[{"_id":"2476","year":"2012","title":"Virus-mediated swapping of zolpidem-insensitive with zolpidem-sensitive GABA A receptors in cortical pyramidal cells","status":"public","publication_status":"published","intvolume":" 590","publisher":"Wiley-Blackwell","author":[{"first_name":"Máté","last_name":"Sümegi","full_name":"Sümegi, Máté"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"full_name":"Matsui, Ko","last_name":"Matsui","first_name":"Ko"},{"last_name":"Lörincz","first_name":"Andrea","full_name":"Lörincz, Andrea"},{"last_name":"Eyre","first_name":"Mark","full_name":"Eyre, Mark D"},{"first_name":"Zoltán","last_name":"Nusser","full_name":"Nusser, Zoltán"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Ryuichi Shigemoto"}],"date_updated":"2021-01-12T06:57:43Z","date_created":"2018-12-11T11:57:53Z","volume":590,"type":"journal_article","abstract":[{"text":"Recently developed pharmacogenetic and optogenetic approaches, with their own advantages and disadvantages, have become indispensable tools in modern neuroscience. Here, we employed a previously described knock-in mouse line (GABA ARγ2 77Ilox) in which the γ2 subunit of the GABA A receptor (GABA AR) was mutated to become zolpidem insensitive (γ2 77I) and used viral vectors to swap γ2 77I with wild-type, zolpidem-sensitive γ2 subunits (γ2 77F). The verification of unaltered density and subcellular distribution of the virally introduced γ2 subunits requires their selective labelling. For this we generated six N- and six C-terminal-tagged γ2 subunits, with which cortical cultures of GABA ARγ2 -/- mice were transduced using lentiviruses. We found that the N-terminal AU1 tag resulted in excellent immunodetection and unimpaired synaptic localization. Unaltered kinetic properties of the AU1-tagged γ2 ( AU1γ2 77F) channels were demonstrated with whole-cell patch-clamp recordings of spontaneous IPSCs from cultured cells. Next, we carried out stereotaxic injections of lenti- and adeno-associated viruses containing Cre-recombinase and the AU1γ2 77F subunit (Cre-2A- AU1γ2 77F) into the neocortex of GABA ARγ2 77Ilox mice. Light microscopic immunofluorescence and electron microscopic freeze-fracture replica immunogold labelling demonstrated the efficient immunodetection of the AU1 tag and the normal enrichment of the AU1γ2 77F subunits in perisomatic GABAergic synapses. In line with this, miniature and action potential-evoked IPSCs whole-cell recorded from transduced cells had unaltered amplitudes, kinetics and restored zolpidem sensitivity. Our results obtained with a wide range of structural and functional verification methods reveal unaltered subcellular distributions and functional properties of γ2 77I and AU1γ2 77F GABA ARs in cortical pyramidal cells. This transgenic-viral pharmacogenetic approach has the advantage that it does not require any extrinsic protein that might endow some unforeseen alterations of the genetically modified cells. In addition, this virus-based approach opens up the possibility of modifying multiple cell types in distinct brain regions and performing alternative recombination-based intersectional genetic manipulations.","lang":"eng"}],"publist_id":"4425","issue":"7","extern":1,"publication":"Journal of Physiology","citation":{"ama":"Sümegi M, Fukazawa Y, Matsui K, et al. Virus-mediated swapping of zolpidem-insensitive with zolpidem-sensitive GABA A receptors in cortical pyramidal cells. Journal of Physiology. 2012;590(7):1517-1534. doi:10.1113/jphysiol.2012.227538","ista":"Sümegi M, Fukazawa Y, Matsui K, Lörincz A, Eyre M, Nusser Z, Shigemoto R. 2012. Virus-mediated swapping of zolpidem-insensitive with zolpidem-sensitive GABA A receptors in cortical pyramidal cells. Journal of Physiology. 590(7), 1517–1534.","ieee":"M. Sümegi et al., “Virus-mediated swapping of zolpidem-insensitive with zolpidem-sensitive GABA A receptors in cortical pyramidal cells,” Journal of Physiology, vol. 590, no. 7. Wiley-Blackwell, pp. 1517–1534, 2012.","apa":"Sümegi, M., Fukazawa, Y., Matsui, K., Lörincz, A., Eyre, M., Nusser, Z., & Shigemoto, R. (2012). Virus-mediated swapping of zolpidem-insensitive with zolpidem-sensitive GABA A receptors in cortical pyramidal cells. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2012.227538","mla":"Sümegi, Máté, et al. “Virus-Mediated Swapping of Zolpidem-Insensitive with Zolpidem-Sensitive GABA A Receptors in Cortical Pyramidal Cells.” Journal of Physiology, vol. 590, no. 7, Wiley-Blackwell, 2012, pp. 1517–34, doi:10.1113/jphysiol.2012.227538.","short":"M. Sümegi, Y. Fukazawa, K. Matsui, A. Lörincz, M. Eyre, Z. Nusser, R. Shigemoto, Journal of Physiology 590 (2012) 1517–1534.","chicago":"Sümegi, Máté, Yugo Fukazawa, Ko Matsui, Andrea Lörincz, Mark Eyre, Zoltán Nusser, and Ryuichi Shigemoto. “Virus-Mediated Swapping of Zolpidem-Insensitive with Zolpidem-Sensitive GABA A Receptors in Cortical Pyramidal Cells.” Journal of Physiology. Wiley-Blackwell, 2012. https://doi.org/10.1113/jphysiol.2012.227538."},"quality_controlled":0,"page":"1517 - 1534","date_published":"2012-04-07T00:00:00Z","doi":"10.1113/jphysiol.2012.227538","day":"07","month":"04"},{"volume":7,"date_created":"2018-12-11T11:57:53Z","date_updated":"2021-01-12T06:57:42Z","author":[{"full_name":"Saito, Yuhki","last_name":"Saito","first_name":"Yuhki"},{"full_name":"Inoue, Tsuyoshi","last_name":"Inoue","first_name":"Tsuyoshi"},{"full_name":"Zhu, Gang","last_name":"Zhu","first_name":"Gang"},{"full_name":"Kimura, Naoki","last_name":"Kimura","first_name":"Naoki"},{"last_name":"Okada","first_name":"Motohiro","full_name":"Okada, Motohiro"},{"first_name":"Masaki","last_name":"Nishimura","full_name":"Nishimura, Masaki"},{"full_name":"Murayama, Shigeo","first_name":"Shigeo","last_name":"Murayama"},{"last_name":"Kaneko","first_name":"Sunao","full_name":"Kaneko, Sunao"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Ryuichi Shigemoto"},{"full_name":"Imoto, Keiji","first_name":"Keiji","last_name":"Imoto"},{"full_name":"Suzuki, Toshiharu","first_name":"Toshiharu","last_name":"Suzuki"}],"intvolume":" 7","publisher":"BioMed Central","status":"public","publication_status":"published","title":"Hyperpolarization-activated cyclic nucleotide gated channels: A potential molecular link between epileptic seizures and Aβ generation in Alzheimer's disease","year":"2012","_id":"2475","extern":1,"publist_id":"4426","issue":"1","abstract":[{"text":"Background: One of the best-characterized causative factors of Alzheimer's disease (AD) is the generation of amyloid-β peptide (Aβ). AD subjects are at high risk of epileptic seizures accompanied by aberrant neuronal excitability, which in itself enhances Aβ generation. However, the molecular linkage between epileptic seizures and Aβ generation in AD remains unclear. Results: X11 and X11-like (X11L) gene knockout mice suffered from epileptic seizures, along with a malfunction of hyperpolarization-activated cyclic nucleotide gated (HCN) channels. Genetic ablation of HCN1 in mice and HCN1 channel blockage in cultured Neuro2a (N2a) cells enhanced Aβ generation. Interestingly, HCN1 levels dramatically decreased in the temporal lobe of cynomolgus monkeys (Macaca fascicularis) during aging and were significantly diminished in the temporal lobe of sporadic AD patients. Conclusion: Because HCN1 associates with amyloid-β precursor protein (APP) and X11/X11L in the brain, genetic deficiency of X11/X11L may induce aberrant HCN1 distribution along with epilepsy. Moreover, the reduction in HCN1 levels in aged primates may contribute to augmented Aβ generation. Taken together, HCN1 is proposed to play an important role in the molecular linkage between epileptic seizures and Aβ generation, and in the aggravation of sporadic AD.","lang":"eng"}],"type":"journal_article","date_published":"2012-10-03T00:00:00Z","doi":"10.1186/1750-1326-7-50","quality_controlled":0,"citation":{"chicago":"Saito, Yuhki, Tsuyoshi Inoue, Gang Zhu, Naoki Kimura, Motohiro Okada, Masaki Nishimura, Shigeo Murayama, et al. “Hyperpolarization-Activated Cyclic Nucleotide Gated Channels: A Potential Molecular Link between Epileptic Seizures and Aβ Generation in Alzheimer’s Disease.” Molecular Neurodegeneration. BioMed Central, 2012. https://doi.org/10.1186/1750-1326-7-50.","short":"Y. Saito, T. Inoue, G. Zhu, N. Kimura, M. Okada, M. Nishimura, S. Murayama, S. Kaneko, R. Shigemoto, K. Imoto, T. Suzuki, Molecular Neurodegeneration 7 (2012).","mla":"Saito, Yuhki, et al. “Hyperpolarization-Activated Cyclic Nucleotide Gated Channels: A Potential Molecular Link between Epileptic Seizures and Aβ Generation in Alzheimer’s Disease.” Molecular Neurodegeneration, vol. 7, no. 1, BioMed Central, 2012, doi:10.1186/1750-1326-7-50.","apa":"Saito, Y., Inoue, T., Zhu, G., Kimura, N., Okada, M., Nishimura, M., … Suzuki, T. (2012). Hyperpolarization-activated cyclic nucleotide gated channels: A potential molecular link between epileptic seizures and Aβ generation in Alzheimer’s disease. Molecular Neurodegeneration. BioMed Central. https://doi.org/10.1186/1750-1326-7-50","ieee":"Y. Saito et al., “Hyperpolarization-activated cyclic nucleotide gated channels: A potential molecular link between epileptic seizures and Aβ generation in Alzheimer’s disease,” Molecular Neurodegeneration, vol. 7, no. 1. BioMed Central, 2012.","ista":"Saito Y, Inoue T, Zhu G, Kimura N, Okada M, Nishimura M, Murayama S, Kaneko S, Shigemoto R, Imoto K, Suzuki T. 2012. Hyperpolarization-activated cyclic nucleotide gated channels: A potential molecular link between epileptic seizures and Aβ generation in Alzheimer’s disease. Molecular Neurodegeneration. 7(1).","ama":"Saito Y, Inoue T, Zhu G, et al. Hyperpolarization-activated cyclic nucleotide gated channels: A potential molecular link between epileptic seizures and Aβ generation in Alzheimer’s disease. Molecular Neurodegeneration. 2012;7(1). doi:10.1186/1750-1326-7-50"},"publication":"Molecular Neurodegeneration","month":"10","day":"03"},{"_id":"2477","year":"2012","publisher":"National Academy of Sciences","intvolume":" 109","publication_status":"published","status":"public","title":"Application of an optogenetic byway for perturbing neuronal activity via glial photostimulation","author":[{"full_name":"Sasaki, Takuya","first_name":"Takuya","last_name":"Sasaki"},{"full_name":"Beppu, Kaoru","last_name":"Beppu","first_name":"Kaoru"},{"last_name":"Tanaka","first_name":"Kenji","full_name":"Tanaka, Kenji F"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"full_name":"Ryuichi Shigemoto","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Matsui, Ko","last_name":"Matsui","first_name":"Ko"}],"volume":109,"date_created":"2018-12-11T11:57:54Z","date_updated":"2021-01-12T06:57:43Z","type":"journal_article","issue":"50","publist_id":"4424","abstract":[{"lang":"eng","text":"Dynamic activity of glia has repeatedly been demonstrated, but if such activity is independent from neuronal activity, glia would not have any role in the information processing in the brain or in the generation of animal behavior. Evidence for neurons communicating with glia is solid, but the signaling pathway leading back from glial-to-neuronal activity was often difficult to study. Here, we introduced a transgenic mouse line in which channelrhodopsin-2, a light-gated cation channel, was expressed in astrocytes. Selective photostimulation of these astrocytes in vivo triggered neuronal activation. Using slice preparations, we show that glial photostimulation leads to release of glutamate, which was sufficient to activate AMPA receptors on Purkinje cells and to induce long-term depression of parallel fiber-to-Purkinje cell synapses through activation of metabotropic glutamate receptors. In contrast to neuronal synaptic vesicular release, glial activation likely causes preferential activation of extrasynaptic receptors that appose glial membrane. Finally, we show that neuronal activation by glial stimulation can lead to perturbation of cerebellar modulated motor behavior. These findings demonstrate that glia can modulate the tone of neuronal activity and behavior. This animal model is expected to be a potentially powerful approach to study the role of glia in brain function."}],"extern":1,"citation":{"ama":"Sasaki T, Beppu K, Tanaka K, Fukazawa Y, Shigemoto R, Matsui K. Application of an optogenetic byway for perturbing neuronal activity via glial photostimulation. PNAS. 2012;109(50):20720-20725. doi:10.1073/pnas.1213458109","apa":"Sasaki, T., Beppu, K., Tanaka, K., Fukazawa, Y., Shigemoto, R., & Matsui, K. (2012). Application of an optogenetic byway for perturbing neuronal activity via glial photostimulation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1213458109","ieee":"T. Sasaki, K. Beppu, K. Tanaka, Y. Fukazawa, R. Shigemoto, and K. Matsui, “Application of an optogenetic byway for perturbing neuronal activity via glial photostimulation,” PNAS, vol. 109, no. 50. National Academy of Sciences, pp. 20720–20725, 2012.","ista":"Sasaki T, Beppu K, Tanaka K, Fukazawa Y, Shigemoto R, Matsui K. 2012. Application of an optogenetic byway for perturbing neuronal activity via glial photostimulation. PNAS. 109(50), 20720–20725.","short":"T. Sasaki, K. Beppu, K. Tanaka, Y. Fukazawa, R. Shigemoto, K. Matsui, PNAS 109 (2012) 20720–20725.","mla":"Sasaki, Takuya, et al. “Application of an Optogenetic Byway for Perturbing Neuronal Activity via Glial Photostimulation.” PNAS, vol. 109, no. 50, National Academy of Sciences, 2012, pp. 20720–25, doi:10.1073/pnas.1213458109.","chicago":"Sasaki, Takuya, Kaoru Beppu, Kenji Tanaka, Yugo Fukazawa, Ryuichi Shigemoto, and Ko Matsui. “Application of an Optogenetic Byway for Perturbing Neuronal Activity via Glial Photostimulation.” PNAS. National Academy of Sciences, 2012. https://doi.org/10.1073/pnas.1213458109."},"publication":"PNAS","page":"20720 - 20725","quality_controlled":0,"date_published":"2012-12-11T00:00:00Z","doi":"10.1073/pnas.1213458109","day":"11","month":"12"},{"day":"22","month":"03","publication":"Neuron","citation":{"chicago":"Abrahamsson, Therese, Laurence Cathala, Ko Matsui, Ryuichi Shigemoto, and David Digregorio. “Thin Dendrites of Cerebellar Interneurons Confer Sublinear Synaptic Integration and a Gradient of Short-Term Plasticity.” Neuron. Elsevier, 2012. https://doi.org/10.1016/j.neuron.2012.01.027.","mla":"Abrahamsson, Therese, et al. “Thin Dendrites of Cerebellar Interneurons Confer Sublinear Synaptic Integration and a Gradient of Short-Term Plasticity.” Neuron, vol. 73, no. 6, Elsevier, 2012, pp. 1159–72, doi:10.1016/j.neuron.2012.01.027.","short":"T. Abrahamsson, L. Cathala, K. Matsui, R. Shigemoto, D. Digregorio, Neuron 73 (2012) 1159–1172.","ista":"Abrahamsson T, Cathala L, Matsui K, Shigemoto R, Digregorio D. 2012. Thin dendrites of cerebellar interneurons confer sublinear synaptic integration and a gradient of short-term plasticity. Neuron. 73(6), 1159–1172.","apa":"Abrahamsson, T., Cathala, L., Matsui, K., Shigemoto, R., & Digregorio, D. (2012). Thin dendrites of cerebellar interneurons confer sublinear synaptic integration and a gradient of short-term plasticity. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2012.01.027","ieee":"T. Abrahamsson, L. Cathala, K. Matsui, R. Shigemoto, and D. Digregorio, “Thin dendrites of cerebellar interneurons confer sublinear synaptic integration and a gradient of short-term plasticity,” Neuron, vol. 73, no. 6. Elsevier, pp. 1159–1172, 2012.","ama":"Abrahamsson T, Cathala L, Matsui K, Shigemoto R, Digregorio D. Thin dendrites of cerebellar interneurons confer sublinear synaptic integration and a gradient of short-term plasticity. Neuron. 2012;73(6):1159-1172. doi:10.1016/j.neuron.2012.01.027"},"quality_controlled":0,"page":"1159 - 1172","date_published":"2012-03-22T00:00:00Z","doi":"10.1016/j.neuron.2012.01.027","type":"journal_article","abstract":[{"lang":"eng","text":"Interneurons are critical for neuronal circuit function, but how their dendritic morphologies and membrane properties influence information flow within neuronal circuits is largely unknown. We studied the spatiotemporal profile of synaptic integration and short-term plasticity in dendrites of mature cerebellar stellate cells by combining two-photon guided electrical stimulation, glutamate uncaging, electron microscopy, and modeling. Synaptic activation within thin (0.4 μm) dendrites produced somatic responses that became smaller and slower with increasing distance from the soma, sublinear subthreshold input-output relationships, and a somatodendritic gradient of short-term plasticity. Unlike most studies showing that neurons employ active dendritic mechanisms, we found that passive cable properties of thin dendrites determine the sublinear integration and plasticity gradient, which both result from large dendritic depolarizations that reduce synaptic driving force. These integrative properties allow stellate cells to act as spatiotemporal filters of synaptic input patterns, thereby biasing their output in favor of sparse presynaptic activity. Stellate cells are critical sources of inhibition in the cerebellum, but how their dendrites integrate excitatory synaptic inputs is unknown. Abrahamsson et al. show that thin dendrites and passive membrane properties of SCs promote sublinear synaptic summation and distance-dependent short-term plasticity. "}],"publist_id":"4427","issue":"6","extern":1,"year":"2012","_id":"2474","status":"public","publication_status":"published","title":"Thin dendrites of cerebellar interneurons confer sublinear synaptic integration and a gradient of short-term plasticity","publisher":"Elsevier","intvolume":" 73","author":[{"last_name":"Abrahamsson","first_name":"Therese","full_name":"Abrahamsson, Therese"},{"full_name":"Cathala, Laurence","last_name":"Cathala","first_name":"Laurence"},{"full_name":"Matsui, Ko","first_name":"Ko","last_name":"Matsui"},{"full_name":"Ryuichi Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"},{"full_name":"DiGregorio, David A","first_name":"David","last_name":"Digregorio"}],"date_created":"2018-12-11T11:57:52Z","date_updated":"2021-01-12T06:57:42Z","volume":73},{"type":"journal_article","extern":1,"abstract":[{"lang":"eng","text":"We investigated the temporal and spatial expression of SK2 in the developing mouse hippocampus using molecular and biochemical techniques, quantitative immunogold electron microscopy, and electrophysiology. The mRNA encoding SK2 was expressed in the developing and adult hippocampus. Western blotting and immunohistochemistry showed that SK2 protein increased with age. This was accompanied by a shift in subcellular localization. Early in development (P5), SK2 was predominantly localized to the endoplasmic reticulum in the pyramidal cell layer. But by P30 SK2 was almost exclusively expressed in the dendrites and spines. The level of SK2 at the postsynaptic density (PSD) also increased during development. In the adult, SK2 expression on the spine plasma membrane showed a proximal-to-distal gradient. Consistent with this redistribution and gradient of SK2, the selective SK channel blocker apamin increased evoked excitatory postsynaptic potentials (EPSPs) only in CA1 pyramidal neurons from mice older than P15. However, the effect of apamin on EPSPs was not different between synapses in proximal or distal stratum radiatum or stratum lacunosum-moleculare in adult. These results show a developmental increase and gradient in SK2-containing channel surface expression that underlie their influence on neurotransmission, and that may contribute to increased memory acquisition during early development."}],"issue":"6","publist_id":"4386","status":"public","publication_status":"published","title":" Developmental profile of SK2 channel expression and function in CA1 neurons","publisher":"Wiley-Blackwell","intvolume":" 22","_id":"2515","year":"2012","date_updated":"2021-01-12T06:57:57Z","date_created":"2018-12-11T11:58:07Z","volume":22,"author":[{"full_name":"Ballesteros-Merino, Carmen","first_name":"Carmen","last_name":"Ballesteros Merino"},{"full_name":"Lin, Michael","last_name":"Lin","first_name":"Michael"},{"first_name":"Wendy","last_name":"Wu","full_name":"Wu, Wendy W"},{"last_name":"Ferrándiz Huertas","first_name":"Clotilde","full_name":"Ferrándiz-Huertas, Clotilde"},{"first_name":"María","last_name":"Cabañero","full_name":"Cabañero, María José"},{"full_name":"Watanabe, Masahiko","first_name":"Masahiko","last_name":"Watanabe"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Ryuichi Shigemoto"},{"full_name":"Maylie, James G","last_name":"Maylie","first_name":"James"},{"first_name":"John","last_name":"Adelman","full_name":"Adelman, John P"},{"last_name":"Luján","first_name":"Rafael","full_name":"Luján, Rafael"}],"month":"06","day":"01","quality_controlled":0,"page":"1467 - 1480","publication":"Hippocampus","citation":{"mla":"Ballesteros Merino, Carmen, et al. “ Developmental Profile of SK2 Channel Expression and Function in CA1 Neurons.” Hippocampus, vol. 22, no. 6, Wiley-Blackwell, 2012, pp. 1467–80, doi:10.1002/hipo.20986.","short":"C. Ballesteros Merino, M. Lin, W. Wu, C. Ferrándiz Huertas, M. Cabañero, M. Watanabe, Y. Fukazawa, R. Shigemoto, J. Maylie, J. Adelman, R. Luján, Hippocampus 22 (2012) 1467–1480.","chicago":"Ballesteros Merino, Carmen, Michael Lin, Wendy Wu, Clotilde Ferrándiz Huertas, María Cabañero, Masahiko Watanabe, Yugo Fukazawa, et al. “ Developmental Profile of SK2 Channel Expression and Function in CA1 Neurons.” Hippocampus. Wiley-Blackwell, 2012. https://doi.org/10.1002/hipo.20986.","ama":"Ballesteros Merino C, Lin M, Wu W, et al. Developmental profile of SK2 channel expression and function in CA1 neurons. Hippocampus. 2012;22(6):1467-1480. doi:10.1002/hipo.20986","ista":"Ballesteros Merino C, Lin M, Wu W, Ferrándiz Huertas C, Cabañero M, Watanabe M, Fukazawa Y, Shigemoto R, Maylie J, Adelman J, Luján R. 2012. Developmental profile of SK2 channel expression and function in CA1 neurons. Hippocampus. 22(6), 1467–1480.","apa":"Ballesteros Merino, C., Lin, M., Wu, W., Ferrándiz Huertas, C., Cabañero, M., Watanabe, M., … Luján, R. (2012). Developmental profile of SK2 channel expression and function in CA1 neurons. Hippocampus. Wiley-Blackwell. https://doi.org/10.1002/hipo.20986","ieee":"C. Ballesteros Merino et al., “ Developmental profile of SK2 channel expression and function in CA1 neurons,” Hippocampus, vol. 22, no. 6. Wiley-Blackwell, pp. 1467–1480, 2012."},"date_published":"2012-06-01T00:00:00Z","doi":"10.1002/hipo.20986"},{"day":"15","month":"02","date_published":"2012-02-15T00:00:00Z","doi":"10.1523/JNEUROSCI.5243-11.2012","quality_controlled":0,"page":"2357 - 2376","publication":"Journal of Neuroscience","citation":{"ieee":"T. Budisantoso, K. Matsui, N. Kamasawa, Y. Fukazawa, and R. Shigemoto, “Mechanisms underlying signal filtering at a multisynapse contact,” Journal of Neuroscience, vol. 32, no. 7. Society for Neuroscience, pp. 2357–2376, 2012.","apa":"Budisantoso, T., Matsui, K., Kamasawa, N., Fukazawa, Y., & Shigemoto, R. (2012). Mechanisms underlying signal filtering at a multisynapse contact. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.5243-11.2012","ista":"Budisantoso T, Matsui K, Kamasawa N, Fukazawa Y, Shigemoto R. 2012. Mechanisms underlying signal filtering at a multisynapse contact. Journal of Neuroscience. 32(7), 2357–2376.","ama":"Budisantoso T, Matsui K, Kamasawa N, Fukazawa Y, Shigemoto R. Mechanisms underlying signal filtering at a multisynapse contact. Journal of Neuroscience. 2012;32(7):2357-2376. doi:10.1523/JNEUROSCI.5243-11.2012","chicago":"Budisantoso, Timotheus, Ko Matsui, Naomi Kamasawa, Yugo Fukazawa, and Ryuichi Shigemoto. “Mechanisms Underlying Signal Filtering at a Multisynapse Contact.” Journal of Neuroscience. Society for Neuroscience, 2012. https://doi.org/10.1523/JNEUROSCI.5243-11.2012.","short":"T. Budisantoso, K. Matsui, N. Kamasawa, Y. Fukazawa, R. Shigemoto, Journal of Neuroscience 32 (2012) 2357–2376.","mla":"Budisantoso, Timotheus, et al. “Mechanisms Underlying Signal Filtering at a Multisynapse Contact.” Journal of Neuroscience, vol. 32, no. 7, Society for Neuroscience, 2012, pp. 2357–76, doi:10.1523/JNEUROSCI.5243-11.2012."},"extern":1,"abstract":[{"text":"Visual information must be relayed through the lateral geniculate nucleus before it reaches the visual cortex. However, not all spikes created in the retina lead to postsynaptic spikes and properties of the retinogeniculate synapse contribute to this filtering. To understand the mechanisms underlying this filtering process, we conducted electrophysiology to assess the properties of signal transmission in the Long-Evans rat. We also performed SDS-digested freeze-fracture replica labeling to quantify the receptor and transporter distribution, as well as EM reconstruction to describe the 3D structure. To analyze the impact of transmitter diffusion on the activity of the receptors, simulations were integrated. We identified that a large contributor to the filtering is the marked paired-pulse depression at this synapse, which was intensified by the morphological characteristics of the contacts. The broad presynaptic and postsynaptic contact area restricts transmitter diffusion two dimensionally. Additionally, the presence of multiple closely arranged release sites invites intersynaptic spillover, which causes desensitization of AMPA receptors. The presence of AMPA receptors that slowly recover from desensitization along with the high presynaptic release probability and multivesicular release at each synapse also contribute to the depression. These features contrast with many other synapses where spatiotemporal spread of transmitter is limited by rapid transmitter clearance allowing synapses to operate more independently. We propose that the micrometer-order structure can ultimately affect the visual information processing.","lang":"eng"}],"issue":"7","publist_id":"4387","type":"journal_article","date_updated":"2021-01-12T06:57:57Z","date_created":"2018-12-11T11:58:07Z","volume":32,"author":[{"full_name":"Budisantoso, Timotheus","first_name":"Timotheus","last_name":"Budisantoso"},{"full_name":"Matsui, Ko","first_name":"Ko","last_name":"Matsui"},{"full_name":"Kamasawa, Naomi","last_name":"Kamasawa","first_name":"Naomi"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Ryuichi Shigemoto"}],"title":"Mechanisms underlying signal filtering at a multisynapse contact","status":"public","publication_status":"published","publisher":"Society for Neuroscience","intvolume":" 32","_id":"2514","year":"2012"},{"date_published":"2012-09-26T00:00:00Z","doi":"10.1523/JNEUROSCI.1142-12.2012","citation":{"chicago":"Parajuli, Laxmi, Chikako Nakajima, Ákos Kulik, Ko Matsui, Toni Schneider, Ryuichi Shigemoto, and Yugo Fukazawa. “Quantitative Regional and Ultra Structural Localization of the Ca v2 3 Subunit of R Type Calcium Channel in Mouse Brain.” Journal of Neuroscience. Society for Neuroscience, 2012. https://doi.org/10.1523/JNEUROSCI.1142-12.2012.","mla":"Parajuli, Laxmi, et al. “Quantitative Regional and Ultra Structural Localization of the Ca v2 3 Subunit of R Type Calcium Channel in Mouse Brain.” Journal of Neuroscience, vol. 32, no. 39, Society for Neuroscience, 2012, pp. 13555–67, doi:10.1523/JNEUROSCI.1142-12.2012.","short":"L. Parajuli, C. Nakajima, Á. Kulik, K. Matsui, T. Schneider, R. Shigemoto, Y. Fukazawa, Journal of Neuroscience 32 (2012) 13555–13567.","ista":"Parajuli L, Nakajima C, Kulik Á, Matsui K, Schneider T, Shigemoto R, Fukazawa Y. 2012. Quantitative regional and ultra structural localization of the Ca v2 3 subunit of R type calcium channel in mouse brain. Journal of Neuroscience. 32(39), 13555–13567.","ieee":"L. Parajuli et al., “Quantitative regional and ultra structural localization of the Ca v2 3 subunit of R type calcium channel in mouse brain,” Journal of Neuroscience, vol. 32, no. 39. Society for Neuroscience, pp. 13555–13567, 2012.","apa":"Parajuli, L., Nakajima, C., Kulik, Á., Matsui, K., Schneider, T., Shigemoto, R., & Fukazawa, Y. (2012). Quantitative regional and ultra structural localization of the Ca v2 3 subunit of R type calcium channel in mouse brain. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1142-12.2012","ama":"Parajuli L, Nakajima C, Kulik Á, et al. Quantitative regional and ultra structural localization of the Ca v2 3 subunit of R type calcium channel in mouse brain. Journal of Neuroscience. 2012;32(39):13555-13567. doi:10.1523/JNEUROSCI.1142-12.2012"},"publication":"Journal of Neuroscience","page":"13555 - 13567","quality_controlled":0,"month":"09","day":"26","author":[{"full_name":"Parajuli, Laxmi K","first_name":"Laxmi","last_name":"Parajuli"},{"full_name":"Nakajima, Chikako","last_name":"Nakajima","first_name":"Chikako"},{"first_name":"Ákos","last_name":"Kulik","full_name":"Kulik, Ákos"},{"first_name":"Ko","last_name":"Matsui","full_name":"Matsui, Ko"},{"last_name":"Schneider","first_name":"Toni","full_name":"Schneider, Toni"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Ryuichi Shigemoto"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"}],"volume":32,"date_created":"2018-12-11T11:59:05Z","date_updated":"2021-01-12T06:59:04Z","year":"2012","_id":"2689","intvolume":" 32","publisher":"Society for Neuroscience","publication_status":"published","title":"Quantitative regional and ultra structural localization of the Ca v2 3 subunit of R type calcium channel in mouse brain","status":"public","issue":"39","publist_id":"4208","abstract":[{"lang":"eng","text":"R-type calcium channels (RTCCs) are well known for their role in synaptic plasticity, but little is known about their subcellular distribution across various neuronal compartments. Using subtype-specific antibodies, we characterized the regional and subcellular localization of Ca v2.3 in mice and rats at both light and electron microscopic levels. Ca v2.3 immunogold particles were found to be predominantly presynaptic in the interpeduncular nucleus, but postsynaptic in other brain regions. Serial section analysis of electron microscopic images from the hippocampal CA1 revealed a higher density of immunogold particles in the dendritic shaft plasma membrane compared with the pyramidal cell somata. However, the labeling densities were not significantly different among the apical, oblique, or basal dendrites. Immunogold particles were also observed over the plasma membrane of dendritic spines, including both synaptic and extrasynaptic sites. Individual spine heads contained <20 immunogold particles, with an average density of ~260 immunoparticles per μm 3 spine head volume, in accordance with the density of RTCCs estimated using calcium imaging (Sabatini and Svoboda, 2000). The Ca v2.3 density was variable among similar-sized spine heads and did not correlate with the density in the parent dendrite, implying that spines are individual calcium compartments operating autonomously from their parent dendrites."}],"extern":1,"type":"journal_article"},{"month":"01","day":"01","page":"117 - 121","quality_controlled":0,"citation":{"ista":"Shinohara Y, Hosoya A, Yamasaki N, Ahmed H, Hattori S, Eguchi M, Yamaguchi S, Miyakawa T, Hirase H, Shigemoto R. 2012. Right-hemispheric dominance of spatial memory in split-brain mice. Hippocampus. 22(2), 117–121.","apa":"Shinohara, Y., Hosoya, A., Yamasaki, N., Ahmed, H., Hattori, S., Eguchi, M., … Shigemoto, R. (2012). Right-hemispheric dominance of spatial memory in split-brain mice. Hippocampus. Wiley-Blackwell. https://doi.org/10.1002/hipo.20886","ieee":"Y. Shinohara et al., “Right-hemispheric dominance of spatial memory in split-brain mice,” Hippocampus, vol. 22, no. 2. Wiley-Blackwell, pp. 117–121, 2012.","ama":"Shinohara Y, Hosoya A, Yamasaki N, et al. Right-hemispheric dominance of spatial memory in split-brain mice. Hippocampus. 2012;22(2):117-121. doi:10.1002/hipo.20886","chicago":"Shinohara, Yoshiaki, Aki Hosoya, Nobuyuki Yamasaki, Hassan Ahmed, Satoko Hattori, Megumi Eguchi, Shun Yamaguchi, Tsuyoshi Miyakawa, Hajime Hirase, and Ryuichi Shigemoto. “Right-Hemispheric Dominance of Spatial Memory in Split-Brain Mice.” Hippocampus. Wiley-Blackwell, 2012. https://doi.org/10.1002/hipo.20886.","mla":"Shinohara, Yoshiaki, et al. “Right-Hemispheric Dominance of Spatial Memory in Split-Brain Mice.” Hippocampus, vol. 22, no. 2, Wiley-Blackwell, 2012, pp. 117–21, doi:10.1002/hipo.20886.","short":"Y. Shinohara, A. Hosoya, N. Yamasaki, H. Ahmed, S. Hattori, M. Eguchi, S. Yamaguchi, T. Miyakawa, H. Hirase, R. Shigemoto, Hippocampus 22 (2012) 117–121."},"publication":"Hippocampus","doi":"10.1002/hipo.20886","date_published":"2012-01-01T00:00:00Z","type":"journal_article","extern":1,"issue":"2","publist_id":"4210","abstract":[{"lang":"eng","text":"Left-right asymmetry of human brain function has been known for a century, although much of molecular and cellular basis of brain laterality remains to be elusive. Recent studies suggest that hippocampal CA3-CA1 excitatory synapses are asymmetrically arranged, however, the functional implication of the asymmetrical circuitry has not been studied at the behavioral level. In order to address the left-right asymmetry of hippocampal function in behaving mice, we analyzed the performance of "split-brain" mice in the Barnes maze. The "split-brain" mice received ventral hippocampal commissure and corpus callosum transection in addition to deprivation of visual input from one eye. In such mice, the hippocampus in the side of visual deprivation receives sensory-driven input. Better spatial task performance was achieved by the mice which were forced to use the right hippocampus than those which were forced to use the left hippocampus. In two-choice spatial maze, forced usage of left hippocampus resulted in a comparable performance to the right counterpart, suggesting that both hippocampal hemispheres are capable of conducting spatial learning. Therefore, the results obtained from the Barnes maze suggest that the usage of the right hippocampus improves the accuracy of spatial memory. Performance of non-spatial yet hippocampus-dependent tasks (e.g. fear conditioning) was not influenced by the laterality of the hippocampus."}],"publisher":"Wiley-Blackwell","intvolume":" 22","publication_status":"published","title":"Right-hemispheric dominance of spatial memory in split-brain mice","status":"public","_id":"2687","year":"2012","volume":22,"date_created":"2018-12-11T11:59:04Z","date_updated":"2021-01-12T06:59:03Z","author":[{"first_name":"Yoshiaki","last_name":"Shinohara","full_name":"Shinohara, Yoshiaki"},{"full_name":"Hosoya, Aki","last_name":"Hosoya","first_name":"Aki"},{"full_name":"Yamasaki, Nobuyuki","last_name":"Yamasaki","first_name":"Nobuyuki"},{"full_name":"Ahmed, Hassan","last_name":"Ahmed","first_name":"Hassan"},{"last_name":"Hattori","first_name":"Satoko","full_name":"Hattori, Satoko"},{"last_name":"Eguchi","first_name":"Megumi","full_name":"Eguchi, Megumi"},{"full_name":"Yamaguchi, Shun","last_name":"Yamaguchi","first_name":"Shun"},{"full_name":"Miyakawa, Tsuyoshi","last_name":"Miyakawa","first_name":"Tsuyoshi"},{"full_name":"Hirase, Hajime","last_name":"Hirase","first_name":"Hajime"},{"full_name":"Ryuichi Shigemoto","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}]},{"day":"01","month":"06","citation":{"mla":"Fukazawa, Yugo, and Ryuichi Shigemoto. “Intra-Synapse-Type and Inter-Synapse-Type Relationships between Synaptic Size and AMPAR Expression.” Current Opinion in Neurobiology, vol. 22, no. 3, Elsevier, 2012, pp. 446–52, doi:10.1016/j.conb.2012.01.006.","short":"Y. Fukazawa, R. Shigemoto, Current Opinion in Neurobiology 22 (2012) 446–452.","chicago":"Fukazawa, Yugo, and Ryuichi Shigemoto. “Intra-Synapse-Type and Inter-Synapse-Type Relationships between Synaptic Size and AMPAR Expression.” Current Opinion in Neurobiology. Elsevier, 2012. https://doi.org/10.1016/j.conb.2012.01.006.","ama":"Fukazawa Y, Shigemoto R. Intra-synapse-type and inter-synapse-type relationships between synaptic size and AMPAR expression. Current Opinion in Neurobiology. 2012;22(3):446-452. doi:10.1016/j.conb.2012.01.006","ista":"Fukazawa Y, Shigemoto R. 2012. Intra-synapse-type and inter-synapse-type relationships between synaptic size and AMPAR expression. Current Opinion in Neurobiology. 22(3), 446–452.","apa":"Fukazawa, Y., & Shigemoto, R. (2012). Intra-synapse-type and inter-synapse-type relationships between synaptic size and AMPAR expression. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2012.01.006","ieee":"Y. Fukazawa and R. Shigemoto, “Intra-synapse-type and inter-synapse-type relationships between synaptic size and AMPAR expression,” Current Opinion in Neurobiology, vol. 22, no. 3. Elsevier, pp. 446–452, 2012."},"publication":"Current Opinion in Neurobiology","page":"446 - 452","quality_controlled":0,"date_published":"2012-06-01T00:00:00Z","doi":"10.1016/j.conb.2012.01.006","type":"journal_article","publist_id":"4209","issue":"3","abstract":[{"lang":"eng","text":"To gain insights into structure-function relationship of excitatory synapses, we revisit our quantitative analysis of synaptic AMPAR by highly sensitive freeze-fracture replica labeling in eight different connections. All of these connections showed linear correlation between synapse size and AMPAR number indicating a common intra-synapse-type relationship in CNS synapses. On the contrary, inter-synapse-type relationship is unexpected indicating no correlation between averages of synapse size and AMPAR number. Interestingly, connections with large average synapse size and low AMPAR density showed high variability of AMPAR number and mosaic distribution within the postsynaptic membrane. We propose an idea that these connections may quickly exhibit synaptic plasticity by modifying AMPAR density/number whereas those with high AMPAR density change their efficacy by modifying synapse size."}],"extern":1,"year":"2012","_id":"2688","publisher":"Elsevier","intvolume":" 22","publication_status":"published","title":"Intra-synapse-type and inter-synapse-type relationships between synaptic size and AMPAR expression","status":"public","author":[{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Ryuichi Shigemoto"}],"volume":22,"date_created":"2018-12-11T11:59:04Z","date_updated":"2021-01-12T06:59:03Z"},{"year":"2012","_id":"2696","publisher":"ArXiv","status":"public","title":"Universality for random matrices and log-gases","publication_status":"published","author":[{"full_name":"László Erdös","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T06:59:06Z","date_created":"2018-12-11T11:59:07Z","type":"preprint","publist_id":"4201","extern":1,"citation":{"chicago":"Erdös, László. “Universality for Random Matrices and Log-Gases.” ArXiv. ArXiv, 2012.","short":"L. Erdös, ArXiv (2012).","mla":"Erdös, László. “Universality for Random Matrices and Log-Gases.” ArXiv, ArXiv, 2012.","apa":"Erdös, L. (2012). Universality for random matrices and log-gases. ArXiv. ArXiv.","ieee":"L. Erdös, “Universality for random matrices and log-gases,” ArXiv. ArXiv, 2012.","ista":"Erdös L. 2012. Universality for random matrices and log-gases. ArXiv, .","ama":"Erdös L. Universality for random matrices and log-gases. ArXiv. 2012."},"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1212.0839"}],"publication":"ArXiv","quality_controlled":0,"date_published":"2012-12-04T00:00:00Z","day":"04","month":"12"},{"intvolume":" 95","publisher":"Oxford University Press","status":"public","title":"Lecture notes on quantum Brownian motion","publication_status":"published","year":"2012","_id":"2700","volume":95,"date_updated":"2021-01-12T06:59:08Z","date_created":"2018-12-11T11:59:08Z","author":[{"full_name":"László Erdös","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"}],"alternative_title":["Quantum Theory from Small to Large Scales"],"type":"conference","extern":1,"publist_id":"4196","page":"3 - 98","quality_controlled":0,"oa":1,"citation":{"ista":"Erdös L. 2012. Lecture notes on quantum Brownian motion. Les Houches Summer School 2010, Quantum Theory from Small to Large Scales, vol. 95, 3–98.","ieee":"L. Erdös, “Lecture notes on quantum Brownian motion,” presented at the Les Houches Summer School 2010, 2012, vol. 95, pp. 3–98.","apa":"Erdös, L. (2012). Lecture notes on quantum Brownian motion (Vol. 95, pp. 3–98). Presented at the Les Houches Summer School 2010, Oxford University Press.","ama":"Erdös L. Lecture notes on quantum Brownian motion. In: Vol 95. Oxford University Press; 2012:3-98.","chicago":"Erdös, László. “Lecture Notes on Quantum Brownian Motion,” 95:3–98. Oxford University Press, 2012.","mla":"Erdös, László. Lecture Notes on Quantum Brownian Motion. Vol. 95, Oxford University Press, 2012, pp. 3–98.","short":"L. Erdös, in:, Oxford University Press, 2012, pp. 3–98."},"main_file_link":[{"url":"http://arxiv.org/abs/1009.0843","open_access":"1"}],"date_published":"2012-05-24T00:00:00Z","conference":{"name":"Les Houches Summer School 2010"},"month":"05","day":"24"},{"date_updated":"2023-02-23T10:06:04Z","date_created":"2018-12-11T11:59:13Z","volume":18,"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Manas","last_name":"Joglekar","full_name":"Joglekar, Manas"},{"full_name":"Shah, Nisarg","last_name":"Shah","first_name":"Nisarg"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"1598"}]},"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrCh"}],"year":"2012","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2020-07-14T12:45:45Z","publist_id":"4180","ec_funded":1,"language":[{"iso":"eng"}],"conference":{"name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","start_date":"2012-12-15","location":"Hyderabad, India","end_date":"2012-12-17"},"doi":"10.4230/LIPIcs.FSTTCS.2012.461","quality_controlled":"1","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"month":"12","oa_version":"Published Version","file":[{"file_id":"5040","relation":"main_file","date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-12T10:13:53Z","checksum":"d4d644ed1a885dbfc4fa1ef4c5724dab","file_name":"IST-2016-525-v1+1_42_1_.pdf","access_level":"open_access","creator":"system","file_size":519040,"content_type":"application/pdf"}],"pubrep_id":"525","title":"Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives","ddc":["000"],"status":"public","intvolume":" 18","_id":"2715","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) with specifications given as Büchi (liveness) objectives. We consider the problem of computing the set of almost-sure winning vertices from where the objective can be ensured with probability 1. We study for the first time the average case complexity of the classical algorithm for computing the set of almost-sure winning vertices for MDPs with Büchi objectives. Our contributions are as follows: First, we show that for MDPs with constant out-degree the expected number of iterations is at most logarithmic and the average case running time is linear (as compared to the worst case linear number of iterations and quadratic time complexity). Second, for the average case analysis over all MDPs we show that the expected number of iterations is constant and the average case running time is linear (again as compared to the worst case linear number of iterations and quadratic time complexity). Finally we also show that given that all MDPs are equally likely, the probability that the classical algorithm requires more than constant number of iterations is exponentially small."}],"alternative_title":["LIPIcs"],"type":"conference","date_published":"2012-12-10T00:00:00Z","page":"461 - 473","citation":{"ama":"Chatterjee K, Joglekar M, Shah N. Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. In: Vol 18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2012:461-473. doi:10.4230/LIPIcs.FSTTCS.2012.461","ista":"Chatterjee K, Joglekar M, Shah N. 2012. Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 18, 461–473.","ieee":"K. Chatterjee, M. Joglekar, and N. Shah, “Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Hyderabad, India, 2012, vol. 18, pp. 461–473.","apa":"Chatterjee, K., Joglekar, M., & Shah, N. (2012). Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives (Vol. 18, pp. 461–473). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Hyderabad, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461","mla":"Chatterjee, Krishnendu, et al. Average Case Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives. Vol. 18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 461–73, doi:10.4230/LIPIcs.FSTTCS.2012.461.","short":"K. Chatterjee, M. Joglekar, N. Shah, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 461–473.","chicago":"Chatterjee, Krishnendu, Manas Joglekar, and Nisarg Shah. “Average Case Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives,” 18:461–73. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012. https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461."},"day":"10","has_accepted_license":"1","scopus_import":1},{"page":"115-131","citation":{"ama":"Chatterjee K, Randour M, Raskin J-F. Strategy synthesis for multi-dimensional quantitative objectives. In: Koutny M, Ulidowski I, eds. CONCUR 2012 - Concurrency Theory. Vol 7454. Berlin, Heidelberg: Springer; 2012:115-131. doi:10.1007/978-3-642-32940-1_10","ista":"Chatterjee K, Randour M, Raskin J-F. 2012. Strategy synthesis for multi-dimensional quantitative objectives. CONCUR 2012 - Concurrency Theory. CONCUR: Conference on Concurrency Theory, LNCS, vol. 7454, 115–131.","ieee":"K. Chatterjee, M. Randour, and J.-F. Raskin, “Strategy synthesis for multi-dimensional quantitative objectives,” in CONCUR 2012 - Concurrency Theory, Newcastle upon Tyne, United Kingdom, 2012, vol. 7454, pp. 115–131.","apa":"Chatterjee, K., Randour, M., & Raskin, J.-F. (2012). Strategy synthesis for multi-dimensional quantitative objectives. In M. Koutny & I. Ulidowski (Eds.), CONCUR 2012 - Concurrency Theory (Vol. 7454, pp. 115–131). Berlin, Heidelberg: Springer. https://doi.org/10.1007/978-3-642-32940-1_10","mla":"Chatterjee, Krishnendu, et al. “Strategy Synthesis for Multi-Dimensional Quantitative Objectives.” CONCUR 2012 - Concurrency Theory, edited by Maciej Koutny and Irek Ulidowski, vol. 7454, Springer, 2012, pp. 115–31, doi:10.1007/978-3-642-32940-1_10.","short":"K. Chatterjee, M. Randour, J.-F. Raskin, in:, M. Koutny, I. Ulidowski (Eds.), CONCUR 2012 - Concurrency Theory, Springer, Berlin, Heidelberg, 2012, pp. 115–131.","chicago":"Chatterjee, Krishnendu, Mickael Randour, and Jean-François Raskin. “Strategy Synthesis for Multi-Dimensional Quantitative Objectives.” In CONCUR 2012 - Concurrency Theory, edited by Maciej Koutny and Irek Ulidowski, 7454:115–31. Berlin, Heidelberg: Springer, 2012. https://doi.org/10.1007/978-3-642-32940-1_10."},"publication":"CONCUR 2012 - Concurrency Theory","date_published":"2012-09-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"15","intvolume":" 7454","title":"Strategy synthesis for multi-dimensional quantitative objectives","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10904","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"Multi-dimensional mean-payoff and energy games provide the mathematical foundation for the quantitative study of reactive systems, and play a central role in the emerging quantitative theory of verification and synthesis. In this work, we study the strategy synthesis problem for games with such multi-dimensional objectives along with a parity condition, a canonical way to express ω-regular conditions. While in general, the winning strategies in such games may require infinite memory, for synthesis the most relevant problem is the construction of a finite-memory winning strategy (if one exists). Our main contributions are as follows. First, we show a tight exponential bound (matching upper and lower bounds) on the memory required for finite-memory winning strategies in both multi-dimensional mean-payoff and energy games along with parity objectives. This significantly improves the triple exponential upper bound for multi energy games (without parity) that could be derived from results in literature for games on VASS (vector addition systems with states). Second, we present an optimal symbolic and incremental algorithm to compute a finite-memory winning strategy (if one exists) in such games. Finally, we give a complete characterization of when finite memory of strategies can be traded off for randomness. In particular, we show that for one-dimension mean-payoff parity games, randomized memoryless strategies are as powerful as their pure finite-memory counterparts."}],"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","external_id":{"arxiv":["1201.5073"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-32940-1_10","conference":{"start_date":"2012-09-04","location":"Newcastle upon Tyne, United Kingdom","end_date":"2012-09-07","name":"CONCUR: Conference on Concurrency Theory"},"publication_identifier":{"eisbn":["9783642329401"],"issn":["0302-9743","1611-3349"],"isbn":["9783642329395"]},"month":"09","editor":[{"full_name":"Koutny, Maciej","first_name":"Maciej","last_name":"Koutny"},{"first_name":"Irek","last_name":"Ulidowski","full_name":"Ulidowski, Irek"}],"publisher":"Springer","department":[{"_id":"KrCh"}],"publication_status":"published","acknowledgement":"Author supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407 (RiSE), ERC Start Grant (279307: Graph Games), Microsoft faculty fellowship.","year":"2012","volume":7454,"date_created":"2022-03-21T08:00:21Z","date_updated":"2023-02-23T10:55:06Z","related_material":{"record":[{"id":"2716","status":"public","relation":"later_version"}]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Randour","first_name":"Mickael","full_name":"Randour, Mickael"},{"last_name":"Raskin","first_name":"Jean-François","full_name":"Raskin, Jean-François"}],"place":"Berlin, Heidelberg","ec_funded":1},{"doi":"10.1016/j.aim.2011.12.010","date_published":"2012-02-15T00:00:00Z","page":"1435 - 1515","quality_controlled":0,"citation":{"short":"L. Erdös, H. Yau, J. Yin, Advances in Mathematics 229 (2012) 1435–1515.","mla":"Erdös, László, et al. “Rigidity of Eigenvalues of Generalized Wigner Matrices.” Advances in Mathematics, vol. 229, no. 3, Academic Press, 2012, pp. 1435–515, doi:10.1016/j.aim.2011.12.010.","chicago":"Erdös, László, Horng Yau, and Jun Yin. “Rigidity of Eigenvalues of Generalized Wigner Matrices.” Advances in Mathematics. Academic Press, 2012. https://doi.org/10.1016/j.aim.2011.12.010.","ama":"Erdös L, Yau H, Yin J. Rigidity of eigenvalues of generalized Wigner matrices. Advances in Mathematics. 2012;229(3):1435-1515. doi:10.1016/j.aim.2011.12.010","ieee":"L. Erdös, H. Yau, and J. Yin, “Rigidity of eigenvalues of generalized Wigner matrices,” Advances in Mathematics, vol. 229, no. 3. Academic Press, pp. 1435–1515, 2012.","apa":"Erdös, L., Yau, H., & Yin, J. (2012). Rigidity of eigenvalues of generalized Wigner matrices. Advances in Mathematics. Academic Press. https://doi.org/10.1016/j.aim.2011.12.010","ista":"Erdös L, Yau H, Yin J. 2012. Rigidity of eigenvalues of generalized Wigner matrices. Advances in Mathematics. 229(3), 1435–1515."},"publication":"Advances in Mathematics","day":"15","month":"02","volume":229,"date_updated":"2021-01-12T06:59:35Z","date_created":"2018-12-11T11:59:30Z","author":[{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"László Erdös"},{"full_name":"Yau, Horng-Tzer","first_name":"Horng","last_name":"Yau"},{"first_name":"Jun","last_name":"Yin","full_name":"Yin, Jun"}],"publisher":"Academic Press","intvolume":" 229","title":"Rigidity of eigenvalues of generalized Wigner matrices","status":"public","publication_status":"published","year":"2012","_id":"2770","extern":1,"publist_id":"4120","issue":"3","abstract":[{"lang":"eng","text":"Consider N×N Hermitian or symmetric random matrices H with independent entries, where the distribution of the (i,j) matrix element is given by the probability measure vij with zero expectation and with variance σ ιj 2. We assume that the variances satisfy the normalization condition Σiσij2=1 for all j and that there is a positive constant c such that c≤Nσ ιj 2 ιc -1. We further assume that the probability distributions νij have a uniform subexponential decay. We prove that the Stieltjes transform of the empirical eigenvalue distribution of H is given by the Wigner semicircle law uniformly up to the edges of the spectrum with an error of order (Nη) -1 where η is the imaginary part of the spectral parameter in the Stieltjes transform. There are three corollaries to this strong local semicircle law: (1) Rigidity of eigenvalues: If γj=γj,N denotes the classical location of the j-th eigenvalue under the semicircle law ordered in increasing order, then the j-th eigenvalue λj is close to γj in the sense that for some positive constants C, c P{double-struck}(∃j:|λ j-γ j|≥(logN) CloglogN[min(j,N-j+1)] -1/3N -2/3)≤ C exp[-(logN) cloglogN] for N large enough. (2) The proof of Dyson's conjecture (Dyson, 1962 [15]) which states that the time scale of the Dyson Brownian motion to reach local equilibrium is of order N -1 up to logarithmic corrections. (3) The edge universality holds in the sense that the probability distributions of the largest (and the smallest) eigenvalues of two generalized Wigner ensembles are the same in the large N limit provided that the second moments of the two ensembles are identical."}],"type":"journal_article"},{"day":"01","month":"02","page":"1 - 46","quality_controlled":0,"citation":{"chicago":"Erdös, László, Benjamin Schlein, Horng Yau, and Jun Yin. “The Local Relaxation Flow Approach to Universality of the Local Statistics for Random Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2012. https://doi.org/10.1214/10-AIHP388.","mla":"Erdös, László, et al. “The Local Relaxation Flow Approach to Universality of the Local Statistics for Random Matrices.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 48, no. 1, Institute of Mathematical Statistics, 2012, pp. 1–46, doi:10.1214/10-AIHP388.","short":"L. Erdös, B. Schlein, H. Yau, J. Yin, Annales de l’institut Henri Poincare (B) Probability and Statistics 48 (2012) 1–46.","ista":"Erdös L, Schlein B, Yau H, Yin J. 2012. The local relaxation flow approach to universality of the local statistics for random matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 48(1), 1–46.","ieee":"L. Erdös, B. Schlein, H. Yau, and J. Yin, “The local relaxation flow approach to universality of the local statistics for random matrices,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 48, no. 1. Institute of Mathematical Statistics, pp. 1–46, 2012.","apa":"Erdös, L., Schlein, B., Yau, H., & Yin, J. (2012). The local relaxation flow approach to universality of the local statistics for random matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/10-AIHP388","ama":"Erdös L, Schlein B, Yau H, Yin J. The local relaxation flow approach to universality of the local statistics for random matrices. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2012;48(1):1-46. doi:10.1214/10-AIHP388"},"publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","date_published":"2012-02-01T00:00:00Z","doi":"10.1214/10-AIHP388","type":"journal_article","extern":1,"issue":"1","publist_id":"4121","abstract":[{"lang":"eng","text":"We present a generalization of the method of the local relaxation flow to establish the universality of local spectral statistics of a broad class of large random matrices. We show that the local distribution of the eigenvalues coincides with the local statistics of the corresponding Gaussian ensemble provided the distribution of the individual matrix element is smooth and the eigenvalues {X J} N j=1 are close to their classical location {y j} N j=1 determined by the limiting density of eigenvalues. Under the scaling where the typical distance between neighboring eigenvalues is of order 1/N, the necessary apriori estimate on the location of eigenvalues requires only to know that E|x j - γ j| 2 ≤ N-1-ε on average. This information can be obtained by well established methods for various matrix ensembles. We demonstrate the method by proving local spectral universality for sample covariance matrices."}],"publisher":"Institute of Mathematical Statistics","intvolume":" 48","status":"public","publication_status":"published","title":"The local relaxation flow approach to universality of the local statistics for random matrices","year":"2012","_id":"2769","volume":48,"date_updated":"2021-01-12T06:59:34Z","date_created":"2018-12-11T11:59:30Z","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"László Erdös"},{"full_name":"Schlein, Benjamin","first_name":"Benjamin","last_name":"Schlein"},{"full_name":"Yau, Horng-Tzer","first_name":"Horng","last_name":"Yau"},{"full_name":"Yin, Jun","first_name":"Jun","last_name":"Yin"}]},{"extern":1,"publist_id":"4123","issue":"1-2","abstract":[{"text":"Consider N × N Hermitian or symmetric random matrices H where the distribution of the (i, j) matrix element is given by a probability measure ν ij with a subexponential decay. Let σ ij 2 be the variance for the probability measure ν ij with the normalization property that Σ iσ i,j 2 = 1 for all j. Under essentially the only condition that c ≤ N σ ij 2 ≤ c -1 for some constant c > 0, we prove that, in the limit N → ∞, the eigenvalue spacing statistics of H in the bulk of the spectrum coincide with those of the Gaussian unitary or orthogonal ensemble (GUE or GOE). We also show that for band matrices with bandwidth M the local semicircle law holds to the energy scale M -1. ","lang":"eng"}],"type":"journal_article","volume":154,"date_updated":"2021-01-12T06:59:33Z","date_created":"2018-12-11T11:59:29Z","author":[{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"László Erdös"},{"last_name":"Yau","first_name":"Horng","full_name":"Yau, Horng-Tzer"},{"first_name":"Jun","last_name":"Yin","full_name":"Yin, Jun"}],"publisher":"Springer","intvolume":" 154","status":"public","publication_status":"published","title":"Bulk universality for generalized Wigner matrices","year":"2012","_id":"2767","day":"01","month":"10","doi":"10.1007/s00440-011-0390-3","date_published":"2012-10-01T00:00:00Z","page":"341 - 407","quality_controlled":0,"citation":{"mla":"Erdös, László, et al. “Bulk Universality for Generalized Wigner Matrices.” Probability Theory and Related Fields, vol. 154, no. 1–2, Springer, 2012, pp. 341–407, doi:10.1007/s00440-011-0390-3.","short":"L. Erdös, H. Yau, J. Yin, Probability Theory and Related Fields 154 (2012) 341–407.","chicago":"Erdös, László, Horng Yau, and Jun Yin. “Bulk Universality for Generalized Wigner Matrices.” Probability Theory and Related Fields. Springer, 2012. https://doi.org/10.1007/s00440-011-0390-3.","ama":"Erdös L, Yau H, Yin J. Bulk universality for generalized Wigner matrices. Probability Theory and Related Fields. 2012;154(1-2):341-407. doi:10.1007/s00440-011-0390-3","ista":"Erdös L, Yau H, Yin J. 2012. Bulk universality for generalized Wigner matrices. Probability Theory and Related Fields. 154(1–2), 341–407.","ieee":"L. Erdös, H. Yau, and J. Yin, “Bulk universality for generalized Wigner matrices,” Probability Theory and Related Fields, vol. 154, no. 1–2. Springer, pp. 341–407, 2012.","apa":"Erdös, L., Yau, H., & Yin, J. (2012). Bulk universality for generalized Wigner matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-011-0390-3"},"publication":"Probability Theory and Related Fields"},{"month":"01","day":"01","doi":"10.1007/s00220-011-1373-z","date_published":"2012-01-01T00:00:00Z","citation":{"chicago":"Erdös, László, and David Hasler. “Wegner Estimate and Anderson Localization for Random Magnetic Fields.” Communications in Mathematical Physics. Springer, 2012. https://doi.org/10.1007/s00220-011-1373-z.","short":"L. Erdös, D. Hasler, Communications in Mathematical Physics 309 (2012) 507–542.","mla":"Erdös, László, and David Hasler. “Wegner Estimate and Anderson Localization for Random Magnetic Fields.” Communications in Mathematical Physics, vol. 309, no. 2, Springer, 2012, pp. 507–42, doi:10.1007/s00220-011-1373-z.","apa":"Erdös, L., & Hasler, D. (2012). Wegner estimate and Anderson localization for random magnetic fields. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-011-1373-z","ieee":"L. Erdös and D. Hasler, “Wegner estimate and Anderson localization for random magnetic fields,” Communications in Mathematical Physics, vol. 309, no. 2. Springer, pp. 507–542, 2012.","ista":"Erdös L, Hasler D. 2012. Wegner estimate and Anderson localization for random magnetic fields. Communications in Mathematical Physics. 309(2), 507–542.","ama":"Erdös L, Hasler D. Wegner estimate and Anderson localization for random magnetic fields. Communications in Mathematical Physics. 2012;309(2):507-542. doi:10.1007/s00220-011-1373-z"},"publication":"Communications in Mathematical Physics","page":"507 - 542","quality_controlled":0,"issue":"2","publist_id":"4122","abstract":[{"text":"We consider a two dimensional magnetic Schrödinger operator with a spatially stationary random magnetic field. We assume that the magnetic field has a positive lower bound and that it has Fourier modes on arbitrarily short scales. We prove the Wegner estimate at arbitrary energy, i. e. we show that the averaged density of states is finite throughout the whole spectrum. We also prove Anderson localization at the bottom of the spectrum.","lang":"eng"}],"extern":1,"type":"journal_article","author":[{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"László Erdös"},{"first_name":"David","last_name":"Hasler","full_name":"Hasler, David G"}],"volume":309,"date_created":"2018-12-11T11:59:30Z","date_updated":"2021-01-12T06:59:34Z","_id":"2768","year":"2012","intvolume":" 309","publisher":"Springer","title":"Wegner estimate and Anderson localization for random magnetic fields","status":"public","publication_status":"published"},{"type":"journal_article","extern":1,"abstract":[{"text":"The Wigner-Dyson-Gaudin-Mehta conjecture asserts that the local eigenvalue statistics of large random matrices exhibit universal behavior depending only on the symmetry class of the matrix ensemble. For invariant matrix models, the eigenvalue distributions are given by a log-gas with potential V and inverse temperature β = 1, 2, 4, corresponding to the orthogonal, unitary and symplectic ensembles. For β ∉ {1, 2, 4}, there is no natural random matrix ensemble behind this model, but the statistical physics interpretation of the log-gas is still valid for all β > 0. The universality conjecture for invariant ensembles asserts that the local eigenvalue statistics are independent of V. In this article, we review our recent solution to the universality conjecture for both invariant and non-invariant ensembles. We will also demonstrate that the local ergodicity of the Dyson Brownian motion is the intrinsic mechanism behind the universality. Furthermore, we review the solution of Dyson's conjecture on the local relaxation time of the Dyson Brownian motion. Related questions such as delocalization of eigenvectors and local version of Wigner's semicircle law will also be discussed.","lang":"eng"}],"publist_id":"4115","issue":"3","title":"Universality of local spectral statistics of random matrices","publication_status":"published","status":"public","publisher":"American Mathematical Society","intvolume":" 49","_id":"2775","year":"2012","date_updated":"2021-01-12T06:59:36Z","date_created":"2018-12-11T11:59:32Z","volume":49,"author":[{"full_name":"László Erdös","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Yau","first_name":"Horng","full_name":"Yau, Horng-Tzer"}],"day":"30","month":"01","quality_controlled":0,"page":"377 - 414","publication":"Bulletin of the American Mathematical Society","citation":{"apa":"Erdös, L., & Yau, H. (2012). Universality of local spectral statistics of random matrices. Bulletin of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0273-0979-2012-01372-1","ieee":"L. Erdös and H. Yau, “Universality of local spectral statistics of random matrices,” Bulletin of the American Mathematical Society, vol. 49, no. 3. American Mathematical Society, pp. 377–414, 2012.","ista":"Erdös L, Yau H. 2012. Universality of local spectral statistics of random matrices. Bulletin of the American Mathematical Society. 49(3), 377–414.","ama":"Erdös L, Yau H. Universality of local spectral statistics of random matrices. Bulletin of the American Mathematical Society. 2012;49(3):377-414. doi:10.1090/S0273-0979-2012-01372-1","chicago":"Erdös, László, and Horng Yau. “Universality of Local Spectral Statistics of Random Matrices.” Bulletin of the American Mathematical Society. American Mathematical Society, 2012. https://doi.org/10.1090/S0273-0979-2012-01372-1.","short":"L. Erdös, H. Yau, Bulletin of the American Mathematical Society 49 (2012) 377–414.","mla":"Erdös, László, and Horng Yau. “Universality of Local Spectral Statistics of Random Matrices.” Bulletin of the American Mathematical Society, vol. 49, no. 3, American Mathematical Society, 2012, pp. 377–414, doi:10.1090/S0273-0979-2012-01372-1."},"doi":"10.1090/S0273-0979-2012-01372-1","date_published":"2012-01-30T00:00:00Z"},{"quality_controlled":0,"publication":"Journal of Mathematical Physics","citation":{"ama":"Erdös L, Fournais S, Solovej J. Relativistic Scott correction in self-generated magnetic fields. Journal of Mathematical Physics. 2012;53(9). doi:10.1063/1.3697417","ista":"Erdös L, Fournais S, Solovej J. 2012. Relativistic Scott correction in self-generated magnetic fields. Journal of Mathematical Physics. 53(9).","apa":"Erdös, L., Fournais, S., & Solovej, J. (2012). Relativistic Scott correction in self-generated magnetic fields. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.3697417","ieee":"L. Erdös, S. Fournais, and J. Solovej, “Relativistic Scott correction in self-generated magnetic fields,” Journal of Mathematical Physics, vol. 53, no. 9. American Institute of Physics, 2012.","mla":"Erdös, László, et al. “Relativistic Scott Correction in Self-Generated Magnetic Fields.” Journal of Mathematical Physics, vol. 53, no. 9, American Institute of Physics, 2012, doi:10.1063/1.3697417.","short":"L. Erdös, S. Fournais, J. Solovej, Journal of Mathematical Physics 53 (2012).","chicago":"Erdös, László, Søren Fournais, and Jan Solovej. “Relativistic Scott Correction in Self-Generated Magnetic Fields.” Journal of Mathematical Physics. American Institute of Physics, 2012. https://doi.org/10.1063/1.3697417."},"doi":"10.1063/1.3697417","date_published":"2012-09-28T00:00:00Z","day":"28","month":"09","status":"public","title":"Relativistic Scott correction in self-generated magnetic fields","publication_status":"published","publisher":"American Institute of Physics","intvolume":" 53","year":"2012","_id":"2777","date_updated":"2021-01-12T06:59:37Z","date_created":"2018-12-11T11:59:32Z","volume":53,"author":[{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"László Erdös"},{"first_name":"Søren","last_name":"Fournais","full_name":"Fournais, Søren"},{"full_name":"Solovej, Jan P","first_name":"Jan","last_name":"Solovej"}],"type":"journal_article","extern":1,"abstract":[{"lang":"eng","text":"We consider a large neutral molecule with total nuclear charge Z in a model with self-generated classical magnetic field and where the kinetic energy of the electrons is treated relativistically. To ensure stability, we assume that Zα < 2/π, where α denotes the fine structure constant. We are interested in the ground state energy in the simultaneous limit Z → ∞, α → 0 such that κ = Zα is fixed. The leading term in the energy asymptotics is independent of κ, it is given by the Thomas-Fermi energy of order Z7/3 and it is unchanged by including the self-generated magnetic field. We prove the first correction term to this energy, the so-called Scott correction of the form S(αZ)Z2. The current paper extends the result of Solovej et al. [Commun. Pure Appl. Math.LXIII, 39-118 (2010)] on the Scott correction for relativistic molecules to include a self-generated magnetic field. Furthermore, we show that the corresponding Scott correction function S, first identified by Solovej et al. [Commun. Pure Appl. Math.LXIII, 39-118 (2010)], is unchanged by including a magnetic field. We also prove new Lieb-Thirring inequalities for the relativistic kinetic energy with magnetic fields."}],"publist_id":"4113","issue":"9"},{"page":"671 - 730","quality_controlled":0,"citation":{"short":"L. Erdös, S. Fournais, J. Solovej, Annales Henri Poincare 13 (2012) 671–730.","mla":"Erdös, László, et al. “Second Order Semiclassics with Self Generated Magnetic Fields.” Annales Henri Poincare, vol. 13, no. 4, Birkhäuser, 2012, pp. 671–730, doi:10.1007/s00023-011-0150-z.","chicago":"Erdös, László, Søren Fournais, and Jan Solovej. “Second Order Semiclassics with Self Generated Magnetic Fields.” Annales Henri Poincare. Birkhäuser, 2012. https://doi.org/10.1007/s00023-011-0150-z.","ama":"Erdös L, Fournais S, Solovej J. Second order semiclassics with self generated magnetic fields. Annales Henri Poincare. 2012;13(4):671-730. doi:10.1007/s00023-011-0150-z","ieee":"L. Erdös, S. Fournais, and J. Solovej, “Second order semiclassics with self generated magnetic fields,” Annales Henri Poincare, vol. 13, no. 4. Birkhäuser, pp. 671–730, 2012.","apa":"Erdös, L., Fournais, S., & Solovej, J. (2012). Second order semiclassics with self generated magnetic fields. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-011-0150-z","ista":"Erdös L, Fournais S, Solovej J. 2012. Second order semiclassics with self generated magnetic fields. Annales Henri Poincare. 13(4), 671–730."},"publication":"Annales Henri Poincare","date_published":"2012-05-01T00:00:00Z","doi":"10.1007/s00023-011-0150-z","day":"01","month":"05","intvolume":" 13","publisher":"Birkhäuser","status":"public","title":"Second order semiclassics with self generated magnetic fields","publication_status":"published","year":"2012","_id":"2772","volume":13,"date_created":"2018-12-11T11:59:31Z","date_updated":"2021-01-12T06:59:36Z","author":[{"full_name":"László Erdös","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"last_name":"Fournais","first_name":"Søren","full_name":"Fournais, Søren"},{"full_name":"Solovej, Jan P","first_name":"Jan","last_name":"Solovej"}],"type":"journal_article","extern":1,"issue":"4","publist_id":"4118","abstract":[{"lang":"eng","text":"We consider the semiclassical asymptotics of the sum of negative eigenvalues of the three-dimensional Pauli operator with an external potential and a self-generated magnetic field B. We also add the field energy β ∫ B 2 and we minimize over all magnetic fields. The parameter β effectively determines the strength of the field. We consider the weak field regime with βh 2 ≥ const > 0, where h is the semiclassical parameter. For smooth potentials we prove that the semiclassical asymptotics of the total energy is given by the non-magnetic Weyl term to leading order with an error bound that is smaller by a factor h 1+e{open}, i. e. the subleading term vanishes. However for potentials with a Coulomb singularity, the subleading term does not vanish due to the non-semiclassical effect of the singularity. Combined with a multiscale technique, this refined estimate is used in the companion paper (Erdo{double acute}s et al. in Scott correction for large molecules with a self-generated magnetic field, Preprint, 2011) to prove the second order Scott correction to the ground state energy of large atoms and molecules."}]},{"_id":"2776","year":"2012","title":"Spectral statistics of Erdős-Rényi graphs II: Eigenvalue spacing and the extreme eigenvalues","publication_status":"published","status":"public","intvolume":" 314","publisher":"Springer","author":[{"full_name":"László Erdös","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Knowles","first_name":"Antti","full_name":"Knowles, Antti"},{"full_name":"Yau, Horng-Tzer","first_name":"Horng","last_name":"Yau"},{"full_name":"Yin, Jun","first_name":"Jun","last_name":"Yin"}],"date_created":"2018-12-11T11:59:32Z","date_updated":"2021-01-12T06:59:37Z","volume":314,"type":"journal_article","abstract":[{"text":"We consider the ensemble of adjacency matrices of Erdős-Rényi random graphs, i.e. graphs on N vertices where every edge is chosen independently and with probability p ≡ p(N). We rescale the matrix so that its bulk eigenvalues are of order one. Under the assumption pN≫N2/3 , we prove the universality of eigenvalue distributions both in the bulk and at the edge of the spectrum. More precisely, we prove (1) that the eigenvalue spacing of the Erdős-Rényi graph in the bulk of the spectrum has the same distribution as that of the Gaussian orthogonal ensemble; and (2) that the second largest eigenvalue of the Erdős-Rényi graph has the same distribution as the largest eigenvalue of the Gaussian orthogonal ensemble. As an application of our method, we prove the bulk universality of generalized Wigner matrices under the assumption that the matrix entries have at least 4 + ε moments.","lang":"eng"}],"publist_id":"4114","issue":"3","extern":1,"publication":"Communications in Mathematical Physics","citation":{"ama":"Erdös L, Knowles A, Yau H, Yin J. Spectral statistics of Erdős-Rényi graphs II: Eigenvalue spacing and the extreme eigenvalues. Communications in Mathematical Physics. 2012;314(3):587-640. doi:10.1007/s00220-012-1527-7","ista":"Erdös L, Knowles A, Yau H, Yin J. 2012. Spectral statistics of Erdős-Rényi graphs II: Eigenvalue spacing and the extreme eigenvalues. Communications in Mathematical Physics. 314(3), 587–640.","ieee":"L. Erdös, A. Knowles, H. Yau, and J. Yin, “Spectral statistics of Erdős-Rényi graphs II: Eigenvalue spacing and the extreme eigenvalues,” Communications in Mathematical Physics, vol. 314, no. 3. Springer, pp. 587–640, 2012.","apa":"Erdös, L., Knowles, A., Yau, H., & Yin, J. (2012). Spectral statistics of Erdős-Rényi graphs II: Eigenvalue spacing and the extreme eigenvalues. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-012-1527-7","mla":"Erdös, László, et al. “Spectral Statistics of Erdős-Rényi Graphs II: Eigenvalue Spacing and the Extreme Eigenvalues.” Communications in Mathematical Physics, vol. 314, no. 3, Springer, 2012, pp. 587–640, doi:10.1007/s00220-012-1527-7.","short":"L. Erdös, A. Knowles, H. Yau, J. Yin, Communications in Mathematical Physics 314 (2012) 587–640.","chicago":"Erdös, László, Antti Knowles, Horng Yau, and Jun Yin. “Spectral Statistics of Erdős-Rényi Graphs II: Eigenvalue Spacing and the Extreme Eigenvalues.” Communications in Mathematical Physics. Springer, 2012. https://doi.org/10.1007/s00220-012-1527-7."},"quality_controlled":0,"page":"587 - 640","date_published":"2012-09-01T00:00:00Z","doi":"10.1007/s00220-012-1527-7","day":"01","month":"09"},{"month":"06","day":"01","page":"847 - 882","quality_controlled":0,"citation":{"chicago":"Erdös, László, Søren Fournais, and Jan Solovej. “Scott Correction for Large Atoms and Molecules in a Self-Generated Magnetic Field.” Communications in Mathematical Physics. Springer, 2012. https://doi.org/10.1007/s00220-012-1468-1.","mla":"Erdös, László, et al. “Scott Correction for Large Atoms and Molecules in a Self-Generated Magnetic Field.” Communications in Mathematical Physics, vol. 312, no. 3, Springer, 2012, pp. 847–82, doi:10.1007/s00220-012-1468-1.","short":"L. Erdös, S. Fournais, J. Solovej, Communications in Mathematical Physics 312 (2012) 847–882.","ista":"Erdös L, Fournais S, Solovej J. 2012. Scott correction for large atoms and molecules in a self-generated magnetic field. Communications in Mathematical Physics. 312(3), 847–882.","apa":"Erdös, L., Fournais, S., & Solovej, J. (2012). Scott correction for large atoms and molecules in a self-generated magnetic field. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-012-1468-1","ieee":"L. Erdös, S. Fournais, and J. Solovej, “Scott correction for large atoms and molecules in a self-generated magnetic field,” Communications in Mathematical Physics, vol. 312, no. 3. Springer, pp. 847–882, 2012.","ama":"Erdös L, Fournais S, Solovej J. Scott correction for large atoms and molecules in a self-generated magnetic field. Communications in Mathematical Physics. 2012;312(3):847-882. doi:10.1007/s00220-012-1468-1"},"publication":"Communications in Mathematical Physics","date_published":"2012-06-01T00:00:00Z","doi":"10.1007/s00220-012-1468-1","type":"journal_article","extern":1,"issue":"3","publist_id":"4116","abstract":[{"lang":"eng","text":"We consider a large neutral molecule with total nuclear charge Z in non-relativistic quantum mechanics with a self-generated classical electromagnetic field. To ensure stability, we assume that Zα 2 ≤ κ 0 for a sufficiently small κ 0, where α denotes the fine structure constant. We show that, in the simultaneous limit Z → ∞, α → 0 such that κ = Zα 2 is fixed, the ground state energy of the system is given by a two term expansion c 1Z 7/3 + c 2(κ) Z 2 + o(Z 2). The leading term is given by the non-magnetic Thomas-Fermi theory. Our result shows that the magnetic field affects only the second (so-called Scott) term in the expansion."}],"publisher":"Springer","intvolume":" 312","title":"Scott correction for large atoms and molecules in a self-generated magnetic field","status":"public","publication_status":"published","_id":"2774","year":"2012","volume":312,"date_created":"2018-12-11T11:59:31Z","date_updated":"2021-01-12T06:59:36Z","author":[{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"László Erdös"},{"full_name":"Fournais, Søren","last_name":"Fournais","first_name":"Søren"},{"full_name":"Solovej, Jan P","first_name":"Jan","last_name":"Solovej"}]},{"day":"10","month":"04","quality_controlled":0,"publication":"Electronic Journal of Probability","citation":{"ista":"Erdös L, Yau H. 2012. A comment on the Wigner-Dyson-Mehta bulk universality conjecture for Wigner matrices. Electronic Journal of Probability. 17.","apa":"Erdös, L., & Yau, H. (2012). A comment on the Wigner-Dyson-Mehta bulk universality conjecture for Wigner matrices. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/EJP.v17-1779","ieee":"L. Erdös and H. Yau, “A comment on the Wigner-Dyson-Mehta bulk universality conjecture for Wigner matrices,” Electronic Journal of Probability, vol. 17. Institute of Mathematical Statistics, 2012.","ama":"Erdös L, Yau H. A comment on the Wigner-Dyson-Mehta bulk universality conjecture for Wigner matrices. Electronic Journal of Probability. 2012;17. doi:10.1214/EJP.v17-1779","chicago":"Erdös, László, and Horng Yau. “A Comment on the Wigner-Dyson-Mehta Bulk Universality Conjecture for Wigner Matrices.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2012. https://doi.org/10.1214/EJP.v17-1779.","mla":"Erdös, László, and Horng Yau. “A Comment on the Wigner-Dyson-Mehta Bulk Universality Conjecture for Wigner Matrices.” Electronic Journal of Probability, vol. 17, Institute of Mathematical Statistics, 2012, doi:10.1214/EJP.v17-1779.","short":"L. Erdös, H. Yau, Electronic Journal of Probability 17 (2012)."},"doi":"10.1214/EJP.v17-1779","date_published":"2012-04-10T00:00:00Z","type":"journal_article","extern":1,"abstract":[{"lang":"eng","text":"Recently we proved [3, 4, 6, 7, 9, 10, 11] that the eigenvalue correlation functions of a general class of random matrices converge, weakly with respect to the energy, to the corresponding ones of Gaussian matrices. Tao and Vu [15] gave a proof that for the special case of Hermitian Wigner matrices the convergence can be strengthened to vague convergence at any fixed energy in the bulk. In this article we show that this theorem is an immediate corollary of our earlier results. Indeed, a more general form of this theorem also follows directly from our work [2]."}],"publist_id":"4117","title":"A comment on the Wigner-Dyson-Mehta bulk universality conjecture for Wigner matrices","publication_status":"published","status":"public","intvolume":" 17","publisher":"Institute of Mathematical Statistics","_id":"2773","year":"2012","date_updated":"2021-01-12T06:59:36Z","date_created":"2018-12-11T11:59:31Z","volume":17,"author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"László Erdös"},{"full_name":"Yau, Horng-Tzer","last_name":"Yau","first_name":"Horng"}]},{"type":"journal_article","extern":1,"abstract":[{"lang":"eng","text":"We consider a magnetic Schrödinger operator in two dimensions. The magnetic field is given as the sum of a large and constant magnetic field and a random magnetic field. Moreover, we allow for an additional deterministic potential as well as a magnetic field which are both periodic. We show that the spectrum of this operator is contained in broadened bands around the Landau levels and that the edges of these bands consist of pure point spectrum with exponentially decaying eigenfunctions. The proof is based on a recent Wegner estimate obtained in Erdos and Hasler (Commun. Math. Phys., preprint, arXiv:1012.5185) and a multiscale analysis."}],"issue":"5","publist_id":"4119","publication_status":"published","title":"Anderson localization at band edges for random magnetic fields","status":"public","publisher":"Springer","intvolume":" 146","_id":"2771","year":"2012","date_created":"2018-12-11T11:59:31Z","date_updated":"2021-01-12T06:59:35Z","volume":146,"author":[{"orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","first_name":"László","full_name":"László Erdös"},{"full_name":"Hasler, David G","first_name":"David","last_name":"Hasler"}],"day":"01","month":"03","quality_controlled":0,"page":"900 - 923","publication":"Journal of Statistical Physics","citation":{"short":"L. Erdös, D. Hasler, Journal of Statistical Physics 146 (2012) 900–923.","mla":"Erdös, László, and David Hasler. “Anderson Localization at Band Edges for Random Magnetic Fields.” Journal of Statistical Physics, vol. 146, no. 5, Springer, 2012, pp. 900–23, doi:10.1007/s10955-012-0445-6.","chicago":"Erdös, László, and David Hasler. “Anderson Localization at Band Edges for Random Magnetic Fields.” Journal of Statistical Physics. Springer, 2012. https://doi.org/10.1007/s10955-012-0445-6.","ama":"Erdös L, Hasler D. Anderson localization at band edges for random magnetic fields. Journal of Statistical Physics. 2012;146(5):900-923. doi:10.1007/s10955-012-0445-6","apa":"Erdös, L., & Hasler, D. (2012). Anderson localization at band edges for random magnetic fields. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-012-0445-6","ieee":"L. Erdös and D. Hasler, “Anderson localization at band edges for random magnetic fields,” Journal of Statistical Physics, vol. 146, no. 5. Springer, pp. 900–923, 2012.","ista":"Erdös L, Hasler D. 2012. Anderson localization at band edges for random magnetic fields. Journal of Statistical Physics. 146(5), 900–923."},"doi":"10.1007/s10955-012-0445-6","date_published":"2012-03-01T00:00:00Z"},{"doi":"10.1063/1.4751478","date_published":"2012-09-28T00:00:00Z","quality_controlled":0,"publication":"Journal of Mathematical Physics","citation":{"ista":"Bourgade P, Erdös L, Yau H. 2012. Bulk universality of general β-ensembles with non-convex potential. Journal of Mathematical Physics. 53(9).","apa":"Bourgade, P., Erdös, L., & Yau, H. (2012). Bulk universality of general β-ensembles with non-convex potential. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4751478","ieee":"P. Bourgade, L. Erdös, and H. Yau, “Bulk universality of general β-ensembles with non-convex potential,” Journal of Mathematical Physics, vol. 53, no. 9. American Institute of Physics, 2012.","ama":"Bourgade P, Erdös L, Yau H. Bulk universality of general β-ensembles with non-convex potential. Journal of Mathematical Physics. 2012;53(9). doi:10.1063/1.4751478","chicago":"Bourgade, Paul, László Erdös, and Horng Yau. “Bulk Universality of General β-Ensembles with Non-Convex Potential.” Journal of Mathematical Physics. American Institute of Physics, 2012. https://doi.org/10.1063/1.4751478.","mla":"Bourgade, Paul, et al. “Bulk Universality of General β-Ensembles with Non-Convex Potential.” Journal of Mathematical Physics, vol. 53, no. 9, American Institute of Physics, 2012, doi:10.1063/1.4751478.","short":"P. Bourgade, L. Erdös, H. Yau, Journal of Mathematical Physics 53 (2012)."},"day":"28","month":"09","date_created":"2018-12-11T11:59:33Z","date_updated":"2021-01-12T06:59:38Z","volume":53,"author":[{"full_name":"Bourgade, Paul","last_name":"Bourgade","first_name":"Paul"},{"full_name":"László Erdös","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"full_name":"Yau, Horng-Tzer","last_name":"Yau","first_name":"Horng"}],"title":"Bulk universality of general β-ensembles with non-convex potential","publication_status":"published","status":"public","intvolume":" 53","publisher":"American Institute of Physics","_id":"2778","year":"2012","extern":1,"abstract":[{"text":"We prove the bulk universality of the β-ensembles with non-convex regular analytic potentials for any β > 0. This removes the convexity assumption appeared in the earlier work [P. Bourgade, L. Erdös, and H.-T. Yau, Universality of general β-ensembles, preprint arXiv:0907.5605 (2011)]. The convexity condition enabled us to use the logarithmic Sobolev inequality to estimate events with small probability. The new idea is to introduce a "convexified measure" so that the local statistics are preserved under this convexification.","lang":"eng"}],"publist_id":"4112","issue":"9","type":"journal_article"},{"type":"journal_article","extern":1,"issue":"8","publist_id":"4111","abstract":[{"text":"We consider a two-dimensional magnetic Schrödinger operator on a square lattice with a spatially stationary random magnetic field. We prove Anderson localization near the spectral edges. We use a new approach to establish a Wegner estimate that does not rely on the monotonicity of the energy on the random parameters.","lang":"eng"}],"publisher":"Birkhäuser","intvolume":" 13","title":"Wegner estimate for random magnetic Laplacian on ℤ 2","publication_status":"published","status":"public","year":"2012","_id":"2779","volume":13,"date_updated":"2021-01-12T06:59:38Z","date_created":"2018-12-11T11:59:33Z","author":[{"first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","full_name":"László Erdös"},{"last_name":"Hasler","first_name":"David","full_name":"Hasler, David G"}],"month":"12","day":"01","page":"1719 - 1731","quality_controlled":0,"citation":{"short":"L. Erdös, D. Hasler, Annales Henri Poincare 13 (2012) 1719–1731.","mla":"Erdös, László, and David Hasler. “Wegner Estimate for Random Magnetic Laplacian on ℤ 2.” Annales Henri Poincare, vol. 13, no. 8, Birkhäuser, 2012, pp. 1719–31, doi:10.1007/s00023-012-0177-9.","chicago":"Erdös, László, and David Hasler. “Wegner Estimate for Random Magnetic Laplacian on ℤ 2.” Annales Henri Poincare. Birkhäuser, 2012. https://doi.org/10.1007/s00023-012-0177-9.","ama":"Erdös L, Hasler D. Wegner estimate for random magnetic Laplacian on ℤ 2. Annales Henri Poincare. 2012;13(8):1719-1731. doi:10.1007/s00023-012-0177-9","apa":"Erdös, L., & Hasler, D. (2012). Wegner estimate for random magnetic Laplacian on ℤ 2. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-012-0177-9","ieee":"L. Erdös and D. Hasler, “Wegner estimate for random magnetic Laplacian on ℤ 2,” Annales Henri Poincare, vol. 13, no. 8. Birkhäuser, pp. 1719–1731, 2012.","ista":"Erdös L, Hasler D. 2012. Wegner estimate for random magnetic Laplacian on ℤ 2. Annales Henri Poincare. 13(8), 1719–1731."},"publication":"Annales Henri Poincare","doi":"10.1007/s00023-012-0177-9","date_published":"2012-12-01T00:00:00Z"},{"page":"1187 - 1200","quality_controlled":0,"citation":{"ista":"Lapp T, Rohloff M, Vollmer J, Hof B. 2012. Particle tracking for polydisperse sedimenting droplets in phase separation. Experiments in Fluids. 52(5), 1187–1200.","apa":"Lapp, T., Rohloff, M., Vollmer, J., & Hof, B. (2012). Particle tracking for polydisperse sedimenting droplets in phase separation. Experiments in Fluids. Springer. https://doi.org/10.1007/s00348-011-1243-7","ieee":"T. Lapp, M. Rohloff, J. Vollmer, and B. Hof, “Particle tracking for polydisperse sedimenting droplets in phase separation,” Experiments in Fluids, vol. 52, no. 5. Springer, pp. 1187–1200, 2012.","ama":"Lapp T, Rohloff M, Vollmer J, Hof B. Particle tracking for polydisperse sedimenting droplets in phase separation. Experiments in Fluids. 2012;52(5):1187-1200. doi:10.1007/s00348-011-1243-7","chicago":"Lapp, Tobias, Martin Rohloff, Jürgen Vollmer, and Björn Hof. “Particle Tracking for Polydisperse Sedimenting Droplets in Phase Separation.” Experiments in Fluids. Springer, 2012. https://doi.org/10.1007/s00348-011-1243-7.","mla":"Lapp, Tobias, et al. “Particle Tracking for Polydisperse Sedimenting Droplets in Phase Separation.” Experiments in Fluids, vol. 52, no. 5, Springer, 2012, pp. 1187–200, doi:10.1007/s00348-011-1243-7.","short":"T. Lapp, M. Rohloff, J. Vollmer, B. Hof, Experiments in Fluids 52 (2012) 1187–1200."},"publication":"Experiments in Fluids","date_published":"2012-05-05T00:00:00Z","doi":"10.1007/s00348-011-1243-7","day":"05","month":"05","intvolume":" 52","publisher":"Springer","status":"public","title":"Particle tracking for polydisperse sedimenting droplets in phase separation","publication_status":"published","_id":"2802","year":"2012","volume":52,"date_created":"2018-12-11T11:59:40Z","date_updated":"2021-01-12T06:59:49Z","author":[{"full_name":"Lapp, Tobias","last_name":"Lapp","first_name":"Tobias"},{"first_name":"Martin","last_name":"Rohloff","full_name":"Rohloff, Martin"},{"first_name":"Jürgen","last_name":"Vollmer","full_name":"Vollmer, Jürgen T"},{"last_name":"Hof","first_name":"Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Björn Hof"}],"type":"journal_article","extern":1,"publist_id":"4087","issue":"5","abstract":[{"lang":"eng","text":"When a binary fluid demixes under a slow temperature ramp, nucleation, coarsening and sedimentation of droplets lead to an oscillatory evolution of the phase-separating system. The advection of the sedimenting droplets is found to be chaotic. The flow is driven by density differences between two phases. Here, we show how image processing can be combined with particle tracking to resolve droplet size and velocity simultaneously. Droplets are used as tracer particles, and the sedimentation velocity is determined. Taking these effects into account, droplets with radii in the range of 4-40 μm are detected and tracked. Based on these data, we resolve the oscillations in the droplet size distribution that are coupled to the convective flow."}]},{"date_created":"2018-12-11T11:59:41Z","date_updated":"2021-01-12T06:59:49Z","volume":108,"author":[{"full_name":"de Lózar, Alberto","last_name":"De Lózar","first_name":"Alberto"},{"full_name":"Mellibovsky, Fernando","first_name":"Fernando","last_name":"Mellibovsky"},{"first_name":"Marc","last_name":"Avila","full_name":"Avila, Marc"},{"full_name":"Björn Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"}],"title":"Edge state in pipe flow experiments","status":"public","publication_status":"published","intvolume":" 108","publisher":"American Physical Society","year":"2012","_id":"2803","extern":1,"abstract":[{"lang":"eng","text":"Recent numerical studies suggest that in pipe and related shear flows, the region of phase space separating laminar from turbulent motion is organized by a chaotic attractor, called an edge state, which mediates the transition process. We here confirm the existence of the edge state in laboratory experiments. We observe that it governs the dynamics during the decay of turbulence underlining its potential relevance for turbulence control. In addition we unveil two unstable traveling wave solutions underlying the experimental flow fields. This observation corroborates earlier suggestions that unstable solutions organize turbulence and its stability border."}],"publist_id":"4086","issue":"21","type":"journal_article","doi":"10.1103/PhysRevLett.108.214502","date_published":"2012-05-21T00:00:00Z","quality_controlled":0,"publication":"Physical Review Letters","citation":{"ama":"De Lózar A, Mellibovsky F, Avila M, Hof B. Edge state in pipe flow experiments. Physical Review Letters. 2012;108(21). doi:10.1103/PhysRevLett.108.214502","ieee":"A. De Lózar, F. Mellibovsky, M. Avila, and B. Hof, “Edge state in pipe flow experiments,” Physical Review Letters, vol. 108, no. 21. American Physical Society, 2012.","apa":"De Lózar, A., Mellibovsky, F., Avila, M., & Hof, B. (2012). Edge state in pipe flow experiments. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.108.214502","ista":"De Lózar A, Mellibovsky F, Avila M, Hof B. 2012. Edge state in pipe flow experiments. Physical Review Letters. 108(21).","short":"A. De Lózar, F. Mellibovsky, M. Avila, B. Hof, Physical Review Letters 108 (2012).","mla":"De Lózar, Alberto, et al. “Edge State in Pipe Flow Experiments.” Physical Review Letters, vol. 108, no. 21, American Physical Society, 2012, doi:10.1103/PhysRevLett.108.214502.","chicago":"De Lózar, Alberto, Fernando Mellibovsky, Marc Avila, and Björn Hof. “Edge State in Pipe Flow Experiments.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.108.214502."},"month":"05","day":"21"},{"citation":{"ista":"Blaschke J, Lapp T, Hof B, Vollmer J. 2012. Breath figures: Nucleation, growth, coalescence, and the size distribution of droplets. Physical Review Letters. 109(6).","ieee":"J. Blaschke, T. Lapp, B. Hof, and J. Vollmer, “Breath figures: Nucleation, growth, coalescence, and the size distribution of droplets,” Physical Review Letters, vol. 109, no. 6. American Physical Society, 2012.","apa":"Blaschke, J., Lapp, T., Hof, B., & Vollmer, J. (2012). Breath figures: Nucleation, growth, coalescence, and the size distribution of droplets. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.068701","ama":"Blaschke J, Lapp T, Hof B, Vollmer J. Breath figures: Nucleation, growth, coalescence, and the size distribution of droplets. Physical Review Letters. 2012;109(6). doi:10.1103/PhysRevLett.109.068701","chicago":"Blaschke, Johannes, Tobias Lapp, Björn Hof, and Jürgen Vollmer. “Breath Figures: Nucleation, Growth, Coalescence, and the Size Distribution of Droplets.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.068701.","mla":"Blaschke, Johannes, et al. “Breath Figures: Nucleation, Growth, Coalescence, and the Size Distribution of Droplets.” Physical Review Letters, vol. 109, no. 6, American Physical Society, 2012, doi:10.1103/PhysRevLett.109.068701.","short":"J. Blaschke, T. Lapp, B. Hof, J. Vollmer, Physical Review Letters 109 (2012)."},"publication":"Physical Review Letters","quality_controlled":0,"date_published":"2012-08-10T00:00:00Z","doi":"10.1103/PhysRevLett.109.068701","month":"08","day":"10","_id":"2804","year":"2012","intvolume":" 109","publisher":"American Physical Society","publication_status":"published","title":"Breath figures: Nucleation, growth, coalescence, and the size distribution of droplets","status":"public","author":[{"first_name":"Johannes","last_name":"Blaschke","full_name":"Blaschke, Johannes"},{"full_name":"Lapp, Tobias","last_name":"Lapp","first_name":"Tobias"},{"full_name":"Björn Hof","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn"},{"full_name":"Vollmer, Jürgen T","first_name":"Jürgen","last_name":"Vollmer"}],"volume":109,"date_updated":"2021-01-12T06:59:50Z","date_created":"2018-12-11T11:59:41Z","type":"journal_article","publist_id":"4085","issue":"6","abstract":[{"lang":"eng","text":"The analysis of the size distribution of droplets condensing on a substrate (breath figures) is a test ground for scaling theories. Here, we show that a faithful description of these distributions must explicitly deal with the growth mechanisms of the droplets. This finding establishes a gateway connecting nucleation and growth of the smallest droplets on surfaces to gross features of the evolution of the droplet size distribution"}],"extern":1},{"day":"01","month":"12","scopus_import":1,"conference":{"name":"NIPS: Neural Information Processing Systems","end_date":"2012-12-06","start_date":"2012-12-03","location":"Lake Tahoe, NV, United States"},"date_published":"2012-12-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Lampert C. Dynamic pruning of factor graphs for maximum marginal prediction. In: Vol 1. Neural Information Processing Systems; 2012:82-90.","ista":"Lampert C. 2012. Dynamic pruning of factor graphs for maximum marginal prediction. NIPS: Neural Information Processing Systems vol. 1, 82–90.","apa":"Lampert, C. (2012). Dynamic pruning of factor graphs for maximum marginal prediction (Vol. 1, pp. 82–90). Presented at the NIPS: Neural Information Processing Systems, Lake Tahoe, NV, United States: Neural Information Processing Systems.","ieee":"C. Lampert, “Dynamic pruning of factor graphs for maximum marginal prediction,” presented at the NIPS: Neural Information Processing Systems, Lake Tahoe, NV, United States, 2012, vol. 1, pp. 82–90.","mla":"Lampert, Christoph. Dynamic Pruning of Factor Graphs for Maximum Marginal Prediction. Vol. 1, Neural Information Processing Systems, 2012, pp. 82–90.","short":"C. Lampert, in:, Neural Information Processing Systems, 2012, pp. 82–90.","chicago":"Lampert, Christoph. “Dynamic Pruning of Factor Graphs for Maximum Marginal Prediction,” 1:82–90. Neural Information Processing Systems, 2012."},"quality_controlled":"1","page":"82 - 90","abstract":[{"text":"We study the problem of maximum marginal prediction (MMP) in probabilistic graphical models, a task that occurs, for example, as the Bayes optimal decision rule under a Hamming loss. MMP is typically performed as a two-stage procedure: one estimates each variable's marginal probability and then forms a prediction from the states of maximal probability. In this work we propose a simple yet effective technique for accelerating MMP when inference is sampling-based: instead of the above two-stage procedure we directly estimate the posterior probability of each decision variable. This allows us to identify the point of time when we are sufficiently certain about any individual decision. Whenever this is the case, we dynamically prune the variables we are confident about from the underlying factor graph. Consequently, at any time only samples of variables whose decision is still uncertain need to be created. Experiments in two prototypical scenarios, multi-label classification and image inpainting, show that adaptive sampling can drastically accelerate MMP without sacrificing prediction accuracy.","lang":"eng"}],"publist_id":"3975","type":"conference","author":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"date_created":"2018-12-11T11:59:48Z","date_updated":"2021-01-12T06:59:59Z","volume":1,"oa_version":"None","_id":"2825","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Dynamic pruning of factor graphs for maximum marginal prediction","publication_status":"published","publisher":"Neural Information Processing Systems","intvolume":" 1","department":[{"_id":"ChLa"}]},{"day":"21","scopus_import":1,"date_published":"2012-05-21T00:00:00Z","citation":{"ama":"Chatterjee K, Zufferey D, Nowak M. Evolutionary game dynamics in populations with different learners. Journal of Theoretical Biology. 2012;301:161-173. doi:10.1016/j.jtbi.2012.02.021","apa":"Chatterjee, K., Zufferey, D., & Nowak, M. (2012). Evolutionary game dynamics in populations with different learners. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2012.02.021","ieee":"K. Chatterjee, D. Zufferey, and M. Nowak, “Evolutionary game dynamics in populations with different learners,” Journal of Theoretical Biology, vol. 301. Elsevier, pp. 161–173, 2012.","ista":"Chatterjee K, Zufferey D, Nowak M. 2012. Evolutionary game dynamics in populations with different learners. Journal of Theoretical Biology. 301, 161–173.","short":"K. Chatterjee, D. Zufferey, M. Nowak, Journal of Theoretical Biology 301 (2012) 161–173.","mla":"Chatterjee, Krishnendu, et al. “Evolutionary Game Dynamics in Populations with Different Learners.” Journal of Theoretical Biology, vol. 301, Elsevier, 2012, pp. 161–73, doi:10.1016/j.jtbi.2012.02.021.","chicago":"Chatterjee, Krishnendu, Damien Zufferey, and Martin Nowak. “Evolutionary Game Dynamics in Populations with Different Learners.” Journal of Theoretical Biology. Elsevier, 2012. https://doi.org/10.1016/j.jtbi.2012.02.021."},"publication":"Journal of Theoretical Biology","page":"161 - 173","abstract":[{"lang":"eng","text":"We study evolutionary game theory in a setting where individuals learn from each other. We extend the traditional approach by assuming that a population contains individuals with different learning abilities. In particular, we explore the situation where individuals have different search spaces, when attempting to learn the strategies of others. The search space of an individual specifies the set of strategies learnable by that individual. The search space is genetically given and does not change under social evolutionary dynamics. We introduce a general framework and study a specific example in the context of direct reciprocity. For this example, we obtain the counter intuitive result that cooperation can only evolve for intermediate benefit-to-cost ratios, while small and large benefit-to-cost ratios favor defection. Our paper is a step toward making a connection between computational learning theory and evolutionary game dynamics."}],"type":"journal_article","oa_version":"Submitted Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2848","intvolume":" 301","status":"public","title":"Evolutionary game dynamics in populations with different learners","month":"05","doi":"10.1016/j.jtbi.2012.02.021","language":[{"iso":"eng"}],"external_id":{"pmid":["22394652"]},"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322297/","open_access":"1"}],"project":[{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","publist_id":"3946","ec_funded":1,"author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Zufferey, Damien","last_name":"Zufferey","first_name":"Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"volume":301,"date_created":"2018-12-11T11:59:55Z","date_updated":"2021-01-12T07:00:12Z","pmid":1,"year":"2012","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"Elsevier","publication_status":"published"},{"file":[{"checksum":"44ee8d173487e8ed41a51136816bbeb4","date_created":"2018-12-12T10:14:26Z","date_updated":"2020-07-14T12:45:51Z","relation":"main_file","file_id":"5078","file_size":392021,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-546-v1+1_2014-J-05-SteinerMinTrees.pdf"}],"oa_version":"Submitted Version","pubrep_id":"546","status":"public","title":"On the configuration space of Steiner minimal trees","ddc":["000"],"intvolume":" 67","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2849","issue":"6","type":"journal_article","date_published":"2012-01-01T00:00:00Z","page":"1167 - 1168","publication":"Russian Mathematical Surveys","citation":{"ama":"Edelsbrunner H, Strelkova N. On the configuration space of Steiner minimal trees. Russian Mathematical Surveys. 2012;67(6):1167-1168. doi:10.1070/RM2012v067n06ABEH004820","ista":"Edelsbrunner H, Strelkova N. 2012. On the configuration space of Steiner minimal trees. Russian Mathematical Surveys. 67(6), 1167–1168.","apa":"Edelsbrunner, H., & Strelkova, N. (2012). On the configuration space of Steiner minimal trees. Russian Mathematical Surveys. IOP Publishing Ltd. https://doi.org/10.1070/RM2012v067n06ABEH004820","ieee":"H. Edelsbrunner and N. Strelkova, “On the configuration space of Steiner minimal trees,” Russian Mathematical Surveys, vol. 67, no. 6. IOP Publishing Ltd., pp. 1167–1168, 2012.","mla":"Edelsbrunner, Herbert, and Nataliya Strelkova. “On the Configuration Space of Steiner Minimal Trees.” Russian Mathematical Surveys, vol. 67, no. 6, IOP Publishing Ltd., 2012, pp. 1167–68, doi:10.1070/RM2012v067n06ABEH004820.","short":"H. Edelsbrunner, N. Strelkova, Russian Mathematical Surveys 67 (2012) 1167–1168.","chicago":"Edelsbrunner, Herbert, and Nataliya Strelkova. “On the Configuration Space of Steiner Minimal Trees.” Russian Mathematical Surveys. IOP Publishing Ltd., 2012. https://doi.org/10.1070/RM2012v067n06ABEH004820."},"day":"01","has_accepted_license":"1","scopus_import":1,"date_created":"2018-12-11T11:59:55Z","date_updated":"2021-01-12T07:00:13Z","volume":67,"author":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nataliya","last_name":"Strelkova","full_name":"Strelkova, Nataliya"}],"publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"IOP Publishing Ltd.","year":"2012","file_date_updated":"2020-07-14T12:45:51Z","publist_id":"3943","language":[{"iso":"eng"}],"doi":"10.1070/RM2012v067n06ABEH004820","quality_controlled":"1","oa":1,"month":"01"},{"month":"07","day":"01","citation":{"ista":"Kiran N, Benková E, Reková A, Dubová J, Malbeck J, Palme K, Brzobohatý B. 2012. Retargeting a maize β-glucosidase to the vacuole - Evidence from intact plants that zeatin-O-glucoside is stored in the vacuole. Phytochemistry. 79, 67–77.","apa":"Kiran, N., Benková, E., Reková, A., Dubová, J., Malbeck, J., Palme, K., & Brzobohatý, B. (2012). Retargeting a maize β-glucosidase to the vacuole - Evidence from intact plants that zeatin-O-glucoside is stored in the vacuole. Phytochemistry. Elsevier. https://doi.org/10.1016/j.phytochem.2012.03.012","ieee":"N. Kiran et al., “Retargeting a maize β-glucosidase to the vacuole - Evidence from intact plants that zeatin-O-glucoside is stored in the vacuole,” Phytochemistry, vol. 79. Elsevier, pp. 67–77, 2012.","ama":"Kiran N, Benková E, Reková A, et al. Retargeting a maize β-glucosidase to the vacuole - Evidence from intact plants that zeatin-O-glucoside is stored in the vacuole. Phytochemistry. 2012;79:67-77. doi:10.1016/j.phytochem.2012.03.012","chicago":"Kiran, Nagavalli, Eva Benková, Alena Reková, Jaroslava Dubová, Jiří Malbeck, Klaus Palme, and Břetislav Brzobohatý. “Retargeting a Maize β-Glucosidase to the Vacuole - Evidence from Intact Plants That Zeatin-O-Glucoside Is Stored in the Vacuole.” Phytochemistry. Elsevier, 2012. https://doi.org/10.1016/j.phytochem.2012.03.012.","mla":"Kiran, Nagavalli, et al. “Retargeting a Maize β-Glucosidase to the Vacuole - Evidence from Intact Plants That Zeatin-O-Glucoside Is Stored in the Vacuole.” Phytochemistry, vol. 79, Elsevier, 2012, pp. 67–77, doi:10.1016/j.phytochem.2012.03.012.","short":"N. Kiran, E. Benková, A. Reková, J. Dubová, J. Malbeck, K. Palme, B. Brzobohatý, Phytochemistry 79 (2012) 67–77."},"publication":"Phytochemistry","page":"67 - 77","quality_controlled":0,"doi":"10.1016/j.phytochem.2012.03.012","date_published":"2012-07-01T00:00:00Z","type":"journal_article","publist_id":"3886","abstract":[{"lang":"eng","text":"Cytokinin (CK) activity is regulated by the complex interplay of their metabolism, transport, stability and cellular/tissue localization. O-glucosides of zeatin-type CKs are postulated to be storage and/or transport forms. Active CK levels are determined in part by their differential distribution of CK metabolites across different subcellular compartments. We have previously shown that overexpressing chloroplast-localized Zm-p60.1, a maize β-glucosidase capable of releasing active cytokinins from their O- and N3-glucosides, perturbs CK homeostasis in transgenic tobacco. We obtained tobacco (Nicotiana tabacum L., cv Petit Havana SR1) plants overexpressing a recombinant Zm-p60.1 that is targeted to the vacuole. The protein is correctly processed and localized to the vacuole. When grown on medium containing exogenous zeatin, transgenic seedlings rapidly accumulate fresh weight due to ectopic growths at the base of the hypocotyl. The presence of the enzyme in these ectopic structures is shown by histochemical staining. CK quantification reveals that these transgenic seedlings are unable to accumulate zeatin-O-glucoside to levels similar to those observed in the wild type. When crossed with tobacco overexpressing the zeatin-O-glucosyltransferase gene from Phaseolus, the vacuolar variant shows an almost complete reversion in the root elongation assay. This is the first evidence from intact plants that the vacuole is the storage organelle for CK O-glucosides and that they are available to attack by Zm-p60.1. We propose the use of Zm-p60.1 as a robust molecular tool that exploits the reversibility of O-glucosylation and enables delicate manipulations of active CK content at the cellular level."}],"extern":1,"_id":"2876","year":"2012","intvolume":" 79","publisher":"Elsevier","status":"public","title":"Retargeting a maize β-glucosidase to the vacuole - Evidence from intact plants that zeatin-O-glucoside is stored in the vacuole","publication_status":"published","author":[{"full_name":"Kiran, Nagavalli S","last_name":"Kiran","first_name":"Nagavalli"},{"full_name":"Eva Benková","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alena","last_name":"Reková","full_name":"Reková, Alena"},{"last_name":"Dubová","first_name":"Jaroslava","full_name":"Dubová, Jaroslava"},{"first_name":"Jiří","last_name":"Malbeck","full_name":"Malbeck, Jiří"},{"first_name":"Klaus","last_name":"Palme","full_name":"Palme, Klaus"},{"last_name":"Brzobohatý","first_name":"Břetislav","full_name":"Brzobohatý, Břetislav"}],"volume":79,"date_created":"2018-12-11T12:00:05Z","date_updated":"2021-01-12T07:00:25Z"},{"extern":1,"issue":"1595","publist_id":"3887","abstract":[{"text":"Phytohormones are important plant growth regulators that control many developmental processes, such as cell division, cell differentiation, organogenesis and morphogenesis. They regulate a multitude of apparently unrelated physiological processes, often with overlapping roles, and they mutually modulate their effects. These features imply important synergistic and antagonistic interactions between the various plant hormones. Auxin and cytokinin are central hormones involved in the regulation of plant growth and development, including processes determining root architecture, such as root pole establishment during early embryogenesis, root meristem maintenance and lateral root organogenesis. Thus, to control root development both pathways put special demands on the mechanisms that balance their activities and mediate their interactions. Here, we summarize recent knowledge on the role of auxin and cytokinin in the regulation of root architecture with special focus on lateral root organogenesis, discuss the latest findings on the molecular mechanisms of their interactions, and present forward genetic screen as a tool to identify novel molecular components of the auxin and cytokinin crosstalk.","lang":"eng"}],"type":"journal_article","volume":367,"date_updated":"2021-01-12T07:00:25Z","date_created":"2018-12-11T12:00:05Z","author":[{"full_name":"Bielach, Agnieszka","first_name":"Agnieszka","last_name":"Bielach"},{"full_name":"Duclercq, Jérôme","last_name":"Duclercq","first_name":"Jérôme"},{"full_name":"Peter Marhavy","id":"3F45B078-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5227-5741","first_name":"Peter","last_name":"Marhavy"},{"full_name":"Eva Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"}],"intvolume":" 367","publisher":"Royal Society, The","title":"Genetic approach towards the identification of auxin - cytokinin crosstalk components involved in root development","publication_status":"published","status":"public","_id":"2875","year":"2012","month":"06","day":"05","date_published":"2012-06-05T00:00:00Z","doi":"10.1098/rstb.2011.0233","page":"1469 - 1478","quality_controlled":0,"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3321684/"}],"citation":{"ama":"Bielach A, Duclercq J, Marhavý P, Benková E. Genetic approach towards the identification of auxin - cytokinin crosstalk components involved in root development. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2012;367(1595):1469-1478. doi:10.1098/rstb.2011.0233","ista":"Bielach A, Duclercq J, Marhavý P, Benková E. 2012. Genetic approach towards the identification of auxin - cytokinin crosstalk components involved in root development. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 367(1595), 1469–1478.","ieee":"A. Bielach, J. Duclercq, P. Marhavý, and E. Benková, “Genetic approach towards the identification of auxin - cytokinin crosstalk components involved in root development,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 367, no. 1595. Royal Society, The, pp. 1469–1478, 2012.","apa":"Bielach, A., Duclercq, J., Marhavý, P., & Benková, E. (2012). Genetic approach towards the identification of auxin - cytokinin crosstalk components involved in root development. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The. https://doi.org/10.1098/rstb.2011.0233","mla":"Bielach, Agnieszka, et al. “Genetic Approach towards the Identification of Auxin - Cytokinin Crosstalk Components Involved in Root Development.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 367, no. 1595, Royal Society, The, 2012, pp. 1469–78, doi:10.1098/rstb.2011.0233.","short":"A. Bielach, J. Duclercq, P. Marhavý, E. Benková, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 367 (2012) 1469–1478.","chicago":"Bielach, Agnieszka, Jérôme Duclercq, Peter Marhavý, and Eva Benková. “Genetic Approach towards the Identification of Auxin - Cytokinin Crosstalk Components Involved in Root Development.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, The, 2012. https://doi.org/10.1098/rstb.2011.0233."},"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences"},{"day":"01","month":"08","citation":{"chicago":"Guenot, Bernadette, Emmanuelle Bayer, Daniel Kierzkowski, Richard Smith, Therese Mandel, Petra Žádníková, Eva Benková, and Cris Kuhlemeier. “Pin1 Independent Leaf Initiation in Arabidopsis.” Plant Physiology. American Society of Plant Biologists, 2012. https://doi.org/10.1104/pp.112.200402.","short":"B. Guenot, E. Bayer, D. Kierzkowski, R. Smith, T. Mandel, P. Žádníková, E. Benková, C. Kuhlemeier, Plant Physiology 159 (2012) 1501–1510.","mla":"Guenot, Bernadette, et al. “Pin1 Independent Leaf Initiation in Arabidopsis.” Plant Physiology, vol. 159, no. 4, American Society of Plant Biologists, 2012, pp. 1501–10, doi:10.1104/pp.112.200402.","ieee":"B. Guenot et al., “Pin1 independent leaf initiation in Arabidopsis,” Plant Physiology, vol. 159, no. 4. American Society of Plant Biologists, pp. 1501–1510, 2012.","apa":"Guenot, B., Bayer, E., Kierzkowski, D., Smith, R., Mandel, T., Žádníková, P., … Kuhlemeier, C. (2012). Pin1 independent leaf initiation in Arabidopsis. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.112.200402","ista":"Guenot B, Bayer E, Kierzkowski D, Smith R, Mandel T, Žádníková P, Benková E, Kuhlemeier C. 2012. Pin1 independent leaf initiation in Arabidopsis. Plant Physiology. 159(4), 1501–1510.","ama":"Guenot B, Bayer E, Kierzkowski D, et al. Pin1 independent leaf initiation in Arabidopsis. Plant Physiology. 2012;159(4):1501-1510. doi:10.1104/pp.112.200402"},"publication":"Plant Physiology","page":"1501 - 1510","quality_controlled":0,"date_published":"2012-08-01T00:00:00Z","doi":"10.1104/pp.112.200402","type":"journal_article","issue":"4","publist_id":"3884","abstract":[{"lang":"eng","text":"Phyllotaxis, the regular arrangement of leaves and flowers around the stem, is a key feature of plant architecture. Current models propose that the spatiotemporal regulation of organ initiation is controlled by a positive feedback loop between the plant hormone auxin and its efflux carrier PIN-FORMED1 (PIN1). Consequently, pin1 mutants give rise to naked inflorescence stalks with few or no flowers, indicating that PIN1 plays a crucial role in organ initiation. However, pin1 mutants do produce leaves. In order to understand the regulatory mechanisms controlling leaf initiation in Arabidopsis (Arabidopsis thaliana) rosettes, we have characterized the vegetative pin1 phenotype in detail. We show that although the timing of leaf initiation in vegetative pin1 mutants is variable and divergence angles clearly deviate from the canonical 137° value, leaves are not positioned at random during early developmental stages. Our data further indicate that other PIN proteins are unlikely to explain the persistence of leaf initiation and positioning during pin1 vegetative development. Thus, phyllotaxis appears to be more complex than suggested by current mechanistic models."}],"extern":1,"_id":"2878","year":"2012","publisher":"American Society of Plant Biologists","intvolume":" 159","publication_status":"published","title":"Pin1 independent leaf initiation in Arabidopsis","status":"public","author":[{"full_name":"Guenot, Bernadette","last_name":"Guenot","first_name":"Bernadette"},{"first_name":"Emmanuelle","last_name":"Bayer","full_name":"Bayer, Emmanuelle"},{"full_name":"Kierzkowski, Daniel","first_name":"Daniel","last_name":"Kierzkowski"},{"full_name":"Smith, Richard S","last_name":"Smith","first_name":"Richard"},{"full_name":"Mandel, Therese","last_name":"Mandel","first_name":"Therese"},{"first_name":"Petra","last_name":"Žádníková","full_name":"Žádníková, Petra"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková","full_name":"Eva Benková"},{"first_name":"Cris","last_name":"Kuhlemeier","full_name":"Kuhlemeier, Cris"}],"volume":159,"date_updated":"2021-01-12T07:00:26Z","date_created":"2018-12-11T12:00:06Z"},{"type":"journal_article","abstract":[{"text":"Hormones, such as auxin and cytokinin, are involved in the complex molecular network that regulates the coordinated development of plant organs. Genes controlling ovule patterning have been identified and studied in detail; however, the roles of auxin and cytokinin in ovule development are largely unknown. Here we show that key cytokinin pathway genes, such as isopentenyltransferase and cytokinin receptors, are expressed during ovule development. Also, in a cre1-12 ahk2-2 ahk3-3 triple mutant with severely reduced cytokinin perception, expression of the auxin efflux facilitator PIN-FORMED 1 (PIN1) was severely reduced. In sporocyteless/nozzle (spl/nzz) mutants, which show a similar phenotype to the cre1-12 ahk2-2 ahk3-3 triple mutant, PIN1 expression is also reduced. Treatment with the exogenous cytokinin N6-benzylaminopurine also altered both auxin distribution and patterning of the ovule; this process required the homeodomain transcription factor BELL1 (BEL1). Thus, this article shows that cytokinin regulates ovule development through the regulation of PIN1. Furthermore, the transcription factors BEL1 and SPL/NZZ, previously described as key regulators of ovule development, are needed for the auxin and cytokinin signaling pathways for the correct patterning of the ovule.","lang":"eng"}],"publist_id":"3885","issue":"7","extern":1,"year":"2012","_id":"2879","status":"public","publication_status":"published","title":"The transcription factors BEL1 and SPL are required for cytokinin and auxin signaling during ovule development in Arabidopsis","publisher":"American Society of Plant Biologists","intvolume":" 24","author":[{"full_name":"Bencivenga, Stefano","last_name":"Bencivenga","first_name":"Stefano"},{"first_name":"Sara","last_name":"Simonini","full_name":"Simonini, Sara"},{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Eva Benková"},{"full_name":"Colombo, Lucia","last_name":"Colombo","first_name":"Lucia"}],"date_updated":"2021-01-12T07:00:26Z","date_created":"2018-12-11T12:00:06Z","volume":24,"day":"01","month":"07","publication":"Plant Cell","citation":{"chicago":"Bencivenga, Stefano, Sara Simonini, Eva Benková, and Lucia Colombo. “The Transcription Factors BEL1 and SPL Are Required for Cytokinin and Auxin Signaling during Ovule Development in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2012. https://doi.org/10.1105/tpc.112.100164.","short":"S. Bencivenga, S. Simonini, E. Benková, L. Colombo, Plant Cell 24 (2012) 2886–2897.","mla":"Bencivenga, Stefano, et al. “The Transcription Factors BEL1 and SPL Are Required for Cytokinin and Auxin Signaling during Ovule Development in Arabidopsis.” Plant Cell, vol. 24, no. 7, American Society of Plant Biologists, 2012, pp. 2886–97, doi:10.1105/tpc.112.100164.","apa":"Bencivenga, S., Simonini, S., Benková, E., & Colombo, L. (2012). The transcription factors BEL1 and SPL are required for cytokinin and auxin signaling during ovule development in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.112.100164","ieee":"S. Bencivenga, S. Simonini, E. Benková, and L. Colombo, “The transcription factors BEL1 and SPL are required for cytokinin and auxin signaling during ovule development in Arabidopsis,” Plant Cell, vol. 24, no. 7. American Society of Plant Biologists, pp. 2886–2897, 2012.","ista":"Bencivenga S, Simonini S, Benková E, Colombo L. 2012. The transcription factors BEL1 and SPL are required for cytokinin and auxin signaling during ovule development in Arabidopsis. Plant Cell. 24(7), 2886–2897.","ama":"Bencivenga S, Simonini S, Benková E, Colombo L. The transcription factors BEL1 and SPL are required for cytokinin and auxin signaling during ovule development in Arabidopsis. Plant Cell. 2012;24(7):2886-2897. doi:10.1105/tpc.112.100164"},"quality_controlled":0,"page":"2886 - 2897","date_published":"2012-07-01T00:00:00Z","doi":"10.1105/tpc.112.100164"},{"day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2012-12-01T00:00:00Z","publication":"Leibniz International Proceedings in Informatics","citation":{"ama":"Boker U, Henzinger TA. Approximate determinization of quantitative automata. In: Leibniz International Proceedings in Informatics. Vol 18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2012:362-373. doi:10.4230/LIPIcs.FSTTCS.2012.362","apa":"Boker, U., & Henzinger, T. A. (2012). Approximate determinization of quantitative automata. In Leibniz International Proceedings in Informatics (Vol. 18, pp. 362–373). Hyderabad, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2012.362","ieee":"U. Boker and T. A. Henzinger, “Approximate determinization of quantitative automata,” in Leibniz International Proceedings in Informatics, Hyderabad, India, 2012, vol. 18, pp. 362–373.","ista":"Boker U, Henzinger TA. 2012. Approximate determinization of quantitative automata. Leibniz International Proceedings in Informatics. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 18, 362–373.","short":"U. Boker, T.A. Henzinger, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 362–373.","mla":"Boker, Udi, and Thomas A. Henzinger. “Approximate Determinization of Quantitative Automata.” Leibniz International Proceedings in Informatics, vol. 18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 362–73, doi:10.4230/LIPIcs.FSTTCS.2012.362.","chicago":"Boker, Udi, and Thomas A Henzinger. “Approximate Determinization of Quantitative Automata.” In Leibniz International Proceedings in Informatics, 18:362–73. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012. https://doi.org/10.4230/LIPIcs.FSTTCS.2012.362."},"page":"362 - 373","abstract":[{"text":"Quantitative automata are nondeterministic finite automata with edge weights. They value a\r\nrun by some function from the sequence of visited weights to the reals, and value a word by its\r\nminimal/maximal run. They generalize boolean automata, and have gained much attention in\r\nrecent years. Unfortunately, important automaton classes, such as sum, discounted-sum, and\r\nlimit-average automata, cannot be determinized. Yet, the quantitative setting provides the potential\r\nof approximate determinization. We define approximate determinization with respect to\r\na distance function, and investigate this potential.\r\nWe show that sum automata cannot be determinized approximately with respect to any\r\ndistance function. However, restricting to nonnegative weights allows for approximate determinization\r\nwith respect to some distance functions.\r\nDiscounted-sum automata allow for approximate determinization, as the influence of a word’s\r\nsuffix is decaying. However, the naive approach, of unfolding the automaton computations up\r\nto a sufficient level, is shown to be doubly exponential in the discount factor. We provide an\r\nalternative construction that is singly exponential in the discount factor, in the precision, and\r\nin the number of states. We prove matching lower bounds, showing exponential dependency on\r\neach of these three parameters.\r\nAverage and limit-average automata are shown to prohibit approximate determinization with\r\nrespect to any distance function, and this is the case even for two weights, 0 and 1.","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"pubrep_id":"805","file":[{"content_type":"application/pdf","file_size":559069,"creator":"system","access_level":"open_access","file_name":"IST-2017-805-v1+1_34.pdf","checksum":"88da18d3e2cb2e5011d7d10ce38a3864","date_created":"2018-12-12T10:10:37Z","date_updated":"2020-07-14T12:45:52Z","relation":"main_file","file_id":"4826"}],"oa_version":"Published Version","_id":"2891","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["004"],"title":"Approximate determinization of quantitative automata","status":"public","intvolume":" 18","month":"12","conference":{"end_date":"2012-12-17","location":"Hyderabad, India","start_date":"2012-12-15","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science"},"doi":"10.4230/LIPIcs.FSTTCS.2012.362","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"}],"file_date_updated":"2020-07-14T12:45:52Z","publist_id":"3867","ec_funded":1,"author":[{"full_name":"Boker, Udi","last_name":"Boker","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"}],"date_updated":"2021-01-12T07:00:31Z","date_created":"2018-12-11T12:00:10Z","volume":18,"year":"2012","acknowledgement":"We thank Laurent Doyen for great ideas and valuable help in analyzing discounted-sum automata.","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}]},{"language":[{"iso":"eng"}],"conference":{"name":"EMSOFT: Embedded Software ","location":"Tampere, Finland","start_date":"2012-10-07","end_date":"2012-10-12"},"doi":"10.1145/2380356.2380371","date_published":"2012-10-01T00:00:00Z","quality_controlled":"1","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"page":"53 - 62","publication":"Proceedings of the tenth ACM international conference on Embedded software","citation":{"ista":"Cerny P, Gopi S, Henzinger TA, Radhakrishna A, Totla N. 2012. Synthesis from incompatible specifications. Proceedings of the tenth ACM international conference on Embedded software. EMSOFT: Embedded Software , 53–62.","apa":"Cerny, P., Gopi, S., Henzinger, T. A., Radhakrishna, A., & Totla, N. (2012). Synthesis from incompatible specifications. In Proceedings of the tenth ACM international conference on Embedded software (pp. 53–62). Tampere, Finland: ACM. https://doi.org/10.1145/2380356.2380371","ieee":"P. Cerny, S. Gopi, T. A. Henzinger, A. Radhakrishna, and N. Totla, “Synthesis from incompatible specifications,” in Proceedings of the tenth ACM international conference on Embedded software, Tampere, Finland, 2012, pp. 53–62.","ama":"Cerny P, Gopi S, Henzinger TA, Radhakrishna A, Totla N. Synthesis from incompatible specifications. In: Proceedings of the Tenth ACM International Conference on Embedded Software. ACM; 2012:53-62. doi:10.1145/2380356.2380371","chicago":"Cerny, Pavol, Sivakanth Gopi, Thomas A Henzinger, Arjun Radhakrishna, and Nishant Totla. “Synthesis from Incompatible Specifications.” In Proceedings of the Tenth ACM International Conference on Embedded Software, 53–62. ACM, 2012. https://doi.org/10.1145/2380356.2380371.","mla":"Cerny, Pavol, et al. “Synthesis from Incompatible Specifications.” Proceedings of the Tenth ACM International Conference on Embedded Software, ACM, 2012, pp. 53–62, doi:10.1145/2380356.2380371.","short":"P. Cerny, S. Gopi, T.A. Henzinger, A. Radhakrishna, N. Totla, in:, Proceedings of the Tenth ACM International Conference on Embedded Software, ACM, 2012, pp. 53–62."},"month":"10","day":"01","scopus_import":1,"date_created":"2018-12-11T12:00:10Z","date_updated":"2021-01-12T07:00:30Z","oa_version":"None","author":[{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","first_name":"Pavol"},{"full_name":"Gopi, Sivakanth","first_name":"Sivakanth","last_name":"Gopi"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Arjun","last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun"},{"full_name":"Totla, Nishant","last_name":"Totla","first_name":"Nishant"}],"publication_status":"published","status":"public","title":"Synthesis from incompatible specifications","department":[{"_id":"ToHe"}],"publisher":"ACM","year":"2012","_id":"2890","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Systems are often specified using multiple requirements on their behavior. In practice, these requirements can be contradictory. The classical approach to specification, verification, and synthesis demands more detailed specifications that resolve any contradictions in the requirements. These detailed specifications are usually large, cumbersome, and hard to maintain or modify. In contrast, quantitative frameworks allow the formalization of the intuitive idea that what is desired is an implementation that comes "closest" to satisfying the mutually incompatible requirements, according to a measure of fit that can be defined by the requirements engineer. One flexible framework for quantifying how "well" an implementation satisfies a specification is offered by simulation distances that are parameterized by an error model. We introduce this framework, study its properties, and provide an algorithmic solution for the following quantitative synthesis question: given two (or more) behavioral requirements specified by possibly incompatible finite-state machines, and an error model, find the finite-state implementation that minimizes the maximal simulation distance to the given requirements. Furthermore, we generalize the framework to handle infinite alphabets (for example, realvalued domains). We also demonstrate how quantitative specifications based on simulation distances might lead to smaller and easier to modify specifications. Finally, we illustrate our approach using case studies on error correcting codes and scheduler synthesis."}],"publist_id":"3868","ec_funded":1,"type":"conference"},{"quality_controlled":"1","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"conference":{"name":"MODELS: Model-driven Engineering Languages and Systems","location":"Innsbruck, Austria","start_date":"2012-09-30","end_date":"2012-10-05"},"doi":"10.1007/978-3-642-33666-9_1","language":[{"iso":"eng"}],"month":"09","year":"2012","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"date_updated":"2021-01-12T07:00:29Z","date_created":"2018-12-11T12:00:09Z","volume":7590,"publist_id":"3870","ec_funded":1,"publication":"Conference proceedings MODELS 2012","citation":{"ama":"Henzinger TA. Quantitative reactive models. In: Conference Proceedings MODELS 2012. Vol 7590. Springer; 2012:1-2. doi:10.1007/978-3-642-33666-9_1","ieee":"T. A. Henzinger, “Quantitative reactive models,” in Conference proceedings MODELS 2012, Innsbruck, Austria, 2012, vol. 7590, pp. 1–2.","apa":"Henzinger, T. A. (2012). Quantitative reactive models. In Conference proceedings MODELS 2012 (Vol. 7590, pp. 1–2). Innsbruck, Austria: Springer. https://doi.org/10.1007/978-3-642-33666-9_1","ista":"Henzinger TA. 2012. Quantitative reactive models. Conference proceedings MODELS 2012. MODELS: Model-driven Engineering Languages and Systems, LNCS, vol. 7590, 1–2.","short":"T.A. Henzinger, in:, Conference Proceedings MODELS 2012, Springer, 2012, pp. 1–2.","mla":"Henzinger, Thomas A. “Quantitative Reactive Models.” Conference Proceedings MODELS 2012, vol. 7590, Springer, 2012, pp. 1–2, doi:10.1007/978-3-642-33666-9_1.","chicago":"Henzinger, Thomas A. “Quantitative Reactive Models.” In Conference Proceedings MODELS 2012, 7590:1–2. Springer, 2012. https://doi.org/10.1007/978-3-642-33666-9_1."},"page":"1 - 2","date_published":"2012-09-01T00:00:00Z","scopus_import":1,"day":"01","_id":"2888","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Quantitative reactive models","intvolume":" 7590","oa_version":"None","type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Formal verification aims to improve the quality of hardware and software by detecting errors before they do harm. At the basis of formal verification lies the logical notion of correctness, which purports to capture whether or not a circuit or program behaves as desired. We suggest that the boolean partition into correct and incorrect systems falls short of the practical need to assess the behavior of hardware and software in a more nuanced fashion against multiple criteria.","lang":"eng"}]},{"type":"conference","abstract":[{"text":"In order to enjoy a digital version of the Jordan Curve Theorem, it is common to use the closed topology for the foreground and the open topology for the background of a 2-dimensional binary image. In this paper, we introduce a single topology that enjoys this theorem for all thresholds decomposing a real-valued image into foreground and background. This topology is easy to construct and it generalizes to n-dimensional images.","lang":"eng"}],"ddc":["000"],"status":"public","title":"The adaptive topology of a digital image","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2903","file":[{"access_level":"open_access","file_name":"IST-2016-545-v1+1_2012-P-10-AdaptiveTopology.pdf","creator":"system","content_type":"application/pdf","file_size":760548,"file_id":"4765","relation":"main_file","checksum":"444869a4e8abf07834f88b6e5cb5e9c3","date_updated":"2020-07-14T12:45:52Z","date_created":"2018-12-12T10:09:41Z"}],"oa_version":"Submitted Version","pubrep_id":"545","scopus_import":1,"has_accepted_license":"1","day":"06","page":"41 - 48","citation":{"ama":"Edelsbrunner H, Symonova O. The adaptive topology of a digital image. In: IEEE; 2012:41-48. doi:10.1109/ISVD.2012.11","apa":"Edelsbrunner, H., & Symonova, O. (2012). The adaptive topology of a digital image (pp. 41–48). Presented at the ISVD: International Symposium on Voronoi Diagrams in Science and Engineering, New Brunswick, NJ, USA : IEEE. https://doi.org/10.1109/ISVD.2012.11","ieee":"H. Edelsbrunner and O. Symonova, “The adaptive topology of a digital image,” presented at the ISVD: International Symposium on Voronoi Diagrams in Science and Engineering, New Brunswick, NJ, USA , 2012, pp. 41–48.","ista":"Edelsbrunner H, Symonova O. 2012. The adaptive topology of a digital image. ISVD: International Symposium on Voronoi Diagrams in Science and Engineering, 41–48.","short":"H. Edelsbrunner, O. Symonova, in:, IEEE, 2012, pp. 41–48.","mla":"Edelsbrunner, Herbert, and Olga Symonova. The Adaptive Topology of a Digital Image. IEEE, 2012, pp. 41–48, doi:10.1109/ISVD.2012.11.","chicago":"Edelsbrunner, Herbert, and Olga Symonova. “The Adaptive Topology of a Digital Image,” 41–48. IEEE, 2012. https://doi.org/10.1109/ISVD.2012.11."},"date_published":"2012-08-06T00:00:00Z","publist_id":"3844","file_date_updated":"2020-07-14T12:45:52Z","publisher":"IEEE","department":[{"_id":"HeEd"},{"_id":"MaJö"}],"publication_status":"published","year":"2012","date_created":"2018-12-11T12:00:15Z","date_updated":"2021-01-12T07:00:35Z","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","first_name":"Olga","last_name":"Symonova","full_name":"Symonova, Olga"}],"month":"08","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1109/ISVD.2012.11","conference":{"end_date":"2012-06-29","location":"New Brunswick, NJ, USA ","start_date":"2012-06-27","name":"ISVD: International Symposium on Voronoi Diagrams in Science and Engineering"}},{"conference":{"end_date":"2012-09-08","location":"Napoli, Italy","start_date":"2012-09-06","name":"GandALF: Games, Automata, Logic, and Formal Verification"},"doi":"10.4204/EPTCS.96.3","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1210.2450"}],"external_id":{"arxiv":["1210.2450"]},"oa":1,"quality_controlled":"1","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"month":"10","author":[{"last_name":"Cerny","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Radhakrishna","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun"}],"related_material":{"record":[{"id":"1733","status":"public","relation":"later_version"}]},"date_updated":"2023-02-23T10:12:05Z","date_created":"2018-12-11T12:00:19Z","volume":96,"year":"2012","publication_status":"published","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"EPTCS","publist_id":"3827","ec_funded":1,"date_published":"2012-10-07T00:00:00Z","publication":"Electronic Proceedings in Theoretical Computer Science","citation":{"chicago":"Cerny, Pavol, Martin Chmelik, Thomas A Henzinger, and Arjun Radhakrishna. “Interface Simulation Distances.” In Electronic Proceedings in Theoretical Computer Science, 96:29–42. EPTCS, 2012. https://doi.org/10.4204/EPTCS.96.3.","short":"P. Cerny, M. Chmelik, T.A. Henzinger, A. Radhakrishna, in:, Electronic Proceedings in Theoretical Computer Science, EPTCS, 2012, pp. 29–42.","mla":"Cerny, Pavol, et al. “Interface Simulation Distances.” Electronic Proceedings in Theoretical Computer Science, vol. 96, EPTCS, 2012, pp. 29–42, doi:10.4204/EPTCS.96.3.","apa":"Cerny, P., Chmelik, M., Henzinger, T. A., & Radhakrishna, A. (2012). Interface Simulation Distances. In Electronic Proceedings in Theoretical Computer Science (Vol. 96, pp. 29–42). Napoli, Italy: EPTCS. https://doi.org/10.4204/EPTCS.96.3","ieee":"P. Cerny, M. Chmelik, T. A. Henzinger, and A. Radhakrishna, “Interface Simulation Distances,” in Electronic Proceedings in Theoretical Computer Science, Napoli, Italy, 2012, vol. 96, pp. 29–42.","ista":"Cerny P, Chmelik M, Henzinger TA, Radhakrishna A. 2012. Interface Simulation Distances. Electronic Proceedings in Theoretical Computer Science. GandALF: Games, Automata, Logic, and Formal Verification vol. 96, 29–42.","ama":"Cerny P, Chmelik M, Henzinger TA, Radhakrishna A. Interface Simulation Distances. In: Electronic Proceedings in Theoretical Computer Science. Vol 96. EPTCS; 2012:29-42. doi:10.4204/EPTCS.96.3"},"page":"29 - 42","day":"07","scopus_import":1,"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2916","title":"Interface Simulation Distances","status":"public","intvolume":" 96","abstract":[{"lang":"eng","text":"The classical (boolean) notion of refinement for behavioral interfaces of system components is the alternating refinement preorder. In this paper, we define a quantitative measure for interfaces, called interface simulation distance. It makes the alternating refinement preorder quantitative by, intu- itively, tolerating errors (while counting them) in the alternating simulation game. We show that the interface simulation distance satisfies the triangle inequality, that the distance between two interfaces does not increase under parallel composition with a third interface, and that the distance between two interfaces can be bounded from above and below by distances between abstractions of the two interfaces. We illustrate the framework, and the properties of the distances under composition of interfaces, with two case studies."}],"type":"conference"},{"scopus_import":1,"month":"11","day":"06","citation":{"mla":"de Vladar, Harold. “The Game of Active Search for Extra Terrestrial Intelligence Breaking the Great Silence .” International Journal of Astrobiology, vol. 12, no. 1, Cambridge University Press, 2012, pp. 53–62, doi:10.1017/S1473550412000407.","short":"H. de Vladar, International Journal of Astrobiology 12 (2012) 53–62.","chicago":"Vladar, Harold de. “The Game of Active Search for Extra Terrestrial Intelligence Breaking the Great Silence .” International Journal of Astrobiology. Cambridge University Press, 2012. https://doi.org/10.1017/S1473550412000407.","ama":"de Vladar H. The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. 2012;12(1):53-62. doi:10.1017/S1473550412000407","ista":"de Vladar H. 2012. The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. 12(1), 53–62.","ieee":"H. de Vladar, “The game of active search for extra terrestrial intelligence Breaking the Great Silence ,” International Journal of Astrobiology, vol. 12, no. 1. Cambridge University Press, pp. 53–62, 2012.","apa":"de Vladar, H. (2012). The game of active search for extra terrestrial intelligence Breaking the Great Silence . International Journal of Astrobiology. Cambridge University Press. https://doi.org/10.1017/S1473550412000407"},"publication":"International Journal of Astrobiology","page":"53 - 62","quality_controlled":"1","date_published":"2012-11-06T00:00:00Z","doi":"10.1017/S1473550412000407","language":[{"iso":"eng"}],"type":"journal_article","publist_id":"3821","issue":"1","abstract":[{"lang":"eng","text":"The search for extra-terrestrial intelligence (SETI) has been performed principally as a one-way survey, listening of radio frequencies across the Milky Way and other galaxies. However, scientists have engaged in an active messaging only rarely. This suggests the simple rationale that if other civilizations exist and take a similar approach to ours, namely listening but not broadcasting, the result is a silent universe. A simple game theoretical model, the prisoner's dilemma, explains this situation: each player (civilization) can passively search (defect), or actively search and broadcast (cooperate). In order to maximize the payoff (or, equivalently, minimize the risks) the best strategy is not to broadcast. In fact, the active search has been opposed on the basis that it might be dangerous to expose ourselves. However, most of these ideas have not been based on objective arguments, and ignore accounting of the possible gains and losses. Thus, the question stands: should we perform an active search? I develop a game-theoretical framework where civilizations can be of different types, and explicitly apply it to a situation where societies are either interested in establishing a two-way communication or belligerent and in urge to exploit ours. The framework gives a quantitative solution (a mixed-strategy), which is how frequent we should perform the active SETI. This frequency is roughly proportional to the inverse of the risk, and can be extremely small. However, given the immense amount of stars being scanned, it supports active SETI. The model is compared with simulations, and the possible actions are evaluated through the San Marino scale, measuring the risks of messaging."}],"year":"2012","_id":"2917","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"publisher":"Cambridge University Press","intvolume":" 12","publication_status":"published","title":"The game of active search for extra terrestrial intelligence Breaking the Great Silence ","status":"public","author":[{"full_name":"Vladar, Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"Vladar","first_name":"Harold"}],"volume":12,"oa_version":"None","date_created":"2018-12-11T12:00:19Z","date_updated":"2021-01-12T07:00:41Z"},{"citation":{"chicago":"Edelsbrunner, Herbert, Alexander Ivanov, and Roman Karasev. “Open Problems in Discrete and Computational Geometry.” Automatic Control and Computer Sciences. Springer, 2012.","short":"H. Edelsbrunner, A. Ivanov, R. Karasev, Automatic Control and Computer Sciences in print (2012).","mla":"Edelsbrunner, Herbert, et al. “Open Problems in Discrete and Computational Geometry.” Automatic Control and Computer Sciences, vol. in print, Springer, 2012.","ieee":"H. Edelsbrunner, A. Ivanov, and R. Karasev, “Open problems in discrete and computational geometry,” Automatic Control and Computer Sciences, vol. in print. Springer, 2012.","apa":"Edelsbrunner, H., Ivanov, A., & Karasev, R. (2012). Open problems in discrete and computational geometry. Automatic Control and Computer Sciences. Springer.","ista":"Edelsbrunner H, Ivanov A, Karasev R. 2012. Open problems in discrete and computational geometry. Automatic Control and Computer Sciences. in print.","ama":"Edelsbrunner H, Ivanov A, Karasev R. Open problems in discrete and computational geometry. Automatic Control and Computer Sciences. 2012;in print."},"publication":"Automatic Control and Computer Sciences","quality_controlled":0,"date_published":"2012-01-01T00:00:00Z","month":"01","day":"01","year":"2012","_id":"2911","publisher":"Springer","publication_status":"published","status":"public","title":"Open problems in discrete and computational geometry","author":[{"full_name":"Herbert Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"first_name":"Alexander","last_name":"Ivanov","full_name":"Ivanov, Alexander"},{"full_name":"Karasev, Roman","last_name":"Karasev","first_name":"Roman"}],"volume":"in print","date_updated":"2021-01-12T07:00:38Z","date_created":"2018-12-11T12:00:18Z","type":"journal_article","publist_id":"3832","abstract":[{"lang":"eng","text":"We have selected problems that may not yet be well known, but have the\npotential to push the research in interesting directions. In particular, we state\nproblems that do not require specific knowledge outside the standard circle of ideas\nin discrete geometry. Despite the relatively simple statements, these problems are\nrelated to current research and their solutions are likely to require new ideas and\napproaches. We have chosen problems from different fields to make this short paper\nattractive to a wide range of specialists."}],"extern":1},{"month":"04","main_file_link":[{"url":"http://arxiv.org/abs/1309.5469","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.1007/978-3-642-32147-4_40","conference":{"location":"Athens, Greece","start_date":"2012-04-19","end_date":"2012-04-21","name":"ISCO: International Symposium on Combinatorial Optimization"},"language":[{"iso":"eng"}],"publist_id":"3806","acknowledgement":"We would like to thank Andrei Krokhin for encourag- ing our cooperation, for helpful discussions, and for his critical reading of the manuscript.\r\n","year":"2012","publisher":"Springer","department":[{"_id":"VlKo"}],"publication_status":"published","author":[{"full_name":"Huber, Anna","first_name":"Anna","last_name":"Huber"},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"volume":7422,"date_created":"2018-12-11T12:00:24Z","date_updated":"2021-01-12T07:00:46Z","scopus_import":1,"day":"01","citation":{"chicago":"Huber, Anna, and Vladimir Kolmogorov. “Towards Minimizing K-Submodular Functions,” 7422:451–62. Springer, 2012. https://doi.org/10.1007/978-3-642-32147-4_40.","short":"A. Huber, V. Kolmogorov, in:, Springer, 2012, pp. 451–462.","mla":"Huber, Anna, and Vladimir Kolmogorov. Towards Minimizing K-Submodular Functions. Vol. 7422, Springer, 2012, pp. 451–62, doi:10.1007/978-3-642-32147-4_40.","apa":"Huber, A., & Kolmogorov, V. (2012). Towards minimizing k-submodular functions (Vol. 7422, pp. 451–462). Presented at the ISCO: International Symposium on Combinatorial Optimization, Athens, Greece: Springer. https://doi.org/10.1007/978-3-642-32147-4_40","ieee":"A. Huber and V. Kolmogorov, “Towards minimizing k-submodular functions,” presented at the ISCO: International Symposium on Combinatorial Optimization, Athens, Greece, 2012, vol. 7422, pp. 451–462.","ista":"Huber A, Kolmogorov V. 2012. Towards minimizing k-submodular functions. ISCO: International Symposium on Combinatorial Optimization, LNCS, vol. 7422, 451–462.","ama":"Huber A, Kolmogorov V. Towards minimizing k-submodular functions. In: Vol 7422. Springer; 2012:451-462. doi:10.1007/978-3-642-32147-4_40"},"page":"451 - 462","date_published":"2012-04-01T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"In this paper we investigate k-submodular functions. This natural family of discrete functions includes submodular and bisubmodular functions as the special cases k = 1 and k = 2 respectively.\r\n\r\nIn particular we generalize the known Min-Max-Theorem for submodular and bisubmodular functions. This theorem asserts that the minimum of the (bi)submodular function can be found by solving a maximization problem over a (bi)submodular polyhedron. We define a k-submodular polyhedron, prove a Min-Max-Theorem for k-submodular functions, and give a greedy algorithm to construct the vertices of the polyhedron.\r\n"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2930","intvolume":" 7422","title":"Towards minimizing k-submodular functions","status":"public","oa_version":"Preprint"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2928","year":"2012","status":"public","publication_status":"published","title":"Generalized sequential tree-reweighted message passing","publisher":"ArXiv","department":[{"_id":"VlKo"}],"author":[{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"},{"first_name":"Thomas","last_name":"Schoenemann","full_name":"Schoenemann, Thomas"}],"date_created":"2018-12-11T12:00:23Z","date_updated":"2021-01-12T07:00:45Z","oa_version":"Preprint","type":"preprint","abstract":[{"lang":"eng","text":" This paper addresses the problem of approximate MAP-MRF inference in general graphical models. Following [36], we consider a family of linear programming relaxations of the problem where each relaxation is specified by a set of nested pairs of factors for which the marginalization constraint needs to be enforced. We develop a generalization of the TRW-S algorithm [9] for this problem, where we use a decomposition into junction chains, monotonic w.r.t. some ordering on the nodes. This generalizes the monotonic chains in [9] in a natural way. We also show how to deal with nested factors in an efficient way. Experiments show an improvement over min-sum diffusion, MPLP and subgradient ascent algorithms on a number of computer vision and natural language processing problems. "}],"publist_id":"3809","publication":"arXiv","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1205.6352"}],"external_id":{"arxiv":["1205.6352"]},"oa":1,"citation":{"ista":"Kolmogorov V, Schoenemann T. 2012. Generalized sequential tree-reweighted message passing. arXiv, .","apa":"Kolmogorov, V., & Schoenemann, T. (2012). Generalized sequential tree-reweighted message passing. arXiv. ArXiv.","ieee":"V. Kolmogorov and T. Schoenemann, “Generalized sequential tree-reweighted message passing,” arXiv. ArXiv, 2012.","ama":"Kolmogorov V, Schoenemann T. Generalized sequential tree-reweighted message passing. arXiv. 2012.","chicago":"Kolmogorov, Vladimir, and Thomas Schoenemann. “Generalized Sequential Tree-Reweighted Message Passing.” ArXiv. ArXiv, 2012.","mla":"Kolmogorov, Vladimir, and Thomas Schoenemann. “Generalized Sequential Tree-Reweighted Message Passing.” ArXiv, ArXiv, 2012.","short":"V. Kolmogorov, T. Schoenemann, ArXiv (2012)."},"page":"16","date_published":"2012-05-29T00:00:00Z","language":[{"iso":"eng"}],"month":"05","day":"29","article_processing_charge":"No"},{"type":"report","extern":1,"publist_id":"3807","status":"public","publication_status":"published","title":"The power of linear programming for valued CSPs: a constructive characterization","publisher":"Unknown","_id":"2929","year":"2012","date_updated":"2019-04-26T07:22:21Z","date_created":"2018-12-11T12:00:24Z","author":[{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"day":"01","month":"01","quality_controlled":0,"citation":{"mla":"Kolmogorov, Vladimir. The Power of Linear Programming for Valued CSPs: A Constructive Characterization. Unknown, 2012.","short":"V. Kolmogorov, The Power of Linear Programming for Valued CSPs: A Constructive Characterization, Unknown, 2012.","chicago":"Kolmogorov, Vladimir. The Power of Linear Programming for Valued CSPs: A Constructive Characterization. Unknown, 2012.","ama":"Kolmogorov V. The Power of Linear Programming for Valued CSPs: A Constructive Characterization. Unknown; 2012.","ista":"Kolmogorov V. 2012. The power of linear programming for valued CSPs: a constructive characterization, Unknown,p.","ieee":"V. Kolmogorov, The power of linear programming for valued CSPs: a constructive characterization. Unknown, 2012.","apa":"Kolmogorov, V. (2012). The power of linear programming for valued CSPs: a constructive characterization. Unknown."},"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1207.7213","open_access":"1"}],"date_published":"2012-01-01T00:00:00Z"},{"type":"conference","publist_id":"3798","abstract":[{"lang":"eng","text":"Developers building cryptography into security-sensitive applications face a daunting task. Not only must they understand the security guarantees delivered by the constructions they choose, they must also implement and combine them correctly and efficiently. Cryptographic compilers free developers from this task by turning high-level specifications of security goals into efficient implementations. Yet, trusting such tools is hard as they rely on complex mathematical machinery and claim security properties that are subtle and difficult to verify. In this paper we present ZKCrypt, an optimizing cryptographic compiler achieving an unprecedented level of assurance without sacrificing practicality for a comprehensive class of cryptographic protocols, known as Zero-Knowledge Proofs of Knowledge. The pipeline of ZKCrypt integrates purpose-built verified compilers and verifying compilers producing formal proofs in the CertiCrypt framework. By combining the guarantees delivered by each stage, ZKCrypt provides assurance that the output implementation securely realizes the abstract proof goal given as input. We report on the main characteristics of ZKCrypt, highlight new definitions and concepts at its foundations, and illustrate its applicability through a representative example of an anonymous credential system."}],"department":[{"_id":"KrPi"}],"publisher":"ACM","title":"Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols","publication_status":"published","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2937","acknowledgement":"This work was partially funded by National Funds through the FCT - Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project ENI-AC/2224/2009, by ENIAC Joint Undertaking under grant agreement number 120224, European Projects FP7-256980 NESSoS and FP7-229599 AMAROUT, Spanish National project TIN2009-14599 DESAFIOS 10, and Madrid Regional project S2009TIC-1465 PROMETIDOS.","year":"2012","oa_version":"Submitted Version","date_updated":"2021-01-12T07:39:53Z","date_created":"2018-12-11T12:00:26Z","author":[{"first_name":"José","last_name":"Almeida","full_name":"Almeida, José"},{"first_name":"Manuel","last_name":"Barbosa","full_name":"Barbosa, Manuel"},{"full_name":"Bangerter, Endre","last_name":"Bangerter","first_name":"Endre"},{"first_name":"Gilles","last_name":"Barthe","full_name":"Barthe, Gilles"},{"orcid":"0000-0003-2835-9093","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","last_name":"Krenn","first_name":"Stephan","full_name":"Krenn, Stephan"},{"full_name":"Béguelin, Santiago","last_name":"Béguelin","first_name":"Santiago"}],"scopus_import":1,"day":"01","month":"10","page":"488 - 500","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2012/258"}],"oa":1,"citation":{"chicago":"Almeida, José, Manuel Barbosa, Endre Bangerter, Gilles Barthe, Stephan Krenn, and Santiago Béguelin. “Full Proof Cryptography: Verifiable Compilation of Efficient Zero-Knowledge Protocols.” In Proceedings of the 2012 ACM Conference on Computer and Communications Security, 488–500. ACM, 2012. https://doi.org/10.1145/2382196.2382249.","short":"J. Almeida, M. Barbosa, E. Bangerter, G. Barthe, S. Krenn, S. Béguelin, in:, Proceedings of the 2012 ACM Conference on Computer and Communications Security, ACM, 2012, pp. 488–500.","mla":"Almeida, José, et al. “Full Proof Cryptography: Verifiable Compilation of Efficient Zero-Knowledge Protocols.” Proceedings of the 2012 ACM Conference on Computer and Communications Security, ACM, 2012, pp. 488–500, doi:10.1145/2382196.2382249.","ieee":"J. Almeida, M. Barbosa, E. Bangerter, G. Barthe, S. Krenn, and S. Béguelin, “Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols,” in Proceedings of the 2012 ACM conference on Computer and communications security, Raleigh, NC, USA, 2012, pp. 488–500.","apa":"Almeida, J., Barbosa, M., Bangerter, E., Barthe, G., Krenn, S., & Béguelin, S. (2012). Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols. In Proceedings of the 2012 ACM conference on Computer and communications security (pp. 488–500). Raleigh, NC, USA: ACM. https://doi.org/10.1145/2382196.2382249","ista":"Almeida J, Barbosa M, Bangerter E, Barthe G, Krenn S, Béguelin S. 2012. Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols. Proceedings of the 2012 ACM conference on Computer and communications security. CCS: Computer and Communications Security, 488–500.","ama":"Almeida J, Barbosa M, Bangerter E, Barthe G, Krenn S, Béguelin S. Full proof cryptography: Verifiable compilation of efficient zero-knowledge protocols. In: Proceedings of the 2012 ACM Conference on Computer and Communications Security. ACM; 2012:488-500. doi:10.1145/2382196.2382249"},"publication":"Proceedings of the 2012 ACM conference on Computer and communications security","language":[{"iso":"eng"}],"doi":"10.1145/2382196.2382249","date_published":"2012-10-01T00:00:00Z","conference":{"name":"CCS: Computer and Communications Security","end_date":"2012-10-18","location":"Raleigh, NC, USA","start_date":"2012-10-16"}},{"oa_version":"Preprint","status":"public","title":"Finite automata with time delay blocks","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2936","abstract":[{"text":"The notion of delays arises naturally in many computational models, such as, in the design of circuits, control systems, and dataflow languages. In this work, we introduce automata with delay blocks (ADBs), extending finite state automata with variable time delay blocks, for deferring individual transition output symbols, in a discrete-time setting. We show that the ADB languages strictly subsume the regular languages, and are incomparable in expressive power to the context-free languages. We show that ADBs are closed under union, concatenation and Kleene star, and under intersection with regular languages, but not closed under complementation and intersection with other ADB languages. We show that the emptiness and the membership problems are decidable in polynomial time for ADBs, whereas the universality problem is undecidable. Finally we consider the linear-time model checking problem, i.e., whether the language of an ADB is contained in a regular language, and show that the model checking problem is PSPACE-complete. Copyright 2012 ACM.","lang":"eng"}],"type":"conference","date_published":"2012-10-01T00:00:00Z","page":"43 - 52","publication":"roceedings of the tenth ACM international conference on Embedded software","citation":{"ama":"Chatterjee K, Henzinger TA, Prabhu V. Finite automata with time delay blocks. In: Roceedings of the Tenth ACM International Conference on Embedded Software. ACM; 2012:43-52. doi:10.1145/2380356.2380370","ieee":"K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Finite automata with time delay blocks,” in roceedings of the tenth ACM international conference on Embedded software, Tampere, Finland, 2012, pp. 43–52.","apa":"Chatterjee, K., Henzinger, T. A., & Prabhu, V. (2012). Finite automata with time delay blocks. In roceedings of the tenth ACM international conference on Embedded software (pp. 43–52). Tampere, Finland: ACM. https://doi.org/10.1145/2380356.2380370","ista":"Chatterjee K, Henzinger TA, Prabhu V. 2012. Finite automata with time delay blocks. roceedings of the tenth ACM international conference on Embedded software. EMSOFT: Embedded Software , 43–52.","short":"K. Chatterjee, T.A. Henzinger, V. Prabhu, in:, Roceedings of the Tenth ACM International Conference on Embedded Software, ACM, 2012, pp. 43–52.","mla":"Chatterjee, Krishnendu, et al. “Finite Automata with Time Delay Blocks.” Roceedings of the Tenth ACM International Conference on Embedded Software, ACM, 2012, pp. 43–52, doi:10.1145/2380356.2380370.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Finite Automata with Time Delay Blocks.” In Roceedings of the Tenth ACM International Conference on Embedded Software, 43–52. ACM, 2012. https://doi.org/10.1145/2380356.2380370."},"day":"01","scopus_import":1,"date_created":"2018-12-11T12:00:26Z","date_updated":"2021-01-12T07:39:53Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"first_name":"Vinayak","last_name":"Prabhu","full_name":"Prabhu, Vinayak"}],"publication_status":"published","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publisher":"ACM","year":"2012","acknowledgement":"This work has been financially supported in part by the European Commission FP7-ICT Cognitive Systems, Interaction, and Robotics under the contract # 270180 (NOPTILUS); by Fundacao para Ciencia e Tecnologia under project PTDC/EEA-CRO/104901/2008 (Modeling and control of Networked vehicle systems in persistent autonomous operations); by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification; FWF NFN Grant No S11407-N23 (RiSE); ERC Start grant (279307: Graph Games); Microsoft faculty fellows award; ERC Advanced grant QUAREM; and FWF Grant No S11403-N23 (RiSE).","ec_funded":1,"publist_id":"3799","language":[{"iso":"eng"}],"conference":{"start_date":"2012-10-07","location":"Tampere, Finland","end_date":"2012-10-12","name":"EMSOFT: Embedded Software "},"doi":"10.1145/2380356.2380370","quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"main_file_link":[{"url":"http://arxiv.org/abs/1207.7019","open_access":"1"}],"oa":1,"month":"10"},{"abstract":[{"lang":"eng","text":"Social insects have a very high potential to become invasive pest species. Here, we explore how their social lifestyle and their interaction with parasites may contribute to this invasive success. Similar to solitary species, parasite release followed by the evolution of increased competitive ability can promote establishment of introduced social insect hosts in their introduced range. Genetic bottlenecks during introduction of low numbers of founder individuals decrease the genetic diversity at three levels: the population, the colony and the individual, with the colony level being specific to social insects. Reduced genetic diversity can affect both the individual immune system and the collective colony-level disease defences (social immunity). Still, the dual immune system is likely to make social insects more robust to parasite attack. Changes in social structure from small, family-based, territorially aggressive societies in native populations towards huge networks of cooperating nests (unicoloniality) occur in some invasive social insects, for example, most invasive ants and some termites. Unicoloniality is likely to affect disease dynamics in multiple ways. The free exchange of individuals within the population leads to an increased genetic heterogeneity among individuals of a single nest, thereby decreasing disease transmission. However, the multitude of reproductively active queens per colony buffers the effect of individual diseased queens and their offspring, which may result in a higher level of vertical disease transmission in unicolonial societies. Lastly, unicoloniality provides a competitive advantage over native species, allowing them to quickly become the dominant species in the habitat, which in turn selects for parasite adaptation to this common host genotype and thus eventually a high parasite pressure. Overall, invasions by insect societies are characterized by general features applying to all introduced species, as well as idiosyncrasies that emerge from their social lifestyle. It is important to study these effects in concert to be able to develop efficient management and biocontrol strategies. © 2012 British Ecological Society."}],"publist_id":"3797","issue":"6","type":"journal_article","date_created":"2018-12-11T12:00:27Z","date_updated":"2021-01-12T07:39:54Z","volume":26,"oa_version":"None","author":[{"orcid":"0000-0003-1832-8883","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","first_name":"Line V","full_name":"Ugelvig, Line V"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"title":"Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies","publication_status":"published","status":"public","intvolume":" 26","publisher":"Wiley-Blackwell","department":[{"_id":"SyCr"}],"_id":"2938","acknowledgement":"We thank Mark Brown, Christopher Pull, Meghan L. Vyleta, Miriam Stock, Barbara Casillas-Perez and three anonymous reviewers for valuable comments on the manuscript and Eva Sixt for ant drawings. Funding was obtained from the German Science Foundation (DFG, by an Individual Research Grant to S.C.) and the European Research Council (ERC, by an ERC-Starting Grant to SC and an Individual Marie Curie EIF fellowship to L.desU.). The authors declare no conflict of interests.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2012","month":"01","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1111/1365-2435.12013","date_published":"2012-01-01T00:00:00Z","quality_controlled":"1","page":"1300 - 1312","publication":"Functional Ecology","citation":{"ama":"Ugelvig LV, Cremer S. Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies. Functional Ecology. 2012;26(6):1300-1312. doi:10.1111/1365-2435.12013","apa":"Ugelvig, L. V., & Cremer, S. (2012). Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12013","ieee":"L. V. Ugelvig and S. Cremer, “Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies,” Functional Ecology, vol. 26, no. 6. Wiley-Blackwell, pp. 1300–1312, 2012.","ista":"Ugelvig LV, Cremer S. 2012. Effects of social immunity and unicoloniality on host parasite interactions in invasive insect societies. Functional Ecology. 26(6), 1300–1312.","short":"L.V. Ugelvig, S. Cremer, Functional Ecology 26 (2012) 1300–1312.","mla":"Ugelvig, Line V., and Sylvia Cremer. “Effects of Social Immunity and Unicoloniality on Host Parasite Interactions in Invasive Insect Societies.” Functional Ecology, vol. 26, no. 6, Wiley-Blackwell, 2012, pp. 1300–12, doi:10.1111/1365-2435.12013.","chicago":"Ugelvig, Line V, and Sylvia Cremer. “Effects of Social Immunity and Unicoloniality on Host Parasite Interactions in Invasive Insect Societies.” Functional Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/1365-2435.12013."}},{"scopus_import":1,"day":"08","month":"05","project":[{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"page":"259 - 271","quality_controlled":"1","citation":{"ieee":"L. Torresani, V. Kolmogorov, and C. Rother, “A dual decomposition approach to feature correspondence,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 35, no. 2. IEEE, pp. 259–271, 2012.","apa":"Torresani, L., Kolmogorov, V., & Rother, C. (2012). A dual decomposition approach to feature correspondence. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2012.105","ista":"Torresani L, Kolmogorov V, Rother C. 2012. A dual decomposition approach to feature correspondence. IEEE Transactions on Pattern Analysis and Machine Intelligence. 35(2), 259–271.","ama":"Torresani L, Kolmogorov V, Rother C. A dual decomposition approach to feature correspondence. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2012;35(2):259-271. doi:10.1109/TPAMI.2012.105","chicago":"Torresani, Lorenzo, Vladimir Kolmogorov, and Carsten Rother. “A Dual Decomposition Approach to Feature Correspondence.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2012. https://doi.org/10.1109/TPAMI.2012.105.","short":"L. Torresani, V. Kolmogorov, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence 35 (2012) 259–271.","mla":"Torresani, Lorenzo, et al. “A Dual Decomposition Approach to Feature Correspondence.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 35, no. 2, IEEE, 2012, pp. 259–71, doi:10.1109/TPAMI.2012.105."},"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","language":[{"iso":"eng"}],"date_published":"2012-05-08T00:00:00Z","doi":"10.1109/TPAMI.2012.105","type":"journal_article","issue":"2","publist_id":"3805","abstract":[{"text":"In this paper, we present a new approach for establishing correspondences between sparse image features related by an unknown nonrigid mapping and corrupted by clutter and occlusion, such as points extracted from images of different instances of the same object category. We formulate this matching task as an energy minimization problem by defining an elaborate objective function of the appearance and the spatial arrangement of the features. Optimization of this energy is an instance of graph matching, which is in general an NP-hard problem. We describe a novel graph matching optimization technique, which we refer to as dual decomposition (DD), and demonstrate on a variety of examples that this method outperforms existing graph matching algorithms. In the majority of our examples, DD is able to find the global minimum within a minute. The ability to globally optimize the objective allows us to accurately learn the parameters of our matching model from training examples. We show on several matching tasks that our learned model yields results superior to those of state-of-the-art methods.\r\n","lang":"eng"}],"department":[{"_id":"VlKo"}],"intvolume":" 35","publisher":"IEEE","publication_status":"published","status":"public","title":"A dual decomposition approach to feature correspondence","_id":"2931","acknowledgement":"This research was funded in part by Microsoft Research.","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"None","volume":35,"date_updated":"2021-01-12T07:00:46Z","date_created":"2018-12-11T12:00:24Z","author":[{"first_name":"Lorenzo","last_name":"Torresani","full_name":"Torresani, Lorenzo"},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"}]},{"month":"09","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-34059-8_20","conference":{"location":"Oxford, UK","start_date":"2012-03-19","end_date":"2012-03-21","name":"Monterey Workshop 2012"},"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","ec_funded":1,"publist_id":"3791","volume":7539,"date_created":"2018-12-11T12:00:28Z","date_updated":"2021-01-12T07:39:56Z","author":[{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","last_name":"Henzinger"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan","last_name":"Nickovic","full_name":"Nickovic, Dejan"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","acknowledgement":"ERC Advanced Grant QUAREM (Quantitative Reactive Modeling), FWF National Research Network RISE (Rigorous Systems Engineering)","year":"2012","day":"16","scopus_import":1,"date_published":"2012-09-16T00:00:00Z","page":"380 - 395","citation":{"ista":"Henzinger TA, Nickovic D. 2012. Independent implementability of viewpoints. Conference proceedings Monterey Workshop 2012. Monterey Workshop 2012, LNCS, vol. 7539, 380–395.","ieee":"T. A. Henzinger and D. Nickovic, “Independent implementability of viewpoints,” in Conference proceedings Monterey Workshop 2012, Oxford, UK, 2012, vol. 7539, pp. 380–395.","apa":"Henzinger, T. A., & Nickovic, D. (2012). Independent implementability of viewpoints. In Conference proceedings Monterey Workshop 2012 (Vol. 7539, pp. 380–395). Oxford, UK: Springer. https://doi.org/10.1007/978-3-642-34059-8_20","ama":"Henzinger TA, Nickovic D. Independent implementability of viewpoints. In: Conference Proceedings Monterey Workshop 2012. Vol 7539. Springer; 2012:380-395. doi:10.1007/978-3-642-34059-8_20","chicago":"Henzinger, Thomas A, and Dejan Nickovic. “Independent Implementability of Viewpoints.” In Conference Proceedings Monterey Workshop 2012, 7539:380–95. Springer, 2012. https://doi.org/10.1007/978-3-642-34059-8_20.","mla":"Henzinger, Thomas A., and Dejan Nickovic. “Independent Implementability of Viewpoints.” Conference Proceedings Monterey Workshop 2012, vol. 7539, Springer, 2012, pp. 380–95, doi:10.1007/978-3-642-34059-8_20.","short":"T.A. Henzinger, D. Nickovic, in:, Conference Proceedings Monterey Workshop 2012, Springer, 2012, pp. 380–395."},"publication":" Conference proceedings Monterey Workshop 2012","abstract":[{"lang":"eng","text":"Interface theories provide a formal framework for component-based development of software and hardware which supports the incremental design of systems and the independent implementability of components. These capabilities are ensured through mathematical properties of the parallel composition operator and the refinement relation for components. More recently, a conjunction operation was added to interface theories in order to provide support for handling multiple viewpoints, requirements engineering, and component reuse. Unfortunately, the conjunction operator does not allow independent implementability in general. In this paper, we study conditions that need to be imposed on interface models in order to enforce independent implementability with respect to conjunction. We focus on multiple viewpoint specifications and propose a new compatibility criterion between two interfaces, which we call orthogonality. We show that orthogonal interfaces can be refined separately, while preserving both orthogonality and composability with other interfaces. We illustrate the independent implementability of different viewpoints with a FIFO buffer example."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"None","intvolume":" 7539","status":"public","title":"Independent implementability of viewpoints","_id":"2942","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"publist_id":"3790","publisher":"Wiley-Blackwell","department":[{"_id":"CaGu"}],"publication_status":"published","acknowledgement":"We thank Professor Philippe Cluzel and Mr Lance Min for providing advice and materials. Jeannette Chau provided technical support. Work at NU was supported by NSF Grants DMR-0715099, MCB-1022117, DMR-1206868, DMR-0520513 and DMR-1121262 (NU-MRSEC), by NIH-NCI Grant U54CA143869-01 (NU-PS-OC) and by the Chicago Biomedical Consortium with support from the Searle Funds at the Chicago Community Trust. Work at UCLA was supported by NIH Grant GM038509.","year":"2012","volume":86,"date_created":"2018-12-11T12:00:28Z","date_updated":"2021-01-12T07:39:56Z","author":[{"full_name":"Hadizadeh Yazdi, Nastaran","last_name":"Hadizadeh Yazdi","first_name":"Nastaran"},{"full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"},{"last_name":"Johnson","first_name":"Reid","full_name":"Johnson, Reid"},{"first_name":"John","last_name":"Marko","full_name":"Marko, John"}],"month":"11","quality_controlled":"1","main_file_link":[{"url":"http://europepmc.org/articles/pmc3524407","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/mmi.12071","type":"journal_article","issue":"6","abstract":[{"lang":"eng","text":"We examine whether the Escherichia coli chromosome is folded into a self-adherent nucleoprotein complex, or alternately is a confined but otherwise unconstrained self-avoiding polymer. We address this through in vivo visualization, using an inducible GFP fusion to the nucleoid-associated protein Fis to non-specifically decorate the entire chromosome. For a range of different growth conditions, the chromosome is a compact structure that does not fill the volume of the cell, and which moves from the new pole to the cell centre. During rapid growth, chromosome segregation occurs well before cell division, with daughter chromosomes coupled by a thin inter-daughter filament before complete segregation, whereas during slow growth chromosomes stay adjacent until cell division occurs. Image correlation analysis indicates that sub-nucleoid structure is stable on a 1min timescale, comparable to the timescale for redistribution time measured for GFP-Fis after photobleaching. Optical deconvolution and writhe calculation analysis indicate that the nucleoid has a large-scale coiled organization rather than being an amorphous mass. Our observations are consistent with the chromosome having a self-adherent filament organization."}],"intvolume":" 86","title":"Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2943","oa_version":"Submitted Version","scopus_import":1,"day":"09","page":"1318 - 1333","citation":{"chicago":"Hadizadeh Yazdi, Nastaran, Calin C Guet, Reid Johnson, and John Marko. “Variation of the Folding and Dynamics of the Escherichia Coli Chromosome with Growth Conditions.” Molecular Microbiology. Wiley-Blackwell, 2012. https://doi.org/10.1111/mmi.12071.","short":"N. Hadizadeh Yazdi, C.C. Guet, R. Johnson, J. Marko, Molecular Microbiology 86 (2012) 1318–1333.","mla":"Hadizadeh Yazdi, Nastaran, et al. “Variation of the Folding and Dynamics of the Escherichia Coli Chromosome with Growth Conditions.” Molecular Microbiology, vol. 86, no. 6, Wiley-Blackwell, 2012, pp. 1318–33, doi:10.1111/mmi.12071.","apa":"Hadizadeh Yazdi, N., Guet, C. C., Johnson, R., & Marko, J. (2012). Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. Wiley-Blackwell. https://doi.org/10.1111/mmi.12071","ieee":"N. Hadizadeh Yazdi, C. C. Guet, R. Johnson, and J. Marko, “Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions,” Molecular Microbiology, vol. 86, no. 6. Wiley-Blackwell, pp. 1318–1333, 2012.","ista":"Hadizadeh Yazdi N, Guet CC, Johnson R, Marko J. 2012. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. 86(6), 1318–1333.","ama":"Hadizadeh Yazdi N, Guet CC, Johnson R, Marko J. Variation of the folding and dynamics of the Escherichia coli chromosome with growth conditions. Molecular Microbiology. 2012;86(6):1318-1333. doi:10.1111/mmi.12071"},"publication":"Molecular Microbiology","date_published":"2012-11-09T00:00:00Z"},{"publication":"Russian Mathematical Surveys","citation":{"ama":"Dolbilin N, Edelsbrunner H, Musin O. On the optimality of functionals over triangulations of Delaunay sets. Russian Mathematical Surveys. 2012;67(4):781-783. doi:10.1070/RM2012v067n04ABEH004807","apa":"Dolbilin, N., Edelsbrunner, H., & Musin, O. (2012). On the optimality of functionals over triangulations of Delaunay sets. Russian Mathematical Surveys. IOP Publishing. https://doi.org/10.1070/RM2012v067n04ABEH004807","ieee":"N. Dolbilin, H. Edelsbrunner, and O. Musin, “On the optimality of functionals over triangulations of Delaunay sets,” Russian Mathematical Surveys, vol. 67, no. 4. IOP Publishing, pp. 781–783, 2012.","ista":"Dolbilin N, Edelsbrunner H, Musin O. 2012. On the optimality of functionals over triangulations of Delaunay sets. Russian Mathematical Surveys. 67(4), 781–783.","short":"N. Dolbilin, H. Edelsbrunner, O. Musin, Russian Mathematical Surveys 67 (2012) 781–783.","mla":"Dolbilin, Nikolai, et al. “On the Optimality of Functionals over Triangulations of Delaunay Sets.” Russian Mathematical Surveys, vol. 67, no. 4, IOP Publishing, 2012, pp. 781–83, doi:10.1070/RM2012v067n04ABEH004807.","chicago":"Dolbilin, Nikolai, Herbert Edelsbrunner, and Oleg Musin. “On the Optimality of Functionals over Triangulations of Delaunay Sets.” Russian Mathematical Surveys. IOP Publishing, 2012. https://doi.org/10.1070/RM2012v067n04ABEH004807."},"page":"781 - 783","date_published":"2012-11-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2941","status":"public","title":"On the optimality of functionals over triangulations of Delaunay sets","ddc":["510"],"intvolume":" 67","pubrep_id":"132","file":[{"date_updated":"2020-07-14T12:45:55Z","date_created":"2018-12-12T10:16:49Z","checksum":"389a5ae53d6347de36c3468034f2821d","file_id":"5239","relation":"main_file","creator":"system","file_size":253816,"content_type":"application/pdf","file_name":"IST-2013-132-v1+1_2012-J-04-Functional-E.pdf","access_level":"open_access"}],"oa_version":"Submitted Version","type":"journal_article","issue":"4","oa":1,"quality_controlled":"1","doi":"10.1070/RM2012v067n04ABEH004807","language":[{"iso":"eng"}],"month":"11","year":"2012","publication_status":"published","publisher":"IOP Publishing","department":[{"_id":"HeEd"}],"author":[{"first_name":"Nikolai","last_name":"Dolbilin","full_name":"Dolbilin, Nikolai"},{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"full_name":"Musin, Oleg","first_name":"Oleg","last_name":"Musin"}],"date_updated":"2021-01-12T07:39:55Z","date_created":"2018-12-11T12:00:28Z","volume":67,"file_date_updated":"2020-07-14T12:45:55Z","publist_id":"3792"},{"month":"10","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","doi":"10.1093/nar/gks705","language":[{"iso":"eng"}],"publist_id":"3786","file_date_updated":"2020-07-14T12:45:55Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","year":"2012","acknowledgement":"Deutsche Forschungsgemeinschaft (DFG) (SFB 960 and FOR855); European Research Council (ERC grant ‘sRNAs’); European Union (FP7 project ‘ONCOMIRs’); German Bundesministerium für Bildung und Forschung (BMBF, NGFN+, FKZ PIM-01GS0804-5); Bavarian Genome Research Network (BayGene to G.M.); The Netherlands Organization for Scientific Research (NWO, VIDI grant to E.B.). Funding for open access charge: DFG via the open access publishing program. \r\n\r\nWe thank Sigrun Ammon and Corinna Friederich for technical assistance and Sebastian Petri and Daniel Schraivogel for helpful discussions.","department":[{"_id":"MiSi"}],"publisher":"Oxford University Press","publication_status":"published","author":[{"full_name":"Dueck, Anne","first_name":"Anne","last_name":"Dueck"},{"first_name":"Christian","last_name":"Ziegler","full_name":"Ziegler, Christian"},{"id":"4DFA52AE-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","last_name":"Eichner","full_name":"Eichner, Alexander"},{"first_name":"Eugène","last_name":"Berezikov","full_name":"Berezikov, Eugène"},{"last_name":"Meister","first_name":"Gunter","full_name":"Meister, Gunter"}],"volume":40,"date_updated":"2021-01-12T07:39:57Z","date_created":"2018-12-11T12:00:29Z","scopus_import":1,"has_accepted_license":"1","day":"01","citation":{"ama":"Dueck A, Ziegler C, Eichner A, Berezikov E, Meister G. MicroRNAs associated with the different human Argonaute proteins. Nucleic Acids Research. 2012;40(19):9850-9862. doi:10.1093/nar/gks705","ista":"Dueck A, Ziegler C, Eichner A, Berezikov E, Meister G. 2012. MicroRNAs associated with the different human Argonaute proteins. Nucleic Acids Research. 40(19), 9850–9862.","ieee":"A. Dueck, C. Ziegler, A. Eichner, E. Berezikov, and G. Meister, “MicroRNAs associated with the different human Argonaute proteins,” Nucleic Acids Research, vol. 40, no. 19. Oxford University Press, pp. 9850–9862, 2012.","apa":"Dueck, A., Ziegler, C., Eichner, A., Berezikov, E., & Meister, G. (2012). MicroRNAs associated with the different human Argonaute proteins. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gks705","mla":"Dueck, Anne, et al. “MicroRNAs Associated with the Different Human Argonaute Proteins.” Nucleic Acids Research, vol. 40, no. 19, Oxford University Press, 2012, pp. 9850–62, doi:10.1093/nar/gks705.","short":"A. Dueck, C. Ziegler, A. Eichner, E. Berezikov, G. Meister, Nucleic Acids Research 40 (2012) 9850–9862.","chicago":"Dueck, Anne, Christian Ziegler, Alexander Eichner, Eugène Berezikov, and Gunter Meister. “MicroRNAs Associated with the Different Human Argonaute Proteins.” Nucleic Acids Research. Oxford University Press, 2012. https://doi.org/10.1093/nar/gks705."},"publication":"Nucleic Acids Research","page":"9850 - 9862","date_published":"2012-10-01T00:00:00Z","type":"journal_article","issue":"19","abstract":[{"lang":"eng","text":"MicroRNAs (miRNAs) are small noncoding RNAs that function in literally all cellular processes. miRNAs interact with Argonaute (Ago) proteins and guide them to specific target sites located in the 3′-untranslated region (3′-UTR) of target mRNAs leading to translational repression and deadenylation-induced mRNA degradation. Most miRNAs are processed from hairpin-structured precursors by the consecutive action of the RNase III enzymes Drosha and Dicer. However, processing of miR-451 is Dicer independent and cleavage is mediated by the endonuclease Ago2. Here we have characterized miR-451 sequence and structure requirements for processing as well as sorting of miRNAs into different Ago proteins. Pre-miR-451 appears to be optimized for Ago2 cleavage and changes result in reduced processing. In addition, we show that the mature miR-451 only associates with Ago2 suggesting that mature miRNAs are not exchanged between different members of the Ago protein family. Based on cloning and deep sequencing of endogenous miRNAs associated with Ago1-3, we do not find evidence for miRNA sorting in human cells. However, Ago identity appears to influence the length of some miRNAs, while others remain unaffected."}],"_id":"2946","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 40","ddc":["570"],"title":"MicroRNAs associated with the different human Argonaute proteins","status":"public","pubrep_id":"383","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"4993","checksum":"1bb8d1ff894014b481657a21083c941c","date_created":"2018-12-12T10:13:12Z","date_updated":"2020-07-14T12:45:55Z","access_level":"open_access","file_name":"IST-2015-383-v1+1_Nucl._Acids_Res.-2012-Dueck-9850-62.pdf","content_type":"application/pdf","file_size":8126936,"creator":"system"}]},{"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Chmelik, Martin","last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Majumdar","first_name":"Ritankar","full_name":"Majumdar, Ritankar"}],"volume":7561,"date_created":"2018-12-11T12:00:29Z","date_updated":"2021-01-12T07:39:58Z","year":"2012","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","ec_funded":1,"publist_id":"3785","doi":"10.1007/978-3-642-33386-6_30","conference":{"location":"Thiruvananthapuram, India","start_date":"2012-10-03","end_date":"2012-10-06","name":" ATVA: Automated Technology for Verification and Analysis"},"language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1202.4140"}],"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","month":"06","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2947","intvolume":" 7561","status":"public","title":"Equivalence of games with probabilistic uncertainty and partial observation games","abstract":[{"text":"We introduce games with probabilistic uncertainty, a model for controller synthesis in which the controller observes the state through imprecise sensors that provide correct information about the current state with a fixed probability. That is, in each step, the sensors return an observed state, and given the observed state, there is a probability distribution (due to the estimation error) over the actual current state. The controller must base its decision on the observed state (rather than the actual current state, which it does not know). On the other hand, we assume that the environment can perfectly observe the current state. We show that controller synthesis for qualitative ω-regular objectives in our model can be reduced in polynomial time to standard partial-observation stochastic games, and vice-versa. As a consequence we establish the precise decidability frontier for the new class of games, and establish optimal complexity results for all the decidable problems.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"date_published":"2012-06-01T00:00:00Z","citation":{"short":"K. Chatterjee, M. Chmelik, R. Majumdar, in:, Springer, 2012, pp. 385–399.","mla":"Chatterjee, Krishnendu, et al. Equivalence of Games with Probabilistic Uncertainty and Partial Observation Games. Vol. 7561, Springer, 2012, pp. 385–99, doi:10.1007/978-3-642-33386-6_30.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Ritankar Majumdar. “Equivalence of Games with Probabilistic Uncertainty and Partial Observation Games,” 7561:385–99. Springer, 2012. https://doi.org/10.1007/978-3-642-33386-6_30.","ama":"Chatterjee K, Chmelik M, Majumdar R. Equivalence of games with probabilistic uncertainty and partial observation games. In: Vol 7561. Springer; 2012:385-399. doi:10.1007/978-3-642-33386-6_30","apa":"Chatterjee, K., Chmelik, M., & Majumdar, R. (2012). Equivalence of games with probabilistic uncertainty and partial observation games (Vol. 7561, pp. 385–399). Presented at the ATVA: Automated Technology for Verification and Analysis, Thiruvananthapuram, India: Springer. https://doi.org/10.1007/978-3-642-33386-6_30","ieee":"K. Chatterjee, M. Chmelik, and R. Majumdar, “Equivalence of games with probabilistic uncertainty and partial observation games,” presented at the ATVA: Automated Technology for Verification and Analysis, Thiruvananthapuram, India, 2012, vol. 7561, pp. 385–399.","ista":"Chatterjee K, Chmelik M, Majumdar R. 2012. Equivalence of games with probabilistic uncertainty and partial observation games. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 7561, 385–399."},"page":"385 - 399","day":"01","scopus_import":1},{"page":"762 - 773","quality_controlled":"1","citation":{"apa":"Girard, J., Moussion, C., & Förster, R. (2012). HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes. Nature Reviews Immunology. Nature Publishing Group. https://doi.org/10.1038/nri3298","ieee":"J. Girard, C. Moussion, and R. Förster, “HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes,” Nature Reviews Immunology, vol. 12, no. 11. Nature Publishing Group, pp. 762–773, 2012.","ista":"Girard J, Moussion C, Förster R. 2012. HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes. Nature Reviews Immunology. 12(11), 762–773.","ama":"Girard J, Moussion C, Förster R. HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes. Nature Reviews Immunology. 2012;12(11):762-773. doi:10.1038/nri3298","chicago":"Girard, Jean, Christine Moussion, and Reinhold Förster. “HEVs, Lymphatics and Homeostatic Immune Cell Trafficking in Lymph Nodes.” Nature Reviews Immunology. Nature Publishing Group, 2012. https://doi.org/10.1038/nri3298.","short":"J. Girard, C. Moussion, R. Förster, Nature Reviews Immunology 12 (2012) 762–773.","mla":"Girard, Jean, et al. “HEVs, Lymphatics and Homeostatic Immune Cell Trafficking in Lymph Nodes.” Nature Reviews Immunology, vol. 12, no. 11, Nature Publishing Group, 2012, pp. 762–73, doi:10.1038/nri3298."},"publication":"Nature Reviews Immunology","language":[{"iso":"eng"}],"date_published":"2012-11-01T00:00:00Z","doi":"10.1038/nri3298","scopus_import":1,"month":"11","day":"01","publisher":"Nature Publishing Group","intvolume":" 12","department":[{"_id":"MiSi"}],"title":"HEVs, lymphatics and homeostatic immune cell trafficking in lymph nodes","status":"public","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2945","acknowledgement":"We thank M. Sixt and A. Peixoto for helpful comments on the manuscript. Work in the laboratory of J.-P.G. is supported by grants from Fondation ARC pour la Recherche sur le Cancer, Agence Nationale de la Recherche (ANR), Institut National du Cancer (INCA), Fondation RITC and Région Midi-Pyrénées. Research by R.F. is supported by Deutsche Forschungsgemeinschaft (DFG) grants SFB621-A1, SFB738-B5, SFB587-B3, SFB900-B1 and KFO 250-FO 334/2-1. We regret that, owing to space limitations, we could not always quote the work of colleagues who have contributed to the field.","year":"2012","volume":12,"oa_version":"None","date_updated":"2021-01-12T07:39:57Z","date_created":"2018-12-11T12:00:29Z","author":[{"full_name":"Girard, Jean","first_name":"Jean","last_name":"Girard"},{"full_name":"Moussion, Christine","id":"3356F664-F248-11E8-B48F-1D18A9856A87","last_name":"Moussion","first_name":"Christine"},{"last_name":"Förster","first_name":"Reinhold","full_name":"Förster, Reinhold"}],"type":"journal_article","issue":"11","publist_id":"3787","abstract":[{"text":"In search of foreign antigens, lymphocytes recirculate from the blood, through lymph nodes, into lymphatics and back to the blood. Dendritic cells also migrate to lymph nodes for optimal interaction with lymphocytes. This continuous trafficking of immune cells into and out of lymph nodes is essential for immune surveillance of foreign invaders. In this article, we review our current understanding of the functions of high endothelial venules (HEVs), stroma and lymphatics in the entry, positioning and exit of immune cells in lymph nodes during homeostasis, and we highlight the unexpected role of dendritic cells in the control of lymphocyte homing through HEVs.","lang":"eng"}]},{"day":"01","month":"11","scopus_import":1,"date_published":"2012-11-01T00:00:00Z","doi":"10.1038/nn.3245","language":[{"iso":"eng"}],"publication":"Nature Neuroscience","citation":{"chicago":"Dupret, David, and Jozsef L Csicsvari. “The Medial Entorhinal Cortex Keeps Up.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3245.","short":"D. Dupret, J.L. Csicsvari, Nature Neuroscience 15 (2012) 1471–1472.","mla":"Dupret, David, and Jozsef L. Csicsvari. “The Medial Entorhinal Cortex Keeps Up.” Nature Neuroscience, vol. 15, no. 11, Nature Publishing Group, 2012, pp. 1471–72, doi:10.1038/nn.3245.","ieee":"D. Dupret and J. L. Csicsvari, “The medial entorhinal cortex keeps Up,” Nature Neuroscience, vol. 15, no. 11. Nature Publishing Group, pp. 1471–1472, 2012.","apa":"Dupret, D., & Csicsvari, J. L. (2012). The medial entorhinal cortex keeps Up. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3245","ista":"Dupret D, Csicsvari JL. 2012. The medial entorhinal cortex keeps Up. Nature Neuroscience. 15(11), 1471–1472.","ama":"Dupret D, Csicsvari JL. The medial entorhinal cortex keeps Up. Nature Neuroscience. 2012;15(11):1471-1472. doi:10.1038/nn.3245"},"main_file_link":[{"url":"http://www.mrcbndu.ox.ac.uk/publications/medial-entorhinal-cortex-keeps"}],"quality_controlled":"1","page":"1471 - 1472","publist_id":"3782","issue":"11","type":"journal_article","author":[{"full_name":"Dupret, David","last_name":"Dupret","first_name":"David"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"}],"date_created":"2018-12-11T12:00:30Z","date_updated":"2021-01-12T07:39:59Z","oa_version":"None","volume":15,"_id":"2949","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","title":"The medial entorhinal cortex keeps Up","publication_status":"published","status":"public","publisher":"Nature Publishing Group","intvolume":" 15","department":[{"_id":"JoCs"}]},{"intvolume":" 103","title":"A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2954","oa_version":"Submitted Version","type":"journal_article","issue":"7","abstract":[{"text":"Spontaneous postsynaptic currents (PSCs) provide key information about the mechanisms of synaptic transmission and the activity modes of neuronal networks. However, detecting spontaneous PSCs in vitro and in vivo has been challenging, because of the small amplitude, the variable kinetics, and the undefined time of generation of these events. Here, we describe a, to our knowledge, new method for detecting spontaneous synaptic events by deconvolution, using a template that approximates the average time course of spontaneous PSCs. A recorded PSC trace is deconvolved from the template, resulting in a series of delta-like functions. The maxima of these delta-like events are reliably detected, revealing the precise onset times of the spontaneous PSCs. Among all detection methods, the deconvolution-based method has a unique temporal resolution, allowing the detection of individual events in high-frequency bursts. Furthermore, the deconvolution-based method has a high amplitude resolution, because deconvolution can substantially increase the signal/noise ratio. When tested against previously published methods using experimental data, the deconvolution-based method was superior for spontaneous PSCs recorded in vivo. Using the high-resolution deconvolution-based detection algorithm, we show that the frequency of spontaneous excitatory postsynaptic currents in dentate gyrus granule cells is 4.5 times higher in vivo than in vitro.","lang":"eng"}],"page":"1429 - 1439","citation":{"apa":"Pernia-Andrade, A., Goswami, S., Stickler, Y., Fröbe, U., Schlögl, A., & Jonas, P. M. (2012). A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophysical Journal. Biophysical. https://doi.org/10.1016/j.bpj.2012.08.039","ieee":"A. Pernia-Andrade, S. Goswami, Y. Stickler, U. Fröbe, A. Schlögl, and P. M. Jonas, “A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo,” Biophysical Journal, vol. 103, no. 7. Biophysical, pp. 1429–1439, 2012.","ista":"Pernia-Andrade A, Goswami S, Stickler Y, Fröbe U, Schlögl A, Jonas PM. 2012. A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophysical Journal. 103(7), 1429–1439.","ama":"Pernia-Andrade A, Goswami S, Stickler Y, Fröbe U, Schlögl A, Jonas PM. A deconvolution based method with high sensitivity and temporal resolution for detection of spontaneous synaptic currents in vitro and in vivo. Biophysical Journal. 2012;103(7):1429-1439. doi:10.1016/j.bpj.2012.08.039","chicago":"Pernia-Andrade, Alejandro, Sarit Goswami, Yvonne Stickler, Ulrich Fröbe, Alois Schlögl, and Peter M Jonas. “A Deconvolution Based Method with High Sensitivity and Temporal Resolution for Detection of Spontaneous Synaptic Currents in Vitro and in Vivo.” Biophysical Journal. Biophysical, 2012. https://doi.org/10.1016/j.bpj.2012.08.039.","short":"A. Pernia-Andrade, S. Goswami, Y. Stickler, U. Fröbe, A. Schlögl, P.M. Jonas, Biophysical Journal 103 (2012) 1429–1439.","mla":"Pernia-Andrade, Alejandro, et al. “A Deconvolution Based Method with High Sensitivity and Temporal Resolution for Detection of Spontaneous Synaptic Currents in Vitro and in Vivo.” Biophysical Journal, vol. 103, no. 7, Biophysical, 2012, pp. 1429–39, doi:10.1016/j.bpj.2012.08.039."},"publication":"Biophysical Journal","date_published":"2012-10-03T00:00:00Z","scopus_import":1,"day":"03","publisher":"Biophysical","department":[{"_id":"PeJo"},{"_id":"ScienComp"}],"publication_status":"published","pmid":1,"acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (TR3/B10) and a European Research Council Advanced grant to P.J.\r\nWe thank H. Hu, S. J. Guzman, and C. Schmidt-Hieber for critically reading the manuscript, I. Koeva and F. Marr for technical support, and E. Kramberger for editorial assistance.\r\n","year":"2012","volume":103,"date_updated":"2021-01-12T07:40:01Z","date_created":"2018-12-11T12:00:32Z","author":[{"first_name":"Alejandro","last_name":"Pernia-Andrade","id":"36963E98-F248-11E8-B48F-1D18A9856A87","full_name":"Pernia-Andrade, Alejandro"},{"last_name":"Goswami","first_name":"Sarit","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","full_name":"Goswami, Sarit"},{"id":"63B76600-E9CC-11E9-9B5F-82450873F7A1","last_name":"Stickler","first_name":"Yvonne","full_name":"Stickler, Yvonne"},{"last_name":"Fröbe","first_name":"Ulrich","full_name":"Fröbe, Ulrich"},{"last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M"}],"publist_id":"3774","project":[{"grant_number":"SFB-TR3-TP10B","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425","name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3471482/"}],"oa":1,"external_id":{"pmid":["23062335"]},"language":[{"iso":"eng"}],"doi":"10.1016/j.bpj.2012.08.039","month":"10"},{"related_material":{"record":[{"id":"1403","status":"public","relation":"dissertation_contains"}]},"author":[{"id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","first_name":"Martin","full_name":"Behrndt, Martin"},{"last_name":"Salbreux","first_name":"Guillaume","full_name":"Salbreux, Guillaume"},{"first_name":"Pedro","last_name":"Campinho","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416","full_name":"Campinho, Pedro"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"},{"full_name":"Oswald, Felix","last_name":"Oswald","first_name":"Felix"},{"full_name":"Roensch, Julia","id":"4220E59C-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Roensch"},{"last_name":"Grill","first_name":"Stephan","full_name":"Grill, Stephan"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"volume":338,"date_updated":"2023-02-21T17:02:44Z","date_created":"2018-12-11T12:00:30Z","year":"2012","department":[{"_id":"CaHe"},{"_id":"Bio"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","publist_id":"3778","doi":"10.1126/science.1224143","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"project":[{"call_identifier":"FWF","name":"Control of Epithelial Cell Layer Spreading in Zebrafish","grant_number":"I 930-B20","_id":"252ABD0A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","month":"10","oa_version":"None","_id":"2950","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 338","status":"public","title":"Forces driving epithelial spreading in zebrafish gastrulation","issue":"6104","abstract":[{"lang":"eng","text":"Contractile actomyosin rings drive various fundamental morphogenetic processes ranging from cytokinesis to wound healing. Actomyosin rings are generally thought to function by circumferential contraction. Here, we show that the spreading of the enveloping cell layer (EVL) over the yolk cell during zebrafish gastrulation is driven by a contractile actomyosin ring. In contrast to previous suggestions, we find that this ring functions not only by circumferential contraction but also by a flow-friction mechanism. This generates a pulling force through resistance against retrograde actomyosin flow. EVL spreading proceeds normally in situations where circumferential contraction is unproductive, indicating that the flow-friction mechanism is sufficient. Thus, actomyosin rings can function in epithelial morphogenesis through a combination of cable-constriction and flow-friction mechanisms."}],"type":"journal_article","date_published":"2012-10-12T00:00:00Z","citation":{"apa":"Behrndt, M., Salbreux, G., Campinho, P., Hauschild, R., Oswald, F., Roensch, J., … Heisenberg, C.-P. J. (2012). Forces driving epithelial spreading in zebrafish gastrulation. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1224143","ieee":"M. Behrndt et al., “Forces driving epithelial spreading in zebrafish gastrulation,” Science, vol. 338, no. 6104. American Association for the Advancement of Science, pp. 257–260, 2012.","ista":"Behrndt M, Salbreux G, Campinho P, Hauschild R, Oswald F, Roensch J, Grill S, Heisenberg C-PJ. 2012. Forces driving epithelial spreading in zebrafish gastrulation. Science. 338(6104), 257–260.","ama":"Behrndt M, Salbreux G, Campinho P, et al. Forces driving epithelial spreading in zebrafish gastrulation. Science. 2012;338(6104):257-260. doi:10.1126/science.1224143","chicago":"Behrndt, Martin, Guillaume Salbreux, Pedro Campinho, Robert Hauschild, Felix Oswald, Julia Roensch, Stephan Grill, and Carl-Philipp J Heisenberg. “Forces Driving Epithelial Spreading in Zebrafish Gastrulation.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224143.","short":"M. Behrndt, G. Salbreux, P. Campinho, R. Hauschild, F. Oswald, J. Roensch, S. Grill, C.-P.J. Heisenberg, Science 338 (2012) 257–260.","mla":"Behrndt, Martin, et al. “Forces Driving Epithelial Spreading in Zebrafish Gastrulation.” Science, vol. 338, no. 6104, American Association for the Advancement of Science, 2012, pp. 257–60, doi:10.1126/science.1224143."},"publication":"Science","page":"257 - 260","day":"12","scopus_import":1},{"_id":"2951","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2012","department":[{"_id":"CaHe"}],"intvolume":" 338","publisher":"American Association for the Advancement of Science","publication_status":"published","status":"public","title":"Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells","author":[{"orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","last_name":"Maître","first_name":"Jean-Léon","full_name":"Maître, Jean-Léon"},{"full_name":"Berthoumieux, Hélène","last_name":"Berthoumieux","first_name":"Hélène"},{"full_name":"Krens, Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","first_name":"Gabriel","last_name":"Krens"},{"full_name":"Salbreux, Guillaume","last_name":"Salbreux","first_name":"Guillaume"},{"full_name":"Julicher, Frank","first_name":"Frank","last_name":"Julicher"},{"first_name":"Ewa","last_name":"Paluch","full_name":"Paluch, Ewa"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"}],"volume":338,"oa_version":"None","date_updated":"2021-01-12T07:40:00Z","date_created":"2018-12-11T12:00:31Z","type":"journal_article","publist_id":"3777","issue":"6104","abstract":[{"lang":"eng","text":"Differential cell adhesion and cortex tension are thought to drive cell sorting by controlling cell-cell contact formation. Here, we show that cell adhesion and cortex tension have different mechanical functions in controlling progenitor cell-cell contact formation and sorting during zebrafish gastrulation. Cortex tension controls cell-cell contact expansion by modulating interfacial tension at the contact. By contrast, adhesion has little direct function in contact expansion, but instead is needed to mechanically couple the cortices of adhering cells at their contacts, allowing cortex tension to control contact expansion. The coupling function of adhesion is mediated by E-cadherin and limited by the mechanical anchoring of E-cadherin to the cortex. Thus, cell adhesion provides the mechanical scaffold for cell cortex tension to drive cell sorting during gastrulation."}],"citation":{"ama":"Maître J-L, Berthoumieux H, Krens G, et al. Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells. Science. 2012;338(6104):253-256. doi:10.1126/science.1225399","apa":"Maître, J.-L., Berthoumieux, H., Krens, G., Salbreux, G., Julicher, F., Paluch, E., & Heisenberg, C.-P. J. (2012). Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1225399","ieee":"J.-L. Maître et al., “Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells,” Science, vol. 338, no. 6104. American Association for the Advancement of Science, pp. 253–256, 2012.","ista":"Maître J-L, Berthoumieux H, Krens G, Salbreux G, Julicher F, Paluch E, Heisenberg C-PJ. 2012. Adhesion functions in cell sorting by mechanically coupling the cortices of adhering cells. Science. 338(6104), 253–256.","short":"J.-L. Maître, H. Berthoumieux, G. Krens, G. Salbreux, F. Julicher, E. Paluch, C.-P.J. Heisenberg, Science 338 (2012) 253–256.","mla":"Maître, Jean-Léon, et al. “Adhesion Functions in Cell Sorting by Mechanically Coupling the Cortices of Adhering Cells.” Science, vol. 338, no. 6104, American Association for the Advancement of Science, 2012, pp. 253–56, doi:10.1126/science.1225399.","chicago":"Maître, Jean-Léon, Hélène Berthoumieux, Gabriel Krens, Guillaume Salbreux, Frank Julicher, Ewa Paluch, and Carl-Philipp J Heisenberg. “Adhesion Functions in Cell Sorting by Mechanically Coupling the Cortices of Adhering Cells.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1225399."},"publication":"Science","page":"253 - 256","quality_controlled":"1","doi":"10.1126/science.1225399","date_published":"2012-10-12T00:00:00Z","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"SSU"}],"scopus_import":1,"month":"10","day":"12"},{"date_published":"2012-11-01T00:00:00Z","doi":"10.1242/dev.073007","language":[{"iso":"eng"}],"citation":{"chicago":"Tada, Masazumi, and Carl-Philipp J Heisenberg. “Convergent Extension Using Collective Cell Migration and Cell Intercalation to Shape Embryos.” Development. Company of Biologists, 2012. https://doi.org/10.1242/dev.073007.","mla":"Tada, Masazumi, and Carl-Philipp J. Heisenberg. “Convergent Extension Using Collective Cell Migration and Cell Intercalation to Shape Embryos.” Development, vol. 139, no. 21, Company of Biologists, 2012, pp. 3897–904, doi:10.1242/dev.073007.","short":"M. Tada, C.-P.J. Heisenberg, Development 139 (2012) 3897–3904.","ista":"Tada M, Heisenberg C-PJ. 2012. Convergent extension Using collective cell migration and cell intercalation to shape embryos. Development. 139(21), 3897–3904.","ieee":"M. Tada and C.-P. J. Heisenberg, “Convergent extension Using collective cell migration and cell intercalation to shape embryos,” Development, vol. 139, no. 21. Company of Biologists, pp. 3897–3904, 2012.","apa":"Tada, M., & Heisenberg, C.-P. J. (2012). Convergent extension Using collective cell migration and cell intercalation to shape embryos. Development. Company of Biologists. https://doi.org/10.1242/dev.073007","ama":"Tada M, Heisenberg C-PJ. Convergent extension Using collective cell migration and cell intercalation to shape embryos. Development. 2012;139(21):3897-3904. doi:10.1242/dev.073007"},"publication":"Development","page":"3897 - 3904","quality_controlled":"1","day":"01","month":"11","scopus_import":1,"author":[{"last_name":"Tada","first_name":"Masazumi","full_name":"Tada, Masazumi"},{"full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566"}],"volume":139,"oa_version":"None","date_created":"2018-12-11T12:00:31Z","date_updated":"2021-01-12T07:40:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2952","acknowledgement":"M.T. is supported by the UK Medical Research Council (MRC) and Royal Society and C.-P.H. by the Fonds zur Förderung der wissenschaftlichen Forschung (FWF), Deutsche Forschungsgemeinschaft (DFG) and Institute of Science and Technology Austria. ","year":"2012","intvolume":" 139","publisher":"Company of Biologists","department":[{"_id":"CaHe"}],"status":"public","publication_status":"published","title":"Convergent extension Using collective cell migration and cell intercalation to shape embryos","publist_id":"3776","issue":"21","abstract":[{"lang":"eng","text":"Body axis elongation represents a common and fundamental morphogenetic process in development. A key mechanism triggering body axis elongation without additional growth is convergent extension (CE), whereby a tissue undergoes simultaneous narrowing and extension. Both collective cell migration and cell intercalation are thought to drive CE and are used to different degrees in various species as they elongate their body axis. Here, we provide an overview of CE as a general strategy for body axis elongation and discuss conserved and divergent mechanisms underlying CE among different species."}],"type":"journal_article"},{"scopus_import":1,"day":"01","month":"10","page":"559 - 561","quality_controlled":"1","citation":{"short":"C.-P.J. Heisenberg, R. Fässler, Current Opinion in Cell Biology 24 (2012) 559–561.","mla":"Heisenberg, Carl-Philipp J., and Reinhard Fässler. “Cell-Cell Adhesion and Extracellular Matrix Diversity Counts.” Current Opinion in Cell Biology, vol. 24, no. 5, Elsevier, 2012, pp. 559–61, doi:10.1016/j.ceb.2012.09.002.","chicago":"Heisenberg, Carl-Philipp J, and Reinhard Fässler. “Cell-Cell Adhesion and Extracellular Matrix Diversity Counts.” Current Opinion in Cell Biology. Elsevier, 2012. https://doi.org/10.1016/j.ceb.2012.09.002.","ama":"Heisenberg C-PJ, Fässler R. Cell-cell adhesion and extracellular matrix diversity counts. Current Opinion in Cell Biology. 2012;24(5):559-561. doi:10.1016/j.ceb.2012.09.002","ieee":"C.-P. J. Heisenberg and R. Fässler, “Cell-cell adhesion and extracellular matrix diversity counts,” Current Opinion in Cell Biology, vol. 24, no. 5. Elsevier, pp. 559–561, 2012.","apa":"Heisenberg, C.-P. J., & Fässler, R. (2012). Cell-cell adhesion and extracellular matrix diversity counts. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2012.09.002","ista":"Heisenberg C-PJ, Fässler R. 2012. Cell-cell adhesion and extracellular matrix diversity counts. Current Opinion in Cell Biology. 24(5), 559–561."},"publication":"Current Opinion in Cell Biology","language":[{"iso":"eng"}],"date_published":"2012-10-01T00:00:00Z","doi":"10.1016/j.ceb.2012.09.002","type":"journal_article","publist_id":"3773","issue":"5","intvolume":" 24","department":[{"_id":"CaHe"}],"publisher":"Elsevier","publication_status":"published","title":"Cell-cell adhesion and extracellular matrix diversity counts","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2953","year":"2012","oa_version":"None","volume":24,"date_created":"2018-12-11T12:00:31Z","date_updated":"2021-01-12T07:40:01Z","author":[{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Fässler","first_name":"Reinhard","full_name":"Fässler, Reinhard"}]},{"publist_id":"3768","ec_funded":1,"pmid":1,"year":"2012","acknowledgement":"J.C. was supported by a MRC Intramural Programme Grant (U138197111) and a European Research Council Starter Grant (281511). K.A. held a Wellcome Trust PhD studentship and a Humboldt Research Fellowship for Postdoctoral Researchers. D.M.B. was supported by Wellcome Trust Senior Fellowships (074385 and 087736).","department":[{"_id":"JoCs"}],"publisher":"Society for Neuroscience","publication_status":"published","author":[{"full_name":"Allen, Kevin","first_name":"Kevin","last_name":"Allen"},{"first_name":"J Nick","last_name":"Rawlins","full_name":"Rawlins, J Nick"},{"last_name":"Bannerman","first_name":"David","full_name":"Bannerman, David"},{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","full_name":"Csicsvari, Jozsef L"}],"volume":32,"date_updated":"2021-01-12T07:40:03Z","date_created":"2018-12-11T12:00:33Z","month":"10","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531717/","open_access":"1"}],"external_id":{"pmid":["23077060"]},"project":[{"_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511","call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex"}],"quality_controlled":"1","doi":"10.1523/JNEUROSCI.6175-11.2012","language":[{"iso":"eng"}],"type":"journal_article","issue":"42","abstract":[{"text":"The activity of hippocampal pyramidal cells reflects both the current position of the animal and information related to its current behavior. Here we investigated whether single hippocampal neurons can encode several independent features defining trials during a memory task. We also tested whether task-related information is represented by partial remapping of the place cell population or, instead, via firing rate modulation of spatially stable place cells. To address these two questions, the activity of hippocampal neurons was recorded in rats performing a conditional discrimination task on a modified T-maze in which the identity of a food reward guided behavior. When the rat was on the central arm of the maze, the firing rate of pyramidal cells changed depending on two independent factors: (1) the identity of the food reward given to the animal and (2) the previous location of the animal on the maze. Importantly, some pyramidal cells encoded information relative to both factors. This trial-type specific and retrospective coding did not interfere with the spatial representation of the maze: hippocampal cells had stable place fields and their theta-phase precession profiles were unaltered during the task, indicating that trial-related information was encoded via rate remapping. During error trials, encoding of both trial-related information and spatial location was impaired. Finally, we found that pyramidal cells also encode trial-related information via rate remapping during the continuous version of the rewarded alternation task without delays. These results suggest that hippocampal neurons can encode several task-related cognitive aspects via rate remapping.","lang":"eng"}],"_id":"2958","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 32","title":"Hippocampal place cells can encode multiple trial-dependent features through rate remapping","status":"public","oa_version":"Submitted Version","scopus_import":1,"day":"17","citation":{"ieee":"K. Allen, J. N. Rawlins, D. Bannerman, and J. L. Csicsvari, “Hippocampal place cells can encode multiple trial-dependent features through rate remapping,” Journal of Neuroscience, vol. 32, no. 42. Society for Neuroscience, pp. 14752–14766, 2012.","apa":"Allen, K., Rawlins, J. N., Bannerman, D., & Csicsvari, J. L. (2012). Hippocampal place cells can encode multiple trial-dependent features through rate remapping. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.6175-11.2012","ista":"Allen K, Rawlins JN, Bannerman D, Csicsvari JL. 2012. Hippocampal place cells can encode multiple trial-dependent features through rate remapping. Journal of Neuroscience. 32(42), 14752–14766.","ama":"Allen K, Rawlins JN, Bannerman D, Csicsvari JL. Hippocampal place cells can encode multiple trial-dependent features through rate remapping. Journal of Neuroscience. 2012;32(42):14752-14766. doi:10.1523/JNEUROSCI.6175-11.2012","chicago":"Allen, Kevin, J Nick Rawlins, David Bannerman, and Jozsef L Csicsvari. “Hippocampal Place Cells Can Encode Multiple Trial-Dependent Features through Rate Remapping.” Journal of Neuroscience. Society for Neuroscience, 2012. https://doi.org/10.1523/JNEUROSCI.6175-11.2012.","short":"K. Allen, J.N. Rawlins, D. Bannerman, J.L. Csicsvari, Journal of Neuroscience 32 (2012) 14752–14766.","mla":"Allen, Kevin, et al. “Hippocampal Place Cells Can Encode Multiple Trial-Dependent Features through Rate Remapping.” Journal of Neuroscience, vol. 32, no. 42, Society for Neuroscience, 2012, pp. 14752–66, doi:10.1523/JNEUROSCI.6175-11.2012."},"publication":"Journal of Neuroscience","page":"14752 - 14766","date_published":"2012-10-17T00:00:00Z"},{"month":"02","doi":"10.1214/11-AOS957","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1012.2643"}],"oa":1,"quality_controlled":"1","publist_id":"3767","author":[{"id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7008-0216","first_name":"Caroline","last_name":"Uhler","full_name":"Uhler, Caroline"}],"volume":40,"date_updated":"2021-01-12T07:40:04Z","date_created":"2018-12-11T12:00:33Z","acknowledgement":"I wish to thank Bernd Sturmfels for many helpful discus- sions and Steffen Lauritzen for introducing me to the problem of the existence of the MLE in Gaussian graphical models. I would also like to thank two referees who provided helpful comments on the original version of this paper.\r\n","year":"2012","publisher":"Institute of Mathematical Statistics","department":[{"_id":"CaUh"}],"publication_status":"published","day":"01","scopus_import":1,"date_published":"2012-02-01T00:00:00Z","citation":{"ama":"Uhler C. Geometry of maximum likelihood estimation in Gaussian graphical models. Annals of Statistics. 2012;40(1):238-261. doi:10.1214/11-AOS957","ista":"Uhler C. 2012. Geometry of maximum likelihood estimation in Gaussian graphical models. Annals of Statistics. 40(1), 238–261.","ieee":"C. Uhler, “Geometry of maximum likelihood estimation in Gaussian graphical models,” Annals of Statistics, vol. 40, no. 1. Institute of Mathematical Statistics, pp. 238–261, 2012.","apa":"Uhler, C. (2012). Geometry of maximum likelihood estimation in Gaussian graphical models. Annals of Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/11-AOS957","mla":"Uhler, Caroline. “Geometry of Maximum Likelihood Estimation in Gaussian Graphical Models.” Annals of Statistics, vol. 40, no. 1, Institute of Mathematical Statistics, 2012, pp. 238–61, doi:10.1214/11-AOS957.","short":"C. Uhler, Annals of Statistics 40 (2012) 238–261.","chicago":"Uhler, Caroline. “Geometry of Maximum Likelihood Estimation in Gaussian Graphical Models.” Annals of Statistics. Institute of Mathematical Statistics, 2012. https://doi.org/10.1214/11-AOS957."},"publication":"Annals of Statistics","page":"238 - 261","issue":"1","abstract":[{"lang":"eng","text":"We study maximum likelihood estimation in Gaussian graphical models from a geometric point of view. An algebraic elimination criterion allows us to find exact lower bounds on the number of observations needed to ensure that the maximum likelihood estimator (MLE) exists with probability one. This is applied to bipartite graphs, grids and colored graphs. We also study the ML degree, and we present the first instance of a graph for which the MLE exists with probability one, even when the number of observations equals the treewidth."}],"type":"journal_article","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2959","intvolume":" 40","status":"public","title":"Geometry of maximum likelihood estimation in Gaussian graphical models"},{"doi":"10.1186/1472-6785-12-7","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","month":"06","author":[{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"},{"full_name":"Suefuji, Masaki","last_name":"Suefuji","first_name":"Masaki"},{"full_name":"Schrempf, Alexandra","first_name":"Alexandra","last_name":"Schrempf"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"}],"volume":12,"date_created":"2018-12-11T12:00:35Z","date_updated":"2021-01-12T07:40:07Z","year":"2012","publisher":"BioMed Central","department":[{"_id":"SyCr"}],"publication_status":"published","publist_id":"3753","file_date_updated":"2020-07-14T12:45:57Z","license":"https://creativecommons.org/licenses/by/4.0/","article_number":"7","date_published":"2012-06-15T00:00:00Z","citation":{"apa":"Cremer, S., Suefuji, M., Schrempf, A., & Heinze, J. (2012). The dynamics of male-male competition in Cardiocondyla obscurior ants. BMC Ecology. BioMed Central. https://doi.org/10.1186/1472-6785-12-7","ieee":"S. Cremer, M. Suefuji, A. Schrempf, and J. Heinze, “The dynamics of male-male competition in Cardiocondyla obscurior ants,” BMC Ecology, vol. 12. BioMed Central, 2012.","ista":"Cremer S, Suefuji M, Schrempf A, Heinze J. 2012. The dynamics of male-male competition in Cardiocondyla obscurior ants. BMC Ecology. 12, 7.","ama":"Cremer S, Suefuji M, Schrempf A, Heinze J. The dynamics of male-male competition in Cardiocondyla obscurior ants. BMC Ecology. 2012;12. doi:10.1186/1472-6785-12-7","chicago":"Cremer, Sylvia, Masaki Suefuji, Alexandra Schrempf, and Jürgen Heinze. “The Dynamics of Male-Male Competition in Cardiocondyla Obscurior Ants.” BMC Ecology. BioMed Central, 2012. https://doi.org/10.1186/1472-6785-12-7.","short":"S. Cremer, M. Suefuji, A. Schrempf, J. Heinze, BMC Ecology 12 (2012).","mla":"Cremer, Sylvia, et al. “The Dynamics of Male-Male Competition in Cardiocondyla Obscurior Ants.” BMC Ecology, vol. 12, 7, BioMed Central, 2012, doi:10.1186/1472-6785-12-7."},"publication":"BMC Ecology","has_accepted_license":"1","day":"15","scopus_import":1,"pubrep_id":"94","oa_version":"Published Version","file":[{"file_name":"IST-2012-94-v1+1_1472-6785-12-7.pdf","access_level":"open_access","file_size":489994,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4706","date_created":"2018-12-12T10:08:44Z","date_updated":"2020-07-14T12:45:57Z","checksum":"03d004bdff3724fb1627e3f5004bad80"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2966","intvolume":" 12","title":"The dynamics of male-male competition in Cardiocondyla obscurior ants","ddc":["570"],"status":"public","abstract":[{"lang":"eng","text":"Background: The outcome of male-male competition can be predicted from the relative fighting qualities of the opponents, which often depend on their age. In insects, freshly emerged and still sexually inactive males are morphologically indistinct from older, sexually active males. These young inactive males may thus be easy targets for older males if they cannot conceal themselves from their attacks. The ant Cardiocondyla obscurior is characterised by lethal fighting between wingless (" ergatoid" ) males. Here, we analyse for how long young males are defenceless after eclosion, and how early adult males can detect the presence of rival males.Results: We found that old ergatoid males consistently won fights against ergatoid males younger than two days. Old males did not differentiate between different types of unpigmented pupae several days before emergence, but had more frequent contact to ready-to-eclose pupae of female sexuals and winged males than of workers and ergatoid males. In rare cases, old ergatoid males displayed alleviated biting of pigmented ergatoid male pupae shortly before adult eclosion, as well as copulation attempts to dark pupae of female sexuals and winged males. Ergatoid male behaviour may be promoted by a closer similarity of the chemical profile of ready-to-eclose pupae to the profile of adults than that of young pupae several days prior to emergence.Conclusion: Young ergatoid males of C. obscurior would benefit greatly by hiding their identity from older, resident males, as they are highly vulnerable during the first two days of their adult lives. In contrast to the winged males of the same species, which are able to prevent ergatoid male attacks by chemical female mimicry, young ergatoids do not seem to be able to produce a protective chemical profile. Conflicts in male-male competition between ergatoid males of different age thus seem to be resolved in favour of the older males. This might represent selection at the colony level rather than the individual level. © 2012 Cremer et al.; licensee BioMed Central Ltd."}],"type":"journal_article"},{"page":"1027 - 1047","citation":{"ama":"Aeschbacher S, Beaumont M, Futschik A. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 2012;192(3):1027-1047. doi:10.1534/genetics.112.143164","ista":"Aeschbacher S, Beaumont M, Futschik A. 2012. A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. 192(3), 1027–1047.","ieee":"S. Aeschbacher, M. Beaumont, and A. Futschik, “A novel approach for choosing summary statistics in approximate Bayesian computation,” Genetics, vol. 192, no. 3. Genetics Society of America, pp. 1027–1047, 2012.","apa":"Aeschbacher, S., Beaumont, M., & Futschik, A. (2012). A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.112.143164","mla":"Aeschbacher, Simon, et al. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics, vol. 192, no. 3, Genetics Society of America, 2012, pp. 1027–47, doi:10.1534/genetics.112.143164.","short":"S. Aeschbacher, M. Beaumont, A. Futschik, Genetics 192 (2012) 1027–1047.","chicago":"Aeschbacher, Simon, Mark Beaumont, and Andreas Futschik. “A Novel Approach for Choosing Summary Statistics in Approximate Bayesian Computation.” Genetics. Genetics Society of America, 2012. https://doi.org/10.1534/genetics.112.143164."},"publication":"Genetics","date_published":"2012-11-01T00:00:00Z","scopus_import":1,"day":"01","intvolume":" 192","title":"A novel approach for choosing summary statistics in approximate Bayesian computation","status":"public","_id":"2962","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","issue":"3","abstract":[{"text":"The choice of summary statistics is a crucial step in approximate Bayesian computation (ABC). Since statistics are often not sufficient, this choice involves a trade-off between loss of information and reduction of dimensionality. The latter may increase the efficiency of ABC. Here, we propose an approach for choosing summary statistics based on boosting, a technique from the machine learning literature. We consider different types of boosting and compare them to partial least squares regression as an alternative. To mitigate the lack of sufficiency, we also propose an approach for choosing summary statistics locally, in the putative neighborhood of the true parameter value. We study a demographic model motivated by the re-introduction of Alpine ibex (Capra ibex) into the Swiss Alps. The parameters of interest are the mean and standard deviation across microsatellites of the scaled ancestral mutation rate (θanc = 4 Ne u), and the proportion of males obtaining access to matings per breeding season (ω). By simulation, we assess the properties of the posterior distribution obtained with the various methods. According to our criteria, ABC with summary statistics chosen locally via boosting with the L2-loss performs best. Applying that method to the ibex data, we estimate θanc ≈ 1.288, and find that most of the variation across loci of the ancestral mutation rate u is between 7.7×10−4 and 3.5×10−3 per locus per generation. The proportion of males with access to matings is estimated to ω ≈ 0.21, which is in good agreement with recent independent estimates.","lang":"eng"}],"quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522150/","open_access":"1"}],"oa":1,"external_id":{"pmid":["22960215"]},"language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"doi":"10.1534/genetics.112.143164","month":"11","publisher":"Genetics Society of America","department":[{"_id":"NiBa"}],"publication_status":"published","pmid":1,"year":"2012","volume":192,"date_updated":"2021-01-12T07:40:05Z","date_created":"2018-12-11T12:00:34Z","author":[{"full_name":"Aeschbacher, Simon","id":"2D35326E-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Aeschbacher"},{"full_name":"Beaumont, Mark","first_name":"Mark","last_name":"Beaumont"},{"last_name":"Futschik","first_name":"Andreas","full_name":"Futschik, Andreas"}],"publist_id":"3763"},{"scopus_import":1,"has_accepted_license":"1","day":"01","page":"200 - 212","citation":{"ama":"Danowski P. Kontext Open Access: Creative Commons. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 2012;65(2):200-212.","ieee":"P. Danowski, “Kontext Open Access: Creative Commons,” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 65, no. 2. VÖB, pp. 200–212, 2012.","apa":"Danowski, P. (2012). Kontext Open Access: Creative Commons. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB.","ista":"Danowski P. 2012. Kontext Open Access: Creative Commons. Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. 65(2), 200–212.","short":"P. Danowski, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare 65 (2012) 200–212.","mla":"Danowski, Patrick. “Kontext Open Access: Creative Commons.” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare, vol. 65, no. 2, VÖB, 2012, pp. 200–12.","chicago":"Danowski, Patrick. “Kontext Open Access: Creative Commons.” Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare. VÖB, 2012."},"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen & Bibliothekare","date_published":"2012-09-01T00:00:00Z","type":"journal_article","issue":"2","abstract":[{"text":"Dieser Artikel soll die sechs verschiedenen Creative Commons Lizenzen erläutern und ihre Bedeutung im Rahmen des wissenschaftlichen Publizierens und des Open Access erklären (CC-BY, CC-BY-SA, CC-BY-NC, CC-BY-ND, CC-BYNC-SA, CC-BY-NC-ND).","lang":"eng"}],"intvolume":" 65","title":"Kontext Open Access: Creative Commons","status":"public","ddc":["020"],"_id":"2965","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"system","file_size":503345,"content_type":"application/pdf","file_name":"IST-2012-95-v1+1_sp-beitrag_danowski_kontext_open_access_creative_commons.pdf","access_level":"open_access","date_created":"2018-12-12T10:08:42Z","date_updated":"2020-07-14T12:45:57Z","checksum":"162eea47d9d840c26b496ba6ae4d1c09","file_id":"4703","relation":"main_file"}],"pubrep_id":"95","popular_science":"1","month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":" http://hdl.handle.net/10760/17625","open_access":"1"}],"oa":1,"language":[{"iso":"ger"}],"publist_id":"3754","file_date_updated":"2020-07-14T12:45:57Z","publisher":"VÖB","department":[{"_id":"E-Lib"}],"publication_status":"published","year":"2012","volume":65,"date_created":"2018-12-11T12:00:35Z","date_updated":"2021-01-12T07:40:07Z","author":[{"full_name":"Danowski, Patrick","last_name":"Danowski","first_name":"Patrick","orcid":"0000-0002-6026-4409","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87"}]},{"quality_controlled":"1","page":"262 - 266","publication":"Behavioural Processes","citation":{"mla":"Jesse, Fabienne, and Katharina Riebel. “Social Facilitation of Male Song by Male and Female Conspecifics in the Zebra Finch, Taeniopygia Guttata.” Behavioural Processes, vol. 91, no. 3, Elsevier, 2012, pp. 262–66, doi:10.1016/j.beproc.2012.09.006.","short":"F. Jesse, K. Riebel, Behavioural Processes 91 (2012) 262–266.","chicago":"Jesse, Fabienne, and Katharina Riebel. “Social Facilitation of Male Song by Male and Female Conspecifics in the Zebra Finch, Taeniopygia Guttata.” Behavioural Processes. Elsevier, 2012. https://doi.org/10.1016/j.beproc.2012.09.006.","ama":"Jesse F, Riebel K. Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. 2012;91(3):262-266. doi:10.1016/j.beproc.2012.09.006","ista":"Jesse F, Riebel K. 2012. Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. 91(3), 262–266.","ieee":"F. Jesse and K. Riebel, “Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata,” Behavioural Processes, vol. 91, no. 3. Elsevier, pp. 262–266, 2012.","apa":"Jesse, F., & Riebel, K. (2012). Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata. Behavioural Processes. Elsevier. https://doi.org/10.1016/j.beproc.2012.09.006"},"language":[{"iso":"eng"}],"date_published":"2012-11-01T00:00:00Z","doi":"10.1016/j.beproc.2012.09.006","day":"01","month":"11","status":"public","title":"Social facilitation of male song by male and female conspecifics in the zebra finch, Taeniopygia guttata","publication_status":"published","publisher":"Elsevier","department":[{"_id":"JoBo"}],"intvolume":" 91","_id":"2963","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:40:06Z","date_created":"2018-12-11T12:00:35Z","oa_version":"None","volume":91,"author":[{"id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87","last_name":"Jesse","first_name":"Fabienne","full_name":"Jesse, Fabienne"},{"last_name":"Riebel","first_name":"Katharina","full_name":"Riebel, Katharina"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Zebra finches are an ubiquitous model system for the study of vocal learning in animal communication. Their song has been well described, but its possible function(s) in social communication are only partly understood. The so-called ‘directed song’ is a high-intensity, high-performance song given during courtship in close proximity to the female, which is known to mediate mate choice and mating. However, this singing mode constitutes only a fraction of zebra finch males’ prolific song output. Potential communicative functions of their second, ‘undirected’ singing mode remain unresolved in the face of contradicting reports of both facilitating and inhibiting effects of social company on singing. We addressed this issue by experimentally manipulating social contexts in a within-subject design, comparing a solo versus male or female only company condition, each lasting for 24 hours. Males’ total song output was significantly higher when a conspecific was in audible and visible distance than when they were alone. Male and female company had an equally facilitating effect on song output. Our findings thus indicate that singing motivation is facilitated rather than inhibited by social company, suggesting that singing in zebra finches might function both in inter- and intrasexual communication. "}],"issue":"3","publist_id":"3756"},{"citation":{"chicago":"Jain, Abhishek, Stephan Krenn, Krzysztof Z Pietrzak, and Aris Tentes. “Commitments and Efficient Zero Knowledge Proofs from Learning Parity with Noise.” edited by Xiaoyun Wang and Kazue Sako, 7658:663–80. Springer, 2012. https://doi.org/10.1007/978-3-642-34961-4_40.","short":"A. Jain, S. Krenn, K.Z. Pietrzak, A. Tentes, in:, X. Wang, K. Sako (Eds.), Springer, 2012, pp. 663–680.","mla":"Jain, Abhishek, et al. Commitments and Efficient Zero Knowledge Proofs from Learning Parity with Noise. Edited by Xiaoyun Wang and Kazue Sako, vol. 7658, Springer, 2012, pp. 663–80, doi:10.1007/978-3-642-34961-4_40.","apa":"Jain, A., Krenn, S., Pietrzak, K. Z., & Tentes, A. (2012). Commitments and efficient zero knowledge proofs from learning parity with noise. In X. Wang & K. Sako (Eds.) (Vol. 7658, pp. 663–680). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Beijing, China: Springer. https://doi.org/10.1007/978-3-642-34961-4_40","ieee":"A. Jain, S. Krenn, K. Z. Pietrzak, and A. Tentes, “Commitments and efficient zero knowledge proofs from learning parity with noise,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Beijing, China, 2012, vol. 7658, pp. 663–680.","ista":"Jain A, Krenn S, Pietrzak KZ, Tentes A. 2012. Commitments and efficient zero knowledge proofs from learning parity with noise. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 7658, 663–680.","ama":"Jain A, Krenn S, Pietrzak KZ, Tentes A. Commitments and efficient zero knowledge proofs from learning parity with noise. In: Wang X, Sako K, eds. Vol 7658. Springer; 2012:663-680. doi:10.1007/978-3-642-34961-4_40"},"page":"663 - 680","date_published":"2012-12-01T00:00:00Z","scopus_import":1,"day":"01","has_accepted_license":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2974","title":"Commitments and efficient zero knowledge proofs from learning parity with noise","status":"public","ddc":["004","005"],"intvolume":" 7658","pubrep_id":"721","oa_version":"Submitted Version","file":[{"creator":"system","content_type":"application/pdf","file_size":482570,"file_name":"IST-2016-721-v1+1_513.pdf","access_level":"open_access","date_created":"2018-12-12T10:14:00Z","date_updated":"2020-07-14T12:45:58Z","checksum":"ab879537385efc4cb4203e7ef0fea17b","file_id":"5048","relation":"main_file"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We construct a perfectly binding string commitment scheme whose security is based on the learning parity with noise (LPN) assumption, or equivalently, the hardness of decoding random linear codes. Our scheme not only allows for a simple and efficient zero-knowledge proof of knowledge for committed values (essentially a Σ-protocol), but also for such proofs showing any kind of relation amongst committed values, i.e. proving that messages m_0,...,m_u, are such that m_0=C(m_1,...,m_u) for any circuit C.\r\n\r\nTo get soundness which is exponentially small in a security parameter t, and when the zero-knowledge property relies on the LPN problem with secrets of length l, our 3 round protocol has communication complexity O(t|C|l log(l)) and computational complexity of O(t|C|l) bit operations. The hidden constants are small, and the computation consists mostly of computing inner products of bit-vectors."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"conference":{"name":"ASIACRYPT: Theory and Application of Cryptology and Information Security","end_date":"2012-12-06","start_date":"2012-12-02","location":"Beijing, China"},"doi":"10.1007/978-3-642-34961-4_40","language":[{"iso":"eng"}],"month":"12","acknowledgement":"We are grateful to Petros Mol for helpful discussions on the reduction for the hardness of the xLPN problem.\r\n","year":"2012","publication_status":"published","publisher":"Springer","editor":[{"first_name":"Xiaoyun","last_name":"Wang","full_name":"Wang, Xiaoyun"},{"first_name":"Kazue","last_name":"Sako","full_name":"Sako, Kazue"}],"department":[{"_id":"KrPi"}],"author":[{"full_name":"Jain, Abhishek","last_name":"Jain","first_name":"Abhishek"},{"orcid":"0000-0003-2835-9093","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","last_name":"Krenn","first_name":"Stephan","full_name":"Krenn, Stephan"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"full_name":"Tentes, Aris","first_name":"Aris","last_name":"Tentes"}],"date_updated":"2021-01-12T07:40:11Z","date_created":"2018-12-11T12:00:38Z","volume":7658,"file_date_updated":"2020-07-14T12:45:58Z","ec_funded":1,"publist_id":"3730"},{"issue":"41","abstract":[{"text":"The coupling between presynaptic Ca^(2+) channels and Ca^(2+) sensors of exocytosis is a key determinant of synaptic transmission. Evoked release from parvalbumin (PV)-expressing interneurons is triggered by nanodomain coupling of P/Q-type Ca^(2+) channels, whereas release from cholecystokinin (CCK)-containing interneurons is generated by microdomain coupling of N-type channels. Nanodomain coupling has several functional advantages, including speed and efficacy of transmission. One potential disadvantage is that stochastic\r\nopening of presynaptic Ca^(2+) channels may trigger spontaneous transmitter release. We addressed this possibility in rat hippocampal\r\ngranule cells, which receive converging inputs from different inhibitory sources. Both reduction of extracellular Ca^(2+) concentration and the unselective Ca^(2+) channel blocker Cd^(2+) reduced the frequency of miniature IPSCs (mIPSCs) in granule cells by ~50%, suggesting that the opening of presynaptic Ca^(2+) channels contributes to spontaneous release. Application of the selective P/Q-type Ca^(2+) channel blocker\r\nω-agatoxin IVa had no detectable effects, whereas both the N-type blocker ω-conotoxin GVIa and the L-type blocker nimodipine reduced\r\nmIPSC frequency. Furthermore, both the fast Ca^(2+) chelator BAPTA-AM and the slow chelator EGTA-AM reduced the mIPSC frequency,\r\nsuggesting that Ca^(2+)-dependent spontaneous release is triggered by microdomain rather than nanodomain coupling. The CB_(1) receptor\r\nagonist WIN 55212-2 also decreased spontaneous release; this effect was occluded by prior application of ω-conotoxin GVIa, suggesting that a major fraction of Ca^(2+)-dependent spontaneous release was generated at the terminals of CCK-expressing interneurons. Tonic inhibition generated by spontaneous opening of presynaptic N- and L-type Ca^(2+) channels may be important for hippocampal information processing.\r\n","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","intvolume":" 32","title":"Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling","status":"public","_id":"2969","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"10","scopus_import":1,"date_published":"2012-10-10T00:00:00Z","page":"14294 - 14304","citation":{"short":"S. Goswami, I. Bucurenciu, P.M. Jonas, Journal of Neuroscience 32 (2012) 14294–14304.","mla":"Goswami, Sarit, et al. “Miniature IPSCs in Hippocampal Granule Cells Are Triggered by Voltage-Gated Ca^(2+) Channels via Microdomain Coupling.” Journal of Neuroscience, vol. 32, no. 41, Society for Neuroscience, 2012, pp. 14294–304, doi:10.1523/JNEUROSCI.6104-11.2012.","chicago":"Goswami, Sarit, Iancu Bucurenciu, and Peter M Jonas. “Miniature IPSCs in Hippocampal Granule Cells Are Triggered by Voltage-Gated Ca^(2+) Channels via Microdomain Coupling.” Journal of Neuroscience. Society for Neuroscience, 2012. https://doi.org/10.1523/JNEUROSCI.6104-11.2012.","ama":"Goswami S, Bucurenciu I, Jonas PM. Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. Journal of Neuroscience. 2012;32(41):14294-14304. doi:10.1523/JNEUROSCI.6104-11.2012","apa":"Goswami, S., Bucurenciu, I., & Jonas, P. M. (2012). Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.6104-11.2012","ieee":"S. Goswami, I. Bucurenciu, and P. M. Jonas, “Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling,” Journal of Neuroscience, vol. 32, no. 41. Society for Neuroscience, pp. 14294–14304, 2012.","ista":"Goswami S, Bucurenciu I, Jonas PM. 2012. Miniature IPSCs in hippocampal granule cells are triggered by voltage-gated Ca^(2+) channels via microdomain coupling. Journal of Neuroscience. 32(41), 14294–14304."},"publication":"Journal of Neuroscience","publist_id":"3744","volume":32,"date_created":"2018-12-11T12:00:36Z","date_updated":"2021-01-12T07:40:08Z","author":[{"last_name":"Goswami","first_name":"Sarit","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","full_name":"Goswami, Sarit"},{"first_name":"Iancu","last_name":"Bucurenciu","full_name":"Bucurenciu, Iancu"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M"}],"publisher":"Society for Neuroscience","department":[{"_id":"PeJo"}],"publication_status":"published","pmid":1,"year":"2012","acknowledgement":"This work was supported by grants from the Deutsche Forschungsgemeinschaft (TR 3/B10, Leibniz program, GSC-4 Spemann Graduate School) and the European Union (European Research Council Advanced Grant).","month":"10","language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.6104-11.2012","project":[{"name":"Glutamaterge synaptische Übertragung und Plastizität in hippocampalen Mikroschaltkreisen","grant_number":"SFB-TR3-TP10B","_id":"25BDE9A4-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","external_id":{"pmid":["23055500"]},"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632771/","open_access":"1"}],"oa":1},{"doi":"10.1016/j.gde.2012.08.004","date_published":"2012-12-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. 2012;22(6):527-532. doi:10.1016/j.gde.2012.08.004","ista":"Kicheva A, Bollenbach MT, Wartlick O, Julicher F, Gonzalez Gaitan M. 2012. Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. 22(6), 527–532.","apa":"Kicheva, A., Bollenbach, M. T., Wartlick, O., Julicher, F., & Gonzalez Gaitan, M. (2012). Investigating the principles of morphogen gradient formation: from tissues to cells. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2012.08.004","ieee":"A. Kicheva, M. T. Bollenbach, O. Wartlick, F. Julicher, and M. Gonzalez Gaitan, “Investigating the principles of morphogen gradient formation: from tissues to cells,” Current Opinion in Genetics & Development, vol. 22, no. 6. Elsevier, pp. 527–532, 2012.","mla":"Kicheva, Anna, et al. “Investigating the Principles of Morphogen Gradient Formation: From Tissues to Cells.” Current Opinion in Genetics & Development, vol. 22, no. 6, Elsevier, 2012, pp. 527–32, doi:10.1016/j.gde.2012.08.004.","short":"A. Kicheva, M.T. Bollenbach, O. Wartlick, F. Julicher, M. Gonzalez Gaitan, Current Opinion in Genetics & Development 22 (2012) 527–532.","chicago":"Kicheva, Anna, Mark Tobias Bollenbach, Ortrud Wartlick, Frank Julicher, and Marcos Gonzalez Gaitan. “Investigating the Principles of Morphogen Gradient Formation: From Tissues to Cells.” Current Opinion in Genetics & Development. Elsevier, 2012. https://doi.org/10.1016/j.gde.2012.08.004."},"publication":"Current Opinion in Genetics & Development","page":"527 - 532","quality_controlled":"1","month":"12","day":"01","scopus_import":1,"author":[{"orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna"},{"full_name":"Bollenbach, Mark Tobias","first_name":"Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"},{"last_name":"Wartlick","first_name":"Ortrud","full_name":"Wartlick, Ortrud"},{"full_name":"Julicher, Frank","first_name":"Frank","last_name":"Julicher"},{"last_name":"Gonzalez Gaitan","first_name":"Marcos","full_name":"Gonzalez Gaitan, Marcos"}],"volume":22,"oa_version":"None","date_created":"2018-12-11T12:00:37Z","date_updated":"2021-01-12T07:40:09Z","acknowledgement":"AK is currently supported by an MRC CDF. MGG and OW were supported by the Swiss National Science Foundation, grants from the Swiss SystemsX.ch initiative, LipidX-2008/011, an ERC advanced investigator grant and the Polish-Swiss research program.","_id":"2970","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToBo"}],"publisher":"Elsevier","intvolume":" 22","title":"Investigating the principles of morphogen gradient formation: from tissues to cells","status":"public","publication_status":"published","issue":"6","publist_id":"3739","abstract":[{"lang":"eng","text":"Morphogen gradients regulate the patterning and growth of many tissues, hence a key question is how they are established and maintained during development. Theoretical descriptions have helped to explain how gradient shape is controlled by the rates of morphogen production, spreading and degradation. These effective rates have been measured using fluorescence recovery after photobleaching (FRAP) and photoactivation. To unravel which molecular events determine the effective rates, such tissue-level assays have been combined with genetic analysis, high-resolution assays, and models that take into account interactions with receptors, extracellular components and trafficking. Nevertheless, because of the natural and experimental data variability, and the underlying assumptions of transport models, it remains challenging to conclusively distinguish between cellular mechanisms."}],"type":"journal_article"},{"type":"conference","publist_id":"3737","abstract":[{"lang":"eng","text":"We study the task of interactive semantic labeling of a segmentation hierarchy. To this end we propose a framework interleaving two components: an automatic labeling step, based on a Conditional Random Field whose dependencies are defined by the inclusion tree of the segmentation hierarchy, and an interaction step that integrates incremental input from a human user. Evaluated on two distinct datasets, the proposed interactive approach efficiently integrates human interventions and illustrates the advantages of structured prediction in an interactive framework. "}],"department":[{"_id":"HeEd"}],"intvolume":" 7476","publisher":"Springer","publication_status":"published","status":"public","title":"Interactive labeling of image segmentation hierarchies","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"2971","year":"2012","volume":7476,"oa_version":"None","date_updated":"2021-01-12T07:40:10Z","date_created":"2018-12-11T12:00:37Z","author":[{"first_name":"Georg","last_name":"Zankl","full_name":"Zankl, Georg"},{"first_name":"Yll","last_name":"Haxhimusa","full_name":"Haxhimusa, Yll"},{"id":"29F89302-F248-11E8-B48F-1D18A9856A87","last_name":"Ion","first_name":"Adrian","full_name":"Ion, Adrian"}],"scopus_import":1,"day":"01","month":"01","page":"11 - 20","quality_controlled":"1","citation":{"mla":"Zankl, Georg, et al. Interactive Labeling of Image Segmentation Hierarchies. Vol. 7476, Springer, 2012, pp. 11–20, doi:10.1007/978-3-642-32717-9_2.","short":"G. Zankl, Y. Haxhimusa, A. Ion, in:, Springer, 2012, pp. 11–20.","chicago":"Zankl, Georg, Yll Haxhimusa, and Adrian Ion. “Interactive Labeling of Image Segmentation Hierarchies,” 7476:11–20. Springer, 2012. https://doi.org/10.1007/978-3-642-32717-9_2.","ama":"Zankl G, Haxhimusa Y, Ion A. Interactive labeling of image segmentation hierarchies. In: Vol 7476. Springer; 2012:11-20. doi:10.1007/978-3-642-32717-9_2","ista":"Zankl G, Haxhimusa Y, Ion A. 2012. Interactive labeling of image segmentation hierarchies. Pattern Recognition vol. 7476, 11–20.","apa":"Zankl, G., Haxhimusa, Y., & Ion, A. (2012). Interactive labeling of image segmentation hierarchies (Vol. 7476, pp. 11–20). Presented at the Pattern Recognition, Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_2","ieee":"G. Zankl, Y. Haxhimusa, and A. Ion, “Interactive labeling of image segmentation hierarchies,” presented at the Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 11–20."},"language":[{"iso":"eng"}],"date_published":"2012-01-01T00:00:00Z","doi":"10.1007/978-3-642-32717-9_2","conference":{"name":"Pattern Recognition","end_date":"2012-08-31","start_date":"2012-08-28","location":"Graz, Austria"}},{"publisher":"Cell Press","intvolume":" 22","publication_status":"published","status":"public","title":"GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses","_id":"3105","year":"2012","volume":22,"date_updated":"2021-01-12T07:41:06Z","date_created":"2018-12-11T12:01:25Z","author":[{"last_name":"Whitford","first_name":"Ryan","full_name":"Whitford, Ryan"},{"full_name":"Fernandez, Ana","last_name":"Fernandez","first_name":"Ana"},{"full_name":"Tejos, Ricardo","first_name":"Ricardo","last_name":"Tejos"},{"full_name":"Pérez, Amparo Cuéllar","last_name":"Pérez","first_name":"Amparo"},{"first_name":"Jürgen","last_name":"Kleine Vehn","full_name":"Kleine-Vehn, Jürgen"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"full_name":"Drozdzecki, Andrzej","last_name":"Drozdzecki","first_name":"Andrzej"},{"first_name":"Johannes","last_name":"Leitner","full_name":"Leitner, Johannes"},{"first_name":"Lindy","last_name":"Abas","full_name":"Abas, Lindy"},{"last_name":"Aerts","first_name":"Maarten","full_name":"Aerts, Maarten"},{"last_name":"Hoogewijs","first_name":"Kurt","full_name":"Hoogewijs, Kurt"},{"full_name":"Pawel Baster","last_name":"Baster","first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Groodt","first_name":"Ruth","full_name":"De Groodt, Ruth"},{"full_name":"Lin, Yao-Cheng","first_name":"Yao","last_name":"Lin"},{"full_name":"Storme, Véronique","first_name":"Véronique","last_name":"Storme"},{"full_name":"Van de Peer, Yves","first_name":"Yves","last_name":"Van De Peer"},{"full_name":"Beeckman, Tom","last_name":"Beeckman","first_name":"Tom"},{"first_name":"Annemieke","last_name":"Madder","full_name":"Madder, Annemieke"},{"full_name":"Devreese, Bart","last_name":"Devreese","first_name":"Bart"},{"first_name":"Christian","last_name":"Luschnig","full_name":"Luschnig, Christian"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Jirí Friml"},{"first_name":"Pierre","last_name":"Hilson","full_name":"Hilson, Pierre"}],"type":"journal_article","extern":1,"publist_id":"3594","issue":"3","abstract":[{"lang":"eng","text":"Growth and development are coordinated by an array of intercellular communications. Known plant signaling molecules include phytohormones and hormone peptides. Although both classes can be implicated in the same developmental processes, little is known about the interplay between phytohormone action and peptide signaling within the cellular microenvironment. We show that genes coding for small secretory peptides, designated GOLVEN (GLV), modulate the distribution of the phytohormone auxin. The deregulation of the GLV function impairs the formation of auxin gradients and alters the reorientation of shoots and roots after a gravity stimulus. Specifically, the GLV signal modulates the trafficking dynamics of the auxin efflux carrier PIN-FORMED2 involved in root tropic responses and meristem organization. Our work links the local action of secretory peptides with phytohormone transport. Root growth factor (RGF) or GOLVEN (GLV) secreted peptides have previously been implicated in meristem regulation. Whitford et al. now show that RGF/GLV peptides induce rapid relocalization of the auxin efflux regulator PIN2, regulate auxin gradients, and modulate auxin-dependent root responses to specific stimuli."}],"page":"678 - 685","quality_controlled":0,"citation":{"ieee":"R. Whitford et al., “GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses,” Developmental Cell, vol. 22, no. 3. Cell Press, pp. 678–685, 2012.","apa":"Whitford, R., Fernandez, A., Tejos, R., Pérez, A., Kleine Vehn, J., Vanneste, S., … Hilson, P. (2012). GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2012.02.002","ista":"Whitford R, Fernandez A, Tejos R, Pérez A, Kleine Vehn J, Vanneste S, Drozdzecki A, Leitner J, Abas L, Aerts M, Hoogewijs K, Baster P, De Groodt R, Lin Y, Storme V, Van De Peer Y, Beeckman T, Madder A, Devreese B, Luschnig C, Friml J, Hilson P. 2012. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. 22(3), 678–685.","ama":"Whitford R, Fernandez A, Tejos R, et al. GOLVEN secretory peptides regulate auxin carrier turnover during plant gravitropic responses. Developmental Cell. 2012;22(3):678-685. doi:10.1016/j.devcel.2012.02.002","chicago":"Whitford, Ryan, Ana Fernandez, Ricardo Tejos, Amparo Pérez, Jürgen Kleine Vehn, Steffen Vanneste, Andrzej Drozdzecki, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” Developmental Cell. Cell Press, 2012. https://doi.org/10.1016/j.devcel.2012.02.002.","short":"R. Whitford, A. Fernandez, R. Tejos, A. Pérez, J. Kleine Vehn, S. Vanneste, A. Drozdzecki, J. Leitner, L. Abas, M. Aerts, K. Hoogewijs, P. Baster, R. De Groodt, Y. Lin, V. Storme, Y. Van De Peer, T. Beeckman, A. Madder, B. Devreese, C. Luschnig, J. Friml, P. Hilson, Developmental Cell 22 (2012) 678–685.","mla":"Whitford, Ryan, et al. “GOLVEN Secretory Peptides Regulate Auxin Carrier Turnover during Plant Gravitropic Responses.” Developmental Cell, vol. 22, no. 3, Cell Press, 2012, pp. 678–85, doi:10.1016/j.devcel.2012.02.002."},"publication":"Developmental Cell","doi":"10.1016/j.devcel.2012.02.002","date_published":"2012-03-13T00:00:00Z","month":"03","day":"13"},{"month":"06","day":"01","publication":"Nature Chemical Biology","citation":{"ama":"Irani N, Di Rubbo S, Mylle E, et al. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. 2012;8(6):583-589. doi:10.1038/nchembio.958","ista":"Irani N, Di Rubbo S, Mylle E, Van Den Begin J, Schneider Pizoń J, Hniliková J, Šíša M, Buyst D, Vilarrasa Blasi J, Szatmári A, Van Damme D, Mishev K, Codreanu M, Kohout L, Strnad M, Caño Delgado A, Friml J, Madder A, Russinova E. 2012. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. 8(6), 583–589.","apa":"Irani, N., Di Rubbo, S., Mylle, E., Van Den Begin, J., Schneider Pizoń, J., Hniliková, J., … Russinova, E. (2012). Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.958","ieee":"N. Irani et al., “Fluorescent castasterone reveals BRI1 signaling from the plasma membrane,” Nature Chemical Biology, vol. 8, no. 6. Nature Publishing Group, pp. 583–589, 2012.","mla":"Irani, Niloufer, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from the Plasma Membrane.” Nature Chemical Biology, vol. 8, no. 6, Nature Publishing Group, 2012, pp. 583–89, doi:10.1038/nchembio.958.","short":"N. Irani, S. Di Rubbo, E. Mylle, J. Van Den Begin, J. Schneider Pizoń, J. Hniliková, M. Šíša, D. Buyst, J. Vilarrasa Blasi, A. Szatmári, D. Van Damme, K. Mishev, M. Codreanu, L. Kohout, M. Strnad, A. Caño Delgado, J. Friml, A. Madder, E. Russinova, Nature Chemical Biology 8 (2012) 583–589.","chicago":"Irani, Niloufer, Simone Di Rubbo, Evelien Mylle, Jos Van Den Begin, Joanna Schneider Pizoń, Jaroslava Hniliková, Miroslav Šíša, et al. “Fluorescent Castasterone Reveals BRI1 Signaling from the Plasma Membrane.” Nature Chemical Biology. Nature Publishing Group, 2012. https://doi.org/10.1038/nchembio.958."},"quality_controlled":0,"page":"583 - 589","doi":"10.1038/nchembio.958","date_published":"2012-06-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Receptor-mediated endocytosis is an integral part of signal transduction as it mediates signal attenuation and provides spatial and temporal dimensions to signaling events. One of the best-studied leucine-rich repeat receptor-like kinases in plants, BRASSINOSTEROID INSENSITIVE 1 (BRI1), perceives its ligand, the brassinosteroid (BR) hormone, at the cell surface and is constitutively endocytosed. However, the importance of endocytosis for BR signaling remains unclear. Here we developed a bioactive, fluorescent BR analog, Alexa Fluor 647-castasterone (AFCS), and visualized the endocytosis of BRI1-AFCS complexes in living Arabidopsis thaliana cells. Impairment of endocytosis dependent on clathrin and the guanine nucleotide exchange factor for ARF GTPases (ARF-GEF) GNOM enhanced BR signaling by retaining active BRI1-ligand complexes at the plasma membrane. Increasing the trans-Golgi network/early endosome pool of BRI1-BR complexes did not affect BR signaling. Our findings provide what is to our knowledge the first visualization of receptor-ligand complexes in plants and reveal clathrin-and ARF-GEF-dependent endocytic regulation of BR signaling from the plasma membrane.","lang":"eng"}],"publist_id":"3590","issue":"6","extern":1,"year":"2012","_id":"3109","publication_status":"published","status":"public","title":"Fluorescent castasterone reveals BRI1 signaling from the plasma membrane","intvolume":" 8","publisher":"Nature Publishing Group","author":[{"first_name":"Niloufer","last_name":"Irani","full_name":"Irani, Niloufer G"},{"full_name":"Di Rubbo, Simone","first_name":"Simone","last_name":"Di Rubbo"},{"last_name":"Mylle","first_name":"Evelien","full_name":"Mylle, Evelien"},{"first_name":"Jos","last_name":"Van Den Begin","full_name":"Van Den Begin, Jos"},{"last_name":"Schneider Pizoń","first_name":"Joanna","full_name":"Schneider-Pizoń, Joanna"},{"last_name":"Hniliková","first_name":"Jaroslava","full_name":"Hniliková, Jaroslava"},{"last_name":"Šíša","first_name":"Miroslav","full_name":"Šíša, Miroslav"},{"full_name":"Buyst, Dieter","first_name":"Dieter","last_name":"Buyst"},{"full_name":"Vilarrasa-Blasi, Josep","first_name":"Josep","last_name":"Vilarrasa Blasi"},{"first_name":"Anna","last_name":"Szatmári","full_name":"Szatmári, Anna-Maria"},{"full_name":"Van Damme, Daniël","last_name":"Van Damme","first_name":"Daniël"},{"full_name":"Mishev, Kiril","last_name":"Mishev","first_name":"Kiril"},{"full_name":"Codreanu, Mirela-Corina","first_name":"Mirela","last_name":"Codreanu"},{"full_name":"Kohout, Ladislav","first_name":"Ladislav","last_name":"Kohout"},{"full_name":"Strnad, Miroslav","first_name":"Miroslav","last_name":"Strnad"},{"first_name":"Ana","last_name":"Caño Delgado","full_name":"Caño-Delgado, Ana I"},{"full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Madder","first_name":"Annemieke","full_name":"Madder, Annemieke"},{"last_name":"Russinova","first_name":"Eugenia","full_name":"Russinova, Eugenia"}],"date_updated":"2021-01-12T07:41:07Z","date_created":"2018-12-11T12:01:26Z","volume":8},{"author":[{"full_name":"Grunewald, Wim","first_name":"Wim","last_name":"Grunewald"},{"full_name":"De Smet, Ive","first_name":"Ive","last_name":"De Smet"},{"full_name":"Lewis, Daniel R","last_name":"Lewis","first_name":"Daniel"},{"first_name":"Christian","last_name":"Löfke","full_name":"Löfke, Christian"},{"first_name":"Leentje","last_name":"Jansen","full_name":"Jansen, Leentje"},{"full_name":"Goeminne, Geert","first_name":"Geert","last_name":"Goeminne"},{"full_name":"Vanden Bossche, Robin","last_name":"Vanden Bossche","first_name":"Robin"},{"full_name":"Karimi, Mansour","last_name":"Karimi","first_name":"Mansour"},{"full_name":"De Rybel, Bert","first_name":"Bert","last_name":"De Rybel"},{"full_name":"Vanholme, Bartel","first_name":"Bartel","last_name":"Vanholme"},{"full_name":"Teichmann, Thomas","last_name":"Teichmann","first_name":"Thomas"},{"full_name":"Boerjan, Wout","last_name":"Boerjan","first_name":"Wout"},{"first_name":"Marc","last_name":"Van Montagu","full_name":"Van Montagu, Marc C"},{"last_name":"Gheysen","first_name":"Godelieve","full_name":"Gheysen, Godelieve"},{"full_name":"Muday, Gloria K","first_name":"Gloria","last_name":"Muday"},{"full_name":"Jirí Friml","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"}],"volume":109,"date_updated":"2021-01-12T07:41:05Z","date_created":"2018-12-11T12:01:24Z","_id":"3104","year":"2012","intvolume":" 109","publisher":"National Academy of Sciences","status":"public","title":"Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis","publication_status":"published","publist_id":"3595","issue":"5","abstract":[{"text":"\nGradients of the plant hormone auxin, which depend on its active intercellular transport, are crucial for the maintenance of root meristematic activity. This directional transport is largely orchestrated by a complex interaction of specific influx and efflux carriers that mediate the auxin flow into and out of cells, respectively. Besides these transport proteins, plant-specific polyphenolic compounds knownasflavonols have beenshownto act as endogenous regulators of auxin transport. However, only limited information is available on how flavonol synthesis is developmentally regulated. Using reduction-of-function and overexpression approaches in parallel, we demonstrate that the WRKY23 transcription factor is needed for proper root growth and development by stimulating the local biosynthesis of flavonols. The expression of WRKY23 itself is controlled by auxin through the AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 transcriptional response pathway. Our results suggest a model in which WRKY23 is part of a transcriptional feedback loop of auxin on its own transport through local regulation of flavonol biosynthesis.","lang":"eng"}],"extern":1,"type":"journal_article","date_published":"2012-01-31T00:00:00Z","doi":"10.1073/pnas.1121134109","citation":{"mla":"Grunewald, Wim, et al. “Transcription Factor WRKY23 Assists Auxin Distribution Patterns during Arabidopsis Root Development through Local Control on Flavonol Biosynthesis.” PNAS, vol. 109, no. 5, National Academy of Sciences, 2012, pp. 1554–59, doi:10.1073/pnas.1121134109.","short":"W. Grunewald, I. De Smet, D. Lewis, C. Löfke, L. Jansen, G. Goeminne, R. Vanden Bossche, M. Karimi, B. De Rybel, B. Vanholme, T. Teichmann, W. Boerjan, M. Van Montagu, G. Gheysen, G. Muday, J. Friml, T. Beeckman, PNAS 109 (2012) 1554–1559.","chicago":"Grunewald, Wim, Ive De Smet, Daniel Lewis, Christian Löfke, Leentje Jansen, Geert Goeminne, Robin Vanden Bossche, et al. “Transcription Factor WRKY23 Assists Auxin Distribution Patterns during Arabidopsis Root Development through Local Control on Flavonol Biosynthesis.” PNAS. National Academy of Sciences, 2012. https://doi.org/10.1073/pnas.1121134109.","ama":"Grunewald W, De Smet I, Lewis D, et al. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. 2012;109(5):1554-1559. doi:10.1073/pnas.1121134109","ista":"Grunewald W, De Smet I, Lewis D, Löfke C, Jansen L, Goeminne G, Vanden Bossche R, Karimi M, De Rybel B, Vanholme B, Teichmann T, Boerjan W, Van Montagu M, Gheysen G, Muday G, Friml J, Beeckman T. 2012. Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. 109(5), 1554–1559.","ieee":"W. Grunewald et al., “Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis,” PNAS, vol. 109, no. 5. National Academy of Sciences, pp. 1554–1559, 2012.","apa":"Grunewald, W., De Smet, I., Lewis, D., Löfke, C., Jansen, L., Goeminne, G., … Beeckman, T. (2012). Transcription factor WRKY23 assists auxin distribution patterns during Arabidopsis root development through local control on flavonol biosynthesis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1121134109"},"publication":"PNAS","page":"1554 - 1559","quality_controlled":0,"day":"31","month":"01"},{"publication_status":"published","title":"A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants","status":"public","publisher":"Nature Publishing Group","intvolume":" 485","_id":"3108","year":"2012","date_updated":"2021-01-12T07:41:07Z","date_created":"2018-12-11T12:01:26Z","volume":485,"author":[{"last_name":"Barbez","first_name":"Elke","full_name":"Barbez, Elke"},{"full_name":"Kubeš, Martin","first_name":"Martin","last_name":"Kubeš"},{"last_name":"Rolčík","first_name":"Jakub","full_name":"Rolčík, Jakub"},{"first_name":"Chloe","last_name":"Béziat","full_name":"Béziat, Chloe"},{"last_name":"Pěnčík","first_name":"Aleš","full_name":"Pěnčík, Aleš"},{"last_name":"Wang","first_name":"Bangjun","full_name":"Wang, Bangjun"},{"full_name":"Rosquete, Michel Ruiz","last_name":"Rosquete","first_name":"Michel"},{"full_name":"Zhu, Jinsheng","last_name":"Zhu","first_name":"Jinsheng"},{"full_name":"Dobrev, Petre I","first_name":"Petre","last_name":"Dobrev"},{"full_name":"Lee, Yuree","last_name":"Lee","first_name":"Yuree"},{"full_name":"Zašímalová, Eva","first_name":"Eva","last_name":"Zašímalová"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"},{"full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"full_name":"Kleine-Vehn, Jürgen","last_name":"Kleine Vehn","first_name":"Jürgen"}],"type":"journal_article","extern":1,"abstract":[{"text":"The phytohormone auxin acts as a prominent signal, providing, by its local accumulation or depletion in selected cells, a spatial and temporal reference for changes in the developmental program. The distribution of auxin depends on both auxin metabolism (biosynthesis, conjugation and degradation) and cellular auxin transport. We identified in silico a novel putative auxin transport facilitator family, called PIN-LIKES (PILS). Here we illustrate that PILS proteins are required for auxin-dependent regulation of plant growth by determining the cellular sensitivity to auxin. PILS proteins regulate intracellular auxin accumulation at the endoplasmic reticulum and thus auxin availability for nuclear auxin signalling. PILS activity affects the level of endogenous auxin indole-3-acetic acid (IAA), presumably via intracellular accumulation and metabolism. Our findings reveal that the transport machinery to compartmentalize auxin within the cell is of an unexpected molecular complexity and demonstrate this compartmentalization to be functionally important for a number of developmental processes.","lang":"eng"}],"issue":"7396","publist_id":"3591","quality_controlled":0,"page":"119 - 122","publication":"Nature","citation":{"mla":"Barbez, Elke, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular Auxin Homeostasis in Plants.” Nature, vol. 485, no. 7396, Nature Publishing Group, 2012, pp. 119–22, doi:10.1038/nature11001.","short":"E. Barbez, M. Kubeš, J. Rolčík, C. Béziat, A. Pěnčík, B. Wang, M. Rosquete, J. Zhu, P. Dobrev, Y. Lee, E. Zašímalová, J. Petrášek, M. Geisler, J. Friml, J. Kleine Vehn, Nature 485 (2012) 119–122.","chicago":"Barbez, Elke, Martin Kubeš, Jakub Rolčík, Chloe Béziat, Aleš Pěnčík, Bangjun Wang, Michel Rosquete, et al. “A Novel Putative Auxin Carrier Family Regulates Intracellular Auxin Homeostasis in Plants.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11001.","ama":"Barbez E, Kubeš M, Rolčík J, et al. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 2012;485(7396):119-122. doi:10.1038/nature11001","ista":"Barbez E, Kubeš M, Rolčík J, Béziat C, Pěnčík A, Wang B, Rosquete M, Zhu J, Dobrev P, Lee Y, Zašímalová E, Petrášek J, Geisler M, Friml J, Kleine Vehn J. 2012. A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. 485(7396), 119–122.","apa":"Barbez, E., Kubeš, M., Rolčík, J., Béziat, C., Pěnčík, A., Wang, B., … Kleine Vehn, J. (2012). A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11001","ieee":"E. Barbez et al., “A novel putative auxin carrier family regulates intracellular auxin homeostasis in plants,” Nature, vol. 485, no. 7396. Nature Publishing Group, pp. 119–122, 2012."},"doi":"10.1038/nature11001","date_published":"2012-05-03T00:00:00Z","month":"05","day":"03"},{"day":"01","month":"04","date_published":"2012-04-01T00:00:00Z","doi":"10.1371/journal.pbio.1001299","citation":{"chicago":"Nagawa, Shingo, Tongda Xu, Deshu Lin, Pankaj Dhonukshe, Xingxing Zhang, Jiří Friml, Ben Scheres, Ying Fu, and Zhenbiao Yang. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” PLoS Biology. Public Library of Science, 2012. https://doi.org/10.1371/journal.pbio.1001299.","mla":"Nagawa, Shingo, et al. “ROP GTPase-Dependent Actin Microfilaments Promote PIN1 Polarization by Localized Inhibition of Clathrin-Dependent Endocytosis.” PLoS Biology, vol. 10, no. 4, Public Library of Science, 2012, doi:10.1371/journal.pbio.1001299.","short":"S. Nagawa, T. Xu, D. Lin, P. Dhonukshe, X. Zhang, J. Friml, B. Scheres, Y. Fu, Z. Yang, PLoS Biology 10 (2012).","ista":"Nagawa S, Xu T, Lin D, Dhonukshe P, Zhang X, Friml J, Scheres B, Fu Y, Yang Z. 2012. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 10(4).","apa":"Nagawa, S., Xu, T., Lin, D., Dhonukshe, P., Zhang, X., Friml, J., … Yang, Z. (2012). ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1001299","ieee":"S. Nagawa et al., “ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis,” PLoS Biology, vol. 10, no. 4. Public Library of Science, 2012.","ama":"Nagawa S, Xu T, Lin D, et al. ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis. PLoS Biology. 2012;10(4). doi:10.1371/journal.pbio.1001299"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication":"PLoS Biology","quality_controlled":0,"issue":"4","publist_id":"3593","abstract":[{"text":"Cell polarization via asymmetrical distribution of structures or molecules is essential for diverse cellular functions and development of organisms, but how polarity is developmentally controlled has been poorly understood. In plants, the asymmetrical distribution of the PIN-FORMED (PIN) proteins involved in the cellular efflux of the quintessential phytohormone auxin plays a central role in developmental patterning, morphogenesis, and differential growth. Recently we showed that auxin promotes cell interdigitation by activating the Rho family ROP GTPases in leaf epidermal pavement cells. Here we found that auxin activation of the ROP2 signaling pathway regulates the asymmetric distribution of PIN1 by inhibiting its endocytosis. ROP2 inhibits PIN1 endocytosis via the accumulation of cortical actin microfilaments induced by the ROP2 effector protein RIC4. Our findings suggest a link between the developmental auxin signal and polar PIN1 distribution via Rho-dependent cytoskeletal reorganization and reveal the conservation of a design principle for cell polarization that is based on Rho GTPase-mediated inhibition of endocytosis.","lang":"eng"}],"extern":1,"type":"journal_article","author":[{"last_name":"Nagawa","first_name":"Shingo","full_name":"Nagawa, Shingo"},{"full_name":"Xu, Tongda","first_name":"Tongda","last_name":"Xu"},{"first_name":"Deshu","last_name":"Lin","full_name":"Lin, Deshu"},{"full_name":"Dhonukshe, Pankaj","first_name":"Pankaj","last_name":"Dhonukshe"},{"full_name":"Zhang, Xingxing","first_name":"Xingxing","last_name":"Zhang"},{"full_name":"Jirí Friml","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"},{"last_name":"Scheres","first_name":"Ben","full_name":"Scheres, Ben"},{"first_name":"Ying","last_name":"Fu","full_name":"Fu, Ying"},{"full_name":"Yang, Zhenbiao","first_name":"Zhenbiao","last_name":"Yang"}],"volume":10,"date_updated":"2021-01-12T07:41:06Z","date_created":"2018-12-11T12:01:25Z","_id":"3106","year":"2012","publisher":"Public Library of Science","intvolume":" 10","title":"ROP GTPase-dependent actin microfilaments promote PIN1 polarization by localized inhibition of clathrin-dependent endocytosis","status":"public","publication_status":"published"},{"language":[{"iso":"eng"}],"doi":"10.1038/nchembio.943","date_published":"2012-05-01T00:00:00Z","page":"415 - 416","quality_controlled":"1","citation":{"ista":"Vanneste S, Friml J. 2012. Plant signaling: Deconstructing auxin sensing, Nature Publishing Group,p.","apa":"Vanneste, S., & Friml, J. (2012). Plant signaling: Deconstructing auxin sensing. Nature Chemical Biology (Vol. 8, pp. 415–416). Nature Publishing Group. https://doi.org/10.1038/nchembio.943","ieee":"S. Vanneste and J. Friml, Plant signaling: Deconstructing auxin sensing, vol. 8, no. 5. Nature Publishing Group, 2012, pp. 415–416.","ama":"Vanneste S, Friml J. Plant Signaling: Deconstructing Auxin Sensing. Vol 8. Nature Publishing Group; 2012:415-416. doi:10.1038/nchembio.943","chicago":"Vanneste, Steffen, and Jiří Friml. Plant Signaling: Deconstructing Auxin Sensing. Nature Chemical Biology. Vol. 8. Nature Publishing Group, 2012. https://doi.org/10.1038/nchembio.943.","mla":"Vanneste, Steffen, and Jiří Friml. “Plant Signaling: Deconstructing Auxin Sensing.” Nature Chemical Biology, vol. 8, no. 5, Nature Publishing Group, 2012, pp. 415–16, doi:10.1038/nchembio.943.","short":"S. Vanneste, J. Friml, Plant Signaling: Deconstructing Auxin Sensing, Nature Publishing Group, 2012."},"publication":"Nature Chemical Biology","month":"05","day":"01","oa_version":"None","volume":8,"date_created":"2018-12-11T12:01:26Z","date_updated":"2021-01-12T07:41:06Z","author":[{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Nature Publishing Group","intvolume":" 8","status":"public","publication_status":"published","title":"Plant signaling: Deconstructing auxin sensing","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3107","year":"2012","extern":"1","issue":"5","publist_id":"3592","type":"other_academic_publication"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3119","ddc":["000"],"title":"Controlling liquids using meshes","status":"public","pubrep_id":"600","oa_version":"Submitted Version","file":[{"creator":"system","file_size":4939370,"content_type":"application/pdf","file_name":"IST-2016-600-v1+1_ControllingLiquids_Preprint.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:00Z","date_created":"2018-12-12T10:11:23Z","checksum":"babda64c24cf90a4d05ae86d712bed08","file_id":"4877","relation":"main_file"}],"type":"conference","abstract":[{"lang":"eng","text":"We present an approach for artist-directed animation of liquids using multiple levels of control over the simulation, ranging from the overall tracking of desired shapes to highly detailed secondary effects such as dripping streams, separating sheets of fluid, surface waves and ripples. The first portion of our technique is a volume preserving morph that allows the animator to produce a plausible fluid-like motion from a sparse set of control meshes. By rasterizing the resulting control meshes onto the simulation grid, the mesh velocities act as boundary conditions during the projection step of the fluid simulation. We can then blend this motion together with uncontrolled fluid velocities to achieve a more relaxed control over the fluid that captures natural inertial effects. Our method can produce highly detailed liquid surfaces with control over sub-grid details by using a mesh-based surface tracker on top of a coarse grid-based fluid simulation. We can create ripples and waves on the fluid surface attracting the surface mesh to the control mesh with spring-like forces and also by running a wave simulation over the surface mesh. Our video results demonstrate how our control scheme can be used to create animated characters and shapes that are made of water.\r\n"}],"publication":"Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation","citation":{"mla":"Raveendran, Karthik, et al. “Controlling Liquids Using Meshes.” Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–64.","short":"K. Raveendran, N. Thuerey, C. Wojtan, G. Turk, in:, Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–264.","chicago":"Raveendran, Karthik, Nils Thuerey, Chris Wojtan, and Greg Turk. “Controlling Liquids Using Meshes.” In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, 255–64. ACM, 2012.","ama":"Raveendran K, Thuerey N, Wojtan C, Turk G. Controlling liquids using meshes. In: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. ACM; 2012:255-264.","ista":"Raveendran K, Thuerey N, Wojtan C, Turk G. 2012. Controlling liquids using meshes. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 255–264.","ieee":"K. Raveendran, N. Thuerey, C. Wojtan, and G. Turk, “Controlling liquids using meshes,” in Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, Aire-la-Ville, Switzerland, 2012, pp. 255–264.","apa":"Raveendran, K., Thuerey, N., Wojtan, C., & Turk, G. (2012). Controlling liquids using meshes. In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation (pp. 255–264). Aire-la-Ville, Switzerland: ACM."},"page":"255 - 264","date_published":"2012-07-29T00:00:00Z","scopus_import":1,"day":"29","has_accepted_license":"1","acknowledgement":"This work was partially funded by NSF grants CCF-0811485 and IIS-1130934. We would like to thank Scanline VFX for additional funding. We would like to thank Jie Tan as well as our anonymous reviewers for their useful suggestions and feedback.","year":"2012","publication_status":"published","department":[{"_id":"ChWo"}],"publisher":"ACM","author":[{"full_name":"Raveendran, Karthik","first_name":"Karthik","last_name":"Raveendran"},{"full_name":"Thuerey, Nils","first_name":"Nils","last_name":"Thuerey"},{"first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"},{"full_name":"Turk, Greg","first_name":"Greg","last_name":"Turk"}],"related_material":{"link":[{"url":"http://dl.acm.org/citation.cfm?id=2422393","relation":"table_of_contents"}]},"date_created":"2018-12-11T12:01:30Z","date_updated":"2023-02-23T11:13:07Z","file_date_updated":"2020-07-14T12:46:00Z","publist_id":"3580","oa":1,"quality_controlled":"1","conference":{"start_date":"2012-07-29","location":"Aire-la-Ville, Switzerland","end_date":"2012-07-31","name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation"},"language":[{"iso":"eng"}],"month":"07"},{"publication_status":"published","publisher":"ACM","department":[{"_id":"ChWo"}],"acknowledgement":"This work is supported by the SNF fellowship PBEZP2-134464.\r\nWe would like to thank Xiaochen Hu for implementing mesh con- version tools, Duygu Ceylan for helping with the rendering, and Art Tevs for the human performance data comparison. We also thank Nils Thuerey and Christopher Batty for helpful discussions. ","year":"2012","date_created":"2018-12-11T12:01:29Z","date_updated":"2022-05-24T08:21:11Z","volume":31,"author":[{"full_name":"Bojsen-Hansen, Morten","first_name":"Morten","last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4417-3224"},{"last_name":"Li","first_name":"Hao","full_name":"Li, Hao"},{"first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"article_number":"53","file_date_updated":"2020-07-14T12:46:00Z","publist_id":"3581","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1145/2185520.2185549","month":"07","ddc":["000"],"title":"Tracking surfaces with evolving topology","status":"public","intvolume":" 31","_id":"3118","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","file":[{"file_id":"5359","relation":"main_file","date_updated":"2020-07-14T12:46:00Z","date_created":"2018-12-12T10:18:37Z","checksum":"1e219c5bf4e5552c1290c62eefa5cd60","file_name":"IST-2016-602-v1+1_topoReg.pdf","access_level":"open_access","creator":"system","file_size":44538518,"content_type":"application/pdf"}],"pubrep_id":"602","alternative_title":["SIGGRAPH"],"type":"journal_article","abstract":[{"text":"We present a method for recovering a temporally coherent, deforming triangle mesh with arbitrarily changing topology from an incoherent sequence of static closed surfaces. We solve this problem using the surface geometry alone, without any prior information like surface templates or velocity fields. Our system combines a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid registration routine, and a reliable technique for changing surface mesh topology. We also introduce a novel topological constraint enforcement algorithm to ensure that the output and input always have similar topology. We apply our technique to a series of diverse input data from video reconstructions, physics simulations, and artistic morphs. The structured output of our algorithm allows us to efficiently track information like colors and displacement maps, recover velocity information, and solve PDEs on the mesh as a post process.","lang":"eng"}],"issue":"4","article_type":"original","publication":"ACM Transactions on Graphics","citation":{"chicago":"Bojsen-Hansen, Morten, Hao Li, and Chris Wojtan. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics. ACM, 2012. https://doi.org/10.1145/2185520.2185549.","mla":"Bojsen-Hansen, Morten, et al. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics, vol. 31, no. 4, 53, ACM, 2012, doi:10.1145/2185520.2185549.","short":"M. Bojsen-Hansen, H. Li, C. Wojtan, ACM Transactions on Graphics 31 (2012).","ista":"Bojsen-Hansen M, Li H, Wojtan C. 2012. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 31(4), 53.","apa":"Bojsen-Hansen, M., Li, H., & Wojtan, C. (2012). Tracking surfaces with evolving topology. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2185520.2185549","ieee":"M. Bojsen-Hansen, H. Li, and C. Wojtan, “Tracking surfaces with evolving topology,” ACM Transactions on Graphics, vol. 31, no. 4. ACM, 2012.","ama":"Bojsen-Hansen M, Li H, Wojtan C. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 2012;31(4). doi:10.1145/2185520.2185549"},"date_published":"2012-07-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No"},{"language":[{"iso":"eng"}],"date_published":"2012-08-01T00:00:00Z","doi":"10.1111/j.1365-294X.2012.05643.x","page":"3640 - 3643","quality_controlled":"1","citation":{"ista":"Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.","apa":"Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05643.x","ieee":"D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012.","ama":"Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x","chicago":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x.","mla":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x.","short":"D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643."},"publication":"Molecular Ecology","month":"08","day":"01","scopus_import":1,"oa_version":"None","volume":21,"date_created":"2018-12-11T12:01:31Z","date_updated":"2021-01-12T07:41:13Z","author":[{"orcid":"0000-0002-4014-8478","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David"},{"full_name":"Barrett, Spencer","last_name":"Barrett","first_name":"Spencer"}],"publisher":"Wiley-Blackwell","intvolume":" 21","department":[{"_id":"NiBa"}],"publication_status":"published","status":"public","title":"Disassortative mating and the maintenance of sexual polymorphism in painted maple","year":"2012","_id":"3122","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"3577","issue":"15","abstract":[{"lang":"eng","text":"Since Darwin's pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic 'pollen transfer' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. "}],"type":"journal_article"},{"scopus_import":1,"day":"01","publication":"Nature Neuroscience","citation":{"chicago":"Williams, Courtney, Wenyan Chen, Chia Lee, Daniel Yaeger, Nicholas Vyleta, and Stephen Smith. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3162.","mla":"Williams, Courtney, et al. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience, vol. 15, no. 9, Nature Publishing Group, 2012, pp. 1195–97, doi:10.1038/nn.3162.","short":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, S. Smith, Nature Neuroscience 15 (2012) 1195–1197.","ista":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. 2012. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 15(9), 1195–1197.","ieee":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, and S. Smith, “Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA,” Nature Neuroscience, vol. 15, no. 9. Nature Publishing Group, pp. 1195–1197, 2012.","apa":"Williams, C., Chen, W., Lee, C., Yaeger, D., Vyleta, N., & Smith, S. (2012). Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3162","ama":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 2012;15(9):1195-1197. doi:10.1038/nn.3162"},"page":"1195 - 1197","date_published":"2012-09-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Voltage-activated Ca(2+) channels (VACCs) mediate Ca(2+) influx to trigger action potential-evoked neurotransmitter release, but the mechanism by which Ca(2+) regulates spontaneous transmission is unclear. We found that VACCs are the major physiological triggers for spontaneous release at mouse neocortical inhibitory synapses. Moreover, despite the absence of a synchronizing action potential, we found that spontaneous fusion of a GABA-containing vesicle required the activation of multiple tightly coupled VACCs of variable type.","lang":"eng"}],"issue":"9","_id":"3121","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA","intvolume":" 15","oa_version":"Submitted Version","month":"09","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431448/"}],"external_id":{"pmid":["22842148"]},"quality_controlled":"1","doi":"10.1038/nn.3162","language":[{"iso":"eng"}],"publist_id":"3578","year":"2012","acknowledgement":"The work was supported by the US National Institutes of Health (DA027110 and GM097433) and OCTRI. C.W. and N.P.V. were supported by a grant from the National Heart, Lung, and Blood Institute (T32HL033808).\r\nWe thank M. Andresen and K. Khodakhah for helpful comments. ","pmid":1,"publication_status":"published","publisher":"Nature Publishing Group","department":[{"_id":"PeJo"}],"author":[{"full_name":"Williams, Courtney","first_name":"Courtney","last_name":"Williams"},{"first_name":"Wenyan","last_name":"Chen","full_name":"Chen, Wenyan"},{"last_name":"Lee","first_name":"Chia","full_name":"Lee, Chia"},{"first_name":"Daniel","last_name":"Yaeger","full_name":"Yaeger, Daniel"},{"first_name":"Nicholas","last_name":"Vyleta","id":"36C4978E-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Nicholas"},{"first_name":"Stephen","last_name":"Smith","full_name":"Smith, Stephen"}],"date_created":"2018-12-11T12:01:30Z","date_updated":"2021-01-12T07:41:12Z","volume":15},{"language":[{"iso":"eng"}],"doi":"10.1112/S0010437X11007226","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1009.4313","open_access":"1"}],"month":"07","volume":148,"date_updated":"2021-01-12T07:41:12Z","date_created":"2018-12-11T12:01:30Z","author":[{"last_name":"Brown","first_name":"Gavin","full_name":"Brown, Gavin"},{"full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber","first_name":"Michael"},{"last_name":"Reid","first_name":"Miles","full_name":"Reid, Miles"}],"department":[{"_id":"HeEd"}],"publisher":"Cambridge University Press","publication_status":"published","acknowledgement":"This research is supported by the Korean Government WCU Grant R33-2008-000-10101-0.","year":"2012","publist_id":"3579","date_published":"2012-07-01T00:00:00Z","page":"1171 - 1194","citation":{"chicago":"Brown, Gavin, Michael Kerber, and Miles Reid. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica. Cambridge University Press, 2012. https://doi.org/10.1112/S0010437X11007226.","mla":"Brown, Gavin, et al. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica, vol. 148, no. 4, Cambridge University Press, 2012, pp. 1171–94, doi:10.1112/S0010437X11007226.","short":"G. Brown, M. Kerber, M. Reid, Compositio Mathematica 148 (2012) 1171–1194.","ista":"Brown G, Kerber M, Reid M. 2012. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 148(4), 1171–1194.","apa":"Brown, G., Kerber, M., & Reid, M. (2012). Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X11007226","ieee":"G. Brown, M. Kerber, and M. Reid, “Fano 3 folds in codimension 4 Tom and Jerry Part I,” Compositio Mathematica, vol. 148, no. 4. Cambridge University Press, pp. 1171–1194, 2012.","ama":"Brown G, Kerber M, Reid M. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 2012;148(4):1171-1194. doi:10.1112/S0010437X11007226"},"publication":"Compositio Mathematica","day":"01","scopus_import":1,"oa_version":"Preprint","intvolume":" 148","status":"public","title":"Fano 3 folds in codimension 4 Tom and Jerry Part I","_id":"3120","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"4","abstract":[{"lang":"eng","text":"We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica."}],"type":"journal_article"},{"scopus_import":1,"month":"10","day":"01","oa":1,"citation":{"ista":"Kolmogorov V. 2012. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 160(15), 2246–2258.","ieee":"V. Kolmogorov, “Minimizing a sum of submodular functions,” Discrete Applied Mathematics, vol. 160, no. 15. Elsevier, pp. 2246–2258, 2012.","apa":"Kolmogorov, V. (2012). Minimizing a sum of submodular functions. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2012.05.025","ama":"Kolmogorov V. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 2012;160(15):2246-2258. doi:10.1016/j.dam.2012.05.025","chicago":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2012.05.025.","mla":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics, vol. 160, no. 15, Elsevier, 2012, pp. 2246–58, doi:10.1016/j.dam.2012.05.025.","short":"V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 2246–2258."},"main_file_link":[{"url":"http://arxiv.org/abs/1006.1990","open_access":"1"}],"publication":"Discrete Applied Mathematics","page":"2246 - 2258","quality_controlled":"1","doi":"10.1016/j.dam.2012.05.025","date_published":"2012-10-01T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","publist_id":"3582","issue":"15","abstract":[{"lang":"eng","text":"We consider the problem of minimizing a function represented as a sum of submodular terms. We assume each term allows an efficient computation of exchange capacities. This holds, for example, for terms depending on a small number of variables, or for certain cardinality-dependent terms. A naive application of submodular minimization algorithms would not exploit the existence of specialized exchange capacity subroutines for individual terms. To overcome this, we cast the problem as a submodular flow (SF) problem in an auxiliary graph in such a way that applying most existing SF algorithms would rely only on these subroutines. We then explore in more detail Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular, we show how to improve its complexity in the case when the function contains cardinality-dependent terms."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3117","year":"2012","publisher":"Elsevier","intvolume":" 160","department":[{"_id":"VlKo"}],"publication_status":"published","status":"public","title":"Minimizing a sum of submodular functions","author":[{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","volume":160,"date_updated":"2021-01-12T07:41:11Z","date_created":"2018-12-11T12:01:29Z"},{"pubrep_id":"114","file":[{"checksum":"729a4becda7d786c4c3db8f9a1f77953","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:08:00Z","relation":"main_file","file_id":"4659","content_type":"application/pdf","file_size":1284801,"creator":"system","access_level":"open_access","file_name":"IST-2013-114-v1+1_WeissmanBarton2012.pdf"}],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3131","intvolume":" 8","ddc":["570","576"],"status":"public","title":"Limits to the rate of adaptive substitution in sexual populations","issue":"6","abstract":[{"text":"In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.","lang":"eng"}],"type":"journal_article","date_published":"2012-06-07T00:00:00Z","citation":{"ista":"Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740.","ieee":"D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012.","apa":"Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740","ama":"Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740","chicago":"Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002740.","mla":"Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002740.","short":"D. Weissman, N.H. Barton, PLoS Genetics 8 (2012)."},"publication":"PLoS Genetics","has_accepted_license":"1","day":"07","scopus_import":1,"author":[{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Weissman","full_name":"Weissman, Daniel"},{"last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"volume":8,"date_updated":"2021-01-12T07:41:17Z","date_created":"2018-12-11T12:01:34Z","acknowledgement":"The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth, O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers for their helpful suggestions.","year":"2012","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","publication_status":"published","ec_funded":1,"publist_id":"3566","file_date_updated":"2020-07-14T12:46:01Z","article_number":"e1002740","doi":"10.1371/journal.pgen.1002740","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"quality_controlled":"1","month":"06"},{"abstract":[{"text":"Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.","lang":"eng"}],"issue":"6","type":"journal_article","file":[{"date_created":"2018-12-12T10:12:52Z","date_updated":"2020-07-14T12:46:01Z","checksum":"f8506fb579eda6fc5613ba9bf421b86a","file_id":"4973","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":2674138,"file_name":"IST-2015-386-v1+1_journal.pgen.1002803.pdf","access_level":"open_access"}],"oa_version":"Published Version","pubrep_id":"386","ddc":["576"],"status":"public","title":"Patterns of evolutionary conservation of essential genes correlate with their compensability","intvolume":" 8","_id":"3130","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"28","has_accepted_license":"1","scopus_import":1,"date_published":"2012-06-28T00:00:00Z","publication":"PLoS Genetics","citation":{"ista":"Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803.","apa":"Bergmiller, T., Ackermann, M., & Silander, O. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002803","ieee":"T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation of essential genes correlate with their compensability,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012.","ama":"Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002803","chicago":"Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002803.","mla":"Bergmiller, Tobias, et al. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics, vol. 8, no. 6, e1002803, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002803.","short":"T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012)."},"file_date_updated":"2020-07-14T12:46:01Z","publist_id":"3567","article_number":"e1002803","date_created":"2018-12-11T12:01:34Z","date_updated":"2021-01-12T07:41:16Z","volume":8,"author":[{"full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias","last_name":"Bergmiller"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"},{"full_name":"Silander, Olin","last_name":"Silander","first_name":"Olin"}],"publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"CaGu"}],"acknowledgement":"We thank Alex Boehm for discussions and comments.","year":"2012","month":"06","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1002803","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1},{"conference":{"name":"CAV: Computer Aided Verification","end_date":"2012-07-13","location":"Berkeley, CA, USA","start_date":"2012-07-07"},"doi":"10.1007/978-3-642-31424-7_24","date_published":"2012-07-01T00:00:00Z","language":[{"iso":"eng"}],"citation":{"chicago":"Guet, Calin C, Ashutosh Gupta, Thomas A Henzinger, Maria Mateescu, and Ali Sezgin. “Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits,” 7358:294–309. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_24.","mla":"Guet, Calin C., et al. Delayed Continuous Time Markov Chains for Genetic Regulatory Circuits. Vol. 7358, Springer, 2012, pp. 294–309, doi:10.1007/978-3-642-31424-7_24.","short":"C.C. Guet, A. Gupta, T.A. Henzinger, M. Mateescu, A. Sezgin, in:, Springer, 2012, pp. 294–309.","ista":"Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. 2012. Delayed continuous time Markov chains for genetic regulatory circuits. CAV: Computer Aided Verification, LNCS, vol. 7358, 294–309.","apa":"Guet, C. C., Gupta, A., Henzinger, T. A., Mateescu, M., & Sezgin, A. (2012). Delayed continuous time Markov chains for genetic regulatory circuits (Vol. 7358, pp. 294–309). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_24","ieee":"C. C. Guet, A. Gupta, T. A. Henzinger, M. Mateescu, and A. Sezgin, “Delayed continuous time Markov chains for genetic regulatory circuits,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 294–309.","ama":"Guet CC, Gupta A, Henzinger TA, Mateescu M, Sezgin A. Delayed continuous time Markov chains for genetic regulatory circuits. In: Vol 7358. Springer; 2012:294-309. doi:10.1007/978-3-642-31424-7_24"},"quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"page":"294 - 309","day":"01","month":"07","scopus_import":1,"author":[{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Mateescu, Maria","first_name":"Maria","last_name":"Mateescu","id":"3B43276C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin","first_name":"Ali"}],"date_created":"2018-12-11T12:01:36Z","date_updated":"2021-01-12T07:41:18Z","oa_version":"None","volume":"7358 ","_id":"3136","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by the ERC Advanced Investigator grant on Quantitative Reactive Modeling (QUAREM) and by the Swiss National Science Foundation.","publication_status":"published","title":"Delayed continuous time Markov chains for genetic regulatory circuits","status":"public","department":[{"_id":"CaGu"},{"_id":"ToHe"}],"publisher":"Springer","abstract":[{"lang":"eng","text":"Continuous-time Markov chains (CTMC) with their rich theory and efficient simulation algorithms have been successfully used in modeling stochastic processes in diverse areas such as computer science, physics, and biology. However, systems that comprise non-instantaneous events cannot be accurately and efficiently modeled with CTMCs. In this paper we define delayed CTMCs, an extension of CTMCs that allows for the specification of a lower bound on the time interval between an event's initiation and its completion, and we propose an algorithm for the computation of their behavior. Our algorithm effectively decomposes the computation into two stages: a pure CTMC governs event initiations while a deterministic process guarantees lower bounds on event completion times. Furthermore, from the nature of delayed CTMCs, we obtain a parallelized version of our algorithm. We use our formalism to model genetic regulatory circuits (biological systems where delayed events are common) and report on the results of our numerical algorithm as run on a cluster. We compare performance and accuracy of our results with results obtained by using pure CTMCs. © 2012 Springer-Verlag."}],"ec_funded":1,"publist_id":"3561","type":"conference","alternative_title":["LNCS"]},{"oa_version":"Preprint","status":"public","title":"Efficient controller synthesis for consumption games with multiple resource types","intvolume":" 7358","_id":"3135","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We introduce consumption games, a model for discrete interactive system with multiple resources that are consumed or reloaded independently. More precisely, a consumption game is a finite-state graph where each transition is labeled by a vector of resource updates, where every update is a non-positive number or ω. The ω updates model the reloading of a given resource. Each vertex belongs either to player □ or player ◇, where the aim of player □ is to play so that the resources are never exhausted. We consider several natural algorithmic problems about consumption games, and show that although these problems are computationally hard in general, they are solvable in polynomial time for every fixed number of resource types (i.e., the dimension of the update vectors) and bounded resource updates. "}],"alternative_title":["LNCS"],"type":"conference","date_published":"2012-07-01T00:00:00Z","page":"23 - 38","citation":{"mla":"Brázdil, Brázdil, et al. Efficient Controller Synthesis for Consumption Games with Multiple Resource Types. Vol. 7358, Springer, 2012, pp. 23–38, doi:10.1007/978-3-642-31424-7_8.","short":"B. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, in:, Springer, 2012, pp. 23–38.","chicago":"Brázdil, Brázdil, Krishnendu Chatterjee, Antonín Kučera, and Petr Novotný. “Efficient Controller Synthesis for Consumption Games with Multiple Resource Types,” 7358:23–38. Springer, 2012. https://doi.org/10.1007/978-3-642-31424-7_8.","ama":"Brázdil B, Chatterjee K, Kučera A, Novotný P. Efficient controller synthesis for consumption games with multiple resource types. In: Vol 7358. Springer; 2012:23-38. doi:10.1007/978-3-642-31424-7_8","ista":"Brázdil B, Chatterjee K, Kučera A, Novotný P. 2012. Efficient controller synthesis for consumption games with multiple resource types. CAV: Computer Aided Verification, LNCS, vol. 7358, 23–38.","ieee":"B. Brázdil, K. Chatterjee, A. Kučera, and P. Novotný, “Efficient controller synthesis for consumption games with multiple resource types,” presented at the CAV: Computer Aided Verification, Berkeley, CA, USA, 2012, vol. 7358, pp. 23–38.","apa":"Brázdil, B., Chatterjee, K., Kučera, A., & Novotný, P. (2012). Efficient controller synthesis for consumption games with multiple resource types (Vol. 7358, pp. 23–38). Presented at the CAV: Computer Aided Verification, Berkeley, CA, USA: Springer. https://doi.org/10.1007/978-3-642-31424-7_8"},"day":"01","scopus_import":1,"date_updated":"2021-01-12T07:41:18Z","date_created":"2018-12-11T12:01:35Z","volume":7358,"author":[{"last_name":"Brázdil","first_name":"Brázdil","full_name":"Brázdil, Brázdil"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kučera","first_name":"Antonín","full_name":"Kučera, Antonín"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny","first_name":"Petr","full_name":"Novotny, Petr"}],"publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"Springer","year":"2012","acknowledgement":"Tomas Brazdil, Antonin Kucera, and Petr Novotny are supported by the Czech Science Foundation, grant No. P202/10/1469. Krishnendu Chatterjee is supported by the FWF (Austrian Science Fund) NFN Grant No S11407-N23 (RiSE) and ERC Start grant (279307: Graph Games).","publist_id":"3562","ec_funded":1,"language":[{"iso":"eng"}],"conference":{"name":"CAV: Computer Aided Verification","start_date":"2012-07-07","location":"Berkeley, CA, USA","end_date":"2012-07-13"},"doi":"10.1007/978-3-642-31424-7_8","quality_controlled":"1","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1202.0796","open_access":"1"}],"month":"07"},{"status":"public","title":"Alexander duality for functions: The persistent behavior of land and water and shore","publication_status":"published","publisher":"ACM","department":[{"_id":"HeEd"}],"_id":"3133","acknowledgement":"his research is partially supported by the National Science Foundation (NSF) under grant DBI-0820624, the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.\r\nThe authors thank an anonymous referee for suggesting the simplified proof of the Contravariant PE Theorem given in this paper. They also thank Frederick Cohen, Yuriy Mileyko and Amit Patel for helpful discussions.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","date_created":"2018-12-11T12:01:35Z","date_updated":"2021-01-12T07:41:17Z","oa_version":"Preprint","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert"},{"full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber","first_name":"Michael"}],"type":"conference","abstract":[{"lang":"eng","text":"This note contributes to the point calculus of persistent homology by extending Alexander duality from spaces to real-valued functions. Given a perfect Morse function f: S n+1 →[0, 1 and a decomposition S n+1 = U ∪ V into two (n + 1)-manifolds with common boundary M, we prove elementary relationships between the persistence diagrams of f restricted to U, to V, and to M. "}],"publist_id":"3564","quality_controlled":"1","page":"249 - 258","publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry ","oa":1,"citation":{"chicago":"Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” In Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , 249–58. ACM, 2012. https://doi.org/10.1145/2261250.2261287.","mla":"Edelsbrunner, Herbert, and Michael Kerber. “Alexander Duality for Functions: The Persistent Behavior of Land and Water and Shore.” Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–58, doi:10.1145/2261250.2261287.","short":"H. Edelsbrunner, M. Kerber, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 249–258.","ista":"Edelsbrunner H, Kerber M. 2012. Alexander duality for functions: The persistent behavior of land and water and shore. Proceedings of the twenty-eighth annual symposium on Computational geometry . SCG: Symposium on Computational Geometry, 249–258.","ieee":"H. Edelsbrunner and M. Kerber, “Alexander duality for functions: The persistent behavior of land and water and shore,” in Proceedings of the twenty-eighth annual symposium on Computational geometry , Chapel Hill, NC, USA, 2012, pp. 249–258.","apa":"Edelsbrunner, H., & Kerber, M. (2012). Alexander duality for functions: The persistent behavior of land and water and shore. In Proceedings of the twenty-eighth annual symposium on Computational geometry (pp. 249–258). Chapel Hill, NC, USA: ACM. https://doi.org/10.1145/2261250.2261287","ama":"Edelsbrunner H, Kerber M. Alexander duality for functions: The persistent behavior of land and water and shore. In: Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry . ACM; 2012:249-258. doi:10.1145/2261250.2261287"},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.5052"}],"language":[{"iso":"eng"}],"conference":{"name":"SCG: Symposium on Computational Geometry","end_date":"2012-06-20","location":"Chapel Hill, NC, USA","start_date":"2012-06-17"},"doi":"10.1145/2261250.2261287","date_published":"2012-06-20T00:00:00Z","scopus_import":1,"day":"20","month":"06"},{"publist_id":"3563","abstract":[{"lang":"eng","text":"It has been an open question whether the sum of finitely many isotropic Gaussian kernels in n ≥ 2 dimensions can have more modes than kernels, until in 2003 Carreira-Perpiñán and Williams exhibited n +1 isotropic Gaussian kernels in ℝ n with n + 2 modes. We give a detailed analysis of this example, showing that it has exponentially many critical points and that the resilience of the extra mode grows like √n. In addition, we exhibit finite configurations of isotropic Gaussian kernels with superlinearly many modes. "}],"type":"conference","oa_version":"None","date_created":"2018-12-11T12:01:35Z","date_updated":"2023-02-23T10:59:27Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"2815"}]},"author":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"first_name":"Brittany","last_name":"Fasy","full_name":"Fasy, Brittany"},{"last_name":"Rote","first_name":"Günter","full_name":"Rote, Günter"}],"publisher":"ACM","department":[{"_id":"HeEd"}],"status":"public","title":"Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions","publication_status":"published","acknowledgement":"This research is partially supported by the National Science Foun- dation (NSF) under grant DBI-0820624, by the European Science Foundation under the Research Networking Programme, and the Russian Government Project 11.G34.31.0053.","_id":"3134","year":"2012","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"06","day":"20","scopus_import":1,"language":[{"iso":"eng"}],"doi":"10.1145/2261250.2261265","date_published":"2012-06-20T00:00:00Z","conference":{"end_date":"2012-06-20","location":"Chapel Hill, NC, USA","start_date":"2012-06-17","name":"SCG: Symposium on Computational Geometry"},"page":"91 - 100","quality_controlled":"1","citation":{"ieee":"H. Edelsbrunner, B. Fasy, and G. Rote, “Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions,” in Proceedings of the twenty-eighth annual symposium on Computational geometry , Chapel Hill, NC, USA, 2012, pp. 91–100.","apa":"Edelsbrunner, H., Fasy, B., & Rote, G. (2012). Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. In Proceedings of the twenty-eighth annual symposium on Computational geometry (pp. 91–100). Chapel Hill, NC, USA: ACM. https://doi.org/10.1145/2261250.2261265","ista":"Edelsbrunner H, Fasy B, Rote G. 2012. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. Proceedings of the twenty-eighth annual symposium on Computational geometry . SCG: Symposium on Computational Geometry, 91–100.","ama":"Edelsbrunner H, Fasy B, Rote G. Add isotropic Gaussian kernels at own risk: More and more resilient modes in higher dimensions. In: Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry . ACM; 2012:91-100. doi:10.1145/2261250.2261265","chicago":"Edelsbrunner, Herbert, Brittany Fasy, and Günter Rote. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” In Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , 91–100. ACM, 2012. https://doi.org/10.1145/2261250.2261265.","short":"H. Edelsbrunner, B. Fasy, G. Rote, in:, Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100.","mla":"Edelsbrunner, Herbert, et al. “Add Isotropic Gaussian Kernels at Own Risk: More and More Resilient Modes in Higher Dimensions.” Proceedings of the Twenty-Eighth Annual Symposium on Computational Geometry , ACM, 2012, pp. 91–100, doi:10.1145/2261250.2261265."},"publication":"Proceedings of the twenty-eighth annual symposium on Computational geometry "},{"type":"journal_article","publist_id":"3565","issue":"8","abstract":[{"lang":"eng","text":"Reproductive division of labour is a characteristic trait of social insects. The dominant reproductive individual, often the queen, uses chemical communication and/or behaviour to maintain her social status. Queens of many social insects communicate their fertility status via cuticle-bound substances. As these substances usually possess a low volatility, their range in queen–worker communication is potentially limited. Here, we investigate the range and impact of behavioural and chemical queen signals on workers of the ant Temnothorax longispinosus. We compared the behaviour and ovary development of workers subjected to three different treatments: workers with direct chemical and physical contact to the queen, those solely under the influence of volatile queen substances and those entirely separated from the queen. In addition to short-ranged queen signals preventing ovary development in workers, we discovered a novel secondary pathway influencing worker behaviour. Workers with no physical contact to the queen, but exposed to volatile substances, started to develop their ovaries, but did not change their behaviour compared to workers in direct contact to the queen. In contrast, workers in queen-separated groups showed both increased ovary development and aggressive dominance interactions. We conclude that T. longispinosus queens influence worker ovary development and behaviour via two independent signals, both ensuring social harmony within the colony."}],"department":[{"_id":"SyCr"}],"intvolume":" 99","publisher":"Springer","status":"public","publication_status":"published","title":"Two pathways ensuring social harmony","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3132","acknowledgement":"We like to thank the editor and three anonymous reviewers for their time and constructive criticism and Inon Scharf, Volker Witte and Andreas Modlmeier for helpful comments on earlier versions of the manuscript. The first and second authors appear in alphabetical order and contributed equally to this paper.","year":"2012","volume":99,"oa_version":"None","date_created":"2018-12-11T12:01:34Z","date_updated":"2021-01-12T07:41:17Z","author":[{"full_name":"Konrad, Matthias","first_name":"Matthias","last_name":"Konrad","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pamminger, Tobias","last_name":"Pamminger","first_name":"Tobias"},{"full_name":"Foitzik, Susanne","last_name":"Foitzik","first_name":"Susanne"}],"scopus_import":1,"day":"01","month":"08","page":"627 - 636","quality_controlled":"1","citation":{"ieee":"M. Konrad, T. Pamminger, and S. Foitzik, “Two pathways ensuring social harmony,” Naturwissenschaften, vol. 99, no. 8. Springer, pp. 627–636, 2012.","apa":"Konrad, M., Pamminger, T., & Foitzik, S. (2012). Two pathways ensuring social harmony. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-012-0943-z","ista":"Konrad M, Pamminger T, Foitzik S. 2012. Two pathways ensuring social harmony. Naturwissenschaften. 99(8), 627–636.","ama":"Konrad M, Pamminger T, Foitzik S. Two pathways ensuring social harmony. Naturwissenschaften. 2012;99(8):627-636. doi:10.1007/s00114-012-0943-z","chicago":"Konrad, Matthias, Tobias Pamminger, and Susanne Foitzik. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften. Springer, 2012. https://doi.org/10.1007/s00114-012-0943-z.","short":"M. Konrad, T. Pamminger, S. Foitzik, Naturwissenschaften 99 (2012) 627–636.","mla":"Konrad, Matthias, et al. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften, vol. 99, no. 8, Springer, 2012, pp. 627–36, doi:10.1007/s00114-012-0943-z."},"publication":"Naturwissenschaften","language":[{"iso":"eng"}],"doi":"10.1007/s00114-012-0943-z","date_published":"2012-08-01T00:00:00Z"},{"month":"05","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1371/journal.pone.0036044","language":[{"iso":"eng"}],"article_number":"e36044","publist_id":"3526","file_date_updated":"2020-07-14T12:46:01Z","year":"2012","acknowledgement":"Supported by National Institutes of Health grants GM071338 (ML) and AI059355 (BM).\r\nWe acknowledge the expertise of Dr. Martina Ralle in Department of Biochemistry and Molecular Biology at OHSU for measurements of potassium using inductively coupled plasma mass spectrometry.","publisher":"Public Library of Science","department":[{"_id":"SyCr"}],"publication_status":"published","author":[{"full_name":"Vyleta, Meghan","first_name":"Meghan","last_name":"Vyleta","id":"418901AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"John","last_name":"Wong","full_name":"Wong, John"},{"first_name":"Bruce","last_name":"Magun","full_name":"Magun, Bruce"}],"volume":7,"date_created":"2018-12-11T12:01:45Z","date_updated":"2021-01-12T07:41:29Z","scopus_import":1,"has_accepted_license":"1","day":"14","citation":{"short":"M. Vyleta, J. Wong, B. Magun, PLoS One 7 (2012).","mla":"Vyleta, Meghan, et al. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” PLoS One, vol. 7, no. 5, e36044, Public Library of Science, 2012, doi:10.1371/journal.pone.0036044.","chicago":"Vyleta, Meghan, John Wong, and Bruce Magun. “Suppression of Ribosomal Function Triggers Innate Immune Signaling through Activation of the NLRP3 Inflammasome.” PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0036044.","ama":"Vyleta M, Wong J, Magun B. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. 2012;7(5). doi:10.1371/journal.pone.0036044","ieee":"M. Vyleta, J. Wong, and B. Magun, “Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome,” PLoS One, vol. 7, no. 5. Public Library of Science, 2012.","apa":"Vyleta, M., Wong, J., & Magun, B. (2012). Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0036044","ista":"Vyleta M, Wong J, Magun B. 2012. Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome. PLoS One. 7(5), e36044."},"publication":"PLoS One","date_published":"2012-05-14T00:00:00Z","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"Some inflammatory stimuli trigger activation of the NLRP3 inflammasome by inducing efflux of cellular potassium. Loss of cellular potassium is known to potently suppress protein synthesis, leading us to test whether the inhibition of protein synthesis itself serves as an activating signal for the NLRP3 inflammasome. Murine bone marrow-derived macrophages, either primed by LPS or unprimed, were exposed to a panel of inhibitors of ribosomal function: ricin, cycloheximide, puromycin, pactamycin, and anisomycin. Macrophages were also exposed to nigericin, ATP, monosodium urate (MSU), and poly I:C. Synthesis of pro-IL-ß and release of IL-1ß from cells in response to these agents was detected by immunoblotting and ELISA. Release of intracellular potassium was measured by mass spectrometry. Inhibition of translation by each of the tested translation inhibitors led to processing of IL-1ß, which was released from cells. Processing and release of IL-1ß was reduced or absent from cells deficient in NLRP3, ASC, or caspase-1, demonstrating the role of the NLRP3 inflammasome. Despite the inability of these inhibitors to trigger efflux of intracellular potassium, the addition of high extracellular potassium suppressed activation of the NLRP3 inflammasome. MSU and double-stranded RNA, which are known to activate the NLRP3 inflammasome, also substantially inhibited protein translation, supporting a close association between inhibition of translation and inflammasome activation. These data demonstrate that translational inhibition itself constitutes a heretofore-unrecognized mechanism underlying IL-1ß dependent inflammatory signaling and that other physical, chemical, or pathogen-associated agents that impair translation may lead to IL-1ß-dependent inflammation through activation of the NLRP3 inflammasome. For agents that inhibit translation through decreased cellular potassium, the application of high extracellular potassium restores protein translation and suppresses activation of the NLRP inflammasome. For agents that inhibit translation through mechanisms that do not involve loss of potassium, high extracellular potassium suppresses IL-1ß processing through a mechanism that remains undefined."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3161","intvolume":" 7","title":"Suppression of ribosomal function triggers innate immune signaling through activation of the NLRP3 inflammasome","ddc":["610"],"status":"public","pubrep_id":"97","oa_version":"Published Version","file":[{"creator":"system","file_size":2984012,"content_type":"application/pdf","file_name":"IST-2012-97-v1+1_journal.pone.0036044.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:14:30Z","checksum":"30cef37e27eaa467f6571b3640282010","file_id":"5082","relation":"main_file"}]},{"has_accepted_license":"1","article_processing_charge":"No","day":"01","scopus_import":1,"date_published":"2012-01-01T00:00:00Z","citation":{"ama":"Asarin E, Donzé A, Maler O, Nickovic D. Parametric identification of temporal properties. In: Vol 7186. Springer; 2012:147-160. doi:10.1007/978-3-642-29860-8_12","ista":"Asarin E, Donzé A, Maler O, Nickovic D. 2012. Parametric identification of temporal properties. RV: Runtime Verification, LNCS, vol. 7186, 147–160.","ieee":"E. Asarin, A. Donzé, O. Maler, and D. Nickovic, “Parametric identification of temporal properties,” presented at the RV: Runtime Verification, San Francisco, CA, United States, 2012, vol. 7186, pp. 147–160.","apa":"Asarin, E., Donzé, A., Maler, O., & Nickovic, D. (2012). Parametric identification of temporal properties (Vol. 7186, pp. 147–160). Presented at the RV: Runtime Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-642-29860-8_12","mla":"Asarin, Eugene, et al. Parametric Identification of Temporal Properties. Vol. 7186, Springer, 2012, pp. 147–60, doi:10.1007/978-3-642-29860-8_12.","short":"E. Asarin, A. Donzé, O. Maler, D. Nickovic, in:, Springer, 2012, pp. 147–160.","chicago":"Asarin, Eugene, Alexandre Donzé, Oded Maler, and Dejan Nickovic. “Parametric Identification of Temporal Properties,” 7186:147–60. Springer, 2012. https://doi.org/10.1007/978-3-642-29860-8_12."},"page":"147 - 160","abstract":[{"text":"Given a dense-time real-valued signal and a parameterized temporal logic formula with both magnitude and timing parameters, we compute the subset of the parameter space that renders the formula satisfied by the trace. We provide two preliminary implementations, one which follows the exact semantics and attempts to compute the validity domain by quantifier elimination in linear arithmetics and one which conducts adaptive search in the parameter space.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Submitted Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":374726,"access_level":"open_access","file_name":"2012_RV_Asarin.pdf","checksum":"ba4a75287008fc64b8fbf78a7476ec32","date_created":"2020-05-15T12:50:15Z","date_updated":"2020-07-14T12:46:01Z","file_id":"7862","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3162","intvolume":" 7186","title":"Parametric identification of temporal properties","ddc":["000"],"status":"public","month":"01","doi":"10.1007/978-3-642-29860-8_12","conference":{"name":"RV: Runtime Verification","end_date":"2011-09-30","location":"San Francisco, CA, United States","start_date":"2011-09-27"},"language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1","publist_id":"3525","file_date_updated":"2020-07-14T12:46:01Z","author":[{"full_name":"Asarin, Eugene","first_name":"Eugene","last_name":"Asarin"},{"full_name":"Donzé, Alexandre","last_name":"Donzé","first_name":"Alexandre"},{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"},{"id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","first_name":"Dejan","full_name":"Nickovic, Dejan"}],"volume":7186,"date_updated":"2021-01-12T07:41:29Z","date_created":"2018-12-11T12:01:45Z","year":"2012","department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published"},{"type":"journal_article","issue":"11","publist_id":"3531","abstract":[{"lang":"eng","text":"There is a long-running controversy about how early cell fate decisions are made in the developing mammalian embryo. 1,2 In particular, it is controversial when the first events that can predict the establishment of the pluripotent and extra-embryonic lineages in the blastocyst of the pre-implantation embryo occur. It has long been proposed that the position and polarity of cells at the 16- to 32-cell stage embryo influence their decision to either give rise to the pluripotent cell lineage that eventually contributes to the inner cell mass (ICM), comprising the primitive endoderm (PE) and the epiblast (EPI), or the extra-embryonic trophectoderm (TE) surrounding the blastocoel. The positioning of cells in the embryo at this developmental stage could largely be the result of random events, making this a stochastic model of cell lineage allocation. Contrary to such a stochastic model, some studies have detected putative differences in the lineage potential of individual blastomeres before compaction, indicating that the first cell fate decisions may occur as early as at the 4-cell stage. Using a non-invasive, quantitative in vivo imaging assay to study the kinetic behavior of Oct4 (also known as POU5F1), a key transcription factor (TF) controlling pre-implantation development in the mouse embryo, 3-5 a recent study identifies Oct4 kinetics as a predictive measure of cell lineage patterning in the early mouse embryo. 6 Here, we discuss the implications of such molecular heterogeneities in early development and offer potential avenues toward a mechanistic understanding of these observations, contributing to the resolution of the controversy of developmental cell lineage allocation."}],"publisher":"Taylor and Francis","department":[{"_id":"ToBo"}],"intvolume":" 11","publication_status":"published","title":"Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo","status":"public","_id":"3160","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","volume":11,"oa_version":"None","date_created":"2018-12-11T12:01:44Z","date_updated":"2021-01-12T07:41:28Z","author":[{"last_name":"Pantazis","first_name":"Periklis","full_name":"Pantazis, Periklis"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias"}],"scopus_import":1,"month":"06","day":"01","page":"2055 - 2058","quality_controlled":"1","citation":{"apa":"Pantazis, P., & Bollenbach, M. T. (2012). Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. Taylor and Francis. https://doi.org/10.4161/cc.20118","ieee":"P. Pantazis and M. T. Bollenbach, “Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo,” Cell Cycle, vol. 11, no. 11. Taylor and Francis, pp. 2055–2058, 2012.","ista":"Pantazis P, Bollenbach MT. 2012. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. 11(11), 2055–2058.","ama":"Pantazis P, Bollenbach MT. Transcription factor kinetics and the emerging asymmetry in the early mammalian embryo. Cell Cycle. 2012;11(11):2055-2058. doi:10.4161/cc.20118","chicago":"Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle. Taylor and Francis, 2012. https://doi.org/10.4161/cc.20118.","short":"P. Pantazis, M.T. Bollenbach, Cell Cycle 11 (2012) 2055–2058.","mla":"Pantazis, Periklis, and Mark Tobias Bollenbach. “Transcription Factor Kinetics and the Emerging Asymmetry in the Early Mammalian Embryo.” Cell Cycle, vol. 11, no. 11, Taylor and Francis, 2012, pp. 2055–58, doi:10.4161/cc.20118."},"publication":"Cell Cycle","language":[{"iso":"eng"}],"date_published":"2012-06-01T00:00:00Z","doi":"10.4161/cc.20118"},{"date_published":"2012-09-01T00:00:00Z","doi":"10.1007/s11263-012-0530-y","language":[{"iso":"eng"}],"publication":"International Journal of Computer Vision","citation":{"ama":"Blaschko M, Lampert C. Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. 2012;99(3):257-258. doi:10.1007/s11263-012-0530-y","ista":"Blaschko M, Lampert C. 2012. Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. 99(3), 257–258.","apa":"Blaschko, M., & Lampert, C. (2012). Guest editorial: Special issue on structured prediction and inference. International Journal of Computer Vision. Springer. https://doi.org/10.1007/s11263-012-0530-y","ieee":"M. Blaschko and C. Lampert, “Guest editorial: Special issue on structured prediction and inference,” International Journal of Computer Vision, vol. 99, no. 3. Springer, pp. 257–258, 2012.","mla":"Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue on Structured Prediction and Inference.” International Journal of Computer Vision, vol. 99, no. 3, Springer, 2012, pp. 257–58, doi:10.1007/s11263-012-0530-y.","short":"M. Blaschko, C. Lampert, International Journal of Computer Vision 99 (2012) 257–258.","chicago":"Blaschko, Matthew, and Christoph Lampert. “Guest Editorial: Special Issue on Structured Prediction and Inference.” International Journal of Computer Vision. Springer, 2012. https://doi.org/10.1007/s11263-012-0530-y."},"quality_controlled":"1","page":"257 - 258","month":"09","day":"01","scopus_import":1,"author":[{"full_name":"Blaschko, Matthew","last_name":"Blaschko","first_name":"Matthew"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph"}],"date_updated":"2021-01-12T07:41:30Z","date_created":"2018-12-11T12:01:46Z","volume":99,"oa_version":"None","_id":"3164","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","year":"2012","publication_status":"published","status":"public","title":"Guest editorial: Special issue on structured prediction and inference","publisher":"Springer","department":[{"_id":"ChLa"}],"intvolume":" 99","abstract":[{"lang":"eng","text":"Overview of the Special Issue on structured prediction and inference."}],"publist_id":"3521","issue":"3","type":"journal_article"},{"publication":"Biology Direct","citation":{"chicago":"Vladar, Harold de. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct. BioMed Central, 2012. https://doi.org/10.1186/1745-6150-7-6.","mla":"de Vladar, Harold. “Amino Acid Fermentation at the Origin of the Genetic Code.” Biology Direct, vol. 7, 6, BioMed Central, 2012, doi:10.1186/1745-6150-7-6.","short":"H. de Vladar, Biology Direct 7 (2012).","ista":"de Vladar H. 2012. Amino acid fermentation at the origin of the genetic code. Biology Direct. 7, 6.","apa":"de Vladar, H. (2012). Amino acid fermentation at the origin of the genetic code. Biology Direct. BioMed Central. https://doi.org/10.1186/1745-6150-7-6","ieee":"H. de Vladar, “Amino acid fermentation at the origin of the genetic code,” Biology Direct, vol. 7. BioMed Central, 2012.","ama":"de Vladar H. Amino acid fermentation at the origin of the genetic code. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-6"},"date_published":"2012-02-10T00:00:00Z","day":"10","has_accepted_license":"1","title":"Amino acid fermentation at the origin of the genetic code","ddc":["570","576"],"status":"public","intvolume":" 7","_id":"3166","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"creator":"system","file_size":4099536,"content_type":"application/pdf","access_level":"open_access","file_name":"IST-2012-99-v1+1_1745-6150-7-6.pdf","checksum":"e511e401e239ef608a7fd79b21a06d78","date_created":"2018-12-12T10:15:44Z","date_updated":"2020-07-14T12:46:02Z","file_id":"5166","relation":"main_file"}],"pubrep_id":"99","type":"journal_article","abstract":[{"text":"There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eors Szathmary (nominated by Dr. Gaspar Jekely) and Dr. Adam Kun (nominated by Dr. Sandor Pongor)","lang":"eng"}],"quality_controlled":"1","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"doi":"10.1186/1745-6150-7-6","month":"02","publication_status":"published","publisher":"BioMed Central","department":[{"_id":"NiBa"}],"acknowledgement":"The author was supported by the ERC-2009-AdG Grant for project 250152 SELECTIONINFORMATION. ","year":"2012","date_updated":"2021-01-12T07:41:31Z","date_created":"2018-12-11T12:01:46Z","volume":7,"author":[{"orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","last_name":"Vladar","first_name":"Harold","full_name":"Vladar, Harold"}],"article_number":"6","file_date_updated":"2020-07-14T12:46:02Z","publist_id":"3518","ec_funded":1},{"issue":"6077","publist_id":"3516","type":"journal_article","author":[{"full_name":"Weber, Michele","id":"3A3FC708-F248-11E8-B48F-1D18A9856A87","first_name":"Michele","last_name":"Weber"}],"popular_science":"1","volume":336,"oa_version":"None","date_updated":"2021-01-12T07:41:32Z","date_created":"2018-12-11T12:01:47Z","pmid":1,"_id":"3167","year":"2012","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MiSi"}],"publisher":"American Association for the Advancement of Science","intvolume":" 336","publication_status":"published","status":"public","title":"NextGen speaks 13 ","month":"04","day":"06","doi":"10.1126/science.336.6077.32","date_published":"2012-04-06T00:00:00Z","language":[{"iso":"eng"}],"external_id":{"pmid":["22491839"]},"citation":{"chicago":"Weber, Michele. “NextGen Speaks 13 .” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.336.6077.32.","short":"M. Weber, Science 336 (2012) 32–34.","mla":"Weber, Michele. “NextGen Speaks 13 .” Science, vol. 336, no. 6077, American Association for the Advancement of Science, 2012, pp. 32–34, doi:10.1126/science.336.6077.32.","apa":"Weber, M. (2012). NextGen speaks 13 . Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.336.6077.32","ieee":"M. Weber, “NextGen speaks 13 ,” Science, vol. 336, no. 6077. American Association for the Advancement of Science, pp. 32–34, 2012.","ista":"Weber M. 2012. NextGen speaks 13 . Science. 336(6077), 32–34.","ama":"Weber M. NextGen speaks 13 . Science. 2012;336(6077):32-34. doi:10.1126/science.336.6077.32"},"publication":"Science","page":"32-34","article_type":"letter_note"},{"month":"11","day":"01","publication":"Journal of Cryptology","citation":{"short":"K.Z. Pietrzak, D. Wikström, Journal of Cryptology 25 (2012) 116–135.","mla":"Pietrzak, Krzysztof Z., and Douglas Wikström. “Parallel Repetition of Computationally Sound Protocols Revisited.” Journal of Cryptology, vol. 25, no. 1, Springer, 2012, pp. 116–35, doi:10.1007/s00145-010-9090-x.","chicago":"Pietrzak, Krzysztof Z, and Douglas Wikström. “Parallel Repetition of Computationally Sound Protocols Revisited.” Journal of Cryptology. Springer, 2012. https://doi.org/10.1007/s00145-010-9090-x.","ama":"Pietrzak KZ, Wikström D. Parallel repetition of computationally sound protocols revisited. Journal of Cryptology. 2012;25(1):116-135. doi:10.1007/s00145-010-9090-x","ieee":"K. Z. Pietrzak and D. Wikström, “Parallel repetition of computationally sound protocols revisited,” Journal of Cryptology, vol. 25, no. 1. Springer, pp. 116–135, 2012.","apa":"Pietrzak, K. Z., & Wikström, D. (2012). Parallel repetition of computationally sound protocols revisited. Journal of Cryptology. Springer. https://doi.org/10.1007/s00145-010-9090-x","ista":"Pietrzak KZ, Wikström D. 2012. Parallel repetition of computationally sound protocols revisited. Journal of Cryptology. 25(1), 116–135."},"quality_controlled":0,"page":"116 - 135","doi":"10.1007/s00145-010-9090-x","date_published":"2012-11-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We prove a negative result concerning error reduction by parallel repetition for computationally sound protocols, e.g., interactive arguments. Our main result is a complete and computationally sound eight round interactive argument for which k-fold parallel repetition does not reduce the error below a constant for any polynomial k. The starting point for our construction is the work of Bellare, Impagliazzo and Naor (FOCS'97). For any fixed k, they construct a four round protocol for which k-fold parallel repetition does not lower the soundness error. The communication complexity of this protocol is linear in k. By using universal arguments due to Barak and Goldreich (CCC 2002), we turn this protocol into an eight-round protocol whose complexity is basically independent of k. "}],"issue":"1","publist_id":"3439","extern":1,"_id":"3241","year":"2012","status":"public","title":"Parallel repetition of computationally sound protocols revisited","publication_status":"published","intvolume":" 25","publisher":"Springer","author":[{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Krzysztof Pietrzak"},{"full_name":"Wikström, Douglas","last_name":"Wikström","first_name":"Douglas"}],"date_created":"2018-12-11T12:02:12Z","date_updated":"2021-01-12T07:42:03Z","volume":25},{"day":"20","scopus_import":1,"date_published":"2012-01-20T00:00:00Z","citation":{"chicago":"Chatterjee, Krishnendu, and Vishwanath Raman. “Synthesizing Protocols for Digital Contract Signing,” 7148:152–68. Springer, 2012. https://doi.org/10.1007/978-3-642-27940-9_11.","short":"K. Chatterjee, V. Raman, in:, Springer, 2012, pp. 152–168.","mla":"Chatterjee, Krishnendu, and Vishwanath Raman. Synthesizing Protocols for Digital Contract Signing. Vol. 7148, Springer, 2012, pp. 152–68, doi:10.1007/978-3-642-27940-9_11.","apa":"Chatterjee, K., & Raman, V. (2012). Synthesizing protocols for digital contract signing (Vol. 7148, pp. 152–168). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA: Springer. https://doi.org/10.1007/978-3-642-27940-9_11","ieee":"K. Chatterjee and V. Raman, “Synthesizing protocols for digital contract signing,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, Philadelphia, PA, USA, 2012, vol. 7148, pp. 152–168.","ista":"Chatterjee K, Raman V. 2012. Synthesizing protocols for digital contract signing. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 7148, 152–168.","ama":"Chatterjee K, Raman V. Synthesizing protocols for digital contract signing. In: Vol 7148. Springer; 2012:152-168. doi:10.1007/978-3-642-27940-9_11"},"page":"152 - 168","abstract":[{"text":"We study the automatic synthesis of fair non-repudiation protocols, a class of fair exchange protocols, used for digital contract signing. First, we show how to specify the objectives of the participating agents, the trusted third party (TTP) and the protocols as path formulas in Linear Temporal Logic (LTL) and prove that the satisfaction of the objectives of the agents and the TTP imply satisfaction of the protocol objectives. We then show that weak (co-operative) co-synthesis and classical (strictly competitive) co-synthesis fail in synthesizing these protocols, whereas assume-guarantee synthesis (AGS) succeeds. We demonstrate the success of assume-guarantee synthesis as follows: (a) any solution of assume-guarantee synthesis is attack-free; no subset of participants can violate the objectives of the other participants without violating their own objectives; (b) the Asokan-Shoup-Waidner (ASW) certified mail protocol that has known vulnerabilities is not a solution of AGS; and (c) the Kremer-Markowitch (KM) non-repudiation protocol is a solution of AGS. To our knowledge this is the first application of synthesis to fair non-repudiation protocols, and our results show how synthesis can generate correct protocols and automatically discover vulnerabilities. The solution to assume-guarantee synthesis can be computed efficiently as the secure equilibrium solution of three-player graph games. © 2012 Springer-Verlag.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3252","status":"public","title":"Synthesizing protocols for digital contract signing","intvolume":" 7148","month":"01","conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","start_date":"2012-01-22","location":"Philadelphia, PA, USA","end_date":"2012-01-24"},"doi":"10.1007/978-3-642-27940-9_11","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.2697"}],"quality_controlled":"1","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"ec_funded":1,"publist_id":"3405","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Raman, Vishwanath","last_name":"Raman","first_name":"Vishwanath"}],"date_created":"2018-12-11T12:02:16Z","date_updated":"2021-01-12T07:42:08Z","volume":7148,"year":"2012","acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No P 23499-N23 (Modern Graph Algorithmic Techniques in Formal Verification), FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.\r\nThe authors would like to thank Avik Chaudhuri for his invaluable help and feedback.","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"}]},{"article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2012-01-01T00:00:00Z","page":"37 - 46","citation":{"mla":"Chatterjee, Krishnendu, and Laurent Doyen. Games and Markov Decision Processes with Mean Payoff Parity and Energy Parity Objectives. Vol. 7119, Springer, 2012, pp. 37–46, doi:10.1007/978-3-642-25929-6_3.","short":"K. Chatterjee, L. Doyen, in:, Springer, 2012, pp. 37–46.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Games and Markov Decision Processes with Mean Payoff Parity and Energy Parity Objectives,” 7119:37–46. Springer, 2012. https://doi.org/10.1007/978-3-642-25929-6_3.","ama":"Chatterjee K, Doyen L. Games and Markov decision processes with mean payoff parity and energy parity objectives. In: Vol 7119. Springer; 2012:37-46. doi:10.1007/978-3-642-25929-6_3","ista":"Chatterjee K, Doyen L. 2012. Games and Markov decision processes with mean payoff parity and energy parity objectives. MEMICS: Mathematical and Engineering Methods in Computer Science, LNCS, vol. 7119, 37–46.","ieee":"K. Chatterjee and L. Doyen, “Games and Markov decision processes with mean payoff parity and energy parity objectives,” presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Lednice, Czech Republic, 2012, vol. 7119, pp. 37–46.","apa":"Chatterjee, K., & Doyen, L. (2012). Games and Markov decision processes with mean payoff parity and energy parity objectives (Vol. 7119, pp. 37–46). Presented at the MEMICS: Mathematical and Engineering Methods in Computer Science, Lednice, Czech Republic: Springer. https://doi.org/10.1007/978-3-642-25929-6_3"},"abstract":[{"text":"In this paper we survey results of two-player games on graphs and Markov decision processes with parity, mean-payoff and energy objectives, and the combination of mean-payoff and energy objectives with parity objectives. These problems have applications in verification and synthesis of reactive systems in resource-constrained environments.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","file":[{"relation":"main_file","file_id":"7863","date_created":"2020-05-15T12:53:12Z","date_updated":"2020-07-14T12:46:05Z","checksum":"eed2cc1e76b160418c977e76e8899a60","file_name":"2012_MEMICS_Chatterjee.pdf","access_level":"open_access","file_size":114060,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Submitted Version","intvolume":" 7119","status":"public","ddc":["000"],"title":"Games and Markov decision processes with mean payoff parity and energy parity objectives","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3255","month":"01","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-25929-6_3","conference":{"name":"MEMICS: Mathematical and Engineering Methods in Computer Science","location":"Lednice, Czech Republic","start_date":"2011-10-14","end_date":"2011-10-16"},"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"publist_id":"3400","file_date_updated":"2020-07-14T12:46:05Z","volume":7119,"date_updated":"2021-01-12T07:42:10Z","date_created":"2018-12-11T12:02:17Z","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"}],"department":[{"_id":"KrCh"}],"publisher":"Springer","publication_status":"published","acknowledgement":"This work was partially supported by FWF NFN Grant S11407-N23 (RiSE) and a Microsoft faculty fellowship.","year":"2012"}]