[{"date_created":"2018-12-11T12:02:01Z","publisher":"IEEE","citation":{"short":"S. Vicente, C. Rother, V. Kolmogorov, in:, IEEE, 2011, pp. 2217–2224.","ista":"Vicente S, Rother C, Kolmogorov V. 2011. Object cosegmentation. CVPR: Computer Vision and Pattern Recognition, 2217–2224.","ama":"Vicente S, Rother C, Kolmogorov V. Object cosegmentation. In: IEEE; 2011:2217-2224. doi:<a href=\"https://doi.org/10.1109/CVPR.2011.5995530\">10.1109/CVPR.2011.5995530</a>","chicago":"Vicente, Sara, Carsten Rother, and Vladimir Kolmogorov. “Object Cosegmentation,” 2217–24. IEEE, 2011. <a href=\"https://doi.org/10.1109/CVPR.2011.5995530\">https://doi.org/10.1109/CVPR.2011.5995530</a>.","mla":"Vicente, Sara, et al. <i>Object Cosegmentation</i>. IEEE, 2011, pp. 2217–24, doi:<a href=\"https://doi.org/10.1109/CVPR.2011.5995530\">10.1109/CVPR.2011.5995530</a>.","ieee":"S. Vicente, C. Rother, and V. Kolmogorov, “Object cosegmentation,” presented at the CVPR: Computer Vision and Pattern Recognition, 2011, pp. 2217–2224.","apa":"Vicente, S., Rother, C., &#38; Kolmogorov, V. (2011). Object cosegmentation (pp. 2217–2224). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPR.2011.5995530\">https://doi.org/10.1109/CVPR.2011.5995530</a>"},"page":"2217 - 2224","publist_id":"3477","title":"Object cosegmentation","doi":"10.1109/CVPR.2011.5995530","publication_status":"published","year":"2011","quality_controlled":0,"status":"public","_id":"3207","type":"conference","date_updated":"2021-01-12T07:41:48Z","abstract":[{"lang":"eng","text":"Cosegmentation is typically defined as the task of jointly segmenting something similar in a given set of images. Existing methods are too generic and so far have not demonstrated competitive results for any specific task. In this paper we overcome this limitation by adding two new aspects to cosegmentation: (1) the &quot;something&quot; has to be an object, and (2) the &quot;similarity&quot; measure is learned. In this way, we are able to achieve excellent results on the recently introduced iCoseg dataset, which contains small sets of images of either the same object instance or similar objects of the same class. The challenge of this dataset lies in the extreme changes in viewpoint, lighting, and object deformations within each set. We are able to considerably outperform several competitors. To achieve this performance, we borrow recent ideas from object recognition: the use of powerful features extracted from a pool of candidate object-like segmentations. We believe that our work will be beneficial to several application areas, such as image retrieval."}],"conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"day":"22","author":[{"first_name":"Sara","full_name":"Vicente, Sara","last_name":"Vicente"},{"first_name":"Carsten","full_name":"Rother, Carsten","last_name":"Rother"},{"last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Vladimir Kolmogorov"}],"date_published":"2011-08-22T00:00:00Z","extern":1,"month":"08"},{"status":"public","quality_controlled":0,"date_updated":"2021-01-12T07:42:00Z","_id":"3236","type":"conference","volume":"6597 ","day":"01","conference":{"name":"TCC: Theory of Cryptography Conference"},"abstract":[{"lang":"eng","text":"If a cryptographic primitive remains secure even if ℓ bits about the secret key are leaked to the adversary, one would expect that at least one of n independent instantiations of the scheme remains secure given n·ℓ bits of leakage. This intuition has been proven true for schemes satisfying some special information-theoretic properties by Alwen et al. [Eurocrypt'10]. On the negative side, Lewko and Waters [FOCS'10] construct a CPA secure public-key encryption scheme for which this intuition fails. The counterexample of Lewko and Waters leaves open the interesting possibility that for any scheme there exists a constant c&gt;0, such that n fold repetition remains secure against c·n·ℓ bits of leakage. Furthermore, their counterexample requires the n copies of the encryption scheme to share a common reference parameter, leaving open the possibility that the intuition is true for all schemes without common setup. In this work we give a stronger counterexample ruling out these possibilities. We construct a signature scheme such that: 1. a single instantiation remains secure given ℓ = log(k) bits of leakage where k is a security parameter. 2. any polynomial number of independent instantiations can be broken (in the strongest sense of key-recovery) given ℓ′ = poly(k) bits of leakage. Note that ℓ does not depend on the number of instances. The computational assumption underlying our counterexample is that non-interactive computationally sound proofs exist. Moreover, under a stronger (non-standard) assumption about such proofs, our counterexample does not require a common reference parameter. The underlying idea of our counterexample is rather generic and can be applied to other primitives like encryption schemes. © 2011 International Association for Cryptologic Research."}],"extern":1,"date_published":"2011-01-01T00:00:00Z","month":"01","author":[{"first_name":"Abhishek","full_name":"Jain, Abhishek","last_name":"Jain"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Krzysztof Pietrzak","first_name":"Krzysztof Z"}],"page":"58 - 69","citation":{"short":"A. Jain, K.Z. Pietrzak, in:, Springer, 2011, pp. 58–69.","ista":"Jain A, Pietrzak KZ. 2011. Parallel repetition for leakage resilience amplification revisited. TCC: Theory of Cryptography Conference, LNCS, vol. 6597, 58–69.","ama":"Jain A, Pietrzak KZ. Parallel repetition for leakage resilience amplification revisited. In: Vol 6597. Springer; 2011:58-69. doi:<a href=\"https://doi.org/10.1007/978-3-642-19571-6_5\">10.1007/978-3-642-19571-6_5</a>","chicago":"Jain, Abhishek, and Krzysztof Z Pietrzak. “Parallel Repetition for Leakage Resilience Amplification Revisited,” 6597:58–69. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-19571-6_5\">https://doi.org/10.1007/978-3-642-19571-6_5</a>.","mla":"Jain, Abhishek, and Krzysztof Z. Pietrzak. <i>Parallel Repetition for Leakage Resilience Amplification Revisited</i>. Vol. 6597, Springer, 2011, pp. 58–69, doi:<a href=\"https://doi.org/10.1007/978-3-642-19571-6_5\">10.1007/978-3-642-19571-6_5</a>.","ieee":"A. Jain and K. Z. Pietrzak, “Parallel repetition for leakage resilience amplification revisited,” presented at the TCC: Theory of Cryptography Conference, 2011, vol. 6597, pp. 58–69.","apa":"Jain, A., &#38; Pietrzak, K. Z. (2011). Parallel repetition for leakage resilience amplification revisited (Vol. 6597, pp. 58–69). Presented at the TCC: Theory of Cryptography Conference, Springer. <a href=\"https://doi.org/10.1007/978-3-642-19571-6_5\">https://doi.org/10.1007/978-3-642-19571-6_5</a>"},"publisher":"Springer","date_created":"2018-12-11T12:02:11Z","doi":"10.1007/978-3-642-19571-6_5","publist_id":"3443","title":"Parallel repetition for leakage resilience amplification revisited","year":"2011","publication_status":"published","alternative_title":["LNCS"]},{"oa_version":"None","conference":{"name":"EUROCRYPT: Theory and Applications of Cryptographic Techniques","end_date":"2011-05-19","location":"Tallinn, Estonia","start_date":"2011-05-15"},"day":"01","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"1187"}]},"abstract":[{"text":"We construct efficient authentication protocols and message-authentication codes (MACs) whose security can be reduced to the learning parity with noise (LPN) problem. Despite a large body of work - starting with the HB protocol of Hopper and Blum in 2001 - until now it was not even known how to construct an efficient authentication protocol from LPN which is secure against man-in-the-middle (MIM) attacks. A MAC implies such a (two-round) protocol. © 2011 International Association for Cryptologic Research","lang":"eng"}],"date_published":"2011-05-01T00:00:00Z","extern":"1","month":"05","author":[{"last_name":"Kiltz","first_name":"Eike","full_name":"Kiltz, Eike"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"David","full_name":"Cash, David","last_name":"Cash"},{"first_name":"Abhishek","full_name":"Jain, Abhishek","last_name":"Jain"},{"full_name":"Venturi, Daniele","first_name":"Daniele","last_name":"Venturi"}],"status":"public","quality_controlled":"1","type":"conference","_id":"3238","date_updated":"2023-09-20T11:20:57Z","volume":6632,"year":"2011","publication_status":"published","alternative_title":["LNCS"],"acknowledgement":"The European Regional Development Fund (ERDF),Guardtime,Qualcomm,Swedbank","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kiltz, Eike, et al. <i>Efficient Authentication from Hard Learning Problems</i>. Vol. 6632, Springer, 2011, pp. 7–26, doi:<a href=\"https://doi.org/10.1007/978-3-642-20465-4_3\">10.1007/978-3-642-20465-4_3</a>.","chicago":"Kiltz, Eike, Krzysztof Z Pietrzak, David Cash, Abhishek Jain, and Daniele Venturi. “Efficient Authentication from Hard Learning Problems,” 6632:7–26. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-20465-4_3\">https://doi.org/10.1007/978-3-642-20465-4_3</a>.","ama":"Kiltz E, Pietrzak KZ, Cash D, Jain A, Venturi D. Efficient authentication from hard learning problems. In: Vol 6632. Springer; 2011:7-26. doi:<a href=\"https://doi.org/10.1007/978-3-642-20465-4_3\">10.1007/978-3-642-20465-4_3</a>","ista":"Kiltz E, Pietrzak KZ, Cash D, Jain A, Venturi D. 2011. Efficient authentication from hard learning problems. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 6632, 7–26.","short":"E. Kiltz, K.Z. Pietrzak, D. Cash, A. Jain, D. Venturi, in:, Springer, 2011, pp. 7–26.","apa":"Kiltz, E., Pietrzak, K. Z., Cash, D., Jain, A., &#38; Venturi, D. (2011). Efficient authentication from hard learning problems (Vol. 6632, pp. 7–26). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Tallinn, Estonia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-20465-4_3\">https://doi.org/10.1007/978-3-642-20465-4_3</a>","ieee":"E. Kiltz, K. Z. Pietrzak, D. Cash, A. Jain, and D. Venturi, “Efficient authentication from hard learning problems,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Tallinn, Estonia, 2011, vol. 6632, pp. 7–26."},"page":"7 - 26","date_created":"2018-12-11T12:02:11Z","publisher":"Springer","intvolume":"      6632","doi":"10.1007/978-3-642-20465-4_3","title":"Efficient authentication from hard learning problems","publist_id":"3442"},{"alternative_title":["LNCS"],"year":"2011","publication_status":"published","doi":"10.1007/978-3-642-22006-7_33","publist_id":"3441","title":"Tamper proof circuits How to trade leakage for tamper resilience","citation":{"chicago":"Faust, Sebastian, Krzysztof Z Pietrzak, and Daniele Venturi. “Tamper Proof Circuits How to Trade Leakage for Tamper Resilience,” 6755:391–402. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-22006-7_33\">https://doi.org/10.1007/978-3-642-22006-7_33</a>.","ama":"Faust S, Pietrzak KZ, Venturi D. Tamper proof circuits How to trade leakage for tamper resilience. In: Vol 6755. Springer; 2011:391-402. doi:<a href=\"https://doi.org/10.1007/978-3-642-22006-7_33\">10.1007/978-3-642-22006-7_33</a>","mla":"Faust, Sebastian, et al. <i>Tamper Proof Circuits How to Trade Leakage for Tamper Resilience</i>. Vol. 6755, no. Part 1, Springer, 2011, pp. 391–402, doi:<a href=\"https://doi.org/10.1007/978-3-642-22006-7_33\">10.1007/978-3-642-22006-7_33</a>.","short":"S. Faust, K.Z. Pietrzak, D. Venturi, in:, Springer, 2011, pp. 391–402.","ista":"Faust S, Pietrzak KZ, Venturi D. 2011. Tamper proof circuits How to trade leakage for tamper resilience. ICALP: Automata, Languages and Programming, LNCS, vol. 6755, 391–402.","ieee":"S. Faust, K. Z. Pietrzak, and D. Venturi, “Tamper proof circuits How to trade leakage for tamper resilience,” presented at the ICALP: Automata, Languages and Programming, 2011, vol. 6755, no. Part 1, pp. 391–402.","apa":"Faust, S., Pietrzak, K. Z., &#38; Venturi, D. (2011). Tamper proof circuits How to trade leakage for tamper resilience (Vol. 6755, pp. 391–402). Presented at the ICALP: Automata, Languages and Programming, Springer. <a href=\"https://doi.org/10.1007/978-3-642-22006-7_33\">https://doi.org/10.1007/978-3-642-22006-7_33</a>"},"page":"391 - 402","date_created":"2018-12-11T12:02:12Z","publisher":"Springer","month":"01","extern":1,"date_published":"2011-01-01T00:00:00Z","author":[{"last_name":"Faust","full_name":"Faust, Sebastian","first_name":"Sebastian"},{"first_name":"Krzysztof Z","full_name":"Krzysztof Pietrzak","orcid":"0000-0002-9139-1654","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Venturi","full_name":"Venturi, Daniele","first_name":"Daniele"}],"conference":{"name":"ICALP: Automata, Languages and Programming"},"day":"01","issue":"Part 1","abstract":[{"text":"Tampering attacks are cryptanalytic attacks on the implementation of cryptographic algorithms (e.g., smart cards), where an adversary introduces faults with the hope that the tampered device will reveal secret information. Inspired by the work of Ishai et al. [Eurocrypt'06], we propose a compiler that transforms any circuit into a new circuit with the same functionality, but which is resilient against a well-defined and powerful tampering adversary. More concretely, our transformed circuits remain secure even if the adversary can adaptively tamper with every wire in the circuit as long as the tampering fails with some probability δ&gt;0. This additional requirement is motivated by practical tampering attacks, where it is often difficult to guarantee the success of a specific attack. Formally, we show that a q-query tampering attack against the transformed circuit can be &quot;simulated&quot; with only black-box access to the original circuit and log(q) bits of additional auxiliary information. Thus, if the implemented cryptographic scheme is secure against log(q) bits of leakage, then our implementation is tamper-proof in the above sense. Surprisingly, allowing for this small amount of information leakage allows for much more efficient compilers, which moreover do not require randomness during evaluation. Similar to earlier works our compiler requires small, stateless and computation-independent tamper-proof gadgets. Thus, our result can be interpreted as reducing the problem of shielding arbitrary complex computation to protecting simple components. © 2011 Springer-Verlag.","lang":"eng"}],"_id":"3239","date_updated":"2021-01-12T07:42:02Z","type":"conference","volume":"6755 ","status":"public","quality_controlled":0},{"type":"conference","_id":"3240","date_updated":"2021-01-12T07:42:03Z","volume":6841,"status":"public","quality_controlled":0,"date_published":"2011-01-01T00:00:00Z","extern":1,"month":"01","author":[{"full_name":"Barak,  Boaz","first_name":"Boaz","last_name":"Barak"},{"full_name":"Dodis, Yevgeniy","first_name":"Yevgeniy","last_name":"Dodis"},{"last_name":"Krawczyk","first_name":"Hugo","full_name":"Krawczyk, Hugo"},{"last_name":"Pereira","full_name":"Pereira, Olivier","first_name":"Olivier"},{"first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","full_name":"Krzysztof Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"},{"full_name":"Standaert, François-Xavier","first_name":"François","last_name":"Standaert"},{"full_name":"Yu, Yu","first_name":"Yu","last_name":"Yu"}],"day":"01","conference":{"name":"CRYPTO: International Cryptology Conference"},"abstract":[{"lang":"eng","text":"The famous Leftover Hash Lemma (LHL) states that (almost) universal hash functions are good randomness extractors. Despite its numerous applications, LHL-based extractors suffer from the following two limitations: - Large Entropy Loss: to extract v bits from distribution X of min-entropy m which are ε-close to uniform, one must set v ≤ m - 2log(1/ε), meaning that the entropy loss L = def m - v ≥ 2 log(1/ε). For many applications, such entropy loss is too large. - Large Seed Length: the seed length n of (almost) universal hash function required by the LHL must be at least n ≥ min (u - v, v + 2log(1/ε)) - O(1), where u is the length of the source, and must grow with the number of extracted bits. Quite surprisingly, we show that both limitations of the LHL - large entropy loss and large seed - can be overcome (or, at least, mitigated) in various important scenarios. First, we show that entropy loss could be reduced to L = log(1/ε) for the setting of deriving secret keys for a wide range of cryptographic applications. Specifically, the security of these schemes with an LHL-derived key gracefully degrades from ε to at most ε + √ε2-L. (Notice that, unlike standard LHL, this bound is meaningful even when one extracts more bits than the min-entropy we have!) Based on these results we build a general computational extractor that enjoys low entropy loss and can be used to instantiate a generic key derivation function for any cryptographic application. Second, we study the soundness of the natural expand-then-extract approach, where one uses a pseudorandom generator (PRG) to expand a short &quot;input seed&quot; S into a longer &quot;output seed&quot; S′, and then use the resulting S′ as the seed required by the LHL (or, more generally, by any randomness extractor). We show that, in general, the expand-then-extract approach is not sound if the Decisional Diffie-Hellman assumption is true. Despite that, we show that it is sound either: (1) when extracting a &quot;small&quot; (logarithmic in the security of the PRG) number of bits; or (2) in minicrypt. Implication (2) suggests that the expand-then-extract approach is likely secure when used with &quot;practical&quot; PRGs, despite lacking a reductionist proof of security! © 2011 International Association for Cryptologic Research."}],"intvolume":"      6841","doi":" 10.1007/978-3-642-22792-9_1","title":"Leftover hash lemma revisited","publist_id":"3440","page":"1 - 20","citation":{"mla":"Barak, Boaz, et al. <i>Leftover Hash Lemma Revisited</i>. Vol. 6841, Springer, 2011, pp. 1–20, doi:<a href=\"https://doi.org/ 10.1007/978-3-642-22792-9_1\"> 10.1007/978-3-642-22792-9_1</a>.","chicago":"Barak, Boaz, Yevgeniy Dodis, Hugo Krawczyk, Olivier Pereira, Krzysztof Z Pietrzak, François Standaert, and Yu Yu. “Leftover Hash Lemma Revisited,” 6841:1–20. Springer, 2011. <a href=\"https://doi.org/ 10.1007/978-3-642-22792-9_1\">https://doi.org/ 10.1007/978-3-642-22792-9_1</a>.","ama":"Barak B, Dodis Y, Krawczyk H, et al. Leftover hash lemma revisited. In: Vol 6841. Springer; 2011:1-20. doi:<a href=\"https://doi.org/ 10.1007/978-3-642-22792-9_1\"> 10.1007/978-3-642-22792-9_1</a>","ista":"Barak B, Dodis Y, Krawczyk H, Pereira O, Pietrzak KZ, Standaert F, Yu Y. 2011. Leftover hash lemma revisited. CRYPTO: International Cryptology Conference, LNCS, vol. 6841, 1–20.","short":"B. Barak, Y. Dodis, H. Krawczyk, O. Pereira, K.Z. Pietrzak, F. Standaert, Y. Yu, in:, Springer, 2011, pp. 1–20.","apa":"Barak, B., Dodis, Y., Krawczyk, H., Pereira, O., Pietrzak, K. Z., Standaert, F., &#38; Yu, Y. (2011). Leftover hash lemma revisited (Vol. 6841, pp. 1–20). Presented at the CRYPTO: International Cryptology Conference, Springer. <a href=\"https://doi.org/ 10.1007/978-3-642-22792-9_1\">https://doi.org/ 10.1007/978-3-642-22792-9_1</a>","ieee":"B. Barak <i>et al.</i>, “Leftover hash lemma revisited,” presented at the CRYPTO: International Cryptology Conference, 2011, vol. 6841, pp. 1–20."},"publisher":"Springer","date_created":"2018-12-11T12:02:12Z","alternative_title":["LNCS"],"year":"2011","publication_status":"published"},{"day":"05","oa_version":"None","conference":{"location":"Kenting, Taiwan","start_date":"2011-12-05","name":"APLAS: Asian Symposium on Programming Languages and Systems","end_date":"2011-12-07"},"abstract":[{"lang":"eng","text":"Verification of programs with procedures, multi-threaded programs, and higher-order functional programs can be effectively au- tomated using abstraction and refinement schemes that rely on spurious counterexamples for abstraction discovery. The analysis of counterexam- ples can be automated by a series of interpolation queries, or, alterna- tively, as a constraint solving query expressed by a set of recursion free Horn clauses. (A set of interpolation queries can be formulated as a single constraint over Horn clauses with linear dependency structure between the unknown relations.) In this paper we present an algorithm for solving recursion free Horn clauses over a combined theory of linear real/rational arithmetic and uninterpreted functions. Our algorithm performs resolu- tion to deal with the clausal structure and relies on partial solutions to deal with (non-local) instances of functionality axioms."}],"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"month":"12","date_published":"2011-12-05T00:00:00Z","author":[{"last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh","first_name":"Ashutosh"},{"first_name":"Corneliu","full_name":"Popeea, Corneliu","last_name":"Popeea"},{"last_name":"Rybalchenko","full_name":"Rybalchenko, Andrey","first_name":"Andrey"}],"status":"public","quality_controlled":"1","_id":"3264","type":"conference","date_updated":"2021-01-12T07:42:15Z","volume":7078,"year":"2011","publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"}],"page":"188 - 203","citation":{"ista":"Gupta A, Popeea C, Rybalchenko A. 2011. Solving recursion-free Horn clauses over LI+UIF. APLAS: Asian Symposium on Programming Languages and Systems, LNCS, vol. 7078, 188–203.","short":"A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011, pp. 188–203.","mla":"Gupta, Ashutosh, et al. <i>Solving Recursion-Free Horn Clauses over LI+UIF</i>. Edited by Hongseok Yang, vol. 7078, Springer, 2011, pp. 188–203, doi:<a href=\"https://doi.org/10.1007/978-3-642-25318-8_16\">10.1007/978-3-642-25318-8_16</a>.","ama":"Gupta A, Popeea C, Rybalchenko A. Solving recursion-free Horn clauses over LI+UIF. In: Yang H, ed. Vol 7078. Springer; 2011:188-203. doi:<a href=\"https://doi.org/10.1007/978-3-642-25318-8_16\">10.1007/978-3-642-25318-8_16</a>","chicago":"Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Solving Recursion-Free Horn Clauses over LI+UIF.” edited by Hongseok Yang, 7078:188–203. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-25318-8_16\">https://doi.org/10.1007/978-3-642-25318-8_16</a>.","apa":"Gupta, A., Popeea, C., &#38; Rybalchenko, A. (2011). Solving recursion-free Horn clauses over LI+UIF. In H. Yang (Ed.) (Vol. 7078, pp. 188–203). Presented at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan: Springer. <a href=\"https://doi.org/10.1007/978-3-642-25318-8_16\">https://doi.org/10.1007/978-3-642-25318-8_16</a>","ieee":"A. Gupta, C. Popeea, and A. Rybalchenko, “Solving recursion-free Horn clauses over LI+UIF,” presented at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan, 2011, vol. 7078, pp. 188–203."},"editor":[{"first_name":"Hongseok","full_name":"Yang, Hongseok","last_name":"Yang"}],"publisher":"Springer","date_created":"2018-12-11T12:02:20Z","intvolume":"      7078","doi":"10.1007/978-3-642-25318-8_16","publist_id":"3383","title":"Solving recursion-free Horn clauses over LI+UIF","ec_funded":1},{"intvolume":"        24","publist_id":"3381","title":"Probabilistic joint image segmentation and labeling","page":"1827 - 1835","citation":{"apa":"Ion, A., Carreira, J., &#38; Sminchisescu, C. (2011). Probabilistic joint image segmentation and labeling. In <i>NIPS Proceedings</i> (Vol. 24, pp. 1827–1835). Granada, Spain: Neural Information Processing Systems Foundation.","ieee":"A. Ion, J. Carreira, and C. Sminchisescu, “Probabilistic joint image segmentation and labeling,” in <i>NIPS Proceedings</i>, Granada, Spain, 2011, vol. 24, pp. 1827–1835.","mla":"Ion, Adrian, et al. “Probabilistic Joint Image Segmentation and Labeling.” <i>NIPS Proceedings</i>, vol. 24, Neural Information Processing Systems Foundation, 2011, pp. 1827–35.","ama":"Ion A, Carreira J, Sminchisescu C. Probabilistic joint image segmentation and labeling. In: <i>NIPS Proceedings</i>. Vol 24. Neural Information Processing Systems Foundation; 2011:1827-1835.","chicago":"Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Probabilistic Joint Image Segmentation and Labeling.” In <i>NIPS Proceedings</i>, 24:1827–35. Neural Information Processing Systems Foundation, 2011.","ista":"Ion A, Carreira J, Sminchisescu C. 2011. Probabilistic joint image segmentation and labeling. NIPS Proceedings. NIPS: Neural Information Processing Systems vol. 24, 1827–1835.","short":"A. Ion, J. Carreira, C. Sminchisescu, in:, NIPS Proceedings, Neural Information Processing Systems Foundation, 2011, pp. 1827–1835."},"publisher":"Neural Information Processing Systems Foundation","publication":"NIPS Proceedings","date_created":"2018-12-11T12:02:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2011","publication_status":"published","date_updated":"2021-01-12T07:42:15Z","_id":"3266","type":"conference","volume":24,"status":"public","quality_controlled":"1","date_published":"2011-12-01T00:00:00Z","month":"12","department":[{"_id":"HeEd"}],"author":[{"full_name":"Ion, Adrian","first_name":"Adrian","last_name":"Ion","id":"29F89302-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Carreira, Joao","first_name":"Joao","last_name":"Carreira"},{"last_name":"Sminchisescu","first_name":"Cristian","full_name":"Sminchisescu, Cristian"}],"scopus_import":1,"day":"01","conference":{"end_date":"2011-12-14","name":"NIPS: Neural Information Processing Systems","start_date":"2011-12-12","location":"Granada, Spain"},"oa_version":"None","abstract":[{"text":"We present a joint image segmentation and labeling model (JSL) which, given a bag of figure-ground segment hypotheses extracted at multiple image locations and scales, constructs a joint probability distribution over both the compatible image interpretations (tilings or image segmentations) composed from those segments, and over their labeling into categories. The process of drawing samples from the joint distribution can be interpreted as first sampling tilings, modeled as maximal cliques, from a graph connecting spatially non-overlapping segments in the bag [1], followed by sampling labels for those segments, conditioned on the choice of a particular tiling. We learn the segmentation and labeling parameters jointly, based on Maximum Likelihood with a novel Incremental Saddle Point estimation procedure. The partition function over tilings and labelings is increasingly more accurately approximated by including incorrect configurations that a not-yet-competent model rates probable during learning. We show that the proposed methodologymatches the current state of the art in the Stanford dataset [2], as well as in VOC2010, where 41.7% accuracy on the test set is achieved.","lang":"eng"}],"language":[{"iso":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2011","title":"Hardness results for homology localization","publist_id":"3379","doi":"10.1007/s00454-010-9322-8","intvolume":"        45","date_created":"2018-12-11T12:02:21Z","publication":"Discrete & Computational Geometry","publisher":"Springer","citation":{"ieee":"C. Chen and D. Freedman, “Hardness results for homology localization,” <i>Discrete &#38; Computational Geometry</i>, vol. 45, no. 3. Springer, pp. 425–448, 2011.","apa":"Chen, C., &#38; Freedman, D. (2011). Hardness results for homology localization. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-010-9322-8\">https://doi.org/10.1007/s00454-010-9322-8</a>","ama":"Chen C, Freedman D. Hardness results for homology localization. <i>Discrete &#38; Computational Geometry</i>. 2011;45(3):425-448. doi:<a href=\"https://doi.org/10.1007/s00454-010-9322-8\">10.1007/s00454-010-9322-8</a>","chicago":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s00454-010-9322-8\">https://doi.org/10.1007/s00454-010-9322-8</a>.","mla":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” <i>Discrete &#38; Computational Geometry</i>, vol. 45, no. 3, Springer, 2011, pp. 425–48, doi:<a href=\"https://doi.org/10.1007/s00454-010-9322-8\">10.1007/s00454-010-9322-8</a>.","short":"C. Chen, D. Freedman, Discrete &#38; Computational Geometry 45 (2011) 425–448.","ista":"Chen C, Freedman D. 2011. Hardness results for homology localization. Discrete &#38; Computational Geometry. 45(3), 425–448."},"page":"425 - 448","scopus_import":1,"author":[{"last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","full_name":"Chen, Chao"},{"full_name":"Freedman, Daniel","first_name":"Daniel","last_name":"Freedman"}],"department":[{"_id":"HeEd"}],"month":"01","date_published":"2011-01-14T00:00:00Z","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10909"}]},"abstract":[{"lang":"eng","text":"We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We study the problem with different measures: volume, diameter and radius. For volume, that is, the 1-norm of a cycle, two main results are presented. First, we prove that the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). The latter result leads to the inapproximability of the problem of computing the nonbounding cycle with the smallest volume and computing cycles representing a homology basis with the minimal total volume. As for the other two measures defined by pairwise geodesic distance, diameter and radius, we show that the localization problem is NP-hard for diameter but is polynomial for radius. Our work is restricted to homology over the ℤ2 field."}],"oa_version":"None","day":"14","issue":"3","volume":45,"type":"journal_article","_id":"3267","date_updated":"2023-02-21T16:07:10Z","quality_controlled":"1","status":"public"},{"status":"public","quality_controlled":"1","_id":"3268","date_updated":"2021-01-12T07:42:16Z","type":"book_chapter","oa_version":"None","day":"30","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Algebraic topology is generally considered one of the purest subfield of mathematics. However, over the last decade two interesting new lines of research have emerged, one focusing on algorithms for algebraic topology, and the other on applications of algebraic topology in engineering and science. Amongst the new areas in which the techniques have been applied are computer vision and image processing. In this paper, we survey the results of these endeavours. Because algebraic topology is an area of mathematics with which most computer vision practitioners have no experience, we review the machinery behind the theories of homology and persistent homology; our review emphasizes intuitive explanations. In terms of applications to computer vision, we focus on four illustrative problems: shape signatures, natural image statistics, image denoising, and segmentation. Our hope is that this review will stimulate interest on the part of computer vision researchers to both use and extend the tools of this new field. "}],"extern":"1","month":"11","date_published":"2011-11-30T00:00:00Z","author":[{"full_name":"Freedman, Daniel","first_name":"Daniel","last_name":"Freedman"},{"last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","full_name":"Chen, Chao"}],"citation":{"short":"D. Freedman, C. Chen, in:, Computer Vision, Nova Science Publishers, 2011, pp. 239–268.","ista":"Freedman D, Chen C. 2011.Algebraic topology for computer vision. In: Computer Vision. Computer Science, Technology and Applications, , 239–268.","ama":"Freedman D, Chen C. Algebraic topology for computer vision. In: <i>Computer Vision</i>. Nova Science Publishers; 2011:239-268.","chicago":"Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.” In <i>Computer Vision</i>, 239–68. Nova Science Publishers, 2011.","mla":"Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.” <i>Computer Vision</i>, Nova Science Publishers, 2011, pp. 239–68.","ieee":"D. Freedman and C. Chen, “Algebraic topology for computer vision,” in <i>Computer Vision</i>, Nova Science Publishers, 2011, pp. 239–268.","apa":"Freedman, D., &#38; Chen, C. (2011). Algebraic topology for computer vision. In <i>Computer Vision</i> (pp. 239–268). Nova Science Publishers."},"page":"239 - 268","date_created":"2018-12-11T12:02:22Z","publication":"Computer Vision","publisher":"Nova Science Publishers","title":"Algebraic topology for computer vision","publist_id":"3378","year":"2011","publication_status":"published","main_file_link":[{"url":"http://www.hpl.hp.com/techreports/2009/HPL-2009-375.pdf"}],"alternative_title":["Computer Science, Technology and Applications"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"main_file_link":[{"url":"http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf","open_access":"1"}],"oa":1,"publication_status":"published","year":"2011","publist_id":"3377","intvolume":"        30","publisher":"Wiley-Blackwell","citation":{"ama":"Sheng Y, Cutler B, Chen C, Nasman J. Perceptual global illumination cancellation in complex projection environments. <i>Computer Graphics Forum</i>. 2011;30(4):1261-1268. doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">10.1111/j.1467-8659.2011.01985.x</a>","chicago":"Sheng, Yu, Barbara Cutler, Chao Chen, and Joshua Nasman. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” <i>Computer Graphics Forum</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">https://doi.org/10.1111/j.1467-8659.2011.01985.x</a>.","mla":"Sheng, Yu, et al. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” <i>Computer Graphics Forum</i>, vol. 30, no. 4, Wiley-Blackwell, 2011, pp. 1261–68, doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">10.1111/j.1467-8659.2011.01985.x</a>.","short":"Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011) 1261–1268.","ista":"Sheng Y, Cutler B, Chen C, Nasman J. 2011. Perceptual global illumination cancellation in complex projection environments. Computer Graphics Forum. 30(4), 1261–1268.","ieee":"Y. Sheng, B. Cutler, C. Chen, and J. Nasman, “Perceptual global illumination cancellation in complex projection environments,” <i>Computer Graphics Forum</i>, vol. 30, no. 4. Wiley-Blackwell, pp. 1261–1268, 2011.","apa":"Sheng, Y., Cutler, B., Chen, C., &#38; Nasman, J. (2011). Perceptual global illumination cancellation in complex projection environments. <i>Computer Graphics Forum</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">https://doi.org/10.1111/j.1467-8659.2011.01985.x</a>"},"article_processing_charge":"No","month":"07","department":[{"_id":"HeEd"}],"abstract":[{"text":"The unintentional scattering of light between neighboring surfaces in complex projection environments increases the brightness and decreases the contrast, disrupting the appearance of the desired imagery. To achieve satisfactory projection results, the inverse problem of global illumination must be solved to cancel this secondary scattering. In this paper, we propose a global illumination cancellation method that minimizes the perceptual difference between the desired imagery and the actual total illumination in the resulting physical environment. Using Gauss-Newton and active set methods, we design a fast solver for the bound constrained nonlinear least squares problem raised by the perceptual error metrics. Our solver is further accelerated with a CUDA implementation and multi-resolution method to achieve 1–2 fps for problems with approximately 3000 variables. We demonstrate the global illumination cancellation algorithm with our multi-projector system. Results show that our method preserves the color fidelity of the desired imagery significantly better than previous methods.","lang":"eng"}],"article_type":"original","issue":"4","day":"19","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Perceptual global illumination cancellation in complex projection environments","doi":"10.1111/j.1467-8659.2011.01985.x","publication":"Computer Graphics Forum","date_created":"2018-12-11T12:02:22Z","page":"1261 - 1268","author":[{"first_name":"Yu","full_name":"Sheng, Yu","last_name":"Sheng"},{"first_name":"Barbara","full_name":"Cutler, Barbara","last_name":"Cutler"},{"full_name":"Chen, Chao","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen"},{"last_name":"Nasman","full_name":"Nasman, Joshua","first_name":"Joshua"}],"scopus_import":1,"date_published":"2011-07-19T00:00:00Z","language":[{"iso":"eng"}],"volume":30,"date_updated":"2021-01-12T07:42:16Z","_id":"3269","type":"journal_article","quality_controlled":"1","status":"public"},{"year":"2011","publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Chen C, Kerber M. 2011. Persistent homology computation with a twist. EuroCG: European Workshop on Computational Geometry, 197–200.","short":"C. Chen, M. Kerber, in:, TU Dortmund, 2011, pp. 197–200.","mla":"Chen, Chao, and Michael Kerber. <i>Persistent Homology Computation with a Twist</i>. TU Dortmund, 2011, pp. 197–200.","ama":"Chen C, Kerber M. Persistent homology computation with a twist. In: TU Dortmund; 2011:197-200.","chicago":"Chen, Chao, and Michael Kerber. “Persistent Homology Computation with a Twist,” 197–200. TU Dortmund, 2011.","apa":"Chen, C., &#38; Kerber, M. (2011). Persistent homology computation with a twist (pp. 197–200). Presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland: TU Dortmund.","ieee":"C. Chen and M. Kerber, “Persistent homology computation with a twist,” presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland, 2011, pp. 197–200."},"page":"197 - 200","date_created":"2018-12-11T12:02:22Z","publisher":"TU Dortmund","publist_id":"3376","title":"Persistent homology computation with a twist","conference":{"end_date":"2011-03-30","name":"EuroCG: European Workshop on Computational Geometry","start_date":"2011-03-28","location":"Morschach, Switzerland"},"oa_version":"None","day":"01","language":[{"iso":"eng"}],"abstract":[{"text":"The persistence diagram of a filtered simplicial com- plex is usually computed by reducing the boundary matrix of the complex. We introduce a simple op- timization technique: by processing the simplices of the complex in decreasing dimension, we can “kill” columns (i.e., set them to zero) without reducing them. This technique completely avoids reduction on roughly half of the columns. We demonstrate that this idea significantly improves the running time of the reduction algorithm in practice. We also give an output-sensitive complexity analysis for the new al- gorithm which yields to sub-cubic asymptotic bounds under certain assumptions.","lang":"eng"}],"date_published":"2011-01-01T00:00:00Z","department":[{"_id":"HeEd"}],"month":"01","author":[{"full_name":"Chen, Chao","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen"},{"full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","first_name":"Michael","last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"}],"status":"public","quality_controlled":"1","_id":"3270","date_updated":"2021-01-12T07:42:17Z","type":"conference"},{"title":"Efficient computation of persistent homology for cubical data","publist_id":"3375","doi":"10.1007/978-3-642-23175-9_7","editor":[{"full_name":"Peikert, Ronald","first_name":"Ronald","last_name":"Peikert"},{"last_name":"Hauser","full_name":"Hauser, Helwig","first_name":"Helwig"},{"first_name":"Hamish","full_name":"Carr, Hamish","last_name":"Carr"},{"first_name":"Raphael","full_name":"Fuchs, Raphael","last_name":"Fuchs"}],"publisher":"Springer","publication":"Topological Methods in Data Analysis and Visualization II","date_created":"2018-12-11T12:02:23Z","page":"91 - 106","citation":{"ista":"Wagner H, Chen C, Vuçini E. 2011.Efficient computation of persistent homology for cubical data. In: Topological Methods in Data Analysis and Visualization II. Theory, Algorithms, and Applications, , 91–106.","short":"H. Wagner, C. Chen, E. Vuçini, in:, R. Peikert, H. Hauser, H. Carr, R. Fuchs (Eds.), Topological Methods in Data Analysis and Visualization II, Springer, 2011, pp. 91–106.","mla":"Wagner, Hubert, et al. “Efficient Computation of Persistent Homology for Cubical Data.” <i>Topological Methods in Data Analysis and Visualization II</i>, edited by Ronald Peikert et al., Springer, 2011, pp. 91–106, doi:<a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">10.1007/978-3-642-23175-9_7</a>.","chicago":"Wagner, Hubert, Chao Chen, and Erald Vuçini. “Efficient Computation of Persistent Homology for Cubical Data.” In <i>Topological Methods in Data Analysis and Visualization II</i>, edited by Ronald Peikert, Helwig Hauser, Hamish Carr, and Raphael Fuchs, 91–106. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">https://doi.org/10.1007/978-3-642-23175-9_7</a>.","ama":"Wagner H, Chen C, Vuçini E. Efficient computation of persistent homology for cubical data. In: Peikert R, Hauser H, Carr H, Fuchs R, eds. <i>Topological Methods in Data Analysis and Visualization II</i>. Springer; 2011:91-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">10.1007/978-3-642-23175-9_7</a>","apa":"Wagner, H., Chen, C., &#38; Vuçini, E. (2011). Efficient computation of persistent homology for cubical data. In R. Peikert, H. Hauser, H. Carr, &#38; R. Fuchs (Eds.), <i>Topological Methods in Data Analysis and Visualization II</i> (pp. 91–106). Springer. <a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">https://doi.org/10.1007/978-3-642-23175-9_7</a>","ieee":"H. Wagner, C. Chen, and E. Vuçini, “Efficient computation of persistent homology for cubical data,” in <i>Topological Methods in Data Analysis and Visualization II</i>, R. Peikert, H. Hauser, H. Carr, and R. Fuchs, Eds. Springer, 2011, pp. 91–106."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","alternative_title":["Theory, Algorithms, and Applications"],"publication_status":"published","year":"2011","date_updated":"2021-01-12T07:42:18Z","_id":"3271","type":"book_chapter","quality_controlled":"1","status":"public","author":[{"last_name":"Wagner","full_name":"Wagner, Hubert","first_name":"Hubert"},{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao"},{"first_name":"Erald","full_name":"Vuçini, Erald","last_name":"Vuçini"}],"scopus_import":1,"department":[{"_id":"HeEd"}],"date_published":"2011-11-14T00:00:00Z","month":"11","abstract":[{"lang":"eng","text":"In this paper we present an efficient framework for computation of persis- tent homology of cubical data in arbitrary dimensions. An existing algorithm using simplicial complexes is adapted to the setting of cubical complexes. The proposed approach enables efficient application of persistent homology in domains where the data is naturally given in a cubical form. By avoiding triangulation of the data, we significantly reduce the size of the complex. We also present a data-structure de- signed to compactly store and quickly manipulate cubical complexes. By means of numerical experiments, we show high speed and memory efficiency of our ap- proach. We compare our framework to other available implementations, showing its superiority. Finally, we report performance on selected 3D and 4D data-sets."}],"language":[{"iso":"eng"}],"day":"14","oa_version":"None"},{"publication_identifier":{"issn":["2663-337X"]},"publist_id":"3373","title":"Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors","date_created":"2018-12-11T12:02:23Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","citation":{"chicago":"Maître, Jean-Léon. “Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors.” Institute of Science and Technology Austria, 2011.","ama":"Maître J-L. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. 2011.","mla":"Maître, Jean-Léon. <i>Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors</i>. Institute of Science and Technology Austria, 2011.","short":"J.-L. Maître, Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors, Institute of Science and Technology Austria, 2011.","ista":"Maître J-L. 2011. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. Institute of Science and Technology Austria.","ieee":"J.-L. Maître, “Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors,” Institute of Science and Technology Austria, 2011.","apa":"Maître, J.-L. (2011). <i>Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors</i>. Institute of Science and Technology Austria."},"alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","year":"2011","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"_id":"3273","date_updated":"2023-09-07T11:30:16Z","type":"dissertation","status":"public","author":[{"first_name":"Jean-Léon","full_name":"Maître, Jean-Léon","orcid":"0000-0002-3688-1474","last_name":"Maître","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"CaHe"}],"month":"12","date_published":"2011-12-12T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"oa_version":"None","day":"12"},{"ddc":["570","579"],"year":"2011","oa":1,"publication_status":"published","alternative_title":["ISTA Thesis"],"file":[{"file_size":4487708,"date_created":"2019-03-26T08:12:21Z","file_name":"2011_Thesis_Kathrin_Schumann.pdf","date_updated":"2020-07-14T12:46:06Z","content_type":"application/pdf","relation":"main_file","checksum":"e69eee6252660f0b694a2ea8923ddc72","creator":"dernst","access_level":"closed","file_id":"6177"},{"date_created":"2021-02-22T11:24:30Z","file_size":4313127,"file_name":"2011_Thesis_Schumann_noS.pdf","success":1,"content_type":"application/pdf","date_updated":"2021-02-22T11:24:30Z","checksum":"71727d63f424b5b446f68f4b87ecadc0","relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"9175"}],"citation":{"apa":"Schumann, K. (2011). <i>The role of chemotactic gradients in dendritic cell migration</i>. Institute of Science and Technology Austria.","ieee":"K. Schumann, “The role of chemotactic gradients in dendritic cell migration,” Institute of Science and Technology Austria, 2011.","mla":"Schumann, Kathrin. <i>The Role of Chemotactic Gradients in Dendritic Cell Migration</i>. Institute of Science and Technology Austria, 2011.","chicago":"Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell Migration.” Institute of Science and Technology Austria, 2011.","ama":"Schumann K. The role of chemotactic gradients in dendritic cell migration. 2011.","ista":"Schumann K. 2011. The role of chemotactic gradients in dendritic cell migration. Institute of Science and Technology Austria.","short":"K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration, Institute of Science and Technology Austria, 2011."},"publisher":"Institute of Science and Technology Austria","publist_id":"3371","publication_identifier":{"issn":["2663-337X"]},"day":"01","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Chemokines organize immune cell trafficking by inducing either directed (tactic) or random (kinetic) migration and by activating integrins in order to support surface adhesion (haptic). Beyond that the same chemokines can establish clearly defined functional areas in secondary lymphoid organs. Until now it is unclear how chemokines can fulfill such diverse functions. One decisive prerequisite to explain these capacities is to know how chemokines are presented in tissue. In theory chemokines could occur either soluble or immobilized, and could be distributed either homogenously or as a concentration gradient. To dissect if and how the presenting mode of chemokines influences immune cells, I tested the response of dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen presenting cells that reside in the periphery and migrate into draining lymph nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs are guided to and within the LN by the chemokine receptor CCR7, which has two ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic reticular cells in the LN, but differ in their ability to bind to heparan sulfate residues. CCL21 has a highly charged C-terminal extension, which mediates binding to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes as a soluble molecule. This study shows that surface-bound CCL21 causes random, haptokinetic DC motility, which is confined to the chemokine coated area by insideout activation of β2 integrins that mediate cell binding to the surface. CCL19 on the other hand forms concentration gradients which trigger directional, chemotactic movement, but no surface adhesion. In addition DCs can actively manipulate this system by recruiting and activating serine proteases on their surfaces, which create - by proteolytically removing the adhesive C-terminus - a solubilized variant of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration gradient DCs establish a positive feedback loop to recruit further DCs from the periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients as well as immobilized haptokinetic fields at the same time and integrate these signals. The result is chemotactically biased haptokinesis - directional migration confined to a chemokine coated track or area - which could explain the dynamic but spatially tightly controlled swarming leukocyte locomotion patterns that have been observed in lymphatic organs by intravital microscopists. The finding that DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces coated with immobilized cues raises the question how these cells transmit intracellular forces to the environment, especially in the non-adherent migration mode. In order to migrate, cells have to generate and transmit force to the extracellular substrate. Force transmission is the prerequisite to procure an expansion of the leading edge and a forward motion of the whole cell body. In the current conceptions actin polymerization at the leading edge is coupled to extracellular ligands via the integrin family of transmembrane receptors, which allows the transmission of intracellular force. Against the paradigm of force transmission during migration, leukocytes, like DCs, are able to migrate in threedimensional environments without using integrin transmembrane receptors (Lämmermann et al., 2008). This reflects the biological function of leukocytes, as they can invade almost all tissues, whereby their migration has to be independent from the extracellular environment. How the cells can achieve this is unclear. For this study I examined DC migration in a defined threedimensional environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result was that chemotactic DCs can switch between integrin-dependent and integrin- independent locomotion and can thereby adapt to the adhesive properties of their environment. If the cells are able to couple their actin cytoskeleton to the substrate, actin polymerization is entirely converted into protrusion. Without coupling the actin cortex undergoes slippage and retrograde actin flow can be observed. But retrograde actin flow can be completely compensated by higher actin polymerization rate keeping the migration velocity and the shape of the cells unaltered. Mesenchymal cells like fibroblast cannot balance the loss of adhesive interaction, cannot protrude into open space and, therefore, strictly depend on integrinmediated force coupling. This leukocyte specific phenomenon of “adaptive force transmission” endows these cells with the unique ability to transit and invade almost every type of tissue. "}],"article_processing_charge":"No","month":"03","department":[{"_id":"MiSi"}],"file_date_updated":"2021-02-22T11:24:30Z","acknowledgement":"I would like to express my sincere gratitude to the following people who made with their continuous support and encouragement this thesis possible: First, I want to thank Prof. Dr. Michael Sixt for his excellent supervision and mentoring, especially for the nice, relaxed working atmosphere, a lot of brilliant ideas and the freedom to work in my own way.\r\n\r\nProf. Dr. Reinhard Fässler for his constant support of the Sixt lab and for providing excellent working conditions. \r\n\r\nProf. Dr. Sanjiv Luther and Prof. Dr. Tobias Bollenbach for agreeing to be member of my thesis committee and to evaluate my work.\r\n\r\nDr. Walther Göhring, Carmen Schmitz, the Recombinant Protein Production core facility and the animal care takers for providing the “infrastructure” for this thesis. \r\n\r\nProf. Dr. Daniel Legler, Markus Bruckner and Dr. Julien Polleux for very fruitful collaborations and discussions.\r\n\r\nMy labmates for their help, a lot of discussions and to make the Sixt lab to a convenient place to work : Karin Hirsch, Tim Lämmeramnn, Holger Pflicke, Jörg Renkawitz, Michele Weber and Alexander Eichner All members of the Department of Molecular Medicine for their help. Especially I want to thank Sarah Schmidt, Karin Hirsch and Raphael Ruppert for their friendship, nice chats and their uncensored point of view. ","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"141","has_accepted_license":"1","degree_awarded":"PhD","date_created":"2018-12-11T12:02:24Z","title":"The role of chemotactic gradients in dendritic cell migration","language":[{"iso":"eng"}],"pubrep_id":"11","date_published":"2011-03-01T00:00:00Z","author":[{"id":"F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F","last_name":"Schumann","first_name":"Kathrin","full_name":"Schumann, Kathrin"}],"status":"public","_id":"3275","type":"dissertation","date_updated":"2023-09-07T11:31:48Z","supervisor":[{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K"}]},{"abstract":[{"text":"We present an algorithm to identify individual neural spikes observed on high-density multi-electrode arrays (MEAs). Our method can distinguish large numbers of distinct neural units, even when spikes overlap, and accounts for intrinsic variability of spikes from each unit. As MEAs grow larger, it is important to find spike-identification methods that are scalable, that is, the computational cost of spike fitting should scale well with the number of units observed. Our algorithm accomplishes this goal, and is fast, because it exploits the spatial locality of each unit and the basic biophysics of extracellular signal propagation. Human interaction plays a key role in our method; but effort is minimized and streamlined via a graphical interface. We illustrate our method on data from guinea pig retinal ganglion cells and document its performance on simulated data consisting of spikes added to experimentally measured background noise. We present several tests demonstrating that the algorithm is highly accurate: it exhibits low error rates on fits to synthetic data, low refractory violation rates, good receptive field coverage, and consistency across users.","lang":"eng"}],"day":"20","issue":"7","author":[{"first_name":"Jason","full_name":"Prentice, Jason S","last_name":"Prentice"},{"last_name":"Homann","full_name":"Homann, Jan","first_name":"Jan"},{"full_name":"Simmons, Kristina D","first_name":"Kristina","last_name":"Simmons"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Gasper Tkacik","orcid":"0000-0002-6699-1455"},{"first_name":"Vijay","full_name":"Balasubramanian, Vijay","last_name":"Balasubramanian"},{"last_name":"Nelson","full_name":"Nelson, Philip C","first_name":"Philip"}],"extern":1,"date_published":"2011-07-20T00:00:00Z","pubrep_id":"381","month":"07","quality_controlled":0,"status":"public","file_date_updated":"2020-07-14T12:46:06Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"volume":6,"date_updated":"2021-01-12T07:42:19Z","_id":"3276","type":"journal_article","oa":1,"publication_status":"published","year":"2011","acknowledgement":"This work was supported by National Science Foundation (NSF) grants IBN-0344678, EF-0928048, National Institutes of Health (NIH) grant RO1 EY08124, NIH training grant T32-07035, and NIH training grant 5T90DA022763-04.\n\nMichael Berry and Olivier Marre have developed an algorithm similar to, but different from, ours (manuscript in preparation). We thank them for discussions of their work, and specifically thank Olivier Marre for suggesting to us that the most complete subtraction of a spike can be obtained by refitting the spike without a prior.\n\n","publisher":"Public Library of Science","date_created":"2018-12-11T12:02:24Z","publication":"PLoS One","citation":{"mla":"Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” <i>PLoS One</i>, vol. 6, no. 7, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pone.0019884\">10.1371/journal.pone.0019884</a>.","ama":"Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. Fast, scalable, Bayesian spike identification for multi-electrode arrays. <i>PLoS One</i>. 2011;6(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0019884\">10.1371/journal.pone.0019884</a>","chicago":"Prentice, Jason, Jan Homann, Kristina Simmons, Gašper Tkačik, Vijay Balasubramanian, and Philip Nelson. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” <i>PLoS One</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pone.0019884\">https://doi.org/10.1371/journal.pone.0019884</a>.","ista":"Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. 2011. Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. 6(7).","short":"J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, P. Nelson, PLoS One 6 (2011).","apa":"Prentice, J., Homann, J., Simmons, K., Tkačik, G., Balasubramanian, V., &#38; Nelson, P. (2011). Fast, scalable, Bayesian spike identification for multi-electrode arrays. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0019884\">https://doi.org/10.1371/journal.pone.0019884</a>","ieee":"J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, and P. Nelson, “Fast, scalable, Bayesian spike identification for multi-electrode arrays,” <i>PLoS One</i>, vol. 6, no. 7. Public Library of Science, 2011."},"file":[{"relation":"main_file","checksum":"654464e99683b55a699734213d5356f1","creator":"system","access_level":"open_access","file_id":"4894","file_size":885464,"date_created":"2018-12-12T10:11:38Z","file_name":"IST-2015-381-v1+1_journal.pone.0019884.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:06Z"}],"publist_id":"3370","title":"Fast, scalable, Bayesian spike identification for multi-electrode arrays","intvolume":"         6","doi":"10.1371/journal.pone.0019884","license":"https://creativecommons.org/licenses/by/4.0/"},{"abstract":[{"text":"Despite much research on the socially parasitic large blue butterflies (genus Maculinea) in the past 40 years, their relationship to their closest relatives, Phengaris, is controversial and the relationships among the remaining genera in the Glaucopsyche section are largely unresolved. The evolutionary history of this butterfly section is particularly important to understand the evolution of life history diversity con- nected to food-plant and host-ant associations in the larval stage. In the present study, we use a combi- nation of four nuclear and two mitochondrial genes to reconstruct the phylogeny of the Glaucopsyche section, and in particular, to study the relationships among and within the Phengaris–Maculinea species.\nWe find a clear pattern between the clades recovered in the Glaucopsyche section phylogeny and their food-plant associations, with only the Phengaris–Maculinea clade utilising more than one plant family. Maculinea is, for the first time, recovered with strong support as a monophyletic group nested within Phengaris, with the closest relative being the rare genus Caerulea. The genus Glaucopsyche is polyphyletic, including the genera Sinia and Iolana. Interestingly, we find evidence for additional potential cryptic spe- cies within the highly endangered Maculinea, which has long been suspected from morphological, ecolog- ical and molecular studies.","lang":"eng"}],"issue":"1","day":"01","author":[{"first_name":"Roger","full_name":"Vila, Roger","last_name":"Vila"},{"first_name":"Naomi","full_name":"Pierce, Naomi E","last_name":"Pierce"},{"last_name":"Nash","first_name":"David","full_name":"Nash, David R"},{"id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","first_name":"Line V","orcid":"0000-0003-1832-8883","full_name":"Line Ugelvig"}],"extern":1,"date_published":"2011-10-01T00:00:00Z","month":"10","quality_controlled":0,"status":"public","volume":61,"type":"journal_article","_id":"3278","date_updated":"2021-01-12T07:42:20Z","publication_status":"published","year":"2011","date_created":"2018-12-11T12:02:25Z","publication":"Molecular Phylogenetics and Evolution","publisher":"Elsevier","citation":{"ieee":"R. Vila, N. Pierce, D. Nash, and L. V. Ugelvig, “A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade,” <i>Molecular Phylogenetics and Evolution</i>, vol. 61, no. 1. Elsevier, pp. 237–243, 2011.","apa":"Vila, R., Pierce, N., Nash, D., &#38; Ugelvig, L. V. (2011). A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. <i>Molecular Phylogenetics and Evolution</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ympev.2011.05.016\">https://doi.org/10.1016/j.ympev.2011.05.016</a>","short":"R. Vila, N. Pierce, D. Nash, L.V. Ugelvig, Molecular Phylogenetics and Evolution 61 (2011) 237–243.","ista":"Vila R, Pierce N, Nash D, Ugelvig LV. 2011. A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution. 61(1), 237–243.","ama":"Vila R, Pierce N, Nash D, Ugelvig LV. A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. <i>Molecular Phylogenetics and Evolution</i>. 2011;61(1):237-243. doi:<a href=\"https://doi.org/10.1016/j.ympev.2011.05.016\">10.1016/j.ympev.2011.05.016</a>","chicago":"Vila, Roger, Naomi Pierce, David Nash, and Line V Ugelvig. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” <i>Molecular Phylogenetics and Evolution</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.ympev.2011.05.016\">https://doi.org/10.1016/j.ympev.2011.05.016</a>.","mla":"Vila, Roger, et al. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” <i>Molecular Phylogenetics and Evolution</i>, vol. 61, no. 1, Elsevier, 2011, pp. 237–43, doi:<a href=\"https://doi.org/10.1016/j.ympev.2011.05.016\">10.1016/j.ympev.2011.05.016</a>."},"page":"237 - 243","publist_id":"3368","title":"A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade","doi":"10.1016/j.ympev.2011.05.016","intvolume":"        61"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Y 250-B03/Austrian Science Fund FWF/Austria","publication_status":"published","year":"2011","publist_id":"3360","title":"Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes","doi":"10.1016/j.bpj.2011.04.035","intvolume":"       100","date_created":"2018-12-11T12:02:27Z","publication":"Biophysical Journal","publisher":"Biophysical Society","citation":{"ista":"Ruprecht V, Wieser S, Marguet D, Schuetz G. 2011. Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. Biophysical Journal. 100(11), 2839–2845.","short":"V. Ruprecht, S. Wieser, D. Marguet, G. Schuetz, Biophysical Journal 100 (2011) 2839–2845.","mla":"Ruprecht, Verena, et al. “Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” <i>Biophysical Journal</i>, vol. 100, no. 11, Biophysical Society, 2011, pp. 2839–45, doi:<a href=\"https://doi.org/10.1016/j.bpj.2011.04.035\">10.1016/j.bpj.2011.04.035</a>.","chicago":"Ruprecht, Verena, Stefan Wieser, Didier Marguet, and Gerhard Schuetz. “Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” <i>Biophysical Journal</i>. Biophysical Society, 2011. <a href=\"https://doi.org/10.1016/j.bpj.2011.04.035\">https://doi.org/10.1016/j.bpj.2011.04.035</a>.","ama":"Ruprecht V, Wieser S, Marguet D, Schuetz G. Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. <i>Biophysical Journal</i>. 2011;100(11):2839-2845. doi:<a href=\"https://doi.org/10.1016/j.bpj.2011.04.035\">10.1016/j.bpj.2011.04.035</a>","apa":"Ruprecht, V., Wieser, S., Marguet, D., &#38; Schuetz, G. (2011). Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2011.04.035\">https://doi.org/10.1016/j.bpj.2011.04.035</a>","ieee":"V. Ruprecht, S. Wieser, D. Marguet, and G. Schuetz, “Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes,” <i>Biophysical Journal</i>, vol. 100, no. 11. Biophysical Society, pp. 2839–2845, 2011."},"page":"2839 - 2845","author":[{"id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","first_name":"Verena","orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena"},{"last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217","first_name":"Stefan"},{"first_name":"Didier","full_name":"Marguet, Didier","last_name":"Marguet"},{"first_name":"Gerhard","full_name":"Schuetz, Gerhard","last_name":"Schuetz"}],"date_published":"2011-06-08T00:00:00Z","extern":"1","month":"06","language":[{"iso":"eng"}],"abstract":[{"text":"Resolving the dynamical interplay of proteins and lipids in the live-cell plasma membrane represents a central goal in current cell biology. Superresolution concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic length scale. Similar concepts for detecting dynamical transitions (superresolution chronoscopy) are still lacking. Here, we show that recently introduced spot-variation fluorescence correlation spectroscopy allows for sensing transient confinement times of membrane constituents at dramatically improved resolution. Using standard diffraction-limited optics, spot-variation fluorescence correlation spectroscopy captures signatures of single retardation events far below the transit time of the tracer through the focal spot. We provide an analytical description of special cases of transient binding of a tracer to pointlike traps, or association of a tracer with nanodomains. The influence of trap mobility and the underlying binding kinetics are quantified. Experimental approaches are suggested that allow for gaining quantitative mechanistic insights into the interaction processes of membrane constituents.","lang":"eng"}],"oa_version":"None","day":"08","issue":"11","volume":100,"date_updated":"2021-01-12T07:42:23Z","_id":"3285","type":"journal_article","status":"public"},{"publist_id":"3359","title":"Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","intvolume":"      1808","doi":"10.1016/j.bbamem.2011.06.007","publication":"Biochimica et Biophysica Acta (BBA) - Biomembranes","date_created":"2018-12-11T12:02:28Z","publisher":"Elsevier","citation":{"mla":"Weghuber, Julian, et al. “Cationic Amphipathic Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” <i>Biochimica et Biophysica Acta (BBA) - Biomembranes</i>, vol. 1808, no. 10, Elsevier, 2011, pp. 2581–90, doi:<a href=\"https://doi.org/10.1016/j.bbamem.2011.06.007\">10.1016/j.bbamem.2011.06.007</a>.","chicago":"Weghuber, Julian, Michael Aichinger, Mario Brameshuber, Stefan Wieser, Verena Ruprecht, Birgit Plochberger, Josef Madl, et al. “Cationic Amphipathic Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” <i>Biochimica et Biophysica Acta (BBA) - Biomembranes</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.bbamem.2011.06.007\">https://doi.org/10.1016/j.bbamem.2011.06.007</a>.","ama":"Weghuber J, Aichinger M, Brameshuber M, et al. Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. <i>Biochimica et Biophysica Acta (BBA) - Biomembranes</i>. 2011;1808(10):2581-2590. doi:<a href=\"https://doi.org/10.1016/j.bbamem.2011.06.007\">10.1016/j.bbamem.2011.06.007</a>","ista":"Weghuber J, Aichinger M, Brameshuber M, Wieser S, Ruprecht V, Plochberger B, Madl J, Horner A, Reipert S, Lohner K, Henics T, Schuetz G. 2011. Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1808(10), 2581–2590.","short":"J. Weghuber, M. Aichinger, M. Brameshuber, S. Wieser, V. Ruprecht, B. Plochberger, J. Madl, A. Horner, S. Reipert, K. Lohner, T. Henics, G. Schuetz, Biochimica et Biophysica Acta (BBA) - Biomembranes 1808 (2011) 2581–2590.","apa":"Weghuber, J., Aichinger, M., Brameshuber, M., Wieser, S., Ruprecht, V., Plochberger, B., … Schuetz, G. (2011). Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. <i>Biochimica et Biophysica Acta (BBA) - Biomembranes</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbamem.2011.06.007\">https://doi.org/10.1016/j.bbamem.2011.06.007</a>","ieee":"J. Weghuber <i>et al.</i>, “Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells,” <i>Biochimica et Biophysica Acta (BBA) - Biomembranes</i>, vol. 1808, no. 10. Elsevier, pp. 2581–2590, 2011."},"page":"2581 - 2590","acknowledgement":"This work was funded by the GEN-AU project of the Austrian Research Promotion Agency, the Austrian Science Fund (FWF; project Y250-B03) and Intercell AG.\nWe thank the following colleagues for providing plasmids and cells: Daniel Legler (University of Konstanz, Switzerland), Jennifer Lippincott-Schwartz (NIH, Bethesda, USA), Hannes Stockinger (Medical University Vienna, Austria), Katharina Strub (University of Geneva, Switzerland), Lawrence Rajendran (ETH Zurich, Switzerland), Eileen M. Lafer (UTHSC San Antonio, Texas, USA), Mark McNiven (Mayo Clinic, Minnesota, USA), John Silvius (McGill University, Montreal, Canada), Christoph Romanin (JKU Linz, Austria), Herbert Stangl (Medical University Vienna, Austria) and Anton van der Merwe (Oxford University, Oxford, UK). We thank Harald Kotisch (MFPL, Vienna) for excellent technical assistance in the processing of samples for electron microscopy and Sergio Grinstein (Hospital for Sick Children Research Institute, Toronto) for fruitful discussions. ","publication_status":"published","year":"2011","volume":1808,"type":"journal_article","_id":"3286","date_updated":"2021-01-12T07:42:24Z","quality_controlled":0,"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","author":[{"first_name":"Julian","full_name":"Weghuber, Julian","last_name":"Weghuber"},{"first_name":"Michael","full_name":"Aichinger, Michael C.","last_name":"Aichinger"},{"full_name":"Brameshuber, Mario","first_name":"Mario","last_name":"Brameshuber"},{"full_name":"Stefan Wieser","orcid":"0000-0002-2670-2217","first_name":"Stefan","last_name":"Wieser","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4088-8633","full_name":"Verena Ruprecht","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht"},{"last_name":"Plochberger","first_name":"Birgit","full_name":"Plochberger, Birgit"},{"first_name":"Josef","full_name":"Madl, Josef","last_name":"Madl"},{"last_name":"Horner","full_name":"Horner, Andreas","first_name":"Andreas"},{"last_name":"Reipert","first_name":"Siegfried","full_name":"Reipert, Siegfried"},{"last_name":"Lohner","first_name":"Karl","full_name":"Lohner, Karl"},{"last_name":"Henics","full_name":"Henics, Tamas","first_name":"Tamas"},{"first_name":"Gerhard","full_name":"Schuetz, Gerhard J","last_name":"Schuetz"}],"date_published":"2011-10-01T00:00:00Z","extern":1,"month":"10","abstract":[{"text":"Cationic antimicrobial peptides (CAMPs) selectively target bacterial membranes by electrostatic interactions with negatively charged lipids. It turned out that for inhibition of microbial growth a high CAMP membrane concentration is required, which can be realized by the incorporation of hydrophobic groups within the peptide. Increasing hydrophobicity, however, reduces the CAMP selectivity for bacterial over eukaryotic host membranes, thereby causing the risk of detrimental side-effects. In this study we addressed how cationic amphipathic peptides—in particular a CAMP with Lysine–Leucine–Lysine repeats (termed KLK)—affect the localization and dynamics of molecules in eukaryotic membranes. We found KLK to selectively inhibit the endocytosis of a subgroup of membrane proteins and lipids by electrostatically interacting with negatively charged sialic acid moieties. Ultrastructural characterization revealed the formation of membrane invaginations representing fission or fusion intermediates, in which the sialylated proteins and lipids were immobilized. Experiments on structurally different cationic amphipathic peptides (KLK, 6-MO-LF11-322 and NK14-2) indicated a cooperation of electrostatic and hydrophobic forces that selectively arrest sialylated membrane constituents.","lang":"eng"}],"day":"01","issue":"10"},{"author":[{"orcid":"0000-0003-4088-8633","full_name":"Ruprecht, Verena","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht"},{"first_name":"Markus","full_name":"Axmann, Markus","last_name":"Axmann"},{"orcid":"0000-0002-2670-2217","full_name":"Wieser, Stefan","first_name":"Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","last_name":"Wieser"},{"last_name":"Schuetz","full_name":"Schuetz, Gerhard","first_name":"Gerhard"}],"scopus_import":1,"month":"12","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"date_published":"2011-12-01T00:00:00Z","abstract":[{"text":"Diffusing membrane constituents are constantly exposed to a variety of forces that influence their stochastic path. Single molecule experiments allow for resolving trajectories at extremely high spatial and temporal accuracy, thereby offering insights into en route interactions of the tracer. In this review we discuss approaches to derive information about the underlying processes, based on single molecule tracking experiments. In particular, we focus on a new versatile way to analyze single molecule diffusion in the absence of a full analytical treatment. The method is based on comprehensive comparison of an experimental data set against the hypothetical outcome of multiple experiments performed on the computer. Since Monte Carlo simulations can be easily and rapidly performed even on state-of-the-art PCs, our method provides a simple way for testing various - even complicated - diffusion models. We describe the new method in detail, and show the applicability on two specific examples: firstly, kinetic rate constants can be derived for the transient interaction of mobile membrane proteins; secondly, residence time and corral size can be extracted for confined diffusion.","lang":"eng"}],"language":[{"iso":"eng"}],"issue":"8","day":"01","oa_version":"None","volume":12,"type":"journal_article","_id":"3287","date_updated":"2021-01-12T07:42:24Z","quality_controlled":"1","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2011","title":"What can we learn from single molecule trajectories?","publist_id":"3358","doi":"10.2174/138920311798841753","intvolume":"        12","publisher":"Bentham Science Publishers","publication":"Current Protein & Peptide Science","date_created":"2018-12-11T12:02:28Z","page":"714 - 724","citation":{"short":"V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein &#38; Peptide Science 12 (2011) 714–724.","ista":"Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single molecule trajectories? Current Protein &#38; Peptide Science. 12(8), 714–724.","ama":"Ruprecht V, Axmann M, Wieser S, Schuetz G. What can we learn from single molecule trajectories? <i>Current Protein &#38; Peptide Science</i>. 2011;12(8):714-724. doi:<a href=\"https://doi.org/10.2174/138920311798841753\">10.2174/138920311798841753</a>","chicago":"Ruprecht, Verena, Markus Axmann, Stefan Wieser, and Gerhard Schuetz. “What Can We Learn from Single Molecule Trajectories?” <i>Current Protein &#38; Peptide Science</i>. Bentham Science Publishers, 2011. <a href=\"https://doi.org/10.2174/138920311798841753\">https://doi.org/10.2174/138920311798841753</a>.","mla":"Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?” <i>Current Protein &#38; Peptide Science</i>, vol. 12, no. 8, Bentham Science Publishers, 2011, pp. 714–24, doi:<a href=\"https://doi.org/10.2174/138920311798841753\">10.2174/138920311798841753</a>.","ieee":"V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from single molecule trajectories?,” <i>Current Protein &#38; Peptide Science</i>, vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011.","apa":"Ruprecht, V., Axmann, M., Wieser, S., &#38; Schuetz, G. (2011). What can we learn from single molecule trajectories? <i>Current Protein &#38; Peptide Science</i>. Bentham Science Publishers. <a href=\"https://doi.org/10.2174/138920311798841753\">https://doi.org/10.2174/138920311798841753</a>"}},{"citation":{"ista":"Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. 2011. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. 6(7).","short":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).","mla":"Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” <i>PLoS One</i>, vol. 6, no. 7, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pone.0022458\">10.1371/journal.pone.0022458</a>.","chicago":"Smutny, Michael, Selwin Wu, Guillermo Gomez, Sabine Mangold, Alpha Yap, and Nicholas Hamilton. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” <i>PLoS One</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pone.0022458\">https://doi.org/10.1371/journal.pone.0022458</a>.","ama":"Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. <i>PLoS One</i>. 2011;6(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0022458\">10.1371/journal.pone.0022458</a>","apa":"Smutny, M., Wu, S., Gomez, G., Mangold, S., Yap, A., &#38; Hamilton, N. (2011). Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0022458\">https://doi.org/10.1371/journal.pone.0022458</a>","ieee":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, and N. Hamilton, “Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens,” <i>PLoS One</i>, vol. 6, no. 7. Public Library of Science, 2011."},"file":[{"creator":"dernst","relation":"main_file","checksum":"57a5eb11dd05241c48c44f492b3ec3ac","file_id":"6399","access_level":"open_access","date_created":"2019-05-10T10:51:43Z","file_size":1984567,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:06Z","file_name":"2011_PLOS_Smutny.PDF"}],"publisher":"Public Library of Science","intvolume":"         6","publist_id":"3357","ddc":["570"],"year":"2011","publication_status":"published","oa":1,"file_date_updated":"2020-07-14T12:46:06Z","day":"22","issue":"7","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion where cellular forces are exerted and resisted. Increasing evidence indicates that E-cadherin adhesion molecules at the ZA serve to sense force applied on the junctions and coordinate cytoskeletal responses to those forces. Efforts to understand the role that cadherins play in mechanotransduction have been limited by the lack of assays to measure the impact of forces on the ZA. In this study we used 4D imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions in confluent epithelial monolayers displayed prominent movements oriented orthogonal (perpendicular) to the ZA itself. Two components were identified in these movements: a relatively slow unidirectional (translational) component that could be readily fitted by least-squares regression analysis, upon which were superimposed more rapid oscillatory movements. Myosin IIB was a dominant factor responsible for driving the unilateral translational movements. In contrast, frequency spectrum analysis revealed that depletion of Myosin IIA increased the power of the oscillatory movements. This implies that Myosin IIA may serve to dampen oscillatory movements of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate that Myosin IIA and Myosin IIB make distinct contributions to junctional movement at the ZA."}],"department":[{"_id":"CaHe"}],"month":"07","has_accepted_license":"1","publication":"PLoS One","date_created":"2018-12-11T12:02:28Z","doi":"10.1371/journal.pone.0022458","title":"Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"his work was funded by the National Health and Medical Research Council (NHMRC) of Australia. M.S. was an Erwin Schroedinger postdoctoral fellow of the Austrian Science Fund (FWF), S.K.W. is supported by a UQ International Research Tuition Award and Research Scholarship, S.M .by an ANZ Trustees PhD Scholarship. A.S.Y. is a Research Fellow of the NHMRC. Confocal imaging was performed at the Australian Cancer Research Foundation (ACRF) Cancer Biology Imaging Centre at the Institute for Molecular Bioscience, established with the generous support of the ACRF.","status":"public","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","_id":"3288","type":"journal_article","date_updated":"2021-01-12T07:42:25Z","volume":6,"language":[{"iso":"eng"}],"date_published":"2011-07-22T00:00:00Z","author":[{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","last_name":"Smutny","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","first_name":"Michael"},{"last_name":"Wu","full_name":"Wu, Selwin","first_name":"Selwin"},{"last_name":"Gomez","full_name":"Gomez, Guillermo","first_name":"Guillermo"},{"last_name":"Mangold","first_name":"Sabine","full_name":"Mangold, Sabine"},{"last_name":"Yap","full_name":"Yap, Alpha","first_name":"Alpha"},{"first_name":"Nicholas","full_name":"Hamilton, Nicholas","last_name":"Hamilton"}]}]