Retrieval Mechanism Research Articles

Cognitive memory control in borderline personality disorder patients

It has been demonstrated that the mechanism of cognitive memory control in humans is sustained by the hippocampus and prefrontal cortices, which have been found to be structurally and functionally abnormal in borderline personality disorder (BPD). We investigated whether the memory control mechanism is affected in BPD. Nineteen Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV BPD patients and 19 matched healthy controls (HC) performed a specific think/no-think paradigm exploring the capacity of remembering and suppressing pair of words previously learned. After the think-no think phase, the second member of each word pair has to be remembered either when subjects are presented with the cue word showed at the beginning of the test (Same Probe Test; SPT) or when they are presented with an extra-list categorical word (Independent Probe Test; IPT). We evaluated the effect of suppression and of retrieval activity on later retention of words. Both on the SPT and on the IPT, HC showed the expected improvement of memory retrieval on to-be-remembered words, unlike BPD patients. On the SPT, HC, but not BPD patients, correctly recalled significantly more words among remembered words (RW) than among suppressed words (SW). Similarly to HC, subjects with BPD without a history of childhood abuse showed a significantly higher percentage of correctly recalled words among RW than among SW. The mechanism of active retrieval of memories and of improvement through repetition is impaired in BPD, particularly in those who experienced traumatic experiences. This impairment might play an important role, possibly resulting in the emergence of unwanted memories and dissociative symptoms.

Retrieval of online handwriting by synthesis and matching

Search and retrieval is gaining importance in the ink domain due to the increase in the availability of online handwritten data. However, the problem is challenging due to variations in handwriting between various writers, digitizers and writing conditions. In this paper, we propose a retrieval mechanism for online handwriting, which can handle different writing styles, specifically for Indian languages. The proposed approach provides a keyboard-based search interface that enables to search handwritten data from any platform, in addition to pen-based and example-based queries. One of the major advantages of this framework is that information retrieval techniques such as ranking relevance, detecting stopwords and controlling word forms can be extended to work with search and retrieval in the ink domain. The framework also allows cross-lingual document retrieval across Indian languages.

A CBR method for CFW prevention and treatment

Different from the conventional methods, this paper presents a case-based reasoning (CBR) method for cucumber fusarium wilt (CFW) prevention and treatment, with vantage case-based indexing and retrieval mechanism, sensitivity analysis based reasoning method and Recall evaluation based case retaining strategy. The optimal interval of case dissimilarity distance threshold T is inferred from the experimental results by X fold cross-validation method. The experiments and application show that useful information can be generated for CFW prevention and treatment and the dynamic adjustment for decision-making of cucumber planting can be assisted by the proposed CBR system.

Glance project: a database retrieval mechanism for the ATLAS detector

During the construction and commissioning phases of the ATLAS detector, data related to the installation, placement, testing and performance of the equipment are stored in relational databases. Each group acquires and saves information in different servers, using diverse technologies, data modeling and terminologies. Installation and maintenance during the experiment construction and operation depends on the access to this information, as well as imply in its update. The development of retrieval and update systems for each data set requires too much effort and high maintenance cost. The Glance system retrieves and inserts/updates data independently of the modeling and technology used for the storage, recognizes the repositories internal structure and guides the user through the creation of search and insertion interfaces. Distinct and spread data sets can be transparently integrated in one interface. Data can be exported/imported to/from various formats. The system handles many independent interfaces, which can be accessed by users or other applications at any time. This paper describes the Glance conception, its development and features. The system usage is illustrated with examples. Current status and future work are also discussed.

Phase-contrast X-ray tomography: Contrast mechanism and roles of phase retrieval

The direct phase-contrast X-ray tomography, which reconstructs tomograms directly from projection phase-contrast images without the phase retrievals, finds many interesting applications for detection of interfaces for different tissues. In this work we explore and clarify the contrast mechanism of the direct phase-contrast tomography, and show that the direct phase-contrast tomogram is a mixture of three components: the 3D map of the imaged object's linear attenuation coefficients, the map of the rescaled 3D Laplacians of its refraction indices, and artifacts related to the global distribution of the attenuation coefficients and refraction indices. The need of phase retrieval for accurate and quantitative tomography for medical applications is pointed out. A phase tomography reconstruction formula for soft tissue imaging, which requires just a single phase-contrast image per projection for reconstruction, is presented.

Interactions between multiple sources of short‐term plasticity during evoked and spontaneous activity at the rat calyx of Held

Sustained activity at most central synapses is accompanied by a number of short-term changes in synaptic strength which act over a range of time scales. Here we examine experimental data and develop a model of synaptic depression at the calyx of Held synaptic terminal that combines many of these mechanisms (acting at differing sites and across a range of time scales). This new model incorporates vesicle recycling, facilitation, activity-dependent vesicle retrieval and multiple mechanisms affecting calcium channel activity and release probability. It can accurately reproduce the time course of experimentally measured short-term depression across different stimulus frequencies and exhibits a slow decay in EPSC amplitude during sustained stimulation. We show that the slow decay is a consequence of vesicle release inhibition by multiple mechanisms and is accompanied by a partial recovery of the releasable vesicle pool. This prediction is supported by patch-clamp data, using long duration repetitive EPSC stimulation at up to 400 Hz. The model also explains the recovery from depression in terms of interaction between these multiple processes, which together generate a stimulus-history-dependent recovery after repetitive stimulation. Given the high rates of spontaneous activity in the auditory pathway, the model also demonstrates how these multiple interactions cause chronic synaptic depression under in vivo conditions. While the magnitude of the depression converges to the same steady state for a given frequency, the time courses of onset and recovery are faster in the presence of spontaneous activity. We conclude that interactions between multiple sources of short-term plasticity can account for the complex kinetics during high frequency stimulation and cause stimulus-history-dependent recovery at this relay synapse.

Hypothesis for the mechanism for heat-induced antigen retrieval occurring on fresh frozen sections without formalin-fixation in immunohistochemistry

The mechanism involved in heat-induced antigen retrieval (AR) remains unproven but probably utilizes the breaking of formalin-induced cross-linkages. We investigated the effectiveness of heat-induced AR on immunohistochemistry and dot-blot analysis using rat uterus tissue sections and protein extracts without formalin-fixation. The unfixed frozen sections, which did not show immunostaining with nine antibodies, were clearly stained after heating the sections. In the dot-blot analysis, the immunoblot sensitivity of detection was greatly enhanced by heating the protein-blotted membrane. These results indicate that other mechanisms of breaking formalin-induced cross-linkages may be present. We propose that one of the other mechanisms for heat-induced AR is that accessibility to the target epitopes of antigenic proteins is limited by natural steric barriers even in the fresh state caused by the antigenic protein itself.

Federated repositories of X-ray diffraction images

There is a pressing need for the archiving and curation of raw X-ray diffraction data. This information is critical for validation, methods development and improvement of archived structures. However, the relatively large size of these data sets has presented challenges for storage in a single worldwide repository such as the Protein Data Bank archive. This problem can be avoided by using a federated approach, where each institution utilizes its institutional repository for storage, with a discovery service overlaid. Institutional repositories are relatively stable and adequately funded, ensuring persistence. Here, a simple repository solution is described, utilizing Fedora open-source database software and data-annotation and deposition tools that can be deployed at any site cheaply and easily. Data sets and associated metadata from federated repositories are given a unique and persistent handle, providing a simple mechanism for search and retrieval via web interfaces. In addition to ensuring that valuable data is not lost, the provision of raw data has several uses for the crystallographic community. Most importantly, structure determination can only be truly repeated or verified when the raw data are available. Moreover, the availability of raw data is extremely useful for the development of improved methods of image analysis and data processing.

Data Integration for Spatio-Temporal Patterns of Gene Expression of Zebrafish development: the GEMS database

SummaryThe Gene Expression Management System (GEMS) is a database system for patterns of gene expression. These patterns result from systematic whole-mount fluorescent in situ hybridization studies on zebrafish embryos. GEMS is an integrative platform that addresses one of the important challenges of developmental biology: how to integrate genetic data that underpin morphological changes during embryogenesis. Our motivation to build this system was by the need to be able to organize and compare multiple patterns of gene expression at tissue level. Integration with other developmental and biomolecular databases will further support our understanding of development. The GEMS operates in concert with a database containing a digital atlas of zebrafish embryo; this digital atlas of zebrafish development has been conceived prior to the expansion of the GEMS. The atlas contains 3D volume models of canonical stages of zebrafish development in which in each volume model element is annotated with an anatomical term. These terms are extracted from a formal anatomical ontology, i.e. the Developmental Anatomy Ontology of Zebrafish (DAOZ). In the GEMS, anatomical terms from this ontology together with terms from the Gene Ontology (GO) are also used to annotate patterns of gene expression and in this manner providing mechanisms for integration and retrieval . The annotations are the glue for integration of patterns of gene expression in GEMS as well as in other biomolecular databases. At the one hand, zebrafish anatomy terminology allows gene expression data within GEMS to be integrated with phenotypical data in the 3D atlas of zebrafish development. At the other hand, GO terms extend GEMS expression patterns integration to a wide range of bioinformatics resources.

Subcortical ischemic vascular disease and cognition: A systematic review.

Subcortical Ischemic Vascular Disease (SIVD) is underdiagnosed. This review investigates the relationship among SIVD severity, cognitive status and neuroimaging markers.MethodsCohort, cross-sectional and case control studies were searched on ISI, Medline, Scielo, PsychoInfo and LILACS databases published between 1995 and 2006.ResultsThe most impaired cognitive domains were executive, attentional and memory retrieval mechanisms. These cognitive features were frequently associated to White Matter Lesions (WML).ConclusionsWML is an independent factor in cognitive decline. However, the threshold for this impact is not yet clearly established.

Efficient Query-by-Content Audio Retrieval by Locality Sensitive Hashing and Partial Sequence Comparison

This paper investigates suitable indexing techniques to enable efficient content-based audio retrieval in large acoustic databases. To make an index-based retrieval mechanism applicable to audio content, we investigate the design of Locality Sensitive Hashing (LSH) and the partial sequence comparison. We propose a fast and efficient audio retrieval framework of query-by-content and develop an audio retrieval system. Based on this framework, four different audio retrieval schemes, LSH-Dynamic Programming (DP), LSH-Sparse DP (SDP), Exact Euclidian LSH (E2LSH)-DP, E2LSH-SDP, are introduced and evaluated in order to better understand the performance of audio retrieval algorithms. The experimental results indicate that compared with the traditional DP and the other three compititive schemes, E2LSH-SDP exhibits the best tradeoff in terms of the response time, retrieval accuracy and computation cost.

The absence of the clathrin-dependent endocytosis in rod bipolar cells of the FVB/N mouse retina

The high rate of exocytosis at the ribbon synapses is balanced by following compensatory endocytosis. Unlike conventional synaptic terminals where clathrin-mediated endocytosis (CME) is a predominant mechanism for membrane retrieval, CME is thought to be only a minor mechanism of endocytosis at the retinal ribbon synapses, but CME is present there and it works. We examined the clathrin expression in the FVB/N rd1 mouse, which is an animal model of retinitis pigmentosa. The broadly distributed pattern of clathrin immunoreactivity in the inner plexiform layer was similar in both the control and FVB/N mouse retinas, but the immunoreactive punta within the rod bipolar axon terminals located in the proximal IPL were decreased in number and reduced in size at postnatal days 14 and they came to disappear at postnatal days 21. This preferential decrease of the clathrin expression at ribbon synapses in the rod bipolar cell axon terminals of the FVB/N mouse retina demonstrates another plastic change after photoreceptor degeneration and this suggests that clathrin may be important for normal synaptic function at the rod bipolar ribbon synapses in the mammalian retina.

Waiting to retrieve: possible implications for brain function

There is evidence that the mid-ventrolateral prefrontal cortex is involved in control processing necessary for the active retrieval of mnemonic information when retrieval cannot be triggered automatically by unique/constant associations within memory. We hypothesized that this process is initiated as soon as an instructional cue to retrieve a particular aspect of an encoded stimulus is presented prior to the appearance of the test stimulus that prompts the subjects' response. To test this hypothesis, we provided the subjects with a delay period following the presentation of the instructional cue. Across delays, the subjects took longer to respond during the active retrieval compared with the automatic retrieval trials. Importantly, for both trial types, delays of up to 300 ms improved the subjects' reaction times during the test period by an average of 101 ms. Retrieval mechanisms, therefore, are initiated early during the post-instruction delay period prior to the presentation of the test stimulus needed for the decision.

Endocytosis Is Required for Synaptic Activity-Dependent Release of Amyloid-β In Vivo

Aggregation of amyloid-beta (Abeta) peptide into soluble and insoluble forms within the brain extracellular space is central to the pathogenesis of Alzheimer's disease. Full-length amyloid precursor protein (APP) is endocytosed from the cell surface into endosomes where it is cleaved to produce Abeta. Abeta is subsequently released into the brain interstitial fluid (ISF). We hypothesized that synaptic transmission results in more APP endocytosis, thereby increasing Abeta generation and release into the ISF. We found that inhibition of clathrin-mediated endocytosis immediately lowers ISF Abeta levels in vivo. Two distinct methods that increased synaptic transmission resulted in an elevation of ISF Abeta levels. Inhibition of endocytosis, however, prevented the activity-dependent increase in Abeta. We estimate that approximately 70% of ISF Abeta arises from endocytosis-associated mechanisms, with the vast majority of this pool also dependent on synaptic activity. These findings have implications for AD pathogenesis and may provide insights into therapeutic intervention.

Query-Adaptive Fusion for Multimodal Search

We conduct a broad survey of query-adaptive search strategies in a variety of application domains, where the internal retrieval mechanisms used for search are adapted in response to the anticipated needs for each individual query experienced by the system. While these query-adaptive approaches can range from meta-search over text collections to multimodal search over video databases, we propose that all such systems can be framed and discussed in the context of a single, unified framework. In our paper, we keep an eye towards the domain of video search, where search cues are available from a rich set of modalities, including textual speech transcripts, low-level visual features, and high-level semantic concept detectors. The relative efficacy of each of the modalities is highly variant between many types of queries. We observe that the state of the art in query-adaptive retrieval frameworks for video collections is highly dependent upon the definition of classes of queries, which are groups of queries that share similar optimal search strategies, while many applications in text and Web retrieval have included many advanced strategies, such as direct prediction of search method performance and inclusion of contextual cues from the searcher. We conclude that such advanced strategies previously developed for text retrieval have a broad range of possible applications in future research in multimodal video search.

Differential role of the hippocampal endocannabinoid system in the memory consolidation and retrieval mechanisms

CB1 cannabinoid receptors are abundantly expressed in the brain, with large concentrations present in the hippocampus, a brain structure essential for memory processing. In the present study, we have investigated the possible modulatory role of the endocannabinoid system in the dorsal hippocampus upon the different phases of memory processing of an aversive task. AM251, a selective antagonist of CB1 receptors, and anandamide, an endogenous agonist of cannabinoid receptors, were bilaterally infused into the dorsal hippocampus of male Wistar rats either before training, immediately after training, or before test in the step-down inhibitory avoidance (IA) task. Results showed that pre-training infusion of CB1 drugs did not influence the acquisition of the task. In contrast, post-training infusion of the CB1 antagonist disrupted while the antagonist facilitated memory consolidation of IA. The post-training results demonstrate that memory consolidation depends on the integrity of the endocannabinoid system in the CA1 region of the dorsal hippocampus. While we still have no direct proof of endocannabinoids released there after an aversive task such as IA, these results suggests that (a) AM251 acts blocking the binding of endogenously released cannabinoids and (b) exogenously supplemented anandamide may be adding its contribution to the action of the endogenously released pool. Considering our data and the higher density of CB1 receptors present in the GABAergic interneurons, we propose them as the putative target of the endocannabinoid modulation of memory, a hypothesis that needs to be proven. In addition, pre-test infusion of the CB1 receptor antagonist facilitated while infusion of the agonist did not affect memory retrieval of IA. The completely opposite action of the same drug upon memory at the post-training (consolidation) and pre-test (recall) contexts suggests that some durable change took place in the CA1 region during the consolidation process that modified the logical attributes of the pharmacological response, i.e., the drug response changed from memory disruption to memory facilitation. A similar phenomenon was previously described by us in the M4 cholinergic muscarinic subsystem in the hippocampus for the same task (Diehl, F., Fürstenau, L. O., Sanchez, G., Camboim, C., de Oliveira Alvares, L., Lanziotti, V. B., et al. (2007). Facilitatory effect of the intra-hippocampal pretest administration of MT3 in the inhibitory avoidance task. Behavioral Brain Research, 177(2), 227–231), but the biological nature of such change in the local neural circuitry remains to be investigated.

Using genetic algorithms to optimize nearest neighbors for data mining

Case-based reasoning (CBR) is widely used in data mining for managerial applications because it often shows significant promise for improving the effectiveness of complex and unstructured decision making. There are, however, some limitations in designing appropriate case indexing and retrieval mechanisms including feature selection and feature weighting. Some of the prior studies pointed out that finding the optimal k parameter for the k-nearest neighbor (k-NN) is also one of the most important factors for designing an effective CBR system. Nonetheless, there have been few attempts to optimize the number of neighbors, especially using artificial intelligence (AI) techniques. This study proposes a genetic algorithm (GA) approach to optimize the number of neighbors to combine. In this study, we apply this novel model to two real-world cases involving stock market and online purchase prediction problems. Experimental results show that a GA-optimized k-NN approach may outperform traditional k-NN. In addition, these results also show that our proposed method is as good as or sometime better than other AI techniques in performance-comparison.

Auditory event-related potentials during a spatial working memory task

Objective Sensory cortical activity can be jointly governed by bottom–up (e.g. stimulus features) and top–down (e.g. memory, attention) factors. We tested the hypothesis that auditory sensory cortical activity is affected by encoding and retrieval of spatial information. Methods Auditory event-related potentials (ERPs) were recorded during working memory and passive listening conditions. Trials contained three noise bursts (two “items” at different locations, followed by a “probe”). In the working memory task subjects determined if the probe matched an item location. The influence of long-term memory was evaluated by training to one location that was always a non-match. Auditory ERPs were analyzed to items and probes (N100, P200, late positive wave-LPW). Results Reaction times varied significantly among probes (trained non-match < matches < non-match). In only the Passive condition N100 and P200 amplitudes to the first item were significantly larger than the second item. Probe ERP amplitudes (N100, LPW) were comparable for match and trained non-match probes relative to non-matches. Conclusions Findings suggest that top–down factors during encoding modify sensory responses to successive items. Probe ERPs reflect sequence factors, such as recency and stimulus probability, and retrieval mechanisms not evident in passive listening. Significance Results support a contribution of auditory cortex to working memory.

Influence of protein–protein interactions on the cellular localization of cytochrome P450

Background: Microsomal CYPs are integral membrane proteins that are localized in the endoplasmic reticulum (ER), which is critical for their function. CYPs are co-translationally inserted into the rough ER membrane and are then either directly retained in the smooth ER or retained by a retrieval mechanism or targeted for ER-associated degradation. Protein–protein interactions are likely to be important for proper cellular targeting of CYPs. Objective: Progress in understanding the mechanisms of cellular targeting and ER retention of CYPs is reviewed with emphasis on the role of protein–protein interactions. Possible mechanisms of direct retention are the incorporation of CYPs into an immobile complex in the ER membrane, homooligomerization that prevents inclusion in transport vesicles, exclusion of CYP monomers from transport vesicles or targeting of CYPs to an ER subdomain away from sites of transport vesicle formation. Degradation of CYPs occurs either by lysosomal mechanisms or by the ubiquitin–proteasomal pathway. Methods: The scope of this review includes studies published in the research literature that have defined the targeting of CYPs to the ER, the retention of CYPs in the ER and the degradation of CYPs. Results/conclusion: Targeting of CYPs to the ER is well understood and involves signal recognition particle-mediated delivery to the sec61 complex. The mechanism of ER retention of CYPs remains unclear, but self-oligomerization or binding to large immobile networks do not underlie ER retention of CYPs. An ER retention ‘receptor’ remains elusive, but BAP31 is important for the proper cellular localization of CYPs and Dap1p is a CYP-binding protein that is a candidate for such a receptor. Identification of protein binding partners of CYPs will be critical to understanding the mechanism of ER retention.

Ancient rules of memory

The first kiss, the smell of mother's cooking or the vision of a beautiful landscape; memories such as these are etched firmly into our brains for recall in vivid detail, even decades later. Memories and experience influence our decisions throughout life, both consciously and subconsciously—in a sense, our memories make us what we are. Yet, understanding how information is encoded in our brains and how memories are maintained, both at the conceptual and molecular levels, remains one of the greatest challenges in the life sciences. Through decades of research, biologists have answered many fundamental questions about the brain, and more recent work has revealed the identity of several crucial molecules involved in the storage and retrieval of information. This has at last begun to shed light on the major scientific puzzle: how do we form and maintain long‐term memories? ![][1] The field of neurobiology had made relatively little progress toward understanding memory since the Canadian psychologist Donald Hebb (1904–1985) introduced the idea of synaptic plasticity nearly 60 years ago (Hebb, 1949). Hebb explained the establishment of memory by changes in the number and strength of synaptic connections between neurons. According to his theory, synapses respond to stimulation by neurotransmitters in a cumulative manner, and repeated stimulation—for example, by learning—leads to ever‐stronger connections between specific neurons until they become permanent. Over time, neuroscientists accepted Hebb's idea of synaptic plasticity, despite a lack of direct molecular evidence. In fact, it was not until recently that scientists—in large part Eric Kandel at Columbia University in New York, NY, USA—discovered several biochemical mechanisms that now support Hebb's idea. Kandel himself won the Nobel Prize for medicine in 2000 for his discovery that the syntheses of different proteins relate to short‐term and long‐term memory in the sea slug Aplysia . The foundations for this work and … [1]: /embed/graphic-1.gif