[{"title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","project":[{"_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","grant_number":"715257"}],"publication_status":"published","citation":{"ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome biology and evolution</i>. 2019;11(4):1033-1044. doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., &#38; Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>."},"author":[{"full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","first_name":"Ann K","last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Melissa A","last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","full_name":"Toups, Melissa A","orcid":"0000-0002-9752-7380"},{"first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","full_name":"Macon, Ariana"},{"orcid":"0000-0001-9638-1220","full_name":"Gammerdinger, William J","first_name":"William J","last_name":"Gammerdinger","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","first_name":"Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","type":"journal_article","department":[{"_id":"BeVi"}],"intvolume":"        11","_id":"6418","language":[{"iso":"eng"}],"issue":"4","isi":1,"scopus_import":"1","related_material":{"record":[{"status":"public","id":"6060","relation":"popular_science"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2019","day":"01","doi":"10.1093/gbe/evz053","date_updated":"2025-04-14T07:41:21Z","date_published":"2019-04-01T00:00:00Z","external_id":{"isi":["000476569800003"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"content_type":"application/pdf","file_name":"2019_GBE_Huylmans.pdf","checksum":"7d0ede297b6741f3dc89cd59017c7642","file_size":1256303,"relation":"main_file","date_updated":"2020-07-14T12:47:29Z","file_id":"6446","access_level":"open_access","date_created":"2019-05-14T08:29:38Z","creator":"dernst"}],"ec_funded":1,"publication":"Genome biology and evolution","publication_identifier":{"eissn":["1759-6653"]},"publisher":"Oxford University Press","file_date_updated":"2020-07-14T12:47:29Z","ddc":["570"],"quality_controlled":"1","date_created":"2019-05-13T07:58:38Z","oa":1,"volume":11,"article_processing_charge":"No","month":"04","status":"public","abstract":[{"text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general.","lang":"eng"}],"page":"1033-1044"},{"month":"07","status":"public","abstract":[{"lang":"eng","text":"This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples."}],"quality_controlled":"1","date_created":"2019-05-14T07:04:06Z","oa":1,"article_processing_charge":"No","volume":38,"publisher":"ACM","file_date_updated":"2020-07-14T12:47:30Z","article_number":"130","ddc":["000","005"],"ec_funded":1,"publication":"ACM Transactions on Graphics","date_updated":"2024-10-22T09:58:22Z","date_published":"2019-07-01T00:00:00Z","external_id":{"isi":["000475740600104"]},"file":[{"file_id":"6443","creator":"dernst","date_created":"2019-05-14T07:03:55Z","access_level":"open_access","file_size":44328918,"checksum":"1b737dfe3e051aba8f3f4ab1dceda673","file_name":"2019_ACM_Schreck.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:47:30Z","relation":"main_file"}],"day":"01","year":"2019","doi":"10.1145/3306346.3323002","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/","relation":"press_release"}]},"scopus_import":"1","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"issue":"4","isi":1,"intvolume":"        38","department":[{"_id":"ChWo"}],"_id":"6442","oa_version":"Submitted Version","type":"journal_article","title":"Fundamental solutions for water wave animation","project":[{"grant_number":"638176","call_identifier":"H2020","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"author":[{"id":"2B14B676-F248-11E8-B48F-1D18A9856A87","last_name":"Schreck","first_name":"Camille","full_name":"Schreck, Camille"},{"last_name":"Hafner","id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hafner, Christian"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"publication_status":"published","citation":{"apa":"Schreck, C., Hafner, C., &#38; Wojtan, C. (2019). Fundamental solutions for water wave animation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3306346.3323002\">https://doi.org/10.1145/3306346.3323002</a>","ieee":"C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4. ACM, 2019.","ama":"Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. <i>ACM Transactions on Graphics</i>. 2019;38(4). doi:<a href=\"https://doi.org/10.1145/3306346.3323002\">10.1145/3306346.3323002</a>","mla":"Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4, 130, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3306346.3323002\">10.1145/3306346.3323002</a>.","ista":"Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130.","short":"C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).","chicago":"Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3306346.3323002\">https://doi.org/10.1145/3306346.3323002</a>."}},{"publisher":"AAAS","article_number":"eaaw9144","quality_controlled":"1","date_created":"2019-09-07T19:04:45Z","article_processing_charge":"No","volume":365,"month":"08","status":"public","abstract":[{"lang":"eng","text":"V (vacuolar)/A (archaeal)-type adenosine triphosphatases (ATPases), found in archaeaand eubacteria, couple ATP hydrolysis or synthesis to proton translocation across theplasma membrane using the rotary-catalysis mechanism. They belong to the V-typeATPase family, which differs from the mitochondrial/chloroplast F-type ATP synthasesin overall architecture. We solved cryo–electron microscopy structures of the intactThermus thermophilusV/A-ATPase, reconstituted into lipid nanodiscs, in three rotationalstates and two substates. These structures indicate substantial flexibility betweenV1and Voin a working enzyme, which results from mechanical competition between centralshaft rotation and resistance from the peripheral stalks. We also describedetails of adenosine diphosphate inhibition release, V1-Votorque transmission, andproton translocation, which are relevant for the entire V-type ATPase family."}],"publication":"Science","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"language":[{"iso":"eng"}],"issue":"6455","isi":1,"related_material":{"link":[{"description":"News on IST Website","relation":"press_release","url":"https://ist.ac.at/en/news/structure-of-protein-nano-turbine-revealed/"}]},"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"ScienComp"}],"pmid":1,"day":"23","year":"2019","doi":"10.1126/science.aaw9144","date_published":"2019-08-23T00:00:00Z","date_updated":"2023-08-29T07:52:02Z","external_id":{"pmid":["31439765"],"isi":["000482464000043"]},"title":"Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase","author":[{"full_name":"Zhou, Long","orcid":"0000-0002-1864-8951","id":"3E751364-F248-11E8-B48F-1D18A9856A87","last_name":"Zhou","first_name":"Long"},{"full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov"}],"publication_status":"published","citation":{"ama":"Zhou L, Sazanov LA. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. <i>Science</i>. 2019;365(6455). doi:<a href=\"https://doi.org/10.1126/science.aaw9144\">10.1126/science.aaw9144</a>","ieee":"L. Zhou and L. A. Sazanov, “Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase,” <i>Science</i>, vol. 365, no. 6455. AAAS, 2019.","apa":"Zhou, L., &#38; Sazanov, L. A. (2019). Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. <i>Science</i>. AAAS. <a href=\"https://doi.org/10.1126/science.aaw9144\">https://doi.org/10.1126/science.aaw9144</a>","mla":"Zhou, Long, and Leonid A. Sazanov. “Structure and Conformational Plasticity of the Intact Thermus Thermophilus V/A-Type ATPase.” <i>Science</i>, vol. 365, no. 6455, eaaw9144, AAAS, 2019, doi:<a href=\"https://doi.org/10.1126/science.aaw9144\">10.1126/science.aaw9144</a>.","chicago":"Zhou, Long, and Leonid A Sazanov. “Structure and Conformational Plasticity of the Intact Thermus Thermophilus V/A-Type ATPase.” <i>Science</i>. AAAS, 2019. <a href=\"https://doi.org/10.1126/science.aaw9144\">https://doi.org/10.1126/science.aaw9144</a>.","short":"L. Zhou, L.A. Sazanov, Science 365 (2019).","ista":"Zhou L, Sazanov LA. 2019. Structure and conformational plasticity of the intact Thermus thermophilus V/A-type ATPase. Science. 365(6455), eaaw9144."},"oa_version":"None","type":"journal_article","intvolume":"       365","department":[{"_id":"LeSa"}],"_id":"6859"},{"month":"10","status":"public","abstract":[{"text":"In  pipes  and  channels,  the  onset  of  turbulence  is  initially  dominated  by  localizedtransients,  which  lead  to  sustained  turbulence  through  their  collective  dynamics.  In  thepresent work, we study numerically the localized turbulence in pipe flow and elucidate astate space structure that gives rise to transient chaos. Starting from the basin boundaryseparating  laminar  and  turbulent  flow,  we  identify  transverse  homoclinic  orbits,  thepresence of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which wasconjectured in various earlier studies. By mapping the transverse intersections between thestable and unstable manifold of a periodic orbit, we identify the gateways that promote anescape from turbulence.","lang":"eng"}],"page":"102401","publisher":"American Physical Society","article_type":"original","quality_controlled":"1","date_created":"2019-11-04T10:04:01Z","oa":1,"volume":4,"article_processing_charge":"No","publication":"Physical Review Fluids","day":"01","year":"2019","doi":"10.1103/PhysRevFluids.4.102401","date_updated":"2023-08-30T07:20:03Z","date_published":"2019-10-01T00:00:00Z","external_id":{"arxiv":["1810.02211"],"isi":["000493510400001"]},"language":[{"iso":"eng"}],"issue":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.02211"}],"isi":1,"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Preprint","type":"journal_article","department":[{"_id":"BjHo"}],"intvolume":"         4","_id":"6978","arxiv":1,"title":"Geometry of transient chaos in streamwise-localized pipe flow turbulence","publication_status":"published","citation":{"ama":"Budanur NB, Dogra A, Hof B. Geometry of transient chaos in streamwise-localized pipe flow turbulence. <i>Physical Review Fluids</i>. 2019;4(10):102401. doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.4.102401\">10.1103/PhysRevFluids.4.102401</a>","apa":"Budanur, N. B., Dogra, A., &#38; Hof, B. (2019). Geometry of transient chaos in streamwise-localized pipe flow turbulence. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.4.102401\">https://doi.org/10.1103/PhysRevFluids.4.102401</a>","ieee":"N. B. Budanur, A. Dogra, and B. Hof, “Geometry of transient chaos in streamwise-localized pipe flow turbulence,” <i>Physical Review Fluids</i>, vol. 4, no. 10. American Physical Society, p. 102401, 2019.","mla":"Budanur, Nazmi B., et al. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” <i>Physical Review Fluids</i>, vol. 4, no. 10, American Physical Society, 2019, p. 102401, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.4.102401\">10.1103/PhysRevFluids.4.102401</a>.","short":"N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 102401.","chicago":"Budanur, Nazmi B, Akshunna Dogra, and Björn Hof. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” <i>Physical Review Fluids</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevFluids.4.102401\">https://doi.org/10.1103/PhysRevFluids.4.102401</a>.","ista":"Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 4(10), 102401."},"author":[{"orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"},{"full_name":"Dogra, Akshunna","last_name":"Dogra","first_name":"Akshunna"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"}]},{"publication":"Nature","ec_funded":1,"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"abstract":[{"text":"Proton-translocating transhydrogenase (also known as nicotinamide nucleotide transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride between NADH and NADP+, coupled to the translocation of one proton across the membrane. Its main physiological function is the generation of NADPH, which is a substrate in anabolic reactions and a regulator of oxidative status; however, NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid deficiency in humans and metabolic abnormalities in mice, similar to those observed in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve a rotation of around 180° of the entire NADP(H)-binding domain that alternately participates in hydride transfer and proton-channel gating. However, owing to the lack of high-resolution structures of intact NNT, the details of this process remain unclear5,6. Here we present the cryo-electron microscopy structure of intact mammalian NNT in different conformational states. We show how the NADP(H)-binding domain opens the proton channel to the opposite sides of the membrane, and we provide structures of these two states. We also describe the catalytically important interfaces and linkers between the membrane and the soluble domains and their roles in nucleotide exchange. These structures enable us to propose a revised mechanism for a coupling process in NNT that is consistent with a large body of previous biochemical work. Our results are relevant to the development of currently unavailable NNT inhibitors, which may have therapeutic potential in ischaemia reperfusion injury, metabolic syndrome and some cancers7,8,9.","lang":"eng"}],"status":"public","month":"09","page":"291–295","ddc":["572"],"article_type":"letter_note","file_date_updated":"2020-11-26T16:33:44Z","publisher":"Springer Nature","volume":573,"article_processing_charge":"No","oa":1,"date_created":"2019-09-04T06:21:41Z","quality_controlled":"1","type":"journal_article","oa_version":"Submitted Version","_id":"6848","department":[{"_id":"LeSa"}],"intvolume":"       573","citation":{"ama":"Kampjut D, Sazanov LA. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. <i>Nature</i>. 2019;573(7773):291–295. doi:<a href=\"https://doi.org/10.1038/s41586-019-1519-2\">10.1038/s41586-019-1519-2</a>","ieee":"D. Kampjut and L. A. Sazanov, “Structure and mechanism of mitochondrial proton-translocating transhydrogenase,” <i>Nature</i>, vol. 573, no. 7773. Springer Nature, pp. 291–295, 2019.","apa":"Kampjut, D., &#38; Sazanov, L. A. (2019). Structure and mechanism of mitochondrial proton-translocating transhydrogenase. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1519-2\">https://doi.org/10.1038/s41586-019-1519-2</a>","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” <i>Nature</i>, vol. 573, no. 7773, Springer Nature, 2019, pp. 291–295, doi:<a href=\"https://doi.org/10.1038/s41586-019-1519-2\">10.1038/s41586-019-1519-2</a>.","short":"D. Kampjut, L.A. Sazanov, Nature 573 (2019) 291–295.","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1519-2\">https://doi.org/10.1038/s41586-019-1519-2</a>.","ista":"Kampjut D, Sazanov LA. 2019. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. 573(7773), 291–295."},"author":[{"full_name":"Kampjut, Domen","orcid":"0000-0002-6018-3422","first_name":"Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989"}],"publication_status":"published","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"title":"Structure and mechanism of mitochondrial proton-translocating transhydrogenase","doi":"10.1038/s41586-019-1519-2","day":"12","year":"2019","pmid":1,"external_id":{"pmid":["31462775"],"isi":["000485415400061"]},"file":[{"date_updated":"2020-11-26T16:33:44Z","relation":"main_file","file_size":3066206,"file_name":"Manuscript_final_acc_withFigs_SI_opt_red.pdf","checksum":"52728cda5210a3e9b74cc204e8aed3d5","content_type":"application/pdf","creator":"lsazanov","date_created":"2020-11-26T16:33:44Z","access_level":"open_access","file_id":"8821","success":1}],"date_updated":"2026-07-25T22:30:45Z","date_published":"2019-09-12T00:00:00Z","isi":1,"issue":"7773","language":[{"iso":"eng"}],"acknowledgement":" We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing was performed at the IST high-performance computing cluster.\r\nThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385.","acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","scopus_import":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/high-end-microscopy-reveals-structure-and-function-of-crucial-metabolic-enzyme/","relation":"press_release","description":"News on IST Website"}],"record":[{"id":"8340","relation":"dissertation_contains","status":"public"}]}},{"ec_funded":1,"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"month":"05","status":"public","abstract":[{"text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour.","lang":"eng"}],"page":"183","publisher":"Institute of Science and Technology Austria","file_date_updated":"2021-02-11T11:17:15Z","ddc":["570","006","578","592"],"date_created":"2019-05-13T08:58:35Z","oa":1,"article_processing_charge":"No","oa_version":"Published Version","type":"dissertation","supervisor":[{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia M","first_name":"Sylvia M","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"}],"department":[{"_id":"SyCr"}],"_id":"6435","title":"Collective defenses of garden ants against a fungal pathogen","OA_place":"publisher","project":[{"name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"771402"}],"corr_author":"1","publication_status":"published","citation":{"ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","apa":"Casillas Perez, B. E. (2019). <i>Collective defenses of garden ants against a fungal pathogen</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>","mla":"Casillas Perez, Barbara E. <i>Collective Defenses of Garden Ants against a Fungal Pathogen</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>.","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>.","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria."},"author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez","first_name":"Barbara E","full_name":"Casillas Perez, Barbara E"}],"year":"2019","day":"07","doi":"10.15479/AT:ISTA:6435","date_published":"2019-05-07T00:00:00Z","date_updated":"2026-04-08T14:02:12Z","file":[{"content_type":"application/pdf","file_name":"tesisDoctoradoBC.pdf","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","embargo":"2020-05-08","file_size":3895187,"relation":"main_file","date_updated":"2021-02-11T11:17:15Z","file_id":"6438","access_level":"open_access","date_created":"2019-05-13T09:16:20Z","creator":"casillas"},{"file_id":"6439","access_level":"closed","date_created":"2019-05-13T09:16:20Z","creator":"casillas","content_type":"application/zip","checksum":"3d221aaff7559a7060230a1ff610594f","file_name":"tesisDoctoradoBC.zip","embargo_to":"open_access","file_size":7365118,"relation":"source_file","date_updated":"2020-07-14T12:47:30Z"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1999","status":"public"}]},"keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}]},{"month":"07","abstract":[{"lang":"eng","text":"The current state of the art in real-time two-dimensional water wave simulation requires developers to choose between efficient Fourier-based methods, which lack interactions with moving obstacles, and finite-difference or finite element methods, which handle environmental interactions but are significantly more expensive. This paper attempts to bridge this long-standing gap between complexity and performance, by proposing a new wave simulation method that can faithfully simulate wave interactions with moving obstacles in real time while simultaneously preserving minute details and accommodating very large simulation domains.\r\n\r\nPrevious methods for simulating 2D water waves directly compute the change in height of the water surface, a strategy which imposes limitations based on the CFL condition (fast moving waves require small time steps) and Nyquist's limit (small wave details require closely-spaced simulation variables). This paper proposes a novel wavelet transformation that discretizes the liquid motion in terms of amplitude-like functions that vary over space, frequency, and direction, effectively generalizing Fourier-based methods to handle local interactions. Because these new variables change much more slowly over space than the original water height function, our change of variables drastically reduces the limitations of the CFL condition and Nyquist limit, allowing us to simulate highly detailed water waves at very large visual resolutions. Our discretization is amenable to fast summation and easy to parallelize. We also present basic extensions like pre-computed wave paths and two-way solid fluid coupling. Finally, we argue that our discretization provides a convenient set of variables for artistic manipulation, which we illustrate with a novel wave-painting interface."}],"status":"public","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2020-07-14T12:44:45Z","publisher":"ACM","article_number":"94","ddc":["000"],"date_created":"2018-12-11T11:44:48Z","oa":1,"quality_controlled":"1","article_processing_charge":"No","volume":37,"ec_funded":1,"publication":"ACM Transactions on Graphics","year":"2018","day":"30","doi":"10.1145/3197517.3201336","date_published":"2018-07-30T00:00:00Z","date_updated":"2024-10-22T09:58:20Z","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"external_id":{"isi":["000448185000055"]},"file":[{"file_id":"5744","access_level":"open_access","date_created":"2018-12-18T09:59:23Z","creator":"dernst","content_type":"application/pdf","checksum":"db75ebabe2ec432bf41389e614d6ef62","file_name":"2018_ACM_Jeschke.pdf","file_size":22185016,"relation":"main_file","date_updated":"2020-07-14T12:44:45Z"}],"language":[{"iso":"eng"}],"isi":1,"issue":"4","alternative_title":["SIGGRAPH"],"user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-water-simulation-captures-small-details-even-in-large-scenes/"}]},"scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Published Version","type":"journal_article","department":[{"_id":"ChWo"}],"intvolume":"        37","_id":"134","publist_id":"7789","title":"Water surface wavelets","author":[{"full_name":"Jeschke, Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"first_name":"Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87","last_name":"Skrivan","full_name":"Skrivan, Tomas"},{"last_name":"Mueller Fischer","first_name":"Matthias","full_name":"Mueller Fischer, Matthias"},{"last_name":"Chentanez","first_name":"Nuttapong","full_name":"Chentanez, Nuttapong"},{"full_name":"Macklin, Miles","first_name":"Miles","last_name":"Macklin"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan"}],"publication_status":"published","citation":{"mla":"Jeschke, Stefan, et al. “Water Surface Wavelets.” <i>ACM Transactions on Graphics</i>, vol. 37, no. 4, 94, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3197517.3201336\">10.1145/3197517.3201336</a>.","ista":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. 2018. Water surface wavelets. ACM Transactions on Graphics. 37(4), 94.","short":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, C. Wojtan, ACM Transactions on Graphics 37 (2018).","chicago":"Jeschke, Stefan, Tomas Skrivan, Matthias Mueller Fischer, Nuttapong Chentanez, Miles Macklin, and Chris Wojtan. “Water Surface Wavelets.” <i>ACM Transactions on Graphics</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3197517.3201336\">https://doi.org/10.1145/3197517.3201336</a>.","ieee":"S. Jeschke, T. Skrivan, M. Mueller Fischer, N. Chentanez, M. Macklin, and C. Wojtan, “Water surface wavelets,” <i>ACM Transactions on Graphics</i>, vol. 37, no. 4. ACM, 2018.","apa":"Jeschke, S., Skrivan, T., Mueller Fischer, M., Chentanez, N., Macklin, M., &#38; Wojtan, C. (2018). Water surface wavelets. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3197517.3201336\">https://doi.org/10.1145/3197517.3201336</a>","ama":"Jeschke S, Skrivan T, Mueller Fischer M, Chentanez N, Macklin M, Wojtan C. Water surface wavelets. <i>ACM Transactions on Graphics</i>. 2018;37(4). doi:<a href=\"https://doi.org/10.1145/3197517.3201336\">10.1145/3197517.3201336</a>"},"project":[{"call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","grant_number":"638176"},{"grant_number":"665385","call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}]},{"status":"public","abstract":[{"lang":"eng","text":"Recent realization of a kinetically constrained chain of Rydberg atoms by Bernien et al., [Nature (London) 551, 579 (2017)] resulted in the observation of unusual revivals in the many-body quantum dynamics. In our previous work [C. J. Turner et al., Nat. Phys. 14, 745 (2018)], such dynamics was attributed to the existence of “quantum scarred” eigenstates in the many-body spectrum of the experimentally realized model. Here, we present a detailed study of the eigenstate properties of the same model. We find that the majority of the eigenstates exhibit anomalous thermalization: the observable expectation values converge to their Gibbs ensemble values, but parametrically slower compared to the predictions of the eigenstate thermalization hypothesis (ETH). Amidst the thermalizing spectrum, we identify nonergodic eigenstates that strongly violate the ETH, whose number grows polynomially with system size. Previously, the same eigenstates were identified via large overlaps with certain product states, and were used to explain the revivals observed in experiment. Here, we find that these eigenstates, in addition to highly atypical expectation values of local observables, also exhibit subthermal entanglement entropy that scales logarithmically with the system size. Moreover, we identify an additional class of quantum scarred eigenstates, and discuss their manifestations in the dynamics starting from initial product states. We use forward scattering approximation to describe the structure and physical properties of quantum scarred eigenstates. Finally, we discuss the stability of quantum scars to various perturbations. We observe that quantum scars remain robust when the introduced perturbation is compatible with the forward scattering approximation. In contrast, the perturbations which most efficiently destroy quantum scars also lead to the restoration of “canonical” thermalization."}],"month":"10","article_number":"155134","publisher":"American Physical Society","volume":98,"article_processing_charge":"No","quality_controlled":"1","date_created":"2018-12-11T11:44:19Z","oa":1,"publication":"Physical Review B","doi":"10.1103/PhysRevB.98.155134","day":"22","year":"2018","external_id":{"arxiv":["1806.10933"],"isi":["000447919100001"]},"date_published":"2018-10-22T00:00:00Z","date_updated":"2023-10-10T13:28:49Z","issue":"15","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10933"}],"isi":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa_version":"Preprint","_id":"44","department":[{"_id":"MaSe"}],"intvolume":"        98","publist_id":"8010","arxiv":1,"publication_status":"published","author":[{"first_name":"C J","last_name":"Turner","full_name":"Turner, C J"},{"id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","last_name":"Michailidis","first_name":"Alexios","full_name":"Michailidis, Alexios","orcid":"0000-0002-8443-1064"},{"first_name":"D A","last_name":"Abanin","full_name":"Abanin, D A"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Papić","first_name":"Z","full_name":"Papić, Z"}],"citation":{"apa":"Turner, C. J., Michailidis, A., Abanin, D. A., Serbyn, M., &#38; Papić, Z. (2018). Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">https://doi.org/10.1103/PhysRevB.98.155134</a>","ieee":"C. J. Turner, A. Michailidis, D. A. Abanin, M. Serbyn, and Z. Papić, “Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations,” <i>Physical Review B</i>, vol. 98, no. 15. American Physical Society, 2018.","ama":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. <i>Physical Review B</i>. 2018;98(15). doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">10.1103/PhysRevB.98.155134</a>","mla":"Turner, C. J., et al. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” <i>Physical Review B</i>, vol. 98, no. 15, 155134, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">10.1103/PhysRevB.98.155134</a>.","ista":"Turner CJ, Michailidis A, Abanin DA, Serbyn M, Papić Z. 2018. Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations. Physical Review B. 98(15), 155134.","short":"C.J. Turner, A. Michailidis, D.A. Abanin, M. Serbyn, Z. Papić, Physical Review B 98 (2018).","chicago":"Turner, C J, Alexios Michailidis, D A Abanin, Maksym Serbyn, and Z Papić. “Quantum Scarred Eigenstates in a Rydberg Atom Chain: Entanglement, Breakdown of Thermalization, and Stability to Perturbations.” <i>Physical Review B</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.98.155134\">https://doi.org/10.1103/PhysRevB.98.155134</a>."},"title":"Quantum scarred eigenstates in a Rydberg atom chain: Entanglement, breakdown of thermalization, and stability to perturbations"},{"publication":"Journal of Fluid Mechanics","ec_funded":1,"publication_identifier":{"issn":["0022-1120"]},"abstract":[{"lang":"eng","text":"Using extensive direct numerical simulations, the dynamics of laminar-turbulent fronts in pipe flow is investigated for Reynolds numbers between and 5500. We here investigate the physical distinction between the fronts of weak and strong slugs both by analysing the turbulent kinetic energy budget and by comparing the downstream front motion to the advection speed of bulk turbulent structures. Our study shows that weak downstream fronts travel slower than turbulent structures in the bulk and correspond to decaying turbulence at the front. At the downstream front speed becomes faster than the advection speed, marking the onset of strong fronts. In contrast to weak fronts, turbulent eddies are generated at strong fronts by feeding on the downstream laminar flow. Our study also suggests that temporal fluctuations of production and dissipation at the downstream laminar-turbulent front drive the dynamical switches between the two types of front observed up to."}],"status":"public","month":"02","page":"1045 - 1059","publisher":"Cambridge University Press","volume":813,"article_processing_charge":"No","date_created":"2018-12-11T11:50:04Z","oa":1,"quality_controlled":"1","type":"journal_article","oa_version":"Submitted Version","_id":"1087","intvolume":"       813","department":[{"_id":"BjHo"}],"publist_id":"6290","arxiv":1,"author":[{"full_name":"Song, Baofang","last_name":"Song","first_name":"Baofang"},{"full_name":"Barkley, Dwight","last_name":"Barkley","first_name":"Dwight"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754","full_name":"Hof, Björn"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"}],"publication_status":"published","citation":{"mla":"Song, Baofang, et al. “Speed and Structure of Turbulent Fronts in Pipe Flow.” <i>Journal of Fluid Mechanics</i>, vol. 813, Cambridge University Press, 2017, pp. 1045–59, doi:<a href=\"https://doi.org/10.1017/jfm.2017.14\">10.1017/jfm.2017.14</a>.","chicago":"Song, Baofang, Dwight Barkley, Björn Hof, and Marc Avila. “Speed and Structure of Turbulent Fronts in Pipe Flow.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2017. <a href=\"https://doi.org/10.1017/jfm.2017.14\">https://doi.org/10.1017/jfm.2017.14</a>.","short":"B. Song, D. Barkley, B. Hof, M. Avila, Journal of Fluid Mechanics 813 (2017) 1045–1059.","ista":"Song B, Barkley D, Hof B, Avila M. 2017. Speed and structure of turbulent fronts in pipe flow. Journal of Fluid Mechanics. 813, 1045–1059.","ama":"Song B, Barkley D, Hof B, Avila M. Speed and structure of turbulent fronts in pipe flow. <i>Journal of Fluid Mechanics</i>. 2017;813:1045-1059. doi:<a href=\"https://doi.org/10.1017/jfm.2017.14\">10.1017/jfm.2017.14</a>","ieee":"B. Song, D. Barkley, B. Hof, and M. Avila, “Speed and structure of turbulent fronts in pipe flow,” <i>Journal of Fluid Mechanics</i>, vol. 813. Cambridge University Press, pp. 1045–1059, 2017.","apa":"Song, B., Barkley, D., Hof, B., &#38; Avila, M. (2017). Speed and structure of turbulent fronts in pipe flow. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2017.14\">https://doi.org/10.1017/jfm.2017.14</a>"},"project":[{"_id":"25152F3A-B435-11E9-9278-68D0E5697425","name":"Decoding the complexity of turbulence at its origin","call_identifier":"FP7","grant_number":"306589"}],"title":"Speed and structure of turbulent fronts in pipe flow","doi":"10.1017/jfm.2017.14","year":"2017","day":"25","external_id":{"isi":["000394376400044"],"arxiv":["1603.04077"]},"date_updated":"2025-06-04T08:35:11Z","date_published":"2017-02-25T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1603.04077"}],"isi":1,"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1"},{"ec_funded":1,"publication":"Neuron","pubrep_id":"752","month":"01","status":"public","abstract":[{"text":"Sharp wave-ripple (SWR) oscillations play a key role in memory consolidation during non-rapid eye movement sleep, immobility, and consummatory behavior. However, whether temporally modulated synaptic excitation or inhibition underlies the ripples is controversial. To address this question, we performed simultaneous recordings of excitatory and inhibitory postsynaptic currents (EPSCs and IPSCs) and local field potentials (LFPs) in the CA1 region of awake mice in vivo. During SWRs, inhibition dominated over excitation, with a peak conductance ratio of 4.1 ± 0.5. Furthermore, the amplitude of SWR-associated IPSCs was positively correlated with SWR magnitude, whereas that of EPSCs was not. Finally, phase analysis indicated that IPSCs were phase-locked to individual ripple cycles, whereas EPSCs were uniformly distributed in phase space. Optogenetic inhibition indicated that PV+ interneurons provided a major contribution to SWR-associated IPSCs. Thus, phasic inhibition, but not excitation, shapes SWR oscillations in the hippocampal CA1 region in vivo.","lang":"eng"}],"page":"308 - 314","publisher":"Elsevier","file_date_updated":"2018-12-12T10:08:56Z","ddc":["571"],"quality_controlled":"1","oa":1,"date_created":"2018-12-11T11:50:15Z","volume":93,"article_processing_charge":"No","oa_version":"Published Version","type":"journal_article","department":[{"_id":"PeJo"},{"_id":"JoCs"}],"intvolume":"        93","_id":"1118","publist_id":"6244","title":"Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo","project":[{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF","grant_number":"P24909-B24"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548"}],"citation":{"mla":"Gan, Jian, et al. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal Ripple Oscillations in Awake Mice in Vivo.” <i>Neuron</i>, vol. 93, no. 2, Elsevier, 2017, pp. 308–14, doi:<a href=\"https://doi.org/10.1016/j.neuron.2016.12.018\">10.1016/j.neuron.2016.12.018</a>.","chicago":"Gan, Jian, Shih-Ming Weng, Alejandro Pernia-Andrade, Jozsef L Csicsvari, and Peter M Jonas. “Phase-Locked Inhibition, but Not Excitation, Underlies Hippocampal Ripple Oscillations in Awake Mice in Vivo.” <i>Neuron</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.neuron.2016.12.018\">https://doi.org/10.1016/j.neuron.2016.12.018</a>.","short":"J. Gan, S.-M. Weng, A. Pernia-Andrade, J.L. Csicsvari, P.M. Jonas, Neuron 93 (2017) 308–314.","ista":"Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. 2017. Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo. Neuron. 93(2), 308–314.","ama":"Gan J, Weng S-M, Pernia-Andrade A, Csicsvari JL, Jonas PM. Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo. <i>Neuron</i>. 2017;93(2):308-314. doi:<a href=\"https://doi.org/10.1016/j.neuron.2016.12.018\">10.1016/j.neuron.2016.12.018</a>","apa":"Gan, J., Weng, S.-M., Pernia-Andrade, A., Csicsvari, J. L., &#38; Jonas, P. M. (2017). Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2016.12.018\">https://doi.org/10.1016/j.neuron.2016.12.018</a>","ieee":"J. Gan, S.-M. Weng, A. Pernia-Andrade, J. L. Csicsvari, and P. M. Jonas, “Phase-locked inhibition, but not excitation, underlies hippocampal ripple oscillations in awake mice in vivo,” <i>Neuron</i>, vol. 93, no. 2. Elsevier, pp. 308–314, 2017."},"publication_status":"published","author":[{"first_name":"Jian","id":"3614E438-F248-11E8-B48F-1D18A9856A87","last_name":"Gan","full_name":"Gan, Jian"},{"first_name":"Shih-Ming","id":"2F9C5AC8-F248-11E8-B48F-1D18A9856A87","last_name":"Weng","full_name":"Weng, Shih-Ming"},{"full_name":"Pernia-Andrade, Alejandro","id":"36963E98-F248-11E8-B48F-1D18A9856A87","last_name":"Pernia-Andrade","first_name":"Alejandro"},{"orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"},{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"day":"18","year":"2017","doi":"10.1016/j.neuron.2016.12.018","date_updated":"2025-04-15T07:20:01Z","date_published":"2017-01-18T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"access_level":"open_access","date_created":"2018-12-12T10:08:56Z","creator":"system","file_id":"4719","relation":"main_file","date_updated":"2018-12-12T10:08:56Z","content_type":"application/pdf","file_name":"IST-2017-752-v1+1_1-s2.0-S0896627316309606-main.pdf","file_size":2738950}],"external_id":{"isi":["000396428200010"]},"language":[{"iso":"eng"}],"issue":"2","isi":1,"scopus_import":"1","has_accepted_license":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"ScienComp"},{"_id":"PreCl"}]},{"abstract":[{"text":"This paper presents a method for simulating water surface waves as a displacement field on a 2D domain. Our method relies on Lagrangian particles that carry packets of water wave energy; each packet carries information about an entire group of wave trains, as opposed to only a single wave crest. Our approach is unconditionally stable and can simulate high resolution geometric details. This approach also presents a straightforward interface for artistic control, because it is essentially a particle system with intuitive parameters like wavelength and amplitude. Our implementation parallelizes well and runs in real time for moderately challenging scenarios.","lang":"eng"}],"status":"public","month":"07","volume":36,"article_processing_charge":"Yes (in subscription journal)","oa":1,"date_created":"2018-12-11T11:46:39Z","quality_controlled":"1","ddc":["006"],"article_number":"103","file_date_updated":"2020-07-14T12:46:34Z","article_type":"original","publisher":"ACM","publication_identifier":{"issn":["0730-0301"]},"publication":"ACM Transactions on Graphics","ec_funded":1,"file":[{"relation":"main_file","date_updated":"2020-07-14T12:46:34Z","content_type":"application/pdf","checksum":"82a3b2bfeee4ddef16ecc21675d1a48a","file_name":"wavepackets_final.pdf","file_size":13131683,"access_level":"open_access","date_created":"2020-01-24T09:32:35Z","creator":"wojtan","file_id":"7359"}],"external_id":{"isi":["000406432100071"]},"date_updated":"2026-04-16T09:58:39Z","date_published":"2017-07-01T00:00:00Z","doi":"10.1145/3072959.3073678","year":"2017","day":"01","acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","isi":1,"issue":"4","language":[{"iso":"eng"}],"_id":"470","intvolume":"        36","department":[{"_id":"ChWo"}],"type":"journal_article","oa_version":"Published Version","author":[{"full_name":"Jeschke, Stefan","orcid":"0000-0003-4330-8884","first_name":"Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"citation":{"ama":"Jeschke S, Wojtan C. Water wave packets. <i>ACM Transactions on Graphics</i>. 2017;36(4). doi:<a href=\"https://doi.org/10.1145/3072959.3073678\">10.1145/3072959.3073678</a>","ieee":"S. Jeschke and C. Wojtan, “Water wave packets,” <i>ACM Transactions on Graphics</i>, vol. 36, no. 4. ACM, 2017.","apa":"Jeschke, S., &#38; Wojtan, C. (2017). Water wave packets. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3072959.3073678\">https://doi.org/10.1145/3072959.3073678</a>","chicago":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” <i>ACM Transactions on Graphics</i>. ACM, 2017. <a href=\"https://doi.org/10.1145/3072959.3073678\">https://doi.org/10.1145/3072959.3073678</a>.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 36 (2017).","ista":"Jeschke S, Wojtan C. 2017. Water wave packets. ACM Transactions on Graphics. 36(4), 103.","mla":"Jeschke, Stefan, and Chris Wojtan. “Water Wave Packets.” <i>ACM Transactions on Graphics</i>, vol. 36, no. 4, 103, ACM, 2017, doi:<a href=\"https://doi.org/10.1145/3072959.3073678\">10.1145/3072959.3073678</a>."},"publication_status":"published","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176"}],"title":"Water wave packets","publist_id":"7350"},{"article_processing_charge":"No","volume":13,"quality_controlled":"1","date_created":"2018-12-11T11:48:35Z","oa":1,"publisher":"American Chemical Society","page":"5039 - 5053","status":"public","abstract":[{"lang":"eng","text":"Polysaccharides (carbohydrates) are key regulators of a large number of cell biological processes. However, precise biochemical or genetic manipulation of these often complex structures is laborious and hampers experimental structure–function studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool to generate and test hypotheses on saccharide function. Yet, currently used MD force fields often overestimate the aggregation propensity of polysaccharides, affecting the usability of those simulations. Here we tested MARTINI, a popular coarse-grained (CG) force field for biological macromolecules, for its ability to accurately represent molecular forces between saccharides. To this end, we calculated a thermodynamic solution property, the second virial coefficient of the osmotic pressure (B22). Comparison with light scattering experiments revealed a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing at an imbalance of the nonbonded solute–solute, solute–water, and water–water interactions. This finding also applies to smaller oligosaccharides which were all found to aggregate in simulations even at moderate concentrations, well below their solubility limit. Finally, we explored the influence of the Lennard-Jones (LJ) interaction between saccharide molecules and propose a simple scaling of the LJ interaction strength that makes MARTINI more reliable for the simulation of saccharides."}],"month":"10","publication_identifier":{"issn":["1549-9618"]},"publication":"Journal of Chemical Theory and Computation","acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"10","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1704.03773"}],"isi":1,"acknowledgement":"P.S.S. was supported by research fellowship 2811/1-1 from the German Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF 187-2013 and Grant GC65-32 from the  Interdisciplinary Centre for Mathematical and Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions and the IST Austria Scientific Computing Facility for support.","language":[{"iso":"eng"}],"external_id":{"isi":["000412965700036"],"arxiv":["1704.03773"]},"date_published":"2017-10-10T00:00:00Z","date_updated":"2025-06-04T09:49:02Z","doi":"10.1021/acs.jctc.7b00374","day":"10","year":"2017","corr_author":"1","author":[{"full_name":"Schmalhorst, Philipp S","orcid":"0000-0002-5795-0133","last_name":"Schmalhorst","id":"309D50DA-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp S"},{"first_name":"Felix","last_name":"Deluweit","full_name":"Deluweit, Felix"},{"last_name":"Scherrers","first_name":"Roger","full_name":"Scherrers, Roger"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"},{"full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","last_name":"Sikora","first_name":"Mateusz K"}],"citation":{"apa":"Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., &#38; Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. <i>Journal of Chemical Theory and Computation</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">https://doi.org/10.1021/acs.jctc.7b00374</a>","ieee":"P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M. K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations of polysaccharides,” <i>Journal of Chemical Theory and Computation</i>, vol. 13, no. 10. American Chemical Society, pp. 5039–5053, 2017.","ama":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. <i>Journal of Chemical Theory and Computation</i>. 2017;13(10):5039-5053. doi:<a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">10.1021/acs.jctc.7b00374</a>","mla":"Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory and Computation</i>, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53, doi:<a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">10.1021/acs.jctc.7b00374</a>.","ista":"Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017. Overcoming the limitations of the MARTINI force field in simulations of polysaccharides. Journal of Chemical Theory and Computation. 13(10), 5039–5053.","short":"P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora, Journal of Chemical Theory and Computation 13 (2017) 5039–5053.","chicago":"Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides.” <i>Journal of Chemical Theory and Computation</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.jctc.7b00374\">https://doi.org/10.1021/acs.jctc.7b00374</a>."},"publication_status":"published","title":"Overcoming the limitations of the MARTINI force field in simulations of polysaccharides","publist_id":"6847","arxiv":1,"_id":"804","intvolume":"        13","department":[{"_id":"CaHe"}],"type":"journal_article","oa_version":"Submitted Version"},{"volume":171,"article_processing_charge":"No","date_created":"2018-12-11T11:48:10Z","quality_controlled":"1","publisher":"Cell Press","page":"188 - 200","abstract":[{"text":"Actin filaments polymerizing against membranes power endocytosis, vesicular traffic, and cell motility. In vitro reconstitution studies suggest that the structure and the dynamics of actin networks respond to mechanical forces. We demonstrate that lamellipodial actin of migrating cells responds to mechanical load when membrane tension is modulated. In a steady state, migrating cell filaments assume the canonical dendritic geometry, defined by Arp2/3-generated 70° branch points. Increased tension triggers a dense network with a broadened range of angles, whereas decreased tension causes a shift to a sparse configuration dominated by filaments growing perpendicularly to the plasma membrane. We show that these responses emerge from the geometry of branched actin: when load per filament decreases, elongation speed increases and perpendicular filaments gradually outcompete others because they polymerize the shortest distance to the membrane, where they are protected from capping. This network-intrinsic geometrical adaptation mechanism tunes protrusive force in response to mechanical load.","lang":"eng"}],"status":"public","month":"09","publication_identifier":{"issn":["0092-8674"]},"publication":"Cell","ec_funded":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","isi":1,"issue":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000411331800020"]},"date_published":"2017-09-21T00:00:00Z","date_updated":"2025-07-10T11:54:27Z","doi":"10.1016/j.cell.2017.07.051","year":"2017","day":"21","citation":{"apa":"Mueller, J., Szep, G., Nemethova, M., de Vries, I., Lieber, A., Winkler, C., … Sixt, M. K. (2017). Load adaptation of lamellipodial actin networks. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2017.07.051\">https://doi.org/10.1016/j.cell.2017.07.051</a>","ieee":"J. Mueller <i>et al.</i>, “Load adaptation of lamellipodial actin networks,” <i>Cell</i>, vol. 171, no. 1. Cell Press, pp. 188–200, 2017.","ama":"Mueller J, Szep G, Nemethova M, et al. Load adaptation of lamellipodial actin networks. <i>Cell</i>. 2017;171(1):188-200. doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.051\">10.1016/j.cell.2017.07.051</a>","mla":"Mueller, Jan, et al. “Load Adaptation of Lamellipodial Actin Networks.” <i>Cell</i>, vol. 171, no. 1, Cell Press, 2017, pp. 188–200, doi:<a href=\"https://doi.org/10.1016/j.cell.2017.07.051\">10.1016/j.cell.2017.07.051</a>.","ista":"Mueller J, Szep G, Nemethova M, de Vries I, Lieber A, Winkler C, Kruse K, Small J, Schmeiser C, Keren K, Hauschild R, Sixt MK. 2017. Load adaptation of lamellipodial actin networks. Cell. 171(1), 188–200.","chicago":"Mueller, Jan, Gregory Szep, Maria Nemethova, Ingrid de Vries, Arnon Lieber, Christoph Winkler, Karsten Kruse, et al. “Load Adaptation of Lamellipodial Actin Networks.” <i>Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cell.2017.07.051\">https://doi.org/10.1016/j.cell.2017.07.051</a>.","short":"J. Mueller, G. Szep, M. Nemethova, I. de Vries, A. Lieber, C. Winkler, K. Kruse, J. Small, C. Schmeiser, K. Keren, R. Hauschild, M.K. Sixt, Cell 171 (2017) 188–200."},"publication_status":"published","author":[{"first_name":"Jan","last_name":"Mueller","full_name":"Mueller, Jan"},{"last_name":"Szep","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","first_name":"Gregory","full_name":"Szep, Gregory"},{"full_name":"Nemethova, Maria","last_name":"Nemethova","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"De Vries","full_name":"De Vries, Ingrid"},{"full_name":"Lieber, Arnon","first_name":"Arnon","last_name":"Lieber"},{"last_name":"Winkler","first_name":"Christoph","full_name":"Winkler, Christoph"},{"last_name":"Kruse","first_name":"Karsten","full_name":"Kruse, Karsten"},{"last_name":"Small","first_name":"John","full_name":"Small, John"},{"full_name":"Schmeiser, Christian","first_name":"Christian","last_name":"Schmeiser"},{"last_name":"Keren","first_name":"Kinneret","full_name":"Keren, Kinneret"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"project":[{"name":"Modeling of Polarization and Motility of Leukocytes in Three-Dimensional Environments","_id":"25AD6156-B435-11E9-9278-68D0E5697425","grant_number":"LS13-029"},{"grant_number":"281556","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425"}],"corr_author":"1","title":"Load adaptation of lamellipodial actin networks","publist_id":"6951","_id":"727","intvolume":"       171","department":[{"_id":"MiSi"},{"_id":"Bio"}],"type":"journal_article","oa_version":"None"},{"page":"1117 - 1123","month":"09","abstract":[{"text":"The hippocampal CA3 region plays a key role in learning and memory. Recurrent CA3–CA3\r\nsynapses are thought to be the subcellular substrate of pattern completion. However, the\r\nsynaptic mechanisms of this network computation remain enigmatic. To investigate these mechanisms, we combined functional connectivity analysis with network modeling.\r\nSimultaneous recording fromup to eight CA3 pyramidal neurons revealed that connectivity was sparse, spatially uniform, and highly enriched in disynaptic motifs (reciprocal, convergence,divergence, and chain motifs). Unitary connections were composed of one or two synaptic contacts, suggesting efficient use of postsynaptic space. Real-size modeling indicated that CA3 networks with sparse connectivity, disynaptic motifs, and single-contact connections robustly generated pattern completion.Thus, macro- and microconnectivity contribute to efficient\r\nmemory storage and retrieval in hippocampal networks.","lang":"eng"}],"status":"public","oa":1,"date_created":"2018-12-11T11:51:31Z","quality_controlled":"1","article_processing_charge":"No","volume":353,"file_date_updated":"2020-07-14T12:44:46Z","publisher":"American Association for the Advancement of Science","ddc":["570"],"ec_funded":1,"publication":"Science","pubrep_id":"823","date_published":"2016-09-09T00:00:00Z","date_updated":"2025-09-22T08:12:10Z","external_id":{"isi":["000382626800045"]},"file":[{"file_size":19408143,"content_type":"application/pdf","file_name":"IST-2017-823-v1+1_aaf1836_CombinedPDF_v2-1.pdf","checksum":"89caefa4e181424cbf0aecc835fcc5ec","date_updated":"2020-07-14T12:44:46Z","relation":"main_file","file_id":"4945","date_created":"2018-12-12T10:12:27Z","creator":"system","access_level":"open_access"}],"year":"2016","day":"09","doi":"10.1126/science.aaf1836","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","has_accepted_license":"1","scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"isi":1,"issue":"6304","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"intvolume":"       353","_id":"1350","oa_version":"Preprint","type":"journal_article","title":"Synaptic mechanisms of pattern completion in the hippocampal CA3 network","author":[{"first_name":"José","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José","orcid":"0000-0003-2209-5242"},{"orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois"},{"full_name":"Frotscher, Michael","last_name":"Frotscher","first_name":"Michael"},{"full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"citation":{"mla":"Guzmán, José, et al. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” <i>Science</i>, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1117–23, doi:<a href=\"https://doi.org/10.1126/science.aaf1836\">10.1126/science.aaf1836</a>.","ista":"Guzmán J, Schlögl A, Frotscher M, Jonas PM. 2016. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. Science. 353(6304), 1117–1123.","short":"J. Guzmán, A. Schlögl, M. Frotscher, P.M. Jonas, Science 353 (2016) 1117–1123.","chicago":"Guzmán, José, Alois Schlögl, Michael Frotscher, and Peter M Jonas. “Synaptic Mechanisms of Pattern Completion in the Hippocampal CA3 Network.” <i>Science</i>. American Association for the Advancement of Science, 2016. <a href=\"https://doi.org/10.1126/science.aaf1836\">https://doi.org/10.1126/science.aaf1836</a>.","ieee":"J. Guzmán, A. Schlögl, M. Frotscher, and P. M. Jonas, “Synaptic mechanisms of pattern completion in the hippocampal CA3 network,” <i>Science</i>, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1117–1123, 2016.","apa":"Guzmán, J., Schlögl, A., Frotscher, M., &#38; Jonas, P. M. (2016). Synaptic mechanisms of pattern completion in the hippocampal CA3 network. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaf1836\">https://doi.org/10.1126/science.aaf1836</a>","ama":"Guzmán J, Schlögl A, Frotscher M, Jonas PM. Synaptic mechanisms of pattern completion in the hippocampal CA3 network. <i>Science</i>. 2016;353(6304):1117-1123. doi:<a href=\"https://doi.org/10.1126/science.aaf1836\">10.1126/science.aaf1836</a>"},"publication_status":"published","project":[{"grant_number":"268548","call_identifier":"FP7","_id":"25C0F108-B435-11E9-9278-68D0E5697425","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"},{"name":"Mechanisms of transmitter release at GABAergic synapses","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P24909-B24"}],"corr_author":"1","publist_id":"5899"},{"date_updated":"2025-09-22T07:43:01Z","date_published":"2016-07-11T00:00:00Z","file":[{"file_id":"4981","access_level":"open_access","creator":"system","date_created":"2018-12-12T10:13:00Z","file_name":"IST-2016-631-v1+2_a96-bojsen-hansen.pdf","checksum":"140b5532f0a2a006a0149cab7c73c17c","content_type":"application/pdf","file_size":12422760,"relation":"main_file","date_updated":"2020-07-14T12:44:47Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000380112400066"]},"day":"11","year":"2016","doi":"10.1145/2897824.2925963","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"acknowledgement":"We thank the IST Austria Visual Computing group for helpful feedback throughout the project. ","isi":1,"issue":"4","alternative_title":["ACM Transactions on Graphics"],"intvolume":"        35","department":[{"_id":"ChWo"}],"_id":"1363","oa_version":"Published Version","type":"conference","title":"Generalized non-reflecting boundaries for fluid re-simulation","citation":{"mla":"Bojsen-Hansen, Morten, and Chris Wojtan. <i>Generalized Non-Reflecting Boundaries for Fluid Re-Simulation</i>. Vol. 35, no. 4, 96, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2897824.2925963\">10.1145/2897824.2925963</a>.","chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Generalized Non-Reflecting Boundaries for Fluid Re-Simulation,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2897824.2925963\">https://doi.org/10.1145/2897824.2925963</a>.","short":"M. Bojsen-Hansen, C. Wojtan, in:, ACM, 2016.","ista":"Bojsen-Hansen M, Wojtan C. 2016. Generalized non-reflecting boundaries for fluid re-simulation. ACM SIGGRAPH, ACM Transactions on Graphics, vol. 35, 96.","ama":"Bojsen-Hansen M, Wojtan C. Generalized non-reflecting boundaries for fluid re-simulation. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2897824.2925963\">10.1145/2897824.2925963</a>","apa":"Bojsen-Hansen, M., &#38; Wojtan, C. (2016). Generalized non-reflecting boundaries for fluid re-simulation (Vol. 35). Presented at the ACM SIGGRAPH, Anaheim, CA, USA: ACM. <a href=\"https://doi.org/10.1145/2897824.2925963\">https://doi.org/10.1145/2897824.2925963</a>","ieee":"M. Bojsen-Hansen and C. Wojtan, “Generalized non-reflecting boundaries for fluid re-simulation,” presented at the ACM SIGGRAPH, Anaheim, CA, USA, 2016, vol. 35, no. 4."},"author":[{"last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","first_name":"Morten","orcid":"0000-0002-4417-3224","full_name":"Bojsen-Hansen, Morten"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"publication_status":"published","project":[{"grant_number":"638176","call_identifier":"H2020","_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Big Splash: Efficient Simulation of Natural Phenomena at Extremely Large Scales"}],"corr_author":"1","publist_id":"5879","month":"07","abstract":[{"text":"When aiming to seamlessly integrate a fluid simulation into a larger scenario (like an open ocean), careful attention must be paid to boundary conditions. In particular, one must implement special &quot;non-reflecting&quot; boundary conditions, which dissipate out-going waves as they exit the simulation. Unfortunately, the state of the art in non-reflecting boundary conditions (perfectly-matched layers, or PMLs) only permits trivially simple inflow/outflow conditions, so there is no reliable way to integrate a fluid simulation into a more complicated environment like a stormy ocean or a turbulent river. This paper introduces the first method for combining nonreflecting boundary conditions based on PMLs with inflow/outflow boundary conditions that vary arbitrarily throughout space and time. Our algorithm is a generalization of stateof- the-art mean-flow boundary conditions in the computational fluid dynamics literature, and it allows for seamless integration of a fluid simulation into much more complicated environments. Our method also opens the door for previously-unseen postprocess effects like retroactively changing the location of solid obstacles, and locally increasing the visual detail of a pre-existing simulation.","lang":"eng"}],"status":"public","date_created":"2018-12-11T11:51:35Z","oa":1,"quality_controlled":"1","volume":35,"article_processing_charge":"No","file_date_updated":"2020-07-14T12:44:47Z","publisher":"ACM","article_number":"96","ddc":["000"],"conference":{"location":"Anaheim, CA, USA","end_date":"2016-07-28","name":"ACM SIGGRAPH","start_date":"2016-07-24"},"ec_funded":1,"pubrep_id":"631"},{"doi":"10.1111/mec.12165","day":"01","year":"2013","external_id":{"isi":["000314220900008"]},"date_updated":"2025-09-29T13:25:36Z","date_published":"2013-02-01T00:00:00Z","issue":"4","isi":1,"acknowledgement":"This study has made use of the computational resources provided by IST Austria and the Edinburgh Compute and Data Facility (ECDF; http://www.ecdf.ed.ac.uk). The ECDF is partially supported by the eDIKT initiative (http://www.edikt.org.uk). S.A. acknowledges financial support by IST Austria, the Janggen-Pöhn Foundation, St. Gallen, the Roche Research Foundation, Basel, the University of Edinburgh in the form of a Torrance Studentship, and the Austrian Science Fund (FWF P21305-N13).","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"scopus_import":"1","related_material":{"record":[{"status":"public","id":"9758","relation":"research_data"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"journal_article","oa_version":"None","_id":"2944","department":[{"_id":"NiBa"}],"intvolume":"        22","publist_id":"3788","corr_author":"1","author":[{"full_name":"Aeschbacher, Simon","last_name":"Aeschbacher","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"full_name":"Futschik, Andreas","first_name":"Andreas","last_name":"Futschik"},{"full_name":"Beaumont, Mark","first_name":"Mark","last_name":"Beaumont"}],"citation":{"mla":"Aeschbacher, Simon, et al. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>, vol. 22, no. 4, Wiley-Blackwell, 2013, pp. 987–1002, doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>.","ista":"Aeschbacher S, Futschik A, Beaumont M. 2013. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . Molecular Ecology. 22(4), 987–1002.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, Molecular Ecology 22 (2013) 987–1002.","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates. .” <i>Molecular Ecology</i>. Wiley-Blackwell, 2013. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>.","apa":"Aeschbacher, S., Futschik, A., &#38; Beaumont, M. (2013). Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/mec.12165\">https://doi.org/10.1111/mec.12165</a>","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ,” <i>Molecular Ecology</i>, vol. 22, no. 4. Wiley-Blackwell, pp. 987–1002, 2013.","ama":"Aeschbacher S, Futschik A, Beaumont M. Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. . <i>Molecular Ecology</i>. 2013;22(4):987-1002. doi:<a href=\"https://doi.org/10.1111/mec.12165\">10.1111/mec.12165</a>"},"publication_status":"published","title":"Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. ","status":"public","abstract":[{"lang":"eng","text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction."}],"month":"02","page":"987 - 1002","publisher":"Wiley-Blackwell","volume":22,"article_processing_charge":"No","quality_controlled":"1","date_created":"2018-12-11T12:00:28Z","publication":"Molecular Ecology"},{"month":"11","status":"public","abstract":[{"lang":"eng","text":"The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine learning literature. We consider different types of boosting and compare them to partial least squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the re-introduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find that most of the variation across loci of the ancestral mutation rate u is between 7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent estimates."}],"page":"1027 - 1047","publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"date_created":"2018-12-11T12:00:34Z","article_processing_charge":"No","volume":192,"publication":"Genetics","pmid":1,"year":"2012","day":"01","doi":"10.1534/genetics.112.143164","date_published":"2012-11-01T00:00:00Z","date_updated":"2025-09-30T08:06:06Z","external_id":{"pmid":["22960215"],"isi":["000310793900018"]},"language":[{"iso":"eng"}],"issue":"3","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/"}],"isi":1,"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledged_ssus":[{"_id":"ScienComp"}],"oa_version":"Submitted Version","type":"journal_article","intvolume":"       192","department":[{"_id":"NiBa"}],"_id":"2962","publist_id":"3763","title":"A novel approach for choosing summary statistics in approximate Bayesian computation","corr_author":"1","publication_status":"published","author":[{"full_name":"Aeschbacher, Simon","last_name":"Aeschbacher","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Mark","last_name":"Beaumont","full_name":"Beaumont, Mark"},{"full_name":"Futschik, Andreas","last_name":"Futschik","first_name":"Andreas"}],"citation":{"chicago":"Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” <i>Genetics</i>. Genetics Society of America, 2012. <a href=\"https://doi.org/10.1534/genetics.112.143164\">https://doi.org/10.1534/genetics.112.143164</a>.","short":"S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047.","ista":"Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047.","mla":"Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” <i>Genetics</i>, vol. 192, no. 3, Genetics Society of America, 2012, pp. 1027–47, doi:<a href=\"https://doi.org/10.1534/genetics.112.143164\">10.1534/genetics.112.143164</a>.","ama":"Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary statistics in approximate Bayesian computation. <i>Genetics</i>. 2012;192(3):1027-1047. doi:<a href=\"https://doi.org/10.1534/genetics.112.143164\">10.1534/genetics.112.143164</a>","ieee":"S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing summary statistics in approximate Bayesian computation,” <i>Genetics</i>, vol. 192, no. 3. Genetics Society of America, pp. 1027–1047, 2012.","apa":"Aeschbacher, S., Beaumont, M., &#38; Futschik, A. (2012). A novel approach for choosing summary statistics in approximate Bayesian computation. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.112.143164\">https://doi.org/10.1534/genetics.112.143164</a>"}}]