[{"title":"Nonadiabatic preparation of spin crystals with ultracold polar molecules","author":[{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"},{"last_name":"Krems","full_name":"Krems, Roman","first_name":"Roman"},{"first_name":"Hendrik","last_name":"Weimer","full_name":"Weimer, Hendrik"}],"publist_id":"4772","article_processing_charge":"No","extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Lemeshko, Mikhail, Roman Krems, and Hendrik Weimer. “Nonadiabatic Preparation of Spin Crystals with Ultracold Polar Molecules.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.035301.","ista":"Lemeshko M, Krems R, Weimer H. 2012. Nonadiabatic preparation of spin crystals with ultracold polar molecules. Physical Review Letters. 109(3).","mla":"Lemeshko, Mikhail, et al. “Nonadiabatic Preparation of Spin Crystals with Ultracold Polar Molecules.” Physical Review Letters, vol. 109, no. 3, American Physical Society, 2012, doi:10.1103/PhysRevLett.109.035301.","short":"M. Lemeshko, R. Krems, H. Weimer, Physical Review Letters 109 (2012).","ieee":"M. Lemeshko, R. Krems, and H. Weimer, “Nonadiabatic preparation of spin crystals with ultracold polar molecules,” Physical Review Letters, vol. 109, no. 3. American Physical Society, 2012.","ama":"Lemeshko M, Krems R, Weimer H. Nonadiabatic preparation of spin crystals with ultracold polar molecules. Physical Review Letters. 2012;109(3). doi:10.1103/PhysRevLett.109.035301","apa":"Lemeshko, M., Krems, R., & Weimer, H. (2012). Nonadiabatic preparation of spin crystals with ultracold polar molecules. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.035301"},"date_updated":"2021-11-16T08:01:02Z","status":"public","type":"journal_article","_id":"2201","related_material":{"link":[{"url":"https://doi.org/10.1103/PhysRevLett.109.049901","relation":"erratum"}]},"volume":109,"issue":"3","doi":"10.1103/PhysRevLett.109.035301","date_published":"2012-07-16T00:00:00Z","date_created":"2018-12-11T11:56:17Z","day":"16","publication":"Physical Review Letters","language":[{"iso":"eng"}],"year":"2012","publication_status":"published","month":"07","intvolume":" 109","publisher":"American Physical Society","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1203.0010"}],"oa_version":"None","abstract":[{"lang":"eng","text":"We study the growth dynamics of ordered structures of strongly interacting polar molecules in optical lattices. Using a dipole blockade of microwave excitations, we map the system onto an interacting spin-1/2 model possessing ground states with crystalline order, and describe a way to prepare these states by nonadiabatically driving the transitions between molecular rotational levels. The proposed technique bypasses the need to cross a phase transition and allows for the creation of ordered domains of considerably larger size compared to approaches relying on adiabatic preparation."}]},{"publication_status":"published","year":"2012","day":"13","publication":"Physical Review A - Atomic, Molecular, and Optical Physics","doi":"10.1103/PhysRevA.86.013409","date_published":"2012-07-13T00:00:00Z","volume":86,"issue":"1","date_created":"2018-12-11T11:56:18Z","abstract":[{"text":"We propose a method for sensitive parallel detection of low-frequency electromagnetic fields based on the fine structure interactions in paramagnetic polar molecules. Compared to the recently implemented scheme employing ultracold 87Rb atoms by Böhi, the technique based on molecules offers a 100-fold higher sensitivity, the possibility to measure both the electric and magnetic field components, and a probe of a wide range of frequencies from the dc limit to the THz regime.","lang":"eng"}],"publisher":"American Physical Society","quality_controlled":0,"oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1202.1857","open_access":"1"}],"month":"07","intvolume":" 86","date_updated":"2021-01-12T06:55:57Z","citation":{"chicago":"Alyabyshev, Sergey, Mikhail Lemeshko, and Roman Krems. “Sensitive Imaging of Electromagnetic Fields with Paramagnetic Polar Molecules.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2012. https://doi.org/10.1103/PhysRevA.86.013409.","ista":"Alyabyshev S, Lemeshko M, Krems R. 2012. Sensitive imaging of electromagnetic fields with paramagnetic polar molecules. Physical Review A - Atomic, Molecular, and Optical Physics. 86(1).","mla":"Alyabyshev, Sergey, et al. “Sensitive Imaging of Electromagnetic Fields with Paramagnetic Polar Molecules.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 86, no. 1, American Physical Society, 2012, doi:10.1103/PhysRevA.86.013409.","apa":"Alyabyshev, S., Lemeshko, M., & Krems, R. (2012). Sensitive imaging of electromagnetic fields with paramagnetic polar molecules. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.86.013409","ama":"Alyabyshev S, Lemeshko M, Krems R. Sensitive imaging of electromagnetic fields with paramagnetic polar molecules. Physical Review A - Atomic, Molecular, and Optical Physics. 2012;86(1). doi:10.1103/PhysRevA.86.013409","ieee":"S. Alyabyshev, M. Lemeshko, and R. Krems, “Sensitive imaging of electromagnetic fields with paramagnetic polar molecules,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 86, no. 1. American Physical Society, 2012.","short":"S. Alyabyshev, M. Lemeshko, R. Krems, Physical Review A - Atomic, Molecular, and Optical Physics 86 (2012)."},"extern":1,"author":[{"first_name":"Sergey","last_name":"Alyabyshev","full_name":"Alyabyshev, Sergey V"},{"orcid":"0000-0002-6990-7802","full_name":"Mikhail Lemeshko","last_name":"Lemeshko","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail"},{"first_name":"Roman","full_name":"Krems, Roman V","last_name":"Krems"}],"publist_id":"4773","title":"Sensitive imaging of electromagnetic fields with paramagnetic polar molecules","_id":"2202","type":"journal_article","status":"public"},{"quality_controlled":"1","publisher":"The Company of Biologists","oa":1,"page":"1200 - 1203","date_published":"2012-12-15T00:00:00Z","doi":"10.1242/bio.20122287","date_created":"2018-12-11T11:56:38Z","has_accepted_license":"1","year":"2012","day":"15","publication":"Biology open","author":[{"last_name":"Liang","full_name":"Liang, Huixuan","first_name":"Huixuan"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"full_name":"Ghashghaei, H.","last_name":"Ghashghaei","first_name":"H."}],"publist_id":"4682","title":"A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors","citation":{"mla":"Liang, Huixuan, et al. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.” Biology Open, vol. 1, no. 12, The Company of Biologists, 2012, pp. 1200–03, doi:10.1242/bio.20122287.","ama":"Liang H, Hippenmeyer S, Ghashghaei H. A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. Biology open. 2012;1(12):1200-1203. doi:10.1242/bio.20122287","apa":"Liang, H., Hippenmeyer, S., & Ghashghaei, H. (2012). A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. Biology Open. The Company of Biologists. https://doi.org/10.1242/bio.20122287","short":"H. Liang, S. Hippenmeyer, H. Ghashghaei, Biology Open 1 (2012) 1200–1203.","ieee":"H. Liang, S. Hippenmeyer, and H. Ghashghaei, “A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors,” Biology open, vol. 1, no. 12. The Company of Biologists, pp. 1200–1203, 2012.","chicago":"Liang, Huixuan, Simon Hippenmeyer, and H. Ghashghaei. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.” Biology Open. The Company of Biologists, 2012. https://doi.org/10.1242/bio.20122287.","ista":"Liang H, Hippenmeyer S, Ghashghaei H. 2012. A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. Biology open. 1(12), 1200–1203."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"month":"12","intvolume":" 1","abstract":[{"lang":"eng","text":"Nestin-cre transgenic mice have been widely used to direct recombination to neural stem cells (NSCs) and intermediate neural progenitor cells (NPCs). Here we report that a readily utilized, and the only commercially available, Nestin-cre line is insufficient for directing recombination in early embryonic NSCs and NPCs. Analysis of recombination efficiency in multiple cre-dependent reporters and a genetic mosaic line revealed consistent temporal and spatial patterns of recombination in NSCs and NPCs. For comparison we utilized a knock-in Emx1cre line and found robust recombination in NSCs and NPCs in ventricular and subventricular zones of the cerebral cortices as early as embryonic day 12.5. In addition we found that the rate of Nestin-cre driven recombination only reaches sufficiently high levels in NSCs and NPCs during late embryonic and early postnatal periods. These findings are important when commercially available cre lines are considered for directing recombination to embryonic NSCs and NPCs."}],"oa_version":"Published Version","issue":"12","volume":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","publication_status":"published","file":[{"file_id":"4990","checksum":"605a1800b81227848c361fd6ba7d22ba","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2015-387-v1+1_1200.full.pdf","date_created":"2018-12-12T10:13:09Z","file_size":726695,"date_updated":"2020-07-14T12:45:35Z","creator":"system"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","pubrep_id":"387","_id":"2263","file_date_updated":"2020-07-14T12:45:35Z","department":[{"_id":"SiHi"}],"date_updated":"2021-01-12T06:56:23Z","ddc":["576"]},{"status":"public","pubrep_id":"572","type":"conference","conference":{"name":"EGPGV: Eurographics Symposium on Parallel Graphics and Visualization","start_date":"2012-05-13","end_date":"2012-05-14","location":"Calgari, Italy"},"_id":"2267","title":"Auto splats: Dynamic point cloud visualization on the GPU","file_date_updated":"2020-07-14T12:45:35Z","author":[{"full_name":"Preiner, Reinhold","last_name":"Preiner","first_name":"Reinhold"},{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Wimmer","full_name":"Wimmer, Michael"}],"publist_id":"4677","extern":"1","ddc":["000"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Preiner, Reinhold, Stefan Jeschke, and Michael Wimmer. “Auto Splats: Dynamic Point Cloud Visualization on the GPU,” 139–48. Eurographics Association, 2012. https://doi.org/10.2312/EGPGV/EGPGV12/139-148.","ista":"Preiner R, Jeschke S, Wimmer M. 2012. Auto splats: Dynamic point cloud visualization on the GPU. EGPGV: Eurographics Symposium on Parallel Graphics and Visualization, 139–148.","mla":"Preiner, Reinhold, et al. Auto Splats: Dynamic Point Cloud Visualization on the GPU. Eurographics Association, 2012, pp. 139–48, doi:10.2312/EGPGV/EGPGV12/139-148.","ieee":"R. Preiner, S. Jeschke, and M. Wimmer, “Auto splats: Dynamic point cloud visualization on the GPU,” presented at the EGPGV: Eurographics Symposium on Parallel Graphics and Visualization, Calgari, Italy, 2012, pp. 139–148.","short":"R. Preiner, S. Jeschke, M. Wimmer, in:, Eurographics Association, 2012, pp. 139–148.","ama":"Preiner R, Jeschke S, Wimmer M. Auto splats: Dynamic point cloud visualization on the GPU. In: Eurographics Association; 2012:139-148. doi:10.2312/EGPGV/EGPGV12/139-148","apa":"Preiner, R., Jeschke, S., & Wimmer, M. (2012). Auto splats: Dynamic point cloud visualization on the GPU (pp. 139–148). Presented at the EGPGV: Eurographics Symposium on Parallel Graphics and Visualization, Calgari, Italy: Eurographics Association. https://doi.org/10.2312/EGPGV/EGPGV12/139-148"},"date_updated":"2021-01-12T06:56:24Z","month":"05","publisher":"Eurographics Association","quality_controlled":"1","oa":1,"oa_version":"Submitted Version","abstract":[{"text":"Capturing real-world objects with laser-scanning technology has become an everyday task. Recently, the acquisition of dynamic scenes at interactive frame rates has become feasible. A high-quality visualization of the resulting point cloud stream would require a per-frame reconstruction of object surfaces. Unfortunately, reconstruction computations are still too time-consuming to be applied interactively. In this paper we present a local surface reconstruction and visualization technique that provides interactive feedback for reasonably sized point clouds, while achieving high image quality. Our method is performed entirely on the GPU and in screen pace, exploiting the efficiency of the common rasterization pipeline. The approach is very general, as no assumption is made about point connectivity or sampling density. This naturally allows combining the outputs of multiple scanners in a single visualization, which is useful for many virtual and augmented reality applications. ","lang":"eng"}],"doi":"10.2312/EGPGV/EGPGV12/139-148","date_published":"2012-05-13T00:00:00Z","date_created":"2018-12-11T11:56:40Z","page":"139 - 148","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"5495bb6ee8662cd401b34afb04dfb40f","file_id":"4866","creator":"system","file_size":14903860,"date_updated":"2020-07-14T12:45:35Z","file_name":"IST-2016-572-v1+1_preiner_2012_AS-draft.pdf","date_created":"2018-12-12T10:11:13Z"}],"day":"13","language":[{"iso":"eng"}],"has_accepted_license":"1","year":"2012","publication_status":"published"},{"publisher":"Public Library of Science","quality_controlled":0,"month":"03","intvolume":" 7","abstract":[{"text":"Mosaic Analysis with Double Markers (MADM) is a method for generating genetically mosaic mice, in which sibling mutant and wild-type cells are labeled with different fluorescent markers. It is a powerful tool that enables analysis of gene function at the single cell level in vivo. It requires transgenic cassettes to be located between the centromere and the mutation in the gene of interest on the same chromosome. Here we compare procedures for introduction of MADM cassettes into new loci in the mouse genome, and describe new approaches for expanding the utility of MADM. We show that: 1) Targeted homologous recombination outperforms random transgenesis in generation of reliably expressed MADM cassettes, 2) MADM cassettes in new genomic loci need to be validated for biallelic and ubiquitous expression, 3) Recombination between MADM cassettes on different chromosomes can be used to study reciprocal chromosomal deletions/duplications, and 4) MADM can be modified to permit transgene expression by combining it with a binary expression system. The advances described in this study expand current, and enable new and more versatile applications of MADM.","lang":"eng"}],"acknowledgement":"This work was supported by a National Institutes of Health grant to LL (R01-NS050835). BT was a Damon Runyon Fellow and was supported by the Damon Runyon Cancer Research Foundation Grant DRG-1819-04. KM was supported by the Japan Society for the Promotion of Science program for Research Abroad and Human Frontier Science Program Organization (LT00300/2007-L). SH was supported by postdoctoral fellowships from the European Molecular Biology Organization (ALTF 851-2005), Human Frontier Science Program Organization (LT00805/2006-L), and Swiss National Science Foundation (PA00P3_124160 and PA00P3_136482). HZ is a Pew Scholar in Biomedical Sciences, supported by The Pew Charitable Trusts. LL is an investigator of the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","volume":7,"issue":"3","date_published":"2012-03-27T00:00:00Z","doi":"10.1371/journal.pone.0033332","date_created":"2018-12-11T11:56:38Z","license":"https://creativecommons.org/licenses/by/4.0/","publication_status":"published","year":"2012","day":"27","publication":"PLoS One","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"2262","author":[{"first_name":"Bosiljka","full_name":"Tasic, Bosiljka","last_name":"Tasic"},{"first_name":"Kazunari","full_name":"Miyamichi, Kazunari","last_name":"Miyamichi"},{"full_name":"Simon Hippenmeyer","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vardhan","last_name":"Dani","full_name":"Dani, Vardhan S."},{"first_name":"H.","last_name":"Zeng","full_name":"Zeng, H."},{"last_name":"Joo","full_name":"Joo, William","first_name":"William"},{"first_name":"Hui","last_name":"Zong","full_name":"Zong, Hui"},{"full_name":"Chen-Tsai, Yanru","last_name":"Chen Tsai","first_name":"Yanru"},{"first_name":"Liqun","full_name":"Luo, Liqun","last_name":"Luo"}],"publist_id":"4683","title":"Extensions of MADM (Mosaic Analysis with Double Markers) in Mice ","citation":{"ista":"Tasic B, Miyamichi K, Hippenmeyer S, Dani V, Zeng H, Joo W, Zong H, Chen Tsai Y, Luo L. 2012. Extensions of MADM (Mosaic Analysis with Double Markers) in Mice . PLoS One. 7(3).","chicago":"Tasic, Bosiljka, Kazunari Miyamichi, Simon Hippenmeyer, Vardhan Dani, H. Zeng, William Joo, Hui Zong, Yanru Chen Tsai, and Liqun Luo. “Extensions of MADM (Mosaic Analysis with Double Markers) in Mice .” PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0033332.","ieee":"B. Tasic et al., “Extensions of MADM (Mosaic Analysis with Double Markers) in Mice ,” PLoS One, vol. 7, no. 3. Public Library of Science, 2012.","short":"B. Tasic, K. Miyamichi, S. Hippenmeyer, V. Dani, H. Zeng, W. Joo, H. Zong, Y. Chen Tsai, L. Luo, PLoS One 7 (2012).","apa":"Tasic, B., Miyamichi, K., Hippenmeyer, S., Dani, V., Zeng, H., Joo, W., … Luo, L. (2012). Extensions of MADM (Mosaic Analysis with Double Markers) in Mice . PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0033332","ama":"Tasic B, Miyamichi K, Hippenmeyer S, et al. Extensions of MADM (Mosaic Analysis with Double Markers) in Mice . PLoS One. 2012;7(3). doi:10.1371/journal.pone.0033332","mla":"Tasic, Bosiljka, et al. “Extensions of MADM (Mosaic Analysis with Double Markers) in Mice .” PLoS One, vol. 7, no. 3, Public Library of Science, 2012, doi:10.1371/journal.pone.0033332."},"date_updated":"2021-01-12T06:56:22Z","extern":1},{"_id":"2268","conference":{"name":"EUROGRAPHICS: European Association for Computer Graphics"},"type":"conference","status":"public","citation":{"ista":"Auzinger T, Guthe M, Jeschke S. 2012. Analytic anti-aliasing of linear functions on polytopes. EUROGRAPHICS: European Association for Computer Graphics, Computer Graphics Forum, vol. 31, 335–344.","chicago":"Auzinger, Thomas, Michael Guthe, and Stefan Jeschke. “Analytic Anti-Aliasing of Linear Functions on Polytopes,” 31:335–44. Wiley-Blackwell, 2012. http://dx.doi.org/10.1111/j.1467-8659.2012.03012.x.","ieee":"T. Auzinger, M. Guthe, and S. Jeschke, “Analytic anti-aliasing of linear functions on polytopes,” presented at the EUROGRAPHICS: European Association for Computer Graphics, 2012, vol. 31, no. 121, pp. 335–344.","short":"T. Auzinger, M. Guthe, S. Jeschke, in:, Wiley-Blackwell, 2012, pp. 335–344.","ama":"Auzinger T, Guthe M, Jeschke S. Analytic anti-aliasing of linear functions on polytopes. In: Vol 31. Wiley-Blackwell; 2012:335-344. doi:http://dx.doi.org/10.1111/j.1467-8659.2012.03012.x","apa":"Auzinger, T., Guthe, M., & Jeschke, S. (2012). Analytic anti-aliasing of linear functions on polytopes (Vol. 31, pp. 335–344). Presented at the EUROGRAPHICS: European Association for Computer Graphics, Wiley-Blackwell. http://dx.doi.org/10.1111/j.1467-8659.2012.03012.x","mla":"Auzinger, Thomas, et al. Analytic Anti-Aliasing of Linear Functions on Polytopes. Vol. 31, no. 121, Wiley-Blackwell, 2012, pp. 335–44, doi:http://dx.doi.org/10.1111/j.1467-8659.2012.03012.x."},"date_updated":"2021-01-12T06:56:24Z","extern":1,"publist_id":"4676","author":[{"last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Thomas Auzinger","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"last_name":"Guthe","full_name":"Guthe, Michael","first_name":"Michael"},{"id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","full_name":"Stefan Jeschke","last_name":"Jeschke"}],"title":"Analytic anti-aliasing of linear functions on polytopes","abstract":[{"text":"This paper presents an analytic formulation for anti-aliased sampling of 2D polygons and 3D polyhedra. Our framework allows the exact evaluation of the convolution integral with a linear function defined on the polytopes. The filter is a spherically symmetric polynomial of any order, supporting approximations to refined variants such as the Mitchell-Netravali filter family. This enables high-quality rasterization of triangles and tetrahedra with linearly interpolated vertex values to regular and non-regular grids. A closed form solution of the convolution is presented and an efficient implementation on the GPU using DirectX and CUDA C is described. ","lang":"eng"}],"acknowledgement":"Funding was provided by the FWF grant P20768-N13.\nWe want to thank the reviewers for their insightful and helpful remarks, Hang Si for making available TetGen and Stefan Bruckner for VolumeShop.","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.cg.tuwien.ac.at/research/publications/2012/Auzinger_2012_AAA/"}],"quality_controlled":0,"alternative_title":["Computer Graphics Forum"],"publisher":"Wiley-Blackwell","intvolume":" 31","month":"05","publication_status":"published","year":"2012","day":"13","page":"335 - 344","date_created":"2018-12-11T11:56:40Z","date_published":"2012-05-13T00:00:00Z","doi":"http://dx.doi.org/10.1111/j.1467-8659.2012.03012.x","volume":31,"issue":121},{"title":"The propagation approach for computing biochemical reaction networks","external_id":{"pmid":["22778152"]},"publist_id":"4625","author":[{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"id":"3B43276C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Mateescu","full_name":"Mateescu, Maria"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Henzinger TA, Mateescu M. 2012. The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. 10(2), 310–322.","chicago":"Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” IEEE ACM Transactions on Computational Biology and Bioinformatics. IEEE, 2012. https://doi.org/10.1109/TCBB.2012.91.","short":"T.A. Henzinger, M. Mateescu, IEEE ACM Transactions on Computational Biology and Bioinformatics 10 (2012) 310–322.","ieee":"T. A. Henzinger and M. Mateescu, “The propagation approach for computing biochemical reaction networks,” IEEE ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 2. IEEE, pp. 310–322, 2012.","apa":"Henzinger, T. A., & Mateescu, M. (2012). The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. IEEE. https://doi.org/10.1109/TCBB.2012.91","ama":"Henzinger TA, Mateescu M. The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. 2012;10(2):310-322. doi:10.1109/TCBB.2012.91","mla":"Henzinger, Thomas A., and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” IEEE ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 2, IEEE, 2012, pp. 310–22, doi:10.1109/TCBB.2012.91."},"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"date_created":"2018-12-11T11:56:52Z","doi":"10.1109/TCBB.2012.91","date_published":"2012-07-03T00:00:00Z","page":"310 - 322","publication":"IEEE ACM Transactions on Computational Biology and Bioinformatics","day":"03","year":"2012","quality_controlled":"1","publisher":"IEEE","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"date_updated":"2021-01-12T06:56:38Z","status":"public","type":"journal_article","_id":"2302","ec_funded":1,"volume":10,"issue":"2","language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 10","month":"07","scopus_import":1,"pmid":1,"oa_version":"None","abstract":[{"text":"We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only "significant" mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model's variables.","lang":"eng"}]},{"abstract":[{"text":"The translation of "next-generation" sequencing directly to the clinic is still being assessed but has the potential for genetic diseases to reduce costs, advance accuracy, and point to unsuspected yet treatable conditions. To study its capability in the clinic, we performed whole-exome sequencing in 118 probands with a diagnosis of a pediatric-onset neurodevelopmental disease in which most known causes had been excluded. Twenty-two genes not previously identified as disease-causing were identified in this study (19% of cohort), further establishing exome sequencing as a useful tool for gene discovery. New genes identified included EXOC8 in Joubert syndrome and GFM2 in a patient with microcephaly, simplified gyral pattern, and insulin-dependent diabetes. Exome sequencing uncovered 10 probands (8% of cohort) with mutations in genes known to cause a disease different from the initial diagnosis. Upon further medical evaluation, these mutations were found to account for each proband's disease, leading to a change in diagnosis, some of which led to changes in patient management. Our data provide proof of principle that genomic strategies are useful in clarifying diagnosis in a proportion of patients with neurodevelopmental disorders.","lang":"eng"}],"quality_controlled":0,"publisher":"American Association for the Advancement of Science","intvolume":" 4","month":"06","year":"2012","publication_status":"published","publication":"Science Translational Medicine","day":"13","date_created":"2018-12-11T11:56:56Z","issue":"138","doi":"10.1126/scitranslmed.3003544","date_published":"2012-06-13T00:00:00Z","volume":4,"_id":"2313","type":"journal_article","status":"public","date_updated":"2021-01-12T06:56:43Z","citation":{"chicago":"Dixon Salazar, Tracy, Jennifer Silhavy, Nitin Udpa, Jana Schroth, Stephanie Bielas, Ashleigh Schaffer, Jesus Olvera, et al. “Exome Sequencing Can Improve Diagnosis and Alter Patient Management.” Science Translational Medicine. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/scitranslmed.3003544.","ista":"Dixon Salazar T, Silhavy J, Udpa N, Schroth J, Bielas S, Schaffer A, Olvera J, Bafna V, Zaki M, Abdel Salam G, Mansour L, Selim L, Abdel Hadi S, Marzouki N, Ben Omran T, Al Saana N, Sönmez F, Celep F, Azam M, Hill K, Collazo A, Fenstermaker A, Novarino G, Akizu N, Garimella K, Sougnez C, Russ C, Gabriel S, Gleeson J. 2012. Exome sequencing can improve diagnosis and alter patient management. Science Translational Medicine. 4(138).","mla":"Dixon Salazar, Tracy, et al. “Exome Sequencing Can Improve Diagnosis and Alter Patient Management.” Science Translational Medicine, vol. 4, no. 138, American Association for the Advancement of Science, 2012, doi:10.1126/scitranslmed.3003544.","short":"T. Dixon Salazar, J. Silhavy, N. Udpa, J. Schroth, S. Bielas, A. Schaffer, J. Olvera, V. Bafna, M. Zaki, G. Abdel Salam, L. Mansour, L. Selim, S. Abdel Hadi, N. Marzouki, T. Ben Omran, N. Al Saana, F. Sönmez, F. Celep, M. Azam, K. Hill, A. Collazo, A. Fenstermaker, G. Novarino, N. Akizu, K. Garimella, C. Sougnez, C. Russ, S. Gabriel, J. Gleeson, Science Translational Medicine 4 (2012).","ieee":"T. Dixon Salazar et al., “Exome sequencing can improve diagnosis and alter patient management,” Science Translational Medicine, vol. 4, no. 138. American Association for the Advancement of Science, 2012.","ama":"Dixon Salazar T, Silhavy J, Udpa N, et al. Exome sequencing can improve diagnosis and alter patient management. Science Translational Medicine. 2012;4(138). doi:10.1126/scitranslmed.3003544","apa":"Dixon Salazar, T., Silhavy, J., Udpa, N., Schroth, J., Bielas, S., Schaffer, A., … Gleeson, J. (2012). Exome sequencing can improve diagnosis and alter patient management. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.3003544"},"extern":1,"author":[{"first_name":"Tracy","full_name":"Dixon-Salazar, Tracy J","last_name":"Dixon Salazar"},{"first_name":"Jennifer","last_name":"Silhavy","full_name":"Silhavy, Jennifer L"},{"first_name":"Nitin","last_name":"Udpa","full_name":"Udpa, Nitin"},{"first_name":"Jana","full_name":"Schroth, Jana","last_name":"Schroth"},{"last_name":"Bielas","full_name":"Bielas, Stephanie L","first_name":"Stephanie"},{"full_name":"Schaffer, Ashleigh E","last_name":"Schaffer","first_name":"Ashleigh"},{"first_name":"Jesus","last_name":"Olvera","full_name":"Olvera, Jesus"},{"first_name":"Vineet","full_name":"Bafna, Vineet K","last_name":"Bafna"},{"full_name":"Zaki, Maha S","last_name":"Zaki","first_name":"Maha"},{"full_name":"Abdel-Salam, Ghada M","last_name":"Abdel Salam","first_name":"Ghada"},{"first_name":"Lobna","last_name":"Mansour","full_name":"Mansour, Lobna A"},{"first_name":"Laila","last_name":"Selim","full_name":"Selim, Laila A"},{"first_name":"Sawsan","last_name":"Abdel Hadi","full_name":"Abdel-Hadi, Sawsan S"},{"last_name":"Marzouki","full_name":"Marzouki, Naima","first_name":"Naima"},{"full_name":"Ben-Omran, Tawfeg I","last_name":"Ben Omran","first_name":"Tawfeg"},{"first_name":"Nouriya","last_name":"Al Saana","full_name":"Al-Saana, Nouriya A"},{"first_name":"Fatma","full_name":"Sönmez, Fatma M","last_name":"Sönmez"},{"full_name":"Celep, Figen","last_name":"Celep","first_name":"Figen"},{"full_name":"Azam, Matloob","last_name":"Azam","first_name":"Matloob"},{"last_name":"Hill","full_name":"Hill, Kiley J","first_name":"Kiley"},{"last_name":"Collazo","full_name":"Collazo, Adrienne","first_name":"Adrienne"},{"last_name":"Fenstermaker","full_name":"Fenstermaker, Ali G","first_name":"Ali"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia","last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Gaia Novarino"},{"first_name":"Naiara","last_name":"Akizu","full_name":"Akizu, Naiara"},{"first_name":"Kiran","last_name":"Garimella","full_name":"Garimella, Kiran V"},{"last_name":"Sougnez","full_name":"Sougnez, Carrie L","first_name":"Carrie"},{"full_name":"Russ, Carsten","last_name":"Russ","first_name":"Carsten"},{"first_name":"Stacey","last_name":"Gabriel","full_name":"Gabriel, Stacey B"},{"first_name":"Joseph","full_name":"Gleeson, Joseph G","last_name":"Gleeson"}],"publist_id":"4614","title":"Exome sequencing can improve diagnosis and alter patient management"},{"intvolume":" 338","month":"10","publisher":"American Association for the Advancement of Science","quality_controlled":0,"abstract":[{"text":"Autism spectrum disorders are a genetically heterogeneous constellation of syndromes characterized by impairments in reciprocal social interaction. Available somatic treatments have limited efficacy. We have identified inactivating mutations in the gene BCKDK (Branched Chain Ketoacid Dehydrogenase Kinase) in consanguineous families with autism, epilepsy, and intellectual disability. The encoded protein is responsible for phosphorylation-mediated inactivation of the E1α subunit of branched-chain ketoacid dehydrogenase (BCKDH). Patients with homozygous BCKDK mutations display reductions in BCKDK messenger RNA and protein, E1α phosphorylation, and plasma branched-chain amino acids. Bckdk knockout mice show abnormal brain amino acid profiles and neurobehavioral deficits that respond to dietary supplementation. Thus, autism presenting with intellectual disability and epilepsy caused by BCKDK mutations represents a potentially treatable syndrome.","lang":"eng"}],"date_created":"2018-12-11T11:56:56Z","doi":"10.1126/science.1224631","date_published":"2012-10-19T00:00:00Z","volume":338,"issue":"6105","page":"394 - 397","publication":"Science","day":"19","publication_status":"published","year":"2012","status":"public","type":"journal_article","_id":"2314","title":"Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy","author":[{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Gaia Novarino","last_name":"Novarino"},{"first_name":"Paul","last_name":"El Fishawy","full_name":"El-Fishawy, Paul"},{"last_name":"Kayserili","full_name":"Kayserili, Hülya","first_name":"Hülya"},{"first_name":"Nagwa","last_name":"Meguid","full_name":"Meguid, Nagwa A"},{"first_name":"Eric","last_name":"Scott","full_name":"Scott, Eric M"},{"full_name":"Schroth, Jana","last_name":"Schroth","first_name":"Jana"},{"first_name":"Jennifer","full_name":"Silhavy, Jennifer L","last_name":"Silhavy"},{"full_name":"Kara, Majdi","last_name":"Kara","first_name":"Majdi"},{"first_name":"Rehab","last_name":"Khalil","full_name":"Khalil, Rehab O"},{"last_name":"Ben Omran","full_name":"Ben-Omran, Tawfeg I","first_name":"Tawfeg"},{"last_name":"Ercan Sencicek","full_name":"Ercan-Sencicek, Adife G","first_name":"Adife"},{"first_name":"Adel","full_name":"Hashish, Adel F","last_name":"Hashish"},{"full_name":"Sanders, Stephan J","last_name":"Sanders","first_name":"Stephan"},{"full_name":"Gupta, Abha R","last_name":"Gupta","first_name":"Abha"},{"full_name":"Hashem, Hebatalla S","last_name":"Hashem","first_name":"Hebatalla"},{"last_name":"Matern","full_name":"Matern, Dietrich","first_name":"Dietrich"},{"first_name":"Stacey","last_name":"Gabriel","full_name":"Gabriel, Stacey B"},{"first_name":"Lawrence","full_name":"Sweetman, Lawrence","last_name":"Sweetman"},{"first_name":"Yasmeen","last_name":"Rahimi","full_name":"Rahimi, Yasmeen"},{"first_name":"Robert","full_name":"Harris, Robert A","last_name":"Harris"},{"first_name":"Matthew","full_name":"State, Matthew W","last_name":"State"},{"first_name":"Joseph","last_name":"Gleeson","full_name":"Gleeson, Joseph G"}],"publist_id":"4613","extern":1,"citation":{"ieee":"G. Novarino et al., “Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy,” Science, vol. 338, no. 6105. American Association for the Advancement of Science, pp. 394–397, 2012.","short":"G. Novarino, P. El Fishawy, H. Kayserili, N. Meguid, E. Scott, J. Schroth, J. Silhavy, M. Kara, R. Khalil, T. Ben Omran, A. Ercan Sencicek, A. Hashish, S. Sanders, A. Gupta, H. Hashem, D. Matern, S. Gabriel, L. Sweetman, Y. Rahimi, R. Harris, M. State, J. Gleeson, Science 338 (2012) 394–397.","apa":"Novarino, G., El Fishawy, P., Kayserili, H., Meguid, N., Scott, E., Schroth, J., … Gleeson, J. (2012). Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1224631","ama":"Novarino G, El Fishawy P, Kayserili H, et al. Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy. Science. 2012;338(6105):394-397. doi:10.1126/science.1224631","mla":"Novarino, Gaia, et al. “Mutations in BCKD-Kinase Lead to a Potentially Treatable Form of Autism with Epilepsy.” Science, vol. 338, no. 6105, American Association for the Advancement of Science, 2012, pp. 394–97, doi:10.1126/science.1224631.","ista":"Novarino G, El Fishawy P, Kayserili H, Meguid N, Scott E, Schroth J, Silhavy J, Kara M, Khalil R, Ben Omran T, Ercan Sencicek A, Hashish A, Sanders S, Gupta A, Hashem H, Matern D, Gabriel S, Sweetman L, Rahimi Y, Harris R, State M, Gleeson J. 2012. Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy. Science. 338(6105), 394–397.","chicago":"Novarino, Gaia, Paul El Fishawy, Hülya Kayserili, Nagwa Meguid, Eric Scott, Jana Schroth, Jennifer Silhavy, et al. “Mutations in BCKD-Kinase Lead to a Potentially Treatable Form of Autism with Epilepsy.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224631."},"date_updated":"2021-01-12T06:56:43Z"},{"publist_id":"4609","author":[{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"department":[{"_id":"RoSe"}],"title":"Absence of bound states implies non-negativity of the scattering length","citation":{"ista":"Seiringer R. 2012. Absence of bound states implies non-negativity of the scattering length. Journal of Spectral Theory. 2(3), 321–328.","chicago":"Seiringer, Robert. “Absence of Bound States Implies Non-Negativity of the Scattering Length.” Journal of Spectral Theory. European Mathematical Society, 2012. https://doi.org/10.4171/JST/31.","ama":"Seiringer R. Absence of bound states implies non-negativity of the scattering length. Journal of Spectral Theory. 2012;2(3):321-328. doi:10.4171/JST/31","apa":"Seiringer, R. (2012). Absence of bound states implies non-negativity of the scattering length. Journal of Spectral Theory. European Mathematical Society. https://doi.org/10.4171/JST/31","ieee":"R. Seiringer, “Absence of bound states implies non-negativity of the scattering length,” Journal of Spectral Theory, vol. 2, no. 3. European Mathematical Society, pp. 321–328, 2012.","short":"R. Seiringer, Journal of Spectral Theory 2 (2012) 321–328.","mla":"Seiringer, Robert. “Absence of Bound States Implies Non-Negativity of the Scattering Length.” Journal of Spectral Theory, vol. 2, no. 3, European Mathematical Society, 2012, pp. 321–28, doi:10.4171/JST/31."},"date_updated":"2021-01-12T06:56:44Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","status":"public","_id":"2318","page":"321-328","doi":"10.4171/JST/31","issue":"3","date_published":"2012-06-24T00:00:00Z","volume":2,"date_created":"2018-12-11T11:56:58Z","publication_status":"published","year":"2012","day":"24","publication":"Journal of Spectral Theory","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"European Mathematical Society","main_file_link":[{"url":"http://arxiv.org/abs/1204.0435","open_access":"1"}],"oa":1,"month":"06","intvolume":" 2","abstract":[{"text":"We show that bosons interacting via pair potentials with negative scattering length form bound states for a suitable number of particles. In other words, the absence of many-particle bound states of any kind implies the non-negativity of the scattering length of the interaction potential. ","lang":"eng"}],"oa_version":"Preprint","acknowledgement":"Partial financial support by NSERC "}]