[{"edition":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:33Z","volume":40,"page":"257 - 267","title":"Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature","quality_controlled":"1","author":[{"full_name":"Zobel, Valentin","first_name":"Valentin","last_name":"Zobel"},{"first_name":"Jan","full_name":"Reininghaus, Jan","last_name":"Reininghaus","id":"4505473A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hotz","full_name":"Hotz, Ingrid","first_name":"Ingrid"}],"language":[{"iso":"eng"}],"intvolume":"        40","status":"public","oa_version":"None","publication_status":"published","article_processing_charge":"No","publisher":"Springer","date_published":"2015-01-01T00:00:00Z","year":"2015","scopus_import":"1","abstract":[{"lang":"eng","text":"The Heat Kernel Signature (HKS) is a scalar quantity which is derived from the heat kernel of a given shape. Due to its robustness, isometry invariance, and multiscale nature, it has been successfully applied in many geometric applications. From a more general point of view, the HKS can be considered as a descriptor of the metric of a Riemannian manifold. Given a symmetric positive definite tensor field we may interpret it as the metric of some Riemannian manifold and thereby apply the HKS to visualize and analyze the given tensor data. In this paper, we propose a generalization of this approach that enables the treatment of indefinite tensor fields, like the stress tensor, by interpreting them as a generator of a positive definite tensor field. To investigate the usefulness of this approach we consider the stress tensor from the two-point-load model example and from a mechanical work piece."}],"alternative_title":["Mathematics and Visualization"],"month":"01","date_updated":"2022-06-10T09:50:14Z","_id":"1531","day":"01","editor":[{"full_name":"Hotz, Ingrid","first_name":"Ingrid","last_name":"Hotz"},{"first_name":"Thomas","full_name":"Schultz, Thomas","last_name":"Schultz"}],"publist_id":"5640","publication":"Visualization and Processing of Higher Order Descriptors for Multi-Valued Data","citation":{"ieee":"V. Zobel, J. Reininghaus, and I. Hotz, “Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature,” in <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, 1st ed., vol. 40, I. Hotz and T. Schultz, Eds. Springer, 2015, pp. 257–267.","chicago":"Zobel, Valentin, Jan Reininghaus, and Ingrid Hotz. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” In <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, edited by Ingrid Hotz and Thomas Schultz, 1st ed., 40:257–67. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">https://doi.org/10.1007/978-3-319-15090-1_13</a>.","short":"V. Zobel, J. Reininghaus, I. Hotz, in:, I. Hotz, T. Schultz (Eds.), Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, 1st ed., Springer, 2015, pp. 257–267.","ama":"Zobel V, Reininghaus J, Hotz I. Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Hotz I, Schultz T, eds. <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>. Vol 40. 1st ed. Springer; 2015:257-267. doi:<a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">10.1007/978-3-319-15090-1_13</a>","mla":"Zobel, Valentin, et al. “Visualizing Symmetric Indefinite 2D Tensor Fields Using The Heat Kernel Signature.” <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i>, edited by Ingrid Hotz and Thomas Schultz, 1st ed., vol. 40, Springer, 2015, pp. 257–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">10.1007/978-3-319-15090-1_13</a>.","apa":"Zobel, V., Reininghaus, J., &#38; Hotz, I. (2015). Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In I. Hotz &#38; T. Schultz (Eds.), <i>Visualization and Processing of Higher Order Descriptors for Multi-Valued Data</i> (1st ed., Vol. 40, pp. 257–267). Springer. <a href=\"https://doi.org/10.1007/978-3-319-15090-1_13\">https://doi.org/10.1007/978-3-319-15090-1_13</a>","ista":"Zobel V, Reininghaus J, Hotz I. 2015.Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature. In: Visualization and Processing of Higher Order Descriptors for Multi-Valued Data. Mathematics and Visualization, vol. 40, 257–267."},"department":[{"_id":"HeEd"}],"type":"book_chapter","publication_identifier":{"isbn":["978-3-319-15089-5"]},"doi":"10.1007/978-3-319-15090-1_13"},{"publication_status":"published","article_processing_charge":"No","oa_version":"None","year":"2015","scopus_import":"1","abstract":[{"lang":"eng","text":"Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels."}],"date_updated":"2025-09-23T07:59:44Z","isi":1,"month":"03","date_published":"2015-03-01T00:00:00Z","publisher":"CSIRO","issue":"3","publication":"Functional Plant Biology","_id":"1532","day":"01","publist_id":"5639","doi":"10.1071/FP14171","publication_identifier":{"issn":["1445-4408"]},"department":[{"_id":"JiFr"}],"type":"journal_article","citation":{"ista":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. 2015. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology. 42(3), 239–251.","apa":"Yang, H., Von Der Fecht Bartenbach, J., Friml, J., Lohmann, J., Neuhäuser, B., &#38; Ludewig, U. (2015). Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. <i>Functional Plant Biology</i>. CSIRO. <a href=\"https://doi.org/10.1071/FP14171\">https://doi.org/10.1071/FP14171</a>","short":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251.","mla":"Yang, Huaiyu, et al. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” <i>Functional Plant Biology</i>, vol. 42, no. 3, CSIRO, 2015, pp. 239–51, doi:<a href=\"https://doi.org/10.1071/FP14171\">10.1071/FP14171</a>.","ama":"Yang H, Von Der Fecht Bartenbach J, Friml J, Lohmann J, Neuhäuser B, Ludewig U. Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. <i>Functional Plant Biology</i>. 2015;42(3):239-251. doi:<a href=\"https://doi.org/10.1071/FP14171\">10.1071/FP14171</a>","chicago":"Yang, Huaiyu, Jenny Von Der Fecht Bartenbach, Jiří Friml, Jan Lohmann, Benjamin Neuhäuser, and Uwe Ludewig. “Auxin-Modulated Root Growth Inhibition in Arabidopsis Thaliana Seedlings with Ammonium as the Sole Nitrogen Source.” <i>Functional Plant Biology</i>. CSIRO, 2015. <a href=\"https://doi.org/10.1071/FP14171\">https://doi.org/10.1071/FP14171</a>.","ieee":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, and U. Ludewig, “Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source,” <i>Functional Plant Biology</i>, vol. 42, no. 3. CSIRO, pp. 239–251, 2015."},"article_type":"original","date_created":"2018-12-11T11:52:34Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"volume":42,"quality_controlled":"1","title":"Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source","page":"239 - 251","intvolume":"        42","status":"public","language":[{"iso":"eng"}],"author":[{"full_name":"Yang, Huaiyu","first_name":"Huaiyu","last_name":"Yang"},{"full_name":"Von Der Fecht Bartenbach, Jenny","first_name":"Jenny","last_name":"Von Der Fecht Bartenbach"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"full_name":"Lohmann, Jan","first_name":"Jan","last_name":"Lohmann"},{"last_name":"Neuhäuser","full_name":"Neuhäuser, Benjamin","first_name":"Benjamin"},{"first_name":"Uwe","full_name":"Ludewig, Uwe","last_name":"Ludewig"}],"external_id":{"isi":["000349635900003"],"pmid":["32480670"]}},{"status":"public","intvolume":"        25","author":[{"last_name":"Xia","first_name":"Wei","full_name":"Xia, Wei"},{"last_name":"Domokos","full_name":"Domokos, Csaba","first_name":"Csaba","id":"492DACF8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Junjun","full_name":"Xiong, Junjun","last_name":"Xiong"},{"last_name":"Cheong","first_name":"Loongfah","full_name":"Cheong, Loongfah"},{"last_name":"Yan","first_name":"Shuicheng","full_name":"Yan, Shuicheng"}],"external_id":{"isi":["000359213400004"]},"language":[{"iso":"eng"}],"title":"Segmentation over detection via optimal sparse reconstructions","quality_controlled":"1","page":"1295 - 1308","volume":25,"date_created":"2018-12-11T11:52:34Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1109/TCSVT.2014.2379972","department":[{"_id":"ChLa"}],"type":"journal_article","citation":{"ama":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. Segmentation over detection via optimal sparse reconstructions. <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. 2015;25(8):1295-1308. doi:<a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">10.1109/TCSVT.2014.2379972</a>","mla":"Xia, Wei, et al. “Segmentation over Detection via Optimal Sparse Reconstructions.” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>, vol. 25, no. 8, IEEE, 2015, pp. 1295–308, doi:<a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">10.1109/TCSVT.2014.2379972</a>.","short":"W. Xia, C. Domokos, J. Xiong, L. Cheong, S. Yan, IEEE Transactions on Circuits and Systems for Video Technology 25 (2015) 1295–1308.","apa":"Xia, W., Domokos, C., Xiong, J., Cheong, L., &#38; Yan, S. (2015). Segmentation over detection via optimal sparse reconstructions. <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. IEEE. <a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">https://doi.org/10.1109/TCSVT.2014.2379972</a>","ista":"Xia W, Domokos C, Xiong J, Cheong L, Yan S. 2015. Segmentation over detection via optimal sparse reconstructions. IEEE Transactions on Circuits and Systems for Video Technology. 25(8), 1295–1308.","ieee":"W. Xia, C. Domokos, J. Xiong, L. Cheong, and S. Yan, “Segmentation over detection via optimal sparse reconstructions,” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>, vol. 25, no. 8. IEEE, pp. 1295–1308, 2015.","chicago":"Xia, Wei, Csaba Domokos, Junjun Xiong, Loongfah Cheong, and Shuicheng Yan. “Segmentation over Detection via Optimal Sparse Reconstructions.” <i>IEEE Transactions on Circuits and Systems for Video Technology</i>. IEEE, 2015. <a href=\"https://doi.org/10.1109/TCSVT.2014.2379972\">https://doi.org/10.1109/TCSVT.2014.2379972</a>."},"publication":"IEEE Transactions on Circuits and Systems for Video Technology","issue":"8","publist_id":"5638","day":"01","_id":"1533","isi":1,"month":"08","date_updated":"2025-09-23T10:44:22Z","scopus_import":"1","abstract":[{"text":"This paper addresses the problem of semantic segmentation, where the possible class labels are from a predefined set. We exploit top-down guidance, i.e., the coarse localization of the objects and their class labels provided by object detectors. For each detected bounding box, figure-ground segmentation is performed and the final result is achieved by merging the figure-ground segmentations. The main idea of the proposed approach, which is presented in our preliminary work, is to reformulate the figure-ground segmentation problem as sparse reconstruction pursuing the object mask in a nonparametric manner. The latent segmentation mask should be coherent subject to sparse error caused by intra-category diversity; thus, the object mask is inferred by making use of sparse representations over the training set. To handle local spatial deformations, local patch-level masks are also considered and inferred by sparse representations over the spatially nearby patches. The sparse reconstruction coefficients and the latent mask are alternately optimized by applying the Lasso algorithm and the accelerated proximal gradient method. The proposed formulation results in a convex optimization problem; thus, the global optimal solution is achieved. In this paper, we provide theoretical analysis of the convergence and optimality. We also give an extended numerical analysis of the proposed algorithm and a comprehensive comparison with the related semantic segmentation methods on the challenging PASCAL visual object class object segmentation datasets and the Weizmann horse dataset. The experimental results demonstrate that the proposed algorithm achieves a competitive performance when compared with the state of the arts.","lang":"eng"}],"year":"2015","publisher":"IEEE","date_published":"2015-08-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","oa_version":"None"},{"language":[{"iso":"eng"}],"author":[{"last_name":"Wang","full_name":"Wang, Hongzhe","first_name":"Hongzhe"},{"last_name":"Yang","first_name":"Kezhen","full_name":"Yang, Kezhen"},{"last_name":"Zou","first_name":"Junjie","full_name":"Zou, Junjie"},{"first_name":"Lingling","full_name":"Zhu, Lingling","last_name":"Zhu"},{"full_name":"Xie, Zidian","first_name":"Zidian","last_name":"Xie"},{"first_name":"Miyoterao","full_name":"Morita, Miyoterao","last_name":"Morita"},{"full_name":"Tasaka, Masao","first_name":"Masao","last_name":"Tasaka"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grotewold, Erich","first_name":"Erich","last_name":"Grotewold"},{"first_name":"Tom","full_name":"Beeckman, Tom","last_name":"Beeckman"},{"last_name":"Vanneste","first_name":"Steffen","full_name":"Vanneste, Steffen"},{"last_name":"Sack","first_name":"Fred","full_name":"Sack, Fred"},{"first_name":"Jie","full_name":"Le, Jie","last_name":"Le"}],"external_id":{"isi":["000366295500008"]},"status":"public","intvolume":"         6","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","has_accepted_license":"1","ec_funded":1,"volume":6,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"8822","date_created":"2018-12-11T11:52:34Z","ddc":["570"],"department":[{"_id":"JiFr"}],"citation":{"ieee":"H. Wang <i>et al.</i>, “Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism,” <i>Nature Communications</i>, vol. 6. Nature Publishing Group, 2015.","chicago":"Wang, Hongzhe, Kezhen Yang, Junjie Zou, Lingling Zhu, Zidian Xie, Miyoterao Morita, Masao Tasaka, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” <i>Nature Communications</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/ncomms9822\">https://doi.org/10.1038/ncomms9822</a>.","short":"H. Wang, K. Yang, J. Zou, L. Zhu, Z. Xie, M. Morita, M. Tasaka, J. Friml, E. Grotewold, T. Beeckman, S. Vanneste, F. Sack, J. Le, Nature Communications 6 (2015).","mla":"Wang, Hongzhe, et al. “Transcriptional Regulation of PIN Genes by FOUR LIPS and MYB88 during Arabidopsis Root Gravitropism.” <i>Nature Communications</i>, vol. 6, 8822, Nature Publishing Group, 2015, doi:<a href=\"https://doi.org/10.1038/ncomms9822\">10.1038/ncomms9822</a>.","ama":"Wang H, Yang K, Zou J, et al. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. <i>Nature Communications</i>. 2015;6. doi:<a href=\"https://doi.org/10.1038/ncomms9822\">10.1038/ncomms9822</a>","ista":"Wang H, Yang K, Zou J, Zhu L, Xie Z, Morita M, Tasaka M, Friml J, Grotewold E, Beeckman T, Vanneste S, Sack F, Le J. 2015. Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. Nature Communications. 6, 8822.","apa":"Wang, H., Yang, K., Zou, J., Zhu, L., Xie, Z., Morita, M., … Le, J. (2015). Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms9822\">https://doi.org/10.1038/ncomms9822</a>"},"type":"journal_article","oa":1,"doi":"10.1038/ncomms9822","publist_id":"5637","_id":"1534","day":"18","publication":"Nature Communications","file_date_updated":"2020-07-14T12:45:01Z","pubrep_id":"485","date_published":"2015-11-18T00:00:00Z","publisher":"Nature Publishing Group","date_updated":"2025-09-23T14:55:59Z","month":"11","isi":1,"scopus_import":"1","year":"2015","abstract":[{"text":"PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity.","lang":"eng"}],"file":[{"file_size":1852268,"date_updated":"2020-07-14T12:45:01Z","content_type":"application/pdf","file_name":"IST-2016-485-v1+1_ncomms9822.pdf","checksum":"3c06735fc7cd7e482ca830cbd26001bf","access_level":"open_access","creator":"system","date_created":"2018-12-12T10:17:07Z","relation":"main_file","file_id":"5259"}],"oa_version":"Published Version","article_processing_charge":"No","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"publication_status":"published"},{"volume":8,"article_type":"original","date_created":"2018-12-11T11:52:35Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"intvolume":"         8","status":"public","author":[{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","first_name":"David H","full_name":"Vandael, David H","last_name":"Vandael","orcid":"0000-0001-7577-1676"},{"full_name":"Marcantoni, Andrea","first_name":"Andrea","last_name":"Marcantoni"},{"first_name":"Emilio","full_name":"Carbone, Emilio","last_name":"Carbone"}],"external_id":{"isi":["000217186100005"],"pmid":["25966692"]},"language":[{"iso":"eng"}],"title":"Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells","quality_controlled":"1","page":"149 - 161","year":"2015","abstract":[{"lang":"eng","text":"Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open readily at relatively low membrane potentials and allow Ca2+ to enter the cells near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation, hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the pacemaking current that sustains action potential (AP) firings and part of the catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating BK channels and drives the resting SK currents. These latter set the inter-spike interval duration between consecutive spikes during spontaneous firing and the rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a primary role in the switch from “tonic” to “burst” firing that occurs in mouse CCs when either the availability of voltage-gated Na channels (Nav) is reduced or the β2 subunit featuring the fast inactivating BK channels is deleted. Here, we discuss the functional role of these “neuronlike” firing modes in CCs and how Cav1.3 contributes to them. The open issue is to understand how these novel firing patterns are adapted to regulate the quantity of circulating catecholamines during resting condition or in response to acute and chronic stress."}],"scopus_import":"1","month":"10","isi":1,"date_updated":"2025-09-23T08:12:18Z","publisher":"Bentham Science Publishers","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/","open_access":"1"}],"date_published":"2015-10-01T00:00:00Z","publication_status":"published","article_processing_charge":"No","oa_version":"Submitted Version","acknowledgement":"This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino.","doi":"10.2174/1874467208666150507105443","oa":1,"type":"journal_article","department":[{"_id":"PeJo"}],"citation":{"chicago":"Vandael, David H, Andrea Marcantoni, and Emilio Carbone. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” <i>Current Molecular Pharmacology</i>. Bentham Science Publishers, 2015. <a href=\"https://doi.org/10.2174/1874467208666150507105443\">https://doi.org/10.2174/1874467208666150507105443</a>.","ieee":"D. H. Vandael, A. Marcantoni, and E. Carbone, “Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells,” <i>Current Molecular Pharmacology</i>, vol. 8, no. 2. Bentham Science Publishers, pp. 149–161, 2015.","apa":"Vandael, D. H., Marcantoni, A., &#38; Carbone, E. (2015). Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. <i>Current Molecular Pharmacology</i>. Bentham Science Publishers. <a href=\"https://doi.org/10.2174/1874467208666150507105443\">https://doi.org/10.2174/1874467208666150507105443</a>","ista":"Vandael DH, Marcantoni A, Carbone E. 2015. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. Current Molecular Pharmacology. 8(2), 149–161.","ama":"Vandael DH, Marcantoni A, Carbone E. Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells. <i>Current Molecular Pharmacology</i>. 2015;8(2):149-161. doi:<a href=\"https://doi.org/10.2174/1874467208666150507105443\">10.2174/1874467208666150507105443</a>","mla":"Vandael, David H., et al. “Cav1.3 Channels as Key Regulators of Neuron-like Firings and Catecholamine Release in Chromaffin Cells.” <i>Current Molecular Pharmacology</i>, vol. 8, no. 2, Bentham Science Publishers, 2015, pp. 149–61, doi:<a href=\"https://doi.org/10.2174/1874467208666150507105443\">10.2174/1874467208666150507105443</a>.","short":"D.H. Vandael, A. Marcantoni, E. Carbone, Current Molecular Pharmacology 8 (2015) 149–161."},"issue":"2","publication":"Current Molecular Pharmacology","day":"01","_id":"1535","publist_id":"5636"},{"date_published":"2015-02-12T00:00:00Z","publisher":"Cell Press","scopus_import":"1","abstract":[{"lang":"eng","text":"Strigolactones, first discovered as germination stimulants for parasitic weeds [1], are carotenoid-derived phytohormones that play major roles in inhibiting lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore, strigolactones are involved in the regulation of lateral and adventitious root development, root cell division [5, 6], secondary growth [7], and leaf senescence [8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the apical membrane of root hypodermal cells, presumably mediating the shootward transport of strigolactone. Above the root tip, in the hypodermal passage cells that form gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral membrane, compatible with its postulated function as strigolactone exporter from root to soil. Transport studies are in line with our localization studies since (1) a papdr1 mutant displays impaired transport of strigolactones out of the root tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2 levels change in plants deregulated for PDR1 expression, suggestive of variations in endogenous strigolactone contents. In conclusion, our results indicate that the polar localizations of PaPDR1 mediate directional shootward strigolactone transport as well as localized exudation into the soil."}],"year":"2015","date_updated":"2025-09-23T07:57:02Z","isi":1,"month":"02","oa_version":"None","publication_status":"published","article_processing_charge":"No","department":[{"_id":"JiFr"}],"citation":{"ama":"Sasse J, Simon S, Gübeli C, et al. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. <i>Current Biology</i>. 2015;25(5):647-655. doi:<a href=\"https://doi.org/10.1016/j.cub.2015.01.015\">10.1016/j.cub.2015.01.015</a>","mla":"Sasse, Joëlle, et al. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” <i>Current Biology</i>, vol. 25, no. 5, Cell Press, 2015, pp. 647–55, doi:<a href=\"https://doi.org/10.1016/j.cub.2015.01.015\">10.1016/j.cub.2015.01.015</a>.","short":"J. Sasse, S. Simon, C. Gübeli, G. Liu, X. Cheng, J. Friml, H. Bouwmeester, E. Martinoia, L. Borghi, Current Biology 25 (2015) 647–655.","apa":"Sasse, J., Simon, S., Gübeli, C., Liu, G., Cheng, X., Friml, J., … Borghi, L. (2015). Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2015.01.015\">https://doi.org/10.1016/j.cub.2015.01.015</a>","ista":"Sasse J, Simon S, Gübeli C, Liu G, Cheng X, Friml J, Bouwmeester H, Martinoia E, Borghi L. 2015. Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport. Current Biology. 25(5), 647–655.","ieee":"J. Sasse <i>et al.</i>, “Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport,” <i>Current Biology</i>, vol. 25, no. 5. Cell Press, pp. 647–655, 2015.","chicago":"Sasse, Joëlle, Sibu Simon, Christian Gübeli, Guowei Liu, Xi Cheng, Jiří Friml, Harro Bouwmeester, Enrico Martinoia, and Lorenzo Borghi. “Asymmetric Localizations of the ABC Transporter PaPDR1 Trace Paths of Directional Strigolactone Transport.” <i>Current Biology</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cub.2015.01.015\">https://doi.org/10.1016/j.cub.2015.01.015</a>."},"type":"journal_article","doi":"10.1016/j.cub.2015.01.015","acknowledgement":"This work was funded by a grant of the Swiss National Foundation to E.M.\r\nWe thank Dr. José María Mateos (University of Zurich) for providing us with the vibratome, Prof. Dolf Weijers (Wageningen University, the Netherlands) for shipping us his set of ligation-independent cloning vectors, Prof. Bruno Humbel (University of Lausanne) for suggestions on GFP-PDR1 detection, and Dr. Undine Krügel (University of Zurich) and Prof. Michal Jasinski (Polish Academy of Science) for hints on protein quantification.","_id":"1536","day":"12","publist_id":"5635","issue":"5","publication":"Current Biology","volume":25,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:35Z","language":[{"iso":"eng"}],"external_id":{"isi":["000350708800029"]},"author":[{"full_name":"Sasse, Joëlle","first_name":"Joëlle","last_name":"Sasse"},{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","full_name":"Simon, Sibu","first_name":"Sibu","last_name":"Simon","orcid":"0000-0002-1998-6741"},{"last_name":"Gübeli","full_name":"Gübeli, Christian","first_name":"Christian"},{"first_name":"Guowei","full_name":"Liu, Guowei","last_name":"Liu"},{"first_name":"Xi","full_name":"Cheng, Xi","last_name":"Cheng"},{"first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Harro","full_name":"Bouwmeester, Harro","last_name":"Bouwmeester"},{"full_name":"Martinoia, Enrico","first_name":"Enrico","last_name":"Martinoia"},{"last_name":"Borghi","first_name":"Lorenzo","full_name":"Borghi, Lorenzo"}],"intvolume":"        25","status":"public","page":"647 - 655","quality_controlled":"1","title":"Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport"},{"title":"Iterative experiment design guides the characterization of a light-inducible gene expression circuit","quality_controlled":"1","page":"8148 - 8153","status":"public","intvolume":"       112","author":[{"orcid":"0000-0003-1615-3282","last_name":"Ruess","full_name":"Ruess, Jakob","first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Parise","full_name":"Parise, Francesca","first_name":"Francesca"},{"full_name":"Milias Argeitis, Andreas","first_name":"Andreas","last_name":"Milias Argeitis"},{"last_name":"Khammash","first_name":"Mustafa","full_name":"Khammash, Mustafa"},{"last_name":"Lygeros","first_name":"John","full_name":"Lygeros, John"}],"external_id":{"pmid":["26085136"],"isi":["000357079400070"]},"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:52:36Z","pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"volume":112,"publication":"PNAS","issue":"26","publist_id":"5633","_id":"1538","day":"30","acknowledgement":"J.R., F.P., and J.L. acknowledge support from the European Commission under the Network of Excellence HYCON2 (highly-complex and networked control systems) and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). ","doi":"10.1073/pnas.1423947112","citation":{"short":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.","ama":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. <i>PNAS</i>. 2015;112(26):8148-8153. doi:<a href=\"https://doi.org/10.1073/pnas.1423947112\">10.1073/pnas.1423947112</a>","mla":"Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” <i>PNAS</i>, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi:<a href=\"https://doi.org/10.1073/pnas.1423947112\">10.1073/pnas.1423947112</a>.","apa":"Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., &#38; Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1423947112\">https://doi.org/10.1073/pnas.1423947112</a>","ista":"Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153.","ieee":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” <i>PNAS</i>, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015.","chicago":"Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” <i>PNAS</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1423947112\">https://doi.org/10.1073/pnas.1423947112</a>."},"type":"journal_article","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"oa":1,"article_processing_charge":"No","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"publication_status":"published","oa_version":"Submitted Version","isi":1,"month":"06","date_updated":"2025-09-23T09:24:24Z","abstract":[{"lang":"eng","text":"Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time."}],"scopus_import":"1","year":"2015","publisher":"National Academy of Sciences","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/"}],"date_published":"2015-06-30T00:00:00Z"},{"pubrep_id":"593","date_published":"2015-12-22T00:00:00Z","publisher":"American Institute of Physics","date_updated":"2025-09-23T09:34:48Z","month":"12","isi":1,"scopus_import":"1","abstract":[{"text":"Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. ","lang":"eng"}],"year":"2015","oa_version":"Published Version","file":[{"file_name":"IST-2016-593-v1+1_Minimal_moment_equations.pdf","checksum":"838657118ae286463a2b7737319f35ce","content_type":"application/pdf","date_updated":"2020-07-14T12:45:01Z","file_size":605355,"file_id":"4641","date_created":"2018-12-12T10:07:43Z","relation":"main_file","access_level":"open_access","creator":"system"}],"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","grant_number":"Z211","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"article_processing_charge":"No","publication_status":"published","citation":{"ieee":"J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” <i>Journal of Chemical Physics</i>, vol. 143, no. 24. American Institute of Physics, 2015.","chicago":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” <i>Journal of Chemical Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1063/1.4937937\">https://doi.org/10.1063/1.4937937</a>.","mla":"Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” <i>Journal of Chemical Physics</i>, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1063/1.4937937\">10.1063/1.4937937</a>.","ama":"Ruess J. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. <i>Journal of Chemical Physics</i>. 2015;143(24). doi:<a href=\"https://doi.org/10.1063/1.4937937\">10.1063/1.4937937</a>","short":"J. Ruess, Journal of Chemical Physics 143 (2015).","apa":"Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. <i>Journal of Chemical Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1063/1.4937937\">https://doi.org/10.1063/1.4937937</a>","ista":"Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103."},"type":"journal_article","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"oa":1,"doi":"10.1063/1.4937937","publist_id":"5632","day":"22","_id":"1539","publication":"Journal of Chemical Physics","file_date_updated":"2020-07-14T12:45:01Z","issue":"24","has_accepted_license":"1","ec_funded":1,"volume":143,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"244103","date_created":"2018-12-11T11:52:36Z","ddc":["000"],"corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000370412900068"]},"author":[{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob","full_name":"Ruess, Jakob","last_name":"Ruess","orcid":"0000-0003-1615-3282"}],"status":"public","intvolume":"       143","quality_controlled":"1","title":"Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space"},{"page":"5029 - 5042","quality_controlled":"1","title":"The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis","language":[{"iso":"eng"}],"external_id":{"isi":["000359688300015"]},"author":[{"last_name":"Robert","first_name":"Hélène","full_name":"Robert, Hélène"},{"last_name":"Crhák Khaitová","first_name":"Lucie","full_name":"Crhák Khaitová, Lucie"},{"last_name":"Mroue","first_name":"Souad","full_name":"Mroue, Souad"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739"}],"status":"public","intvolume":"        66","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:36Z","volume":66,"publist_id":"5631","_id":"1540","day":"05","publication":"Journal of Experimental Botany","issue":"16","citation":{"ama":"Robert H, Crhák Khaitová L, Mroue S, Benková E. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. <i>Journal of Experimental Botany</i>. 2015;66(16):5029-5042. doi:<a href=\"https://doi.org/10.1093/jxb/erv256\">10.1093/jxb/erv256</a>","mla":"Robert, Hélène, et al. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” <i>Journal of Experimental Botany</i>, vol. 66, no. 16, Oxford University Press, 2015, pp. 5029–42, doi:<a href=\"https://doi.org/10.1093/jxb/erv256\">10.1093/jxb/erv256</a>.","short":"H. Robert, L. Crhák Khaitová, S. Mroue, E. Benková, Journal of Experimental Botany 66 (2015) 5029–5042.","apa":"Robert, H., Crhák Khaitová, L., Mroue, S., &#38; Benková, E. (2015). The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/erv256\">https://doi.org/10.1093/jxb/erv256</a>","ista":"Robert H, Crhák Khaitová L, Mroue S, Benková E. 2015. The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis. Journal of Experimental Botany. 66(16), 5029–5042.","ieee":"H. Robert, L. Crhák Khaitová, S. Mroue, and E. Benková, “The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis,” <i>Journal of Experimental Botany</i>, vol. 66, no. 16. Oxford University Press, pp. 5029–5042, 2015.","chicago":"Robert, Hélène, Lucie Crhák Khaitová, Souad Mroue, and Eva Benková. “The Importance of Localized Auxin Production for Morphogenesis of Reproductive Organs and Embryos in Arabidopsis.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/jxb/erv256\">https://doi.org/10.1093/jxb/erv256</a>."},"type":"journal_article","department":[{"_id":"EvBe"}],"doi":"10.1093/jxb/erv256","acknowledgement":"The work was supported by grants from: the Employment of Best Young Scientists for International Cooperation Empowerment/OPVKII programme (CZ.1.07/2.3.00/30.0037) to HSR and LCK; the Czech Science Foundation (GA13-39982S) to EB, LCK and SM; and the SoMoPro II programme (3SGA5602), cofinanced by the South-Moravian Region and the EU (FP7/2007–2013 People Programme), to HSR.","oa_version":"None","article_processing_charge":"No","publication_status":"published","date_published":"2015-05-05T00:00:00Z","publisher":"Oxford University Press","date_updated":"2025-09-23T13:51:25Z","month":"05","isi":1,"abstract":[{"text":"Plant sexual reproduction involves highly structured and specialized organs: stamens (male) and gynoecia (female, containing ovules). These organs synchronously develop within protective flower buds, until anthesis, via tightly coordinated mechanisms that are essential for effective fertilization and production of viable seeds. The phytohormone auxin is one of the key endogenous signalling molecules controlling initiation and development of these, and other, plant organs. In particular, its uneven distribution, resulting from tightly controlled production, metabolism and directional transport, is an important morphogenic factor. In this review we discuss how developmentally controlled and localized auxin biosynthesis and transport contribute to the coordinated development of plants' reproductive organs, and their fertilized derivatives (embryos) via the regulation of auxin levels and distribution within and around them. Current understanding of the links between de novo local auxin biosynthesis, auxin transport and/or signalling is presented to highlight the importance of the non-cell autonomous action of auxin production on development and morphogenesis of reproductive organs and embryos. An overview of transcription factor families, which spatiotemporally define local auxin production by controlling key auxin biosynthetic enzymes, is also presented.","lang":"eng"}],"scopus_import":"1","year":"2015"},{"date_created":"2018-12-11T11:52:37Z","conference":{"location":"Haifa, Israel","start_date":"2015-11-17","name":"HVC: Haifa Verification Conference","end_date":"2015-11-19"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"volume":9434,"title":"XSpeed: Accelerating reachability analysis on multi-core processors","quality_controlled":"1","page":"3 - 18","status":"public","intvolume":"      9434","author":[{"last_name":"Ray","first_name":"Rajarshi","full_name":"Ray, Rajarshi"},{"first_name":"Amit","full_name":"Gurung, Amit","last_name":"Gurung"},{"first_name":"Binayak","full_name":"Das, Binayak","last_name":"Das"},{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","orcid":"0000-0002-0686-0365","first_name":"Sergiy","full_name":"Bogomolov, Sergiy"},{"last_name":"Grosu","first_name":"Radu","full_name":"Grosu, Radu"}],"language":[{"iso":"eng"}],"project":[{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"series_title":"Lecture Notes in Computer Science","publication_status":"published","oa_version":"None","month":"11","date_updated":"2025-04-15T06:26:02Z","scopus_import":1,"year":"2015","abstract":[{"lang":"eng","text":"We present XSpeed a parallel state-space exploration algorithm for continuous systems with linear dynamics and nondeterministic inputs. The motivation of having parallel algorithms is to exploit the computational power of multi-core processors to speed-up performance. The parallelization is achieved on two fronts. First, we propose a parallel implementation of the support function algorithm by sampling functions in parallel. Second, we propose a parallel state-space exploration by slicing the time horizon and computing the reachable states in the time slices in parallel. The second method can be however applied only to a class of linear systems with invertible dynamics and fixed input. A GP-GPU implementation is also presented following a lazy evaluation strategy on support functions. The parallel algorithms are implemented in the tool XSpeed. We evaluated the performance on two benchmarks including an 28 dimension Helicopter model. Comparison with the sequential counterpart shows a maximum speed-up of almost 7× on a 6 core, 12 thread Intel Xeon CPU E5-2420 processor. Our GP-GPU implementation shows a maximum speed-up of 12× over the sequential implementation and 53× over SpaceEx (LGG scenario), the state of the art tool for reachability analysis of linear hybrid systems. Experiments illustrate that our parallel algorithm with time slicing not only speeds-up performance but also improves precision."}],"alternative_title":["LNCS"],"publisher":"Springer","date_published":"2015-11-28T00:00:00Z","publist_id":"5630","day":"28","_id":"1541","acknowledgement":"This work was supported in part by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","doi":"10.1007/978-3-319-26287-1_1","department":[{"_id":"ToHe"}],"type":"conference","citation":{"ama":"Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. XSpeed: Accelerating reachability analysis on multi-core processors. 2015;9434:3-18. doi:<a href=\"https://doi.org/10.1007/978-3-319-26287-1_1\">10.1007/978-3-319-26287-1_1</a>","mla":"Ray, Rajarshi, et al. <i>XSpeed: Accelerating Reachability Analysis on Multi-Core Processors</i>. Vol. 9434, Springer, 2015, pp. 3–18, doi:<a href=\"https://doi.org/10.1007/978-3-319-26287-1_1\">10.1007/978-3-319-26287-1_1</a>.","short":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, R. Grosu, 9434 (2015) 3–18.","ista":"Ray R, Gurung A, Das B, Bartocci E, Bogomolov S, Grosu R. 2015. XSpeed: Accelerating reachability analysis on multi-core processors. 9434, 3–18.","apa":"Ray, R., Gurung, A., Das, B., Bartocci, E., Bogomolov, S., &#38; Grosu, R. (2015). XSpeed: Accelerating reachability analysis on multi-core processors. Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. <a href=\"https://doi.org/10.1007/978-3-319-26287-1_1\">https://doi.org/10.1007/978-3-319-26287-1_1</a>","ieee":"R. Ray, A. Gurung, B. Das, E. Bartocci, S. Bogomolov, and R. Grosu, “XSpeed: Accelerating reachability analysis on multi-core processors,” vol. 9434. Springer, pp. 3–18, 2015.","chicago":"Ray, Rajarshi, Amit Gurung, Binayak Das, Ezio Bartocci, Sergiy Bogomolov, and Radu Grosu. “XSpeed: Accelerating Reachability Analysis on Multi-Core Processors.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-26287-1_1\">https://doi.org/10.1007/978-3-319-26287-1_1</a>."}},{"corr_author":"1","ddc":["570"],"date_created":"2018-12-11T11:52:37Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":383,"ec_funded":1,"has_accepted_license":"1","title":"Toward a unifying framework for evolutionary processes","quality_controlled":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"page":"28 - 43","intvolume":"       383","status":"public","author":[{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago","full_name":"Paixao, Tiago"},{"first_name":"Golnaz","full_name":"Badkobeh, Golnaz","last_name":"Badkobeh"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"last_name":"Çörüş","first_name":"Doğan","full_name":"Çörüş, Doğan"},{"first_name":"Duccuong","full_name":"Dang, Duccuong","last_name":"Dang"},{"last_name":"Friedrich","full_name":"Friedrich, Tobias","first_name":"Tobias"},{"first_name":"Per","full_name":"Lehre, Per","last_name":"Lehre"},{"last_name":"Sudholt","first_name":"Dirk","full_name":"Sudholt, Dirk"},{"last_name":"Sutton","full_name":"Sutton, Andrew","first_name":"Andrew"},{"orcid":"0000-0002-6873-2967","last_name":"Trubenova","first_name":"Barbora","full_name":"Trubenova, Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000362056300005"]},"language":[{"iso":"eng"}],"publication_status":"published","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618091"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152"}],"article_processing_charge":"No","file":[{"checksum":"33b60ecfea60764756a9ee9df5eb65ca","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:01Z","file_size":595307,"file_id":"5244","relation":"main_file","date_created":"2018-12-12T10:16:53Z","creator":"system","access_level":"open_access"}],"oa_version":"Published Version","year":"2015","abstract":[{"text":"The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. ","lang":"eng"}],"scopus_import":"1","isi":1,"month":"10","date_updated":"2025-09-23T14:55:02Z","publisher":"Elsevier","date_published":"2015-10-21T00:00:00Z","pubrep_id":"483","file_date_updated":"2020-07-14T12:45:01Z","publication":" Journal of Theoretical Biology","_id":"1542","day":"21","publist_id":"5629","doi":"10.1016/j.jtbi.2015.07.011","oa":1,"citation":{"ieee":"T. Paixao <i>et al.</i>, “Toward a unifying framework for evolutionary processes,” <i> Journal of Theoretical Biology</i>, vol. 383. Elsevier, pp. 28–43, 2015.","chicago":"Paixao, Tiago, Golnaz Badkobeh, Nicholas H Barton, Doğan Çörüş, Duccuong Dang, Tobias Friedrich, Per Lehre, Dirk Sudholt, Andrew Sutton, and Barbora Trubenova. “Toward a Unifying Framework for Evolutionary Processes.” <i> Journal of Theoretical Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>.","short":"T. Paixao, G. Badkobeh, N.H. Barton, D. Çörüş, D. Dang, T. Friedrich, P. Lehre, D. Sudholt, A. Sutton, B. Trubenova,  Journal of Theoretical Biology 383 (2015) 28–43.","mla":"Paixao, Tiago, et al. “Toward a Unifying Framework for Evolutionary Processes.” <i> Journal of Theoretical Biology</i>, vol. 383, Elsevier, 2015, pp. 28–43, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>.","ama":"Paixao T, Badkobeh G, Barton NH, et al. Toward a unifying framework for evolutionary processes. <i> Journal of Theoretical Biology</i>. 2015;383:28-43. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">10.1016/j.jtbi.2015.07.011</a>","ista":"Paixao T, Badkobeh G, Barton NH, Çörüş D, Dang D, Friedrich T, Lehre P, Sudholt D, Sutton A, Trubenova B. 2015. Toward a unifying framework for evolutionary processes.  Journal of Theoretical Biology. 383, 28–43.","apa":"Paixao, T., Badkobeh, G., Barton, N. H., Çörüş, D., Dang, D., Friedrich, T., … Trubenova, B. (2015). Toward a unifying framework for evolutionary processes. <i> Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2015.07.011\">https://doi.org/10.1016/j.jtbi.2015.07.011</a>"},"type":"journal_article","department":[{"_id":"NiBa"},{"_id":"CaGu"}]},{"intvolume":"       169","doi":"10.1104/pp.15.00769","status":"public","author":[{"last_name":"Olvera Carrillo","full_name":"Olvera Carrillo, Yadira","first_name":"Yadira"},{"first_name":"Michiel","full_name":"Van Bel, Michiel","last_name":"Van Bel"},{"last_name":"Van Hautegem","full_name":"Van Hautegem, Tom","first_name":"Tom"},{"id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","full_name":"Fendrych, Matyas","last_name":"Fendrych","orcid":"0000-0002-9767-8699"},{"full_name":"Huysmans, Marlies","first_name":"Marlies","last_name":"Huysmans"},{"first_name":"Mária","full_name":"Šimášková, Mária","last_name":"Šimášková"},{"first_name":"Matthias","full_name":"Van Durme, Matthias","last_name":"Van Durme"},{"last_name":"Buscaill","full_name":"Buscaill, Pierre","first_name":"Pierre"},{"last_name":"Rivas","first_name":"Susana","full_name":"Rivas, Susana"},{"last_name":"Coll","full_name":"Coll, Núria","first_name":"Núria"},{"first_name":"Frederik","full_name":"Coppens, Frederik","last_name":"Coppens"},{"last_name":"Maere","first_name":"Steven","full_name":"Maere, Steven"},{"full_name":"Nowack, Moritz","first_name":"Moritz","last_name":"Nowack"}],"external_id":{"isi":["000368472700025"]},"language":[{"iso":"eng"}],"type":"journal_article","citation":{"short":"Y. Olvera Carrillo, M. Van Bel, T. Van Hautegem, M. Fendrych, M. Huysmans, M. Šimášková, M. Van Durme, P. Buscaill, S. Rivas, N. Coll, F. Coppens, S. Maere, M. Nowack, Plant Physiology 169 (2015) 2684–2699.","ama":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, et al. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. <i>Plant Physiology</i>. 2015;169(4):2684-2699. doi:<a href=\"https://doi.org/10.1104/pp.15.00769\">10.1104/pp.15.00769</a>","mla":"Olvera Carrillo, Yadira, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” <i>Plant Physiology</i>, vol. 169, no. 4, American Society of Plant Biologists, 2015, pp. 2684–99, doi:<a href=\"https://doi.org/10.1104/pp.15.00769\">10.1104/pp.15.00769</a>.","ista":"Olvera Carrillo Y, Van Bel M, Van Hautegem T, Fendrych M, Huysmans M, Šimášková M, Van Durme M, Buscaill P, Rivas S, Coll N, Coppens F, Maere S, Nowack M. 2015. A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. Plant Physiology. 169(4), 2684–2699.","apa":"Olvera Carrillo, Y., Van Bel, M., Van Hautegem, T., Fendrych, M., Huysmans, M., Šimášková, M., … Nowack, M. (2015). A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.15.00769\">https://doi.org/10.1104/pp.15.00769</a>","ieee":"Y. Olvera Carrillo <i>et al.</i>, “A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants,” <i>Plant Physiology</i>, vol. 169, no. 4. American Society of Plant Biologists, pp. 2684–2699, 2015.","chicago":"Olvera Carrillo, Yadira, Michiel Van Bel, Tom Van Hautegem, Matyas Fendrych, Marlies Huysmans, Mária Šimášková, Matthias Van Durme, et al. “A Conserved Core of Programmed Cell Death Indicator Genes Discriminates Developmentally and Environmentally Induced Programmed Cell Death in Plants.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2015. <a href=\"https://doi.org/10.1104/pp.15.00769\">https://doi.org/10.1104/pp.15.00769</a>."},"department":[{"_id":"JiFr"}],"issue":"4","title":"A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants","publication":"Plant Physiology","day":"01","_id":"1543","page":"2684 - 2699","publist_id":"5628","year":"2015","scopus_import":"1","abstract":[{"text":"A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta.","lang":"eng"}],"volume":169,"month":"12","isi":1,"date_updated":"2025-09-22T14:28:43Z","publisher":"American Society of Plant Biologists","date_published":"2015-12-01T00:00:00Z","publication_status":"published","article_processing_charge":"No","date_created":"2018-12-11T11:52:38Z","oa_version":"None","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"pmid":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:38Z","corr_author":"1","volume":128,"page":"223 - 241","title":"Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins","quality_controlled":"1","external_id":{"isi":["000370490800013"],"pmid":["25997350"]},"author":[{"first_name":"Phuong","full_name":"Nguyen, Phuong","last_name":"Nguyen"},{"first_name":"Christine","full_name":"Field, Christine","last_name":"Field"},{"last_name":"Groen","full_name":"Groen, Aaron","first_name":"Aaron"},{"last_name":"Mitchison","first_name":"Timothy","full_name":"Mitchison, Timothy"},{"full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"status":"public","intvolume":"       128","oa_version":"Submitted Version","article_processing_charge":"No","publication_status":"published","publisher":"Academic Press","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/","open_access":"1"}],"date_published":"2015-04-08T00:00:00Z","month":"04","isi":1,"date_updated":"2025-09-29T11:03:06Z","abstract":[{"lang":"eng","text":"Cell division in prokaryotes and eukaryotes is commonly initiated by the well-controlled binding of proteins to the cytoplasmic side of the cell membrane. However, a precise characterization of the spatiotemporal dynamics of membrane-bound proteins is often difficult to achieve in vivo. Here, we present protocols for the use of supported lipid bilayers to rebuild the cytokinetic machineries of cells with greatly different dimensions: the bacterium Escherichia coli and eggs of the vertebrate Xenopus laevis. Combined with total internal reflection fluorescence microscopy, these experimental setups allow for precise quantitative analyses of membrane-bound proteins. The protocols described to obtain glass-supported membranes from bacterial and vertebrate lipids can be used as starting points for other reconstitution experiments. We believe that similar biochemical assays will be instrumental to study the biochemistry and biophysics underlying a variety of complex cellular tasks, such as signaling, vesicle trafficking, and cell motility."}],"year":"2015","scopus_import":"1","publist_id":"5627","_id":"1544","day":"08","publication":"Building a Cell from its Components Parts","type":"book_chapter","department":[{"_id":"MaLo"}],"citation":{"apa":"Nguyen, P., Field, C., Groen, A., Mitchison, T., &#38; Loose, M. (2015). Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In <i>Building a Cell from its Components Parts</i> (Vol. 128, pp. 223–241). Academic Press. <a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">https://doi.org/10.1016/bs.mcb.2015.01.007</a>","ista":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. 2015.Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: Building a Cell from its Components Parts. vol. 128, 223–241.","mla":"Nguyen, Phuong, et al. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” <i>Building a Cell from Its Components Parts</i>, vol. 128, Academic Press, 2015, pp. 223–41, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">10.1016/bs.mcb.2015.01.007</a>.","ama":"Nguyen P, Field C, Groen A, Mitchison T, Loose M. Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins. In: <i>Building a Cell from Its Components Parts</i>. Vol 128. Academic Press; 2015:223-241. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">10.1016/bs.mcb.2015.01.007</a>","short":"P. Nguyen, C. Field, A. Groen, T. Mitchison, M. Loose, in:, Building a Cell from Its Components Parts, Academic Press, 2015, pp. 223–241.","chicago":"Nguyen, Phuong, Christine Field, Aaron Groen, Timothy Mitchison, and Martin Loose. “Using Supported Bilayers to Study the Spatiotemporal Organization of Membrane-Bound Proteins.” In <i>Building a Cell from Its Components Parts</i>, 128:223–41. Academic Press, 2015. <a href=\"https://doi.org/10.1016/bs.mcb.2015.01.007\">https://doi.org/10.1016/bs.mcb.2015.01.007</a>.","ieee":"P. Nguyen, C. Field, A. Groen, T. Mitchison, and M. Loose, “Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins,” in <i>Building a Cell from its Components Parts</i>, vol. 128, Academic Press, 2015, pp. 223–241."},"oa":1,"doi":"10.1016/bs.mcb.2015.01.007"},{"publication":"Frontiers in Environmental Science","file_date_updated":"2022-02-25T11:55:26Z","day":"10","_id":"10794","doi":"10.3389/fenvs.2015.00042","publication_identifier":{"issn":["2296-665X"]},"acknowledgement":"The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX.","type":"journal_article","citation":{"ieee":"F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” <i>Frontiers in Environmental Science</i>, vol. 3. Frontiers, 2015.","chicago":"Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>. Frontiers, 2015. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>.","short":"F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).","ama":"Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. 2015;3. doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>","mla":"Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>, vol. 3, 42, Frontiers, 2015, doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>.","ista":"Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.","apa":"Parise, F., Lygeros, J., &#38; Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>"},"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"oa":1,"article_processing_charge":"No","project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"publication_status":"published","file":[{"file_name":"2015_FrontiersEnvironmScience_Parise.pdf","checksum":"26c222487564e1be02a11d688d6f769d","content_type":"application/pdf","success":1,"date_updated":"2022-02-25T11:55:26Z","file_size":1371201,"file_id":"10795","date_created":"2022-02-25T11:55:26Z","relation":"main_file","access_level":"open_access","creator":"dernst"}],"oa_version":"Published Version","date_updated":"2025-04-15T06:50:01Z","month":"06","scopus_import":"1","year":"2015","abstract":[{"text":"Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation.","lang":"eng"}],"date_published":"2015-06-10T00:00:00Z","publisher":"Frontiers","quality_controlled":"1","title":"Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","intvolume":"         3","language":[{"iso":"eng"}],"author":[{"full_name":"Parise, Francesca","first_name":"Francesca","last_name":"Parise"},{"first_name":"John","full_name":"Lygeros, John","last_name":"Lygeros"},{"full_name":"Ruess, Jakob","first_name":"Jakob","orcid":"0000-0003-1615-3282","last_name":"Ruess","id":"4A245D00-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2022-02-25T11:42:25Z","ddc":["000","570"],"corr_author":"1","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"42","keyword":["General Environmental Science"],"ec_funded":1,"volume":3,"has_accepted_license":"1"},{"issue":"1","publication":"Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms","day":"01","_id":"10796","acknowledgement":"The research was partly supported by FWF Grant No P 23499-N23, FWF NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","publication_identifier":{"isbn":["978-161197374-7"]},"doi":"10.1137/1.9781611973730.69","oa":1,"type":"conference","department":[{"_id":"KrCh"}],"citation":{"ieee":"K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory strategies for concurrent mean-payoff games,” in <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, San Diego, CA, United States, 2015, vol. 2015, no. 1, pp. 1018–1029.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2015:1018–29. SIAM, 2015. <a href=\"https://doi.org/10.1137/1.9781611973730.69\">https://doi.org/10.1137/1.9781611973730.69</a>.","ama":"Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In: <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2015. SIAM; 2015:1018-1029. doi:<a href=\"https://doi.org/10.1137/1.9781611973730.69\">10.1137/1.9781611973730.69</a>","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2015, no. 1, SIAM, 2015, pp. 1018–29, doi:<a href=\"https://doi.org/10.1137/1.9781611973730.69\">10.1137/1.9781611973730.69</a>.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029.","apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2015, pp. 1018–1029). San Diego, CA, United States: SIAM. <a href=\"https://doi.org/10.1137/1.9781611973730.69\">https://doi.org/10.1137/1.9781611973730.69</a>","ista":"Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2015, 1018–1029."},"OA_place":"publisher","publication_status":"published","article_processing_charge":"No","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa_version":"Preprint","year":"2015","scopus_import":"1","abstract":[{"lang":"eng","text":"We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy)."}],"month":"01","arxiv":1,"date_updated":"2025-06-26T06:54:08Z","publisher":"SIAM","date_published":"2015-01-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1409.6690"}],"title":"The value 1 problem under finite-memory strategies for concurrent mean-payoff games","quality_controlled":"1","page":"1018-1029","intvolume":"      2015","status":"public","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","id":"3B699956-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1409.6690"]},"language":[{"iso":"eng"}],"corr_author":"1","date_created":"2022-02-25T12:18:43Z","conference":{"start_date":"2015-01-04","name":"SODA: Symposium on Discrete Algorithms","end_date":"2015-01-06","location":"San Diego, CA, United States"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":2015,"ec_funded":1,"OA_type":"green"},{"issue":"2","publication":"Archive for Rational Mechanics and Analysis","day":"01","_id":"2085","publist_id":"4951","doi":"10.1007/s00205-014-0781-6","oa":1,"type":"journal_article","department":[{"_id":"RoSe"}],"citation":{"short":"P. Nam, R. Seiringer, Archive for Rational Mechanics and Analysis 215 (2015) 381–417.","ama":"Nam P, Seiringer R. Collective excitations of Bose gases in the mean-field regime. <i>Archive for Rational Mechanics and Analysis</i>. 2015;215(2):381-417. doi:<a href=\"https://doi.org/10.1007/s00205-014-0781-6\">10.1007/s00205-014-0781-6</a>","mla":"Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the Mean-Field Regime.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 215, no. 2, Springer, 2015, pp. 381–417, doi:<a href=\"https://doi.org/10.1007/s00205-014-0781-6\">10.1007/s00205-014-0781-6</a>.","apa":"Nam, P., &#38; Seiringer, R. (2015). Collective excitations of Bose gases in the mean-field regime. <i>Archive for Rational Mechanics and Analysis</i>. Springer. <a href=\"https://doi.org/10.1007/s00205-014-0781-6\">https://doi.org/10.1007/s00205-014-0781-6</a>","ista":"Nam P, Seiringer R. 2015. Collective excitations of Bose gases in the mean-field regime. Archive for Rational Mechanics and Analysis. 215(2), 381–417.","ieee":"P. Nam and R. Seiringer, “Collective excitations of Bose gases in the mean-field regime,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 215, no. 2. Springer, pp. 381–417, 2015.","chicago":"Nam, Phan, and Robert Seiringer. “Collective Excitations of Bose Gases in the Mean-Field Regime.” <i>Archive for Rational Mechanics and Analysis</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00205-014-0781-6\">https://doi.org/10.1007/s00205-014-0781-6</a>."},"publication_status":"published","article_processing_charge":"No","oa_version":"Preprint","abstract":[{"text":"We study the spectrum of a large system of N identical bosons interacting via a two-body potential with strength 1/N. In this mean-field regime, Bogoliubov's theory predicts that the spectrum of the N-particle Hamiltonian can be approximated by that of an effective quadratic Hamiltonian acting on Fock space, which describes the fluctuations around a condensed state. Recently, Bogoliubov's theory has been justified rigorously in the case that the low-energy eigenvectors of the N-particle Hamiltonian display complete condensation in the unique minimizer of the corresponding Hartree functional. In this paper, we shall justify Bogoliubov's theory for the high-energy part of the spectrum of the N-particle Hamiltonian corresponding to (non-linear) excited states of the Hartree functional. Moreover, we shall extend the existing results on the excitation spectrum to the case of non-uniqueness and/or degeneracy of the Hartree minimizer. In particular, the latter covers the case of rotating Bose gases, when the rotation speed is large enough to break the symmetry and to produce multiple quantized vortices in the Hartree minimizer. ","lang":"eng"}],"year":"2015","scopus_import":"1","month":"02","isi":1,"date_updated":"2025-09-23T08:17:14Z","arxiv":1,"publisher":"Springer","date_published":"2015-02-01T00:00:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1402.1153","open_access":"1"}],"title":"Collective excitations of Bose gases in the mean-field regime","quality_controlled":"1","page":"381 - 417","intvolume":"       215","status":"public","author":[{"id":"404092F4-F248-11E8-B48F-1D18A9856A87","first_name":"Phan","full_name":"Nam, Phan","last_name":"Nam"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1402.1153"],"isi":["000347150400002"]},"language":[{"iso":"eng"}],"corr_author":"1","date_created":"2018-12-11T11:55:37Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":215},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:56:05Z","volume":333,"page":"1365 - 1416","title":"The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case","quality_controlled":"1","external_id":{"isi":["000348303100008"],"arxiv":["1309.5106"]},"author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László","first_name":"László"},{"full_name":"Knowles, Antti","first_name":"Antti","last_name":"Knowles"}],"language":[{"iso":"eng"}],"intvolume":"       333","status":"public","oa_version":"Preprint","publication_status":"published","article_processing_charge":"No","publisher":"Springer","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1309.5106"}],"date_published":"2015-02-01T00:00:00Z","year":"2015","scopus_import":"1","abstract":[{"text":"We consider the spectral statistics of large random band matrices on mesoscopic energy scales. We show that the correlation function of the local eigenvalue density exhibits a universal power law behaviour that differs from the Wigner-Dyson- Mehta statistics. This law had been predicted in the physics literature by Altshuler and Shklovskii in (Zh Eksp Teor Fiz (Sov Phys JETP) 91(64):220(127), 1986); it describes the correlations of the eigenvalue density in general metallic sampleswith weak disorder. Our result rigorously establishes the Altshuler-Shklovskii formulas for band matrices. In two dimensions, where the leading term vanishes owing to an algebraic cancellation, we identify the first non-vanishing term and show that it differs substantially from the prediction of Kravtsov and Lerner in (Phys Rev Lett 74:2563-2566, 1995). The proof is given in the current paper and its companion (Ann. H. Poincaré. arXiv:1309.5107, 2014). ","lang":"eng"}],"isi":1,"month":"02","arxiv":1,"date_updated":"2025-09-23T13:39:37Z","_id":"2166","day":"01","publist_id":"4818","issue":"3","publication":"Communications in Mathematical Physics","oa":1,"citation":{"ieee":"L. Erdös and A. Knowles, “The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case,” <i>Communications in Mathematical Physics</i>, vol. 333, no. 3. Springer, pp. 1365–1416, 2015.","chicago":"Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random Band Matrices I: The Unimodular Case.” <i>Communications in Mathematical Physics</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s00220-014-2119-5\">https://doi.org/10.1007/s00220-014-2119-5</a>.","mla":"Erdös, László, and Antti Knowles. “The Altshuler-Shklovskii Formulas for Random Band Matrices I: The Unimodular Case.” <i>Communications in Mathematical Physics</i>, vol. 333, no. 3, Springer, 2015, pp. 1365–416, doi:<a href=\"https://doi.org/10.1007/s00220-014-2119-5\">10.1007/s00220-014-2119-5</a>.","ama":"Erdös L, Knowles A. The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. <i>Communications in Mathematical Physics</i>. 2015;333(3):1365-1416. doi:<a href=\"https://doi.org/10.1007/s00220-014-2119-5\">10.1007/s00220-014-2119-5</a>","short":"L. Erdös, A. Knowles, Communications in Mathematical Physics 333 (2015) 1365–1416.","apa":"Erdös, L., &#38; Knowles, A. (2015). The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-014-2119-5\">https://doi.org/10.1007/s00220-014-2119-5</a>","ista":"Erdös L, Knowles A. 2015. The Altshuler-Shklovskii formulas for random band matrices I: the unimodular case. Communications in Mathematical Physics. 333(3), 1365–1416."},"type":"journal_article","department":[{"_id":"LaEr"}],"doi":"10.1007/s00220-014-2119-5"},{"publication":"SIAM Journal on Computing","issue":"1","publist_id":"4673","_id":"2271","day":"01","doi":"10.1137/130945648","citation":{"ieee":"V. Kolmogorov, J. Thapper, and S. Živný, “The power of linear programming for general-valued CSPs,” <i>SIAM Journal on Computing</i>, vol. 44, no. 1. SIAM, pp. 1–36, 2015.","chicago":"Kolmogorov, Vladimir, Johan Thapper, and Stanislav Živný. “The Power of Linear Programming for General-Valued CSPs.” <i>SIAM Journal on Computing</i>. SIAM, 2015. <a href=\"https://doi.org/10.1137/130945648\">https://doi.org/10.1137/130945648</a>.","ama":"Kolmogorov V, Thapper J, Živný S. The power of linear programming for general-valued CSPs. <i>SIAM Journal on Computing</i>. 2015;44(1):1-36. doi:<a href=\"https://doi.org/10.1137/130945648\">10.1137/130945648</a>","mla":"Kolmogorov, Vladimir, et al. “The Power of Linear Programming for General-Valued CSPs.” <i>SIAM Journal on Computing</i>, vol. 44, no. 1, SIAM, 2015, pp. 1–36, doi:<a href=\"https://doi.org/10.1137/130945648\">10.1137/130945648</a>.","short":"V. Kolmogorov, J. Thapper, S. Živný, SIAM Journal on Computing 44 (2015) 1–36.","apa":"Kolmogorov, V., Thapper, J., &#38; Živný, S. (2015). The power of linear programming for general-valued CSPs. <i>SIAM Journal on Computing</i>. SIAM. <a href=\"https://doi.org/10.1137/130945648\">https://doi.org/10.1137/130945648</a>","ista":"Kolmogorov V, Thapper J, Živný S. 2015. The power of linear programming for general-valued CSPs. SIAM Journal on Computing. 44(1), 1–36."},"type":"journal_article","department":[{"_id":"VlKo"}],"oa":1,"article_processing_charge":"No","publication_status":"published","oa_version":"Preprint","date_updated":"2025-09-23T14:14:57Z","arxiv":1,"isi":1,"month":"02","scopus_import":"1","abstract":[{"text":"A class of valued constraint satisfaction problems (VCSPs) is characterised by a valued constraint language, a fixed set of cost functions on a finite domain. Finite-valued constraint languages contain functions that take on rational costs and general-valued constraint languages contain functions that take on rational or infinite costs. An instance of the problem is specified by a sum of functions from the language with the goal to minimise the sum. This framework includes and generalises well-studied constraint satisfaction problems (CSPs) and maximum constraint satisfaction problems (Max-CSPs).\r\nOur main result is a precise algebraic characterisation of valued constraint languages whose instances can be solved exactly by the basic linear programming relaxation (BLP). For a general-valued constraint language Γ, BLP is a decision procedure for Γ if and only if Γ admits a symmetric fractional polymorphism of every arity. For a finite-valued constraint language Γ, BLP is a decision procedure if and only if Γ admits a symmetric fractional polymorphism of some arity, or equivalently, if Γ admits a symmetric fractional polymorphism of arity 2.\r\nUsing these results, we obtain tractability of several novel and previously widely-open classes of VCSPs, including problems over valued constraint languages that are: (1) submodular on arbitrary lattices; (2) bisubmodular (also known as k-submodular) on arbitrary finite domains; (3) weakly (and hence strongly) tree-submodular on arbitrary trees. ","lang":"eng"}],"year":"2015","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.4219"}],"date_published":"2015-02-01T00:00:00Z","publisher":"SIAM","quality_controlled":"1","title":"The power of linear programming for general-valued CSPs","page":"1 - 36","status":"public","intvolume":"        44","language":[{"iso":"eng"}],"author":[{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Thapper, Johan","first_name":"Johan","last_name":"Thapper"},{"first_name":"Stanislav","full_name":"Živný, Stanislav","last_name":"Živný"}],"external_id":{"arxiv":["1311.4219"],"isi":["000353967100001"]},"date_created":"2018-12-11T11:56:41Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":44,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2518"}]}},{"oa":1,"type":"journal_article","citation":{"chicago":"Nakamura, Yukihiro, Harumi Harada, Naomi Kamasawa, Ko Matsui, Jason Rothman, Ryuichi Shigemoto, R Angus Silver, David Digregorio, and Tomoyuki Takahashi. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” <i>Neuron</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">https://doi.org/10.1016/j.neuron.2014.11.019</a>.","ieee":"Y. Nakamura <i>et al.</i>, “Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development,” <i>Neuron</i>, vol. 85, no. 1. Elsevier, pp. 145–158, 2015.","ista":"Nakamura Y, Harada H, Kamasawa N, Matsui K, Rothman J, Shigemoto R, Silver RA, Digregorio D, Takahashi T. 2015. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. Neuron. 85(1), 145–158.","apa":"Nakamura, Y., Harada, H., Kamasawa, N., Matsui, K., Rothman, J., Shigemoto, R., … Takahashi, T. (2015). Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">https://doi.org/10.1016/j.neuron.2014.11.019</a>","short":"Y. Nakamura, H. Harada, N. Kamasawa, K. Matsui, J. Rothman, R. Shigemoto, R.A. Silver, D. Digregorio, T. Takahashi, Neuron 85 (2015) 145–158.","ama":"Nakamura Y, Harada H, Kamasawa N, et al. Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development. <i>Neuron</i>. 2015;85(1):145-158. doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">10.1016/j.neuron.2014.11.019</a>","mla":"Nakamura, Yukihiro, et al. “Nanoscale Distribution of Presynaptic Ca2+ Channels and Its Impact on Vesicular Release during Development.” <i>Neuron</i>, vol. 85, no. 1, Elsevier, 2015, pp. 145–58, doi:<a href=\"https://doi.org/10.1016/j.neuron.2014.11.019\">10.1016/j.neuron.2014.11.019</a>."},"department":[{"_id":"RySh"}],"doi":"10.1016/j.neuron.2014.11.019","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"acknowledgement":"This work was supported by the Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency to T.T. and R.S.; by the funding provided by Okinawa Institute of Science and Technology (OIST) to T.T. and Y.N.; by JSPS Core-to-Core Program, A. Advanced Networks to T.T.; by the Grant-in-Aid for Young Scientists from the Japanese Ministry of Education, Culture, Sports, Science and Technology (#23700474) to Y.N.; by the Centre National de la Recherche Scientifique through the Actions Thematiques et Initatives sur Programme, Fondation Fyssen, Fondation pour la Recherche Medicale, Federation pour la Recherche sur le Cerveau, Agence Nationale de la Recherche (ANR-2007-Neuro-008-01 and ANR-2010-BLAN-1411-01) to D.D. and Y.N.; and by the European Commission Coordination Action ENINET (LSHM-CT-2005-19063) to D.D. and R.A.S. R.A.S. and J.S.R. were funded by Wellcome Trust Senior (064413) and Principal (095667) Research Fellowship and an ERC advance grant (294667) to RAS.","day":"07","_id":"1546","publist_id":"5625","file_date_updated":"2020-07-14T12:45:01Z","issue":"1","publication":"Neuron","date_published":"2015-01-07T00:00:00Z","publisher":"Elsevier","pubrep_id":"482","abstract":[{"lang":"eng","text":"Synaptic efficacy and precision are influenced by the coupling of voltage-gated Ca2+ channels (VGCCs) to vesicles. But because the topography of VGCCs and their proximity to vesicles is unknown, a quantitative understanding of the determinants of vesicular release at nanometer scale is lacking. To investigate this, we combined freeze-fracture replica immunogold labeling of Cav2.1 channels, local [Ca2+] imaging, and patch pipette perfusion of EGTA at the calyx of Held. Between postnatal day 7 and 21, VGCCs formed variable sized clusters and vesicular release became less sensitive to EGTA, whereas fixed Ca2+ buffer properties remained constant. Experimentally constrained reaction-diffusion simulations suggest that Ca2+ sensors for vesicular release are located at the perimeter of VGCC clusters (&lt;30nm) and predict that VGCC number per cluster determines vesicular release probability without altering release time course. This &quot;perimeter release model&quot; provides a unifying framework accounting for developmental changes in both synaptic efficacy and time course."}],"year":"2015","scopus_import":"1","date_updated":"2025-09-23T09:38:39Z","isi":1,"month":"01","file":[{"file_id":"5170","relation":"main_file","date_created":"2018-12-12T10:15:47Z","creator":"system","access_level":"open_access","checksum":"725f4d5be2dbb44b283ce722645ef37d","file_name":"IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:01Z","file_size":3080111}],"oa_version":"Published Version","publication_status":"published","OA_place":"publisher","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"external_id":{"pmid":["25533484"],"isi":["000348295100015"]},"author":[{"last_name":"Nakamura","first_name":"Yukihiro","full_name":"Nakamura, Yukihiro"},{"id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi","first_name":"Harumi"},{"last_name":"Kamasawa","first_name":"Naomi","full_name":"Kamasawa, Naomi"},{"first_name":"Ko","full_name":"Matsui, Ko","last_name":"Matsui"},{"full_name":"Rothman, Jason","first_name":"Jason","last_name":"Rothman"},{"first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Silver","first_name":"R Angus","full_name":"Silver, R Angus"},{"last_name":"Digregorio","full_name":"Digregorio, David","first_name":"David"},{"full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki","last_name":"Takahashi"}],"intvolume":"        85","status":"public","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"page":"145 - 158","license":"https://creativecommons.org/licenses/by/3.0/","quality_controlled":"1","title":"Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development","has_accepted_license":"1","OA_type":"hybrid","volume":85,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pmid":1,"article_type":"original","date_created":"2018-12-11T11:52:39Z","ddc":["570"]},{"language":[{"iso":"eng"}],"external_id":{"arxiv":["0901.3015"],"isi":["000355776600024"]},"author":[{"last_name":"Mohammadi","first_name":"Fatemeh","full_name":"Mohammadi, Fatemeh","id":"2C29581E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Moradi, Somayeh","first_name":"Somayeh","last_name":"Moradi"}],"intvolume":"        52","status":"public","page":"977 - 986","quality_controlled":"1","title":"Resolution of unmixed bipartite graphs","volume":52,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:52:39Z","oa":1,"department":[{"_id":"CaUh"}],"type":"journal_article","citation":{"ieee":"F. Mohammadi and S. Moradi, “Resolution of unmixed bipartite graphs,” <i>Bulletin of the Korean Mathematical Society</i>, vol. 52, no. 3. Korean Mathematical Society, pp. 977–986, 2015.","chicago":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” <i>Bulletin of the Korean Mathematical Society</i>. Korean Mathematical Society, 2015. <a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">https://doi.org/10.4134/BKMS.2015.52.3.977</a>.","short":"F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015) 977–986.","mla":"Mohammadi, Fatemeh, and Somayeh Moradi. “Resolution of Unmixed Bipartite Graphs.” <i>Bulletin of the Korean Mathematical Society</i>, vol. 52, no. 3, Korean Mathematical Society, 2015, pp. 977–86, doi:<a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">10.4134/BKMS.2015.52.3.977</a>.","ama":"Mohammadi F, Moradi S. Resolution of unmixed bipartite graphs. <i>Bulletin of the Korean Mathematical Society</i>. 2015;52(3):977-986. doi:<a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">10.4134/BKMS.2015.52.3.977</a>","ista":"Mohammadi F, Moradi S. 2015. Resolution of unmixed bipartite graphs. Bulletin of the Korean Mathematical Society. 52(3), 977–986.","apa":"Mohammadi, F., &#38; Moradi, S. (2015). Resolution of unmixed bipartite graphs. <i>Bulletin of the Korean Mathematical Society</i>. Korean Mathematical Society. <a href=\"https://doi.org/10.4134/BKMS.2015.52.3.977\">https://doi.org/10.4134/BKMS.2015.52.3.977</a>"},"doi":"10.4134/BKMS.2015.52.3.977","publication_identifier":{"eissn":["2234-3016"]},"day":"31","_id":"1547","publist_id":"5624","issue":"3","publication":"Bulletin of the Korean Mathematical Society","main_file_link":[{"url":"http://arxiv.org/abs/0901.3015","open_access":"1"}],"date_published":"2015-05-31T00:00:00Z","publisher":"Korean Mathematical Society","abstract":[{"text":"Let G be a graph on the vertex set V(G) = {x1,…,xn} with the edge set E(G), and let R = K[x1,…, xn] be the polynomial ring over a field K. Two monomial ideals are associated to G, the edge ideal I(G) generated by all monomials xixj with {xi,xj} ∈ E(G), and the vertex cover ideal IG generated by monomials ∏xi∈Cxi for all minimal vertex covers C of G. A minimal vertex cover of G is a subset C ⊂ V(G) such that each edge has at least one vertex in C and no proper subset of C has the same property. Indeed, the vertex cover ideal of G is the Alexander dual of the edge ideal of G. In this paper, for an unmixed bipartite graph G we consider the lattice of vertex covers LG and we explicitly describe the minimal free resolution of the ideal associated to LG which is exactly the vertex cover ideal of G. Then we compute depth, projective dimension, regularity and extremal Betti numbers of R/I(G) in terms of the associated lattice.","lang":"eng"}],"year":"2015","scopus_import":"1","arxiv":1,"date_updated":"2025-09-23T10:36:36Z","month":"05","isi":1,"oa_version":"Preprint","publication_status":"published","article_processing_charge":"No"}]