[{"date_published":"2018-06-07T00:00:00Z","day":"07","volume":54,"date_created":"2023-02-20T08:13:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1029/2017wr021606","extern":"1","author":[{"last_name":"Clemenzi","full_name":"Clemenzi, I.","first_name":"I."},{"first_name":"Francesca","full_name":"Pellicciotti, Francesca","last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"},{"first_name":"P.","full_name":"Burlando, P.","last_name":"Burlando"}],"status":"public","oa_version":"Published Version","publication_identifier":{"eissn":["1944-7973"],"issn":["0043-1397"]},"oa":1,"year":"2018","_id":"12605","date_updated":"2023-02-28T11:42:40Z","title":"Snow depth structure, fractal behavior, and interannual consistency over Haut Glacier d'Arolla, Switzerland","article_processing_charge":"No","scopus_import":"1","publication":"Water Resources Research","publisher":"American Geophysical Union","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Snow depth patterns over glaciers are controlled by precipitation, snow redistribution due to wind and avalanches, and the exchange of energy with the atmosphere that determines snow ablation. While many studies have advanced the understanding of ablation processes, less is known about winter snow patterns and their variability over glaciers. We analyze snow depth on Haut Glacier d'Arolla, Switzerland, in the two winter seasons 2006–2007 and 2010–2011 to (1) understand whether snow depth over an alpine glacier at the end of the accumulation season exhibits a behavior similar to the one observed on single slopes and vegetated areas; and (2) investigate the snow pattern consistency over the two accumulation seasons. We perform this analysis on a data set of high-resolution lidar-derived snow depth using variograms and fractal parameters. Our first main result is that snow depth patterns on the glacier exhibit a multiscale behavior, with a scale break around 20 m after which the fractal dimension increases, indicating more autocorrelated structure before the scale break than after. Second, this behavior is consistent over the two years, with fractal parameters and their spatial variability almost constant in the two seasons. We also show that snow depth patterns exhibit a distinct behavior in the glacier tongue and the upper catchment, with longer correlation distances on the tongue in the direction of the main winds, suggesting spatial distinctions that are likely induced by different processes and that should be taken into account when extrapolating snow depth from limited samples."}],"publication_status":"published","article_type":"original","citation":{"mla":"Clemenzi, I., et al. “Snow Depth Structure, Fractal Behavior, and Interannual Consistency over Haut Glacier d’Arolla, Switzerland.” <i>Water Resources Research</i>, vol. 54, no. 10, American Geophysical Union, 2018, pp. 7929–45, doi:<a href=\"https://doi.org/10.1029/2017wr021606\">10.1029/2017wr021606</a>.","short":"I. Clemenzi, F. Pellicciotti, P. Burlando, Water Resources Research 54 (2018) 7929–7945.","ieee":"I. Clemenzi, F. Pellicciotti, and P. Burlando, “Snow depth structure, fractal behavior, and interannual consistency over Haut Glacier d’Arolla, Switzerland,” <i>Water Resources Research</i>, vol. 54, no. 10. American Geophysical Union, pp. 7929–7945, 2018.","ista":"Clemenzi I, Pellicciotti F, Burlando P. 2018. Snow depth structure, fractal behavior, and interannual consistency over Haut Glacier d’Arolla, Switzerland. Water Resources Research. 54(10), 7929–7945.","chicago":"Clemenzi, I., Francesca Pellicciotti, and P. Burlando. “Snow Depth Structure, Fractal Behavior, and Interannual Consistency over Haut Glacier d’Arolla, Switzerland.” <i>Water Resources Research</i>. American Geophysical Union, 2018. <a href=\"https://doi.org/10.1029/2017wr021606\">https://doi.org/10.1029/2017wr021606</a>.","apa":"Clemenzi, I., Pellicciotti, F., &#38; Burlando, P. (2018). Snow depth structure, fractal behavior, and interannual consistency over Haut Glacier d’Arolla, Switzerland. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2017wr021606\">https://doi.org/10.1029/2017wr021606</a>","ama":"Clemenzi I, Pellicciotti F, Burlando P. Snow depth structure, fractal behavior, and interannual consistency over Haut Glacier d’Arolla, Switzerland. <i>Water Resources Research</i>. 2018;54(10):7929-7945. doi:<a href=\"https://doi.org/10.1029/2017wr021606\">10.1029/2017wr021606</a>"},"keyword":["Water Science and Technology"],"quality_controlled":"1","issue":"10","page":"7929-7945","month":"06","intvolume":"        54","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1029/2017WR021606","open_access":"1"}]},{"scopus_import":"1","publication":"The Cryosphere","publisher":"Copernicus Publications","language":[{"iso":"eng"}],"abstract":[{"text":"Ice cliffs within a supraglacial debris cover have been identified as a source for high ablation relative to the surrounding debris-covered area. Due to their small relative size and steep orientation, ice cliffs are difficult to detect using nadir-looking space borne sensors. The method presented here uses surface slopes calculated from digital elevation model (DEM) data to map ice cliff geometry and produce an ice cliff probability map. Surface slope thresholds, which can be sensitive to geographic location and/or data quality, are selected automatically. The method also attempts to include area at the (often narrowing) ends of ice cliffs which could otherwise be neglected due to signal saturation in surface slope data. The method was calibrated in the eastern Alaska Range, Alaska, USA, against a control ice cliff dataset derived from high-resolution visible and thermal data. Using the same input parameter set that performed best in Alaska, the method was tested against ice cliffs manually mapped in the Khumbu Himal, Nepal. Our results suggest the method can accommodate different glaciological settings and different DEM data sources without a data intensive (high-resolution, multi-data source) recalibration.","lang":"eng"}],"publication_status":"published","article_type":"original","quality_controlled":"1","keyword":["Earth-Surface Processes","Water Science and Technology"],"citation":{"ista":"Herreid S, Pellicciotti F. 2018. Automated detection of ice cliffs within supraglacial debris cover. The Cryosphere. 12(5), 1811–1829.","ieee":"S. Herreid and F. Pellicciotti, “Automated detection of ice cliffs within supraglacial debris cover,” <i>The Cryosphere</i>, vol. 12, no. 5. Copernicus Publications, pp. 1811–1829, 2018.","mla":"Herreid, Sam, and Francesca Pellicciotti. “Automated Detection of Ice Cliffs within Supraglacial Debris Cover.” <i>The Cryosphere</i>, vol. 12, no. 5, Copernicus Publications, 2018, pp. 1811–29, doi:<a href=\"https://doi.org/10.5194/tc-12-1811-2018\">10.5194/tc-12-1811-2018</a>.","short":"S. Herreid, F. Pellicciotti, The Cryosphere 12 (2018) 1811–1829.","ama":"Herreid S, Pellicciotti F. Automated detection of ice cliffs within supraglacial debris cover. <i>The Cryosphere</i>. 2018;12(5):1811-1829. doi:<a href=\"https://doi.org/10.5194/tc-12-1811-2018\">10.5194/tc-12-1811-2018</a>","apa":"Herreid, S., &#38; Pellicciotti, F. (2018). Automated detection of ice cliffs within supraglacial debris cover. <i>The Cryosphere</i>. Copernicus Publications. <a href=\"https://doi.org/10.5194/tc-12-1811-2018\">https://doi.org/10.5194/tc-12-1811-2018</a>","chicago":"Herreid, Sam, and Francesca Pellicciotti. “Automated Detection of Ice Cliffs within Supraglacial Debris Cover.” <i>The Cryosphere</i>. Copernicus Publications, 2018. <a href=\"https://doi.org/10.5194/tc-12-1811-2018\">https://doi.org/10.5194/tc-12-1811-2018</a>."},"issue":"5","page":"1811-1829","month":"05","intvolume":"        12","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5194/tc-12-1811-2018"}],"date_published":"2018-05-31T00:00:00Z","day":"31","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-02-20T08:13:36Z","volume":12,"doi":"10.5194/tc-12-1811-2018","author":[{"last_name":"Herreid","full_name":"Herreid, Sam","first_name":"Sam"},{"last_name":"Pellicciotti","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","full_name":"Pellicciotti, Francesca"}],"status":"public","extern":"1","oa_version":"Published Version","publication_identifier":{"issn":["1994-0424"]},"oa":1,"year":"2018","date_updated":"2023-02-28T11:39:26Z","_id":"12606","title":"Automated detection of ice cliffs within supraglacial debris cover","article_processing_charge":"No"},{"_id":"12607","date_updated":"2023-02-28T11:35:18Z","article_processing_charge":"No","title":"Aspect controls the survival of ice cliffs on debris-covered glaciers","oa":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"year":"2018","doi":"10.1073/pnas.1713892115","volume":115,"date_created":"2023-02-20T08:13:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","extern":"1","status":"public","author":[{"last_name":"Buri","full_name":"Buri, Pascal","first_name":"Pascal"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","first_name":"Francesca","full_name":"Pellicciotti, Francesca"}],"day":"09","date_published":"2018-04-09T00:00:00Z","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1713892115","open_access":"1"}],"page":"4369-4374","issue":"17","intvolume":"       115","month":"04","article_type":"original","publication_status":"published","citation":{"apa":"Buri, P., &#38; Pellicciotti, F. (2018). Aspect controls the survival of ice cliffs on debris-covered glaciers. <i>PNAS</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1713892115\">https://doi.org/10.1073/pnas.1713892115</a>","chicago":"Buri, Pascal, and Francesca Pellicciotti. “Aspect Controls the Survival of Ice Cliffs on Debris-Covered Glaciers.” <i>PNAS</i>. Proceedings of the National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1713892115\">https://doi.org/10.1073/pnas.1713892115</a>.","ama":"Buri P, Pellicciotti F. Aspect controls the survival of ice cliffs on debris-covered glaciers. <i>PNAS</i>. 2018;115(17):4369-4374. doi:<a href=\"https://doi.org/10.1073/pnas.1713892115\">10.1073/pnas.1713892115</a>","short":"P. Buri, F. Pellicciotti, PNAS 115 (2018) 4369–4374.","mla":"Buri, Pascal, and Francesca Pellicciotti. “Aspect Controls the Survival of Ice Cliffs on Debris-Covered Glaciers.” <i>PNAS</i>, vol. 115, no. 17, Proceedings of the National Academy of Sciences, 2018, pp. 4369–74, doi:<a href=\"https://doi.org/10.1073/pnas.1713892115\">10.1073/pnas.1713892115</a>.","ieee":"P. Buri and F. Pellicciotti, “Aspect controls the survival of ice cliffs on debris-covered glaciers,” <i>PNAS</i>, vol. 115, no. 17. Proceedings of the National Academy of Sciences, pp. 4369–4374, 2018.","ista":"Buri P, Pellicciotti F. 2018. Aspect controls the survival of ice cliffs on debris-covered glaciers. PNAS. 115(17), 4369–4374."},"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","publication":"PNAS","scopus_import":"1","abstract":[{"text":"Supraglacial ice cliffs exist on debris-covered glaciers worldwide, but despite their importance as melt hot spots, their life cycle is little understood. Early field observations had advanced a hypothesis of survival of north-facing and disappearance of south-facing cliffs, which is central for predicting the contribution of cliffs to total glacier mass losses. Their role as windows of energy transfer suggests they may explain the anomalously high mass losses of debris-covered glaciers in High Mountain Asia (HMA) despite the insulating debris, currently at the center of a debated controversy. We use a 3D model of cliff evolution coupled to very high-resolution topographic data to demonstrate that ice cliffs facing south (in the Northern Hemisphere) disappear within a few months due to enhanced solar radiation receipts and that aspect is the key control on cliffs evolution. We reproduce continuous flattening of south-facing cliffs, a result of their vertical gradient of incoming solar radiation and sky view factor. Our results establish that only north-facing cliffs are recurrent features and thus stable contributors to the melting of debris-covered glaciers. Satellite observations and mass balance modeling confirms that few south-facing cliffs of small size exist on the glaciers of Langtang, and their contribution to the glacier volume losses is very small (∼1%). This has major implications for the mass balance of HMA debris-covered glaciers as it provides the basis for new parameterizations of cliff evolution and distribution to constrain volume losses in a region where glaciers are highly relevant as water sources for millions of people.","lang":"eng"}],"language":[{"iso":"eng"}]},{"_id":"127","type":"journal_article","date_updated":"2021-01-12T06:49:31Z","title":"Clicks for doughnuts","issue":"8","page":"777 - 778","month":"05","intvolume":"        14","year":"2018","volume":14,"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:46Z","publication_status":"published","doi":"10.1038/s41567-018-0160-6","citation":{"apa":"Waitukaitis, S. R. (2018). Clicks for doughnuts. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41567-018-0160-6\">https://doi.org/10.1038/s41567-018-0160-6</a>","chicago":"Waitukaitis, Scott R. “Clicks for Doughnuts.” <i>Nature Physics</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41567-018-0160-6\">https://doi.org/10.1038/s41567-018-0160-6</a>.","ama":"Waitukaitis SR. Clicks for doughnuts. <i>Nature Physics</i>. 2018;14(8):777-778. doi:<a href=\"https://doi.org/10.1038/s41567-018-0160-6\">10.1038/s41567-018-0160-6</a>","mla":"Waitukaitis, Scott R. “Clicks for Doughnuts.” <i>Nature Physics</i>, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 777–78, doi:<a href=\"https://doi.org/10.1038/s41567-018-0160-6\">10.1038/s41567-018-0160-6</a>.","short":"S.R. Waitukaitis, Nature Physics 14 (2018) 777–778.","ista":"Waitukaitis SR. 2018. Clicks for doughnuts. Nature Physics. 14(8), 777–778.","ieee":"S. R. Waitukaitis, “Clicks for doughnuts,” <i>Nature Physics</i>, vol. 14, no. 8. Nature Publishing Group, pp. 777–778, 2018."},"extern":"1","author":[{"id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","full_name":"Waitukaitis, Scott R","first_name":"Scott R","orcid":"0000-0002-2299-3176"}],"status":"public","oa_version":"None","publication":"Nature Physics","date_published":"2018-05-28T00:00:00Z","day":"28","publisher":"Nature Publishing Group","publist_id":"7926","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The ideas of topology are breaking ground in origami-based metamaterials. Experiments now show that certain shapes — doughnuts included — exhibit topological bistability, and can be made to click between different topologically stable states."}]},{"type":"journal_article","ddc":["004"],"month":"08","isi":1,"article_number":"136","intvolume":"        37","pubrep_id":"1038","issue":"4","ec_funded":1,"citation":{"ama":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds: Computational design of silicone molds. <i>ACM Trans Graph</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201381\">10.1145/3197517.3201381</a>","apa":"Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., &#38; Cignoni, P. (2018). Metamolds: Computational design of silicone molds. <i>ACM Trans. Graph.</i> ACM. <a href=\"https://doi.org/10.1145/3197517.3201381\">https://doi.org/10.1145/3197517.3201381</a>","chicago":"Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.” <i>ACM Trans. Graph.</i> ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201381\">https://doi.org/10.1145/3197517.3201381</a>.","ieee":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni, “Metamolds: Computational design of silicone molds,” <i>ACM Trans. Graph.</i>, vol. 37, no. 4. ACM, 2018.","ista":"Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds: Computational design of silicone molds. ACM Trans. Graph. 37(4), 136.","mla":"Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.” <i>ACM Trans. Graph.</i>, vol. 37, no. 4, 136, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201381\">10.1145/3197517.3201381</a>.","short":"T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM Trans. Graph. 37 (2018)."},"quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"publist_id":"8043","department":[{"_id":"BeBi"}],"abstract":[{"text":"We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery.","lang":"eng"}],"file":[{"relation":"main_file","date_updated":"2020-07-14T12:44:43Z","file_name":"IST-2018-1038-v1+1_metamolds_authorversion.pdf","date_created":"2018-12-12T10:18:52Z","file_size":91939066,"access_level":"open_access","creator":"system","checksum":"61d46273dca4de626accef1d17a0aaad","content_type":"application/pdf","file_id":"5374"}],"scopus_import":"1","publication":"ACM Trans. Graph.","file_date_updated":"2020-07-14T12:44:43Z","publisher":"ACM","article_processing_charge":"No","title":"Metamolds: Computational design of silicone molds","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/metamolds-molding-a-mold/"}]},"_id":"13","date_updated":"2023-09-13T08:56:07Z","has_accepted_license":"1","year":"2018","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767"}],"oa":1,"author":[{"last_name":"Alderighi","full_name":"Alderighi, Thomas","first_name":"Thomas"},{"full_name":"Malomo, Luigi","first_name":"Luigi","last_name":"Malomo"},{"last_name":"Giorgi","first_name":"Daniela","full_name":"Giorgi, Daniela"},{"full_name":"Pietroni, Nico","first_name":"Nico","last_name":"Pietroni"},{"last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","first_name":"Bernd"},{"last_name":"Cignoni","first_name":"Paolo","full_name":"Cignoni, Paolo"}],"status":"public","oa_version":"Submitted Version","volume":37,"date_created":"2018-12-11T11:44:09Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1145/3197517.3201381","external_id":{"isi":["000448185000097"]},"date_published":"2018-08-04T00:00:00Z","day":"04"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-05-23T13:24:51Z","doi":"10.5281/ZENODO.1322669","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Stroeymeyt","first_name":"Nathalie","full_name":"Stroeymeyt, Nathalie"},{"full_name":"Grasse, Anna V","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse"},{"last_name":"Crespi","first_name":"Alessandro","full_name":"Crespi, Alessandro"},{"last_name":"Mersch","full_name":"Mersch, Danielle","first_name":"Danielle"},{"first_name":"Sylvia","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"},{"first_name":"Laurent","full_name":"Keller, Laurent","last_name":"Keller"}],"status":"public","citation":{"apa":"Stroeymeyt, N., Grasse, A. V., Crespi, A., Mersch, D., Cremer, S., &#38; Keller, L. (2018). Social network plasticity decreases disease transmission in a eusocial insect. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.1322669\">https://doi.org/10.5281/ZENODO.1322669</a>","chicago":"Stroeymeyt, Nathalie, Anna V Grasse, Alessandro Crespi, Danielle Mersch, Sylvia Cremer, and Laurent Keller. “Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect.” Zenodo, 2018. <a href=\"https://doi.org/10.5281/ZENODO.1322669\">https://doi.org/10.5281/ZENODO.1322669</a>.","ama":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. Social network plasticity decreases disease transmission in a eusocial insect. 2018. doi:<a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>","mla":"Stroeymeyt, Nathalie, et al. <i>Social Network Plasticity Decreases Disease Transmission in a Eusocial Insect</i>. Zenodo, 2018, doi:<a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>.","short":"N. Stroeymeyt, A.V. Grasse, A. Crespi, D. Mersch, S. Cremer, L. Keller, (2018).","ieee":"N. Stroeymeyt, A. V. Grasse, A. Crespi, D. Mersch, S. Cremer, and L. Keller, “Social network plasticity decreases disease transmission in a eusocial insect.” Zenodo, 2018.","ista":"Stroeymeyt N, Grasse AV, Crespi A, Mersch D, Cremer S, Keller L. 2018. Social network plasticity decreases disease transmission in a eusocial insect, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.1322669\">10.5281/ZENODO.1322669</a>."},"oa_version":"Published Version","date_published":"2018-10-23T00:00:00Z","day":"23","publisher":"Zenodo","department":[{"_id":"SyCr"}],"abstract":[{"text":"Dataset for manuscript 'Social network plasticity decreases disease transmission in a eusocial insect'\r\nCompared to previous versions: - raw image files added\r\n                                                     - correction of URLs within README.txt file\r\n","lang":"eng"}],"related_material":{"record":[{"id":"7","relation":"used_in_publication","status":"public"}]},"ddc":["570"],"date_updated":"2023-10-17T11:50:04Z","_id":"13055","type":"research_data_reference","title":"Social network plasticity decreases disease transmission in a eusocial insect","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.1480665"}],"oa":1,"month":"10","year":"2018"},{"title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.3271452"}],"related_material":{"record":[{"id":"7181","status":"public","relation":"used_in_publication"}]},"_id":"13059","type":"research_data_reference","ddc":["570"],"date_updated":"2023-09-06T14:32:51Z","month":"12","year":"2018","oa":1,"citation":{"ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>","apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>","chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. <a href=\"https://doi.org/10.5281/ZENODO.2025846\">https://doi.org/10.5281/ZENODO.2025846</a>.","ieee":"E. Garriga <i>et al.</i>, “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>.","mla":"Garriga, Edgar, et al. <i>Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method</i>. Zenodo, 2018, doi:<a href=\"https://doi.org/10.5281/ZENODO.2025846\">10.5281/ZENODO.2025846</a>.","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018)."},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"last_name":"Garriga","full_name":"Garriga, Edgar","first_name":"Edgar"},{"full_name":"di Tommaso, Paolo","first_name":"Paolo","last_name":"di Tommaso"},{"first_name":"Cedrik","full_name":"Magis, Cedrik","last_name":"Magis"},{"full_name":"Erb, Ionas","first_name":"Ionas","last_name":"Erb"},{"full_name":"Mansouri, Leila","first_name":"Leila","last_name":"Mansouri"},{"full_name":"Baltzis, Athanasios","first_name":"Athanasios","last_name":"Baltzis"},{"last_name":"Laayouni","full_name":"Laayouni, Hafid","first_name":"Hafid"},{"orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor","first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Floden, Evan","first_name":"Evan","last_name":"Floden"},{"last_name":"Notredame","full_name":"Notredame, Cedric","first_name":"Cedric"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-05-23T16:08:20Z","doi":"10.5281/ZENODO.2025846","department":[{"_id":"FyKo"}],"abstract":[{"text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).","lang":"eng"}],"date_published":"2018-12-07T00:00:00Z","publisher":"Zenodo","day":"07"},{"publisher":"eLife Sciences Publications","file":[{"checksum":"d6331d4385b1fffd6b47b45d5949d841","content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_id":"5695","relation":"main_file","file_size":3158125,"date_created":"2018-12-17T11:55:05Z","date_updated":"2020-07-14T12:44:43Z","file_name":"2018_eLife_Picard.pdf"}],"publication":"eLife","scopus_import":"1","file_date_updated":"2020-07-14T12:44:43Z","abstract":[{"lang":"eng","text":"XY systems usually show chromosome-wide compensation of X-linked genes, while in many ZW systems, compensation is restricted to a minority of dosage-sensitive genes. Why such differences arose is still unclear. Here, we combine comparative genomics, transcriptomics and proteomics to obtain a complete overview of the evolution of gene dosage on the Z-chromosome of Schistosoma parasites. We compare the Z-chromosome gene content of African (Schistosoma mansoni and S. haematobium) and Asian (S. japonicum) schistosomes and describe lineage-specific evolutionary strata. We use these to assess gene expression evolution following sex-linkage. The resulting patterns suggest a reduction in expression of Z-linked genes in females, combined with upregulation of the Z in both sexes, in line with the first step of Ohno’s classic model of dosage compensation evolution. Quantitative proteomics suggest that post-transcriptional mechanisms do not play a major role in balancing the expression of Z-linked genes. "}],"language":[{"iso":"eng"}],"department":[{"_id":"BeVi"}],"publist_id":"7792","article_type":"original","publication_status":"published","quality_controlled":"1","citation":{"mla":"Picard, Marion A. L., et al. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>, vol. 7, e35684, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>.","short":"M.A.L. Picard, C. Cosseau, S. Ferré, T. Quack, C. Grevelding, Y. Couté, B. Vicoso, ELife 7 (2018).","ista":"Picard MAL, Cosseau C, Ferré S, Quack T, Grevelding C, Couté Y, Vicoso B. 2018. Evolution of gene dosage on the Z-chromosome of schistosome parasites. eLife. 7, e35684.","ieee":"M. A. L. Picard <i>et al.</i>, “Evolution of gene dosage on the Z-chromosome of schistosome parasites,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","chicago":"Picard, Marion A L, Celine Cosseau, Sabrina Ferré, Thomas Quack, Christoph Grevelding, Yohann Couté, and Beatriz Vicoso. “Evolution of Gene Dosage on the Z-Chromosome of Schistosome Parasites.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>.","apa":"Picard, M. A. L., Cosseau, C., Ferré, S., Quack, T., Grevelding, C., Couté, Y., &#38; Vicoso, B. (2018). Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.35684\">https://doi.org/10.7554/eLife.35684</a>","ama":"Picard MAL, Cosseau C, Ferré S, et al. Evolution of gene dosage on the Z-chromosome of schistosome parasites. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.35684\">10.7554/eLife.35684</a>"},"intvolume":"         7","article_number":"e35684","month":"08","isi":1,"ddc":["570"],"type":"journal_article","day":"13","date_published":"2018-08-13T00:00:00Z","external_id":{"isi":["000441388200001"]},"doi":"10.7554/eLife.35684","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:44:47Z","volume":7,"oa_version":"Published Version","author":[{"id":"2C921A7A-F248-11E8-B48F-1D18A9856A87","last_name":"Picard","first_name":"Marion A","full_name":"Picard, Marion A","orcid":"0000-0002-8101-2518"},{"last_name":"Cosseau","first_name":"Celine","full_name":"Cosseau, Celine"},{"full_name":"Ferré, Sabrina","first_name":"Sabrina","last_name":"Ferré"},{"last_name":"Quack","full_name":"Quack, Thomas","first_name":"Thomas"},{"first_name":"Christoph","full_name":"Grevelding, Christoph","last_name":"Grevelding"},{"first_name":"Yohann","full_name":"Couté, Yohann","last_name":"Couté"},{"orcid":"0000-0002-4579-8306","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa":1,"year":"2018","project":[{"grant_number":"P28842-B22","call_identifier":"FWF","name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425"}],"acknowledgement":"We are grateful to Lu Dabing (Soochow University, Suzhou, China) for providing Schistosoma japonicum samples, to Ariana Macon (IST Austria) and Georgette Stovall (JLU Giessen) for technical assistance, to IT support at IST Austria for providing optimal environment to bioinformatic analyses, and to the Vicoso lab for comments on the manuscript.","has_accepted_license":"1","date_updated":"2024-02-21T13:45:12Z","_id":"131","related_material":{"record":[{"id":"5586","status":"public","relation":"popular_science"}]},"article_processing_charge":"No","title":"Evolution of gene dosage on the Z-chromosome of schistosome parasites"},{"intvolume":"        46","month":"08","isi":1,"page":"360 - 375","issue":"3","ddc":["570"],"type":"journal_article","abstract":[{"text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments.","lang":"eng"}],"publist_id":"7791","language":[{"iso":"eng"}],"department":[{"_id":"EdHa"}],"publisher":"Cell Press","scopus_import":"1","publication":"Developmental Cell","file_date_updated":"2020-07-14T12:44:43Z","file":[{"creator":"dernst","access_level":"open_access","content_type":"application/pdf","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","file_id":"5694","relation":"main_file","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","date_updated":"2020-07-14T12:44:43Z","file_size":8948384,"date_created":"2018-12-17T10:49:49Z"}],"quality_controlled":"1","citation":{"ieee":"M. Sznurkowska <i>et al.</i>, “Defining lineage potential and fate behavior of precursors during pancreas development,” <i>Developmental Cell</i>, vol. 46, no. 3. Cell Press, pp. 360–375, 2018.","ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375.","mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” <i>Developmental Cell</i>, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">10.1016/j.devcel.2018.06.028</a>.","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375.","ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. <i>Developmental Cell</i>. 2018;46(3):360-375. doi:<a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">10.1016/j.devcel.2018.06.028</a>","chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” <i>Developmental Cell</i>. Cell Press, 2018. <a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">https://doi.org/10.1016/j.devcel.2018.06.028</a>.","apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2018.06.028\">https://doi.org/10.1016/j.devcel.2018.06.028</a>"},"article_type":"original","publication_status":"published","year":"2018","acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support.","has_accepted_license":"1","oa":1,"title":"Defining lineage potential and fate behavior of precursors during pancreas development","article_processing_charge":"No","date_updated":"2023-09-11T12:52:41Z","_id":"132","external_id":{"isi":["000441327300012"]},"day":"06","date_published":"2018-08-06T00:00:00Z","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"author":[{"full_name":"Sznurkowska, Magdalena","first_name":"Magdalena","last_name":"Sznurkowska"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"last_name":"Azzarelli","first_name":"Roberta","full_name":"Azzarelli, Roberta"},{"last_name":"Rulands","full_name":"Rulands, Steffen","first_name":"Steffen"},{"first_name":"Sonia","full_name":"Nestorowa, Sonia","last_name":"Nestorowa"},{"first_name":"Christopher","full_name":"Hindley, Christopher","last_name":"Hindley"},{"first_name":"Jennifer","full_name":"Nichols, Jennifer","last_name":"Nichols"},{"last_name":"Göttgens","first_name":"Berthold","full_name":"Göttgens, Berthold"},{"full_name":"Huch, Meritxell","first_name":"Meritxell","last_name":"Huch"},{"full_name":"Philpott, Anna","first_name":"Anna","last_name":"Philpott"},{"first_name":"Benjamin","full_name":"Simons, Benjamin","last_name":"Simons"}],"status":"public","doi":"10.1016/j.devcel.2018.06.028","date_created":"2018-12-11T11:44:48Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":46},{"year":"2018","publication_identifier":{"issn":["1944-8244","1944-8252"]},"title":"Supported two-dimensional materials under ion irradiation: The substrate governs defect production","article_processing_charge":"No","_id":"13255","date_updated":"2023-08-01T07:18:30Z","external_id":{"pmid":["30117320"]},"date_published":"2018-08-17T00:00:00Z","day":"17","extern":"1","status":"public","author":[{"first_name":"Silvan","full_name":"Kretschmer, Silvan","last_name":"Kretschmer"},{"orcid":"0000-0003-4074-2570","full_name":"Maslov, Mikhail","first_name":"Mikhail","last_name":"Maslov","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ghaderzadeh","first_name":"Sadegh","full_name":"Ghaderzadeh, Sadegh"},{"last_name":"Ghorbani-Asl","full_name":"Ghorbani-Asl, Mahdi","first_name":"Mahdi"},{"first_name":"Gregor","full_name":"Hlawacek, Gregor","last_name":"Hlawacek"},{"first_name":"Arkady V.","full_name":"Krasheninnikov, Arkady V.","last_name":"Krasheninnikov"}],"oa_version":"None","volume":10,"date_created":"2023-07-21T11:43:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1021/acsami.8b08471","pmid":1,"month":"08","intvolume":"        10","issue":"36","page":"30827-30836","type":"journal_article","language":[{"iso":"eng"}],"abstract":[{"text":"Focused ion beams perfectly suit for patterning two-dimensional (2D) materials, but the optimization of irradiation parameters requires full microscopic understanding of defect production mechanisms. In contrast to freestanding 2D systems, the details of damage creation in supported 2D materials are not fully understood, whereas the majority of experiments have been carried out for 2D targets deposited on substrates. Here, we suggest a universal and computationally efficient scheme to model the irradiation of supported 2D materials, which combines analytical potential molecular dynamics with Monte Carlo simulations and makes it possible to independently assess the contributions to the damage from backscattered ions and atoms sputtered from the substrate. Using the scheme, we study the defect production in graphene and MoS2 sheets, which are the two most important and wide-spread 2D materials, deposited on a SiO2 substrate. For helium and neon ions with a wide range of initial ion energies including those used in a commercial helium ion microscope (HIM), we demonstrate that depending on the ion energy and mass, the defect production in 2D systems can be dominated by backscattered ions and sputtered substrate atoms rather than by the direct ion impacts and that the amount of damage in 2D materials heavily depends on whether a substrate is present or not. We also study the factors which limit the spatial resolution of the patterning process. Our results, which agree well with the available experimental data, provide not only insights into defect production but also quantitative information, which can be used for the minimization of damage during imaging in HIM or optimization of the patterning process.","lang":"eng"}],"publication":"ACS Applied Materials & Interfaces","publisher":"American Chemical Society","keyword":["General Materials Science"],"citation":{"apa":"Kretschmer, S., Maslov, M., Ghaderzadeh, S., Ghorbani-Asl, M., Hlawacek, G., &#38; Krasheninnikov, A. V. (2018). Supported two-dimensional materials under ion irradiation: The substrate governs defect production. <i>ACS Applied Materials &#38; Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsami.8b08471\">https://doi.org/10.1021/acsami.8b08471</a>","chicago":"Kretschmer, Silvan, Mikhail Maslov, Sadegh Ghaderzadeh, Mahdi Ghorbani-Asl, Gregor Hlawacek, and Arkady V. Krasheninnikov. “Supported Two-Dimensional Materials under Ion Irradiation: The Substrate Governs Defect Production.” <i>ACS Applied Materials &#38; Interfaces</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acsami.8b08471\">https://doi.org/10.1021/acsami.8b08471</a>.","ama":"Kretschmer S, Maslov M, Ghaderzadeh S, Ghorbani-Asl M, Hlawacek G, Krasheninnikov AV. Supported two-dimensional materials under ion irradiation: The substrate governs defect production. <i>ACS Applied Materials &#38; Interfaces</i>. 2018;10(36):30827-30836. doi:<a href=\"https://doi.org/10.1021/acsami.8b08471\">10.1021/acsami.8b08471</a>","mla":"Kretschmer, Silvan, et al. “Supported Two-Dimensional Materials under Ion Irradiation: The Substrate Governs Defect Production.” <i>ACS Applied Materials &#38; Interfaces</i>, vol. 10, no. 36, American Chemical Society, 2018, pp. 30827–36, doi:<a href=\"https://doi.org/10.1021/acsami.8b08471\">10.1021/acsami.8b08471</a>.","short":"S. Kretschmer, M. Maslov, S. Ghaderzadeh, M. Ghorbani-Asl, G. Hlawacek, A.V. Krasheninnikov, ACS Applied Materials &#38; Interfaces 10 (2018) 30827–30836.","ieee":"S. Kretschmer, M. Maslov, S. Ghaderzadeh, M. Ghorbani-Asl, G. Hlawacek, and A. V. Krasheninnikov, “Supported two-dimensional materials under ion irradiation: The substrate governs defect production,” <i>ACS Applied Materials &#38; Interfaces</i>, vol. 10, no. 36. American Chemical Society, pp. 30827–30836, 2018.","ista":"Kretschmer S, Maslov M, Ghaderzadeh S, Ghorbani-Asl M, Hlawacek G, Krasheninnikov AV. 2018. Supported two-dimensional materials under ion irradiation: The substrate governs defect production. ACS Applied Materials &#38; Interfaces. 10(36), 30827–30836."},"quality_controlled":"1","publication_status":"published","article_type":"original"},{"publication_status":"published","quality_controlled":"1","alternative_title":["LIPIcs"],"citation":{"ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Synchronizing the asynchronous,” presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","ista":"Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 21.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Kragl, Bernhard, et al. <i>Synchronizing the Asynchronous</i>. Vol. 118, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">10.4230/LIPIcs.CONCUR.2018.21</a>.","ama":"Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">10.4230/LIPIcs.CONCUR.2018.21</a>","apa":"Kragl, B., Qadeer, S., &#38; Henzinger, T. A. (2018). Synchronizing the asynchronous (Vol. 118). Presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.21</a>","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2018.21\">https://doi.org/10.4230/LIPIcs.CONCUR.2018.21</a>."},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file_date_updated":"2020-07-14T12:44:44Z","file":[{"relation":"main_file","file_size":745438,"date_created":"2018-12-12T10:18:46Z","file_name":"IST-2018-853-v2+2_concur2018.pdf","date_updated":"2020-07-14T12:44:44Z","checksum":"c90895f4c5fafc18ddc54d1c8848077e","content_type":"application/pdf","creator":"system","access_level":"open_access","file_id":"5368"}],"scopus_import":1,"abstract":[{"text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs.","lang":"eng"}],"publist_id":"7790","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"ddc":["000"],"type":"conference","pubrep_id":"1039","intvolume":"       118","article_number":"21","month":"08","doi":"10.4230/LIPIcs.CONCUR.2018.21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:44:48Z","volume":118,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","first_name":"Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Qadeer, Shaz","first_name":"Shaz","last_name":"Qadeer"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger"}],"day":"13","date_published":"2018-08-13T00:00:00Z","date_updated":"2023-09-07T13:18:00Z","_id":"133","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"6426"},{"status":"public","id":"8332","relation":"dissertation_contains"}]},"conference":{"end_date":"2018-09-07","start_date":"2018-09-04","location":"Beijing, China","name":"CONCUR: International Conference on Concurrency Theory"},"title":"Synchronizing the asynchronous","oa":1,"publication_identifier":{"issn":["18688969"]},"year":"2018","project":[{"name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23"}],"has_accepted_license":"1"},{"oa":1,"has_accepted_license":"1","year":"2018","related_material":{"record":[{"id":"9810","status":"public","relation":"research_data"}]},"_id":"82","date_updated":"2023-09-13T08:45:41Z","article_processing_charge":"Yes","title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","date_published":"2018-08-16T00:00:00Z","day":"16","external_id":{"isi":["000443383300024"]},"volume":16,"date_created":"2018-12-11T11:44:32Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","doi":"10.1371/journal.pbio.2005971","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"last_name":"Chaudhry","first_name":"Waqas","full_name":"Chaudhry, Waqas"},{"last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7460-7479","first_name":"Maros","full_name":"Pleska, Maros"},{"first_name":"Nilang","full_name":"Shah, Nilang","last_name":"Shah"},{"first_name":"Howard","full_name":"Weiss, Howard","last_name":"Weiss"},{"last_name":"Mccall","full_name":"Mccall, Ingrid","first_name":"Ingrid"},{"full_name":"Meyer, Justin","first_name":"Justin","last_name":"Meyer"},{"last_name":"Gupta","first_name":"Animesh","full_name":"Gupta, Animesh"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","last_name":"Guet","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052"},{"first_name":"Bruce","full_name":"Levin, Bruce","last_name":"Levin"}],"oa_version":"Published Version","issue":"8","isi":1,"month":"08","article_number":"2005971","intvolume":"        16","type":"journal_article","ddc":["570"],"scopus_import":"1","file":[{"file_size":4007095,"date_created":"2018-12-17T12:55:31Z","date_updated":"2020-07-14T12:48:10Z","file_name":"2018_Plos_Chaudhry.pdf","relation":"main_file","file_id":"5706","content_type":"application/pdf","checksum":"527076f78265cd4ea192cd1569851587","access_level":"open_access","creator":"dernst"}],"publication":"PLoS Biology","file_date_updated":"2020-07-14T12:48:10Z","publisher":"Public Library of Science","department":[{"_id":"CaGu"}],"publist_id":"7972","language":[{"iso":"eng"}],"abstract":[{"text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term &quot;leaky resistance.&quot; We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”.","lang":"eng"}],"publication_status":"published","citation":{"mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” <i>PLoS Biology</i>, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971\">10.1371/journal.pbio.2005971</a>.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971.","ieee":"W. Chaudhry <i>et al.</i>, “Leaky resistance and the conditions for the existence of lytic bacteriophage,” <i>PLoS Biology</i>, vol. 16, no. 8. Public Library of Science, 2018.","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2005971\">https://doi.org/10.1371/journal.pbio.2005971</a>","chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” <i>PLoS Biology</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pbio.2005971\">https://doi.org/10.1371/journal.pbio.2005971</a>.","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. <i>PLoS Biology</i>. 2018;16(8). doi:<a href=\"https://doi.org/10.1371/journal.pbio.2005971\">10.1371/journal.pbio.2005971</a>"},"quality_controlled":"1"},{"publication_identifier":{"issn":["0091-6749"]},"issue":"3","page":"973-976.e11","oa":1,"month":"09","year":"2018","intvolume":"       142","date_updated":"2021-01-12T08:17:37Z","type":"journal_article","_id":"8231","article_processing_charge":"No","title":"AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jaci.2018.04.021"}],"date_published":"2018-09-01T00:00:00Z","publication":"Journal of Allergy and Clinical Immunology","day":"01","publisher":"Elsevier","language":[{"iso":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-10T11:51:36Z","volume":142,"article_type":"letter_note","doi":"10.1016/j.jaci.2018.04.021","quality_controlled":"1","author":[{"orcid":"0000-0002-8777-3502","first_name":"Judit","full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Josef","full_name":"Singer, Josef","last_name":"Singer"},{"full_name":"Ilieva, Kristina M.","first_name":"Kristina M.","last_name":"Ilieva"},{"full_name":"Matz, Miroslawa","first_name":"Miroslawa","last_name":"Matz"},{"last_name":"Herrmann","full_name":"Herrmann, Ina","first_name":"Ina"},{"full_name":"Spillner, Edzard","first_name":"Edzard","last_name":"Spillner"},{"full_name":"Karagiannis, Sophia N.","first_name":"Sophia N.","last_name":"Karagiannis"},{"full_name":"Jensen-Jarolim, Erika","first_name":"Erika","last_name":"Jensen-Jarolim"}],"status":"public","extern":"1","citation":{"mla":"Singer, Judit, et al. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” <i>Journal of Allergy and Clinical Immunology</i>, vol. 142, no. 3, Elsevier, 2018, p. 973–976.e11, doi:<a href=\"https://doi.org/10.1016/j.jaci.2018.04.021\">10.1016/j.jaci.2018.04.021</a>.","short":"J. Singer, J. Singer, K.M. Ilieva, M. Matz, I. Herrmann, E. Spillner, S.N. Karagiannis, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 142 (2018) 973–976.e11.","ieee":"J. Singer <i>et al.</i>, “AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor,” <i>Journal of Allergy and Clinical Immunology</i>, vol. 142, no. 3. Elsevier, p. 973–976.e11, 2018.","ista":"Singer J, Singer J, Ilieva KM, Matz M, Herrmann I, Spillner E, Karagiannis SN, Jensen-Jarolim E. 2018. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. 142(3), 973–976.e11.","apa":"Singer, J., Singer, J., Ilieva, K. M., Matz, M., Herrmann, I., Spillner, E., … Jensen-Jarolim, E. (2018). AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. <i>Journal of Allergy and Clinical Immunology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jaci.2018.04.021\">https://doi.org/10.1016/j.jaci.2018.04.021</a>","chicago":"Singer, Judit, Josef Singer, Kristina M. Ilieva, Miroslawa Matz, Ina Herrmann, Edzard Spillner, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” <i>Journal of Allergy and Clinical Immunology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jaci.2018.04.021\">https://doi.org/10.1016/j.jaci.2018.04.021</a>.","ama":"Singer J, Singer J, Ilieva KM, et al. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. <i>Journal of Allergy and Clinical Immunology</i>. 2018;142(3):973-976.e11. doi:<a href=\"https://doi.org/10.1016/j.jaci.2018.04.021\">10.1016/j.jaci.2018.04.021</a>"},"oa_version":"Published Version"},{"main_file_link":[{"url":"https://doi.org/10.18632/oncotarget.24876","open_access":"1"}],"article_processing_charge":"No","title":"Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody","_id":"8232","type":"journal_article","date_updated":"2021-01-12T08:17:37Z","year":"2018","intvolume":"         9","month":"04","oa":1,"page":"19026-19038","publication_identifier":{"eissn":["1949-2553"]},"oa_version":"Published Version","citation":{"short":"T. Nagaya, S. Okuyama, F. Ogata, Y. Maruoka, D.W. Knapp, S.N. Karagiannis, J. Singer, P.L. Choyke, A.K. LeBlanc, E. Jensen-Jarolim, H. Kobayashi, Oncotarget 9 (2018) 19026–19038.","mla":"Nagaya, Tadanobu, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” <i>Oncotarget</i>, vol. 9, Impact Journals, 2018, pp. 19026–38, doi:<a href=\"https://doi.org/10.18632/oncotarget.24876\">10.18632/oncotarget.24876</a>.","ieee":"T. Nagaya <i>et al.</i>, “Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody,” <i>Oncotarget</i>, vol. 9. Impact Journals, pp. 19026–19038, 2018.","ista":"Nagaya T, Okuyama S, Ogata F, Maruoka Y, Knapp DW, Karagiannis SN, Singer J, Choyke PL, LeBlanc AK, Jensen-Jarolim E, Kobayashi H. 2018. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 9, 19026–19038.","chicago":"Nagaya, Tadanobu, Shuhei Okuyama, Fusa Ogata, Yasuhiro Maruoka, Deborah W. Knapp, Sophia N. Karagiannis, Judit Singer, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” <i>Oncotarget</i>. Impact Journals, 2018. <a href=\"https://doi.org/10.18632/oncotarget.24876\">https://doi.org/10.18632/oncotarget.24876</a>.","apa":"Nagaya, T., Okuyama, S., Ogata, F., Maruoka, Y., Knapp, D. W., Karagiannis, S. N., … Kobayashi, H. (2018). Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. <i>Oncotarget</i>. Impact Journals. <a href=\"https://doi.org/10.18632/oncotarget.24876\">https://doi.org/10.18632/oncotarget.24876</a>","ama":"Nagaya T, Okuyama S, Ogata F, et al. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. <i>Oncotarget</i>. 2018;9:19026-19038. doi:<a href=\"https://doi.org/10.18632/oncotarget.24876\">10.18632/oncotarget.24876</a>"},"extern":"1","author":[{"last_name":"Nagaya","first_name":"Tadanobu","full_name":"Nagaya, Tadanobu"},{"first_name":"Shuhei","full_name":"Okuyama, Shuhei","last_name":"Okuyama"},{"last_name":"Ogata","full_name":"Ogata, Fusa","first_name":"Fusa"},{"last_name":"Maruoka","full_name":"Maruoka, Yasuhiro","first_name":"Yasuhiro"},{"last_name":"Knapp","first_name":"Deborah W.","full_name":"Knapp, Deborah W."},{"last_name":"Karagiannis","first_name":"Sophia N.","full_name":"Karagiannis, Sophia N."},{"orcid":"0000-0002-8777-3502","first_name":"Judit","full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Choyke","first_name":"Peter L.","full_name":"Choyke, Peter L."},{"full_name":"LeBlanc, Amy K.","first_name":"Amy K.","last_name":"LeBlanc"},{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika","first_name":"Erika"},{"last_name":"Kobayashi","first_name":"Hisataka","full_name":"Kobayashi, Hisataka"}],"status":"public","quality_controlled":"1","doi":"10.18632/oncotarget.24876","article_type":"original","volume":9,"date_created":"2020-08-10T11:52:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","abstract":[{"lang":"eng","text":"Anti-epidermal growth factor receptor (EGFR) antibody therapy is used in EGFR expressing cancers including lung, colon, head and neck, and bladder cancers, however results have been modest. Near infrared photoimmunotherapy (NIR-PIT) is a highly selective tumor treatment that employs an antibody-photo-absorber conjugate which is activated by NIR light. NIR-PIT is in clinical trials in patients with recurrent head and neck cancers using cetuximab-IR700 as the conjugate. However, its use has otherwise been restricted to mouse models. This is an effort to explore larger animal models with NIR-PIT. We describe the use of a recombinant canine anti-EGFR monoclonal antibody (mAb), can225IgG, conjugated to the photo-absorber, IR700DX, in three EGFR expressing canine transitional cell carcinoma (TCC) cell lines as a prelude to possible canine clinical studies. Can225-IR700 conjugate showed specific binding and cell-specific killing after NIR-PIT on EGFR expressing cells in vitro. In the in vivo study, can225-IR700 conjugate demonstrated accumulation of the fluorescent conjugate with high tumor-to-background ratio. Tumor-bearing mice were separated into 4 groups: (1) no treatment; (2) 100 μg of can225-IR700 i.v. only; (3) NIR light exposure only; (4) 100 μg of can225-IR700 i.v., NIR light exposure. Tumor growth was significantly inhibited by NIR-PIT treatment compared with the other groups (p < 0.001), and significantly prolonged survival was achieved (p < 0.001 vs. other groups) in the treatment groups. In conclusion, NIR-PIT with can225-IR700 is a promising treatment for canine EGFR-expressing cancers, including invasive transitional cell carcinoma in pet dogs, that could provide a pathway to translation to humans."}],"language":[{"iso":"eng"}],"publisher":"Impact Journals","day":"10","publication":"Oncotarget","date_published":"2018-04-10T00:00:00Z"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.dci.2018.01.005"}],"type":"journal_article","intvolume":"        82","month":"05","page":"118-127","issue":"5","citation":{"ama":"Herrmann I, Gotovina J, Singer J, et al. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. <i>Developmental &#38; Comparative Immunology</i>. 2018;82(5):118-127. doi:<a href=\"https://doi.org/10.1016/j.dci.2018.01.005\">10.1016/j.dci.2018.01.005</a>","apa":"Herrmann, I., Gotovina, J., Singer, J., Fischer, M. B., Hufnagl, K., Bianchini, R., &#38; Jensen-Jarolim, E. (2018). Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. <i>Developmental &#38; Comparative Immunology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dci.2018.01.005\">https://doi.org/10.1016/j.dci.2018.01.005</a>","chicago":"Herrmann, Ina, Jelena Gotovina, Judit Singer, Michael B. Fischer, Karin Hufnagl, Rodolfo Bianchini, and Erika Jensen-Jarolim. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” <i>Developmental &#38; Comparative Immunology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.dci.2018.01.005\">https://doi.org/10.1016/j.dci.2018.01.005</a>.","ieee":"I. Herrmann <i>et al.</i>, “Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy,” <i>Developmental &#38; Comparative Immunology</i>, vol. 82, no. 5. Elsevier, pp. 118–127, 2018.","ista":"Herrmann I, Gotovina J, Singer J, Fischer MB, Hufnagl K, Bianchini R, Jensen-Jarolim E. 2018. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental &#38; Comparative Immunology. 82(5), 118–127.","short":"I. Herrmann, J. Gotovina, J. Singer, M.B. Fischer, K. Hufnagl, R. Bianchini, E. Jensen-Jarolim, Developmental &#38; Comparative Immunology 82 (2018) 118–127.","mla":"Herrmann, Ina, et al. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” <i>Developmental &#38; Comparative Immunology</i>, vol. 82, no. 5, Elsevier, 2018, pp. 118–27, doi:<a href=\"https://doi.org/10.1016/j.dci.2018.01.005\">10.1016/j.dci.2018.01.005</a>."},"quality_controlled":"1","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"The M2a subtype of macrophages plays an important role in human immunoglobulin E (IgE-mediated allergies) and other Th2 type immune reactions. In contrast, very little is known about these cells in the dog. Here we describe an in vitro method to activate canine histiocytic DH82 cells and primary canine monocyte-derived macrophages (MDMs) toward the M2a macrophages using human cytokines. For a side-by-side comparison, we compared the canine cells to human MDMs, and the human monocytic cell line U937 activated towards M1 and M2a cells on the cellular and molecular level. In analogy to activated human M2a cells, canine M2a, differentiated from both DH82 and MDMs, showed an increase in CD206 surface receptor expression compared to M1. Interestingly, canine M2a, but not M1 derived from MDM, upregulated the high-affinity IgE receptor (FcεRI). Transcription levels of M2a-associated genes (IL10, CCL22, TGFβ, CD163) showed a diverse pattern between the human and dog species, whereas M1 genes (IDO1, CXCL11, IL6, TNF-α) were similarly upregulated in canine and human M1 cells (cell lines and MDMs). We suggest that our novel in vitro method will be suitable in comparative allergology studies focussing on macrophages."}],"language":[{"iso":"eng"}],"publisher":"Elsevier","publication":"Developmental & Comparative Immunology","title":"Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy","article_processing_charge":"No","_id":"8233","date_updated":"2021-01-12T08:17:38Z","year":"2018","oa":1,"publication_identifier":{"issn":["0145-305X"]},"oa_version":"Published Version","extern":"1","author":[{"full_name":"Herrmann, Ina","first_name":"Ina","last_name":"Herrmann"},{"full_name":"Gotovina, Jelena","first_name":"Jelena","last_name":"Gotovina"},{"last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit","first_name":"Judit"},{"first_name":"Michael B.","full_name":"Fischer, Michael B.","last_name":"Fischer"},{"full_name":"Hufnagl, Karin","first_name":"Karin","last_name":"Hufnagl"},{"last_name":"Bianchini","full_name":"Bianchini, Rodolfo","first_name":"Rodolfo"},{"first_name":"Erika","full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim"}],"status":"public","doi":"10.1016/j.dci.2018.01.005","volume":82,"date_created":"2020-08-10T11:53:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","date_published":"2018-05-01T00:00:00Z"},{"oa":1,"publication_identifier":{"issn":["1555-4309","1555-4317"]},"intvolume":"      2018","year":"2018","article_number":"1269830","month":"02","date_updated":"2021-01-12T08:17:38Z","type":"journal_article","_id":"8234","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1155/2018/1269830"}],"article_processing_charge":"No","title":"Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer","publisher":"Hindawi","day":"13","date_published":"2018-02-13T00:00:00Z","publication":"Contrast Media & Molecular Imaging","abstract":[{"lang":"eng","text":"Molecular imaging probes such as PET-tracers have the potential to improve the accuracy of tumor characterization by directly visualizing the biochemical situation. Thus, molecular changes can be detected early before morphological manifestation. The A3 adenosine receptor (A3AR) is described to be highly expressed in colon cancer cell lines and human colorectal cancer (CRC), suggesting this receptor as a tumor marker. The aim of this preclinical study was the evaluation of FE@SUPPY as a PET-tracer for CRC using in vitro imaging and in vivo PET imaging. First, affinity and selectivity of FE@SUPPY and its metabolites were determined, proving the favorable binding profile of FE@SUPPY. The human adenocarcinoma cell line HT-29 was characterized regarding its hA3AR expression and was subsequently chosen as tumor graft. Promising results regarding the potential of FE@SUPPY as a PET-tracer for CRC imaging were obtained by autoradiography as ≥2.3-fold higher accumulation of FE@SUPPY was found in CRC tissue compared to adjacent healthy colon tissue from the same patient. Nevertheless, first in vivo studies using HT-29 xenografts showed insufficient tumor uptake due to (1) poor conservation of target expression in xenografts and (2) unfavorable pharmacokinetics of FE@SUPPY in mice. We therefore conclude that HT-29 xenografts are not adequate to visualize hA3ARs using FE@SUPPY."}],"language":[{"iso":"eng"}],"doi":"10.1155/2018/1269830","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-10T11:53:07Z","publication_status":"published","volume":2018,"oa_version":"Published Version","author":[{"first_name":"T.","full_name":"Balber, T.","last_name":"Balber"},{"orcid":"0000-0002-8777-3502","first_name":"Judit","full_name":"Singer, Judit","last_name":"Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Berroterán-Infante, N.","first_name":"N.","last_name":"Berroterán-Infante"},{"full_name":"Dumanic, M.","first_name":"M.","last_name":"Dumanic"},{"full_name":"Fetty, L.","first_name":"L.","last_name":"Fetty"},{"last_name":"Fazekas-Singer","first_name":"J.","full_name":"Fazekas-Singer, J.","orcid":"0000-0002-8777-3502"},{"full_name":"Vraka, C.","first_name":"C.","last_name":"Vraka"},{"last_name":"Nics","full_name":"Nics, L.","first_name":"L."},{"last_name":"Bergmann","full_name":"Bergmann, M.","first_name":"M."},{"full_name":"Pallitsch, K.","first_name":"K.","last_name":"Pallitsch"},{"first_name":"H.","full_name":"Spreitzer, H.","last_name":"Spreitzer"},{"first_name":"W.","full_name":"Wadsak, W.","orcid":"0000-0003-4479-8053","last_name":"Wadsak"},{"last_name":"Hacker","full_name":"Hacker, M.","first_name":"M."},{"full_name":"Jensen-Jarolim, E.","first_name":"E.","last_name":"Jensen-Jarolim"},{"first_name":"H.","full_name":"Viernstein, H.","last_name":"Viernstein"},{"full_name":"Mitterhauser, M.","first_name":"M.","orcid":"0000-0003-3173-5272","last_name":"Mitterhauser"}],"status":"public","quality_controlled":"1","citation":{"mla":"Balber, T., et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” <i>Contrast Media &#38; Molecular Imaging</i>, vol. 2018, 1269830, Hindawi, 2018, doi:<a href=\"https://doi.org/10.1155/2018/1269830\">10.1155/2018/1269830</a>.","short":"T. Balber, J. Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, L. Nics, M. Bergmann, K. Pallitsch, H. Spreitzer, W. Wadsak, M. Hacker, E. Jensen-Jarolim, H. Viernstein, M. Mitterhauser, Contrast Media &#38; Molecular Imaging 2018 (2018).","ieee":"T. Balber <i>et al.</i>, “Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer,” <i>Contrast Media &#38; Molecular Imaging</i>, vol. 2018. Hindawi, 2018.","ista":"Balber T, Singer J, Berroterán-Infante N, Dumanic M, Fetty L, Fazekas-Singer J, Vraka C, Nics L, Bergmann M, Pallitsch K, Spreitzer H, Wadsak W, Hacker M, Jensen-Jarolim E, Viernstein H, Mitterhauser M. 2018. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media &#38; Molecular Imaging. 2018, 1269830.","chicago":"Balber, T., Judit Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” <i>Contrast Media &#38; Molecular Imaging</i>. Hindawi, 2018. <a href=\"https://doi.org/10.1155/2018/1269830\">https://doi.org/10.1155/2018/1269830</a>.","apa":"Balber, T., Singer, J., Berroterán-Infante, N., Dumanic, M., Fetty, L., Fazekas-Singer, J., … Mitterhauser, M. (2018). Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. <i>Contrast Media &#38; Molecular Imaging</i>. Hindawi. <a href=\"https://doi.org/10.1155/2018/1269830\">https://doi.org/10.1155/2018/1269830</a>","ama":"Balber T, Singer J, Berroterán-Infante N, et al. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. <i>Contrast Media &#38; Molecular Imaging</i>. 2018;2018. doi:<a href=\"https://doi.org/10.1155/2018/1269830\">10.1155/2018/1269830</a>"},"extern":"1"},{"publisher":"Springer Nature","day":"27","date_published":"2018-12-27T00:00:00Z","publication":"BMC Genomics","abstract":[{"lang":"eng","text":"Background: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.\r\n\r\nResults: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.\r\n\r\nConclusions: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei."}],"language":[{"iso":"eng"}],"doi":"10.1186/s12864-018-5245-1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2020-08-15T11:02:08Z","volume":19,"oa_version":"Published Version","quality_controlled":"1","author":[{"orcid":"0000-0003-1006-6639","first_name":"Olga","full_name":"Bochkareva, Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"first_name":"Elena V.","full_name":"Moroz, Elena V.","last_name":"Moroz"},{"full_name":"Davydov, Iakov I.","first_name":"Iakov I.","last_name":"Davydov"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"status":"public","citation":{"ieee":"O. Bochkareva, E. V. Moroz, I. I. Davydov, and M. S. Gelfand, “Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.,” <i>BMC Genomics</i>, vol. 19. Springer Nature, 2018.","ista":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. 2018. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 19, 965.","short":"O. Bochkareva, E.V. Moroz, I.I. Davydov, M.S. Gelfand, BMC Genomics 19 (2018).","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” <i>BMC Genomics</i>, vol. 19, 965, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1186/s12864-018-5245-1\">10.1186/s12864-018-5245-1</a>.","ama":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. <i>BMC Genomics</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s12864-018-5245-1\">10.1186/s12864-018-5245-1</a>","chicago":"Bochkareva, Olga, Elena V. Moroz, Iakov I. Davydov, and Mikhail S. Gelfand. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” <i>BMC Genomics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1186/s12864-018-5245-1\">https://doi.org/10.1186/s12864-018-5245-1</a>.","apa":"Bochkareva, O., Moroz, E. V., Davydov, I. I., &#38; Gelfand, M. S. (2018). Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. <i>BMC Genomics</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12864-018-5245-1\">https://doi.org/10.1186/s12864-018-5245-1</a>"},"extern":"1","oa":1,"publication_identifier":{"issn":["1471-2164"]},"intvolume":"        19","year":"2018","article_number":"965","month":"12","date_updated":"2023-02-23T13:28:52Z","type":"journal_article","_id":"8262","main_file_link":[{"url":"https://doi.org/10.1186/s12864-018-5245-1","open_access":"1"}],"title":"Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.","article_processing_charge":"No"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.7717/peerj.4545"}],"type":"journal_article","intvolume":"         6","article_number":"e4545","month":"03","quality_controlled":"1","citation":{"short":"O. Bochkareva, N.O. Dranenko, E.S. Ocheredko, G.M. Kanevsky, Y.N. Lozinsky, V.A. Khalaycheva, I.I. Artamonova, M.S. Gelfand, PeerJ 6 (2018).","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” <i>PeerJ</i>, vol. 6, e4545, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.4545\">10.7717/peerj.4545</a>.","ista":"Bochkareva O, Dranenko NO, Ocheredko ES, Kanevsky GM, Lozinsky YN, Khalaycheva VA, Artamonova II, Gelfand MS. 2018. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. 6, e4545.","ieee":"O. Bochkareva <i>et al.</i>, “Genome rearrangements and phylogeny reconstruction in Yersinia pestis,” <i>PeerJ</i>, vol. 6. PeerJ, 2018.","apa":"Bochkareva, O., Dranenko, N. O., Ocheredko, E. S., Kanevsky, G. M., Lozinsky, Y. N., Khalaycheva, V. A., … Gelfand, M. S. (2018). Genome rearrangements and phylogeny reconstruction in Yersinia pestis. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.4545\">https://doi.org/10.7717/peerj.4545</a>","chicago":"Bochkareva, Olga, Natalia O. Dranenko, Elena S. Ocheredko, German M. Kanevsky, Yaroslav N. Lozinsky, Vera A. Khalaycheva, Irena I. Artamonova, and Mikhail S. Gelfand. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.4545\">https://doi.org/10.7717/peerj.4545</a>.","ama":"Bochkareva O, Dranenko NO, Ocheredko ES, et al. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. <i>PeerJ</i>. 2018;6. doi:<a href=\"https://doi.org/10.7717/peerj.4545\">10.7717/peerj.4545</a>"},"article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content."}],"language":[{"iso":"eng"}],"publisher":"PeerJ","publication":"PeerJ","title":"Genome rearrangements and phylogeny reconstruction in Yersinia pestis","article_processing_charge":"No","date_updated":"2023-02-23T13:28:57Z","_id":"8265","year":"2018","oa":1,"publication_identifier":{"issn":["2167-8359"]},"oa_version":"Published Version","status":"public","author":[{"last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","first_name":"Olga","full_name":"Bochkareva, Olga"},{"last_name":"Dranenko","full_name":"Dranenko, Natalia O.","first_name":"Natalia O."},{"first_name":"Elena S.","full_name":"Ocheredko, Elena S.","last_name":"Ocheredko"},{"last_name":"Kanevsky","full_name":"Kanevsky, German M.","first_name":"German M."},{"last_name":"Lozinsky","full_name":"Lozinsky, Yaroslav N.","first_name":"Yaroslav N."},{"last_name":"Khalaycheva","first_name":"Vera A.","full_name":"Khalaycheva, Vera A."},{"last_name":"Artamonova","full_name":"Artamonova, Irena I.","first_name":"Irena I."},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"extern":"1","pmid":1,"doi":"10.7717/peerj.4545","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-15T11:08:23Z","volume":6,"external_id":{"pmid":["29607260"]},"day":"27","date_published":"2018-03-27T00:00:00Z"},{"doi":"10.21873/anticanres.12525","article_type":"original","volume":38,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2020-08-17T07:13:55Z","oa_version":"None","extern":"1","citation":{"ama":"Carvalho MI, Bianchini R, Singer J, et al. Bidirectional regulation of COX-2 expression between cancer cells and macrophages. <i>Anticancer Research</i>. 2018;38(5):2811-2817. doi:<a href=\"https://doi.org/10.21873/anticanres.12525\">10.21873/anticanres.12525</a>","apa":"Carvalho, M. I., Bianchini, R., Singer, J., Herrmann, I., Flickinger, I., Thalhammer, J. G., … Queiroga, F. L. (2018). Bidirectional regulation of COX-2 expression between cancer cells and macrophages. <i>Anticancer Research</i>. International Institute of Anticancer Research. <a href=\"https://doi.org/10.21873/anticanres.12525\">https://doi.org/10.21873/anticanres.12525</a>","chicago":"Carvalho, Maria Isabel, Rodolfo Bianchini, Judit Singer, Ina Herrmann, Irene Flickinger, Johann G. Thalhammer, Isabel Pires, Erika Jensen-Jarolim, and Felisbina L. Queiroga. “Bidirectional Regulation of COX-2 Expression between Cancer Cells and Macrophages.” <i>Anticancer Research</i>. International Institute of Anticancer Research, 2018. <a href=\"https://doi.org/10.21873/anticanres.12525\">https://doi.org/10.21873/anticanres.12525</a>.","ista":"Carvalho MI, Bianchini R, Singer J, Herrmann I, Flickinger I, Thalhammer JG, Pires I, Jensen-Jarolim E, Queiroga FL. 2018. Bidirectional regulation of COX-2 expression between cancer cells and macrophages. Anticancer Research. 38(5), 2811–2817.","ieee":"M. I. Carvalho <i>et al.</i>, “Bidirectional regulation of COX-2 expression between cancer cells and macrophages,” <i>Anticancer Research</i>, vol. 38, no. 5. International Institute of Anticancer Research, pp. 2811–2817, 2018.","mla":"Carvalho, Maria Isabel, et al. “Bidirectional Regulation of COX-2 Expression between Cancer Cells and Macrophages.” <i>Anticancer Research</i>, vol. 38, no. 5, International Institute of Anticancer Research, 2018, pp. 2811–17, doi:<a href=\"https://doi.org/10.21873/anticanres.12525\">10.21873/anticanres.12525</a>.","short":"M.I. Carvalho, R. Bianchini, J. Singer, I. Herrmann, I. Flickinger, J.G. Thalhammer, I. Pires, E. Jensen-Jarolim, F.L. Queiroga, Anticancer Research 38 (2018) 2811–2817."},"status":"public","quality_controlled":"1","author":[{"full_name":"Carvalho, Maria Isabel","first_name":"Maria Isabel","last_name":"Carvalho"},{"first_name":"Rodolfo","full_name":"Bianchini, Rodolfo","last_name":"Bianchini"},{"id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Fazekas-Singer","full_name":"Fazekas-Singer, Judit","first_name":"Judit","orcid":"0000-0002-8777-3502"},{"last_name":"Herrmann","full_name":"Herrmann, Ina","first_name":"Ina"},{"full_name":"Flickinger, Irene","first_name":"Irene","last_name":"Flickinger"},{"first_name":"Johann G.","full_name":"Thalhammer, Johann G.","last_name":"Thalhammer"},{"first_name":"Isabel","full_name":"Pires, Isabel","last_name":"Pires"},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"},{"last_name":"Queiroga","first_name":"Felisbina L.","full_name":"Queiroga, Felisbina L."}],"day":"01","publisher":"International Institute of Anticancer Research","publication":"Anticancer Research","date_published":"2018-05-01T00:00:00Z","abstract":[{"text":"Background/Aim: Our aim was to investigate the crosstalk between tumor and immune cells (M2 macrophages) and its effects on cyclo-oxygenase-2 (COX2) regulation in canine mammary tumors (CMT). Materials and Methods: Sh1b CMT cells and human BT474 mammary or HT29 colon cancer cells were co-cultured with canine peripheral blood mononuclear cells (PBMCs) or with macrophage-like differentiated THP1 monocytes (dTHP1). Intracellular COX2 expression by PBMCs, dTHP1 and cancer cells was evaluated by flow cytometry. Results: Co-culturing of Sh1b and canine PBMCs induced COX2 overexpression in CMT cells. In turn, COX2 expression by PBMCs, mostly CD68+ macrophages, was attenuated by co-culture with Sh1b (p=0.0001). In accordance, co-culture with dTHP1 prompted intracellular production of COX2 in both Sh1b CMT cells and HT29 human colon cancer cells and reduced production of COX2 in BT474 human mammary cancer cells. The intracellular COX2 expression from dTHP1 decreased when treated with conditioned medium from cultured Sh1b and HT29 cancer cells. Conclusion: Bidirectional COX2 regulation between cancer and monocytes/macrophages might shape a tolerogenic tumor microenvironment in CMT.","lang":"eng"}],"language":[{"iso":"eng"}],"type":"journal_article","_id":"8274","date_updated":"2021-01-12T08:17:52Z","article_processing_charge":"No","title":"Bidirectional regulation of COX-2 expression between cancer cells and macrophages","page":"2811-2817","issue":"5","publication_identifier":{"issn":["0250-7005"],"eissn":["1791-7530"]},"intvolume":"        38","year":"2018","month":"05"},{"publisher":"IEEE","day":"26","publication":"2018 IEEE Symposium on Security and Privacy","date_published":"2018-07-26T00:00:00Z","abstract":[{"text":"Designing a secure permissionless distributed ledger (blockchain) that performs on par with centralized payment\r\nprocessors, such as Visa, is a challenging task. Most existing distributed ledgers are unable to scale-out, i.e., to grow their totalprocessing capacity with the number of validators; and those that do, compromise security or decentralization. We present OmniLedger, a novel scale-out distributed ledger that preserves longterm security under permissionless operation. It ensures security and correctness by using a bias-resistant public-randomness protocol for choosing large, statistically representative shards that process transactions, and by introducing an efficient crossshard commit protocol that atomically handles transactions affecting multiple shards. OmniLedger also optimizes performance via parallel intra-shard transaction processing, ledger pruning via collectively-signed state blocks, and low-latency “trust-butverify” \r\nvalidation for low-value transactions. An evaluation ofour experimental prototype shows that OmniLedger’s throughput\r\nscales linearly in the number of active validators, supporting Visa-level workloads and beyond, while confirming typical transactions in under two seconds.","lang":"eng"}],"language":[{"iso":"eng"}],"doi":"10.1109/sp.2018.000-5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2020-08-26T11:46:35Z","oa_version":"Preprint","extern":"1","citation":{"ama":"Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. OmniLedger: A secure, scale-out, decentralized ledger via sharding. In: <i>2018 IEEE Symposium on Security and Privacy</i>. IEEE; 2018:583-598. doi:<a href=\"https://doi.org/10.1109/sp.2018.000-5\">10.1109/sp.2018.000-5</a>","apa":"Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Syta, E., &#38; Ford, B. (2018). OmniLedger: A secure, scale-out, decentralized ledger via sharding. In <i>2018 IEEE Symposium on Security and Privacy</i> (pp. 583–598). San Francisco, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/sp.2018.000-5\">https://doi.org/10.1109/sp.2018.000-5</a>","chicago":"Kokoris Kogias, Eleftherios, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, Ewa Syta, and Bryan Ford. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” In <i>2018 IEEE Symposium on Security and Privacy</i>, 583–98. IEEE, 2018. <a href=\"https://doi.org/10.1109/sp.2018.000-5\">https://doi.org/10.1109/sp.2018.000-5</a>.","ista":"Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. 2018. OmniLedger: A secure, scale-out, decentralized ledger via sharding. 2018 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 583–598.","ieee":"E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, and B. Ford, “OmniLedger: A secure, scale-out, decentralized ledger via sharding,” in <i>2018 IEEE Symposium on Security and Privacy</i>, San Francisco, CA, United States, 2018, pp. 583–598.","mla":"Kokoris Kogias, Eleftherios, et al. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” <i>2018 IEEE Symposium on Security and Privacy</i>, IEEE, 2018, pp. 583–98, doi:<a href=\"https://doi.org/10.1109/sp.2018.000-5\">10.1109/sp.2018.000-5</a>.","short":"E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, B. Ford, in:, 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–598."},"author":[{"last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Jovanovic, Philipp","first_name":"Philipp","last_name":"Jovanovic"},{"last_name":"Gasser","full_name":"Gasser, Linus","first_name":"Linus"},{"first_name":"Nicolas","full_name":"Gailly, Nicolas","last_name":"Gailly"},{"last_name":"Syta","full_name":"Syta, Ewa","first_name":"Ewa"},{"last_name":"Ford","first_name":"Bryan","full_name":"Ford, Bryan"}],"quality_controlled":"1","status":"public","oa":1,"page":"583-598","publication_identifier":{"isbn":["9781538643532"],"issn":["2375-1207"]},"year":"2018","month":"07","type":"conference","_id":"8297","date_updated":"2021-01-12T08:17:56Z","conference":{"start_date":"2018-05-20","end_date":"2018-05-24","name":"SP: Symposium on Security and Privacy","location":"San Francisco, CA, United States"},"main_file_link":[{"url":"https://eprint.iacr.org/2017/406","open_access":"1"}],"title":"OmniLedger: A secure, scale-out, decentralized ledger via sharding","article_processing_charge":"No"}]