[{"pmid":1,"title":"Regulation of biological accuracy, precision, and memory by plant chromatin organization","article_processing_charge":"No","publisher":"Elsevier","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-14T08:32:38Z","volume":22,"date_created":"2021-06-08T08:58:52Z","year":"2012","page":"132-138","article_type":"review","status":"public","scopus_import":"1","citation":{"ieee":"J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” <i>Current Opinion in Genetics and Development</i>, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.","mla":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and Development</i>, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:<a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">10.1016/j.gde.2012.01.007</a>.","chicago":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">https://doi.org/10.1016/j.gde.2012.01.007</a>.","ama":"Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>. 2012;22(2):132-138. doi:<a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">10.1016/j.gde.2012.01.007</a>","apa":"Huff, J. T., &#38; Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">https://doi.org/10.1016/j.gde.2012.01.007</a>","ista":"Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 22(2), 132–138.","short":"J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138."},"abstract":[{"lang":"eng","text":"Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory."}],"department":[{"_id":"DaZi"}],"author":[{"first_name":"Jason T.","full_name":"Huff, Jason T.","last_name":"Huff"},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"oa_version":"None","extern":"1","date_published":"2012-04-01T00:00:00Z","doi":"10.1016/j.gde.2012.01.007","_id":"9528","month":"04","external_id":{"pmid":["22336527"]},"quality_controlled":"1","publication_status":"published","publication":"Current Opinion in Genetics and Development","intvolume":"        22","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0959-437X"]},"type":"journal_article","issue":"2"},{"citation":{"ieee":"D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation of constitutive expression,” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012.","mla":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:<a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">10.1101/sqb.2012.77.014944</a>.","ista":"Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 77, 147–154.","chicago":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press, 2012. <a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">https://doi.org/10.1101/sqb.2012.77.014944</a>.","apa":"Coleman-Derr, D., &#38; Zilberman, D. (2012). DNA methylation, H2A.Z, and the regulation of constitutive expression. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">https://doi.org/10.1101/sqb.2012.77.014944</a>","ama":"Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. 2012;77:147-154. doi:<a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">10.1101/sqb.2012.77.014944</a>","short":"D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154."},"day":"18","abstract":[{"lang":"eng","text":"The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies."}],"scopus_import":"1","year":"2012","date_created":"2021-06-08T13:01:23Z","volume":77,"status":"public","article_type":"review","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/sqb.2012.77.014944"}],"page":"147-154","article_processing_charge":"No","pmid":1,"title":"DNA methylation, H2A.Z, and the regulation of constitutive expression","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-14T08:33:09Z","publisher":"Cold Spring Harbor Laboratory Press","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1943-4456"],"issn":["0091-7451"]},"external_id":{"pmid":["23250988"]},"month":"12","_id":"9535","date_published":"2012-12-18T00:00:00Z","extern":"1","doi":"10.1101/sqb.2012.77.014944","publication":"Cold Spring Harbor Symposia on Quantitative Biology","oa":1,"intvolume":"        77","publication_status":"published","quality_controlled":"1","author":[{"last_name":"Coleman-Derr","full_name":"Coleman-Derr, D.","first_name":"D."},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"oa_version":"Published Version","department":[{"_id":"DaZi"}]},{"oa":1,"doi":"10.5061/dryad.sv37s","date_published":"2012-09-27T00:00:00Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"3242"}]},"_id":"9755","month":"09","type":"research_data_reference","abstract":[{"lang":"eng","text":"Due to the omnipresent risk of epidemics, insect societies have evolved sophisticated disease defences at the individual and colony level. An intriguing yet little understood phenomenon is that social contact to pathogen-exposed individuals reduces susceptibility of previously naive nestmates to this pathogen. We tested whether such social immunisation in Lasius ants against the entomopathogenic fungus Metarhizium anisopliae is based on active upregulation of the immune system of nestmates following contact to an infectious individual or passive protection via transfer of immune effectors among group members—that is, active versus passive immunisation. We found no evidence for involvement of passive immunisation via transfer of antimicrobials among colony members. Instead, intensive allogrooming behaviour between naive and pathogen-exposed ants before fungal conidia firmly attached to their cuticle suggested passage of the pathogen from the exposed individuals to their nestmates. By tracing fluorescence-labelled conidia we indeed detected frequent pathogen transfer to the nestmates, where they caused low-level infections as revealed by growth of small numbers of fungal colony forming units from their dissected body content. These infections rarely led to death, but instead promoted an enhanced ability to inhibit fungal growth and an active upregulation of immune genes involved in antifungal defences (defensin and prophenoloxidase, PPO). Contrarily, there was no upregulation of the gene cathepsin L, which is associated with antibacterial and antiviral defences, and we found no increased antibacterial activity of nestmates of fungus-exposed ants. This indicates that social immunisation after fungal exposure is specific, similar to recent findings for individual-level immune priming in invertebrates. Epidemiological modeling further suggests that active social immunisation is adaptive, as it leads to faster elimination of the disease and lower death rates than passive immunisation. Interestingly, humans have also utilised the protective effect of low-level infections to fight smallpox by intentional transfer of low pathogen doses (“variolation” or “inoculation”)."}],"day":"27","citation":{"ista":"Konrad M, Vyleta M, Theis F, Stock M, Klatt M, Drescher V, Marr C, Ugelvig LV, Cremer S. 2012. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies, Dryad, <a href=\"https://doi.org/10.5061/dryad.sv37s\">10.5061/dryad.sv37s</a>.","ama":"Konrad M, Vyleta M, Theis F, et al. Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. 2012. doi:<a href=\"https://doi.org/10.5061/dryad.sv37s\">10.5061/dryad.sv37s</a>","chicago":"Konrad, Matthias, Meghan Vyleta, Fabian Theis, Miriam Stock, Martina Klatt, Verena Drescher, Carsten Marr, Line V Ugelvig, and Sylvia Cremer. “Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.” Dryad, 2012. <a href=\"https://doi.org/10.5061/dryad.sv37s\">https://doi.org/10.5061/dryad.sv37s</a>.","apa":"Konrad, M., Vyleta, M., Theis, F., Stock, M., Klatt, M., Drescher, V., … Cremer, S. (2012). Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies. Dryad. <a href=\"https://doi.org/10.5061/dryad.sv37s\">https://doi.org/10.5061/dryad.sv37s</a>","short":"M. Konrad, M. Vyleta, F. Theis, M. Stock, M. Klatt, V. Drescher, C. Marr, L.V. Ugelvig, S. Cremer, (2012).","ieee":"M. Konrad <i>et al.</i>, “Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies.” Dryad, 2012.","mla":"Konrad, Matthias, et al. <i>Data from: Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/dryad.sv37s\">10.5061/dryad.sv37s</a>."},"date_updated":"2023-02-23T11:18:41Z","publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","department":[{"_id":"SyCr"}],"title":"Data from: Social transfer of pathogenic fungus promotes active immunisation in ant colonies","article_processing_charge":"No","oa_version":"Published Version","author":[{"first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias","last_name":"Konrad"},{"first_name":"Meghan","id":"418901AA-F248-11E8-B48F-1D18A9856A87","full_name":"Vyleta, Meghan","last_name":"Vyleta"},{"first_name":"Fabian","full_name":"Theis, Fabian","last_name":"Theis"},{"full_name":"Stock, Miriam","last_name":"Stock","first_name":"Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martina","id":"E60F29C6-E9AE-11E9-AF6E-D190C7302F38","full_name":"Klatt, Martina","last_name":"Klatt"},{"full_name":"Drescher, Verena","last_name":"Drescher","first_name":"Verena"},{"first_name":"Carsten","last_name":"Marr","full_name":"Marr, Carsten"},{"full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","last_name":"Ugelvig","first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.sv37s"}],"status":"public","date_created":"2021-07-30T08:39:13Z","year":"2012"},{"year":"2012","date_created":"2021-07-30T12:31:31Z","status":"public","main_file_link":[{"url":"https://doi.org/10.5061/dryad.61649","open_access":"1"}],"author":[{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Tragust","full_name":"Tragust, Simon"},{"first_name":"Barbara","id":"479DDAAC-E9CD-11E9-9B5F-82450873F7A1","full_name":"Mitteregger, Barbara","last_name":"Mitteregger"},{"full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367","last_name":"Barone","first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Konrad, Matthias","last_name":"Konrad","first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ugelvig, Line V","orcid":"0000-0003-1832-8883","last_name":"Ugelvig","first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"oa_version":"Published Version","article_processing_charge":"No","department":[{"_id":"SyCr"}],"title":"Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison","publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T11:04:28Z","day":"14","citation":{"short":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, (2012).","chicago":"Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line V Ugelvig, and Sylvia Cremer. “Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” Dryad, 2012. <a href=\"https://doi.org/10.5061/dryad.61649\">https://doi.org/10.5061/dryad.61649</a>.","ista":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2012. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison, Dryad, <a href=\"https://doi.org/10.5061/dryad.61649\">10.5061/dryad.61649</a>.","apa":"Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., &#38; Cremer, S. (2012). Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Dryad. <a href=\"https://doi.org/10.5061/dryad.61649\">https://doi.org/10.5061/dryad.61649</a>","ama":"Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. 2012. doi:<a href=\"https://doi.org/10.5061/dryad.61649\">10.5061/dryad.61649</a>","mla":"Tragust, Simon, et al. <i>Data from: Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/dryad.61649\">10.5061/dryad.61649</a>.","ieee":"S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Data from: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison.” Dryad, 2012."},"abstract":[{"lang":"eng","text":"To fight infectious diseases, host immune defences are employed at multiple levels. Sanitary behaviour, such as pathogen avoidance and removal, acts as a first line of defence to prevent infection [1] before activation of the physiological immune system. Insect societies have evolved a wide range of collective hygiene measures and intensive health care towards pathogen-exposed group members [2]. One of the most common behaviours is allogrooming, in which nestmates remove infectious particles from the body surfaces of exposed individuals [3]. Here we show that, in invasive garden ants, grooming of fungus-exposed brood is effective beyond the sheer mechanical removal of fungal conidiospores as it also includes chemical disinfection through the application of poison produced by the ants themselves. Formic acid is the main active component of the poison. It inhibits fungal growth of conidiospores remaining on the brood surface after grooming and also those collected in the mouth of the grooming ant. This dual function is achieved by uptake of the poison droplet into the mouth through acidopore self-grooming and subsequent application onto the infectious brood via brood grooming. This extraordinary behaviour extends current understanding of grooming and the establishment of social immunity in insect societies."}],"type":"research_data_reference","_id":"9757","related_material":{"record":[{"relation":"used_in_publication","id":"2926","status":"public"}]},"date_published":"2012-12-14T00:00:00Z","doi":"10.5061/dryad.61649","month":"12","oa":1},{"citation":{"mla":"Aeschbacher, Simon, et al. <i>Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/dryad.274b1\">10.5061/dryad.274b1</a>.","ieee":"S. Aeschbacher, A. Futschik, and M. Beaumont, “Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates.” Dryad, 2012.","short":"S. Aeschbacher, A. Futschik, M. Beaumont, (2012).","ama":"Aeschbacher S, Futschik A, Beaumont M. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. 2012. doi:<a href=\"https://doi.org/10.5061/dryad.274b1\">10.5061/dryad.274b1</a>","apa":"Aeschbacher, S., Futschik, A., &#38; Beaumont, M. (2012). Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates. Dryad. <a href=\"https://doi.org/10.5061/dryad.274b1\">https://doi.org/10.5061/dryad.274b1</a>","chicago":"Aeschbacher, Simon, Andreas Futschik, and Mark Beaumont. “Data from: Approximate Bayesian Computation for Modular Inference Problems with Many Parameters: The Example of Migration Rates.” Dryad, 2012. <a href=\"https://doi.org/10.5061/dryad.274b1\">https://doi.org/10.5061/dryad.274b1</a>.","ista":"Aeschbacher S, Futschik A, Beaumont M. 2012. Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates, Dryad, <a href=\"https://doi.org/10.5061/dryad.274b1\">10.5061/dryad.274b1</a>."},"day":"14","type":"research_data_reference","abstract":[{"lang":"eng","text":"We propose a two-step procedure for estimating multiple migration rates in an approximate Bayesian computation (ABC) framework, accounting for global nuisance parameters. The approach is not limited to migration, but generally of interest for inference problems with multiple parameters and a modular structure (e.g. independent sets of demes or loci). We condition on a known, but complex demographic model of a spatially subdivided population, motivated by the reintroduction of Alpine ibex (Capra ibex) into Switzerland. In the first step, the global parameters ancestral mutation rate and male mating skew have been estimated for the whole population in Aeschbacher et al. (Genetics 2012; 192: 1027). In the second step, we estimate in this study the migration rates independently for clusters of demes putatively connected by migration. For large clusters (many migration rates), ABC faces the problem of too many summary statistics. We therefore assess by simulation if estimation per pair of demes is a valid alternative. We find that the trade-off between reduced dimensionality for the pairwise estimation on the one hand and lower accuracy due to the assumption of pairwise independence on the other depends on the number of migration rates to be inferred: the accuracy of the pairwise approach increases with the number of parameters, relative to the joint estimation approach. To distinguish between low and zero migration, we perform ABC-type model comparison between a model with migration and one without. Applying the approach to microsatellite data from Alpine ibex, we find no evidence for substantial gene flow via migration, except for one pair of demes in one direction."}],"month":"11","related_material":{"record":[{"id":"2944","relation":"used_in_publication","status":"public"}]},"date_published":"2012-11-14T00:00:00Z","doi":"10.5061/dryad.274b1","_id":"9758","oa":1,"date_created":"2021-07-30T12:36:39Z","year":"2012","oa_version":"Published Version","author":[{"full_name":"Aeschbacher, Simon","last_name":"Aeschbacher","first_name":"Simon","id":"2D35326E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Futschik, Andreas","last_name":"Futschik","first_name":"Andreas"},{"last_name":"Beaumont","full_name":"Beaumont, Mark","first_name":"Mark"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.274b1","open_access":"1"}],"status":"public","department":[{"_id":"NiBa"}],"title":"Data from: Approximate Bayesian computation for modular inference problems with many parameters: the example of migration rates","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-23T11:05:19Z","publisher":"Dryad"},{"page":"109-129","author":[{"first_name":"Stephanie","id":"3C77F464-F248-11E8-B48F-1D18A9856A87","full_name":"zur Nedden, Stephanie","last_name":"zur Nedden"},{"first_name":"Alexander S.","full_name":"Doney, Alexander S.","last_name":"Doney"},{"first_name":"Bruno G.","full_name":"Frenguelli, Bruno G.","last_name":"Frenguelli"}],"oa_version":"None","status":"public","editor":[{"first_name":"Susan","last_name":"Masino","full_name":"Masino, Susan"},{"last_name":"Boison","full_name":"Boison, Detlev","first_name":"Detlev"}],"acknowledgement":"We are grateful to Research into Ageing/Ageing UK and The Dunhill Trust for funding SzN’s graduate studies, and to Prof Nicholas Dale for his valuable input.","date_created":"2022-03-21T07:16:12Z","year":"2012","edition":"1","place":"New York","date_updated":"2022-06-21T11:51:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","title":"The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books","department":[{"_id":"HaJa"}],"article_processing_charge":"No","publication_identifier":{"eisbn":["9781461439035"],"isbn":["9781461439028"]},"language":[{"iso":"eng"}],"type":"book_chapter","abstract":[{"lang":"eng","text":"Under physiological conditions the brain, via the purine salvage pathway, reuses the preformed purine bases hypoxanthine, derived from ATP degradation, and adenine (Ade), derived from polyamine synthesis, to restore its ATP pool. However, the massive degradation of ATP during ischemia, although providing valuable neuroprotective adenosine, results in the accumulation and loss of diffusible purine metabolites and thereby leads to a protracted reduction in the post-ischemic ATP pool size. In vivo, this may both limit the ability to deploy ATP-dependent reparative mechanisms and reduce the subsequent availability of adenosine, whilst in brain slices results in tissue with substantially lower levels of ATP than in vivo. In the present review, we describe the mechanisms by which brain tissue replenishes its ATP, how this can be improved with the clinically tolerated chemicals D-ribose and adenine, and the functional, and potential therapeutic, implications of doing so."}],"day":"23","citation":{"ama":"zur Nedden S, Doney AS, Frenguelli BG. The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In: Masino S, Boison D, eds. <i>Adenosine</i>. 1st ed. New York: Springer; 2012:109-129. doi:<a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">10.1007/978-1-4614-3903-5_6</a>","chicago":"Nedden, Stephanie zur, Alexander S. Doney, and Bruno G. Frenguelli. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” In <i>Adenosine</i>, edited by Susan Masino and Detlev Boison, 1st ed., 109–29. New York: Springer, 2012. <a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">https://doi.org/10.1007/978-1-4614-3903-5_6</a>.","apa":"zur Nedden, S., Doney, A. S., &#38; Frenguelli, B. G. (2012). The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In S. Masino &#38; D. Boison (Eds.), <i>Adenosine</i> (1st ed., pp. 109–129). New York: Springer. <a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">https://doi.org/10.1007/978-1-4614-3903-5_6</a>","ista":"zur Nedden S, Doney AS, Frenguelli BG. 2012.The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In: Adenosine. , 109–129.","short":"S. zur Nedden, A.S. Doney, B.G. Frenguelli, in:, S. Masino, D. Boison (Eds.), Adenosine, 1st ed., Springer, New York, 2012, pp. 109–129.","ieee":"S. zur Nedden, A. S. Doney, and B. G. Frenguelli, “The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books,” in <i>Adenosine</i>, 1st ed., S. Masino and D. Boison, Eds. New York: Springer, 2012, pp. 109–129.","mla":"zur Nedden, Stephanie, et al. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” <i>Adenosine</i>, edited by Susan Masino and Detlev Boison, 1st ed., Springer, 2012, pp. 109–29, doi:<a href=\"https://doi.org/10.1007/978-1-4614-3903-5_6\">10.1007/978-1-4614-3903-5_6</a>."},"quality_controlled":"1","publication_status":"published","publication":"Adenosine","date_published":"2012-07-23T00:00:00Z","doi":"10.1007/978-1-4614-3903-5_6","_id":"10896","month":"07","scopus_import":"1"},{"day":"15","citation":{"ieee":"A. Bouajjani, C. Dragoi, C. Enea, and M. Sighireanu, “Accurate invariant checking for programs manipulating lists and arrays with infinite data,” in <i>Automated Technology for Verification and Analysis</i>, Thiruvananthapuram, India, 2012, vol. 7561, pp. 167–182.","mla":"Bouajjani, Ahmed, et al. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Springer, 2012, pp. 167–82, doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">10.1007/978-3-642-33386-6_14</a>.","ista":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. 2012. Accurate invariant checking for programs manipulating lists and arrays with infinite data. Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and AnalysisLNCS, LNCS, vol. 7561, 167–182.","ama":"Bouajjani A, Dragoi C, Enea C, Sighireanu M. Accurate invariant checking for programs manipulating lists and arrays with infinite data. In: <i>Automated Technology for Verification and Analysis</i>. Vol 7561. LNCS. Berlin, Heidelberg: Springer; 2012:167-182. doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">10.1007/978-3-642-33386-6_14</a>","apa":"Bouajjani, A., Dragoi, C., Enea, C., &#38; Sighireanu, M. (2012). Accurate invariant checking for programs manipulating lists and arrays with infinite data. In <i>Automated Technology for Verification and Analysis</i> (Vol. 7561, pp. 167–182). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">https://doi.org/10.1007/978-3-642-33386-6_14</a>","chicago":"Bouajjani, Ahmed, Cezara Dragoi, Constantin Enea, and Mihaela Sighireanu. “Accurate Invariant Checking for Programs Manipulating Lists and Arrays with Infinite Data.” In <i>Automated Technology for Verification and Analysis</i>, 7561:167–82. LNCS. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_14\">https://doi.org/10.1007/978-3-642-33386-6_14</a>.","short":"A. Bouajjani, C. Dragoi, C. Enea, M. Sighireanu, in:, Automated Technology for Verification and Analysis, Springer, Berlin, Heidelberg, 2012, pp. 167–182."},"abstract":[{"lang":"eng","text":"We propose a logic-based framework for automated reasoning about sequential programs manipulating singly-linked lists and arrays with unbounded data. We introduce the logic SLAD, which allows combining shape constraints, written in a fragment of Separation Logic, with data and size constraints. We address the problem of checking the entailment between SLAD formulas, which is crucial in performing pre-post condition reasoning. Although this problem is undecidable in general for SLAD, we propose a sound and powerful procedure that is able to solve this problem for a large class of formulas, beyond the capabilities of existing techniques and tools. We prove that this procedure is complete, i.e., it is actually a decision procedure for this problem, for an important fragment of SLAD including known decidable logics. We implemented this procedure and shown its preciseness and its efficiency on a significant benchmark of formulas."}],"scopus_import":"1","acknowledgement":"This work has been partially supported by the French ANR project Veridyc","volume":7561,"year":"2012","date_created":"2022-03-21T07:58:39Z","page":"167-182","status":"public","article_processing_charge":"No","title":"Accurate invariant checking for programs manipulating lists and arrays with infinite data","date_updated":"2023-09-05T14:07:24Z","publisher":"Springer","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9783642333866"],"isbn":["9783642333859"],"issn":["0302-9743"],"eissn":["1611-3349"]},"type":"conference","_id":"10903","doi":"10.1007/978-3-642-33386-6_14","date_published":"2012-10-15T00:00:00Z","conference":{"start_date":"2012-10-03","name":"ATVA: Automated Technology for Verification and Analysis","location":"Thiruvananthapuram, India","end_date":"2012-10-06"},"month":"10","publication_status":"published","quality_controlled":"1","publication":"Automated Technology for Verification and Analysis","intvolume":"      7561","series_title":"LNCS","author":[{"full_name":"Bouajjani, Ahmed","last_name":"Bouajjani","first_name":"Ahmed"},{"full_name":"Dragoi, Cezara","last_name":"Dragoi","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Constantin","last_name":"Enea","full_name":"Enea, Constantin"},{"first_name":"Mihaela","full_name":"Sighireanu, Mihaela","last_name":"Sighireanu"}],"oa_version":"None","department":[{"_id":"ToHe"}],"place":"Berlin, Heidelberg"},{"abstract":[{"lang":"eng","text":"Multi-dimensional mean-payoff and energy games provide the mathematical foundation for the quantitative study of reactive systems, and play a central role in the emerging quantitative theory of verification and synthesis. In this work, we study the strategy synthesis problem for games with such multi-dimensional objectives along with a parity condition, a canonical way to express ω-regular conditions. While in general, the winning strategies in such games may require infinite memory, for synthesis the most relevant problem is the construction of a finite-memory winning strategy (if one exists). Our main contributions are as follows. First, we show a tight exponential bound (matching upper and lower bounds) on the memory required for finite-memory winning strategies in both multi-dimensional mean-payoff and energy games along with parity objectives. This significantly improves the triple exponential upper bound for multi energy games (without parity) that could be derived from results in literature for games on VASS (vector addition systems with states). Second, we present an optimal symbolic and incremental algorithm to compute a finite-memory winning strategy (if one exists) in such games. Finally, we give a complete characterization of when finite memory of strategies can be traded off for randomness. In particular, we show that for one-dimension mean-payoff parity games, randomized memoryless strategies are as powerful as their pure finite-memory counterparts."}],"day":"15","citation":{"ista":"Chatterjee K, Randour M, Raskin J-F. 2012. Strategy synthesis for multi-dimensional quantitative objectives. CONCUR 2012 - Concurrency Theory. CONCUR: Conference on Concurrency Theory, LNCS, vol. 7454, 115–131.","apa":"Chatterjee, K., Randour, M., &#38; Raskin, J.-F. (2012). Strategy synthesis for multi-dimensional quantitative objectives. In M. Koutny &#38; I. Ulidowski (Eds.), <i>CONCUR 2012 - Concurrency Theory</i> (Vol. 7454, pp. 115–131). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">https://doi.org/10.1007/978-3-642-32940-1_10</a>","ama":"Chatterjee K, Randour M, Raskin J-F. Strategy synthesis for multi-dimensional quantitative objectives. In: Koutny M, Ulidowski I, eds. <i>CONCUR 2012 - Concurrency Theory</i>. Vol 7454. Berlin, Heidelberg: Springer; 2012:115-131. doi:<a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">10.1007/978-3-642-32940-1_10</a>","chicago":"Chatterjee, Krishnendu, Mickael Randour, and Jean-François Raskin. “Strategy Synthesis for Multi-Dimensional Quantitative Objectives.” In <i>CONCUR 2012 - Concurrency Theory</i>, edited by Maciej Koutny and Irek Ulidowski, 7454:115–31. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">https://doi.org/10.1007/978-3-642-32940-1_10</a>.","short":"K. Chatterjee, M. Randour, J.-F. Raskin, in:, M. Koutny, I. Ulidowski (Eds.), CONCUR 2012 - Concurrency Theory, Springer, Berlin, Heidelberg, 2012, pp. 115–131.","ieee":"K. Chatterjee, M. Randour, and J.-F. Raskin, “Strategy synthesis for multi-dimensional quantitative objectives,” in <i>CONCUR 2012 - Concurrency Theory</i>, Newcastle upon Tyne, United Kingdom, 2012, vol. 7454, pp. 115–131.","mla":"Chatterjee, Krishnendu, et al. “Strategy Synthesis for Multi-Dimensional Quantitative Objectives.” <i>CONCUR 2012 - Concurrency Theory</i>, edited by Maciej Koutny and Irek Ulidowski, vol. 7454, Springer, 2012, pp. 115–31, doi:<a href=\"https://doi.org/10.1007/978-3-642-32940-1_10\">10.1007/978-3-642-32940-1_10</a>."},"related_material":{"record":[{"id":"2716","relation":"later_version","status":"public"}]},"scopus_import":"1","page":"115-131","status":"public","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"acknowledgement":"Author supported by Austrian Science Fund (FWF) Grant No P 23499-N23, FWF NFN Grant No S11407 (RiSE), ERC Start Grant (279307: Graph Games), Microsoft faculty fellowship.","volume":7454,"year":"2012","date_created":"2022-03-21T08:00:21Z","date_updated":"2023-02-23T10:55:06Z","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","title":"Strategy synthesis for multi-dimensional quantitative objectives","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783642329395"],"eisbn":["9783642329401"],"issn":["0302-9743","1611-3349"]},"type":"conference","alternative_title":["LNCS"],"publication_status":"published","quality_controlled":"1","publication":"CONCUR 2012 - Concurrency Theory","intvolume":"      7454","_id":"10904","doi":"10.1007/978-3-642-32940-1_10","date_published":"2012-09-15T00:00:00Z","conference":{"location":"Newcastle upon Tyne, United Kingdom","end_date":"2012-09-07","name":"CONCUR: Conference on Concurrency Theory","start_date":"2012-09-04"},"arxiv":1,"external_id":{"arxiv":["1201.5073"]},"month":"09","oa_version":"Preprint","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Mickael","last_name":"Randour","full_name":"Randour, Mickael"},{"full_name":"Raskin, Jean-François","last_name":"Raskin","first_name":"Jean-François"}],"editor":[{"full_name":"Koutny, Maciej","last_name":"Koutny","first_name":"Maciej"},{"full_name":"Ulidowski, Irek","last_name":"Ulidowski","first_name":"Irek"}],"place":"Berlin, Heidelberg","ec_funded":1,"department":[{"_id":"KrCh"}]},{"ec_funded":1,"department":[{"_id":"KrCh"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Sebastian","full_name":"Krinninger, Sebastian","last_name":"Krinninger"},{"last_name":"Nanongkai","full_name":"Nanongkai, Danupon","first_name":"Danupon"}],"oa_version":"Preprint","external_id":{"arxiv":["1604.08234"]},"arxiv":1,"conference":{"name":"ESA: European Symposium on Algorithms","start_date":"2012-09-10","location":"Ljubljana, Slovenia","end_date":"2012-09-12"},"month":"10","_id":"10905","doi":"10.1007/978-3-642-33090-2_27","date_published":"2012-10-01T00:00:00Z","publication":"Algorithms – ESA 2012","intvolume":"      7501","oa":1,"publication_status":"published","quality_controlled":"1","alternative_title":["LNCS"],"type":"conference","publication_identifier":{"eisbn":["9783642330902"],"isbn":["9783642330896"],"issn":["0302-9743"],"eissn":["1611-3349"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Polynomial-time algorithms for energy games with special weight structures","publisher":"Springer","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-05T14:09:30Z","year":"2012","date_created":"2022-03-21T08:01:45Z","acknowledgement":"Supported by the Austrian Science Fund (FWF): P23499-N23, the Austrian Science Fund (FWF): S11407-N23 (RiSE), an ERC Start Grant (279307: Graph Games), and a Microsoft Faculty Fellows Award","volume":7501,"status":"public","project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08234"}],"page":"301-312","scopus_import":"1","related_material":{"record":[{"relation":"later_version","id":"535","status":"public"}]},"citation":{"mla":"Chatterjee, Krishnendu, et al. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” <i>Algorithms – ESA 2012</i>, vol. 7501, Springer, 2012, pp. 301–12, doi:<a href=\"https://doi.org/10.1007/978-3-642-33090-2_27\">10.1007/978-3-642-33090-2_27</a>.","ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Polynomial-time algorithms for energy games with special weight structures,” in <i>Algorithms – ESA 2012</i>, Ljubljana, Slovenia, 2012, vol. 7501, pp. 301–312.","short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, Algorithms – ESA 2012, Springer, 2012, pp. 301–312.","ista":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. 2012. Polynomial-time algorithms for energy games with special weight structures. Algorithms – ESA 2012. ESA: European Symposium on Algorithms, LNCS, vol. 7501, 301–312.","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., &#38; Nanongkai, D. (2012). Polynomial-time algorithms for energy games with special weight structures. In <i>Algorithms – ESA 2012</i> (Vol. 7501, pp. 301–312). Ljubljana, Slovenia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33090-2_27\">https://doi.org/10.1007/978-3-642-33090-2_27</a>","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, and Danupon Nanongkai. “Polynomial-Time Algorithms for Energy Games with Special Weight Structures.” In <i>Algorithms – ESA 2012</i>, 7501:301–12. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33090-2_27\">https://doi.org/10.1007/978-3-642-33090-2_27</a>.","ama":"Chatterjee K, Henzinger MH, Krinninger S, Nanongkai D. Polynomial-time algorithms for energy games with special weight structures. In: <i>Algorithms – ESA 2012</i>. Vol 7501. Springer; 2012:301-312. doi:<a href=\"https://doi.org/10.1007/978-3-642-33090-2_27\">10.1007/978-3-642-33090-2_27</a>"},"day":"01","abstract":[{"lang":"eng","text":"Energy games belong to a class of turn-based two-player infinite-duration games played on a weighted directed graph. It is one of the rare and intriguing combinatorial problems that lie in NP ∩ co−NP, but are not known to be in P. While the existence of polynomial-time algorithms has been a major open problem for decades, there is no algorithm that solves any non-trivial subclass in polynomial time.\r\nIn this paper, we give several results based on the weight structures of the graph. First, we identify a notion of penalty and present a polynomial-time algorithm when the penalty is large. Our algorithm is the first polynomial-time algorithm on a large class of weighted graphs. It includes several counter examples that show that many previous algorithms, such as value iteration and random facet algorithms, require at least sub-exponential time. Our main technique is developing the first non-trivial approximation algorithm and showing how to convert it to an exact algorithm. Moreover, we show that in a practical case in verification where weights are clustered around a constant number of values, the energy game problem can be solved in polynomial time. We also show that the problem is still as hard as in general when the clique-width is bounded or the graph is strongly ergodic, suggesting that restricting graph structures need not help."}]},{"oa_version":"Published Version","author":[{"first_name":"Sergey","last_name":"Grebenshchikov","full_name":"Grebenshchikov, Sergey"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nuno P.","last_name":"Lopes","full_name":"Lopes, Nuno P."},{"first_name":"Corneliu","last_name":"Popeea","full_name":"Popeea, Corneliu"},{"first_name":"Andrey","last_name":"Rybalchenko","full_name":"Rybalchenko, Andrey"}],"series_title":"LNCS","editor":[{"first_name":"Cormac","full_name":"Flanagan, Cormac","last_name":"Flanagan"},{"full_name":"König, Barbara","last_name":"König","first_name":"Barbara"}],"place":"Berlin, Heidelberg","department":[{"_id":"ToHe"}],"type":"conference","publication_identifier":{"eisbn":["9783642287565"],"isbn":["9783642287558"],"issn":["0302-9743"],"eissn":["1611-3349"]},"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"oa":1,"publication":"Tools and Algorithms for the Construction and Analysis of Systems","intvolume":"      7214","quality_controlled":"1","publication_status":"published","month":"04","conference":{"end_date":"2012-04-01","location":"Tallinn, Estonia","start_date":"2012-03-24","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"doi":"10.1007/978-3-642-28756-5_46","date_published":"2012-04-01T00:00:00Z","_id":"10906","main_file_link":[{"url":"https://doi.org/10.1007/978-3-642-28756-5_46","open_access":"1"}],"status":"public","page":"549-551","date_created":"2022-03-21T08:03:30Z","year":"2012","volume":7214,"date_updated":"2023-09-05T14:09:54Z","publisher":"Springer","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"HSF(C): A software verifier based on Horn clauses","article_processing_charge":"No","abstract":[{"text":"HSF(C) is a tool that automates verification of safety and liveness properties for C programs. This paper describes the verification approach taken by HSF(C) and provides instructions on how to install and use the tool.","lang":"eng"}],"citation":{"mla":"Grebenshchikov, Sergey, et al. “HSF(C): A Software Verifier Based on Horn Clauses.” <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, edited by Cormac Flanagan and Barbara König, vol. 7214, Springer, 2012, pp. 549–51, doi:<a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">10.1007/978-3-642-28756-5_46</a>.","ieee":"S. Grebenshchikov, A. Gupta, N. P. Lopes, C. Popeea, and A. Rybalchenko, “HSF(C): A software verifier based on Horn clauses,” in <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, Tallinn, Estonia, 2012, vol. 7214, pp. 549–551.","short":"S. Grebenshchikov, A. Gupta, N.P. Lopes, C. Popeea, A. Rybalchenko, in:, C. Flanagan, B. König (Eds.), Tools and Algorithms for the Construction and Analysis of Systems, Springer, Berlin, Heidelberg, 2012, pp. 549–551.","ista":"Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. 2012. HSF(C): A software verifier based on Horn clauses. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of SystemsLNCS, LNCS, vol. 7214, 549–551.","ama":"Grebenshchikov S, Gupta A, Lopes NP, Popeea C, Rybalchenko A. HSF(C): A software verifier based on Horn clauses. In: Flanagan C, König B, eds. <i>Tools and Algorithms for the Construction and Analysis of Systems</i>. Vol 7214. LNCS. Berlin, Heidelberg: Springer; 2012:549-551. doi:<a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">10.1007/978-3-642-28756-5_46</a>","chicago":"Grebenshchikov, Sergey, Ashutosh Gupta, Nuno P. Lopes, Corneliu Popeea, and Andrey Rybalchenko. “HSF(C): A Software Verifier Based on Horn Clauses.” In <i>Tools and Algorithms for the Construction and Analysis of Systems</i>, edited by Cormac Flanagan and Barbara König, 7214:549–51. LNCS. Berlin, Heidelberg: Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">https://doi.org/10.1007/978-3-642-28756-5_46</a>.","apa":"Grebenshchikov, S., Gupta, A., Lopes, N. P., Popeea, C., &#38; Rybalchenko, A. (2012). HSF(C): A software verifier based on Horn clauses. In C. Flanagan &#38; B. König (Eds.), <i>Tools and Algorithms for the Construction and Analysis of Systems</i> (Vol. 7214, pp. 549–551). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-28756-5_46\">https://doi.org/10.1007/978-3-642-28756-5_46</a>"},"day":"01","scopus_import":"1"},{"has_accepted_license":"1","scopus_import":1,"day":"15","citation":{"mla":"Liang, Huixuan, et al. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.” <i>Biology Open</i>, vol. 1, no. 12, The Company of Biologists, 2012, pp. 1200–03, doi:<a href=\"https://doi.org/10.1242/bio.20122287\">10.1242/bio.20122287</a>.","ieee":"H. Liang, S. Hippenmeyer, and H. Ghashghaei, “A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors,” <i>Biology open</i>, vol. 1, no. 12. The Company of Biologists, pp. 1200–1203, 2012.","short":"H. Liang, S. Hippenmeyer, H. Ghashghaei, Biology Open 1 (2012) 1200–1203.","chicago":"Liang, Huixuan, Simon Hippenmeyer, and H. Ghashghaei. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.” <i>Biology Open</i>. The Company of Biologists, 2012. <a href=\"https://doi.org/10.1242/bio.20122287\">https://doi.org/10.1242/bio.20122287</a>.","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.","ama":"Liang H, Hippenmeyer S, Ghashghaei H. A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. <i>Biology open</i>. 2012;1(12):1200-1203. doi:<a href=\"https://doi.org/10.1242/bio.20122287\">10.1242/bio.20122287</a>","apa":"Liang, H., Hippenmeyer, S., &#38; Ghashghaei, H. (2012). A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. <i>Biology Open</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/bio.20122287\">https://doi.org/10.1242/bio.20122287</a>"},"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."}],"title":"A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors","ddc":["576"],"date_updated":"2021-01-12T06:56:23Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"The Company of Biologists","pubrep_id":"387","volume":1,"year":"2012","date_created":"2018-12-11T11:56:38Z","page":"1200 - 1203","status":"public","_id":"2263","date_published":"2012-12-15T00:00:00Z","doi":"10.1242/bio.20122287","month":"12","publication_status":"published","quality_controlled":"1","oa":1,"publication":"Biology open","intvolume":"         1","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:35Z","issue":"12","type":"journal_article","file":[{"creator":"system","file_size":726695,"date_created":"2018-12-12T10:13:09Z","file_id":"4990","relation":"main_file","date_updated":"2020-07-14T12:45:35Z","file_name":"IST-2015-387-v1+1_1200.full.pdf","checksum":"605a1800b81227848c361fd6ba7d22ba","access_level":"open_access","content_type":"application/pdf"}],"department":[{"_id":"SiHi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"publist_id":"4682","author":[{"first_name":"Huixuan","last_name":"Liang","full_name":"Liang, Huixuan"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"last_name":"Ghashghaei","full_name":"Ghashghaei, H.","first_name":"H."}],"oa_version":"Published Version"},{"pmid":1,"title":"The propagation approach for computing biochemical reaction networks","publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:56:38Z","volume":10,"date_created":"2018-12-11T11:56:52Z","year":"2012","page":"310 - 322","status":"public","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"scopus_import":1,"day":"03","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.","ama":"Henzinger TA, Mateescu M. The propagation approach for computing biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. 2012;10(2):310-322. doi:<a href=\"https://doi.org/10.1109/TCBB.2012.91\">10.1109/TCBB.2012.91</a>","chicago":"Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. IEEE, 2012. <a href=\"https://doi.org/10.1109/TCBB.2012.91\">https://doi.org/10.1109/TCBB.2012.91</a>.","apa":"Henzinger, T. A., &#38; Mateescu, M. (2012). The propagation approach for computing biochemical reaction networks. <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>. IEEE. <a href=\"https://doi.org/10.1109/TCBB.2012.91\">https://doi.org/10.1109/TCBB.2012.91</a>","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,” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>, vol. 10, no. 2. IEEE, pp. 310–322, 2012.","mla":"Henzinger, Thomas A., and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” <i>IEEE ACM Transactions on Computational Biology and Bioinformatics</i>, vol. 10, no. 2, IEEE, 2012, pp. 310–22, doi:<a href=\"https://doi.org/10.1109/TCBB.2012.91\">10.1109/TCBB.2012.91</a>."},"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 &quot;significant&quot; 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"}],"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"ec_funded":1,"oa_version":"None","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Mateescu, Maria","last_name":"Mateescu","first_name":"Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"4625","date_published":"2012-07-03T00:00:00Z","doi":"10.1109/TCBB.2012.91","_id":"2302","month":"07","external_id":{"pmid":["22778152"]},"quality_controlled":"1","publication_status":"published","publication":"IEEE ACM Transactions on Computational Biology and Bioinformatics","intvolume":"        10","language":[{"iso":"eng"}],"type":"journal_article","issue":"2"},{"acknowledgement":"Partial financial support by NSERC ","volume":2,"year":"2012","date_created":"2018-12-11T11:56:58Z","page":"321-328","publist_id":"4609","status":"public","oa_version":"Preprint","main_file_link":[{"url":"http://arxiv.org/abs/1204.0435","open_access":"1"}],"author":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"RoSe"}],"title":"Absence of bound states implies non-negativity of the scattering length","publisher":"European Mathematical Society","date_updated":"2021-01-12T06:56:44Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"24","citation":{"short":"R. Seiringer, Journal of Spectral Theory 2 (2012) 321–328.","ista":"Seiringer R. 2012. Absence of bound states implies non-negativity of the scattering length. Journal of Spectral Theory. 2(3), 321–328.","apa":"Seiringer, R. (2012). Absence of bound states implies non-negativity of the scattering length. <i>Journal of Spectral Theory</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/JST/31\">https://doi.org/10.4171/JST/31</a>","chicago":"Seiringer, Robert. “Absence of Bound States Implies Non-Negativity of the Scattering Length.” <i>Journal of Spectral Theory</i>. European Mathematical Society, 2012. <a href=\"https://doi.org/10.4171/JST/31\">https://doi.org/10.4171/JST/31</a>.","ama":"Seiringer R. Absence of bound states implies non-negativity of the scattering length. <i>Journal of Spectral Theory</i>. 2012;2(3):321-328. doi:<a href=\"https://doi.org/10.4171/JST/31\">10.4171/JST/31</a>","mla":"Seiringer, Robert. “Absence of Bound States Implies Non-Negativity of the Scattering Length.” <i>Journal of Spectral Theory</i>, vol. 2, no. 3, European Mathematical Society, 2012, pp. 321–28, doi:<a href=\"https://doi.org/10.4171/JST/31\">10.4171/JST/31</a>.","ieee":"R. Seiringer, “Absence of bound states implies non-negativity of the scattering length,” <i>Journal of Spectral Theory</i>, vol. 2, no. 3. European Mathematical Society, pp. 321–328, 2012."},"language":[{"iso":"eng"}],"issue":"3","abstract":[{"lang":"eng","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. "}],"type":"journal_article","_id":"2318","doi":"10.4171/JST/31","date_published":"2012-06-24T00:00:00Z","month":"06","publication_status":"published","quality_controlled":"1","publication":"Journal of Spectral Theory","oa":1,"intvolume":"         2"},{"page":"1319 - 1334","status":"public","volume":29,"year":"2012","date_created":"2018-12-11T11:57:30Z","ddc":["570","576"],"date_updated":"2021-01-12T06:57:19Z","publisher":"Oxford University Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pubrep_id":"384","title":"A consistent phylogenetic backbone for the fungi","abstract":[{"lang":"eng","text":"The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses."}],"day":"01","citation":{"ieee":"I. Ebersberger <i>et al.</i>, “A consistent phylogenetic backbone for the fungi,” <i>Molecular Biology and Evolution</i>, vol. 29, no. 5. Oxford University Press, pp. 1319–1334, 2012.","mla":"Ebersberger, Ingo, et al. “A Consistent Phylogenetic Backbone for the Fungi.” <i>Molecular Biology and Evolution</i>, vol. 29, no. 5, Oxford University Press, 2012, pp. 1319–34, doi:<a href=\"https://doi.org/10.1093/molbev/msr285\">10.1093/molbev/msr285</a>.","chicago":"Ebersberger, Ingo, Ricardo De Matos Simoes, Anne Kupczok, Matthias Gube, Erika Kothe, Kerstin Voigt, and Arndt Von Haeseler. “A Consistent Phylogenetic Backbone for the Fungi.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2012. <a href=\"https://doi.org/10.1093/molbev/msr285\">https://doi.org/10.1093/molbev/msr285</a>.","ama":"Ebersberger I, De Matos Simoes R, Kupczok A, et al. A consistent phylogenetic backbone for the fungi. <i>Molecular Biology and Evolution</i>. 2012;29(5):1319-1334. doi:<a href=\"https://doi.org/10.1093/molbev/msr285\">10.1093/molbev/msr285</a>","apa":"Ebersberger, I., De Matos Simoes, R., Kupczok, A., Gube, M., Kothe, E., Voigt, K., &#38; Von Haeseler, A. (2012). A consistent phylogenetic backbone for the fungi. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msr285\">https://doi.org/10.1093/molbev/msr285</a>","ista":"Ebersberger I, De Matos Simoes R, Kupczok A, Gube M, Kothe E, Voigt K, Von Haeseler A. 2012. A consistent phylogenetic backbone for the fungi. Molecular Biology and Evolution. 29(5), 1319–1334.","short":"I. Ebersberger, R. De Matos Simoes, A. Kupczok, M. Gube, E. Kothe, K. Voigt, A. Von Haeseler, Molecular Biology and Evolution 29 (2012) 1319–1334."},"has_accepted_license":"1","scopus_import":1,"publist_id":"4515","oa_version":"Published Version","author":[{"first_name":"Ingo","full_name":"Ebersberger, Ingo","last_name":"Ebersberger"},{"first_name":"Ricardo","last_name":"De Matos Simoes","full_name":"De Matos Simoes, Ricardo"},{"id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","last_name":"Kupczok","full_name":"Kupczok, Anne"},{"first_name":"Matthias","full_name":"Gube, Matthias","last_name":"Gube"},{"last_name":"Kothe","full_name":"Kothe, Erika","first_name":"Erika"},{"last_name":"Voigt","full_name":"Voigt, Kerstin","first_name":"Kerstin"},{"full_name":"Von Haeseler, Arndt","last_name":"Von Haeseler","first_name":"Arndt"}],"tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"file":[{"date_updated":"2020-07-14T12:45:40Z","file_name":"IST-2015-384-v1+1_Mol_Biol_Evol-2012-Ebersberger-1319-34.pdf","access_level":"open_access","checksum":"d565dcac27d1736c0c378ea6fcf22d69","content_type":"application/pdf","creator":"system","file_size":754922,"date_created":"2018-12-12T10:13:30Z","relation":"main_file","file_id":"5013"}],"department":[{"_id":"JoBo"}],"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:40Z","issue":"5","type":"journal_article","publication_status":"published","quality_controlled":"1","intvolume":"        29","publication":"Molecular Biology and Evolution","oa":1,"_id":"2411","doi":"10.1093/molbev/msr285","date_published":"2012-05-01T00:00:00Z","month":"05"},{"ddc":["000"],"date_updated":"2023-02-23T10:06:04Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","pubrep_id":"525","title":"Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives","page":"461 - 473","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"status":"public","volume":18,"year":"2012","date_created":"2018-12-11T11:59:13Z","has_accepted_license":"1","related_material":{"record":[{"id":"1598","relation":"later_version","status":"public"}]},"scopus_import":1,"abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) with specifications given as Büchi (liveness) objectives. We consider the problem of computing the set of almost-sure winning vertices from where the objective can be ensured with probability 1. We study for the first time the average case complexity of the classical algorithm for computing the set of almost-sure winning vertices for MDPs with Büchi objectives. Our contributions are as follows: First, we show that for MDPs with constant out-degree the expected number of iterations is at most logarithmic and the average case running time is linear (as compared to the worst case linear number of iterations and quadratic time complexity). Second, for the average case analysis over all MDPs we show that the expected number of iterations is constant and the average case running time is linear (again as compared to the worst case linear number of iterations and quadratic time complexity). Finally we also show that given that all MDPs are equally likely, the probability that the classical algorithm requires more than constant number of iterations is exponentially small."}],"day":"10","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Average Case Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives</i>. Vol. 18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 461–73, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461\">10.4230/LIPIcs.FSTTCS.2012.461</a>.","ieee":"K. Chatterjee, M. Joglekar, and N. Shah, “Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Hyderabad, India, 2012, vol. 18, pp. 461–473.","short":"K. Chatterjee, M. Joglekar, N. Shah, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 461–473.","ista":"Chatterjee K, Joglekar M, Shah N. 2012. Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 18, 461–473.","apa":"Chatterjee, K., Joglekar, M., &#38; Shah, N. (2012). Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives (Vol. 18, pp. 461–473). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Hyderabad, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461\">https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461</a>","ama":"Chatterjee K, Joglekar M, Shah N. Average case analysis of the classical algorithm for Markov decision processes with Büchi objectives. In: Vol 18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2012:461-473. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461\">10.4230/LIPIcs.FSTTCS.2012.461</a>","chicago":"Chatterjee, Krishnendu, Manas Joglekar, and Nisarg Shah. “Average Case Analysis of the Classical Algorithm for Markov Decision Processes with Büchi Objectives,” 18:461–73. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461\">https://doi.org/10.4230/LIPIcs.FSTTCS.2012.461</a>."},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"file":[{"creator":"system","file_size":519040,"date_created":"2018-12-12T10:13:53Z","relation":"main_file","file_id":"5040","access_level":"open_access","content_type":"application/pdf","checksum":"d4d644ed1a885dbfc4fa1ef4c5724dab","file_name":"IST-2016-525-v1+1_42_1_.pdf","date_updated":"2020-07-14T12:45:45Z"}],"ec_funded":1,"department":[{"_id":"KrCh"}],"publist_id":"4180","oa_version":"Published Version","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"last_name":"Joglekar","full_name":"Joglekar, Manas","first_name":"Manas"},{"full_name":"Shah, Nisarg","last_name":"Shah","first_name":"Nisarg"}],"publication_status":"published","quality_controlled":"1","oa":1,"intvolume":"        18","_id":"2715","doi":"10.4230/LIPIcs.FSTTCS.2012.461","date_published":"2012-12-10T00:00:00Z","conference":{"end_date":"2012-12-17","location":"Hyderabad, India","start_date":"2012-12-15","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science"},"month":"12","file_date_updated":"2020-07-14T12:45:45Z","language":[{"iso":"eng"}],"type":"conference","alternative_title":["LIPIcs"]},{"department":[{"_id":"ChLa"}],"title":"Dynamic pruning of factor graphs for maximum marginal prediction","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:59:59Z","publisher":"Neural Information Processing Systems","volume":1,"year":"2012","date_created":"2018-12-11T11:59:48Z","page":"82 - 90","status":"public","publist_id":"3975","author":[{"last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"oa_version":"None","_id":"2825","date_published":"2012-12-01T00:00:00Z","scopus_import":1,"conference":{"name":"NIPS: Neural Information Processing Systems","start_date":"2012-12-03","location":"Lake Tahoe, NV, United States","end_date":"2012-12-06"},"month":"12","publication_status":"published","quality_controlled":"1","intvolume":"         1","day":"01","citation":{"ieee":"C. Lampert, “Dynamic pruning of factor graphs for maximum marginal prediction,” presented at the NIPS: Neural Information Processing Systems, Lake Tahoe, NV, United States, 2012, vol. 1, pp. 82–90.","mla":"Lampert, Christoph. <i>Dynamic Pruning of Factor Graphs for Maximum Marginal Prediction</i>. Vol. 1, Neural Information Processing Systems, 2012, pp. 82–90.","ista":"Lampert C. 2012. Dynamic pruning of factor graphs for maximum marginal prediction. NIPS: Neural Information Processing Systems vol. 1, 82–90.","chicago":"Lampert, Christoph. “Dynamic Pruning of Factor Graphs for Maximum Marginal Prediction,” 1:82–90. Neural Information Processing Systems, 2012.","apa":"Lampert, C. (2012). Dynamic pruning of factor graphs for maximum marginal prediction (Vol. 1, pp. 82–90). Presented at the NIPS: Neural Information Processing Systems, Lake Tahoe, NV, United States: Neural Information Processing Systems.","ama":"Lampert C. Dynamic pruning of factor graphs for maximum marginal prediction. In: Vol 1. Neural Information Processing Systems; 2012:82-90.","short":"C. Lampert, in:, Neural Information Processing Systems, 2012, pp. 82–90."},"language":[{"iso":"eng"}],"abstract":[{"text":"We study the problem of maximum marginal prediction (MMP) in probabilistic graphical models, a task that occurs, for example, as the Bayes optimal decision rule under a Hamming loss. MMP is typically performed as a two-stage procedure: one estimates each variable's marginal probability and then forms a prediction from the states of maximal probability. In this work we propose a simple yet effective technique for accelerating MMP when inference is sampling-based: instead of the above two-stage procedure we directly estimate the posterior probability of each decision variable. This allows us to identify the point of time when we are sufficiently certain about any individual decision. Whenever this is the case, we dynamically prune the variables we are confident about from the underlying factor graph. Consequently, at any time only samples of variables whose decision is still uncertain need to be created. Experiments in two prototypical scenarios, multi-label classification and image inpainting, show that adaptive sampling can drastically accelerate MMP without sacrificing prediction accuracy.","lang":"eng"}],"type":"conference"},{"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ec_funded":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Zufferey","full_name":"Zufferey, Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"oa_version":"Submitted Version","publist_id":"3946","quality_controlled":"1","publication_status":"published","intvolume":"       301","oa":1,"publication":"Journal of Theoretical Biology","doi":"10.1016/j.jtbi.2012.02.021","date_published":"2012-05-21T00:00:00Z","_id":"2848","month":"05","external_id":{"pmid":["22394652"]},"language":[{"iso":"eng"}],"type":"journal_article","date_updated":"2021-01-12T07:00:12Z","publisher":"Elsevier","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Evolutionary game dynamics in populations with different learners","pmid":1,"page":"161 - 173","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322297/","open_access":"1"}],"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"status":"public","volume":301,"date_created":"2018-12-11T11:59:55Z","year":"2012","scopus_import":1,"abstract":[{"text":"We study evolutionary game theory in a setting where individuals learn from each other. We extend the traditional approach by assuming that a population contains individuals with different learning abilities. In particular, we explore the situation where individuals have different search spaces, when attempting to learn the strategies of others. The search space of an individual specifies the set of strategies learnable by that individual. The search space is genetically given and does not change under social evolutionary dynamics. We introduce a general framework and study a specific example in the context of direct reciprocity. For this example, we obtain the counter intuitive result that cooperation can only evolve for intermediate benefit-to-cost ratios, while small and large benefit-to-cost ratios favor defection. Our paper is a step toward making a connection between computational learning theory and evolutionary game dynamics.","lang":"eng"}],"day":"21","citation":{"apa":"Chatterjee, K., Zufferey, D., &#38; Nowak, M. (2012). Evolutionary game dynamics in populations with different learners. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2012.02.021\">https://doi.org/10.1016/j.jtbi.2012.02.021</a>","ama":"Chatterjee K, Zufferey D, Nowak M. Evolutionary game dynamics in populations with different learners. <i>Journal of Theoretical Biology</i>. 2012;301:161-173. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2012.02.021\">10.1016/j.jtbi.2012.02.021</a>","chicago":"Chatterjee, Krishnendu, Damien Zufferey, and Martin Nowak. “Evolutionary Game Dynamics in Populations with Different Learners.” <i>Journal of Theoretical Biology</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.jtbi.2012.02.021\">https://doi.org/10.1016/j.jtbi.2012.02.021</a>.","ista":"Chatterjee K, Zufferey D, Nowak M. 2012. Evolutionary game dynamics in populations with different learners. Journal of Theoretical Biology. 301, 161–173.","short":"K. Chatterjee, D. Zufferey, M. Nowak, Journal of Theoretical Biology 301 (2012) 161–173.","ieee":"K. Chatterjee, D. Zufferey, and M. Nowak, “Evolutionary game dynamics in populations with different learners,” <i>Journal of Theoretical Biology</i>, vol. 301. Elsevier, pp. 161–173, 2012.","mla":"Chatterjee, Krishnendu, et al. “Evolutionary Game Dynamics in Populations with Different Learners.” <i>Journal of Theoretical Biology</i>, vol. 301, Elsevier, 2012, pp. 161–73, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2012.02.021\">10.1016/j.jtbi.2012.02.021</a>."}},{"file":[{"checksum":"44ee8d173487e8ed41a51136816bbeb4","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2016-546-v1+1_2014-J-05-SteinerMinTrees.pdf","date_updated":"2020-07-14T12:45:51Z","creator":"system","file_size":392021,"relation":"main_file","file_id":"5078","date_created":"2018-12-12T10:14:26Z"}],"department":[{"_id":"HeEd"}],"publist_id":"3943","oa_version":"Submitted Version","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"full_name":"Strelkova, Nataliya","last_name":"Strelkova","first_name":"Nataliya"}],"_id":"2849","date_published":"2012-01-01T00:00:00Z","doi":"10.1070/RM2012v067n06ABEH004820","month":"01","publication_status":"published","quality_controlled":"1","intvolume":"        67","publication":"Russian Mathematical Surveys","oa":1,"file_date_updated":"2020-07-14T12:45:51Z","language":[{"iso":"eng"}],"issue":"6","type":"journal_article","title":"On the configuration space of Steiner minimal trees","ddc":["000"],"publisher":"IOP Publishing Ltd.","date_updated":"2021-01-12T07:00:13Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pubrep_id":"546","volume":67,"year":"2012","date_created":"2018-12-11T11:59:55Z","page":"1167 - 1168","status":"public","has_accepted_license":"1","scopus_import":1,"day":"01","citation":{"mla":"Edelsbrunner, Herbert, and Nataliya Strelkova. “On the Configuration Space of Steiner Minimal Trees.” <i>Russian Mathematical Surveys</i>, vol. 67, no. 6, IOP Publishing Ltd., 2012, pp. 1167–68, doi:<a href=\"https://doi.org/10.1070/RM2012v067n06ABEH004820\">10.1070/RM2012v067n06ABEH004820</a>.","ieee":"H. Edelsbrunner and N. Strelkova, “On the configuration space of Steiner minimal trees,” <i>Russian Mathematical Surveys</i>, vol. 67, no. 6. IOP Publishing Ltd., pp. 1167–1168, 2012.","short":"H. Edelsbrunner, N. Strelkova, Russian Mathematical Surveys 67 (2012) 1167–1168.","ista":"Edelsbrunner H, Strelkova N. 2012. On the configuration space of Steiner minimal trees. Russian Mathematical Surveys. 67(6), 1167–1168.","apa":"Edelsbrunner, H., &#38; Strelkova, N. (2012). On the configuration space of Steiner minimal trees. <i>Russian Mathematical Surveys</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1070/RM2012v067n06ABEH004820\">https://doi.org/10.1070/RM2012v067n06ABEH004820</a>","chicago":"Edelsbrunner, Herbert, and Nataliya Strelkova. “On the Configuration Space of Steiner Minimal Trees.” <i>Russian Mathematical Surveys</i>. IOP Publishing Ltd., 2012. <a href=\"https://doi.org/10.1070/RM2012v067n06ABEH004820\">https://doi.org/10.1070/RM2012v067n06ABEH004820</a>.","ama":"Edelsbrunner H, Strelkova N. On the configuration space of Steiner minimal trees. <i>Russian Mathematical Surveys</i>. 2012;67(6):1167-1168. doi:<a href=\"https://doi.org/10.1070/RM2012v067n06ABEH004820\">10.1070/RM2012v067n06ABEH004820</a>"}},{"publist_id":"3870","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"oa_version":"None","ec_funded":1,"department":[{"_id":"ToHe"}],"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"type":"conference","_id":"2888","date_published":"2012-09-01T00:00:00Z","doi":"10.1007/978-3-642-33666-9_1","conference":{"end_date":"2012-10-05","location":"Innsbruck, Austria","name":"MODELS: Model-driven Engineering Languages and Systems","start_date":"2012-09-30"},"month":"09","publication_status":"published","quality_controlled":"1","intvolume":"      7590","publication":"Conference proceedings MODELS 2012","volume":7590,"year":"2012","date_created":"2018-12-11T12:00:09Z","page":"1 - 2","status":"public","project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"title":"Quantitative reactive models","publisher":"Springer","date_updated":"2021-01-12T07:00:29Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"01","citation":{"ista":"Henzinger TA. 2012. Quantitative reactive models. Conference proceedings MODELS 2012. MODELS: Model-driven Engineering Languages and Systems, LNCS, vol. 7590, 1–2.","apa":"Henzinger, T. A. (2012). Quantitative reactive models. In <i>Conference proceedings MODELS 2012</i> (Vol. 7590, pp. 1–2). Innsbruck, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-642-33666-9_1\">https://doi.org/10.1007/978-3-642-33666-9_1</a>","ama":"Henzinger TA. Quantitative reactive models. In: <i>Conference Proceedings MODELS 2012</i>. Vol 7590. Springer; 2012:1-2. doi:<a href=\"https://doi.org/10.1007/978-3-642-33666-9_1\">10.1007/978-3-642-33666-9_1</a>","chicago":"Henzinger, Thomas A. “Quantitative Reactive Models.” In <i>Conference Proceedings MODELS 2012</i>, 7590:1–2. Springer, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33666-9_1\">https://doi.org/10.1007/978-3-642-33666-9_1</a>.","short":"T.A. Henzinger, in:, Conference Proceedings MODELS 2012, Springer, 2012, pp. 1–2.","ieee":"T. A. Henzinger, “Quantitative reactive models,” in <i>Conference proceedings MODELS 2012</i>, Innsbruck, Austria, 2012, vol. 7590, pp. 1–2.","mla":"Henzinger, Thomas A. “Quantitative Reactive Models.” <i>Conference Proceedings MODELS 2012</i>, vol. 7590, Springer, 2012, pp. 1–2, doi:<a href=\"https://doi.org/10.1007/978-3-642-33666-9_1\">10.1007/978-3-642-33666-9_1</a>."},"abstract":[{"lang":"eng","text":"Formal verification aims to improve the quality of hardware and software by detecting errors before they do harm. At the basis of formal verification lies the logical notion of correctness, which purports to capture whether or not a circuit or program behaves as desired. We suggest that the boolean partition into correct and incorrect systems falls short of the practical need to assess the behavior of hardware and software in a more nuanced fashion against multiple criteria."}],"scopus_import":1},{"page":"53 - 62","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"status":"public","publist_id":"3868","oa_version":"None","author":[{"last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"last_name":"Gopi","full_name":"Gopi, Sivakanth","first_name":"Sivakanth"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna"},{"first_name":"Nishant","full_name":"Totla, Nishant","last_name":"Totla"}],"year":"2012","date_created":"2018-12-11T12:00:10Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","date_updated":"2021-01-12T07:00:30Z","ec_funded":1,"department":[{"_id":"ToHe"}],"title":"Synthesis from incompatible specifications","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Systems are often specified using multiple requirements on their behavior. In practice, these requirements can be contradictory. The classical approach to specification, verification, and synthesis demands more detailed specifications that resolve any contradictions in the requirements. These detailed specifications are usually large, cumbersome, and hard to maintain or modify. In contrast, quantitative frameworks allow the formalization of the intuitive idea that what is desired is an implementation that comes &quot;closest&quot; to satisfying the mutually incompatible requirements, according to a measure of fit that can be defined by the requirements engineer. One flexible framework for quantifying how &quot;well&quot; an implementation satisfies a specification is offered by simulation distances that are parameterized by an error model. We introduce this framework, study its properties, and provide an algorithmic solution for the following quantitative synthesis question: given two (or more) behavioral requirements specified by possibly incompatible finite-state machines, and an error model, find the finite-state implementation that minimizes the maximal simulation distance to the given requirements. Furthermore, we generalize the framework to handle infinite alphabets (for example, realvalued domains). We also demonstrate how quantitative specifications based on simulation distances might lead to smaller and easier to modify specifications. Finally, we illustrate our approach using case studies on error correcting codes and scheduler synthesis."}],"type":"conference","day":"01","citation":{"short":"P. Cerny, S. Gopi, T.A. Henzinger, A. Radhakrishna, N. Totla, in:, Proceedings of the Tenth ACM International Conference on Embedded Software, ACM, 2012, pp. 53–62.","chicago":"Cerny, Pavol, Sivakanth Gopi, Thomas A Henzinger, Arjun Radhakrishna, and Nishant Totla. “Synthesis from Incompatible Specifications.” In <i>Proceedings of the Tenth ACM International Conference on Embedded Software</i>, 53–62. ACM, 2012. <a href=\"https://doi.org/10.1145/2380356.2380371\">https://doi.org/10.1145/2380356.2380371</a>.","ama":"Cerny P, Gopi S, Henzinger TA, Radhakrishna A, Totla N. Synthesis from incompatible specifications. In: <i>Proceedings of the Tenth ACM International Conference on Embedded Software</i>. ACM; 2012:53-62. doi:<a href=\"https://doi.org/10.1145/2380356.2380371\">10.1145/2380356.2380371</a>","apa":"Cerny, P., Gopi, S., Henzinger, T. A., Radhakrishna, A., &#38; Totla, N. (2012). Synthesis from incompatible specifications. In <i>Proceedings of the tenth ACM international conference on Embedded software</i> (pp. 53–62). Tampere, Finland: ACM. <a href=\"https://doi.org/10.1145/2380356.2380371\">https://doi.org/10.1145/2380356.2380371</a>","ista":"Cerny P, Gopi S, Henzinger TA, Radhakrishna A, Totla N. 2012. Synthesis from incompatible specifications. Proceedings of the tenth ACM international conference on Embedded software. EMSOFT: Embedded Software , 53–62.","mla":"Cerny, Pavol, et al. “Synthesis from Incompatible Specifications.” <i>Proceedings of the Tenth ACM International Conference on Embedded Software</i>, ACM, 2012, pp. 53–62, doi:<a href=\"https://doi.org/10.1145/2380356.2380371\">10.1145/2380356.2380371</a>.","ieee":"P. Cerny, S. Gopi, T. A. Henzinger, A. Radhakrishna, and N. Totla, “Synthesis from incompatible specifications,” in <i>Proceedings of the tenth ACM international conference on Embedded software</i>, Tampere, Finland, 2012, pp. 53–62."},"publication_status":"published","quality_controlled":"1","publication":"Proceedings of the tenth ACM international conference on Embedded software","_id":"2890","date_published":"2012-10-01T00:00:00Z","doi":"10.1145/2380356.2380371","scopus_import":1,"conference":{"location":"Tampere, Finland","end_date":"2012-10-12","start_date":"2012-10-07","name":"EMSOFT: Embedded Software "},"month":"10"}]