[{"date_published":"2011-06-27T00:00:00Z","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"}],"publisher":"IST Austria","date_updated":"2023-02-23T11:23:01Z","date_created":"2018-12-12T11:39:00Z","status":"public","type":"technical_report","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"id":"3341","status":"public","relation":"later_version"}]},"file_date_updated":"2020-07-14T12:46:40Z","day":"27","oa_version":"Published Version","has_accepted_license":"1","pubrep_id":"18","ddc":["000","005"],"abstract":[{"lang":"eng","text":"We consider two-player stochastic games played on a finite state space for an infinite num- ber of rounds. The games are concurrent: in each round, the two players (player 1 and player 2) choose their moves independently and simultaneously; the current state and the two moves determine a probability distribution over the successor states. We also consider the important special case of turn-based stochastic games where players make moves in turns, rather than concurrently. We study concurrent games with ω-regular winning conditions specified as parity objectives. The value for player 1 for a parity objective is the maximal probability with which the player can guarantee the satisfaction of the objective against all strategies of the opponent. We study the problem of continuity and robustness of the value function in concurrent and turn-based stochastic parity games with respect to imprecision in the transition probabilities. We present quantitative bounds on the difference of the value function (in terms of the imprecision of the transition probabilities) and show the value continuity for structurally equivalent concurrent games (two games are structurally equivalent if the support of the transition func- tion is same and the probabilities differ). We also show robustness of optimal strategies for structurally equivalent turn-based stochastic parity games. Finally we show that the value continuity property breaks without the structurally equivalent assumption (even for Markov chains) and show that our quantitative bound is asymptotically optimal. Hence our results are tight (the assumption is both necessary and sufficient) and optimal (our quantitative bound is asymptotically optimal)."}],"department":[{"_id":"KrCh"}],"page":"18","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu. <i>Robustness of Structurally Equivalent Concurrent Parity Games</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0006\">https://doi.org/10.15479/AT:IST-2011-0006</a>.","ieee":"K. Chatterjee, <i>Robustness of structurally equivalent concurrent parity games</i>. IST Austria, 2011.","ama":"Chatterjee K. <i>Robustness of Structurally Equivalent Concurrent Parity Games</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0006\">10.15479/AT:IST-2011-0006</a>","apa":"Chatterjee, K. (2011). <i>Robustness of structurally equivalent concurrent parity games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0006\">https://doi.org/10.15479/AT:IST-2011-0006</a>","mla":"Chatterjee, Krishnendu. <i>Robustness of Structurally Equivalent Concurrent Parity Games</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0006\">10.15479/AT:IST-2011-0006</a>.","short":"K. Chatterjee, Robustness of Structurally Equivalent Concurrent Parity Games, IST Austria, 2011.","ista":"Chatterjee K. 2011. Robustness of structurally equivalent concurrent parity games, IST Austria, 18p."},"oa":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2011-0006","publication_status":"published","file":[{"access_level":"open_access","file_name":"IST-2011-0006_IST-2011-0006.pdf","content_type":"application/pdf","file_id":"5546","file_size":335997,"creator":"system","checksum":"1322b652d6ab07eb5248298a3f91c1cf","relation":"main_file","date_created":"2018-12-12T11:54:24Z","date_updated":"2020-07-14T12:46:40Z"}],"year":"2011","publication_identifier":{"issn":["2664-1690"]},"_id":"5382","title":"Robustness of structurally equivalent concurrent parity games"},{"status":"public","type":"technical_report","day":"26","file_date_updated":"2020-07-14T12:46:40Z","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"relation":"later_version","status":"public","id":"3323"}]},"ddc":["000","006"],"pubrep_id":"19","has_accepted_license":"1","oa_version":"Published Version","abstract":[{"text":"We present a new decidable logic called TREX for expressing constraints about imperative tree data structures. In particular, TREX supports a transitive closure operator that can express reachability constraints, which often appear in data structure invariants. We show that our logic is closed under weakest precondition computation, which enables its use for automated software verification. We further show that satisfiability of formulas in TREX is decidable in NP. The low complexity makes it an attractive alternative to more expensive logics such as monadic second-order logic (MSOL) over trees, which have been traditionally used for reasoning about tree data structures.","lang":"eng"}],"date_published":"2011-04-26T00:00:00Z","publisher":"IST Austria","author":[{"last_name":"Wies","full_name":"Wies, Thomas","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Muñiz","full_name":"Muñiz, Marco","first_name":"Marco"},{"first_name":"Viktor","full_name":"Kuncak, Viktor","last_name":"Kuncak"}],"date_created":"2018-12-12T11:39:01Z","date_updated":"2023-02-23T11:22:16Z","citation":{"chicago":"Wies, Thomas, Marco Muñiz, and Viktor Kuncak. <i>On an Efficient Decision Procedure for Imperative Tree Data Structures</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0005\">https://doi.org/10.15479/AT:IST-2011-0005</a>.","ieee":"T. Wies, M. Muñiz, and V. Kuncak, <i>On an efficient decision procedure for imperative tree data structures</i>. IST Austria, 2011.","ama":"Wies T, Muñiz M, Kuncak V. <i>On an Efficient Decision Procedure for Imperative Tree Data Structures</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0005\">10.15479/AT:IST-2011-0005</a>","apa":"Wies, T., Muñiz, M., &#38; Kuncak, V. (2011). <i>On an efficient decision procedure for imperative tree data structures</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0005\">https://doi.org/10.15479/AT:IST-2011-0005</a>","mla":"Wies, Thomas, et al. <i>On an Efficient Decision Procedure for Imperative Tree Data Structures</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0005\">10.15479/AT:IST-2011-0005</a>.","ista":"Wies T, Muñiz M, Kuncak V. 2011. On an efficient decision procedure for imperative tree data structures, IST Austria, 25p.","short":"T. Wies, M. Muñiz, V. Kuncak, On an Efficient Decision Procedure for Imperative Tree Data Structures, IST Austria, 2011."},"oa":1,"year":"2011","file":[{"checksum":"b20029184c4a819c5f4466a4a3d238b5","file_size":619053,"creator":"system","date_created":"2018-12-12T11:53:01Z","relation":"main_file","date_updated":"2020-07-14T12:46:40Z","access_level":"open_access","file_name":"IST-2011-0005_IST-2011-0005.pdf","file_id":"5462","content_type":"application/pdf"}],"publication_status":"published","doi":"10.15479/AT:IST-2011-0005","language":[{"iso":"eng"}],"title":"On an efficient decision procedure for imperative tree data structures","_id":"5383","publication_identifier":{"issn":["2664-1690"]},"page":"25","department":[{"_id":"ToHe"}],"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"page":"30","file":[{"date_created":"2018-12-12T11:54:23Z","relation":"main_file","date_updated":"2020-07-14T12:46:40Z","checksum":"f5a0f664fadc335990f5fcf138df19f1","file_size":570827,"creator":"system","file_name":"IST-2011-004_IST-2011-0004.pdf","file_id":"5545","content_type":"application/pdf","access_level":"open_access"}],"year":"2011","publication_status":"published","language":[{"iso":"eng"}],"doi":"10.15479/AT:IST-2011-0004","title":"Decidable problems for probabilistic automata on infinite words","_id":"5384","publication_identifier":{"issn":["2664-1690"]},"citation":{"ieee":"K. Chatterjee and M. Tracol, <i>Decidable problems for probabilistic automata on infinite words</i>. IST Austria, 2011.","ama":"Chatterjee K, Tracol M. <i>Decidable Problems for Probabilistic Automata on Infinite Words</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0004\">10.15479/AT:IST-2011-0004</a>","chicago":"Chatterjee, Krishnendu, and Mathieu Tracol. <i>Decidable Problems for Probabilistic Automata on Infinite Words</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0004\">https://doi.org/10.15479/AT:IST-2011-0004</a>.","apa":"Chatterjee, K., &#38; Tracol, M. (2011). <i>Decidable problems for probabilistic automata on infinite words</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0004\">https://doi.org/10.15479/AT:IST-2011-0004</a>","mla":"Chatterjee, Krishnendu, and Mathieu Tracol. <i>Decidable Problems for Probabilistic Automata on Infinite Words</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0004\">10.15479/AT:IST-2011-0004</a>.","ista":"Chatterjee K, Tracol M. 2011. Decidable problems for probabilistic automata on infinite words, IST Austria, 30p.","short":"K. Chatterjee, M. Tracol, Decidable Problems for Probabilistic Automata on Infinite Words, IST Austria, 2011."},"oa":1,"date_created":"2018-12-12T11:39:01Z","date_updated":"2023-02-23T11:05:53Z","date_published":"2011-04-11T00:00:00Z","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Tracol","first_name":"Mathieu","full_name":"Tracol, Mathieu","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87"}],"publisher":"IST Austria","pubrep_id":"20","ddc":["000","005"],"oa_version":"Published Version","has_accepted_license":"1","abstract":[{"text":"We consider probabilistic automata on infinite words with acceptance defined by parity conditions. We consider three qualitative decision problems: (i) the positive decision problem asks whether there is a word that is accepted with positive probability; (ii) the almost decision problem asks whether there is a word that is accepted with probability 1; and (iii) the limit decision problem asks whether for every ε > 0 there is a word that is accepted with probability at least 1 − ε. We unify and generalize several decidability results for probabilistic automata over infinite words, and identify a robust (closed under union and intersection) subclass of probabilistic automata for which all the qualitative decision problems are decidable for parity conditions. We also show that if the input words are restricted to lasso shape words, then the positive and almost problems are decidable for all probabilistic automata with parity conditions.","lang":"eng"}],"type":"technical_report","status":"public","day":"11","file_date_updated":"2020-07-14T12:46:40Z","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"status":"public","id":"2957","relation":"later_version"}]}},{"month":"04","page":"14","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publication_identifier":{"issn":["2664-1690"]},"project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Design for Embedded Systems"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"language":[{"iso":"eng"}],"year":"2011","date_created":"2018-12-12T11:39:02Z","publisher":"IST Austria","abstract":[{"text":"There is recently a significant effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions, aiming for a general and flexible framework for quantitative-oriented specifications. In the heart of quantitative objectives lies the accumulation of values along a computation. It is either the accumulated summation, as with the energy objectives, or the accumulated average, as with the mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point of time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire computation. We study the border of decidability for extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities by prefix-accumulation assertions and extending LTL with path-accumulation assertions, result in temporal logics whose model-checking problem is decidable. The extended logics allow to significantly extend the currently known energy and mean-payoff objectives. Moreover, the prefix-accumulation assertions may be refined with “controlled-accumulation”, allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that the fragment we point to is, in a sense, the maximal logic whose extension with prefix-accumulation assertions permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, and in particular CTL and LTL, makes the problem undecidable.","lang":"eng"}],"has_accepted_license":"1","ddc":["000","004"],"related_material":{"record":[{"relation":"later_version","status":"public","id":"2038"},{"relation":"later_version","id":"3356","status":"public"}]},"file_date_updated":"2020-07-14T12:46:41Z","day":"04","status":"public","type":"technical_report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5385","title":"Temporal specifications with accumulative values","doi":"10.15479/AT:IST-2011-0003","file":[{"access_level":"open_access","content_type":"application/pdf","file_id":"5461","file_name":"IST-2011-0003_IST-2011-0003.pdf","checksum":"8491d0d48c4911620ecd5350b413c11e","creator":"system","file_size":366281,"date_updated":"2020-07-14T12:46:41Z","relation":"main_file","date_created":"2018-12-12T11:53:00Z"}],"publication_status":"published","oa":1,"citation":{"chicago":"Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman. <i>Temporal Specifications with Accumulative Values</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">https://doi.org/10.15479/AT:IST-2011-0003</a>.","ieee":"U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, <i>Temporal specifications with accumulative values</i>. IST Austria, 2011.","ama":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. <i>Temporal Specifications with Accumulative Values</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">10.15479/AT:IST-2011-0003</a>","short":"U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, Temporal Specifications with Accumulative Values, IST Austria, 2011.","ista":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2011. Temporal specifications with accumulative values, IST Austria, 14p.","mla":"Boker, Udi, et al. <i>Temporal Specifications with Accumulative Values</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">10.15479/AT:IST-2011-0003</a>.","apa":"Boker, U., Chatterjee, K., Henzinger, T. A., &#38; Kupferman, O. (2011). <i>Temporal specifications with accumulative values</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0003\">https://doi.org/10.15479/AT:IST-2011-0003</a>"},"date_updated":"2023-02-23T11:23:41Z","ec_funded":1,"author":[{"id":"31E297B6-F248-11E8-B48F-1D18A9856A87","full_name":"Boker, Udi","first_name":"Udi","last_name":"Boker"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Kupferman","first_name":"Orna","full_name":"Kupferman, Orna"}],"date_published":"2011-04-04T00:00:00Z","oa_version":"Published Version","pubrep_id":"21","alternative_title":["IST Austria Technical Report"]},{"date_updated":"2023-02-23T11:22:48Z","date_created":"2018-12-12T11:39:02Z","publisher":"IST Austria","author":[{"last_name":"Chen","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"},{"first_name":"Daniel","full_name":"Freedman, Daniel","last_name":"Freedman"},{"orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"date_published":"2011-03-28T00:00:00Z","abstract":[{"text":"We introduce TopoCut: a new way to integrate knowledge about topological properties (TPs) into random field image segmentation model. Instead of including TPs as additional constraints during minimization of the energy function, we devise an efficient algorithm for modifying the unary potentials such that the resulting segmentation is guaranteed with the desired properties. Our method is more flexible in the sense that it handles more topology constraints than previous methods, which were only able to enforce pairwise or global connectivity. In particular, our method is very fast, making it for the first time possible to enforce global topological properties in practical image segmentation tasks.","lang":"eng"}],"oa_version":"Published Version","has_accepted_license":"1","pubrep_id":"22","ddc":["000"],"alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"id":"3336","status":"public","relation":"later_version"}]},"day":"28","file_date_updated":"2020-07-14T12:46:41Z","type":"technical_report","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","page":"69","department":[{"_id":"ChLa"}],"publication_identifier":{"issn":["2664-1690"]},"_id":"5386","title":"Enforcing topological constraints in random field image segmentation","doi":"10.15479/AT:IST-2011-0002","language":[{"iso":"eng"}],"publication_status":"published","year":"2011","file":[{"creator":"system","file_size":26390601,"checksum":"ad64c2add5fe2ad10e9d5c669f3f9526","date_updated":"2020-07-14T12:46:41Z","relation":"main_file","date_created":"2018-12-12T11:53:34Z","access_level":"open_access","content_type":"application/pdf","file_id":"5495","file_name":"IST-2011-0002_IST-2011-0002.pdf"}],"oa":1,"citation":{"short":"C. Chen, D. Freedman, C. Lampert, Enforcing Topological Constraints in Random Field Image Segmentation, IST Austria, 2011.","ista":"Chen C, Freedman D, Lampert C. 2011. Enforcing topological constraints in random field image segmentation, IST Austria, 69p.","mla":"Chen, Chao, et al. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">10.15479/AT:IST-2011-0002</a>.","apa":"Chen, C., Freedman, D., &#38; Lampert, C. (2011). <i>Enforcing topological constraints in random field image segmentation</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">https://doi.org/10.15479/AT:IST-2011-0002</a>","ieee":"C. Chen, D. Freedman, and C. Lampert, <i>Enforcing topological constraints in random field image segmentation</i>. IST Austria, 2011.","ama":"Chen C, Freedman D, Lampert C. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">10.15479/AT:IST-2011-0002</a>","chicago":"Chen, Chao, Daniel Freedman, and Christoph Lampert. <i>Enforcing Topological Constraints in Random Field Image Segmentation</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0002\">https://doi.org/10.15479/AT:IST-2011-0002</a>."}},{"status":"public","type":"journal_article","extern":"1","day":"15","abstract":[{"text":"The four microsporangia of the flowering plant anther develop from archesporial cells in the L2 of the primordium. Within each microsporangium, developing microsporocytes are surrounded by concentric monolayers of tapetal, middle layer and endothecial cells. How this intricate array of tissues, each containing relatively few cells, is established in an organ possessing no formal meristems is poorly understood. We describe here the pivotal role of the LRR receptor kinase EXCESS MICROSPOROCYTES 1 (EMS1) in forming the monolayer of tapetal nurse cells in Arabidopsis. Unusually for plants, tapetal cells are specified very early in development, and are subsequently stimulated to proliferate by a receptor-like kinase (RLK) complex that includes EMS1. Mutations in members of this EMS1 signalling complex and its putative ligand result in male-sterile plants in which tapetal initials fail to proliferate. Surprisingly, these cells continue to develop, isolated at the locular periphery. Mutant and wild-type microsporangia expand at similar rates and the ‘tapetal’ space at the periphery of mutant locules becomes occupied by microsporocytes. However, induction of late expression of EMS1 in the few tapetal initials in ems1 plants results in their proliferation to generate a functional tapetum, and this proliferation suppresses microsporocyte number. Our experiments also show that integrity of the tapetal monolayer is crucial for the maintenance of the polarity of divisions within it. This unexpected autonomy of the tapetal ‘lineage’ is discussed in the context of tissue development in complex plant organs, where constancy in size, shape and cell number is crucial.","lang":"eng"}],"external_id":{"pmid":["20570940"]},"publisher":"The Company of Biologists","quality_controlled":"1","date_created":"2023-01-16T09:21:54Z","language":[{"iso":"eng"}],"year":"2010","publication_identifier":{"issn":["1477-9129","0950-1991"]},"volume":137,"page":"2409-2416","department":[{"_id":"XiFe"}],"pmid":1,"article_type":"original","month":"07","scopus_import":"1","oa_version":"None","date_published":"2010-07-15T00:00:00Z","author":[{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng"},{"first_name":"Hugh G.","full_name":"Dickinson, Hugh G.","last_name":"Dickinson"}],"issue":"14","date_updated":"2023-05-08T10:57:11Z","intvolume":"       137","citation":{"mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation in the Arabidopsis Anther.” <i>Development</i>, vol. 137, no. 14, The Company of Biologists, 2010, pp. 2409–16, doi:<a href=\"https://doi.org/10.1242/dev.049320\">10.1242/dev.049320</a>.","apa":"Feng, X., &#38; Dickinson, H. G. (2010). Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.049320\">https://doi.org/10.1242/dev.049320</a>","short":"X. Feng, H.G. Dickinson, Development 137 (2010) 2409–2416.","ista":"Feng X, Dickinson HG. 2010. Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. Development. 137(14), 2409–2416.","ieee":"X. Feng and H. G. Dickinson, “Tapetal cell fate, lineage and proliferation in the Arabidopsis anther,” <i>Development</i>, vol. 137, no. 14. The Company of Biologists, pp. 2409–2416, 2010.","ama":"Feng X, Dickinson HG. Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. <i>Development</i>. 2010;137(14):2409-2416. doi:<a href=\"https://doi.org/10.1242/dev.049320\">10.1242/dev.049320</a>","chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation in the Arabidopsis Anther.” <i>Development</i>. The Company of Biologists, 2010. <a href=\"https://doi.org/10.1242/dev.049320\">https://doi.org/10.1242/dev.049320</a>."},"acknowledgement":"We thank the following for providing mutant lines and reagents: Hong Ma, De Ye, Sacco De Vries, and Rod Scott for providing the pA9::Barnase lines and information on A9 expression patterns. Carla Galinha and Paolo Piazza gave valuable help with in situ hybridisation and qRT-PCR, respectively, and we acknowledge Qing Zhang, Helen Prescott and Matthew Dicks for providing excellent technical assistance. We are indebted to Miltos Tsiantis and Angela Hay for helpful discussion, and the research was funded by Oxford University through a Clarendon Scholarship to X.F., with additional financial support from Magdalen College (Oxford).","doi":"10.1242/dev.049320","publication_status":"published","article_processing_charge":"No","_id":"12199","publication":"Development","title":"Tapetal cell fate, lineage and proliferation in the Arabidopsis anther","keyword":["Developmental Biology","Molecular Biology","Anther Tapetum","Arabidopsis","Cell Fate Establishment","EMS1","Reproductive Cell Lineage"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","type":"journal_article","extern":"1","day":"22","abstract":[{"text":"Key steps in the evolution of the angiosperm anther include the patterning of the concentrically organized microsporangium and the incorporation of four such microsporangia into a leaf-like structure. Mutant studies in the model plant Arabidopsis thaliana are leading to an increasingly accurate picture of (i) the cell lineages culminating in the different cell types present in the microsporangium (the microsporocytes, the tapetum, and the middle and endothecial layers), and (ii) some of the genes responsible for specifying their fates. However, the processes that confer polarity on the developing anther and position the microsporangia within it remain unclear. Certainly, data from a range of experimental strategies suggest that hormones play a central role in establishing polarity and the patterning of the anther initial, and may be responsible for locating the microsporangia. But the fact that microsporangia were originally positioned externally suggests that their development is likely to be autonomous, perhaps with the reproductive cells generating signals controlling the growth and division of the investing anther epidermis. These possibilities are discussed in the context of the expression of genes which initiate and maintain male and female reproductive development, and in the perspective of our current views of anther evolution.","lang":"eng"}],"publisher":"Portland Press Ltd.","quality_controlled":"1","external_id":{"pmid":["20298223"]},"date_created":"2023-01-16T09:22:18Z","year":"2010","language":[{"iso":"eng"}],"volume":38,"publication_identifier":{"issn":["0300-5127","1470-8752"]},"page":"571-576","department":[{"_id":"XiFe"}],"pmid":1,"month":"03","article_type":"original","scopus_import":"1","oa_version":"None","date_published":"2010-03-22T00:00:00Z","author":[{"last_name":"Feng","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi"},{"last_name":"Dickinson","first_name":"Hugh G.","full_name":"Dickinson, Hugh G."}],"issue":"2","intvolume":"        38","date_updated":"2023-05-08T10:57:59Z","citation":{"chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning of the <i>Arabidopsis</i> Anther.” <i>Biochemical Society Transactions</i>. Portland Press Ltd., 2010. <a href=\"https://doi.org/10.1042/bst0380571\">https://doi.org/10.1042/bst0380571</a>.","ieee":"X. Feng and H. G. Dickinson, “Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther,” <i>Biochemical Society Transactions</i>, vol. 38, no. 2. Portland Press Ltd., pp. 571–576, 2010.","ama":"Feng X, Dickinson HG. Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. <i>Biochemical Society Transactions</i>. 2010;38(2):571-576. doi:<a href=\"https://doi.org/10.1042/bst0380571\">10.1042/bst0380571</a>","apa":"Feng, X., &#38; Dickinson, H. G. (2010). Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. <i>Biochemical Society Transactions</i>. Portland Press Ltd. <a href=\"https://doi.org/10.1042/bst0380571\">https://doi.org/10.1042/bst0380571</a>","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning of the <i>Arabidopsis</i> Anther.” <i>Biochemical Society Transactions</i>, vol. 38, no. 2, Portland Press Ltd., 2010, pp. 571–76, doi:<a href=\"https://doi.org/10.1042/bst0380571\">10.1042/bst0380571</a>.","ista":"Feng X, Dickinson HG. 2010. Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. Biochemical Society Transactions. 38(2), 571–576.","short":"X. Feng, H.G. Dickinson, Biochemical Society Transactions 38 (2010) 571–576."},"publication_status":"published","doi":"10.1042/bst0380571","_id":"12200","title":"Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther","publication":"Biochemical Society Transactions","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Biochemistry","Anther Development","Arabidopsis","Cell Fate","Microsporangium","Polarity","Receptor Kinase"]},{"oa":1,"article_number":"W10522","citation":{"apa":"Pellicciotti, F., Bauder, A., &#38; Parola, M. (2010). Effect of glaciers on streamflow trends in the Swiss Alps. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2009wr009039\">https://doi.org/10.1029/2009wr009039</a>","mla":"Pellicciotti, Francesca, et al. “Effect of Glaciers on Streamflow Trends in the Swiss Alps.” <i>Water Resources Research</i>, vol. 46, no. 10, W10522, American Geophysical Union, 2010, doi:<a href=\"https://doi.org/10.1029/2009wr009039\">10.1029/2009wr009039</a>.","ista":"Pellicciotti F, Bauder A, Parola M. 2010. Effect of glaciers on streamflow trends in the Swiss Alps. Water Resources Research. 46(10), W10522.","short":"F. Pellicciotti, A. Bauder, M. Parola, Water Resources Research 46 (2010).","chicago":"Pellicciotti, Francesca, A. Bauder, and M. Parola. “Effect of Glaciers on Streamflow Trends in the Swiss Alps.” <i>Water Resources Research</i>. American Geophysical Union, 2010. <a href=\"https://doi.org/10.1029/2009wr009039\">https://doi.org/10.1029/2009wr009039</a>.","ama":"Pellicciotti F, Bauder A, Parola M. Effect of glaciers on streamflow trends in the Swiss Alps. <i>Water Resources Research</i>. 2010;46(10). doi:<a href=\"https://doi.org/10.1029/2009wr009039\">10.1029/2009wr009039</a>","ieee":"F. Pellicciotti, A. Bauder, and M. Parola, “Effect of glaciers on streamflow trends in the Swiss Alps,” <i>Water Resources Research</i>, vol. 46, no. 10. American Geophysical Union, 2010."},"_id":"12653","article_processing_charge":"No","publication":"Water Resources Research","title":"Effect of glaciers on streamflow trends in the Swiss Alps","doi":"10.1029/2009wr009039","publication_status":"published","keyword":["Water Science and Technology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"Published Version","author":[{"last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70"},{"first_name":"A.","full_name":"Bauder, A.","last_name":"Bauder"},{"last_name":"Parola","full_name":"Parola, M.","first_name":"M."}],"date_published":"2010-10-01T00:00:00Z","date_updated":"2023-02-20T09:39:29Z","intvolume":"        46","issue":"10","publication_identifier":{"issn":["0043-1397"],"eissn":["1944-7973"]},"volume":46,"language":[{"iso":"eng"}],"year":"2010","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1029/2009WR009039"}],"month":"10","extern":"1","day":"01","status":"public","type":"journal_article","abstract":[{"lang":"eng","text":"Daily streamflow from stations close to five Swiss glaciers is analyzed for trends with the Mann-Kendall test. We consider a common period of record (1974–2004) and longer periods based on data availability. The trend statistical significance is tested on annual and seasonal bases. We also examine changes in precipitation, temperature, and snow cover characteristics. Highly glacierized basins show statistically significant positive trends in annual streamflow caused by increasing streamflow in spring and summer. Trends are more numerous and stronger at lower and mid than at the upper quantiles. The basin characterized by lower glacier coverage, conversely, does not exhibit consistently statistically significant trends. Changes in precipitation are not sufficient to explain the observed streamflow trends. Air temperature sees an increase in mean, minimum, and maximum values at all sites. Variations in the seasonal snow accumulation and ablation process are evident. Solid precipitation is decreasing at all sites and trends may be due to a shift from snowfall into rainfall. Mean snow depth is also decreasing, and its duration is getting shorter because of a decrease in solid precipitation and enhanced melting. Trend magnitude attenuates with longer time series. Contrasting trends are detected for different subperiods in the last 70 years: statistically significant negative trends are observed in the periods 1944–1974 and 1954–1984 for Aletschgletscher, in contrast with the results for the common period. These trends are explained by different rates of ice volume changes, and the sign of trends is clearly related to phases of positive or negative glacier mass balance."}],"quality_controlled":"1","publisher":"American Geophysical Union","date_created":"2023-02-20T08:18:27Z"},{"citation":{"mla":"Jösch, Maximilian A., et al. “ON and off Pathways in Drosophila Motion Vision.” <i>Nature</i>, vol. 468, no. 7321, Nature Publishing Group, 2010, pp. 300–04, doi:<a href=\"https://doi.org/10.1038/nature09545\">10.1038/nature09545</a>.","apa":"Jösch, M. A., Schnell, B., Raghu, S., Reiff, D., &#38; Borst, A. (2010). ON and off pathways in Drosophila motion vision. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09545\">https://doi.org/10.1038/nature09545</a>","ista":"Jösch MA, Schnell B, Raghu S, Reiff D, Borst A. 2010. ON and off pathways in Drosophila motion vision. Nature. 468(7321), 300–304.","short":"M.A. Jösch, B. Schnell, S. Raghu, D. Reiff, A. Borst, Nature 468 (2010) 300–304.","ieee":"M. A. Jösch, B. Schnell, S. Raghu, D. Reiff, and A. Borst, “ON and off pathways in Drosophila motion vision,” <i>Nature</i>, vol. 468, no. 7321. Nature Publishing Group, pp. 300–304, 2010.","ama":"Jösch MA, Schnell B, Raghu S, Reiff D, Borst A. ON and off pathways in Drosophila motion vision. <i>Nature</i>. 2010;468(7321):300-304. doi:<a href=\"https://doi.org/10.1038/nature09545\">10.1038/nature09545</a>","chicago":"Jösch, Maximilian A, Bettina Schnell, Shamprasad Raghu, Dierk Reiff, and Alexander Borst. “ON and off Pathways in Drosophila Motion Vision.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature09545\">https://doi.org/10.1038/nature09545</a>."},"publication":"Nature","_id":"1300","title":"ON and off pathways in Drosophila motion vision","volume":468,"year":"2010","publication_status":"published","doi":"10.1038/nature09545","page":"300 - 304","month":"11","extern":1,"day":"11","status":"public","type":"journal_article","abstract":[{"lang":"eng","text":"Motion vision is a major function of all visual systems, yet the underlying neural mechanisms and circuits are still elusive. In the lamina, the first optic neuropile of Drosophila melanogaster, photoreceptor signals split into five parallel pathways, L1-L5. Here we examine how these pathways contribute to visual motion detection by combining genetic block and reconstitution of neural activity in different lamina cell types with whole-cell recordings from downstream motion-sensitive neurons. We find reduced responses to moving gratings if L1 or L2 is blocked; however, reconstitution of photoreceptor input to only L1 or L2 results in wild-type responses. Thus, the first experiment indicates the necessity of both pathways, whereas the second indicates sufficiency of each single pathway. This contradiction can be explained by electrical coupling between L1 and L2, allowing for activation of both pathways even when only one of them receives photoreceptor input. A fundamental difference between the L1 pathway and the L2 pathway is uncovered when blocking L1 or L2 output while presenting moving edges of positive (ON) or negative (OFF) contrast polarity: blocking L1 eliminates the response to moving ON edges, whereas blocking L2 eliminates the response to moving OFF edges. Thus, similar to the segregation of photoreceptor signals in ON and OFF bipolar cell pathways in the vertebrate retina, photoreceptor signals segregate into ON-L1 and OFF-L2 channels in the lamina of Drosophila."}],"publist_id":"5970","author":[{"last_name":"Jösch","orcid":"0000-0002-3937-1330","full_name":"Maximilian Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A"},{"full_name":"Schnell, Bettina","first_name":"Bettina","last_name":"Schnell"},{"last_name":"Raghu","full_name":"Raghu, Shamprasad V","first_name":"Shamprasad"},{"full_name":"Reiff, Dierk F","first_name":"Dierk","last_name":"Reiff"},{"last_name":"Borst","full_name":"Borst, Alexander","first_name":"Alexander"}],"publisher":"Nature Publishing Group","quality_controlled":0,"date_published":"2010-11-11T00:00:00Z","date_created":"2018-12-11T11:51:14Z","intvolume":"       468","date_updated":"2021-01-12T06:49:44Z","issue":"7321"},{"pmid":1,"page":"1646 - 1657","month":"03","article_type":"original","volume":103,"publication_identifier":{"eissn":["1522-1598"],"issn":[" 0022-3077"]},"year":"2010","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"American Physiological Society","external_id":{"pmid":["20089816"]},"date_created":"2018-12-11T11:51:14Z","day":"01","extern":"1","status":"public","type":"journal_article","abstract":[{"text":"Motion vision is essential for navigating through the environment. Due to its genetic amenability, the fruit fly Drosophila has been serving for a lengthy period as a model organism for studying optomotor behavior as elicited by large-field horizontal motion. However, the neurons underlying the control of this behavior have not been studied in Drosophila so far. Here we report the first whole cell recordings from three cells of the horizontal system (HSN, HSE, and HSS) in the lobula plate of Drosophila. All three HS cells are tuned to large-field horizontal motion in a direction-selective way; they become excited by front-to-back motion and inhibited by back-to-front motion in the ipsilateral field of view. The response properties of HS cells such as contrast and velocity dependence are in accordance with the correlation-type model of motion detection. Neurobiotin injection suggests extensive coupling among ipsilateral HS cells and additional coupling to tangential cells that have their dendrites in the contralateral hemisphere of the brain. This connectivity scheme accounts for the complex layout of their receptive fields and explains their sensitivity both to ipsilateral and to contralateral motion. Thus the main response properties of Drosophila HS cells are strikingly similar to the responses of their counterparts in the blowfly Calliphora, although we found substantial differences with respect to their dendritic structure and connectivity. This long-awaited functional characterization of HS cells in Drosophila provides the basis for the future dissection of optomotor behavior and the underlying neural circuitry by combining genetics, physiology, and behavior.","lang":"eng"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","acknowledgement":"This work was supported by the Max-Planck-Society and by a Human Frontier Science Program grant to K. Ito, A. Borst, and B. Nelson.","citation":{"chicago":"Schnell, Bettina, Maximilian A Jösch, Friedrich Förstner, Shamprasad Raghu, Hideo Otsuna, Kei Ito, Alexander Borst, and Dierk Reiff. “Processing of Horizontal Optic Flow in Three Visual Interneurons of the Drosophila Brain.” <i>Journal of Neurophysiology</i>. American Physiological Society, 2010. <a href=\"https://doi.org/10.1152/jn.00950.2009\">https://doi.org/10.1152/jn.00950.2009</a>.","ieee":"B. Schnell <i>et al.</i>, “Processing of horizontal optic flow in three visual interneurons of the Drosophila brain,” <i>Journal of Neurophysiology</i>, vol. 103, no. 3. American Physiological Society, pp. 1646–1657, 2010.","ama":"Schnell B, Jösch MA, Förstner F, et al. Processing of horizontal optic flow in three visual interneurons of the Drosophila brain. <i>Journal of Neurophysiology</i>. 2010;103(3):1646-1657. doi:<a href=\"https://doi.org/10.1152/jn.00950.2009\">10.1152/jn.00950.2009</a>","short":"B. Schnell, M.A. Jösch, F. Förstner, S. Raghu, H. Otsuna, K. Ito, A. Borst, D. Reiff, Journal of Neurophysiology 103 (2010) 1646–1657.","ista":"Schnell B, Jösch MA, Förstner F, Raghu S, Otsuna H, Ito K, Borst A, Reiff D. 2010. Processing of horizontal optic flow in three visual interneurons of the Drosophila brain. Journal of Neurophysiology. 103(3), 1646–1657.","apa":"Schnell, B., Jösch, M. A., Förstner, F., Raghu, S., Otsuna, H., Ito, K., … Reiff, D. (2010). Processing of horizontal optic flow in three visual interneurons of the Drosophila brain. <i>Journal of Neurophysiology</i>. American Physiological Society. <a href=\"https://doi.org/10.1152/jn.00950.2009\">https://doi.org/10.1152/jn.00950.2009</a>","mla":"Schnell, Bettina, et al. “Processing of Horizontal Optic Flow in Three Visual Interneurons of the Drosophila Brain.” <i>Journal of Neurophysiology</i>, vol. 103, no. 3, American Physiological Society, 2010, pp. 1646–57, doi:<a href=\"https://doi.org/10.1152/jn.00950.2009\">10.1152/jn.00950.2009</a>."},"_id":"1301","article_processing_charge":"No","title":"Processing of horizontal optic flow in three visual interneurons of the Drosophila brain","publication":"Journal of Neurophysiology","publication_status":"published","doi":"10.1152/jn.00950.2009","author":[{"last_name":"Schnell","full_name":"Schnell, Bettina","first_name":"Bettina"},{"first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","full_name":"Jösch, Maximilian A","last_name":"Jösch","orcid":"0000-0002-3937-1330"},{"full_name":"Förstner, Friedrich","first_name":"Friedrich","last_name":"Förstner"},{"full_name":"Raghu, Shamprasad","first_name":"Shamprasad","last_name":"Raghu"},{"full_name":"Otsuna, Hideo","first_name":"Hideo","last_name":"Otsuna"},{"full_name":"Ito, Kei","first_name":"Kei","last_name":"Ito"},{"last_name":"Borst","full_name":"Borst, Alexander","first_name":"Alexander"},{"full_name":"Reiff, Dierk","first_name":"Dierk","last_name":"Reiff"}],"date_published":"2010-03-01T00:00:00Z","intvolume":"       103","date_updated":"2021-01-12T06:49:44Z","issue":"3","publist_id":"5971","oa_version":"None"},{"date_updated":"2021-01-12T08:19:30Z","date_created":"2020-09-18T10:11:13Z","intvolume":"       132","issue":"45","author":[{"orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Meier","first_name":"Beat H.","full_name":"Meier, Beat H."},{"last_name":"Ernst","full_name":"Ernst, Matthias","first_name":"Matthias"}],"publisher":"American Chemical Society","quality_controlled":"1","date_published":"2010-10-26T00:00:00Z","abstract":[{"lang":"eng","text":"Characterization of protein dynamics by solid-state NMR spectroscopy requires robust and accurate measurement protocols, which are not yet fully developed. In this study, we investigate the backbone dynamics of microcrystalline ubiquitin using different approaches. A rotational-echo double-resonance type (REDOR-type) methodology allows one to accurately measure 1H−15N order parameters in highly deuterated samples. We show that the systematic errors in the REDOR experiment are as low as 1% or even less, giving access to accurate data for the amplitudes of backbone mobility. Combining such dipolar-coupling-derived order parameters with autocorrelated and cross-correlated 15N relaxation rates, we are able to quantitate amplitudes and correlation times of backbone dynamics on picosecond and nanosecond time scales in a residue-resolved manner. While the mobility on picosecond time scales appears to have rather uniform amplitude throughout the protein, we unambiguously identify and quantitate nanosecond mobility with order parameters S2 as low as 0.8 in some regions of the protein, where nanosecond dynamics has also been revealed in solution state. The methodology used here, a combination of accurate dipolar-coupling measurements and different relaxation parameters, yields details about dynamics on different time scales and can be applied to solid protein samples such as amyloid fibrils or membrane proteins."}],"oa_version":"None","extern":"1","day":"26","status":"public","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","month":"10","page":"15957-15967","publication_identifier":{"issn":["0002-7863","1520-5126"]},"_id":"8472","publication":"Journal of the American Chemical Society","volume":132,"article_processing_charge":"No","title":"Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy","language":[{"iso":"eng"}],"doi":"10.1021/ja100726a","publication_status":"published","year":"2010","citation":{"mla":"Schanda, Paul, et al. “Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>, vol. 132, no. 45, American Chemical Society, 2010, pp. 15957–67, doi:<a href=\"https://doi.org/10.1021/ja100726a\">10.1021/ja100726a</a>.","apa":"Schanda, P., Meier, B. H., &#38; Ernst, M. (2010). Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/ja100726a\">https://doi.org/10.1021/ja100726a</a>","short":"P. Schanda, B.H. Meier, M. Ernst, Journal of the American Chemical Society 132 (2010) 15957–15967.","ista":"Schanda P, Meier BH, Ernst M. 2010. Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. Journal of the American Chemical Society. 132(45), 15957–15967.","ieee":"P. Schanda, B. H. Meier, and M. Ernst, “Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy,” <i>Journal of the American Chemical Society</i>, vol. 132, no. 45. American Chemical Society, pp. 15957–15967, 2010.","ama":"Schanda P, Meier BH, Ernst M. Quantitative analysis of protein backbone dynamics in microcrystalline ubiquitin by solid-state NMR spectroscopy. <i>Journal of the American Chemical Society</i>. 2010;132(45):15957-15967. doi:<a href=\"https://doi.org/10.1021/ja100726a\">10.1021/ja100726a</a>","chicago":"Schanda, Paul, Beat H. Meier, and Matthias Ernst. “Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2010. <a href=\"https://doi.org/10.1021/ja100726a\">https://doi.org/10.1021/ja100726a</a>."}},{"publisher":"American Society for Biochemistry & Molecular Biology","quality_controlled":"1","author":[{"last_name":"Corazza","full_name":"Corazza, Alessandra","first_name":"Alessandra"},{"last_name":"Rennella","first_name":"Enrico","full_name":"Rennella, Enrico"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606"},{"last_name":"Mimmi","full_name":"Mimmi, Maria Chiara","first_name":"Maria Chiara"},{"full_name":"Cutuil, Thomas","first_name":"Thomas","last_name":"Cutuil"},{"last_name":"Raimondi","first_name":"Sara","full_name":"Raimondi, Sara"},{"full_name":"Giorgetti, Sofia","first_name":"Sofia","last_name":"Giorgetti"},{"last_name":"Fogolari","first_name":"Federico","full_name":"Fogolari, Federico"},{"last_name":"Viglino","first_name":"Paolo","full_name":"Viglino, Paolo"},{"full_name":"Frydman, Lucio","first_name":"Lucio","last_name":"Frydman"},{"full_name":"Gal, Maayan","first_name":"Maayan","last_name":"Gal"},{"full_name":"Bellotti, Vittorio","first_name":"Vittorio","last_name":"Bellotti"},{"last_name":"Brutscher","full_name":"Brutscher, Bernhard","first_name":"Bernhard"},{"last_name":"Esposito","first_name":"Gennaro","full_name":"Esposito, Gennaro"}],"date_published":"2010-02-19T00:00:00Z","date_created":"2020-09-18T10:11:23Z","intvolume":"       285","date_updated":"2021-01-12T08:19:31Z","issue":"8","day":"19","extern":"1","type":"journal_article","status":"public","abstract":[{"lang":"eng","text":"β2-microglobulin (β2m), the light chain of class I major histocompatibility complex, is responsible for the dialysis-related amyloidosis and, in patients undergoing long term dialysis, the full-length and chemically unmodified β2m converts into amyloid fibrils. The protein, belonging to the immunoglobulin superfamily, in common to other members of this family, experiences during its folding a long-lived intermediate associated to the trans-to-cis isomerization of Pro-32 that has been addressed as the precursor of the amyloid fibril formation. In this respect, previous studies on the W60G β2m mutant, showing that the lack of Trp-60 prevents fibril formation in mild aggregating condition, prompted us to reinvestigate the refolding kinetics of wild type and W60G β2m at atomic resolution by real-time NMR. The analysis, conducted at ambient temperature by the band selective flip angle short transient real-time two-dimensional NMR techniques and probing the β2m states every 15 s, revealed a more complex folding energy landscape than previously reported for wild type β2m, involving more than a single intermediate species, and shedding new light into the fibrillogenic pathway. Moreover, a significant difference in the kinetic scheme previously characterized by optical spectroscopic methods was discovered for the W60G β2m mutant."}],"oa_version":"None","page":"5827-5835","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","keyword":["Cell Biology","Biochemistry","Molecular Biology"],"month":"02","article_type":"original","citation":{"chicago":"Corazza, Alessandra, Enrico Rennella, Paul Schanda, Maria Chiara Mimmi, Thomas Cutuil, Sara Raimondi, Sofia Giorgetti, et al. “Native-Unlike Long-Lived Intermediates along the Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin Revealed by Real-Time Two-Dimensional NMR.” <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology, 2010. <a href=\"https://doi.org/10.1074/jbc.m109.061168\">https://doi.org/10.1074/jbc.m109.061168</a>.","ieee":"A. Corazza <i>et al.</i>, “Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR,” <i>Journal of Biological Chemistry</i>, vol. 285, no. 8. American Society for Biochemistry &#38; Molecular Biology, pp. 5827–5835, 2010.","ama":"Corazza A, Rennella E, Schanda P, et al. Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR. <i>Journal of Biological Chemistry</i>. 2010;285(8):5827-5835. doi:<a href=\"https://doi.org/10.1074/jbc.m109.061168\">10.1074/jbc.m109.061168</a>","short":"A. Corazza, E. Rennella, P. Schanda, M.C. Mimmi, T. Cutuil, S. Raimondi, S. Giorgetti, F. Fogolari, P. Viglino, L. Frydman, M. Gal, V. Bellotti, B. Brutscher, G. Esposito, Journal of Biological Chemistry 285 (2010) 5827–5835.","ista":"Corazza A, Rennella E, Schanda P, Mimmi MC, Cutuil T, Raimondi S, Giorgetti S, Fogolari F, Viglino P, Frydman L, Gal M, Bellotti V, Brutscher B, Esposito G. 2010. Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR. Journal of Biological Chemistry. 285(8), 5827–5835.","mla":"Corazza, Alessandra, et al. “Native-Unlike Long-Lived Intermediates along the Folding Pathway of the Amyloidogenic Protein Β2-Microglobulin Revealed by Real-Time Two-Dimensional NMR.” <i>Journal of Biological Chemistry</i>, vol. 285, no. 8, American Society for Biochemistry &#38; Molecular Biology, 2010, pp. 5827–35, doi:<a href=\"https://doi.org/10.1074/jbc.m109.061168\">10.1074/jbc.m109.061168</a>.","apa":"Corazza, A., Rennella, E., Schanda, P., Mimmi, M. C., Cutuil, T., Raimondi, S., … Esposito, G. (2010). Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR. <i>Journal of Biological Chemistry</i>. American Society for Biochemistry &#38; Molecular Biology. <a href=\"https://doi.org/10.1074/jbc.m109.061168\">https://doi.org/10.1074/jbc.m109.061168</a>"},"_id":"8473","publication":"Journal of Biological Chemistry","volume":285,"title":"Native-unlike long-lived intermediates along the folding pathway of the amyloidogenic protein β2-Microglobulin revealed by real-time two-dimensional NMR","article_processing_charge":"No","publication_identifier":{"issn":["0021-9258","1083-351X"]},"year":"2010","publication_status":"published","doi":"10.1074/jbc.m109.061168","language":[{"iso":"eng"}]},{"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"43-87","publication_status":"published","year":"2010","doi":"10.1016/s1874-575x(10)00310-3","language":[{"iso":"eng"}],"publication":"Handbook of Dynamical Systems","_id":"8506","volume":3,"title":"Prevalence","article_processing_charge":"No","publication_identifier":{"isbn":["9780444531414"],"issn":["1874-575X"]},"citation":{"chicago":"Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” In <i>Handbook of Dynamical Systems</i>, 3:43–87. Elsevier, 2010. <a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">https://doi.org/10.1016/s1874-575x(10)00310-3</a>.","ieee":"B. R. Hunt and V. Kaloshin, “Prevalence,” in <i>Handbook of Dynamical Systems</i>, vol. 3, Elsevier, 2010, pp. 43–87.","ama":"Hunt BR, Kaloshin V. Prevalence. In: <i>Handbook of Dynamical Systems</i>. Vol 3. Elsevier; 2010:43-87. doi:<a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">10.1016/s1874-575x(10)00310-3</a>","short":"B.R. Hunt, V. Kaloshin, in:, Handbook of Dynamical Systems, Elsevier, 2010, pp. 43–87.","ista":"Hunt BR, Kaloshin V. 2010.Prevalence. In: Handbook of Dynamical Systems. vol. 3, 43–87.","apa":"Hunt, B. R., &#38; Kaloshin, V. (2010). Prevalence. In <i>Handbook of Dynamical Systems</i> (Vol. 3, pp. 43–87). Elsevier. <a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">https://doi.org/10.1016/s1874-575x(10)00310-3</a>","mla":"Hunt, Brian R., and Vadim Kaloshin. “Prevalence.” <i>Handbook of Dynamical Systems</i>, vol. 3, Elsevier, 2010, pp. 43–87, doi:<a href=\"https://doi.org/10.1016/s1874-575x(10)00310-3\">10.1016/s1874-575x(10)00310-3</a>."},"date_created":"2020-09-18T10:47:48Z","intvolume":"         3","date_updated":"2021-01-12T08:19:45Z","date_published":"2010-01-01T00:00:00Z","publisher":"Elsevier","quality_controlled":"1","author":[{"last_name":"Hunt","full_name":"Hunt, Brian R.","first_name":"Brian R."},{"first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"}],"oa_version":"None","status":"public","type":"book_chapter","extern":"1","day":"01"},{"conference":{"start_date":"2009-08-03","name":"International Congress on Mathematical Physics","location":"Prague, Czech Republic","end_date":"2009-08-08"},"citation":{"chicago":"Kaloshin, Vadim, KE ZHANG, and YONG ZHENG. “Almost Dense Orbit on Energy Surface.” In <i>XVIth International Congress on Mathematical Physics</i>, 314–22. World Scientific, 2010. <a href=\"https://doi.org/10.1142/9789814304634_0017\">https://doi.org/10.1142/9789814304634_0017</a>.","ama":"Kaloshin V, ZHANG K, ZHENG Y. Almost dense orbit on energy surface. In: <i>XVIth International Congress on Mathematical Physics</i>. World Scientific; 2010:314-322. doi:<a href=\"https://doi.org/10.1142/9789814304634_0017\">10.1142/9789814304634_0017</a>","ieee":"V. Kaloshin, K. ZHANG, and Y. ZHENG, “Almost dense orbit on energy surface,” in <i>XVIth International Congress on Mathematical Physics</i>, Prague, Czech Republic, 2010, pp. 314–322.","ista":"Kaloshin V, ZHANG K, ZHENG Y. 2010. Almost dense orbit on energy surface. XVIth International Congress on Mathematical Physics. International Congress on Mathematical Physics, 314–322.","short":"V. Kaloshin, K. ZHANG, Y. ZHENG, in:, XVIth International Congress on Mathematical Physics, World Scientific, 2010, pp. 314–322.","apa":"Kaloshin, V., ZHANG, K., &#38; ZHENG, Y. (2010). Almost dense orbit on energy surface. In <i>XVIth International Congress on Mathematical Physics</i> (pp. 314–322). Prague, Czech Republic: World Scientific. <a href=\"https://doi.org/10.1142/9789814304634_0017\">https://doi.org/10.1142/9789814304634_0017</a>","mla":"Kaloshin, Vadim, et al. “Almost Dense Orbit on Energy Surface.” <i>XVIth International Congress on Mathematical Physics</i>, World Scientific, 2010, pp. 314–22, doi:<a href=\"https://doi.org/10.1142/9789814304634_0017\">10.1142/9789814304634_0017</a>."},"publication_identifier":{"isbn":["9789814304627","9789814304634"]},"_id":"8507","publication":"XVIth International Congress on Mathematical Physics","title":"Almost dense orbit on energy surface","article_processing_charge":"No","doi":"10.1142/9789814304634_0017","language":[{"iso":"eng"}],"year":"2010","publication_status":"published","page":"314-322","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","day":"01","extern":"1","status":"public","type":"conference","abstract":[{"text":"We study a Cr nearly integrable Hamiltonian system  defined on 𝕋3 × ℝ3. Let  and µΣ1 be the restriction of Lebesgue measure on 𝕋3 × ℝ3 to ∑. We prove there is a perturbation ,  and an orbit (q(t), p(t)): ℝ → 𝕋3 × ℝ3 of the Hamiltonian equation  such that .","lang":"eng"}],"oa_version":"None","publisher":"World Scientific","author":[{"first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","last_name":"Kaloshin"},{"full_name":"ZHANG, KE","first_name":"KE","last_name":"ZHANG"},{"full_name":"ZHENG, YONG","first_name":"YONG","last_name":"ZHENG"}],"quality_controlled":"1","date_published":"2010-03-01T00:00:00Z","date_updated":"2021-01-12T08:19:46Z","date_created":"2020-09-18T10:47:56Z"},{"doi":"10.1038/nature09105","publication_status":"published","year":"2010","_id":"857","publication":"Nature","title":"Sequence space and the ongoing expansion of the protein universe","volume":465,"citation":{"chicago":"Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature09105\">https://doi.org/10.1038/nature09105</a>.","ama":"Povolotskaya I, Kondrashov F. Sequence space and the ongoing expansion of the protein universe. <i>Nature</i>. 2010;465(7300):922-926. doi:<a href=\"https://doi.org/10.1038/nature09105\">10.1038/nature09105</a>","ieee":"I. Povolotskaya and F. Kondrashov, “Sequence space and the ongoing expansion of the protein universe,” <i>Nature</i>, vol. 465, no. 7300. Nature Publishing Group, pp. 922–926, 2010.","short":"I. Povolotskaya, F. Kondrashov, Nature 465 (2010) 922–926.","ista":"Povolotskaya I, Kondrashov F. 2010. Sequence space and the ongoing expansion of the protein universe. Nature. 465(7300), 922–926.","apa":"Povolotskaya, I., &#38; Kondrashov, F. (2010). Sequence space and the ongoing expansion of the protein universe. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09105\">https://doi.org/10.1038/nature09105</a>","mla":"Povolotskaya, Inna, and Fyodor Kondrashov. “Sequence Space and the Ongoing Expansion of the Protein Universe.” <i>Nature</i>, vol. 465, no. 7300, Nature Publishing Group, 2010, pp. 922–26, doi:<a href=\"https://doi.org/10.1038/nature09105\">10.1038/nature09105</a>."},"acknowledgement":"We thank E. Koonin, Y. Wolf, A. Lobkovsky, D. Petrov, D. Ivankov, J. Sharpe, B. Lehner, Y. Jaeger, P. Vlasov, M. Ptitsyn and M. Roytberg for discussions and A. Kondrashov for extensive feedback on our manuscript. We thank D. Tawfik for inspiring us to start the investigation of the functional limits in sequence space.\n","month":"06","page":"922 - 926","publist_id":"6791","abstract":[{"text":"The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, 3.5 × 10 9 yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.","lang":"eng"}],"status":"public","type":"journal_article","day":"17","extern":1,"issue":"7300","date_updated":"2021-01-12T08:20:05Z","date_created":"2018-12-11T11:48:52Z","intvolume":"       465","date_published":"2010-06-17T00:00:00Z","publisher":"Nature Publishing Group","author":[{"last_name":"Povolotskaya","first_name":"Inna","full_name":"Povolotskaya, Inna"},{"full_name":"Fyodor Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"}],"quality_controlled":0},{"doi":"10.1038/nature08691","year":"2010","publication_status":"published","_id":"862","title":"Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness","publication":"Nature","volume":464,"citation":{"mla":"Meer, Margarita, et al. “Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.” <i>Nature</i>, vol. 464, no. 7286, Nature Publishing Group, 2010, pp. 279–82, doi:<a href=\"https://doi.org/10.1038/nature08691\">10.1038/nature08691</a>.","apa":"Meer, M., Kondrashov, A., Artzy Randrup, Y., &#38; Kondrashov, F. (2010). Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature08691\">https://doi.org/10.1038/nature08691</a>","ista":"Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. 2010. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. Nature. 464(7286), 279–282.","short":"M. Meer, A. Kondrashov, Y. Artzy Randrup, F. Kondrashov, Nature 464 (2010) 279–282.","chicago":"Meer, Margarita, Alexey Kondrashov, Yael Artzy Randrup, and Fyodor Kondrashov. “Compensatory Evolution in Mitochondrial TRNAs Navigates Valleys of Low Fitness.” <i>Nature</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nature08691\">https://doi.org/10.1038/nature08691</a>.","ama":"Meer M, Kondrashov A, Artzy Randrup Y, Kondrashov F. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness. <i>Nature</i>. 2010;464(7286):279-282. doi:<a href=\"https://doi.org/10.1038/nature08691\">10.1038/nature08691</a>","ieee":"M. Meer, A. Kondrashov, Y. Artzy Randrup, and F. Kondrashov, “Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness,” <i>Nature</i>, vol. 464, no. 7286. Nature Publishing Group, pp. 279–282, 2010."},"acknowledgement":"We thank H. Innan, M. Laessig, R. Guigo, I. Povolotskaya, D. Ivankov and M. Breen for thoughtful discussions and critical reading of the manuscript.","month":"03","page":"279 - 282","publist_id":"6784","abstract":[{"text":"A long-standing controversy in evolutionary biology is whether or not evolving lineages can cross valleys on the fitness landscape that correspond to low-fitness genotypes, which can eventually enable them to reach isolated fitness peaks1-9. Here we study the fitness landscapes traversed by switches between different AU and GC Watson-Crick nucleotide pairs at complementary sites of mitochondrial transfer RNA stem regions in 83 mammalian species. We find that such Watson-Crick switches occur 30-40 times more slowly than pairs of neutral substitutions, and that alleles corresponding to GU and AC non-Watson-Crick intermediate states segregate within human populations at low frequencies, similar to those of non-synonymous alleles. Substitutions leading to a Watson-Crick switch are strongly correlated, especially in mitochondrial tRNAs encoded on the GT-nucleotide-rich strand of the mitochondrial genome. Using these data we estimate that a typical Watson-Crick switch involves crossing a fitness valley of a depth of about 10-3 or even about 10-2, with AC intermediates being slightly more deleterious than GU intermediates. This compensatory evolution must proceed through rare intermediate variants that never reach fixation. The ubiquitous nature of compensatory evolution in mammalian mitochondrial tRNAs and other molecules implies that simultaneous fixation of two alleles that are individually deleterious may be a common phenomenon at the molecular level.","lang":"eng"}],"type":"journal_article","status":"public","extern":1,"day":"11","issue":"7286","date_updated":"2021-01-12T08:20:20Z","intvolume":"       464","date_created":"2018-12-11T11:48:54Z","date_published":"2010-03-11T00:00:00Z","quality_controlled":0,"author":[{"full_name":"Meer, Margarita V","first_name":"Margarita","last_name":"Meer"},{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey S"},{"first_name":"Yael","full_name":"Artzy-Randrup, Yael","last_name":"Artzy Randrup"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Nature Publishing Group"},{"publisher":"Royal Society, The","quality_controlled":0,"author":[{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","full_name":"Fyodor Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kondrashov, Alexey S","first_name":"Alexey","last_name":"Kondrashov"}],"date_published":"2010-04-27T00:00:00Z","intvolume":"       365","date_created":"2018-12-11T11:48:57Z","date_updated":"2021-01-12T08:20:43Z","issue":"1544","extern":1,"day":"27","type":"journal_article","status":"public","abstract":[{"text":"The rate of spontaneous mutation in natural populations is a fundamental parameter for many evolutionary phenomena. Because the rate of mutation is generally low, most of what is currently known about mutation has been obtained through indirect, complex and imprecise methodological approaches. However, in the past few years genome-wide sequencing of closely related individuals has made it possible to estimate the rates of mutation directly at the level of the DNA, avoiding most of the problems associated with using indirect methods. Here, we review the methods used in the past with an emphasis on next generation sequencing, which may soon make the accurate measurement of spontaneous mutation rates a matter of routine.","lang":"eng"}],"publist_id":"6772","page":"1169 - 1176","month":"04","citation":{"apa":"Kondrashov, F., &#38; Kondrashov, A. (2010). Measurements of spontaneous rates of mutations in the recent past and the near future. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rstb.2009.0286\">https://doi.org/10.1098/rstb.2009.0286</a>","mla":"Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous Rates of Mutations in the Recent Past and the near Future.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544, Royal Society, The, 2010, pp. 1169–76, doi:<a href=\"https://doi.org/10.1098/rstb.2009.0286\">10.1098/rstb.2009.0286</a>.","short":"F. Kondrashov, A. Kondrashov, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1169–1176.","ista":"Kondrashov F, Kondrashov A. 2010. Measurements of spontaneous rates of mutations in the recent past and the near future. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1169–1176.","ama":"Kondrashov F, Kondrashov A. Measurements of spontaneous rates of mutations in the recent past and the near future. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1544):1169-1176. doi:<a href=\"https://doi.org/10.1098/rstb.2009.0286\">10.1098/rstb.2009.0286</a>","ieee":"F. Kondrashov and A. Kondrashov, “Measurements of spontaneous rates of mutations in the recent past and the near future,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544. Royal Society, The, pp. 1169–1176, 2010.","chicago":"Kondrashov, Fyodor, and Alexey Kondrashov. “Measurements of Spontaneous Rates of Mutations in the Recent Past and the near Future.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, The, 2010. <a href=\"https://doi.org/10.1098/rstb.2009.0286\">https://doi.org/10.1098/rstb.2009.0286</a>."},"_id":"872","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","volume":365,"title":"Measurements of spontaneous rates of mutations in the recent past and the near future","year":"2010","publication_status":"published","doi":"10.1098/rstb.2009.0286"},{"date_updated":"2021-01-12T08:21:15Z","date_created":"2018-12-11T11:49:00Z","intvolume":"         5","publisher":"BioMed Central","author":[{"first_name":"Alexey","full_name":"Kondrashov, Alexey S","last_name":"Kondrashov"},{"first_name":"Inna","full_name":"Povolotskaya, Inna","last_name":"Povolotskaya"},{"full_name":"Ivankov, Dmitry N","first_name":"Dmitry","last_name":"Ivankov"},{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Fyodor Kondrashov"}],"quality_controlled":0,"date_published":"2010-01-21T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"Background: Divergence of two independently evolving sequences that originated from a common ancestor can be described by two parameters, the asymptotic level of divergence E and the rate r at which this level of divergence is approached. Constant negative selection impedes allele replacements and, therefore, is routinely assumed to decelerate sequence divergence. However, its impact on E and on r has not been formally investigated.Results: Strong selection that favors only one allele can make E arbitrarily small and r arbitrarily large. In contrast, in the case of 4 possible alleles and equal mutation rates, the lowest value of r, attained when two alleles confer equal fitnesses and the other two are strongly deleterious, is only two times lower than its value under selective neutrality.Conclusions: Constant selection can strongly constrain the level of sequence divergence, but cannot reduce substantially the rate at which this level is approached. In particular, under any constant selection the divergence of sequences that accumulated one substitution per neutral site since their origin from the common ancestor must already constitute at least one half of the asymptotic divergence at sites under such selection.Reviewers: This article was reviewed by Drs. Nicolas Galtier, Sergei Maslov, and Nick Grishin.","lang":"eng"}],"publist_id":"6762","extern":1,"day":"21","status":"public","type":"journal_article","month":"01","license":"https://creativecommons.org/licenses/by/4.0/","_id":"884","volume":5,"publication":"Biology Direct","title":"Rate of sequence divergence under constant selection","doi":"10.1186/1745-6150-5-5","year":"2010","publication_status":"published","citation":{"ama":"Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. Rate of sequence divergence under constant selection. <i>Biology Direct</i>. 2010;5. doi:<a href=\"https://doi.org/10.1186/1745-6150-5-5\">10.1186/1745-6150-5-5</a>","ieee":"A. Kondrashov, I. Povolotskaya, D. Ivankov, and F. Kondrashov, “Rate of sequence divergence under constant selection,” <i>Biology Direct</i>, vol. 5. BioMed Central, 2010.","chicago":"Kondrashov, Alexey, Inna Povolotskaya, Dmitry Ivankov, and Fyodor Kondrashov. “Rate of Sequence Divergence under Constant Selection.” <i>Biology Direct</i>. BioMed Central, 2010. <a href=\"https://doi.org/10.1186/1745-6150-5-5\">https://doi.org/10.1186/1745-6150-5-5</a>.","ista":"Kondrashov A, Povolotskaya I, Ivankov D, Kondrashov F. 2010. Rate of sequence divergence under constant selection. Biology Direct. 5.","short":"A. Kondrashov, I. Povolotskaya, D. Ivankov, F. Kondrashov, Biology Direct 5 (2010).","mla":"Kondrashov, Alexey, et al. “Rate of Sequence Divergence under Constant Selection.” <i>Biology Direct</i>, vol. 5, BioMed Central, 2010, doi:<a href=\"https://doi.org/10.1186/1745-6150-5-5\">10.1186/1745-6150-5-5</a>.","apa":"Kondrashov, A., Povolotskaya, I., Ivankov, D., &#38; Kondrashov, F. (2010). Rate of sequence divergence under constant selection. <i>Biology Direct</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1745-6150-5-5\">https://doi.org/10.1186/1745-6150-5-5</a>"}},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"07","pmid":1,"page":"2360 - 2364","_id":"89","volume":2,"publication":"ACS Applied Materials and Interfaces","title":"Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution","publication_status":"published","year":"2010","doi":"10.1021/am100375w","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the National Science Foundation under Grants PHY-0456898 and PHY-0757989, and acknowledgment is made to the Donors of the Petroleum Research Fund administered by the American Chemical Society for partial support of this research.","citation":{"chicago":"Wright, Ian, Andrew P Higginbotham, Shenda Baker, and Tom Donnelly. “Generation of Nanoparticles of Controlled Size Using Ultrasonic Piezoelectric Oscillators in Solution.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society, 2010. <a href=\"https://doi.org/10.1021/am100375w\">https://doi.org/10.1021/am100375w</a>.","ieee":"I. Wright, A. P. Higginbotham, S. Baker, and T. Donnelly, “Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution,” <i>ACS Applied Materials and Interfaces</i>, vol. 2, no. 8. American Chemical Society, pp. 2360–2364, 2010.","ama":"Wright I, Higginbotham AP, Baker S, Donnelly T. Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution. <i>ACS Applied Materials and Interfaces</i>. 2010;2(8):2360-2364. doi:<a href=\"https://doi.org/10.1021/am100375w\">10.1021/am100375w</a>","short":"I. Wright, A.P. Higginbotham, S. Baker, T. Donnelly, ACS Applied Materials and Interfaces 2 (2010) 2360–2364.","ista":"Wright I, Higginbotham AP, Baker S, Donnelly T. 2010. Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution. ACS Applied Materials and Interfaces. 2(8), 2360–2364.","apa":"Wright, I., Higginbotham, A. P., Baker, S., &#38; Donnelly, T. (2010). Generation of nanoparticles of controlled size using ultrasonic piezoelectric oscillators in solution. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/am100375w\">https://doi.org/10.1021/am100375w</a>","mla":"Wright, Ian, et al. “Generation of Nanoparticles of Controlled Size Using Ultrasonic Piezoelectric Oscillators in Solution.” <i>ACS Applied Materials and Interfaces</i>, vol. 2, no. 8, American Chemical Society, 2010, pp. 2360–64, doi:<a href=\"https://doi.org/10.1021/am100375w\">10.1021/am100375w</a>."},"date_created":"2018-12-11T11:44:34Z","intvolume":"         2","date_updated":"2021-01-12T08:21:17Z","issue":"8","quality_controlled":"1","publisher":"American Chemical Society","author":[{"last_name":"Wright","first_name":"Ian","full_name":"Wright, Ian"},{"full_name":"Higginbotham, Andrew P","first_name":"Andrew P","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363"},{"first_name":"Shenda","full_name":"Baker, Shenda","last_name":"Baker"},{"last_name":"Donnelly","full_name":"Donnelly, Tom","first_name":"Tom"}],"external_id":{"pmid":["    20735108"]},"date_published":"2010-07-20T00:00:00Z","abstract":[{"text":"We demonstrate the operation of a device that can produce chitosan nanoparticles in a tunable size range from 50-300 nm with small size dispersion. A piezoelectric oscillator operated at megahertz frequencies is used to aerosolize a solution containing dissolved chitosan. The solvent is then evaporated from the aerosolized droplets in a heat pipe, leaving monodisperse nanoparticles to be collected. The nanoparticle size is controlled both by the concentration of the dissolved polymer and by the size of the aerosol droplets that are created. Our device can be used with any polymer or polymer/therapeutic combination that can be prepared in a homogeneous solution and vaporized.","lang":"eng"}],"publist_id":"7965","oa_version":"None","extern":"1","day":"20","status":"public","type":"journal_article"},{"publist_id":"6755","abstract":[{"text":"Gene duplications and their subsequent divergence play an important part in the evolution of novel gene functions. Several models for the emergence, maintenance and evolution of gene copies have been proposed. However, a clear consensus on how gene duplications are fixed and maintained in genomes is lacking. Here, we present a comprehensive classification of the models that are relevant to all stages of the evolution of gene duplications. Each model predicts a unique combination of evolutionary dynamics and functional properties. Setting out these predictions is an important step towards identifying the main mechanisms that are involved in the evolution of gene duplications.","lang":"eng"}],"status":"public","type":"journal_article","day":"01","extern":1,"issue":"2","date_updated":"2021-01-12T08:21:19Z","intvolume":"        11","date_created":"2018-12-11T11:49:03Z","date_published":"2010-02-01T00:00:00Z","publisher":"Nature Publishing Group","author":[{"last_name":"Innan","full_name":"Innan, Hideki","first_name":"Hideki"},{"last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Fyodor Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":0,"doi":"10.1038/nrg2689","publication_status":"published","year":"2010","volume":11,"_id":"891","title":"The evolution of gene duplications: Classifying and distinguishing between models","publication":"Nature Reviews Genetics","citation":{"ieee":"H. Innan and F. Kondrashov, “The evolution of gene duplications: Classifying and distinguishing between models,” <i>Nature Reviews Genetics</i>, vol. 11, no. 2. Nature Publishing Group, pp. 97–108, 2010.","ama":"Innan H, Kondrashov F. The evolution of gene duplications: Classifying and distinguishing between models. <i>Nature Reviews Genetics</i>. 2010;11(2):97-108. doi:<a href=\"https://doi.org/10.1038/nrg2689\">10.1038/nrg2689</a>","chicago":"Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications: Classifying and Distinguishing between Models.” <i>Nature Reviews Genetics</i>. Nature Publishing Group, 2010. <a href=\"https://doi.org/10.1038/nrg2689\">https://doi.org/10.1038/nrg2689</a>.","apa":"Innan, H., &#38; Kondrashov, F. (2010). The evolution of gene duplications: Classifying and distinguishing between models. <i>Nature Reviews Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nrg2689\">https://doi.org/10.1038/nrg2689</a>","mla":"Innan, Hideki, and Fyodor Kondrashov. “The Evolution of Gene Duplications: Classifying and Distinguishing between Models.” <i>Nature Reviews Genetics</i>, vol. 11, no. 2, Nature Publishing Group, 2010, pp. 97–108, doi:<a href=\"https://doi.org/10.1038/nrg2689\">10.1038/nrg2689</a>.","ista":"Innan H, Kondrashov F. 2010. The evolution of gene duplications: Classifying and distinguishing between models. Nature Reviews Genetics. 11(2), 97–108.","short":"H. Innan, F. Kondrashov, Nature Reviews Genetics 11 (2010) 97–108."},"acknowledgement":"We thank M. Lynch for insightful comments on the manuscript.\n","month":"02","page":"97 - 108"}]