The Simplest Evaluation Measures for XML Information Retrieval that Could Possibly Work

This paper reviews several evaluation measures developed for evaluating XML information retrieval (IR) systems. We argue that these measures, some of which are currently in use by the INitiative for the Evaluation of XML Retrieval (INEX), are complicated, hard to understand, and hard to explain to users of XML IR systems. To show the value of keeping things simple, we report alternative evaluation results of official evaluation runs submitted to INEX 2004 using simple metrics, and show its value for INEX

Report on the first Twente Data Management Workshop on XML Databases and Information Retrieval

The Database Group of the University of Twente initiated a new series of workshops called Twente Data Management workshops (TDM), starting with one on XML Databases and Information Retrieval which took place on 21 June 2004 at the University of Twente. We have set ourselves two goals for the workshop series: i) To provide a forum to share original ideas as well as research results on data management problems; ii) To bring together researchers from the database community and researchers from related research fields

On Region Algebras, XML Databases, and Information Retrieval

This paper describes some new ideas on developing a logical algebra for databases that manage textual data and support information retrieval functionality. We describe a first prototype of such a system

Exploiting Query Structure and Document Structure to Improve Document Retrieval Effectiveness

In this paper we present a systematic analysis of document retrieval using unstructured and structured queries within the score region algebra (SRA) structured retrieval framework. The behavior of di®erent retrieval models, namely Boolean, tf.idf, GPX, language models, and Okapi, is tested using the transparent SRA framework in our three-level structured retrieval system called TIJAH. The retrieval models are implemented along four elementary retrieval aspects: element and term selection, element score computation, score combination, and score propagation. The analysis is performed on a numerous experiments evaluated on TREC and CLEF collections, using manually generated unstructured and structured queries. Unstructured queries range from the short title queries to long title + description + narrative queries. For generating structured queries we exploit the knowledge of the document structure and the content used to semantically describe or classify documents. We show that such structured information can be utilized in retrieval engines to give more precise answers to user queries then when using unstructured queries

A database approach to information retrieval:The remarkable relationship between language models and region models

In this report, we unify two quite distinct approaches to information retrieval: region models and language models. Region models were developed for structured document retrieval. They provide a well-defined behaviour as well as a simple query language that allows application developers to rapidly develop applications. Language models are particularly useful to reason about the ranking of search results, and for developing new ranking approaches. The unified model allows application developers to define complex language modeling approaches as logical queries on a textual database. We show a remarkable one-to-one relationship between region queries and the language models they represent for a wide variety of applications: simple ad-hoc search, cross-language retrieval, video retrieval, and web search

Vague element selection and query rewriting for XML retrieval

In this paper we present the extension of our prototype three-level database system (TIJAH) developed for struc-tured information retrieval. The extension is aimed at mod-eling vague search on XML elements. All three levels (con-ceptual, logical, and physical) of the TIJAH system are enhanced to support vague search concepts. The vague search is implemented as vague selection of XML elements using XML element name expansion lists and rewriting tech-niques. We test the performance of retrieval models us-ing automatically generated expansion lists and compared them with models that use manual ones. The goal is to find the best approach for structured information retrieval with vague structural constraints on element names expressed in the query. 1

Free energy barrier for melittin reorientation from a membrane-bound state to a transmembrane state

An important step in a phospholipid membrane pore formation by melittin antimicrobial peptide is a reorientation of the peptide from a surface into a transmembrane conformation. In this work we perform umbrella sampling simulations to calculate the potential of mean force (PMF) for the reorientation of melittin from a surface-bound state to a transmembrane state and provide a molecular level insight into understanding peptide and lipid properties that influence the existence of the free energy barrier. The PMFs were calculated for a peptide to lipid (P/L) ratio of 1/128 and 4/128. We observe that the free energy barrier is reduced when the P/L ratio increased. In addition, we study the cooperative effect; specifically we investigate if the barrier is smaller for a second melittin reorientation, given that another neighboring melittin was already in the transmembrane state. We observe that indeed the barrier of the PMF curve is reduced in this case, thus confirming the presence of a cooperative effect

The cooperative behaviour of antimicrobial peptides in model membranes

A systematic analysis of the hypothesis of the antimicrobial peptides' (AMPs) cooperative action is performed by means of full atomistic molecular dynamics simulations accompanied by circular dichroism experiments. Several AMPs from the aurein family (2.5,2.6, 3.1), have a similar sequence in the first ten amino acids, are investigated in different environments including aqueous solution, trifluoroethanol (TFE), palmitoyloleoylphosphatidylethanolamine (POPE), and palmitoyloleoylphosphatidylglycerol (POPG) lipid bilayers. It is found that the cooperative effect is stronger in aqueous solution and weaker in TFE. Moreover, in the presence of membranes, the cooperative effect plays an important role in the peptide/lipid bilayer interaction. The action of AMPs is a competition of the hydrophobic interactions between the side chains of the peptides and the hydrophobic region of lipid molecules, as well as the intra peptide interaction. The aureins 2.5-COOH and 2.6-COOH form a hydrophobic aggregate to minimize the interaction between the hydrophobic group and the water. Once that the peptides reach the water/lipid interface the hydrophobic aggregate becomes smaller and the peptides start to penetrate into the membrane. In contrast, aurein 3.1-COOH forms only a transient aggregate which disintegrates once the peptides reached the membrane, and it shows no cooperativity in membrane penetratio