--- _id: '1405' abstract: - lang: eng text: "Motivated by the analysis of highly dynamic message-passing systems, i.e. unbounded thread creation, mobility, etc. we present a framework for the analysis of depth-bounded systems. Depth-bounded systems are one of the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. Even though they are infinite state systems depth-bounded systems are well-structured, thus can be analyzed algorithmically. We give an interpretation of depth-bounded systems as graph-rewriting systems. This gives more flexibility and ease of use to apply depth-bounded systems to other type of systems like shared memory concurrency.\r\n\r\nFirst, we develop an adequate domain of limits for depth-bounded systems, a prerequisite for the effective representation of downward-closed sets. Downward-closed sets are needed by forward saturation-based algorithms to represent potentially infinite sets of states. Then, we present an abstract interpretation framework to compute the covering set of well-structured transition systems. Because, in general, the covering set is not computable, our abstraction over-approximates the actual covering set. Our abstraction captures the essence of acceleration based-algorithms while giving up enough precision to ensure convergence. We have implemented the analysis in the PICASSO tool and show that it is accurate in practice. Finally, we build some further analyses like termination using the covering set as starting point." acknowledgement: "This work was supported in part by the Austrian Science Fund NFN RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant QUAREM (Quantitative Reactve Modeling).\r\nChapter 2, 3, and 4 are joint work with Thomas A. Henzinger and Thomas Wies. Chapter 2 was published in FoSSaCS 2010 as “Forward Analysis of Depth-Bounded Processes” [112]. Chapter 3 was published in VMCAI 2012 as “Ideal Abstractions for Well-Structured Transition Systems” [114]. Chap- ter 5.1 is joint work with Kshitij Bansal, Eric Koskinen, and Thomas Wies. It was published in TACAS 2013 as “Structural Counter Abstraction” [13]. The author’s contribution in this part is mostly related to the implementation. The theory required to understand the method and its implementation is quickly recalled to make the thesis self-contained, but should not be considered as a contribution. For the details of the methods, we refer the reader to the orig- inal publication [13] and the corresponding technical report [14]. Chapter 5.2 is ongoing work with Shahram Esmaeilsabzali, Rupak Majumdar, and Thomas Wies. I also would like to thank the people who supported over the past 4 years. My advisor Thomas A. Henzinger who gave me a lot of freedom to work on projects I was interested in. My collaborators, especially Thomas Wies with whom I worked since the beginning. The members of my thesis committee, Viktor Kun- cak and Rupak Majumdar, who also agreed to advise me. Simon Aeschbacher, Pavol Cerny, Cezara Dragoi, Arjun Radhakrishna, my family, friends and col- leagues who created an enjoyable environment. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: Zufferey D. Analysis of dynamic message passing programs. 2013. doi:10.15479/at:ista:1405 apa: Zufferey, D. (2013). Analysis of dynamic message passing programs. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:1405 chicago: Zufferey, Damien. “Analysis of Dynamic Message Passing Programs.” Institute of Science and Technology Austria, 2013. https://doi.org/10.15479/at:ista:1405. ieee: D. Zufferey, “Analysis of dynamic message passing programs,” Institute of Science and Technology Austria, 2013. ista: Zufferey D. 2013. Analysis of dynamic message passing programs. Institute of Science and Technology Austria. mla: Zufferey, Damien. Analysis of Dynamic Message Passing Programs. Institute of Science and Technology Austria, 2013, doi:10.15479/at:ista:1405. short: D. Zufferey, Analysis of Dynamic Message Passing Programs, Institute of Science and Technology Austria, 2013. date_created: 2018-12-11T11:51:50Z date_published: 2013-09-05T00:00:00Z date_updated: 2023-09-07T11:36:37Z day: '05' ddc: - '000' degree_awarded: PhD department: - _id: ToHe - _id: GradSch doi: 10.15479/at:ista:1405 ec_funded: 1 file: - access_level: open_access checksum: ed2d7b52933d134e8dc69d569baa284e content_type: application/pdf creator: dernst date_created: 2021-02-22T11:28:36Z date_updated: 2021-02-22T11:28:36Z file_id: '9176' file_name: 2013_Zufferey_thesis_final.pdf file_size: 1514906 relation: main_file success: 1 - access_level: closed checksum: cecc4c4b14225bee973d32e3dba91a55 content_type: application/pdf creator: cchlebak date_created: 2021-11-16T14:42:52Z date_updated: 2021-11-17T13:47:58Z file_id: '10298' file_name: 2013_Zufferey_thesis_final_pdfa.pdf file_size: 1378313 relation: main_file file_date_updated: 2021-11-17T13:47:58Z has_accepted_license: '1' language: - iso: eng main_file_link: - url: http://dzufferey.github.io/files/2013_thesis.pdf month: '09' oa: 1 oa_version: Published Version page: '134' project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '5802' related_material: record: - id: '2847' relation: part_of_dissertation status: public - id: '3251' relation: part_of_dissertation status: public - id: '4361' relation: part_of_dissertation status: public status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 title: Analysis of dynamic message passing programs type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2013' ... --- _id: '2847' abstract: - lang: eng text: Depth-Bounded Systems form an expressive class of well-structured transition systems. They can model a wide range of concurrent infinite-state systems including those with dynamic thread creation, dynamically changing communication topology, and complex shared heap structures. We present the first method to automatically prove fair termination of depth-bounded systems. Our method uses a numerical abstraction of the system, which we obtain by systematically augmenting an over-approximation of the system’s reachable states with a finite set of counters. This numerical abstraction can be analyzed with existing termination provers. What makes our approach unique is the way in which it exploits the well-structuredness of the analyzed system. We have implemented our work in a prototype tool and used it to automatically prove liveness properties of complex concurrent systems, including nonblocking algorithms such as Treiber’s stack and several distributed processes. Many of these examples are beyond the scope of termination analyses that are based on traditional counter abstractions. alternative_title: - LNCS author: - first_name: Kshitij full_name: Bansal, Kshitij last_name: Bansal - first_name: Eric full_name: Koskinen, Eric last_name: Koskinen - first_name: Thomas full_name: Wies, Thomas id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: Bansal K, Koskinen E, Wies T, Zufferey D. Structural Counter Abstraction. Piterman N, Smolka S, eds. 2013;7795:62-77. doi:10.1007/978-3-642-36742-7_5 apa: 'Bansal, K., Koskinen, E., Wies, T., & Zufferey, D. (2013). Structural Counter Abstraction. (N. Piterman & S. Smolka, Eds.). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Rome, Italy: Springer. https://doi.org/10.1007/978-3-642-36742-7_5' chicago: Bansal, Kshitij, Eric Koskinen, Thomas Wies, and Damien Zufferey. “Structural Counter Abstraction.” Edited by Nir Piterman and Scott Smolka. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-36742-7_5. ieee: K. Bansal, E. Koskinen, T. Wies, and D. Zufferey, “Structural Counter Abstraction,” vol. 7795. Springer, pp. 62–77, 2013. ista: Bansal K, Koskinen E, Wies T, Zufferey D. 2013. Structural Counter Abstraction (eds. N. Piterman & S. Smolka). 7795, 62–77. mla: Bansal, Kshitij, et al. Structural Counter Abstraction. Edited by Nir Piterman and Scott Smolka, vol. 7795, Springer, 2013, pp. 62–77, doi:10.1007/978-3-642-36742-7_5. short: K. Bansal, E. Koskinen, T. Wies, D. Zufferey, 7795 (2013) 62–77. conference: end_date: 2013-03-24 location: Rome, Italy name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2013-03-16 date_created: 2018-12-11T11:59:54Z date_published: 2013-03-01T00:00:00Z date_updated: 2023-09-07T11:36:36Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-642-36742-7_5 ec_funded: 1 editor: - first_name: Nir full_name: Piterman, Nir last_name: Piterman - first_name: Scott full_name: Smolka, Scott last_name: Smolka intvolume: ' 7795' language: - iso: eng main_file_link: - open_access: '1' url: http://arise.or.at/pubpdf/Structural_Counter_Abstraction.pdf month: '03' oa: 1 oa_version: Submitted Version page: 62 - 77 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '3947' quality_controlled: '1' related_material: record: - id: '1405' relation: dissertation_contains status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Structural Counter Abstraction type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7795 year: '2013' ... --- _id: '1406' abstract: - lang: eng text: Epithelial spreading is a critical part of various developmental and wound repair processes. Here we use zebrafish epiboly as a model system to study the cellular and molecular mechanisms underlying the spreading of epithelial sheets. During zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the embryo to eventually cover the entire yolk cell by the end of gastrulation. The EVL leading edge is anchored through tight junctions to the yolk syncytial layer (YSL), where directly adjacent to the EVL margin a contractile actomyosin ring is formed that is thought to drive EVL epiboly. The prevalent view in the field was that the contractile ring exerts a pulling force on the EVL margin, which pulls the EVL towards the vegetal pole. However, how this force is generated and how it affects EVL morphology still remains elusive. Moreover, the cellular mechanisms mediating the increase in EVL surface area, while maintaining tissue integrity and function are still unclear. Here we show that the YSL actomyosin ring pulls on the EVL margin by two distinct force-generating mechanisms. One mechanism is based on contraction of the ring around its circumference, as previously proposed. The second mechanism is based on actomyosin retrogade flows, generating force through resistance against the substrate. The latter can function at any epiboly stage even in situations where the contraction-based mechanism is unproductive. Additionally, we demonstrate that during epiboly the EVL is subjected to anisotropic tension, which guides the orientation of EVL cell division along the main axis (animal-vegetal) of tension. The influence of tension in cell division orientation involves cell elongation and requires myosin-2 activity for proper spindle alignment. Strikingly, we reveal that tension-oriented cell divisions release anisotropic tension within the EVL and that in the absence of such divisions, EVL cells undergo ectopic fusions. We conclude that forces applied to the EVL by the action of the YSL actomyosin ring generate a tension anisotropy in the EVL that orients cell divisions, which in turn limit tissue tension increase thereby facilitating tissue spreading. acknowledged_ssus: - _id: Bio - _id: PreCl alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Pedro full_name: Campinho, Pedro id: 3AFBBC42-F248-11E8-B48F-1D18A9856A87 last_name: Campinho orcid: 0000-0002-8526-5416 citation: ama: 'Campinho P. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. 2013.' apa: 'Campinho, P. (2013). Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. Institute of Science and Technology Austria.' chicago: 'Campinho, Pedro. “Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading.” Institute of Science and Technology Austria, 2013.' ieee: 'P. Campinho, “Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading,” Institute of Science and Technology Austria, 2013.' ista: 'Campinho P. 2013. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. Institute of Science and Technology Austria.' mla: 'Campinho, Pedro. Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading. Institute of Science and Technology Austria, 2013.' short: 'P. Campinho, Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading, Institute of Science and Technology Austria, 2013.' date_created: 2018-12-11T11:51:50Z date_published: 2013-10-01T00:00:00Z date_updated: 2023-09-07T11:36:07Z day: '01' degree_awarded: PhD department: - _id: CaHe language: - iso: eng month: '10' oa_version: None page: '123' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '5801' status: public supervisor: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 title: 'Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading' type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2013' ... --- _id: '2247' abstract: - lang: eng text: Cooperative behavior, where one individual incurs a cost to help another, is a wide spread phenomenon. Here we study direct reciprocity in the context of the alternating Prisoner's Dilemma. We consider all strategies that can be implemented by one and two-state automata. We calculate the payoff matrix of all pairwise encounters in the presence of noise. We explore deterministic selection dynamics with and without mutation. Using different error rates and payoff values, we observe convergence to a small number of distinct equilibria. Two of them are uncooperative strict Nash equilibria representing always-defect (ALLD) and Grim. The third equilibrium is mixed and represents a cooperative alliance of several strategies, dominated by a strategy which we call Forgiver. Forgiver cooperates whenever the opponent has cooperated; it defects once when the opponent has defected, but subsequently Forgiver attempts to re-establish cooperation even if the opponent has defected again. Forgiver is not an evolutionarily stable strategy, but the alliance, which it rules, is asymptotically stable. For a wide range of parameter values the most commonly observed outcome is convergence to the mixed equilibrium, dominated by Forgiver. Our results show that although forgiving might incur a short-term loss it can lead to a long-term gain. Forgiveness facilitates stable cooperation in the presence of exploitation and noise. article_number: e80814 author: - first_name: Benjamin full_name: Zagorsky, Benjamin last_name: Zagorsky - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Zagorsky B, Reiter J, Chatterjee K, Nowak M. Forgiver triumphs in alternating prisoner’s dilemma . PLoS One. 2013;8(12). doi:10.1371/journal.pone.0080814 apa: Zagorsky, B., Reiter, J., Chatterjee, K., & Nowak, M. (2013). Forgiver triumphs in alternating prisoner’s dilemma . PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0080814 chicago: Zagorsky, Benjamin, Johannes Reiter, Krishnendu Chatterjee, and Martin Nowak. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” PLoS One. Public Library of Science, 2013. https://doi.org/10.1371/journal.pone.0080814. ieee: B. Zagorsky, J. Reiter, K. Chatterjee, and M. Nowak, “Forgiver triumphs in alternating prisoner’s dilemma ,” PLoS One, vol. 8, no. 12. Public Library of Science, 2013. ista: Zagorsky B, Reiter J, Chatterjee K, Nowak M. 2013. Forgiver triumphs in alternating prisoner’s dilemma . PLoS One. 8(12), e80814. mla: Zagorsky, Benjamin, et al. “Forgiver Triumphs in Alternating Prisoner’s Dilemma .” PLoS One, vol. 8, no. 12, e80814, Public Library of Science, 2013, doi:10.1371/journal.pone.0080814. short: B. Zagorsky, J. Reiter, K. Chatterjee, M. Nowak, PLoS One 8 (2013). date_created: 2018-12-11T11:56:33Z date_published: 2013-12-12T00:00:00Z date_updated: 2023-09-07T11:40:43Z day: '12' ddc: - '000' department: - _id: KrCh doi: 10.1371/journal.pone.0080814 ec_funded: 1 file: - access_level: open_access checksum: 808e8b9e6e89658bee4ffbbfac1bd19d content_type: application/pdf creator: system date_created: 2018-12-12T10:11:15Z date_updated: 2020-07-14T12:45:34Z file_id: '4868' file_name: IST-2016-409-v1+1_journal.pone.0080814.pdf file_size: 1050042 relation: main_file file_date_updated: 2020-07-14T12:45:34Z has_accepted_license: '1' intvolume: ' 8' issue: '12' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '12' oa: 1 oa_version: Published Version project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4702' pubrep_id: '409' quality_controlled: '1' related_material: record: - id: '9749' relation: research_data status: public - id: '1400' relation: dissertation_contains status: public scopus_import: 1 status: public title: 'Forgiver triumphs in alternating prisoner''s dilemma ' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ... --- _id: '2858' abstract: - lang: eng text: Tumor growth is caused by the acquisition of driver mutations, which enhance the net reproductive rate of cells. Driver mutations may increase cell division, reduce cell death, or allow cells to overcome density-limiting effects. We study the dynamics of tumor growth as one additional driver mutation is acquired. Our models are based on two-type branching processes that terminate in either tumor disappearance or tumor detection. In our first model, both cell types grow exponentially, with a faster rate for cells carrying the additional driver. We find that the additional driver mutation does not affect the survival probability of the lesion, but can substantially reduce the time to reach the detectable size if the lesion is slow growing. In our second model, cells lacking the additional driver cannot exceed a fixed carrying capacity, due to density limitations. In this case, the time to detection depends strongly on this carrying capacity. Our model provides a quantitative framework for studying tumor dynamics during different stages of progression. We observe that early, small lesions need additional drivers, while late stage metastases are only marginally affected by them. These results help to explain why additional driver mutations are typically not detected in fast-growing metastases. author: - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Ivana full_name: Božić, Ivana last_name: Božić - first_name: Benjamin full_name: Allen, Benjamin id: 135B5B70-E9D2-11E9-BD74-BB415DA2B523 last_name: Allen - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. The effect of one additional driver mutation on tumor progression. Evolutionary Applications. 2013;6(1):34-45. doi:10.1111/eva.12020 apa: Reiter, J., Božić, I., Allen, B., Chatterjee, K., & Nowak, M. (2013). The effect of one additional driver mutation on tumor progression. Evolutionary Applications. Wiley-Blackwell. https://doi.org/10.1111/eva.12020 chicago: Reiter, Johannes, Ivana Božić, Benjamin Allen, Krishnendu Chatterjee, and Martin Nowak. “The Effect of One Additional Driver Mutation on Tumor Progression.” Evolutionary Applications. Wiley-Blackwell, 2013. https://doi.org/10.1111/eva.12020. ieee: J. Reiter, I. Božić, B. Allen, K. Chatterjee, and M. Nowak, “The effect of one additional driver mutation on tumor progression,” Evolutionary Applications, vol. 6, no. 1. Wiley-Blackwell, pp. 34–45, 2013. ista: Reiter J, Božić I, Allen B, Chatterjee K, Nowak M. 2013. The effect of one additional driver mutation on tumor progression. Evolutionary Applications. 6(1), 34–45. mla: Reiter, Johannes, et al. “The Effect of One Additional Driver Mutation on Tumor Progression.” Evolutionary Applications, vol. 6, no. 1, Wiley-Blackwell, 2013, pp. 34–45, doi:10.1111/eva.12020. short: J. Reiter, I. Božić, B. Allen, K. Chatterjee, M. Nowak, Evolutionary Applications 6 (2013) 34–45. date_created: 2018-12-11T11:59:58Z date_published: 2013-01-01T00:00:00Z date_updated: 2023-09-07T11:40:43Z day: '01' ddc: - '570' department: - _id: KrCh doi: 10.1111/eva.12020 ec_funded: 1 file: - access_level: open_access checksum: e2955b3889f8a823c3d5a72cb16f8957 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:50Z date_updated: 2020-07-14T12:45:51Z file_id: '5173' file_name: IST-2016-415-v1+1_Reiter_et_al-2013-Evolutionary_Applications.pdf file_size: 1172037 relation: main_file file_date_updated: 2020-07-14T12:45:51Z has_accepted_license: '1' intvolume: ' 6' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 34 - 45 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: Evolutionary Applications publication_status: published publisher: Wiley-Blackwell publist_id: '3931' pubrep_id: '415' quality_controlled: '1' related_material: record: - id: '1400' relation: dissertation_contains status: public scopus_import: 1 status: public title: The effect of one additional driver mutation on tumor progression tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2013' ... --- _id: '2816' abstract: - lang: eng text: In solid tumors, targeted treatments can lead to dramatic regressions, but responses are often short-lived because resistant cancer cells arise. The major strategy proposed for overcoming resistance is combination therapy. We present a mathematical model describing the evolutionary dynamics of lesions in response to treatment. We first studied 20 melanoma patients receiving vemurafenib. We then applied our model to an independent set of pancreatic, colorectal, and melanoma cancer patients with metastatic disease. We find that dual therapy results in long-term disease control for most patients, if there are no single mutations that cause cross-resistance to both drugs; in patients with large disease burden, triple therapy is needed. We also find that simultaneous therapy with two drugs is much more effective than sequential therapy. Our results provide realistic expectations for the efficacy of new drug combinations and inform the design of trials for new cancer therapeutics. article_number: e00747 author: - first_name: Ivana full_name: Božić, Ivana last_name: Božić - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Benjamin full_name: Allen, Benjamin last_name: Allen - first_name: Tibor full_name: Antal, Tibor last_name: Antal - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Preya full_name: Shah, Preya last_name: Shah - first_name: Yo full_name: Moon, Yo last_name: Moon - first_name: Amin full_name: Yaqubie, Amin last_name: Yaqubie - first_name: Nicole full_name: Kelly, Nicole last_name: Kelly - first_name: Dung full_name: Le, Dung last_name: Le - first_name: Evan full_name: Lipson, Evan last_name: Lipson - first_name: Paul full_name: Chapman, Paul last_name: Chapman - first_name: Luis full_name: Diaz, Luis last_name: Diaz - first_name: Bert full_name: Vogelstein, Bert last_name: Vogelstein - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Božić I, Reiter J, Allen B, et al. Evolutionary dynamics of cancer in response to targeted combination therapy. eLife. 2013;2. doi:10.7554/eLife.00747 apa: Božić, I., Reiter, J., Allen, B., Antal, T., Chatterjee, K., Shah, P., … Nowak, M. (2013). Evolutionary dynamics of cancer in response to targeted combination therapy. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.00747 chicago: Božić, Ivana, Johannes Reiter, Benjamin Allen, Tibor Antal, Krishnendu Chatterjee, Preya Shah, Yo Moon, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” ELife. eLife Sciences Publications, 2013. https://doi.org/10.7554/eLife.00747. ieee: I. Božić et al., “Evolutionary dynamics of cancer in response to targeted combination therapy,” eLife, vol. 2. eLife Sciences Publications, 2013. ista: Božić I, Reiter J, Allen B, Antal T, Chatterjee K, Shah P, Moon Y, Yaqubie A, Kelly N, Le D, Lipson E, Chapman P, Diaz L, Vogelstein B, Nowak M. 2013. Evolutionary dynamics of cancer in response to targeted combination therapy. eLife. 2, e00747. mla: Božić, Ivana, et al. “Evolutionary Dynamics of Cancer in Response to Targeted Combination Therapy.” ELife, vol. 2, e00747, eLife Sciences Publications, 2013, doi:10.7554/eLife.00747. short: I. Božić, J. Reiter, B. Allen, T. Antal, K. Chatterjee, P. Shah, Y. Moon, A. Yaqubie, N. Kelly, D. Le, E. Lipson, P. Chapman, L. Diaz, B. Vogelstein, M. Nowak, ELife 2 (2013). date_created: 2018-12-11T11:59:45Z date_published: 2013-06-25T00:00:00Z date_updated: 2023-09-07T11:40:43Z day: '25' ddc: - '570' - '610' department: - _id: KrCh doi: 10.7554/eLife.00747 file: - access_level: open_access checksum: 2c38c47815eacd8fa66cb8b404cf7c61 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:48Z date_updated: 2020-07-14T12:45:49Z file_id: '4967' file_name: IST-2013-134-v1+1_e00747.full.pdf file_size: 3358321 relation: main_file file_date_updated: 2020-07-14T12:45:49Z has_accepted_license: '1' intvolume: ' 2' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '3985' pubrep_id: '134' quality_controlled: '1' related_material: record: - id: '1400' relation: dissertation_contains status: public scopus_import: 1 status: public title: Evolutionary dynamics of cancer in response to targeted combination therapy tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2013' ... --- _id: '2000' abstract: - lang: eng text: In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics. alternative_title: - LNCS author: - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Ivana full_name: Božić, Ivana last_name: Božić - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: 'Reiter J, Božić I, Chatterjee K, Nowak M. TTP: Tool for tumor progression. In: Proceedings of 25th Int. Conf. on Computer Aided Verification. Vol 8044. Lecture Notes in Computer Science. Springer; 2013:101-106. doi:10.1007/978-3-642-39799-8_6' apa: 'Reiter, J., Božić, I., Chatterjee, K., & Nowak, M. (2013). TTP: Tool for tumor progression. In Proceedings of 25th Int. Conf. on Computer Aided Verification (Vol. 8044, pp. 101–106). St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_6' chicago: 'Reiter, Johannes, Ivana Božić, Krishnendu Chatterjee, and Martin Nowak. “TTP: Tool for Tumor Progression.” In Proceedings of 25th Int. Conf. on Computer Aided Verification, 8044:101–6. Lecture Notes in Computer Science. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_6.' ieee: 'J. Reiter, I. Božić, K. Chatterjee, and M. Nowak, “TTP: Tool for tumor progression,” in Proceedings of 25th Int. Conf. on Computer Aided Verification, St. Petersburg, Russia, 2013, vol. 8044, pp. 101–106.' ista: 'Reiter J, Božić I, Chatterjee K, Nowak M. 2013. TTP: Tool for tumor progression. Proceedings of 25th Int. Conf. on Computer Aided Verification. CAV: Computer Aided VerificationLecture Notes in Computer Science, LNCS, vol. 8044, 101–106.' mla: 'Reiter, Johannes, et al. “TTP: Tool for Tumor Progression.” Proceedings of 25th Int. Conf. on Computer Aided Verification, vol. 8044, Springer, 2013, pp. 101–06, doi:10.1007/978-3-642-39799-8_6.' short: J. Reiter, I. Božić, K. Chatterjee, M. Nowak, in:, Proceedings of 25th Int. Conf. on Computer Aided Verification, Springer, 2013, pp. 101–106. conference: end_date: 2013-07-19 location: St. Petersburg, Russia name: 'CAV: Computer Aided Verification' start_date: 2013-07-13 date_created: 2018-12-11T11:55:08Z date_published: 2013-01-01T00:00:00Z date_updated: 2023-09-07T11:40:43Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-642-39799-8_6 ec_funded: 1 external_id: arxiv: - '1303.5251' intvolume: ' 8044' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1303.5251 month: '01' oa: 1 oa_version: Preprint page: 101 - 106 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Proceedings of 25th Int. Conf. on Computer Aided Verification publication_status: published publisher: Springer publist_id: '5077' quality_controlled: '1' related_material: record: - id: '5399' relation: earlier_version status: public - id: '1400' relation: dissertation_contains status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: 'TTP: Tool for tumor progression' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8044 year: '2013' ... --- _id: '2445' abstract: - lang: eng text: We develop program synthesis techniques that can help programmers fix concurrency-related bugs. We make two new contributions to synthesis for concurrency, the first improving the efficiency of the synthesized code, and the second improving the efficiency of the synthesis procedure itself. The first contribution is to have the synthesis procedure explore a variety of (sequential) semantics-preserving program transformations. Classically, only one such transformation has been considered, namely, the insertion of synchronization primitives (such as locks). Based on common manual bug-fixing techniques used by Linux device-driver developers, we explore additional, more efficient transformations, such as the reordering of independent instructions. The second contribution is to speed up the counterexample-guided removal of concurrency bugs within the synthesis procedure by considering partial-order traces (instead of linear traces) as counterexamples. A partial-order error trace represents a set of linear (interleaved) traces of a concurrent program all of which lead to the same error. By eliminating a partial-order error trace, we eliminate in a single iteration of the synthesis procedure all linearizations of the partial-order trace. We evaluated our techniques on several simplified examples of real concurrency bugs that occurred in Linux device drivers. alternative_title: - LNCS author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna - first_name: Leonid full_name: Ryzhyk, Leonid last_name: Ryzhyk - first_name: Thorsten full_name: Tarrach, Thorsten id: 3D6E8F2C-F248-11E8-B48F-1D18A9856A87 last_name: Tarrach orcid: 0000-0003-4409-8487 citation: ama: 'Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Efficient synthesis for concurrency by semantics-preserving transformations. In: Vol 8044. Springer; 2013:951-967. doi:10.1007/978-3-642-39799-8_68' apa: 'Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., & Tarrach, T. (2013). Efficient synthesis for concurrency by semantics-preserving transformations (Vol. 8044, pp. 951–967). Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. https://doi.org/10.1007/978-3-642-39799-8_68' chicago: Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and Thorsten Tarrach. “Efficient Synthesis for Concurrency by Semantics-Preserving Transformations,” 8044:951–67. Springer, 2013. https://doi.org/10.1007/978-3-642-39799-8_68. ieee: 'P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Efficient synthesis for concurrency by semantics-preserving transformations,” presented at the CAV: Computer Aided Verification, St. Petersburg, Russia, 2013, vol. 8044, pp. 951–967.' ista: 'Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2013. Efficient synthesis for concurrency by semantics-preserving transformations. CAV: Computer Aided Verification, LNCS, vol. 8044, 951–967.' mla: Cerny, Pavol, et al. Efficient Synthesis for Concurrency by Semantics-Preserving Transformations. Vol. 8044, Springer, 2013, pp. 951–67, doi:10.1007/978-3-642-39799-8_68. short: P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2013, pp. 951–967. conference: end_date: 2013-07-19 location: St. Petersburg, Russia name: 'CAV: Computer Aided Verification' start_date: 2013-07-13 date_created: 2018-12-11T11:57:42Z date_published: 2013-07-01T00:00:00Z date_updated: 2023-09-07T11:57:01Z day: '01' ddc: - '000' - '004' department: - _id: ToHe doi: 10.1007/978-3-642-39799-8_68 ec_funded: 1 file: - access_level: open_access checksum: 70c70ca5487faba82262c63e1b678a27 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:37Z date_updated: 2020-07-14T12:45:40Z file_id: '5158' file_name: IST-2014-199-v1+1_cav2013-final.pdf file_size: 365548 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 8044' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 951 - 967 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '4458' pubrep_id: '199' quality_controlled: '1' related_material: record: - id: '1130' relation: dissertation_contains status: public scopus_import: 1 status: public title: Efficient synthesis for concurrency by semantics-preserving transformations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8044 year: '2013' ... --- _id: '2926' abstract: - lang: eng text: To fight infectious diseases, host immune defenses are employed at multiple levels. Sanitary behavior, such as pathogen avoidance and removal, acts as a first line of defense 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 toward pathogen-exposed group members [2]. One of the most common behaviors 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; 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 behavior extends the current understanding of grooming and the establishment of social immunity in insect societies. acknowledgement: "Funding for this project was obtained by the German Research Foundation (DFG, to S.C.) and the European Research Council (ERC, through an ERC-Starting Grant to S.C. and an Individual Marie Curie IEF fellowship to L.V.U.).\r\nWe thank Jørgen Eilenberg, Bernhardt Steinwender, Miriam Stock, and Meghan L. Vyleta for the fungal strain and its characterization; Volker Witte for chemical information; Eva Sixt for ant drawings; and Robert Hauschild for help with image analysis. We further thank Martin Kaltenpoth, Michael Sixt, Jürgen Heinze, and Joachim Ruther for discussion and Daria Siekhaus, Sophie A.O. Armitage, and Leila Masri for comments on the manuscript. \r\n" author: - first_name: Simon full_name: Tragust, Simon id: 35A7A418-F248-11E8-B48F-1D18A9856A87 last_name: Tragust - first_name: Barbara full_name: Mitteregger, Barbara id: 479DDAAC-E9CD-11E9-9B5F-82450873F7A1 last_name: Mitteregger - first_name: Vanessa full_name: Barone, Vanessa id: 419EECCC-F248-11E8-B48F-1D18A9856A87 last_name: Barone orcid: 0000-0003-2676-3367 - first_name: Matthias full_name: Konrad, Matthias id: 46528076-F248-11E8-B48F-1D18A9856A87 last_name: Konrad - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Current Biology. 2013;23(1):76-82. doi:10.1016/j.cub.2012.11.034 apa: Tragust, S., Mitteregger, B., Barone, V., Konrad, M., Ugelvig, L. V., & Cremer, S. (2013). Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2012.11.034 chicago: Tragust, Simon, Barbara Mitteregger, Vanessa Barone, Matthias Konrad, Line V Ugelvig, and Sylvia Cremer. “Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” Current Biology. Cell Press, 2013. https://doi.org/10.1016/j.cub.2012.11.034. ieee: S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L. V. Ugelvig, and S. Cremer, “Ants disinfect fungus-exposed brood by oral uptake and spread of their poison,” Current Biology, vol. 23, no. 1. Cell Press, pp. 76–82, 2013. ista: Tragust S, Mitteregger B, Barone V, Konrad M, Ugelvig LV, Cremer S. 2013. Ants disinfect fungus-exposed brood by oral uptake and spread of their poison. Current Biology. 23(1), 76–82. mla: Tragust, Simon, et al. “Ants Disinfect Fungus-Exposed Brood by Oral Uptake and Spread of Their Poison.” Current Biology, vol. 23, no. 1, Cell Press, 2013, pp. 76–82, doi:10.1016/j.cub.2012.11.034. short: S. Tragust, B. Mitteregger, V. Barone, M. Konrad, L.V. Ugelvig, S. Cremer, Current Biology 23 (2013) 76–82. date_created: 2018-12-11T12:00:23Z date_published: 2013-01-07T00:00:00Z date_updated: 2023-09-07T12:05:08Z day: '07' department: - _id: SyCr - _id: CaHe doi: 10.1016/j.cub.2012.11.034 ec_funded: 1 intvolume: ' 23' issue: '1' language: - iso: eng month: '01' oa_version: None page: 76 - 82 project: - _id: 25DAF0B2-B435-11E9-9278-68D0E5697425 grant_number: CR-118/3-1 name: Host-Parasite Coevolution - _id: 25DC711C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '243071' name: 'Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects' - _id: 25DDF0F0-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '302004' name: 'Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach' publication: Current Biology publication_status: published publisher: Cell Press publist_id: '3811' quality_controlled: '1' related_material: record: - id: '9757' relation: research_data status: public - id: '961' relation: dissertation_contains status: public scopus_import: 1 status: public title: Ants disinfect fungus-exposed brood by oral uptake and spread of their poison type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2013' ... --- _id: '2305' abstract: - lang: eng text: We study the complexity of central controller synthesis problems for finite-state Markov decision processes, where the objective is to optimize both the expected mean-payoff performance of the system and its stability. e argue that the basic theoretical notion of expressing the stability in terms of the variance of the mean-payoff (called global variance in our paper) is not always sufficient, since it ignores possible instabilities on respective runs. For this reason we propose alernative definitions of stability, which we call local and hybrid variance, and which express how rewards on each run deviate from the run's own mean-payoff and from the expected mean-payoff, respectively. We show that a strategy ensuring both the expected mean-payoff and the variance below given bounds requires randomization and memory, under all the above semantics of variance. We then look at the problem of determining whether there is a such a strategy. For the global variance, we show that the problem is in PSPACE, and that the answer can be approximated in pseudo-polynomial time. For the hybrid variance, the analogous decision problem is in NP, and a polynomial-time approximating algorithm also exists. For local variance, we show that the decision problem is in NP. Since the overall performance can be traded for stability (and vice versa), we also present algorithms for approximating the associated Pareto curve in all the three cases. Finally, we study a special case of the decision problems, where we require a given expected mean-payoff together with zero variance. Here we show that the problems can be all solved in polynomial time. author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vojtěch full_name: Forejt, Vojtěch last_name: Forejt - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera citation: ama: 'Brázdil T, Chatterjee K, Forejt V, Kučera A. Trading performance for stability in Markov decision processes. In: 28th Annual ACM/IEEE Symposium. IEEE; 2013:331-340. doi:10.1109/LICS.2013.39' apa: 'Brázdil, T., Chatterjee, K., Forejt, V., & Kučera, A. (2013). Trading performance for stability in Markov decision processes. In 28th Annual ACM/IEEE Symposium (pp. 331–340). New Orleans, LA, United States: IEEE. https://doi.org/10.1109/LICS.2013.39' chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Vojtěch Forejt, and Antonín Kučera. “Trading Performance for Stability in Markov Decision Processes.” In 28th Annual ACM/IEEE Symposium, 331–40. IEEE, 2013. https://doi.org/10.1109/LICS.2013.39. ieee: T. Brázdil, K. Chatterjee, V. Forejt, and A. Kučera, “Trading performance for stability in Markov decision processes,” in 28th Annual ACM/IEEE Symposium, New Orleans, LA, United States, 2013, pp. 331–340. ista: 'Brázdil T, Chatterjee K, Forejt V, Kučera A. 2013. Trading performance for stability in Markov decision processes. 28th Annual ACM/IEEE Symposium. LICS: Logic in Computer Science, 331–340.' mla: Brázdil, Tomáš, et al. “Trading Performance for Stability in Markov Decision Processes.” 28th Annual ACM/IEEE Symposium, IEEE, 2013, pp. 331–40, doi:10.1109/LICS.2013.39. short: T. Brázdil, K. Chatterjee, V. Forejt, A. Kučera, in:, 28th Annual ACM/IEEE Symposium, IEEE, 2013, pp. 331–340. conference: end_date: 2013-06-28 location: New Orleans, LA, United States name: 'LICS: Logic in Computer Science' start_date: 2013-06-25 date_created: 2018-12-11T11:56:53Z date_published: 2013-08-01T00:00:00Z date_updated: 2023-09-20T11:15:30Z day: '01' department: - _id: KrCh doi: 10.1109/LICS.2013.39 ec_funded: 1 external_id: arxiv: - '1305.4103' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1305.4103 month: '08' oa: 1 oa_version: Preprint page: 331 - 340 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: 28th Annual ACM/IEEE Symposium publication_status: published publisher: IEEE publist_id: '4622' quality_controlled: '1' related_material: record: - id: '1294' relation: later_version status: public scopus_import: 1 status: public title: Trading performance for stability in Markov decision processes type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2820' abstract: - lang: eng text: 'In this paper, we introduce the powerful framework of graph games for the analysis of real-time scheduling with firm deadlines. We introduce a novel instance of a partial-observation game that is suitable for this purpose, and prove decidability of all the involved decision problems. We derive a graph game that allows the automated computation of the competitive ratio (along with an optimal witness algorithm for the competitive ratio) and establish an NP-completeness proof for the graph game problem. For a given on-line algorithm, we present polynomial time solution for computing (i) the worst-case utility; (ii) the worst-case utility ratio w.r.t. a clairvoyant off-line algorithm; and (iii) the competitive ratio. A major strength of the proposed approach lies in its flexibility w.r.t. incorporating additional constraints on the adversary and/or the algorithm, including limited maximum or average load, finiteness of periods of overload, etc., which are easily added by means of additional instances of standard objective functions for graph games. ' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Alexander full_name: Kößler, Alexander last_name: Kößler - first_name: Ulrich full_name: Schmid, Ulrich last_name: Schmid citation: ama: 'Chatterjee K, Kößler A, Schmid U. Automated analysis of real-time scheduling using graph games. In: Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control. ACM; 2013:163-172. doi:10.1145/2461328.2461356' apa: 'Chatterjee, K., Kößler, A., & Schmid, U. (2013). Automated analysis of real-time scheduling using graph games. In Proceedings of the 16th International conference on Hybrid systems: Computation and control (pp. 163–172). Philadelphia, PA, United States: ACM. https://doi.org/10.1145/2461328.2461356' chicago: 'Chatterjee, Krishnendu, Alexander Kößler, and Ulrich Schmid. “Automated Analysis of Real-Time Scheduling Using Graph Games.” In Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, 163–72. ACM, 2013. https://doi.org/10.1145/2461328.2461356.' ieee: 'K. Chatterjee, A. Kößler, and U. Schmid, “Automated analysis of real-time scheduling using graph games,” in Proceedings of the 16th International conference on Hybrid systems: Computation and control, Philadelphia, PA, United States, 2013, pp. 163–172.' ista: 'Chatterjee K, Kößler A, Schmid U. 2013. Automated analysis of real-time scheduling using graph games. Proceedings of the 16th International conference on Hybrid systems: Computation and control. HSCC: Hybrid Systems - Computation and Control, 163–172.' mla: 'Chatterjee, Krishnendu, et al. “Automated Analysis of Real-Time Scheduling Using Graph Games.” Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, ACM, 2013, pp. 163–72, doi:10.1145/2461328.2461356.' short: 'K. Chatterjee, A. Kößler, U. Schmid, in:, Proceedings of the 16th International Conference on Hybrid Systems: Computation and Control, ACM, 2013, pp. 163–172.' conference: end_date: 2013-04-11 location: Philadelphia, PA, United States name: 'HSCC: Hybrid Systems - Computation and Control' start_date: 2013-04-08 date_created: 2018-12-11T11:59:46Z date_published: 2013-04-01T00:00:00Z date_updated: 2023-09-27T12:52:38Z day: '01' department: - _id: KrCh doi: 10.1145/2461328.2461356 ec_funded: 1 language: - iso: eng month: '04' oa_version: None page: 163 - 172 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: 'Proceedings of the 16th International conference on Hybrid systems: Computation and control' publication_identifier: isbn: - '978-1-4503-1567-8 ' publication_status: published publisher: ACM publist_id: '3981' quality_controlled: '1' related_material: record: - id: '738' relation: later_version status: public scopus_import: 1 status: public title: Automated analysis of real-time scheduling using graph games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '2272' abstract: - lang: eng text: "We consider Conditional Random Fields (CRFs) with pattern-based potentials defined on a chain. In this model the energy of a string (labeling) x1...xn is the sum of terms over intervals [i,j] where each term is non-zero only if the substring xi...xj equals a prespecified pattern α. Such CRFs can be naturally applied to many sequence tagging problems.\r\nWe present efficient algorithms for the three standard inference tasks in a CRF, namely computing (i) the partition function, (ii) marginals, and (iii) computing the MAP. Their complexities are respectively O(nL), O(nLℓmax) and O(nLmin{|D|,log(ℓmax+1)}) where L is the combined length of input patterns, ℓmax is the maximum length of a pattern, and D is the input alphabet. This improves on the previous algorithms of (Ye et al., 2009) whose complexities are respectively O(nL|D|), O(n|Γ|L2ℓ2max) and O(nL|D|), where |Γ| is the number of input patterns.\r\nIn addition, we give an efficient algorithm for sampling. Finally, we consider the case of non-positive weights. (Komodakis & Paragios, 2009) gave an O(nL) algorithm for computing the MAP. We present a modification that has the same worst-case complexity but can beat it in the best case. " alternative_title: - JMLR article_processing_charge: No author: - first_name: Rustem full_name: Takhanov, Rustem id: 2CCAC26C-F248-11E8-B48F-1D18A9856A87 last_name: Takhanov - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: 'Takhanov R, Kolmogorov V. Inference algorithms for pattern-based CRFs on sequence data. In: ICML’13 Proceedings of the 30th International Conference on International. Vol 28. ML Research Press; 2013:145-153.' apa: 'Takhanov, R., & Kolmogorov, V. (2013). Inference algorithms for pattern-based CRFs on sequence data. In ICML’13 Proceedings of the 30th International Conference on International (Vol. 28, pp. 145–153). Atlanta, GA, USA: ML Research Press.' chicago: Takhanov, Rustem, and Vladimir Kolmogorov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” In ICML’13 Proceedings of the 30th International Conference on International, 28:145–53. ML Research Press, 2013. ieee: R. Takhanov and V. Kolmogorov, “Inference algorithms for pattern-based CRFs on sequence data,” in ICML’13 Proceedings of the 30th International Conference on International, Atlanta, GA, USA, 2013, vol. 28, no. 3, pp. 145–153. ista: 'Takhanov R, Kolmogorov V. 2013. Inference algorithms for pattern-based CRFs on sequence data. ICML’13 Proceedings of the 30th International Conference on International. ICML: International Conference on Machine Learning, JMLR, vol. 28, 145–153.' mla: Takhanov, Rustem, and Vladimir Kolmogorov. “Inference Algorithms for Pattern-Based CRFs on Sequence Data.” ICML’13 Proceedings of the 30th International Conference on International, vol. 28, no. 3, ML Research Press, 2013, pp. 145–53. short: R. Takhanov, V. Kolmogorov, in:, ICML’13 Proceedings of the 30th International Conference on International, ML Research Press, 2013, pp. 145–153. conference: end_date: 2013-06-21 location: Atlanta, GA, USA name: 'ICML: International Conference on Machine Learning' start_date: 2013-06-16 date_created: 2018-12-11T11:56:41Z date_published: 2013-06-01T00:00:00Z date_updated: 2023-10-17T09:51:32Z day: '01' department: - _id: VlKo intvolume: ' 28' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://proceedings.mlr.press/v28/takhanov13.pdf?CFID=105472548&CFTOKEN=5c5859b5d97b4439-27B4AC58-BA92-A964-B598CAACEE6CC515 month: '06' oa: 1 oa_version: Submitted Version page: 145 - 153 publication: ICML'13 Proceedings of the 30th International Conference on International publication_status: published publisher: ML Research Press publist_id: '4672' quality_controlled: '1' related_material: record: - id: '1794' relation: later_version status: public scopus_import: '1' status: public title: Inference algorithms for pattern-based CRFs on sequence data type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2013' ... --- _id: '2448' abstract: - lang: eng text: Cell-to-cell directional flow of the phytohormone auxin is primarily established by polar localization of the PIN auxin transporters, a process tightly regulated at multiple levels by auxin itself. We recently reported that, in the context of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular, ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal root tip cells under conditions normally triggering PIN2 degradation. Here, we show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts as a general positive modulator of polar auxin transport in roots. article_number: e25688 article_processing_charge: No article_type: original author: - first_name: Estelle full_name: Remy, Estelle last_name: Remy - first_name: Pawel full_name: Baster, Pawel id: 3028BD74-F248-11E8-B48F-1D18A9856A87 last_name: Baster - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Paula full_name: Duque, Paula last_name: Duque citation: ama: Remy E, Baster P, Friml J, Duque P. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. Plant Signaling & Behavior. 2013;8(10). doi:10.4161/psb.25688 apa: Remy, E., Baster, P., Friml, J., & Duque, P. (2013). ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. Plant Signaling & Behavior. Taylor & Francis. https://doi.org/10.4161/psb.25688 chicago: Remy, Estelle, Pawel Baster, Jiří Friml, and Paula Duque. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” Plant Signaling & Behavior. Taylor & Francis, 2013. https://doi.org/10.4161/psb.25688. ieee: E. Remy, P. Baster, J. Friml, and P. Duque, “ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip,” Plant Signaling & Behavior, vol. 8, no. 10. Taylor & Francis, 2013. ista: Remy E, Baster P, Friml J, Duque P. 2013. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. Plant Signaling & Behavior. 8(10), e25688. mla: Remy, Estelle, et al. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” Plant Signaling & Behavior, vol. 8, no. 10, e25688, Taylor & Francis, 2013, doi:10.4161/psb.25688. short: E. Remy, P. Baster, J. Friml, P. Duque, Plant Signaling & Behavior 8 (2013). date_created: 2018-12-11T11:57:43Z date_published: 2013-07-10T00:00:00Z date_updated: 2023-10-17T11:15:14Z day: '10' department: - _id: JiFr doi: 10.4161/psb.25688 ec_funded: 1 external_id: pmid: - '23857365' intvolume: ' 8' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091088/ month: '07' oa: 1 oa_version: Submitted Version pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Plant Signaling & Behavior publication_status: published publisher: Taylor & Francis publist_id: '4455' quality_controlled: '1' scopus_import: '1' status: public title: ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2013' ... --- _id: '2853' abstract: - lang: eng text: High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared with its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low, because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation. article_processing_charge: No article_type: original author: - first_name: Dominik full_name: Refardt, Dominik last_name: Refardt - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Rolf full_name: Kümmerli, Rolf last_name: Kümmerli citation: ama: 'Refardt D, Bergmiller T, Kümmerli R. Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. Proceedings of the Royal Society of London Series B Biological Sciences. 2013;280(1759). doi:10.1098/rspb.2012.3035' apa: 'Refardt, D., Bergmiller, T., & Kümmerli, R. (2013). Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2012.3035' chicago: 'Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2013. https://doi.org/10.1098/rspb.2012.3035.' ieee: 'D. Refardt, T. Bergmiller, and R. Kümmerli, “Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1759. The Royal Society, 2013.' ista: 'Refardt D, Bergmiller T, Kümmerli R. 2013. Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection. Proceedings of the Royal Society of London Series B Biological Sciences. 280(1759).' mla: 'Refardt, Dominik, et al. “Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 280, no. 1759, The Royal Society, 2013, doi:10.1098/rspb.2012.3035.' short: D. Refardt, T. Bergmiller, R. Kümmerli, Proceedings of the Royal Society of London Series B Biological Sciences 280 (2013). date_created: 2018-12-11T11:59:56Z date_published: 2013-05-22T00:00:00Z date_updated: 2023-10-18T06:43:23Z day: '22' department: - _id: CaGu doi: 10.1098/rspb.2012.3035 external_id: pmid: - '23516238' intvolume: ' 280' issue: '1759' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3619501/ month: '05' oa: 1 oa_version: Submitted Version pmid: 1 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_identifier: eissn: - 1471-2954 publication_status: published publisher: The Royal Society publist_id: '3939' quality_controlled: '1' related_material: record: - id: '9751' relation: research_data status: public scopus_import: '1' status: public title: 'Altruism can evolve when relatedness is low: Evidence from bacteria committing suicide upon phage infection' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 280 year: '2013' ... --- _id: '9751' abstract: - lang: eng text: High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent parasite transmission to nearby relatives. We found that bacterial suicide provides large benefits to survivors at marginal costs to committers. The cost of suicide was low because infected cells are moribund, rapidly dying upon phage infection, such that no more opportunity for reproduction remains. As a consequence of its marginal cost, host suicide was selectively favoured even when relatedness between committers and survivors approached zero. Altogether, our findings demonstrate that low-cost suicide can evolve with ease, represents an effective host-defence strategy, and seems to be widespread among microbes. Moreover, low-cost suicide might also occur in higher organisms as exemplified by infected social insect workers leaving the colony to die in isolation. article_processing_charge: No author: - first_name: Dominik full_name: Refardt, Dominik last_name: Refardt - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Rolf full_name: Kümmerli, Rolf last_name: Kümmerli citation: ama: 'Refardt D, Bergmiller T, Kümmerli R. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. 2013. doi:10.5061/dryad.b1q2n' apa: 'Refardt, D., Bergmiller, T., & Kümmerli, R. (2013). Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection. Dryad. https://doi.org/10.5061/dryad.b1q2n' chicago: 'Refardt, Dominik, Tobias Bergmiller, and Rolf Kümmerli. “Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection.” Dryad, 2013. https://doi.org/10.5061/dryad.b1q2n.' ieee: 'D. Refardt, T. Bergmiller, and R. Kümmerli, “Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection.” Dryad, 2013.' ista: 'Refardt D, Bergmiller T, Kümmerli R. 2013. Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection, Dryad, 10.5061/dryad.b1q2n.' mla: 'Refardt, Dominik, et al. Data from: Altruism Can Evolve When Relatedness Is Low: Evidence from Bacteria Committing Suicide upon Phage Infection. Dryad, 2013, doi:10.5061/dryad.b1q2n.' short: D. Refardt, T. Bergmiller, R. Kümmerli, (2013). date_created: 2021-07-30T08:08:09Z date_published: 2013-03-21T00:00:00Z date_updated: 2023-10-18T06:43:22Z day: '21' department: - _id: CaGu doi: 10.5061/dryad.b1q2n main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.b1q2n month: '03' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '2853' relation: used_in_publication status: public status: public title: 'Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2013' ... --- _id: '7785' abstract: - lang: eng text: Neural circuit assembly requires selection of specific cell fates, axonal trajectories, and synaptic targets. By analyzing the function of a secreted semaphorin, Sema-2b, in Drosophila olfactory receptor neuron (ORN) development, we identified multiple molecular and cellular mechanisms that link these events. Notch signaling limits Sema-2b expression to ventromedial ORN classes, within which Sema-2b cell-autonomously sensitizes ORN axons to external semaphorins. Central-brain-derived Sema-2a and Sema-2b attract Sema-2b-expressing axons to the ventromedial trajectory. In addition, Sema-2b/PlexB-mediated axon-axon interactions consolidate this trajectory choice and promote ventromedial axon-bundle formation. Selecting the correct developmental trajectory is ultimately essential for proper target choice. These findings demonstrate that Sema-2b couples ORN axon guidance to postsynaptic target neuron dendrite patterning well before the final target selection phase, and exemplify how a single guidance molecule can drive consecutive stages of neural circuit assembly with the help of sophisticated spatial and temporal regulation. article_processing_charge: No article_type: original author: - first_name: William J. full_name: Joo, William J. last_name: Joo - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 - first_name: Liang full_name: Liang, Liang last_name: Liang - first_name: Liqun full_name: Luo, Liqun last_name: Luo citation: ama: 'Joo WJ, Sweeney LB, Liang L, Luo L. Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. Neuron. 2013;78(4):673-686. doi:10.1016/j.neuron.2013.03.022' apa: 'Joo, W. J., Sweeney, L. B., Liang, L., & Luo, L. (2013). Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2013.03.022' chicago: 'Joo, William J., Lora B. Sweeney, Liang Liang, and Liqun Luo. “Linking Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” Neuron. Elsevier, 2013. https://doi.org/10.1016/j.neuron.2013.03.022.' ieee: 'W. J. Joo, L. B. Sweeney, L. Liang, and L. Luo, “Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting,” Neuron, vol. 78, no. 4. Elsevier, pp. 673–686, 2013.' ista: 'Joo WJ, Sweeney LB, Liang L, Luo L. 2013. Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting. Neuron. 78(4), 673–686.' mla: 'Joo, William J., et al. “Linking Cell Fate, Trajectory Choice, and Target Selection: Genetic Analysis of Sema-2b in Olfactory Axon Targeting.” Neuron, vol. 78, no. 4, Elsevier, 2013, pp. 673–86, doi:10.1016/j.neuron.2013.03.022.' short: W.J. Joo, L.B. Sweeney, L. Liang, L. Luo, Neuron 78 (2013) 673–686. date_created: 2020-04-30T13:19:59Z date_published: 2013-05-22T00:00:00Z date_updated: 2024-01-31T10:15:25Z day: '22' doi: 10.1016/j.neuron.2013.03.022 extern: '1' intvolume: ' 78' issue: '4' language: - iso: eng month: '05' oa_version: None page: 673-686 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'Linking cell fate, trajectory choice, and target selection: Genetic analysis of sema-2b in olfactory axon targeting' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 78 year: '2013' ... --- _id: '2274' abstract: - lang: eng text: "Proofs of work (PoW) have been suggested by Dwork and Naor (Crypto'92) as protection to a shared resource. The basic idea is to ask the service requestor to dedicate some non-trivial amount of computational work to every request. The original applications included prevention of spam and protection against denial of service attacks. More recently, PoWs have been used to prevent double spending in the Bitcoin digital currency system.\r\n\r\nIn this work, we put forward an alternative concept for PoWs -- so-called proofs of space (PoS), where a service requestor must dedicate a significant amount of disk space as opposed to computation. We construct secure PoS schemes in the random oracle model, using graphs with high "pebbling complexity" and Merkle hash-trees. " author: - first_name: Stefan full_name: Dziembowski, Stefan last_name: Dziembowski - first_name: Sebastian full_name: Faust, Sebastian last_name: Faust - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. Proofs of Space. IST Austria; 2013. apa: Dziembowski, S., Faust, S., Kolmogorov, V., & Pietrzak, K. Z. (2013). Proofs of Space. IST Austria. chicago: Dziembowski, Stefan, Sebastian Faust, Vladimir Kolmogorov, and Krzysztof Z Pietrzak. Proofs of Space. IST Austria, 2013. ieee: S. Dziembowski, S. Faust, V. Kolmogorov, and K. Z. Pietrzak, Proofs of Space. IST Austria, 2013. ista: Dziembowski S, Faust S, Kolmogorov V, Pietrzak KZ. 2013. Proofs of Space, IST Austria,p. mla: Dziembowski, Stefan, et al. Proofs of Space. IST Austria, 2013. short: S. Dziembowski, S. Faust, V. Kolmogorov, K.Z. Pietrzak, Proofs of Space, IST Austria, 2013. date_created: 2018-12-11T11:56:42Z date_published: 2013-11-28T00:00:00Z date_updated: 2024-03-20T08:31:49Z day: '28' ddc: - '530' department: - _id: VlKo - _id: KrPi file: - access_level: open_access checksum: 37b61637b62fc079d9141c59d9f1a94f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:11Z date_updated: 2020-07-14T12:45:36Z file_id: '5197' file_name: IST-2016-671-v1+1_796.pdf file_size: 405870 relation: main_file file_date_updated: 2020-07-14T12:45:36Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication_status: published publisher: IST Austria publist_id: '4670' pubrep_id: '671' related_material: record: - id: '1675' relation: later_version status: public scopus_import: 1 status: public title: Proofs of Space type: report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2013' ... --- _id: '15162' abstract: - lang: eng text: Cytological profiling (CP) is an unbiased image-based screening technique that uses automated microscopy and image analysis to profile compounds based on numerous quantifiable phenotypic features. We used CP to evaluate a library of nearly 500 compounds with documented mechanisms of action (MOAs) spanning a wide range of biological pathways. We developed informatics techniques for generating dosage-independent phenotypic “fingerprints” for each compound, and for quantifying the likelihood that a compound's CP fingerprint corresponds to its annotated MOA. We identified groups of features that distinguish classes with closely related phenotypes, such as microtubule poisons vs. HSP90 inhibitors, and DNA synthesis vs. proteasome inhibitors. We tested several cases in which cytological profiles indicated novel mechanisms, including a tyrphostin kinase inhibitor involved in mitochondrial uncoupling, novel microtubule poisons, and a nominal PPAR-gamma ligand that acts as a proteasome inhibitor, using independent biochemical assays to confirm the MOAs predicted by the CP signatures. We also applied maximal-information statistics to identify correlations between cytological features and kinase inhibitory activities by combining the CP fingerprints of 24 kinase inhibitors with published data on their specificities against a diverse panel of kinases. The resulting analysis suggests a strategy for probing the biological functions of specific kinases by compiling cytological data from inhibitors of varying specificities. article_number: '2604' article_processing_charge: No article_type: original author: - first_name: Marcos H. full_name: Woehrmann, Marcos H. last_name: Woehrmann - first_name: Walter M. full_name: Bray, Walter M. last_name: Bray - first_name: James K. full_name: Durbin, James K. last_name: Durbin - first_name: Sean C. full_name: Nisam, Sean C. last_name: Nisam - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Emerson full_name: Glassey, Emerson last_name: Glassey - first_name: Joshua M. full_name: Stuart, Joshua M. last_name: Stuart - first_name: R. Scott full_name: Lokey, R. Scott last_name: Lokey citation: ama: Woehrmann MH, Bray WM, Durbin JK, et al. Large-scale cytological profiling for functional analysis of bioactive compounds. Molecular BioSystems. 2013;9(11). doi:10.1039/c3mb70245f apa: Woehrmann, M. H., Bray, W. M., Durbin, J. K., Nisam, S. C., Michael, A. K., Glassey, E., … Lokey, R. S. (2013). Large-scale cytological profiling for functional analysis of bioactive compounds. Molecular BioSystems. Royal Society of Chemistry. https://doi.org/10.1039/c3mb70245f chicago: Woehrmann, Marcos H., Walter M. Bray, James K. Durbin, Sean C. Nisam, Alicia K. Michael, Emerson Glassey, Joshua M. Stuart, and R. Scott Lokey. “Large-Scale Cytological Profiling for Functional Analysis of Bioactive Compounds.” Molecular BioSystems. Royal Society of Chemistry, 2013. https://doi.org/10.1039/c3mb70245f. ieee: M. H. Woehrmann et al., “Large-scale cytological profiling for functional analysis of bioactive compounds,” Molecular BioSystems, vol. 9, no. 11. Royal Society of Chemistry, 2013. ista: Woehrmann MH, Bray WM, Durbin JK, Nisam SC, Michael AK, Glassey E, Stuart JM, Lokey RS. 2013. Large-scale cytological profiling for functional analysis of bioactive compounds. Molecular BioSystems. 9(11), 2604. mla: Woehrmann, Marcos H., et al. “Large-Scale Cytological Profiling for Functional Analysis of Bioactive Compounds.” Molecular BioSystems, vol. 9, no. 11, 2604, Royal Society of Chemistry, 2013, doi:10.1039/c3mb70245f. short: M.H. Woehrmann, W.M. Bray, J.K. Durbin, S.C. Nisam, A.K. Michael, E. Glassey, J.M. Stuart, R.S. Lokey, Molecular BioSystems 9 (2013). date_created: 2024-03-21T07:58:57Z date_published: 2013-08-20T00:00:00Z date_updated: 2024-03-25T11:45:46Z day: '20' doi: 10.1039/c3mb70245f extern: '1' intvolume: ' 9' issue: '11' keyword: - Molecular Biology - Biotechnology language: - iso: eng month: '08' oa_version: None publication: Molecular BioSystems publication_identifier: eissn: - 1742-2051 issn: - 1742-206X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Large-scale cytological profiling for functional analysis of bioactive compounds type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2013' ... --- _id: '10387' abstract: - lang: eng text: We report numerical simulations of membrane tubulation driven by large colloidal particles. Using Monte Carlo simulations we study how the process depends on particle size and binding strength, and present accurate free energy calculations to sort out how tube formation compares with the competing budding process. We find that tube formation is a result of the collective behavior of the particles adhering on the surface, and it occurs for binding strengths that are smaller than those required for budding. We also find that long linear aggregates of particles forming on the membrane surface act as nucleation seeds for tubulation by lowering the free energy barrier associated to the process. article_number: '188101' article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Angelo full_name: Cacciuto, Angelo last_name: Cacciuto citation: ama: Šarić A, Cacciuto A. Mechanism of membrane tube formation induced by adhesive nanocomponents. Physical Review Letters. 2012;109(18). doi:10.1103/physrevlett.109.188101 apa: Šarić, A., & Cacciuto, A. (2012). Mechanism of membrane tube formation induced by adhesive nanocomponents. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.109.188101 chicago: Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced by Adhesive Nanocomponents.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/physrevlett.109.188101. ieee: A. Šarić and A. Cacciuto, “Mechanism of membrane tube formation induced by adhesive nanocomponents,” Physical Review Letters, vol. 109, no. 18. American Physical Society, 2012. ista: Šarić A, Cacciuto A. 2012. Mechanism of membrane tube formation induced by adhesive nanocomponents. Physical Review Letters. 109(18), 188101. mla: Šarić, Anđela, and Angelo Cacciuto. “Mechanism of Membrane Tube Formation Induced by Adhesive Nanocomponents.” Physical Review Letters, vol. 109, no. 18, 188101, American Physical Society, 2012, doi:10.1103/physrevlett.109.188101. short: A. Šarić, A. Cacciuto, Physical Review Letters 109 (2012). date_created: 2021-11-29T14:08:00Z date_published: 2012-10-31T00:00:00Z date_updated: 2021-11-29T14:29:25Z day: '31' doi: 10.1103/physrevlett.109.188101 extern: '1' external_id: arxiv: - '1206.3528' pmid: - '23215334' intvolume: ' 109' issue: '18' keyword: - general physics and astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1206.3528 month: '10' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Mechanism of membrane tube formation induced by adhesive nanocomponents type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 109 year: '2012' ... --- _id: '10388' abstract: - lang: eng text: Using computer simulations, we show that lipid membranes can mediate linear aggregation of spherical nanoparticles binding to it for a wide range of biologically relevant bending rigidities. This result is in net contrast with the isotropic aggregation of nanoparticles on fluid interfaces or the expected clustering of isotropic insertions in biological membranes. We present a phase diagram indicating where linear aggregation is expected and compute explicitly the free-energy barriers associated with linear and isotropic aggregation. Finally, we provide simple scaling arguments to explain this phenomenology. acknowledgement: "This work was supported by the National Science Foundation under Career Grant No. DMR-0846426.\r\n" article_number: '118101' article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Angelo full_name: Cacciuto, Angelo last_name: Cacciuto citation: ama: Šarić A, Cacciuto A. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. Physical Review Letters. 2012;108(11). doi:10.1103/physrevlett.108.118101 apa: Šarić, A., & Cacciuto, A. (2012). Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.108.118101 chicago: Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/physrevlett.108.118101. ieee: A. Šarić and A. Cacciuto, “Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles,” Physical Review Letters, vol. 108, no. 11. American Physical Society, 2012. ista: Šarić A, Cacciuto A. 2012. Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles. Physical Review Letters. 108(11), 118101. mla: Šarić, Anđela, and Angelo Cacciuto. “Fluid Membranes Can Drive Linear Aggregation of Adsorbed Spherical Nanoparticles.” Physical Review Letters, vol. 108, no. 11, 118101, American Physical Society, 2012, doi:10.1103/physrevlett.108.118101. short: A. Šarić, A. Cacciuto, Physical Review Letters 108 (2012). date_created: 2021-11-29T14:30:05Z date_published: 2012-03-14T00:00:00Z date_updated: 2021-11-29T15:12:13Z day: '14' doi: 10.1103/physrevlett.108.118101 extern: '1' external_id: arxiv: - '1201.0036' pmid: - '22540513' intvolume: ' 108' issue: '11' keyword: - general physics and astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1201.0036 month: '03' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 108 year: '2012' ... --- _id: '1055' abstract: - lang: eng text: In July, 2011, a 32-year-old man presented with thoracic pain radiating to the left arm and upper dorsum, shortness of breath, and palpitations. He had had upper back tension for 6 months. Medical history was unremarkable apart from moderate nicotine use (two pack-years). Echocardiography, electrocardiography, and laboratory tests were unremarkable, excluding a cardiac event. CT of the chest after chest radiography showed a large bulla of 16 cm diameter in the right hemithorax (figure A). We did not detect radiological evidence of underlying pulmonary disease. The bulla wall was unremarkable and no structures were seen within the bulla. acknowledgement: We thank the interdisciplinary team at the ELK Berlin Chest Hospital. article_processing_charge: No author: - first_name: Barbara full_name: Erne, Barbara last_name: Erne - first_name: Mareike full_name: Graff, Mareike last_name: Graff - first_name: Wolfram full_name: Klemm, Wolfram last_name: Klemm - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Gunda full_name: Leschber, Gunda last_name: Leschber citation: ama: Erne B, Graff M, Klemm W, Danzl JG, Leschber G. Bulla in the lung. The Lancet. 2012;380(9849). doi:10.1016/S0140-6736(12)60690-4 apa: Erne, B., Graff, M., Klemm, W., Danzl, J. G., & Leschber, G. (2012). Bulla in the lung. The Lancet. Elsevier. https://doi.org/10.1016/S0140-6736(12)60690-4 chicago: Erne, Barbara, Mareike Graff, Wolfram Klemm, Johann G Danzl, and Gunda Leschber. “Bulla in the Lung.” The Lancet. Elsevier, 2012. https://doi.org/10.1016/S0140-6736(12)60690-4. ieee: B. Erne, M. Graff, W. Klemm, J. G. Danzl, and G. Leschber, “Bulla in the lung,” The Lancet, vol. 380, no. 9849. Elsevier, 2012. ista: Erne B, Graff M, Klemm W, Danzl JG, Leschber G. 2012. Bulla in the lung. The Lancet. 380(9849). mla: Erne, Barbara, et al. “Bulla in the Lung.” The Lancet, vol. 380, no. 9849, Elsevier, 2012, doi:10.1016/S0140-6736(12)60690-4. short: B. Erne, M. Graff, W. Klemm, J.G. Danzl, G. Leschber, The Lancet 380 (2012). date_created: 2018-12-11T11:49:54Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T06:47:57Z day: '01' doi: 10.1016/S0140-6736(12)60690-4 extern: '1' intvolume: ' 380' issue: '9849' language: - iso: eng month: '10' oa_version: None publication: The Lancet publication_status: published publisher: Elsevier publist_id: '6333' status: public title: Bulla in the lung type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 380 year: '2012' ... --- _id: '1056' abstract: - lang: eng text: We prepare and study a metastable attractive Mott-insulator state formed with bosonic atoms in a three-dimensional optical lattice. Starting from a Mott insulator with Cs atoms at weak repulsive interactions, we use a magnetic Feshbach resonance to tune the interactions to large attractive values and produce a metastable state pinned by attractive interactions with a lifetime on the order of 10 s. We probe the (de)excitation spectrum via lattice modulation spectroscopy, measuring the interaction dependence of two- and three-body bound-state energies. As a result of increased on-site three-body loss we observe resonance broadening and suppression of tunneling processes that produce three-body occupation. acknowledgement: We are indebted to R. Grimm for generous support. We thank J. von Stecher, P. Johnson, and E. Tiesinga for fruitful discussions. We gratefully acknowledge funding by the Austrian Science Fund (FWF) within Project No. I153-N16 and within the framework of the European Science Foundation (ESF) EuroQUASAR collective research project QuDeGPM, and by the European Research Council (ERC) under Project No. 278417. article_processing_charge: No author: - first_name: Manfred full_name: Mark, Manfred last_name: Mark - first_name: Elmar full_name: Haller, Elmar last_name: Haller - first_name: Katharina full_name: Lauber, Katharina last_name: Lauber - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Alexander full_name: Janisch, Alexander last_name: Janisch - first_name: Hans full_name: Büchler, Hans last_name: Büchler - first_name: Andrew full_name: Daley, Andrew last_name: Daley - first_name: Hanns full_name: Nägerl, Hanns last_name: Nägerl citation: ama: Mark M, Haller E, Lauber K, et al. Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. Physical Review Letters. 2012;108(21). doi:10.1103/PhysRevLett.108.215302 apa: Mark, M., Haller, E., Lauber, K., Danzl, J. G., Janisch, A., Büchler, H., … Nägerl, H. (2012). Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.108.215302 chicago: Mark, Manfred, Elmar Haller, Katharina Lauber, Johann G Danzl, Alexander Janisch, Hans Büchler, Andrew Daley, and Hanns Nägerl. “Preparation and Spectroscopy of a Metastable Mott-Insulator State with Attractive Interactions.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.108.215302. ieee: M. Mark et al., “Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions,” Physical Review Letters, vol. 108, no. 21. American Physical Society, 2012. ista: Mark M, Haller E, Lauber K, Danzl JG, Janisch A, Büchler H, Daley A, Nägerl H. 2012. Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions. Physical Review Letters. 108(21). mla: Mark, Manfred, et al. “Preparation and Spectroscopy of a Metastable Mott-Insulator State with Attractive Interactions.” Physical Review Letters, vol. 108, no. 21, American Physical Society, 2012, doi:10.1103/PhysRevLett.108.215302. short: M. Mark, E. Haller, K. Lauber, J.G. Danzl, A. Janisch, H. Büchler, A. Daley, H. Nägerl, Physical Review Letters 108 (2012). date_created: 2018-12-11T11:49:55Z date_published: 2012-05-25T00:00:00Z date_updated: 2021-01-12T06:47:58Z day: '25' doi: 10.1103/PhysRevLett.108.215302 extern: '1' external_id: arxiv: - '1201.1008' intvolume: ' 108' issue: '21' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1201.1008 month: '05' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '6334' status: public title: Preparation and spectroscopy of a metastable mott-insulator state with attractive interactions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 108 year: '2012' ... --- _id: '10750' abstract: - lang: eng text: The goal of this work is to study the superconducting coherence length in the fluctuation regime in cuprate superconductors. In this work we present cantilever torque magnetometry measurements of micron-size BSCCO flakes patterned with arrays of nanometer scale rings or holes. Using ultrasensitive dynamic torque magnetometry, oscillations in magnetization are observed near Tc as a function of the applied magnetic flux threading the array. Special effort was made to detect the oscillations in magnetization at temperatures above Tc, where the Nernst effect and magnetization measurements suggest the possibility of pairing. To constrain the magnitude of the coherence length in the fluctuation regime, we will present the dependence of the amplitude of the h/2e period oscillations as a function of temperature and hole size. acknowledgement: This work was supported by the Center for Emergent Superconductivity, an Energy Frontier Research Center funded by the U.S. DOE, Office of Science, under Award No. DE-AC0298CH1088. alternative_title: - Bulletin of the American Physical Society article_number: X21.00008 article_processing_charge: No author: - first_name: Hryhoriy full_name: Polshyn, Hryhoriy id: edfc7cb1-526e-11ec-b05a-e6ecc27e4e48 last_name: Polshyn orcid: 0000-0001-8223-8896 - first_name: Raffi full_name: Budakian, Raffi last_name: Budakian citation: ama: 'Polshyn H, Budakian R. Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc. In: APS March Meeting 2012. Vol 57. American Physical Society; 2012.' apa: 'Polshyn, H., & Budakian, R. (2012). Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc. In APS March Meeting 2012 (Vol. 57). Boston, MA, United States: American Physical Society.' chicago: Polshyn, Hryhoriy, and Raffi Budakian. “Cantilever Torque Magnetometry Study of Multiply Connected BSCCO Arrays near Tc.” In APS March Meeting 2012, Vol. 57. American Physical Society, 2012. ieee: H. Polshyn and R. Budakian, “Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc,” in APS March Meeting 2012, Boston, MA, United States, 2012, vol. 57, no. 1. ista: 'Polshyn H, Budakian R. 2012. Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc. APS March Meeting 2012. APS: American Physical Society, Bulletin of the American Physical Society, vol. 57, X21.00008.' mla: Polshyn, Hryhoriy, and Raffi Budakian. “Cantilever Torque Magnetometry Study of Multiply Connected BSCCO Arrays near Tc.” APS March Meeting 2012, vol. 57, no. 1, X21.00008, American Physical Society, 2012. short: H. Polshyn, R. Budakian, in:, APS March Meeting 2012, American Physical Society, 2012. conference: end_date: 2012-03-02 location: Boston, MA, United States name: 'APS: American Physical Society' start_date: 2012-02-27 date_created: 2022-02-08T10:39:08Z date_published: 2012-02-01T00:00:00Z date_updated: 2022-02-08T10:48:01Z day: '01' extern: '1' intvolume: ' 57' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://meetings.aps.org/Meeting/MAR12/Event/167014 month: '02' oa: 1 oa_version: Published Version publication: APS March Meeting 2012 publication_identifier: issn: - 0003-0503 publication_status: published publisher: American Physical Society quality_controlled: '1' status: public title: Cantilever torque magnetometry study of multiply connected BSCCO arrays near Tc type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 57 year: '2012' ... --- _id: '10896' 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. 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. article_processing_charge: No author: - first_name: Stephanie full_name: zur Nedden, Stephanie id: 3C77F464-F248-11E8-B48F-1D18A9856A87 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 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. Adenosine. 1st ed. New York: Springer; 2012:109-129. doi:10.1007/978-1-4614-3903-5_6' apa: 'zur Nedden, S., Doney, A. S., & Frenguelli, B. G. (2012). The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books. In S. Masino & D. Boison (Eds.), Adenosine (1st ed., pp. 109–129). New York: Springer. https://doi.org/10.1007/978-1-4614-3903-5_6' 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 Adenosine, edited by Susan Masino and Detlev Boison, 1st ed., 109–29. New York: Springer, 2012. https://doi.org/10.1007/978-1-4614-3903-5_6.' 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 Adenosine, 1st ed., S. Masino and D. Boison, Eds. New York: Springer, 2012, pp. 109–129.' 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.' mla: 'zur Nedden, Stephanie, et al. “The Double-Edged Sword: Gaining Adenosine at the Expense of ATP. How to Balance the Books.” Adenosine, edited by Susan Masino and Detlev Boison, 1st ed., Springer, 2012, pp. 109–29, doi:10.1007/978-1-4614-3903-5_6.' 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. date_created: 2022-03-21T07:16:12Z date_published: 2012-07-23T00:00:00Z date_updated: 2022-06-21T11:51:58Z day: '23' department: - _id: HaJa doi: 10.1007/978-1-4614-3903-5_6 edition: '1' editor: - first_name: Susan full_name: Masino, Susan last_name: Masino - first_name: Detlev full_name: Boison, Detlev last_name: Boison language: - iso: eng month: '07' oa_version: None page: 109-129 place: New York publication: Adenosine publication_identifier: eisbn: - '9781461439035' isbn: - '9781461439028' publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: 'The double-edged sword: Gaining Adenosine at the expense of ATP. How to balance the books' type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '11089' abstract: - lang: eng text: The Nuclear Envelope (NE) contains over 100 different proteins that associate with nuclear components such as chromatin, the lamina and the transcription machinery. Mutations in genes encoding NE proteins have been shown to result in tissue-specific defects and disease, suggesting cell-type specific differences in NE composition and function. Consistent with these observations, recent studies have revealed unexpected functions for numerous NE associated proteins during cell differentiation and development. Here we review the latest insights into the roles played by the NE in cell differentiation, development, disease and aging, focusing primarily on inner nuclear membrane (INM) proteins and nuclear pore components. article_processing_charge: No article_type: original author: - first_name: J Sebastian full_name: Gomez-Cavazos, J Sebastian last_name: Gomez-Cavazos - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: 'Gomez-Cavazos JS, Hetzer M. Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins. Current Opinion in Cell Biology. 2012;24(6):775-783. doi:10.1016/j.ceb.2012.08.008' apa: 'Gomez-Cavazos, J. S., & Hetzer, M. (2012). Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2012.08.008' chicago: 'Gomez-Cavazos, J Sebastian, and Martin Hetzer. “Outfits for Different Occasions: Tissue-Specific Roles of Nuclear Envelope Proteins.” Current Opinion in Cell Biology. Elsevier, 2012. https://doi.org/10.1016/j.ceb.2012.08.008.' ieee: 'J. S. Gomez-Cavazos and M. Hetzer, “Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins,” Current Opinion in Cell Biology, vol. 24, no. 6. Elsevier, pp. 775–783, 2012.' ista: 'Gomez-Cavazos JS, Hetzer M. 2012. Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins. Current Opinion in Cell Biology. 24(6), 775–783.' mla: 'Gomez-Cavazos, J. Sebastian, and Martin Hetzer. “Outfits for Different Occasions: Tissue-Specific Roles of Nuclear Envelope Proteins.” Current Opinion in Cell Biology, vol. 24, no. 6, Elsevier, 2012, pp. 775–83, doi:10.1016/j.ceb.2012.08.008.' short: J.S. Gomez-Cavazos, M. Hetzer, Current Opinion in Cell Biology 24 (2012) 775–783. date_created: 2022-04-07T07:51:37Z date_published: 2012-12-01T00:00:00Z date_updated: 2022-07-18T08:38:47Z day: '01' doi: 10.1016/j.ceb.2012.08.008 extern: '1' external_id: pmid: - '22995343' intvolume: ' 24' issue: '6' keyword: - Cell Biology language: - iso: eng month: '12' oa_version: None page: 775-783 pmid: 1 publication: Current Opinion in Cell Biology publication_identifier: issn: - 0955-0674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Outfits for different occasions: tissue-specific roles of Nuclear Envelope proteins' type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 24 year: '2012' ... --- _id: '11091' abstract: - lang: eng text: Neoplastic cells are often characterized by specific morphological abnormalities of the nuclear envelope (NE), which have been used for cancer diagnosis for more than a century. The NE is a double phospholipid bilayer that encapsulates the nuclear genome, regulates all nuclear trafficking of RNAs and proteins and prevents the passive diffusion of macromolecules between the nucleoplasm and the cytoplasm. Whether there is a consequence to the proper functioning of the cell and loss of structural integrity of the nucleus remains unclear. Using live cell imaging, we characterize a phenomenon wherein nuclei of several proliferating human cancer cell lines become temporarily ruptured during interphase. Strikingly, NE rupturing was associated with the mislocalization of nucleoplasmic and cytoplasmic proteins and, in the most extreme cases, the entrapment of cytoplasmic organelles in the nuclear interior. In addition, we observed the formation of micronuclei-like structures during interphase and the movement of chromatin out of the nuclear space. The frequency of these NE rupturing events was higher in cells in which the nuclear lamina, a network of intermediate filaments providing mechanical support to the NE, was not properly formed. Our data uncover the existence of a NE instability that has the potential to change the genomic landscape of cancer cells. article_processing_charge: No article_type: original author: - first_name: Jesse D. full_name: Vargas, Jesse D. last_name: Vargas - first_name: Emily M. full_name: Hatch, Emily M. last_name: Hatch - first_name: Daniel J. full_name: Anderson, Daniel J. last_name: Anderson - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Vargas JD, Hatch EM, Anderson DJ, Hetzer M. Transient nuclear envelope rupturing during interphase in human cancer cells. Nucleus. 2012;3(1):88-100. doi:10.4161/nucl.18954 apa: Vargas, J. D., Hatch, E. M., Anderson, D. J., & Hetzer, M. (2012). Transient nuclear envelope rupturing during interphase in human cancer cells. Nucleus. Taylor & Francis. https://doi.org/10.4161/nucl.18954 chicago: Vargas, Jesse D., Emily M. Hatch, Daniel J. Anderson, and Martin Hetzer. “Transient Nuclear Envelope Rupturing during Interphase in Human Cancer Cells.” Nucleus. Taylor & Francis, 2012. https://doi.org/10.4161/nucl.18954. ieee: J. D. Vargas, E. M. Hatch, D. J. Anderson, and M. Hetzer, “Transient nuclear envelope rupturing during interphase in human cancer cells,” Nucleus, vol. 3, no. 1. Taylor & Francis, pp. 88–100, 2012. ista: Vargas JD, Hatch EM, Anderson DJ, Hetzer M. 2012. Transient nuclear envelope rupturing during interphase in human cancer cells. Nucleus. 3(1), 88–100. mla: Vargas, Jesse D., et al. “Transient Nuclear Envelope Rupturing during Interphase in Human Cancer Cells.” Nucleus, vol. 3, no. 1, Taylor & Francis, 2012, pp. 88–100, doi:10.4161/nucl.18954. short: J.D. Vargas, E.M. Hatch, D.J. Anderson, M. Hetzer, Nucleus 3 (2012) 88–100. date_created: 2022-04-07T07:51:53Z date_published: 2012-01-01T00:00:00Z date_updated: 2022-07-18T08:52:53Z day: '01' doi: 10.4161/nucl.18954 extern: '1' external_id: pmid: - '22567193' intvolume: ' 3' issue: '1' keyword: - Cell Biology language: - iso: eng month: '01' oa_version: None page: 88-100 pmid: 1 publication: Nucleus publication_identifier: eissn: - 1949-1042 issn: - 1949-1034 publication_status: published publisher: Taylor & Francis quality_controlled: '1' scopus_import: '1' status: public title: Transient nuclear envelope rupturing during interphase in human cancer cells type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 3 year: '2012' ... --- _id: '11093' abstract: - lang: eng text: Nuclear pore complexes (NPCs) are built from ∼30 different proteins called nucleoporins or Nups. Previous studies have shown that several Nups exhibit cell-type-specific expression and that mutations in NPC components result in tissue-specific diseases. Here we show that a specific change in NPC composition is required for both myogenic and neuronal differentiation. The transmembrane nucleoporin Nup210 is absent in proliferating myoblasts and embryonic stem cells (ESCs) but becomes expressed and incorporated into NPCs during cell differentiation. Preventing Nup210 production by RNAi blocks myogenesis and the differentiation of ESCs into neuroprogenitors. We found that the addition of Nup210 to NPCs does not affect nuclear transport but is required for the induction of genes that are essential for cell differentiation. Our results identify a single change in NPC composition as an essential step in cell differentiation and establish a role for Nup210 in gene expression regulation and cell fate determination. article_processing_charge: No article_type: original author: - first_name: Maximiliano A. full_name: D'Angelo, Maximiliano A. last_name: D'Angelo - first_name: J. Sebastian full_name: Gomez-Cavazos, J. Sebastian last_name: Gomez-Cavazos - first_name: Arianna full_name: Mei, Arianna last_name: Mei - first_name: Daniel H. full_name: Lackner, Daniel H. last_name: Lackner - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: D’Angelo MA, Gomez-Cavazos JS, Mei A, Lackner DH, Hetzer M. A change in nuclear pore complex composition regulates cell differentiation. Developmental Cell. 2012;22(2):446-458. doi:10.1016/j.devcel.2011.11.021 apa: D’Angelo, M. A., Gomez-Cavazos, J. S., Mei, A., Lackner, D. H., & Hetzer, M. (2012). A change in nuclear pore complex composition regulates cell differentiation. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2011.11.021 chicago: D’Angelo, Maximiliano A., J. Sebastian Gomez-Cavazos, Arianna Mei, Daniel H. Lackner, and Martin Hetzer. “A Change in Nuclear Pore Complex Composition Regulates Cell Differentiation.” Developmental Cell. Elsevier, 2012. https://doi.org/10.1016/j.devcel.2011.11.021. ieee: M. A. D’Angelo, J. S. Gomez-Cavazos, A. Mei, D. H. Lackner, and M. Hetzer, “A change in nuclear pore complex composition regulates cell differentiation,” Developmental Cell, vol. 22, no. 2. Elsevier, pp. 446–458, 2012. ista: D’Angelo MA, Gomez-Cavazos JS, Mei A, Lackner DH, Hetzer M. 2012. A change in nuclear pore complex composition regulates cell differentiation. Developmental Cell. 22(2), 446–458. mla: D’Angelo, Maximiliano A., et al. “A Change in Nuclear Pore Complex Composition Regulates Cell Differentiation.” Developmental Cell, vol. 22, no. 2, Elsevier, 2012, pp. 446–58, doi:10.1016/j.devcel.2011.11.021. short: M.A. D’Angelo, J.S. Gomez-Cavazos, A. Mei, D.H. Lackner, M. Hetzer, Developmental Cell 22 (2012) 446–458. date_created: 2022-04-07T07:52:10Z date_published: 2012-01-19T00:00:00Z date_updated: 2022-07-18T08:53:16Z day: '19' doi: 10.1016/j.devcel.2011.11.021 extern: '1' external_id: pmid: - '22264802' intvolume: ' 22' issue: '2' keyword: - Developmental Biology - Cell Biology - General Biochemistry - Genetics and Molecular Biology - Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2011.11.021 month: '01' oa: 1 oa_version: Published Version page: 446-458 pmid: 1 publication: Developmental Cell publication_identifier: issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: A change in nuclear pore complex composition regulates cell differentiation type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 22 year: '2012' ... --- _id: '11092' abstract: - lang: eng text: To combat the functional decline of the proteome, cells use the process of protein turnover to replace potentially impaired polypeptides with new functional copies. We found that extremely long-lived proteins (ELLPs) did not turn over in postmitotic cells of the rat central nervous system. These ELLPs were associated with chromatin and the nuclear pore complex, the central transport channels that mediate all molecular trafficking in and out of the nucleus. The longevity of these proteins would be expected to expose them to potentially harmful metabolites, putting them at risk of accumulating damage over extended periods of time. Thus, it is possible that failure to maintain proper levels and functional integrity of ELLPs in nonproliferative cells might contribute to age-related deterioration in cell and tissue function. article_processing_charge: No article_type: letter_note author: - first_name: Jeffrey N. full_name: Savas, Jeffrey N. last_name: Savas - first_name: Brandon H. full_name: Toyama, Brandon H. last_name: Toyama - first_name: Tao full_name: Xu, Tao last_name: Xu - first_name: John R. full_name: Yates, John R. last_name: Yates - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Savas JN, Toyama BH, Xu T, Yates JR, Hetzer M. Extremely long-lived nuclear pore proteins in the rat brain. Science. 2012;335(6071):942-942. doi:10.1126/science.1217421 apa: Savas, J. N., Toyama, B. H., Xu, T., Yates, J. R., & Hetzer, M. (2012). Extremely long-lived nuclear pore proteins in the rat brain. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1217421 chicago: Savas, Jeffrey N., Brandon H. Toyama, Tao Xu, John R. Yates, and Martin Hetzer. “Extremely Long-Lived Nuclear Pore Proteins in the Rat Brain.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1217421. ieee: J. N. Savas, B. H. Toyama, T. Xu, J. R. Yates, and M. Hetzer, “Extremely long-lived nuclear pore proteins in the rat brain,” Science, vol. 335, no. 6071. American Association for the Advancement of Science, pp. 942–942, 2012. ista: Savas JN, Toyama BH, Xu T, Yates JR, Hetzer M. 2012. Extremely long-lived nuclear pore proteins in the rat brain. Science. 335(6071), 942–942. mla: Savas, Jeffrey N., et al. “Extremely Long-Lived Nuclear Pore Proteins in the Rat Brain.” Science, vol. 335, no. 6071, American Association for the Advancement of Science, 2012, pp. 942–942, doi:10.1126/science.1217421. short: J.N. Savas, B.H. Toyama, T. Xu, J.R. Yates, M. Hetzer, Science 335 (2012) 942–942. date_created: 2022-04-07T07:52:01Z date_published: 2012-02-02T00:00:00Z date_updated: 2022-07-18T08:53:06Z day: '02' doi: 10.1126/science.1217421 extern: '1' external_id: pmid: - '22300851' intvolume: ' 335' issue: '6071' keyword: - Multidisciplinary language: - iso: eng month: '02' oa_version: None page: 942-942 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Extremely long-lived nuclear pore proteins in the rat brain type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 335 year: '2012' ... --- _id: '11090' abstract: - lang: eng text: Nuclear export of mRNAs is thought to occur exclusively through nuclear pore complexes. In this issue of Cell, Speese et al. identify an alternate pathway for mRNA export in muscle cells where ribonucleoprotein complexes involved in forming neuromuscular junctions transit the nuclear envelope by fusing with and budding through the nuclear membrane. article_processing_charge: No article_type: letter_note author: - first_name: Emily M. full_name: Hatch, Emily M. last_name: Hatch - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Hatch EM, Hetzer M. RNP export by nuclear envelope budding. Cell. 2012;149(4):733-735. doi:10.1016/j.cell.2012.04.018 apa: Hatch, E. M., & Hetzer, M. (2012). RNP export by nuclear envelope budding. Cell. Elsevier. https://doi.org/10.1016/j.cell.2012.04.018 chicago: Hatch, Emily M., and Martin Hetzer. “RNP Export by Nuclear Envelope Budding.” Cell. Elsevier, 2012. https://doi.org/10.1016/j.cell.2012.04.018. ieee: E. M. Hatch and M. Hetzer, “RNP export by nuclear envelope budding,” Cell, vol. 149, no. 4. Elsevier, pp. 733–735, 2012. ista: Hatch EM, Hetzer M. 2012. RNP export by nuclear envelope budding. Cell. 149(4), 733–735. mla: Hatch, Emily M., and Martin Hetzer. “RNP Export by Nuclear Envelope Budding.” Cell, vol. 149, no. 4, Elsevier, 2012, pp. 733–35, doi:10.1016/j.cell.2012.04.018. short: E.M. Hatch, M. Hetzer, Cell 149 (2012) 733–735. date_created: 2022-04-07T07:51:45Z date_published: 2012-05-11T00:00:00Z date_updated: 2022-07-18T08:58:48Z day: '11' doi: 10.1016/j.cell.2012.04.018 extern: '1' external_id: pmid: - '22579277' intvolume: ' 149' issue: '4' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2012.04.018 month: '05' oa: 1 oa_version: Published Version page: 733-735 pmid: 1 publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: RNP export by nuclear envelope budding type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 149 year: '2012' ... --- _id: '113' abstract: - lang: eng text: 'Although liquids typically flow around intruding objects, a counterintuitive phenomenon occurs in dense suspensions of micrometre-sized particles: they become liquid-like when perturbed lightly, but harden when driven strongly. Rheological experiments have investigated how such thickening arises under shear, and linked it to hydrodynamic interactions or granular dilation. However, neither of these mechanisms alone can explain the ability of suspensions to generate very large, positive normal stresses under impact. To illustrate the phenomenon, such stresses can be large enough to allow a person to run across a suspension without sinking, and far exceed the upper limit observed under shear or extension. Here we show that these stresses originate from an impact-generated solidification front that transforms an initially compressible particle matrix into a rapidly growing jammed region, ultimately leading to extraordinary amounts of momentum absorption. Using high-speed videography, embedded force sensing and X-ray imaging, we capture the detailed dynamics of this process as it decelerates a metal rod hitting a suspension of cornflour (cornstarch) in water. We develop a model for the dynamic solidification and its effect on the surrounding suspension that reproduces the observed behaviour quantitatively. Our findings suggest that prior interpretations of the impact resistance as dominated by shear thickening need to be revisited.' acknowledgement: This work was supported by NSF through its MRSEC programme (DMR-0820054) and by the US Army Research Office through grant number W911NF-12-1-0182. S.R.W. acknowledges support from a Millikan fellowship. author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Heinrich full_name: Jaeger, Heinrich last_name: Jaeger citation: ama: Waitukaitis SR, Jaeger H. Impact-activated solidification of dense suspensions via dynamic jamming fronts. Nature. 2012;487(7406):205-209. doi:10.1038/nature11187 apa: Waitukaitis, S. R., & Jaeger, H. (2012). Impact-activated solidification of dense suspensions via dynamic jamming fronts. Nature. Nature Publishing Group. https://doi.org/10.1038/nature11187 chicago: Waitukaitis, Scott R, and Heinrich Jaeger. “Impact-Activated Solidification of Dense Suspensions via Dynamic Jamming Fronts.” Nature. Nature Publishing Group, 2012. https://doi.org/10.1038/nature11187. ieee: S. R. Waitukaitis and H. Jaeger, “Impact-activated solidification of dense suspensions via dynamic jamming fronts,” Nature, vol. 487, no. 7406. Nature Publishing Group, pp. 205–209, 2012. ista: Waitukaitis SR, Jaeger H. 2012. Impact-activated solidification of dense suspensions via dynamic jamming fronts. Nature. 487(7406), 205–209. mla: Waitukaitis, Scott R., and Heinrich Jaeger. “Impact-Activated Solidification of Dense Suspensions via Dynamic Jamming Fronts.” Nature, vol. 487, no. 7406, Nature Publishing Group, 2012, pp. 205–09, doi:10.1038/nature11187. short: S.R. Waitukaitis, H. Jaeger, Nature 487 (2012) 205–209. date_created: 2018-12-11T11:44:42Z date_published: 2012-07-12T00:00:00Z date_updated: 2021-01-12T06:48:30Z day: '12' doi: 10.1038/nature11187 extern: '1' intvolume: ' 487' issue: '7406' language: - iso: eng month: '07' oa_version: None page: 205 - 209 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '7941' status: public title: Impact-activated solidification of dense suspensions via dynamic jamming fronts type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 487 year: '2012' ... --- _id: '114' abstract: - lang: eng text: We report on an investigation of the solidification of a cornstarch and water suspension during normal impact on its surface. We find that a finite time after impact, the suspension displays characteristics reminiscent of a solid, including localized stress transmission, the development of a yield stress, and some elastic energy storage. The time dependence of these characteristics depends on the thickness of the cornstarch layer, showing that the solidification is a dynamic process driven by the impacting object. These findings confirm previous speculations that rapidly applied normal stress transforms the normally fluid-like suspension into a temporarily jammed solid and draw a clear distinction between the effects of normal stress and shear stress in dense suspensions. acknowledgement: This work was supported by the NSF through its MRSEC program (DMR-0820054). S. R. W. acknowledges support from a Millikan fellowship. author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Heinrich full_name: Jaeger, Heinrich last_name: Jaeger citation: ama: Waitukaitis SR, Jaeger H. Solidification of a cornstarch and water suspension. Revista Cubana de Fisica. 2012;29(1E):1E31-1E33. apa: Waitukaitis, S. R., & Jaeger, H. (2012). Solidification of a cornstarch and water suspension. Revista Cubana de Fisica. Universidad de La Habana. chicago: Waitukaitis, Scott R, and Heinrich Jaeger. “Solidification of a Cornstarch and Water Suspension.” Revista Cubana de Fisica. Universidad de La Habana, 2012. ieee: S. R. Waitukaitis and H. Jaeger, “Solidification of a cornstarch and water suspension,” Revista Cubana de Fisica, vol. 29, no. 1E. Universidad de La Habana, p. 1E31-1E33, 2012. ista: Waitukaitis SR, Jaeger H. 2012. Solidification of a cornstarch and water suspension. Revista Cubana de Fisica. 29(1E), 1E31-1E33. mla: Waitukaitis, Scott R., and Heinrich Jaeger. “Solidification of a Cornstarch and Water Suspension.” Revista Cubana de Fisica, vol. 29, no. 1E, Universidad de La Habana, 2012, p. 1E31-1E33. short: S.R. Waitukaitis, H. Jaeger, Revista Cubana de Fisica 29 (2012) 1E31-1E33. date_created: 2018-12-11T11:44:42Z date_published: 2012-08-14T00:00:00Z date_updated: 2021-01-12T06:48:34Z day: '14' ddc: - '530' extern: '1' file: - access_level: open_access content_type: application/pdf creator: kschuh date_created: 2019-05-16T11:08:52Z date_updated: 2019-05-16T11:08:52Z file_id: '6461' file_name: 2012_RCF_Waitukaitis.pdf file_size: 589776 relation: main_file success: 1 file_date_updated: 2019-05-16T11:08:52Z has_accepted_license: '1' intvolume: ' 29' issue: 1E language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '08' oa: 1 oa_version: Published Version page: 1E31 - 1E33 publication: Revista Cubana de Fisica publication_status: published publisher: Universidad de La Habana publist_id: '7940' quality_controlled: '1' status: public title: Solidification of a cornstarch and water suspension 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) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2012' ... --- _id: '11656' abstract: - lang: eng text: "Suppose your sole interest in recommending a product to me is to maximize the amount paid to you by the seller for a sequence of recommendations. How should you recommend optimally if I become more inclined to ignore you with each irrelevant recommendation you make? Finding an answer to this question is a key challenge in all forms of marketing that rely on and explore social ties; ranging from personal recommendations to viral marketing.\r\n\r\nWe prove that even if the recommendee regains her initial trust on each successful recommendation, the expected revenue the recommender can make over an infinite period due to payments by the seller is bounded. This can only be overcome when the recommendee also incrementally regains trust during periods without any recommendation. Here, we see a connection to \"banner blindness,\" suggesting that showing fewer ads can lead to a higher long-term revenue." article_processing_charge: No author: - first_name: Paul full_name: Dütting, Paul last_name: Dütting - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Ingmar full_name: Weber, Ingmar last_name: Weber citation: ama: 'Dütting P, Henzinger MH, Weber I. Maximizing revenue from strategic recommendations under decaying trust. In: Proceedings of the 21st ACM International Conference on Information and Knowledge Management. Association for Computing Machinery; 2012:2268-2286. doi:10.1145/2396761.2398621' apa: 'Dütting, P., Henzinger, M. H., & Weber, I. (2012). Maximizing revenue from strategic recommendations under decaying trust. In Proceedings of the 21st ACM international conference on Information and knowledge management (pp. 2268–2286). Maui, HI, United States: Association for Computing Machinery. https://doi.org/10.1145/2396761.2398621' chicago: Dütting, Paul, Monika H Henzinger, and Ingmar Weber. “Maximizing Revenue from Strategic Recommendations under Decaying Trust.” In Proceedings of the 21st ACM International Conference on Information and Knowledge Management, 2268–86. Association for Computing Machinery, 2012. https://doi.org/10.1145/2396761.2398621. ieee: P. Dütting, M. H. Henzinger, and I. Weber, “Maximizing revenue from strategic recommendations under decaying trust,” in Proceedings of the 21st ACM international conference on Information and knowledge management, Maui, HI, United States, 2012, pp. 2268–2286. ista: 'Dütting P, Henzinger MH, Weber I. 2012. Maximizing revenue from strategic recommendations under decaying trust. Proceedings of the 21st ACM international conference on Information and knowledge management. CIKM: Conference on Information and Knowledge Management, 2268–2286.' mla: Dütting, Paul, et al. “Maximizing Revenue from Strategic Recommendations under Decaying Trust.” Proceedings of the 21st ACM International Conference on Information and Knowledge Management, Association for Computing Machinery, 2012, pp. 2268–86, doi:10.1145/2396761.2398621. short: P. Dütting, M.H. Henzinger, I. Weber, in:, Proceedings of the 21st ACM International Conference on Information and Knowledge Management, Association for Computing Machinery, 2012, pp. 2268–2286. conference: end_date: 2012-11-02 location: Maui, HI, United States name: 'CIKM: Conference on Information and Knowledge Management' start_date: 2012-10-29 date_created: 2022-07-27T06:47:53Z date_published: 2012-10-29T00:00:00Z date_updated: 2023-02-09T09:19:49Z day: '29' doi: 10.1145/2396761.2398621 extern: '1' language: - iso: eng month: '10' oa_version: None page: 2268-2286 publication: Proceedings of the 21st ACM international conference on Information and knowledge management publication_identifier: isbn: - '9781450311564' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Maximizing revenue from strategic recommendations under decaying trust type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '11751' abstract: - lang: eng text: The Seebeck coefficients, electrical resistivities, total thermal conductivities, and magnetization are reported for temperatures between 5 and 350 K for n-type Bi0.88Sb0.12 nano-composite alloys made by Ho-doping at the 0, 1, and 3 % atomic levels. The alloys were prepared using a dc hot-pressing method, and are shown to be single phase for both Ho contents with grain sizes on the average of 900 nm. We find the parent compound has a maximum of ZT = 0.28 at 231 K, while doping 1 % Ho increases the maximum ZT to 0.31 at 221 K and the 3 % doped sample suppresses the maximum ZT = 0.24 at a temperature of 260 K. article_processing_charge: No article_type: original author: - first_name: K. C. full_name: Lukas, K. C. last_name: Lukas - first_name: G. full_name: Joshi, G. last_name: Joshi - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Z. F. full_name: Ren, Z. F. last_name: Ren - first_name: C. P. full_name: Opeil, C. P. last_name: Opeil citation: ama: Lukas KC, Joshi G, Modic KA, Ren ZF, Opeil CP. Thermoelectric properties of Ho-doped Bi0.88Sb0.12. Journal of Materials Science. 2012;47(15):5729-5734. doi:10.1007/s10853-012-6463-6 apa: Lukas, K. C., Joshi, G., Modic, K. A., Ren, Z. F., & Opeil, C. P. (2012). Thermoelectric properties of Ho-doped Bi0.88Sb0.12. Journal of Materials Science. Springer Nature. https://doi.org/10.1007/s10853-012-6463-6 chicago: Lukas, K. C., G. Joshi, Kimberly A Modic, Z. F. Ren, and C. P. Opeil. “Thermoelectric Properties of Ho-Doped Bi0.88Sb0.12.” Journal of Materials Science. Springer Nature, 2012. https://doi.org/10.1007/s10853-012-6463-6. ieee: K. C. Lukas, G. Joshi, K. A. Modic, Z. F. Ren, and C. P. Opeil, “Thermoelectric properties of Ho-doped Bi0.88Sb0.12,” Journal of Materials Science, vol. 47, no. 15. Springer Nature, pp. 5729–5734, 2012. ista: Lukas KC, Joshi G, Modic KA, Ren ZF, Opeil CP. 2012. Thermoelectric properties of Ho-doped Bi0.88Sb0.12. Journal of Materials Science. 47(15), 5729–5734. mla: Lukas, K. C., et al. “Thermoelectric Properties of Ho-Doped Bi0.88Sb0.12.” Journal of Materials Science, vol. 47, no. 15, Springer Nature, 2012, pp. 5729–34, doi:10.1007/s10853-012-6463-6. short: K.C. Lukas, G. Joshi, K.A. Modic, Z.F. Ren, C.P. Opeil, Journal of Materials Science 47 (2012) 5729–5734. date_created: 2022-08-08T08:28:20Z date_published: 2012-08-01T00:00:00Z date_updated: 2022-08-11T09:34:39Z day: '01' doi: 10.1007/s10853-012-6463-6 extern: '1' external_id: arxiv: - '1201.6304' intvolume: ' 47' issue: '15' language: - iso: eng month: '08' oa_version: Preprint page: 5729-5734 publication: Journal of Materials Science publication_identifier: eissn: - 1573-4803 issn: - 0022-2461 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Thermoelectric properties of Ho-doped Bi0.88Sb0.12 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2012' ... --- _id: '11794' abstract: - lang: eng text: We study individual rational, Pareto optimal, and incentive compatible mechanisms for auctions with heterogeneous items and budget limits. For multi-dimensional valuations we show that there can be no deterministic mechanism with these properties for divisible items. We use this to show that there can also be no randomized mechanism that achieves this for either divisible or indivisible items. For single-dimensional valuations we show that there can be no deterministic mechanism with these properties for indivisible items, but that there is a randomized mechanism that achieves this for either divisible or indivisible items. The impossibility results hold for public budgets, while the mechanism allows private budgets, which is in both cases the harder variant to show. While all positive results are polynomial-time algorithms, all negative results hold independent of complexity considerations. alternative_title: - LNCS article_processing_charge: No author: - first_name: Paul full_name: Dütting, Paul last_name: Dütting - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Martin full_name: Starnberger, Martin last_name: Starnberger citation: ama: 'Dütting P, Henzinger MH, Starnberger M. Auctions with heterogeneous items and budget limits. In: 8th International Workshop on Internet and Network Economics. Vol 7695. Springer Nature; 2012:44–57. doi:10.1007/978-3-642-35311-6_4' apa: 'Dütting, P., Henzinger, M. H., & Starnberger, M. (2012). Auctions with heterogeneous items and budget limits. In 8th International Workshop on Internet and Network Economics (Vol. 7695, pp. 44–57). Liverpool, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-642-35311-6_4' chicago: Dütting, Paul, Monika H Henzinger, and Martin Starnberger. “Auctions with Heterogeneous Items and Budget Limits.” In 8th International Workshop on Internet and Network Economics, 7695:44–57. Springer Nature, 2012. https://doi.org/10.1007/978-3-642-35311-6_4. ieee: P. Dütting, M. H. Henzinger, and M. Starnberger, “Auctions with heterogeneous items and budget limits,” in 8th International Workshop on Internet and Network Economics, Liverpool, United Kingdom, 2012, vol. 7695, pp. 44–57. ista: 'Dütting P, Henzinger MH, Starnberger M. 2012. Auctions with heterogeneous items and budget limits. 8th International Workshop on Internet and Network Economics. WINE: International Conference on Web and Internet Economics, LNCS, vol. 7695, 44–57.' mla: Dütting, Paul, et al. “Auctions with Heterogeneous Items and Budget Limits.” 8th International Workshop on Internet and Network Economics, vol. 7695, Springer Nature, 2012, pp. 44–57, doi:10.1007/978-3-642-35311-6_4. short: P. Dütting, M.H. Henzinger, M. Starnberger, in:, 8th International Workshop on Internet and Network Economics, Springer Nature, 2012, pp. 44–57. conference: end_date: 2012-12-14 location: Liverpool, United Kingdom name: 'WINE: International Conference on Web and Internet Economics' start_date: 2012-12-11 date_created: 2022-08-11T11:32:25Z date_published: 2012-12-01T00:00:00Z date_updated: 2023-02-21T16:28:29Z day: '01' doi: 10.1007/978-3-642-35311-6_4 extern: '1' external_id: arxiv: - '1209.6448' intvolume: ' 7695' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1209.6448 month: '12' oa: 1 oa_version: Preprint page: 44–57 publication: 8th International Workshop on Internet and Network Economics publication_identifier: isbn: - '9783642353109' issn: - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '11794' relation: later_version status: public scopus_import: '1' status: public title: Auctions with heterogeneous items and budget limits type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7695 year: '2012' ... --- _id: '11795' abstract: - lang: eng text: "We study multiple keyword sponsored search auctions with budgets. Each keyword has multiple ad slots with a click-through rate. The bidders have additive valuations, which are linear in the click-through rates, and budgets, which are restricting their overall payments. Additionally, the number of slots per keyword assigned to a bidder is bounded.\r\n\r\nWe show the following results: (1) We give the first mechanism for multiple keywords, where click-through rates differ among slots. Our mechanism is incentive compatible in expectation, individually rational in expectation, and Pareto optimal. (2) We study the combinatorial setting, where each bidder is only interested in a subset of the keywords. We give an incentive compatible, individually rational, Pareto optimal, and deterministic mechanism for identical click-through rates. (3) We give an impossibility result for incentive compatible, individually rational, Pareto optimal, and deterministic mechanisms for bidders with diminishing marginal valuations." alternative_title: - LNCS article_processing_charge: No author: - first_name: Riccardo full_name: Colini-Baldeschi, Riccardo last_name: Colini-Baldeschi - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Stefano full_name: Leonardi, Stefano last_name: Leonardi - first_name: Martin full_name: Starnberger, Martin last_name: Starnberger citation: ama: 'Colini-Baldeschi R, Henzinger MH, Leonardi S, Starnberger M. On multiple keyword sponsored search auctions with budgets. In: 39th International Colloquium on Automata, Languages, and Programming. Vol 7392. Springer Nature; 2012:1–12. doi:10.1007/978-3-642-31585-5_1' apa: 'Colini-Baldeschi, R., Henzinger, M. H., Leonardi, S., & Starnberger, M. (2012). On multiple keyword sponsored search auctions with budgets. In 39th International Colloquium on Automata, Languages, and Programming (Vol. 7392, pp. 1–12). Warwick, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-642-31585-5_1' chicago: Colini-Baldeschi, Riccardo, Monika H Henzinger, Stefano Leonardi, and Martin Starnberger. “On Multiple Keyword Sponsored Search Auctions with Budgets.” In 39th International Colloquium on Automata, Languages, and Programming, 7392:1–12. Springer Nature, 2012. https://doi.org/10.1007/978-3-642-31585-5_1. ieee: R. Colini-Baldeschi, M. H. Henzinger, S. Leonardi, and M. Starnberger, “On multiple keyword sponsored search auctions with budgets,” in 39th International Colloquium on Automata, Languages, and Programming, Warwick, United Kingdom, 2012, vol. 7392, pp. 1–12. ista: 'Colini-Baldeschi R, Henzinger MH, Leonardi S, Starnberger M. 2012. On multiple keyword sponsored search auctions with budgets. 39th International Colloquium on Automata, Languages, and Programming. ICALP: International Colloquium on Automata, Languages, and Programming, LNCS, vol. 7392, 1–12.' mla: Colini-Baldeschi, Riccardo, et al. “On Multiple Keyword Sponsored Search Auctions with Budgets.” 39th International Colloquium on Automata, Languages, and Programming, vol. 7392, Springer Nature, 2012, pp. 1–12, doi:10.1007/978-3-642-31585-5_1. short: R. Colini-Baldeschi, M.H. Henzinger, S. Leonardi, M. Starnberger, in:, 39th International Colloquium on Automata, Languages, and Programming, Springer Nature, 2012, pp. 1–12. conference: end_date: 2012-07-13 location: Warwick, United Kingdom name: 'ICALP: International Colloquium on Automata, Languages, and Programming' start_date: 2012-07-09 date_created: 2022-08-11T11:46:51Z date_published: 2012-07-01T00:00:00Z date_updated: 2023-02-21T16:28:31Z day: '01' doi: 10.1007/978-3-642-31585-5_1 extern: '1' intvolume: ' 7392' language: - iso: eng month: '07' oa_version: None page: 1–12 publication: 39th International Colloquium on Automata, Languages, and Programming publication_identifier: isbn: - '9783642315848' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '11795' relation: later_version status: public scopus_import: '1' status: public title: On multiple keyword sponsored search auctions with budgets type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7392 year: '2012' ... --- _id: '11964' abstract: - lang: eng text: A detailed investigation on the direct arylation of benzene with aryl bromides by using first-row transition metals under high-temperature/high-pressure (high-T/p) conditions is described. By employing a parallel reactor platform for rapid reaction screening and discovery at elevated temperatures, various metal/ligand/base combinations were evaluated for their ability to enable biaryl formation through C-H activation. The combination of cobalt(III) acetylacetonate and lithium bis(trimethylsilyl)amide was subjected to further process intensification at 200 °C (15 bar), allowing a significant reduction of the catalyst/base loading and a dramatic increase in catalytic efficiency (turnover frequency) by a factor of 1000 compared to traditional protocols. The high-throughput screening additionally identified novel nickel- and copper-based metal/ligand combinations that favored an amination pathway competing with C-H activation, with the addition of ligands, such as 1,10-phenanthroline, having a profound influence on the selectivity. In addition to metal-based catalysts, high-T/p process windows were also successfully applied to transition-metal-free systems, utilizing 1,10-phenanthroline as organocatalyst. article_processing_charge: No article_type: original author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: David full_name: Cantillo, David last_name: Cantillo - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe citation: ama: 'Pieber B, Cantillo D, Kappe CO. Direct arylation of benzene with aryl bromides using high‐temperature/high‐pressure process windows: Expanding the scope of C-H activation chemistry. Chemistry – A European Journal. 2012;18(16):5047-5055. doi:10.1002/chem.201103748' apa: 'Pieber, B., Cantillo, D., & Kappe, C. O. (2012). Direct arylation of benzene with aryl bromides using high‐temperature/high‐pressure process windows: Expanding the scope of C-H activation chemistry. Chemistry – A European Journal. Wiley. https://doi.org/10.1002/chem.201103748' chicago: 'Pieber, Bartholomäus, David Cantillo, and C. Oliver Kappe. “Direct Arylation of Benzene with Aryl Bromides Using High‐temperature/High‐pressure Process Windows: Expanding the Scope of C-H Activation Chemistry.” Chemistry – A European Journal. Wiley, 2012. https://doi.org/10.1002/chem.201103748.' ieee: 'B. Pieber, D. Cantillo, and C. O. Kappe, “Direct arylation of benzene with aryl bromides using high‐temperature/high‐pressure process windows: Expanding the scope of C-H activation chemistry,” Chemistry – A European Journal, vol. 18, no. 16. Wiley, pp. 5047–5055, 2012.' ista: 'Pieber B, Cantillo D, Kappe CO. 2012. Direct arylation of benzene with aryl bromides using high‐temperature/high‐pressure process windows: Expanding the scope of C-H activation chemistry. Chemistry – A European Journal. 18(16), 5047–5055.' mla: 'Pieber, Bartholomäus, et al. “Direct Arylation of Benzene with Aryl Bromides Using High‐temperature/High‐pressure Process Windows: Expanding the Scope of C-H Activation Chemistry.” Chemistry – A European Journal, vol. 18, no. 16, Wiley, 2012, pp. 5047–55, doi:10.1002/chem.201103748.' short: B. Pieber, D. Cantillo, C.O. Kappe, Chemistry – A European Journal 18 (2012) 5047–5055. date_created: 2022-08-24T12:48:28Z date_published: 2012-04-16T00:00:00Z date_updated: 2023-02-21T10:09:35Z day: '16' doi: 10.1002/chem.201103748 extern: '1' external_id: pmid: - '22396386' intvolume: ' 18' issue: '16' language: - iso: eng month: '04' oa_version: None page: 5047-5055 pmid: 1 publication: Chemistry – A European Journal publication_identifier: eissn: - 1521-3765 issn: - 0947-6539 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Direct arylation of benzene with aryl bromides using high‐temperature/high‐pressure process windows: Expanding the scope of C-H activation chemistry' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2012' ... --- _id: '11963' abstract: - lang: eng text: 'Peroxides and ethers in flow: 2-Carbonyl-substituted phenols and β-ketoesters react safely with ethers in a microreactor environment using a copper catalyst and an organic peroxide (TBHP). This protocol results in unsymmetrical acetal scaffolds not easily available otherwise (see scheme).' article_processing_charge: No article_type: letter_note author: - first_name: G. Sathish full_name: Kumar, G. Sathish last_name: Kumar - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: K. Rajender full_name: Reddy, K. Rajender last_name: Reddy - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe citation: ama: Kumar GS, Pieber B, Reddy KR, Kappe CO. Copper-catalyzed formation of C-O bonds by direct α-C-H bond activation of ethers using stoichiometric amounts of peroxide in batch and continuous-flow formats. Chemistry - A European Journal. 2012;18(20):6124-6128. doi:10.1002/chem.201200815 apa: Kumar, G. S., Pieber, B., Reddy, K. R., & Kappe, C. O. (2012). Copper-catalyzed formation of C-O bonds by direct α-C-H bond activation of ethers using stoichiometric amounts of peroxide in batch and continuous-flow formats. Chemistry - A European Journal. Wiley. https://doi.org/10.1002/chem.201200815 chicago: Kumar, G. Sathish, Bartholomäus Pieber, K. Rajender Reddy, and C. Oliver Kappe. “Copper-Catalyzed Formation of C-O Bonds by Direct α-C-H Bond Activation of Ethers Using Stoichiometric Amounts of Peroxide in Batch and Continuous-Flow Formats.” Chemistry - A European Journal. Wiley, 2012. https://doi.org/10.1002/chem.201200815. ieee: G. S. Kumar, B. Pieber, K. R. Reddy, and C. O. Kappe, “Copper-catalyzed formation of C-O bonds by direct α-C-H bond activation of ethers using stoichiometric amounts of peroxide in batch and continuous-flow formats,” Chemistry - A European Journal, vol. 18, no. 20. Wiley, pp. 6124–6128, 2012. ista: Kumar GS, Pieber B, Reddy KR, Kappe CO. 2012. Copper-catalyzed formation of C-O bonds by direct α-C-H bond activation of ethers using stoichiometric amounts of peroxide in batch and continuous-flow formats. Chemistry - A European Journal. 18(20), 6124–6128. mla: Kumar, G. Sathish, et al. “Copper-Catalyzed Formation of C-O Bonds by Direct α-C-H Bond Activation of Ethers Using Stoichiometric Amounts of Peroxide in Batch and Continuous-Flow Formats.” Chemistry - A European Journal, vol. 18, no. 20, Wiley, 2012, pp. 6124–28, doi:10.1002/chem.201200815. short: G.S. Kumar, B. Pieber, K.R. Reddy, C.O. Kappe, Chemistry - A European Journal 18 (2012) 6124–6128. date_created: 2022-08-24T12:33:05Z date_published: 2012-05-14T00:00:00Z date_updated: 2023-02-21T10:09:33Z day: '14' doi: 10.1002/chem.201200815 extern: '1' external_id: pmid: - '22492535' intvolume: ' 18' issue: '20' language: - iso: eng month: '05' oa_version: None page: 6124-6128 pmid: 1 publication: Chemistry - A European Journal publication_identifier: eissn: - 1521-3765 issn: - 0947-6539 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Copper-catalyzed formation of C-O bonds by direct α-C-H bond activation of ethers using stoichiometric amounts of peroxide in batch and continuous-flow formats type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2012' ... --- _id: '12644' abstract: - lang: eng text: In the Dry Andes of central Chile, summer water resources originate mostly from snowmelt and ice melt. We use the physically based, spatially distributed hydrological model TOPKAPI to study the exchange between glaciers and climate in the upper Aconcagua River Basin during the summer season and identify the model parameters that are robust and transferable and those that are more dependent on calibration. TOPKAPI has recently been adapted to incorporate an enhanced temperature index approach for snow and ice melting. We suggest a calibration procedure that allows calibration of parameters in three steps by separating parameters governing distinct processes. We evaluate the parameters' transferability in time and in space by applying the model at two spatial scales. TOPKAPI's ability to simulate the relevant processes is tested against meteorological, ablation, and glacier runoff data measured on Juncal Norte Glacier during two glacier ablation seasons. The model was applied successfully to the climatic setting of the Dry Andes once its parameters were recalibrated. We found a clear distinction between parameters that are stable in time and those that need recalibration. The parameters of the melt model are transferable from one season to the other, while the parameters governing the extrapolation of meteorological input data and the routing of glacier meltwater need recalibration from one season to the other. Sensitivity analysis revealed that the model is most sensitive to the temperature lapse rate governing the extrapolation of air temperature from point measurements to the glacier scale and to the melt parameter that multiplies the shortwave radiation balance. article_number: W03509 article_processing_charge: No article_type: original author: - first_name: S. full_name: Ragettli, S. last_name: Ragettli - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: 'Ragettli S, Pellicciotti F. Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters. Water Resources Research. 2012;48(3). doi:10.1029/2011wr010559' apa: 'Ragettli, S., & Pellicciotti, F. (2012). Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters. Water Resources Research. American Geophysical Union. https://doi.org/10.1029/2011wr010559' chicago: 'Ragettli, S., and Francesca Pellicciotti. “Calibration of a Physically Based, Spatially Distributed Hydrological Model in a Glacierized Basin: On the Use of Knowledge from Glaciometeorological Processes to Constrain Model Parameters.” Water Resources Research. American Geophysical Union, 2012. https://doi.org/10.1029/2011wr010559.' ieee: 'S. Ragettli and F. Pellicciotti, “Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters,” Water Resources Research, vol. 48, no. 3. American Geophysical Union, 2012.' ista: 'Ragettli S, Pellicciotti F. 2012. Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters. Water Resources Research. 48(3), W03509.' mla: 'Ragettli, S., and Francesca Pellicciotti. “Calibration of a Physically Based, Spatially Distributed Hydrological Model in a Glacierized Basin: On the Use of Knowledge from Glaciometeorological Processes to Constrain Model Parameters.” Water Resources Research, vol. 48, no. 3, W03509, American Geophysical Union, 2012, doi:10.1029/2011wr010559.' short: S. Ragettli, F. Pellicciotti, Water Resources Research 48 (2012). date_created: 2023-02-20T08:17:39Z date_published: 2012-03-01T00:00:00Z date_updated: 2023-02-21T09:38:36Z day: '01' doi: 10.1029/2011wr010559 extern: '1' intvolume: ' 48' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1029/2011WR010559 month: '03' oa: 1 oa_version: Published Version publication: Water Resources Research publication_identifier: issn: - 0043-1397 publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: 'Calibration of a physically based, spatially distributed hydrological model in a glacierized basin: On the use of knowledge from glaciometeorological processes to constrain model parameters' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2012' ... --- _id: '12646' abstract: - lang: eng text: Assessment of water resources from remote mountainous catchments plays a crucial role for the development of rural areas in or in the vicinity of mountain ranges. The scarcity of data, however, prevents the application of standard approaches that are based on data-driven models. The Hindu Kush–Karakoram–Himalaya mountain range is a crucial area in terms of water resources, but our understanding of the response of its high-elevation catchments to a changing climate is hindered by lack of hydro-meteorological and cryospheric data. Hydrological modeling is challenging here because internal inconsistencies—such as an underestimation of precipitation input that can be compensated for by an overestimation of meltwater—might be hidden due to the complexity of feedback mechanisms that govern melt and runoff generation in such basins. Data scarcity adds to this difficulty by preventing the application of systematic calibration procedures that would allow identification of the parameter set that could guarantee internal consistency in the simulation of the single hydrological components. In this work, we use simulations from the Hunza River Basin in the Karakoram region obtained with the hydrological model TOPKAPI to quantify the predictive power of discharge and snow-cover data sets, as well as the combination of both. We also show that short-term measurements of meteorological variables such as radiative fluxes, wind speed, relative humidity, and air temperature from glacio-meteorological experiments are crucial for a correct parameterization of surface melt processes. They enable detailed simulations of the energy fluxes governing glacier–atmosphere interaction and the resulting ablation through energy-balance modeling. These simulations are used to derive calibrated parameters for the simplified snow and glacier routines in TOPKAPI. We demonstrate that such parameters are stable in space and time in similar climatic regions, thus reducing the number of parameters requiring calibration. article_processing_charge: No article_type: original author: - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: Cyrill full_name: Buergi, Cyrill last_name: Buergi - first_name: Walter Willem full_name: Immerzeel, Walter Willem last_name: Immerzeel - first_name: Markus full_name: Konz, Markus last_name: Konz - first_name: Arun B. full_name: Shrestha, Arun B. last_name: Shrestha citation: ama: 'Pellicciotti F, Buergi C, Immerzeel WW, Konz M, Shrestha AB. Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies. Mountain Research and Development. 2012;32(1):39-50. doi:10.1659/mrd-journal-d-11-00092.1' apa: 'Pellicciotti, F., Buergi, C., Immerzeel, W. W., Konz, M., & Shrestha, A. B. (2012). Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies. Mountain Research and Development. International Mountain Society. https://doi.org/10.1659/mrd-journal-d-11-00092.1' chicago: 'Pellicciotti, Francesca, Cyrill Buergi, Walter Willem Immerzeel, Markus Konz, and Arun B. Shrestha. “Challenges and Uncertainties in Hydrological Modeling of Remote Hindu Kush–Karakoram–Himalayan (HKH) Basins: Suggestions for Calibration Strategies.” Mountain Research and Development. International Mountain Society, 2012. https://doi.org/10.1659/mrd-journal-d-11-00092.1.' ieee: 'F. Pellicciotti, C. Buergi, W. W. Immerzeel, M. Konz, and A. B. Shrestha, “Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies,” Mountain Research and Development, vol. 32, no. 1. International Mountain Society, pp. 39–50, 2012.' ista: 'Pellicciotti F, Buergi C, Immerzeel WW, Konz M, Shrestha AB. 2012. Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies. Mountain Research and Development. 32(1), 39–50.' mla: 'Pellicciotti, Francesca, et al. “Challenges and Uncertainties in Hydrological Modeling of Remote Hindu Kush–Karakoram–Himalayan (HKH) Basins: Suggestions for Calibration Strategies.” Mountain Research and Development, vol. 32, no. 1, International Mountain Society, 2012, pp. 39–50, doi:10.1659/mrd-journal-d-11-00092.1.' short: F. Pellicciotti, C. Buergi, W.W. Immerzeel, M. Konz, A.B. Shrestha, Mountain Research and Development 32 (2012) 39–50. date_created: 2023-02-20T08:17:47Z date_published: 2012-02-01T00:00:00Z date_updated: 2023-02-21T09:31:54Z day: '01' doi: 10.1659/mrd-journal-d-11-00092.1 extern: '1' intvolume: ' 32' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1659/MRD-JOURNAL-D-11-00092.1 month: '02' oa: 1 oa_version: Published Version page: 39-50 publication: Mountain Research and Development publication_identifier: eissn: - 1994-7151 issn: - 0276-4741 publication_status: published publisher: International Mountain Society quality_controlled: '1' scopus_import: '1' status: public title: 'Challenges and uncertainties in hydrological modeling of remote Hindu Kush–Karakoram–Himalayan (HKH) basins: Suggestions for calibration strategies' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2012' ... --- _id: '12647' abstract: - lang: eng text: Accurate quantification of the spatial distribution of precipitation in mountain regions is crucial for assessments of water resources and for the understanding of high-altitude hydrology, yet it is one of the largest unknowns due to the lack of high-altitude observations. The Hunza basin in Pakistan contains very large glacier systems, which, given the melt, cannot persist unless precipitation (snow input) is much higher than what is observed at the meteorological stations, mostly located in mountain valleys. Several studies, therefore, suggest strong positive vertical precipitation lapse rates; in the present study, we quantify this lapse rate by using glaciers as a proxy. We assume a neutral mass balance for the glaciers for the period from 2001 to 2003, and we inversely model the precipitation lapse by balancing the total accumulation in the catchment area and the ablation over the glacier area for the 50 largest glacier systems in the Hunza basin in the Karakoram. Our results reveal a vertical precipitation lapse rate that equals 0.21 ± 0.12% m−1, with a maximum precipitation at an elevation of 5500 masl. We showed that the total annual basin precipitation (828 mm) is 260% higher than what is estimated based on interpolated observations (319 mm); this has major consequences for hydrological modeling and water resource assessments in general. Our results were validated by using previously published studies on individual glaciers as well as the water balance of the Hunza basin. The approach is more widely applicable in mountain ranges where precipitation measurements at high altitude are lacking. article_processing_charge: No article_type: original author: - first_name: Walter Willem full_name: Immerzeel, Walter Willem last_name: Immerzeel - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: Arun B. full_name: Shrestha, Arun B. last_name: Shrestha citation: ama: Immerzeel WW, Pellicciotti F, Shrestha AB. Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin. Mountain Research and Development. 2012;32(1):30-38. doi:10.1659/mrd-journal-d-11-00097.1 apa: Immerzeel, W. W., Pellicciotti, F., & Shrestha, A. B. (2012). Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin. Mountain Research and Development. International Mountain Society. https://doi.org/10.1659/mrd-journal-d-11-00097.1 chicago: Immerzeel, Walter Willem, Francesca Pellicciotti, and Arun B. Shrestha. “Glaciers as a Proxy to Quantify the Spatial Distribution of Precipitation in the Hunza Basin.” Mountain Research and Development. International Mountain Society, 2012. https://doi.org/10.1659/mrd-journal-d-11-00097.1. ieee: W. W. Immerzeel, F. Pellicciotti, and A. B. Shrestha, “Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin,” Mountain Research and Development, vol. 32, no. 1. International Mountain Society, pp. 30–38, 2012. ista: Immerzeel WW, Pellicciotti F, Shrestha AB. 2012. Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin. Mountain Research and Development. 32(1), 30–38. mla: Immerzeel, Walter Willem, et al. “Glaciers as a Proxy to Quantify the Spatial Distribution of Precipitation in the Hunza Basin.” Mountain Research and Development, vol. 32, no. 1, International Mountain Society, 2012, pp. 30–38, doi:10.1659/mrd-journal-d-11-00097.1. short: W.W. Immerzeel, F. Pellicciotti, A.B. Shrestha, Mountain Research and Development 32 (2012) 30–38. date_created: 2023-02-20T08:17:52Z date_published: 2012-02-01T00:00:00Z date_updated: 2023-02-21T08:56:29Z day: '01' doi: 10.1659/mrd-journal-d-11-00097.1 extern: '1' intvolume: ' 32' issue: '1' keyword: - General Environmental Science - Development - Environmental Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1659/MRD-JOURNAL-D-11-00097.1 month: '02' oa: 1 oa_version: Published Version page: 30-38 publication: Mountain Research and Development publication_identifier: eissn: - 1994-7151 issn: - 0276-4741 publication_status: published publisher: International Mountain Society quality_controlled: '1' scopus_import: '1' status: public title: Glaciers as a proxy to quantify the spatial distribution of precipitation in the Hunza basin type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2012' ... --- _id: '12648' abstract: - lang: eng text: Distributed glacier melt models generally assume that the glacier surface consists of bare exposed ice and snow. In reality, many glaciers are wholly or partially covered in layers of debris that tend to suppress ablation rates. In this paper, an existing physically based point model for the ablation of debris-covered ice is incorporated in a distributed melt model and applied to Haut Glacier d'Arolla, Switzerland, which has three large patches of debris cover on its surface. The model is based on a 10 m resolution digital elevation model (DEM) of the area; each glacier pixel in the DEM is defined as either bare or debris-covered ice, and may be covered in snow that must be melted off before ice ablation is assumed to occur. Each debris-covered pixel is assigned a debris thickness value using probability distributions based on over 1000 manual thickness measurements. Locally observed meteorological data are used to run energy balance calculations in every pixel, using an approach suitable for snow, bare ice or debris-covered ice as appropriate. The use of the debris model significantly reduces the total ablation in the debris-covered areas, however the precise reduction is sensitive to the temperature extrapolation used in the model distribution because air near the debris surface tends to be slightly warmer than over bare ice. Overall results suggest that the debris patches, which cover 10% of the glacierized area, reduce total runoff from the glacierized part of the basin by up to 7%. article_number: D18105 article_processing_charge: No article_type: original author: - first_name: T. D. full_name: Reid, T. D. last_name: Reid - first_name: M. full_name: Carenzo, M. last_name: Carenzo - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: B. W. full_name: Brock, B. W. last_name: Brock citation: ama: 'Reid TD, Carenzo M, Pellicciotti F, Brock BW. Including debris cover effects in a distributed model of glacier ablation. Journal of Geophysical Research: Atmospheres. 2012;117(D18). doi:10.1029/2012jd017795' apa: 'Reid, T. D., Carenzo, M., Pellicciotti, F., & Brock, B. W. (2012). Including debris cover effects in a distributed model of glacier ablation. Journal of Geophysical Research: Atmospheres. American Geophysical Union. https://doi.org/10.1029/2012jd017795' chicago: 'Reid, T. D., M. Carenzo, Francesca Pellicciotti, and B. W. Brock. “Including Debris Cover Effects in a Distributed Model of Glacier Ablation.” Journal of Geophysical Research: Atmospheres. American Geophysical Union, 2012. https://doi.org/10.1029/2012jd017795.' ieee: 'T. D. Reid, M. Carenzo, F. Pellicciotti, and B. W. Brock, “Including debris cover effects in a distributed model of glacier ablation,” Journal of Geophysical Research: Atmospheres, vol. 117, no. D18. American Geophysical Union, 2012.' ista: 'Reid TD, Carenzo M, Pellicciotti F, Brock BW. 2012. Including debris cover effects in a distributed model of glacier ablation. Journal of Geophysical Research: Atmospheres. 117(D18), D18105.' mla: 'Reid, T. D., et al. “Including Debris Cover Effects in a Distributed Model of Glacier Ablation.” Journal of Geophysical Research: Atmospheres, vol. 117, no. D18, D18105, American Geophysical Union, 2012, doi:10.1029/2012jd017795.' short: 'T.D. Reid, M. Carenzo, F. Pellicciotti, B.W. Brock, Journal of Geophysical Research: Atmospheres 117 (2012).' date_created: 2023-02-20T08:17:57Z date_published: 2012-09-27T00:00:00Z date_updated: 2023-02-20T10:57:31Z day: '27' doi: 10.1029/2012jd017795 extern: '1' intvolume: ' 117' issue: D18 keyword: - Paleontology - Space and Planetary Science - Earth and Planetary Sciences (miscellaneous) - Atmospheric Science - Earth-Surface Processes - Geochemistry and Petrology - Soil Science - Water Science and Technology - Ecology - Aquatic Science - Forestry - Oceanography - Geophysics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1029/2012JD017795 month: '09' oa: 1 oa_version: Published Version publication: 'Journal of Geophysical Research: Atmospheres' publication_identifier: issn: - 0148-0227 publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: Including debris cover effects in a distributed model of glacier ablation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 117 year: '2012' ... --- _id: '1384' abstract: - lang: eng text: 'Software model checking, as an undecidable problem, has three possible outcomes: (1) the program satisfies the specification, (2) the program does not satisfy the specification, and (3) the model checker fails. The third outcome usually manifests itself in a space-out, time-out, or one component of the verification tool giving up; in all of these failing cases, significant computation is performed by the verification tool before the failure, but no result is reported. We propose to reformulate the model-checking problem as follows, in order to have the verification tool report a summary of the performed work even in case of failure: given a program and a specification, the model checker returns a condition Ψ - usually a state predicate - such that the program satisfies the specification under the condition Ψ - that is, as long as the program does not leave the states in which Ψ is satisfied. In our experiments, we investigated as one major application of conditional model checking the sequential combination of model checkers with information passing. We give the condition that one model checker produces, as input to a second conditional model checker, such that the verification problem for the second is restricted to the part of the state space that is not covered by the condition, i.e., the second model checker works on the problems that the first model checker could not solve. Our experiments demonstrate that repeated application of conditional model checkers, passing information from one model checker to the next, can significantly improve the verification results and performance, i.e., we can now verify programs that we could not verify before.' acknowledgement: This research was supported by the Canadian NSERC grant RGPIN 341819-07, the ERC Advanced Grant QUAREM, and the Austrian Science Fund NFN RiSE. article_number: '57' author: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Mehmet full_name: Keremoglu, Mehmet last_name: Keremoglu - first_name: Philipp full_name: Wendler, Philipp last_name: Wendler citation: ama: 'Beyer D, Henzinger TA, Keremoglu M, Wendler P. Conditional model checking: A technique to pass information between verifiers. In: Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering. ACM; 2012. doi:10.1145/2393596.2393664' apa: 'Beyer, D., Henzinger, T. A., Keremoglu, M., & Wendler, P. (2012). Conditional model checking: A technique to pass information between verifiers. In Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering. Cary, NC, USA: ACM. https://doi.org/10.1145/2393596.2393664' chicago: 'Beyer, Dirk, Thomas A Henzinger, Mehmet Keremoglu, and Philipp Wendler. “Conditional Model Checking: A Technique to Pass Information between Verifiers.” In Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering. ACM, 2012. https://doi.org/10.1145/2393596.2393664.' ieee: 'D. Beyer, T. A. Henzinger, M. Keremoglu, and P. Wendler, “Conditional model checking: A technique to pass information between verifiers,” in Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering, Cary, NC, USA, 2012.' ista: 'Beyer D, Henzinger TA, Keremoglu M, Wendler P. 2012. Conditional model checking: A technique to pass information between verifiers. Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering. FSE: Foundations of Software Engineering, 57.' mla: 'Beyer, Dirk, et al. “Conditional Model Checking: A Technique to Pass Information between Verifiers.” Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering, 57, ACM, 2012, doi:10.1145/2393596.2393664.' short: D. Beyer, T.A. Henzinger, M. Keremoglu, P. Wendler, in:, Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering, ACM, 2012. conference: end_date: 2012-11-16 location: Cary, NC, USA name: 'FSE: Foundations of Software Engineering' start_date: 2012-11-11 date_created: 2018-12-11T11:51:42Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T06:50:18Z day: '01' department: - _id: ToHe doi: 10.1145/2393596.2393664 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1109.6926 month: '11' oa: 1 oa_version: Preprint project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering publication_status: published publisher: ACM publist_id: '5826' quality_controlled: '1' scopus_import: 1 status: public title: 'Conditional model checking: A technique to pass information between verifiers' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '1472' abstract: - lang: eng text: For G = GL 2, PGL 2, SL 2 we prove that the perverse filtration associated with the Hitchin map on the rational cohomology of the moduli space of twisted G-Higgs bundles on a compact Riemann surface C agrees with the weight filtration on the rational cohomology of the twisted G character variety of C when the cohomologies are identified via non-Abelian Hodge theory. The proof is accomplished by means of a study of the topology of the Hitchin map over the locus of integral spectral curves. acknowledgement: Mark Andrea A. de Cataldo was partially supported by N.S.A. and N.S.F. Tamás Hausel was supported by a Royal Society University Research Fellowship. Luca Migliorini was partially supported by PRIN 2007 project "Spazi di moduli e teoria di Lie" author: - first_name: Mark full_name: De Cataldo, Mark A last_name: De Cataldo - first_name: Tamas full_name: Tamas Hausel id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Luca full_name: Migliorini, Luca last_name: Migliorini citation: ama: 'De Cataldo M, Hausel T, Migliorini L. Topology of hitchin systems and Hodge theory of character varieties: The case A 1. Annals of Mathematics. 2012;175(3):1329-1407. doi:10.4007/annals.2012.175.3.7' apa: 'De Cataldo, M., Hausel, T., & Migliorini, L. (2012). Topology of hitchin systems and Hodge theory of character varieties: The case A 1. Annals of Mathematics. Princeton University Press. https://doi.org/10.4007/annals.2012.175.3.7' chicago: 'De Cataldo, Mark, Tamás Hausel, and Luca Migliorini. “Topology of Hitchin Systems and Hodge Theory of Character Varieties: The Case A 1.” Annals of Mathematics. Princeton University Press, 2012. https://doi.org/10.4007/annals.2012.175.3.7.' ieee: 'M. De Cataldo, T. Hausel, and L. Migliorini, “Topology of hitchin systems and Hodge theory of character varieties: The case A 1,” Annals of Mathematics, vol. 175, no. 3. Princeton University Press, pp. 1329–1407, 2012.' ista: 'De Cataldo M, Hausel T, Migliorini L. 2012. Topology of hitchin systems and Hodge theory of character varieties: The case A 1. Annals of Mathematics. 175(3), 1329–1407.' mla: 'De Cataldo, Mark, et al. “Topology of Hitchin Systems and Hodge Theory of Character Varieties: The Case A 1.” Annals of Mathematics, vol. 175, no. 3, Princeton University Press, 2012, pp. 1329–407, doi:10.4007/annals.2012.175.3.7.' short: M. De Cataldo, T. Hausel, L. Migliorini, Annals of Mathematics 175 (2012) 1329–1407. date_created: 2018-12-11T11:52:13Z date_published: 2012-05-01T00:00:00Z date_updated: 2021-01-12T06:50:59Z day: '01' doi: 10.4007/annals.2012.175.3.7 extern: 1 intvolume: ' 175' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1004.1420 month: '05' oa: 1 page: 1329 - 1407 publication: Annals of Mathematics publication_status: published publisher: Princeton University Press publist_id: '5727' quality_controlled: 0 status: public title: 'Topology of hitchin systems and Hodge theory of character varieties: The case A 1' type: journal_article volume: 175 year: '2012' ... --- _id: '1471' abstract: - lang: eng text: 'Given a possibly reducible and non-reduced spectral cover π: X → C over a smooth projective complex curve C we determine the group of connected components of the Prym variety Prym(X/C). As an immediate application we show that the finite group of n-torsion points of the Jacobian of C acts trivially on the cohomology of the twisted SL n-Higgs moduli space up to the degree which is predicted by topological mirror symmetry. In particular this yields a new proof of a result of Harder-Narasimhan, showing that this finite group acts trivially on the cohomology of the twisted SL n stable bundle moduli space.' author: - first_name: Tamas full_name: Tamas Hausel id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Christian full_name: Pauly, Christian last_name: Pauly citation: ama: Hausel T, Pauly C. Prym varieties of spectral covers. Geometry and Topology. 2012;16(3):1609-1638. doi:10.2140/gt.2012.16.1609 apa: Hausel, T., & Pauly, C. (2012). Prym varieties of spectral covers. Geometry and Topology. University of Warwick. https://doi.org/10.2140/gt.2012.16.1609 chicago: Hausel, Tamás, and Christian Pauly. “Prym Varieties of Spectral Covers.” Geometry and Topology. University of Warwick, 2012. https://doi.org/10.2140/gt.2012.16.1609. ieee: T. Hausel and C. Pauly, “Prym varieties of spectral covers,” Geometry and Topology, vol. 16, no. 3. University of Warwick, pp. 1609–1638, 2012. ista: Hausel T, Pauly C. 2012. Prym varieties of spectral covers. Geometry and Topology. 16(3), 1609–1638. mla: Hausel, Tamás, and Christian Pauly. “Prym Varieties of Spectral Covers.” Geometry and Topology, vol. 16, no. 3, University of Warwick, 2012, pp. 1609–38, doi:10.2140/gt.2012.16.1609. short: T. Hausel, C. Pauly, Geometry and Topology 16 (2012) 1609–1638. date_created: 2018-12-11T11:52:13Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T06:50:58Z day: '01' doi: 10.2140/gt.2012.16.1609 extern: 1 intvolume: ' 16' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1012.4748 month: '08' oa: 1 page: 1609 - 1638 publication: Geometry and Topology publication_status: published publisher: University of Warwick publist_id: '5726' quality_controlled: 0 status: public title: Prym varieties of spectral covers type: journal_article volume: 16 year: '2012' ... --- _id: '171' abstract: - lang: eng text: For given non-zero integers a, b, q we investigate the density of solutions (x, y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined over ℚ. author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Stephan full_name: Baier, Stephan last_name: Baier citation: ama: Browning TD, Baier S. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. 2012;2013(680):1-65. doi:https://doi.org/10.1515/crelle.2012.039 apa: Browning, T. D., & Baier, S. (2012). Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle.2012.039 chicago: Browning, Timothy D, and Stephan Baier. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte Mathematik. Walter de Gruyter, 2012. https://doi.org/10.1515/crelle.2012.039. ieee: T. D. Browning and S. Baier, “Inhomogeneous cubic congruences and rational points on del Pezzo surfaces,” Journal fur die Reine und Angewandte Mathematik, vol. 2013, no. 680. Walter de Gruyter, pp. 1–65, 2012. ista: Browning TD, Baier S. 2012. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. 2013(680), 1–65. mla: Browning, Timothy D., and Stephan Baier. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte Mathematik, vol. 2013, no. 680, Walter de Gruyter, 2012, pp. 1–65, doi:https://doi.org/10.1515/crelle.2012.039. short: T.D. Browning, S. Baier, Journal Fur Die Reine Und Angewandte Mathematik 2013 (2012) 1–65. date_created: 2018-12-11T11:45:00Z date_published: 2012-04-03T00:00:00Z date_updated: 2021-01-12T06:52:41Z day: '03' doi: https://doi.org/10.1515/crelle.2012.039 extern: 1 intvolume: ' 2013' issue: '680' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1011.3434 month: '04' oa: 1 page: 1 - 65 publication: Journal fur die Reine und Angewandte Mathematik publication_status: published publisher: Walter de Gruyter publist_id: '7750' quality_controlled: 0 status: public title: Inhomogeneous cubic congruences and rational points on del Pezzo surfaces type: journal_article volume: 2013 year: '2012' ... --- _id: '1725' abstract: - lang: eng text: The spatial organization of cell fates during development involves the interpretation of morphogen gradients by cellular signaling cascades and transcriptional networks. Recent studies use biophysical models, genetics, and quantitative imaging to unravel how tissue-level morphogen behavior arises from subcellular events. Moreover, data from several systems show that morphogen gradients, downstream signaling, and the activity of cell-intrinsic transcriptional networks change dynamically during pattern formation. Studies from Drosophila and now also vertebrates suggest that transcriptional network dynamics are central to the generation of gene expression patterns. Together, this leads to the view that pattern formation is an emergent behavior that results from the coordination of events occurring across molecular, cellular, and tissue scales. The development of novel approaches to study this complex process remains a challenge. acknowledgement: 'Funding provided by the Medical Research Council (UK). ' author: - first_name: Anna full_name: Anna Kicheva id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Michael full_name: Cohen, Michael H last_name: Cohen - first_name: James full_name: Briscoe, James last_name: Briscoe citation: ama: 'Kicheva A, Cohen M, Briscoe J. Developmental pattern formation: Insights from physics and biology. Science. 2012;338(6104):210-212. doi:10.1126/science.1225182' apa: 'Kicheva, A., Cohen, M., & Briscoe, J. (2012). Developmental pattern formation: Insights from physics and biology. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1225182' chicago: 'Kicheva, Anna, Michael Cohen, and James Briscoe. “Developmental Pattern Formation: Insights from Physics and Biology.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1225182.' ieee: 'A. Kicheva, M. Cohen, and J. Briscoe, “Developmental pattern formation: Insights from physics and biology,” Science, vol. 338, no. 6104. American Association for the Advancement of Science, pp. 210–212, 2012.' ista: 'Kicheva A, Cohen M, Briscoe J. 2012. Developmental pattern formation: Insights from physics and biology. Science. 338(6104), 210–212.' mla: 'Kicheva, Anna, et al. “Developmental Pattern Formation: Insights from Physics and Biology.” Science, vol. 338, no. 6104, American Association for the Advancement of Science, 2012, pp. 210–12, doi:10.1126/science.1225182.' short: A. Kicheva, M. Cohen, J. Briscoe, Science 338 (2012) 210–212. date_created: 2018-12-11T11:53:40Z date_published: 2012-10-12T00:00:00Z date_updated: 2021-01-12T06:52:47Z day: '12' doi: 10.1126/science.1225182 extern: 1 intvolume: ' 338' issue: '6104' month: '10' page: 210 - 212 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5404' quality_controlled: 0 status: public title: 'Developmental pattern formation: Insights from physics and biology' type: journal_article volume: 338 year: '2012' ... --- _id: '1757' abstract: - lang: eng text: Self-assembled Ge wires with a height of only 3 unit cells and a length of up to 2 micrometers were grown on Si(001) by means of a catalyst-free method based on molecular beam epitaxy. The wires grow horizontally along either the [100] or the [010] direction. On atomically flat surfaces, they exhibit a highly uniform, triangular cross section. A simple thermodynamic model accounts for the existence of a preferential base width for longitudinal expansion, in quantitative agreement with the experimental findings. Despite the absence of intentional doping, the first transistor-type devices made from single wires show low-resistive electrical contacts and single-hole transport at sub-Kelvin temperatures. In view of their exceptionally small and self-defined cross section, these Ge wires hold promise for the realization of hole systems with exotic properties and provide a new development route for silicon-based nanoelectronics. acknowledgement: We acknowledge the financial support by the DFG SPP1386, P. Chen and D. J. Thurmer for MBE assistance, R. Wacquez for providing the ultrathin SOI wafers, and G. Bauer, Y. Hu, X. Jehl, S. Kiravittaya, C. Klöffel, E. J. H. Lee, F. Liu, D. Loss, and S. Mahapatra for helpful discussions. G. K. acknowledges support from the European commission via a Marie Curie Carrer Integration Grant. S. D. F. acknowledges support from the European Research Council through the starting grant program author: - first_name: Jianjun full_name: Zhang, Jianjun last_name: Zhang - first_name: Georgios full_name: Georgios Katsaros id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros - first_name: Francesco full_name: Montalenti, Francesco last_name: Montalenti - first_name: Daniele full_name: Scopece, Daniele last_name: Scopece - first_name: Roman full_name: Rezaev, Roman O last_name: Rezaev - first_name: Christine full_name: Mickel, Christine H last_name: Mickel - first_name: Bernd full_name: Rellinghaus, Bernd last_name: Rellinghaus - first_name: Leo full_name: Miglio, Leo P last_name: Miglio - first_name: Silvano full_name: De Franceschi, Silvano last_name: De Franceschi - first_name: Armando full_name: Rastelli, Armando last_name: Rastelli - first_name: Oliver full_name: Schmidt, Oliver G last_name: Schmidt citation: ama: Zhang J, Katsaros G, Montalenti F, et al. Monolithic growth of ultrathin Ge nanowires on Si(001) . Physical Review Letters. 2012;109(8). doi:10.1103/PhysRevLett.109.085502 apa: Zhang, J., Katsaros, G., Montalenti, F., Scopece, D., Rezaev, R., Mickel, C., … Schmidt, O. (2012). Monolithic growth of ultrathin Ge nanowires on Si(001) . Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.085502 chicago: Zhang, Jianjun, Georgios Katsaros, Francesco Montalenti, Daniele Scopece, Roman Rezaev, Christine Mickel, Bernd Rellinghaus, et al. “Monolithic Growth of Ultrathin Ge Nanowires on Si(001) .” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.085502. ieee: J. Zhang et al., “Monolithic growth of ultrathin Ge nanowires on Si(001) ,” Physical Review Letters, vol. 109, no. 8. American Physical Society, 2012. ista: Zhang J, Katsaros G, Montalenti F, Scopece D, Rezaev R, Mickel C, Rellinghaus B, Miglio L, De Franceschi S, Rastelli A, Schmidt O. 2012. Monolithic growth of ultrathin Ge nanowires on Si(001) . Physical Review Letters. 109(8). mla: Zhang, Jianjun, et al. “Monolithic Growth of Ultrathin Ge Nanowires on Si(001) .” Physical Review Letters, vol. 109, no. 8, American Physical Society, 2012, doi:10.1103/PhysRevLett.109.085502. short: J. Zhang, G. Katsaros, F. Montalenti, D. Scopece, R. Rezaev, C. Mickel, B. Rellinghaus, L. Miglio, S. De Franceschi, A. Rastelli, O. Schmidt, Physical Review Letters 109 (2012). date_created: 2018-12-11T11:53:51Z date_published: 2012-08-23T00:00:00Z date_updated: 2021-01-12T06:53:00Z day: '23' doi: 10.1103/PhysRevLett.109.085502 extern: 1 intvolume: ' 109' issue: '8' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1208.0666 month: '08' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5367' quality_controlled: 0 status: public title: 'Monolithic growth of ultrathin Ge nanowires on Si(001) ' type: journal_article volume: 109 year: '2012' ... --- _id: '1758' abstract: - lang: eng text: We studied the low-energy states of spin-1/2 quantum dots defined in InAs/InP nanowires and coupled to aluminum superconducting leads. By varying the superconducting gap Δ with a magnetic field B we investigated the transition from strong coupling Δ≪T K to weak-coupling Δ≫T K, where T K is the Kondo temperature. Below the critical field, we observe a persisting zero-bias Kondo resonance that vanishes only for low B or higher temperatures, leaving the room to more robust subgap structures at bias voltages between Δ and 2Δ. For strong and approximately symmetric tunnel couplings, a Josephson supercurrent is observed in addition to the Kondo peak. We ascribe the coexistence of a Kondo resonance and a superconducting gap to a significant density of intragap quasiparticle states, and the finite-bias subgap structures to tunneling through Shiba states. Our results, supported by numerical calculations, own relevance also in relation to tunnel-spectroscopy experiments aiming at the observation of Majorana fermions in hybrid nanostructures. acknowledgement: This work was supported by the EU Marie Curie program and by the Agence Nationale de la Recherche. R. A. acknowledges support from the Spanish Ministry of Science and Innovation through Grant No. FIS2009-08744 author: - first_name: Eduardo full_name: Lee, Eduardo J last_name: Lee - first_name: Xiaocheng full_name: Jiang, Xiaocheng last_name: Jiang - first_name: Ramón full_name: Aguado, Ramón last_name: Aguado - first_name: Georgios full_name: Georgios Katsaros id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros - first_name: Charles full_name: Lieber, Charles M last_name: Lieber - first_name: Silvano full_name: De Franceschi, Silvano last_name: De Franceschi citation: ama: Lee E, Jiang X, Aguado R, Katsaros G, Lieber C, De Franceschi S. Zero-bias anomaly in a nanowire quantum dot coupled to superconductors. Physical Review Letters. 2012;109(18). doi:10.1103/PhysRevLett.109.186802 apa: Lee, E., Jiang, X., Aguado, R., Katsaros, G., Lieber, C., & De Franceschi, S. (2012). Zero-bias anomaly in a nanowire quantum dot coupled to superconductors. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.186802 chicago: Lee, Eduardo, Xiaocheng Jiang, Ramón Aguado, Georgios Katsaros, Charles Lieber, and Silvano De Franceschi. “Zero-Bias Anomaly in a Nanowire Quantum Dot Coupled to Superconductors.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.186802. ieee: E. Lee, X. Jiang, R. Aguado, G. Katsaros, C. Lieber, and S. De Franceschi, “Zero-bias anomaly in a nanowire quantum dot coupled to superconductors,” Physical Review Letters, vol. 109, no. 18. American Physical Society, 2012. ista: Lee E, Jiang X, Aguado R, Katsaros G, Lieber C, De Franceschi S. 2012. Zero-bias anomaly in a nanowire quantum dot coupled to superconductors. Physical Review Letters. 109(18). mla: Lee, Eduardo, et al. “Zero-Bias Anomaly in a Nanowire Quantum Dot Coupled to Superconductors.” Physical Review Letters, vol. 109, no. 18, American Physical Society, 2012, doi:10.1103/PhysRevLett.109.186802. short: E. Lee, X. Jiang, R. Aguado, G. Katsaros, C. Lieber, S. De Franceschi, Physical Review Letters 109 (2012). date_created: 2018-12-11T11:53:51Z date_published: 2012-10-31T00:00:00Z date_updated: 2021-01-12T06:53:01Z day: '31' doi: 10.1103/PhysRevLett.109.186802 extern: 1 intvolume: ' 109' issue: '18' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1207.1259 month: '10' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5366' quality_controlled: 0 status: public title: Zero-bias anomaly in a nanowire quantum dot coupled to superconductors type: journal_article volume: 109 year: '2012' ... --- _id: '1756' abstract: - lang: eng text: We report on the electronic transport properties of multiple-gate devices fabricated from undoped silicon nanowires. Understanding and control of the relevant transport mechanisms was achieved by means of local electrostatic gating and temperature-dependent measurements. The roles of the source/drain contacts and of the silicon channel could be independently evaluated and tuned. Wrap gates surrounding the silicide-silicon contact interfaces were proved to be effective in inducing a full suppression of the contact Schottky barriers, thereby enabling carrier injection down to liquid helium temperature. By independently tuning the effective Schottky barrier heights, a variety of reconfigurable device functionalities could be obtained. In particular, the same nanowire device could be configured to work as a Schottky barrier transistor, a Schottky diode, or a p-n diode with tunable polarities. This versatility was eventually exploited to realize a NAND logic gate with gain well above one. acknowledgement: This work was supported by the Agence Nationale de la Recherche (ANR) through the ACCESS and COHESION projects and by the European Commission through the Chemtronics program MEST-CT-2005-020513 author: - first_name: Massimo full_name: Mongillo, Massimo last_name: Mongillo - first_name: Panayotis full_name: Spathis, Panayotis N last_name: Spathis - first_name: Georgios full_name: Georgios Katsaros id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros - first_name: Pascal full_name: Gentile, Pascal last_name: Gentile - first_name: Silvano full_name: De Franceschi, Silvano last_name: De Franceschi citation: ama: Mongillo M, Spathis P, Katsaros G, Gentile P, De Franceschi S. Multifunctional devices and logic gates with undoped silicon nanowires. Nano Letters. 2012;12(6):3074-3079. doi:10.1021/nl300930m apa: Mongillo, M., Spathis, P., Katsaros, G., Gentile, P., & De Franceschi, S. (2012). Multifunctional devices and logic gates with undoped silicon nanowires. Nano Letters. American Chemical Society. https://doi.org/10.1021/nl300930m chicago: Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Pascal Gentile, and Silvano De Franceschi. “Multifunctional Devices and Logic Gates with Undoped Silicon Nanowires.” Nano Letters. American Chemical Society, 2012. https://doi.org/10.1021/nl300930m. ieee: M. Mongillo, P. Spathis, G. Katsaros, P. Gentile, and S. De Franceschi, “Multifunctional devices and logic gates with undoped silicon nanowires,” Nano Letters, vol. 12, no. 6. American Chemical Society, pp. 3074–3079, 2012. ista: Mongillo M, Spathis P, Katsaros G, Gentile P, De Franceschi S. 2012. Multifunctional devices and logic gates with undoped silicon nanowires. Nano Letters. 12(6), 3074–3079. mla: Mongillo, Massimo, et al. “Multifunctional Devices and Logic Gates with Undoped Silicon Nanowires.” Nano Letters, vol. 12, no. 6, American Chemical Society, 2012, pp. 3074–79, doi:10.1021/nl300930m. short: M. Mongillo, P. Spathis, G. Katsaros, P. Gentile, S. De Franceschi, Nano Letters 12 (2012) 3074–3079. date_created: 2018-12-11T11:53:50Z date_published: 2012-06-13T00:00:00Z date_updated: 2021-01-12T06:53:00Z day: '13' doi: 10.1021/nl300930m extern: 1 intvolume: ' 12' issue: '6' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1208.1465 month: '06' oa: 1 page: 3074 - 3079 publication: Nano Letters publication_status: published publisher: American Chemical Society publist_id: '5368' quality_controlled: 0 status: public title: Multifunctional devices and logic gates with undoped silicon nanowires type: journal_article volume: 12 year: '2012' ... --- _id: '1783' abstract: - lang: eng text: Nonlinearity and entanglement are two important properties by which physical systems can be identified as nonclassical. We study the dynamics of the resonant interaction of up to N=3 two-level systems and a single mode of the electromagnetic field sharing a single excitation dynamically. We observe coherent vacuum Rabi oscillations and their nonlinear √N speedup by tracking the populations of all qubits and the resonator in time. We use quantum state tomography to show explicitly that the dynamics generates maximally entangled states of the W class in a time limited only by the collective interaction rate. We use an entanglement witness and the 3-tangle to characterize the state whose fidelity F=78% is limited in our experiments by crosstalk arising during the simultaneous qubit manipulations which is absent in a sequential approach with F=91%. acknowledgement: This work was supported by the Swiss National Science Foundation (SNF) and the EU IP SOLID author: - first_name: Jonas full_name: Mlynek, Jonas A last_name: Mlynek - first_name: Abdufarrukh full_name: Abdumalikov, Abdufarrukh A last_name: Abdumalikov - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Matthias full_name: Baur, Matthias P last_name: Baur - first_name: C full_name: Lang, C last_name: Lang - first_name: Arjan full_name: Van Loo, Arjan F last_name: Van Loo - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Mlynek J, Abdumalikov A, Fink JM, et al. Demonstrating W-type entanglement of Dicke states in resonant cavity quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 2012;86(5). doi:10.1103/PhysRevA.86.053838 apa: Mlynek, J., Abdumalikov, A., Fink, J. M., Steffen, L., Baur, M., Lang, C., … Wallraff, A. (2012). Demonstrating W-type entanglement of Dicke states in resonant cavity quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.86.053838 chicago: Mlynek, Jonas, Abdufarrukh Abdumalikov, Johannes M Fink, L. Steffen, Matthias Baur, C Lang, Arjan Van Loo, and Andreas Wallraff. “Demonstrating W-Type Entanglement of Dicke States in Resonant Cavity Quantum Electrodynamics.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2012. https://doi.org/10.1103/PhysRevA.86.053838. ieee: J. Mlynek et al., “Demonstrating W-type entanglement of Dicke states in resonant cavity quantum electrodynamics,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 86, no. 5. American Physical Society, 2012. ista: Mlynek J, Abdumalikov A, Fink JM, Steffen L, Baur M, Lang C, Van Loo A, Wallraff A. 2012. Demonstrating W-type entanglement of Dicke states in resonant cavity quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics. 86(5). mla: Mlynek, Jonas, et al. “Demonstrating W-Type Entanglement of Dicke States in Resonant Cavity Quantum Electrodynamics.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 86, no. 5, American Physical Society, 2012, doi:10.1103/PhysRevA.86.053838. short: J. Mlynek, A. Abdumalikov, J.M. Fink, L. Steffen, M. Baur, C. Lang, A. Van Loo, A. Wallraff, Physical Review A - Atomic, Molecular, and Optical Physics 86 (2012). date_created: 2018-12-11T11:53:59Z date_published: 2012-11-30T00:00:00Z date_updated: 2021-01-12T06:53:10Z day: '30' doi: 10.1103/PhysRevA.86.053838 extern: 1 intvolume: ' 86' issue: '5' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1202.5191 month: '11' oa: 1 publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '5332' quality_controlled: 0 status: public title: Demonstrating W-type entanglement of Dicke states in resonant cavity quantum electrodynamics type: journal_article volume: 86 year: '2012' ... --- _id: '1782' abstract: - lang: eng text: Steering a quantum harmonic oscillator state along cyclic trajectories leads to a path-dependent geometric phase. Here we describe its experimental observation in an electronic harmonic oscillator. We use a superconducting qubit as a nonlinear probe of the phase, which is otherwise unobservable due to the linearity of the oscillator. We show that the geometric phase is, for a variety of cyclic paths, proportional to the area enclosed in the quadrature plane. At the transition to the nonadiabatic regime, we study corrections to the phase and dephasing of the qubit caused by qubit-resonator entanglement. In particular, we identify parameters for which this dephasing mechanism is negligible even in the nonadiabatic regime. The demonstrated controllability makes our system a versatile tool to study geometric phases in open quantum systems and to investigate their potential for quantum information processing. acknowledgement: This work is supported by the EU project GEOMDISS, the Austrian Science Foundation (S. F.), and the Swiss National Science Foundation (SNSF) author: - first_name: M full_name: Pechal, M last_name: Pechal - first_name: Stefan full_name: Berger, Stefan T last_name: Berger - first_name: Abdufarrukh full_name: Abdumalikov, Abdufarrukh A last_name: Abdumalikov - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Jonas full_name: Mlynek, Jonas A last_name: Mlynek - first_name: L. full_name: Steffen, L. Kraig last_name: Steffen - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp citation: ama: Pechal M, Berger S, Abdumalikov A, et al. Geometric phase and nonadiabatic effects in an electronic harmonic oscillator. Physical Review Letters. 2012;108(17). doi:10.1103/PhysRevLett.108.170401 apa: Pechal, M., Berger, S., Abdumalikov, A., Fink, J. M., Mlynek, J., Steffen, L., … Filipp, S. (2012). Geometric phase and nonadiabatic effects in an electronic harmonic oscillator. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.108.170401 chicago: Pechal, M, Stefan Berger, Abdufarrukh Abdumalikov, Johannes M Fink, Jonas Mlynek, L. Steffen, Andreas Wallraff, and Stefan Filipp. “Geometric Phase and Nonadiabatic Effects in an Electronic Harmonic Oscillator.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.108.170401. ieee: M. Pechal et al., “Geometric phase and nonadiabatic effects in an electronic harmonic oscillator,” Physical Review Letters, vol. 108, no. 17. American Physical Society, 2012. ista: Pechal M, Berger S, Abdumalikov A, Fink JM, Mlynek J, Steffen L, Wallraff A, Filipp S. 2012. Geometric phase and nonadiabatic effects in an electronic harmonic oscillator. Physical Review Letters. 108(17). mla: Pechal, M., et al. “Geometric Phase and Nonadiabatic Effects in an Electronic Harmonic Oscillator.” Physical Review Letters, vol. 108, no. 17, American Physical Society, 2012, doi:10.1103/PhysRevLett.108.170401. short: M. Pechal, S. Berger, A. Abdumalikov, J.M. Fink, J. Mlynek, L. Steffen, A. Wallraff, S. Filipp, Physical Review Letters 108 (2012). date_created: 2018-12-11T11:53:59Z date_published: 2012-04-23T00:00:00Z date_updated: 2021-01-12T06:53:10Z day: '23' doi: 10.1103/PhysRevLett.108.170401 extern: 1 intvolume: ' 108' issue: '17' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1109.1157 month: '04' oa: 1 publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5333' quality_controlled: 0 status: public title: Geometric phase and nonadiabatic effects in an electronic harmonic oscillator type: journal_article volume: 108 year: '2012' ... --- _id: '1784' abstract: - lang: eng text: A localized qubit entangled with a propagating quantum field is well suited to study nonlocal aspects of quantum mechanics and may also provide a channel to communicate between spatially separated nodes in a quantum network. Here, we report the on-demand generation and characterization of Bell-type entangled states between a superconducting qubit and propagating microwave fields composed of zero-, one-, and two-photon Fock states. Using low noise linear amplification and efficient data acquisition we extract all relevant correlations between the qubit and the photon states and demonstrate entanglement with high fidelity. acknowledgement: This work was supported by the European Research Council (ERC) through a Starting Grant and by ETHZ author: - first_name: Christopher full_name: Eichler, Christopher last_name: Eichler - first_name: C full_name: Lang, C last_name: Lang - first_name: Johannes M full_name: Johannes Fink id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: J full_name: Govenius, J last_name: Govenius - first_name: Stefan full_name: Filipp, Stefan last_name: Filipp - first_name: Andreas full_name: Wallraff, Andreas last_name: Wallraff citation: ama: Eichler C, Lang C, Fink JM, Govenius J, Filipp S, Wallraff A. Observation of entanglement between itinerant microwave photons and a superconducting qubit. Physical Review Letters. 2012;109(24). doi:10.1103/PhysRevLett.109.240501 apa: Eichler, C., Lang, C., Fink, J. M., Govenius, J., Filipp, S., & Wallraff, A. (2012). Observation of entanglement between itinerant microwave photons and a superconducting qubit. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.240501 chicago: Eichler, Christopher, C Lang, Johannes M Fink, J Govenius, Stefan Filipp, and Andreas Wallraff. “Observation of Entanglement between Itinerant Microwave Photons and a Superconducting Qubit.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.240501. ieee: C. Eichler, C. Lang, J. M. Fink, J. Govenius, S. Filipp, and A. Wallraff, “Observation of entanglement between itinerant microwave photons and a superconducting qubit,” Physical Review Letters, vol. 109, no. 24. American Physical Society, 2012. ista: Eichler C, Lang C, Fink JM, Govenius J, Filipp S, Wallraff A. 2012. Observation of entanglement between itinerant microwave photons and a superconducting qubit. Physical Review Letters. 109(24). mla: Eichler, Christopher, et al. “Observation of Entanglement between Itinerant Microwave Photons and a Superconducting Qubit.” Physical Review Letters, vol. 109, no. 24, American Physical Society, 2012, doi:10.1103/PhysRevLett.109.240501. short: C. Eichler, C. Lang, J.M. Fink, J. Govenius, S. Filipp, A. Wallraff, Physical Review Letters 109 (2012). date_created: 2018-12-11T11:53:59Z date_published: 2012-12-10T00:00:00Z date_updated: 2021-01-12T06:53:10Z day: '10' doi: 10.1103/PhysRevLett.109.240501 extern: 1 intvolume: ' 109' issue: '24' main_file_link: - open_access: '0' url: http://arxiv.org/abs/1209.0441 month: '12' publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5330' quality_controlled: 0 status: public title: Observation of entanglement between itinerant microwave photons and a superconducting qubit type: journal_article volume: 109 year: '2012' ... --- _id: '1801' abstract: - lang: eng text: Brain circuits are assembled from a large variety of morphologically and functionally diverse cell types. It is not known how the intermingled cell types of an individual adult brain region differ in their expressed genomes. Here we describe an atlas of cell type transcriptomes in one brain region, the mouse retina. We found that each adult cell type expressed a specific set of genes, including a unique set of transcription factors, forming a 'barcode' for cell identity. Cell type transcriptomes carried enough information to categorize cells into morphological classes and types. Several genes that were specifically expressed in particular retinal circuit elements, such as inhibitory neuron types, are associated with eye diseases. The resource described here allows gene expression to be compared across adult retinal cell types, experimenting with specific transcription factors to differentiate stem or somatic cells to retinal cell types, and predicting cellular targets of newly discovered disease-associated genes. acknowledgement: The study was supported by Friedrich Miescher Institute funds, Alcon award, a National Center of Competence in Research Genetics grant, a European Research Council grant, a Swiss-Hungarian grant, and RETICIRC, TREATRUSH, SEEBETTER and OPTONEURO grants from the European Union to B.R. author: - first_name: Sandra full_name: Sandra Siegert id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 - first_name: Erik full_name: Cabuy, Erik last_name: Cabuy - first_name: Brigitte full_name: Scherf, Brigitte G last_name: Scherf - first_name: Hubertus full_name: Kohler, Hubertus last_name: Kohler - first_name: Satchidananda full_name: Panda, Satchidananda last_name: Panda - first_name: Yunzheng full_name: Le, Yunzheng last_name: Le - first_name: Hans full_name: Fehling, Hans J last_name: Fehling - first_name: Dimos full_name: Gaidatzis, Dimos last_name: Gaidatzis - first_name: Michael full_name: Stadler, Michael B last_name: Stadler - first_name: Botond full_name: Roska, Botond M last_name: Roska citation: ama: Siegert S, Cabuy E, Scherf B, et al. Transcriptional code and disease map for adult retinal cell types. Nature Neuroscience. 2012;15(3):487-495. doi:10.1038/nn.3032 apa: Siegert, S., Cabuy, E., Scherf, B., Kohler, H., Panda, S., Le, Y., … Roska, B. (2012). Transcriptional code and disease map for adult retinal cell types. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3032 chicago: Siegert, Sandra, Erik Cabuy, Brigitte Scherf, Hubertus Kohler, Satchidananda Panda, Yunzheng Le, Hans Fehling, Dimos Gaidatzis, Michael Stadler, and Botond Roska. “Transcriptional Code and Disease Map for Adult Retinal Cell Types.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3032. ieee: S. Siegert et al., “Transcriptional code and disease map for adult retinal cell types,” Nature Neuroscience, vol. 15, no. 3. Nature Publishing Group, pp. 487–495, 2012. ista: Siegert S, Cabuy E, Scherf B, Kohler H, Panda S, Le Y, Fehling H, Gaidatzis D, Stadler M, Roska B. 2012. Transcriptional code and disease map for adult retinal cell types. Nature Neuroscience. 15(3), 487–495. mla: Siegert, Sandra, et al. “Transcriptional Code and Disease Map for Adult Retinal Cell Types.” Nature Neuroscience, vol. 15, no. 3, Nature Publishing Group, 2012, pp. 487–95, doi:10.1038/nn.3032. short: S. Siegert, E. Cabuy, B. Scherf, H. Kohler, S. Panda, Y. Le, H. Fehling, D. Gaidatzis, M. Stadler, B. Roska, Nature Neuroscience 15 (2012) 487–495. date_created: 2018-12-11T11:54:05Z date_published: 2012-03-01T00:00:00Z date_updated: 2021-01-12T06:53:17Z day: '01' doi: 10.1038/nn.3032 extern: 1 intvolume: ' 15' issue: '3' month: '03' page: 487 - 495 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '5309' quality_controlled: 0 status: public title: Transcriptional code and disease map for adult retinal cell types type: journal_article volume: 15 year: '2012' ... --- _id: '1976' abstract: - lang: eng text: 'Complex I is a key enzyme of the respiratory chain in many organisms. This multi-protein complex with an intricate evolutionary history originated from the unification of prebuilt modules of hydrogenases and transporters. Using recently determined crystallographic structures of complex I we reanalyzed evolutionarily related complexes that couple oxidoreduction to trans-membrane ion translocation. Our analysis points to the previously unnoticed structural homology of the electron input module of formate dehydrogenlyases and subunit NuoG of complex I. We also show that all related to complex I hydrogenases likely operate via a conformation driven mechanism with structural changes generated in the conserved coupling site located at the interface of subunits NuoB/D/H. The coupling apparently originated once in evolutionary history, together with subunit NuoH joining hydrogenase and transport modules. Analysis of quinone oxidoreduction properties and the structure of complex I allows us to suggest a fully reversible coupling mechanism. Our model predicts that: 1) proton access to the ketone groups of the bound quinone is rigorously controlled by the protein, 2) the negative electric charge of the anionic ubiquinol head group is a major driving force for conformational changes.' acknowledgement: The work in authors' laboratory was funded by the Medical Research Council. author: - first_name: Rouslan full_name: Efremov, Rouslan G last_name: Efremov - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Efremov R, Sazanov LA. The coupling mechanism of respiratory complex i - A structural and evolutionary perspective. Biochimica et Biophysica Acta - Bioenergetics. 2012;1817(10):1785-1795. doi:10.1016/j.bbabio.2012.02.015 apa: Efremov, R., & Sazanov, L. A. (2012). The coupling mechanism of respiratory complex i - A structural and evolutionary perspective. Biochimica et Biophysica Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2012.02.015 chicago: Efremov, Rouslan, and Leonid A Sazanov. “The Coupling Mechanism of Respiratory Complex i - A Structural and Evolutionary Perspective.” Biochimica et Biophysica Acta - Bioenergetics. Elsevier, 2012. https://doi.org/10.1016/j.bbabio.2012.02.015. ieee: R. Efremov and L. A. Sazanov, “The coupling mechanism of respiratory complex i - A structural and evolutionary perspective,” Biochimica et Biophysica Acta - Bioenergetics, vol. 1817, no. 10. Elsevier, pp. 1785–1795, 2012. ista: Efremov R, Sazanov LA. 2012. The coupling mechanism of respiratory complex i - A structural and evolutionary perspective. Biochimica et Biophysica Acta - Bioenergetics. 1817(10), 1785–1795. mla: Efremov, Rouslan, and Leonid A. Sazanov. “The Coupling Mechanism of Respiratory Complex i - A Structural and Evolutionary Perspective.” Biochimica et Biophysica Acta - Bioenergetics, vol. 1817, no. 10, Elsevier, 2012, pp. 1785–95, doi:10.1016/j.bbabio.2012.02.015. short: R. Efremov, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1817 (2012) 1785–1795. date_created: 2018-12-11T11:55:00Z date_published: 2012-10-01T00:00:00Z date_updated: 2019-04-26T07:22:06Z day: '01' doi: 10.1016/j.bbabio.2012.02.015 extern: 1 intvolume: ' 1817' issue: '10' month: '10' page: 1785 - 1795 publication: Biochimica et Biophysica Acta - Bioenergetics publication_status: published publisher: Elsevier publist_id: '5108' quality_controlled: 0 status: public title: The coupling mechanism of respiratory complex i - A structural and evolutionary perspective type: review volume: 1817 year: '2012' ... --- _id: '1972' abstract: - lang: eng text: Outer membrane protein F, a major component of the Escherichia coli outer membrane, was crystallized for the first time in lipidic mesophase of monoolein in novel space groups, P1 and H32. Due to ease of its purification and crystallization OmpF can be used as a benchmark protein for establishing membrane protein crystallization in meso, as a "membrane lyzozyme" The packing of porin trimers in the crystals of space group H32 is similar to natural outer membranes, providing the first high-resolution insight into the close to native packing of OmpF. Surprisingly, interaction between trimers is mediated exclusively by lipids, without direct protein-protein contacts. Multiple ordered lipids are observed and many of them occupy identical positions independently of the space group, identifying preferential interaction sites of lipid acyl chains. Presence of ordered aliphatic chains close to a positively charged area on the porin surface suggests a position for a lipopolysaccharide binding site on the surface of the major E. coli porins. acknowledgement: This work was funded by the Medical Research Council. author: - first_name: Rouslan full_name: Efremov, Rouslan G last_name: Efremov - first_name: Leonid A full_name: Leonid Sazanov id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Efremov R, Sazanov LA. Structure of Escherichia coli OmpF porin from lipidic mesophase. Journal of Structural Biology. 2012;178(3):311-318. doi:10.1016/j.jsb.2012.03.005 apa: Efremov, R., & Sazanov, L. A. (2012). Structure of Escherichia coli OmpF porin from lipidic mesophase. Journal of Structural Biology. Academic Press. https://doi.org/10.1016/j.jsb.2012.03.005 chicago: Efremov, Rouslan, and Leonid A Sazanov. “Structure of Escherichia Coli OmpF Porin from Lipidic Mesophase.” Journal of Structural Biology. Academic Press, 2012. https://doi.org/10.1016/j.jsb.2012.03.005. ieee: R. Efremov and L. A. Sazanov, “Structure of Escherichia coli OmpF porin from lipidic mesophase,” Journal of Structural Biology, vol. 178, no. 3. Academic Press, pp. 311–318, 2012. ista: Efremov R, Sazanov LA. 2012. Structure of Escherichia coli OmpF porin from lipidic mesophase. Journal of Structural Biology. 178(3), 311–318. mla: Efremov, Rouslan, and Leonid A. Sazanov. “Structure of Escherichia Coli OmpF Porin from Lipidic Mesophase.” Journal of Structural Biology, vol. 178, no. 3, Academic Press, 2012, pp. 311–18, doi:10.1016/j.jsb.2012.03.005. short: R. Efremov, L.A. Sazanov, Journal of Structural Biology 178 (2012) 311–318. date_created: 2018-12-11T11:54:59Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T06:54:26Z day: '01' doi: 10.1016/j.jsb.2012.03.005 extern: 1 intvolume: ' 178' issue: '3' month: '06' page: 311 - 318 publication: Journal of Structural Biology publication_status: published publisher: Academic Press publist_id: '5109' quality_controlled: 0 status: public title: Structure of Escherichia coli OmpF porin from lipidic mesophase type: journal_article volume: 178 year: '2012' ... --- _id: '1987' abstract: - lang: eng text: | In the living cell, proteins are able to organize space much larger than their dimensions. In return, changes of intracellular space can influence biochemical reactions, allowing cells to sense their size and shape. Despite the possibility to reconstitute protein self-organization with only a few purified components, we still lack knowledge of how geometrical boundaries affect spatiotemporal protein patterns. Following a minimal systems approach, we used purified proteins and photolithographically patterned membranes to study the influence of spatial confinement on the self-organization of the Min system, a spatial regulator of bacterial cytokinesis, in vitro. We found that the emerging protein pattern responds even to the lateral, two-dimensional geometry of the membrane such that, as in the three-dimensional cell, Min protein waves travel along the longest axis of the membrane patch. This shows that for spatial sensing the Min system does not need to be enclosed in a three-dimensional compartment. Using a computational model we quantitatively analyzed our experimental findings and identified persistent binding of MinE to the membrane as requirement for the Min system to sense geometry. Our results give insight into the interplay between geometrical confinement and biochemical patterns emerging from a nonlinear reaction-diffusion system. acknowledgement: 'This work was supported by the Max-Planck-Society (P.S. and M.L.) and by the German Research Foundation as part of the Research Training Group “Nano- and Biotechnologies for Electronic Device Packaging” (GRK 1401) (J.S.) and by the Leibniz-Award (P.S.). ' author: - first_name: Jakob full_name: Schweizer, Jakob last_name: Schweizer - first_name: Martin full_name: Martin Loose id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - first_name: Mike full_name: 'Bonny, Mike ' last_name: Bonny - first_name: Karsten full_name: Kruse, Karsten last_name: Kruse - first_name: Ingolf full_name: Mönch, Ingolf last_name: Mönch - first_name: Petra full_name: 'Schwille, Petra ' last_name: Schwille citation: ama: Schweizer J, Loose M, Bonny M, Kruse K, Mönch I, Schwille P. Geometry sensing by self-organized protein patterns. PNAS. 2012;109(38):15283-15288. doi:10.1073/pnas.1206953109 apa: Schweizer, J., Loose, M., Bonny, M., Kruse, K., Mönch, I., & Schwille, P. (2012). Geometry sensing by self-organized protein patterns. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1206953109 chicago: Schweizer, Jakob, Martin Loose, Mike Bonny, Karsten Kruse, Ingolf Mönch, and Petra Schwille. “Geometry Sensing by Self-Organized Protein Patterns.” PNAS. National Academy of Sciences, 2012. https://doi.org/10.1073/pnas.1206953109. ieee: J. Schweizer, M. Loose, M. Bonny, K. Kruse, I. Mönch, and P. Schwille, “Geometry sensing by self-organized protein patterns,” PNAS, vol. 109, no. 38. National Academy of Sciences, pp. 15283–15288, 2012. ista: Schweizer J, Loose M, Bonny M, Kruse K, Mönch I, Schwille P. 2012. Geometry sensing by self-organized protein patterns. PNAS. 109(38), 15283–15288. mla: Schweizer, Jakob, et al. “Geometry Sensing by Self-Organized Protein Patterns.” PNAS, vol. 109, no. 38, National Academy of Sciences, 2012, pp. 15283–88, doi:10.1073/pnas.1206953109. short: J. Schweizer, M. Loose, M. Bonny, K. Kruse, I. Mönch, P. Schwille, PNAS 109 (2012) 15283–15288. date_created: 2018-12-11T11:55:04Z date_published: 2012-09-18T00:00:00Z date_updated: 2021-01-12T06:54:31Z day: '18' doi: 10.1073/pnas.1206953109 extern: 1 intvolume: ' 109' issue: '38' month: '09' page: 15283 - 15288 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5096' quality_controlled: 0 status: public title: Geometry sensing by self-organized protein patterns type: journal_article volume: 109 year: '2012' ... --- _id: '2048' abstract: - lang: eng text: Leakage resilient cryptography attempts to incorporate side-channel leakage into the black-box security model and designs cryptographic schemes that are provably secure within it. Informally, a scheme is leakage-resilient if it remains secure even if an adversary learns a bounded amount of arbitrary information about the schemes internal state. Unfortunately, most leakage resilient schemes are unnecessarily complicated in order to achieve strong provable security guarantees. As advocated by Yu et al. [CCS’10], this mostly is an artefact of the security proof and in practice much simpler construction may already suffice to protect against realistic side-channel attacks. In this paper, we show that indeed for simpler constructions leakage-resilience can be obtained when we aim for relaxed security notions where the leakage-functions and/or the inputs to the primitive are chosen non-adaptively. For example, we show that a three round Feistel network instantiated with a leakage resilient PRF yields a leakage resilient PRP if the inputs are chosen non-adaptively (This complements the result of Dodis and Pietrzak [CRYPTO’10] who show that if a adaptive queries are allowed, a superlogarithmic number of rounds is necessary.) We also show that a minor variation of the classical GGM construction gives a leakage resilient PRF if both, the leakage-function and the inputs, are chosen non-adaptively. acknowledgement: "Sebastian Faust acknowledges support from the Danish National Research Foundation and The National Science Foundation of China (under the grant 61061130540) for the Sino-Danish Center for the Theory of Interactive Computation, within part of this work was performed; and from the CFEM research center, supported by the Danish Strategic Research Council. \r\nSupported by the European Research Council/ERC Starting Grant 259668-PSPC.\r\n" alternative_title: - LNCS author: - first_name: Sebastian full_name: Faust, Sebastian last_name: Faust - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Joachim full_name: Schipper, Joachim id: 7BE863D4-E9CF-11E9-9EDB-90527418172C last_name: Schipper citation: ama: 'Faust S, Pietrzak KZ, Schipper J. Practical leakage-resilient symmetric cryptography. In: Conference Proceedings CHES 2012. Vol 7428. Springer; 2012:213-232. doi:10.1007/978-3-642-33027-8_13' apa: 'Faust, S., Pietrzak, K. Z., & Schipper, J. (2012). Practical leakage-resilient symmetric cryptography. In Conference proceedings CHES 2012 (Vol. 7428, pp. 213–232). Leuven, Belgium: Springer. https://doi.org/10.1007/978-3-642-33027-8_13' chicago: Faust, Sebastian, Krzysztof Z Pietrzak, and Joachim Schipper. “Practical Leakage-Resilient Symmetric Cryptography.” In Conference Proceedings CHES 2012, 7428:213–32. Springer, 2012. https://doi.org/10.1007/978-3-642-33027-8_13. ieee: S. Faust, K. Z. Pietrzak, and J. Schipper, “Practical leakage-resilient symmetric cryptography,” in Conference proceedings CHES 2012, Leuven, Belgium, 2012, vol. 7428, pp. 213–232. ista: 'Faust S, Pietrzak KZ, Schipper J. 2012. Practical leakage-resilient symmetric cryptography. Conference proceedings CHES 2012. CHES: Cryptographic Hardware and Embedded Systems, LNCS, vol. 7428, 213–232.' mla: Faust, Sebastian, et al. “Practical Leakage-Resilient Symmetric Cryptography.” Conference Proceedings CHES 2012, vol. 7428, Springer, 2012, pp. 213–32, doi:10.1007/978-3-642-33027-8_13. short: S. Faust, K.Z. Pietrzak, J. Schipper, in:, Conference Proceedings CHES 2012, Springer, 2012, pp. 213–232. conference: end_date: 2012-09-12 location: Leuven, Belgium name: 'CHES: Cryptographic Hardware and Embedded Systems' start_date: 2012-09-09 date_created: 2018-12-11T11:55:25Z date_published: 2012-09-01T00:00:00Z date_updated: 2021-01-12T06:54:58Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-642-33027-8_13 ec_funded: 1 intvolume: ' 7428' language: - iso: eng main_file_link: - open_access: '1' url: http://www.iacr.org/archive/ches2012/74280211/74280211.pdf month: '09' oa: 1 oa_version: Preprint page: 213 - 232 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: ' Conference proceedings CHES 2012' publication_status: published publisher: Springer publist_id: '5003' quality_controlled: '1' scopus_import: 1 status: public title: Practical leakage-resilient symmetric cryptography type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7428 year: '2012' ... --- _id: '2049' abstract: - lang: eng text: "We propose a new authentication protocol that is provably secure based on a ring variant of the learning parity with noise (LPN) problem. The protocol follows the design principle of the LPN-based protocol from Eurocrypt’11 (Kiltz et al.), and like it, is a two round protocol secure against active attacks. Moreover, our protocol has small communication complexity and a very small footprint which makes it applicable in scenarios that involve low-cost, resource-constrained devices.\r\n\r\nPerformance-wise, our protocol is more efficient than previous LPN-based schemes, such as the many variants of the Hopper-Blum (HB) protocol and the aforementioned protocol from Eurocrypt’11. Our implementation results show that it is even comparable to the standard challenge-and-response protocols based on the AES block-cipher. Our basic protocol is roughly 20 times slower than AES, but with the advantage of having 10 times smaller code size. Furthermore, if a few hundred bytes of non-volatile memory are available to allow the storage of some off-line pre-computations, then the online phase of our protocols is only twice as slow as AES.\r\n" acknowledgement: "Supported by the European Research Council / ERC Starting Grant (259668- PSPC)\r\nWe would like to thank the anonymous referees of this confer- ence and those of the ECRYPT Workshop on Lightweight Cryptography for very useful comments, and in particular for the suggestion that the scheme is somewhat vulnerable to a man-in-the-middle attack whenever an adversary observes two reader challenges that are the same. We hope that the attack we described in Appendix A corresponds to what the reviewer had in mind. We also thank Tanja Lange for pointing us to the pa- per of [Kir11] and for discussions of some of her recent work. " alternative_title: - LNCS author: - first_name: Stefan full_name: Heyse, Stefan last_name: Heyse - first_name: Eike full_name: Kiltz, Eike last_name: Kiltz - first_name: Vadim full_name: Lyubashevsky, Vadim last_name: Lyubashevsky - first_name: Christof full_name: Paar, Christof last_name: Paar - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Heyse S, Kiltz E, Lyubashevsky V, Paar C, Pietrzak KZ. Lapin: An efficient authentication protocol based on ring-LPN. In: Conference Proceedings FSE 2012. Vol 7549. Springer; 2012:346-365. doi:10.1007/978-3-642-34047-5_20' apa: 'Heyse, S., Kiltz, E., Lyubashevsky, V., Paar, C., & Pietrzak, K. Z. (2012). Lapin: An efficient authentication protocol based on ring-LPN. In Conference proceedings FSE 2012 (Vol. 7549, pp. 346–365). Washington, DC, USA: Springer. https://doi.org/10.1007/978-3-642-34047-5_20' chicago: 'Heyse, Stefan, Eike Kiltz, Vadim Lyubashevsky, Christof Paar, and Krzysztof Z Pietrzak. “Lapin: An Efficient Authentication Protocol Based on Ring-LPN.” In Conference Proceedings FSE 2012, 7549:346–65. Springer, 2012. https://doi.org/10.1007/978-3-642-34047-5_20.' ieee: 'S. Heyse, E. Kiltz, V. Lyubashevsky, C. Paar, and K. Z. Pietrzak, “Lapin: An efficient authentication protocol based on ring-LPN,” in Conference proceedings FSE 2012, Washington, DC, USA, 2012, vol. 7549, pp. 346–365.' ista: 'Heyse S, Kiltz E, Lyubashevsky V, Paar C, Pietrzak KZ. 2012. Lapin: An efficient authentication protocol based on ring-LPN. Conference proceedings FSE 2012. FSE: Fast Software Encryption, LNCS, vol. 7549, 346–365.' mla: 'Heyse, Stefan, et al. “Lapin: An Efficient Authentication Protocol Based on Ring-LPN.” Conference Proceedings FSE 2012, vol. 7549, Springer, 2012, pp. 346–65, doi:10.1007/978-3-642-34047-5_20.' short: S. Heyse, E. Kiltz, V. Lyubashevsky, C. Paar, K.Z. Pietrzak, in:, Conference Proceedings FSE 2012, Springer, 2012, pp. 346–365. conference: end_date: 2012-03-21 location: Washington, DC, USA name: 'FSE: Fast Software Encryption' start_date: 2012-03-19 date_created: 2018-12-11T11:55:25Z date_published: 2012-03-01T00:00:00Z date_updated: 2021-01-12T06:54:58Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-642-34047-5_20 ec_funded: 1 intvolume: ' 7549' language: - iso: eng main_file_link: - open_access: '1' url: http://www.iacr.org/archive/fse2012/75490350/75490350.pdf month: '03' oa: 1 oa_version: Preprint page: 346 - 365 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: ' Conference proceedings FSE 2012' publication_status: published publisher: Springer publist_id: '5002' quality_controlled: '1' scopus_import: 1 status: public title: 'Lapin: An efficient authentication protocol based on ring-LPN' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7549 year: '2012' ... --- _id: '2073' abstract: - lang: eng text: 'Background: Drosophila albomicans is a unique model organism for studying both sex chromosome and B chromosome evolution. A pair of its autosomes comprising roughly 40% of the whole genome has fused to the ancient X and Y chromosomes only about 0.12 million years ago, thereby creating the youngest and most gene-rich neo-sex system reported to date. This species also possesses recently derived B chromosomes that show non-Mendelian inheritance and significantly influence fertility.Methods: We sequenced male flies with B chromosomes at 124.5-fold genome coverage using next-generation sequencing. To characterize neo-Y specific changes and B chromosome sequences, we also sequenced inbred female flies derived from the same strain but without B''s at 28.5-fold.Results: We assembled a female genome and placed 53% of the sequence and 85% of the annotated proteins into specific chromosomes, by comparison with the 12 Drosophila genomes. Despite its very recent origin, the non-recombining neo-Y chromosome shows various signs of degeneration, including a significant enrichment of non-functional genes compared to the neo-X, and an excess of tandem duplications relative to other chromosomes. We also characterized a B-chromosome linked scaffold that contains an actively transcribed unit and shows sequence similarity to the subcentromeric regions of both the ancient X and the neo-X chromosome.Conclusions: Our results provide novel insights into the very early stages of sex chromosome evolution and B chromosome origination, and suggest an unprecedented connection between the births of these two systems in D. albomicans.' author: - first_name: Qi full_name: Zhou, Qi last_name: Zhou - first_name: Hongmei full_name: Zhu, Hongmei last_name: Zhu - first_name: Quanfei full_name: Huang, Quanfei last_name: Huang - first_name: Li full_name: Zhao, Li last_name: Zhao - first_name: Guo full_name: Zhang, Guo J last_name: Zhang - first_name: Scott full_name: Roy, Scott W last_name: Roy - first_name: Beatriz full_name: Beatriz Vicoso id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Zhaolin full_name: Xuan, Zhaolin last_name: Xuan - first_name: Jue full_name: Ruan, Jue last_name: Ruan - first_name: Yue full_name: Zhang, Yue last_name: Zhang - first_name: Ruoping full_name: Zhao, Ruoping last_name: Zhao - first_name: Chen full_name: Ye, Chen last_name: Ye - first_name: Xiuqing full_name: Zhang, Xiuqing last_name: Zhang - first_name: Jùn full_name: Wang, Jùn last_name: Wang - first_name: Wen full_name: Wang, Wen last_name: Wang - first_name: Doris full_name: Bachtrog, Doris last_name: Bachtrog citation: ama: Zhou Q, Zhu H, Huang Q, et al. Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans. BMC Genomics. 2012;13(1). doi:10.1186/1471-2164-13-109 apa: Zhou, Q., Zhu, H., Huang, Q., Zhao, L., Zhang, G., Roy, S., … Bachtrog, D. (2012). Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans. BMC Genomics. BioMed Central. https://doi.org/10.1186/1471-2164-13-109 chicago: Zhou, Qi, Hongmei Zhu, Quanfei Huang, Li Zhao, Guo Zhang, Scott Roy, Beatriz Vicoso, et al. “Deciphering Neo-Sex and B Chromosome Evolution by the Draft Genome of Drosophila Albomicans.” BMC Genomics. BioMed Central, 2012. https://doi.org/10.1186/1471-2164-13-109. ieee: Q. Zhou et al., “Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans,” BMC Genomics, vol. 13, no. 1. BioMed Central, 2012. ista: Zhou Q, Zhu H, Huang Q, Zhao L, Zhang G, Roy S, Vicoso B, Xuan Z, Ruan J, Zhang Y, Zhao R, Ye C, Zhang X, Wang J, Wang W, Bachtrog D. 2012. Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans. BMC Genomics. 13(1). mla: Zhou, Qi, et al. “Deciphering Neo-Sex and B Chromosome Evolution by the Draft Genome of Drosophila Albomicans.” BMC Genomics, vol. 13, no. 1, BioMed Central, 2012, doi:10.1186/1471-2164-13-109. short: Q. Zhou, H. Zhu, Q. Huang, L. Zhao, G. Zhang, S. Roy, B. Vicoso, Z. Xuan, J. Ruan, Y. Zhang, R. Zhao, C. Ye, X. Zhang, J. Wang, W. Wang, D. Bachtrog, BMC Genomics 13 (2012). date_created: 2018-12-11T11:55:33Z date_published: 2012-03-22T00:00:00Z date_updated: 2021-01-12T06:55:08Z day: '22' doi: 10.1186/1471-2164-13-109 extern: 1 intvolume: ' 13' issue: '1' month: '03' publication: BMC Genomics publication_status: published publisher: BioMed Central publist_id: '4965' quality_controlled: 0 status: public title: Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 13 year: '2012' ... --- _id: '2079' abstract: - lang: eng text: We introduce an algorithm and representation for fabricating 3D shape abstractions using mutually intersecting planar cut-outs. The planes have prefabricated slits at their intersections and are assembled by sliding them together. Often such abstractions are used as a sculptural art form or in architecture and are colloquially called ‘cardboard sculptures’. Based on an analysis of construction rules, we propose an extended binary space partitioning tree as an efficient representation of such cardboard models which allows us to quickly evaluate the feasibility of newly added planar elements. The complexity of insertion order quickly increases with the number of planar elements and manual analysis becomes intractable. We provide tools for generating cardboard sculptures with guaranteed constructibility. In combination with a simple optimization and sampling strategy for new elements, planar shape abstraction models can be designed by iteratively adding elements. As an output, we obtain a fabrication plan that can be printed or sent to a laser cutter. We demonstrate the complete process by designing and fabricating cardboard models of various well-known 3D shapes. author: - first_name: Kristian full_name: Hildebrand, Kristian last_name: Hildebrand - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Marc full_name: Alexa, Marc last_name: Alexa citation: ama: 'Hildebrand K, Bickel B, Alexa M. crdbrd: Shape fabrication by sliding planar slices. Computer Graphics Forum. 2012;31(2pt3):583-592. doi:10.1111/j.1467-8659.2012.03037.x' apa: 'Hildebrand, K., Bickel, B., & Alexa, M. (2012). crdbrd: Shape fabrication by sliding planar slices. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2012.03037.x' chicago: 'Hildebrand, Kristian, Bernd Bickel, and Marc Alexa. “Crdbrd: Shape Fabrication by Sliding Planar Slices.” Computer Graphics Forum. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1467-8659.2012.03037.x.' ieee: 'K. Hildebrand, B. Bickel, and M. Alexa, “crdbrd: Shape fabrication by sliding planar slices,” Computer Graphics Forum, vol. 31, no. 2pt3. Wiley-Blackwell, pp. 583–592, 2012.' ista: 'Hildebrand K, Bickel B, Alexa M. 2012. crdbrd: Shape fabrication by sliding planar slices. Computer Graphics Forum. 31(2pt3), 583–592.' mla: 'Hildebrand, Kristian, et al. “Crdbrd: Shape Fabrication by Sliding Planar Slices.” Computer Graphics Forum, vol. 31, no. 2pt3, Wiley-Blackwell, 2012, pp. 583–92, doi:10.1111/j.1467-8659.2012.03037.x.' short: K. Hildebrand, B. Bickel, M. Alexa, Computer Graphics Forum 31 (2012) 583–592. date_created: 2018-12-11T11:55:35Z date_published: 2012-05-01T00:00:00Z date_updated: 2021-01-12T06:55:10Z day: '01' doi: 10.1111/j.1467-8659.2012.03037.x extern: 1 intvolume: ' 31' issue: 2pt3 month: '05' page: 583 - 592 publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '4959' quality_controlled: 0 status: public title: 'crdbrd: Shape fabrication by sliding planar slices' type: journal_article volume: 31 year: '2012' ... --- _id: '2103' abstract: - lang: eng text: Although facial hair plays an important role in individual expression, facial-hair reconstruction is not addressed by current facecapture systems. Our research addresses this limitation with an algorithm that treats hair and skin surface capture together in a coupled fashion so that a high-quality representation of hair fibers as well as the underlying skin surface can be reconstructed. We propose a passive, camera-based system that is robust against arbitrary motion since all data is acquired within the time period of a single exposure. Our reconstruction algorithm detects and traces hairs in the captured images and reconstructs them in 3D using a multiview stereo approach. Our coupled skin-reconstruction algorithm uses information about the detected hairs to deliver a skin surface that lies underneath all hairs irrespective of occlusions. In dense regions like eyebrows, we employ a hair-synthesis method to create hair fibers that plausibly match the image data. We demonstrate our scanning system on a number of individuals and show that it can successfully reconstruct a variety of facial-hair styles together with the underlying skin surface. author: - first_name: Thabo full_name: Beeler, Thabo last_name: Beeler - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Gioacchino full_name: Noris, Gioacchino last_name: Noris - first_name: Paul full_name: Beardsley, Paul A last_name: Beardsley - first_name: Steve full_name: Marschner, Steve last_name: Marschner - first_name: Robert full_name: Sumner, Robert W last_name: Sumner - first_name: Markus full_name: Groß, Markus S last_name: Groß citation: ama: Beeler T, Bickel B, Noris G, et al. Coupled 3D reconstruction of sparse facial hair and skin. ACM Transactions on Graphics. 2012;31(4). doi:10.1145/2185520.2185613 apa: Beeler, T., Bickel, B., Noris, G., Beardsley, P., Marschner, S., Sumner, R., & Groß, M. (2012). Coupled 3D reconstruction of sparse facial hair and skin. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2185520.2185613 chicago: Beeler, Thabo, Bernd Bickel, Gioacchino Noris, Paul Beardsley, Steve Marschner, Robert Sumner, and Markus Groß. “Coupled 3D Reconstruction of Sparse Facial Hair and Skin.” ACM Transactions on Graphics. ACM, 2012. https://doi.org/10.1145/2185520.2185613. ieee: T. Beeler et al., “Coupled 3D reconstruction of sparse facial hair and skin,” ACM Transactions on Graphics, vol. 31, no. 4. ACM, 2012. ista: Beeler T, Bickel B, Noris G, Beardsley P, Marschner S, Sumner R, Groß M. 2012. Coupled 3D reconstruction of sparse facial hair and skin. ACM Transactions on Graphics. 31(4). mla: Beeler, Thabo, et al. “Coupled 3D Reconstruction of Sparse Facial Hair and Skin.” ACM Transactions on Graphics, vol. 31, no. 4, ACM, 2012, doi:10.1145/2185520.2185613. short: T. Beeler, B. Bickel, G. Noris, P. Beardsley, S. Marschner, R. Sumner, M. Groß, ACM Transactions on Graphics 31 (2012). date_created: 2018-12-11T11:55:44Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T06:55:20Z day: '01' doi: 10.1145/2185520.2185613 extern: 1 intvolume: ' 31' issue: '4' month: '01' publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4932' quality_controlled: 0 status: public title: Coupled 3D reconstruction of sparse facial hair and skin type: journal_article volume: 31 year: '2012' ... --- _id: '2101' abstract: - lang: eng text: 'Articulated deformable characters are widespread in computer animation. Unfortunately, we lack methods for their automatic fabrication using modern additive manufacturing (AM) technologies. We propose a method that takes a skinned mesh as input, then estimates a fabricatable single-material model that approximates the 3D kinematics of the corresponding virtual articulated character in a piecewise linear manner. We first extract a set of potential joint locations. From this set, together with optional, user-specified range constraints, we then estimate mechanical friction joints that satisfy inter-joint non-penetration and other fabrication constraints. To avoid brittle joint designs, we place joint centers on an approximate medial axis representation of the input geometry, and maximize each joint''s minimal cross-sectional area. We provide several demonstrations, manufactured as single, assembled pieces using 3D printers. ' acknowledgement: This work was partially supported by NSF grant IIS-1116619. Doug James acknowledges support from Pixar and a fellowship from the John Simon Guggenheim Memorial Foundation author: - first_name: Moritz full_name: Bac̈her, Moritz last_name: Bac̈Her - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Doug full_name: James, Doug L last_name: James - first_name: Hanspeter full_name: Pfister, Hanspeter last_name: Pfister citation: ama: Bac̈Her M, Bickel B, James D, Pfister H. Fabricating articulated characters from skinned meshes. ACM Transactions on Graphics. 2012;31(4). doi:10.1145/2185520.2185543 apa: Bac̈Her, M., Bickel, B., James, D., & Pfister, H. (2012). Fabricating articulated characters from skinned meshes. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2185520.2185543 chicago: Bac̈Her, Moritz, Bernd Bickel, Doug James, and Hanspeter Pfister. “Fabricating Articulated Characters from Skinned Meshes.” ACM Transactions on Graphics. ACM, 2012. https://doi.org/10.1145/2185520.2185543. ieee: M. Bac̈Her, B. Bickel, D. James, and H. Pfister, “Fabricating articulated characters from skinned meshes,” ACM Transactions on Graphics, vol. 31, no. 4. ACM, 2012. ista: Bac̈Her M, Bickel B, James D, Pfister H. 2012. Fabricating articulated characters from skinned meshes. ACM Transactions on Graphics. 31(4). mla: Bac̈Her, Moritz, et al. “Fabricating Articulated Characters from Skinned Meshes.” ACM Transactions on Graphics, vol. 31, no. 4, ACM, 2012, doi:10.1145/2185520.2185543. short: M. Bac̈Her, B. Bickel, D. James, H. Pfister, ACM Transactions on Graphics 31 (2012). date_created: 2018-12-11T11:55:43Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T06:55:19Z day: '01' doi: 10.1145/2185520.2185543 extern: 1 intvolume: ' 31' issue: '4' month: '01' publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4933' quality_controlled: 0 status: public title: Fabricating articulated characters from skinned meshes type: journal_article volume: 31 year: '2012' ... --- _id: '2102' abstract: - lang: eng text: 'We propose a complete process for designing, simulating, and fabricating synthetic skin for an animatronics character that mimics the face of a given subject and its expressions. The process starts with measuring the elastic properties of a material used to manufacture synthetic soft tissue. Given these measurements we use physicsbased simulation to predict the behavior of a face when it is driven by the underlying robotic actuation. Next, we capture 3D facial expressions for a given target subject. As the key component of our process, we present a novel optimization scheme that determines the shape of the synthetic skin as well as the actuation parameters that provide the best match to the target expressions. We demonstrate this computational skin design by physically cloning a real human face onto an animatronics figure. ' acknowledgement: This work was supported in part by the NCCR Co-Me of the Swiss NSF author: - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Peter full_name: Kaufmann, Peter last_name: Kaufmann - first_name: Mélina full_name: Skouras, Mélina last_name: Skouras - first_name: Bernhard full_name: Thomaszewski, Bernhard last_name: Thomaszewski - first_name: Derek full_name: Bradley, Derek J last_name: Bradley - first_name: Thabo full_name: Beeler, Thabo last_name: Beeler - first_name: Philip full_name: Jackson, Philip V last_name: Jackson - first_name: Steve full_name: Marschner, Steve last_name: Marschner - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Markus full_name: Groß, Markus S last_name: Groß citation: ama: Bickel B, Kaufmann P, Skouras M, et al. Physical face cloning. ACM Transactions on Graphics. 2012;31(4). doi:10.1145/2185520.2185614 apa: Bickel, B., Kaufmann, P., Skouras, M., Thomaszewski, B., Bradley, D., Beeler, T., … Groß, M. (2012). Physical face cloning. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2185520.2185614 chicago: Bickel, Bernd, Peter Kaufmann, Mélina Skouras, Bernhard Thomaszewski, Derek Bradley, Thabo Beeler, Philip Jackson, Steve Marschner, Wojciech Matusik, and Markus Groß. “Physical Face Cloning.” ACM Transactions on Graphics. ACM, 2012. https://doi.org/10.1145/2185520.2185614. ieee: B. Bickel et al., “Physical face cloning,” ACM Transactions on Graphics, vol. 31, no. 4. ACM, 2012. ista: Bickel B, Kaufmann P, Skouras M, Thomaszewski B, Bradley D, Beeler T, Jackson P, Marschner S, Matusik W, Groß M. 2012. Physical face cloning. ACM Transactions on Graphics. 31(4). mla: Bickel, Bernd, et al. “Physical Face Cloning.” ACM Transactions on Graphics, vol. 31, no. 4, ACM, 2012, doi:10.1145/2185520.2185614. short: B. Bickel, P. Kaufmann, M. Skouras, B. Thomaszewski, D. Bradley, T. Beeler, P. Jackson, S. Marschner, W. Matusik, M. Groß, ACM Transactions on Graphics 31 (2012). date_created: 2018-12-11T11:55:43Z date_published: 2012-07-04T00:00:00Z date_updated: 2021-01-12T06:55:19Z day: '04' doi: 10.1145/2185520.2185614 extern: 1 intvolume: ' 31' issue: '4' month: '07' publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '4931' quality_controlled: 0 status: public title: Physical face cloning type: journal_article volume: 31 year: '2012' ... --- _id: '2106' abstract: - lang: eng text: Progress in cloth simulation for computer animation and apparel design has led to a multitude of deformation models, each with its own way of relating geometry, deformation, and forces. As simulators improve, differences between these models become more important, but it is difficult to choose a model and a set of parameters to match a given real material simply by looking at simulation results. This paper provides measurement and fitting methods that allow nonlinear models to be fit to the observed deformation of a particular cloth sample. Unlike standard textile testing, our system measures complex 3D deformations of a sheet of cloth, not just one-dimensional force-displacement curves, so it works under a wider range of deformation conditions. The fitted models are then evaluated by comparison to measured deformations with motions very different from those used for fitting. acknowledgement: This work was funded in part by the Spanish Ministry of Science and Innovation, project TIN2009-07942, and by the European Research Council, project ERC-2011-StG-280135 Animetrics. author: - first_name: Eder full_name: Miguel, Eder last_name: Miguel - first_name: Derek full_name: Bradley, Derek J last_name: Bradley - first_name: Bernhard full_name: Thomaszewski, Bernhard last_name: Thomaszewski - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Wojciech full_name: Matusik, Wojciech last_name: Matusik - first_name: Miguel full_name: Otaduy, Miguel A last_name: Otaduy - first_name: Steve full_name: Marschner, Steve last_name: Marschner citation: ama: 'Miguel E, Bradley D, Thomaszewski B, et al. Data-driven estimation of cloth simulation models. In: Vol 31. Wiley-Blackwell; 2012:519-528. doi:10.1111/j.1467-8659.2012.03031.x' apa: Miguel, E., Bradley, D., Thomaszewski, B., Bickel, B., Matusik, W., Otaduy, M., & Marschner, S. (2012). Data-driven estimation of cloth simulation models (Vol. 31, pp. 519–528). Presented at the Computer Graphics Forum, Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2012.03031.x chicago: Miguel, Eder, Derek Bradley, Bernhard Thomaszewski, Bernd Bickel, Wojciech Matusik, Miguel Otaduy, and Steve Marschner. “Data-Driven Estimation of Cloth Simulation Models,” 31:519–28. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1467-8659.2012.03031.x. ieee: E. Miguel et al., “Data-driven estimation of cloth simulation models,” presented at the Computer Graphics Forum, 2012, vol. 31, no. 2, pp. 519–528. ista: Miguel E, Bradley D, Thomaszewski B, Bickel B, Matusik W, Otaduy M, Marschner S. 2012. Data-driven estimation of cloth simulation models. Computer Graphics Forum vol. 31, 519–528. mla: Miguel, Eder, et al. Data-Driven Estimation of Cloth Simulation Models. Vol. 31, no. 2, Wiley-Blackwell, 2012, pp. 519–28, doi:10.1111/j.1467-8659.2012.03031.x. short: E. Miguel, D. Bradley, B. Thomaszewski, B. Bickel, W. Matusik, M. Otaduy, S. Marschner, in:, Wiley-Blackwell, 2012, pp. 519–528. conference: name: Computer Graphics Forum date_created: 2018-12-11T11:55:45Z date_published: 2012-05-01T00:00:00Z date_updated: 2021-01-12T06:55:21Z day: '01' doi: 10.1111/j.1467-8659.2012.03031.x extern: 1 intvolume: ' 31' issue: '2' month: '05' page: 519 - 528 publication_status: published publisher: Wiley-Blackwell publist_id: '4929' quality_controlled: 0 status: public title: Data-driven estimation of cloth simulation models type: conference volume: 31 year: '2012' ... --- _id: '2104' abstract: - lang: eng text: 'In recent years, various methods have been introduced to exploit pre-recorded data to improve the performance and/or realism of dynamic deformations, but their differences and similarities have not been adequately analyzed or discussed. So far, the proposed methods have been explored mainly in the research context. They have not been adopted by the computer graphics industry. This course bridges the gap between research labs and industry to present a unifying theory and understanding of data-driven methods for dynamic deformations that may inspire development of novel solutions. It focuses on application of data-driven methods to three areas of computer animation: dynamic deformation of faces, soft volumetric tissue, and cloth. And it describes how to approach these challenges in a data-driven manner, classifies the various methods, and demonstrates how data-driven methods can work in other settings. ' author: - first_name: Miguel full_name: Otaduy, Miguel A last_name: Otaduy - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Derek full_name: Bradley, Derek J last_name: Bradley - first_name: Huamin full_name: Wang, Huamin last_name: Wang citation: ama: 'Otaduy M, Bickel B, Bradley D, Wang H. Data-driven simulation methods in computer graphics: Cloth, tissue and faces. In: ACM; 2012. doi:10.1145/2343483.2343495' apa: 'Otaduy, M., Bickel, B., Bradley, D., & Wang, H. (2012). Data-driven simulation methods in computer graphics: Cloth, tissue and faces. Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM. https://doi.org/10.1145/2343483.2343495' chicago: 'Otaduy, Miguel, Bernd Bickel, Derek Bradley, and Huamin Wang. “Data-Driven Simulation Methods in Computer Graphics: Cloth, Tissue and Faces.” ACM, 2012. https://doi.org/10.1145/2343483.2343495.' ieee: 'M. Otaduy, B. Bickel, D. Bradley, and H. Wang, “Data-driven simulation methods in computer graphics: Cloth, tissue and faces,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 2012.' ista: 'Otaduy M, Bickel B, Bradley D, Wang H. 2012. Data-driven simulation methods in computer graphics: Cloth, tissue and faces. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques.' mla: 'Otaduy, Miguel, et al. Data-Driven Simulation Methods in Computer Graphics: Cloth, Tissue and Faces. ACM, 2012, doi:10.1145/2343483.2343495.' short: M. Otaduy, B. Bickel, D. Bradley, H. Wang, in:, ACM, 2012. conference: name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' date_created: 2018-12-11T11:55:44Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T06:55:20Z day: '01' doi: 10.1145/2343483.2343495 extern: 1 month: '01' publication_status: published publisher: ACM publist_id: '4930' quality_controlled: 0 status: public title: 'Data-driven simulation methods in computer graphics: Cloth, tissue and faces' type: conference year: '2012' ... --- _id: '2105' acknowledgement: Mélina Skouras was partially supported by the NCCR Co-Me of the Swiss National Science Foundation. author: - first_name: Mélina full_name: Skouras, Mélina last_name: Skouras - first_name: Bernhard full_name: Thomaszewski, Bernhard last_name: Thomaszewski - first_name: Bernd full_name: Bernd Bickel id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Markus full_name: Groß, Markus S last_name: Groß citation: ama: 'Skouras M, Thomaszewski B, Bickel B, Groß M. Computational design of rubber balloons. In: Vol 31. Wiley-Blackwell; 2012:835-844. doi:10.1111/j.1467-8659.2012.03064.x' apa: 'Skouras, M., Thomaszewski, B., Bickel, B., & Groß, M. (2012). Computational design of rubber balloons (Vol. 31, pp. 835–844). Presented at the EUROGRAPHICS: European Association for Computer Graphics, Wiley-Blackwell. https://doi.org/10.1111/j.1467-8659.2012.03064.x' chicago: Skouras, Mélina, Bernhard Thomaszewski, Bernd Bickel, and Markus Groß. “Computational Design of Rubber Balloons,” 31:835–44. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1467-8659.2012.03064.x. ieee: 'M. Skouras, B. Thomaszewski, B. Bickel, and M. Groß, “Computational design of rubber balloons,” presented at the EUROGRAPHICS: European Association for Computer Graphics, 2012, vol. 31, no. 2, pp. 835–844.' ista: 'Skouras M, Thomaszewski B, Bickel B, Groß M. 2012. Computational design of rubber balloons. EUROGRAPHICS: European Association for Computer Graphics vol. 31, 835–844.' mla: Skouras, Mélina, et al. Computational Design of Rubber Balloons. Vol. 31, no. 2, Wiley-Blackwell, 2012, pp. 835–44, doi:10.1111/j.1467-8659.2012.03064.x. short: M. Skouras, B. Thomaszewski, B. Bickel, M. Groß, in:, Wiley-Blackwell, 2012, pp. 835–844. conference: name: 'EUROGRAPHICS: European Association for Computer Graphics' date_created: 2018-12-11T11:55:45Z date_published: 2012-05-01T00:00:00Z date_updated: 2021-01-12T06:55:20Z day: '01' doi: 10.1111/j.1467-8659.2012.03064.x extern: 1 intvolume: ' 31' issue: '2' month: '05' page: 835 - 844 publication_status: published publisher: Wiley-Blackwell publist_id: '4928' quality_controlled: 0 status: public title: Computational design of rubber balloons type: conference volume: 31 year: '2012' ... --- _id: '2125' abstract: - lang: eng text: We consider a class of stochastic PDEs of Burgers type in spatial dimension 1, driven by space–time white noise. Even though it is well known that these equations are well posed, it turns out that if one performs a spatial discretization of the nonlinearity in the “wrong” way, then the sequence of approximate equations does converge to a limit, but this limit exhibits an additional correction term. This correction term is proportional to the local quadratic cross-variation (in space) of the gradient of the conserved quantity with the solution itself. This can be understood as a consequence of the fact that for any fixed time, the law of the solution is locally equivalent to Wiener measure, where space plays the role of time. In this sense, the correction term is similar to the usual Itô–Stratonovich correction term that arises when one considers different temporal discretizations of stochastic ODEs. acknowledgement: Supported by Rubicon Grant 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). Supported by the EPSRC Grants EP/E002269/1 and EP/D071593/1, a Wolfson Research Merit Award of the Royal Society and a Philip Leverhulme prize of the Lev author: - first_name: Martin full_name: Hairer, Martin M last_name: Hairer - first_name: Jan full_name: Jan Maas id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: Hairer M, Maas J. A spatial version of the Itô-Stratonovich correction. Annals of Probability. 2012;40(4):1675-1714. doi:10.1214/11-AOP662 apa: Hairer, M., & Maas, J. (2012). A spatial version of the Itô-Stratonovich correction. Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/11-AOP662 chicago: Hairer, Martin, and Jan Maas. “A Spatial Version of the Itô-Stratonovich Correction.” Annals of Probability. Institute of Mathematical Statistics, 2012. https://doi.org/10.1214/11-AOP662. ieee: M. Hairer and J. Maas, “A spatial version of the Itô-Stratonovich correction,” Annals of Probability, vol. 40, no. 4. Institute of Mathematical Statistics, pp. 1675–1714, 2012. ista: Hairer M, Maas J. 2012. A spatial version of the Itô-Stratonovich correction. Annals of Probability. 40(4), 1675–1714. mla: Hairer, Martin, and Jan Maas. “A Spatial Version of the Itô-Stratonovich Correction.” Annals of Probability, vol. 40, no. 4, Institute of Mathematical Statistics, 2012, pp. 1675–714, doi:10.1214/11-AOP662. short: M. Hairer, J. Maas, Annals of Probability 40 (2012) 1675–1714. date_created: 2018-12-11T11:55:51Z date_published: 2012-07-01T00:00:00Z date_updated: 2021-01-12T06:55:27Z day: '01' doi: 10.1214/11-AOP662 extern: 1 intvolume: ' 40' issue: '4' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1011.0966 month: '07' oa: 1 page: 1675 - 1714 publication: Annals of Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '4908' quality_controlled: 0 status: public title: A spatial version of the Itô-Stratonovich correction type: journal_article volume: 40 year: '2012' ... --- _id: '2127' abstract: - lang: eng text: We study a new notion of Ricci curvature that applies to Markov chains on discrete spaces. This notion relies on geodesic convexity of the entropy and is analogous to the one introduced by Lott, Sturm, and Villani for geodesic measure spaces. In order to apply to the discrete setting, the role of the Wasserstein metric is taken over by a different metric, having the property that continuous time Markov chains are gradient flows of the entropy. Using this notion of Ricci curvature we prove discrete analogues of fundamental results by Bakry–Émery and Otto–Villani. Further, we show that Ricci curvature bounds are preserved under tensorisation. As a special case we obtain the sharp Ricci curvature lower bound for the discrete hypercube. acknowledgement: Jan Maas is supported by Rubicon subsidy 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). author: - first_name: Matthias full_name: Erbar, Matthias last_name: Erbar - first_name: Jan full_name: Jan Maas id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 citation: ama: Erbar M, Maas J. Ricci curvature of finite Markov chains via convexity of the entropy. Archive for Rational Mechanics and Analysis. 2012;206(3):997-1038. doi:10.1007/s00205-012-0554-z apa: Erbar, M., & Maas, J. (2012). Ricci curvature of finite Markov chains via convexity of the entropy. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-012-0554-z chicago: Erbar, Matthias, and Jan Maas. “Ricci Curvature of Finite Markov Chains via Convexity of the Entropy.” Archive for Rational Mechanics and Analysis. Springer, 2012. https://doi.org/10.1007/s00205-012-0554-z. ieee: M. Erbar and J. Maas, “Ricci curvature of finite Markov chains via convexity of the entropy,” Archive for Rational Mechanics and Analysis, vol. 206, no. 3. Springer, pp. 997–1038, 2012. ista: Erbar M, Maas J. 2012. Ricci curvature of finite Markov chains via convexity of the entropy. Archive for Rational Mechanics and Analysis. 206(3), 997–1038. mla: Erbar, Matthias, and Jan Maas. “Ricci Curvature of Finite Markov Chains via Convexity of the Entropy.” Archive for Rational Mechanics and Analysis, vol. 206, no. 3, Springer, 2012, pp. 997–1038, doi:10.1007/s00205-012-0554-z. short: M. Erbar, J. Maas, Archive for Rational Mechanics and Analysis 206 (2012) 997–1038. date_created: 2018-12-11T11:55:52Z date_published: 2012-12-01T00:00:00Z date_updated: 2021-01-12T06:55:28Z day: '01' doi: 10.1007/s00205-012-0554-z extern: 1 intvolume: ' 206' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1111.2687 month: '12' oa: 1 page: 997 - 1038 publication: Archive for Rational Mechanics and Analysis publication_status: published publisher: Springer publist_id: '4906' quality_controlled: 0 status: public title: Ricci curvature of finite Markov chains via convexity of the entropy type: journal_article volume: 206 year: '2012' ... --- _id: '2128' abstract: - lang: eng text: We introduce a technique for handling Whitney decompositions in Gaussian harmonic analysis and apply it to the study of Gaussian analogues of the classical tent spaces T 1,q of Coifman–Meyer–Stein. acknowledgement: J. Maas was supported by Rubicon subsidy 680-50-0901 of the Netherlands Organisation for Scientific Research (NWO). J. van Neerven was supported by VICI subsidy 639.033.604 of the Netherlands Organisation for Scientific Research (NWO). author: - first_name: Jan full_name: Jan Maas id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Jan full_name: van Neerven, Jan M last_name: Van Neerven - first_name: Pierre full_name: Portal, Pierre last_name: Portal citation: ama: Maas J, Van Neerven J, Portal P. Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure. Arkiv för Matematik. 2012;50(2):379-395. doi:10.1007/s11512-010-0143-z apa: Maas, J., Van Neerven, J., & Portal, P. (2012). Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure. Arkiv För Matematik. Springer. https://doi.org/10.1007/s11512-010-0143-z chicago: Maas, Jan, Jan Van Neerven, and Pierre Portal. “Whitney Coverings and the Tent Spaces T 1,q (γ) for the Gaussian Measure.” Arkiv För Matematik. Springer, 2012. https://doi.org/10.1007/s11512-010-0143-z. ieee: J. Maas, J. Van Neerven, and P. Portal, “Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure,” Arkiv för Matematik, vol. 50, no. 2. Springer, pp. 379–395, 2012. ista: Maas J, Van Neerven J, Portal P. 2012. Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure. Arkiv för Matematik. 50(2), 379–395. mla: Maas, Jan, et al. “Whitney Coverings and the Tent Spaces T 1,q (γ) for the Gaussian Measure.” Arkiv För Matematik, vol. 50, no. 2, Springer, 2012, pp. 379–95, doi:10.1007/s11512-010-0143-z. short: J. Maas, J. Van Neerven, P. Portal, Arkiv För Matematik 50 (2012) 379–395. date_created: 2018-12-11T11:55:52Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T06:55:28Z day: '01' doi: 10.1007/s11512-010-0143-z extern: 1 intvolume: ' 50' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1002.4911 month: '10' oa: 1 page: 379 - 395 publication: Arkiv för Matematik publication_status: published publisher: Springer publist_id: '4907' quality_controlled: 0 status: public title: Whitney coverings and the tent spaces T 1,q (γ) for the Gaussian measure type: journal_article volume: 50 year: '2012' ... --- _id: '2203' abstract: - lang: eng text: We show that the electric dipole-dipole interaction between a pair of polar molecules undergoes an all-out transformation when superimposed by a far-off-resonant optical field. The combined interaction potential becomes tunable by variation of wavelength, polarisation and intensity of the optical field and its dependence on the intermolecular separation exhibits a crossover from an inverse-power to an oscillating behaviour. The ability thereby offered to control molecular interactions opens up avenues toward the creation and manipulation of novel phases of ultracold polar gases among whose characteristics is a long-range entanglement of the dipoles' mutual orientation. We devised an accurate analytic model of such optical-field-dressed dipole-dipole interaction potentials, which enables a straightforward access to the optical-field parameters required for the design of intermolecular interactions in the laboratory. author: - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Břetislav full_name: Friedrich, Břetislav last_name: Friedrich citation: ama: 'Lemeshko M, Friedrich B. Interaction between polar molecules subject to a far-off-resonant optical field: Entangled dipoles up- or down-holding each other. Molecular Physics. 2012;110(15-16):1873-1881. doi:10.1080/00268976.2012.689868' apa: 'Lemeshko, M., & Friedrich, B. (2012). Interaction between polar molecules subject to a far-off-resonant optical field: Entangled dipoles up- or down-holding each other. Molecular Physics. Taylor & Francis. https://doi.org/10.1080/00268976.2012.689868' chicago: 'Lemeshko, Mikhail, and Břetislav Friedrich. “Interaction between Polar Molecules Subject to a Far-off-Resonant Optical Field: Entangled Dipoles up- or down-Holding Each Other.” Molecular Physics. Taylor & Francis, 2012. https://doi.org/10.1080/00268976.2012.689868.' ieee: 'M. Lemeshko and B. Friedrich, “Interaction between polar molecules subject to a far-off-resonant optical field: Entangled dipoles up- or down-holding each other,” Molecular Physics, vol. 110, no. 15–16. Taylor & Francis, pp. 1873–1881, 2012.' ista: 'Lemeshko M, Friedrich B. 2012. Interaction between polar molecules subject to a far-off-resonant optical field: Entangled dipoles up- or down-holding each other. Molecular Physics. 110(15–16), 1873–1881.' mla: 'Lemeshko, Mikhail, and Břetislav Friedrich. “Interaction between Polar Molecules Subject to a Far-off-Resonant Optical Field: Entangled Dipoles up- or down-Holding Each Other.” Molecular Physics, vol. 110, no. 15–16, Taylor & Francis, 2012, pp. 1873–81, doi:10.1080/00268976.2012.689868.' short: M. Lemeshko, B. Friedrich, Molecular Physics 110 (2012) 1873–1881. date_created: 2018-12-11T11:56:18Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T06:55:58Z day: '01' doi: 10.1080/00268976.2012.689868 extern: 1 intvolume: ' 110' issue: 15-16 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1108.4583 month: '01' oa: 1 page: 1873 - 1881 publication: Molecular Physics publication_status: published publisher: Taylor & Francis publist_id: '4770' quality_controlled: 0 status: public title: 'Interaction between polar molecules subject to a far-off-resonant optical field: Entangled dipoles up- or down-holding each other' type: journal_article volume: 110 year: '2012' ... --- _id: '2201' abstract: - lang: eng text: We study the growth dynamics of ordered structures of strongly interacting polar molecules in optical lattices. Using a dipole blockade of microwave excitations, we map the system onto an interacting spin-1/2 model possessing ground states with crystalline order, and describe a way to prepare these states by nonadiabatically driving the transitions between molecular rotational levels. The proposed technique bypasses the need to cross a phase transition and allows for the creation of ordered domains of considerably larger size compared to approaches relying on adiabatic preparation. article_processing_charge: No author: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Roman full_name: Krems, Roman last_name: Krems - first_name: Hendrik full_name: Weimer, Hendrik last_name: Weimer citation: ama: Lemeshko M, Krems R, Weimer H. Nonadiabatic preparation of spin crystals with ultracold polar molecules. Physical Review Letters. 2012;109(3). doi:10.1103/PhysRevLett.109.035301 apa: Lemeshko, M., Krems, R., & Weimer, H. (2012). Nonadiabatic preparation of spin crystals with ultracold polar molecules. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.035301 chicago: Lemeshko, Mikhail, Roman Krems, and Hendrik Weimer. “Nonadiabatic Preparation of Spin Crystals with Ultracold Polar Molecules.” Physical Review Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.035301. ieee: M. Lemeshko, R. Krems, and H. Weimer, “Nonadiabatic preparation of spin crystals with ultracold polar molecules,” Physical Review Letters, vol. 109, no. 3. American Physical Society, 2012. ista: Lemeshko M, Krems R, Weimer H. 2012. Nonadiabatic preparation of spin crystals with ultracold polar molecules. Physical Review Letters. 109(3). mla: Lemeshko, Mikhail, et al. “Nonadiabatic Preparation of Spin Crystals with Ultracold Polar Molecules.” Physical Review Letters, vol. 109, no. 3, American Physical Society, 2012, doi:10.1103/PhysRevLett.109.035301. short: M. Lemeshko, R. Krems, H. Weimer, Physical Review Letters 109 (2012). date_created: 2018-12-11T11:56:17Z date_published: 2012-07-16T00:00:00Z date_updated: 2021-11-16T08:01:02Z day: '16' doi: 10.1103/PhysRevLett.109.035301 extern: '1' intvolume: ' 109' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1203.0010 month: '07' oa: 1 oa_version: None publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '4772' related_material: link: - relation: erratum url: https://doi.org/10.1103/PhysRevLett.109.049901 status: public title: Nonadiabatic preparation of spin crystals with ultracold polar molecules type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 109 year: '2012' ... --- _id: '2202' abstract: - lang: eng text: We propose a method for sensitive parallel detection of low-frequency electromagnetic fields based on the fine structure interactions in paramagnetic polar molecules. Compared to the recently implemented scheme employing ultracold 87Rb atoms by Böhi, the technique based on molecules offers a 100-fold higher sensitivity, the possibility to measure both the electric and magnetic field components, and a probe of a wide range of frequencies from the dc limit to the THz regime. author: - first_name: Sergey full_name: Alyabyshev, Sergey V last_name: Alyabyshev - first_name: Mikhail full_name: Mikhail Lemeshko id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 - first_name: Roman full_name: Krems, Roman V last_name: Krems citation: ama: Alyabyshev S, Lemeshko M, Krems R. Sensitive imaging of electromagnetic fields with paramagnetic polar molecules. Physical Review A - Atomic, Molecular, and Optical Physics. 2012;86(1). doi:10.1103/PhysRevA.86.013409 apa: Alyabyshev, S., Lemeshko, M., & Krems, R. (2012). Sensitive imaging of electromagnetic fields with paramagnetic polar molecules. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.86.013409 chicago: Alyabyshev, Sergey, Mikhail Lemeshko, and Roman Krems. “Sensitive Imaging of Electromagnetic Fields with Paramagnetic Polar Molecules.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2012. https://doi.org/10.1103/PhysRevA.86.013409. ieee: S. Alyabyshev, M. Lemeshko, and R. Krems, “Sensitive imaging of electromagnetic fields with paramagnetic polar molecules,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 86, no. 1. American Physical Society, 2012. ista: Alyabyshev S, Lemeshko M, Krems R. 2012. Sensitive imaging of electromagnetic fields with paramagnetic polar molecules. Physical Review A - Atomic, Molecular, and Optical Physics. 86(1). mla: Alyabyshev, Sergey, et al. “Sensitive Imaging of Electromagnetic Fields with Paramagnetic Polar Molecules.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 86, no. 1, American Physical Society, 2012, doi:10.1103/PhysRevA.86.013409. short: S. Alyabyshev, M. Lemeshko, R. Krems, Physical Review A - Atomic, Molecular, and Optical Physics 86 (2012). date_created: 2018-12-11T11:56:18Z date_published: 2012-07-13T00:00:00Z date_updated: 2021-01-12T06:55:57Z day: '13' doi: 10.1103/PhysRevA.86.013409 extern: 1 intvolume: ' 86' issue: '1' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1202.1857 month: '07' oa: 1 publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '4773' quality_controlled: 0 status: public title: Sensitive imaging of electromagnetic fields with paramagnetic polar molecules type: journal_article volume: 86 year: '2012' ... --- _id: '2263' 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. author: - first_name: Huixuan full_name: Liang, Huixuan last_name: Liang - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: H. full_name: Ghashghaei, H. last_name: Ghashghaei citation: ama: Liang H, Hippenmeyer S, Ghashghaei H. A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. Biology open. 2012;1(12):1200-1203. doi:10.1242/bio.20122287 apa: Liang, H., Hippenmeyer, S., & Ghashghaei, H. (2012). A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors. Biology Open. The Company of Biologists. https://doi.org/10.1242/bio.20122287 chicago: Liang, Huixuan, Simon Hippenmeyer, and H. Ghashghaei. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.” Biology Open. The Company of Biologists, 2012. https://doi.org/10.1242/bio.20122287. ieee: H. Liang, S. Hippenmeyer, and H. Ghashghaei, “A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors,” Biology open, vol. 1, no. 12. The Company of Biologists, pp. 1200–1203, 2012. 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. mla: Liang, Huixuan, et al. “A Nestin-Cre Transgenic Mouse Is Insufficient for Recombination in Early Embryonic Neural Progenitors.” Biology Open, vol. 1, no. 12, The Company of Biologists, 2012, pp. 1200–03, doi:10.1242/bio.20122287. short: H. Liang, S. Hippenmeyer, H. Ghashghaei, Biology Open 1 (2012) 1200–1203. date_created: 2018-12-11T11:56:38Z date_published: 2012-12-15T00:00:00Z date_updated: 2021-01-12T06:56:23Z day: '15' ddc: - '576' department: - _id: SiHi doi: 10.1242/bio.20122287 file: - access_level: open_access checksum: 605a1800b81227848c361fd6ba7d22ba content_type: application/pdf creator: system date_created: 2018-12-12T10:13:09Z date_updated: 2020-07-14T12:45:35Z file_id: '4990' file_name: IST-2015-387-v1+1_1200.full.pdf file_size: 726695 relation: main_file file_date_updated: 2020-07-14T12:45:35Z has_accepted_license: '1' intvolume: ' 1' issue: '12' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '12' oa: 1 oa_version: Published Version page: 1200 - 1203 publication: Biology open publication_status: published publisher: The Company of Biologists publist_id: '4682' pubrep_id: '387' quality_controlled: '1' scopus_import: 1 status: public title: A Nestin-cre transgenic mouse is insufficient for recombination in early embryonic neural progenitors tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2012' ... --- _id: '2267' abstract: - lang: eng text: 'Capturing real-world objects with laser-scanning technology has become an everyday task. Recently, the acquisition of dynamic scenes at interactive frame rates has become feasible. A high-quality visualization of the resulting point cloud stream would require a per-frame reconstruction of object surfaces. Unfortunately, reconstruction computations are still too time-consuming to be applied interactively. In this paper we present a local surface reconstruction and visualization technique that provides interactive feedback for reasonably sized point clouds, while achieving high image quality. Our method is performed entirely on the GPU and in screen pace, exploiting the efficiency of the common rasterization pipeline. The approach is very general, as no assumption is made about point connectivity or sampling density. This naturally allows combining the outputs of multiple scanners in a single visualization, which is useful for many virtual and augmented reality applications. ' author: - first_name: Reinhold full_name: Preiner, Reinhold last_name: Preiner - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Michael full_name: Wimmer, Michael last_name: Wimmer citation: ama: 'Preiner R, Jeschke S, Wimmer M. Auto splats: Dynamic point cloud visualization on the GPU. In: Eurographics Association; 2012:139-148. doi:10.2312/EGPGV/EGPGV12/139-148' apa: 'Preiner, R., Jeschke, S., & Wimmer, M. (2012). Auto splats: Dynamic point cloud visualization on the GPU (pp. 139–148). Presented at the EGPGV: Eurographics Symposium on Parallel Graphics and Visualization, Calgari, Italy: Eurographics Association. https://doi.org/10.2312/EGPGV/EGPGV12/139-148' chicago: 'Preiner, Reinhold, Stefan Jeschke, and Michael Wimmer. “Auto Splats: Dynamic Point Cloud Visualization on the GPU,” 139–48. Eurographics Association, 2012. https://doi.org/10.2312/EGPGV/EGPGV12/139-148.' ieee: 'R. Preiner, S. Jeschke, and M. Wimmer, “Auto splats: Dynamic point cloud visualization on the GPU,” presented at the EGPGV: Eurographics Symposium on Parallel Graphics and Visualization, Calgari, Italy, 2012, pp. 139–148.' ista: 'Preiner R, Jeschke S, Wimmer M. 2012. Auto splats: Dynamic point cloud visualization on the GPU. EGPGV: Eurographics Symposium on Parallel Graphics and Visualization, 139–148.' mla: 'Preiner, Reinhold, et al. Auto Splats: Dynamic Point Cloud Visualization on the GPU. Eurographics Association, 2012, pp. 139–48, doi:10.2312/EGPGV/EGPGV12/139-148.' short: R. Preiner, S. Jeschke, M. Wimmer, in:, Eurographics Association, 2012, pp. 139–148. conference: end_date: 2012-05-14 location: Calgari, Italy name: 'EGPGV: Eurographics Symposium on Parallel Graphics and Visualization' start_date: 2012-05-13 date_created: 2018-12-11T11:56:40Z date_published: 2012-05-13T00:00:00Z date_updated: 2021-01-12T06:56:24Z day: '13' ddc: - '000' doi: 10.2312/EGPGV/EGPGV12/139-148 extern: '1' file: - access_level: open_access checksum: 5495bb6ee8662cd401b34afb04dfb40f content_type: application/pdf creator: system date_created: 2018-12-12T10:11:13Z date_updated: 2020-07-14T12:45:35Z file_id: '4866' file_name: IST-2016-572-v1+1_preiner_2012_AS-draft.pdf file_size: 14903860 relation: main_file file_date_updated: 2020-07-14T12:45:35Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 139 - 148 publication_status: published publisher: Eurographics Association publist_id: '4677' pubrep_id: '572' quality_controlled: '1' status: public title: 'Auto splats: Dynamic point cloud visualization on the GPU' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2012' ... --- _id: '2262' abstract: - lang: eng text: 'Mosaic Analysis with Double Markers (MADM) is a method for generating genetically mosaic mice, in which sibling mutant and wild-type cells are labeled with different fluorescent markers. It is a powerful tool that enables analysis of gene function at the single cell level in vivo. It requires transgenic cassettes to be located between the centromere and the mutation in the gene of interest on the same chromosome. Here we compare procedures for introduction of MADM cassettes into new loci in the mouse genome, and describe new approaches for expanding the utility of MADM. We show that: 1) Targeted homologous recombination outperforms random transgenesis in generation of reliably expressed MADM cassettes, 2) MADM cassettes in new genomic loci need to be validated for biallelic and ubiquitous expression, 3) Recombination between MADM cassettes on different chromosomes can be used to study reciprocal chromosomal deletions/duplications, and 4) MADM can be modified to permit transgene expression by combining it with a binary expression system. The advances described in this study expand current, and enable new and more versatile applications of MADM.' acknowledgement: This work was supported by a National Institutes of Health grant to LL (R01-NS050835). BT was a Damon Runyon Fellow and was supported by the Damon Runyon Cancer Research Foundation Grant DRG-1819-04. KM was supported by the Japan Society for the Promotion of Science program for Research Abroad and Human Frontier Science Program Organization (LT00300/2007-L). SH was supported by postdoctoral fellowships from the European Molecular Biology Organization (ALTF 851-2005), Human Frontier Science Program Organization (LT00805/2006-L), and Swiss National Science Foundation (PA00P3_124160 and PA00P3_136482). HZ is a Pew Scholar in Biomedical Sciences, supported by The Pew Charitable Trusts. LL is an investigator of the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. author: - first_name: Bosiljka full_name: Tasic, Bosiljka last_name: Tasic - first_name: Kazunari full_name: Miyamichi, Kazunari last_name: Miyamichi - first_name: Simon full_name: Simon Hippenmeyer id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Vardhan full_name: Dani, Vardhan S. last_name: Dani - first_name: H. full_name: Zeng, H. last_name: Zeng - first_name: William full_name: Joo, William last_name: Joo - first_name: Hui full_name: Zong, Hui last_name: Zong - first_name: Yanru full_name: Chen-Tsai, Yanru last_name: Chen Tsai - first_name: Liqun full_name: Luo, Liqun last_name: Luo citation: ama: Tasic B, Miyamichi K, Hippenmeyer S, et al. Extensions of MADM (Mosaic Analysis with Double Markers) in Mice . PLoS One. 2012;7(3). doi:10.1371/journal.pone.0033332 apa: Tasic, B., Miyamichi, K., Hippenmeyer, S., Dani, V., Zeng, H., Joo, W., … Luo, L. (2012). Extensions of MADM (Mosaic Analysis with Double Markers) in Mice . PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0033332 chicago: Tasic, Bosiljka, Kazunari Miyamichi, Simon Hippenmeyer, Vardhan Dani, H. Zeng, William Joo, Hui Zong, Yanru Chen Tsai, and Liqun Luo. “Extensions of MADM (Mosaic Analysis with Double Markers) in Mice .” PLoS One. Public Library of Science, 2012. https://doi.org/10.1371/journal.pone.0033332. ieee: B. Tasic et al., “Extensions of MADM (Mosaic Analysis with Double Markers) in Mice ,” PLoS One, vol. 7, no. 3. Public Library of Science, 2012. ista: Tasic B, Miyamichi K, Hippenmeyer S, Dani V, Zeng H, Joo W, Zong H, Chen Tsai Y, Luo L. 2012. Extensions of MADM (Mosaic Analysis with Double Markers) in Mice . PLoS One. 7(3). mla: Tasic, Bosiljka, et al. “Extensions of MADM (Mosaic Analysis with Double Markers) in Mice .” PLoS One, vol. 7, no. 3, Public Library of Science, 2012, doi:10.1371/journal.pone.0033332. short: B. Tasic, K. Miyamichi, S. Hippenmeyer, V. Dani, H. Zeng, W. Joo, H. Zong, Y. Chen Tsai, L. Luo, PLoS One 7 (2012). date_created: 2018-12-11T11:56:38Z date_published: 2012-03-27T00:00:00Z date_updated: 2021-01-12T06:56:22Z day: '27' doi: 10.1371/journal.pone.0033332 extern: 1 intvolume: ' 7' issue: '3' month: '03' publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '4683' quality_controlled: 0 status: public title: 'Extensions of MADM (Mosaic Analysis with Double Markers) in Mice ' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 7 year: '2012' ... --- _id: '2268' abstract: - lang: eng text: 'This paper presents an analytic formulation for anti-aliased sampling of 2D polygons and 3D polyhedra. Our framework allows the exact evaluation of the convolution integral with a linear function defined on the polytopes. The filter is a spherically symmetric polynomial of any order, supporting approximations to refined variants such as the Mitchell-Netravali filter family. This enables high-quality rasterization of triangles and tetrahedra with linearly interpolated vertex values to regular and non-regular grids. A closed form solution of the convolution is presented and an efficient implementation on the GPU using DirectX and CUDA C is described. ' acknowledgement: |- Funding was provided by the FWF grant P20768-N13. We want to thank the reviewers for their insightful and helpful remarks, Hang Si for making available TetGen and Stefan Bruckner for VolumeShop. alternative_title: - Computer Graphics Forum author: - first_name: Thomas full_name: Thomas Auzinger id: 4718F954-F248-11E8-B48F-1D18A9856A87 last_name: Auzinger orcid: 0000-0002-1546-3265 - first_name: Michael full_name: Guthe, Michael last_name: Guthe - first_name: Stefan full_name: Stefan Jeschke id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke citation: ama: 'Auzinger T, Guthe M, Jeschke S. Analytic anti-aliasing of linear functions on polytopes. In: Vol 31. Wiley-Blackwell; 2012:335-344. doi:http://dx.doi.org/10.1111/j.1467-8659.2012.03012.x' apa: 'Auzinger, T., Guthe, M., & Jeschke, S. (2012). Analytic anti-aliasing of linear functions on polytopes (Vol. 31, pp. 335–344). Presented at the EUROGRAPHICS: European Association for Computer Graphics, Wiley-Blackwell. http://dx.doi.org/10.1111/j.1467-8659.2012.03012.x' chicago: Auzinger, Thomas, Michael Guthe, and Stefan Jeschke. “Analytic Anti-Aliasing of Linear Functions on Polytopes,” 31:335–44. Wiley-Blackwell, 2012. http://dx.doi.org/10.1111/j.1467-8659.2012.03012.x. ieee: 'T. Auzinger, M. Guthe, and S. Jeschke, “Analytic anti-aliasing of linear functions on polytopes,” presented at the EUROGRAPHICS: European Association for Computer Graphics, 2012, vol. 31, no. 121, pp. 335–344.' ista: 'Auzinger T, Guthe M, Jeschke S. 2012. Analytic anti-aliasing of linear functions on polytopes. EUROGRAPHICS: European Association for Computer Graphics, Computer Graphics Forum, vol. 31, 335–344.' mla: Auzinger, Thomas, et al. Analytic Anti-Aliasing of Linear Functions on Polytopes. Vol. 31, no. 121, Wiley-Blackwell, 2012, pp. 335–44, doi:http://dx.doi.org/10.1111/j.1467-8659.2012.03012.x. short: T. Auzinger, M. Guthe, S. Jeschke, in:, Wiley-Blackwell, 2012, pp. 335–344. conference: name: 'EUROGRAPHICS: European Association for Computer Graphics' date_created: 2018-12-11T11:56:40Z date_published: 2012-05-13T00:00:00Z date_updated: 2021-01-12T06:56:24Z day: '13' doi: http://dx.doi.org/10.1111/j.1467-8659.2012.03012.x extern: 1 intvolume: ' 31' issue: 121 main_file_link: - open_access: '1' url: https://www.cg.tuwien.ac.at/research/publications/2012/Auzinger_2012_AAA/ month: '05' oa: 1 page: 335 - 344 publication_status: published publisher: Wiley-Blackwell publist_id: '4676' quality_controlled: 0 status: public title: Analytic anti-aliasing of linear functions on polytopes type: conference volume: 31 year: '2012' ... --- _id: '2302' abstract: - lang: eng text: 'We introduce propagation models (PMs), a formalism able to express several kinds of equations that describe the behavior of biochemical reaction networks. Furthermore, we introduce the propagation abstract data type (PADT), which separates concerns regarding different numerical algorithms for the transient analysis of biochemical reaction networks from concerns regarding their implementation, thus allowing for portable and efficient solutions. The state of a propagation abstract data type is given by a vector that assigns mass values to a set of nodes, and its (next) operator propagates mass values through this set of nodes. We propose an approximate implementation of the (next) operator, based on threshold abstraction, which propagates only "significant" mass values and thus achieves a compromise between efficiency and accuracy. Finally, we give three use cases for propagation models: the chemical master equation (CME), the reaction rate equation (RRE), and a hybrid method that combines these two equations. These three applications use propagation models in order to propagate probabilities and/or expected values and variances of the model''s variables.' author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Maria full_name: Mateescu, Maria id: 3B43276C-F248-11E8-B48F-1D18A9856A87 last_name: Mateescu citation: ama: Henzinger TA, Mateescu M. The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. 2012;10(2):310-322. doi:10.1109/TCBB.2012.91 apa: Henzinger, T. A., & Mateescu, M. (2012). The propagation approach for computing biochemical reaction networks. IEEE ACM Transactions on Computational Biology and Bioinformatics. IEEE. https://doi.org/10.1109/TCBB.2012.91 chicago: Henzinger, Thomas A, and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” IEEE ACM Transactions on Computational Biology and Bioinformatics. IEEE, 2012. https://doi.org/10.1109/TCBB.2012.91. ieee: T. A. Henzinger and M. Mateescu, “The propagation approach for computing biochemical reaction networks,” IEEE ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 2. IEEE, pp. 310–322, 2012. 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. mla: Henzinger, Thomas A., and Maria Mateescu. “The Propagation Approach for Computing Biochemical Reaction Networks.” IEEE ACM Transactions on Computational Biology and Bioinformatics, vol. 10, no. 2, IEEE, 2012, pp. 310–22, doi:10.1109/TCBB.2012.91. short: T.A. Henzinger, M. Mateescu, IEEE ACM Transactions on Computational Biology and Bioinformatics 10 (2012) 310–322. date_created: 2018-12-11T11:56:52Z date_published: 2012-07-03T00:00:00Z date_updated: 2021-01-12T06:56:38Z day: '03' department: - _id: ToHe - _id: CaGu doi: 10.1109/TCBB.2012.91 ec_funded: 1 external_id: pmid: - '22778152' intvolume: ' 10' issue: '2' language: - iso: eng month: '07' oa_version: None page: 310 - 322 pmid: 1 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: IEEE ACM Transactions on Computational Biology and Bioinformatics publication_status: published publisher: IEEE publist_id: '4625' quality_controlled: '1' scopus_import: 1 status: public title: The propagation approach for computing biochemical reaction networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2012' ... --- _id: '2313' abstract: - lang: eng text: The translation of "next-generation" sequencing directly to the clinic is still being assessed but has the potential for genetic diseases to reduce costs, advance accuracy, and point to unsuspected yet treatable conditions. To study its capability in the clinic, we performed whole-exome sequencing in 118 probands with a diagnosis of a pediatric-onset neurodevelopmental disease in which most known causes had been excluded. Twenty-two genes not previously identified as disease-causing were identified in this study (19% of cohort), further establishing exome sequencing as a useful tool for gene discovery. New genes identified included EXOC8 in Joubert syndrome and GFM2 in a patient with microcephaly, simplified gyral pattern, and insulin-dependent diabetes. Exome sequencing uncovered 10 probands (8% of cohort) with mutations in genes known to cause a disease different from the initial diagnosis. Upon further medical evaluation, these mutations were found to account for each proband's disease, leading to a change in diagnosis, some of which led to changes in patient management. Our data provide proof of principle that genomic strategies are useful in clarifying diagnosis in a proportion of patients with neurodevelopmental disorders. author: - first_name: Tracy full_name: Dixon-Salazar, Tracy J last_name: Dixon Salazar - first_name: Jennifer full_name: Silhavy, Jennifer L last_name: Silhavy - first_name: Nitin full_name: Udpa, Nitin last_name: Udpa - first_name: Jana full_name: Schroth, Jana last_name: Schroth - first_name: Stephanie full_name: Bielas, Stephanie L last_name: Bielas - first_name: Ashleigh full_name: Schaffer, Ashleigh E last_name: Schaffer - first_name: Jesus full_name: Olvera, Jesus last_name: Olvera - first_name: Vineet full_name: Bafna, Vineet K last_name: Bafna - first_name: Maha full_name: Zaki, Maha S last_name: Zaki - first_name: Ghada full_name: Abdel-Salam, Ghada M last_name: Abdel Salam - first_name: Lobna full_name: Mansour, Lobna A last_name: Mansour - first_name: Laila full_name: Selim, Laila A last_name: Selim - first_name: Sawsan full_name: Abdel-Hadi, Sawsan S last_name: Abdel Hadi - first_name: Naima full_name: Marzouki, Naima last_name: Marzouki - first_name: Tawfeg full_name: Ben-Omran, Tawfeg I last_name: Ben Omran - first_name: Nouriya full_name: Al-Saana, Nouriya A last_name: Al Saana - first_name: Fatma full_name: Sönmez, Fatma M last_name: Sönmez - first_name: Figen full_name: Celep, Figen last_name: Celep - first_name: Matloob full_name: Azam, Matloob last_name: Azam - first_name: Kiley full_name: Hill, Kiley J last_name: Hill - first_name: Adrienne full_name: Collazo, Adrienne last_name: Collazo - first_name: Ali full_name: Fenstermaker, Ali G last_name: Fenstermaker - first_name: Gaia full_name: Gaia Novarino id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Naiara full_name: Akizu, Naiara last_name: Akizu - first_name: Kiran full_name: Garimella, Kiran V last_name: Garimella - first_name: Carrie full_name: Sougnez, Carrie L last_name: Sougnez - first_name: Carsten full_name: Russ, Carsten last_name: Russ - first_name: Stacey full_name: Gabriel, Stacey B last_name: Gabriel - first_name: Joseph full_name: Gleeson, Joseph G last_name: Gleeson citation: ama: Dixon Salazar T, Silhavy J, Udpa N, et al. Exome sequencing can improve diagnosis and alter patient management. Science Translational Medicine. 2012;4(138). doi:10.1126/scitranslmed.3003544 apa: Dixon Salazar, T., Silhavy, J., Udpa, N., Schroth, J., Bielas, S., Schaffer, A., … Gleeson, J. (2012). Exome sequencing can improve diagnosis and alter patient management. Science Translational Medicine. American Association for the Advancement of Science. https://doi.org/10.1126/scitranslmed.3003544 chicago: Dixon Salazar, Tracy, Jennifer Silhavy, Nitin Udpa, Jana Schroth, Stephanie Bielas, Ashleigh Schaffer, Jesus Olvera, et al. “Exome Sequencing Can Improve Diagnosis and Alter Patient Management.” Science Translational Medicine. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/scitranslmed.3003544. ieee: T. Dixon Salazar et al., “Exome sequencing can improve diagnosis and alter patient management,” Science Translational Medicine, vol. 4, no. 138. American Association for the Advancement of Science, 2012. ista: Dixon Salazar T, Silhavy J, Udpa N, Schroth J, Bielas S, Schaffer A, Olvera J, Bafna V, Zaki M, Abdel Salam G, Mansour L, Selim L, Abdel Hadi S, Marzouki N, Ben Omran T, Al Saana N, Sönmez F, Celep F, Azam M, Hill K, Collazo A, Fenstermaker A, Novarino G, Akizu N, Garimella K, Sougnez C, Russ C, Gabriel S, Gleeson J. 2012. Exome sequencing can improve diagnosis and alter patient management. Science Translational Medicine. 4(138). mla: Dixon Salazar, Tracy, et al. “Exome Sequencing Can Improve Diagnosis and Alter Patient Management.” Science Translational Medicine, vol. 4, no. 138, American Association for the Advancement of Science, 2012, doi:10.1126/scitranslmed.3003544. short: T. Dixon Salazar, J. Silhavy, N. Udpa, J. Schroth, S. Bielas, A. Schaffer, J. Olvera, V. Bafna, M. Zaki, G. Abdel Salam, L. Mansour, L. Selim, S. Abdel Hadi, N. Marzouki, T. Ben Omran, N. Al Saana, F. Sönmez, F. Celep, M. Azam, K. Hill, A. Collazo, A. Fenstermaker, G. Novarino, N. Akizu, K. Garimella, C. Sougnez, C. Russ, S. Gabriel, J. Gleeson, Science Translational Medicine 4 (2012). date_created: 2018-12-11T11:56:56Z date_published: 2012-06-13T00:00:00Z date_updated: 2021-01-12T06:56:43Z day: '13' doi: 10.1126/scitranslmed.3003544 extern: 1 intvolume: ' 4' issue: '138' month: '06' publication: Science Translational Medicine publication_status: published publisher: American Association for the Advancement of Science publist_id: '4614' quality_controlled: 0 status: public title: Exome sequencing can improve diagnosis and alter patient management type: journal_article volume: 4 year: '2012' ... --- _id: '2314' abstract: - lang: eng text: Autism spectrum disorders are a genetically heterogeneous constellation of syndromes characterized by impairments in reciprocal social interaction. Available somatic treatments have limited efficacy. We have identified inactivating mutations in the gene BCKDK (Branched Chain Ketoacid Dehydrogenase Kinase) in consanguineous families with autism, epilepsy, and intellectual disability. The encoded protein is responsible for phosphorylation-mediated inactivation of the E1α subunit of branched-chain ketoacid dehydrogenase (BCKDH). Patients with homozygous BCKDK mutations display reductions in BCKDK messenger RNA and protein, E1α phosphorylation, and plasma branched-chain amino acids. Bckdk knockout mice show abnormal brain amino acid profiles and neurobehavioral deficits that respond to dietary supplementation. Thus, autism presenting with intellectual disability and epilepsy caused by BCKDK mutations represents a potentially treatable syndrome. author: - first_name: Gaia full_name: Gaia Novarino id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Paul full_name: El-Fishawy, Paul last_name: El Fishawy - first_name: Hülya full_name: Kayserili, Hülya last_name: Kayserili - first_name: Nagwa full_name: Meguid, Nagwa A last_name: Meguid - first_name: Eric full_name: Scott, Eric M last_name: Scott - first_name: Jana full_name: Schroth, Jana last_name: Schroth - first_name: Jennifer full_name: Silhavy, Jennifer L last_name: Silhavy - first_name: Majdi full_name: Kara, Majdi last_name: Kara - first_name: Rehab full_name: Khalil, Rehab O last_name: Khalil - first_name: Tawfeg full_name: Ben-Omran, Tawfeg I last_name: Ben Omran - first_name: Adife full_name: Ercan-Sencicek, Adife G last_name: Ercan Sencicek - first_name: Adel full_name: Hashish, Adel F last_name: Hashish - first_name: Stephan full_name: Sanders, Stephan J last_name: Sanders - first_name: Abha full_name: Gupta, Abha R last_name: Gupta - first_name: Hebatalla full_name: Hashem, Hebatalla S last_name: Hashem - first_name: Dietrich full_name: Matern, Dietrich last_name: Matern - first_name: Stacey full_name: Gabriel, Stacey B last_name: Gabriel - first_name: Lawrence full_name: Sweetman, Lawrence last_name: Sweetman - first_name: Yasmeen full_name: Rahimi, Yasmeen last_name: Rahimi - first_name: Robert full_name: Harris, Robert A last_name: Harris - first_name: Matthew full_name: State, Matthew W last_name: State - first_name: Joseph full_name: Gleeson, Joseph G last_name: Gleeson citation: ama: Novarino G, El Fishawy P, Kayserili H, et al. Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy. Science. 2012;338(6105):394-397. doi:10.1126/science.1224631 apa: Novarino, G., El Fishawy, P., Kayserili, H., Meguid, N., Scott, E., Schroth, J., … Gleeson, J. (2012). Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1224631 chicago: Novarino, Gaia, Paul El Fishawy, Hülya Kayserili, Nagwa Meguid, Eric Scott, Jana Schroth, Jennifer Silhavy, et al. “Mutations in BCKD-Kinase Lead to a Potentially Treatable Form of Autism with Epilepsy.” Science. American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224631. ieee: G. Novarino et al., “Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy,” Science, vol. 338, no. 6105. American Association for the Advancement of Science, pp. 394–397, 2012. ista: Novarino G, El Fishawy P, Kayserili H, Meguid N, Scott E, Schroth J, Silhavy J, Kara M, Khalil R, Ben Omran T, Ercan Sencicek A, Hashish A, Sanders S, Gupta A, Hashem H, Matern D, Gabriel S, Sweetman L, Rahimi Y, Harris R, State M, Gleeson J. 2012. Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy. Science. 338(6105), 394–397. mla: Novarino, Gaia, et al. “Mutations in BCKD-Kinase Lead to a Potentially Treatable Form of Autism with Epilepsy.” Science, vol. 338, no. 6105, American Association for the Advancement of Science, 2012, pp. 394–97, doi:10.1126/science.1224631. short: G. Novarino, P. El Fishawy, H. Kayserili, N. Meguid, E. Scott, J. Schroth, J. Silhavy, M. Kara, R. Khalil, T. Ben Omran, A. Ercan Sencicek, A. Hashish, S. Sanders, A. Gupta, H. Hashem, D. Matern, S. Gabriel, L. Sweetman, Y. Rahimi, R. Harris, M. State, J. Gleeson, Science 338 (2012) 394–397. date_created: 2018-12-11T11:56:56Z date_published: 2012-10-19T00:00:00Z date_updated: 2021-01-12T06:56:43Z day: '19' doi: 10.1126/science.1224631 extern: 1 intvolume: ' 338' issue: '6105' month: '10' page: 394 - 397 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '4613' quality_controlled: 0 status: public title: Mutations in BCKD-kinase lead to a potentially treatable form of autism with epilepsy type: journal_article volume: 338 year: '2012' ... --- _id: '2318' 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. ' acknowledgement: 'Partial financial support by NSERC ' author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Seiringer R. Absence of bound states implies non-negativity of the scattering length. Journal of Spectral Theory. 2012;2(3):321-328. doi:10.4171/JST/31 apa: Seiringer, R. (2012). Absence of bound states implies non-negativity of the scattering length. Journal of Spectral Theory. European Mathematical Society. https://doi.org/10.4171/JST/31 chicago: Seiringer, Robert. “Absence of Bound States Implies Non-Negativity of the Scattering Length.” Journal of Spectral Theory. European Mathematical Society, 2012. https://doi.org/10.4171/JST/31. ieee: R. Seiringer, “Absence of bound states implies non-negativity of the scattering length,” Journal of Spectral Theory, vol. 2, no. 3. European Mathematical Society, pp. 321–328, 2012. ista: Seiringer R. 2012. Absence of bound states implies non-negativity of the scattering length. Journal of Spectral Theory. 2(3), 321–328. mla: Seiringer, Robert. “Absence of Bound States Implies Non-Negativity of the Scattering Length.” Journal of Spectral Theory, vol. 2, no. 3, European Mathematical Society, 2012, pp. 321–28, doi:10.4171/JST/31. short: R. Seiringer, Journal of Spectral Theory 2 (2012) 321–328. date_created: 2018-12-11T11:56:58Z date_published: 2012-06-24T00:00:00Z date_updated: 2021-01-12T06:56:44Z day: '24' department: - _id: RoSe doi: 10.4171/JST/31 intvolume: ' 2' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1204.0435 month: '06' oa: 1 oa_version: Preprint page: 321-328 publication: Journal of Spectral Theory publication_status: published publisher: European Mathematical Society publist_id: '4609' quality_controlled: '1' status: public title: Absence of bound states implies non-negativity of the scattering length type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2012' ... --- _id: '2317' abstract: - lang: eng text: 'We present a summary of our recent rigorous derivation of the celebrated Ginzburg-Landau (GL) theory, starting from the microscopic Bardeen-Cooper-Schrieffer (BCS) model. Close to the critical temperature, GL arises as an effective theory on the macroscopic scale. The relevant scaling limit is semiclassical in nature, and semiclassical analysis, with minimal regularity assumptions, plays an important part in our proof. ' author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jan full_name: Solovej, Jan P last_name: Solovej citation: ama: 'Frank R, Hainzl C, Seiringer R, Solovej J. Microscopic derivation of the Ginzburg-Landau model. In: World Scientific Publishing; 2012:575-583. doi:10.1142/9789814449243_0060' apa: 'Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2012). Microscopic derivation of the Ginzburg-Landau model (pp. 575–583). Presented at the ICMP: International Congress on Mathematical Physics, World Scientific Publishing. https://doi.org/10.1142/9789814449243_0060' chicago: Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “Microscopic Derivation of the Ginzburg-Landau Model,” 575–83. World Scientific Publishing, 2012. https://doi.org/10.1142/9789814449243_0060. ieee: 'R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “Microscopic derivation of the Ginzburg-Landau model,” presented at the ICMP: International Congress on Mathematical Physics, 2012, pp. 575–583.' ista: 'Frank R, Hainzl C, Seiringer R, Solovej J. 2012. Microscopic derivation of the Ginzburg-Landau model. ICMP: International Congress on Mathematical Physics, 575–583.' mla: Frank, Rupert, et al. Microscopic Derivation of the Ginzburg-Landau Model. World Scientific Publishing, 2012, pp. 575–83, doi:10.1142/9789814449243_0060. short: R. Frank, C. Hainzl, R. Seiringer, J. Solovej, in:, World Scientific Publishing, 2012, pp. 575–583. conference: name: 'ICMP: International Congress on Mathematical Physics' date_created: 2018-12-11T11:56:57Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T06:56:44Z day: '01' doi: 10.1142/9789814449243_0060 extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1209.1080 month: '08' oa: 1 page: 575 - 583 publication_status: published publisher: World Scientific Publishing publist_id: '4610' quality_controlled: 0 status: public title: Microscopic derivation of the Ginzburg-Landau model type: conference year: '2012' ... --- _id: '2316' abstract: - lang: eng text: 'We summarize our recent results on the ground state energy of multi-polaron systems. In particular, we discuss stability and existence of the thermodynamic limit, and we discuss the absence of binding in the case of large Coulomb repulsion and the corresponding binding-unbinding transition. We also consider the Pekar-Tomasevich approximation to the ground state energy and we study radial symmetry of the ground state density. ' author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Lawrence full_name: Thomas, Lawrence E last_name: Thomas citation: ama: 'Frank R, Lieb É, Seiringer R, Thomas L. Ground state properties of multi-polaron systems. In: World Scientific Publishing; 2012:477-485. doi:10.1142/9789814449243_0045' apa: 'Frank, R., Lieb, É., Seiringer, R., & Thomas, L. (2012). Ground state properties of multi-polaron systems (pp. 477–485). Presented at the ICMP: International Congress on Mathematical Physics, World Scientific Publishing. https://doi.org/10.1142/9789814449243_0045' chicago: Frank, Rupert, Élliott Lieb, Robert Seiringer, and Lawrence Thomas. “Ground State Properties of Multi-Polaron Systems,” 477–85. World Scientific Publishing, 2012. https://doi.org/10.1142/9789814449243_0045. ieee: 'R. Frank, É. Lieb, R. Seiringer, and L. Thomas, “Ground state properties of multi-polaron systems,” presented at the ICMP: International Congress on Mathematical Physics, 2012, pp. 477–485.' ista: 'Frank R, Lieb É, Seiringer R, Thomas L. 2012. Ground state properties of multi-polaron systems. ICMP: International Congress on Mathematical Physics, 477–485.' mla: Frank, Rupert, et al. Ground State Properties of Multi-Polaron Systems. World Scientific Publishing, 2012, pp. 477–85, doi:10.1142/9789814449243_0045. short: R. Frank, É. Lieb, R. Seiringer, L. Thomas, in:, World Scientific Publishing, 2012, pp. 477–485. conference: name: 'ICMP: International Congress on Mathematical Physics' date_created: 2018-12-11T11:56:57Z date_published: 2012-08-01T00:00:00Z date_updated: 2021-01-12T06:56:44Z day: '01' doi: 10.1142/9789814449243_0045 extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/1209.3717 month: '08' oa: 1 page: 477 - 485 publication_status: published publisher: World Scientific Publishing publist_id: '4611' quality_controlled: 0 status: public title: Ground state properties of multi-polaron systems type: conference year: '2012' ... --- _id: '237' abstract: - lang: eng text: The Manin conjecture is established for Châtelet surfaces over Q aris-ing as minimal proper smooth models of the surface Y 2 + Z 2 = f(X) in A 3 Q, where f ∈ Z[X] is a totally reducible polynomial of degree 3 without repeated roots. These surfaces do not satisfy weak approximation. acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council" author: - first_name: Régis full_name: de la Bretèche, Régis last_name: De La Bretèche - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Emmanuel full_name: Peyre, Emmanuel last_name: Peyre citation: ama: De La Bretèche R, Browning TD, Peyre E. On Manin’s conjecture for a family of Châtelet surfaces. Annals of Mathematics. 2012;175(1):297-343. doi:10.4007/annals.2012.175.1.8 apa: De La Bretèche, R., Browning, T. D., & Peyre, E. (2012). On Manin’s conjecture for a family of Châtelet surfaces. Annals of Mathematics. Princeton University Press. https://doi.org/10.4007/annals.2012.175.1.8 chicago: De La Bretèche, Régis, Timothy D Browning, and Emmanuel Peyre. “On Manin’s Conjecture for a Family of Châtelet Surfaces.” Annals of Mathematics. Princeton University Press, 2012. https://doi.org/10.4007/annals.2012.175.1.8. ieee: R. De La Bretèche, T. D. Browning, and E. Peyre, “On Manin’s conjecture for a family of Châtelet surfaces,” Annals of Mathematics, vol. 175, no. 1. Princeton University Press, pp. 297–343, 2012. ista: De La Bretèche R, Browning TD, Peyre E. 2012. On Manin’s conjecture for a family of Châtelet surfaces. Annals of Mathematics. 175(1), 297–343. mla: De La Bretèche, Régis, et al. “On Manin’s Conjecture for a Family of Châtelet Surfaces.” Annals of Mathematics, vol. 175, no. 1, Princeton University Press, 2012, pp. 297–343, doi:10.4007/annals.2012.175.1.8. short: R. De La Bretèche, T.D. Browning, E. Peyre, Annals of Mathematics 175 (2012) 297–343. date_created: 2018-12-11T11:45:22Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T06:57:04Z day: '01' doi: 10.4007/annals.2012.175.1.8 extern: 1 intvolume: ' 175' issue: '1' month: '01' page: 297 - 343 publication: Annals of Mathematics publication_status: published publisher: Princeton University Press publist_id: '7667' quality_controlled: 0 status: public title: On Manin's conjecture for a family of Châtelet surfaces type: journal_article volume: 175 year: '2012' ... --- _id: '238' abstract: - lang: eng text: For given positive integers a, b, q we investigate the density of solutions (x, y) ∈ Z2 to congruences ax + by2 ≡ 0 mod q. acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council" author: - first_name: Stephan full_name: Baier, Stephan last_name: Baier - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: Baier S, Browning TD. Inhomogeneous quadratic congruences. Functiones et Approximatio, Commentarii Mathematici. 2012;47(2):267-286. doi:10.7169/facm/2012.47.2.9 apa: Baier, S., & Browning, T. D. (2012). Inhomogeneous quadratic congruences. Functiones et Approximatio, Commentarii Mathematici. Adam Mickiewicz University Press. https://doi.org/10.7169/facm/2012.47.2.9 chicago: Baier, Stephan, and Timothy D Browning. “Inhomogeneous Quadratic Congruences.” Functiones et Approximatio, Commentarii Mathematici. Adam Mickiewicz University Press, 2012. https://doi.org/10.7169/facm/2012.47.2.9. ieee: S. Baier and T. D. Browning, “Inhomogeneous quadratic congruences,” Functiones et Approximatio, Commentarii Mathematici, vol. 47, no. 2. Adam Mickiewicz University Press, pp. 267–286, 2012. ista: Baier S, Browning TD. 2012. Inhomogeneous quadratic congruences. Functiones et Approximatio, Commentarii Mathematici. 47(2), 267–286. mla: Baier, Stephan, and Timothy D. Browning. “Inhomogeneous Quadratic Congruences.” Functiones et Approximatio, Commentarii Mathematici, vol. 47, no. 2, Adam Mickiewicz University Press, 2012, pp. 267–86, doi:10.7169/facm/2012.47.2.9. short: S. Baier, T.D. Browning, Functiones et Approximatio, Commentarii Mathematici 47 (2012) 267–286. date_created: 2018-12-11T11:45:22Z date_published: 2012-12-20T00:00:00Z date_updated: 2021-01-12T06:57:08Z day: '20' doi: 10.7169/facm/2012.47.2.9 extern: 1 intvolume: ' 47' issue: '2' month: '12' page: 267 - 286 publication: Functiones et Approximatio, Commentarii Mathematici publication_status: published publisher: Adam Mickiewicz University Press publist_id: '7666' quality_controlled: 0 status: public title: Inhomogeneous quadratic congruences type: journal_article volume: 47 year: '2012' ... --- _id: '2399' abstract: - lang: eng text: | Bose–Einstein condensation (BEC) in cold atomic gases was first achieved experimentally in 1995 [1, 6]. After initial failed attempts with spin-polarized atomic hydrogen, the first successful demonstrations of this phenomenon used gases of rubidium and sodium atoms, respectively. Since then there has been a surge of activity in this field, with ingenious experiments putting forth more and more astonishing results about the behavior of matter at very cold temperatures. alternative_title: - Lecture Notes in Mathematics author: - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Seiringer R. Cold quantum gases and bose einstein condensation. In: Rivasseau V, Seiringer R, Solovej J, Spencer T, eds. Quantum Many Body Systems. Vol 2051. Springer; 2012:55-92. doi:10.1007/978-3-642-29511-9_2' apa: Seiringer, R. (2012). Cold quantum gases and bose einstein condensation. In V. Rivasseau, R. Seiringer, J. Solovej, & T. Spencer (Eds.), Quantum Many Body Systems (Vol. 2051, pp. 55–92). Springer. https://doi.org/10.1007/978-3-642-29511-9_2 chicago: Seiringer, Robert. “Cold Quantum Gases and Bose Einstein Condensation.” In Quantum Many Body Systems, edited by Vincent Rivasseau, Robert Seiringer, Jan Solovej, and Thomas Spencer, 2051:55–92. Springer, 2012. https://doi.org/10.1007/978-3-642-29511-9_2. ieee: R. Seiringer, “Cold quantum gases and bose einstein condensation,” in Quantum Many Body Systems, vol. 2051, V. Rivasseau, R. Seiringer, J. Solovej, and T. Spencer, Eds. Springer, 2012, pp. 55–92. ista: 'Seiringer R. 2012.Cold quantum gases and bose einstein condensation. In: Quantum Many Body Systems. Lecture Notes in Mathematics, vol. 2051, 55–92.' mla: Seiringer, Robert. “Cold Quantum Gases and Bose Einstein Condensation.” Quantum Many Body Systems, edited by Vincent Rivasseau et al., vol. 2051, Springer, 2012, pp. 55–92, doi:10.1007/978-3-642-29511-9_2. short: R. Seiringer, in:, V. Rivasseau, R. Seiringer, J. Solovej, T. Spencer (Eds.), Quantum Many Body Systems, Springer, 2012, pp. 55–92. date_created: 2018-12-11T11:57:26Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T06:57:14Z day: '01' doi: 10.1007/978-3-642-29511-9_2 editor: - first_name: Vincent full_name: Rivasseau, Vincent last_name: Rivasseau - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jan full_name: Solovej, Jan P last_name: Solovej - first_name: Thomas full_name: Spencer, Thomas last_name: Spencer extern: 1 intvolume: ' 2051' month: '01' page: 55 - 92 publication: Quantum Many Body Systems publication_status: published publisher: Springer publist_id: '4526' quality_controlled: 0 status: public title: Cold quantum gases and bose einstein condensation type: book_chapter volume: 2051 year: '2012' ... --- _id: '2394' abstract: - lang: eng text: We study the BCS gap equation for a Fermi gas with unequal population of spin-up and spin-down states. For cosh (δ μ/T) ≤ 2, with T the temperature and δμ the chemical potential difference, the question of existence of non-trivial solutions can be reduced to spectral properties of a linear operator, similar to the unpolarized case studied previously in [Frank, R. L., Hainzl, C., Naboko, S., and Seiringer, R., J., Geom. Anal.17, 559-567 (2007)10.1007/BF02937429; Hainzl, C., Hamza, E., Seiringer, R., and Solovej, J. P., Commun., Math. Phys.281, 349-367 (2008)10.1007/s00220-008-0489-2; and Hainzl, C. and Seiringer, R., Phys. Rev. B77, 184517-110 435 (2008)]10.1103/PhysRevB.77.184517. For cosh (δ μ/T) > 2 the phase diagram is more complicated, however. We derive upper and lower bounds for the critical temperature, and study their behavior in the small coupling limit. author: - first_name: Abraham full_name: Freiji, Abraham last_name: Freiji - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Freiji A, Hainzl C, Seiringer R. The gap equation for spin-polarized fermions. Journal of Mathematical Physics. 2012;53(1). doi:10.1063/1.3670747 apa: Freiji, A., Hainzl, C., & Seiringer, R. (2012). The gap equation for spin-polarized fermions. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.3670747 chicago: Freiji, Abraham, Christian Hainzl, and Robert Seiringer. “The Gap Equation for Spin-Polarized Fermions.” Journal of Mathematical Physics. American Institute of Physics, 2012. https://doi.org/10.1063/1.3670747. ieee: A. Freiji, C. Hainzl, and R. Seiringer, “The gap equation for spin-polarized fermions,” Journal of Mathematical Physics, vol. 53, no. 1. American Institute of Physics, 2012. ista: Freiji A, Hainzl C, Seiringer R. 2012. The gap equation for spin-polarized fermions. Journal of Mathematical Physics. 53(1). mla: Freiji, Abraham, et al. “The Gap Equation for Spin-Polarized Fermions.” Journal of Mathematical Physics, vol. 53, no. 1, American Institute of Physics, 2012, doi:10.1063/1.3670747. short: A. Freiji, C. Hainzl, R. Seiringer, Journal of Mathematical Physics 53 (2012). date_created: 2018-12-11T11:57:25Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T06:57:13Z day: '01' doi: 10.1063/1.3670747 extern: 1 intvolume: ' 53' issue: '1' month: '01' publication: Journal of Mathematical Physics publication_status: published publisher: American Institute of Physics publist_id: '4532' quality_controlled: 0 status: public title: The gap equation for spin-polarized fermions type: journal_article volume: 53 year: '2012' ... --- _id: '2395' abstract: - lang: eng text: 'We give the first rigorous derivation of the celebrated Ginzburg-Landau (GL) theory, starting from the microscopic Bardeen-Cooper-Schrieffer (BCS) model. Close to the critical temperature, GL arises as an effective theory on the macroscopic scale. The relevant scaling limit is semiclassical in nature, and semiclassical analysis, with minimal regularity assumptions, plays an important part in our proof. ' author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jan full_name: Solovej, Jan P last_name: Solovej citation: ama: Frank R, Hainzl C, Seiringer R, Solovej J. Microscopic derivation of Ginzburg-Landau theory. Journal of the American Mathematical Society. 2012;25(3):667-713. doi:10.1090/S0894-0347-2012-00735-8 apa: Frank, R., Hainzl, C., Seiringer, R., & Solovej, J. (2012). Microscopic derivation of Ginzburg-Landau theory. Journal of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0894-0347-2012-00735-8 chicago: Frank, Rupert, Christian Hainzl, Robert Seiringer, and Jan Solovej. “Microscopic Derivation of Ginzburg-Landau Theory.” Journal of the American Mathematical Society. American Mathematical Society, 2012. https://doi.org/10.1090/S0894-0347-2012-00735-8. ieee: R. Frank, C. Hainzl, R. Seiringer, and J. Solovej, “Microscopic derivation of Ginzburg-Landau theory,” Journal of the American Mathematical Society, vol. 25, no. 3. American Mathematical Society, pp. 667–713, 2012. ista: Frank R, Hainzl C, Seiringer R, Solovej J. 2012. Microscopic derivation of Ginzburg-Landau theory. Journal of the American Mathematical Society. 25(3), 667–713. mla: Frank, Rupert, et al. “Microscopic Derivation of Ginzburg-Landau Theory.” Journal of the American Mathematical Society, vol. 25, no. 3, American Mathematical Society, 2012, pp. 667–713, doi:10.1090/S0894-0347-2012-00735-8. short: R. Frank, C. Hainzl, R. Seiringer, J. Solovej, Journal of the American Mathematical Society 25 (2012) 667–713. date_created: 2018-12-11T11:57:25Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T06:57:13Z day: '01' doi: 10.1090/S0894-0347-2012-00735-8 extern: 1 intvolume: ' 25' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1102.4001 month: '01' oa: 1 page: 667 - 713 publication: Journal of the American Mathematical Society publication_status: published publisher: American Mathematical Society publist_id: '4531' quality_controlled: 0 status: public title: Microscopic derivation of Ginzburg-Landau theory type: journal_article volume: 25 year: '2012' ... --- _id: '2396' abstract: - lang: eng text: A positive temperature analogue of the scattering length of a potential V can be defined via integrating the difference of the heat kernels of -Δ and, with Δ the Laplacian. An upper bound on this quantity is a crucial input in the derivation of a bound on the critical temperature of a dilute Bose gas (Seiringer and Ueltschi in Phys Rev B 80:014502, 2009). In (Seiringer and Ueltschi in Phys Rev B 80:014502, 2009), a bound was given in the case of finite range potentials and sufficiently low temperature. In this paper, we improve the bound and extend it to potentials of infinite range. author: - first_name: Benjamin full_name: Landon, Benjamin last_name: Landon - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Landon B, Seiringer R. The scattering length at positive temperature. Letters in Mathematical Physics. 2012;100(3):237-243. doi:10.1007/s11005-012-0566-5 apa: Landon, B., & Seiringer, R. (2012). The scattering length at positive temperature. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-012-0566-5 chicago: Landon, Benjamin, and Robert Seiringer. “The Scattering Length at Positive Temperature.” Letters in Mathematical Physics. Springer, 2012. https://doi.org/10.1007/s11005-012-0566-5. ieee: B. Landon and R. Seiringer, “The scattering length at positive temperature,” Letters in Mathematical Physics, vol. 100, no. 3. Springer, pp. 237–243, 2012. ista: Landon B, Seiringer R. 2012. The scattering length at positive temperature. Letters in Mathematical Physics. 100(3), 237–243. mla: Landon, Benjamin, and Robert Seiringer. “The Scattering Length at Positive Temperature.” Letters in Mathematical Physics, vol. 100, no. 3, Springer, 2012, pp. 237–43, doi:10.1007/s11005-012-0566-5. short: B. Landon, R. Seiringer, Letters in Mathematical Physics 100 (2012) 237–243. date_created: 2018-12-11T11:57:25Z date_published: 2012-06-01T00:00:00Z date_updated: 2021-01-12T06:57:13Z day: '01' doi: 10.1007/s11005-012-0566-5 extern: 1 intvolume: ' 100' issue: '3' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1111.1683 month: '06' oa: 1 page: 237 - 243 publication: Letters in Mathematical Physics publication_status: published publisher: Springer publist_id: '4529' quality_controlled: 0 status: public title: The scattering length at positive temperature type: journal_article volume: 100 year: '2012' ... --- _id: '2398' abstract: - lang: eng text: We extend the mathematical theory of quantum hypothesis testing to the general W*-algebraic setting and explore its relation with recent developments in non-equilibrium quantum statistical mechanics. In particular, we relate the large deviation principle for the full counting statistics of entropy flow to quantum hypothesis testing of the arrow of time. author: - first_name: Vojkan full_name: Jakšić, Vojkan last_name: Jakšić - first_name: Yoshiko full_name: Ogata, Yoshiko last_name: Ogata - first_name: Claude full_name: Pillet, Claude A last_name: Pillet - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Jakšić V, Ogata Y, Pillet C, Seiringer R. Quantum hypothesis testing and non-equilibrium statistical mechanics. Reviews in Mathematical Physics. 2012;24(6). doi:10.1142/S0129055X12300026 apa: Jakšić, V., Ogata, Y., Pillet, C., & Seiringer, R. (2012). Quantum hypothesis testing and non-equilibrium statistical mechanics. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X12300026 chicago: Jakšić, Vojkan, Yoshiko Ogata, Claude Pillet, and Robert Seiringer. “Quantum Hypothesis Testing and Non-Equilibrium Statistical Mechanics.” Reviews in Mathematical Physics. World Scientific Publishing, 2012. https://doi.org/10.1142/S0129055X12300026. ieee: V. Jakšić, Y. Ogata, C. Pillet, and R. Seiringer, “Quantum hypothesis testing and non-equilibrium statistical mechanics,” Reviews in Mathematical Physics, vol. 24, no. 6. World Scientific Publishing, 2012. ista: Jakšić V, Ogata Y, Pillet C, Seiringer R. 2012. Quantum hypothesis testing and non-equilibrium statistical mechanics. Reviews in Mathematical Physics. 24(6). mla: Jakšić, Vojkan, et al. “Quantum Hypothesis Testing and Non-Equilibrium Statistical Mechanics.” Reviews in Mathematical Physics, vol. 24, no. 6, World Scientific Publishing, 2012, doi:10.1142/S0129055X12300026. short: V. Jakšić, Y. Ogata, C. Pillet, R. Seiringer, Reviews in Mathematical Physics 24 (2012). date_created: 2018-12-11T11:57:26Z date_published: 2012-07-01T00:00:00Z date_updated: 2020-07-14T12:45:40Z day: '01' doi: 10.1142/S0129055X12300026 extern: 1 intvolume: ' 24' issue: '6' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1109.3804 month: '07' oa: 1 publication: Reviews in Mathematical Physics publication_status: published publisher: World Scientific Publishing publist_id: '4528' quality_controlled: 0 status: public title: Quantum hypothesis testing and non-equilibrium statistical mechanics type: review volume: 24 year: '2012' ... --- _id: '2397' abstract: - lang: eng text: We consider the low-density limit of a Fermi gas in the BCS approximation. We show that if the interaction potential allows for a two-particle bound state, the system at zero temperature is well approximated by the Gross-Pitaevskii functional, describing a Bose-Einstein condensate of fermion pairs. author: - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Hainzl C, Seiringer R. Low density limit of BCS theory and Bose-Einstein condensation of Fermion pairs. Letters in Mathematical Physics. 2012;100(2):119-138. doi:10.1007/s11005-011-0535-4 apa: Hainzl, C., & Seiringer, R. (2012). Low density limit of BCS theory and Bose-Einstein condensation of Fermion pairs. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-011-0535-4 chicago: Hainzl, Christian, and Robert Seiringer. “Low Density Limit of BCS Theory and Bose-Einstein Condensation of Fermion Pairs.” Letters in Mathematical Physics. Springer, 2012. https://doi.org/10.1007/s11005-011-0535-4. ieee: C. Hainzl and R. Seiringer, “Low density limit of BCS theory and Bose-Einstein condensation of Fermion pairs,” Letters in Mathematical Physics, vol. 100, no. 2. Springer, pp. 119–138, 2012. ista: Hainzl C, Seiringer R. 2012. Low density limit of BCS theory and Bose-Einstein condensation of Fermion pairs. Letters in Mathematical Physics. 100(2), 119–138. mla: Hainzl, Christian, and Robert Seiringer. “Low Density Limit of BCS Theory and Bose-Einstein Condensation of Fermion Pairs.” Letters in Mathematical Physics, vol. 100, no. 2, Springer, 2012, pp. 119–38, doi:10.1007/s11005-011-0535-4. short: C. Hainzl, R. Seiringer, Letters in Mathematical Physics 100 (2012) 119–138. date_created: 2018-12-11T11:57:25Z date_published: 2012-05-01T00:00:00Z date_updated: 2021-01-12T06:57:14Z day: '01' doi: 10.1007/s11005-011-0535-4 extern: 1 intvolume: ' 100' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1105.1100 month: '05' oa: 1 page: 119 - 138 publication: Letters in Mathematical Physics publication_status: published publisher: Springer publist_id: '4530' quality_controlled: 0 status: public title: Low density limit of BCS theory and Bose-Einstein condensation of Fermion pairs type: journal_article volume: 100 year: '2012' ... --- _id: '240' abstract: - lang: eng text: We investigate the frequency of positive squareful numbers x, y, z≤B for which x+y=z and present a conjecture concerning its asymptotic behavior. acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council" author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: K Van full_name: Valckenborgh, K Van last_name: Valckenborgh citation: ama: Browning TD, Valckenborgh KV. Sums of three squareful numbers. Experimental Mathematics. 2012;21(2):204-211. doi:10.1080/10586458.2011.605733 apa: Browning, T. D., & Valckenborgh, K. V. (2012). Sums of three squareful numbers. Experimental Mathematics. Taylor & Francis. https://doi.org/10.1080/10586458.2011.605733 chicago: Browning, Timothy D, and K Van Valckenborgh. “Sums of Three Squareful Numbers.” Experimental Mathematics. Taylor & Francis, 2012. https://doi.org/10.1080/10586458.2011.605733. ieee: T. D. Browning and K. V. Valckenborgh, “Sums of three squareful numbers,” Experimental Mathematics, vol. 21, no. 2. Taylor & Francis, pp. 204–211, 2012. ista: Browning TD, Valckenborgh KV. 2012. Sums of three squareful numbers. Experimental Mathematics. 21(2), 204–211. mla: Browning, Timothy D., and K. Van Valckenborgh. “Sums of Three Squareful Numbers.” Experimental Mathematics, vol. 21, no. 2, Taylor & Francis, 2012, pp. 204–11, doi:10.1080/10586458.2011.605733. short: T.D. Browning, K.V. Valckenborgh, Experimental Mathematics 21 (2012) 204–211. date_created: 2018-12-11T11:45:23Z date_published: 2012-05-23T00:00:00Z date_updated: 2021-01-12T06:57:15Z day: '23' doi: 10.1080/10586458.2011.605733 extern: 1 intvolume: ' 21' issue: '2' month: '05' page: 204 - 211 publication: Experimental Mathematics publication_status: published publisher: Taylor & Francis publist_id: '7664' quality_controlled: 0 status: public title: Sums of three squareful numbers type: journal_article volume: 21 year: '2012' ... --- _id: '2400' abstract: - lang: eng text: If the polaron coupling constant α is large enough, bipolarons or multi-polarons will form. When passing through the critical α c from above, does the radius of the system simply get arbitrarily large or does it reach a maximum and then explode? We prove that it is always the latter. We also prove the analogous statement for the Pekar-Tomasevich (PT) approximation to the energy, in which case there is a solution to the PT equation at α c. Similarly, we show that the same phenomenon occurs for atoms, e. g., helium, at the critical value of the nuclear charge. Our proofs rely only on energy estimates, not on a detailed analysis of the Schrödinger equation, and are very general. They use the fact that the Coulomb repulsion decays like 1/r, while 'uncertainty principle' localization energies decay more rapidly, as 1/r 2. author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Frank R, Lieb É, Seiringer R. Binding of polarons and atoms at threshold. Communications in Mathematical Physics. 2012;313(2):405-424. doi:10.1007/s00220-012-1436-9 apa: Frank, R., Lieb, É., & Seiringer, R. (2012). Binding of polarons and atoms at threshold. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-012-1436-9 chicago: Frank, Rupert, Élliott Lieb, and Robert Seiringer. “Binding of Polarons and Atoms at Threshold.” Communications in Mathematical Physics. Springer, 2012. https://doi.org/10.1007/s00220-012-1436-9. ieee: R. Frank, É. Lieb, and R. Seiringer, “Binding of polarons and atoms at threshold,” Communications in Mathematical Physics, vol. 313, no. 2. Springer, pp. 405–424, 2012. ista: Frank R, Lieb É, Seiringer R. 2012. Binding of polarons and atoms at threshold. Communications in Mathematical Physics. 313(2), 405–424. mla: Frank, Rupert, et al. “Binding of Polarons and Atoms at Threshold.” Communications in Mathematical Physics, vol. 313, no. 2, Springer, 2012, pp. 405–24, doi:10.1007/s00220-012-1436-9. short: R. Frank, É. Lieb, R. Seiringer, Communications in Mathematical Physics 313 (2012) 405–424. date_created: 2018-12-11T11:57:27Z date_published: 2012-07-01T00:00:00Z date_updated: 2021-01-12T06:57:15Z day: '01' doi: 10.1007/s00220-012-1436-9 extern: 1 intvolume: ' 313' issue: '2' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1106.0729 month: '07' oa: 1 page: 405 - 424 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '4527' quality_controlled: 0 status: public title: Binding of polarons and atoms at threshold type: journal_article volume: 313 year: '2012' ... --- _id: '2403' abstract: - lang: eng text: We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval in the Gross-Pitaevskii regime. We prove that Bose-Einstein condensation survives even a strong random potential with a high density of scatterers. The character of the wavefunction of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers and strong interactions the wavefunction extends over the whole interval. A high density of scatterers and weak interactions, on the other hand, lead to localization of the wavefunction in a fragmented subset of the interval. author: - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason - first_name: Valentin full_name: Zagrebnov, Valentin A last_name: Zagrebnov citation: ama: Seiringer R, Yngvason J, Zagrebnov V. Disordered Bose-Einstein condensates with interaction in one dimension. Journal of Statistical Mechanics Theory and Experiment. 2012;2012(11). doi:10.1088/1742-5468/2012/11/P11007 apa: Seiringer, R., Yngvason, J., & Zagrebnov, V. (2012). Disordered Bose-Einstein condensates with interaction in one dimension. Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd. https://doi.org/10.1088/1742-5468/2012/11/P11007 chicago: Seiringer, Robert, Jakob Yngvason, and Valentin Zagrebnov. “Disordered Bose-Einstein Condensates with Interaction in One Dimension.” Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2012. https://doi.org/10.1088/1742-5468/2012/11/P11007. ieee: R. Seiringer, J. Yngvason, and V. Zagrebnov, “Disordered Bose-Einstein condensates with interaction in one dimension,” Journal of Statistical Mechanics Theory and Experiment, vol. 2012, no. 11. IOP Publishing Ltd., 2012. ista: Seiringer R, Yngvason J, Zagrebnov V. 2012. Disordered Bose-Einstein condensates with interaction in one dimension. Journal of Statistical Mechanics Theory and Experiment. 2012(11). mla: Seiringer, Robert, et al. “Disordered Bose-Einstein Condensates with Interaction in One Dimension.” Journal of Statistical Mechanics Theory and Experiment, vol. 2012, no. 11, IOP Publishing Ltd., 2012, doi:10.1088/1742-5468/2012/11/P11007. short: R. Seiringer, J. Yngvason, V. Zagrebnov, Journal of Statistical Mechanics Theory and Experiment 2012 (2012). date_created: 2018-12-11T11:57:28Z date_published: 2012-11-01T00:00:00Z date_updated: 2021-01-12T06:57:16Z day: '01' doi: 10.1088/1742-5468/2012/11/P11007 extern: 1 intvolume: ' 2012' issue: '11' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1207.7054 month: '11' oa: 1 publication: Journal of Statistical Mechanics Theory and Experiment publication_status: published publisher: IOP Publishing Ltd. publist_id: '4523' quality_controlled: 0 status: public title: Disordered Bose-Einstein condensates with interaction in one dimension type: journal_article volume: 2012 year: '2012' ... --- _id: '2402' abstract: - lang: eng text: We consider a model of quantum-mechanical particles interacting via point interactions of infinite scattering length. In the case of fermions we prove a Lieb-Thirring inequality for the energy, i.e., we show that the energy is bounded from below by a constant times the integral of the particle density to the power. author: - first_name: Rupert full_name: Frank, Rupert L last_name: Frank - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Frank R, Seiringer R. Lieb-Thirring inequality for a model of particles with point interactions. Journal of Mathematical Physics. 2012;53(9). doi:10.1063/1.3697416 apa: Frank, R., & Seiringer, R. (2012). Lieb-Thirring inequality for a model of particles with point interactions. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.3697416 chicago: Frank, Rupert, and Robert Seiringer. “Lieb-Thirring Inequality for a Model of Particles with Point Interactions.” Journal of Mathematical Physics. American Institute of Physics, 2012. https://doi.org/10.1063/1.3697416. ieee: R. Frank and R. Seiringer, “Lieb-Thirring inequality for a model of particles with point interactions,” Journal of Mathematical Physics, vol. 53, no. 9. American Institute of Physics, 2012. ista: Frank R, Seiringer R. 2012. Lieb-Thirring inequality for a model of particles with point interactions. Journal of Mathematical Physics. 53(9). mla: Frank, Rupert, and Robert Seiringer. “Lieb-Thirring Inequality for a Model of Particles with Point Interactions.” Journal of Mathematical Physics, vol. 53, no. 9, American Institute of Physics, 2012, doi:10.1063/1.3697416. short: R. Frank, R. Seiringer, Journal of Mathematical Physics 53 (2012). date_created: 2018-12-11T11:57:27Z date_published: 2012-09-28T00:00:00Z date_updated: 2021-01-12T06:57:16Z day: '28' doi: 10.1063/1.3697416 extern: 1 intvolume: ' 53' issue: '9' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1112.5617 month: '09' oa: 1 publication: Journal of Mathematical Physics publication_status: published publisher: American Institute of Physics publist_id: '4524' quality_controlled: 0 status: public title: Lieb-Thirring inequality for a model of particles with point interactions type: journal_article volume: 53 year: '2012' ... --- _id: '2401' abstract: - lang: eng text: We find further implications of the BMV conjecture, which states that for hermitian matrices B≥0 and A, the function λ {mapping} Tr exp(A - λB) is the Laplace transform of a positive measure supported on [0,∞]. author: - first_name: Élliott full_name: Lieb, Élliott H last_name: Lieb - first_name: Robert full_name: Robert Seiringer id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Lieb É, Seiringer R. Further implications of the Bessis-Moussa-Villani conjecture. Journal of Statistical Physics. 2012;149(1):86-91. doi:10.1007/s10955-012-0585-8 apa: Lieb, É., & Seiringer, R. (2012). Further implications of the Bessis-Moussa-Villani conjecture. Journal of Statistical Physics. Springer. https://doi.org/10.1007/s10955-012-0585-8 chicago: Lieb, Élliott, and Robert Seiringer. “Further Implications of the Bessis-Moussa-Villani Conjecture.” Journal of Statistical Physics. Springer, 2012. https://doi.org/10.1007/s10955-012-0585-8. ieee: É. Lieb and R. Seiringer, “Further implications of the Bessis-Moussa-Villani conjecture,” Journal of Statistical Physics, vol. 149, no. 1. Springer, pp. 86–91, 2012. ista: Lieb É, Seiringer R. 2012. Further implications of the Bessis-Moussa-Villani conjecture. Journal of Statistical Physics. 149(1), 86–91. mla: Lieb, Élliott, and Robert Seiringer. “Further Implications of the Bessis-Moussa-Villani Conjecture.” Journal of Statistical Physics, vol. 149, no. 1, Springer, 2012, pp. 86–91, doi:10.1007/s10955-012-0585-8. short: É. Lieb, R. Seiringer, Journal of Statistical Physics 149 (2012) 86–91. date_created: 2018-12-11T11:57:27Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T06:57:16Z day: '01' doi: 10.1007/s10955-012-0585-8 extern: 1 intvolume: ' 149' issue: '1' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1206.0460 month: '10' oa: 1 page: 86 - 91 publication: Journal of Statistical Physics publication_status: published publisher: Springer publist_id: '4525' quality_controlled: 0 status: public title: Further implications of the Bessis-Moussa-Villani conjecture type: journal_article volume: 149 year: '2012' ... --- _id: '2411' 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. author: - first_name: Ingo full_name: Ebersberger, Ingo last_name: Ebersberger - first_name: Ricardo full_name: De Matos Simoes, Ricardo last_name: De Matos Simoes - first_name: Anne full_name: Kupczok, Anne id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Matthias full_name: Gube, Matthias last_name: Gube - first_name: Erika full_name: Kothe, Erika last_name: Kothe - first_name: Kerstin full_name: Voigt, Kerstin last_name: Voigt - first_name: Arndt full_name: Von Haeseler, Arndt last_name: Von Haeseler citation: ama: Ebersberger I, De Matos Simoes R, Kupczok A, et al. A consistent phylogenetic backbone for the fungi. Molecular Biology and Evolution. 2012;29(5):1319-1334. doi:10.1093/molbev/msr285 apa: 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. Oxford University Press. https://doi.org/10.1093/molbev/msr285 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.” Molecular Biology and Evolution. Oxford University Press, 2012. https://doi.org/10.1093/molbev/msr285. ieee: I. Ebersberger et al., “A consistent phylogenetic backbone for the fungi,” Molecular Biology and Evolution, vol. 29, no. 5. Oxford University Press, pp. 1319–1334, 2012. 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. mla: Ebersberger, Ingo, et al. “A Consistent Phylogenetic Backbone for the Fungi.” Molecular Biology and Evolution, vol. 29, no. 5, Oxford University Press, 2012, pp. 1319–34, doi:10.1093/molbev/msr285. 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. date_created: 2018-12-11T11:57:30Z date_published: 2012-05-01T00:00:00Z date_updated: 2021-01-12T06:57:19Z day: '01' ddc: - '570' - '576' department: - _id: JoBo doi: 10.1093/molbev/msr285 file: - access_level: open_access checksum: d565dcac27d1736c0c378ea6fcf22d69 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:30Z date_updated: 2020-07-14T12:45:40Z file_id: '5013' file_name: IST-2015-384-v1+1_Mol_Biol_Evol-2012-Ebersberger-1319-34.pdf file_size: 754922 relation: main_file file_date_updated: 2020-07-14T12:45:40Z has_accepted_license: '1' intvolume: ' 29' issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1319 - 1334 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '4515' pubrep_id: '384' quality_controlled: '1' scopus_import: 1 status: public title: A consistent phylogenetic backbone for the fungi 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) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2012' ... --- _id: '241' abstract: - lang: eng text: The representation of integral binary forms as sums of two squares is discussed and applied to establish the Manin conjecture for certain Châtelet surfaces over ℚ. author: - first_name: Régis full_name: de la Bretèche, Régis last_name: De La Bretèche - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 citation: ama: De La Bretèche R, Browning TD. Binary forms as sums of two squares and Châtelet surfaces. Israel Journal of Mathematics. 2012;191(2):973-1012. doi:10.1007/s11856-012-0019-y apa: De La Bretèche, R., & Browning, T. D. (2012). Binary forms as sums of two squares and Châtelet surfaces. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-012-0019-y chicago: De La Bretèche, Régis, and Timothy D Browning. “Binary Forms as Sums of Two Squares and Châtelet Surfaces.” Israel Journal of Mathematics. Springer, 2012. https://doi.org/10.1007/s11856-012-0019-y. ieee: R. De La Bretèche and T. D. Browning, “Binary forms as sums of two squares and Châtelet surfaces,” Israel Journal of Mathematics, vol. 191, no. 2. Springer, pp. 973–1012, 2012. ista: De La Bretèche R, Browning TD. 2012. Binary forms as sums of two squares and Châtelet surfaces. Israel Journal of Mathematics. 191(2), 973–1012. mla: De La Bretèche, Régis, and Timothy D. Browning. “Binary Forms as Sums of Two Squares and Châtelet Surfaces.” Israel Journal of Mathematics, vol. 191, no. 2, Springer, 2012, pp. 973–1012, doi:10.1007/s11856-012-0019-y. short: R. De La Bretèche, T.D. Browning, Israel Journal of Mathematics 191 (2012) 973–1012. date_created: 2018-12-11T11:45:23Z date_published: 2012-02-28T00:00:00Z date_updated: 2021-01-12T06:57:19Z day: '28' doi: 10.1007/s11856-012-0019-y extern: 1 intvolume: ' 191' issue: '2' month: '02' page: 973 - 1012 publication: Israel Journal of Mathematics publication_status: published publisher: Springer publist_id: '7663' quality_controlled: 0 status: public title: Binary forms as sums of two squares and Châtelet surfaces type: journal_article volume: 191 year: '2012' ... --- _id: '242' abstract: - lang: eng text: We investigate the first and second moments of shifted convolutions of the generalized divisor function d 3(n). acknowledgement: "EP/E053262/1\tEngineering and Physical Sciences Research Council" author: - first_name: Stephan full_name: Baier, Stephan last_name: Baier - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Gihan full_name: Marasingha, Gihan last_name: Marasingha - first_name: Liangyi full_name: Zhao, Liangyi last_name: Zhao citation: ama: Baier S, Browning TD, Marasingha G, Zhao L. Averages of shifted convolutions of d3 (n). Proceedings of the Edinburgh Mathematical Society. 2012;55(3):551-576. doi:10.1017/S001309151100037X apa: Baier, S., Browning, T. D., Marasingha, G., & Zhao, L. (2012). Averages of shifted convolutions of d3 (n). Proceedings of the Edinburgh Mathematical Society. Cambridge University Press. https://doi.org/10.1017/S001309151100037X chicago: Baier, Stephan, Timothy D Browning, Gihan Marasingha, and Liangyi Zhao. “Averages of Shifted Convolutions of D3 (N).” Proceedings of the Edinburgh Mathematical Society. Cambridge University Press, 2012. https://doi.org/10.1017/S001309151100037X. ieee: S. Baier, T. D. Browning, G. Marasingha, and L. Zhao, “Averages of shifted convolutions of d3 (n),” Proceedings of the Edinburgh Mathematical Society, vol. 55, no. 3. Cambridge University Press, pp. 551–576, 2012. ista: Baier S, Browning TD, Marasingha G, Zhao L. 2012. Averages of shifted convolutions of d3 (n). Proceedings of the Edinburgh Mathematical Society. 55(3), 551–576. mla: Baier, Stephan, et al. “Averages of Shifted Convolutions of D3 (N).” Proceedings of the Edinburgh Mathematical Society, vol. 55, no. 3, Cambridge University Press, 2012, pp. 551–76, doi:10.1017/S001309151100037X. short: S. Baier, T.D. Browning, G. Marasingha, L. Zhao, Proceedings of the Edinburgh Mathematical Society 55 (2012) 551–576. date_created: 2018-12-11T11:45:23Z date_published: 2012-10-01T00:00:00Z date_updated: 2021-01-12T06:57:23Z day: '01' doi: 10.1017/S001309151100037X extern: 1 intvolume: ' 55' issue: '3' main_file_link: - open_access: '1' url: https://arxiv.org/abs/1101.5464 month: '10' oa: 1 page: 551 - 576 publication: Proceedings of the Edinburgh Mathematical Society publication_status: published publisher: Cambridge University Press publist_id: '7662' quality_controlled: 0 status: public title: Averages of shifted convolutions of d3 (n) type: journal_article volume: 55 year: '2012' ... --- _id: '243' abstract: - lang: eng text: Let P(t) ∈ ℚ[t] be an irreducible quadratic polynomial and suppose that K is a quartic extension of ℚ containing the roots of P(t). Let N K/ℚ(X) be a full norm form for the extension K/ℚ. We show that the variety P(t) =N K/ℚ(X)≠ 0 satisfies the Hasse principle and weak approximation. The proof uses analytic methods. author: - first_name: Timothy D full_name: Timothy Browning id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Roger full_name: Heath-Brown, Roger last_name: Heath Brown citation: ama: Browning TD, Heath Brown R. Quadratic polynomials represented by norm forms. Geometric and Functional Analysis. 2012;22(5):1124-1190. doi:10.1007/s00039-012-0168-5 apa: Browning, T. D., & Heath Brown, R. (2012). Quadratic polynomials represented by norm forms. Geometric and Functional Analysis. Springer Basel. https://doi.org/10.1007/s00039-012-0168-5 chicago: Browning, Timothy D, and Roger Heath Brown. “Quadratic Polynomials Represented by Norm Forms.” Geometric and Functional Analysis. Springer Basel, 2012. https://doi.org/10.1007/s00039-012-0168-5. ieee: T. D. Browning and R. Heath Brown, “Quadratic polynomials represented by norm forms,” Geometric and Functional Analysis, vol. 22, no. 5. Springer Basel, pp. 1124–1190, 2012. ista: Browning TD, Heath Brown R. 2012. Quadratic polynomials represented by norm forms. Geometric and Functional Analysis. 22(5), 1124–1190. mla: Browning, Timothy D., and Roger Heath Brown. “Quadratic Polynomials Represented by Norm Forms.” Geometric and Functional Analysis, vol. 22, no. 5, Springer Basel, 2012, pp. 1124–90, doi:10.1007/s00039-012-0168-5. short: T.D. Browning, R. Heath Brown, Geometric and Functional Analysis 22 (2012) 1124–1190. date_created: 2018-12-11T11:45:24Z date_published: 2012-08-25T00:00:00Z date_updated: 2021-01-12T06:57:26Z day: '25' doi: 10.1007/s00039-012-0168-5 extern: 1 intvolume: ' 22' issue: '5' month: '08' page: 1124 - 1190 publication: Geometric and Functional Analysis publication_status: published publisher: Springer Basel publist_id: '7661' quality_controlled: 0 status: public title: Quadratic polynomials represented by norm forms type: journal_article volume: 22 year: '2012' ... --- _id: '2440' abstract: - lang: eng text: We present an algorithm for computing [X, Y], i.e., all homotopy classes of continuous maps X → Y, where X, Y are topological spaces given as finite simplicial complexes, Y is (d - 1)-connected for some d ≥ 2 (for example, Y can be the d-dimensional sphere S d), and dim X ≤ 2d - 2. These conditions on X, Y guarantee that [X, Y] has a natural structure of a finitely generated Abelian group, and the algorithm finds generators and relations for it. We combine several tools and ideas from homotopy theory (such as Postnikov systems, simplicial sets, and obstruction theory) with algorithmic tools from effective algebraic topology (objects with effective homology). We hope that a further extension of the methods developed here will yield an algorithm for computing, in some cases of interest, the ℤ 2-index, which is a quantity playing a prominent role in Borsuk-Ulam style applications of topology in combinatorics and geometry, e.g., in topological lower bounds for the chromatic number of a graph. In a certain range of dimensions, deciding the embeddability of a simplicial complex into ℝ d also amounts to a ℤ 2-index computation. This is the main motivation of our work. We believe that investigating the computational complexity of questions in homotopy theory and similar areas presents a fascinating research area, and we hope that our work may help bridge the cultural gap between algebraic topology and theoretical computer science. author: - first_name: Martin full_name: Čadek, Martin last_name: Čadek - first_name: Marek full_name: Marek Krcál id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál - first_name: Jiří full_name: Matoušek, Jiří last_name: Matoušek - first_name: Francis full_name: Sergeraert, Francis last_name: Sergeraert - first_name: Lukáš full_name: Vokřínek, Lukáš last_name: Vokřínek - first_name: Uli full_name: Uli Wagner id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: 'Čadek M, Krcál M, Matoušek J, Sergeraert F, Vokřínek L, Wagner U. Computing all maps into a sphere. In: SIAM; 2012:1-10.' apa: 'Čadek, M., Krcál, M., Matoušek, J., Sergeraert, F., Vokřínek, L., & Wagner, U. (2012). Computing all maps into a sphere (pp. 1–10). Presented at the SODA: Symposium on Discrete Algorithms, SIAM.' chicago: Čadek, Martin, Marek Krcál, Jiří Matoušek, Francis Sergeraert, Lukáš Vokřínek, and Uli Wagner. “Computing All Maps into a Sphere,” 1–10. SIAM, 2012. ieee: 'M. Čadek, M. Krcál, J. Matoušek, F. Sergeraert, L. Vokřínek, and U. Wagner, “Computing all maps into a sphere,” presented at the SODA: Symposium on Discrete Algorithms, 2012, pp. 1–10.' ista: 'Čadek M, Krcál M, Matoušek J, Sergeraert F, Vokřínek L, Wagner U. 2012. Computing all maps into a sphere. SODA: Symposium on Discrete Algorithms, 1–10.' mla: Čadek, Martin, et al. Computing All Maps into a Sphere. SIAM, 2012, pp. 1–10. short: M. Čadek, M. Krcál, J. Matoušek, F. Sergeraert, L. Vokřínek, U. Wagner, in:, SIAM, 2012, pp. 1–10. conference: name: 'SODA: Symposium on Discrete Algorithms' date_created: 2018-12-11T11:57:40Z date_published: 2012-01-01T00:00:00Z date_updated: 2021-01-12T06:57:30Z day: '01' extern: 1 main_file_link: - open_access: '0' url: http://arxiv.org/abs/1105.6257 month: '01' page: 1 - 10 publication_status: published publisher: SIAM publist_id: '4466' quality_controlled: 0 status: public title: Computing all maps into a sphere type: conference year: '2012' ...