Retrieval Mechanism Research Articles

Aspects of ‘relevance’ in the alignment of curriculum with educational standards

With over 60,000 US K-12 science and mathematics education standards and a rapid proliferation of Web-enabled curriculum, retrieving curriculum that aligns with the standards to which teachers must teach is a key objective for educational digital libraries. However, previous studies of such alignment use single-dimensional and binary measures of the alignment concept. As a consequence, they suffer from low inter-rater reliability (IRR), with experts agreeing about alignments only some 20–40% of the time. We present the results of an experiment in which the alignment variable was operationalized using the Saracevic model of relevance ‘clues’ taken from the everyday practice of K-12 teaching. Results show high IRR across all clues with IRR on several specific alignment dimensions significantly higher than on overall alignment. In addition, a model of overall alignment is derived and estimated. The structure and explanatory power of the model as well as the relationships between alignment clues differ significantly between alignments of curriculum found by users themselves and curriculum found by others. These results illustrate the usefulness of clue-based relevance measures for information retrieval and have important consequences for both the formulation of automated retrieval mechanisms and the construction of a gold standard or benchmark set of standard-curriculum alignments.

Molecular mechanisms of antigen retrieval: antigen retrieval reverses steric interference caused by formalin-induced cross-links

The overwhelming majority of antibodies useful for formalin fixed, paraffin embedded (FFPE) tissues require antigen retrieval to reverse the effect of formalin fixation and re-establish immunoreactivity. How this reversal happens is poorly understood. We developed a new experimental model for studying the mechanism of formalin fixation and antigen retrieval. Epitope mapping studies on nine antibodies useful for FFPE tissues revealed that each consisted of a contiguous stretch of amino acids in the native protein (linear epitope). Small peptides representing the epitopes of antibodies to human epidermal growth factor receptor type (HER2), estrogen, and progesterone receptors were attached covalently to glass microscope slides in a peptide array. Most peptides retained immunoreactivity after formalin fixation. Immunoreactivity was completely abrogated for all peptides, however, if an irrelevant large protein was present during formalin-induced cross-linking. We hypothesize that cross-linking the irrelevant protein to the peptide epitopes sterically blocked antibodies from binding. Antigen retrieval dissociates irrelevant proteins and restores immunoreactivity. Because the epitopes for clinical antibodies require only primary protein structure, the fact that antigen retrieval probably denatures the secondary and tertiary structure of the protein is irrelevant. The same mechanism may occur in tissue samples subjected to formalin fixation and antigen retrieval.

Applying Biomedical Ontologies on Semantic Query Expansion

Abstract*1- Introduction*The interpretation of a question (or information need) depends, among other things, of a series of lexicalsemantic relations that complement and help the cognitive process of answering that information need. Despite this fact, currently used information retrieval mechanisms take few advantages of the semantic interpretation of users’ information needs (usually specified through keywords). In most of the cases, those mechanisms are based on keyword matching, and thus are excessively dependant on the query and document terms.There are several past results showing that, in general, information retrieval based on domain knowledge decreases the accuracy of keyword based search engines. We believe this approach deserves further discussion and experimentation, looking for more strong evidences that these negative results can really be generalized. Moreover, there are some questions left unanswered by previous work that our experiment is addressing:(i) Using a scientific ontology, with formal construction and maintenance processes, such as the OBO ontologies, would produce better results? (ii) Are there more efficient query expansion techniques using available domain knowledge?(iii) Is a scientific ontology complete enough to fulfill the information retrieval researchers’ needs, in general?*2- Semantic Query Expansion*To try to answer some of these questions, we run a query expansion experiment using the Gene Ontology (GO) as domain knowledge. As the document repository, we used an extraction of 10 years of PubMed publications (from 1994 to 2004), which contains approximately 4.6 Million documents. This dataset is a test collection used by the information retrieval community, called Genomic TREC.*3- Results*To evaluate our ontology-based semantic query expansion technique, we measured the effectiveness of the information retrieval mechanism with and without expansion. In a nutshell, the average result showed an increase of 28% on synonyms relations and a small decrease on other relations.Our results show a lot of consistence with past related work. In fact, if the expansion strategy does not selectively choose when and how to expand, only synonym relations are worth to be used. However, looking further, it is possible to find several opportunities to try other expansion strategies. For example, the problem with query expansion using generalization/specialization relationships is that, if it is always applied, the bad results are more frequent than the good ones. But, if the strategy is to be selective on when to use these relations for expansion, the increasing on accuracy can be outstanding. As shown by our experiment, there was a query with 98% increment on effectiveness. *4- Conclusion*We strongly believe that it is premature to assume that semantics-based query expansion is, in general, a recall-enhancing, precision-degrading technique. Our experiments suggest that by using scientific based ontologies (like OBO ontologies) with formal relations, it is possible to increase both recall and precision. Our group is currently revising this first experiment towards a better semantic query expansion strategy.*5- Acknowledgements*This work was partially funded by CAPES and CNPq research grants 311454/2006-2, 306889/2007-2 and 484713/2007-8.*References*_Fox E. Lexical relations enhancing effectiveness of information retrieval systems. SIGIR Forum, New York, v.15, n.3, p.5-3.__Voorhees E. Query expansion using lexicalsemantic relations. In: ACM SIGIR conference on research and development in information retrieval, Proceedings, Dublin:17, p.61–69, 1994_

Pollen Tube Growth: a Delicate Equilibrium Between Secretory and Endocytic Pathways

Although pollen tube growth is a prerequisite for higher plant fertilization and seed production, the processes leading to pollen tube emission and elongation are crucial for understanding the basic mechanisms of tip growth. It was generally accepted that pollen tube elongation occurs by accumulation and fusion of Golgi-derived secretory vesicles (SVs) in the apical region, or clear zone, where they were thought to fuse with a restricted area of the apical plasma membrane (PM), defining the apical growth domain. Fusion of SVs at the tip reverses outside cell wall material and provides new segments of PM. However, electron microscopy studies have clearly shown that the PM incorporated at the tip greatly exceeds elongation and a mechanism of PM retrieval was already postulated in the mid-nineteenth century. Recent studies on endocytosis during pollen tube growth showed that different endocytic pathways occurred in distinct zones of the tube, including the apex, and led to a new hypothesis to explain vesicle accumulation at the tip; namely, that endocytic vesicles contribute substantially to V-shaped vesicle accumulation in addition to SVs and that exocytosis does not involve the entire apical domain. New insights suggested the intriguing hypothesis that modulation between exo- and endocytosis in the apex contributes to maintain PM polarity in terms of lipid/protein composition and showed distinct degradation pathways that could have different functions in the physiology of the cell. Pollen tube growth in vivo is closely regulated by interaction with style molecules. The study of endocytosis and membrane recycling in pollen tubes opens new perspectives to studying pollen tube-style interactions in vivo.

Optimising context data dissemination and storage in distributed pervasive computing systems

Context management systems are expected to administrate large volumes of spatial and non-spatial information in geographical disperse domains. In particular, when these systems cover wide areas such as cities, countries or even the entire planet, the design of scalable storage, retrieval and propagation mechanisms is paramount. This paper elaborates on mechanisms that address advanced requirements, including support for distributed context databases management; efficient query handling; innovative management of mobile physical objects and optimization strategies for distributed context data dissemination. These mechanisms establish a robust spatially-enhanced distributed context management framework that has already been designed and carefully implemented and thoroughly evaluated.

Graded information extraction by neural-network dynamics with multihysteretic neurons

A major goal in the study of neural networks is to create novel information-processing algorithms inferred from the real brain. Recent neurophysiological evidence of graded persistent activity suggests that the brain possesses neural mechanisms for retrieval of graded information, which could be described by the neural-network dynamics with attractors that are continuously dependent on the initial state. Theoretical studies have also demonstrated that model neurons with a multihysteretic response property can generate robust continuous attractors. Inspired by these lines of evidence, we proposed an algorithm given by the multihysteretic neuron-network dynamics, devised to retrieve graded information specific to a given topic (i.e., context, represented by the initial state). To demonstrate the validity of the proposed algorithm, we examined keyword extraction from documents, which is best fitted for evaluating the appropriateness of retrieval of graded information. The performance of keyword extraction by using our algorithm was significantly high (measured by the average precision of document retrieval, for which the appropriateness of keyword extraction is crucial) compared with standard document-retrieval methods. Moreover, our algorithm exhibited much higher performance than the neural-network dynamics with bistable neurons, which can also produce robust continuous attractors but only represent dichotomous information at the single-cell level. These findings indicate that the capability to manage graded information at the single-cell level was essential for obtaining a high performing algorithm.

Case-Based Reasoning Approach to Construction Safety Hazard Identification: Adaptation and Utilization

Risk assessment, consisting of hazard identification and risk analysis, is an important process that can prevent costly incidents. However, due to operational pressures and lack of construction experience, risk assessments are frequently poorly conducted. In order to improve the quality of risk assessments in the construction industry, it is important to explore the use of artificial intelligence methods to ensure that the process is efficient and at the same time thorough. This paper describes the adaptation process of a case-based reasoning (CBR) approach for construction safety hazard identification. The CBR approach aims to utilize past knowledge in the form of past hazard identification and incident cases to improve the efficiency and quality of new hazard identification. The overall approach and retrieval mechanism are described in earlier papers. This paper is focused on the adaptation process for hazard identification. Using the proposed CBR approach, for a new work scenario (the input case), a most relevant hazard identification tree and a set of incident cases will be retrieved to facilitate hazard identification. However, not all information contained in these cases are relevant. Thus, less relevant information has to be pruned off and all the retrieved information has to be integrated into a hazard identification tree. The proposed adaptation is conducted in three steps: (1) pruning of the retrieved hazard identification tree; (2) pruning of the incident cases; and (3) insertion of incident cases into the hazard identification tree. The adaptation process is based on the calculation of similarity scores of indexes. A case study based on actual hazard identifications and incident cases is used to validate the feasibility of the proposed adaptation techniques.

EEG Activity Underlying Successful Study of Associative and Order Information

Two of the most well studied and ecologically relevant memory paradigms are memory for pairs ("associations") and ordered sequences ("serial lists"). Behavioral theories comprise two classes: those that use common mechanisms and those that use distinct mechanisms for study and retrieval of associations versus serial lists. We tested the common-mechanisms hypothesis by recording electroencephalographic activity related to successful study ("subsequent memory effect" [SME]) of pairs and short lists (triples) of nouns. Multivariate analysis identified four distributed patterns of brain activity: (1) right parietal activity throughout most of the study period that differentiated study of pairs from triples within subjects as well as exhibiting an SME that was significant for pairs but not for triples; (2) a left parietal and fronto-polar activity pattern that was reliable around 500 msec and later in the study trial, exhibiting an SME for pairs and a weaker, nonsignificant SME for triples; (3) a left frontal/right parietal topography in the middle of the study interval which covaried with speed and accuracy across subjects; and (4) a pattern resembling the late positive component preceded by an early potential which together covaried with accuracy in triples but slow response times for both pairs and triples. These patterns point to the relevance of three classic SME components (early, late positive, and slow components) from single-item memory to memory for structured information, but suggest that they reflect subsets of more complex spatio-temporal patterns. Our findings support common underlying mechanisms for study and recall of pairs and lists. However, existing models must be modified to account for differences in both the presence of certain study-relevant processes and in the relevance of these processes to performance measures for pairs versus serial lists.

An Adaptive and Context-Aware Scenario Model Based on a Web Service Architecture for Pervasive Learning Systems

Pervasive learning will become increasingly important in technology-enhanced learning (TEL). In this context, development efforts focus on features such as context-awareness, adaptation, services retrieval and orchestration mechanisms. This paper proposes a process to assist the development of such systems, from conception through to execution. This paper focuses mainly on pervasive TEL systems in a learning situation at the workplace. We introduce a context-aware scenario model of corporate learning and working scenarios in e-retail environments such as shops and hypermarkets. This model enables us to integrate contextual information into scenarios and to select how to perform activities according to the current situation. Our pervasive learning system is based on a service oriented architecture that consists of an infrastructure for service management and execution that is flexible enough to reuse learning components and to deal with context changes that are not known in advance and discovered on the fly.

Salient cues enhance strategy monitoring and task switching for prospective memory:An ERP study

Objective To investigate the retrieval mechanism of prospective memory,spatiotemporal patterns of event-related potentials (ERP) were used to reveal neural correlates of the prospective interference effect. Methods A task of matching two sequential patterns was taken as the ongoing task and the detection of patterns with two salient levels as prospective memory tasks. Experiments were performed in blocks for single ongoing task block and two prospective memory blocks. Results No significant behavioral effect was found for prospective interference [reaction time(ms):control blocks 750.29±161.33,high salience blocks 770.94±174.89,low salience bocks 764.79±174.12,F(1.52,25.82)=0.48,P =0.57 and correction rate(%):control blocks 85.89±8.07,high salience blocks 88.26±7.00,low salience blocks 87.91±7.28,F(1.50,25.57)=2.46,P =0.12].But significant ERP effect was found at bilateral frontal regions from 160 ms to 240 ms for both two prospective memory blocks. Moreover,greater negativity at the right frontal polar region appeared significantly at 360'440 ms for higher salient patterns. Conclusion Prospective memory is retrieved based on strategic monitoring and high salient stimuli may enhance to keep the prospective goal and improve task switching. Key words: Prospective memory; Prospective interference effect; Event related potentials

Data modeling and retrieval in semantic grid based on RDF

The data processed by semantic grid are often semi-structured data.Therefore,how to model and retrieve these semi-structured data is a key issue of semantic Web.The presenting model for semi-structured data base Resource Description Framework(RDF) and its information retrieval mechanism were proposed in this paper.Then a semantic grid infrastructure was described,which implemented knowledge sharing and retrieval in chemical engineering domain based on a chemical computing grid platform.

Agreement attraction in comprehension: Representations and processes

Much work has demonstrated so-called attraction errors in the production of subject–verb agreement (e.g., ‘The key to the cabinets are on the table’, [Bock, J. K., & Miller, C. A. (1991). Broken agreement. Cognitive Psychology, 23, 45–93]), in which a verb erroneously agrees with an intervening noun. Six self-paced reading experiments examined the online mechanisms underlying the analogous attraction effects that have been shown in comprehension; namely reduced disruption for subject–verb agreement violations when these ‘attractor’ nouns intervene. One class of theories suggests that these effects are rooted in faulty representation of the number of the subject, while another class of theories suggests instead that such effects arise in the process of re-accessing subject number at the verb. Two main findings provide evidence against the first class of theories. First, attraction also occurs in relative clause configurations in which the attractor noun does not intervene between subject and verb and is not in a direct structural relationship with the subject head (e.g., ‘The drivers who the runner wave to each morning’). Second, we observe a ‘grammatical asymmetry’: attraction effects are limited to ungrammatical sentences, which would be unexpected if the representation of subject number were inherently prone to error. We argue that agreement attraction in comprehension instead reflects a cue-based retrieval mechanism that is subject to retrieval errors. The grammatical asymmetry can be accounted for under one implementation that we propose, or if the mechanism is only called upon when the predicted agreement features fail to be instantiated on the verb.

Developing a semantic-enable information retrieval mechanism

The existing information retrieval systems are mostly keyword-based and retrieve relevant documents or information by matching keywords. Keyword-based search, in spite of its merits of expedient query for information and ease-of-use, has failed to represent the complete semantics contained in the content and has let to the retrieval failure. In a textual content, the author’s intention is represented in a semantic format of various combinations of word–word relations that are comprehensible to human beings. Query constructed by descriptions in natural language best reflects querist’s intention. This study developed a semantic-enable information retrieval mechanism that handles the processing, recognition, extraction, extensions and matching of content semantics to achieve the following objectives: (1) to analyze and determine the semantic features of content, to develop a semantic pattern that represents semantic features of the content, and to structuralize and materialize semantic features; (2) to analyze user’s query and extend its implied semantics through semantic extension so as to identify more semantic features for matching; and (3) to generate contents with approximate semantics by matching against the extended query to provide correct contents to the querist. This mechanism is capable of improving the traditional problem of keyword search and enables the user to perform a semantic-based query and search for the required information, thereby improving the reusing and sharing of information.

Case-Based Reasoning for Construction Hazard Identification: Case Representation and Retrieval

This paper proposes a case-based reasoning (CBR) approach to construction hazard identification that facilitates systematic feedback of past knowledge in the form of incident cases and hazard identification. This paper focuses on two of the key components of the CBR approach: (1) a detailed knowledge representation scheme, developed based on the modified loss causation model, to codify incident cases and past hazard identification and (2) an intelligent retrieval mechanism that can automatically retrieve relevant past cases. The detailed knowledge representation scheme presented herein is designed to model both incident cases and hazard identification so that both types of knowledge repository can be retrieved simultaneously and adapted for use. The scheme also includes a linguistic structure used to facilitate indexing of cases. The retrieval mechanism is based on the concept of similarity scoring. In this paper, a novel scoring technique based on semantic networks is presented. A case study is presented to demonstrate and validate the proposed approach.

Prediction, sequences and the hippocampus.

Recordings of rat hippocampal place cells have provided information about how the hippocampus retrieves memory sequences. One line of evidence has to do with phase precession, a process organized by theta and gamma oscillations. This precession can be interpreted as the cued prediction of the sequence of upcoming positions. In support of this interpretation, experiments in two-dimensional environments and on a cue-rich linear track demonstrate that many cells represent a position ahead of the animal and that this position is the same irrespective of which direction the rat is coming from. Other lines of investigation have demonstrated that such predictive processes also occur in the non-spatial domain and that retrieval can be internally or externally cued. The mechanism of sequence retrieval and the usefulness of this retrieval to guide behaviour are discussed.

A single‐trace dual‐process model of episodic memory: A novel computational account of familiarity and recollection

Dual-process theories of episodic memory state that retrieval is contingent on two independent processes: familiarity (providing a sense of oldness) and recollection (recovering events and their context). A variety of studies have reported distinct neural signatures for familiarity and recollection, supporting dual-process theory. One outstanding question is whether these signatures reflect the activation of distinct memory traces or the operation of different retrieval mechanisms on a single memory trace. We present a computational model that uses a single neuronal network to store memory traces, but two distinct and independent retrieval processes access the memory. The model is capable of performing familiarity and recollection-based discrimination between old and new patterns, demonstrating that dual-process models need not to rely on multiple independent memory traces, but can use a single trace. Importantly, our putative familiarity and recollection processes exhibit distinct characteristics analogous to those found in empirical data; they diverge in capacity and sensitivity to sparse and correlated patterns, exhibit distinct ROC curves, and account for performance on both item and associative recognition tests. The demonstration that a single-trace, dual-process model can account for a range of empirical findings highlights the importance of distinguishing between neuronal processes and the neuronal representations on which they operate.

Identifying deliberate attempts to fake memory impairment through the combined use of reaction time and event-related potential measures

The central aim of this study was to evaluate the value of reaction time (RT) measures and event-related potentials (ERPs) for the assessment of simulated memory impairment. In two identical experiments (N=24), healthy volunteers carried out an adapted version of the Amsterdam Short-Term Memory (ASTM) test. In half of the cases participants were instructed to perform to their best of abilities (control condition) while in the other half participants were asked to feign a believable memory deficit (simulation condition). Compared to controls, simulating participants were found to produce longer and more variable RTs. In addition, they took longer to respond to new words than to old words, while control participants showed the opposite pattern. Both early (300–500 ms) and late (500–800 ms) ERP old/new effects were similar in magnitude and scalp distribution for both groups of participants, regardless of the fact that simulating participants had significantly lower recognition accuracy than controls. The ERP old/new effect was assumed to reflect unaffected retrieval mechanisms and thus the discrepancy between this measure and recognition performance was interpreted as evidence for intentional underperformance. Results are discussed in relation to clinical observations and deception detection studies. It was concluded that the combined use of RT and ERP measures could be useful to detect and evaluate simulation of memory impairment but that future studies should include patient groups to test some of our assumptions.

A New Interactive Video Retrieval Framework Using Semantic Matching

摘要: 近年来基于内容的视频检索技术受到人们越来越多的关注. 本文提出了一套基于语义匹配的交互式视频检索框架, 其贡献主要为以下三方面: 1)定义新型的视频高层特征---语义直方图用以描述视频的高层语义信息; 2)使用主导集聚类算法建立基于非监督学习的检索机制, 用以降低在线计算复杂度和提高检索效率; 3)提出新型的相关反馈机制---基于语义的分支反馈, 该机制采用分支反馈结构和分支更新策略实现检索性能的提升. 实验结果表明了本框架的有效性. 关键词: 语义匹配直方图 / 基于非监督学习的检索机制 / 基于语义的分支反馈

Qp: A tool for generating 3D models of ancient Greek pottery

Abstract The development of content based retrieval mechanisms is a very active research area. Present studies are mainly focused on automating the information extraction and indexing processes. Usually for the development and evaluation of such mechanisms, there is always a need for a ground-truth database. In this paper, we present a software tool named qp that is able to semi-automatically produce a collection of random 3D vessels, with morphological characteristics similar to those found in ancient Greek pottery, a ceramic group exhibited worldwide with great impact to scholars as well as general public. A 3D vessel collection has been produced by qp and can be used as a test bed dataset for the development of shape-based 3D descriptors applicable to pottery. Additionally, qp can be considered as a 3D vessel modelling software tool which can be used by people not related to computer graphics technology and particularly to 3D modelling.

The Endoplasmic Reticulum-associated Degradation of Transthyretin Variants Is Negatively Regulated by BiP in Mammalian Cells

Amyloid fibril formation of mutant transthyretin (TTR) that causes familial amyloid polyneuropathy occurs in the extracellular space. Thus, secretion of TTR variants contributes to the pathogenesis of amyloidosis. However, the molecular mechanisms underlying the endoplasmic reticulum (ER) exit or retention and subsequent degradation of TTR variants remain unclear. Here, we demonstrated that the nonsecreted TTR variants, such as D18G TTR and amyloidogenic TTRs with introduced monomeric mutation (M-TTRs), stably interact with the ER chaperone BiP in mammalian cells. These proteins were co-secreted with the secreted form of BiP in which the KDEL signal was removed, indicating that BiP partially contributes to the ER retention of nonsecreted TTR variants. More interestingly, the degradation efficiency of nonsecreted TTRs was increased when BiP was down-regulated by small interfering RNA. Thus, BiP protects the TTR variants from immediate degradation. Additionally, we showed that the stability of nonsecreted TTR variants is not disturbed in the coat complex II-deficient conditions, which are enough to inhibit the ER export of secreted TTR variants, including wild-type TTR. Therefore, the post-ER retrieval mechanism might not contribute to the ER-associated degradation of nonsecreted TTR variants. These findings suggest that the affinity to the ER-resident protein BiP regulates the fate of TTR variants in the ER.