| 1. |
- Wiedorn, Max O., et al.
(författare)
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Megahertz serial crystallography
- 2018
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a beta-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.
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| 2. |
- Kontopoulos, E., et al.
(författare)
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Deliverable 4.5: Context-aware Content Interpretation
- 2016
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Rapport (refereegranskat)abstract
- The current deliverable summarises the work conducted within task T4.5 of WP4, presenting our proposed approaches for contextualised content interpretation, aimed at gaining insightful contextualised views on content semantics. This is achieved through the adoption of appropriate context-aware semantic models developed within the project, and via enriching the semantic descriptions with background knowledge, deriving thus higher level contextualised content interpretations that are closer to human perception and appraisal needs. More specifically, the main contributions of the deliverable are the following: A theoretical framework using physics as a metaphor to develop different models of evolving semantic content. A set of proof-of-concept models for semantic drifts due to field dynamics, introducing two methods to identify quantum-like (QL) patterns in evolving information searching behaviour, and a QL model akin to particle-wave duality for semantic content classification. Integration of two specific tools, Somoclu for drift detection and Ncpol2spda for entanglement detection. An “energetic” hypothesis accounting for contextualized evolving semantic structures over time. A proposed semantic interpretation framework, integrating (a) an ontological inference scheme based on Description Logics (DL), (b) a rule-based reasoning layer built on SPARQL Inference Notation (SPIN), (c) an uncertainty management framework based on non-monotonic logics. A novel scheme for contextualized reasoning on semantic drift, based on LRM dependencies and OWL’s punning mechanism. An implementation of SPIN rules for policy and ecosystem change management, with the adoption of LRM preconditions and impacts. Specific use case scenarios demonstrate the context under development and the efficiency of the approach. Respective open-source implementations and experimental results that validate all the above.All these contributions are tightly interlinked with the other PERICLES work packages: WP2 supplies the use cases and sample datasets for validating our proposed approaches, WP3 provides the models (LRM and Digital Ecosystem models) that form the basis for our semantic representations of content and context, WP5 provides the practical application of the technologies developed to preservation processes, while the tools and algorithms presented in this deliverable can be deployed in combination with test scenarios, which will be part of the WP6 test beds.
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| 3. |
- Maronidis, A., et al.
(författare)
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PERICLES Deliverable 4.3: Content Semantics and Use Context Analysis Techniques
- 2016
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Rapport (refereegranskat)abstract
- The current deliverable summarises the work conducted within task T4.3 of WP4, focusing on the extraction and the subsequent analysis of semantic information from digital content, which is imperative for its preservability. More specifically, the deliverable defines content semantic information from a visual and textual perspective, explains how this information can be exploited in long-term digital preservation and proposes novel approaches for extracting this information in a scalable manner. Additionally, the deliverable discusses novel techniques for retrieving and analysing the context of use of digital objects. Although this topic has not been extensively studied by existing literature, we believe use context is vital in augmenting the semantic information and maintaining the usability and preservability of the digital objects, as well as their ability to be accurately interpreted as initially intended.
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| 4. |
- Kontopoulos, Efstratios, et al.
(författare)
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PERICLES Deliverable 4.4: Modelling Contextualised Semantics
- 2016
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Rapport (refereegranskat)abstract
- The current deliverable summarises the work conducted within task T4.4 of WP4, presenting our proposed models for semantically representing digital content and its respective context – the latter refers to any information coming from the environment of the digital object (DO) that offers a better insight into the object’s status, its interrelationships with other content items and information about the object’s context of use. Within PERICLES, we refer to the content semantics enriched with the contextual perspective as “contextualised semantics”. The deliverable presents two complementary modelling approaches, based respectively on (a) ontologies and logics, and, (b) multivariate statistics.
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| 5. |
- Bender, Michael A., et al.
(författare)
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The minimum backlog problem
- 2015
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Ingår i: Theoretical Computer Science. - : ELSEVIER SCIENCE BV. - 0304-3975 .- 1879-2294. ; 605, s. 51-61
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Tidskriftsartikel (refereegranskat)abstract
- We study the minimum backlog problem (MBP). This online problem arises, e.g., in the context of sensor networks. We focus on two main variants of MBP. The discrete MBP is a 2-person game played on a graph G = (V, E). The player is initially located at a vertex of the graph. In each time step, the adversary pours a total of one unit of water into cups that are located on the vertices of the graph, arbitrarily distributing the water among the cups. The player then moves from her current vertex to an adjacent vertex and empties the cup at that vertex. The players objective is to minimize the backlog, i.e., the maximum amount of water in any cup at any time. The geometric MBP is a continuous-time version of the MBP: the cups are points in the two-dimensional plane, the adversary pours water continuously at a constant rate, and the player moves in the plane with unit speed. Again, the players objective is to minimize the backlog. We show that the competitive ratio of any algorithm for the MBP has a lower bound of Omega (D), where D is the diameter of the graph (for the discrete MBP) or the diameter of the point set (for the geometric MBP). Therefore we focus on determining a strategy for the player that guarantees a uniform upper bound on the absolute value of the backlog. For the absolute value of the backlog there is a trivial lower bound of Omega (D), and the deamortization analysis of Dietz and Sleator gives an upper bound of O (D log N) for N cups. Our main result is a tight upper bound for the geometric MBP: we show that there is a strategy for the player that guarantees a backlog of O(D), independently of the number of cups. We also study a localized version of the discrete MBP: the adversary has a location within the graph and must act locally (filling cups) with respect to his position, just as the player acts locally (emptying cups) with respect to her position. We prove that deciding the value of this game is PSPACE-hard. (C) 2015 Elsevier B.V. All rights reserved.
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| 6. |
- Efrat, Alon, et al.
(författare)
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Improved Approximation Algorithms for Relay Placement
- 2016
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Ingår i: ACM Transactions on Algorithms. - : ACM Press. - 1549-6325 .- 1549-6333. ; 12:2, s. 20-
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Tidskriftsartikel (refereegranskat)abstract
- In the relay placement problem, the input is a set of sensors and a number r >= 1, the communication range of a relay. In the one-tier version of the problem, the objective is to place a minimum number of relays so that between every pair of sensors there is a path through sensors and/or relays such that the consecutive vertices of the path are within distance r if both vertices are relays and within distance 1 otherwise. The two-tier version adds the restrictions that the path must go through relays, and not through sensors. We present a 3.11-approximation algorithm for the one-tier version and a polynomial-time approximation scheme (PTAS) for the two-tier version. We also show that the one-tier version admits no PTAS, assuming P not equal NP.
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