MonetDB/XQuery: a fast XQuery processor powered by a relational engine

Relational XQuery systems try to re-use mature relational data management infrastructures to create fast and scalable XML database technology. This paper describes the main features, key contributions, and lessons learned while implementing such a system. Its architecture consists of (i) a range-based encoding of XML documents into relational tables, (ii) a compilation technique that translates XQuery into a basic relational algebra, (iii) a restricted (order) property-aware peephole relational query optimization strategy, and (iv) a mapping from XML update statements into relational updates. Thus, this system implements all essential XML database functionalities (rather than a single feature) such that we can learn from the full consequences of our architectural decisions. While implementing this system, we had to extend the state-of-the-art with a number of new technical contributions, such as loop-lifted staircase join and efficient relational query evaluation strategies for XQuery theta-joins with existential semantics. These contributions as well as the architectural lessons learned are also deemed valuable for other relational back-end engines. The performance and scalability of the resulting system is evaluated on the XMark benchmark up to data sizes of 11GB. The performance section also provides an extensive benchmark comparison of all major XMark results published previously, which confirm that the goal of purely relational XQuery processing, namely speed and scalability, was met

Pathfinder: relational XQuery over multi-gigabyte XML inputs in interactive time

Using a relational DBMS as back-end engine for an XQuery processing system leverages relational query optimization and scalable query processing strategies provided by mature DBMS engines in the XML domain. Though a lot of theoretical work has been done in this area and various solutions have been proposed, no complete systems have been made available so far to give the practical evidence that this is a viable approach. In this paper, we describe the ourely relational XQuery processor Pathfinder that has been built on top of the extensible RDBMS MonetDB. Performance results indicate that the system is capable of evaluating XQuery queries efficiently, even if the input XML documents become huge. We additionally present further contributions such as loop-lifted staircase join, techniques to derive order properties and to reduce sorting effort in the generated relational algebra plans, as well as methods for optimizing XQuery joins, which, taken together, enabled us to reach our performance and scalability goal

Molecular mechanism of influenza A NS1-mediated TRIM25 recognition and inhibition

RIG-I is a viral RNA sensor that induces the production of type I interferon (IFN) in response to infection with a variety of viruses. Modification of RIG-I with K63-linked poly-ubiquitin chains, synthesised by TRIM25, is crucial for activation of the RIG-I/MAVS signalling pathway. TRIM25 activity is targeted by influenza A virus non-structural protein 1 (NS1) to suppress IFN production and prevent an efficient host immune response. Here we present structures of the human TRIM25 coiled-coil-PRYSPRY module and of complexes between the TRIM25 coiled-coil domain and NS1. These structures show that binding of NS1 interferes with the correct positioning of the PRYSPRY domain of TRIM25 required for substrate ubiquitination and provide a mechanistic explanation for how NS1 suppresses RIG-I ubiquitination and hence downstream signalling. In contrast, the formation of unanchored K63-linked poly-ubiquitin chains is unchanged by NS1 binding, indicating that RING dimerisation of TRIM25 is not affected by NS1

Adler Function, Sum Rules and Crewther Relation of Order O(alpha_s^4): the Singlet Case

The analytic result for the singlet part of the Adler function of the vector current in a general gauge theory is presented in five-loop approximation. Comparing this result with the corresponding singlet part of the Gross-Llewellyn Smith sum rule [1], we successfully demonstrate the validity of the generalized Crewther relation for the singlet part. This provides a non-trivial test of both our calculations and the generalized Crewther relation. Combining the result with the already available non-singlet part of the Adler function [2,3] we arrive at the complete ${\cal O}(\alpha_s^4)$ expression for the Adler function and, as a direct consequence, at the complete ${\cal O}(\alpha_s^4)$ correction to the $e^+ e^-$ annihilation into hadrons in a general gauge theory.Comment: 4 pages, 1 figure. Final published versio