, et al. “The Persistent Homology of a Self-Map.” <i>Foundations of Computational Mathematics</i>, vol. 15, no. 5, Springer, 2015, pp. 1213–44, doi:<a href=\"https://doi.org/10.1007/s10208-014-9223-y\">10.1007/s10208-014-9223-y</a>.","chicago":"Edelsbrunner, Herbert, Grzegorz Jablonski, and Marian Mrozek. “The Persistent Homology of a Self-Map.” <i>Foundations of Computational Mathematics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s10208-014-9223-y\">https://doi.org/10.1007/s10208-014-9223-y</a>.","ista":"Edelsbrunner H, Jablonski G, Mrozek M. 2015. The persistent homology of a self-map. Foundations of Computational Mathematics. 15(5), 1213–1244.","ama":"Edelsbrunner H, Jablonski G, Mrozek M. The persistent homology of a self-map. <i>Foundations of Computational Mathematics</i>. 2015;15(5):1213-1244. doi:<a href=\"https://doi.org/10.1007/s10208-014-9223-y\">10.1007/s10208-014-9223-y</a>","short":"H. Edelsbrunner, G. Jablonski, M. Mrozek, Foundations of Computational Mathematics 15 (2015) 1213–1244.","apa":"Edelsbrunner, H., Jablonski, G., &#38; Mrozek, M. (2015). The persistent homology of a self-map. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-014-9223-y\">https://doi.org/10.1007/s10208-014-9223-y</a>"},"type":"journal_article"},{"type":"journal_article","citation":{"mla":"Boccara, Charlotte N., et al. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” <i>Hippocampus</i>, vol. 25, no. 7, Wiley, 2015, pp. 838–57, doi:<a href=\"https://doi.org/10.1002/hipo.22407\">10.1002/hipo.22407</a>.","ieee":"C. N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, and M. Witter, “A three-plane architectonic atlas of the rat hippocampal region,” <i>Hippocampus</i>, vol. 25, no. 7. Wiley, pp. 838–857, 2015.","chicago":"Boccara, Charlotte N., Lisa Kjønigsen, Ingvild Hammer, Jan Bjaalie, Trygve Leergaard, and Menno Witter. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” <i>Hippocampus</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/hipo.22407\">https://doi.org/10.1002/hipo.22407</a>.","ista":"Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. 2015. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. 25(7), 838–857.","ama":"Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. A three-plane architectonic atlas of the rat hippocampal region. <i>Hippocampus</i>. 2015;25(7):838-857. doi:<a href=\"https://doi.org/10.1002/hipo.22407\">10.1002/hipo.22407</a>","short":"C.N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, M. Witter, Hippocampus 25 (2015) 838–857.","apa":"Boccara, C. N., Kjønigsen, L., Hammer, I., Bjaalie, J., Leergaard, T., &#38; Witter, M. (2015). A three-plane architectonic atlas of the rat hippocampal region. <i>Hippocampus</i>. Wiley. <a href=\"https://doi.org/10.1002/hipo.22407\">https://doi.org/10.1002/hipo.22407</a>"},"month":"07","page":"838 - 857","abstract":[{"lang":"eng","text":"The hippocampal region, comprising the hippocampal formation and the parahippocampal region, has been one of the most intensively studied parts of the brain for decades. Better understanding of its functional diversity and complexity has led to an increased demand for specificity in experimental procedures and manipulations. In view of the complex 3D structure of the hippocampal region, precisely positioned experimental approaches require a fine-grained architectural description that is available and readable to experimentalists lacking detailed anatomical experience. In this paper, we provide the first cyto- and chemoarchitectural description of the hippocampal formation and parahippocampal region in the rat at high resolution and in the three standard sectional planes: coronal, horizontal and sagittal. The atlas uses a series of adjacent sections stained for neurons and for a number of chemical marker substances, particularly parvalbumin and calbindin. All the borders defined in one plane have been cross-checked against their counterparts in the other two planes. The entire dataset will be made available as a web-based interactive application through the Rodent Brain WorkBench (http://www.rbwb.org) which, together with this paper, provides a unique atlas resource."}],"publist_id":"5222","_id":"1874","language":[{"iso":"eng"}],"date_updated":"2025-09-23T07:29:29Z","oa_version":"None","quality_controlled":"1","publisher":"Wiley","issue":"7","date_created":"2018-12-11T11:54:29Z","author":[{"first_name":"Charlotte","full_name":"Boccara, Charlotte","id":"3FC06552-F248-11E8-B48F-1D18A9856A87","last_name":"Boccara","orcid":"0000-0001-7237-5109"},{"last_name":"Kjønigsen","full_name":"Kjønigsen, Lisa","first_name":"Lisa"},{"last_name":"Hammer","first_name":"Ingvild","full_name":"Hammer, Ingvild"},{"last_name":"Bjaalie","first_name":"Jan","full_name":"Bjaalie, Jan"},{"first_name":"Trygve","full_name":"Leergaard, Trygve","last_name":"Leergaard"},{"last_name":"Witter","first_name":"Menno","full_name":"Witter, Menno"}],"title":"A three-plane architectonic atlas of the rat hippocampal region","date_published":"2015-07-01T00:00:00Z","volume":25,"publication":"Hippocampus","year":"2015","scopus_import":"1","intvolume":"        25","doi":"10.1002/hipo.22407","article_processing_charge":"No","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"JoCs"}],"external_id":{"isi":["000356812700007"]},"publication_status":"published","status":"public","isi":1,"day":"01"}]