[{"department":[{"_id":"HeEd"}],"article_processing_charge":"No","date_created":"2018-12-11T11:52:33Z","publication_status":"published","intvolume":"        40","title":"Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature","alternative_title":["Mathematics and Visualization"],"scopus_import":"1","_id":"1531","author":[{"full_name":"Zobel, Valentin","first_name":"Valentin","last_name":"Zobel"},{"id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Reininghaus","full_name":"Reininghaus, Jan"},{"full_name":"Hotz, Ingrid","last_name":"Hotz","first_name":"Ingrid"}],"editor":[{"last_name":"Hotz","first_name":"Ingrid","full_name":"Hotz, Ingrid"},{"first_name":"Thomas","last_name":"Schultz","full_name":"Schultz, Thomas"}],"publisher":"Springer","quality_controlled":"1","page":"257 - 267","day":"01","edition":"1","doi":"10.1007/978-3-319-15090-1_13","abstract":[{"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.","lang":"eng"}],"year":"2015","citation":{"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>.","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.","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.","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>","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>","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>."},"date_updated":"2022-06-10T09:50:14Z","volume":40,"oa_version":"None","month":"01","publication":"Visualization and Processing of Higher Order Descriptors for Multi-Valued Data","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-319-15089-5"]},"publist_id":"5640","type":"book_chapter","date_published":"2015-01-01T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"quality_controlled":"1","page":"239 - 251","publisher":"CSIRO","article_type":"original","scopus_import":"1","_id":"1532","pmid":1,"issue":"3","author":[{"last_name":"Yang","first_name":"Huaiyu","full_name":"Yang, Huaiyu"},{"full_name":"Von Der Fecht Bartenbach, Jenny","first_name":"Jenny","last_name":"Von Der Fecht Bartenbach"},{"last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lohmann, Jan","last_name":"Lohmann","first_name":"Jan"},{"first_name":"Benjamin","last_name":"Neuhäuser","full_name":"Neuhäuser, Benjamin"},{"full_name":"Ludewig, Uwe","first_name":"Uwe","last_name":"Ludewig"}],"department":[{"_id":"JiFr"}],"date_created":"2018-12-11T11:52:34Z","article_processing_charge":"No","publication_status":"published","intvolume":"        42","title":"Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source","volume":42,"citation":{"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.","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>","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>","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.","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>.","short":"H. Yang, J. Von Der Fecht Bartenbach, J. Friml, J. Lohmann, B. Neuhäuser, U. Ludewig, Functional Plant Biology 42 (2015) 239–251."},"year":"2015","date_updated":"2022-05-24T09:02:24Z","external_id":{"pmid":["32480670"]},"day":"01","doi":"10.1071/FP14171","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"publication":"Functional Plant Biology","oa_version":"None","month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"journal_article","date_published":"2015-03-01T00:00:00Z","publication_identifier":{"issn":["1445-4408"]},"publist_id":"5639"},{"volume":25,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:26Z","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>","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>","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>.","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.","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.","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."},"year":"2015","date_published":"2015-08-01T00:00:00Z","type":"journal_article","doi":"10.1109/TCSVT.2014.2379972","day":"01","abstract":[{"lang":"eng","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."}],"publist_id":"5638","page":"1295 - 1308","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"IEEE","_id":"1533","publication":"IEEE Transactions on Circuits and Systems for Video Technology","scopus_import":1,"author":[{"full_name":"Xia, Wei","last_name":"Xia","first_name":"Wei"},{"id":"492DACF8-F248-11E8-B48F-1D18A9856A87","full_name":"Domokos, Csaba","last_name":"Domokos","first_name":"Csaba"},{"full_name":"Xiong, Junjun","last_name":"Xiong","first_name":"Junjun"},{"first_name":"Loongfah","last_name":"Cheong","full_name":"Cheong, Loongfah"},{"first_name":"Shuicheng","last_name":"Yan","full_name":"Yan, Shuicheng"}],"issue":"8","oa_version":"None","publication_status":"published","date_created":"2018-12-11T11:52:34Z","department":[{"_id":"ChLa"}],"month":"08","title":"Segmentation over detection via optimal sparse reconstructions","intvolume":"        25"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2015-11-18T00:00:00Z","publist_id":"5637","oa":1,"file":[{"date_created":"2018-12-12T10:17:07Z","checksum":"3c06735fc7cd7e482ca830cbd26001bf","file_size":1852268,"date_updated":"2020-07-14T12:45:01Z","content_type":"application/pdf","file_name":"IST-2016-485-v1+1_ncomms9822.pdf","relation":"main_file","access_level":"open_access","file_id":"5259","creator":"system"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","has_accepted_license":"1","publication":"Nature Communications","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","article_number":"8822","month":"11","language":[{"iso":"eng"}],"year":"2015","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>.","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>","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>","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.","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>."},"date_updated":"2021-01-12T06:51:26Z","day":"18","doi":"10.1038/ncomms9822","abstract":[{"lang":"eng","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."}],"volume":6,"ddc":["570"],"scopus_import":1,"_id":"1534","author":[{"full_name":"Wang, Hongzhe","last_name":"Wang","first_name":"Hongzhe"},{"full_name":"Yang, Kezhen","first_name":"Kezhen","last_name":"Yang"},{"last_name":"Zou","first_name":"Junjie","full_name":"Zou, Junjie"},{"first_name":"Lingling","last_name":"Zhu","full_name":"Zhu, Lingling"},{"full_name":"Xie, Zidian","last_name":"Xie","first_name":"Zidian"},{"full_name":"Morita, Miyoterao","last_name":"Morita","first_name":"Miyoterao"},{"first_name":"Masao","last_name":"Tasaka","full_name":"Tasaka, Masao"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"},{"full_name":"Grotewold, Erich","last_name":"Grotewold","first_name":"Erich"},{"first_name":"Tom","last_name":"Beeckman","full_name":"Beeckman, Tom"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Sack, Fred","first_name":"Fred","last_name":"Sack"},{"full_name":"Le, Jie","first_name":"Jie","last_name":"Le"}],"date_created":"2018-12-11T11:52:34Z","department":[{"_id":"JiFr"}],"publication_status":"published","intvolume":"         6","title":"Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism","pubrep_id":"485","quality_controlled":"1","ec_funded":1,"file_date_updated":"2020-07-14T12:45:01Z","publisher":"Nature Publishing Group"},{"abstract":[{"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.","lang":"eng"}],"day":"01","doi":"10.2174/1874467208666150507105443","external_id":{"pmid":["25966692"]},"year":"2015","citation":{"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.","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>.","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>","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>","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.","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."},"date_updated":"2021-01-12T06:51:26Z","volume":8,"acknowledgement":"This work was supported by the Italian MIUR (PRIN 2010/2011 project 2010JFYFY2) and the University of Torino.","intvolume":"         8","title":"Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells","department":[{"_id":"PeJo"}],"date_created":"2018-12-11T11:52:35Z","article_processing_charge":"No","publication_status":"published","issue":"2","author":[{"id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","last_name":"Vandael","first_name":"David H"},{"full_name":"Marcantoni, Andrea","first_name":"Andrea","last_name":"Marcantoni"},{"first_name":"Emilio","last_name":"Carbone","full_name":"Carbone, Emilio"}],"scopus_import":1,"pmid":1,"_id":"1535","article_type":"original","publisher":"Bentham Science Publishers","quality_controlled":"1","page":"149 - 161","publist_id":"5636","oa":1,"type":"journal_article","date_published":"2015-10-01T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384372/","open_access":"1"}],"month":"10","oa_version":"Submitted Version","publication":"Current Molecular Pharmacology","language":[{"iso":"eng"}]},{"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.","volume":25,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:51:27Z","year":"2015","citation":{"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.","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.","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>.","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>.","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.","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>","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>"},"date_published":"2015-02-12T00:00:00Z","type":"journal_article","doi":"10.1016/j.cub.2015.01.015","day":"12","abstract":[{"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.","lang":"eng"}],"publist_id":"5635","page":"647 - 655","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Cell Press","_id":"1536","publication":"Current Biology","scopus_import":1,"author":[{"full_name":"Sasse, Joëlle","last_name":"Sasse","first_name":"Joëlle"},{"first_name":"Sibu","last_name":"Simon","orcid":"0000-0002-1998-6741","full_name":"Simon, Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gübeli","first_name":"Christian","full_name":"Gübeli, Christian"},{"first_name":"Guowei","last_name":"Liu","full_name":"Liu, Guowei"},{"first_name":"Xi","last_name":"Cheng","full_name":"Cheng, Xi"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bouwmeester, Harro","last_name":"Bouwmeester","first_name":"Harro"},{"last_name":"Martinoia","first_name":"Enrico","full_name":"Martinoia, Enrico"},{"last_name":"Borghi","first_name":"Lorenzo","full_name":"Borghi, Lorenzo"}],"issue":"5","publication_status":"published","oa_version":"None","department":[{"_id":"JiFr"}],"date_created":"2018-12-11T11:52:35Z","title":"Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport","month":"02","intvolume":"        25"},{"file":[{"date_created":"2018-12-12T10:13:21Z","file_size":4362653,"checksum":"228d3edf40627d897b3875088a0ac51f","date_updated":"2020-07-14T12:45:01Z","content_type":"application/pdf","file_name":"IST-2016-484-v1+1_1-s2.0-S0092867415000094-main.pdf","relation":"main_file","access_level":"open_access","file_id":"5003","creator":"system"}],"status":"public","related_material":{"record":[{"status":"public","id":"961","relation":"dissertation_contains"}]},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"publist_id":"5634","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2015-02-12T00:00:00Z","language":[{"iso":"eng"}],"project":[{"grant_number":"T 560-B17","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","call_identifier":"FWF","_id":"2529486C-B435-11E9-9278-68D0E5697425"},{"name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","grant_number":"I 812-B12","call_identifier":"FWF","_id":"2527D5CC-B435-11E9-9278-68D0E5697425"}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Published Version","month":"02","has_accepted_license":"1","publication":"Cell","acknowledgement":"We would like to thank R. Hausschild and E. Papusheva for technical assistance and the service facilities at the IST Austria for continuous support. The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel and E. Paluch for exchanging unpublished data. ","volume":160,"ddc":["570"],"day":"12","doi":"10.1016/j.cell.2015.01.008","abstract":[{"lang":"eng","text":"3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype."}],"year":"2015","citation":{"chicago":"Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” <i>Cell</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">https://doi.org/10.1016/j.cell.2015.01.008</a>.","ieee":"V. Ruprecht <i>et al.</i>, “Cortical contractility triggers a stochastic switch to fast amoeboid cell motility,” <i>Cell</i>, vol. 160, no. 4. Cell Press, pp. 673–685, 2015.","apa":"Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K., … Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">https://doi.org/10.1016/j.cell.2015.01.008</a>","ama":"Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. <i>Cell</i>. 2015;160(4):673-685. doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">10.1016/j.cell.2015.01.008</a>","ista":"Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V, Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685.","mla":"Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” <i>Cell</i>, vol. 160, no. 4, Cell Press, 2015, pp. 673–85, doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">10.1016/j.cell.2015.01.008</a>.","short":"V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V. Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160 (2015) 673–685."},"date_updated":"2023-09-07T12:05:08Z","publisher":"Cell Press","quality_controlled":"1","page":"673 - 685","file_date_updated":"2020-07-14T12:45:01Z","date_created":"2018-12-11T11:52:35Z","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"publication_status":"published","intvolume":"       160","title":"Cortical contractility triggers a stochastic switch to fast amoeboid cell motility","pubrep_id":"484","scopus_import":1,"_id":"1537","issue":"4","author":[{"id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","last_name":"Ruprecht","first_name":"Verena"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217","last_name":"Wieser","first_name":"Stefan"},{"first_name":"Andrew","last_name":"Callan Jones","full_name":"Callan Jones, Andrew"},{"orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","first_name":"Michael","last_name":"Smutny","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi","first_name":"Hitoshi","last_name":"Morita"},{"id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","last_name":"Sako","first_name":"Keisuke","full_name":"Sako, Keisuke","orcid":"0000-0002-6453-8075"},{"orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa","first_name":"Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Monika","last_name":"Ritsch Marte","full_name":"Ritsch Marte, Monika"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","first_name":"Michael K"},{"last_name":"Voituriez","first_name":"Raphaël","full_name":"Voituriez, Raphaël"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}]},{"day":"30","doi":"10.1073/pnas.1423947112","abstract":[{"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.","lang":"eng"}],"year":"2015","citation":{"short":"J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153.","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>.","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.","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>","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>","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>."},"date_updated":"2021-01-12T06:51:27Z","external_id":{"pmid":["26085136"]},"volume":112,"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). ","date_created":"2018-12-11T11:52:36Z","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"publication_status":"published","intvolume":"       112","title":"Iterative experiment design guides the characterization of a light-inducible gene expression circuit","scopus_import":1,"_id":"1538","pmid":1,"issue":"26","author":[{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","last_name":"Ruess","first_name":"Jakob","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282"},{"full_name":"Parise, Francesca","first_name":"Francesca","last_name":"Parise"},{"last_name":"Milias Argeitis","first_name":"Andreas","full_name":"Milias Argeitis, Andreas"},{"first_name":"Mustafa","last_name":"Khammash","full_name":"Khammash, Mustafa"},{"full_name":"Lygeros, John","last_name":"Lygeros","first_name":"John"}],"publisher":"National Academy of Sciences","ec_funded":1,"quality_controlled":"1","page":"8148 - 8153","publist_id":"5633","oa":1,"type":"journal_article","date_published":"2015-06-30T00:00:00Z","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa_version":"Submitted Version","month":"06","publication":"PNAS","language":[{"iso":"eng"}]},{"file":[{"creator":"system","file_id":"4641","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-593-v1+1_Minimal_moment_equations.pdf","date_updated":"2020-07-14T12:45:01Z","checksum":"838657118ae286463a2b7737319f35ce","file_size":605355,"date_created":"2018-12-12T10:07:43Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publist_id":"5632","oa":1,"date_published":"2015-12-22T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"month":"12","article_number":"244103","publication":"Journal of Chemical Physics","has_accepted_license":"1","volume":143,"ddc":["000"],"doi":"10.1063/1.4937937","day":"22","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"}],"date_updated":"2021-01-12T06:51:28Z","citation":{"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.","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>.","short":"J. Ruess, Journal of Chemical Physics 143 (2015).","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>.","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>","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>"},"year":"2015","publisher":"American Institute of Physics","ec_funded":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:01Z","publication_status":"published","date_created":"2018-12-11T11:52:36Z","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"title":"Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space","pubrep_id":"593","intvolume":"       143","_id":"1539","scopus_import":1,"author":[{"id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob","orcid":"0000-0003-1615-3282","last_name":"Ruess","first_name":"Jakob"}],"issue":"24"},{"date_published":"2015-05-05T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T06:51:29Z","citation":{"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>","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>","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>.","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.","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."},"year":"2015","abstract":[{"lang":"eng","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."}],"publist_id":"5631","doi":"10.1093/jxb/erv256","day":"05","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","volume":66,"author":[{"full_name":"Robert, Hélène","last_name":"Robert","first_name":"Hélène"},{"last_name":"Crhák Khaitová","first_name":"Lucie","full_name":"Crhák Khaitová, Lucie"},{"full_name":"Mroue, Souad","last_name":"Mroue","first_name":"Souad"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"}],"issue":"16","_id":"1540","publication":"Journal of Experimental Botany","scopus_import":1,"month":"05","title":"The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis","intvolume":"        66","oa_version":"None","publication_status":"published","department":[{"_id":"EvBe"}],"date_created":"2018-12-11T11:52:36Z","language":[{"iso":"eng"}],"page":"5029 - 5042","quality_controlled":"1","publisher":"Oxford University Press"},{"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).","volume":9434,"day":"28","doi":"10.1007/978-3-319-26287-1_1","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."}],"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>","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>.","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."},"year":"2015","date_updated":"2020-08-11T10:09:17Z","publisher":"Springer","series_title":"Lecture Notes in Computer Science","ec_funded":1,"quality_controlled":"1","page":"3 - 18","date_created":"2018-12-11T11:52:37Z","department":[{"_id":"ToHe"}],"publication_status":"published","intvolume":"      9434","alternative_title":["LNCS"],"title":"XSpeed: Accelerating reachability analysis on multi-core processors","scopus_import":1,"_id":"1541","author":[{"full_name":"Ray, Rajarshi","last_name":"Ray","first_name":"Rajarshi"},{"full_name":"Gurung, Amit","first_name":"Amit","last_name":"Gurung"},{"first_name":"Binayak","last_name":"Das","full_name":"Das, Binayak"},{"last_name":"Bartocci","first_name":"Ezio","full_name":"Bartocci, Ezio"},{"id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","first_name":"Sergiy","full_name":"Bogomolov, Sergiy","orcid":"0000-0002-0686-0365"},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publist_id":"5630","type":"conference","date_published":"2015-11-28T00:00:00Z","conference":{"name":"HVC: Haifa Verification Conference","start_date":"2015-11-17","end_date":"2015-11-19","location":"Haifa, Israel"},"language":[{"iso":"eng"}],"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"oa_version":"None","month":"11"},{"ddc":["570"],"volume":383,"abstract":[{"lang":"eng","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. "}],"doi":"10.1016/j.jtbi.2015.07.011","day":"21","date_updated":"2021-01-12T06:51:29Z","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>.","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>","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>","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.","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>."},"year":"2015","publisher":"Elsevier","file_date_updated":"2020-07-14T12:45:01Z","page":"28 - 43","ec_funded":1,"quality_controlled":"1","title":"Toward a unifying framework for evolutionary processes","pubrep_id":"483","intvolume":"       383","publication_status":"published","date_created":"2018-12-11T11:52:37Z","department":[{"_id":"NiBa"},{"_id":"CaGu"}],"author":[{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953","last_name":"Paixao","first_name":"Tiago"},{"full_name":"Badkobeh, Golnaz","first_name":"Golnaz","last_name":"Badkobeh"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Çörüş, Doğan","last_name":"Çörüş","first_name":"Doğan"},{"first_name":"Duccuong","last_name":"Dang","full_name":"Dang, Duccuong"},{"last_name":"Friedrich","first_name":"Tobias","full_name":"Friedrich, Tobias"},{"first_name":"Per","last_name":"Lehre","full_name":"Lehre, Per"},{"first_name":"Dirk","last_name":"Sudholt","full_name":"Sudholt, Dirk"},{"full_name":"Sutton, Andrew","last_name":"Sutton","first_name":"Andrew"},{"full_name":"Trubenova, Barbora","orcid":"0000-0002-6873-2967","last_name":"Trubenova","first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87"}],"_id":"1542","scopus_import":1,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","relation":"main_file","creator":"system","file_id":"5244","checksum":"33b60ecfea60764756a9ee9df5eb65ca","file_size":595307,"date_created":"2018-12-12T10:16:53Z","file_name":"IST-2016-483-v1+1_1-s2.0-S0022519315003409-main.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:45:01Z"}],"publist_id":"5629","oa":1,"date_published":"2015-10-21T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"language":[{"iso":"eng"}],"month":"10","oa_version":"Published Version","project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"}],"publication":" Journal of Theoretical Biology","has_accepted_license":"1"},{"date_updated":"2021-01-12T06:51:30Z","year":"2015","citation":{"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>.","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.","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>","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>","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.","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>.","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."},"date_published":"2015-12-01T00:00:00Z","type":"journal_article","doi":"10.1104/pp.15.00769","day":"01","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"}],"publist_id":"5628","volume":169,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication":"Plant Physiology","_id":"1543","scopus_import":1,"author":[{"full_name":"Olvera Carrillo, Yadira","last_name":"Olvera Carrillo","first_name":"Yadira"},{"full_name":"Van Bel, Michiel","last_name":"Van Bel","first_name":"Michiel"},{"first_name":"Tom","last_name":"Van Hautegem","full_name":"Van Hautegem, Tom"},{"first_name":"Matyas","last_name":"Fendrych","orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Huysmans, Marlies","first_name":"Marlies","last_name":"Huysmans"},{"full_name":"Šimášková, Mária","last_name":"Šimášková","first_name":"Mária"},{"first_name":"Matthias","last_name":"Van Durme","full_name":"Van Durme, Matthias"},{"full_name":"Buscaill, Pierre","last_name":"Buscaill","first_name":"Pierre"},{"last_name":"Rivas","first_name":"Susana","full_name":"Rivas, Susana"},{"full_name":"Coll, Núria","last_name":"Coll","first_name":"Núria"},{"last_name":"Coppens","first_name":"Frederik","full_name":"Coppens, Frederik"},{"full_name":"Maere, Steven","last_name":"Maere","first_name":"Steven"},{"last_name":"Nowack","first_name":"Moritz","full_name":"Nowack, Moritz"}],"issue":"4","oa_version":"None","publication_status":"published","department":[{"_id":"JiFr"}],"date_created":"2018-12-11T11:52:38Z","month":"12","title":"A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants","intvolume":"       169","page":"2684 - 2699","language":[{"iso":"eng"}],"publisher":"American Society of Plant Biologists"},{"doi":"10.1016/bs.mcb.2015.01.007","day":"08","abstract":[{"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.","lang":"eng"}],"date_updated":"2021-01-12T06:51:30Z","citation":{"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.","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>.","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.","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>","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>","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."},"year":"2015","external_id":{"pmid":["25997350"]},"volume":128,"publication_status":"published","date_created":"2018-12-11T11:52:38Z","department":[{"_id":"MaLo"}],"title":"Using supported bilayers to study the spatiotemporal organization of membrane-bound proteins","intvolume":"       128","pmid":1,"_id":"1544","scopus_import":1,"author":[{"full_name":"Nguyen, Phuong","last_name":"Nguyen","first_name":"Phuong"},{"last_name":"Field","first_name":"Christine","full_name":"Field, Christine"},{"full_name":"Groen, Aaron","first_name":"Aaron","last_name":"Groen"},{"full_name":"Mitchison, Timothy","first_name":"Timothy","last_name":"Mitchison"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"}],"publisher":"Academic Press","page":"223 - 241","quality_controlled":"1","oa":1,"publist_id":"5627","date_published":"2015-04-08T00:00:00Z","type":"book_chapter","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578691/"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa_version":"Submitted Version","month":"04","publication":"Building a Cell from its Components Parts","language":[{"iso":"eng"}]},{"type":"journal_article","date_published":"2015-01-07T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publist_id":"5625","oa":1,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"content_type":"application/pdf","file_name":"IST-2016-482-v1+1_1-s2.0-S0896627314010472-main.pdf","date_updated":"2020-07-14T12:45:01Z","file_size":3080111,"checksum":"725f4d5be2dbb44b283ce722645ef37d","date_created":"2018-12-12T10:15:47Z","creator":"system","file_id":"5170","access_level":"open_access","relation":"main_file"}],"has_accepted_license":"1","publication":"Neuron","month":"01","oa_version":"Published Version","language":[{"iso":"eng"}],"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.","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>","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>","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.","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>.","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."},"year":"2015","date_updated":"2021-01-12T06:51:31Z","abstract":[{"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.","lang":"eng"}],"day":"07","doi":"10.1016/j.neuron.2014.11.019","ddc":["570"],"volume":85,"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.","issue":"1","author":[{"full_name":"Nakamura, Yukihiro","last_name":"Nakamura","first_name":"Yukihiro"},{"id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Harumi","last_name":"Harada","orcid":"0000-0001-7429-7896","full_name":"Harada, Harumi"},{"first_name":"Naomi","last_name":"Kamasawa","full_name":"Kamasawa, Naomi"},{"full_name":"Matsui, Ko","first_name":"Ko","last_name":"Matsui"},{"first_name":"Jason","last_name":"Rothman","full_name":"Rothman, Jason"},{"last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Silver, R Angus","first_name":"R Angus","last_name":"Silver"},{"last_name":"Digregorio","first_name":"David","full_name":"Digregorio, David"},{"last_name":"Takahashi","first_name":"Tomoyuki","full_name":"Takahashi, Tomoyuki"}],"scopus_import":1,"_id":"1546","intvolume":"        85","title":"Nanoscale distribution of presynaptic Ca2+ channels and its impact on vesicular release during development","pubrep_id":"482","department":[{"_id":"RySh"}],"date_created":"2018-12-11T11:52:39Z","publication_status":"published","file_date_updated":"2020-07-14T12:45:01Z","quality_controlled":"1","page":"145 - 158","publisher":"Elsevier"},{"month":"05","oa_version":"Preprint","publication":"Bulletin of the Korean Mathematical Society","language":[{"iso":"eng"}],"publist_id":"5624","oa":1,"publication_identifier":{"eissn":["2234-3016"]},"date_published":"2015-05-31T00:00:00Z","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/0901.3015"}],"title":"Resolution of unmixed bipartite graphs","intvolume":"        52","publication_status":"published","department":[{"_id":"CaUh"}],"date_created":"2018-12-11T11:52:39Z","author":[{"id":"2C29581E-F248-11E8-B48F-1D18A9856A87","full_name":"Mohammadi, Fatemeh","last_name":"Mohammadi","first_name":"Fatemeh"},{"first_name":"Somayeh","last_name":"Moradi","full_name":"Moradi, Somayeh"}],"issue":"3","_id":"1547","scopus_import":1,"publisher":"Korean Mathematical Society","page":"977 - 986","quality_controlled":"1","abstract":[{"lang":"eng","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."}],"doi":"10.4134/BKMS.2015.52.3.977","day":"31","date_updated":"2021-01-12T06:51:31Z","year":"2015","citation":{"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>.","short":"F. Mohammadi, S. Moradi, Bulletin of the Korean Mathematical Society 52 (2015) 977–986.","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>","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>","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>."},"volume":52},{"volume":81,"year":"2015","citation":{"chicago":"Milutinovic, Barbara, Christina Höfling, Momir Futo, Jörn Scharsack, and Joachim Kurtz. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” <i>Applied and Environmental Microbiology</i>. American Society for Microbiology, 2015. <a href=\"https://doi.org/10.1128/AEM.02051-15\">https://doi.org/10.1128/AEM.02051-15</a>.","ieee":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, and J. Kurtz, “Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination,” <i>Applied and Environmental Microbiology</i>, vol. 81, no. 23. American Society for Microbiology, pp. 8135–8144, 2015.","apa":"Milutinovic, B., Höfling, C., Futo, M., Scharsack, J., &#38; Kurtz, J. (2015). Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. <i>Applied and Environmental Microbiology</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/AEM.02051-15\">https://doi.org/10.1128/AEM.02051-15</a>","ama":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. <i>Applied and Environmental Microbiology</i>. 2015;81(23):8135-8144. doi:<a href=\"https://doi.org/10.1128/AEM.02051-15\">10.1128/AEM.02051-15</a>","ista":"Milutinovic B, Höfling C, Futo M, Scharsack J, Kurtz J. 2015. Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination. Applied and Environmental Microbiology. 81(23), 8135–8144.","short":"B. Milutinovic, C. Höfling, M. Futo, J. Scharsack, J. Kurtz, Applied and Environmental Microbiology 81 (2015) 8135–8144.","mla":"Milutinovic, Barbara, et al. “Infection of Tribolium Castaneum with Bacillus Thuringiensis: Quantification of Bacterial Replication within Cadavers, Transmission via Cannibalism, and Inhibition of Spore Germination.” <i>Applied and Environmental Microbiology</i>, vol. 81, no. 23, American Society for Microbiology, 2015, pp. 8135–44, doi:<a href=\"https://doi.org/10.1128/AEM.02051-15\">10.1128/AEM.02051-15</a>."},"date_updated":"2021-01-12T06:51:31Z","external_id":{"pmid":["26386058"]},"day":"01","doi":"10.1128/AEM.02051-15","abstract":[{"text":"Reproduction within a host and transmission to the next host are crucial for the virulence and fitness of pathogens. Nevertheless, basic knowledge about such parameters is often missing from the literature, even for well-studied bacteria, such as Bacillus thuringiensis, an endospore-forming insect pathogen, which infects its hosts via the oral route. To characterize bacterial replication success, we made use of an experimental oral infection system for the red flour beetle Tribolium castaneum and developed a flow cytometric assay for the quantification of both spore ingestion by the individual beetle larvae and the resulting spore load after bacterial replication and resporulation within cadavers. On average, spore numbers increased 460-fold, showing that Bacillus thuringiensis grows and replicates successfully in insect cadavers. By inoculating cadaver-derived spores and spores from bacterial stock cultures into nutrient medium, we next investigated outgrowth characteristics of vegetative cells and found that cadaver- derived bacteria showed reduced growth compared to bacteria from the stock cultures. Interestingly, this reduced growth was a consequence of inhibited spore germination, probably originating from the host and resulting in reduced host mortality in subsequent infections by cadaver-derived spores. Nevertheless, we further showed that Bacillus thuringiensis transmission was possible via larval cannibalism when no other food was offered. These results contribute to our understanding of the ecology of Bacillus thuringiensis as an insect pathogen.","lang":"eng"}],"quality_controlled":"1","page":"8135 - 8144","publisher":"American Society for Microbiology","scopus_import":1,"pmid":1,"_id":"1548","issue":"23","author":[{"id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","last_name":"Milutinovic","orcid":"0000-0002-8214-4758","full_name":"Milutinovic, Barbara"},{"last_name":"Höfling","first_name":"Christina","full_name":"Höfling, Christina"},{"full_name":"Futo, Momir","last_name":"Futo","first_name":"Momir"},{"last_name":"Scharsack","first_name":"Jörn","full_name":"Scharsack, Jörn"},{"full_name":"Kurtz, Joachim","first_name":"Joachim","last_name":"Kurtz"}],"date_created":"2018-12-11T11:52:39Z","department":[{"_id":"SyCr"}],"publication_status":"published","intvolume":"        81","title":"Infection of Tribolium castaneum with Bacillus thuringiensis: Quantification of bacterial replication within cadavers, transmission via cannibalism, and inhibition of spore germination","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651099/"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","type":"journal_article","date_published":"2015-12-01T00:00:00Z","publist_id":"5623","oa":1,"language":[{"iso":"eng"}],"publication":"Applied and Environmental Microbiology","oa_version":"Submitted Version","month":"12"},{"abstract":[{"lang":"eng","text":"Nature has incorporated small photochromic molecules, colloquially termed 'photoswitches', in photoreceptor proteins to sense optical cues in photo-taxis and vision. While Nature's ability to employ light-responsive functionalities has long been recognized, it was not until recently that scientists designed, synthesized and applied synthetic photochromes to manipulate many of which open rapidly and locally in their native cell types, biological processes with the temporal and spatial resolution of light. Ion channels in particular have come to the forefront of proteins that can be put under the designer control of synthetic photochromes. Photochromic ion channel controllers are comprised of three classes, photochromic soluble ligands (PCLs), photochromic tethered ligands (PTLs) and photochromic crosslinkers (PXs), and in each class ion channel functionality is controlled through reversible changes in photochrome structure. By acting as light-dependent ion channel agonists, antagonist or modulators, photochromic controllers effectively converted a wide range of ion channels, including voltage-gated ion channels, 'leak channels', tri-, tetra- and pentameric ligand-gated ion channels, and temperaturesensitive ion channels, into man-made photoreceptors. Control by photochromes can be reversible, unlike in the case of 'caged' compounds, and non-invasive with high spatial precision, unlike pharmacology and electrical manipulation. Here, we introduce design principles of emerging photochromic molecules that act on ion channels and discuss the impact that these molecules are beginning to have on ion channel biophysics and neuronal physiology."}],"doi":"10.1007/978-1-4939-2845-3_6","day":"18","date_updated":"2021-01-12T06:51:32Z","citation":{"chicago":"Mckenzie, Catherine, Inmaculada Sanchez-Romero, and Harald L Janovjak. “Flipping the Photoswitch: Ion Channels under Light Control.” In <i>Novel Chemical Tools to Study Ion Channel Biology</i>, 869:101–17. Advances in Experimental Medicine and Biology. Springer, 2015. <a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">https://doi.org/10.1007/978-1-4939-2845-3_6</a>.","ieee":"C. Mckenzie, I. Sanchez-Romero, and H. L. Janovjak, “Flipping the photoswitch: Ion channels under light control,” in <i>Novel chemical tools to study ion channel biology</i>, vol. 869, Springer, 2015, pp. 101–117.","apa":"Mckenzie, C., Sanchez-Romero, I., &#38; Janovjak, H. L. (2015). Flipping the photoswitch: Ion channels under light control. In <i>Novel chemical tools to study ion channel biology</i> (Vol. 869, pp. 101–117). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">https://doi.org/10.1007/978-1-4939-2845-3_6</a>","ama":"Mckenzie C, Sanchez-Romero I, Janovjak HL. Flipping the photoswitch: Ion channels under light control. In: <i>Novel Chemical Tools to Study Ion Channel Biology</i>. Vol 869. Advances in Experimental Medicine and Biology. Springer; 2015:101-117. doi:<a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">10.1007/978-1-4939-2845-3_6</a>","ista":"Mckenzie C, Sanchez-Romero I, Janovjak HL. 2015.Flipping the photoswitch: Ion channels under light control. In: Novel chemical tools to study ion channel biology. vol. 869, 101–117.","mla":"Mckenzie, Catherine, et al. “Flipping the Photoswitch: Ion Channels under Light Control.” <i>Novel Chemical Tools to Study Ion Channel Biology</i>, vol. 869, Springer, 2015, pp. 101–17, doi:<a href=\"https://doi.org/10.1007/978-1-4939-2845-3_6\">10.1007/978-1-4939-2845-3_6</a>.","short":"C. Mckenzie, I. Sanchez-Romero, H.L. Janovjak, in:, Novel Chemical Tools to Study Ion Channel Biology, Springer, 2015, pp. 101–117."},"year":"2015","ddc":["571","576"],"volume":869,"title":"Flipping the photoswitch: Ion channels under light control","pubrep_id":"839","intvolume":"       869","publication_status":"published","department":[{"_id":"HaJa"}],"date_created":"2018-12-11T11:52:39Z","author":[{"id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","full_name":"Mckenzie, Catherine","first_name":"Catherine","last_name":"Mckenzie"},{"full_name":"Sanchez Romero, Inmaculada","last_name":"Sanchez Romero","first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"_id":"1549","scopus_import":1,"publisher":"Springer","file_date_updated":"2020-07-14T12:45:01Z","page":"101 - 117","series_title":"Advances in Experimental Medicine and Biology","quality_controlled":"1","publist_id":"5622","oa":1,"publication_identifier":{"isbn":["978-1-4939-2844-6"]},"date_published":"2015-09-18T00:00:00Z","type":"book_chapter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"relation":"main_file","access_level":"open_access","creator":"system","file_id":"4854","file_size":1919655,"checksum":"bd1bfdf2423a0c3b6e7cabfa8b44bc0f","date_created":"2018-12-12T10:11:02Z","content_type":"application/pdf","file_name":"IST-2017-839-v1+1_mckenzie.pdf","date_updated":"2020-07-14T12:45:01Z"}],"month":"09","oa_version":"Submitted Version","publication":"Novel chemical tools to study ion channel biology","has_accepted_license":"1","language":[{"iso":"eng"}]},{"publication":"Neuron","month":"09","oa_version":"Submitted Version","language":[{"iso":"eng"}],"date_published":"2015-09-02T00:00:00Z","type":"journal_article","oa":1,"publist_id":"5621","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560602/"}],"author":[{"full_name":"Mayer, Christian","last_name":"Mayer","first_name":"Christian"},{"first_name":"Xavier","last_name":"Jaglin","full_name":"Jaglin, Xavier"},{"first_name":"Lucy","last_name":"Cobbs","full_name":"Cobbs, Lucy"},{"full_name":"Bandler, Rachel","first_name":"Rachel","last_name":"Bandler"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","last_name":"Streicher","full_name":"Streicher, Carmen"},{"full_name":"Cepko, Constance","first_name":"Constance","last_name":"Cepko"},{"first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fishell","first_name":"Gord","full_name":"Fishell, Gord"}],"issue":"5","_id":"1550","pmid":1,"scopus_import":1,"title":"Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries","intvolume":"        87","publication_status":"published","department":[{"_id":"SiHi"}],"date_created":"2018-12-11T11:52:40Z","page":"989 - 998","quality_controlled":"1","publisher":"Elsevier","external_id":{"pmid":["26299473"]},"date_updated":"2021-01-12T06:51:32Z","year":"2015","citation":{"apa":"Mayer, C., Jaglin, X., Cobbs, L., Bandler, R., Streicher, C., Cepko, C., … Fishell, G. (2015). Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2015.07.011\">https://doi.org/10.1016/j.neuron.2015.07.011</a>","ama":"Mayer C, Jaglin X, Cobbs L, et al. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. <i>Neuron</i>. 2015;87(5):989-998. doi:<a href=\"https://doi.org/10.1016/j.neuron.2015.07.011\">10.1016/j.neuron.2015.07.011</a>","chicago":"Mayer, Christian, Xavier Jaglin, Lucy Cobbs, Rachel Bandler, Carmen Streicher, Constance Cepko, Simon Hippenmeyer, and Gord Fishell. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” <i>Neuron</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.neuron.2015.07.011\">https://doi.org/10.1016/j.neuron.2015.07.011</a>.","ieee":"C. Mayer <i>et al.</i>, “Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries,” <i>Neuron</i>, vol. 87, no. 5. Elsevier, pp. 989–998, 2015.","mla":"Mayer, Christian, et al. “Clonally Related Forebrain Interneurons Disperse Broadly across Both Functional Areas and Structural Boundaries.” <i>Neuron</i>, vol. 87, no. 5, Elsevier, 2015, pp. 989–98, doi:<a href=\"https://doi.org/10.1016/j.neuron.2015.07.011\">10.1016/j.neuron.2015.07.011</a>.","short":"C. Mayer, X. Jaglin, L. Cobbs, R. Bandler, C. Streicher, C. Cepko, S. Hippenmeyer, G. Fishell, Neuron 87 (2015) 989–998.","ista":"Mayer C, Jaglin X, Cobbs L, Bandler R, Streicher C, Cepko C, Hippenmeyer S, Fishell G. 2015. Clonally related forebrain interneurons disperse broadly across both functional areas and structural boundaries. Neuron. 87(5), 989–998."},"abstract":[{"lang":"eng","text":"The medial ganglionic eminence (MGE) gives rise to the majority of mouse forebrain interneurons. Here, we examine the lineage relationship among MGE-derived interneurons using a replication-defective retroviral library containing a highly diverse set of DNA barcodes. Recovering the barcodes from the mature progeny of infected progenitor cells enabled us to unambiguously determine their respective lineal relationship. We found that clonal dispersion occurs across large areas of the brain and is not restricted by anatomical divisions. As such, sibling interneurons can populate the cortex, hippocampus striatum, and globus pallidus. The majority of interneurons appeared to be generated from asymmetric divisions of MGE progenitor cells, followed by symmetric divisions within the subventricular zone. Altogether, our findings uncover that lineage relationships do not appear to determine interneuron allocation to particular regions. As such, it is likely that clonally related interneurons have considerable flexibility as to the particular forebrain circuits to which they can contribute."}],"doi":"10.1016/j.neuron.2015.07.011","day":"02","volume":87,"acknowledgement":"Research in the G.F. laboratory is supported by NIH (NS 081297, MH095147, and P01NS074972) and the Simons Foundation. Research in the S.H. laboratory is supported by the European Union (FP7-CIG618444). C.M. is supported by EMBO ALTF (1295-2012). X.H.J. is supported by EMBO (ALTF 303-2010) and HFSP (LT000078/2011-L).\r\n\r\n"},{"language":[{"iso":"eng"}],"month":"06","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"oa_version":"Published Version","has_accepted_license":"1","publication":"PLoS Biology","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"date_updated":"2020-07-14T12:45:02Z","content_type":"application/pdf","file_name":"IST-2016-481-v1+1_journal.pbio.1002169.pdf","date_created":"2018-12-12T10:14:13Z","checksum":"30dee7a2c11ed09f2f5634655c0146f8","file_size":3468956,"file_id":"5063","creator":"system","relation":"main_file","access_level":"open_access"}],"oa":1,"publist_id":"5620","type":"journal_article","date_published":"2015-06-04T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"Public Library of Science","file_date_updated":"2020-07-14T12:45:02Z","quality_controlled":"1","ec_funded":1,"page":"1 - 30","intvolume":"        13","title":"Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes","pubrep_id":"481","date_created":"2018-12-11T11:52:40Z","department":[{"_id":"SyCr"}],"publication_status":"published","issue":"6","author":[{"id":"349A6E66-F248-11E8-B48F-1D18A9856A87","full_name":"El Masri, Leila","first_name":"Leila","last_name":"El Masri"},{"full_name":"Branca, Antoine","last_name":"Branca","first_name":"Antoine"},{"last_name":"Sheppard","first_name":"Anna","full_name":"Sheppard, Anna"},{"full_name":"Papkou, Andrei","last_name":"Papkou","first_name":"Andrei"},{"first_name":"David","last_name":"Laehnemann","full_name":"Laehnemann, David"},{"first_name":"Patrick","last_name":"Guenther","full_name":"Guenther, Patrick"},{"full_name":"Prahl, Swantje","first_name":"Swantje","last_name":"Prahl"},{"full_name":"Saebelfeld, Manja","last_name":"Saebelfeld","first_name":"Manja"},{"full_name":"Hollensteiner, Jacqueline","last_name":"Hollensteiner","first_name":"Jacqueline"},{"full_name":"Liesegang, Heiko","first_name":"Heiko","last_name":"Liesegang"},{"last_name":"Brzuszkiewicz","first_name":"Elzbieta","full_name":"Brzuszkiewicz, Elzbieta"},{"first_name":"Rolf","last_name":"Daniel","full_name":"Daniel, Rolf"},{"last_name":"Michiels","first_name":"Nico","full_name":"Michiels, Nico"},{"last_name":"Schulte","first_name":"Rebecca","full_name":"Schulte, Rebecca"},{"first_name":"Joachim","last_name":"Kurtz","full_name":"Kurtz, Joachim"},{"full_name":"Rosenstiel, Philip","first_name":"Philip","last_name":"Rosenstiel"},{"full_name":"Telschow, Arndt","first_name":"Arndt","last_name":"Telschow"},{"full_name":"Bornberg Bauer, Erich","last_name":"Bornberg Bauer","first_name":"Erich"},{"last_name":"Schulenburg","first_name":"Hinrich","full_name":"Schulenburg, Hinrich"}],"scopus_import":1,"_id":"1551","ddc":["570"],"volume":13,"acknowledgement":"We are very grateful for funding from the German Science Foundation (DFG) to HS (SCHU 1415/8, SCHU 1415/9), PR (RO 2994/3), EBB (BO 2544/7), HL (LI 1690/2), AT (TE 976/2), RDS (SCHU 2522/1), JK (KU 1929/4); from the Kiel Excellence Cluster Inflammation at Interfaces to HS and PR; and from the ISTFELLOW program (Co-fund Marie Curie Actions of the European Commission) to LM.","abstract":[{"lang":"eng","text":"Reciprocal coevolution between host and pathogen is widely seen as a major driver of evolution and biological innovation. Yet, to date, the underlying genetic mechanisms and associated trait functions that are unique to rapid coevolutionary change are generally unknown. We here combined experimental evolution of the bacterial biocontrol agent Bacillus thuringiensis and its nematode host Caenorhabditis elegans with large-scale phenotyping, whole genome analysis, and functional genetics to demonstrate the selective benefit of pathogen virulence and the underlying toxin genes during the adaptation process. We show that: (i) high virulence was specifically favoured during pathogen–host coevolution rather than pathogen one-sided adaptation to a nonchanging host or to an environment without host; (ii) the pathogen genotype BT-679 with known nematocidal toxin genes and high virulence specifically swept to fixation in all of the independent replicate populations under coevolution but only some under one-sided adaptation; (iii) high virulence in the BT-679-dominated populations correlated with elevated copy numbers of the plasmid containing the nematocidal toxin genes; (iv) loss of virulence in a toxin-plasmid lacking BT-679 isolate was reconstituted by genetic reintroduction or external addition of the toxins.We conclude that sustained coevolution is distinct from unidirectional selection in shaping the pathogen's genome and life history characteristics. To our knowledge, this study is the first to characterize the pathogen genes involved in coevolutionary adaptation in an animal host–pathogen interaction system."}],"day":"04","doi":"10.1371/journal.pbio.1002169","year":"2015","citation":{"chicago":"El Masri, Leila, Antoine Branca, Anna Sheppard, Andrei Papkou, David Laehnemann, Patrick Guenther, Swantje Prahl, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” <i>PLoS Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002169\">https://doi.org/10.1371/journal.pbio.1002169</a>.","ieee":"L. El Masri <i>et al.</i>, “Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes,” <i>PLoS Biology</i>, vol. 13, no. 6. Public Library of Science, pp. 1–30, 2015.","ama":"El Masri L, Branca A, Sheppard A, et al. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. <i>PLoS Biology</i>. 2015;13(6):1-30. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002169\">10.1371/journal.pbio.1002169</a>","apa":"El Masri, L., Branca, A., Sheppard, A., Papkou, A., Laehnemann, D., Guenther, P., … Schulenburg, H. (2015). Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002169\">https://doi.org/10.1371/journal.pbio.1002169</a>","ista":"El Masri L, Branca A, Sheppard A, Papkou A, Laehnemann D, Guenther P, Prahl S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels N, Schulte R, Kurtz J, Rosenstiel P, Telschow A, Bornberg Bauer E, Schulenburg H. 2015. Host–pathogen coevolution: The selective advantage of Bacillus thuringiensis virulence and its cry toxin genes. PLoS Biology. 13(6), 1–30.","mla":"El Masri, Leila, et al. “Host–Pathogen Coevolution: The Selective Advantage of Bacillus Thuringiensis Virulence and Its Cry Toxin Genes.” <i>PLoS Biology</i>, vol. 13, no. 6, Public Library of Science, 2015, pp. 1–30, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002169\">10.1371/journal.pbio.1002169</a>.","short":"L. El Masri, A. Branca, A. Sheppard, A. Papkou, D. Laehnemann, P. Guenther, S. Prahl, M. Saebelfeld, J. Hollensteiner, H. Liesegang, E. Brzuszkiewicz, R. Daniel, N. Michiels, R. Schulte, J. Kurtz, P. Rosenstiel, A. Telschow, E. Bornberg Bauer, H. Schulenburg, PLoS Biology 13 (2015) 1–30."},"date_updated":"2021-01-12T06:51:33Z"}]