--- _id: '5998' abstract: - lang: eng text: Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) β-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy-limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM. article_number: e1007698 article_processing_charge: No author: - first_name: Philipp full_name: Velicky, Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Gudrun full_name: Meinhardt, Gudrun last_name: Meinhardt - first_name: Kerstin full_name: Plessl, Kerstin last_name: Plessl - first_name: Sigrid full_name: Vondra, Sigrid last_name: Vondra - first_name: Tamara full_name: Weiss, Tamara last_name: Weiss - first_name: Peter full_name: Haslinger, Peter last_name: Haslinger - first_name: Thomas full_name: Lendl, Thomas last_name: Lendl - first_name: Karin full_name: Aumayr, Karin last_name: Aumayr - first_name: Mario full_name: Mairhofer, Mario last_name: Mairhofer - first_name: Xiaowei full_name: Zhu, Xiaowei last_name: Zhu - first_name: Birgit full_name: Schütz, Birgit last_name: Schütz - first_name: Roberta L. full_name: Hannibal, Roberta L. last_name: Hannibal - first_name: Robert full_name: Lindau, Robert last_name: Lindau - first_name: Beatrix full_name: Weil, Beatrix last_name: Weil - first_name: Jan full_name: Ernerudh, Jan last_name: Ernerudh - first_name: Jürgen full_name: Neesen, Jürgen last_name: Neesen - first_name: Gerda full_name: Egger, Gerda last_name: Egger - first_name: Mario full_name: Mikula, Mario last_name: Mikula - first_name: Clemens full_name: Röhrl, Clemens last_name: Röhrl - first_name: Alexander E. full_name: Urban, Alexander E. last_name: Urban - first_name: Julie full_name: Baker, Julie last_name: Baker - first_name: Martin full_name: Knöfler, Martin last_name: Knöfler - first_name: Jürgen full_name: Pollheimer, Jürgen last_name: Pollheimer citation: ama: Velicky P, Meinhardt G, Plessl K, et al. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 2018;14(10). doi:10.1371/journal.pgen.1007698 apa: Velicky, P., Meinhardt, G., Plessl, K., Vondra, S., Weiss, T., Haslinger, P., … Pollheimer, J. (2018). Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007698 chicago: Velicky, Philipp, Gudrun Meinhardt, Kerstin Plessl, Sigrid Vondra, Tamara Weiss, Peter Haslinger, Thomas Lendl, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007698. ieee: P. Velicky et al., “Genome amplification and cellular senescence are hallmarks of human placenta development,” PLOS Genetics, vol. 14, no. 10. Public Library of Science, 2018. ista: Velicky P, Meinhardt G, Plessl K, Vondra S, Weiss T, Haslinger P, Lendl T, Aumayr K, Mairhofer M, Zhu X, Schütz B, Hannibal RL, Lindau R, Weil B, Ernerudh J, Neesen J, Egger G, Mikula M, Röhrl C, Urban AE, Baker J, Knöfler M, Pollheimer J. 2018. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 14(10), e1007698. mla: Velicky, Philipp, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics, vol. 14, no. 10, e1007698, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007698. short: P. Velicky, G. Meinhardt, K. Plessl, S. Vondra, T. Weiss, P. Haslinger, T. Lendl, K. Aumayr, M. Mairhofer, X. Zhu, B. Schütz, R.L. Hannibal, R. Lindau, B. Weil, J. Ernerudh, J. Neesen, G. Egger, M. Mikula, C. Röhrl, A.E. Urban, J. Baker, M. Knöfler, J. Pollheimer, PLOS Genetics 14 (2018). date_created: 2019-02-14T13:07:45Z date_published: 2018-10-12T00:00:00Z date_updated: 2023-09-19T14:31:43Z day: '12' ddc: - '570' department: - _id: JoDa doi: 10.1371/journal.pgen.1007698 external_id: isi: - '000449328500025' file: - access_level: open_access checksum: 34aa9a5972f61889c19f18be8ee787a0 content_type: application/pdf creator: kschuh date_created: 2019-02-14T13:14:35Z date_updated: 2020-07-14T12:47:15Z file_id: '6000' file_name: 2018_PLOS_Velicky.pdf file_size: 4592947 relation: main_file file_date_updated: 2020-07-14T12:47:15Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '10' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '10' oa: 1 oa_version: Published Version publication: PLOS Genetics publication_identifier: issn: - 1553-7404 publication_status: published publisher: Public Library of Science quality_controlled: '1' scopus_import: '1' status: public title: Genome amplification and cellular senescence are hallmarks of human placenta development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2018' ... --- _id: '5995' abstract: - lang: eng text: "Motivation\r\nComputational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here." article_processing_charge: No author: - first_name: Dinara R full_name: Usmanova, Dinara R last_name: Usmanova - first_name: Natalya S full_name: Bogatyreva, Natalya S last_name: Bogatyreva - first_name: Joan full_name: Ariño Bernad, Joan last_name: Ariño Bernad - first_name: Aleksandra A full_name: Eremina, Aleksandra A last_name: Eremina - first_name: Anastasiya A full_name: Gorshkova, Anastasiya A last_name: Gorshkova - first_name: German M full_name: Kanevskiy, German M last_name: Kanevskiy - first_name: Lyubov R full_name: Lonishin, Lyubov R last_name: Lonishin - first_name: Alexander V full_name: Meister, Alexander V last_name: Meister - first_name: Alisa G full_name: Yakupova, Alisa G last_name: Yakupova - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Dmitry full_name: Ivankov, Dmitry id: 49FF1036-F248-11E8-B48F-1D18A9856A87 last_name: Ivankov citation: ama: Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 2018;34(21):3653-3658. doi:10.1093/bioinformatics/bty340 apa: Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. Oxford University Press . https://doi.org/10.1093/bioinformatics/bty340 chicago: Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics. Oxford University Press , 2018. https://doi.org/10.1093/bioinformatics/bty340. ieee: D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018. ista: Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658. mla: Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics, vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340. short: D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658. date_created: 2019-02-14T12:48:00Z date_published: 2018-11-01T00:00:00Z date_updated: 2023-09-19T14:31:13Z day: '01' ddc: - '570' department: - _id: FyKo doi: 10.1093/bioinformatics/bty340 ec_funded: 1 external_id: isi: - '000450038900008' pmid: - '29722803' file: - access_level: open_access checksum: 7e0495153f44211479674601d7f6ee03 content_type: application/pdf creator: kschuh date_created: 2019-02-14T13:00:55Z date_updated: 2020-07-14T12:47:15Z file_id: '5997' file_name: 2018_Oxford_Usmanova.pdf file_size: 291969 relation: main_file file_date_updated: 2020-07-14T12:47:15Z has_accepted_license: '1' intvolume: ' 34' isi: 1 issue: '21' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '11' oa: 1 oa_version: Published Version page: 3653-3658 pmid: 1 project: - _id: 26120F5C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335980' name: Systematic investigation of epistasis in molecular evolution publication: Bioinformatics publication_identifier: issn: - 1367-4803 - 1460-2059 publication_status: published publisher: 'Oxford University Press ' quality_controlled: '1' scopus_import: '1' status: public title: Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 34 year: '2018' ... --- _id: '5992' abstract: - lang: eng text: Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the F-actin density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the F-actin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive F-actin network retrograde flow. article_processing_charge: No author: - first_name: Setareh full_name: Dolati, Setareh last_name: Dolati - first_name: Frieda full_name: Kage, Frieda last_name: Kage - first_name: Jan full_name: Mueller, Jan last_name: Mueller - first_name: Mathias full_name: Müsken, Mathias last_name: Müsken - first_name: Marieluise full_name: Kirchner, Marieluise last_name: Kirchner - first_name: Gunnar full_name: Dittmar, Gunnar last_name: Dittmar - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Klemens full_name: Rottner, Klemens last_name: Rottner - first_name: Martin full_name: Falcke, Martin last_name: Falcke citation: ama: Dolati S, Kage F, Mueller J, et al. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 2018;29(22):2674-2686. doi:10.1091/mbc.e18-02-0082 apa: Dolati, S., Kage, F., Mueller, J., Müsken, M., Kirchner, M., Dittmar, G., … Falcke, M. (2018). On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. American Society for Cell Biology . https://doi.org/10.1091/mbc.e18-02-0082 chicago: Dolati, Setareh, Frieda Kage, Jan Mueller, Mathias Müsken, Marieluise Kirchner, Gunnar Dittmar, Michael K Sixt, Klemens Rottner, and Martin Falcke. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell. American Society for Cell Biology , 2018. https://doi.org/10.1091/mbc.e18-02-0082. ieee: S. Dolati et al., “On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility,” Molecular Biology of the Cell, vol. 29, no. 22. American Society for Cell Biology , pp. 2674–2686, 2018. ista: Dolati S, Kage F, Mueller J, Müsken M, Kirchner M, Dittmar G, Sixt MK, Rottner K, Falcke M. 2018. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 29(22), 2674–2686. mla: Dolati, Setareh, et al. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell, vol. 29, no. 22, American Society for Cell Biology , 2018, pp. 2674–86, doi:10.1091/mbc.e18-02-0082. short: S. Dolati, F. Kage, J. Mueller, M. Müsken, M. Kirchner, G. Dittmar, M.K. Sixt, K. Rottner, M. Falcke, Molecular Biology of the Cell 29 (2018) 2674–2686. date_created: 2019-02-14T12:25:47Z date_published: 2018-11-01T00:00:00Z date_updated: 2023-09-19T14:30:23Z day: '01' ddc: - '570' department: - _id: MiSi doi: 10.1091/mbc.e18-02-0082 external_id: isi: - '000455641000011' pmid: - '30156465' file: - access_level: open_access checksum: e98465b4416b3e804c47f40086932af2 content_type: application/pdf creator: kschuh date_created: 2019-02-14T12:34:29Z date_updated: 2020-07-14T12:47:15Z file_id: '5994' file_name: 2018_ASCB_Dolati.pdf file_size: 6668971 relation: main_file file_date_updated: 2020-07-14T12:47:15Z has_accepted_license: '1' intvolume: ' 29' isi: 1 issue: '22' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '11' oa: 1 oa_version: Published Version page: 2674-2686 pmid: 1 publication: Molecular Biology of the Cell publication_identifier: eissn: - 1939-4586 publication_status: published publisher: 'American Society for Cell Biology ' quality_controlled: '1' scopus_import: '1' status: public title: On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 29 year: '2018' ... --- _id: '6010' abstract: - lang: eng text: The optic tectum (TeO), or superior colliculus, is a multisensory midbrain center that organizes spatially orienting responses to relevant stimuli. To define the stimulus with the highest priority at each moment, a network of reciprocal connections between the TeO and the isthmi promotes competition between concurrent tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression of tectal inputs are located in separate isthmic nuclei, facilitating the analysis of the neural processes that mediate competition. A specific subset of radial neurons in the intermediate tectal layers relay retinal inputs to the isthmi, but at present it is unclear whether separate neurons innervate individual nuclei or a single neural type sends a common input to several of them. In this study, we used in vitro neural tracing and cell-filling experiments in chickens to show that single neurons innervate, via axon collaterals, the three nuclei that comprise the isthmotectal network. This demonstrates that the input signals representing the strength of the incoming stimuli are simultaneously relayed to the mechanisms promoting both enhancement and suppression of the input signals. By performing in vivo recordings in anesthetized chicks, we also show that this common input generates synchrony between both antagonistic mechanisms, demonstrating that activity enhancement and suppression are closely coordinated. From a computational point of view, these results suggest that these tectal neurons constitute integrative nodes that combine inputs from different sources to drive in parallel several concurrent neural processes, each performing complementary functions within the network through different firing patterns and connectivity. article_processing_charge: No author: - first_name: Florencia full_name: Garrido-Charad, Florencia last_name: Garrido-Charad - first_name: Tomas A full_name: Vega Zuniga, Tomas A id: 2E7C4E78-F248-11E8-B48F-1D18A9856A87 last_name: Vega Zuniga - first_name: Cristián full_name: Gutiérrez-Ibáñez, Cristián last_name: Gutiérrez-Ibáñez - first_name: Pedro full_name: Fernandez, Pedro last_name: Fernandez - first_name: Luciana full_name: López-Jury, Luciana last_name: López-Jury - first_name: Cristian full_name: González-Cabrera, Cristian last_name: González-Cabrera - first_name: Harvey J. full_name: Karten, Harvey J. last_name: Karten - first_name: Harald full_name: Luksch, Harald last_name: Luksch - first_name: Gonzalo J. full_name: Marín, Gonzalo J. last_name: Marín citation: ama: Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, et al. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 2018;115(32):E7615-E7623. doi:10.1073/pnas.1804517115 apa: Garrido-Charad, F., Vega Zuniga, T. A., Gutiérrez-Ibáñez, C., Fernandez, P., López-Jury, L., González-Cabrera, C., … Marín, G. J. (2018). “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1804517115 chicago: Garrido-Charad, Florencia, Tomas A Vega Zuniga, Cristián Gutiérrez-Ibáñez, Pedro Fernandez, Luciana López-Jury, Cristian González-Cabrera, Harvey J. Karten, Harald Luksch, and Gonzalo J. Marín. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1804517115. ieee: F. Garrido-Charad et al., ““Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network,” Proceedings of the National Academy of Sciences, vol. 115, no. 32. National Academy of Sciences, pp. E7615–E7623, 2018. ista: Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, Fernandez P, López-Jury L, González-Cabrera C, Karten HJ, Luksch H, Marín GJ. 2018. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 115(32), E7615–E7623. mla: Garrido-Charad, Florencia, et al. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” Proceedings of the National Academy of Sciences, vol. 115, no. 32, National Academy of Sciences, 2018, pp. E7615–23, doi:10.1073/pnas.1804517115. short: F. Garrido-Charad, T.A. Vega Zuniga, C. Gutiérrez-Ibáñez, P. Fernandez, L. López-Jury, C. González-Cabrera, H.J. Karten, H. Luksch, G.J. Marín, Proceedings of the National Academy of Sciences 115 (2018) E7615–E7623. date_created: 2019-02-14T14:33:34Z date_published: 2018-08-07T00:00:00Z date_updated: 2023-09-19T14:35:36Z day: '07' department: - _id: MaJö doi: 10.1073/pnas.1804517115 external_id: isi: - '000440982000020' pmid: - '30026198' intvolume: ' 115' isi: 1 issue: '32' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30026198 month: '08' oa: 1 oa_version: Submitted Version page: E7615-E7623 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '6003' abstract: - lang: eng text: Digital fabrication devices are powerful tools for creating tangible reproductions of 3D digital models. Most available printing technologies aim at producing an accurate copy of a tridimensional shape. However, fabrication technologies can also be used to create a stylistic representation of a digital shape. We refer to this class of methods as ‘stylized fabrication methods’. These methods abstract geometric and physical features of a given shape to create an unconventional representation, to produce an optical illusion or to devise a particular interaction with the fabricated model. In this state‐of‐the‐art report, we classify and overview this broad and emerging class of approaches and also propose possible directions for future research. article_processing_charge: No author: - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Paolo full_name: Cignoni, Paolo last_name: Cignoni - first_name: Luigi full_name: Malomo, Luigi last_name: Malomo - first_name: Nico full_name: Pietroni, Nico last_name: Pietroni citation: ama: Bickel B, Cignoni P, Malomo L, Pietroni N. State of the art on stylized fabrication. Computer Graphics Forum. 2018;37(6):325-342. doi:10.1111/cgf.13327 apa: Bickel, B., Cignoni, P., Malomo, L., & Pietroni, N. (2018). State of the art on stylized fabrication. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13327 chicago: Bickel, Bernd, Paolo Cignoni, Luigi Malomo, and Nico Pietroni. “State of the Art on Stylized Fabrication.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13327. ieee: B. Bickel, P. Cignoni, L. Malomo, and N. Pietroni, “State of the art on stylized fabrication,” Computer Graphics Forum, vol. 37, no. 6. Wiley, pp. 325–342, 2018. ista: Bickel B, Cignoni P, Malomo L, Pietroni N. 2018. State of the art on stylized fabrication. Computer Graphics Forum. 37(6), 325–342. mla: Bickel, Bernd, et al. “State of the Art on Stylized Fabrication.” Computer Graphics Forum, vol. 37, no. 6, Wiley, 2018, pp. 325–42, doi:10.1111/cgf.13327. short: B. Bickel, P. Cignoni, L. Malomo, N. Pietroni, Computer Graphics Forum 37 (2018) 325–342. date_created: 2019-02-14T13:52:25Z date_published: 2018-09-01T00:00:00Z date_updated: 2023-09-19T14:33:40Z day: '01' ddc: - '004' department: - _id: BeBi doi: 10.1111/cgf.13327 ec_funded: 1 external_id: isi: - '000437272800019' file: - access_level: open_access checksum: d2bbe5c658d8159fbe9016a4f5e82b19 content_type: application/pdf creator: kschuh date_created: 2019-02-14T14:09:28Z date_updated: 2020-07-14T12:47:15Z file_id: '6004' file_name: StylizedFabricationSTAR-Personal.pdf file_size: 6209349 relation: main_file file_date_updated: 2020-07-14T12:47:15Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '6' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 325-342 project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: Computer Graphics Forum publication_identifier: issn: - 0167-7055 publication_status: published publisher: Wiley pubrep_id: '1051' quality_controlled: '1' scopus_import: '1' status: public title: State of the art on stylized fabrication type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2018' ... --- _id: '6002' abstract: - lang: eng text: The Bogoliubov free energy functional is analysed. The functional serves as a model of a translation-invariant Bose gas at positive temperature. We prove the existence of minimizers in the case of repulsive interactions given by a sufficiently regular two-body potential. Furthermore, we prove the existence of a phase transition in this model and provide its phase diagram. article_processing_charge: No author: - first_name: Marcin M full_name: Napiórkowski, Marcin M id: 4197AD04-F248-11E8-B48F-1D18A9856A87 last_name: Napiórkowski - first_name: Robin full_name: Reuvers, Robin last_name: Reuvers - first_name: Jan Philip full_name: Solovej, Jan Philip last_name: Solovej citation: ama: 'Napiórkowski MM, Reuvers R, Solovej JP. The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. 2018;229(3):1037-1090. doi:10.1007/s00205-018-1232-6' apa: 'Napiórkowski, M. M., Reuvers, R., & Solovej, J. P. (2018). The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-018-1232-6' chicago: 'Napiórkowski, Marcin M, Robin Reuvers, and Jan Philip Solovej. “The Bogoliubov Free Energy Functional I: Existence of Minimizers and Phase Diagram.” Archive for Rational Mechanics and Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00205-018-1232-6.' ieee: 'M. M. Napiórkowski, R. Reuvers, and J. P. Solovej, “The Bogoliubov free energy functional I: Existence of minimizers and phase diagram,” Archive for Rational Mechanics and Analysis, vol. 229, no. 3. Springer Nature, pp. 1037–1090, 2018.' ista: 'Napiórkowski MM, Reuvers R, Solovej JP. 2018. The Bogoliubov free energy functional I: Existence of minimizers and phase diagram. Archive for Rational Mechanics and Analysis. 229(3), 1037–1090.' mla: 'Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional I: Existence of Minimizers and Phase Diagram.” Archive for Rational Mechanics and Analysis, vol. 229, no. 3, Springer Nature, 2018, pp. 1037–90, doi:10.1007/s00205-018-1232-6.' short: M.M. Napiórkowski, R. Reuvers, J.P. Solovej, Archive for Rational Mechanics and Analysis 229 (2018) 1037–1090. date_created: 2019-02-14T13:40:53Z date_published: 2018-09-01T00:00:00Z date_updated: 2023-09-19T14:33:12Z day: '01' department: - _id: RoSe doi: 10.1007/s00205-018-1232-6 external_id: arxiv: - '1511.05935' isi: - '000435367300003' intvolume: ' 229' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.05935 month: '09' oa: 1 oa_version: Preprint page: 1037-1090 project: - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems publication: Archive for Rational Mechanics and Analysis publication_identifier: eissn: - 1432-0673 issn: - 0003-9527 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'The Bogoliubov free energy functional I: Existence of minimizers and phase diagram' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 229 year: '2018' ... --- _id: '5996' abstract: - lang: eng text: 'In pipes, turbulence sets in despite the linear stability of the laminar Hagen–Poiseuille flow. The Reynolds number ( ) for which turbulence first appears in a given experiment – the ‘natural transition point’ – depends on imperfections of the set-up, or, more precisely, on the magnitude of finite amplitude perturbations. At onset, turbulence typically only occupies a certain fraction of the flow, and this fraction equally is found to differ from experiment to experiment. Despite these findings, Reynolds proposed that after sufficiently long times, flows may settle to steady conditions: below a critical velocity, flows should (regardless of initial conditions) always return to laminar, while above this velocity, eddying motion should persist. As will be shown, even in pipes several thousand diameters long, the spatio-temporal intermittent flow patterns observed at the end of the pipe strongly depend on the initial conditions, and there is no indication that different flow patterns would eventually settle to a (statistical) steady state. Exploiting the fact that turbulent puffs do not age (i.e. they are memoryless), we continuously recreate the puff sequence exiting the pipe at the pipe entrance, and in doing so introduce periodic boundary conditions for the puff pattern. This procedure allows us to study the evolution of the flow patterns for arbitrary long times, and we find that after times in excess of advective time units, indeed a statistical steady state is reached. Although the resulting flows remain spatio-temporally intermittent, puff splitting and decay rates eventually reach a balance, so that the turbulent fraction fluctuates around a well-defined level which only depends on . In accordance with Reynolds’ proposition, we find that at lower (here 2020), flows eventually always resume to laminar, while for higher ( ), turbulence persists. The critical point for pipe flow hence falls in the interval of $2020 , which is in very good agreement with the recently proposed value of . The latter estimate was based on single-puff statistics and entirely neglected puff interactions. Unlike in typical contact processes where such interactions strongly affect the percolation threshold, in pipe flow, the critical point is only marginally influenced. Interactions, on the other hand, are responsible for the approach to the statistical steady state. As shown, they strongly affect the resulting flow patterns, where they cause ‘puff clustering’, and these regions of large puff densities are observed to travel across the puff pattern in a wave-like fashion.' acknowledgement: ' We also thank Philipp Maier and the IST Austria workshop for theirdedicated technical support' article_processing_charge: No article_type: original author: - first_name: Mukund full_name: Vasudevan, Mukund id: 3C5A959A-F248-11E8-B48F-1D18A9856A87 last_name: Vasudevan - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Vasudevan M, Hof B. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 2018;839:76-94. doi:10.1017/jfm.2017.923 apa: Vasudevan, M., & Hof, B. (2018). The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2017.923 chicago: Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” Journal of Fluid Mechanics. Cambridge University Press, 2018. https://doi.org/10.1017/jfm.2017.923. ieee: M. Vasudevan and B. Hof, “The critical point of the transition to turbulence in pipe flow,” Journal of Fluid Mechanics, vol. 839. Cambridge University Press, pp. 76–94, 2018. ista: Vasudevan M, Hof B. 2018. The critical point of the transition to turbulence in pipe flow. Journal of Fluid Mechanics. 839, 76–94. mla: Vasudevan, Mukund, and Björn Hof. “The Critical Point of the Transition to Turbulence in Pipe Flow.” Journal of Fluid Mechanics, vol. 839, Cambridge University Press, 2018, pp. 76–94, doi:10.1017/jfm.2017.923. short: M. Vasudevan, B. Hof, Journal of Fluid Mechanics 839 (2018) 76–94. date_created: 2019-02-14T12:50:50Z date_published: 2018-03-25T00:00:00Z date_updated: 2023-09-19T14:37:49Z day: '25' department: - _id: BjHo doi: 10.1017/jfm.2017.923 ec_funded: 1 external_id: arxiv: - '1709.06372' isi: - '000437858300003' intvolume: ' 839' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.06372 month: '03' oa: 1 oa_version: Preprint page: 76-94 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Journal of Fluid Mechanics publication_identifier: eissn: - 1469-7645 issn: - 0022-1120 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: The critical point of the transition to turbulence in pipe flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 839 year: '2018' ... --- _id: '5993' abstract: - lang: eng text: 'In this article, we consider the termination problem of probabilistic programs with real-valued variables. Thequestions concerned are: qualitative ones that ask (i) whether the program terminates with probability 1(almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); andquantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) tocompute a boundBsuch that the probability not to terminate afterBsteps decreases exponentially (con-centration problem). To solve these questions, we utilize the notion of ranking supermartingales, which isa powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmicsynthesis of linear ranking-supermartingales over affine probabilistic programs (Apps) with both angelic anddemonic non-determinism. An important subclass of Apps is LRApp which is defined as the class of all Appsover which a linear ranking-supermartingale exists.Our main contributions are as follows. Firstly, we show that the membership problem of LRApp (i) canbe decided in polynomial time for Apps with at most demonic non-determinism, and (ii) isNP-hard and inPSPACEfor Apps with angelic non-determinism. Moreover, theNP-hardness result holds already for Appswithout probability and demonic non-determinism. Secondly, we show that the concentration problem overLRApp can be solved in the same complexity as for the membership problem of LRApp. Finally, we show thatthe expectation problem over LRApp can be solved in2EXPTIMEand isPSPACE-hard even for Apps withoutprobability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate theeffectiveness of our approach to answer the qualitative and quantitative questions over Apps with at mostdemonic non-determinism.' article_number: '7' article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Hongfei full_name: Fu, Hongfei id: 3AAD03D6-F248-11E8-B48F-1D18A9856A87 last_name: Fu - first_name: Petr full_name: Novotný, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotný - first_name: Rouzbeh full_name: Hasheminezhad, Rouzbeh last_name: Hasheminezhad citation: ama: Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. 2018;40(2). doi:10.1145/3174800 apa: Chatterjee, K., Fu, H., Novotný, P., & Hasheminezhad, R. (2018). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM). https://doi.org/10.1145/3174800 chicago: Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs.” ACM Transactions on Programming Languages and Systems. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3174800. ieee: K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” ACM Transactions on Programming Languages and Systems, vol. 40, no. 2. Association for Computing Machinery (ACM), 2018. ista: Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2018. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. ACM Transactions on Programming Languages and Systems. 40(2), 7. mla: Chatterjee, Krishnendu, et al. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs.” ACM Transactions on Programming Languages and Systems, vol. 40, no. 2, 7, Association for Computing Machinery (ACM), 2018, doi:10.1145/3174800. short: K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, ACM Transactions on Programming Languages and Systems 40 (2018). date_created: 2019-02-14T12:29:10Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-19T14:38:42Z day: '01' department: - _id: KrCh doi: 10.1145/3174800 ec_funded: 1 external_id: arxiv: - '1510.08517' isi: - '000434634500003' intvolume: ' 40' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1510.08517 month: '06' oa: 1 oa_version: Submitted Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ACM Transactions on Programming Languages and Systems publication_identifier: issn: - 0164-0925 publication_status: published publisher: Association for Computing Machinery (ACM) quality_controlled: '1' related_material: record: - id: '1438' relation: earlier_version status: public scopus_import: '1' status: public title: Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 40 year: '2018' ... --- _id: '5999' abstract: - lang: eng text: "We introduce for each quiver Q and each algebraic oriented cohomology theory A, the cohomological Hall algebra (CoHA) of Q, as the A-homology of the moduli of representations of the preprojective algebra of Q. This generalizes the K-theoretic Hall algebra of commuting varieties defined by Schiffmann-Vasserot. When A is the Morava K-theory, we show evidence that this algebra is a candidate for Lusztig's reformulated conjecture on modular representations of algebraic groups.\r\nWe construct an action of the preprojective CoHA on the A-homology of Nakajima quiver varieties. We compare this with the action of the Borel subalgebra of Yangian when A is the intersection theory. We also give a shuffle algebra description of this CoHA in terms of the underlying formal group law of A. As applications, we obtain a shuffle description of the Yangian. " article_processing_charge: No author: - first_name: Yaping full_name: Yang, Yaping last_name: Yang - first_name: Gufang full_name: Zhao, Gufang id: 2BC2AC5E-F248-11E8-B48F-1D18A9856A87 last_name: Zhao citation: ama: Yang Y, Zhao G. The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. 2018;116(5):1029-1074. doi:10.1112/plms.12111 apa: Yang, Y., & Zhao, G. (2018). The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. Oxford University Press. https://doi.org/10.1112/plms.12111 chicago: Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective Algebra.” Proceedings of the London Mathematical Society. Oxford University Press, 2018. https://doi.org/10.1112/plms.12111. ieee: Y. Yang and G. Zhao, “The cohomological Hall algebra of a preprojective algebra,” Proceedings of the London Mathematical Society, vol. 116, no. 5. Oxford University Press, pp. 1029–1074, 2018. ista: Yang Y, Zhao G. 2018. The cohomological Hall algebra of a preprojective algebra. Proceedings of the London Mathematical Society. 116(5), 1029–1074. mla: Yang, Yaping, and Gufang Zhao. “The Cohomological Hall Algebra of a Preprojective Algebra.” Proceedings of the London Mathematical Society, vol. 116, no. 5, Oxford University Press, 2018, pp. 1029–74, doi:10.1112/plms.12111. short: Y. Yang, G. Zhao, Proceedings of the London Mathematical Society 116 (2018) 1029–1074. date_created: 2019-02-14T13:14:22Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-09-19T14:37:19Z day: '01' department: - _id: TaHa doi: 10.1112/plms.12111 external_id: arxiv: - '1407.7994' isi: - '000431506400001' intvolume: ' 116' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1407.7994 month: '05' oa: 1 oa_version: Preprint page: 1029-1074 publication: Proceedings of the London Mathematical Society publication_identifier: issn: - 0024-6115 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: The cohomological Hall algebra of a preprojective algebra type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 116 year: '2018' ... --- _id: '5989' abstract: - lang: eng text: Schistosomes are the causative agents of schistosomiasis, a neglected tropical disease affecting over 230 million people worldwide.Additionally to their major impact on human health, they are also models of choice in evolutionary biology. These parasitic flatwormsare unique among the common hermaphroditic trematodes as they have separate sexes. This so-called “evolutionary scandal”displays a female heterogametic genetic sex-determination system (ZZ males and ZW females), as well as a pronounced adult sexualdimorphism. These phenotypic differences are determined by a shared set of genes in both sexes, potentially leading to intralocussexual conflicts. To resolve these conflicts in sexually selected traits, molecular mechanisms such as sex-biased gene expression couldoccur, but parent-of-origin gene expression also provides an alternative. In this work we investigated the latter mechanism, that is,genes expressed preferentially from either the maternal or the paternal allele, inSchistosoma mansonispecies. To this end, tran-scriptomes from male and female hybrid adults obtained by strain crosses were sequenced. Strain-specific single nucleotide poly-morphism (SNP) markers allowed us to discriminate the parental origin, while reciprocal crosses helped to differentiate parentalexpression from strain-specific expression. We identified genes containing SNPs expressed in a parent-of-origin manner consistentwith paternal and maternal imprints. Although the majority of the SNPs was identified in mitochondrial and Z-specific loci, theremaining SNPs found in male and female transcriptomes were situated in genes that have the potential to explain sexual differencesin schistosome parasites. Furthermore, we identified and validated four new Z-specific scaffolds. article_processing_charge: No author: - first_name: Julien full_name: Kincaid-Smith, Julien last_name: Kincaid-Smith - first_name: Marion A L full_name: Picard, Marion A L id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 - first_name: Céline full_name: Cosseau, Céline last_name: Cosseau - first_name: Jérôme full_name: Boissier, Jérôme last_name: Boissier - first_name: Dany full_name: Severac, Dany last_name: Severac - first_name: Christoph full_name: Grunau, Christoph last_name: Grunau - first_name: Eve full_name: Toulza, Eve last_name: Toulza citation: ama: Kincaid-Smith J, Picard MAL, Cosseau C, et al. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. 2018;10(3):840-856. doi:10.1093/gbe/evy037 apa: Kincaid-Smith, J., Picard, M. A. L., Cosseau, C., Boissier, J., Severac, D., Grunau, C., & Toulza, E. (2018). Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy037 chicago: Kincaid-Smith, Julien, Marion A L Picard, Céline Cosseau, Jérôme Boissier, Dany Severac, Christoph Grunau, and Eve Toulza. “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy037. ieee: J. Kincaid-Smith et al., “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 840–856, 2018. ista: Kincaid-Smith J, Picard MAL, Cosseau C, Boissier J, Severac D, Grunau C, Toulza E. 2018. Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites. Genome Biology and Evolution. 10(3), 840–856. mla: Kincaid-Smith, Julien, et al. “Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 840–56, doi:10.1093/gbe/evy037. short: J. Kincaid-Smith, M.A.L. Picard, C. Cosseau, J. Boissier, D. Severac, C. Grunau, E. Toulza, Genome Biology and Evolution 10 (2018) 840–856. date_created: 2019-02-14T12:13:52Z date_published: 2018-03-01T00:00:00Z date_updated: 2023-09-19T14:39:08Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/gbe/evy037 external_id: isi: - '000429483700013' file: - access_level: open_access checksum: 736a459cb77de5824354466bb0331caf content_type: application/pdf creator: dernst date_created: 2019-02-14T12:20:01Z date_updated: 2020-07-14T12:47:15Z file_id: '5991' file_name: 2018_GBE_Kincaid_Smith.pdf file_size: 529755 relation: main_file file_date_updated: 2020-07-14T12:47:15Z has_accepted_license: '1' intvolume: ' 10' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 840-856 publication: Genome Biology and Evolution publication_identifier: issn: - 1759-6653 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Parent-of-Origin-Dependent Gene Expression in Male and Female Schistosome Parasites tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10 year: '2018' ... --- _id: '6031' abstract: - lang: eng text: We introduce Clover, a new library for efficient computation using low-precision data, providing mathematical routines required by fundamental methods in optimization and sparse recovery. Our library faithfully implements variants of stochastic quantization that guarantee convergence at low precision, and supports data formats from 4-bit quantized to 32-bit IEEE-754 on current Intel processors. In particular, we show that 4-bit can be implemented efficiently using Intel AVX despite the lack of native support for this data format. Experimental results with dot product, matrix-vector multiplication (MVM), gradient descent (GD), and iterative hard thresholding (IHT) demonstrate that the attainable speedups are in many cases close to linear with respect to the reduction of precision due to reduced data movement. Finally, for GD and IHT, we show examples of absolute speedup achieved by 4-bit versus 32-bit, by iterating until a given target error is achieved. article_number: '8598402' article_processing_charge: No author: - first_name: Alen full_name: Stojanov, Alen last_name: Stojanov - first_name: Tyler Michael full_name: Smith, Tyler Michael last_name: Smith - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Markus full_name: Puschel, Markus last_name: Puschel citation: ama: 'Stojanov A, Smith TM, Alistarh D-A, Puschel M. Fast quantized arithmetic on x86: Trading compute for data movement. In: 2018 IEEE International Workshop on Signal Processing Systems. Vol 2018-October. IEEE; 2018. doi:10.1109/SiPS.2018.8598402' apa: 'Stojanov, A., Smith, T. M., Alistarh, D.-A., & Puschel, M. (2018). Fast quantized arithmetic on x86: Trading compute for data movement. In 2018 IEEE International Workshop on Signal Processing Systems (Vol. 2018–October). Cape Town, South Africa: IEEE. https://doi.org/10.1109/SiPS.2018.8598402' chicago: 'Stojanov, Alen, Tyler Michael Smith, Dan-Adrian Alistarh, and Markus Puschel. “Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” In 2018 IEEE International Workshop on Signal Processing Systems, Vol. 2018–October. IEEE, 2018. https://doi.org/10.1109/SiPS.2018.8598402.' ieee: 'A. Stojanov, T. M. Smith, D.-A. Alistarh, and M. Puschel, “Fast quantized arithmetic on x86: Trading compute for data movement,” in 2018 IEEE International Workshop on Signal Processing Systems, Cape Town, South Africa, 2018, vol. 2018–October.' ista: 'Stojanov A, Smith TM, Alistarh D-A, Puschel M. 2018. Fast quantized arithmetic on x86: Trading compute for data movement. 2018 IEEE International Workshop on Signal Processing Systems. SiPS: Workshop on Signal Processing Systems vol. 2018–October, 8598402.' mla: 'Stojanov, Alen, et al. “Fast Quantized Arithmetic on X86: Trading Compute for Data Movement.” 2018 IEEE International Workshop on Signal Processing Systems, vol. 2018–October, 8598402, IEEE, 2018, doi:10.1109/SiPS.2018.8598402.' short: A. Stojanov, T.M. Smith, D.-A. Alistarh, M. Puschel, in:, 2018 IEEE International Workshop on Signal Processing Systems, IEEE, 2018. conference: end_date: 2018-10-24 location: Cape Town, South Africa name: 'SiPS: Workshop on Signal Processing Systems' start_date: 2018-10-21 date_created: 2019-02-17T22:59:25Z date_published: 2018-12-31T00:00:00Z date_updated: 2023-09-19T14:41:51Z day: '31' department: - _id: DaAl doi: 10.1109/SiPS.2018.8598402 external_id: isi: - '000465106800060' isi: 1 language: - iso: eng month: '12' oa_version: None publication: 2018 IEEE International Workshop on Signal Processing Systems publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: 'Fast quantized arithmetic on x86: Trading compute for data movement' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2018-October year: '2018' ... --- _id: '25' abstract: - lang: eng text: 'Partially observable Markov decision processes (POMDPs) are the standard models for planning under uncertainty with both finite and infinite horizon. Besides the well-known discounted-sum objective, indefinite-horizon objective (aka Goal-POMDPs) is another classical objective for POMDPs. In this case, given a set of target states and a positive cost for each transition, the optimization objective is to minimize the expected total cost until a target state is reached. In the literature, RTDP-Bel or heuristic search value iteration (HSVI) have been used for solving Goal-POMDPs. Neither of these algorithms has theoretical convergence guarantees, and HSVI may even fail to terminate its trials. We give the following contributions: (1) We discuss the challenges introduced in Goal-POMDPs and illustrate how they prevent the original HSVI from converging. (2) We present a novel algorithm inspired by HSVI, termed Goal-HSVI, and show that our algorithm has convergence guarantees. (3) We show that Goal-HSVI outperforms RTDP-Bel on a set of well-known examples.' acknowledgement: '∗This work has been supported by Vienna Science and Technology Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Starting grant (279307: Graph Games). This research was sponsored by the Army Research Laboratory and was accomplished under Cooperative Agreement Number W911NF-13-2-0045 (ARL Cyber Security CRA). ' article_processing_charge: No author: - first_name: Karel full_name: Horák, Karel last_name: Horák - first_name: Branislav full_name: Bošanský, Branislav last_name: Bošanský - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Horák K, Bošanský B, Chatterjee K. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. Vol 2018-July. IJCAI; 2018:4764-4770. doi:10.24963/ijcai.2018/662' apa: 'Horák, K., Bošanský, B., & Chatterjee, K. (2018). Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence (Vol. 2018–July, pp. 4764–4770). Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/662' chicago: 'Horák, Karel, Branislav Bošanský, and Krishnendu Chatterjee. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” In Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, 2018–July:4764–70. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/662.' ieee: 'K. Horák, B. Bošanský, and K. Chatterjee, “Goal-HSVI: Heuristic search value iteration for goal-POMDPs,” in Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018–July, pp. 4764–4770.' ista: 'Horák K, Bošanský B, Chatterjee K. 2018. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018–July, 4764–4770.' mla: 'Horák, Karel, et al. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, vol. 2018–July, IJCAI, 2018, pp. 4764–70, doi:10.24963/ijcai.2018/662.' short: K. Horák, B. Bošanský, K. Chatterjee, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4764–4770. conference: end_date: 2018-07-19 location: Stockholm, Sweden name: 'IJCAI: International Joint Conference on Artificial Intelligence' start_date: 2018-07-13 date_created: 2018-12-11T11:44:13Z date_published: 2018-07-01T00:00:00Z date_updated: 2023-09-19T14:44:59Z day: '01' department: - _id: KrCh doi: 10.24963/ijcai.2018/662 ec_funded: 1 external_id: isi: - '000764175404127' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.24963/ijcai.2018/662 month: '07' oa: 1 oa_version: Published Version page: 4764 - 4770 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence publication_status: published publisher: IJCAI publist_id: '8030' quality_controlled: '1' scopus_import: '1' status: public title: 'Goal-HSVI: Heuristic search value iteration for goal-POMDPs' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2018-July year: '2018' ... --- _id: '24' abstract: - lang: eng text: Partially-observable Markov decision processes (POMDPs) with discounted-sum payoff are a standard framework to model a wide range of problems related to decision making under uncertainty. Traditionally, the goal has been to obtain policies that optimize the expectation of the discounted-sum payoff. A key drawback of the expectation measure is that even low probability events with extreme payoff can significantly affect the expectation, and thus the obtained policies are not necessarily risk-averse. An alternate approach is to optimize the probability that the payoff is above a certain threshold, which allows obtaining risk-averse policies, but ignores optimization of the expectation. We consider the expectation optimization with probabilistic guarantee (EOPG) problem, where the goal is to optimize the expectation ensuring that the payoff is above a given threshold with at least a specified probability. We present several results on the EOPG problem, including the first algorithm to solve it. acknowledgement: "This research was supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003; Austrian Science Fund (FWF): S11407-N23(RiSE/SHiNE);and an ERC Start Grant (279307:Graph Games).\r\n" article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Adrian full_name: Elgyütt, Adrian id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87 last_name: Elgyütt - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny - first_name: Owen full_name: Rouillé, Owen last_name: Rouillé citation: ama: 'Chatterjee K, Elgyütt A, Novotný P, Rouillé O. Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives. In: Vol 2018. IJCAI; 2018:4692-4699. doi:10.24963/ijcai.2018/652' apa: 'Chatterjee, K., Elgyütt, A., Novotný, P., & Rouillé, O. (2018). Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives (Vol. 2018, pp. 4692–4699). Presented at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm, Sweden: IJCAI. https://doi.org/10.24963/ijcai.2018/652' chicago: Chatterjee, Krishnendu, Adrian Elgyütt, Petr Novotný, and Owen Rouillé. “Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum Objectives,” 2018:4692–99. IJCAI, 2018. https://doi.org/10.24963/ijcai.2018/652. ieee: 'K. Chatterjee, A. Elgyütt, P. Novotný, and O. Rouillé, “Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives,” presented at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018, pp. 4692–4699.' ista: 'Chatterjee K, Elgyütt A, Novotný P, Rouillé O. 2018. Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018, 4692–4699.' mla: Chatterjee, Krishnendu, et al. Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum Objectives. Vol. 2018, IJCAI, 2018, pp. 4692–99, doi:10.24963/ijcai.2018/652. short: K. Chatterjee, A. Elgyütt, P. Novotný, O. Rouillé, in:, IJCAI, 2018, pp. 4692–4699. conference: end_date: 2018-07-19 location: Stockholm, Sweden name: 'IJCAI: International Joint Conference on Artificial Intelligence' start_date: 2018-07-13 date_created: 2018-12-11T11:44:13Z date_published: 2018-07-01T00:00:00Z date_updated: 2023-09-19T14:45:48Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.24963/ijcai.2018/652 ec_funded: 1 external_id: arxiv: - '1804.10601' isi: - '000764175404117' intvolume: ' 2018' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.10601 month: '07' oa: 1 oa_version: Preprint page: 4692 - 4699 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: IJCAI publist_id: '8031' quality_controlled: '1' scopus_import: '1' status: public title: Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2018 year: '2018' ... --- _id: '34' abstract: - lang: eng text: Partially observable Markov decision processes (POMDPs) are widely used in probabilistic planning problems in which an agent interacts with an environment using noisy and imprecise sensors. We study a setting in which the sensors are only partially defined and the goal is to synthesize “weakest” additional sensors, such that in the resulting POMDP, there is a small-memory policy for the agent that almost-surely (with probability 1) satisfies a reachability objective. We show that the problem is NP-complete, and present a symbolic algorithm by encoding the problem into SAT instances. We illustrate trade-offs between the amount of memory of the policy and the number of additional sensors on a simple example. We have implemented our approach and consider three classical POMDP examples from the literature, and show that in all the examples the number of sensors can be significantly decreased (as compared to the existing solutions in the literature) without increasing the complexity of the policies. alternative_title: - ICAPS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chemlík, Martin last_name: Chemlík - first_name: Ufuk full_name: Topcu, Ufuk last_name: Topcu citation: ama: 'Chatterjee K, Chemlík M, Topcu U. Sensor synthesis for POMDPs with reachability objectives. In: Vol 2018. AAAI Press; 2018:47-55.' apa: 'Chatterjee, K., Chemlík, M., & Topcu, U. (2018). Sensor synthesis for POMDPs with reachability objectives (Vol. 2018, pp. 47–55). Presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands: AAAI Press.' chicago: Chatterjee, Krishnendu, Martin Chemlík, and Ufuk Topcu. “Sensor Synthesis for POMDPs with Reachability Objectives,” 2018:47–55. AAAI Press, 2018. ieee: 'K. Chatterjee, M. Chemlík, and U. Topcu, “Sensor synthesis for POMDPs with reachability objectives,” presented at the ICAPS: International Conference on Automated Planning and Scheduling, Delft, Netherlands, 2018, vol. 2018, pp. 47–55.' ista: 'Chatterjee K, Chemlík M, Topcu U. 2018. Sensor synthesis for POMDPs with reachability objectives. ICAPS: International Conference on Automated Planning and Scheduling, ICAPS, vol. 2018, 47–55.' mla: Chatterjee, Krishnendu, et al. Sensor Synthesis for POMDPs with Reachability Objectives. Vol. 2018, AAAI Press, 2018, pp. 47–55. short: K. Chatterjee, M. Chemlík, U. Topcu, in:, AAAI Press, 2018, pp. 47–55. conference: end_date: 2018-06-29 location: Delft, Netherlands name: 'ICAPS: International Conference on Automated Planning and Scheduling' start_date: 2018-06-24 date_created: 2018-12-11T11:44:16Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-19T14:44:14Z day: '01' department: - _id: KrCh ec_funded: 1 external_id: arxiv: - '1710.00675' isi: - '000492986200006' intvolume: ' 2018' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1710.00675 month: '06' oa: 1 oa_version: Preprint page: 47 - 55 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: AAAI Press publist_id: '8021' quality_controlled: '1' scopus_import: '1' status: public title: Sensor synthesis for POMDPs with reachability objectives type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2018 year: '2018' ... --- _id: '18' abstract: - lang: eng text: An N-superconcentrator is a directed, acyclic graph with N input nodes and N output nodes such that every subset of the inputs and every subset of the outputs of same cardinality can be connected by node-disjoint paths. It is known that linear-size and bounded-degree superconcentrators exist. We prove the existence of such superconcentrators with asymptotic density 25.3 (where the density is the number of edges divided by N). The previously best known densities were 28 [12] and 27.4136 [17]. article_processing_charge: No author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek citation: ama: Kolmogorov V, Rolinek M. Superconcentrators of density 25.3. Ars Combinatoria. 2018;141(10):269-304. apa: Kolmogorov, V., & Rolinek, M. (2018). Superconcentrators of density 25.3. Ars Combinatoria. Charles Babbage Research Centre. chicago: Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.” Ars Combinatoria. Charles Babbage Research Centre, 2018. ieee: V. Kolmogorov and M. Rolinek, “Superconcentrators of density 25.3,” Ars Combinatoria, vol. 141, no. 10. Charles Babbage Research Centre, pp. 269–304, 2018. ista: Kolmogorov V, Rolinek M. 2018. Superconcentrators of density 25.3. Ars Combinatoria. 141(10), 269–304. mla: Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.” Ars Combinatoria, vol. 141, no. 10, Charles Babbage Research Centre, 2018, pp. 269–304. short: V. Kolmogorov, M. Rolinek, Ars Combinatoria 141 (2018) 269–304. date_created: 2018-12-11T11:44:11Z date_published: 2018-10-01T00:00:00Z date_updated: 2023-09-19T14:46:18Z day: '01' department: - _id: VlKo external_id: arxiv: - '1405.7828' isi: - '000446809500022' intvolume: ' 141' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1405.7828 month: '10' oa: 1 oa_version: Preprint page: 269 - 304 publication: Ars Combinatoria publication_identifier: issn: - 0381-7032 publication_status: published publisher: Charles Babbage Research Centre publist_id: '8037' quality_controlled: '1' scopus_import: '1' status: public title: Superconcentrators of density 25.3 type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 141 year: '2018' ... --- _id: '6355' abstract: - lang: eng text: We prove that any cyclic quadrilateral can be inscribed in any closed convex C1-curve. The smoothness condition is not required if the quadrilateral is a rectangle. article_number: e7 article_processing_charge: No author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov citation: ama: Akopyan A, Avvakumov S. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. 2018;6. doi:10.1017/fms.2018.7 apa: Akopyan, A., & Avvakumov, S. (2018). Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2018.7 chicago: Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma. Cambridge University Press, 2018. https://doi.org/10.1017/fms.2018.7. ieee: A. Akopyan and S. Avvakumov, “Any cyclic quadrilateral can be inscribed in any closed convex smooth curve,” Forum of Mathematics, Sigma, vol. 6. Cambridge University Press, 2018. ista: Akopyan A, Avvakumov S. 2018. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. 6, e7. mla: Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma, vol. 6, e7, Cambridge University Press, 2018, doi:10.1017/fms.2018.7. short: A. Akopyan, S. Avvakumov, Forum of Mathematics, Sigma 6 (2018). date_created: 2019-04-30T06:09:57Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-09-19T14:50:12Z day: '31' ddc: - '510' department: - _id: UlWa - _id: HeEd - _id: JaMa doi: 10.1017/fms.2018.7 ec_funded: 1 external_id: arxiv: - '1712.10205' isi: - '000433915500001' file: - access_level: open_access checksum: 5a71b24ba712a3eb2e46165a38fbc30a content_type: application/pdf creator: dernst date_created: 2019-04-30T06:14:58Z date_updated: 2020-07-14T12:47:28Z file_id: '6356' file_name: 2018_ForumMahtematics_Akopyan.pdf file_size: 249246 relation: main_file file_date_updated: 2020-07-14T12:47:28Z has_accepted_license: '1' intvolume: ' 6' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics publication: Forum of Mathematics, Sigma publication_identifier: issn: - 2050-5094 publication_status: published publisher: Cambridge University Press quality_controlled: '1' related_material: record: - id: '8156' relation: dissertation_contains status: public status: public title: Any cyclic quadrilateral can be inscribed in any closed convex smooth curve tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 6 year: '2018' ... --- _id: '6195' abstract: - lang: eng text: In the context of robotic manipulation and grasping, the shift from a view that is static (force closure of a single posture) and contact-deprived (only contact for force closure is allowed, everything else is obstacle) towards a view that is dynamic and contact-rich (soft manipulation) has led to an increased interest in soft hands. These hands can easily exploit environmental constraints and object surfaces without risk, and safely interact with humans, but present also some challenges. Designing them is difficult, as well as predicting, modelling, and “programming” their interactions with the objects and the environment. This paper tackles the problem of simulating them in a fast and effective way, leveraging on novel and existing simulation technologies. We present a triple-layered simulation framework where dynamic properties such as stiffness are determined from slow but accurate FEM simulation data once, and then condensed into a lumped parameter model that can be used to fast simulate soft fingers and soft hands. We apply our approach to the simulation of soft pneumatic fingers. article_number: '8461106' article_processing_charge: No author: - first_name: Maria full_name: Pozzi, Maria last_name: Pozzi - first_name: Eder full_name: Miguel Villalba, Eder id: 3FB91342-F248-11E8-B48F-1D18A9856A87 last_name: Miguel Villalba orcid: 0000-0001-5665-0430 - first_name: Raphael full_name: Deimel, Raphael last_name: Deimel - first_name: Monica full_name: Malvezzi, Monica last_name: Malvezzi - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Oliver full_name: Brock, Oliver last_name: Brock - first_name: Domenico full_name: Prattichizzo, Domenico last_name: Prattichizzo citation: ama: 'Pozzi M, Miguel Villalba E, Deimel R, et al. Efficient FEM-based simulation of soft robots modeled as kinematic chains. In: IEEE; 2018. doi:10.1109/icra.2018.8461106' apa: 'Pozzi, M., Miguel Villalba, E., Deimel, R., Malvezzi, M., Bickel, B., Brock, O., & Prattichizzo, D. (2018). Efficient FEM-based simulation of soft robots modeled as kinematic chains. Presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia: IEEE. https://doi.org/10.1109/icra.2018.8461106' chicago: Pozzi, Maria, Eder Miguel Villalba, Raphael Deimel, Monica Malvezzi, Bernd Bickel, Oliver Brock, and Domenico Prattichizzo. “Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains.” IEEE, 2018. https://doi.org/10.1109/icra.2018.8461106. ieee: 'M. Pozzi et al., “Efficient FEM-based simulation of soft robots modeled as kinematic chains,” presented at the ICRA: International Conference on Robotics and Automation, Brisbane, Australia, 2018.' ista: 'Pozzi M, Miguel Villalba E, Deimel R, Malvezzi M, Bickel B, Brock O, Prattichizzo D. 2018. Efficient FEM-based simulation of soft robots modeled as kinematic chains. ICRA: International Conference on Robotics and Automation, 8461106.' mla: Pozzi, Maria, et al. Efficient FEM-Based Simulation of Soft Robots Modeled as Kinematic Chains. 8461106, IEEE, 2018, doi:10.1109/icra.2018.8461106. short: M. Pozzi, E. Miguel Villalba, R. Deimel, M. Malvezzi, B. Bickel, O. Brock, D. Prattichizzo, in:, IEEE, 2018. conference: end_date: 2018-05-25 location: Brisbane, Australia name: 'ICRA: International Conference on Robotics and Automation' start_date: 2018-05-21 date_created: 2019-04-04T09:50:38Z date_published: 2018-09-10T00:00:00Z date_updated: 2023-09-19T14:49:03Z day: '10' department: - _id: BeBi doi: 10.1109/icra.2018.8461106 external_id: isi: - '000446394503031' isi: 1 language: - iso: eng month: '09' oa_version: None publication_identifier: isbn: - '9781538630815' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Efficient FEM-based simulation of soft robots modeled as kinematic chains type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '6941' abstract: - lang: eng text: "Bitcoin has become the most successful cryptocurrency ever deployed, and its most distinctive feature is that it is decentralized. Its underlying protocol (Nakamoto consensus) achieves this by using proof of work, which has the drawback that it causes the consumption of vast amounts of energy to maintain the ledger. Moreover, Bitcoin mining dynamics have become less distributed over time.\r\n\r\nTowards addressing these issues, we propose SpaceMint, a cryptocurrency based on proofs of space instead of proofs of work. Miners in SpaceMint dedicate disk space rather than computation. We argue that SpaceMint’s design solves or alleviates several of Bitcoin’s issues: most notably, its large energy consumption. SpaceMint also rewards smaller miners fairly according to their contribution to the network, thus incentivizing more distributed participation.\r\n\r\nThis paper adapts proof of space to enable its use in cryptocurrency, studies the attacks that can arise against a Bitcoin-like blockchain that uses proof of space, and proposes a new blockchain format and transaction types to address these attacks. Our prototype shows that initializing 1 TB for mining takes about a day (a one-off setup cost), and miners spend on average just a fraction of a second per block mined. Finally, we provide a game-theoretic analysis modeling SpaceMint as an extensive game (the canonical game-theoretic notion for games that take place over time) and show that this stylized game satisfies a strong equilibrium notion, thereby arguing for SpaceMint ’s stability and consensus." alternative_title: - LNCS article_processing_charge: No author: - first_name: Sunoo full_name: Park, Sunoo last_name: Park - first_name: Albert full_name: Kwon, Albert last_name: Kwon - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. SpaceMint: A cryptocurrency based on proofs of space. In: 22nd International Conference on Financial Cryptography and Data Security. Vol 10957. Springer Nature; 2018:480-499. doi:10.1007/978-3-662-58387-6_26' apa: 'Park, S., Kwon, A., Fuchsbauer, G., Gazi, P., Alwen, J. F., & Pietrzak, K. Z. (2018). SpaceMint: A cryptocurrency based on proofs of space. In 22nd International Conference on Financial Cryptography and Data Security (Vol. 10957, pp. 480–499). Nieuwpoort, Curacao: Springer Nature. https://doi.org/10.1007/978-3-662-58387-6_26' chicago: 'Park, Sunoo, Albert Kwon, Georg Fuchsbauer, Peter Gazi, Joel F Alwen, and Krzysztof Z Pietrzak. “SpaceMint: A Cryptocurrency Based on Proofs of Space.” In 22nd International Conference on Financial Cryptography and Data Security, 10957:480–99. Springer Nature, 2018. https://doi.org/10.1007/978-3-662-58387-6_26.' ieee: 'S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J. F. Alwen, and K. Z. Pietrzak, “SpaceMint: A cryptocurrency based on proofs of space,” in 22nd International Conference on Financial Cryptography and Data Security, Nieuwpoort, Curacao, 2018, vol. 10957, pp. 480–499.' ista: 'Park S, Kwon A, Fuchsbauer G, Gazi P, Alwen JF, Pietrzak KZ. 2018. SpaceMint: A cryptocurrency based on proofs of space. 22nd International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 10957, 480–499.' mla: 'Park, Sunoo, et al. “SpaceMint: A Cryptocurrency Based on Proofs of Space.” 22nd International Conference on Financial Cryptography and Data Security, vol. 10957, Springer Nature, 2018, pp. 480–99, doi:10.1007/978-3-662-58387-6_26.' short: S. Park, A. Kwon, G. Fuchsbauer, P. Gazi, J.F. Alwen, K.Z. Pietrzak, in:, 22nd International Conference on Financial Cryptography and Data Security, Springer Nature, 2018, pp. 480–499. conference: end_date: 2018-03-02 location: Nieuwpoort, Curacao name: 'FC: Financial Cryptography and Data Security' start_date: 2018-02-26 date_created: 2019-10-14T06:35:38Z date_published: 2018-12-07T00:00:00Z date_updated: 2023-09-19T15:02:13Z day: '07' department: - _id: KrPi doi: 10.1007/978-3-662-58387-6_26 ec_funded: 1 external_id: isi: - '000540656400026' intvolume: ' 10957' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2015/528 month: '12' oa: 1 oa_version: Submitted Version page: 480-499 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: 22nd International Conference on Financial Cryptography and Data Security publication_identifier: eissn: - 1611-3349 isbn: - '9783662583869' - '9783662583876' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'SpaceMint: A cryptocurrency based on proofs of space' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10957 year: '2018' ... --- _id: '6497' abstract: - lang: eng text: T cells are actively scanning pMHC-presenting cells in lymphoid organs and nonlymphoid tissues (NLTs) with divergent topologies and confinement. How the T cell actomyosin cytoskeleton facilitates this task in distinct environments is incompletely understood. Here, we show that lack of Myosin IXb (Myo9b), a negative regulator of the small GTPase Rho, led to increased Rho-GTP levels and cell surface stiffness in primary T cells. Nonetheless, intravital imaging revealed robust motility of Myo9b−/− CD8+ T cells in lymphoid tissue and similar expansion and differentiation during immune responses. In contrast, accumulation of Myo9b−/− CD8+ T cells in NLTs was strongly impaired. Specifically, Myo9b was required for T cell crossing of basement membranes, such as those which are present between dermis and epidermis. As consequence, Myo9b−/− CD8+ T cells showed impaired control of skin infections. In sum, we show that Myo9b is critical for the CD8+ T cell adaptation from lymphoid to NLT surveillance and the establishment of protective tissue–resident T cell populations. article_processing_charge: No author: - first_name: Federica full_name: Moalli, Federica last_name: Moalli - first_name: Xenia full_name: Ficht, Xenia last_name: Ficht - first_name: Philipp full_name: Germann, Philipp last_name: Germann - first_name: Mykhailo full_name: Vladymyrov, Mykhailo last_name: Vladymyrov - first_name: Bettina full_name: Stolp, Bettina last_name: Stolp - first_name: Ingrid full_name: de Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: de Vries - first_name: Ruth full_name: Lyck, Ruth last_name: Lyck - first_name: Jasmin full_name: Balmer, Jasmin last_name: Balmer - first_name: Amleto full_name: Fiocchi, Amleto last_name: Fiocchi - first_name: Mario full_name: Kreutzfeldt, Mario last_name: Kreutzfeldt - first_name: Doron full_name: Merkler, Doron last_name: Merkler - first_name: Matteo full_name: Iannacone, Matteo last_name: Iannacone - first_name: Akitaka full_name: Ariga, Akitaka last_name: Ariga - first_name: Michael H. full_name: Stoffel, Michael H. last_name: Stoffel - first_name: James full_name: Sharpe, James last_name: Sharpe - first_name: Martin full_name: Bähler, Martin last_name: Bähler - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Alba full_name: Diz-Muñoz, Alba last_name: Diz-Muñoz - first_name: Jens V. full_name: Stein, Jens V. last_name: Stein citation: ama: Moalli F, Ficht X, Germann P, et al. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2018;2015(7):1869–1890. doi:10.1084/jem.20170896 apa: Moalli, F., Ficht, X., Germann, P., Vladymyrov, M., Stolp, B., de Vries, I., … Stein, J. V. (2018). The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20170896 chicago: Moalli, Federica, Xenia Ficht, Philipp Germann, Mykhailo Vladymyrov, Bettina Stolp, Ingrid de Vries, Ruth Lyck, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine. Rockefeller University Press, 2018. https://doi.org/10.1084/jem.20170896. ieee: F. Moalli et al., “The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells,” The Journal of Experimental Medicine, vol. 2015, no. 7. Rockefeller University Press, pp. 1869–1890, 2018. ista: Moalli F, Ficht X, Germann P, Vladymyrov M, Stolp B, de Vries I, Lyck R, Balmer J, Fiocchi A, Kreutzfeldt M, Merkler D, Iannacone M, Ariga A, Stoffel MH, Sharpe J, Bähler M, Sixt MK, Diz-Muñoz A, Stein JV. 2018. The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells. The Journal of Experimental Medicine. 2015(7), 1869–1890. mla: Moalli, Federica, et al. “The Rho Regulator Myosin IXb Enables Nonlymphoid Tissue Seeding of Protective CD8+T Cells.” The Journal of Experimental Medicine, vol. 2015, no. 7, Rockefeller University Press, 2018, pp. 1869–1890, doi:10.1084/jem.20170896. short: F. Moalli, X. Ficht, P. Germann, M. Vladymyrov, B. Stolp, I. de Vries, R. Lyck, J. Balmer, A. Fiocchi, M. Kreutzfeldt, D. Merkler, M. Iannacone, A. Ariga, M.H. Stoffel, J. Sharpe, M. Bähler, M.K. Sixt, A. Diz-Muñoz, J.V. Stein, The Journal of Experimental Medicine 2015 (2018) 1869–1890. date_created: 2019-05-28T12:36:47Z date_published: 2018-06-06T00:00:00Z date_updated: 2023-09-19T14:52:08Z day: '06' ddc: - '570' department: - _id: MiSi doi: 10.1084/jem.20170896 external_id: isi: - '000440822900011' file: - access_level: open_access checksum: 86ae5331f9bfced9a6358a790a04bef4 content_type: application/pdf creator: kschuh date_created: 2019-05-28T12:40:05Z date_updated: 2020-07-14T12:47:32Z file_id: '6498' file_name: 2018_rupress_Moalli.pdf file_size: 3841660 relation: main_file file_date_updated: 2020-07-14T12:47:32Z has_accepted_license: '1' intvolume: ' 2015' isi: 1 issue: '7' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1869–1890 publication: The Journal of Experimental Medicine publication_identifier: eissn: - 1540-9538 issn: - 0022-1007 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: The Rho regulator Myosin IXb enables nonlymphoid tissue seeding of protective CD8+T cells tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2015 year: '2018' ... --- _id: '6499' abstract: - lang: eng text: Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge. article_number: e45836 article_processing_charge: No author: - first_name: Sven M full_name: Truckenbrodt, Sven M id: 45812BD4-F248-11E8-B48F-1D18A9856A87 last_name: Truckenbrodt - first_name: Manuel full_name: Maidorn, Manuel last_name: Maidorn - first_name: Dagmar full_name: Crzan, Dagmar last_name: Crzan - first_name: Hanna full_name: Wildhagen, Hanna last_name: Wildhagen - first_name: Selda full_name: Kabatas, Selda last_name: Kabatas - first_name: Silvio O full_name: Rizzoli, Silvio O last_name: Rizzoli citation: ama: Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 2018;19(9). doi:10.15252/embr.201845836 apa: Truckenbrodt, S. M., Maidorn, M., Crzan, D., Wildhagen, H., Kabatas, S., & Rizzoli, S. O. (2018). X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO Reports. EMBO. https://doi.org/10.15252/embr.201845836 chicago: Truckenbrodt, Sven M, Manuel Maidorn, Dagmar Crzan, Hanna Wildhagen, Selda Kabatas, and Silvio O Rizzoli. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” EMBO Reports. EMBO, 2018. https://doi.org/10.15252/embr.201845836. ieee: S. M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, and S. O. Rizzoli, “X10 expansion microscopy enables 25‐nm resolution on conventional microscopes,” EMBO reports, vol. 19, no. 9. EMBO, 2018. ista: Truckenbrodt SM, Maidorn M, Crzan D, Wildhagen H, Kabatas S, Rizzoli SO. 2018. X10 expansion microscopy enables 25‐nm resolution on conventional microscopes. EMBO reports. 19(9), e45836. mla: Truckenbrodt, Sven M., et al. “X10 Expansion Microscopy Enables 25‐nm Resolution on Conventional Microscopes.” EMBO Reports, vol. 19, no. 9, e45836, EMBO, 2018, doi:10.15252/embr.201845836. short: S.M. Truckenbrodt, M. Maidorn, D. Crzan, H. Wildhagen, S. Kabatas, S.O. Rizzoli, EMBO Reports 19 (2018). date_created: 2019-05-28T13:16:08Z date_published: 2018-09-01T00:00:00Z date_updated: 2023-09-19T14:52:32Z day: '01' ddc: - '580' department: - _id: JoDa doi: 10.15252/embr.201845836 external_id: isi: - '000443682200009' file: - access_level: open_access checksum: 6ec90abc637f09cca3a7b6424d7e7a26 content_type: application/pdf creator: kschuh date_created: 2019-05-28T13:17:19Z date_updated: 2020-07-14T12:47:32Z file_id: '6500' file_name: 2018_embo_Truckenbrodt.pdf file_size: 2005572 relation: main_file file_date_updated: 2020-07-14T12:47:32Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: EMBO reports publication_identifier: eissn: - 1469-3178 issn: - 1469-221X publication_status: published publisher: EMBO quality_controlled: '1' scopus_import: '1' status: public title: X10 expansion microscopy enables 25‐nm resolution on conventional microscopes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ...