[{"language":[{"iso":"eng"}],"publist_id":"5198","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"article_processing_charge":"No","title":"Mathematical model of alternative mechanism of telomere length maintenance","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kollár, Richard","first_name":"Richard","last_name":"Kollár"},{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína","last_name":"Bod'ová","orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína"},{"full_name":"Nosek, Jozef","first_name":"Jozef","last_name":"Nosek"},{"last_name":"Tomáška","first_name":"Ľubomír","full_name":"Tomáška, Ľubomír"}],"publisher":"American Institute of Physics","publication_status":"published","_id":"1896","type":"journal_article","abstract":[{"text":"Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.","lang":"eng"}],"scopus_import":"1","citation":{"apa":"Kollár, R., Bodova, K., Nosek, J., &#38; Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">https://doi.org/10.1103/PhysRevE.89.032701</a>","mla":"Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">10.1103/PhysRevE.89.032701</a>.","ama":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2014;89(3). doi:<a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">10.1103/PhysRevE.89.032701</a>","short":"R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","ista":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701.","ieee":"R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 89, no. 3. American Institute of Physics, 2014.","chicago":"Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2014. <a href=\"https://doi.org/10.1103/PhysRevE.89.032701\">https://doi.org/10.1103/PhysRevE.89.032701</a>."},"year":"2014","issue":"3","oa":1,"date_updated":"2022-08-01T10:50:10Z","acknowledgement":"The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.).","article_number":"032701","month":"03","intvolume":"        89","date_published":"2014-03-04T00:00:00Z","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.0430"}],"doi":"10.1103/PhysRevE.89.032701","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","status":"public","day":"04","date_created":"2018-12-11T11:54:35Z","volume":89},{"doi":"10.1105/tpc.114.125880","publication_status":"published","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/"}],"publication":"Plant Cell","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"GNOM is one of the most characterized membrane trafficking regulators in plants, with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor) class to mediate vesicle budding at endomembranes. The crucial role of GNOM in recycling of PIN auxin transporters and other proteins to the plasma membrane was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM, the most prominent regulator of recycling in plants, has been proposed to act and localize at so far elusive recycling endosomes. Here, we report the GNOM localization in context of its cellular function in Arabidopsis thaliana. State-of-the-art imaging, pharmacological interference, and ultrastructure analysis show that GNOM predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus, whereas prolonged exposures results in GNOM translocation to trans-Golgi network (TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role for GNOM in maintaining TGN/EE function. Our results redefine the subcellular action of GNOM and reevaluate the identity and function of recycling endosomes in plants."}],"scopus_import":1,"citation":{"chicago":"Naramoto, Satoshi, Marisa Otegui, Natsumaro Kutsuna, Riet De Rycke, Tomoko Dainobu, Michael Karampelias, Masaru Fujimoto, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” <i>Plant Cell</i>. American Society of Plant Biologists, 2014. <a href=\"https://doi.org/10.1105/tpc.114.125880\">https://doi.org/10.1105/tpc.114.125880</a>.","ama":"Naramoto S, Otegui M, Kutsuna N, et al. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. <i>Plant Cell</i>. 2014;26(7):3062-3076. doi:<a href=\"https://doi.org/10.1105/tpc.114.125880\">10.1105/tpc.114.125880</a>","ista":"Naramoto S, Otegui M, Kutsuna N, De Rycke R, Dainobu T, Karampelias M, Fujimoto M, Feraru E, Miki D, Fukuda H, Nakano A, Friml J. 2014. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 26(7), 3062–3076.","ieee":"S. Naramoto <i>et al.</i>, “Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,” <i>Plant Cell</i>, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076, 2014.","short":"S. Naramoto, M. Otegui, N. Kutsuna, R. De Rycke, T. Dainobu, M. Karampelias, M. Fujimoto, E. Feraru, D. Miki, H. Fukuda, A. Nakano, J. Friml, Plant Cell 26 (2014) 3062–3076.","mla":"Naramoto, Satoshi, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” <i>Plant Cell</i>, vol. 26, no. 7, American Society of Plant Biologists, 2014, pp. 3062–76, doi:<a href=\"https://doi.org/10.1105/tpc.114.125880\">10.1105/tpc.114.125880</a>.","apa":"Naramoto, S., Otegui, M., Kutsuna, N., De Rycke, R., Dainobu, T., Karampelias, M., … Friml, J. (2014). Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.114.125880\">https://doi.org/10.1105/tpc.114.125880</a>"},"volume":26,"status":"public","day":"01","_id":"1897","date_created":"2018-12-11T11:54:36Z","publist_id":"5199","department":[{"_id":"JiFr"}],"page":"3062 - 3076","year":"2014","language":[{"iso":"eng"}],"publisher":"American Society of Plant Biologists","acknowledgement":"This work was supported by the Odysseus Program of the Research Foundation-Flanders (J.F.).","intvolume":"        26","month":"07","date_published":"2014-07-01T00:00:00Z","issue":"7","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"first_name":"Marisa","last_name":"Otegui","full_name":"Otegui, Marisa"},{"full_name":"Kutsuna, Natsumaro","first_name":"Natsumaro","last_name":"Kutsuna"},{"full_name":"De Rycke, Riet","first_name":"Riet","last_name":"De Rycke"},{"full_name":"Dainobu, Tomoko","first_name":"Tomoko","last_name":"Dainobu"},{"first_name":"Michael","last_name":"Karampelias","full_name":"Karampelias, Michael"},{"last_name":"Fujimoto","first_name":"Masaru","full_name":"Fujimoto, Masaru"},{"first_name":"Elena","last_name":"Feraru","full_name":"Feraru, Elena"},{"full_name":"Miki, Daisuke","first_name":"Daisuke","last_name":"Miki"},{"full_name":"Fukuda, Hiroo","last_name":"Fukuda","first_name":"Hiroo"},{"last_name":"Nakano","first_name":"Akihiko","full_name":"Nakano, Akihiko"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"title":"Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis","date_updated":"2021-01-12T06:53:55Z"},{"abstract":[{"text":"Fast synaptic transmission is important for rapid information processing. To explore the maximal rate of neuronal signaling and to analyze the presynaptic mechanisms, we focused on the input layer of the cerebellar cortex, where exceptionally high action potential (AP) frequencies have been reported invivo. With paired recordings between presynaptic cerebellar mossy fiber boutons and postsynaptic granule cells, we demonstrate reliable neurotransmission upto ~1 kHz. Presynaptic APs are ultrafast, with ~100μs half-duration. Both Kv1 and Kv3 potassium channels mediate the fast repolarization, rapidly inactivating sodium channels ensure metabolic efficiency, and little AP broadening occurs during bursts of up to 1.5 kHz. Presynaptic Cav2.1 (P/Q-type) calcium channels open efficiently during ultrafast APs. Furthermore, a subset of synaptic vesicles is tightly coupled to Ca2+ channels, and vesicles are rapidly recruited to the release site. These data reveal mechanisms of presynaptic AP generation and transmitter release underlying neuronal kHz signaling.","lang":"eng"}],"scopus_import":1,"type":"journal_article","volume":84,"citation":{"apa":"Ritzau Jost, A., Delvendahl, I., Rings, A., Byczkowicz, N., Harada, H., Shigemoto, R., … Hallermann, S. (2014). Ultrafast action potentials mediate kilohertz signaling at a central synapse. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2014.08.036\">https://doi.org/10.1016/j.neuron.2014.08.036</a>","mla":"Ritzau Jost, Andreas, et al. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” <i>Neuron</i>, vol. 84, no. 1, Elsevier, 2014, pp. 152–63, doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.08.036\">10.1016/j.neuron.2014.08.036</a>.","ama":"Ritzau Jost A, Delvendahl I, Rings A, et al. Ultrafast action potentials mediate kilohertz signaling at a central synapse. <i>Neuron</i>. 2014;84(1):152-163. doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.08.036\">10.1016/j.neuron.2014.08.036</a>","ieee":"A. Ritzau Jost <i>et al.</i>, “Ultrafast action potentials mediate kilohertz signaling at a central synapse,” <i>Neuron</i>, vol. 84, no. 1. Elsevier, pp. 152–163, 2014.","short":"A. Ritzau Jost, I. Delvendahl, A. Rings, N. Byczkowicz, H. Harada, R. Shigemoto, J. Hirrlinger, J. Eilers, S. Hallermann, Neuron 84 (2014) 152–163.","ista":"Ritzau Jost A, Delvendahl I, Rings A, Byczkowicz N, Harada H, Shigemoto R, Hirrlinger J, Eilers J, Hallermann S. 2014. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 84(1), 152–163.","chicago":"Ritzau Jost, Andreas, Igor Delvendahl, Annika Rings, Niklas Byczkowicz, Harumi Harada, Ryuichi Shigemoto, Johannes Hirrlinger, Jens Eilers, and Stefan Hallermann. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2014.08.036\">https://doi.org/10.1016/j.neuron.2014.08.036</a>."},"status":"public","day":"01","quality_controlled":"1","date_created":"2018-12-11T11:54:36Z","_id":"1898","publication":"Neuron","doi":"10.1016/j.neuron.2014.08.036","publication_status":"published","oa_version":"None","publisher":"Elsevier","date_published":"2014-10-01T00:00:00Z","intvolume":"        84","month":"10","title":"Ultrafast action potentials mediate kilohertz signaling at a central synapse","author":[{"last_name":"Ritzau Jost","first_name":"Andreas","full_name":"Ritzau Jost, Andreas"},{"full_name":"Delvendahl, Igor","first_name":"Igor","last_name":"Delvendahl"},{"full_name":"Rings, Annika","last_name":"Rings","first_name":"Annika"},{"full_name":"Byczkowicz, Niklas","first_name":"Niklas","last_name":"Byczkowicz"},{"first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","last_name":"Shigemoto"},{"full_name":"Hirrlinger, Johannes","last_name":"Hirrlinger","first_name":"Johannes"},{"full_name":"Eilers, Jens","first_name":"Jens","last_name":"Eilers"},{"first_name":"Stefan","last_name":"Hallermann","full_name":"Hallermann, Stefan"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","issue":"1","date_updated":"2021-01-12T06:53:55Z","publist_id":"5197","department":[{"_id":"RySh"}],"page":"152 - 163","year":"2014","language":[{"iso":"eng"}]},{"oa_version":"Submitted Version","doi":"10.1038/ncb3001","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159251/"}],"publication":"Nature Cell Biology","date_created":"2018-12-11T11:54:36Z","day":"13","status":"public","pmid":1,"volume":16,"year":"2014","page":"758 - 769","external_id":{"pmid":["25016959"]},"date_updated":"2021-01-12T06:53:55Z","issue":"8","oa":1,"intvolume":"        16","month":"07","date_published":"2014-07-13T00:00:00Z","publication_status":"published","_id":"1899","quality_controlled":"1","citation":{"chicago":"Williams, Scott, Lyndsay Ratliff, Maria P Postiglione, Juergen Knoblich, and Elaine Fuchs. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/ncb3001\">https://doi.org/10.1038/ncb3001</a>.","short":"S. Williams, L. Ratliff, M.P. Postiglione, J. Knoblich, E. Fuchs, Nature Cell Biology 16 (2014) 758–769.","ista":"Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. 2014. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 16(8), 758–769.","ieee":"S. Williams, L. Ratliff, M. P. Postiglione, J. Knoblich, and E. Fuchs, “Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN,” <i>Nature Cell Biology</i>, vol. 16, no. 8. Nature Publishing Group, pp. 758–769, 2014.","ama":"Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. <i>Nature Cell Biology</i>. 2014;16(8):758-769. doi:<a href=\"https://doi.org/10.1038/ncb3001\">10.1038/ncb3001</a>","mla":"Williams, Scott, et al. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” <i>Nature Cell Biology</i>, vol. 16, no. 8, Nature Publishing Group, 2014, pp. 758–69, doi:<a href=\"https://doi.org/10.1038/ncb3001\">10.1038/ncb3001</a>.","apa":"Williams, S., Ratliff, L., Postiglione, M. P., Knoblich, J., &#38; Fuchs, E. (2014). Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb3001\">https://doi.org/10.1038/ncb3001</a>"},"type":"journal_article","abstract":[{"text":"Asymmetric cell divisions allow stem cells to balance proliferation and differentiation. During embryogenesis, murine epidermis expands rapidly from a single layer of unspecified basal layer progenitors to a stratified, differentiated epithelium. Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation protein LGN, but little is known about how the apical localization of LGN is regulated. Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to explore the functions of the LGN-interacting proteins Par3, mInsc and Gα i3. Whereas loss of each gene alone leads to randomized division angles, combined loss of Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of LGN. These findings lend experimental support for the hitherto untested model that Par3-mInsc and Gα i3 act cooperatively to polarize LGN and promote perpendicular divisions. Finally, we uncover a developmental switch between delamination-driven early stratification and spindle-orientation-dependent differentiation that occurs around E15, revealing a two-step mechanism underlying epidermal maturation.","lang":"eng"}],"scopus_import":1,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","publist_id":"5196","department":[{"_id":"SiHi"}],"title":"Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Williams, Scott","last_name":"Williams","first_name":"Scott"},{"full_name":"Ratliff, Lyndsay","last_name":"Ratliff","first_name":"Lyndsay"},{"full_name":"Postiglione, Maria P","last_name":"Postiglione","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","first_name":"Maria P"},{"first_name":"Juergen","last_name":"Knoblich","full_name":"Knoblich, Juergen"},{"full_name":"Fuchs, Elaine","first_name":"Elaine","last_name":"Fuchs"}],"publisher":"Nature Publishing Group"},{"date_published":"2014-01-31T00:00:00Z","intvolume":"        16","month":"01","publisher":"Nature Publishing Group","date_updated":"2021-01-12T06:53:56Z","author":[{"full_name":"Behrndt, Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Lateral junction dynamics lead the way out","issue":"2","page":"127 - 129","publist_id":"5195","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"year":"2014","volume":16,"citation":{"ieee":"M. Behrndt and C.-P. J. Heisenberg, “Lateral junction dynamics lead the way out,” <i>Nature Cell Biology</i>, vol. 16, no. 2. Nature Publishing Group, pp. 127–129, 2014.","short":"M. Behrndt, C.-P.J. Heisenberg, Nature Cell Biology 16 (2014) 127–129.","ista":"Behrndt M, Heisenberg C-PJ. 2014. Lateral junction dynamics lead the way out. Nature Cell Biology. 16(2), 127–129.","ama":"Behrndt M, Heisenberg C-PJ. Lateral junction dynamics lead the way out. <i>Nature Cell Biology</i>. 2014;16(2):127-129. doi:<a href=\"https://doi.org/10.1038/ncb2913\">10.1038/ncb2913</a>","chicago":"Behrndt, Martin, and Carl-Philipp J Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” <i>Nature Cell Biology</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/ncb2913\">https://doi.org/10.1038/ncb2913</a>.","apa":"Behrndt, M., &#38; Heisenberg, C.-P. J. (2014). Lateral junction dynamics lead the way out. <i>Nature Cell Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncb2913\">https://doi.org/10.1038/ncb2913</a>","mla":"Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” <i>Nature Cell Biology</i>, vol. 16, no. 2, Nature Publishing Group, 2014, pp. 127–29, doi:<a href=\"https://doi.org/10.1038/ncb2913\">10.1038/ncb2913</a>."},"scopus_import":1,"abstract":[{"lang":"eng","text":"Epithelial cell layers need to be tightly regulated to maintain their integrity and correct function. Cell integration into epithelial sheets is now shown to depend on the N-WASP-regulated stabilization of cortical F-actin, which generates distinct patterns of apical-lateral contractility at E-cadherin-based cell-cell junctions."}],"type":"journal_article","_id":"1900","date_created":"2018-12-11T11:54:37Z","quality_controlled":"1","day":"31","status":"public","publication":"Nature Cell Biology","doi":"10.1038/ncb2913","publication_status":"published","oa_version":"None"},{"date_updated":"2021-01-12T06:53:57Z","issue":"2","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Huiyu","last_name":"Tian","full_name":"Tian, Huiyu"},{"full_name":"Wabnik, Krzysztof T","first_name":"Krzysztof T","last_name":"Wabnik"},{"full_name":"Niu, Tiantian","last_name":"Niu","first_name":"Tiantian"},{"full_name":"Li, Hongjiang","last_name":"Li","first_name":"Hongjiang"},{"full_name":"Yu, Qianqian","last_name":"Yu","first_name":"Qianqian"},{"full_name":"Pollmann, Stephan","last_name":"Pollmann","first_name":"Stephan"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Govaerts, Willy","last_name":"Govaerts","first_name":"Willy"},{"first_name":"Jakub","last_name":"Rolčík","full_name":"Rolčík, Jakub"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Ding, Zhaojun","last_name":"Ding","first_name":"Zhaojun"}],"title":"WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis","month":"02","intvolume":"         7","date_published":"2014-02-01T00:00:00Z","publisher":"Oxford University Press","acknowledgement":"This work was supported by funding from the projects CZ.1.07/2.3.00/20.0043 and CZ.1.05/1.1.00/02.0068 (to CEITEC, Central European Institute of Technology) and the Odysseus program of the Research Foundation-Flanders to J.F\r\n","language":[{"iso":"eng"}],"year":"2014","page":"277 - 289","publist_id":"5194","department":[{"_id":"JiFr"}],"_id":"1901","date_created":"2018-12-11T11:54:37Z","status":"public","day":"01","citation":{"ama":"Tian H, Wabnik KT, Niu T, et al. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. <i>Molecular Plant</i>. 2014;7(2):277-289. doi:<a href=\"https://doi.org/10.1093/mp/sst118\">10.1093/mp/sst118</a>","short":"H. Tian, K.T. Wabnik, T. Niu, H. Li, Q. Yu, S. Pollmann, S. Vanneste, W. Govaerts, J. Rolčík, M. Geisler, J. Friml, Z. Ding, Molecular Plant 7 (2014) 277–289.","ista":"Tian H, Wabnik KT, Niu T, Li H, Yu Q, Pollmann S, Vanneste S, Govaerts W, Rolčík J, Geisler M, Friml J, Ding Z. 2014. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 7(2), 277–289.","ieee":"H. Tian <i>et al.</i>, “WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis,” <i>Molecular Plant</i>, vol. 7, no. 2. Oxford University Press, pp. 277–289, 2014.","chicago":"Tian, Huiyu, Krzysztof T Wabnik, Tiantian Niu, Hongjiang Li, Qianqian Yu, Stephan Pollmann, Steffen Vanneste, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” <i>Molecular Plant</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/mp/sst118\">https://doi.org/10.1093/mp/sst118</a>.","apa":"Tian, H., Wabnik, K. T., Niu, T., Li, H., Yu, Q., Pollmann, S., … Ding, Z. (2014). WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. <i>Molecular Plant</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/mp/sst118\">https://doi.org/10.1093/mp/sst118</a>","mla":"Tian, Huiyu, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” <i>Molecular Plant</i>, vol. 7, no. 2, Oxford University Press, 2014, pp. 277–89, doi:<a href=\"https://doi.org/10.1093/mp/sst118\">10.1093/mp/sst118</a>."},"volume":7,"type":"journal_article","abstract":[{"lang":"eng","text":"In plants, the patterning of stem cell-enriched meristems requires a graded auxin response maximum that emerges from the concerted action of polar auxin transport, auxin biosynthesis, auxin metabolism, and cellular auxin response machinery. However, mechanisms underlying this auxin response maximum-mediated root stem cell maintenance are not fully understood. Here, we present unexpected evidence that WUSCHEL-RELATED HOMEOBOX 5 (WOX5) transcription factor modulates expression of auxin biosynthetic genes in the quiescent center (QC) of the root and thus provides a robust mechanism for the maintenance of auxin response maximum in the root tip. This WOX5 action is balanced through the activity of indole-3-acetic acid 17 (IAA17) auxin response repressor. Our combined genetic, cell biology, and computational modeling studies revealed a previously uncharacterized feedback loop linking WOX5-mediated auxin production to IAA17-dependent repression of auxin responses. This WOX5-IAA17 feedback circuit further assures the maintenance of auxin response maximum in the root tip and thereby contributes to the maintenance of distal stem cell (DSC) populations. Our experimental studies and in silico computer simulations both demonstrate that the WOX5-IAA17 feedback circuit is essential for the maintenance of auxin gradient in the root tip and the auxin-mediated root DSC differentiation."}],"scopus_import":1,"oa_version":"None","doi":"10.1093/mp/sst118","publication_status":"published","publication":"Molecular Plant"},{"publisher":"Oxford University Press","author":[{"first_name":"Barry","last_name":"Hall","full_name":"Hall, Barry"},{"first_name":"Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","last_name":"Acar","orcid":"0000-0003-1986-9753","full_name":"Acar, Hande"},{"full_name":"Nandipati, Anna","last_name":"Nandipati","first_name":"Anna"},{"first_name":"Miriam","last_name":"Barlow","full_name":"Barlow, Miriam"}],"title":"Growth rates made easy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","department":[{"_id":"JoBo"}],"publist_id":"5193","language":[{"iso":"eng"}],"article_type":"original","citation":{"apa":"Hall, B., Acar, H., Nandipati, A., &#38; Barlow, M. (2014). Growth rates made easy. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/mst187\">https://doi.org/10.1093/molbev/mst187</a>","mla":"Hall, Barry, et al. “Growth Rates Made Easy.” <i>Molecular Biology and Evolution</i>, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:<a href=\"https://doi.org/10.1093/molbev/mst187\">10.1093/molbev/mst187</a>.","ista":"Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular Biology and Evolution. 31(1), 232–238.","ieee":"B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” <i>Molecular Biology and Evolution</i>, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014.","short":"B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238.","ama":"Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. <i>Molecular Biology and Evolution</i>. 2014;31(1):232-238. doi:<a href=\"https://doi.org/10.1093/molbev/mst187\">10.1093/molbev/mst187</a>","chicago":"Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/molbev/mst187\">https://doi.org/10.1093/molbev/mst187</a>."},"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"In the 1960s-1980s, determination of bacterial growth rates was an important tool in microbial genetics, biochemistry, molecular biology, and microbial physiology. The exciting technical developments of the 1990s and the 2000s eclipsed that tool; as a result, many investigators today lack experience with growth rate measurements. Recently, investigators in a number of areas have started to use measurements of bacterial growth rates for a variety of purposes. Those measurements have been greatly facilitated by the availability of microwell plate readers that permit the simultaneous measurements on up to 384 different cultures. Only the exponential (logarithmic) portions of the resulting growth curves are useful for determining growth rates, and manual determination of that portion and calculation of growth rates can be tedious for high-throughput purposes. Here, we introduce the program GrowthRates that uses plate reader output files to automatically determine the exponential portion of the curve and to automatically calculate the growth rate, the maximum culture density, and the duration of the growth lag phase. GrowthRates is freely available for Macintosh, Windows, and Linux.We discuss the effects of culture volume, the classical bacterial growth curve, and the differences between determinations in rich media and minimal (mineral salts) media. This protocol covers calibration of the plate reader, growth of culture inocula for both rich and minimal media, and experimental setup. As a guide to reliability, we report typical day-to-day variation in growth rates and variation within experiments with respect to position of wells within the plates."}],"type":"journal_article","_id":"1902","quality_controlled":"1","publication_status":"published","date_published":"2014-01-01T00:00:00Z","month":"01","intvolume":"        31","date_updated":"2022-06-07T11:08:13Z","issue":"1","external_id":{"pmid":["24170494"]},"page":"232 - 238","year":"2014","volume":31,"pmid":1,"date_created":"2018-12-11T11:54:37Z","day":"01","status":"public","publication":"Molecular Biology and Evolution","doi":"10.1093/molbev/mst187","oa_version":"None"},{"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","_id":"1903","quality_controlled":"1","citation":{"chicago":"Chatterjee, Krishnendu. “Partial-Observation Stochastic Reachability and Parity Games,” 8634:1–4. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-662-44522-8_1\">https://doi.org/10.1007/978-3-662-44522-8_1</a>.","short":"K. Chatterjee, in:, Springer, 2014, pp. 1–4.","ista":"Chatterjee K. 2014. Partial-observation stochastic reachability and parity games. MFCS: Mathematical Foundations of Computer Science, LNCS, vol. 8634, 1–4.","ieee":"K. Chatterjee, “Partial-observation stochastic reachability and parity games,” presented at the MFCS: Mathematical Foundations of Computer Science, Budapest, Hungary, 2014, vol. 8634, no. PART 1, pp. 1–4.","ama":"Chatterjee K. Partial-observation stochastic reachability and parity games. In: Vol 8634. Springer; 2014:1-4. doi:<a href=\"https://doi.org/10.1007/978-3-662-44522-8_1\">10.1007/978-3-662-44522-8_1</a>","mla":"Chatterjee, Krishnendu. <i>Partial-Observation Stochastic Reachability and Parity Games</i>. Vol. 8634, no. PART 1, Springer, 2014, pp. 1–4, doi:<a href=\"https://doi.org/10.1007/978-3-662-44522-8_1\">10.1007/978-3-662-44522-8_1</a>.","apa":"Chatterjee, K. (2014). Partial-observation stochastic reachability and parity games (Vol. 8634, pp. 1–4). Presented at the MFCS: Mathematical Foundations of Computer Science, Budapest, Hungary: Springer. <a href=\"https://doi.org/10.1007/978-3-662-44522-8_1\">https://doi.org/10.1007/978-3-662-44522-8_1</a>"},"scopus_import":1,"abstract":[{"text":"We consider two-player zero-sum partial-observation stochastic games on graphs. Based on the information available to the players these games can be classified as follows: (a) general partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) perfect-observation (both players have complete view of the game). The one-sided partial-observation games subsumes the important special case of one-player partial-observation stochastic games (or partial-observation Markov decision processes (POMDPs)). Based on the randomization available for the strategies, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization. We consider all these classes of games with reachability, and parity objectives that can express all ω-regular objectives. The analysis problems are classified into the qualitative analysis that asks for the existence of a strategy that ensures the objective with probability 1; and the quantitative analysis that asks for the existence of a strategy that ensures the objective with probability at least λ (0,1). In this talk we will cover a wide range of results: for perfect-observation games; for POMDPs; for one-sided partial-observation games; and for general partial-observation games.","lang":"eng"}],"type":"conference","language":[{"iso":"eng"}],"pubrep_id":"141","department":[{"_id":"KrCh"}],"publist_id":"5192","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Partial-observation stochastic reachability and parity games","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"publisher":"Springer","related_material":{"record":[{"relation":"later_version","status":"public","id":"2211"},{"id":"5381","status":"public","relation":"earlier_version"}]},"ec_funded":1,"oa_version":"None","doi":"10.1007/978-3-662-44522-8_1","date_created":"2018-12-11T11:54:38Z","status":"public","day":"01","volume":8634,"year":"2014","page":"1 - 4","conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2014-08-25","end_date":"2014-08-29","location":"Budapest, Hungary"},"date_updated":"2023-02-23T12:23:43Z","issue":"PART 1","alternative_title":["LNCS"],"date_published":"2014-01-01T00:00:00Z","month":"01","intvolume":"      8634"},{"publisher":"European Mathematical Society","title":"Strichartz inequality for orthonormal functions","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Frank, Rupert","last_name":"Frank","first_name":"Rupert"},{"last_name":"Lewin","first_name":"Mathieu","full_name":"Lewin, Mathieu"},{"last_name":"Lieb","first_name":"Élliott","full_name":"Lieb, Élliott"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"publist_id":"5191","department":[{"_id":"RoSe"}],"language":[{"iso":"eng"}],"citation":{"apa":"Frank, R., Lewin, M., Lieb, É., &#38; Seiringer, R. (2014). Strichartz inequality for orthonormal functions. <i>Journal of the European Mathematical Society</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/JEMS/467\">https://doi.org/10.4171/JEMS/467</a>","mla":"Frank, Rupert, et al. “Strichartz Inequality for Orthonormal Functions.” <i>Journal of the European Mathematical Society</i>, vol. 16, no. 7, European Mathematical Society, 2014, pp. 1507–26, doi:<a href=\"https://doi.org/10.4171/JEMS/467\">10.4171/JEMS/467</a>.","ama":"Frank R, Lewin M, Lieb É, Seiringer R. Strichartz inequality for orthonormal functions. <i>Journal of the European Mathematical Society</i>. 2014;16(7):1507-1526. doi:<a href=\"https://doi.org/10.4171/JEMS/467\">10.4171/JEMS/467</a>","ieee":"R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “Strichartz inequality for orthonormal functions,” <i>Journal of the European Mathematical Society</i>, vol. 16, no. 7. European Mathematical Society, pp. 1507–1526, 2014.","short":"R. Frank, M. Lewin, É. Lieb, R. Seiringer, Journal of the European Mathematical Society 16 (2014) 1507–1526.","ista":"Frank R, Lewin M, Lieb É, Seiringer R. 2014. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 16(7), 1507–1526.","chicago":"Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “Strichartz Inequality for Orthonormal Functions.” <i>Journal of the European Mathematical Society</i>. European Mathematical Society, 2014. <a href=\"https://doi.org/10.4171/JEMS/467\">https://doi.org/10.4171/JEMS/467</a>."},"type":"journal_article","abstract":[{"lang":"eng","text":"We prove a Strichartz inequality for a system of orthonormal functions, with an optimal behavior of the constant in the limit of a large number of functions. The estimate generalizes the usual Strichartz inequality, in the same fashion as the Lieb-Thirring inequality generalizes the Sobolev inequality. As an application, we consider the Schrödinger equation with a time-dependent potential and we show the existence of the wave operator in Schatten spaces."}],"scopus_import":1,"_id":"1904","quality_controlled":"1","project":[{"_id":"26450934-B435-11E9-9278-68D0E5697425","name":"NSERC Postdoctoral fellowship"}],"publication_status":"published","intvolume":"        16","month":"08","date_published":"2014-08-23T00:00:00Z","date_updated":"2021-01-12T06:53:58Z","issue":"7","oa":1,"page":"1507 - 1526","year":"2014","volume":16,"date_created":"2018-12-11T11:54:38Z","day":"23","status":"public","main_file_link":[{"url":"http://arxiv.org/abs/1306.1309","open_access":"1"}],"doi":"10.4171/JEMS/467","publication":"Journal of the European Mathematical Society","oa_version":"Submitted Version"},{"quality_controlled":"1","_id":"1905","type":"journal_article","abstract":[{"text":"The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution).","lang":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"citation":{"chicago":"Tobler, Michael, Martin Plath, Rüdiger Riesch, Ingo Schlupp, Anna V Grasse, Gopi Munimanda, C Setzer, Dustin Penn, and Yoshan Moodley. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” <i>Journal of Evolutionary Biology</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/jeb.12370\">https://doi.org/10.1111/jeb.12370</a>.","ama":"Tobler M, Plath M, Riesch R, et al. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. <i>Journal of Evolutionary Biology</i>. 2014;27(5):960-974. doi:<a href=\"https://doi.org/10.1111/jeb.12370\">10.1111/jeb.12370</a>","ista":"Tobler M, Plath M, Riesch R, Schlupp I, Grasse AV, Munimanda G, Setzer C, Penn D, Moodley Y. 2014. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 27(5), 960–974.","short":"M. Tobler, M. Plath, R. Riesch, I. Schlupp, A.V. Grasse, G. Munimanda, C. Setzer, D. Penn, Y. Moodley, Journal of Evolutionary Biology 27 (2014) 960–974.","ieee":"M. Tobler <i>et al.</i>, “Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations,” <i>Journal of Evolutionary Biology</i>, vol. 27, no. 5. Wiley, pp. 960–974, 2014.","mla":"Tobler, Michael, et al. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” <i>Journal of Evolutionary Biology</i>, vol. 27, no. 5, Wiley, 2014, pp. 960–74, doi:<a href=\"https://doi.org/10.1111/jeb.12370\">10.1111/jeb.12370</a>.","apa":"Tobler, M., Plath, M., Riesch, R., Schlupp, I., Grasse, A. V., Munimanda, G., … Moodley, Y. (2014). Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.12370\">https://doi.org/10.1111/jeb.12370</a>"},"publication_status":"published","author":[{"last_name":"Tobler","first_name":"Michael","full_name":"Tobler, Michael"},{"last_name":"Plath","first_name":"Martin","full_name":"Plath, Martin"},{"first_name":"Rüdiger","last_name":"Riesch","full_name":"Riesch, Rüdiger"},{"first_name":"Ingo","last_name":"Schlupp","full_name":"Schlupp, Ingo"},{"last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","full_name":"Grasse, Anna V"},{"first_name":"Gopi","last_name":"Munimanda","full_name":"Munimanda, Gopi"},{"first_name":"C","last_name":"Setzer","full_name":"Setzer, C"},{"full_name":"Penn, Dustin","last_name":"Penn","first_name":"Dustin"},{"last_name":"Moodley","first_name":"Yoshan","full_name":"Moodley, Yoshan"}],"title":"Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Wiley","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"SyCr"}],"publist_id":"5190","article_processing_charge":"No","day":"12","status":"public","date_created":"2018-12-11T11:54:38Z","pmid":1,"volume":27,"oa_version":"None","doi":"10.1111/jeb.12370","publication":"Journal of Evolutionary Biology","issue":"5","date_updated":"2022-06-07T09:22:20Z","acknowledgement":"This study was funded by grants from the National Science Foundation (NSF) to MT (IOS-1121832) and IS (DEB-0743406) and from the German Science Foundation (DFG; PL 470/1-2) and ‘LOEWE − Landesoffensive zur Entwicklung wissenschaftlich-ökonomischer Exzellenz’ of Hesse's Ministry of Higher Education, Research, and the Arts, to MP.","intvolume":"        27","month":"04","date_published":"2014-04-12T00:00:00Z","year":"2014","external_id":{"pmid":["24725091"]},"page":"960 - 974"},{"pubrep_id":"573","language":[{"iso":"eng"}],"department":[{"_id":"ChWo"}],"publist_id":"5189","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Large-scale point-cloud visualization through localized textured surface reconstruction","author":[{"last_name":"Arikan","first_name":"Murat","full_name":"Arikan, Murat"},{"full_name":"Preiner, Reinhold","last_name":"Preiner","first_name":"Reinhold"},{"full_name":"Scheiblauer, Claus","first_name":"Claus","last_name":"Scheiblauer"},{"full_name":"Jeschke, Stefan","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","last_name":"Jeschke"},{"last_name":"Wimmer","first_name":"Michael","full_name":"Wimmer, Michael"}],"file":[{"date_updated":"2020-07-14T12:45:20Z","date_created":"2018-12-12T10:17:41Z","file_name":"IST-2016-573-v1+1_arikan-2014-pcvis-draft.pdf","access_level":"open_access","checksum":"5bf58942d2eb20adf03c7f9ea2e68124","relation":"main_file","file_id":"5297","content_type":"application/pdf","file_size":13594598,"creator":"system"}],"publisher":"IEEE","has_accepted_license":"1","publication_status":"published","project":[{"call_identifier":"FWF","grant_number":"P 24352-N23","name":"Deep Pictures: Creating Visual and Haptic Vector Images","_id":"25357BD2-B435-11E9-9278-68D0E5697425"}],"_id":"1906","scopus_import":1,"abstract":[{"text":"In this paper, we introduce a novel scene representation for the visualization of large-scale point clouds accompanied by a set of high-resolution photographs. Many real-world applications deal with very densely sampled point-cloud data, which are augmented with photographs that often reveal lighting variations and inaccuracies in registration. Consequently, the high-quality representation of the captured data, i.e., both point clouds and photographs together, is a challenging and time-consuming task. We propose a two-phase approach, in which the first (preprocessing) phase generates multiple overlapping surface patches and handles the problem of seamless texture generation locally for each patch. The second phase stitches these patches at render-time to produce a high-quality visualization of the data. As a result of the proposed localization of the global texturing problem, our algorithm is more than an order of magnitude faster than equivalent mesh-based texturing techniques. Furthermore, since our preprocessing phase requires only a minor fraction of the whole data set at once, we provide maximum flexibility when dealing with growing data sets.","lang":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:45:20Z","citation":{"ama":"Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. Large-scale point-cloud visualization through localized textured surface reconstruction. <i>IEEE Transactions on Visualization and Computer Graphics</i>. 2014;20(9):1280-1292. doi:<a href=\"https://doi.org/10.1109/TVCG.2014.2312011\">10.1109/TVCG.2014.2312011</a>","ieee":"M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, and M. Wimmer, “Large-scale point-cloud visualization through localized textured surface reconstruction,” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 20, no. 9. IEEE, pp. 1280–1292, 2014.","short":"M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, M. Wimmer, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 1280–1292.","ista":"Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. 2014. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 20(9), 1280–1292.","chicago":"Arikan, Murat, Reinhold Preiner, Claus Scheiblauer, Stefan Jeschke, and Michael Wimmer. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/TVCG.2014.2312011\">https://doi.org/10.1109/TVCG.2014.2312011</a>.","apa":"Arikan, M., Preiner, R., Scheiblauer, C., Jeschke, S., &#38; Wimmer, M. (2014). Large-scale point-cloud visualization through localized textured surface reconstruction. <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE. <a href=\"https://doi.org/10.1109/TVCG.2014.2312011\">https://doi.org/10.1109/TVCG.2014.2312011</a>","mla":"Arikan, Murat, et al. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 20, no. 9, IEEE, 2014, pp. 1280–92, doi:<a href=\"https://doi.org/10.1109/TVCG.2014.2312011\">10.1109/TVCG.2014.2312011</a>."},"year":"2014","page":"1280 - 1292","oa":1,"issue":"9","date_updated":"2021-01-12T06:53:59Z","acknowledgement":"This research was supported by the Austrian Research Promotion Agency (FFG) project REPLICATE (no. 835948), the EU FP7 project HARVEST4D (no. 323567).","date_published":"2014-09-09T00:00:00Z","month":"09","intvolume":"        20","oa_version":"Submitted Version","publication":"IEEE Transactions on Visualization and Computer Graphics","doi":"10.1109/TVCG.2014.2312011","status":"public","day":"09","ddc":["000"],"date_created":"2018-12-11T11:54:39Z","volume":20},{"abstract":[{"text":"Most cryptographic security proofs require showing that two systems are indistinguishable. A central tool in such proofs is that of a game, where winning the game means provoking a certain condition, and it is shown that the two systems considered cannot be distinguished unless this condition is provoked. Upper bounding the probability of winning such a game, i.e., provoking this condition, for an arbitrary strategy is usually hard, except in the special case where the best strategy for winning such a game is known to be non-adaptive. A sufficient criterion for ensuring the optimality of non-adaptive strategies is that of conditional equivalence to a system, a notion introduced in [1]. In this paper, we show that this criterion is not necessary to ensure the optimality of non-adaptive strategies by giving two results of independent interest: 1) the optimality of non-adaptive strategies is not preserved under parallel composition; 2) in contrast, conditional equivalence is preserved under parallel composition.","lang":"eng"}],"scopus_import":1,"type":"conference","citation":{"apa":"Demay, G., Gazi, P., Maurer, U., &#38; Tackmann, B. (2014). Optimality of non-adaptive strategies: The case of parallel games. In <i>IEEE International Symposium on Information Theory</i>. Honolulu, USA: IEEE. <a href=\"https://doi.org/10.1109/ISIT.2014.6875125\">https://doi.org/10.1109/ISIT.2014.6875125</a>","mla":"Demay, Grégory, et al. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” <i>IEEE International Symposium on Information Theory</i>, 6875125, IEEE, 2014, doi:<a href=\"https://doi.org/10.1109/ISIT.2014.6875125\">10.1109/ISIT.2014.6875125</a>.","short":"G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, IEEE International Symposium on Information Theory, IEEE, 2014.","ieee":"G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Optimality of non-adaptive strategies: The case of parallel games,” in <i>IEEE International Symposium on Information Theory</i>, Honolulu, USA, 2014.","ista":"Demay G, Gazi P, Maurer U, Tackmann B. 2014. Optimality of non-adaptive strategies: The case of parallel games. IEEE International Symposium on Information Theory. IEEE International Symposium on Information Theory Proceedings, 6875125.","ama":"Demay G, Gazi P, Maurer U, Tackmann B. Optimality of non-adaptive strategies: The case of parallel games. In: <i>IEEE International Symposium on Information Theory</i>. IEEE; 2014. doi:<a href=\"https://doi.org/10.1109/ISIT.2014.6875125\">10.1109/ISIT.2014.6875125</a>","chicago":"Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” In <i>IEEE International Symposium on Information Theory</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/ISIT.2014.6875125\">https://doi.org/10.1109/ISIT.2014.6875125</a>."},"day":"01","status":"public","quality_controlled":"1","_id":"1907","date_created":"2018-12-11T11:54:39Z","publication":"IEEE International Symposium on Information Theory","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2014/299"}],"publication_status":"published","doi":"10.1109/ISIT.2014.6875125","oa_version":"Submitted Version","publisher":"IEEE","article_number":"6875125","date_published":"2014-01-01T00:00:00Z","month":"01","oa":1,"author":[{"full_name":"Demay, Grégory","last_name":"Demay","first_name":"Grégory"},{"id":"3E0BFE38-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","last_name":"Gazi","full_name":"Gazi, Peter"},{"full_name":"Maurer, Ueli","first_name":"Ueli","last_name":"Maurer"},{"first_name":"Björn","last_name":"Tackmann","full_name":"Tackmann, Björn"}],"title":"Optimality of non-adaptive strategies: The case of parallel games","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:53:59Z","department":[{"_id":"KrPi"}],"publist_id":"5188","conference":{"location":"Honolulu, USA","name":"IEEE International Symposium on Information Theory Proceedings","end_date":"2014-07-04","start_date":"2014-06-29"},"year":"2014","language":[{"iso":"eng"}]},{"oa_version":"Submitted Version","ec_funded":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.0737"}],"doi":"10.1534/genetics.113.160705","publication":"Genetics","date_created":"2018-12-11T11:54:39Z","day":"01","status":"public","volume":196,"year":"2014","page":"1167 - 1183","date_updated":"2021-01-12T06:53:59Z","issue":"4","oa":1,"intvolume":"       196","month":"04","date_published":"2014-04-01T00:00:00Z","project":[{"name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7"}],"publication_status":"published","_id":"1908","quality_controlled":"1","citation":{"ieee":"D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations with linear chromosomes,” <i>Genetics</i>, vol. 196, no. 4. Genetics Society of America, pp. 1167–1183, 2014.","short":"D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183.","ista":"Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 196(4), 1167–1183.","ama":"Weissman D, Hallatschek O. The rate of adaptation in large sexual populations with linear chromosomes. <i>Genetics</i>. 2014;196(4):1167-1183. doi:<a href=\"https://doi.org/10.1534/genetics.113.160705\">10.1534/genetics.113.160705</a>","chicago":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” <i>Genetics</i>. Genetics Society of America, 2014. <a href=\"https://doi.org/10.1534/genetics.113.160705\">https://doi.org/10.1534/genetics.113.160705</a>.","apa":"Weissman, D., &#38; Hallatschek, O. (2014). The rate of adaptation in large sexual populations with linear chromosomes. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.113.160705\">https://doi.org/10.1534/genetics.113.160705</a>","mla":"Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” <i>Genetics</i>, vol. 196, no. 4, Genetics Society of America, 2014, pp. 1167–83, doi:<a href=\"https://doi.org/10.1534/genetics.113.160705\">10.1534/genetics.113.160705</a>."},"type":"journal_article","abstract":[{"lang":"eng","text":"In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations."}],"scopus_import":1,"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"publist_id":"5187","author":[{"full_name":"Weissman, Daniel","last_name":"Weissman","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel"},{"first_name":"Oskar","last_name":"Hallatschek","full_name":"Hallatschek, Oskar"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"The rate of adaptation in large sexual populations with linear chromosomes","publisher":"Genetics Society of America"},{"date_updated":"2021-01-12T06:54:00Z","issue":"3","oa":1,"month":"06","intvolume":"        28","date_published":"2014-06-01T00:00:00Z","acknowledgement":"Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1","year":"2014","page":"693 - 701","date_created":"2018-12-11T11:54:40Z","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)"},"ddc":["570"],"day":"01","status":"public","volume":28,"oa_version":"Published Version","doi":"10.1111/1365-2435.12207","publication":"Functional Ecology","file":[{"file_name":"IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf","date_created":"2018-12-12T10:15:45Z","date_updated":"2020-07-14T12:45:20Z","creator":"system","file_size":536154,"content_type":"application/pdf","file_id":"5167","relation":"main_file","access_level":"open_access","checksum":"3cbe8623174709a8ceec2103246f8fe0"}],"title":"The fitness costs of adaptation via phenotypic plasticity and maternal effects","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Ezard, Thomas","last_name":"Ezard","first_name":"Thomas"},{"first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","full_name":"Prizak, Roshan"},{"last_name":"Hoyle","first_name":"Rebecca","full_name":"Hoyle, Rebecca"}],"has_accepted_license":"1","publisher":"Wiley-Blackwell","language":[{"iso":"eng"}],"pubrep_id":"419","publist_id":"5186","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"_id":"1909","citation":{"chicago":"Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” <i>Functional Ecology</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/1365-2435.12207\">https://doi.org/10.1111/1365-2435.12207</a>.","short":"T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701.","ista":"Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701.","ieee":"T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” <i>Functional Ecology</i>, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014.","ama":"Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. <i>Functional Ecology</i>. 2014;28(3):693-701. doi:<a href=\"https://doi.org/10.1111/1365-2435.12207\">10.1111/1365-2435.12207</a>","mla":"Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” <i>Functional Ecology</i>, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:<a href=\"https://doi.org/10.1111/1365-2435.12207\">10.1111/1365-2435.12207</a>.","apa":"Ezard, T., Prizak, R., &#38; Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. <i>Functional Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/1365-2435.12207\">https://doi.org/10.1111/1365-2435.12207</a>"},"file_date_updated":"2020-07-14T12:45:20Z","type":"journal_article","scopus_import":1,"abstract":[{"text":"Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution.","lang":"eng"}],"publication_status":"published"},{"language":[{"iso":"eng"}],"year":"2014","page":"553 - 560","department":[{"_id":"MiSi"}],"publist_id":"5185","date_updated":"2021-01-12T06:54:01Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Sabine","last_name":"Konradi","full_name":"Konradi, Sabine"},{"full_name":"Yasmin, Nighat","first_name":"Nighat","last_name":"Yasmin"},{"last_name":"Haslwanter","first_name":"Denise","full_name":"Haslwanter, Denise"},{"first_name":"Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","last_name":"Weber","full_name":"Weber, Michele"},{"last_name":"Gesslbauer","first_name":"Bernd","full_name":"Gesslbauer, Bernd"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"last_name":"Strobl","first_name":"Herbert","full_name":"Strobl, Herbert"}],"title":"Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2","issue":"2","date_published":"2014-02-01T00:00:00Z","intvolume":"        44","month":"02","acknowledgement":"FWF. Grant Number: P22058-B20","publisher":"Wiley-Blackwell","oa_version":"None","publication":"European Journal of Immunology","publication_status":"published","doi":"10.1002/eji.201343681","date_created":"2018-12-11T11:54:40Z","_id":"1910","day":"01","status":"public","volume":44,"citation":{"short":"S. Konradi, N. Yasmin, D. Haslwanter, M. Weber, B. Gesslbauer, M.K. Sixt, H. Strobl, European Journal of Immunology 44 (2014) 553–560.","ista":"Konradi S, Yasmin N, Haslwanter D, Weber M, Gesslbauer B, Sixt MK, Strobl H. 2014. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 44(2), 553–560.","ieee":"S. Konradi <i>et al.</i>, “Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2,” <i>European Journal of Immunology</i>, vol. 44, no. 2. Wiley-Blackwell, pp. 553–560, 2014.","ama":"Konradi S, Yasmin N, Haslwanter D, et al. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. <i>European Journal of Immunology</i>. 2014;44(2):553-560. doi:<a href=\"https://doi.org/10.1002/eji.201343681\">10.1002/eji.201343681</a>","chicago":"Konradi, Sabine, Nighat Yasmin, Denise Haslwanter, Michele Weber, Bernd Gesslbauer, Michael K Sixt, and Herbert Strobl. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” <i>European Journal of Immunology</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/eji.201343681\">https://doi.org/10.1002/eji.201343681</a>.","apa":"Konradi, S., Yasmin, N., Haslwanter, D., Weber, M., Gesslbauer, B., Sixt, M. K., &#38; Strobl, H. (2014). Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. <i>European Journal of Immunology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/eji.201343681\">https://doi.org/10.1002/eji.201343681</a>","mla":"Konradi, Sabine, et al. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” <i>European Journal of Immunology</i>, vol. 44, no. 2, Wiley-Blackwell, 2014, pp. 553–60, doi:<a href=\"https://doi.org/10.1002/eji.201343681\">10.1002/eji.201343681</a>."},"abstract":[{"lang":"eng","text":"angerhans cells (LCs) are a unique subset of dendritic cells (DCs) that express epithelial adhesion molecules, allowing them to form contacts with epithelial cells and reside in epidermal/epithelial tissues. The dynamic regulation of epithelial adhesion plays a decisive role in the life cycle of LCs. It controls whether LCs remain immature and sessile within the epidermis or mature and egress to initiate immune responses. So far, the molecular machinery regulating epithelial adhesion molecules during LC maturation remains elusive. Here, we generated pure populations of immature human LCs in vitro to systematically probe for gene-expression changes during LC maturation. LCs down-regulate a set of epithelial genes including E-cadherin, while they upregulate the mesenchymal marker N-cadherin known to facilitate cell migration. In addition, N-cadherin is constitutively expressed by monocyte-derived DCs known to exhibit characteristics of both inflammatory-type and interstitial/dermal DCs. Moreover, the transcription factors ZEB1 and ZEB2 (ZEB is zinc-finger E-box-binding homeobox) are upregulated in migratory LCs. ZEB1 and ZEB2 have been shown to induce epithelial-to-mesenchymal transition (EMT) and invasive behavior in cancer cells undergoing metastasis. Our results provide the first hint that the molecular EMT machinery might facilitate LC mobilization. Moreover, our study suggests that N-cadherin plays a role during DC migration."}],"scopus_import":1,"type":"journal_article"},{"date_updated":"2021-01-12T06:54:01Z","issue":"1","author":[{"last_name":"Engström","first_name":"Alexander","full_name":"Engström, Alexander"},{"id":"46870C74-F248-11E8-B48F-1D18A9856A87","first_name":"Patrik","last_name":"Noren","full_name":"Noren, Patrik"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Tverberg's Theorem and Graph Coloring","intvolume":"        51","month":"01","date_published":"2014-01-01T00:00:00Z","acknowledgement":"Patrik Norén gratefully acknowledges support from the Wallenberg foundation","publisher":"Springer","language":[{"iso":"eng"}],"year":"2014","page":"207 - 220","department":[{"_id":"CaUh"}],"publist_id":"5183","_id":"1911","date_created":"2018-12-11T11:54:40Z","status":"public","day":"01","citation":{"mla":"Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” <i>Discrete &#38; Computational Geometry</i>, vol. 51, no. 1, Springer, 2014, pp. 207–20, doi:<a href=\"https://doi.org/10.1007/s00454-013-9556-3\">10.1007/s00454-013-9556-3</a>.","apa":"Engström, A., &#38; Noren, P. (2014). Tverberg’s Theorem and Graph Coloring. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-013-9556-3\">https://doi.org/10.1007/s00454-013-9556-3</a>","chicago":"Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00454-013-9556-3\">https://doi.org/10.1007/s00454-013-9556-3</a>.","ista":"Engström A, Noren P. 2014. Tverberg’s Theorem and Graph Coloring. Discrete &#38; Computational Geometry. 51(1), 207–220.","short":"A. Engström, P. Noren, Discrete &#38; Computational Geometry 51 (2014) 207–220.","ieee":"A. Engström and P. Noren, “Tverberg’s Theorem and Graph Coloring,” <i>Discrete &#38; Computational Geometry</i>, vol. 51, no. 1. Springer, pp. 207–220, 2014.","ama":"Engström A, Noren P. Tverberg’s Theorem and Graph Coloring. <i>Discrete &#38; Computational Geometry</i>. 2014;51(1):207-220. doi:<a href=\"https://doi.org/10.1007/s00454-013-9556-3\">10.1007/s00454-013-9556-3</a>"},"volume":51,"type":"journal_article","scopus_import":1,"abstract":[{"text":"The topological Tverberg theorem has been generalized in several directions by setting extra restrictions on the Tverberg partitions. Restricted Tverberg partitions, defined by the idea that certain points cannot be in the same part, are encoded with graphs. When two points are adjacent in the graph, they are not in the same part. If the restrictions are too harsh, then the topological Tverberg theorem fails. The colored Tverberg theorem corresponds to graphs constructed as disjoint unions of small complete graphs. Hell studied the case of paths and cycles. In graph theory these partitions are usually viewed as graph colorings. As explored by Aharoni, Haxell, Meshulam and others there are fundamental connections between several notions of graph colorings and topological combinatorics. For ordinary graph colorings it is enough to require that the number of colors q satisfy q&gt;Δ, where Δ is the maximal degree of the graph. It was proven by the first author using equivariant topology that if q&gt;Δ 2 then the topological Tverberg theorem still works. It is conjectured that q&gt;KΔ is also enough for some constant K, and in this paper we prove a fixed-parameter version of that conjecture. The required topological connectivity results are proven with shellability, which also strengthens some previous partial results where the topological connectivity was proven with the nerve lemma.","lang":"eng"}],"oa_version":"None","doi":"10.1007/s00454-013-9556-3","publication_status":"published","publication":"Discrete & Computational Geometry"},{"page":"774 - 783","external_id":{"pmid":["25535919"]},"year":"2014","acknowledgement":"We are grateful to members of the C.-P.H. lab, M. Concha, D. Siekhaus, and J. Vermot for comments on the manuscript and to M. Furutani-Seiki for sharing reagents. This work was supported by the Institute of Science and Technology Austria and an Alexander von Humboldt Foundation fellowship to J.C.","month":"12","intvolume":"        31","date_published":"2014-12-22T00:00:00Z","issue":"6","oa":1,"date_updated":"2023-09-07T12:05:08Z","doi":"10.1016/j.devcel.2014.11.003","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/25535919","open_access":"1"}],"publication":"Developmental Cell","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"961"}]},"pmid":1,"volume":31,"status":"public","day":"22","date_created":"2018-12-11T11:54:41Z","publist_id":"5182","department":[{"_id":"CaHe"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Cell Press","title":"The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ","author":[{"last_name":"Compagnon","id":"2E3E0988-F248-11E8-B48F-1D18A9856A87","first_name":"Julien","full_name":"Compagnon, Julien"},{"full_name":"Barone, Vanessa","first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367","last_name":"Barone"},{"first_name":"Srivarsha","last_name":"Rajshekar","full_name":"Rajshekar, Srivarsha"},{"full_name":"Kottmeier, Rita","first_name":"Rita","last_name":"Kottmeier"},{"full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha","first_name":"Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Behrndt, Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","type":"journal_article","abstract":[{"lang":"eng","text":"Kupffer's vesicle (KV) is the zebrafish organ of laterality, patterning the embryo along its left-right (LR) axis. Regional differences in cell shape within the lumen-lining KV epithelium are essential for its LR patterning function. However, the processes by which KV cells acquire their characteristic shapes are largely unknown. Here, we show that the notochord induces regional differences in cell shape within KV by triggering extracellular matrix (ECM) accumulation adjacent to anterior-dorsal (AD) regions of KV. This localized ECM deposition restricts apical expansion of lumen-lining epithelial cells in AD regions of KV during lumen growth. Our study provides mechanistic insight into the processes by which KV translates global embryonic patterning into regional cell shape differences required for its LR symmetry-breaking function."}],"scopus_import":"1","citation":{"apa":"Compagnon, J., Barone, V., Rajshekar, S., Kottmeier, R., Pranjic-Ferscha, K., Behrndt, M., &#38; Heisenberg, C.-P. J. (2014). The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2014.11.003\">https://doi.org/10.1016/j.devcel.2014.11.003</a>","mla":"Compagnon, Julien, et al. “The Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish Laterality Organ.” <i>Developmental Cell</i>, vol. 31, no. 6, Cell Press, 2014, pp. 774–83, doi:<a href=\"https://doi.org/10.1016/j.devcel.2014.11.003\">10.1016/j.devcel.2014.11.003</a>.","ista":"Compagnon J, Barone V, Rajshekar S, Kottmeier R, Pranjic-Ferscha K, Behrndt M, Heisenberg C-PJ. 2014. The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental Cell. 31(6), 774–783.","ieee":"J. Compagnon <i>et al.</i>, “The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ,” <i>Developmental Cell</i>, vol. 31, no. 6. Cell Press, pp. 774–783, 2014.","short":"J. Compagnon, V. Barone, S. Rajshekar, R. Kottmeier, K. Pranjic-Ferscha, M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 31 (2014) 774–783.","ama":"Compagnon J, Barone V, Rajshekar S, et al. The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. <i>Developmental Cell</i>. 2014;31(6):774-783. doi:<a href=\"https://doi.org/10.1016/j.devcel.2014.11.003\">10.1016/j.devcel.2014.11.003</a>","chicago":"Compagnon, Julien, Vanessa Barone, Srivarsha Rajshekar, Rita Kottmeier, Kornelija Pranjic-Ferscha, Martin Behrndt, and Carl-Philipp J Heisenberg. “The Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish Laterality Organ.” <i>Developmental Cell</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.devcel.2014.11.003\">https://doi.org/10.1016/j.devcel.2014.11.003</a>."},"quality_controlled":"1","_id":"1912"},{"type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"Deposits of phosphorylated tau protein and convergence of pathology in the hippocampus are the hallmarks of neurodegenerative tauopathies. Thus we aimed to evaluate whether regional and cellular vulnerability patterns in the hippocampus distinguish tauopathies or are influenced by their concomitant presence. Methods: We created a heat map of phospho-tau (AT8) immunoreactivity patterns in 24 hippocampal subregions/layers in individuals with Alzheimer's disease (AD)-related neurofibrillary degeneration (n = 40), Pick's disease (n = 8), progressive supranuclear palsy (n = 7), corticobasal degeneration (n = 6), argyrophilic grain disease (AGD, n = 18), globular glial tauopathy (n = 5), and tau-astrogliopathy of the elderly (n = 10). AT8 immunoreactivity patterns were compared by mathematical analysis. Results: Our study reveals disease-specific hot spots and regional selective vulnerability for these disorders. The pattern of hippocampal AD-related tau pathology is strongly influenced by concomitant AGD. Mathematical analysis reveals that hippocampal involvement in primary tauopathies is distinguishable from early-stage AD-related neurofibrillary degeneration. Conclusion: Our data demonstrate disease-specific AT8 immunoreactivity patterns and hot spots in the hippocampus even in tauopathies, which primarily do not affect the hippocampus. These hot spots can be shifted to other regions by the co-occurrence of tauopathies like AGD. Our observations support the notion that globular glial tauopathies and tau-astrogliopathy of the elderly are distinct entities."}],"publication_identifier":{"issn":["1420-8008"]},"citation":{"chicago":"Milenković, Ivan, Tatjana Petrov, and Gábor Kovács. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.” <i>Dementia and Geriatric Cognitive Disorders</i>. Karger Publishers, 2014. <a href=\"https://doi.org/10.1159/000365548\">https://doi.org/10.1159/000365548</a>.","ama":"Milenković I, Petrov T, Kovács G. Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. <i>Dementia and Geriatric Cognitive Disorders</i>. 2014;38(5-6):375-388. doi:<a href=\"https://doi.org/10.1159/000365548\">10.1159/000365548</a>","short":"I. Milenković, T. Petrov, G. Kovács, Dementia and Geriatric Cognitive Disorders 38 (2014) 375–388.","ieee":"I. Milenković, T. Petrov, and G. Kovács, “Patterns of hippocampal tau pathology differentiate neurodegenerative dementias,” <i>Dementia and Geriatric Cognitive Disorders</i>, vol. 38, no. 5–6. Karger Publishers, pp. 375–388, 2014.","ista":"Milenković I, Petrov T, Kovács G. 2014. Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders. 38(5–6), 375–388.","mla":"Milenković, Ivan, et al. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.” <i>Dementia and Geriatric Cognitive Disorders</i>, vol. 38, no. 5–6, Karger Publishers, 2014, pp. 375–88, doi:<a href=\"https://doi.org/10.1159/000365548\">10.1159/000365548</a>.","apa":"Milenković, I., Petrov, T., &#38; Kovács, G. (2014). Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. <i>Dementia and Geriatric Cognitive Disorders</i>. Karger Publishers. <a href=\"https://doi.org/10.1159/000365548\">https://doi.org/10.1159/000365548</a>"},"quality_controlled":"1","_id":"1913","publication_status":"published","publisher":"Karger Publishers","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Milenković, Ivan","last_name":"Milenković","first_name":"Ivan"},{"orcid":"0000-0002-9041-0905","last_name":"Petrov","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","full_name":"Petrov, Tatjana"},{"full_name":"Kovács, Gábor","first_name":"Gábor","last_name":"Kovács"}],"title":"Patterns of hippocampal tau pathology differentiate neurodegenerative dementias","publist_id":"5181","department":[{"_id":"CaGu"}],"article_processing_charge":"No","article_type":"original","language":[{"iso":"eng"}],"pmid":1,"volume":38,"day":"07","status":"public","date_created":"2018-12-11T11:54:41Z","main_file_link":[{"url":"https://kops.uni-konstanz.de/bitstream/123456789/42127/1/Milenkovic_2-17ivylo2up0798.pdf","open_access":"1"}],"doi":"10.1159/000365548","publication":"Dementia and Geriatric Cognitive Disorders","oa_version":"Published Version","acknowledgement":"This study was supported by the European Commission’s 7th Framework Programme under GA No. 278486, ‘DEVELAGE’.","intvolume":"        38","month":"11","date_published":"2014-11-07T00:00:00Z","issue":"5-6","oa":1,"date_updated":"2023-10-17T10:21:17Z","external_id":{"pmid":["25195847"]},"page":"375 - 388","year":"2014"},{"year":"2014","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"publist_id":"5180","page":"R27 - R29","author":[{"full_name":"Sauer, Michael","first_name":"Michael","last_name":"Sauer"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Plant biology: Gatekeepers of the road to protein perdition","issue":"1","date_updated":"2021-01-12T06:54:02Z","publisher":"Cell Press","date_published":"2014-01-06T00:00:00Z","intvolume":"        24","month":"01","oa_version":"None","publication":"Current Biology","publication_status":"published","doi":"10.1016/j.cub.2013.11.019","day":"06","status":"public","quality_controlled":"1","_id":"1914","date_created":"2018-12-11T11:54:41Z","scopus_import":1,"abstract":[{"lang":"eng","text":"Targeting membrane proteins for degradation requires the sequential action of ESCRT sub-complexes ESCRT-0 to ESCRT-III. Although this machinery is generally conserved among kingdoms, plants lack the essential ESCRT-0 components. A new report closes this gap by identifying a novel protein family that substitutes for ESCRT-0 function in plants."}],"type":"journal_article","volume":24,"citation":{"ama":"Sauer M, Friml J. Plant biology: Gatekeepers of the road to protein perdition. <i>Current Biology</i>. 2014;24(1):R27-R29. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.11.019\">10.1016/j.cub.2013.11.019</a>","short":"M. Sauer, J. Friml, Current Biology 24 (2014) R27–R29.","ista":"Sauer M, Friml J. 2014. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 24(1), R27–R29.","ieee":"M. Sauer and J. Friml, “Plant biology: Gatekeepers of the road to protein perdition,” <i>Current Biology</i>, vol. 24, no. 1. Cell Press, pp. R27–R29, 2014.","chicago":"Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” <i>Current Biology</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cub.2013.11.019\">https://doi.org/10.1016/j.cub.2013.11.019</a>.","apa":"Sauer, M., &#38; Friml, J. (2014). Plant biology: Gatekeepers of the road to protein perdition. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.11.019\">https://doi.org/10.1016/j.cub.2013.11.019</a>","mla":"Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” <i>Current Biology</i>, vol. 24, no. 1, Cell Press, 2014, pp. R27–29, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.11.019\">10.1016/j.cub.2013.11.019</a>."}},{"doi":"10.1042/BST20130269","publication":"Biochemical Society Transactions","ec_funded":1,"oa_version":"None","pmid":1,"volume":42,"date_created":"2018-12-11T11:54:41Z","day":"01","status":"public","external_id":{"pmid":["24450654"]},"page":"212 - 218","year":"2014","month":"02","intvolume":"        42","date_published":"2014-02-01T00:00:00Z","acknowledgement":"This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], Central European Institute of Technology (CEITEC) [grant number CZ.1.05/1.1.00/02.0068], European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czec","date_updated":"2025-05-07T11:12:31Z","issue":"1","project":[{"call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","publication_identifier":{"eissn":["1470-8752"],"issn":["0300-5127"]},"citation":{"chicago":"Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” <i>Biochemical Society Transactions</i>. Portland Press, 2014. <a href=\"https://doi.org/10.1042/BST20130269\">https://doi.org/10.1042/BST20130269</a>.","ama":"Chen X, Friml J. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. <i>Biochemical Society Transactions</i>. 2014;42(1):212-218. doi:<a href=\"https://doi.org/10.1042/BST20130269\">10.1042/BST20130269</a>","ista":"Chen X, Friml J. 2014. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 42(1), 212–218.","ieee":"X. Chen and J. Friml, “Rho-GTPase-regulated vesicle trafficking in plant cell polarity,” <i>Biochemical Society Transactions</i>, vol. 42, no. 1. Portland Press, pp. 212–218, 2014.","short":"X. Chen, J. Friml, Biochemical Society Transactions 42 (2014) 212–218.","mla":"Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” <i>Biochemical Society Transactions</i>, vol. 42, no. 1, Portland Press, 2014, pp. 212–18, doi:<a href=\"https://doi.org/10.1042/BST20130269\">10.1042/BST20130269</a>.","apa":"Chen, X., &#38; Friml, J. (2014). Rho-GTPase-regulated vesicle trafficking in plant cell polarity. <i>Biochemical Society Transactions</i>. Portland Press. <a href=\"https://doi.org/10.1042/BST20130269\">https://doi.org/10.1042/BST20130269</a>"},"type":"journal_article","scopus_import":"1","abstract":[{"lang":"eng","text":"ROPs (Rho of plants) belong to a large family of plant-specific Rho-like small GTPases that function as essential molecular switches to control diverse cellular processes including cytoskeleton organization, cell polarization, cytokinesis, cell differentiation and vesicle trafficking. Although the machineries of vesicle trafficking and cell polarity in plants have been individually well addressed, how ROPs co-ordinate those processes is still largely unclear. Recent progress has been made towards an understanding of the coordination of ROP signalling and trafficking of PIN (PINFORMED) transporters for the plant hormone auxin in both root and leaf pavement cells. PIN transporters constantly shuttle between the endosomal compartments and the polar plasma membrane domains, therefore the modulation of PIN-dependent auxin transport between cells is a main developmental output of ROP-regulated vesicle trafficking. The present review focuses on these cellular mechanisms, especially the integration of ROP-based vesicle trafficking and plant cell polarity."}],"_id":"1915","quality_controlled":"1","article_processing_charge":"No","publist_id":"5179","department":[{"_id":"JiFr"}],"language":[{"iso":"eng"}],"article_type":"original","publisher":"Portland Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Rho-GTPase-regulated vesicle trafficking in plant cell polarity","author":[{"last_name":"Chen","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Xu"},{"full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"}]}]