Adapting to Changing Memory Retrieval Demands: Evidence from Event-Related Potentials

Science.gov (United States)

Benoit, Roland G.; Werkle-Bergner, Markus; Mecklinger, Axel; Kray, Jutta

2009-01-01

This study investigated preparatory processes involved in adapting to changing episodic memory retrieval demands. Event-related potentials (ERPs) were recorded while participants performed a general old/new recognition task and a specific task that also required retrieval of perceptual details. The relevant task remained either constant or changed…

Age-Related Decline in Controlled Retrieval: The Role of the PFC and Sleep

Directory of Open Access Journals (Sweden)

Kristine A. Wilckens

2012-01-01

Full Text Available Age-related cognitive impairments often include difficulty retrieving memories, particularly those that rely on executive control. In this paper we discuss the influence of the prefrontal cortex on memory retrieval, and the specific memory processes associated with the prefrontal cortex that decline in late adulthood. We conclude that preretrieval processes associated with preparation to make a memory judgment are impaired, leading to greater reliance on postretrieval processes. This is consistent with the view that impairments in executive control significantly contribute to deficits in controlled retrieval. Finally, we discuss age-related changes in sleep as a potential mechanism that contributes to deficiencies in executive control that are important for efficient retrieval. The sleep literature points to the importance of slow-wave sleep in restoration of prefrontal cortex function. Given that slow-wave sleep significantly declines with age, we hypothesize that age-related changes in slow-wave sleep could mediate age-related decline in executive control, manifesting a robust deficit in controlled memory retrieval processes. Interventions, like physical activity, that improve sleep could be effective methods to enhance controlled memory processes in late life.

[Establishment of a comprehensive database for laryngeal cancer related genes and the miRNAs].

Science.gov (United States)

Li, Mengjiao; E, Qimin; Liu, Jialin; Huang, Tingting; Liang, Chuanyu

2015-09-01

By collecting and analyzing the laryngeal cancer related genes and the miRNAs, to build a comprehensive laryngeal cancer-related gene database, which differs from the current biological information database with complex and clumsy structure and focuses on the theme of gene and miRNA, and it could make the research and teaching more convenient and efficient. Based on the B/S architecture, using Apache as a Web server, MySQL as coding language of database design and PHP as coding language of web design, a comprehensive database for laryngeal cancer-related genes was established, providing with the gene tables, protein tables, miRNA tables and clinical information tables of the patients with laryngeal cancer. The established database containsed 207 laryngeal cancer related genes, 243 proteins, 26 miRNAs, and their particular information such as mutations, methylations, diversified expressions, and the empirical references of laryngeal cancer relevant molecules. The database could be accessed and operated via the Internet, by which browsing and retrieval of the information were performed. The database were maintained and updated regularly. The database for laryngeal cancer related genes is resource-integrated and user-friendly, providing a genetic information query tool for the study of laryngeal cancer.

Genome-Wide Temporal Expression Profiling in Caenorhabditis elegans Identifies a Core Gene Set Related to Long-Term Memory.

Science.gov (United States)

Freytag, Virginie; Probst, Sabine; Hadziselimovic, Nils; Boglari, Csaba; Hauser, Yannick; Peter, Fabian; Gabor Fenyves, Bank; Milnik, Annette; Demougin, Philippe; Vukojevic, Vanja; de Quervain, Dominique J-F; Papassotiropoulos, Andreas; Stetak, Attila

2017-07-12

The identification of genes related to encoding, storage, and retrieval of memories is a major interest in neuroscience. In the current study, we analyzed the temporal gene expression changes in a neuronal mRNA pool during an olfactory long-term associative memory (LTAM) in Caenorhabditis elegans hermaphrodites. Here, we identified a core set of 712 (538 upregulated and 174 downregulated) genes that follows three distinct temporal peaks demonstrating multiple gene regulation waves in LTAM. Compared with the previously published positive LTAM gene set (Lakhina et al., 2015), 50% of the identified upregulated genes here overlap with the previous dataset, possibly representing stimulus-independent memory-related genes. On the other hand, the remaining genes were not previously identified in positive associative memory and may specifically regulate aversive LTAM. Our results suggest a multistep gene activation process during the formation and retrieval of long-term memory and define general memory-implicated genes as well as conditioning-type-dependent gene sets. SIGNIFICANCE STATEMENT The identification of genes regulating different steps of memory is of major interest in neuroscience. Identification of common memory genes across different learning paradigms and the temporal activation of the genes are poorly studied. Here, we investigated the temporal aspects of Caenorhabditis elegans gene expression changes using aversive olfactory associative long-term memory (LTAM) and identified three major gene activation waves. Like in previous studies, aversive LTAM is also CREB dependent, and CREB activity is necessary immediately after training. Finally, we define a list of memory paradigm-independent core gene sets as well as conditioning-dependent genes. Copyright © 2017 the authors 0270-6474/17/376661-12$15.00/0.

Event-related potential evidence for separable automatic and controlled retrieval processes in proactive interference.

Science.gov (United States)

Bergström, Zara M; O'Connor, Richard J; Li, Martin K-H; Simons, Jon S

2012-05-21

Interference between competing memories is a major source of retrieval failure, yet, surprisingly little is known about how competitive memory activation arises in the brain. One possibility is that interference during episodic retrieval might be produced by relatively automatic conceptual priming mechanisms that are independent of strategic retrieval processes. Such priming-driven interference might occur when the competing memories have strong pre-existing associations to the retrieval cue. We used ERPs to measure the neural dynamics of retrieval competition, and investigated whether the ERP correlates of interference were affected by varying task demands for selective retrieval. Participants encoded cue words that were presented either two or four times, paired either with the same or different strongly associated words across repetitions. In a subsequent test, participants either selectively recalled each cue's most recent associate, or simply judged how many times a cue had been presented, without requiring selective recall. Interference effects on test performance were only seen in the recall task. In contrast, ERPs during test revealed an early posterior positivity for high interference items that was present in both retrieval tasks. This early ERP effect likely reflects a conceptual priming-related N400 reduction when many associations to a cue were pre-activated. A later parietal positivity resembling the ERP correlate of conscious recollection was found only in the recall task. The results suggest that early effects of proactive interference are relatively automatic and independent of intentional retrieval processes, consistent with suggestions that interference can arise through conceptual priming. Copyright © 2012 Elsevier B.V. All rights reserved.

Reversible Inactivation of the Higher Order Auditory Cortex during Fear Memory Consolidation Prevents Memory-Related Activity in the Basolateral Amygdala during Remote Memory Retrieval.

Science.gov (United States)

Cambiaghi, Marco; Renna, Annamaria; Milano, Luisella; Sacchetti, Benedetto

2017-01-01

Recent findings have shown that the auditory cortex, and specifically the higher order Te2 area, is necessary for the consolidation of long-term fearful memories and that it interacts with the amygdala during the retrieval of long-term fearful memories. Here, we tested whether the reversible blockade of Te2 during memory consolidation may affect the activity changes occurring in the amygdala during the retrieval of fearful memories. To address this issue, we blocked Te2 in a reversible manner during memory consolidation processes. After 4 weeks, we assessed the activity of Te2 and individual nuclei of the amygdala during the retrieval of long-term memories. Rats in which Te2 was inactivated upon memory encoding showed a decreased freezing and failed to show Te2-to-basolateral amygdala (BLA) synchrony during memory retrieval. In addition, the expression of the immediate early gene zif268 in the lateral, basal and central amygdala nuclei did not show memory-related enhancement. As all sites were intact upon memory retrieval, we propose that the auditory cortex represents a key node in the consolidation of fear memories and it is essential for amygdala nuclei to support memory retrieval process.

A Parallel Relational Database Management System Approach to Relevance Feedback in Information Retrieval.

Science.gov (United States)

Lundquist, Carol; Frieder, Ophir; Holmes, David O.; Grossman, David

1999-01-01

Describes a scalable, parallel, relational database-drive information retrieval engine. To support portability across a wide range of execution environments, all algorithms adhere to the SQL-92 standard. By incorporating relevance feedback algorithms, accuracy is enhanced over prior database-driven information retrieval efforts. Presents…

Retrievable Inferior Vena Cava Filters: Factors that Affect Retrieval Success

Energy Technology Data Exchange (ETDEWEB)

Geisbuesch, Philipp, E-mail: philippgeisbuesch@gmx.de; Benenati, James F.; Pena, Constantino S.; Couvillon, Joseph; Powell, Alex; Gandhi, Ripal; Samuels, Shaun; Uthoff, Heiko [Baptist Cardiac and Vascular Institute, Division of Vascular and Interventional Radiology (United States)

2012-10-15

Purpose: To report and analyze the indications, procedural success, and complications of retrievable inferior vena cava filters (rIVCF) placement and to identify parameters that influence retrieval attempt and failure. Methods: Between January 2005 and December 2010, a total of 200 patients (80 men, median age 67 years, range 11-95 years) received a rIVCF with the clinical possibility that it could be removed. All patients with rIVCF were prospectively entered into a database and followed until retrieval or a decision not to retrieve the filter was made. A retrospective analysis of this database was performed. Results: Sixty-one percent of patients had an accepted indication for filter placement; 39% of patients had a relative indication. There was a tendency toward a higher retrieval rate in patients with relative indications (40% vs. 55%, P = 0.076). Filter placement was technically successful in all patients, with no procedure-related mortality. The retrieval rate was 53%. Patient age of >80 years (odds ratio [OR] 0.056, P > 0.0001) and presence of malignancy (OR 0.303, P = 0.003) was associated with a significantly reduced probability for attempted retrieval. Retrieval failure occurred in 7% (6 of 91) of all retrieval attempts. A time interval of > 90 days between implantation and attempted retrieval was associated with retrieval failure (OR 19.8, P = 0.009). Conclusions: Patient age >80 years and a history of malignancy are predictors of a reduced probability for retrieval attempt. The rate of retrieval failure is low and seems to be associated with a time interval of >90 days between filter placement and retrieval.

Retrievable Inferior Vena Cava Filters: Factors that Affect Retrieval Success

International Nuclear Information System (INIS)

Geisbüsch, Philipp; Benenati, James F.; Peña, Constantino S.; Couvillon, Joseph; Powell, Alex; Gandhi, Ripal; Samuels, Shaun; Uthoff, Heiko

2012-01-01

Purpose: To report and analyze the indications, procedural success, and complications of retrievable inferior vena cava filters (rIVCF) placement and to identify parameters that influence retrieval attempt and failure. Methods: Between January 2005 and December 2010, a total of 200 patients (80 men, median age 67 years, range 11–95 years) received a rIVCF with the clinical possibility that it could be removed. All patients with rIVCF were prospectively entered into a database and followed until retrieval or a decision not to retrieve the filter was made. A retrospective analysis of this database was performed. Results: Sixty-one percent of patients had an accepted indication for filter placement; 39% of patients had a relative indication. There was a tendency toward a higher retrieval rate in patients with relative indications (40% vs. 55%, P = 0.076). Filter placement was technically successful in all patients, with no procedure-related mortality. The retrieval rate was 53%. Patient age of >80 years (odds ratio [OR] 0.056, P > 0.0001) and presence of malignancy (OR 0.303, P = 0.003) was associated with a significantly reduced probability for attempted retrieval. Retrieval failure occurred in 7% (6 of 91) of all retrieval attempts. A time interval of > 90 days between implantation and attempted retrieval was associated with retrieval failure (OR 19.8, P = 0.009). Conclusions: Patient age >80 years and a history of malignancy are predictors of a reduced probability for retrieval attempt. The rate of retrieval failure is low and seems to be associated with a time interval of >90 days between filter placement and retrieval.

Functional-anatomic study of episodic retrieval using fMRI. I. Retrieval effort versus retrieval success.

Science.gov (United States)

Buckner, R L; Koutstaal, W; Schacter, D L; Wagner, A D; Rosen, B R

1998-04-01

A number of recent functional imaging studies have identified brain areas activated during tasks involving episodic memory retrieval. The identification of such areas provides a foundation for targeted hypotheses regarding the more specific contributions that these areas make to episodic retrieval. As a beginning effort toward such an endeavor, whole-brain functional magnetic resonance imaging (fMRI) was used to examine 14 subjects during episodic word recognition in a block-designed fMRI experiment. Study conditions were manipulated by presenting either shallow or deep encoding tasks. This manipulation yielded two recognition conditions that differed with regard to retrieval effort and retrieval success: shallow encoding yielded low levels of recognition success with high levels of retrieval effort, and deep encoding yielded high levels of recognition success with low levels of effort. Many brain areas were activated in common by these two recognition conditions compared to a low-level fixation condition, including left and right prefrontal regions often detected during PET episodic retrieval paradigms (e.g., R. L. Buckner et al., 1996, J. Neurosci. 16, 6219-6235) thereby generalizing these findings to fMRI. Characterization of the activated regions in relation to the separate recognition conditions showed (1) bilateral anterior insular regions and a left dorsal prefrontal region were more active after shallow encoding, when retrieval demanded greatest effort, and (2) right anterior prefrontal cortex, which has been implicated in episodic retrieval, was most active during successful retrieval after deep encoding. We discuss these findings in relation to component processes involved in episodic retrieval and in the context of a companion study using event-related fMRI.

The processing of inter-item relations as a moderating factor of retrieval-induced forgetting

OpenAIRE

Tempel, Tobias; Wippich, Werner

2012-01-01

We investigated influences of item generation and emotional valence on retrieval-induced forgetting. Drawing on postulates of the three-factor theory of generation effects, generation tasks differentially affecting the processing of inter-item relations were applied. Whereas retrieval-induced forgetting of freely generated items was moderated by the emotional valence as well as retrieval-induced forgetting of read items, even though in the reverse direction (Experiment 1), fragment completion...

The role of retrieval mode and retrieval orientation in retrieval practice: insights from comparing recognition memory testing formats and restudying.

Science.gov (United States)

Gao, Chuanji; Rosburg, Timm; Hou, Mingzhu; Li, Bingbing; Xiao, Xin; Guo, Chunyan

2016-12-01

The effectiveness of retrieval practice for aiding long-term memory, referred to as the testing effect, has been widely demonstrated. However, the specific neurocognitive mechanisms underlying this phenomenon remain unclear. In the present study, we sought to explore the role of pre-retrieval processes at initial testing on later recognition performance by using event-related potentials (ERPs). Subjects studied two lists of words (Chinese characters) and then performed a recognition task or a source memory task, or restudied the word lists. At the end of the experiment, subjects received a final recognition test based on the remember-know paradigm. Behaviorally, initial testing (active retrieval) enhanced memory retention relative to restudying (passive retrieval). The retrieval mode at initial testing was indexed by more positive-going ERPs for unstudied items in the active-retrieval tasks than in passive retrieval from 300 to 900 ms. Follow-up analyses showed that the magnitude of the early ERP retrieval mode effect (300-500 ms) was predictive of the behavioral testing effect later on. In addition, the ERPs for correctly rejected new items during initial testing differed between the two active-retrieval tasks from 500 to 900 ms, and this ERP retrieval orientation effect predicted differential behavioral testing gains between the two active-retrieval conditions. Our findings confirm that initial testing promotes later retrieval relative to restudying, and they further suggest that adopting pre-retrieval processing in the forms of retrieval mode and retrieval orientation might contribute to these memory enhancements.

Age-Related Effects of the Apolipoprotein E Gene on Brain Function.

Science.gov (United States)

Matura, Silke; Prvulovic, David; Hartmann, Daniel; Scheibe, Monika; Sepanski, Beate; Butz, Marius; Oertel-Knöchel, Viola; Knöchel, Christian; Karakaya, Tarik; Fußer, Fabian; Hattingen, Elke; Pantel, Johannes

2016-03-16

The apolipoprotein E (ApoE) ɛ4 allele is a well-established genetic risk factor for sporadic Alzheimer's disease. Some evidence suggests a negative role of the ApoE ɛ4 allele for cognitive performance in late life, while beneficial effects on cognition have been shown in young age. We investigated age-related effects of the ApoE gene on brain function by assessing cognitive performance, as well as functional activation patterns during retrieval of Face-Name pairs in a group of young (n = 50; age 26.4±4.6 years, 25 ɛ4 carriers) and old (n = 40; age 66.1±7.0 years, 20 ɛ4 carriers) participants. A cross-sectional factorial design was used to examine the effects of age, ApoE genotype, and their interaction on both cognitive performance and the blood oxygenation level dependent (BOLD) brain response during retrieval of Face-Name pairs. While there were no genotype-related differences in cognitive performance, we found a significant interaction of age and ApoE genotype on task-related activation bilaterally in anterior cingulate gyrus and superior frontal gyrus, as well as left and right insula. Old age was associated with increased activity in ɛ4 carriers. The increased BOLD response in old ɛ4 carriers during retrieval could indicate a neurocognitive disadvantage associated with the ɛ4 allele with increasing age. Furthermore, recruitment of neuronal resources resulted in enhanced memory performance in young ɛ4 carriers, pointing to a better neurofunctional capacity associated with the ApoE4 genotype in young age.

The Role of Medial Temporal Lobe Regions in Incidental and Intentional Retrieval of Item and Relational Information in Aging.

Science.gov (United States)

Wang, Wei-Chun; Giovanello, Kelly S

2016-06-01

Considerable neuropsychological and neuroimaging work indicates that the medial temporal lobes are critical for both item and relational memory retrieval. However, there remain outstanding issues in the literature, namely the extent to which medial temporal lobe regions are differentially recruited during incidental and intentional retrieval of item and relational information, and the extent to which aging may affect these neural substrates. The current fMRI study sought to address these questions; participants incidentally encoded word pairs embedded in sentences and incidental item and relational retrieval were assessed through speeded reading of intact, rearranged, and new word-pair sentences, while intentional item and relational retrieval were assessed through old/new associative recognition of a separate set of intact, rearranged, and new word pairs. Results indicated that, in both younger and older adults, anterior hippocampus and perirhinal cortex indexed incidental and intentional item retrieval in the same manner. In contrast, posterior hippocampus supported incidental and intentional relational retrieval in both age groups and an adjacent cluster in posterior hippocampus was recruited during both forms of relational retrieval for older, but not younger, adults. Our findings suggest that while medial temporal lobe regions do not differentiate between incidental and intentional forms of retrieval, there are distinct roles for anterior and posterior medial temporal lobe regions during retrieval of item and relational information, respectively, and further indicate that posterior regions may, under certain conditions, be over-recruited in healthy aging. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Prospective memory and aging: evidence for preserved spontaneous retrieval with exact but not related cues.

Science.gov (United States)

Mullet, Hillary G; Scullin, Michael K; Hess, Theodore J; Scullin, Rachel B; Arnold, Kathleen M; Einstein, Gilles O

2013-12-01

We examined whether normal aging spares or compromises cue-driven spontaneous retrieval processes that support prospective remembering. In Experiment 1, young and older adults performed prospective-memory tasks that required either strategic monitoring processes for retrieval (nonfocal) or for which participants relied on spontaneous retrieval processes (focal). We found age differences for nonfocal, but not focal, prospective-memory performance. Experiments 2 and 3 used an intention-interference paradigm in which participants were asked to perform a prospective-memory task (e.g., press "Q" when the word money appears) in the context of an image-rating task and were then told to suspend their prospective-memory intention until after completing an intervening lexical-decision task. During the lexical-decision task, we presented the exact prospective-memory cue (e.g., money; Experiments 2 and 3) or a semantically related lure (e.g., wallet; Experiment 3), and we inferred spontaneous retrieval from slowed lexical-decision responses to these items relative to matched control items. Young and older adults showed significant slowing when the exact prospective-memory cue was presented. Only young adults, however, showed significant slowing to the semantically related lure items. Collectively, these results partially support the multiprocess theory prediction that aging spares spontaneous retrieval processes. Spontaneous retrieval processes may become less sensitive with aging, such that older adults are less likely to respond to cues that do not exactly match their encoded targets. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Less we forget: retrieval cues and release from retrieval-induced forgetting.

Science.gov (United States)

Jonker, Tanya R; Seli, Paul; Macleod, Colin M

2012-11-01

Retrieving some items from memory can impair the subsequent recall of other related but not retrieved items, a phenomenon called retrieval-induced forgetting (RIF). The dominant explanation of RIF-the inhibition account-asserts that forgetting occurs because related items are suppressed during retrieval practice to reduce retrieval competition. This item inhibition persists, making it more difficult to recall the related items on a later test. In our set of experiments, each category was designed such that each exemplar belonged to one of two subcategories (e.g., each BIRD exemplar was either a bird of prey or a pet bird), but this subcategory information was not made explicit during study or retrieval practice. Practicing retrieval of items from only one subcategory led to RIF for items from the other subcategory when cued only with the overall category label (BIRD) at test. However, adapting the technique of Gardiner, Craik, and Birtwistle (Journal of Learning and Verbal Behavior 11:778-783, 1972), providing subcategory cues during the final test eliminated RIF. The results challenge the inhibition account's fundamental assumption of cue independence but are consistent with a cue-based interference account.

Concept similarity and related categories in information retrieval using formal concept analysis

Science.gov (United States)

Eklund, P.; Ducrou, J.; Dau, F.

2012-11-01

The application of formal concept analysis to the problem of information retrieval has been shown useful but has lacked any real analysis of the idea of relevance ranking of search results. SearchSleuth is a program developed to experiment with the automated local analysis of Web search using formal concept analysis. SearchSleuth extends a standard search interface to include a conceptual neighbourhood centred on a formal concept derived from the initial query. This neighbourhood of the concept derived from the search terms is decorated with its upper and lower neighbours representing more general and special concepts, respectively. SearchSleuth is in many ways an archetype of search engines based on formal concept analysis with some novel features. In SearchSleuth, the notion of related categories - which are themselves formal concepts - is also introduced. This allows the retrieval focus to shift to a new formal concept called a sibling. This movement across the concept lattice needs to relate one formal concept to another in a principled way. This paper presents the issues concerning exploring, searching, and ordering the space of related categories. The focus is on understanding the use and meaning of proximity and semantic distance in the context of information retrieval using formal concept analysis.

Retrieval of relative humidity from CSIR-NLC mobile LIDAR backscatter measurements

CSIR Research Space (South Africa)

Tesfaye, M

2009-09-01

Full Text Available data was collected over 23 hours. The above data sets were used to determine the retrieved relative humidity and compared with Irene (near to Pretoria) weather balloon humidity measurements. The results of the comparative study are presented...

MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature

Directory of Open Access Journals (Sweden)

Fang Yu-Ching

2011-12-01

Full Text Available Abstract Background DNA methylation is regarded as a potential biomarker in the diagnosis and treatment of cancer. The relations between aberrant gene methylation and cancer development have been identified by a number of recent scientific studies. In a previous work, we used co-occurrences to mine those associations and compiled the MeInfoText 1.0 database. To reduce the amount of manual curation and improve the accuracy of relation extraction, we have now developed MeInfoText 2.0, which uses a machine learning-based approach to extract gene methylation-cancer relations. Description Two maximum entropy models are trained to predict if aberrant gene methylation is related to any type of cancer mentioned in the literature. After evaluation based on 10-fold cross-validation, the average precision/recall rates of the two models are 94.7/90.1 and 91.8/90% respectively. MeInfoText 2.0 provides the gene methylation profiles of different types of human cancer. The extracted relations with maximum probability, evidence sentences, and specific gene information are also retrievable. The database is available at http://bws.iis.sinica.edu.tw:8081/MeInfoText2/. Conclusion The previous version, MeInfoText, was developed by using association rules, whereas MeInfoText 2.0 is based on a new framework that combines machine learning, dictionary lookup and pattern matching for epigenetics information extraction. The results of experiments show that MeInfoText 2.0 outperforms existing tools in many respects. To the best of our knowledge, this is the first study that uses a hybrid approach to extract gene methylation-cancer relations. It is also the first attempt to develop a gene methylation and cancer relation corpus.

Retrieval Attempts Enhance Learning, but Retrieval Success (versus Failure) Does Not Matter

Science.gov (United States)

Kornell, Nate; Klein, Patricia Jacobs; Rawson, Katherine A.

2015-01-01

Retrieving information from memory enhances learning. We propose a 2-stage framework to explain the benefits of retrieval. Stage 1 takes place as one attempts to retrieve an answer, which activates knowledge related to the retrieval cue. Stage 2 begins when the answer becomes available, at which point appropriate connections are strengthened and…

Neural activation patterns during retrieval of schema-related memories: differences and commonalities between children and adults.

Science.gov (United States)

Brod, Garvin; Lindenberger, Ulman; Shing, Yee Lee

2017-11-01

Schemas represent stable properties of individuals' experiences, and allow them to classify new events as being congruent or incongruent with existing knowledge. Research with adults indicates that the prefrontal cortex (PFC) is involved in memory retrieval of schema-related information. However, developmental differences between children and adults in the neural correlates of schema-related memories are not well understood. One reason for this is the inherent confound between schema-relevant experience and maturation, as both are related to time. To overcome this limitation, we used a novel paradigm that experimentally induces, and then probes for, task-relevant knowledge during encoding of new information. Thirty-one children aged 8-12 years and 26 young adults participated in the experiment. While successfully retrieving schema-congruent events, children showed less medial PFC activity than adults. In addition, medial PFC activity during successful retrieval correlated positively with children's age. While successfully retrieving schema-incongruent events, children showed stronger hippocampus (HC) activation as well as weaker connectivity between the striatum and the dorsolateral PFC than adults. These findings were corroborated by an exploratory full-factorial analysis investigating age differences in the retrieval of schema-congruent versus schema-incongruent events, comparing the two conditions directly. Consistent with the findings of the separate analyses, two clusters, one in the medial PFC, one in the HC, were identified that exhibited a memory × congruency × age group interaction. In line with the two-component model of episodic memory development, the present findings point to an age-related shift from a more HC-bound processing to an increasing recruitment of prefrontal brain regions in the retrieval of schema-related events. © 2016 John Wiley & Sons Ltd.

Information Retrieval System Design Issues in a Microcomputer-Based Relational DBMS Environment.

Science.gov (United States)

Wolfram, Dietmar

1992-01-01

Outlines the file structure requirements for a microcomputer-based information retrieval system using FoxPro, a relational database management system (DBMS). Issues relating to the design and implementation of such systems are discussed, and two possible designs are examined in terms of space economy and practicality of implementation. (15…

The Menkes and Wilson disease genes counteract in copper toxicosis in Labrador retrievers: a new canine model for copper-metabolism disorders

Directory of Open Access Journals (Sweden)

Hille Fieten

2016-01-01

Full Text Available The deleterious effects of a disrupted copper metabolism are illustrated by hereditary diseases caused by mutations in the genes coding for the copper transporters ATP7A and ATP7B. Menkes disease, involving ATP7A, is a fatal neurodegenerative disorder of copper deficiency. Mutations in ATP7B lead to Wilson disease, which is characterized by a predominantly hepatic copper accumulation. The low incidence and the phenotypic variability of human copper toxicosis hamper identification of causal genes or modifier genes involved in the disease pathogenesis. The Labrador retriever was recently characterized as a new canine model for copper toxicosis. Purebred dogs have reduced genetic variability, which facilitates identification of genes involved in complex heritable traits that might influence phenotype in both humans and dogs. We performed a genome-wide association study in 235 Labrador retrievers and identified two chromosome regions containing ATP7A and ATP7B that were associated with variation in hepatic copper levels. DNA sequence analysis identified missense mutations in each gene. The amino acid substitution ATP7B:p.Arg1453Gln was associated with copper accumulation, whereas the amino acid substitution ATP7A:p.Thr327Ile partly protected against copper accumulation. Confocal microscopy indicated that aberrant copper metabolism upon expression of the ATP7B variant occurred because of mis-localization of the protein in the endoplasmic reticulum. Dermal fibroblasts derived from ATP7A:p.Thr327Ile dogs showed copper accumulation and delayed excretion. We identified the Labrador retriever as the first natural, non-rodent model for ATP7B-associated copper toxicosis. Attenuation of copper accumulation by the ATP7A mutation sheds an interesting light on the interplay of copper transporters in body copper homeostasis and warrants a thorough investigation of ATP7A as a modifier gene in copper-metabolism disorders. The identification of two new functional

Gene Ontology and KEGG Enrichment Analyses of Genes Related to Age-Related Macular Degeneration

Directory of Open Access Journals (Sweden)

Jian Zhang

2014-01-01

Full Text Available Identifying disease genes is one of the most important topics in biomedicine and may facilitate studies on the mechanisms underlying disease. Age-related macular degeneration (AMD is a serious eye disease; it typically affects older adults and results in a loss of vision due to retina damage. In this study, we attempt to develop an effective method for distinguishing AMD-related genes. Gene ontology and KEGG enrichment analyses of known AMD-related genes were performed, and a classification system was established. In detail, each gene was encoded into a vector by extracting enrichment scores of the gene set, including it and its direct neighbors in STRING, and gene ontology terms or KEGG pathways. Then certain feature-selection methods, including minimum redundancy maximum relevance and incremental feature selection, were adopted to extract key features for the classification system. As a result, 720 GO terms and 11 KEGG pathways were deemed the most important factors for predicting AMD-related genes.

Respecting Relations: Memory Access and Antecedent Retrieval in Incremental Sentence Processing

Science.gov (United States)

Kush, Dave W.

2013-01-01

This dissertation uses the processing of anaphoric relations to probe how linguistic information is encoded in and retrieved from memory during real-time sentence comprehension. More specifically, the dissertation attempts to resolve a tension between the demands of a linguistic processor implemented in a general-purpose cognitive architecture and…

Monetary rewards influence retrieval orientations.

Science.gov (United States)

Halsband, Teresa M; Ferdinand, Nicola K; Bridger, Emma K; Mecklinger, Axel

2012-09-01

Reward anticipation during learning is known to support memory formation, but its role in retrieval processes is so far unclear. Retrieval orientations, as a reflection of controlled retrieval processing, are one aspect of retrieval that might be modulated by reward. These processes can be measured using the event-related potentials (ERPs) elicited by retrieval cues from tasks with different retrieval requirements, such as via changes in the class of targeted memory information. To determine whether retrieval orientations of this kind are modulated by reward during learning, we investigated the effects of high and low reward expectancy on the ERP correlates of retrieval orientation in two separate experiments. The reward manipulation at study in Experiment 1 was associated with later memory performance, whereas in Experiment 2, reward was directly linked to accuracy in the study task. In both studies, the participants encoded mixed lists of pictures and words preceded by high- or low-reward cues. After 24 h, they performed a recognition memory exclusion task, with words as the test items. In addition to a previously reported material-specific effect of retrieval orientation, a frontally distributed, reward-associated retrieval orientation effect was found in both experiments. These findings suggest that reward motivation during learning leads to the adoption of a reward-associated retrieval orientation to support the retrieval of highly motivational information. Thus, ERP retrieval orientation effects not only reflect retrieval processes related to the sought-for materials, but also relate to the reward conditions with which items were combined during encoding.

User centered and ontology based information retrieval system for life sciences.

Science.gov (United States)

Sy, Mohameth-François; Ranwez, Sylvie; Montmain, Jacky; Regnault, Armelle; Crampes, Michel; Ranwez, Vincent

2012-01-25

Because of the increasing number of electronic resources, designing efficient tools to retrieve and exploit them is a major challenge. Some improvements have been offered by semantic Web technologies and applications based on domain ontologies. In life science, for instance, the Gene Ontology is widely exploited in genomic applications and the Medical Subject Headings is the basis of biomedical publications indexation and information retrieval process proposed by PubMed. However current search engines suffer from two main drawbacks: there is limited user interaction with the list of retrieved resources and no explanation for their adequacy to the query is provided. Users may thus be confused by the selection and have no idea on how to adapt their queries so that the results match their expectations. This paper describes an information retrieval system that relies on domain ontology to widen the set of relevant documents that is retrieved and that uses a graphical rendering of query results to favor user interactions. Semantic proximities between ontology concepts and aggregating models are used to assess documents adequacy with respect to a query. The selection of documents is displayed in a semantic map to provide graphical indications that make explicit to what extent they match the user's query; this man/machine interface favors a more interactive and iterative exploration of data corpus, by facilitating query concepts weighting and visual explanation. We illustrate the benefit of using this information retrieval system on two case studies one of which aiming at collecting human genes related to transcription factors involved in hemopoiesis pathway. The ontology based information retrieval system described in this paper (OBIRS) is freely available at: http://www.ontotoolkit.mines-ales.fr/ObirsClient/. This environment is a first step towards a user centred application in which the system enlightens relevant information to provide decision help.

User centered and ontology based information retrieval system for life sciences

Directory of Open Access Journals (Sweden)

Sy Mohameth-François

2012-01-01

Full Text Available Abstract Background Because of the increasing number of electronic resources, designing efficient tools to retrieve and exploit them is a major challenge. Some improvements have been offered by semantic Web technologies and applications based on domain ontologies. In life science, for instance, the Gene Ontology is widely exploited in genomic applications and the Medical Subject Headings is the basis of biomedical publications indexation and information retrieval process proposed by PubMed. However current search engines suffer from two main drawbacks: there is limited user interaction with the list of retrieved resources and no explanation for their adequacy to the query is provided. Users may thus be confused by the selection and have no idea on how to adapt their queries so that the results match their expectations. Results This paper describes an information retrieval system that relies on domain ontology to widen the set of relevant documents that is retrieved and that uses a graphical rendering of query results to favor user interactions. Semantic proximities between ontology concepts and aggregating models are used to assess documents adequacy with respect to a query. The selection of documents is displayed in a semantic map to provide graphical indications that make explicit to what extent they match the user's query; this man/machine interface favors a more interactive and iterative exploration of data corpus, by facilitating query concepts weighting and visual explanation. We illustrate the benefit of using this information retrieval system on two case studies one of which aiming at collecting human genes related to transcription factors involved in hemopoiesis pathway. Conclusions The ontology based information retrieval system described in this paper (OBIRS is freely available at: http://www.ontotoolkit.mines-ales.fr/ObirsClient/. This environment is a first step towards a user centred application in which the system enlightens

PageRank without hyperlinks: Reranking with PubMed related article networks for biomedical text retrieval

Directory of Open Access Journals (Sweden)

Lin Jimmy

2008-06-01

Full Text Available Abstract Background Graph analysis algorithms such as PageRank and HITS have been successful in Web environments because they are able to extract important inter-document relationships from manually-created hyperlinks. We consider the application of these techniques to biomedical text retrieval. In the current PubMed® search interface, a MEDLINE® citation is connected to a number of related citations, which are in turn connected to other citations. Thus, a MEDLINE record represents a node in a vast content-similarity network. This article explores the hypothesis that these networks can be exploited for text retrieval, in the same manner as hyperlink graphs on the Web. Results We conducted a number of reranking experiments using the TREC 2005 genomics track test collection in which scores extracted from PageRank and HITS analysis were combined with scores returned by an off-the-shelf retrieval engine. Experiments demonstrate that incorporating PageRank scores yields significant improvements in terms of standard ranked-retrieval metrics. Conclusion The link structure of content-similarity networks can be exploited to improve the effectiveness of information retrieval systems. These results generalize the applicability of graph analysis algorithms to text retrieval in the biomedical domain.

PageRank without hyperlinks: reranking with PubMed related article networks for biomedical text retrieval.

Science.gov (United States)

Lin, Jimmy

2008-06-06

Graph analysis algorithms such as PageRank and HITS have been successful in Web environments because they are able to extract important inter-document relationships from manually-created hyperlinks. We consider the application of these techniques to biomedical text retrieval. In the current PubMed(R) search interface, a MEDLINE(R) citation is connected to a number of related citations, which are in turn connected to other citations. Thus, a MEDLINE record represents a node in a vast content-similarity network. This article explores the hypothesis that these networks can be exploited for text retrieval, in the same manner as hyperlink graphs on the Web. We conducted a number of reranking experiments using the TREC 2005 genomics track test collection in which scores extracted from PageRank and HITS analysis were combined with scores returned by an off-the-shelf retrieval engine. Experiments demonstrate that incorporating PageRank scores yields significant improvements in terms of standard ranked-retrieval metrics. The link structure of content-similarity networks can be exploited to improve the effectiveness of information retrieval systems. These results generalize the applicability of graph analysis algorithms to text retrieval in the biomedical domain.

Competitive retrieval is not a prerequisite for forgetting in the retrieval practice paradigm.

NARCIS (Netherlands)

Camp, Gino; Dalm, Sander

2018-01-01

Retrieving information from memory can lead to forgetting of other, related information. The inhibition account of this retrieval-induced forgetting effect predicts that this form of forgetting occurs when competition arises between the practiced information and the related information, leading to

Neural correlates of relational memory: successful encoding and retrieval of semantic and perceptual associations

NARCIS (Netherlands)

Prince, S.E.; Daselaar, S.M.; Cabeza, R.

2005-01-01

Using event-related functional magnetic resonance imaging, we identified brain regions involved in successful relational memory (RM) during encoding and retrieval for semantic and perceptual associations or in general, independent of phase and content. Participants were scanned while encoding and

Generic information can retrieve known biological associations: implications for biomedical knowledge discovery.

Directory of Open Access Journals (Sweden)

Herman H H B M van Haagen

Full Text Available MOTIVATION: Weighted semantic networks built from text-mined literature can be used to retrieve known protein-protein or gene-disease associations, and have been shown to anticipate associations years before they are explicitly stated in the literature. Our text-mining system recognizes over 640,000 biomedical concepts: some are specific (i.e., names of genes or proteins others generic (e.g., 'Homo sapiens'. Generic concepts may play important roles in automated information retrieval, extraction, and inference but may also result in concept overload and confound retrieval and reasoning with low-relevance or even spurious links. Here, we attempted to optimize the retrieval performance for protein-protein interactions (PPI by filtering generic concepts (node filtering or links to generic concepts (edge filtering from a weighted semantic network. First, we defined metrics based on network properties that quantify the specificity of concepts. Then using these metrics, we systematically filtered generic information from the network while monitoring retrieval performance of known protein-protein interactions. We also systematically filtered specific information from the network (inverse filtering, and assessed the retrieval performance of networks composed of generic information alone. RESULTS: Filtering generic or specific information induced a two-phase response in retrieval performance: initially the effects of filtering were minimal but beyond a critical threshold network performance suddenly drops. Contrary to expectations, networks composed exclusively of generic information demonstrated retrieval performance comparable to unfiltered networks that also contain specific concepts. Furthermore, an analysis using individual generic concepts demonstrated that they can effectively support the retrieval of known protein-protein interactions. For instance the concept "binding" is indicative for PPI retrieval and the concept "mutation abnormality" is

Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists.

Science.gov (United States)

Wiley, Laura K; Sivley, R Michael; Bush, William S

2013-01-01

Efficient storage and retrieval of genomic annotations based on range intervals is necessary, given the amount of data produced by next-generation sequencing studies. The indexing strategies of relational database systems (such as MySQL) greatly inhibit their use in genomic annotation tasks. This has led to the development of stand-alone applications that are dependent on flat-file libraries. In this work, we introduce MyNCList, an implementation of the NCList data structure within a MySQL database. MyNCList enables the storage, update and rapid retrieval of genomic annotations from the convenience of a relational database system. Range-based annotations of 1 million variants are retrieved in under a minute, making this approach feasible for whole-genome annotation tasks. Database URL: https://github.com/bushlab/mynclist.

Learning related modulation of functional retrieval networks in man.

Science.gov (United States)

Petersson, K M; Sandblom, J; Gisselgård, J; Ingvar, M

2001-07-01

The medial temporal lobe has been implicated in studies of episodic memory tasks involving spatio-temporal context and object-location conjunctions. We have previously demonstrated that an increased level of practice in a free-recall task parallels a decrease in the functional activity of several brain regions, including the medial temporal lobe, the prefrontal, the anterior cingulate, the anterior insular, and the posterior parietal cortices, that in concert demonstrate a move from elaborate controlled processing towards a higher degree of automaticity. Here we report data from two experiments that extend these initial observations. We used a similar experimental approach but probed for effects of retrieval paradigms and stimulus material. In the first experiment we investigated practice related changes during recognition of object-location conjunctions and in the second during free-recall of pseudo-words. Learning in a neural network is a dynamic consequence of information processing and network plasticity. The present and previous PET results indicate that practice can induce a learning related functional restructuring of information processing. Different adaptive processes likely subserve the functional re-organisation observed. These may in part be related to different demands for attentional and working memory processing. It appears that the role(s) of the prefrontal cortex and the medial temporal lobe in memory retrieval are complex, perhaps reflecting several different interacting processes or cognitive components. We suggest that an integrative interactive perspective on the role of the prefrontal and medial temporal lobe is necessary for an understanding of the processing significance of these regions in learning and memory. It appears necessary to develop elaborated and explicit computational models for prefrontal and medial temporal functions in order to derive detailed empirical predictions, and in combination with an efficient use and development of

Encoding and retrieval of landmark-related spatial cues during navigation: an fMRI study.

Science.gov (United States)

Wegman, Joost; Tyborowska, Anna; Janzen, Gabriele

2014-07-01

To successfully navigate, humans can use different cues from their surroundings. Learning locations in an environment can be supported by parallel subsystems in the hippocampus and the striatum. We used fMRI to look at differences in the use of object-related spatial cues while 47 participants actively navigated in an open-field virtual environment. In each trial, participants navigated toward a target object. During encoding, three positional cues (columns) with directional cues (shadows) were available. During retrieval, the removed target had to be replaced while either two objects without shadows (objects trial) or one object with a shadow (shadow trial) were available. Participants were informed in blocks about which type of retrieval trial was most likely to occur, thereby modulating expectations of having to rely on a single landmark or on a configuration of landmarks. How the spatial learning systems in the hippocampus and caudate nucleus were involved in these landmark-based encoding and retrieval processes were investigated. Landmark configurations can create a geometry similar to boundaries in an environment. It was found that the hippocampus was involved in encoding when relying on configurations of landmarks, whereas the caudate nucleus was involved in encoding when relying on single landmarks. This might suggest that the observed hippocampal activation for configurations of objects is linked to a spatial representation observed with environmental boundaries. Retrieval based on configurations of landmarks activated regions associated with the spatial updation of object locations for reorientation. When only a single landmark was available during retrieval, regions associated with updating the location of oneself were activated. There was also evidence that good between-participant performance was predicted by right hippocampal activation. This study therefore sheds light on how the brain deals with changing demands on spatial processing related purely

Mining literature for a comprehensive pathway analysis: A case study for retrieval of homocysteine related genes for genetic and epigenetic studies

Directory of Open Access Journals (Sweden)

Mahajan Anubha

2006-01-01

Full Text Available Abstract Homocysteine is an independent risk factor for cardiovascular diseases. It is also known to be associated with a variety of complex disorders. While there are a large number of independent studies implicating homocysteine in isolated pathways, the mechanism of homocysteine induced adverse effects are not clear. Homocysteine-induced modulation of gene expression through alteration of methylation status or by hitherto unknown mechanisms is predicted to lead to several pathological conditions either directly or indirectly. In the present manuscript, using literature mining approach, we have identified the genes that are modulated directly or indirectly by an elevated level of homocysteine. These genes were then placed in appropriate pathways in an attempt to understand the molecular basis of homocysteine induced complex disorders and to provide a resource for selection of genes for polymorphism screening and analysis of mutations as well as epigenetic modifications in relation to hyperhomocysteinemia. We have identified 135 genes in 1137 abstracts that either modulate the levels of homocysteine or are modulated by elevated levels of homocysteine. Mapping the genes to their respective pathways revealed that an elevated level of homocysteine leads to the atherosclerosis either by directly affecting lipid metabolism and transport or via oxidative stress and/or Endoplasmic Reticulum (ER stress. Elevated levels of homocysteine also decreases the bioavailability of nitric oxide and modulates the levels of other metabolites including S-adenosyl methionine and S-adenosyl homocysteine which may result in cardiovascular or neurological disorders. The ER stress emerges as the common pathway that relates to apoptosis, atherosclerosis and neurological disorders and is modulated by levels of homocysteine. The comprehensive network collated has lead to the identification of genes that are modulated by homocysteine indicating that homocysteine exerts its

Transient acidosis while retrieving a fear-related memory enhances its lability

Science.gov (United States)

Du, Jianyang; Price, Margaret P; Taugher, Rebecca J; Grigsby, Daniel; Ash, Jamison J; Stark, Austin C; Hossain Saad, Md Zubayer; Singh, Kritika; Mandal, Juthika; Wemmie, John A; Welsh, Michael J

2017-01-01

Attenuating the strength of fearful memories could benefit people disabled by memories of past trauma. Pavlovian conditioning experiments indicate that a retrieval cue can return a conditioned aversive memory to a labile state. However, means to enhance retrieval and render a memory more labile are unknown. We hypothesized that augmenting synaptic signaling during retrieval would increase memory lability. To enhance synaptic transmission, mice inhaled CO2 to induce an acidosis and activate acid sensing ion channels. Transient acidification increased the retrieval-induced lability of an aversive memory. The labile memory could then be weakened by an extinction protocol or strengthened by reconditioning. Coupling CO2 inhalation to retrieval increased activation of amygdala neurons bearing the memory trace and increased the synaptic exchange from Ca2+-impermeable to Ca2+-permeable AMPA receptors. The results suggest that transient acidosis during retrieval renders the memory of an aversive event more labile and suggest a strategy to modify debilitating memories. DOI: http://dx.doi.org/10.7554/eLife.22564.001 PMID:28650315

Altered Neural Activity during Semantic Object Memory Retrieval in Amnestic Mild Cognitive Impairment as Measured by Event-Related Potentials.

Science.gov (United States)

Chiang, Hsueh-Sheng; Mudar, Raksha A; Pudhiyidath, Athula; Spence, Jeffrey S; Womack, Kyle B; Cullum, C Munro; Tanner, Jeremy A; Eroh, Justin; Kraut, Michael A; Hart, John

2015-01-01

Deficits in semantic memory in individuals with amnestic mild cognitive impairment (aMCI) have been previously reported, but the underlying neurobiological mechanisms remain to be clarified. We examined event-related potentials (ERPs) associated with semantic memory retrieval in 16 individuals with aMCI as compared to 17 normal controls using the Semantic Object Retrieval Task (EEG SORT). In this task, subjects judged whether pairs of words (object features) elicited retrieval of an object (retrieval trials) or not (non-retrieval trials). Behavioral findings revealed that aMCI subjects had lower accuracy scores and marginally longer reaction time compared to controls. We used a multivariate analytical technique (STAT-PCA) to investigate similarities and differences in ERPs between aMCI and control groups. STAT-PCA revealed a left fronto-temporal component starting at around 750 ms post-stimulus in both groups. However, unlike controls, aMCI subjects showed an increase in the frontal-parietal scalp potential that distinguished retrieval from non-retrieval trials between 950 and 1050 ms post-stimulus negatively correlated with the performance on the logical memory subtest of the Wechsler Memory Scale-III. Thus, individuals with aMCI were not only impaired in their behavioral performance on SORT relative to controls, but also displayed alteration in the corresponding ERPs. The altered neural activity in aMCI compared to controls suggests a more sustained and effortful search during object memory retrieval, which may be a potential marker indicating disease processes at the pre-dementia stage.

Cry-Bt identifier: a biological database for PCR detection of Cry genes present in transgenic plants.

Science.gov (United States)

Singh, Vinay Kumar; Ambwani, Sonu; Marla, Soma; Kumar, Anil

2009-10-23

We describe the development of a user friendly tool that would assist in the retrieval of information relating to Cry genes in transgenic crops. The tool also helps in detection of transformed Cry genes from Bacillus thuringiensis present in transgenic plants by providing suitable designed primers for PCR identification of these genes. The tool designed based on relational database model enables easy retrieval of information from the database with simple user queries. The tool also enables users to access related information about Cry genes present in various databases by interacting with different sources (nucleotide sequences, protein sequence, sequence comparison tools, published literature, conserved domains, evolutionary and structural data). http://insilicogenomics.in/Cry-btIdentifier/welcome.html.

Remembering and knowing personality traits: figure/ground asymmetries in person-related retrieval experience.

Science.gov (United States)

Wehr, Thomas

2008-01-01

In two experiments, the effect of category salience on retrieval experience was investigated. In Experiment 1, participants rated typicality or concreteness of personality traits that differed in stereotype reference (i.e., consistent, inconsistent, and neutral in relation to the age stereotype). More remember judgments were given for consistent and inconsistent traits in contrast to neutral traits, thereby indicating a figure/ground asymmetry. In Experiment 2, neutral traits were excluded and a classical figure/ground phenomenon was demonstrated for the retrieval experience of traits (i.e., reversibility of an ambiguous figure after typicality and untypicality ratings). Altogether, the results suggest that metacognitive trait representations depend on principles of figure/ground asymmetries rather than on functional principles of social information processing.

Retrieval options study

International Nuclear Information System (INIS)

1980-03-01

This Retrieval Options Study is part of the systems analysis activities of the Office of Nuclear Waste Isolation to develop the scientific and technological bases for radioactive waste repositories in various geologic media. The study considers two waste forms, high level waste and spent fuel, and defines various classes of waste retrieval and recovery. A methodology and data base are developed which allow the relative evaluation of retrieval and recovery costs and the following technical criteria: safety; technical feasibility; ease of retrieval; probable intact retrieval time; safeguards; monitoring; criticality; and licensability. A total of 505 repository options are defined and the cost and technical criteria evaluated utilizing a combination of facts and engineering judgments. The repositories evaluated are selected combinations of the following parameters: Geologic Media (salt, granite, basalt, shale); Retrieval Time after Emplacement (5 and 25 years); Emplacement Design (nominal hole, large hole, carbon steel canister, corrosion resistant canister, backfill in hole, nominal sleeves, thick wall sleeves); Emplacement Configuration (single vertical, multiple vertical, single horizontal, multiple horizontal, vaults; Thermal Considerations; (normal design, reduced density, once-through ventilation, recirculated ventilation); Room Backfill; (none, run-of-mine, early, 5 year delay, 25 year delay, decommissioned); and Rate of Retrieval;

Treatment of cuff-related tracheal stenosis with a fully covered retrievable expandable metallic stent

International Nuclear Information System (INIS)

Chen, G.; Wang, Z.; Liang, X.; Wang, Y.; Wang, Y.; Wang, Z.; Xian, J.

2013-01-01

Aim: To investigate the clinical effectiveness, complications, and optimal duration of use of covered retrievable expandable metallic stents in the management of cuff-related tracheal stenosis. Materials and methods: Twenty-one patients with cuff-related tracheal stenosis, Meyer–Cotton grade II (29%) and III (71%), who underwent fluoroscopically guided placement of covered retrievable expandable metallic stents were studied. Sixty-four-section computed tomography (CT) and bronchovideoscopy were performed prior to stent insertion, 1 month after stent insertion, in the case of stent-related complications, and after stent removal. Clinical manifestations, Hugh–Jones classification, and forced expiratory volume in 1 s (FEV1) were used to evaluate respiratory function before and after stent insertion and removal. The diameter of the stricture and FEV1 changes before insertion and after removal were analysed using the paired samples t-test. A p-value of ≤0.05 was considered statistically significant. Results: Twenty-one patients had 27 covered retrievable expandable metallic stents placed. Stents were electively removed from 20 patients. The median duration of stent placement was 5 months (range 4–12 months). One stent was not removed due to mucopolysaccharidosis type II (MPS II or Hunter syndrome) with tracheomalacia. After stent removal, airway dimensions increased and airway occlusion was symptomatically relieved in all patients. CT and bronchovideoscopy showed patent lumens with increased dimensions. Stent-related complications occurred in 19 (91%) patients, including granulation tissue formation (n = 18, 86%), stent migration and stent expectoration (n = 2, 10%), mucus plugging (n = 1, 5%), and halitosis (n = 6, 29%). Some patients experienced multiple complications, which were all managed effectively while the stent was still in place. There was a statistically significant difference in the diameter of the stricture and FEV1 between the time of stent

Treatment of cuff-related tracheal stenosis with a fully covered retrievable expandable metallic stent.

Science.gov (United States)

Chen, G; Wang, Z; Liang, X; Wang, Y; Wang, Y; Wang, Z; Xian, J

2013-04-01

To investigate the clinical effectiveness, complications, and optimal duration of use of covered retrievable expandable metallic stents in the management of cuff-related tracheal stenosis. Twenty-one patients with cuff-related tracheal stenosis, Meyer-Cotton grade II (29%) and III (71%), who underwent fluoroscopically guided placement of covered retrievable expandable metallic stents were studied. Sixty-four-section computed tomography (CT) and bronchovideoscopy were performed prior to stent insertion, 1 month after stent insertion, in the case of stent-related complications, and after stent removal. Clinical manifestations, Hugh-Jones classification, and forced expiratory volume in 1 s (FEV1) were used to evaluate respiratory function before and after stent insertion and removal. The diameter of the stricture and FEV1 changes before insertion and after removal were analysed using the paired samples t-test. A p-value of ≤0.05 was considered statistically significant. Twenty-one patients had 27 covered retrievable expandable metallic stents placed. Stents were electively removed from 20 patients. The median duration of stent placement was 5 months (range 4-12 months). One stent was not removed due to mucopolysaccharidosis type II (MPS II or Hunter syndrome) with tracheomalacia. After stent removal, airway dimensions increased and airway occlusion was symptomatically relieved in all patients. CT and bronchovideoscopy showed patent lumens with increased dimensions. Stent-related complications occurred in 19 (91%) patients, including granulation tissue formation (n = 18, 86%), stent migration and stent expectoration (n = 2, 10%), mucus plugging (n = 1, 5%), and halitosis (n = 6, 29%). Some patients experienced multiple complications, which were all managed effectively while the stent was still in place. There was a statistically significant difference in the diameter of the stricture and FEV1 between the time of stent insertion and removal. An improvement in

Do age-related word retrieval difficulties appear (or disappear) in connected speech?

Science.gov (United States)

Kavé, Gitit; Goral, Mira

2017-09-01

We conducted a comprehensive literature review of studies of word retrieval in connected speech in healthy aging and reviewed relevant aphasia research that could shed light on the aging literature. Four main hypotheses guided the review: (1) Significant retrieval difficulties would lead to reduced output in connected speech. (2) Significant retrieval difficulties would lead to a more limited lexical variety in connected speech. (3) Significant retrieval difficulties would lead to an increase in word substitution errors and in pronoun use as well as to greater dysfluency and hesitation in connected speech. (4) Retrieval difficulties on tests of single-word production would be associated with measures of word retrieval in connected speech. Studies on aging did not confirm these four hypotheses, unlike studies on aphasia that generally did. The review suggests that future research should investigate how context facilitates word production in old age.

UniGene Tabulator: a full parser for the UniGene format.

Science.gov (United States)

Lenzi, Luca; Frabetti, Flavia; Facchin, Federica; Casadei, Raffaella; Vitale, Lorenza; Canaider, Silvia; Carinci, Paolo; Zannotti, Maria; Strippoli, Pierluigi

2006-10-15

UniGene Tabulator 1.0 provides a solution for full parsing of UniGene flat file format; it implements a structured graphical representation of each data field present in UniGene following import into a common database managing system usable in a personal computer. This database includes related tables for sequence, protein similarity, sequence-tagged site (STS) and transcript map interval (TXMAP) data, plus a summary table where each record represents a UniGene cluster. UniGene Tabulator enables full local management of UniGene data, allowing parsing, querying, indexing, retrieving, exporting and analysis of UniGene data in a relational database form, usable on Macintosh (OS X 10.3.9 or later) and Windows (2000, with service pack 4, XP, with service pack 2 or later) operating systems-based computers. The current release, including both the FileMaker runtime applications, is freely available at http://apollo11.isto.unibo.it/software/

Trial-to-trial dynamics of selective long-term-memory retrieval with continuously changing retrieval targets.

Science.gov (United States)

Kizilirmak, Jasmin M; Rösler, Frank; Khader, Patrick H

2014-10-01

How do we control the successive retrieval of behaviorally relevant information from long-term memory (LTM) without being distracted by other potential retrieval targets associated to the same retrieval cues? Here, we approach this question by investigating the nature of trial-by-trial dynamics of selective LTM retrieval, i.e., in how far retrieval in one trial has detrimental or facilitatory effects on selective retrieval in the following trial. Participants first learned associations between retrieval cues and targets, with one cue always being linked to three targets, forming small associative networks. In successive trials, participants had to access either the same or a different target belonging to either the same or a different cue. We found that retrieval times were faster for targets that had already been relevant in the previous trial, with this facilitatory effect being substantially weaker when the associative network changed in which the targets were embedded. Moreover, staying within the same network still had a facilitatory effect even if the target changed, which became evident in a relatively higher memory performance in comparison to a network change. Furthermore, event-related brain potentials (ERPs) showed topographically and temporally dissociable correlates of these effects, suggesting that they result from combined influences of distinct processes that aid memory retrieval when relevant and irrelevant targets change their status from trial to trial. Taken together, the present study provides insight into the different processing stages of memory retrieval when fast switches between retrieval targets are required. Copyright © 2014 Elsevier Inc. All rights reserved.

Retrieval options study

Energy Technology Data Exchange (ETDEWEB)

1980-03-01

This Retrieval Options Study is part of the systems analysis activities of the Office of Nuclear Waste Isolation to develop the scientific and technological bases for radioactive waste repositories in various geologic media. The study considers two waste forms, high level waste and spent fuel, and defines various classes of waste retrieval and recovery. A methodology and data base are developed which allow the relative evaluation of retrieval and recovery costs and the following technical criteria: safety; technical feasibility; ease of retrieval; probable intact retrieval time; safeguards; monitoring; criticality; and licensability. A total of 505 repository options are defined and the cost and technical criteria evaluated utilizing a combination of facts and engineering judgments. The repositories evaluated are selected combinations of the following parameters: Geologic Media (salt, granite, basalt, shale); Retrieval Time after Emplacement (5 and 25 years); Emplacement Design (nominal hole, large hole, carbon steel canister, corrosion resistant canister, backfill in hole, nominal sleeves, thick wall sleeves); Emplacement Configuration (single vertical, multiple vertical, single horizontal, multiple horizontal, vaults; Thermal Considerations; (normal design, reduced density, once-through ventilation, recirculated ventilation); Room Backfill; (none, run-of-mine, early, 5 year delay, 25 year delay, decommissioned); and Rate of Retrieval; (same as emplacement, variably slower depending on repository/canister condition).

Retrieval Cues on Tests: A Strategy for Helping Students Overcome Retrieval Failure

Science.gov (United States)

Gallagher, Kristel M.

2017-01-01

Students often struggle to recall information on tests, frequently claiming to experience a "retrieval failure" of learned information. Thus, the retrieval of information from memory may be a roadblock to student success. I propose a relatively simple adjustment to the wording of test items to help eliminate this potential barrier.…

A LDA-based approach to promoting ranking diversity for genomics information retrieval.

Science.gov (United States)

Chen, Yan; Yin, Xiaoshi; Li, Zhoujun; Hu, Xiaohua; Huang, Jimmy Xiangji

2012-06-11

In the biomedical domain, there are immense data and tremendous increase of genomics and biomedical relevant publications. The wealth of information has led to an increasing amount of interest in and need for applying information retrieval techniques to access the scientific literature in genomics and related biomedical disciplines. In many cases, the desired information of a query asked by biologists is a list of a certain type of entities covering different aspects that are related to the question, such as cells, genes, diseases, proteins, mutations, etc. Hence, it is important of a biomedical IR system to be able to provide relevant and diverse answers to fulfill biologists' information needs. However traditional IR model only concerns with the relevance between retrieved documents and user query, but does not take redundancy between retrieved documents into account. This will lead to high redundancy and low diversity in the retrieval ranked lists. In this paper, we propose an approach which employs a topic generative model called Latent Dirichlet Allocation (LDA) to promoting ranking diversity for biomedical information retrieval. Different from other approaches or models which consider aspects on word level, our approach assumes that aspects should be identified by the topics of retrieved documents. We present LDA model to discover topic distribution of retrieval passages and word distribution of each topic dimension, and then re-rank retrieval results with topic distribution similarity between passages based on N-size slide window. We perform our approach on TREC 2007 Genomics collection and two distinctive IR baseline runs, which can achieve 8% improvement over the highest Aspect MAP reported in TREC 2007 Genomics track. The proposed method is the first study of adopting topic model to genomics information retrieval, and demonstrates its effectiveness in promoting ranking diversity as well as in improving relevance of ranked lists of genomics search

Macular xanthophylls, lipoprotein-related genes, and age-related macular degeneration.

Science.gov (United States)

Koo, Euna; Neuringer, Martha; SanGiovanni, John Paul

2014-07-01

Plant-based macular xanthophylls (MXs; lutein and zeaxanthin) and the lutein metabolite meso-zeaxanthin are the major constituents of macular pigment, a compound concentrated in retinal areas that are responsible for fine-feature visual sensation. There is an unmet need to examine the genetics of factors influencing regulatory mechanisms and metabolic fates of these 3 MXs because they are linked to processes implicated in the pathogenesis of age-related macular degeneration (AMD). In this work we provide an overview of evidence supporting a molecular basis for AMD-MX associations as they may relate to DNA sequence variation in AMD- and lipoprotein-related genes. We recognize a number of emerging research opportunities, barriers, knowledge gaps, and tools offering promise for meaningful investigation and inference in the field. Overviews on AMD- and high-density lipoprotein (HDL)-related genes encoding receptors, transporters, and enzymes affecting or affected by MXs are followed with information on localization of products from these genes to retinal cell types manifesting AMD-related pathophysiology. Evidence on the relation of each gene or gene product with retinal MX response to nutrient intake is discussed. This information is followed by a review of results from mechanistic studies testing gene-disease relations. We then present findings on relations of AMD with DNA sequence variants in MX-associated genes. Our conclusion is that AMD-associated DNA variants that influence the actions and metabolic fates of HDL system constituents should be examined further for concomitant influence on MX absorption, retinal tissue responses to MX intake, and the capacity to modify MX-associated factors and processes implicated in AMD pathogenesis. © 2014 American Society for Nutrition.

[Competition-dependence on retrieval-induced forgetting: the influence of the amount of retrieval cues].

Science.gov (United States)

Yamada, Yohei; Tsukimoto, Takashi; Hirano, Tetsuji

2010-02-01

Remembering some of the studied (target) items impairs subsequent remembrance of relevant (non-target) items. This phenomenon, retrieval-induced forgetting (RIF), occurs when non-targets actively compete with the retrieval of a target. Researchers suggest that suppression mechanisms reduce interference from relevant items to facilitate the retrieval of target items (Anderson, 2003). Competition-dependence is one of the properties that support the suppression hypothesis (Anderson, Bjork, & Bjork, 1994). In the present study, we manipulated the type of retrieval practice (normal, last-letter, or category-name) in order to vary the degree of competition between the target and the non-targets. For the high-scoring retrieval practice group, RIF occurred in the normal retrieval condition, but not in the last-letter or in the category-name conditions. For the low-scoring retrieval practice group, RIF did not occur in any of the conditions. These findings provide new evidence that the occurrence of RIF depends on the degree of competition between a target item and related non-target items during retrieval practice.

Comprehensive analysis of gene expression patterns of hedgehog-related genes

Directory of Open Access Journals (Sweden)

Baillie David

2006-10-01

Full Text Available Abstract Background The Caenorhabditis elegans genome encodes ten proteins that share sequence similarity with the Hedgehog signaling molecule through their C-terminal autoprocessing Hint/Hog domain. These proteins contain novel N-terminal domains, and C. elegans encodes dozens of additional proteins containing only these N-terminal domains. These gene families are called warthog, groundhog, ground-like and quahog, collectively called hedgehog (hh-related genes. Previously, the expression pattern of seventeen genes was examined, which showed that they are primarily expressed in the ectoderm. Results With the completion of the C. elegans genome sequence in November 2002, we reexamined and identified 61 hh-related ORFs. Further, we identified 49 hh-related ORFs in C. briggsae. ORF analysis revealed that 30% of the genes still had errors in their predictions and we improved these predictions here. We performed a comprehensive expression analysis using GFP fusions of the putative intergenic regulatory sequence with one or two transgenic lines for most genes. The hh-related genes are expressed in one or a few of the following tissues: hypodermis, seam cells, excretory duct and pore cells, vulval epithelial cells, rectal epithelial cells, pharyngeal muscle or marginal cells, arcade cells, support cells of sensory organs, and neuronal cells. Using time-lapse recordings, we discovered that some hh-related genes are expressed in a cyclical fashion in phase with molting during larval development. We also generated several translational GFP fusions, but they did not show any subcellular localization. In addition, we also studied the expression patterns of two genes with similarity to Drosophila frizzled, T23D8.1 and F27E11.3A, and the ortholog of the Drosophila gene dally-like, gpn-1, which is a heparan sulfate proteoglycan. The two frizzled homologs are expressed in a few neurons in the head, and gpn-1 is expressed in the pharynx. Finally, we compare the

Determining Semantically Related Significant Genes.

Science.gov (United States)

Taha, Kamal

2014-01-01

GO relation embodies some aspects of existence dependency. If GO term xis existence-dependent on GO term y, the presence of y implies the presence of x. Therefore, the genes annotated with the function of the GO term y are usually functionally and semantically related to the genes annotated with the function of the GO term x. A large number of gene set enrichment analysis methods have been developed in recent years for analyzing gene sets enrichment. However, most of these methods overlook the structural dependencies between GO terms in GO graph by not considering the concept of existence dependency. We propose in this paper a biological search engine called RSGSearch that identifies enriched sets of genes annotated with different functions using the concept of existence dependency. We observe that GO term xcannot be existence-dependent on GO term y, if x- and y- have the same specificity (biological characteristics). After encoding into a numeric format the contributions of GO terms annotating target genes to the semantics of their lowest common ancestors (LCAs), RSGSearch uses microarray experiment to identify the most significant LCA that annotates the result genes. We evaluated RSGSearch experimentally and compared it with five gene set enrichment systems. Results showed marked improvement.

Age-Related Reversals in Neural Recruitment across Memory Retrieval Phases.

Science.gov (United States)

Ford, Jaclyn H; Kensinger, Elizabeth A

2017-05-17

Over the last several decades, neuroimaging research has identified age-related neural changes that occur during cognitive tasks. These changes are used to help researchers identify functional changes that contribute to age-related impairments in cognitive performance. One commonly reported example of such a change is an age-related decrease in the recruitment of posterior sensory regions coupled with an increased recruitment of prefrontal regions across multiple cognitive tasks. This shift is often described as a compensatory recruitment of prefrontal regions due to age-related sensory-processing deficits in posterior regions. However, age is not only associated with spatial shifts in recruitment, but also with temporal shifts, in which younger and older adults recruit the same neural region at different points in a task trial. The current study examines the possible contribution of temporal modifications in the often-reported posterior-anterior shift. Participants, ages 19-85, took part in a memory retrieval task with a protracted retrieval trial consisting of an initial memory search phase and a subsequent detail elaboration phase. Age-related neural patterns during search replicated prior reports of age-related decreases in posterior recruitment and increases in prefrontal recruitment. However, during the later elaboration phase, the same posterior regions were associated with age-related increases in activation. Further, ROI and functional connectivity results suggest that these posterior regions function similarly during search and elaboration. These results suggest that the often-reported posterior-anterior shift may not reflect the inability of older adults to engage in sensory processing, but rather a change in when they recruit this processing. SIGNIFICANCE STATEMENT The current study provides evidence that the often-reported posterior-anterior shift in aging may not reflect a global sensory-processing deficit, as has often been reported, but rather a

Lumbosacral stenosis in Labrador retriever military working dogs - an exomic exploratory study.

Science.gov (United States)

Mukherjee, Meenakshi; Jones, Jeryl C; Yao, Jianbo

2017-01-01

Canine lumbosacral stenosis is defined as narrowing of the caudal lumbar and/or sacral vertebral canal. A risk factor for neurologic problems in many large sized breeds, lumbosacral stenosis can also cause early retirement in Labrador retriever military working dogs. Though vital for conservative management of the condition, early detection is complicated by the ambiguous nature of clinical signs of lumbosacral stenosis in stoic and high-drive Labrador retriever military working dogs. Though clinical diagnoses of lumbosacral stenosis using CT imaging are standard, they are usually not performed unless dogs present with clinical symptoms. Understanding the underlying genomic mechanisms would be beneficial in developing early detection methods for lumbosacral stenosis, which could prevent premature retirement in working dogs. The exomes of 8 young Labrador retriever military working dogs (4 affected and 4 unaffected by lumbosacral stenosis, phenotypically selected by CT image analyses from 40 dogs with no reported clinical signs of the condition) were sequenced to identify and annotate exonic variants between dogs negative and positive for lumbosacral stenosis. Two-hundred and fifty-two variants were detected to be homozygous for the wild allele and either homozygous or heterozygous for the variant allele. Seventeen non-disruptive variants were detected that could affect protein effectiveness in 7 annotated (SCN1B, RGS9BP, ASXL3, TTR, LRRC16B, PTPRO, ZBBX) and 3 predicted genes (EEF1A1, DNAJA1, ZFX). No exonic variants were detected in any of the canine orthologues for human lumbar spinal stenosis candidate genes. TTR (transthyretin) gene could be a possible candidate for lumbosacral stenosis in Labrador retrievers based on previous human studies that have reported an association between human lumbar spinal stenosis and transthyretin protein amyloidosis. Other genes identified with exonic variants in this study but with no known published association with lumbosacral

Noncompetitive retrieval practice causes retrieval-induced forgetting in cued recall but not in recognition.

Science.gov (United States)

Grundgeiger, Tobias

2014-04-01

Retrieving a subset of learned items can lead to the forgetting of related items. Such retrieval-induced forgetting (RIF) can be explained by the inhibition of irrelevant items in order to overcome retrieval competition when the target item is retrieved. According to the retrieval inhibition account, such retrieval competition is a necessary condition for RIF. However, research has indicated that noncompetitive retrieval practice can also cause RIF by strengthening cue-item associations. According to the strength-dependent competition account, the strengthened items interfere with the retrieval of weaker items, resulting in impaired recall of weaker items in the final memory test. The aim of this study was to replicate RIF caused by noncompetitive retrieval practice and to determine whether this forgetting is also observed in recognition tests. In the context of RIF, it has been assumed that recognition tests circumvent interference and, therefore, should not be sensitive to forgetting due to strength-dependent competition. However, this has not been empirically tested, and it has been suggested that participants may reinstate learned cues as retrieval aids during the final test. In the present experiments, competitive practice or noncompetitive practice was followed by either final cued-recall tests or recognition tests. In cued-recall tests, RIF was observed in both competitive and noncompetitive conditions. However, in recognition tests, RIF was observed only in the competitive condition and was absent in the noncompetitive condition. The result underscores the contribution of strength-dependent competition to RIF. However, recognition tests seem to be a reliable way of distinguishing between RIF due to retrieval inhibition or strength-dependent competition.

Macular xanthophylls, lipoprotein-related genes, and age-related macular degeneration1234

Science.gov (United States)

Koo, Euna; Neuringer, Martha; SanGiovanni, John Paul

2014-01-01

Plant-based macular xanthophylls (MXs; lutein and zeaxanthin) and the lutein metabolite meso-zeaxanthin are the major constituents of macular pigment, a compound concentrated in retinal areas that are responsible for fine-feature visual sensation. There is an unmet need to examine the genetics of factors influencing regulatory mechanisms and metabolic fates of these 3 MXs because they are linked to processes implicated in the pathogenesis of age-related macular degeneration (AMD). In this work we provide an overview of evidence supporting a molecular basis for AMD-MX associations as they may relate to DNA sequence variation in AMD- and lipoprotein-related genes. We recognize a number of emerging research opportunities, barriers, knowledge gaps, and tools offering promise for meaningful investigation and inference in the field. Overviews on AMD- and high-density lipoprotein (HDL)–related genes encoding receptors, transporters, and enzymes affecting or affected by MXs are followed with information on localization of products from these genes to retinal cell types manifesting AMD-related pathophysiology. Evidence on the relation of each gene or gene product with retinal MX response to nutrient intake is discussed. This information is followed by a review of results from mechanistic studies testing gene-disease relations. We then present findings on relations of AMD with DNA sequence variants in MX-associated genes. Our conclusion is that AMD-associated DNA variants that influence the actions and metabolic fates of HDL system constituents should be examined further for concomitant influence on MX absorption, retinal tissue responses to MX intake, and the capacity to modify MX-associated factors and processes implicated in AMD pathogenesis. PMID:24829491

Cost-related implications of retrieval: Who should pay? Who should assess the cost/benefit?

International Nuclear Information System (INIS)

Soederberg, O.

2000-01-01

This paper contains an analysis of three different cases when a retrieval operation could take place. For each of the cases, the analysis covers three conceivable reasons for the retrieval. This means a total of nine scenarios to be analysed. One requirement for the analysis should be observed. That requirement is that there is, in a country, a system where assets are set aside today to cover such costs in the future which are caused by the current production of nuclear power. Within this framework, the analysis focuses on the financial implications of costs in connection with retrieval. (Consequences on the total national economy of such a financing system and of a retrieval operation are not discussed.) A financing system along these lines is consistent with two generally acknowledged principles: the polluter pays principle and the principle of not imposing undue burdens on future generations. But how are these principles applicable if, in the future, spent nuclear fuel were to be retrieved? Different time-horizons for a retrieval operation might produce different answers and these answers might also differ depending on the reasons for retrieval. The three chosen approximate times for retrieval are retrieval after a 10 year demonstration period (case 1), retrieval after the repository has ended its operating period but before final sealing has been carried out (case 2) and retrieval after about 50 years from sealing (case 3). The three reasons, which could be relevant in all three cases, can briefly be summarised as ''the solution is not safe enough'', ''the solution is safe enough but a better method than the chosen one has been developed and should be applied'' and ''what was considered as nuclear waste when disposed of now represents an economic asset which should be used by man''. (author)

Evaluation of the Serotonergic Genes htr1A, htr1B, htr2A, and slc6A4 in Aggressive Behavior of Golden Retriever Dogs

NARCIS (Netherlands)

Berg, L. van den; Vos-Loohuis, M.; Schilder, M.B.H.; Oost, B.A. van; Hazewinkel, H.A.W.; Wade, C.M.; Karlsson, E.K.; Lindblad-Toh, K.; Liinamo, A.E.; Leegwater, P.A.J.

2008-01-01

Aggressive behavior displays a high heritability in our study group ofGolden Retriever dogs.Alterations in brain serotonin metabolism have been described in aggressive dogs before. Here, we evaluate whether four genes of the canine serotonergic system, coding for the serotonin receptors 1A, 1B,

Information content of ozone retrieval algorithms

Science.gov (United States)

Rodgers, C.; Bhartia, P. K.; Chu, W. P.; Curran, R.; Deluisi, J.; Gille, J. C.; Hudson, R.; Mateer, C.; Rusch, D.; Thomas, R. J.

1989-01-01

The algorithms are characterized that were used for production processing by the major suppliers of ozone data to show quantitatively: how the retrieved profile is related to the actual profile (This characterizes the altitude range and vertical resolution of the data); the nature of systematic errors in the retrieved profiles, including their vertical structure and relation to uncertain instrumental parameters; how trends in the real ozone are reflected in trends in the retrieved ozone profile; and how trends in other quantities (both instrumental and atmospheric) might appear as trends in the ozone profile. No serious deficiencies were found in the algorithms used in generating the major available ozone data sets. As the measurements are all indirect in someway, and the retrieved profiles have different characteristics, data from different instruments are not directly comparable.

Ontology-Based Retrieval of Spatially Related Objects for Location Based Services

Science.gov (United States)

Haav, Hele-Mai; Kaljuvee, Aivi; Luts, Martin; Vajakas, Toivo

Advanced Location Based Service (LBS) applications have to integrate information stored in GIS, information about users' preferences (profile) as well as contextual information and information about application itself. Ontology engineering provides methods to semantically integrate several data sources. We propose an ontology-driven LBS development framework: the paper describes the architecture of ontologies and their usage for retrieval of spatially related objects relevant to the user. Our main contribution is to enable personalised ontology driven LBS by providing a novel approach for defining personalised semantic spatial relationships by means of ontologies. The approach is illustrated by an industrial case study.

Indirect two-sided relative ranking: a robust similarity measure for gene expression data

Directory of Open Access Journals (Sweden)

Licamele Louis

2010-03-01

Full Text Available Abstract Background There is a large amount of gene expression data that exists in the public domain. This data has been generated under a variety of experimental conditions. Unfortunately, these experimental variations have generally prevented researchers from accurately comparing and combining this wealth of data, which still hides many novel insights. Results In this paper we present a new method, which we refer to as indirect two-sided relative ranking, for comparing gene expression profiles that is robust to variations in experimental conditions. This method extends the current best approach, which is based on comparing the correlations of the up and down regulated genes, by introducing a comparison based on the correlations in rankings across the entire database. Because our method is robust to experimental variations, it allows a greater variety of gene expression data to be combined, which, as we show, leads to richer scientific discoveries. Conclusions We demonstrate the benefit of our proposed indirect method on several datasets. We first evaluate the ability of the indirect method to retrieve compounds with similar therapeutic effects across known experimental barriers, namely vehicle and batch effects, on two independent datasets (one private and one public. We show that our indirect method is able to significantly improve upon the previous state-of-the-art method with a substantial improvement in recall at rank 10 of 97.03% and 49.44%, on each dataset, respectively. Next, we demonstrate that our indirect method results in improved accuracy for classification in several additional datasets. These datasets demonstrate the use of our indirect method for classifying cancer subtypes, predicting drug sensitivity/resistance, and classifying (related cell types. Even in the absence of a known (i.e., labeled experimental barrier, the improvement of the indirect method in each of these datasets is statistically significant.

Data Aggregation System: A system for information retrieval on demand over relational and non-relational distributed data sources

Energy Technology Data Exchange (ETDEWEB)

Ball, G. [Imperial Coll., London; Kuznetsov, V. [Cornell U.; Evans, D. [Fermilab; Metson, S. [Bristol U.

2011-01-01

We present the Data Aggregation System, a system for information retrieval and aggregation from heterogenous sources of relational and non-relational data for the Compact Muon Solenoid experiment on the CERN Large Hadron Collider. The experiment currently has a number of organically-developed data sources, including front-ends to a number of different relational databases and non-database data services which do not share common data structures or APIs (Application Programming Interfaces), and cannot at this stage be readily converged. DAS provides a single interface for querying all these services, a caching layer to speed up access to expensive underlying calls and the ability to merge records from different data services pertaining to a single primary key.

Ontology-based Information Retrieval

DEFF Research Database (Denmark)

Styltsvig, Henrik Bulskov

In this thesis, we will present methods for introducing ontologies in information retrieval. The main hypothesis is that the inclusion of conceptual knowledge such as ontologies in the information retrieval process can contribute to the solution of major problems currently found in information...... retrieval. This utilization of ontologies has a number of challenges. Our focus is on the use of similarity measures derived from the knowledge about relations between concepts in ontologies, the recognition of semantic information in texts and the mapping of this knowledge into the ontologies in use......, as well as how to fuse together the ideas of ontological similarity and ontological indexing into a realistic information retrieval scenario. To achieve the recognition of semantic knowledge in a text, shallow natural language processing is used during indexing that reveals knowledge to the level of noun...

Neural correlates of autobiographical memory retrieval in children and adults.

Science.gov (United States)

Bauer, Patricia J; Pathman, Thanujeni; Inman, Cory; Campanella, Carolina; Hamann, Stephan

2017-04-01

Autobiographical memory (AM) is a critically important form of memory for life events that undergoes substantial developmental changes from childhood to adulthood. Relatively little is known regarding the functional neural correlates of AM retrieval in children as assessed with fMRI, and how they may differ from adults. We investigated this question with 14 children ages 8-11 years and 14 adults ages 19-30 years, contrasting AM retrieval with semantic memory (SM) retrieval. During scanning, participants were cued by verbal prompts to retrieve previously selected recent AMs or to verify semantic properties of words. As predicted, both groups showed AM retrieval-related increased activation in regions implicated in prior studies, including bilateral hippocampus, and prefrontal, posterior cingulate, and parietal cortices. Adults showed greater activation in the hippocampal/parahippocampal region as well as prefrontal and parietal cortex, relative to children; age-related differences were most prominent in the first 8 sec versus the second 8 sec of AM retrieval and when AM retrieval was contrasted with semantic retrieval. This study is the first to characterise similarities and differences during AM retrieval in children and adults using fMRI.

Autophagy-related genes in Helicobacter pylori infection.

Science.gov (United States)

Tanaka, Shingo; Nagashima, Hiroyuki; Uotani, Takahiro; Graham, David Y; Yamaoka, Yoshio

2017-06-01

In vitro studies have shown that Helicobacter pylori (H. pylori) infection induces autophagy in gastric epithelial cells. However, prolonged exposure to H. pylori reduces autophagy by preventing maturation of the autolysosome. The alterations of the autophagy-related genes in H. pylori infection are not yet fully understood. We analyzed autophagy-related gene expression in H. pylori-infected gastric mucosa compared with uninfected gastric mucosa obtained from 136 Bhutanese volunteers with mild dyspeptic symptoms. We also studied single nucleotide polymorphisms (SNPs) of autophagy-related gene in 283 Bhutanese participants to identify the influence on susceptibility to H. pylori infection. Microarray analysis of 226 autophagy-related genes showed that 16 genes were upregulated (7%) and nine were downregulated (4%). We used quantitative reverse transcriptase polymerase chain reaction to measure mRNA levels of the downregulated genes (ATG16L1, ATG5, ATG4D, and ATG9A) that were core molecules of autophagy. ATG16L1 and ATG5 mRNA levels in H. pylori-positive specimens (n=86) were significantly less than those in H. pylori-negative specimens (n=50). ATG16L1 mRNA levels were inversely related to H. pylori density. We also compared SNPs of ATG16L1 (rs2241880) among 206 H. pylori-positive and 77 H. pylori-negative subjects. The odds ratio for the presence of H. pylori in the GG genotype was 0.40 (95% CI: 0.18-0.91) relative to the AA/AG genotypes. Autophagy-related gene expression profiling using high-throughput microarray analysis indicated that downregulation of core autophagy machinery genes may depress autophagy functions and possibly provide a better intracellular habit for H. pylori in gastric epithelial cells. © 2017 John Wiley & Sons Ltd.

Relevance of useful visual words in object retrieval

Science.gov (United States)

Qi, Siyuan; Luo, Yupin

2013-07-01

The most popular methods in object retrieval are almost based on bag-of-words(BOW) which is both effective and efficient. In this paper we present a method use the relations between words of the vocabulary to improve the retrieval performance based on the BOW framework. In basic BOW retrieval framework, only a few words of the vocabulary is useful for retrieval, which are spatial consistent in images. We introduce a method to useful select useful words and build a relevance between these words. We combine useful relevance with basic BOW framework and query expansion as well. The useful relevance is able to discover latent related words which is not exist in the query image, so that we can get a more accurate vector model for retrieval. Combined with query expansion method, the retrieval performance are better and fewer time cost.

Multimedia information retrieval theory and techniques

CERN Document Server

Raieli, Roberto

2013-01-01

Novel processing and searching tools for the management of new multimedia documents have developed. Multimedia Information Retrieval (MMIR) is an organic system made up of Text Retrieval (TR); Visual Retrieval (VR); Video Retrieval (VDR); and Audio Retrieval (AR) systems. So that each type of digital document may be analysed and searched by the elements of language appropriate to its nature, search criteria must be extended. Such an approach is known as the Content Based Information Retrieval (CBIR), and is the core of MMIR. This novel content-based concept of information handling needs to be integrated with more traditional semantics. Multimedia Information Retrieval focuses on the tools of processing and searching applicable to the content-based management of new multimedia documents. Translated from Italian by Giles Smith, the book is divided in to two parts. Part one discusses MMIR and related theories, and puts forward new methodologies; part two reviews various experimental and operating MMIR systems, a...

Retrieval-induced forgetting in schizophrenia.

Science.gov (United States)

Nestor, Paul G; Piech, Richard; Allen, Christopher; Niznikiewicz, Margaret; Shenton, Martha; McCarley, Robert W

2005-06-15

Retrieving category associates (e.g., FRUIT-ORANGE) may induce forgetting other category members (e.g., FRUIT-BANANA), a phenomenon known as retrieval-induced forgetting (RIF). We designed 2 experiments to examine the role of RIF in the associative memory impairment of schizophrenia (SZ). Subjects studied 36 category-exemplar pairs, generated from 6 categories composed of 6 members each. For half of the studied category-exemplar pairs, subjects practiced retrieval by completing word stems, followed by a delayed category-cued recall on all of the practiced and unpracticed items. Experiment 1 used unrelated category exemplars-pairs (e.g., FRUIT-ORANGE, METALS-IRON), whereas experiment 2 included related category exemplar pairs (e.g., COTTON-SHIRT, LEATHER-SKIRT). SZ showed reduced associative memory but normal RIF for unrelated categories used in experiment 1. For experiment 2, SZ showed a significant decline in associative memory for related but not unrelated category-exemplars in comparison to controls. Results suggested faulty specificity/distinctiveness for encoding and retrieval, but not abnormal RIF in the associative memory disturbance of SZ.

Age-related alterations of brain network underlying the retrieval of emotional autobiographical memories: an fMRI study using independent component analysis.

Science.gov (United States)

Ge, Ruiyang; Fu, Yan; Wang, Dahua; Yao, Li; Long, Zhiying

2014-01-01

Normal aging has been shown to modulate the neural underpinnings of autobiographical memory and emotion processing. Moreover, previous researches have suggested that aging produces a "positivity effect" in autobiographical memory. Although a few imaging studies have investigated the neural mechanism of the positivity effect, the neural substrates underlying the positivity effect in emotional autobiographical memory is unclear. To understand the age-related neural changes in emotional autobiographical memory that underlie the positivity effect, the present functional magnetic resonance imaging (fMRI) study used the independent component analysis (ICA) method to compare brain networks in younger and older adults as they retrieved positive and negative autobiographical events. Compared to their younger counterparts, older adults reported relatively higher positive feelings when retrieving emotional autobiographical events. Imaging data indicated an age-related reversal within the ventromedial prefrontal/anterior cingulate cortex (VMPFC/ACC) and the left amygdala of the brain networks that were engaged in the retrieval of autobiographical events with different valence. The retrieval of negative events compared to positive events induced stronger activity in the VMPFC/ACC and weaker activity in the amygdala for the older adults, whereas the younger adults showed a reversed pattern. Moreover, activity in the VMPFC/ACC within the task-related networks showed a negative correlation with the emotional valence intensity. These results may suggest that the positivity effect in older adults' autobiographical memories is potentially due to age-related changes in controlled emotional processing implemented by the VMPFC/ACC-amygdala circuit.

Age-related alterations of brain network underlying the retrieval of emotional autobiographical memories: An fMRI study using independent component analysis

Directory of Open Access Journals (Sweden)

Ruiyang eGe

2014-08-01

Full Text Available Normal aging has been shown to modulate the neural underpinnings of autobiographical memory and emotion processing. Moreover, previous researches have suggested that aging produces a positivity effect in autobiographical memory. Although a few imaging studies have investigated the neural mechanism of the positivity effect, the neural substrates underlying the positivity effect in emotional autobiographical memory is unclear. To understand the age-related neural changes in emotional autobiographical memory that underlie the positivity effect, the present functional magnetic resonance imaging (fMRI study used the independent component analysis (ICA method to compare brain networks in younger and older adults as they retrieved positive and negative autobiographical events. Compared to their younger counterparts, older adults reported relatively higher positive feelings when retrieving emotional autobiographical events. Imaging data indicated an age-related reversal within the ventromedial prefrontal/anterior cingulate cortex (VMPFC/ACC and the left amygdala of the brain networks that were engaged in the retrieval of autobiographical events with different valence. The retrieval of negative events compared to positive events induced stronger activity in the VMPFC/ACC and weaker activity in the amygdala for the older adults, whereas the younger adults showed a reversed pattern. Moreover, activity in the VMPFC/ACC within the task-related networks showed a negative correlation with the emotional valence intensity. These results may suggest that the positivity effect in older adults’ autobiographical memories is potentially due to age-related changes in controlled emotional processing implemented by the VMPFC/ACC-amygdala circuit.

Post-Retrieval Extinction Attenuates Cocaine Memories

OpenAIRE

Sartor, Gregory C; Aston-Jones, Gary

2013-01-01

Recent studies have shown that post-retrieval extinction training attenuates fear and reward-related memories in both humans and rodents. This noninvasive, behavioral approach has the potential to be used in clinical settings to treat maladaptive memories that underlie several psychiatric disorders, including drug addiction. However, few studies to date have used a post-retrieval extinction approach to attenuate addiction-related memories. In the current study, we attempted to disrupt cocaine...

Mapping of olfactory memory circuits: region-specific c-fos activation after odor-reward associative learning or after its retrieval.

Science.gov (United States)

Tronel, Sophie; Sara, Susan J

2002-01-01

Although there is growing knowledge about intracellular mechanisms underlying neuronal plasticity and memory consolidation and reconsolidation after retrieval, information concerning the interaction among brain areas during formation and retrieval of memory is relatively sparse and fragmented. Addressing this question requires simultaneous monitoring of activity in multiple brain regions during learning, the post-acquisition consolidation period, and retrieval and subsequent reconsolidation. Immunoreaction to the immediate early gene c-fos is a powerful tool to mark neuronal activation of specific populations of neurons. Using this method, we are able to report, for the first time, post-training activation of a network of closely related brain regions, particularly in the frontal cortex and the basolateral amygdala (BLA), that is specific to the learning of an odor-reward association. On the other hand, retrieval of a well-established associative memory trace does not seem to differentially activate the same regions. The amygdala, in particular, is not engaged after retrieval, whereas the lateral habenula (LHab) shows strong activation that is restricted to animals having previously learned the association. Although intracellular mechanisms may be similar during consolidation and reconsolidation, this study indicates that different brain circuits are involved in the two processes, at least with respect to a rapidly learned olfactory task.

Guenter Tulip Filter Retrieval Experience: Predictors of Successful Retrieval

International Nuclear Information System (INIS)

Turba, Ulku Cenk; Arslan, Bulent; Meuse, Michael; Sabri, Saher; Macik, Barbara Gail; Hagspiel, Klaus D.; Matsumoto, Alan H.; Angle, John F.

2010-01-01

We report our experience with Guenter Tulip filter placement indications, retrievals, and procedural problems, with emphasis on alternative retrieval techniques. We have identified 92 consecutive patients in whom a Guenter Tulip filter was placed and filter removal attempted. We recorded patient demographic information, filter placement and retrieval indications, procedures, standard and nonstandard filter retrieval techniques, complications, and clinical outcomes. The mean time to retrieval for those who experienced filter strut penetration was statistically significant [F(1,90) = 8.55, p = 0.004]. Filter strut(s) IVC penetration and successful retrieval were found to be statistically significant (p = 0.043). The filter hook-IVC relationship correlated with successful retrieval. A modified guidewire loop technique was applied in 8 of 10 cases where the hook appeared to penetrate the IVC wall and could not be engaged with a loop snare catheter, providing additional technical success in 6 of 8 (75%). Therefore, the total filter retrieval success increased from 88 to 95%. In conclusion, the Guenter Tulip filter has high successful retrieval rates with low rates of complication. Additional maneuvers such as a guidewire loop method can be used to improve retrieval success rates when the filter hook is endothelialized.

Age-related changes in neural oscillations supporting context memory retrieval.

Science.gov (United States)

Strunk, Jonathan; James, Taylor; Arndt, Jason; Duarte, Audrey

2017-06-01

Recent evidence suggests that directing attention toward single item-context associations during encoding improves young and older adults' context memory performance and reduces demands on executive functions during retrieval. In everyday situations, there are many event features competing for our attention, and our ability to successfully recover those details may depend on our ability to ignore others. Failures of selective attention may contribute to older adults' context memory impairments. In the current electroencephalogram (EEG) study, we assessed the effects of age on processes supporting successful context memory retrieval of selectively attended features as indexed by neural oscillations. During encoding, young and older adults were directed to attend to a picture of an object and its relationship to one of two concurrently presented contextual details: a color or scene. At retrieval, we tested their memory for the object, its attended and unattended context features, and their confidence for both the attended and unattended features. Both groups showed greater memory for attended than unattended contextual features. However, older adults showed evidence of hyper-binding between attended and unattended context features while the young adults did not. EEG results in the theta band suggest that young and older adults recollect similar amounts of information but brain-behavior correlations suggest that this information was supportive of contextual memory performance, particularly for young adults. By contrast, sustained beta desynchronization, indicative of sensory reactivation and episodic reconstruction, was correlated with contextual memory performance for older adults only. We conclude that older adults' inhibition deficits during encoding reduced the selectivity of their contextual memories, which led to reliance on executive functions like episodic reconstruction to support successful memory retrieval. Copyright © 2017 Elsevier Ltd. All rights

Retrieval-induced forgetting and interference between cues:Training a cue-outcome association attenuates retrieval by alternative cues

OpenAIRE

Ortega-Castro, Nerea; Vadillo Nistal, Miguel

2013-01-01

Some researchers have attempted to determine whether situations in which a single cue is paired with several outcomes (A-B, A-C interference or interference between outcomes) involve the same learning and retrieval mechanisms as situations in which several cues are paired with a single outcome (A-B, C-B interference or interference between cues). Interestingly, current research on a related effect, which is known as retrieval-induced forgetting, can illuminate this debate. Most retrieval-indu...

EM-21 Retrieval Knowledge Center: Waste Retrieval Challenges

Energy Technology Data Exchange (ETDEWEB)

Fellinger, Andrew P.; Rinker, Michael W.; Berglin, Eric J.; Minichan, Richard L.; Poirier, Micheal R.; Gauglitz, Phillip A.; Martin, Bruce A.; Hatchell, Brian K.; Saldivar, Eloy; Mullen, O Dennis; Chapman, Noel F.; Wells, Beric E.; Gibbons, Peter W.

2009-04-10

EM-21 is the Waste Processing Division of the Office of Engineering and Technology, within the U.S. Department of Energy’s (DOE) Office of Environmental Management (EM). In August of 2008, EM-21 began an initiative to develop a Retrieval Knowledge Center (RKC) to provide the DOE, high level waste retrieval operators, and technology developers with centralized and focused location to share knowledge and expertise that will be used to address retrieval challenges across the DOE complex. The RKC is also designed to facilitate information sharing across the DOE Waste Site Complex through workshops, and a searchable database of waste retrieval technology information. The database may be used to research effective technology approaches for specific retrieval tasks and to take advantage of the lessons learned from previous operations. It is also expected to be effective for remaining current with state-of-the-art of retrieval technologies and ongoing development within the DOE Complex. To encourage collaboration of DOE sites with waste retrieval issues, the RKC team is co-led by the Savannah River National Laboratory (SRNL) and the Pacific Northwest National Laboratory (PNNL). Two RKC workshops were held in the Fall of 2008. The purpose of these workshops was to define top level waste retrieval functional areas, exchange lessons learned, and develop a path forward to support a strategic business plan focused on technology needs for retrieval. The primary participants involved in these workshops included retrieval personnel and laboratory staff that are associated with Hanford and Savannah River Sites since the majority of remaining DOE waste tanks are located at these sites. This report summarizes and documents the results of the initial RKC workshops. Technology challenges identified from these workshops and presented here are expected to be a key component to defining future RKC-directed tasks designed to facilitate tank waste retrieval solutions.

EM-21 Retrieval Knowledge Center: Waste Retrieval Challenges

International Nuclear Information System (INIS)

Fellinger, Andrew P.; Rinker, Michael W.; Berglin, Eric J.; Minichan, Richard L.; Poirier, Micheal R.; Gauglitz, Phillip A.; Martin, Bruce A.; Hatchell, Brian K.; Saldivar, Eloy; Mullen, O Dennis; Chapman, Noel F.; Wells, Beric E.; Gibbons, Peter W.

2009-01-01

EM-21 is the Waste Processing Division of the Office of Engineering and Technology, within the U.S. Department of Energy's (DOE) Office of Environmental Management (EM). In August of 2008, EM-21 began an initiative to develop a Retrieval Knowledge Center (RKC) to provide the DOE, high level waste retrieval operators, and technology developers with centralized and focused location to share knowledge and expertise that will be used to address retrieval challenges across the DOE complex. The RKC is also designed to facilitate information sharing across the DOE Waste Site Complex through workshops, and a searchable database of waste retrieval technology information. The database may be used to research effective technology approaches for specific retrieval tasks and to take advantage of the lessons learned from previous operations. It is also expected to be effective for remaining current with state-of-the-art of retrieval technologies and ongoing development within the DOE Complex. To encourage collaboration of DOE sites with waste retrieval issues, the RKC team is co-led by the Savannah River National Laboratory (SRNL) and the Pacific Northwest National Laboratory (PNNL). Two RKC workshops were held in the Fall of 2008. The purpose of these workshops was to define top level waste retrieval functional areas, exchange lessons learned, and develop a path forward to support a strategic business plan focused on technology needs for retrieval. The primary participants involved in these workshops included retrieval personnel and laboratory staff that are associated with Hanford and Savannah River Sites since the majority of remaining DOE waste tanks are located at these sites. This report summarizes and documents the results of the initial RKC workshops. Technology challenges identified from these workshops and presented here are expected to be a key component to defining future RKC-directed tasks designed to facilitate tank waste retrieval solutions

Age-related changes in the functional network underlying specific and general autobiographical memory retrieval: a pivotal role for the anterior cingulate cortex.

Directory of Open Access Journals (Sweden)

Pénélope Martinelli

Full Text Available Age-related changes in autobiographical memory (AM recall are characterized by a decline in episodic details, while semantic aspects are spared. This deleterious effect is supposed to be mediated by an inefficient recruitment of executive processes during AM retrieval. To date, contrasting evidence has been reported on the neural underpinning of this decline, and none of the previous studies has directly compared the episodic and semantic aspects of AM in elderly. We asked 20 young and 17 older participants to recall specific and general autobiographical events (i.e., episodic and semantic AM elicited by personalized cues while recording their brain activity by means of fMRI. At the behavioral level, we confirmed that the richness of episodic AM retrieval is specifically impoverished in aging and that this decline is related to the reduction of executive functions. At the neural level, in both age groups, we showed the recruitment of a large network during episodic AM retrieval encompassing prefrontal, cortical midline and posterior regions, and medial temporal structures, including the hippocampus. This network was very similar, but less extended, during semantic AM retrieval. Nevertheless, a greater activity was evidenced in the dorsal anterior cingulate cortex (dACC during episodic, compared to semantic AM retrieval in young participants, and a reversed pattern in the elderly. Moreover, activity in dACC during episodic AM retrieval was correlated with inhibition and richness of memories in both groups. Our findings shed light on the direct link between episodic AM retrieval, executive control, and their decline in aging, proposing a possible neuronal signature. They also suggest that increased activity in dACC during semantic AM retrieval in the elderly could be seen as a compensatory mechanism underpinning successful AM performance observed in aging. These results are discussed in the framework of recently proposed models of neural

How to average logarithmic retrievals?

Directory of Open Access Journals (Sweden)

B. Funke

2012-04-01

Full Text Available Calculation of mean trace gas contributions from profiles obtained by retrievals of the logarithm of the abundance rather than retrievals of the abundance itself are prone to biases. By means of a system simulator, biases of linear versus logarithmic averaging were evaluated for both maximum likelihood and maximum a priori retrievals, for various signal to noise ratios and atmospheric variabilities. These biases can easily reach ten percent or more. As a rule of thumb we found for maximum likelihood retrievals that linear averaging better represents the true mean value in cases of large local natural variability and high signal to noise ratios, while for small local natural variability logarithmic averaging often is superior. In the case of maximum a posteriori retrievals, the mean is dominated by the a priori information used in the retrievals and the method of averaging is of minor concern. For larger natural variabilities, the appropriateness of the one or the other method of averaging depends on the particular case because the various biasing mechanisms partly compensate in an unpredictable manner. This complication arises mainly because of the fact that in logarithmic retrievals the weight of the prior information depends on abundance of the gas itself. No simple rule was found on which kind of averaging is superior, and instead of suggesting simple recipes we cannot do much more than to create awareness of the traps related with averaging of mixing ratios obtained from logarithmic retrievals.

Foreign Body Retrieval

Medline Plus

Full Text Available ... object is solid or filled with fluid). In medicine, ultrasound is used to detect changes in appearance, ... Anesthesia Safety X-ray, Interventional Radiology and Nuclear Medicine Radiation Safety Videos related to Foreign Body Retrieval ...

Effects of Level of Retrieval Success on Recall-Related Frontal and Medial Temporal Lobe Activations

Directory of Open Access Journals (Sweden)

Daniela Montaldi

2002-01-01

Full Text Available Brain dedicated single photon emission computed tomography (SPECT was used to compare the neuroactivation produced by the cued recall of response words in a set of studied word pairs with that produced by the cued retrieval of words semantically related to unstudied stimulus words. Six of the 12 subjects scanned were extensively trained so as to have good memory of the studied pairs and the remaining six were minimally trained so as to have poor memory. When comparing episodic with semantic retrieval, the well-trained subjects showed significant left medial temporal lobe activation, which was also significantly greater than that shown by the poorly trained subjects, who failed to show significant medial temporal lobe activation. In contrast, the poorly trained subjects showed significant bilateral frontal lobe activation, which was significantly greater than that shown by the well-trained subjects who failed to show significant frontal lobe activation. The frontal activations occurred mainly in the dorsolateral region, but extended into the ventrolateral and, to a lesser extent, the frontal polar regions. It is argued that whereas the medial temporal lobe activation increased as the proportion of response words successfully recalled increased, the bilateral frontal lobe activation increased in proportion to retrieval effort, which was greater when learning had been less good.

Foreign Body Retrieval

Medline Plus

Full Text Available ... related to Foreign Body Retrieval Sponsored by Please note RadiologyInfo.org is not a medical facility. Please ... is further reviewed by committees from the American College of Radiology (ACR) and the Radiological Society of ...

Validation of commonly used reference genes for sleep-related gene expression studies

Directory of Open Access Journals (Sweden)

Castro Rosa MRPS

2009-05-01

Full Text Available Abstract Background Sleep is a restorative process and is essential for maintenance of mental and physical health. In an attempt to understand the complexity of sleep, multidisciplinary strategies, including genetic approaches, have been applied to sleep research. Although quantitative real time PCR has been used in previous sleep-related gene expression studies, proper validation of reference genes is currently lacking. Thus, we examined the effect of total or paradoxical sleep deprivation (TSD or PSD on the expression stability of the following frequently used reference genes in brain and blood: beta-actin (b-actin, beta-2-microglobulin (B2M, glyceraldehyde-3-phosphate dehydrogenase (GAPDH, and hypoxanthine guanine phosphoribosyl transferase (HPRT. Results Neither TSD nor PSD affected the expression stability of all tested genes in both tissues indicating that b-actin, B2M, GAPDH and HPRT are appropriate reference genes for the sleep-related gene expression studies. In order to further verify these results, the relative expression of brain derived neurotrophic factor (BDNF and glycerol-3-phosphate dehydrogenase1 (GPD1 was evaluated in brain and blood, respectively. The normalization with each of four reference genes produced similar pattern of expression in control and sleep deprived rats, but subtle differences in the magnitude of expression fold change were observed which might affect the statistical significance. Conclusion This study demonstrated that sleep deprivation does not alter the expression stability of commonly used reference genes in brain and blood. Nonetheless, the use of multiple reference genes in quantitative RT-PCR is required for the accurate results.

Cloning arbuscule-related genes from mycorrhizas

DEFF Research Database (Denmark)

Burleigh, Stephen

2000-01-01

Until recently little was known about the identity of the genes expressed in the arbuscules of mycorrhizas, due in part to problems associated with cloning genes from the tissues of an obligate symbiont. However, the combination of advanced molecular techniques, innovative use of the materials...... available and fortuitous cloning has resulted in the recent identification of a number of arbuscule-related genes. This article provides a brief summary of the genes involved in arbuscule development, function and regulation, and the techniques used to study them. Molecular techniques include differential...

Database for High Throughput Screening Hits (dHITS): a simple tool to retrieve gene specific phenotypes from systematic screens done in yeast.

Science.gov (United States)

Chuartzman, Silvia G; Schuldiner, Maya

2018-03-25

In the last decade several collections of Saccharomyces cerevisiae yeast strains have been created. In these collections every gene is modified in a similar manner such as by a deletion or the addition of a protein tag. Such libraries have enabled a diversity of systematic screens, giving rise to large amounts of information regarding gene functions. However, often papers describing such screens focus on a single gene or a small set of genes and all other loci affecting the phenotype of choice ('hits') are only mentioned in tables that are provided as supplementary material and are often hard to retrieve or search. To help unify and make such data accessible, we have created a Database of High Throughput Screening Hits (dHITS). The dHITS database enables information to be obtained about screens in which genes of interest were found as well as the other genes that came up in that screen - all in a readily accessible and downloadable format. The ability to query large lists of genes at the same time provides a platform to easily analyse hits obtained from transcriptional analyses or other screens. We hope that this platform will serve as a tool to facilitate investigation of protein functions to the yeast community. © 2018 The Authors Yeast Published by John Wiley & Sons Ltd.

Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation.

Science.gov (United States)

Huang, Chung-Chi; Lu, Zhiyong

2016-01-01

Identifying relevant papers from the literature is a common task in biocuration. Most current biomedical literature search systems primarily rely on matching user keywords. Semantic search, on the other hand, seeks to improve search accuracy by understanding the entities and contextual relations in user keywords. However, past research has mostly focused on semantically identifying biological entities (e.g. chemicals, diseases and genes) with little effort on discovering semantic relations. In this work, we aim to discover biomedical semantic relations in PubMed queries in an automated and unsupervised fashion. Specifically, we focus on extracting and understanding the contextual information (or context patterns) that is used by PubMed users to represent semantic relations between entities such as 'CHEMICAL-1 compared to CHEMICAL-2' With the advances in automatic named entity recognition, we first tag entities in PubMed queries and then use tagged entities as knowledge to recognize pattern semantics. More specifically, we transform PubMed queries into context patterns involving participating entities, which are subsequently projected to latent topics via latent semantic analysis (LSA) to avoid the data sparseness and specificity issues. Finally, we mine semantically similar contextual patterns or semantic relations based on LSA topic distributions. Our two separate evaluation experiments of chemical-chemical (CC) and chemical-disease (CD) relations show that the proposed approach significantly outperforms a baseline method, which simply measures pattern semantics by similarity in participating entities. The highest performance achieved by our approach is nearly 0.9 and 0.85 respectively for the CC and CD task when compared against the ground truth in terms of normalized discounted cumulative gain (nDCG), a standard measure of ranking quality. These results suggest that our approach can effectively identify and return related semantic patterns in a ranked order

Retrieval from Memory: Vulnerable or Inviolable?

Science.gov (United States)

Jones, Dylan M.; Marsh, John E.; Hughes, Robert W.

2012-01-01

We show that retrieval from semantic memory is vulnerable even to the mere presence of speech. Irrelevant speech impairs semantic fluency--namely, lexical retrieval cued by a semantic category name--but only if it is meaningful (forward speech compared to reversed speech or words compared to nonwords). Moreover, speech related semantically to the…

Event-Related fMRI Studies of Episodic Encoding and Retrieval: Meta-Analyses Using Activation Likelihood Estimation

Science.gov (United States)

Spaniol, Julia; Davidson, Patrick S. R.; Kim, Alice S. N.; Han, Hua; Moscovitch, Morris; Grady, Cheryl L.

2009-01-01

The recent surge in event-related fMRI studies of episodic memory has generated a wealth of information about the neural correlates of encoding and retrieval processes. However, interpretation of individual studies is hampered by methodological differences, and by the fact that sample sizes are typically small. We submitted results from studies of…

High Working Memory Capacity Predicts Less Retrieval Induced Forgetting

NARCIS (Netherlands)

Mall, Jonathan T.; Morey, Candice C.

2013-01-01

Background : Working Memory Capacity (WMC) is thought to be related to executive control and focused memory search abilities. These two hypotheses make contrasting predictions regarding the effects of retrieval on forgetting. Executive control during memory retrieval is believed to lead to retrieval

On the reliability of retrieval-induced forgetting

Directory of Open Access Journals (Sweden)

Christopher eRowland

2014-11-01

Full Text Available Memory is modified through the act of retrieval. Although retrieving a target piece of information may strengthen the retrieved information itself, it may also serve to weaken retention of related information. This phenomenon, termed retrieval-induced forgetting, has garnered substantial interest for its implications as to why forgetting occurs. The present study attempted to replicate the seminal work by Anderson, Bjork, and Bjork (1994 on retrieval-induced forgetting, given the apparent sensitivity of the effect to certain deviations from the original paradigm developed to study the phenomenon. The study extends the conditions under which retrieval-induced forgetting has been examined by utilizing both a traditional college undergraduate sample (Experiment 1, along with a more diverse internet sample (Experiment 2. In addition, Experiment 3 details a replication attempt of retrieval-induced forgetting using Anderson and Spellman’s (1995 independent cue procedure. Retrieval-induced forgetting was observed when using the traditional retrieval practice paradigm with undergraduate (Experiment 1 and internet (Experiment 2 samples, though the effect was not found when using the independent cue procedure (Experiment 3. Thus, the study can provide an indication as to the robustness of retrieval-induced forgetting to deviations from the traditional college undergraduate samples that have been used in the majority of existing research on the effect.

Transcriptomic landscape of Dendrobium huoshanense and its genes related to polysaccharide biosynthesis

Directory of Open Access Journals (Sweden)

Rongchun Han

2018-03-01

Full Text Available Dendrobium huoshanense has long been used to treat various diseases in oriental medicine. In order to study its gene expression profile, transcripts involved in the biosynthesis of precursors of polysaccharides, as well as mechanisms underlining morphological differences between wild and cultivated plants, three organs of both wild type and cultivated D. huoshanense were collected and sequenced by Illumina HiSeq4000 platform, yielding 919,409,540 raw reads in FASTQ format. After Trinity de novo assembly and quality control, 241,242 nonredundant contigs with the average length of 967.5 bp were generated. qRT-PCR experiment on the selected transcripts showed the transcriptomic data were reliable. BLASTx was conducted against NR, SwissProt, String, Pfam, and KEGG. Gene ontology annotation revealed more than 40,000 contigs assigned to catalytic activity and metabolic process, suggesting its dynamic physiological activities. By searching KEGG pathway, six genes potentially involved in mannose biosynthetic pathway were retrieved. Gene expression analysis for stems between wild and cultivated D. huoshanense resulted in 956 genes differentially expressed. Simple sequence repeats (SSRs analysis revealed 143 SSRs with the unit size of 4 and 3,437 SSRs the size of 3. The obtained SSRs are the potential molecular markers for discriminating distinct cultivars of D. huoshanense.

Introduction to information retrieval

CERN Document Server

Manning, Christopher D; Schütze, Hinrich

2008-01-01

Class-tested and coherent, this textbook teaches classical and web information retrieval, including web search and the related areas of text classification and text clustering from basic concepts. It gives an up-to-date treatment of all aspects of the design and implementation of systems for gathering, indexing, and searching documents; methods for evaluating systems; and an introduction to the use of machine learning methods on text collections. All the important ideas are explained using examples and figures, making it perfect for introductory courses in information retrieval for advanced un

Dialog-based Interactive Image Retrieval

OpenAIRE

Guo, Xiaoxiao; Wu, Hui; Cheng, Yu; Rennie, Steven; Feris, Rogerio Schmidt

2018-01-01

Existing methods for interactive image retrieval have demonstrated the merit of integrating user feedback, improving retrieval results. However, most current systems rely on restricted forms of user feedback, such as binary relevance responses, or feedback based on a fixed set of relative attributes, which limits their impact. In this paper, we introduce a new approach to interactive image search that enables users to provide feedback via natural language, allowing for more natural and effect...

Music Retrieval Based on the Relation between Color Association and Lyrics

Science.gov (United States)

Nakamur, Tetsuaki; Utsumi, Akira; Sakamoto, Maki

Various methods for music retrieval have been proposed. Recently, many researchers are tackling developing methods based on the relationship between music and feelings. In our previous psychological study, we found that there was a significant correlation between colors evoked from songs and colors evoked only from lyrics, and showed that the music retrieval system using lyrics could be developed. In this paper, we focus on the relationship among music, lyrics and colors, and propose a music retrieval method using colors as queries and analyzing lyrics. This method estimates colors evoked from songs by analyzing lyrics of the songs. On the first step of our method, words associated with colors are extracted from lyrics. We assumed two types of methods to extract words associated with colors. In the one of two methods, the words are extracted based on the result of a psychological experiment. In the other method, in addition to the words extracted based on the result of the psychological experiment, the words from corpora for the Latent Semantic Analysis are extracted. On the second step, colors evoked from the extracted words are compounded, and the compounded colors are regarded as those evoked from the song. On the last step, colors as queries are compared with colors estimated from lyrics, and the list of songs is presented based on similarities. We evaluated the two methods described above and found that the method based on the psychological experiment and corpora performed better than the method only based on the psychological experiment. As a result, we showed that the method using colors as queries and analyzing lyrics is effective for music retrieval.

Natural language retrieval in nuclear safety information system

International Nuclear Information System (INIS)

Komata, Masaoki; Oosawa, Yasuo; Ujita, Hiroshi

1983-01-01

A natural language retrieval program NATLANG is developed to assist in the retrieval of information from event-and-cause descriptions in Licensee Event Reports (LER). The characteristics of NATLANG are (1) the use of base forms of words to retrieve related forms altered by the addition of prefixes or suffixes or changes in inflection, (2) direct access and short time retrieval with an alphabet pointer, (3) effective determination of the items and entries for a Hitachi event classification in a two step retrieval scheme, and (4) Japanese character output with the PL-1 language. NATLANG output reduces the effort needed to re-classify licensee events in the Hitachi event classification. (author)

The relation of serotonin-related gene and COMT gene polymorphisms with criminal behavior in schizophrenic disorder.

Science.gov (United States)

Koh, Kyung Bong; Choi, Eun Hee; Lee, Young-joon; Han, Mooyoung; Choi, Sang-Sup; Kim, So Won; Lee, Min Goo

2012-02-01

It has been suggested that patients with schizophrenia might be involved in criminal behavior, such as homicidal and violent behavior. However, the relationship between criminal behavior and genes in patients with schizophrenia has not been clearly elucidated. The objective of this study was to examine the relation between criminal behavior and serotonin-related gene or catechol-O-methyltransferase (COMT) gene polymorphisms in patients with schizophrenia. Serotonin-related and COMT polymorphic markers were assessed by using single nucleotide polymorphism (SNP) genotyping. Ninety-nine crime-related inpatients with schizophrenia (57 homicidal and 42 nonhomicidal violent) and 133 healthy subjects were enrolled between October 2005 and May 2008. Diagnoses were made according to the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-IV) criteria. The genotype frequencies of tryptophan hydroxylase-1 (TPH1) A218C and COMT V158M were compared between groups. The TPH1 CC genotype had 2.7-fold higher odds of crime-related schizophrenia compared with A-carrier genotype after the analysis was controlled for sex and age (OR, 2.69; 95% CI, 1.22 - 5.91; P = .01). In addition, the TPH1 CC genotype had 3.4-fold higher odds of homicidal schizophrenia compared with A-carrier genotype after the analysis was controlled for sex and age (OR, 3.38; 95% CI, 1.40 - 8.18; P = .007). However, no significant differences were found in the frequencies of genotype of COMT polymorphism between criminal schizophrenics and healthy subjects, nor were any significant differences found between nonhomicidal schizophrenics and healthy subjects. These results indicate that the TPH1 CC recessive genotype is likely to be a genetic risk factor for criminal behavior, especially homicidal behavior in patients with schizophrenia. However, COMT gene polymorphisms were not associated with criminal behavior in schizophrenic patients. © Copyright 2012 Physicians Postgraduate Press, Inc.

Phase analysis of circadian-related genes in two tissues

Directory of Open Access Journals (Sweden)

Li Leping

2006-02-01

Full Text Available Abstract Background Recent circadian clock studies using gene expression microarray in two different tissues of mouse have revealed not all circadian-related genes are synchronized in phase or peak expression times across tissues in vivo. Instead, some circadian-related genes may be delayed by 4–8 hrs in peak expression in one tissue relative to the other. These interesting biological observations prompt a statistical question regarding how to distinguish the synchronized genes from genes that are systematically lagged in phase/peak expression time across two tissues. Results We propose a set of techniques from circular statistics to analyze phase angles of circadian-related genes in two tissues. We first estimate the phases of a cycling gene separately in each tissue, which are then used to estimate the paired angular difference of the phase angles of the gene in the two tissues. These differences are modeled as a mixture of two von Mises distributions which enables us to cluster genes into two groups; one group having synchronized transcripts with the same phase in the two tissues, the other containing transcripts with a discrepancy in phase between the two tissues. For each cluster of genes we assess the association of phases across the tissue types using circular-circular regression. We also develop a bootstrap methodology based on a circular-circular regression model to evaluate the improvement in fit provided by allowing two components versus a one-component von-Mises model. Conclusion We applied our proposed methodologies to the circadian-related genes common to heart and liver tissues in Storch et al. 2, and found that an estimated 80% of circadian-related transcripts common to heart and liver tissues were synchronized in phase, and the other 20% of transcripts were lagged about 8 hours in liver relative to heart. The bootstrap p-value for being one cluster is 0.063, which suggests the possibility of two clusters. Our methodologies can

Dissociating the two faces of selective memory retrieval.

Science.gov (United States)

Dobler, Ina M; Bäuml, Karl-Heinz T

2012-07-01

Research in the past four decades has repeatedly shown that selective retrieval of some (non-target) memories can impair subsequent retrieval of other (target) information, a finding known as retrieval-induced forgetting. More recently, however, there is evidence that selective retrieval can both impair and enhance recall of related memories (K-H. T. Bäuml & Samenieh, 2010). To identify possible experimental dissociations between the detrimental and the beneficial effects of memory retrieval, we examined retrieval dynamics in listwise directed forgetting, varying the delay between preceding non-target and subsequent target recall. When target recall immediately followed non-target recall, we replicated the prior work and found detrimental effects of memory retrieval on to-be-remembered items but beneficial effects on to-be-forgotten items. In contrast, when a delay was introduced between non-target and target recall, the detrimental effects were present but the beneficial effects were absent. The results demonstrate a first experimental dissociation between the two effects of memory retrieval. They are consistent with a recent two-factor account of the two faces of selective memory retrieval.

Selective memory retrieval can impair and improve retrieval of other memories.

Science.gov (United States)

Bäuml, Karl-Heinz T; Samenieh, Anuscheh

2012-03-01

Research from the past decades has shown that retrieval of a specific memory (e.g., retrieving part of a previous vacation) typically attenuates retrieval of other memories (e.g., memories for other details of the event), causing retrieval-induced forgetting. More recently, however, it has been shown that retrieval can both attenuate and aid recall of other memories (K.-H. T. Bäuml & A. Samenieh, 2010). To identify the circumstances under which retrieval aids recall, the authors examined retrieval dynamics in listwise directed forgetting, context-dependent forgetting, proactive interference, and in the absence of any induced memory impairment. They found beneficial effects of selective retrieval in listwise directed forgetting and context-dependent forgetting but detrimental effects in all the other conditions. Because context-dependent forgetting and listwise directed forgetting arguably reflect impaired context access, the results suggest that memory retrieval aids recall of memories that are subject to impaired context access but attenuates recall in the absence of such circumstances. The findings are consistent with a 2-factor account of memory retrieval and suggest the existence of 2 faces of memory retrieval. 2012 APA, all rights reserved

Plasticity-Related Gene Expression During Eszopiclone-Induced Sleep.

Science.gov (United States)

Gerashchenko, Dmitry; Pasumarthi, Ravi K; Kilduff, Thomas S

2017-07-01

Experimental evidence suggests that restorative processes depend on synaptic plasticity changes in the brain during sleep. We used the expression of plasticity-related genes to assess synaptic plasticity changes during drug-induced sleep. We first characterized sleep induced by eszopiclone in mice during baseline conditions and during the recovery from sleep deprivation. We then compared the expression of 18 genes and two miRNAs critically involved in synaptic plasticity in these mice. Gene expression was assessed in the cerebral cortex and hippocampus by the TaqMan reverse transcription polymerase chain reaction and correlated with sleep parameters. Eszopiclone reduced the latency to nonrapid eye movement (NREM) sleep and increased NREM sleep amounts. Eszopiclone had no effect on slow wave activity (SWA) during baseline conditions but reduced the SWA increase during recovery sleep (RS) after sleep deprivation. Gene expression analyses revealed three distinct patterns: (1) four genes had higher expression either in the cortex or hippocampus in the group of mice with increased amounts of wakefulness; (2) a large proportion of plasticity-related genes (7 out of 18 genes) had higher expression during RS in the cortex but not in the hippocampus; and (3) six genes and the two miRNAs showed no significant changes across conditions. Even at a relatively high dose (20 mg/kg), eszopiclone did not reduce the expression of plasticity-related genes during RS period in the cortex. These results indicate that gene expression associated with synaptic plasticity occurs in the cortex in the presence of a hypnotic medication. © Sleep Research Society 2017. Published by Oxford University Press on behalf of the Sleep Research Society. All rights reserved. For permissions, please e-mail journals.permissions@oup.com.

Care episode retrieval: distributional semantic models for information retrieval in the clinical domain.

Science.gov (United States)

Moen, Hans; Ginter, Filip; Marsi, Erwin; Peltonen, Laura-Maria; Salakoski, Tapio; Salanterä, Sanna

2015-01-01

Patients' health related information is stored in electronic health records (EHRs) by health service providers. These records include sequential documentation of care episodes in the form of clinical notes. EHRs are used throughout the health care sector by professionals, administrators and patients, primarily for clinical purposes, but also for secondary purposes such as decision support and research. The vast amounts of information in EHR systems complicate information management and increase the risk of information overload. Therefore, clinicians and researchers need new tools to manage the information stored in the EHRs. A common use case is, given a--possibly unfinished--care episode, to retrieve the most similar care episodes among the records. This paper presents several methods for information retrieval, focusing on care episode retrieval, based on textual similarity, where similarity is measured through domain-specific modelling of the distributional semantics of words. Models include variants of random indexing and the semantic neural network model word2vec. Two novel methods are introduced that utilize the ICD-10 codes attached to care episodes to better induce domain-specificity in the semantic model. We report on experimental evaluation of care episode retrieval that circumvents the lack of human judgements regarding episode relevance. Results suggest that several of the methods proposed outperform a state-of-the art search engine (Lucene) on the retrieval task.

Foreign Body Retrieval

Medline Plus

Full Text Available ... Physician Resources Professions Site Index A-Z Foreign Body Retrieval Foreign body retrieval is the removal of ... foreign body detection and removal? What is Foreign Body Retrieval? Foreign body retrieval involves the removal of ...

Sugarcane genes related to mitochondrial function

Directory of Open Access Journals (Sweden)

Fonseca Ghislaine V.

2001-01-01

Full Text Available Mitochondria function as metabolic powerhouses by generating energy through oxidative phosphorylation and have become the focus of renewed interest due to progress in understanding the subtleties of their biogenesis and the discovery of the important roles which these organelles play in senescence, cell death and the assembly of iron-sulfur (Fe/S centers. Using proteins from the yeast Saccharomyces cerevisiae, Homo sapiens and Arabidopsis thaliana we searched the sugarcane expressed sequence tag (SUCEST database for the presence of expressed sequence tags (ESTs with similarity to nuclear genes related to mitochondrial functions. Starting with 869 protein sequences, we searched for sugarcane EST counterparts to these proteins using the basic local alignment search tool TBLASTN similarity searching program run against 260,781 sugarcane ESTs contained in 81,223 clusters. We were able to recover 367 clusters likely to represent sugarcane orthologues of the corresponding genes from S. cerevisiae, H. sapiens and A. thaliana with E-value <= 10-10. Gene products belonging to all functional categories related to mitochondrial functions were found and this allowed us to produce an overview of the nuclear genes required for sugarcane mitochondrial biogenesis and function as well as providing a starting point for detailed analysis of sugarcane gene structure and physiology.

Relative skills of soil moisture and vegetation optical depth retrievals for agricultural drought monitoring

Science.gov (United States)

Soil moisture condition is an important indicator for agricultural drought monitoring. Through the Land Parameter Retrieval Model (LPRM), vegetation optical depth (VOD) as well as surface soil moisture (SM) can be retrieved simultaneously from brightness temperature observations from the Advanced Mi...

MARS: Microarray analysis, retrieval, and storage system

Directory of Open Access Journals (Sweden)

Scheideler Marcel

2005-04-01

Full Text Available Abstract Background Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerful and easy to use microarray databases facilitating array fabrication, labeling, hybridization, and data analysis. The wealth of data generated by this high throughput approach renders adequate database and analysis tools crucial for the pursuit of insights into the transcriptomic behavior of cells. Results MARS (Microarray Analysis and Retrieval System provides a comprehensive MIAME supportive suite for storing, retrieving, and analyzing multi color microarray data. The system comprises a laboratory information management system (LIMS, a quality control management, as well as a sophisticated user management system. MARS is fully integrated into an analytical pipeline of microarray image analysis, normalization, gene expression clustering, and mapping of gene expression data onto biological pathways. The incorporation of ontologies and the use of MAGE-ML enables an export of studies stored in MARS to public repositories and other databases accepting these documents. Conclusion We have developed an integrated system tailored to serve the specific needs of microarray based research projects using a unique fusion of Web based and standalone applications connected to the latest J2EE application server technology. The presented system is freely available for academic and non-profit institutions. More information can be found at http://genome.tugraz.at.

Assessing Boundary Conditions of the Testing Effect: On the Relative Efficacy of Covert vs. Overt Retrieval

Directory of Open Access Journals (Sweden)

Max L. Sundqvist

2017-06-01

Full Text Available Repeated testing during learning often improves later memory, which is often referred to as the testing effect. To clarify its boundary conditions, we examined whether the testing effect was selectively affected by covert (retrieved but not articulated or overt (retrieved and articulated response format. In Experiments 1 and 2, we compared immediate (5 min and delayed (1 week cued recall for paired associates following study-only, covert, and overt conditions, including two types of overt articulation (typing and writing. A clear testing effect was observed in both experiments, but with no selective effects of response format. In Experiments 3 and 4, we compared covert and overt retrieval under blocked and random list orders. The effect sizes were small in both experiments, but there was a significant effect of response format, with overt retrieval showing better final recall performance than covert retrieval. There were no significant effects of blocked vs. random list orders with respect to the testing effect produced. Taken together, these findings suggest that, under specific circumstances, overt retrieval may lead to a greater testing effect than that of covert retrieval, but because of small effect sizes, it appears that the testing effect is mainly the result of retrieval processes and that articulation has fairly little to add to its magnitude in a paired-associates learning paradigm.

Gene-Environment Interactions of Circadian-Related Genes for Cardiometabolic Traits

DEFF Research Database (Denmark)

Dashti, Hassan S; Follis, Jack L; Smith, Caren E

2015-01-01

OBJECTIVE: Common circadian-related gene variants associate with increased risk for metabolic alterations including type 2 diabetes. However, little is known about whether diet and sleep could modify associations between circadian-related variants (CLOCK-rs1801260, CRY2-rs11605924, MTNR1B-rs13871...

Gene-environment interactions of circadian-related genes for cardiometabolic traits

Science.gov (United States)

Objective: Common circadian-related gene variants associate with increased risk for metabolic alterations including type 2 diabetes. However, little is known about whether diet and sleep could modify associations between circadian-related variants (CLOCK-rs1801260, CRY2-rs11605924, MTNR1B-rs1387153,...

Genetic variation in aggression-related traits in Golden Retriever dogs

NARCIS (Netherlands)

Liinamo, A.E.; Berg, van den L.; Leegwater, P.A.J.; Schilder, M.B.H.; Arendonk, van J.A.M.; Oost, van B.A.

2007-01-01

In this study, heritabilities of several measures of aggression were estimated in a group of 325 Golden Retrievers, using the Restricted Maximum Likelihood method. The studied measures were obtained either through owner opinions or by using the Canine Behavioural Assessment and Research

Generating Concise Rules for Human Motion Retrieval

Science.gov (United States)

Mukai, Tomohiko; Wakisaka, Ken-Ichi; Kuriyama, Shigeru

This paper proposes a method for retrieving human motion data with concise retrieval rules based on the spatio-temporal features of motion appearance. Our method first converts motion clip into a form of clausal language that represents geometrical relations between body parts and their temporal relationship. A retrieval rule is then learned from the set of manually classified examples using inductive logic programming (ILP). ILP automatically discovers the essential rule in the same clausal form with a user-defined hypothesis-testing procedure. All motions are indexed using this clausal language, and the desired clips are retrieved by subsequence matching using the rule. Such rule-based retrieval offers reasonable performance and the rule can be intuitively edited in the same language form. Consequently, our method enables efficient and flexible search from a large dataset with simple query language.

Individual Differences in Working Memory Capacity Predict Retrieval-Induced Forgetting

Science.gov (United States)

Aslan, Alp; Bauml, Karl-Heinz T.

2011-01-01

Selectively retrieving a subset of previously studied information enhances memory for the retrieved information but causes forgetting of related, nonretrieved information. Such retrieval-induced forgetting (RIF) has often been attributed to inhibitory executive-control processes that supposedly suppress the nonretrieved items' memory…

Cortisol effects on autobiographic memory retrieval in PTSD: an analysis of word valence and time until retrieval.

Science.gov (United States)

Wingenfeld, Katja; Driessen, Martin; Schlosser, Nicole; Terfehr, Kirsten; Carvalho Fernando, Silvia; Wolf, Oliver Tobias

2013-09-01

In healthy participants, cortisol administration has been found to impair autobiographic memory retrieval. We recently reported that administration of 10 mg of hydrocortisone had enhancing effects on autobiographical memory retrieval, i.e. more specific memory retrieval, in patients with posttraumatic stress disorder (PTSD), while in healthy controls the impairing effects were replicated. We here report a re-analysis of these data with respect to cue-word valence and retrieval time. In a placebo-controlled cross-over study, 43 patients with PTSD and 43 age- and sex-matched healthy controls received either placebo or hydrocortisone orally before the autobiographical memory test was performed. We found that the effects of cortisol on memory retrieval depended on cue-word valence and group (significant interaction effects of drug by group and drug by valence by group). The enhancing effect of cortisol on memory retrieval in PTSD seemed to be relatively independent of cue-word valence, while in the control group the impairing effects of cortisol were only seen in response to neutral cue-words. The second result of the study was that in patients as well as in controls, cortisol administration led to faster memory retrieval compared to placebo. This was seen in response to positive and (to lesser extend) to neutral cue-words, but not in response to negative cue-words. Our findings illustrate that the opposing effects of cortisol on autobiographical memory retrieval in PTSD patients and controls are further modulated by the emotionality of the cue-words.

Kinematic gait analyses in healthy Golden Retrievers

OpenAIRE

Silva, Gabriela C.A.; Cardoso, Mariana Trés; Gaiad, Thais P.; Brolio, Marina P.; Oliveira, Vanessa C.; Assis Neto, Antonio; Martins, Daniele S.; Ambrósio, Carlos E.

2014-01-01

Kinematic analysis relates to the relative movement between rigid bodies and finds application in gait analysis and other body movements, interpretation of their data when there is change, determines the choice of treatment to be instituted. The objective of this study was to standardize the march of Dog Golden Retriever Healthy to assist in the diagnosis and treatment of musculoskeletal disorders. We used a kinematic analysis system to analyse the gait of seven dogs Golden Retriever, female,...

Development of retrievability plans

International Nuclear Information System (INIS)

Richardson, P.J.

1999-03-01

regard to the issue of Safeguards, as it relates to the long-term monitoring of fissile material, whilst at the same time incorporates information regarding public perceptions of retrievability wherever possible. Ethical issues concerning responsibilities of present and future generations are included where appropriate. In order to assist in comparing the different strategies envisaged in the different countries examined, in terms of waste types, host rocks and other controlling factors identified by the International Atomic Energy Agency, and described in Section 4, a Table has been included in the report. It is important at the outset to make a comment regarding basic terminology. It is necessary to distinguish between 'retrievability', which is the theoretical ability to recover wastes however difficult that may ultimately prove to be, and 'retrieval', which is the actual act of recovery. Implementing agencies tend to refer to 'retrievability' as an unlikely and probably unnecessary option, whereas the public tends to express concern about how 'retrieval' could actually be carried out

Changing Information Retrieval Behaviours

DEFF Research Database (Denmark)

Constantiou, Ioanna D.; Lehrer, Christiane; Hess, Thomas

2014-01-01

on the continuance of LBS use and indicate changes in individuals' information retrieval behaviours in everyday life. In particular, the distinct value dimension of LBS in specific contexts of use changes individuals' behaviours towards accessing location-related information....

Relative expression of genes related with cold tolerance in ...

African Journals Online (AJOL)

Low temperature is one of the main abiotic stresses affecting rice yield in Chile. Alterations in phenology and physiology of the crop are observed after a cold event. The objective of this work was to study the relative expression of genes related with cold stress in Chilean cultivars of rice. For this, we analyzed the expression ...

State-related alterations of gene expression in bipolar disorder

DEFF Research Database (Denmark)

Munkholm, Klaus; Vinberg, Maj; Berk, Michael

2012-01-01

Munkholm K, Vinberg M, Berk M, Kessing LV. State-related alterations of gene expression in bipolar disorder: a systematic review. Bipolar Disord 2012: 14: 684-696. © 2012 The Authors. Journal compilation © 2012 John Wiley & Sons A/S. Objective:  Alterations in gene expression in bipolar disorder...... have been found in numerous studies. It is unclear whether such alterations are related to specific mood states. As a biphasic disorder, mood state-related alterations in gene expression have the potential to point to markers of disease activity, and trait-related alterations might indicate...... vulnerability pathways. This review therefore evaluated the evidence for whether gene expression in bipolar disorder is state or trait related. Methods:  A systematic review, using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guideline for reporting systematic reviews, based...

INIS retrieval service, towards on-line

International Nuclear Information System (INIS)

Ebinuma, Yukio; Komatsubara, Yasutoshi

1983-01-01

Japan Atomic Energy Research Institute executes the retrieval service of INIS atomic energy information by batch system in cooperation with Genshiryoku Kozaikai. This service is very popular to the users in whole Japan, but the demand of on-line service has increased recently. Therefore, it was decided to begin the INIS on-line service from January, 1984, through the on-line information retrieval system of the Japan Information Center of Science and Technology. It is expected that when the operation will be started, the utilization of INIS atomic energy information in Japan will drastically increase. Also Japan Atomic Energy Research Institute has carried out the retrieval service by on-line system for those in the institute besides the batch system, accordingly, at this opportunity, the state of utilization of both systems and their distinction to use effectively, and the operation and the method of utilization of the on-line information retrieval system of JICST are explained. In the on-line system, the users are accessible to the data base themselves, and immediate information retrieval is possible, while in the batch system, the related information can be retrieved without fail, and the troublesome operation of equipment is not necessary. (Kako, I.)

The List-Strength Effect in Recall: Relative-Strength Competition and Retrieval Inhibition May both Contribute to Forgetting

Science.gov (United States)

Verde, Michael F.

2009-01-01

According to the principle of relative-strength competition, stronger items in memory block the retrieval of weaker items. This principle, integral to many theories of forgetting over the years, derives much of its support from the list-strength effect (LSE), in which strengthening some items in a study list makes it more difficult to recall other…

Assembly of inflammation-related genes for pathway-focused genetic analysis.

Directory of Open Access Journals (Sweden)

Matthew J Loza

2007-10-01

Full Text Available Recent identifications of associations between novel variants in inflammation-related genes and several common diseases emphasize the need for systematic evaluations of these genes in disease susceptibility. Considering that many genes are involved in the complex inflammation responses and many genetic variants in these genes have the potential to alter the functions and expression of these genes, we assembled a list of key inflammation-related genes to facilitate the identification of genetic associations of diseases with an inflammation-related etiology. We first reviewed various phases of inflammation responses, including the development of immune cells, sensing of danger, influx of cells to sites of insult, activation and functional responses of immune and non-immune cells, and resolution of the immune response. Assisted by the Ingenuity Pathway Analysis, we then identified 17 functional sub-pathways that are involved in one or multiple phases. This organization would greatly increase the chance of detecting gene-gene interactions by hierarchical clustering of genes with their functional closeness in a pathway. Finally, as an example application, we have developed tagging single nucleotide polymorphism (tSNP arrays for populations of European and African descent to capture all the common variants of these key inflammation-related genes. Assays of these tSNPs have been designed and assembled into two Affymetrix ParAllele customized chips, one each for European (12,011 SNPs and African (21,542 SNPs populations. These tSNPs have greater coverage for these inflammation-related genes compared to the existing genome-wide arrays, particularly in the African population. These tSNP arrays can facilitate systematic evaluation of inflammation pathways in disease susceptibility. For additional applications, other genotyping platforms could also be employed. For existing genome-wide association data, this list of key inflammation-related genes and

Retrieval-Based Learning: Positive Effects of Retrieval Practice in Elementary School Children

Directory of Open Access Journals (Sweden)

Jeffrey D. Karpicke

2016-03-01

Full Text Available A wealth of research has demonstrated that practicing retrieval is a powerful way to enhance learning. However, nearly all prior research has examined retrieval practice with college students. Little is known about retrieval practice in children, and even less is known about possible individual differences in retrieval practice. In three experiments, 88 children (mean age 10 years studied a list of words and either restudied the items or practiced retrieving them. They then took a final free recall test (Experiments 1 and 2 or recognition test (Experiment 3. In all experiments, children showed robust retrieval practice effects. Although a range of individual differences in reading comprehension and processing speed were observed among these children, the benefits of retrieval practice were independent of these factors. The results contribute to the growing body of research supporting the mnemonic benefits of retrieval practice and provide preliminary evidence that practicing retrieval may be an effective learning strategy for children with varying levels of reading comprehension and processing speed.

What Is the Molecular Signature of Mind–Body Interventions? A Systematic Review of Gene Expression Changes Induced by Meditation and Related Practices

Directory of Open Access Journals (Sweden)

Ivana Buric

2017-06-01

Full Text Available There is considerable evidence for the effectiveness of mind–body interventions (MBIs in improving mental and physical health, but the molecular mechanisms of these benefits remain poorly understood. One hypothesis is that MBIs reverse expression of genes involved in inflammatory reactions that are induced by stress. This systematic review was conducted to examine changes in gene expression that occur after MBIs and to explore how these molecular changes are related to health. We searched PubMed throughout September 2016 to look for studies that have used gene expression analysis in MBIs (i.e., mindfulness, yoga, Tai Chi, Qigong, relaxation response, and breath regulation. Due to the limited quantity of studies, we included both clinical and non-clinical samples with any type of research design. Eighteen relevant studies were retrieved and analyzed. Overall, the studies indicate that these practices are associated with a downregulation of nuclear factor kappa B pathway; this is the opposite of the effects of chronic stress on gene expression and suggests that MBI practices may lead to a reduced risk of inflammation-related diseases. However, it is unclear how the effects of MBIs compare to other healthy interventions such as exercise or nutrition due to the small number of available studies. More research is required to be able to understand the effects of MBIs at the molecular level.

What Is the Molecular Signature of Mind-Body Interventions? A Systematic Review of Gene Expression Changes Induced by Meditation and Related Practices.

Science.gov (United States)

Buric, Ivana; Farias, Miguel; Jong, Jonathan; Mee, Christopher; Brazil, Inti A

2017-01-01

There is considerable evidence for the effectiveness of mind-body interventions (MBIs) in improving mental and physical health, but the molecular mechanisms of these benefits remain poorly understood. One hypothesis is that MBIs reverse expression of genes involved in inflammatory reactions that are induced by stress. This systematic review was conducted to examine changes in gene expression that occur after MBIs and to explore how these molecular changes are related to health. We searched PubMed throughout September 2016 to look for studies that have used gene expression analysis in MBIs (i.e., mindfulness, yoga, Tai Chi, Qigong, relaxation response, and breath regulation). Due to the limited quantity of studies, we included both clinical and non-clinical samples with any type of research design. Eighteen relevant studies were retrieved and analyzed. Overall, the studies indicate that these practices are associated with a downregulation of nuclear factor kappa B pathway; this is the opposite of the effects of chronic stress on gene expression and suggests that MBI practices may lead to a reduced risk of inflammation-related diseases. However, it is unclear how the effects of MBIs compare to other healthy interventions such as exercise or nutrition due to the small number of available studies. More research is required to be able to understand the effects of MBIs at the molecular level.

Bayesian aerosol retrieval algorithm for MODIS AOD retrieval over land

Science.gov (United States)

Lipponen, Antti; Mielonen, Tero; Pitkänen, Mikko R. A.; Levy, Robert C.; Sawyer, Virginia R.; Romakkaniemi, Sami; Kolehmainen, Ville; Arola, Antti

2018-03-01

We have developed a Bayesian aerosol retrieval (BAR) algorithm for the retrieval of aerosol optical depth (AOD) over land from the Moderate Resolution Imaging Spectroradiometer (MODIS). In the BAR algorithm, we simultaneously retrieve all dark land pixels in a granule, utilize spatial correlation models for the unknown aerosol parameters, use a statistical prior model for the surface reflectance, and take into account the uncertainties due to fixed aerosol models. The retrieved parameters are total AOD at 0.55 µm, fine-mode fraction (FMF), and surface reflectances at four different wavelengths (0.47, 0.55, 0.64, and 2.1 µm). The accuracy of the new algorithm is evaluated by comparing the AOD retrievals to Aerosol Robotic Network (AERONET) AOD. The results show that the BAR significantly improves the accuracy of AOD retrievals over the operational Dark Target (DT) algorithm. A reduction of about 29 % in the AOD root mean square error and decrease of about 80 % in the median bias of AOD were found globally when the BAR was used instead of the DT algorithm. Furthermore, the fraction of AOD retrievals inside the ±(0.05+15 %) expected error envelope increased from 55 to 76 %. In addition to retrieving the values of AOD, FMF, and surface reflectance, the BAR also gives pixel-level posterior uncertainty estimates for the retrieved parameters. The BAR algorithm always results in physical, non-negative AOD values, and the average computation time for a single granule was less than a minute on a modern personal computer.

Optimization of Calcine Blending During Retrieval from Binsets

International Nuclear Information System (INIS)

Nelson, Lee Orville; Mohr, Charles Milton; Taylor, Dean Dalton

2000-01-01

This report documents a study performed during advanced feasibility studies for the INTEC Technology Development Facility (ITDF). The study was commissioned to provide information about functional requirements for the ITDF related to development of equipment and procedures for retrieving radioactive calcine from binset storage at the Idaho Nuclear Technology and Engineering Center (INTEC) at the Idaho National Engineering and Environmental Laboratory (INEEL). Calcine will be retrieved prior to treating it for permanent disposal in a national repository for high level waste. The objective this study was to estimate the degree of homogenization of the calcine that might be achieved through optimized retrieval and subsequent blending. Such homogenization has the potential of reducing the costs for treatment of the calcine and for qualifying of the final waste forms for acceptance at the repository. Results from the study indicate that optimized retrieval and blending can reduce the peak concentration variations of key components (Al, Zr, F) in blended batches of retrieved calcine. During un-optimized retrieval these variations are likely to be 81-138% while optimized retrieval can reduce them to the 5-10% range

15 CFR 950.9 - Computerized Environmental Data and Information Retrieval Service.

Science.gov (United States)

2010-01-01

... Information Retrieval Service. 950.9 Section 950.9 Commerce and Foreign Trade Regulations Relating to Commerce... Computerized Environmental Data and Information Retrieval Service. The Environmental Data Index (ENDEX... computerized, information retrieval service provides a parallel subject-author-abstract referral service. A...

The management-retrieval code of nuclear level density sub-library (CENPL-NLD)

International Nuclear Information System (INIS)

Ge Zhigang; Su Zongdi; Huang Zhongfu; Dong Liaoyuan

1995-01-01

The management-retrieval code of the Nuclear Level Density (NLD) is presented. It contains two retrieval ways: single nucleus (SN) and neutron reaction (NR). The latter contains four kinds of retrieval types. This code not only can retrieve level density parameter and the data related to the level density, but also can calculate the relevant data by using different level density parameters and do comparison of the calculated results with related data in order to help user to select level density parameters

An investigation of response competition in retrieval-induced forgetting

Directory of Open Access Journals (Sweden)

Gina A. Glanc

2015-12-01

Full Text Available It has been demonstrated that retrieval practice on a subset of studied items can cause forgetting of different related studied items. This retrieval-induced forgetting (the RIF effect has been demonstrated in a variety of recall studies and has been attributed to an inhibitory mechanism activated during retrieval practice by competition for a shared retrieval cue. The current study generalizes the RIF effect to recognition memory and investigates this competition assumption. Experiment 1 demonstrated an effect of RIF effect in item recognition with incidental encoding of category-exemplar association during the study phase. Experiment 2 demonstrated evidence of RIF with use of an independent retrieval cue during retrieval practice. Results from this study indicate that response competition may occur outside of the retrieval-practice phase, or may not be limited to situations where there is an overt link to a shared category cue.

Modelamiento de un sistema de recuperación de imágenes de recursos acuáticos, basado en contenido y calidad de la información Modeling of an aquatic resource image retrieval system, based on content and information quality

Directory of Open Access Journals (Sweden)

Bell Manrique Losada

2008-07-01

Full Text Available En el marco de los Sistemas de Recuperación de Información, se ubican los Sistemas de Recuperación de Imágenes, los cuales permiten generar procesos de búsqueda y almacenamiento de recursos por medio de coincidencias por palabras claves u otros métodos en tiempo real. Este tipo de sistemas pueden usar como í ndices, contenido visual de las imágenes como color, textura y brillo, y además combinar diferentes atributos para mejorar los procesos de clasificación y relevancia de los resultados del proceso de búsqueda, que se conocen como 'de la calidad de la información'. Este artículo presenta el modelamiento de un Sistema de Recuperación de Imágenes que combina atributos de la recuperación basada en contenido como color, textura y forma, con la recuperación basada en la calidad de la información, como frecuencia de actualización, portabilidad y relevancia, en el contexto de la Colección Digital de Imágenes de Ecosistemas Acuáticos Amazónicos del Grupo CAPREA de la Universidad de la Amazonia.In Information Retrieval Systems, Image Retrieval Systems are located; they allow generating searching and storing processes of resources through coincidences by key words or other real-time methods. This type of systems can use visual content of images (color, texture, and brightness as indices. In addition, these systems combine different attributes to improve the processes of classification and relevance of the searching process results known as 'Information Quality.' This paper presents the modeling of a Image Retrieval System which combines attributes of the contentbased retrieval such as color, texture, and shape, with the Information Quality-based retrieval as updating portability and relevance frequency in the context of Digital Image Collection of Aquatic Amazon Ecosystems of Universidad del Amazonia CAPREA Research Group.

Isolation and characterization of Agouti: a diabetes/obesity related gene

Energy Technology Data Exchange (ETDEWEB)

Woychik, Richard P. (Knoxville, TN)

2000-06-27

The present invention relates to the cloning and expression of the Agouti gene and analogous genes in transformed, transfected and transgenic mice. The present invention provides an animal model for the study of diabetes, obesity and tumors for the testing of potential therapeutic agents. The present invention provides oligonucleotide probes for the detection of the Agouti gene and mutations in the gene. The present invention also relates to the isolation and recombinant production of the Agouti gene product, production of antibodies to the Agouti gene product and their use as diagnostic and therapeutic agents.

Isolation and characterization of Agouti: a diabetes/obesity related gene

Energy Technology Data Exchange (ETDEWEB)

Woychik, Richard P. (Knoxville, TN)

1998-01-01

The present invention relates to the cloning and expression of the Agouti gene and analogous genes in transformed, transfected and transgenic mice. The present invention provides an animal model for the study of diabetes, obesity and tumors for the testing of potential therapeutic agents. The present invention provides oligonucleotide probes for the detection of the Agouti gene and mutations in the gene. The present invention also relates to the isolation and recombinant production of the Agouti gene product, production of antibodies to the Agouti gene product and their use as diagnostic and therapeutic agents.

Pulmonary phenotypes associated with genetic variation in telomere-related genes.

Science.gov (United States)

Hoffman, Thijs W; van Moorsel, Coline H M; Borie, Raphael; Crestani, Bruno

2018-05-01

Genomic mutations in telomere-related genes have been recognized as a cause of familial forms of idiopathic pulmonary fibrosis (IPF). However, it has become increasingly clear that telomere syndromes and telomere shortening are associated with various types of pulmonary disease. Additionally, it was found that also single nucleotide polymorphisms (SNPs) in telomere-related genes are risk factors for the development of pulmonary disease. This review focuses on recent updates on pulmonary phenotypes associated with genetic variation in telomere-related genes. Genomic mutations in seven telomere-related genes cause pulmonary disease. Pulmonary phenotypes associated with these mutations range from many forms of pulmonary fibrosis to emphysema and pulmonary vascular disease. Telomere-related mutations account for up to 10% of sporadic IPF, 25% of familial IPF, 10% of connective-tissue disease-associated interstitial lung disease, and 1% of COPD. Mixed disease forms have also been found. Furthermore, SNPs in TERT, TERC, OBFC1, and RTEL1, as well as short telomere length, have been associated with several pulmonary diseases. Treatment of pulmonary disease caused by telomere-related gene variation is currently based on disease diagnosis and not on the underlying cause. Pulmonary phenotypes found in carriers of telomere-related gene mutations and SNPs are primarily pulmonary fibrosis, sometimes emphysema and rarely pulmonary vascular disease. Genotype-phenotype relations are weak, suggesting that environmental factors and genetic background of patients determine disease phenotypes to a large degree. A disease model is presented wherever genomic variation in telomere-related genes cause specific pulmonary disease phenotypes whenever triggered by environmental exposure, comorbidity, or unknown factors.

Retrieval deficiency in brain activity of working memory in amnesic mild cognitive impairment patients: A brain event-related potentials study

Directory of Open Access Journals (Sweden)

Binyin eLi

2016-03-01

Full Text Available In the early stage of Alzheimer disease (AD or mild cognitive impairment (MCI, working memory (WM deficiency is prominent and could be attributed to failure in encoding, maintenance or retrieval of information. However, evidence for a retention or retrieval deficit remains equivocal. It is also unclear what cognitive mechanism in working memory is impaired in MCI or early AD. We enrolled forty-six subjects from our Memory Clinics and community, with 24 amnesic MCI patients and 22 normal subjects. After neurological and cognitive assessments, they performed a classic delayed match to sample task with simultaneous event-related potential (ERP recorded. The ERPs in encoding and retrieval epoch during WM were analyzed separately. The latency and amplitude of every ERP component were compared between two groups, and then analyzed to explore their relationship with neuropsychological performance. Finally, the locations of maximal difference in cortex were calculated by standard low-resolution tomographic analysis. A total of five components were found: P1, N1, P2, N2 and P300. The amplitude of P2 and P300 was larger in normal subjects than in MCI patients only during retrieval, not encoding epoch, while the latency did not show statistical difference. The latency and amplitude of P1 and N1 were similar in two groups. P2 amplitude in the retrieval epoch positively correlated with memory test (auditory verbal learning test and visual spatial score of Chinese Addenbrooke’s Cognitive Examination-Revised (ACE-R, while P300 amplitude correlated with ACE-R. The activation difference in P2 time range was maximal at medial frontal gyrus. However, the difference in cortex activation during P300 time range did not show significance. The amplitude of P2 indicated deficiency in memory retrieval process, potentially due to dysfunction of central executive in WM model. Regarding the location of P2 during WM task, medial frontal plays important role in memory

Ontology-based literature mining of E. coli vaccine-associated gene interaction networks.

Science.gov (United States)

Hur, Junguk; Özgür, Arzucan; He, Yongqun

2017-03-14

Pathogenic Escherichia coli infections cause various diseases in humans and many animal species. However, with extensive E. coli vaccine research, we are still unable to fully protect ourselves against E. coli infections. To more rational development of effective and safe E. coli vaccine, it is important to better understand E. coli vaccine-associated gene interaction networks. In this study, we first extended the Vaccine Ontology (VO) to semantically represent various E. coli vaccines and genes used in the vaccine development. We also normalized E. coli gene names compiled from the annotations of various E. coli strains using a pan-genome-based annotation strategy. The Interaction Network Ontology (INO) includes a hierarchy of various interaction-related keywords useful for literature mining. Using VO, INO, and normalized E. coli gene names, we applied an ontology-based SciMiner literature mining strategy to mine all PubMed abstracts and retrieve E. coli vaccine-associated E. coli gene interactions. Four centrality metrics (i.e., degree, eigenvector, closeness, and betweenness) were calculated for identifying highly ranked genes and interaction types. Using vaccine-related PubMed abstracts, our study identified 11,350 sentences that contain 88 unique INO interactions types and 1,781 unique E. coli genes. Each sentence contained at least one interaction type and two unique E. coli genes. An E. coli gene interaction network of genes and INO interaction types was created. From this big network, a sub-network consisting of 5 E. coli vaccine genes, including carA, carB, fimH, fepA, and vat, and 62 other E. coli genes, and 25 INO interaction types was identified. While many interaction types represent direct interactions between two indicated genes, our study has also shown that many of these retrieved interaction types are indirect in that the two genes participated in the specified interaction process in a required but indirect process. Our centrality analysis of

Schematic memory components converge within angular gyrus during retrieval

Science.gov (United States)

Wagner, Isabella C; van Buuren, Mariët; Kroes, Marijn CW; Gutteling, Tjerk P; van der Linden, Marieke; Morris, Richard G; Fernández, Guillén

2015-01-01

Mental schemas form associative knowledge structures that can promote the encoding and consolidation of new and related information. Schemas are facilitated by a distributed system that stores components separately, presumably in the form of inter-connected neocortical representations. During retrieval, these components need to be recombined into one representation, but where exactly such recombination takes place is unclear. Thus, we asked where different schema components are neuronally represented and converge during retrieval. Subjects acquired and retrieved two well-controlled, rule-based schema structures during fMRI on consecutive days. Schema retrieval was associated with midline, medial-temporal, and parietal processing. We identified the multi-voxel representations of different schema components, which converged within the angular gyrus during retrieval. Critically, convergence only happened after 24-hour-consolidation and during a transfer test where schema material was applied to novel but related trials. Therefore, the angular gyrus appears to recombine consolidated schema components into one memory representation. DOI: http://dx.doi.org/10.7554/eLife.09668.001 PMID:26575291

Prioritizing chronic obstructive pulmonary disease (COPD) candidate genes in COPD-related networks.

Science.gov (United States)

Zhang, Yihua; Li, Wan; Feng, Yuyan; Guo, Shanshan; Zhao, Xilei; Wang, Yahui; He, Yuehan; He, Weiming; Chen, Lina

2017-11-28

Chronic obstructive pulmonary disease (COPD) is a multi-factor disease, which could be caused by many factors, including disturbances of metabolism and protein-protein interactions (PPIs). In this paper, a weighted COPD-related metabolic network and a weighted COPD-related PPI network were constructed base on COPD disease genes and functional information. Candidate genes in these weighted COPD-related networks were prioritized by making use of a gene prioritization method, respectively. Literature review and functional enrichment analysis of the top 100 genes in these two networks suggested the correlation of COPD and these genes. The performance of our gene prioritization method was superior to that of ToppGene and ToppNet for genes from the COPD-related metabolic network or the COPD-related PPI network after assessing using leave-one-out cross-validation, literature validation and functional enrichment analysis. The top-ranked genes prioritized from COPD-related metabolic and PPI networks could promote the better understanding about the molecular mechanism of this disease from different perspectives. The top 100 genes in COPD-related metabolic network or COPD-related PPI network might be potential markers for the diagnosis and treatment of COPD.

Detecting Horizontal Gene Transfer between Closely Related Taxa.

Directory of Open Access Journals (Sweden)

Orit Adato

2015-10-01

Full Text Available Horizontal gene transfer (HGT, the transfer of genetic material between organisms, is crucial for genetic innovation and the evolution of genome architecture. Existing HGT detection algorithms rely on a strong phylogenetic signal distinguishing the transferred sequence from ancestral (vertically derived genes in its recipient genome. Detecting HGT between closely related species or strains is challenging, as the phylogenetic signal is usually weak and the nucleotide composition is normally nearly identical. Nevertheless, there is a great importance in detecting HGT between congeneric species or strains, especially in clinical microbiology, where understanding the emergence of new virulent and drug-resistant strains is crucial, and often time-sensitive. We developed a novel, self-contained technique named Near HGT, based on the synteny index, to measure the divergence of a gene from its native genomic environment and used it to identify candidate HGT events between closely related strains. The method confirms candidate transferred genes based on the constant relative mutability (CRM. Using CRM, the algorithm assigns a confidence score based on "unusual" sequence divergence. A gene exhibiting exceptional deviations according to both synteny and mutability criteria, is considered a validated HGT product. We first employed the technique to a set of three E. coli strains and detected several highly probable horizontally acquired genes. We then compared the method to existing HGT detection tools using a larger strain data set. When combined with additional approaches our new algorithm provides richer picture and brings us closer to the goal of detecting all newly acquired genes in a particular strain.

Differentiation of subsequent memory effects between retrieval practice and elaborative study.

Science.gov (United States)

Liu, Yi; Rosburg, Timm; Gao, Chuanji; Weber, Christine; Guo, Chunyan

2017-07-01

Retrieval practice enhances memory retention more than re-studying. The underlying mechanisms of this retrieval practice effect have remained widely unclear. According to the elaborative retrieval hypothesis, activation of elaborative information occurs to a larger extent during testing than re-studying. In contrast, the episodic context account has suggested that recollecting prior episodic information (especially the temporal context) contributes to memory retention. To adjudicate the distinction between these two accounts, the present study used the classical retrieval practice effect paradigm to compare retrieval practice and elaborative study. In an initial behavioral experiment, retrieval practice produced greater retention than elaboration and re-studying in a one-week delayed test. In a subsequent event-related potential (ERP) experiment, retrieval practice resulted in reliably superior accuracy in the delayed test compared to elaborative study. In the ERPs, a frontally distributed subsequent memory effect (SME), starting at 300ms, occurred in the elaborative study condition, but not in the retrieval practice condition. A parietal SME emerged in the retrieval practice condition from 500 to 700ms, but was absent in the elaborative study condition. After 700ms, a late SME was present in the retrieval practice condition, but not in the elaborative study condition. Moreover, SMEs lasted longer in retrieval practice than in elaboration. The frontal SME in the elaborative study condition might be related to semantic processing or working memory-based elaboration, whereas the parietal and widespread SME in the retrieval practice condition might be associated with episodic recollection processes. These findings contradict the elaborative retrieval theory, and suggest that contextual recollection rather than activation of semantic information contributes to the retrieval practice effect, supporting the episodic context account. Copyright © 2017. Published by

Optimization of Calcine Blending During Retrieval From Binsets

International Nuclear Information System (INIS)

Taylor, D.D.; Mohr, C.M.; Nelson, L.O.

2000-01-01

This report documents a study performed during advanced feasibility studies for the INTEC Technology Development Facility (ITDF). The study was commissioned to provide information about functional requirements for the ITDF related to development of equipment and procedures for retrieving radioactive calcine from binset storage at the Idaho Nuclear Technology and Engineering Center (INTEC) at the Idaho National Engineering and Environmental Laboratory (INEEL). Calcine will be retrieved prior to treating it for permanent disposal in a national repository for high level waste. The objective this study was to estimate the degree of homogenization of the calcine that might be achieved through optimized retrieval and subsequent blending. Such homogenization has the potential of reducing the costs for treatment of the calcine and for qualifying of the final waste forms for acceptance at the repository. Results from the study indicate that optimized retrieval and blending can reduce the peak c oncentration variations of key components (Al, Zr, F) in blended batches of retrieved calcine. During un-optimized retrieval these variations are likely to be 81-138% while optimized retrieval can reduce them to the 5-10% range

Calcitonin gene-related peptide antagonism and cluster headache

DEFF Research Database (Denmark)

Ashina, Håkan; Newman, Lawrence; Ashina, Sait

2017-01-01

Calcitonin gene-related peptide (CGRP) is a key signaling molecule involved in migraine pathophysiology. Efficacy of CGRP monoclonal antibodies and antagonists in migraine treatment has fueled an increasing interest in the prospect of treating cluster headache (CH) with CGRP antagonism. The exact...... role of CGRP and its mechanism of action in CH have not been fully clarified. A search for original studies and randomized controlled trials (RCTs) published in English was performed in PubMed and in ClinicalTrials.gov . The search term used was "cluster headache and calcitonin gene related peptide......" and "primary headaches and calcitonin gene related peptide." Reference lists of identified articles were also searched for additional relevant papers. Human experimental studies have reported elevated plasma CGRP levels during both spontaneous and glyceryl trinitrate-induced cluster attacks. CGRP may play...

Measuring and Predicting Tag Importance for Image Retrieval.

Science.gov (United States)

Li, Shangwen; Purushotham, Sanjay; Chen, Chen; Ren, Yuzhuo; Kuo, C-C Jay

2017-12-01

Textual data such as tags, sentence descriptions are combined with visual cues to reduce the semantic gap for image retrieval applications in today's Multimodal Image Retrieval (MIR) systems. However, all tags are treated as equally important in these systems, which may result in misalignment between visual and textual modalities during MIR training. This will further lead to degenerated retrieval performance at query time. To address this issue, we investigate the problem of tag importance prediction, where the goal is to automatically predict the tag importance and use it in image retrieval. To achieve this, we first propose a method to measure the relative importance of object and scene tags from image sentence descriptions. Using this as the ground truth, we present a tag importance prediction model to jointly exploit visual, semantic and context cues. The Structural Support Vector Machine (SSVM) formulation is adopted to ensure efficient training of the prediction model. Then, the Canonical Correlation Analysis (CCA) is employed to learn the relation between the image visual feature and tag importance to obtain robust retrieval performance. Experimental results on three real-world datasets show a significant performance improvement of the proposed MIR with Tag Importance Prediction (MIR/TIP) system over other MIR systems.

Memory retrieval of smoking-related images induce greater insula activation as revealed by an fMRI-based delayed matching to sample task.

Science.gov (United States)

Janes, Amy C; Ross, Robert S; Farmer, Stacey; Frederick, Blaise B; Nickerson, Lisa D; Lukas, Scott E; Stern, Chantal E

2015-03-01

Nicotine dependence is a chronic and difficult to treat disorder. While environmental stimuli associated with smoking precipitate craving and relapse, it is unknown whether smoking cues are cognitively processed differently than neutral stimuli. To evaluate working memory differences between smoking-related and neutral stimuli, we conducted a delay-match-to-sample (DMS) task concurrently with functional magnetic resonance imaging (fMRI) in nicotine-dependent participants. The DMS task evaluates brain activation during the encoding, maintenance and retrieval phases of working memory. Smoking images induced significantly more subjective craving, and greater midline cortical activation during encoding in comparison to neutral stimuli that were similar in content yet lacked a smoking component. The insula, which is involved in maintaining nicotine dependence, was active during the successful retrieval of previously viewed smoking versus neutral images. In contrast, neutral images required more prefrontal cortex-mediated active maintenance during the maintenance period. These findings indicate that distinct brain regions are involved in the different phases of working memory for smoking-related versus neutral images. Importantly, the results implicate the insula in the retrieval of smoking-related stimuli, which is relevant given the insula's emerging role in addiction. © 2013 Society for the Study of Addiction.

Water vapour retrieval using the Precision Solar Spectroradiometer

Science.gov (United States)

Raptis, Panagiotis-Ioannis; Kazadzis, Stelios; Gröbner, Julian; Kouremeti, Natalia; Doppler, Lionel; Becker, Ralf; Helmis, Constantinos

2018-02-01

The Precision Solar Spectroradiometer (PSR) is a new spectroradiometer developed at Physikalisch-Meteorologisches Observatorium Davos - World Radiation Center (PMOD-WRC), Davos, measuring direct solar irradiance at the surface, in the 300-1020 nm spectral range and at high temporal resolution. The purpose of this work is to investigate the instrument's potential to retrieve integrated water vapour (IWV) using its spectral measurements. Two different approaches were developed in order to retrieve IWV: the first one uses single-channel and wavelength measurements, following a theoretical water vapour high absorption wavelength, and the second one uses direct sun irradiance integrated at a certain spectral region. IWV results have been validated using a 2-year data set, consisting of an AERONET sun-photometer Cimel CE318, a Global Positioning System (GPS), a microwave radiometer profiler (MWP) and radiosonde retrievals recorded at Meteorological Observatorium Lindenberg, Germany. For the monochromatic approach, better agreement with retrievals from other methods and instruments was achieved using the 946 nm channel, while for the spectral approach the 934-948 nm window was used. Compared to other instruments' retrievals, the monochromatic approach leads to mean relative differences up to 3.3 % with the coefficient of determination (R2) being in the region of 0.87-0.95, while for the spectral approach mean relative differences up to 0.7 % were recorded with R2 in the region of 0.96-0.98. Uncertainties related to IWV retrieval methods were investigated and found to be less than 0.28 cm for both methods. Absolute IWV deviations of differences between PSR and other instruments were determined the range of 0.08-0.30 cm and only in extreme cases would reach up to 15 %.

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean) Cattle.

Science.gov (United States)

Lim, Dajeong; Lee, Seung-Hwan; Kim, Nam-Kuk; Cho, Yong-Min; Chai, Han-Ha; Seong, Hwan-Hoo; Kim, Heebal

2013-01-01

Marbling (intramuscular fat) is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the 'marbling score' trait and systemically analyzed the network topology in Hanwoo (Korean cattle). As a result, we determined 3 modules (gene groups) that showed statistically significant results for marbling score. In particular, one module (denoted as red) has a statistically significant result for marbling score (p = 0.008) and intramuscular fat (p = 0.02) and water capacity (p = 0.006). From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA) have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

Gene Co-expression Analysis to Characterize Genes Related to Marbling Trait in Hanwoo (Korean Cattle

Directory of Open Access Journals (Sweden)

Dajeong Lim

2013-01-01

Full Text Available Marbling (intramuscular fat is an important trait that affects meat quality and is a casual factor determining the price of beef in the Korean beef market. It is a complex trait and has many biological pathways related to muscle and fat. There is a need to identify functional modules or genes related to marbling traits and investigate their relationships through a weighted gene co-expression network analysis based on the system level. Therefore, we investigated the co-expression relationships of genes related to the ‘marbling score’ trait and systemically analyzed the network topology in Hanwoo (Korean cattle. As a result, we determined 3 modules (gene groups that showed statistically significant results for marbling score. In particular, one module (denoted as red has a statistically significant result for marbling score (p = 0.008 and intramuscular fat (p = 0.02 and water capacity (p = 0.006. From functional enrichment and relationship analysis of the red module, the pathway hub genes (IL6, CHRNE, RB1, INHBA and NPPA have a direct interaction relationship and share the biological functions related to fat or muscle, such as adipogenesis or muscle growth. This is the first gene network study with m.logissimus in Hanwoo to observe co-expression patterns in divergent marbling phenotypes. It may provide insights into the functional mechanisms of the marbling trait.

compendiumdb: an R package for retrieval and storage of functional genomics data

NARCIS (Netherlands)

Nandal, Umesh K.; van Kampen, Antoine H. C.; Moerland, Perry D.

2016-01-01

Currently, the Gene Expression Omnibus (GEO) contains public data of over 1 million samples from more than 40 000 microarray-based functional genomics experiments. This provides a rich source of information for novel biological discoveries. However, unlocking this potential often requires retrieving

The development of brain systems associated with successful memory retrieval of scenes.

Science.gov (United States)

Ofen, Noa; Chai, Xiaoqian J; Schuil, Karen D I; Whitfield-Gabrieli, Susan; Gabrieli, John D E

2012-07-18

Neuroanatomical and psychological evidence suggests prolonged maturation of declarative memory systems in the human brain from childhood into young adulthood. Here, we examine functional brain development during successful memory retrieval of scenes in children, adolescents, and young adults ages 8-21 via functional magnetic resonance imaging. Recognition memory improved with age, specifically for accurate identification of studied scenes (hits). Successful retrieval (correct old-new decisions for studied vs unstudied scenes) was associated with activations in frontal, parietal, and medial temporal lobe (MTL) regions. Activations associated with successful retrieval increased with age in left parietal cortex (BA7), bilateral prefrontal, and bilateral caudate regions. In contrast, activations associated with successful retrieval did not change with age in the MTL. Psychophysiological interaction analysis revealed that there were, however, age-relate changes in differential connectivity for successful retrieval between MTL and prefrontal regions. These results suggest that neocortical regions related to attentional or strategic control show the greatest developmental changes for memory retrieval of scenes. Furthermore, these results suggest that functional interactions between MTL and prefrontal regions during memory retrieval also develop into young adulthood. The developmental increase of memory-related activations in frontal and parietal regions for retrieval of scenes and the absence of such an increase in MTL regions parallels what has been observed for memory encoding of scenes.

Arousal?But Not Valence?Reduces False Memories at Retrieval

OpenAIRE

Mirandola, Chiara; Toffalini, Enrico

2016-01-01

Mood affects both memory accuracy and memory distortions. However, some aspects of this relation are still poorly understood: (1) whether valence and arousal equally affect false memory production, and (2) whether retrieval-related processes matter; the extant literature typically shows that mood influences memory performance when it is induced before encoding, leaving unsolved whether mood induced before retrieval also impacts memory. We examined how negative, positive, and neutral mood indu...

Hospital nurses' information retrieval behaviours in relation to evidence based nursing: a literature review.

Science.gov (United States)

Alving, Berit Elisabeth; Christensen, Janne Buck; Thrysøe, Lars

2018-03-01

The purpose of this literature review is to provide an overview of the information retrieval behaviour of clinical nurses, in terms of the use of databases and other information resources and their frequency of use. Systematic searches carried out in five databases and handsearching were used to identify the studies from 2010 to 2016, with a populations, exposures and outcomes (PEO) search strategy, focusing on the question: In which databases or other information resources do hospital nurses search for evidence based information, and how often? Of 5272 titles retrieved based on the search strategy, only nine studies fulfilled the criteria for inclusion. The studies are from the United States, Canada, Taiwan and Nigeria. The results show that hospital nurses' primary choice of source for evidence based information is Google and peers, while bibliographic databases such as PubMed are secondary choices. Data on frequency are only included in four of the studies, and data are heterogenous. The reasons for choosing Google and peers are primarily lack of time; lack of information; lack of retrieval skills; or lack of training in database searching. Only a few studies are published on clinical nurses' retrieval behaviours, and more studies are needed from Europe and Australia. © 2018 Health Libraries Group.

Patterns of expression of cell wall related genes in sugarcane

Directory of Open Access Journals (Sweden)

Lima D.U.

2001-01-01

Full Text Available Our search for genes related to cell wall metabolism in the sugarcane expressed sequence tag (SUCEST database (http://sucest.lbi.dcc.unicamp.br resulted in 3,283 reads (1% of the total reads which were grouped into 459 clusters (potential genes with an average of 7.1 reads per cluster. To more clearly display our correlation coefficients, we constructed surface maps which we used to investigate the relationship between cell wall genes and the sugarcane tissues libraries from which they came. The only significant correlations that we found between cell wall genes and/or their expression within particular libraries were neutral or synergetic. Genes related to cellulose biosynthesis were from the CesA family, and were found to be the most abundant cell wall related genes in the SUCEST database. We found that the highest number of CesA reads came from the root and stem libraries. The genes with the greatest number of reads were those involved in cell wall hydrolases (e.g. beta-1,3-glucanases, xyloglucan endo-beta-transglycosylase, beta-glucosidase and endo-beta-mannanase. Correlation analyses by surface mapping revealed that the expression of genes related to biosynthesis seems to be associated with the hydrolysis of hemicelluloses, pectin hydrolases being mainly associated with xyloglucan hydrolases. The patterns of cell wall related gene expression in sugarcane based on the number of reads per cluster reflected quite well the expected physiological characteristics of the tissues. This is the first work to provide a general view on plant cell wall metabolism through the expression of related genes in almost all the tissues of a plant at the same time. For example, developing flowers behaved similarly to both meristematic tissues and leaf-root transition zone tissues. Besides providing a basis for future research on the mechanisms of plant development which involve the cell wall, our findings will provide valuable tools for plant engineering in the

Transfer Appropriate Forgetting: The Cue-Dependent Nature of Retrieval-Induced Forgetting

Science.gov (United States)

Perfect, Timothy J.; Stark, Louisa-Jayne; Tree, Jeremy J.; Moulin, Christopher J. A.; Ahmed, Lubna; Hutter, Russell

2004-01-01

Retrieval-induced forgetting is the failure to recall a previously studied word following repeated retrieval of a related item. It has been argued that this is due to retrieval competition between practiced and unpracticed items, which results in inhibition of the non-recalled item, detectable with an independent cue at final test. Three…

Concept of Operations for Waste Transport, Emplacement, and Retrieval

International Nuclear Information System (INIS)

Raczka, Norman T.

2001-01-01

The preparation of this technical report has two objectives. The first objective is to discuss the base case concepts of waste transport, emplacement, and retrieval operations and evaluate these operations relative to a lower-temperature repository design. Aspects of the operations involved in waste transport, emplacement and retrieval may be affected by the lower-temperature operating schemes. This report evaluates the effects the lower-temperature alternatives may have on the operational concepts involved in emplacing and retrieving waste. The second objective is to provide backup material for the design description, in a traceable and defensible format, for Section 2 of the Waste Emplacement/Retrieval System Description Document

Emergent web intelligence advanced information retrieval

CERN Document Server

Badr, Youakim; Abraham, Ajith; Hassanien, Aboul-Ella

2010-01-01

Web Intelligence explores the impact of artificial intelligence and advanced information technologies representing the next generation of Web-based systems, services, and environments, and designing hybrid web systems that serve wired and wireless users more efficiently. Multimedia and XML-based data are produced regularly and in increasing way in our daily digital activities, and their retrieval must be explored and studied in this emergent web-based era. 'Emergent Web Intelligence: Advanced information retrieval, provides reviews of the related cutting-edge technologies and insights. It is v

The Effect of Overgeneral Autobiographical Memory Retrieval on Rumination

Directory of Open Access Journals (Sweden)

Filip Raes

2006-03-01

Full Text Available From distinct research traditions rumination and overgeneral autobiographical memory retrieval (OGM have emerged as two vulnerability markers for depression and depressive relapse (Nolen-Hoeksema, 2004; Williams, 2004. Recent research further suggests a causal relation between rumination and OGM (e.g., Watkins & Teasdale, 2001. The present study investigated the inverse relationship, that is, OGM causally influencing ruminative thinking. A scrambled sentences procedure was used to assess the extent to which 112 student participants were engaged in a mental mode consistent with ruminative thinking following either a specific or overgeneral memory retrieval style manipulation. Trait rumination was also assessed prior to the experimental retrieval manipulation, using a self-report scale. It was found that high ruminators, following an overgeneral (as compared to a specific retrieval style, unscrambled sentences relatively more into sentences with a ruminative meaning. In non or low ruminators this retrieval style manipulation had no such effect. Alongside the findings of Watkins and colleagues (e.g., Watkins & Teasdale, 2001, the present results are consistent with the view of rumination and OGM as two mutually reinforcing vulnerability factors for depression (Williams, 1996, 2004.

Gunther Tulip Retrievable Inferior Vena Caval Filters: Indications, Efficacy, Retrieval, and Complications

International Nuclear Information System (INIS)

Looby, S.; Given, M.F.; Geoghegan, T.; McErlean, A.; Lee, M.J.

2007-01-01

Purpose. We evaluated the Gunther Tulip (GT) retrievable inferior vena cava (IVC) filter with regard to indications, filtration efficacy, complications, retrieval window, and use of anticoagulation. Method. A retrospective study was performed of 147 patients (64 men, 83 women; mean age 58.8 years) who underwent retrievable GT filter insertion between 2001 and 2005. The indications for placement included a diagnosis of pulmonary embolism or deep venous thrombosis with a contraindication to anticoagulation (n = 68), pulmonary embolism or deep venous thrombosis while on anticoagulation (n = 49), prophylactic filter placement for high-risk surgical patients with a past history of pulmonary embolism or deep venous thrombosis (n = 20), and a high risk of pulmonary embolism or deep venous thrombosis (n = 10). Forty-nine of the 147 patients did not receive anticoagulation (33.7%) while 96 of 147 patients did, 82 of these receiving warfarin (56.5%), 11 receiving low-molecular weight heparins (7.58%), and 3 receiving antiplatelet agents alone (2.06%). Results. Filter placement was successful in 147 patients (100%). Two patients had two filters inserted. Of the 147 patients, filter deployment was on a permanent basis in 102 and with an intention to retrieve in 45 patients. There were 36 (80%) successful retrievals and 9 (20%) failed retrievals. The mean time to retrieval was 33.6 days. The reasons for failed retrieval included filter struts tightly adherent to the IVC wall (5/9), extreme filter tilt (2/9), and extensive filter thrombus (2/9). Complications included pneumothorax (n = 4), failure of filter expansion (n = 1), and breakthrough pulmonary embolism (n = 1). No IVC thrombotic episodes were recorded. Discussion. The Gunther Tulip retrievable filter can be used as a permanent or a retrievable filter. It is safe and efficacious. GT filters can be safely retrieved at a mean time interval of 33.6 days. The newly developed Celect filter may extend the retrieval interval

Candidate genes and pathogenesis investigation for sepsis-related acute respiratory distress syndrome based on gene expression profile.

Science.gov (United States)

Wang, Min; Yan, Jingjun; He, Xingxing; Zhong, Qiang; Zhan, Chengye; Li, Shusheng

2016-04-18

Acute respiratory distress syndrome (ARDS) is a potentially devastating form of acute inflammatory lung injury as well as a major cause of acute respiratory failure. Although researchers have made significant progresses in elucidating the pathophysiology of this complex syndrome over the years, the absence of a universal detail disease mechanism up until now has led to a series of practical problems for a definitive treatment. This study aimed to predict some genes or pathways associated with sepsis-related ARDS based on a public microarray dataset and to further explore the molecular mechanism of ARDS. A total of 122 up-regulated DEGs and 91 down-regulated differentially expressed genes (DEGs) were obtained. The up- and down-regulated DEGs were mainly involved in functions like mitotic cell cycle and pathway like cell cycle. Protein-protein interaction network of ARDS analysis revealed 20 hub genes including cyclin B1 (CCNB1), cyclin B2 (CCNB2) and topoisomerase II alpha (TOP2A). A total of seven transcription factors including forkhead box protein M1 (FOXM1) and 30 target genes were revealed in the transcription factor-target gene regulation network. Furthermore, co-cited genes including CCNB2-CCNB1 were revealed in literature mining for the relations ARDS related genes. Pathways like mitotic cell cycle were closed related with the development of ARDS. Genes including CCNB1, CCNB2 and TOP2A, as well as transcription factors like FOXM1 might be used as the novel gene therapy targets for sepsis related ARDS.

Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS.

Science.gov (United States)

Pan, David Z; Garske, Kristina M; Alvarez, Marcus; Bhagat, Yash V; Boocock, James; Nikkola, Elina; Miao, Zong; Raulerson, Chelsea K; Cantor, Rita M; Civelek, Mete; Glastonbury, Craig A; Small, Kerrin S; Boehnke, Michael; Lusis, Aldons J; Sinsheimer, Janet S; Mohlke, Karen L; Laakso, Markku; Pajukanta, Päivi; Ko, Arthur

2018-04-17

Increased adiposity is a hallmark of obesity and overweight, which affect 2.2 billion people world-wide. Understanding the genetic and molecular mechanisms that underlie obesity-related phenotypes can help to improve treatment options and drug development. Here we perform promoter Capture Hi-C in human adipocytes to investigate interactions between gene promoters and distal elements as a transcription-regulating mechanism contributing to these phenotypes. We find that promoter-interacting elements in human adipocytes are enriched for adipose-related transcription factor motifs, such as PPARG and CEBPB, and contribute to heritability of cis-regulated gene expression. We further intersect these data with published genome-wide association studies for BMI and BMI-related metabolic traits to identify the genes that are under genetic cis regulation in human adipocytes via chromosomal interactions. This integrative genomics approach identifies four cis-eQTL-eGene relationships associated with BMI or obesity-related traits, including rs4776984 and MAP2K5, which we further confirm by EMSA, and highlights 38 additional candidate genes.

Transformed Neural Pattern Reinstatement during Episodic Memory Retrieval.

Science.gov (United States)

Xiao, Xiaoqian; Dong, Qi; Gao, Jiahong; Men, Weiwei; Poldrack, Russell A; Xue, Gui

2017-03-15

Contemporary models of episodic memory posit that remembering involves the reenactment of encoding processes. Although encoding-retrieval similarity has been consistently reported and linked to memory success, the nature of neural pattern reinstatement is poorly understood. Using high-resolution fMRI on human subjects, our results obtained clear evidence for item-specific pattern reinstatement in the frontoparietal cortex, even when the encoding-retrieval pairs shared no perceptual similarity. No item-specific pattern reinstatement was found in the ventral visual cortex. Importantly, the brain regions and voxels carrying item-specific representation differed significantly between encoding and retrieval, and the item specificity for encoding-retrieval similarity was smaller than that for encoding or retrieval, suggesting different nature of representations between encoding and retrieval. Moreover, cross-region representational similarity analysis suggests that the encoded representation in the ventral visual cortex was reinstated in the frontoparietal cortex during retrieval. Together, these results suggest that, in addition to reinstatement of the originally encoded pattern in the brain regions that perform encoding processes, retrieval may also involve the reinstatement of a transformed representation of the encoded information. These results emphasize the constructive nature of memory retrieval that helps to serve important adaptive functions. SIGNIFICANCE STATEMENT Episodic memory enables humans to vividly reexperience past events, yet how this is achieved at the neural level is barely understood. A long-standing hypothesis posits that memory retrieval involves the faithful reinstatement of encoding-related activity. We tested this hypothesis by comparing the neural representations during encoding and retrieval. We found strong pattern reinstatement in the frontoparietal cortex, but not in the ventral visual cortex, that represents visual details. Critically

Information Retrieval and Graph Analysis Approaches for Book Recommendation

Directory of Open Access Journals (Sweden)

Chahinez Benkoussas

2015-01-01

Full Text Available A combination of multiple information retrieval approaches is proposed for the purpose of book recommendation. In this paper, book recommendation is based on complex user's query. We used different theoretical retrieval models: probabilistic as InL2 (Divergence from Randomness model and language model and tested their interpolated combination. Graph analysis algorithms such as PageRank have been successful in Web environments. We consider the application of this algorithm in a new retrieval approach to related document network comprised of social links. We called Directed Graph of Documents (DGD a network constructed with documents and social information provided from each one of them. Specifically, this work tackles the problem of book recommendation in the context of INEX (Initiative for the Evaluation of XML retrieval Social Book Search track. A series of reranking experiments demonstrate that combining retrieval models yields significant improvements in terms of standard ranked retrieval metrics. These results extend the applicability of link analysis algorithms to different environments.

Thermodynamic and cloud parameter retrieval using infrared spectral data

Science.gov (United States)

Zhou, Daniel K.; Smith, William L., Sr.; Liu, Xu; Larar, Allen M.; Huang, Hung-Lung A.; Li, Jun; McGill, Matthew J.; Mango, Stephen A.

2005-01-01

High-resolution infrared radiance spectra obtained from near nadir observations provide atmospheric, surface, and cloud property information. A fast radiative transfer model, including cloud effects, is used for atmospheric profile and cloud parameter retrieval. The retrieval algorithm is presented along with its application to recent field experiment data from the NPOESS Airborne Sounding Testbed - Interferometer (NAST-I). The retrieval accuracy dependence on cloud properties is discussed. It is shown that relatively accurate temperature and moisture retrievals can be achieved below optically thin clouds. For optically thick clouds, accurate temperature and moisture profiles down to cloud top level are obtained. For both optically thin and thick cloud situations, the cloud top height can be retrieved with an accuracy of approximately 1.0 km. Preliminary NAST-I retrieval results from the recent Atlantic-THORPEX Regional Campaign (ATReC) are presented and compared with coincident observations obtained from dropsondes and the nadir-pointing Cloud Physics Lidar (CPL).

Information Retrieval and Graph Analysis Approaches for Book Recommendation.

Science.gov (United States)

Benkoussas, Chahinez; Bellot, Patrice

2015-01-01

A combination of multiple information retrieval approaches is proposed for the purpose of book recommendation. In this paper, book recommendation is based on complex user's query. We used different theoretical retrieval models: probabilistic as InL2 (Divergence from Randomness model) and language model and tested their interpolated combination. Graph analysis algorithms such as PageRank have been successful in Web environments. We consider the application of this algorithm in a new retrieval approach to related document network comprised of social links. We called Directed Graph of Documents (DGD) a network constructed with documents and social information provided from each one of them. Specifically, this work tackles the problem of book recommendation in the context of INEX (Initiative for the Evaluation of XML retrieval) Social Book Search track. A series of reranking experiments demonstrate that combining retrieval models yields significant improvements in terms of standard ranked retrieval metrics. These results extend the applicability of link analysis algorithms to different environments.

RETRIEVAL EVENTS EVALUATION

International Nuclear Information System (INIS)

Wilson, T.

1999-01-01

The purpose of this analysis is to evaluate impacts to the retrieval concept presented in the Design Analysis ''Retrieval Equipment and Strategy'' (Reference 6), from abnormal events based on Design Basis Events (DBE) and Beyond Design Basis Events (BDBE) as defined in two recent analyses: (1) DBE/Scenario Analysis for Preclosure Repository Subsurface Facilities (Reference 4); and (2) Preliminary Preclosure Design Basis Event Calculations for the Monitored Geologic Repository (Reference 5) The objective of this task is to determine what impacts the DBEs and BDBEs have on the equipment developed for retrieval. The analysis lists potential impacts and recommends changes to be analyzed in subsequent design analyses for developed equipment, or recommend where additional equipment may be needed, to allow retrieval to be performed in all DBE or BDBE situations. This analysis supports License Application design and therefore complies with the requirements of Systems Description Document input criteria comparison as presented in Section 7, Conclusions. In addition, the analysis discusses the impacts associated with not using concrete inverts in the emplacement drifts. The ''Retrieval Equipment and Strategy'' analysis was based on a concrete invert configuration in the emplacement drift. The scope of the analysis, as presented in ''Development Plan for Retrieval Events Evaluation'' (Reference 3) includes evaluation and criteria of the following: Impacts to retrieval from the emplacement drift based on DBE/BDBEs, and changes to the invert configuration for the preclosure period. Impacts to retrieval from the main drifts based on DBE/BDBEs for the preclosure period

Arousal-But Not Valence-Reduces False Memories at Retrieval.

Science.gov (United States)

Mirandola, Chiara; Toffalini, Enrico

2016-01-01

Mood affects both memory accuracy and memory distortions. However, some aspects of this relation are still poorly understood: (1) whether valence and arousal equally affect false memory production, and (2) whether retrieval-related processes matter; the extant literature typically shows that mood influences memory performance when it is induced before encoding, leaving unsolved whether mood induced before retrieval also impacts memory. We examined how negative, positive, and neutral mood induced before retrieval affected inferential false memories and related subjective memory experiences. A recognition-memory paradigm for photographs depicting script-like events was employed. Results showed that individuals in both negative and positive moods-similar in arousal levels-correctly recognized more target events and endorsed fewer false memories (and these errors were linked to remember responses less frequently), compared to individuals in neutral mood. This suggests that arousal (but not valence) predicted memory performance; furthermore, we found that arousal ratings provided by participants were more adequate predictors of memory performance than their actual belonging to either positive, negative or neutral mood groups. These findings suggest that arousal has a primary role in affecting memory, and that mood exerts its power on true and false memory even when induced at retrieval.

Transformation invariant image indexing and retrieval for image databases

NARCIS (Netherlands)

Gevers, Th.; Smeulders, A.W.M.

1994-01-01

This paper presents a novel design of an image database system which supports storage, indexing and retrieval of images by content. The image retrieval methodology is based on the observation that images can be discriminated by the presence of image objects and their spatial relations. Images in the

Retrieval of Embolized Amplatzer Patent Foramen Ovale Occlusion Device: Issues Related to Late Recognition

Directory of Open Access Journals (Sweden)

Allan J. Davies

2017-01-01

Full Text Available Embolization of a percutaneous patent foramen ovale (PFO closure device is a rare but serious complication. While early, periprocedural device embolization can normally be managed with snare and percutaneous retrieval, late embolization requires a different management strategy due to inability of the device to deform to allow passage into a large caliber sheath. We present a case of asymptomatic device embolization recognized six months following implantation and discuss the challenges encountered in successfully retrieving the device.

Cloning of the relative genes of endocrine exophthalmos

International Nuclear Information System (INIS)

Zheng, JG

2004-01-01

Aim: In order to clarify the pathogenesis of endocrine exophthalmos, and lay foundations for finding the new functions of its relative genes, the cloning of its relative genes was carried out. Methods: The thyroid tissues of 10 hyperthyroidism patients, 5 of them with endocrine exophthalmos and 5 without that, were obtained. Their mRNA were collected respectively by using Quick Prep Micro mRNA purification kit. Then the same amount of the mRNA from 5 patients with endocrine exophthalmos was added into an eppendorf tube to form a mRNA pool. And that of the 5 patients without endocrine exophthalmos was also prepared as the other pool. As a model, the pool was used to synthesize the single and double chains of cDNA through SMART Tm PCR cDNA Synthesis Kit. The double chains cDNA from the endocrine exophthalmos patients, being used as tester, and that from the patients without endocrine exophthalmos, being used as driver, were digested by restriction endonucleases Hae III to get the fragments which was less than 500 bases. The tester cDNA was ligated with adapt or 1 or 2 respectively. Then the subtractive suppressive hybridization was performed between tester and driver cDNA. And the efficacies of subtraction were measured. The differential genes between the thyroid tissues of endocrine exophthalmos and the thyroid tissues without endocrine exophthalmos were obtained through two cycles of subtractive hybridization and two cycles PCR. The differential genes were cloned into the vector of pT-Adv, and then transformed into E.coliDH5a. 48 white clonies were selected to build the subtractive suppressive library of the relative genes of endocrine exophthalmos. The primer 2 was applied for the colony PCR of the relative genes. The amplified genes were obtained and purified by using Quaqwich Spine PCR Purification Kit. According to the principle of random primer, the double chains cDNA from the thyroid tissues with or without endocrine exophthalmos were digested by Hae III

Private information retrieval

CERN Document Server

Yi, Xun; Bertino, Elisa

2013-01-01

This book deals with Private Information Retrieval (PIR), a technique allowing a user to retrieve an element from a server in possession of a database without revealing to the server which element is retrieved. PIR has been widely applied to protect the privacy of the user in querying a service provider on the Internet. For example, by PIR, one can query a location-based service provider about the nearest car park without revealing his location to the server.The first PIR approach was introduced by Chor, Goldreich, Kushilevitz and Sudan in 1995 in a multi-server setting, where the user retriev

Evolutionary Computing Methods for Spectral Retrieval

Science.gov (United States)

Terrile, Richard; Fink, Wolfgang; Huntsberger, Terrance; Lee, Seugwon; Tisdale, Edwin; VonAllmen, Paul; Tinetti, Geivanna

2009-01-01

A methodology for processing spectral images to retrieve information on underlying physical, chemical, and/or biological phenomena is based on evolutionary and related computational methods implemented in software. In a typical case, the solution (the information that one seeks to retrieve) consists of parameters of a mathematical model that represents one or more of the phenomena of interest. The methodology was developed for the initial purpose of retrieving the desired information from spectral image data acquired by remote-sensing instruments aimed at planets (including the Earth). Examples of information desired in such applications include trace gas concentrations, temperature profiles, surface types, day/night fractions, cloud/aerosol fractions, seasons, and viewing angles. The methodology is also potentially useful for retrieving information on chemical and/or biological hazards in terrestrial settings. In this methodology, one utilizes an iterative process that minimizes a fitness function indicative of the degree of dissimilarity between observed and synthetic spectral and angular data. The evolutionary computing methods that lie at the heart of this process yield a population of solutions (sets of the desired parameters) within an accuracy represented by a fitness-function value specified by the user. The evolutionary computing methods (ECM) used in this methodology are Genetic Algorithms and Simulated Annealing, both of which are well-established optimization techniques and have also been described in previous NASA Tech Briefs articles. These are embedded in a conceptual framework, represented in the architecture of the implementing software, that enables automatic retrieval of spectral and angular data and analysis of the retrieved solutions for uniqueness.

Expression Analysis of Genes Related to Rice Resistance Against Brown Planthopper, Nilaparvata lugens

Directory of Open Access Journals (Sweden)

Panatda Jannoey

2017-05-01

Full Text Available Brown planthopper (BPH is an insect species that feeds on the vascular system of rice plants. To examine the defence mechanism of rice plants against BPH, the pathogenesis-related genes (PR1a, PR2, PR3, PR4, PR6, PR9, PR10a, PR13, PR15 and PRpha, signaling molecule synthesis genes (AOS, AXR, ACO and LOX, antioxidant-related genes (CAT, TRX, GST and SOD and lignin biosynthesis-related genes (CHS, CHI and C4H were investigated in a resistant rice variety. AOS, PR6, PR9 and PR15 genes showed significantly increased relative expression levels at 24.38-, 19.17-, 14.71-, and 12.74-fold compared to the control. Moderate increased relative expression levels of lignin biosynthesis-related gene (C4H, pathogenesis-related genes (PR4, PR10a and PRpha, and antioxidant-related gene (GST were found, while CHI, LOX, SOD, TRX1 and AXR showed decreased relative expression levels. It was thus clearly shown that wound-induced response genes were activated in rice plants after BPH attacks through AOS activation. Jasmonic acid signaling molecule may activate PR6, PR15, GST and CAT subsequently increasing their expression for H2O2 detoxification. PR6 were expressed at the highest relative level among the PR genes. These genes therefore have also a considerable synergistic role with the other genes against BPH by interfered their digestion tract system.

Statistical Language Models and Information Retrieval: Natural Language Processing Really Meets Retrieval

NARCIS (Netherlands)

Hiemstra, Djoerd; de Jong, Franciska M.G.

2001-01-01

Traditionally, natural language processing techniques for information retrieval have always been studied outside the framework of formal models of information retrieval. In this article, we introduce a new formal model of information retrieval based on the application of statistical language models.

The properties of retrieval cues constrain the picture superiority effect.

Science.gov (United States)

Weldon, M S; Roediger, H L; Challis, B H

1989-01-01

In three experiments, we examined why pictures are remembered better than words on explicit memory tests like recall and recognition, whereas words produce more priming than pictures on some implicit tests, such as word-fragment and word-stem completion (e.g., completing -l-ph-nt or ele----- as elephant). One possibility is that pictures are always more accessible than words if subjects are given explicit retrieval instructions. An alternative possibility is that the properties of the retrieval cues themselves constrain the retrieval processes engaged; word fragments might induce data-driven (perceptually based) retrieval, which favors words regardless of the retrieval instructions. Experiment 1 demonstrated that words were remembered better than pictures on both the word-fragment and word-stem completion tasks under both implicit and explicit retrieval conditions. In Experiment 2, pictures were recalled better than words with semantically related extralist cues. In Experiment 3, when semantic cues were combined with word fragments, pictures and words were recalled equally well under explicit retrieval conditions, but words were superior to pictures under implicit instructions. Thus, the inherently data-limited properties of fragmented words limit their use in accessing conceptual codes. Overall, the results indicate that retrieval operations are largely determined by properties of the retrieval cues under both implicit and explicit retrieval conditions.

Identification of apoptosis-related PLZF target genes

International Nuclear Information System (INIS)

Bernardo, Maria Victoria; Yelo, Estefania; Gimeno, Lourdes; Campillo, Jose Antonio; Parrado, Antonio

2007-01-01

The PLZF gene encodes a BTB/POZ-zinc finger-type transcription factor, involved in physiological development, proliferation, differentiation, and apoptosis. In this paper, we investigate proliferation, survival, and gene expression regulation in stable clones from the human haematopoietic K562, DG75, and Jurkat cell lines with inducible expression of PLZF. In Jurkat cells, but not in K562 and DG75 cells, PLZF induced growth suppression and apoptosis in a cell density-dependent manner. Deletion of the BTB/POZ domain of PLZF abrogated growth suppression and apoptosis. PLZF was expressed with a nuclear speckled pattern distinctively in the full-length PLZF-expressing Jurkat clones, suggesting that the nuclear speckled localization is required for PLZF-induced apoptosis. By microarray analysis, we identified that the apoptosis-inducer TP53INP1, ID1, and ID3 genes were upregulated, and the apoptosis-inhibitor TERT gene was downregulated. The identification of apoptosis-related PLZF target genes may have biological and clinical relevance in cancer typified by altered PLZF expression

Data retrieval systems and models of information situations

International Nuclear Information System (INIS)

Jankowski, L.

1984-01-01

Demands placed on data retrieval systems and their basic parameters are given. According to the stage of development of data collection and processing, data retrieval systems may be divided into systems for the simple recording and provision of data, systems for recording and providing data with integrated statistical functions, and logical information systems. The structure is characterized of the said information systems as are methods of processing and representation of facts. The notion is defined of ''artificial intelligence'' in the development of logical information systems. The structure of representing knowledge in diverse forms of the model is decisive in logical information systems related to nuclear research. The main model elements are the characteristics of data, forms of representation and program. In dependence on the structure of data, the structure of the preparatory and transformation algorithms and on the aim of the system it is possible to classify data retrieval systems related to nuclear research and technology into five logical information models: linear, identification, advisory, theory-experiment models and problem solving models. The characteristics are given of the said models and examples of data retrieval systems for the individual models. (E.S.)

Probabilistic and machine learning-based retrieval approaches for biomedical dataset retrieval

Science.gov (United States)

Karisani, Payam; Qin, Zhaohui S; Agichtein, Eugene

2018-01-01

Abstract The bioCADDIE dataset retrieval challenge brought together different approaches to retrieval of biomedical datasets relevant to a user’s query, expressed as a text description of a needed dataset. We describe experiments in applying a data-driven, machine learning-based approach to biomedical dataset retrieval as part of this challenge. We report on a series of experiments carried out to evaluate the performance of both probabilistic and machine learning-driven techniques from information retrieval, as applied to this challenge. Our experiments with probabilistic information retrieval methods, such as query term weight optimization, automatic query expansion and simulated user relevance feedback, demonstrate that automatically boosting the weights of important keywords in a verbose query is more effective than other methods. We also show that although there is a rich space of potential representations and features available in this domain, machine learning-based re-ranking models are not able to improve on probabilistic information retrieval techniques with the currently available training data. The models and algorithms presented in this paper can serve as a viable implementation of a search engine to provide access to biomedical datasets. The retrieval performance is expected to be further improved by using additional training data that is created by expert annotation, or gathered through usage logs, clicks and other processes during natural operation of the system. Database URL: https://github.com/emory-irlab/biocaddie

ICan: an integrated co-alteration network to identify ovarian cancer-related genes.

Science.gov (United States)

Zhou, Yuanshuai; Liu, Yongjing; Li, Kening; Zhang, Rui; Qiu, Fujun; Zhao, Ning; Xu, Yan

2015-01-01

Over the last decade, an increasing number of integrative studies on cancer-related genes have been published. Integrative analyses aim to overcome the limitation of a single data type, and provide a more complete view of carcinogenesis. The vast majority of these studies used sample-matched data of gene expression and copy number to investigate the impact of copy number alteration on gene expression, and to predict and prioritize candidate oncogenes and tumor suppressor genes. However, correlations between genes were neglected in these studies. Our work aimed to evaluate the co-alteration of copy number, methylation and expression, allowing us to identify cancer-related genes and essential functional modules in cancer. We built the Integrated Co-alteration network (ICan) based on multi-omics data, and analyzed the network to uncover cancer-related genes. After comparison with random networks, we identified 155 ovarian cancer-related genes, including well-known (TP53, BRCA1, RB1 and PTEN) and also novel cancer-related genes, such as PDPN and EphA2. We compared the results with a conventional method: CNAmet, and obtained a significantly better area under the curve value (ICan: 0.8179, CNAmet: 0.5183). In this paper, we describe a framework to find cancer-related genes based on an Integrated Co-alteration network. Our results proved that ICan could precisely identify candidate cancer genes and provide increased mechanistic understanding of carcinogenesis. This work suggested a new research direction for biological network analyses involving multi-omics data.

Dancing your moves away: How memory retrieval shapes complex motor action.

Science.gov (United States)

Tempel, Tobias; Loran, Igor; Frings, Christian

2015-09-01

Human memory is subject to continuous change. Besides the accumulation of contents as a consequence of encoding new information, the accessing of memory influences later accessibility. The authors investigated how retrieval-related memory-shaping processes affect intentionally acquired complex motion patterns. Dance figures served as the material to be learned. The authors found that selectively retrieving a subset of dance moves facilitated later recall of the retrieved dance figures, whereas figures that were related to these but that did not receive selective practice suffered from forgetting. These opposing effects were shown in experiments with different designs involving either the learning of only 1 set of body movements or 2 sets of movements categorized into 2 dances. A 3rd experiment showed that selective restudy also entailed a recall benefit for restudied dance figures but did not induce forgetting for related nonrestudied dance figures. The results suggest that motor programs representing the motion patterns in a format closely corresponding to parameters of movement execution were affected. The reported experiments demonstrate how retrieval determines motor memory plasticity and emphasize the importance of separating restudy and retrieval practice when teaching people new movements. (c) 2015 APA, all rights reserved).

Interference from retrieval cues in Parkinson's disease.

Science.gov (United States)

Crescentini, Cristiano; Marin, Dario; Del Missier, Fabio; Biasutti, Emanuele; Shallice, Tim

2011-11-01

Existing studies on memory interference in Parkinson's disease (PD) patients have provided mixed results and it is unknown whether PD patients have problems in overcoming interference from retrieval cues. We investigated this issue by using a part-list cuing paradigm. In this paradigm, after the study of a list of items, the presentation of some of these items as retrieval cues hinders the recall of the remaining ones. We tested PD patients' (n = 19) and control participants' (n = 16) episodic memory in the presence and absence of part-list cues, using initial-letter probes, and following either weak or strong serial associative encoding of list items. Both PD patients and control participants showed a comparable and significant part-list cuing effect after weak associative encoding (13% vs. 12% decrease in retrieval in part-list cuing vs. no part-list cuing -control- conditions in PD patients and control participants, respectively), denoting a similar effect of cue-driven interference in the two populations when a serial retrieval strategy is hard to develop. However, only PD patients showed a significant part-list cuing effect after strong associative encoding (20% vs. 5% decrease in retrieval in patients and controls, respectively). When encoding promotes the development of an effective serial retrieval strategy, the presentation of part-list cues has a specifically disruptive effect in PD patients. This indicates problems in strategic retrieval, probably related to PD patients' increased tendency to rely on external cues. Findings in control conditions suggest that less effective encoding may have contributed to PD patients' memory performance.

Age-related deficits in selective attention during encoding increase demands on episodic reconstruction during context retrieval: An ERP study.

Science.gov (United States)

James, Taylor; Strunk, Jonathan; Arndt, Jason; Duarte, Audrey

2016-06-01

Previous event-related potential (ERP) and neuroimaging evidence suggests that directing attention toward single item-context associations compared to intra-item features at encoding improves context memory performance and reduces demands on strategic retrieval operations in young and older adults. In everyday situations, however, there are multiple event features competing for our attention. It is not currently known how selectively attending to one contextual feature while attempting to ignore another influences context memory performance and the processes that support successful retrieval in the young and old. We investigated this issue in the current ERP study. Young and older participants studied pictures of objects in the presence of two contextual features: a color and a scene, and their attention was directed to the object's relationship with one of those contexts. Participants made context memory decisions for both attended and unattended contexts and rated their confidence in those decisions. Behavioral results showed that while both groups were generally successful in applying selective attention during context encoding, older adults were less confident in their context memory decisions for attended features and showed greater dependence in context memory accuracy for attended and unattended contextual features (i.e., hyper-binding). ERP results were largely consistent between age groups but older adults showed a more pronounced late posterior negativity (LPN) implicated in episodic reconstruction processes. We conclude that age-related suppression deficits during encoding result in reduced selectivity in context memory, thereby increasing subsequent demands on episodic reconstruction processes when sought after details are not readily retrieved. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optimization of Calcine Blending During Retrieval From Binsets; TOPICAL

International Nuclear Information System (INIS)

Taylor, D.D.; Mohr, C.M.; Nelson, L.O.

2000-01-01

This report documents a study performed during advanced feasibility studies for the INTEC Technology Development Facility (ITDF). The study was commissioned to provide information about functional requirements for the ITDF related to development of equipment and procedures for retrieving radioactive calcine from binset storage at the Idaho Nuclear Technology and Engineering Center (INTEC) at the Idaho National Engineering and Environmental Laboratory (INEEL). Calcine will be retrieved prior to treating it for permanent disposal in a national repository for high level waste. The objective this study was to estimate the degree of homogenization of the calcine that might be achieved through optimized retrieval and subsequent blending. Such homogenization has the potential of reducing the costs for treatment of the calcine and for qualifying of the final waste forms for acceptance at the repository. Results from the study indicate that optimized retrieval and blending can reduce the peak c oncentration variations of key components (Al, Zr, F) in blended batches of retrieved calcine. During un-optimized retrieval these variations are likely to be 81-138% while optimized retrieval can reduce them to the 5-10% range

Automatic medical image annotation and keyword-based image retrieval using relevance feedback.

Science.gov (United States)

Ko, Byoung Chul; Lee, JiHyeon; Nam, Jae-Yeal

2012-08-01

This paper presents novel multiple keywords annotation for medical images, keyword-based medical image retrieval, and relevance feedback method for image retrieval for enhancing image retrieval performance. For semantic keyword annotation, this study proposes a novel medical image classification method combining local wavelet-based center symmetric-local binary patterns with random forests. For keyword-based image retrieval, our retrieval system use the confidence score that is assigned to each annotated keyword by combining probabilities of random forests with predefined body relation graph. To overcome the limitation of keyword-based image retrieval, we combine our image retrieval system with relevance feedback mechanism based on visual feature and pattern classifier. Compared with other annotation and relevance feedback algorithms, the proposed method shows both improved annotation performance and accurate retrieval results.

Retrieval-practice task affects relationship between working memory capacity and retrieval-induced forgetting.

Science.gov (United States)

Storm, Benjamin C; Bui, Dung C

2016-11-01

Retrieving a subset of items from memory can cause forgetting of other items in memory, a phenomenon referred to as retrieval-induced forgetting (RIF). Individuals who exhibit greater amounts of RIF have been shown to also exhibit superior working memory capacity (WMC) and faster stop-signal reaction times (SSRTs), results which have been interpreted as suggesting that RIF reflects an inhibitory process that is mediated by the processes of executive control. Across four experiments, we sought to further elucidate this issue by manipulating the way in which participants retrieved items during retrieval practice and examining how the resulting effects of forgetting correlated with WMC (Experiments 1-3) and SSRT (Experiment 4). Significant correlations were observed when participants retrieved items from an earlier study phase (within-list retrieval practice), but not when participants generated items from semantic memory (extra-list retrieval practice). These results provide important new insight into the role of executive-control processes in RIF.

Gene Transfers Between Distantly Related Organisms

Science.gov (United States)

Doolittle, Russell F.

2003-01-01

With the completion of numerous microbial genome sequences, reports of individual gene transfers between distantly related prokaryotes have become commonplace. On the other hand, transfers between prokaryotes and eukaryotes still excite the imagination. Many of these claims may be premature, but some are certainly valid. In this chapter, the kinds of supporting data needed to propose transfers between distantly related organisms and cite some interesting examples are considered.

Gene expression changes for antioxidants pathways in the mouse cochlea: relations to age-related hearing deficits.

Directory of Open Access Journals (Sweden)

Sherif F Tadros

Full Text Available Age-related hearing loss - presbycusis - is the number one neurodegenerative disorder and top communication deficit of our aged population. Like many aging disorders of the nervous system, damage from free radicals linked to production of reactive oxygen and/or nitrogen species (ROS and RNS, respectively may play key roles in disease progression. The efficacy of the antioxidant systems, e.g., glutathione and thioredoxin, is an important factor in pathophysiology of the aging nervous system. In this investigation, relations between the expression of antioxidant-related genes in the auditory portion of the inner ear - cochlea, and age-related hearing loss was explored for CBA/CaJ mice. Forty mice were classified into four groups according to age and degree of hearing loss. Cochlear mRNA samples were collected and cDNA generated. Using Affymetrix® GeneChip, the expressions of 56 antioxidant-related gene probes were analyzed to estimate the differences in gene expression between the four subject groups. The expression of Glutathione peroxidase 6, Gpx6; Thioredoxin reductase 1, Txnrd1; Isocitrate dehydrogenase 1, Idh1; and Heat shock protein 1, Hspb1; were significantly different, or showed large fold-change differences between subject groups. The Gpx6, Txnrd1 and Hspb1 gene expression changes were validated using qPCR. The Gpx6 gene was upregulated while the Txnrd1 gene was downregulated with age/hearing loss. The Hspb1 gene was found to be downregulated in middle-aged animals as well as those with mild presbycusis, whereas it was upregulated in those with severe presbycusis. These results facilitate development of future interventions to predict, prevent or slow down the progression of presbycusis.

A data mining approach for classifying DNA repair genes into ageing-related or non-ageing-related

Directory of Open Access Journals (Sweden)

Vasieva Olga

2011-01-01

Full Text Available Abstract Background The ageing of the worldwide population means there is a growing need for research on the biology of ageing. DNA damage is likely a key contributor to the ageing process and elucidating the role of different DNA repair systems in ageing is of great interest. In this paper we propose a data mining approach, based on classification methods (decision trees and Naive Bayes, for analysing data about human DNA repair genes. The goal is to build classification models that allow us to discriminate between ageing-related and non-ageing-related DNA repair genes, in order to better understand their different properties. Results The main patterns discovered by the classification methods are as follows: (a the number of protein-protein interactions was a predictor of DNA repair proteins being ageing-related; (b the use of predictor attributes based on protein-protein interactions considerably increased predictive accuracy of attributes based on Gene Ontology (GO annotations; (c GO terms related to "response to stimulus" seem reasonably good predictors of ageing-relatedness for DNA repair genes; (d interaction with the XRCC5 (Ku80 protein is a strong predictor of ageing-relatedness for DNA repair genes; and (e DNA repair genes with a high expression in T lymphocytes are more likely to be ageing-related. Conclusions The above patterns are broadly integrated in an analysis discussing relations between Ku, the non-homologous end joining DNA repair pathway, ageing and lymphocyte development. These patterns and their analysis support non-homologous end joining double strand break repair as central to the ageing-relatedness of DNA repair genes. Our work also showcases the use of protein interaction partners to improve accuracy in data mining methods and our approach could be applied to other ageing-related pathways.

Distinct slow and fast cortical theta dynamics in episodic memory retrieval.

Science.gov (United States)

Pastötter, Bernhard; Bäuml, Karl-Heinz T

2014-07-01

Brain oscillations in the theta frequency band (3-8 Hz) have been shown to be critically involved in human episodic memory retrieval. In prior work, both positive and negative relationships between cortical theta power and retrieval success have been reported. This study examined the hypothesis that slow and fast cortical theta oscillations at the edges of the traditional theta frequency band are differentially related to retrieval success. Scalp EEG was recorded in healthy human participants as they performed a cued-recall episodic memory task. Slow (~3 Hz) and fast (~7 Hz) theta oscillations at retrieval were examined as a function of whether an item was recalled or not and as a function of the items' output position at test. Recall success typically declines with output position, due to increases in interference level. The results showed that slow theta power was positively related but fast theta power was negatively related to retrieval success. Concurrent positive and negative episodic memory effects for slow and fast theta oscillations were dissociable in time and space, showing different time courses and different spatial locations on the scalp. Moreover, fast theta power increased from early to late output positions, whereas slow theta power was unaffected by items' output position. Together with prior work, the results suggest that slow and fast theta oscillations have distinct functional roles in episodic memory retrieval, with slow theta oscillations being related to processes of recollection and conscious awareness, and fast theta oscillations being linked to processes of interference and interference resolution. Copyright © 2014 Elsevier Inc. All rights reserved.

Expression of isgylation related genes in regenerating rat liver

Directory of Open Access Journals (Sweden)

Kuklin A. V.

2015-10-01

Full Text Available Our recent studies have revealed the early up-regulated expression of interferon alpha (IFNα in the liver, induced by partial hepatectomy. The role of this cytokine of innate immune response in liver regeneration is still controversial. Aim. To analyze expression of canonical interferon-stimulated genes Ube1l, Ube2l6, Trim25, Usp18 and Isg15 during the liver transition from quiescence to proliferation induced by partial hepatectomy, and acute phase response induced by laparotomy. These genes are responsible for posttranslational modification of proteins by ISGylation. The expression of genes encoding TATA binding protein (TBP and 18S rRNA served as indirect general markers of transcriptional and translational activities. Methods. The abundance of investigated RNAs was assessed in total liver RNA by real time RT–qPCR. Results. Partial hepatecomy induced steady upregulation of the Tbp and 18S rRNA genes expression during 12 hours post-surgery and downregulation or no change in expression of ISGylation-related genes during the first 3 hours followed by slight upregulation at 12 hours. The level of Isg15 transcripts was permanently below that of the control during the prereplicative period. Laparotomy induced a continuous downregulation of Tbp and 18S rRNA expression and early (1–3h upregulation of ISGylation–related transcripts followed by a sharp drop at 6 hours and slight increase/decrease at 12 hours. The changes in the abundance of Ifnα and ISGylation-related mRNAs were oppositely directed at each stage of the response to partial hepatectomy and laparotomy. Conclusion. We suggest that the expression of ISGylation-related genes does not depend on the expression of Ifnα gene after both surgeries. The indirect indices of transcription and translation as well as the expression of ISGylation-relaled genes are principally different in response to partial hepatectomy and laparotomy and argue for the high specificity of innate immune response.

Research progress on related genes for primary open angle glaucoma

Directory of Open Access Journals (Sweden)

Ailijiang·Aierken

2014-04-01

Full Text Available Primary open angle glaucoma(POAGis the main cause of blindness with visual field damage and optic nerve degeneration. In recent years, a lot of researches have been done, showing that genetic factors and gene mutation play an important role in POAG. There are more than 20 related POAG genes. Now we will review the related genes of POAG, especially the well known causative genes of MYOC, OPTN, WDR36, and CAV1/CAV2, in terms of their locations, structures, research progress, et al, and provide a reference for genetic research in primary open-angle glaucoma.

Divided Attention Improves Delayed, but Not Immediate Retrieval of a Consolidated Memory

OpenAIRE

Kessler, Yoav; Vandermorris, Susan; Gopie, Nigel; Daros, Alexander; Winocur, Gordon; Moscovitch, Morris

2014-01-01

A well-documented dissociation between memory encoding and retrieval concerns the role of attention in the two processes. The typical finding is that divided attention (DA) during encoding impairs future memory, but retrieval is relatively robust to attentional manipulations. However, memory research in the past 20 years had demonstrated that retrieval is a memory-changing process, in which the strength and availability of information are modified by various characteristics of the retrieval p...

ORFer--retrieval of protein sequences and open reading frames from GenBank and storage into relational databases or text files.

Science.gov (United States)

Büssow, Konrad; Hoffmann, Steve; Sievert, Volker

2002-12-19

Functional genomics involves the parallel experimentation with large sets of proteins. This requires management of large sets of open reading frames as a prerequisite of the cloning and recombinant expression of these proteins. A Java program was developed for retrieval of protein and nucleic acid sequences and annotations from NCBI GenBank, using the XML sequence format. Annotations retrieved by ORFer include sequence name, organism and also the completeness of the sequence. The program has a graphical user interface, although it can be used in a non-interactive mode. For protein sequences, the program also extracts the open reading frame sequence, if available, and checks its correct translation. ORFer accepts user input in the form of single or lists of GenBank GI identifiers or accession numbers. It can be used to extract complete sets of open reading frames and protein sequences from any kind of GenBank sequence entry, including complete genomes or chromosomes. Sequences are either stored with their features in a relational database or can be exported as text files in Fasta or tabulator delimited format. The ORFer program is freely available at http://www.proteinstrukturfabrik.de/orfer. The ORFer program allows for fast retrieval of DNA sequences, protein sequences and their open reading frames and sequence annotations from GenBank. Furthermore, storage of sequences and features in a relational database is supported. Such a database can supplement a laboratory information system (LIMS) with appropriate sequence information.

Polymorphism and methylation of the MC4R gene in obese and non-obese dogs.

Science.gov (United States)

Mankowska, Monika; Nowacka-Woszuk, Joanna; Graczyk, Aneta; Ciazynska, Paulina; Stachowiak, Monika; Switonski, Marek

2017-08-01

The dog is considered to be a useful biomedical model for human diseases and disorders, including obesity. One of the numerous genes associated with human polygenic obesity is MC4R, encoding the melanocortin 4 receptor. The aim of our study was to analyze polymorphisms and methylation of the canine MC4R in relation to adiposity. Altogether 270 dogs representing four breeds predisposed to obesity: Labrador Retriever (n = 187), Golden Retriever (n = 38), Beagle (n = 28) and Cocker Spaniel (n = 17), were studied. The dogs were classified into three groups: lean, overweight and obese, according to the 5-point Body Condition Score (BCS) scale. In the cohort of Labradors a complete phenotypic data (age, sex, neutering status, body weight and BCS) were collected for 127 dogs. The entire coding sequence as well as 5' and 3'-flanking regions of the studied gene were sequenced and six polymorphic sites were reported. Genotype frequencies differed considerably between breeds and Labrador Retrievers appeared to be the less polymorphic. Moreover, distribution of some polymorphic variants differed significantly (P C, c.868C>T and c.*33C>G) and Beagles (c.-435T>C and c.637G>T). On the contrary, in Labradors no association between the studied polymorphisms and BCS or body weight was observed. Methylation analysis, using bisulfite DNA conversion followed by Sanger sequencing, was carried out for 12 dogs with BCS = 3 and 12 dogs with BCS = 5. Two intragenic CpG islands, containing 19 cytosines, were analyzed and the methylation profile did not differ significantly between lean and obese animals. We conclude that an association of the MC4R gene polymorphism with dog obesity or body weight is unlikely, in spite of the fact that some associations were found in small cohorts of Beagles and Golden Retrievers. Also methylation level of this gene is not related with dog adiposity.

Microevolution of Virulence-Related Genes in Helicobacter pylori Familial Infection.

Directory of Open Access Journals (Sweden)

Yoshikazu Furuta

Full Text Available Helicobacter pylori, a bacterial pathogen that can infect human stomach causing gastritis, ulcers and cancer, is known to have a high degree of genome/epigenome diversity as the result of mutation and recombination. The bacteria often infect in childhood and persist for the life of the host. One of the reasons of the rapid evolution of H. pylori is that it changes its genome drastically for adaptation to a new host. To investigate microevolution and adaptation of the H. pylori genome, we undertook whole genome sequencing of the same or very similar sequence type in multi-locus sequence typing (MLST with seven genes in members of the same family consisting of parents and children in Japan. Detection of nucleotide substitutions revealed likely transmission pathways involving children. Nonsynonymous (amino acid changing mutations were found in virulence-related genes (cag genes, vacA, hcpDX, tnfα, ggt, htrA and the collagenase gene, outer membrane protein (OMP genes and other cell surface-related protein genes, signal transduction genes and restriction-modification genes. We reconstructed various pathways by which H. pylori can adapt to a new human host, and our results raised the possibility that the mutational changes in virulence-related genes have a role in adaptation to a child host. Changes in restriction-modification genes might remodel the methylome and transcriptome to help adaptation. This study has provided insights into H. pylori transmission and virulence and has implications for basic research as well as clinical practice.

Retrieval-induced forgetting and interference between cues: training a cue-outcome association attenuates retrieval by alternative cues.

Science.gov (United States)

Ortega-Castro, Nerea; Vadillo, Miguel A

2013-03-01

Some researchers have attempted to determine whether situations in which a single cue is paired with several outcomes (A-B, A-C interference or interference between outcomes) involve the same learning and retrieval mechanisms as situations in which several cues are paired with a single outcome (A-B, C-B interference or interference between cues). Interestingly, current research on a related effect, which is known as retrieval-induced forgetting, can illuminate this debate. Most retrieval-induced forgetting experiments are based on an experimental design that closely resembles the A-B, A-C interference paradigm. In the present experiment, we found that a similar effect may be observed when items are rearranged such that the general structure of the task more closely resembles the A-B, C-B interference paradigm. This result suggests that, as claimed by other researchers in the area of contingency learning, the two types of interference, namely A-B, A-C and A-B, C-B interference, may share some basic mechanisms. Moreover, the type of inhibitory processes assumed to underlie retrieval-induced forgetting may also play a role in these phenomena. Copyright © 2012 Elsevier B.V. All rights reserved.

Transcriptomic network analysis of micronuclei-related genes: a case study

DEFF Research Database (Denmark)

van Leeuwen, D. M.; Pedersen, Marie; Knudsen, Lisbeth E.

2011-01-01

checkpoint and aneuploidy. The MN-related gene network was tested against a transcriptomics case study associated with MN measurements. In this case study, transcriptomic data from children and adults differentially exposed to ambient air pollution in the Czech Republic were analysed and visualised......Mechanistically relevant information on responses of humans to xenobiotic exposure in relation to chemically induced biological effects, such as micronuclei (MN) formation can be obtained through large-scale transcriptomics studies. Network analysis may enhance the analysis and visualisation...... of such data. Therefore, this study aimed to develop a 'MN formation' network based on a priori knowledge, by using the pathway tool MetaCore. The gene network contained 27 genes and three gene complexes that are related to processes involved in MN formation, e.g. spindle assembly checkpoint, cell cycle...

Arousal—But Not Valence—Reduces False Memories at Retrieval

Science.gov (United States)

Mirandola, Chiara; Toffalini, Enrico

2016-01-01

Mood affects both memory accuracy and memory distortions. However, some aspects of this relation are still poorly understood: (1) whether valence and arousal equally affect false memory production, and (2) whether retrieval-related processes matter; the extant literature typically shows that mood influences memory performance when it is induced before encoding, leaving unsolved whether mood induced before retrieval also impacts memory. We examined how negative, positive, and neutral mood induced before retrieval affected inferential false memories and related subjective memory experiences. A recognition-memory paradigm for photographs depicting script-like events was employed. Results showed that individuals in both negative and positive moods–similar in arousal levels–correctly recognized more target events and endorsed fewer false memories (and these errors were linked to remember responses less frequently), compared to individuals in neutral mood. This suggests that arousal (but not valence) predicted memory performance; furthermore, we found that arousal ratings provided by participants were more adequate predictors of memory performance than their actual belonging to either positive, negative or neutral mood groups. These findings suggest that arousal has a primary role in affecting memory, and that mood exerts its power on true and false memory even when induced at retrieval. PMID:26938737

Arousal-But Not Valence-Reduces False Memories at Retrieval.

Directory of Open Access Journals (Sweden)

Chiara Mirandola

Full Text Available Mood affects both memory accuracy and memory distortions. However, some aspects of this relation are still poorly understood: (1 whether valence and arousal equally affect false memory production, and (2 whether retrieval-related processes matter; the extant literature typically shows that mood influences memory performance when it is induced before encoding, leaving unsolved whether mood induced before retrieval also impacts memory. We examined how negative, positive, and neutral mood induced before retrieval affected inferential false memories and related subjective memory experiences. A recognition-memory paradigm for photographs depicting script-like events was employed. Results showed that individuals in both negative and positive moods-similar in arousal levels-correctly recognized more target events and endorsed fewer false memories (and these errors were linked to remember responses less frequently, compared to individuals in neutral mood. This suggests that arousal (but not valence predicted memory performance; furthermore, we found that arousal ratings provided by participants were more adequate predictors of memory performance than their actual belonging to either positive, negative or neutral mood groups. These findings suggest that arousal has a primary role in affecting memory, and that mood exerts its power on true and false memory even when induced at retrieval.

Analogical reasoning and prefrontal cortex: evidence for separable retrieval and integration mechanisms.

Science.gov (United States)

Bunge, Silvia A; Wendelken, Carter; Badre, David; Wagner, Anthony D

2005-03-01

The present study examined the contributions of prefrontal cortex (PFC) subregions to two component processes underlying verbal analogical reasoning: semantic retrieval and integration. Event-related functional magnetic resonance imaging data were acquired while subjects performed propositional analogy and semantic decision tasks. On each trial, subjects viewed a pair of words (pair 1), followed by an instructional cue and a second word pair (pair 2). On analogy trials, subjects evaluated whether pair 2 was semantically analogous to pair 1. On semantic trials, subjects indicated whether the pair 2 words were semantically related to each other. Thus, analogy--but not semantic--trials required integration across multiple retrieved relations. To identify regions involved in semantic retrieval, we manipulated the associative strength of pair 1 words in both tasks. Anterior left inferior PFC (aLIPC) was modulated by associative strength, consistent with a role in controlled semantic retrieval. Left frontopolar cortex was insensitive to associative strength, but was more sensitive to integration demands than was aLIPC, consistent with a role in integrating the products of semantic retrieval to evaluate whether distinct representations are analogous. Right dorsolateral PFC exhibited a profile consistent with a role in response selection rather than retrieval or integration. These findings indicate that verbal analogical reasoning depends on multiple, PFC-mediated computations.

Can We Retrieve the Information Which Was Intentionally Forgotten? Electrophysiological Correlates of Strategic Retrieval in Directed Forgetting

Directory of Open Access Journals (Sweden)

Xinrui Mao

2017-08-01

Full Text Available Retrieval inhibition hypothesis of directed forgetting effects assumed TBF (to-be-forgotten items were not retrieved intentionally, while selective rehearsal hypothesis assumed the memory representation of retrieved TBF (to-be-forgotten items was weaker than TBR (to-be-remembered items. Previous studies indicated that directed forgetting effects of item-cueing method resulted from selective rehearsal at encoding, but the mechanism of retrieval inhibition that affected directed forgetting of TBF (to-be-forgotten items was not clear. Strategic retrieval is a control process allowing the selective retrieval of target information, which includes retrieval orientation and strategic recollection. Retrieval orientation via the comparison of tasks refers to the specific form of processing resulted by retrieval efforts. Strategic recollection is the type of strategies to recollect studied items for the retrieval success of targets. Using a “directed forgetting” paradigm combined with a memory exclusion task, our investigation of strategic retrieval in directed forgetting assisted to explore how retrieval inhibition played a role on directed forgetting effects. When TBF items were targeted, retrieval orientation showed more positive ERPs to new items, indicating that TBF items demanded more retrieval efforts. The results of strategic recollection indicated that: (a when TBR items were retrieval targets, late parietal old/new effects were only evoked by TBR items but not TBF items, indicating the retrieval inhibition of TBF items; (b when TBF items were retrieval targets, the late parietal old/new effect were evoked by both TBR items and TBF items, indicating that strategic retrieval could overcome retrieval inhibition of TBF items. These findings suggested the modulation of strategic retrieval on retrieval inhibition of directed forgetting, supporting that directed forgetting effects were not only caused by selective rehearsal, but also retrieval

Information retrieval models foundations and relationships

CERN Document Server

Roelleke, Thomas

2013-01-01

Information Retrieval (IR) models are a core component of IR research and IR systems. The past decade brought a consolidation of the family of IR models, which by 2000 consisted of relatively isolated views on TF-IDF (Term-Frequency times Inverse-Document-Frequency) as the weighting scheme in the vector-space model (VSM), the probabilistic relevance framework (PRF), the binary independence retrieval (BIR) model, BM25 (Best-Match Version 25, the main instantiation of the PRF/BIR), and language modelling (LM). Also, the early 2000s saw the arrival of divergence from randomness (DFR).Regarding in

Anxiety and retrieval inhibition: support for an enhanced inhibition account.

Science.gov (United States)

Nuñez, Mia; Gregory, Josh; Zinbarg, Richard E

2017-02-01

Retrieval inhibition of negative associations is important for exposure therapy for anxiety, but the relationship between memory inhibition and anxiety is not well understood-anxiety could either be associated with enhanced or deficient inhibition. The present study tested these two competing hypotheses by measuring retrieval inhibition of negative stimuli by related neutral stimuli. Non-clinically anxious undergraduates completed measures of trait and state anxiety and completed a retrieval induced forgetting task. Adaptive forgetting varied with state anxiety. Low levels of state anxiety were associated with no evidence for retrieval inhibition for either threatening or non-threatening categories. Participants in the middle tertile of state anxiety scores exhibited retrieval inhibition for non-threatening categories but not for threatening categories. Participants in the highest tertile of state anxiety, however, exhibited retrieval inhibition for both threatening and non-threatening categories with the magnitude of retrieval inhibition being greater for threatening than non-threatening categories. The data are in line with the avoidance aspect of the vigilance-avoidance theory of anxiety and inhibition. Implications for cognitive behavioural therapy practices are discussed.

Uncertainty Assessment of Space-Borne Passive Soil Moisture Retrievals

Science.gov (United States)

Quets, Jan; De Lannoy, Gabrielle; Reichle, Rolf; Cosh, Michael; van der Schalie, Robin; Wigneron, Jean-Pierre

2017-01-01

The uncertainty associated with passive soil moisture retrieval is hard to quantify, and known to be underlain by various, diverse, and complex causes. Factors affecting space-borne retrieved soil moisture estimation include: (i) the optimization or inversion method applied to the radiative transfer model (RTM), such as e.g. the Single Channel Algorithm (SCA), or the Land Parameter Retrieval Model (LPRM), (ii) the selection of the observed brightness temperatures (Tbs), e.g. polarization and incidence angle, (iii) the definition of the cost function and the impact of prior information in it, and (iv) the RTM parameterization (e.g. parameterizations officially used by the SMOS L2 and SMAP L2 retrieval products, ECMWF-based SMOS assimilation product, SMAP L4 assimilation product, and perturbations from those configurations). This study aims at disentangling the relative importance of the above-mentioned sources of uncertainty, by carrying out soil moisture retrieval experiments, using SMOS Tb observations in different settings, of which some are mentioned above. The ensemble uncertainties are evaluated at 11 reference CalVal sites, over a time period of more than 5 years. These experimental retrievals were inter-compared, and further confronted with in situ soil moisture measurements and operational SMOS L2 retrievals, using commonly used skill metrics to quantify the temporal uncertainty in the retrievals.

A Prototype of an Intelligent System for Information Retrieval: IOTA.

Science.gov (United States)

Chiaramella, Y.; Defude, B.

1987-01-01

Discusses expert systems and their value as components of information retrieval systems related to semantic inference, and describes IOTA, a model of an intelligent information retrieval system which emphasizes natural language query processing. Experimental results are discussed and current and future developments are highlighted. (Author/LRW)

Connectionist Interaction Information Retrieval.

Science.gov (United States)

Dominich, Sandor

2003-01-01

Discussion of connectionist views for adaptive clustering in information retrieval focuses on a connectionist clustering technique and activation spreading-based information retrieval model using the interaction information retrieval method. Presents theoretical as well as simulation results as regards computational complexity and includes…

Resistance-related gene transcription and antioxidant enzyme ...

African Journals Online (AJOL)

The two tobacco relatives of Nicotiana alata and Nicotiana longiflora display a high level of resistance against Colletotrichum nicotianae and the two genes NTF6 and NtPAL related to pathogen defense transcription were higher in N. alata and N. longiflora than the commercial cv. K326. Inoculation with C. nicotianae ...

Retrievable disposal - opposing views on ethics

International Nuclear Information System (INIS)

Selling, H.A.

2000-01-01

In the previous decades many research programmes on the disposal of radioactive waste have been completed in the Netherlands. The experts involved have reconfirmed their view that deep underground disposal in suitable geological formations would ensure a safe and prolonged isolation of the waste from the biosphere. Both rock salt and clay formations are considered to qualify as a suitable host rock. In 1993 the government in a position paper stated that such a repository should be designed in a way that the waste can be retrieved from it, should the need arise. In an attempt to involve stakeholders in the decision-making process, a research contract was awarded to an environmental group to study the ethical aspects related to retrievable disposal of radioactive waste. In their report which was published in its final form in January 2000 the authors concluded that retrievable disposal is acceptable from an ethical point of view. However, this conclusion was reached in the understanding that this situation of retrievability would be permanent. From the concept of equity between generations, each successive generation should be offered equal opportunities to decide for itself how to dispose of the radioactive waste. Consequently, the preferred disposal option is retrievable disposal (or long term storage) in a surface facility. Although this view is not in conformity with the ''official'' position on radioactive waste disposal, there is a benefit of having established a dialogue between interested parties in a broad sense. (author)

Introduction to information retrieval

CERN Document Server

Manning, Christopher D; Schütze, Hinrich

2008-01-01

Class-tested and coherent, this textbook teaches classical and web information retrieval, including web search and the related areas of text classification and text clustering from basic concepts. It gives an up-to-date treatment of all aspects of the design and implementation of systems for gathering, indexing, and searching documents; methods for evaluating systems; and an introduction to the use of machine learning methods on text collections. All the important ideas are explained using examples and figures, making it perfect for introductory courses in information retrieval for advanced undergraduates and graduate students in computer science. Based on feedback from extensive classroom experience, the book has been carefully structured in order to make teaching more natural and effective. Slides and additional exercises (with solutions for lecturers) are also available through the book's supporting website to help course instructors prepare their lectures.

Characterization of transformation related genes in oral cancer cells.

Science.gov (United States)

Chang, D D; Park, N H; Denny, C T; Nelson, S F; Pe, M

1998-04-16

A cDNA representational difference analysis (cDNA-RDA) and an arrayed filter technique were used to characterize transformation-related genes in oral cancer. From an initial comparison of normal oral epithelial cells and a human papilloma virus (HPV)-immortalized oral epithelial cell line, we obtained 384 differentially expressed gene fragments and arrayed them on a filter. Two hundred and twelve redundant clones were identified by three rounds of back hybridization. Sequence analysis of the remaining clones revealed 99 unique clones corresponding to 69 genes. The expression of these transformation related gene fragments in three nontumorigenic HPV-immortalized oral epithelial cell lines and three oral cancer cell lines were simultaneously monitored using a cDNA array hybridization. Although there was a considerable cell line-to-cell line variability in the expression of these clones, a reliable prediction of their expression could be made from the cDNA array hybridization. Our study demonstrates the utility of combining cDNA-RDA and arrayed filters in high-throughput gene expression difference analysis. The differentially expressed genes identified in this study should be informative in studying oral epithelial cell carcinogenesis.

Suppression of PCD-related genes affects salt tolerance in Arabidopsis.

Science.gov (United States)

Bahieldin, Ahmed; Alqarni, Dhafer A M; Atef, Ahmed; Gadalla, Nour O; Al-matary, Mohammed; Edris, Sherif; Al-Kordy, Magdy A; Makki, Rania M; Al-Doss, Abdullah A; Sabir, Jamal S M; Mutwakil, Mohammed H Z; El-Domyati, Fotouh M

2016-01-01

This work aims at examining a natural exciting phenomenon suggesting that suppression of genes inducing programmed cell death (PCD) might confer tolerance against abiotic stresses in plants. PCD-related genes were induced in tobacco under oxalic acid (OA) treatment (20 mM), and plant cells were characterized to confirm the incidence of PCD. The results indicated that PCD was triggered 24 h after the exposure to OA. Then, RNAs were extracted from tobacco cells 0, 2, 6, 12 and 24 h after treatment for deep sequencing. RNA-Seq analyses were done with a special emphasis to clusters whose PCD-related genes were upregulated after 2 h of OA exposure. Accordingly, 23 tobacco PCD-related genes were knocked down via virus-induced gene silencing (VIGS), whereas our results indicated the influence of five of them on inducing or suppressing PCD. Knockout T-DNA insertion mutants of these five genes in Arabidopsis were tested under salt stress (0, 100, 150, and 200 mM NaCl), and the results indicated that a mutant of an antiapoptotic gene, namely Bax Inhibitor-1 (BI-1), whose VIGS induced PCD in tobacco, was salt sensitive, while a mutant of an apoptotic gene, namely mildew resistance locus O (Mlo), whose VIGS suppressed PCD, was salt tolerant as compared to the WT (Col) control. These data support our hypothesis that retarding PCD-inducing genes can result in higher levels of salt tolerance, while retarding PCD-suppressing genes can result in lower levels of salt tolerance in plants. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

A BDNF sensitive mechanism is involved in the fear memory resulting from the interaction between stress and the retrieval of an established trace.

Science.gov (United States)

Giachero, Marcelo; Bustos, Silvia G; Calfa, Gaston; Molina, Victor A

2013-04-15

The present study investigates the fear memory resulting from the interaction of a stressful experience and the retrieval of an established fear memory trace. Such a combination enhanced both fear expression and fear retention in adult Wistar rats. Likewise, midazolam intra-basolateral amygdala (BLA) infusion prior to stress attenuated the enhancement of fear memory thus suggesting the involvement of a stress-induced reduction of the GABAergic transmission in BLA in the stress-induced enhancing effect. It has been suggested that, unlike the immediate-early gene Zif268 which is related to the reconsolidation process, the expression of hippocampal brain-derived neurotrophic factor (BDNF) is highly correlated with consolidation. We therefore evaluate the relative contribution of these two neurobiological processes to the fear memory resulting from the above-mentioned interaction. Intra-dorsal hippocampus (DH) infusions of either the antisense Zif268 or the inhibitor of the protein degradation (Clasto-Lactacystin β-Lactone), suggested to be involved in the retrieval-dependent destabilization process, did not affect the resulting contextual memory. In contrast, the knockdown of hippocampal BDNF mitigated the stress-induced facilitating influence on fear retention. In addition, the retrieval experience elevated BDNF level in DH at 60 min after recall exclusively in stressed animals. These findings suggest the involvement of a hippocampal BDNF sensitive mechanism in the stress-promoting influence on the fear memory following retrieval.

Patient and surgery related factors associated with fatigue type polyethylene wear on 49 PCA and DURACON retrievals at autopsy and revision

Directory of Open Access Journals (Sweden)

Ochsner Peter E

2008-02-01

Full Text Available Abstract Background Polyethylene wear is an important factor for longevity of total knee arthroplasty. Proven and suspicious factors causing wear can be grouped as material, patient and surgery related. There are more studies correlating design and/or biomaterial factors to in vivo wear than those to patient and surgery related factors. Many retrieval studies just include revision implants and therefore may not be representative. This study is aimed to correlate patient- and surgery- related factors to visual wear score by minimizing design influence and include both autopsy and revision implants. Comparison between the groups was expected to unmask patient and surgery-related factors responsible for wear. Methods The amount of joint side wear on polyethylene retrievals was measured using a modification of an established visual wear score. Fatigue type wear was defined as summation of the most severe wear modes of delamination, pitting and cracks. Analysis of patient and surgery related variables suspicious to cause wear included prospectively sampled patient activity which was measured by self reported walking capacity. Statistical analysis was done by univariate analysis of variance. Activity level and implantation time were merged to an index of use and correlated to the wear score. Results Wear score after comparable implantation time was significantly less in the autopsy group. Even so, fatigue type wear accounted for 84 and 93 % of total wear score on autopsy and revision implants respectively. A highly significant influence on wear score was found in time of implantation (p = 0.002, level of activity (p = 0.025 and inserts belonging to revision group (p = 0.006. No influence was found for the kind of patella replacement (p = 0.483. Body mass index and accuracy of component alignment had no significant influence on visual wear score. Fatigue-type wear in the medial compartment was closely correlated to the index of use in the autopsy (R2

Beyond information retrieval: information discovery and multimedia information retrieval

OpenAIRE

Roberto Raieli

2017-01-01

The paper compares the current methodologies for search and discovery of information and information resources: terminological search and term-based language, own of information retrieval (IR); semantic search and information discovery, being developed mainly through the language of linked data; semiotic search and content-based language, experienced by multimedia information retrieval (MIR).MIR semiotic methodology is, then, detailed.

AP-102/104 Retrieval control system qualification test procedure

International Nuclear Information System (INIS)

RIECK, C.A.

1999-01-01

This Qualification Test Procedure documents the results of the qualification testing that was performed on the Project W-211, ''Initial Tank Retrieval Systems,'' retrieval control system (RCS) for tanks 241-AP-102 and 241-AP-104. The results confirm that the RCS has been programmed correctly and that the two related hardware enclosures have been assembled in accordance with the design documents

Dissecting Time- from Tumor-Related Gene Expression Variability in Bilateral Breast Cancer

Directory of Open Access Journals (Sweden)

Maurizio Callari

2018-01-01

Full Text Available Metachronous (MBC and synchronous bilateral breast tumors (SBC are mostly distinct primaries, whereas paired primaries and their local recurrences (LRC share a common origin. Intra-pair gene expression variability in MBC, SBC, and LRC derives from time/tumor microenvironment-related and tumor genetic background-related factors and pairs represents an ideal model for trying to dissect tumor-related from microenvironment-related variability. Pairs of tumors derived from women with SBC (n = 18, MBC (n = 11, and LRC (n = 10 undergoing local-regional treatment were profiled for gene expression; similarity between pairs was measured using an intraclass correlation coefficient (ICC computed for each gene and compared using analysis of variance (ANOVA. When considering biologically unselected genes, the highest correlations were found for primaries and paired LRC, and the lowest for MBC pairs. By instead limiting the analysis to the breast cancer intrinsic genes, correlations between primaries and paired LRC were enhanced, while lower similarities were observed for SBC and MBC. Focusing on stromal-related genes, the ICC values decreased for MBC and were significantly different from SBC. These findings indicate that it is possible to dissect intra-pair gene expression variability into components that are associated with genetic origin or with time and microenvironment by using specific gene subsets.

Molecular cloning of allelopathy related genes and their relation to HHO in Eupatorium adenophorum.

Science.gov (United States)

Guo, Huiming; Pei, Xixiang; Wan, Fanghao; Cheng, Hongmei

2011-10-01

In this study, conserved sequence regions of HMGR, DXR, and CHS (encoding 3-hydroxy-3-methylglutaryl-CoA reductase, 1-deoxyxylulose-5-phosphate reductoisomerase and chalcone synthase, respectively) were amplified by reverse transcriptase (RT)-PCR from Eupatorium adenophorum. Quantitative real-time PCR showed that the expression of CHS was related to the level of HHO, an allelochemical isolated from E. adenophorum. Semi-quantitative RT-PCR showed that there was no significant difference in expression of genes among three different tissues, except for CHS. Southern blotting indicated that at least three CHS genes are present in the E. adenophorum genome. A full-length cDNA from CHS genes (named EaCHS1, GenBank ID: FJ913888) was cloned. The 1,455 bp cDNA contained an open reading frame (1,206 bp) encoding a protein of 401 amino acids. Preliminary bioinformatics analysis of EaCHS1 revealed that EaCHS1 was a member of CHS family, the subcellular localization predicted that EaCHS1 was a cytoplasmic protein. To the best of our knowledge, this is the first report of conserved sequences of these genes and of a full-length EaCHS1 gene in E. adenophorum. The results indicated that CHS gene is related to allelopathy of E. adenophorum.

Monetary incentives at retrieval promote recognition of involuntarily learned emotional information.

Science.gov (United States)

Yan, Chunping; Li, Yunyun; Zhang, Qin; Cui, Lixia

2018-03-07

Previous studies have suggested that the effects of reward on memory processes are affected by certain factors, but it remains unclear whether the effects of reward at retrieval on recognition processes are influenced by emotion. The event-related potential was used to investigate the combined effect of reward and emotion on memory retrieval and its neural mechanism. The behavioral results indicated that the reward at retrieval improved recognition performance under positive and negative emotional conditions. The event-related potential results indicated that there were significant interactions between the reward and emotion in the average amplitude during recognition, and the significant reward effects from the frontal to parietal brain areas appeared at 130-800 ms for positive pictures and at 190-800 ms for negative pictures, but there were no significant reward effects of neutral pictures; the reward effect of positive items appeared relatively earlier, starting at 130 ms, and that of negative pictures began at 190 ms. These results indicate that monetary incentives at retrieval promote recognition of involuntarily learned emotional information.

Geological Disposal of Radioactive Waste: Technological Implications for Retrievability

International Nuclear Information System (INIS)

2009-01-01

Various IAEA Member States are discussing whether and to what degree reversibility (including retrievability) might be built into management strategies for radioactive waste. This is particularly the case in relation to the disposal of long lived and/or high level waste and spent nuclear fuel (SNF) in geological repositories. It is generally accepted that such repositories should be designed to be passively safe with no intention of retrieving the waste. Nevertheless, various reasons have been advanced for including the concept of reversibility and the ability to retrieve the emplaced wastes in the disposal strategy. The intention is to increase the level of flexibility and to provide the ability to cope with, or to benefit from, new technical advances in waste management and materials technologies, and to respond to changing social, economic and political opinion. The technological implications of retrievability in geological disposal concepts are explored in this report. Scenarios for retrieving emplaced waste packages are considered and the report aims to identify and describe any related technological provisions that should be incorporated into the design, construction, operational and closure phases of the repository. This is based on a number of reference concepts for the geological disposal of radioactive waste (including SNF) which are currently being developed in Member States with advanced development programmes. The report begins with a brief overview of various repository concepts, starting with a summary of the types of radioactive waste that are typically considered for deep geological disposal. The main host rocks considered are igneous crystalline and volcanic rocks, argillaceous clay rocks and salts. The typical design features of repositories are provided with a description of repository layouts, an overview of the key features of the major repository components, comprising the waste package, the emplacement cells and repository access facilities

Electronic publishing and intelligent information retrieval

Science.gov (United States)

Heck, A.

1992-01-01

Europeans are now taking steps to homogenize policies and standardize procedures in electronic publishing (EP) in astronomy and space sciences. This arose from an open meeting organized in Oct. 1991 at Strasbourg Observatory (France) and another business meeting held late Mar. 1992 with the major publishers and journal editors in astronomy and space sciences. The ultimate aim of EP might be considered as the so-called 'intelligent information retrieval' (IIR) or better named 'advanced information retrieval' (AIR), taking advantage of the fact that the material to be published appears at some stage in a machine-readable form. It is obvious that the combination of desktop and electronic publishing with networking and new structuring of knowledge bases will profoundly reshape not only our ways of publishing, but also our procedures of communicating and retrieving information. It should be noted that a world-wide survey among astronomers and space scientists carried out before the October 1991 colloquium on the various packages and machines used, indicated that TEX-related packages were already in majoritarian use in our community. It has also been stressed at each meeting that the European developments should be carried out in collaboration with what is done in the US (STELLAR project, for instance). American scientists and journal editors actually attended both meetings mentioned above. The paper will offer a review of the status of electronic publishing in astronomy and its possible contribution to advanced information retrieval in this field. It will also report on recent meetings such as the 'Astronomy from Large Databases-2 (ALD-2)' conference dealing with the latest developments in networking, in data, information, and knowledge bases, as well as in the related methodologies.

Electrophysiological correlates of competitor activation predict retrieval-induced forgetting.

Science.gov (United States)

Hellerstedt, Robin; Johansson, Mikael

2014-06-01

The very act of retrieval modifies the accessibility of memory for knowledge and past events and can also cause forgetting. A prominent theory of such retrieval-induced forgetting (RIF) holds that retrieval recruits inhibition to overcome interference from competing memories, rendering these memories inaccessible. The present study tested a fundamental tenet of the inhibitory-control account: The competition-dependence assumption. Event-related potentials (ERPs) were recorded while participants engaged in a competitive retrieval task. Competition levels were manipulated within the retrieval task by varying the cue-item associative strength of competing items. In order to temporally separate ERP correlates of competitor activation and target retrieval, memory was probed with the sequential presentation of 2 cues: A category cue, to reactivate competitors, and a target cue. As predicted by the inhibitory-control account, competitors with strong compared with weak cue-competitor association were more susceptible to forgetting. Furthermore, competition-sensitive ERP modulations, elicited by the category cue, were observed over anterior regions and reflected individual differences in ensuing forgetting. The present study demonstrates ERP correlates of the reactivation of tightly bound associated memories (the competitors) and provides support for the inhibitory-control account of RIF.

Retrieval practice with short-answer, multiple-choice, and hybrid tests.

Science.gov (United States)

Smith, Megan A; Karpicke, Jeffrey D

2014-01-01

Retrieval practice improves meaningful learning, and the most frequent way of implementing retrieval practice in classrooms is to have students answer questions. In four experiments (N=372) we investigated the effects of different question formats on learning. Students read educational texts and practised retrieval by answering short-answer, multiple-choice, or hybrid questions. In hybrid conditions students first attempted to recall answers in short-answer format, then identified answers in multiple-choice format. We measured learning 1 week later using a final assessment with two types of questions: those that could be answered by recalling information verbatim from the texts and those that required inferences. Practising retrieval in all format conditions enhanced retention, relative to a study-only control condition, on both verbatim and inference questions. However, there were little or no advantages of answering short-answer or hybrid format questions over multiple-choice questions in three experiments. In Experiment 4, when retrieval success was improved under initial short-answer conditions, there was an advantage of answering short-answer or hybrid questions over multiple-choice questions. The results challenge the simple conclusion that short-answer questions always produce the best learning, due to increased retrieval effort or difficulty, and demonstrate the importance of retrieval success for retrieval-based learning activities.

Parsimonious Language Models for Information Retrieval

NARCIS (Netherlands)

Hiemstra, Djoerd; Robertson, Stephen; Zaragoza, Hugo

We systematically investigate a new approach to estimating the parameters of language models for information retrieval, called parsimonious language models. Parsimonious language models explicitly address the relation between levels of language models that are typically used for smoothing. As such,

Retrieval practice enhances the accessibility but not the quality of memory.

Science.gov (United States)

Sutterer, David W; Awh, Edward

2016-06-01

Numerous studies have demonstrated that retrieval from long-term memory (LTM) can enhance subsequent memory performance, a phenomenon labeled the retrieval practice effect. However, the almost exclusive reliance on categorical stimuli in this literature leaves open a basic question about the nature of this improvement in memory performance. It has not yet been determined whether retrieval practice improves the probability of successful memory retrieval or the quality of the retrieved representation. To answer this question, we conducted three experiments using a mixture modeling approach (Zhang & Luck, 2008) that provides a measure of both the probability of recall and the quality of the recalled memories. Subjects attempted to memorize the color of 400 unique shapes. After every 10 images were presented, subjects either recalled the last 10 colors (the retrieval practice condition) by clicking on a color wheel with each shape as a retrieval cue or they participated in a control condition that involved no further presentations (Experiment 1) or restudy of the 10 shape/color associations (Experiments 2 and 3). Performance in a subsequent delayed recall test revealed a robust retrieval practice effect. Subjects recalled a significantly higher proportion of items that they had previously retrieved relative to items that were untested or that they had restudied. Interestingly, retrieval practice did not elicit any improvement in the precision of the retrieved memories. The same empirical pattern also was observed following delays of greater than 24 hours. Thus, retrieval practice increases the probability of successful memory retrieval but does not improve memory quality.

Physically-Retrieving Cloud and Thermodynamic Parameters from Ultraspectral IR Measurements

Science.gov (United States)

Zhou, Daniel K.; Smith, William L., Sr.; Liu, Xu; Larar, Allen M.; Mango, Stephen A.; Huang, Hung-Lung

2007-01-01

A physical inversion scheme has been developed, dealing with cloudy as well as cloud-free radiance observed with ultraspectral infrared sounders, to simultaneously retrieve surface, atmospheric thermodynamic, and cloud microphysical parameters. A fast radiative transfer model, which applies to the clouded atmosphere, is used for atmospheric profile and cloud parameter retrieval. A one-dimensional (1-d) variational multi-variable inversion solution is used to improve an iterative background state defined by an eigenvector-regression-retrieval. The solution is iterated in order to account for non-linearity in the 1-d variational solution. It is shown that relatively accurate temperature and moisture retrievals can be achieved below optically thin clouds. For optically thick clouds, accurate temperature and moisture profiles down to cloud top level are obtained. For both optically thin and thick cloud situations, the cloud top height can be retrieved with relatively high accuracy (i.e., error < 1 km). NPOESS Airborne Sounder Testbed Interferometer (NAST-I) retrievals from the Atlantic-THORPEX Regional Campaign are compared with coincident observations obtained from dropsondes and the nadir-pointing Cloud Physics Lidar (CPL). This work was motivated by the need to obtain solutions for atmospheric soundings from infrared radiances observed for every individual field of view, regardless of cloud cover, from future ultraspectral geostationary satellite sounding instruments, such as the Geosynchronous Imaging Fourier Transform Spectrometer (GIFTS) and the Hyperspectral Environmental Suite (HES). However, this retrieval approach can also be applied to the ultraspectral sounding instruments to fly on Polar satellites, such as the Infrared Atmospheric Sounding Interferometer (IASI) on the European MetOp satellite, the Cross-track Infrared Sounder (CrIS) on the NPOESS Preparatory Project and the following NPOESS series of satellites.

A hybrid computational method for the discovery of novel reproduction-related genes.

Science.gov (United States)

Chen, Lei; Chu, Chen; Kong, Xiangyin; Huang, Guohua; Huang, Tao; Cai, Yu-Dong

2015-01-01

Uncovering the molecular mechanisms underlying reproduction is of great importance to infertility treatment and to the generation of healthy offspring. In this study, we discovered novel reproduction-related genes with a hybrid computational method, integrating three different types of method, which offered new clues for further reproduction research. This method was first executed on a weighted graph, constructed based on known protein-protein interactions, to search the shortest paths connecting any two known reproduction-related genes. Genes occurring in these paths were deemed to have a special relationship with reproduction. These newly discovered genes were filtered with a randomization test. Then, the remaining genes were further selected according to their associations with known reproduction-related genes measured by protein-protein interaction score and alignment score obtained by BLAST. The in-depth analysis of the high confidence novel reproduction genes revealed hidden mechanisms of reproduction and provided guidelines for further experimental validations.

Identifying and Analyzing Novel Epilepsy-Related Genes Using Random Walk with Restart Algorithm

Directory of Open Access Journals (Sweden)

Wei Guo

2017-01-01

Full Text Available As a pathological condition, epilepsy is caused by abnormal neuronal discharge in brain which will temporarily disrupt the cerebral functions. Epilepsy is a chronic disease which occurs in all ages and would seriously affect patients’ personal lives. Thus, it is highly required to develop effective medicines or instruments to treat the disease. Identifying epilepsy-related genes is essential in order to understand and treat the disease because the corresponding proteins encoded by the epilepsy-related genes are candidates of the potential drug targets. In this study, a pioneering computational workflow was proposed to predict novel epilepsy-related genes using the random walk with restart (RWR algorithm. As reported in the literature RWR algorithm often produces a number of false positive genes, and in this study a permutation test and functional association tests were implemented to filter the genes identified by RWR algorithm, which greatly reduce the number of suspected genes and result in only thirty-three novel epilepsy genes. Finally, these novel genes were analyzed based upon some recently published literatures. Our findings implicate that all novel genes were closely related to epilepsy. It is believed that the proposed workflow can also be applied to identify genes related to other diseases and deepen our understanding of the mechanisms of these diseases.

Replicon-dependent differentiation of symbiosis-related genes in Sinorhizobium strains nodulating Glycine max.

Science.gov (United States)

Guo, Hui Juan; Wang, En Tao; Zhang, Xing Xing; Li, Qin Qin; Zhang, Yan Ming; Tian, Chang Fu; Chen, Wen Xin

2014-02-01

In order to investigate the genetic differentiation of Sinorhizobium strains nodulating Glycine max and related microevolutionary mechanisms, three housekeeping genes (SMc00019, truA, and thrA) and 16 symbiosis-related genes on the chromosome (7 genes), pSymA (6 genes), and pSymB (3 genes) were analyzed. Five distinct species were identified among the test strains by calculating the average nucleotide identity (ANI) of SMc00019-truA-thrA: Sinorhizobium fredii, Sinorhizobium sojae, Sinorhizobium sp. I, Sinorhizobium sp. II, and Sinorhizobium sp. III. These species assignments were also supported by population genetics and phylogenetic analyses of housekeeping genes and symbiosis-related genes on the chromosome and pSymB. Different levels of genetic differentiation were observed among these species or different replicons. S. sojae was the most divergent from the other test species and was characterized by its low intraspecies diversity and limited geographic distribution. Intergenic recombination dominated the evolution of 19 genes from different replicons. Intraspecies recombination happened frequently in housekeeping genes and symbiosis-related genes on the chromosome and pSymB, whereas pSymA genes showed a clear pattern of lateral-transfer events between different species. Moreover, pSymA genes were characterized by a lower level of polymorphism and recombination than those on the chromosome and pSymB. Taken together, genes from different replicons of rhizobia might be involved in the establishment of symbiosis with legumes, but these symbiosis-related genes might have evolved differently according to their corresponding replicons.

Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span

Directory of Open Access Journals (Sweden)

Jordan MI

2006-05-01

Full Text Available Abstract Background The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caenorhabditis Genetic Center (CGC Bibliography using techniques from statistical information retrieval. Items in the CGC biomedical text corpus were modeled using the Latent Dirichlet Allocation (LDA model. LDA is a hierarchical Bayesian model which represents a document as a random mixture over latent topics; each topic is characterized by a distribution over words. Results An LDA model estimated from CGC items had better predictive performance than two standard models (unigram and mixture of unigrams trained using the same data. To illustrate the practical utility of LDA models of biomedical corpora, a trained CGC LDA model was used for a retrospective study of nematode genes known to be associated with life span modification. Corpus-, document-, and word-level LDA parameters were combined with terms from the Gene Ontology to enhance the explanatory value of the CGC LDA model, and to suggest additional candidates for age-related genes. A novel, pairwise document similarity measure based on the posterior distribution on the topic simplex was formulated and used to search the CGC database for "homologs" of a "query" document discussing the life span-modifying clk-2 gene. Inspection of these document homologs enabled and facilitated the production of hypotheses about the function and role of clk-2. Conclusion Like other graphical models for genetic, genomic and other types of biological data, LDA provides a method for extracting unanticipated insights and generating predictions amenable to subsequent experimental validation.

Encoding and Retrieval Interference in Sentence Comprehension: Evidence from Agreement

Directory of Open Access Journals (Sweden)

Sandra Villata

2018-01-01

Full Text Available Long-distance verb-argument dependencies generally require the integration of a fronted argument when the verb is encountered for sentence interpretation. Under a parsing model that handles long-distance dependencies through a cue-based retrieval mechanism, retrieval is hampered when retrieval cues also resonate with non-target elements (retrieval interference. However, similarity-based interference may also stem from interference arising during the encoding of elements in memory (encoding interference, an effect that is not directly accountable for by a cue-based retrieval mechanism. Although encoding and retrieval interference are clearly distinct at the theoretical level, it is difficult to disentangle the two on empirical grounds, since encoding interference may also manifest at the retrieval region. We report two self-paced reading experiments aimed at teasing apart the role of each component in gender and number subject-verb agreement in Italian and English object relative clauses. In Italian, the verb does not agree in gender with the subject, thus providing no cue for retrieval. In English, although present tense verbs agree in number with the subject, past tense verbs do not, allowing us to test the role of number as a retrieval cue within the same language. Results from both experiments converge, showing similarity-based interference at encoding, and some evidence for an effect at retrieval. After having pointed out the non-negligible role of encoding in sentence comprehension, and noting that Lewis and Vasishth’s (2005 ACT-R model of sentence processing, the most fully developed cue-based retrieval approach to sentence processing does not predict encoding effects, we propose an augmentation of this model that predicts these effects. We then also propose a self-organizing sentence processing model (SOSP, which has the advantage of accounting for retrieval and encoding interference with a single mechanism.

Encoding and Retrieval Interference in Sentence Comprehension: Evidence from Agreement

Science.gov (United States)

Villata, Sandra; Tabor, Whitney; Franck, Julie

2018-01-01

Long-distance verb-argument dependencies generally require the integration of a fronted argument when the verb is encountered for sentence interpretation. Under a parsing model that handles long-distance dependencies through a cue-based retrieval mechanism, retrieval is hampered when retrieval cues also resonate with non-target elements (retrieval interference). However, similarity-based interference may also stem from interference arising during the encoding of elements in memory (encoding interference), an effect that is not directly accountable for by a cue-based retrieval mechanism. Although encoding and retrieval interference are clearly distinct at the theoretical level, it is difficult to disentangle the two on empirical grounds, since encoding interference may also manifest at the retrieval region. We report two self-paced reading experiments aimed at teasing apart the role of each component in gender and number subject-verb agreement in Italian and English object relative clauses. In Italian, the verb does not agree in gender with the subject, thus providing no cue for retrieval. In English, although present tense verbs agree in number with the subject, past tense verbs do not, allowing us to test the role of number as a retrieval cue within the same language. Results from both experiments converge, showing similarity-based interference at encoding, and some evidence for an effect at retrieval. After having pointed out the non-negligible role of encoding in sentence comprehension, and noting that Lewis and Vasishth’s (2005) ACT-R model of sentence processing, the most fully developed cue-based retrieval approach to sentence processing does not predict encoding effects, we propose an augmentation of this model that predicts these effects. We then also propose a self-organizing sentence processing model (SOSP), which has the advantage of accounting for retrieval and encoding interference with a single mechanism. PMID:29403414

Citrus plastid-related gene profiling based on expressed sequence tag analyses

Directory of Open Access Journals (Sweden)

Tercilio Calsa Jr.

2007-01-01

Full Text Available Plastid-related sequences, derived from putative nuclear or plastome genes, were searched in a large collection of expressed sequence tags (ESTs and genomic sequences from the Citrus Biotechnology initiative in Brazil. The identified putative Citrus chloroplast gene sequences were compared to those from Arabidopsis, Eucalyptus and Pinus. Differential expression profiling for plastid-directed nuclear-encoded proteins and photosynthesis-related gene expression variation between Citrus sinensis and Citrus reticulata, when inoculated or not with Xylella fastidiosa, were also analyzed. Presumed Citrus plastome regions were more similar to Eucalyptus. Some putative genes appeared to be preferentially expressed in vegetative tissues (leaves and bark or in reproductive organs (flowers and fruits. Genes preferentially expressed in fruit and flower may be associated with hypothetical physiological functions. Expression pattern clustering analysis suggested that photosynthesis- and carbon fixation-related genes appeared to be up- or down-regulated in a resistant or susceptible Citrus species after Xylella inoculation in comparison to non-infected controls, generating novel information which may be helpful to develop novel genetic manipulation strategies to control Citrus variegated chlorosis (CVC.

Interactions among emotional attention, encoding, and retrieval of ambiguous information: An eye-tracking study.

Science.gov (United States)

Everaert, Jonas; Koster, Ernst H W

2015-10-01

Emotional biases in attention modulate encoding of emotional material into long-term memory, but little is known about the role of such attentional biases during emotional memory retrieval. The present study investigated how emotional biases in memory are related to attentional allocation during retrieval. Forty-nine individuals encoded emotionally positive and negative meanings derived from ambiguous information and then searched their memory for encoded meanings in response to a set of retrieval cues. The remember/know/new procedure was used to classify memories as recollection-based or familiarity-based, and gaze behavior was monitored throughout the task to measure attentional allocation. We found that a bias in sustained attention during recollection-based, but not familiarity-based, retrieval predicted subsequent memory bias toward positive versus negative material following encoding. Thus, during emotional memory retrieval, attention affects controlled forms of retrieval (i.e., recollection) but does not modulate relatively automatic, familiarity-based retrieval. These findings enhance understanding of how distinct components of attention regulate the emotional content of memories. Implications for theoretical models and emotion regulation are discussed. (c) 2015 APA, all rights reserved).

Bioinformatics analysis of breast cancer bone metastasis related gene-CXCR4

Institute of Scientific and Technical Information of China (English)

Heng-Wei Zhang; Xian-Fu Sun; Ya-Ning He; Jun-Tao Li; Xu-Hui Guo; Hui Liu

2013-01-01

Objective: To analyze breast cancer bone metastasis related gene-CXCR4. Methods: This research screened breast cancer bone metastasis related genes by high-flux gene chip. Results:It was found that the expressions of 396 genes were different including 165 up-regulations and 231 down-regulations. The expression of chemokine receptor CXCR4 was obviously up-regulated in the tissue with breast cancer bone metastasis. Compared with the tissue without bone metastasis, there was significant difference, which indicated that CXCR4 played a vital role in breast cancer bone metastasis. Conclusions: The bioinformatics analysis of CXCR4 can provide a certain basis for the occurrence and diagnosis of breast cancer bone metastasis, target gene therapy and evaluation of prognosis.

Retrieval of Legal Information Through Discovery Layers: A Case Study Related to Indian Law Libraries

Directory of Open Access Journals (Sweden)

Kushwah, Shivpal Singh

2016-09-01

Full Text Available Purpose. The purpose of this paper is to analyze and evaluate discovery layer search tools for retrieval of legal information in Indian law libraries. This paper covers current practices in legal information retrieval with special reference to Indian academic law libraries, and analyses its importance in the domain of law.Design/Methodology/Approach. A web survey and observational study method are used to collect the data. Data related to the discovery tools were collected using email and further discussion held with the discovery layer/ tool /product developers and their representatives.Findings. Results show that most of the Indian law libraries are subscribing to bundles of legal information resources such as Hein Online, JSTOR, LexisNexis Academic, Manupatra, Westlaw India, SCC web, AIR Online (CDROM, and so on. International legal and academic resources are compatible with discovery tools because they support various standards related to online publishing and dissemination such as OAI/PMH, Open URL, MARC21, and Z39.50, but Indian legal resources such as Manupatra, Air, and SCC are not compatible with the discovery layers. The central index is one of the important components in a discovery search interface, and discovery layer services/tools could be useful for Indian law libraries also if they can include multiple legal and academic resources in their central index. But present practices and observations reveal that discovery layers are not providing facility to cover legal information resources. Therefore, in the present form, discovery tools are not very useful; they are an incomplete and half solution for Indian libraries because all available Indian legal resources available in the law libraries are not covered.Originality/Value. Very limited research or published literature is available in the area of discovery layers and their compatibility with legal information resources.

A COLQ missense mutation in Labrador Retrievers having congenital myasthenic syndrome.

Directory of Open Access Journals (Sweden)

Caitlin J Rinz

Full Text Available Congenital myasthenic syndromes (CMSs are heterogeneous neuromuscular disorders characterized by skeletal muscle weakness caused by disruption of signal transmission across the neuromuscular junction (NMJ. CMSs are rarely encountered in veterinary medicine, and causative mutations have only been identified in Old Danish Pointing Dogs and Brahman cattle to date. Herein, we characterize a novel CMS in 2 Labrador Retriever littermates with an early onset of marked generalized muscle weakness. Because the sire and dam share 2 recent common ancestors, CMS is likely the result of recessive alleles inherited identical by descent (IBD. Genome-wide SNP profiles generated from the Illumina HD array for 9 nuclear family members were used to determine genomic inheritance patterns in chromosomal regions encompassing 18 functional candidate genes. SNP haplotypes spanning 3 genes were consistent with autosomal recessive transmission, and microsatellite data showed that only the segment encompassing COLQ was inherited IBD. COLQ encodes the collagenous tail of acetylcholinesterase, the enzyme responsible for termination of signal transduction in the NMJ. Sequences from COLQ revealed a variant in exon 14 (c.1010T>C that results in the substitution of a conserved amino acid (I337T within the C-terminal domain. Both affected puppies were homozygous for this variant, and 16 relatives were heterozygous, while 288 unrelated Labrador Retrievers and 112 dogs of other breeds were wild-type. A recent study in which 2 human CMS patients were found to be homozygous for an identical COLQ mutation (c.1010T>C; I337T provides further evidence that this mutation is pathogenic. This report describes the first COLQ mutation in canine CMS and demonstrates the utility of SNP profiles from nuclear family members for the identification of private mutations.

Ontology-based Brucella vaccine literature indexing and systematic analysis of gene-vaccine association network

Science.gov (United States)

2011-01-01

Background Vaccine literature indexing is poorly performed in PubMed due to limited hierarchy of Medical Subject Headings (MeSH) annotation in the vaccine field. Vaccine Ontology (VO) is a community-based biomedical ontology that represents various vaccines and their relations. SciMiner is an in-house literature mining system that supports literature indexing and gene name tagging. We hypothesize that application of VO in SciMiner will aid vaccine literature indexing and mining of vaccine-gene interaction networks. As a test case, we have examined vaccines for Brucella, the causative agent of brucellosis in humans and animals. Results The VO-based SciMiner (VO-SciMiner) was developed to incorporate a total of 67 Brucella vaccine terms. A set of rules for term expansion of VO terms were learned from training data, consisting of 90 biomedical articles related to Brucella vaccine terms. VO-SciMiner demonstrated high recall (91%) and precision (99%) from testing a separate set of 100 manually selected biomedical articles. VO-SciMiner indexing exhibited superior performance in retrieving Brucella vaccine-related papers over that obtained with MeSH-based PubMed literature search. For example, a VO-SciMiner search of "live attenuated Brucella vaccine" returned 922 hits as of April 20, 2011, while a PubMed search of the same query resulted in only 74 hits. Using the abstracts of 14,947 Brucella-related papers, VO-SciMiner identified 140 Brucella genes associated with Brucella vaccines. These genes included known protective antigens, virulence factors, and genes closely related to Brucella vaccines. These VO-interacting Brucella genes were significantly over-represented in biological functional categories, including metabolite transport and metabolism, replication and repair, cell wall biogenesis, intracellular trafficking and secretion, posttranslational modification, and chaperones. Furthermore, a comprehensive interaction network of Brucella vaccines and genes were

Automated Medical Literature Retrieval

Directory of Open Access Journals (Sweden)

David Hawking

2012-09-01

Full Text Available Background The constantly growing publication rate of medical research articles puts increasing pressure on medical specialists who need to be aware of the recent developments in their field. The currently used literature retrieval systems allow researchers to find specific papers; however the search task is still repetitive and time-consuming. Aims In this paper we describe a system that retrieves medical publications by automatically generating queries based on data from an electronic patient record. This allows the doctor to focus on medical issues and provide an improved service to the patient, with higher confidence that it is underpinned by current research. Method Our research prototype automatically generates query terms based on the patient record and adds weight factors for each term. Currently the patient’s age is taken into account with a fuzzy logic derived weight, and terms describing blood-related anomalies are derived from recent blood test results. Conditionally selected homonyms are used for query expansion. The query retrieves matching records from a local index of PubMed publications and displays results in descending relevance for the given patient. Recent publications are clearly highlighted for instant recognition by the researcher. Results Nine medical specialists from the Royal Adelaide Hospital evaluated the system and submitted pre-trial and post-trial questionnaires. Throughout the study we received positive feedback as doctors felt the support provided by the prototype was useful, and which they would like to use in their daily routine. Conclusion By supporting the time-consuming task of query formulation and iterative modification as well as by presenting the search results in order of relevance for the specific patient, literature retrieval becomes part of the daily workflow of busy professionals.

Age differences in the focus of retrieval: Evidence from dual-list free recall.

Science.gov (United States)

Wahlheim, Christopher N; Huff, Mark J

2015-12-01

In the present experiment, we examined age differences in the focus of retrieval using a dual-list free recall paradigm. Younger and older adults studied 2 lists of unrelated words and recalled from the first list, the second list, or both lists. Older adults showed impaired use of control processes to recall items correctly from a target list and prevent intrusions. This pattern reflected a deficit in recollection verified using a process dissociation procedure. We examined the consequences of an age-related deficit in control processes on the focus of retrieval using measures of temporal organization. Evidence that older adults engaged a broader focus of retrieval than younger adults was shown clearly when participants were instructed to recall from both lists. First-recalled items originated from more distant positions across lists for older adults. We interpret older adults' broader retrieval orientation as consistent with their impaired ability to elaborate cues to constrain retrieval. These findings show that age-related deficits in control processes impair context reinstatement and the subsequent focus of retrieval to target episodes. (c) 2015 APA, all rights reserved).

Explaining category-related effects in the retrieval of conceptual and lexical knowledge for concrete entities: operationalization and analysis of factors.

Science.gov (United States)

Tranel, D; Logan, C G; Frank, R J; Damasio, A R

1997-10-01

Category-related effects in the retrieval of conceptual and lexical knowledge for concrete entities have been well documented in lesion studies, and also with functional imaging and electrophysiological approaches. For example, brain-damaged subjects may be impaired in the ability to recognize or to name animals but not tools, or the opposite pattern may obtain. One reason for these dissociations is that different patterns of defects tend to be caused by distinct lesion profiles, suggesting a relative tendency for certain neural systems to be involved in category-related knowledge. But we and others have also hypothesized that a variety of traits of concrete entities co-determine category-related dissociations. Such traits ('factors') include homomorphy (similarity of form), familiarity, value to perceiver, manipulability, characteristic motion, characteristic sensory modality of transaction (vision, touch, hearing), and typical age of acquisition. It is our view that the mix of factors relative to different conceptual categories plays a key role in the neuroanatomical distribution of records for those different categories, and is thus behind the systematic correlations between certain retrieval defects and damage to certain neural systems [12, 52]. In this study, we operationalized these factors and analyzed their intercorrelations. Stimuli were slides of 215 items from the conceptual categories of animals, fruits/vegetables, tools/utensils, vehicles, and musical instruments. The factors were operationalized on the basis of ratings obtained from 227 normal control subjects and on the basis of computer analyses of the digitized outlines of the stimuli. Principal components analysis revealed that 81% of the variability across items could be accounted for by three components: Component 1 (practically useful, common items): high value to perceiver, tactile mode of transaction, high familiarity, low age of acquisition; Component 2 (homomorphic, non-manipulable items

Vasopressin Gene-Related Products in the Management of Breast Cancer

National Research Council Canada - National Science Library

North, William

1998-01-01

.... The VP gene is expressed by seemingly all breast cancers and by all DCIS, and this information coupled with an absence of VP gene-related products from fibrocystic disease potentially provides us...

Innovative grout/retrieval demonstration final report

International Nuclear Information System (INIS)

Loomis, G.G.; Thompson, D.N.

1995-01-01

This report presents the results of an evaluation of an innovative retrieval technique for buried transuranic waste. Application of this retrieval technique was originally designed for full pit retrieval; however, it applies equally to a hot spot retrieval technology. The technique involves grouting the buried soil waste matrix with a jet grouting procedure, applying an expansive demolition grout to the matrix, and retrieving the debris. The grouted matrix provides an agglomeration of fine soil particles and contaminants resulting in an inherent contamination control during the dusty retrieval process. A full-scale field demonstration of this retrieval technique was performed on a simulated waste pit at the Idaho National Engineering Laboratory. Details are reported on all phases of this proof-of-concept demonstration including pit construction, jet grouting activities, application of the demolition grout, and actual retrieval of the grouted pit. A quantitative evaluation of aerosolized soils and rare earth tracer spread is given for all phases of the demonstration, and these results are compared to a baseline retrieval activity using conventional retrieval means. 8 refs., 47 figs., 10 tabs

Preliminary characterization of a death-related gene in silkworm ...

African Journals Online (AJOL)

Through RT-PCR analysis of death-related protein gene in different tissues and different developmental stage of B. mori, it showed the distributed condition of the gene. It was widely expressed in various tissues and mainly expressed in testis, malphigian vessels, posterior intestine, silk gland. Meanwhile, it was widely ...

Mapping and annotating obesity-related genes in pig and human genomes.

Science.gov (United States)

Martelli, Pier Luigi; Fontanesi, Luca; Piovesan, Damiano; Fariselli, Piero; Casadio, Rita

2014-01-01

Background. Obesity is a major health problem in both developed and emerging countries. Obesity is a complex disease whose etiology involves genetic factors in strong interplay with environmental determinants and lifestyle. The discovery of genetic factors and biological pathways underlying human obesity is hampered by the difficulty in controlling the genetic background of human cohorts. Animal models are then necessary to further dissect the genetics of obesity. Pig has emerged as one of the most attractive models, because of the similarity with humans in the mechanisms regulating the fat deposition. Results. We collected the genes related to obesity in humans and to fat deposition traits in pig. We localized them on both human and pig genomes, building a map useful to interpret comparative studies on obesity. We characterized the collected genes structurally and functionally with BAR+ and mapped them on KEGG pathways and on STRING protein interaction network. Conclusions. The collected set consists of 361 obesity related genes in human and pig genomes. All genes were mapped on the human genome, and 54 could not be localized on the pig genome (release 2012). Only for 3 human genes there is no counterpart in pig, confirming that this animal is a good model for human obesity studies. Obesity related genes are mostly involved in regulation and signaling processes/pathways and relevant connection emerges between obesity-related genes and diseases such as cancer and infectious diseases.

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease.

Science.gov (United States)

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. http://rged.wall-eva.net. © The Author(s) 2014. Published by Oxford University Press.

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease

Science.gov (United States)

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Availability and implementation: Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. Database URL: http://rged.wall-eva.net PMID:25252782

Topological Aspects of Information Retrieval.

Science.gov (United States)

Egghe, Leo; Rousseau, Ronald

1998-01-01

Discusses topological aspects of theoretical information retrieval, including retrieval topology; similarity topology; pseudo-metric topology; document spaces as topological spaces; Boolean information retrieval as a subsystem of any topological system; and proofs of theorems. (LRW)

RETRIEVAL EQUIPMENT DESCRIPTIONS

International Nuclear Information System (INIS)

J. Steinhoff

1997-01-01

The objective and the scope of this document are to list and briefly describe the major mobile equipment necessary for waste package (WP) retrieval from the proposed subsurface nuclear waste repository at Yucca Mountain. Primary performance characteristics and some specialized design features of the equipment are explained and summarized in the individual subsections of this document. There are no quality assurance requirements or QA controls in this document. Retrieval under normal conditions is accomplished with the same fleet of equipment as is used for emplacement. Descriptions of equipment used for retrieval under normal conditions is found in Emplacement Equipment Descriptions, DI: BCAF00000-01717-5705-00002 (a document in progress). Equipment used for retrieval under abnormal conditions is addressed in this document and consists of the following: (1) Inclined Plane Hauler; (2) Bottom Lift Transporter; (3) Load Haul Dump (LHD) Loader; (4) Heavy Duty Forklift for Emplacement Drifts; (5) Covered Shuttle Car; (6) Multipurpose Vehicle; and (7) Scaler

Geospatial metadata retrieval from web services

Directory of Open Access Journals (Sweden)

Ivanildo Barbosa

Full Text Available Nowadays, producers of geospatial data in either raster or vector formats are able to make them available on the World Wide Web by deploying web services that enable users to access and query on those contents even without specific software for geoprocessing. Several providers around the world have deployed instances of WMS (Web Map Service, WFS (Web Feature Service and WCS (Web Coverage Service, all of them specified by the Open Geospatial Consortium (OGC. In consequence, metadata about the available contents can be retrieved to be compared with similar offline datasets from other sources. This paper presents a brief summary and describes the matching process between the specifications for OGC web services (WMS, WFS and WCS and the specifications for metadata required by the ISO 19115 - adopted as reference for several national metadata profiles, including the Brazilian one. This process focuses on retrieving metadata about the identification and data quality packages as well as indicates the directions to retrieve metadata related to other packages. Therefore, users are able to assess whether the provided contents fit to their purposes.

RETRIEVING SUSPECT TRANSURANIC WASTE FROM THE HANFORD BURIAL GROUNDS PROGRESS PLANS AND CHALLENGES

International Nuclear Information System (INIS)

FRENCH, M.S.

2006-01-01

This paper describes the scope and status of the program for retrieval of suspect transuranic (TRU) waste stored in the Hanford Site low-level burial grounds. Beginning in 1970 and continuing until the late 1980's, waste suspected of containing significant quantities of transuranic isotopes was placed in ''retrievable'' storage in designated modules in the Hanford burial grounds, with the intent that the waste would be retrieved when a national repository for disposal of such waste became operational. Approximately 15,000 cubic meters of waste, suspected of being TRU, was placed in storage modules in four burial grounds. With the availability of the national repository (the Waste Isolation Pilot Plant), retrieval of the suspect TRU waste is now underway. Retrieval efforts, to date, have been conducted in storage modules that contain waste, which is in general, contact-handled, relatively new (1980's and later), is stacked in neat, engineered configurations, and has a relatively good record of waste characteristics. Even with these optimum conditions, retrieval personnel have had to deal with a large number of structurally degraded containers, radioactive contamination issues, and industrial hazards (including organic vapors). Future retrieval efforts in older, less engineered modules are expected to present additional hazards and difficult challenges

Automatic content linking: Speech-based just-in-time retrieval for multimedia archives

NARCIS (Netherlands)

Popescu-Belis, A.; Kilgour, J.; Poller, P.; Nanchen, A.; Boertjes, E.; Wit, J. de

2010-01-01

The Automatic Content Linking Device monitors a conversation and uses automatically recognized words to retrieve documents that are of potential use to the participants. The document set includes project related reports or emails, transcribed snippets of past meetings, and websites. Retrieval

Abnormalities in alternative splicing of angiogenesis-related genes and their role in HIV-related cancers

Directory of Open Access Journals (Sweden)

Mthembu NN

2017-03-01

Full Text Available Nonkululeko N Mthembu,1 Zukile Mbita,2 Rodney Hull,1 Zodwa Dlamini1 1Research, Innovation and Engagements, Mangosuthu University of Technology, Durban, 2Department of Biochemistry, Microbiology and Biotechnology, University of Limpopo, Sovenga, South Africa Abstract: Alternative splicing of mRNA leads to an increase in proteome biodiversity by allowing the generation of multiple mRNAs, coding for multiple protein isoforms of various structural and functional properties from a single primary pre-mRNA transcript. The protein isoforms produced are tightly regulated in normal development but are mostly deregulated in various cancers. In HIV-infected individuals with AIDS, there is an increase in aberrant alternative splicing, resulting in an increase in HIV/AIDS-related cancers, such as Kaposi’s sarcoma, non-Hodgkin’s lymphoma, and cervical cancer. This aberrant splicing leads to abnormal production of protein and is caused by mutations in cis-acting elements or trans-acting factors in angiogenesis-related genes. Restoring the normal regulation of alternative splicing of angiogenic genes would alter the expression of protein isoforms and may confer normal cell physiology in patients with these cancers. This review highlights the abnormalities in alternative splicing of angiogenesis-related genes and their implication in HIV/AIDS-related cancers. This allows us to gain an insight into the pathogenesis of HIV/AIDS-related cancer and in turn elucidate the therapeutic potential of alternatively spliced genes in HIV/AIDS-related malignancies. Keywords: vascular endothelial growth factor, oncogenic viruses, hypoxia induced factor 1, Kaposi’s sarcoma, non-Hodgkin’s lymphoma, therapies targeting alternative splicing

Infectious Cognition: Risk Perception Affects Socially Shared Retrieval-Induced Forgetting of Medical Information.

Science.gov (United States)

Coman, Alin; Berry, Jessica N

2015-12-01

When speakers selectively retrieve previously learned information, listeners often concurrently, and covertly, retrieve their memories of that information. This concurrent retrieval typically enhances memory for mentioned information (the rehearsal effect) and impairs memory for unmentioned but related information (socially shared retrieval-induced forgetting, SSRIF), relative to memory for unmentioned and unrelated information. Building on research showing that anxiety leads to increased attention to threat-relevant information, we explored whether concurrent retrieval is facilitated in high-anxiety real-world contexts. Participants first learned category-exemplar facts about meningococcal disease. Following a manipulation of perceived risk of infection (low vs. high risk), they listened to a mock radio show in which some of the facts were selectively practiced. Final recall tests showed that the rehearsal effect was equivalent between the two risk conditions, but SSRIF was significantly larger in the high-risk than in the low-risk condition. Thus, the tendency to exaggerate consequences of news events was found to have deleterious consequences. © The Author(s) 2015.

Single-footprint retrievals of temperature, water vapor and cloud properties from AIRS

Science.gov (United States)

Irion, Fredrick W.; Kahn, Brian H.; Schreier, Mathias M.; Fetzer, Eric J.; Fishbein, Evan; Fu, Dejian; Kalmus, Peter; Wilson, R. Chris; Wong, Sun; Yue, Qing

2018-02-01

Single-footprint Atmospheric Infrared Sounder spectra are used in an optimal estimation-based algorithm (AIRS-OE) for simultaneous retrieval of atmospheric temperature, water vapor, surface temperature, cloud-top temperature, effective cloud optical depth and effective cloud particle radius. In a departure from currently operational AIRS retrievals (AIRS V6), cloud scattering and absorption are in the radiative transfer forward model and AIRS single-footprint thermal infrared data are used directly rather than cloud-cleared spectra (which are calculated using nine adjacent AIRS infrared footprints). Coincident MODIS cloud data are used for cloud a priori data. Using single-footprint spectra improves the horizontal resolution of the AIRS retrieval from ˜ 45 to ˜ 13.5 km at nadir, but as microwave data are not used, the retrieval is not made at altitudes below thick clouds. An outline of the AIRS-OE retrieval procedure and information content analysis is presented. Initial comparisons of AIRS-OE to AIRS V6 results show increased horizontal detail in the water vapor and relative humidity fields in the free troposphere above the clouds. Initial comparisons of temperature, water vapor and relative humidity profiles with coincident radiosondes show good agreement. Future improvements to the retrieval algorithm, and to the forward model in particular, are discussed.

Systematically characterizing and prioritizing chemosensitivity related gene based on Gene Ontology and protein interaction network

Directory of Open Access Journals (Sweden)

Chen Xin

2012-10-01

Full Text Available Abstract Background The identification of genes that predict in vitro cellular chemosensitivity of cancer cells is of great importance. Chemosensitivity related genes (CRGs have been widely utilized to guide clinical and cancer chemotherapy decisions. In addition, CRGs potentially share functional characteristics and network features in protein interaction networks (PPIN. Methods In this study, we proposed a method to identify CRGs based on Gene Ontology (GO and PPIN. Firstly, we documented 150 pairs of drug-CCRG (curated chemosensitivity related gene from 492 published papers. Secondly, we characterized CCRGs from the perspective of GO and PPIN. Thirdly, we prioritized CRGs based on CCRGs’ GO and network characteristics. Lastly, we evaluated the performance of the proposed method. Results We found that CCRG enriched GO terms were most often related to chemosensitivity and exhibited higher similarity scores compared to randomly selected genes. Moreover, CCRGs played key roles in maintaining the connectivity and controlling the information flow of PPINs. We then prioritized CRGs using CCRG enriched GO terms and CCRG network characteristics in order to obtain a database of predicted drug-CRGs that included 53 CRGs, 32 of which have been reported to affect susceptibility to drugs. Our proposed method identifies a greater number of drug-CCRGs, and drug-CCRGs are much more significantly enriched in predicted drug-CRGs, compared to a method based on the correlation of gene expression and drug activity. The mean area under ROC curve (AUC for our method is 65.2%, whereas that for the traditional method is 55.2%. Conclusions Our method not only identifies CRGs with expression patterns strongly correlated with drug activity, but also identifies CRGs in which expression is weakly correlated with drug activity. This study provides the framework for the identification of signatures that predict in vitro cellular chemosensitivity and offers a valuable

Laparoscopic specimen retrieval bags.

Science.gov (United States)

Smorgick, Noam

2014-10-01

Specimen retrieval bags have long been used in laparoscopic gynecologic surgery for contained removal of adnexal cysts and masses. More recently, the concerns regarding spread of malignant cells during mechanical morcellation of myoma have led to an additional use of specimen retrieval bags for contained "in-bag" morcellation. This review will discuss the indications for use retrieval bags in gynecologic endoscopy, and describe the different specimen bags available to date.

Information, conservation and retrieval

Energy Technology Data Exchange (ETDEWEB)

Eng, T [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden); Norberg, E [National Swedish Archives, Stockholm (Sweden); Torbacke, J [Stockholm Univ. (Sweden). Dept. of History; Jensen, M [Swedish Radiation Protection Inst., Stockholm (Sweden)

1996-12-01

The seminar took place on the Swedish ship for transportation of radioactive wastes, M/S Sigyn, which at summer time is used for exhibitions. The seminar treated items related to general information needs in society and questions related to radioactive waste, i.e. how knowledge about a waste repository should be passed on to future generations. Three contributions are contained in the report from the seminar and are indexed separately: `Active preservation - otherwise no achieves`; `The conservation and dissemination of information - A democratic issue`; and, `Conservation and retrieval of information - Elements of a strategy to inform future societies about nuclear waste repositories`.

Information, conservation and retrieval

International Nuclear Information System (INIS)

Eng, T.; Norberg, E.; Torbacke, J.

1996-12-01

The seminar took place on the Swedish ship for transportation of radioactive wastes, M/S Sigyn, which at summer time is used for exhibitions. The seminar treated items related to general information needs in society and questions related to radioactive waste, i.e. how knowledge about a waste repository should be passed on to future generations. Three contributions are contained in the report from the seminar and are indexed separately: 'Active preservation - otherwise no achieves'; 'The conservation and dissemination of information - A democratic issue'; and, 'Conservation and retrieval of information - Elements of a strategy to inform future societies about nuclear waste repositories'

Gene expression profiles reveal key genes for early diagnosis and treatment of adamantinomatous craniopharyngioma.

Science.gov (United States)

Yang, Jun; Hou, Ziming; Wang, Changjiang; Wang, Hao; Zhang, Hongbing

2018-04-23

Adamantinomatous craniopharyngioma (ACP) is an aggressive brain tumor that occurs predominantly in the pediatric population. Conventional diagnosis method and standard therapy cannot treat ACPs effectively. In this paper, we aimed to identify key genes for ACP early diagnosis and treatment. Datasets GSE94349 and GSE68015 were obtained from Gene Expression Omnibus database. Consensus clustering was applied to discover the gene clusters in the expression data of GSE94349 and functional enrichment analysis was performed on gene set in each cluster. The protein-protein interaction (PPI) network was built by the Search Tool for the Retrieval of Interacting Genes, and hubs were selected. Support vector machine (SVM) model was built based on the signature genes identified from enrichment analysis and PPI network. Dataset GSE94349 was used for training and testing, and GSE68015 was used for validation. Besides, RT-qPCR analysis was performed to analyze the expression of signature genes in ACP samples compared with normal controls. Seven gene clusters were discovered in the differentially expressed genes identified from GSE94349 dataset. Enrichment analysis of each cluster identified 25 pathways that highly associated with ACP. PPI network was built and 46 hubs were determined. Twenty-five pathway-related genes that overlapped with the hubs in PPI network were used as signatures to establish the SVM diagnosis model for ACP. The prediction accuracy of SVM model for training, testing, and validation data were 94, 85, and 74%, respectively. The expression of CDH1, CCL2, ITGA2, COL8A1, COL6A2, and COL6A3 were significantly upregulated in ACP tumor samples, while CAMK2A, RIMS1, NEFL, SYT1, and STX1A were significantly downregulated, which were consistent with the differentially expressed gene analysis. SVM model is a promising classification tool for screening and early diagnosis of ACP. The ACP-related pathways and signature genes will advance our knowledge of ACP pathogenesis

[Neurons in NAc core and BLA are activated during cocaine context-associated reward memory retrieval in mice].

Science.gov (United States)

Wang, Jun-Jun; Yao, Wen-Qing; Chen, Yue-Jun; Ma, Lan; Tao, Ye-Zheng

2014-10-25

The intense associative memories that develop between cocaine-paired contexts and rewarding stimuli make addiction hard to cure by contributing to cocaine seeking and relapse. So it's of great importance to examine the neurobiological basis of addiction memory. Cocaine conditioned place preference (CPP) used in this study is a form of Pavlovian conditioning which can establish associations between drug and contextual factors. c-Fos and Zif268 are commonly used immediate early gene (IEG) makers to identify neurons that are activated after a stimulus or behavioral conditioning. This study was designed to reveal neuronal c-Fos, Zif268 expression pattern in 10 brain regions following cocaine context-associated reward memory retrieval in mice, combining animal behavioral study and immunofluorescence method. C57BL/6 mice were randomly divided into 3 groups: Saline retrieval, Cocaine retrieval, and No retrieval of cocaine groups. Cocaine retrieval and No retrieval of cocaine underwent CPP training (one side paired with cocaine, and the other side with saline) except that No retrieval of cocaine group didn't undergo CPP test. Saline retrieval group received saline injections (i.p) on both sides. The results showed that: Neuronal c-Fos, Zif268 protein expression levels in nucleus accumbens (NAc) core both were elevated in Cocaine retrieval group compared with those in Saline retrieval (Control) group during cocaine context-associated reward memory retrieval. Zif268 protein expression level in basolateral amygdala (BLA) was also elevated in Cocaine retrieval group compared with that in control mice. Elevation was not seen in other regions such as hippocampus, prefrontal cortex (PFC). Thus, NAc core and BLA were activated during cocaine context-associated reward memory retrieval. The results suggest that neurons that are activated in NAc core and BLA are crucial basis of cocaine context-associated reward memory.

Assessment of Snared-Loop Technique When Standard Retrieval of Inferior Vena Cava Filters Fails

International Nuclear Information System (INIS)

Doody, Orla; Noe, Geertje; Given, Mark F.; Foley, Peter T.; Lyon, Stuart M.

2009-01-01

Purpose To identify the success and complications related to a variant technique used to retrieve inferior vena cava filters when simple snare approach has failed. Methods A retrospective review of all Cook Guenther Tulip filters and Cook Celect filters retrieved between July 2006 and February 2008 was performed. During this period, 130 filter retrievals were attempted. In 33 cases, the standard retrieval technique failed. Retrieval was subsequently attempted with our modified retrieval technique. Results The retrieval was successful in 23 cases (mean dwell time, 171.84 days; range, 5-505 days) and unsuccessful in 10 cases (mean dwell time, 162.2 days; range, 94-360 days). Our filter retrievability rates increased from 74.6% with the standard retrieval method to 92.3% when the snared-loop technique was used. Unsuccessful retrieval was due to significant endothelialization (n = 9) and caval penetration by the filter (n = 1). A single complication occurred in the group, in a patient developing pulmonary emboli after attempted retrieval. Conclusion The technique we describe increased the retrievability of the two filters studied. Hook endothelialization is the main factor resulting in failed retrieval and continues to be a limitation with these filters.

Retrieving autobiographical memories: How different retrieval strategies associated with different cues explain reaction time differences.

Science.gov (United States)

Uzer, Tugba

2016-02-01

Previous research has shown that memories cued by concrete concepts, such as objects, are retrieved faster than those cued by more abstract concepts, such as emotions. This effect has been explained by the fact that more memories are directly retrieved from object versus emotion cues. In the present study, we tested whether RT differences between memories cued by emotion versus object terms occur not only because object cues elicit direct retrieval of more memories (Uzer, Lee, & Brown, 2012), but also because of differences in memory generation in response to emotions versus objects. One hundred university students retrieved memories in response to basic-level (e.g. orange), superordinate-level (e.g. plant), and emotion (e.g. surprised) cues. Retrieval speed was measured and participants reported whether memories were directly retrieved or generated on each trial. Results showed that memories were retrieved faster in response to basic-level versus superordinate-level and emotion cues because a) basic-level cues elicited more directly retrieved memories, and b) generating memories was more difficult when cues were abstract versus concrete. These results suggest that generative retrieval is a cue generation process in which additional cues that provide contextual information including the target event are produced. Memories are retrieved more slowly in response to emotion cues in part because emotion labels are less effective cues of appropriate contextual information. This particular finding is inconsistent with the idea that emotion is a primary organizational unit for autobiographical memories. In contrast, the difficulty of emotional memory generation implies that emotions represent low-level event information in the organization of autobiographical memory. Copyright © 2016 Elsevier B.V. All rights reserved.

Memory networks supporting retrieval effort and retrieval success under conditions of full and divided attention.

Science.gov (United States)

Skinner, Erin I; Fernandes, Myra A; Grady, Cheryl L

2009-01-01

We used a multivariate analysis technique, partial least squares (PLS), to identify distributed patterns of brain activity associated with retrieval effort and retrieval success. Participants performed a recognition memory task under full attention (FA) or two different divided attention (DA) conditions during retrieval. Behaviorally, recognition was disrupted when a word, but not digit-based distracting task, was performed concurrently with retrieval. PLS was used to identify patterns of brain activation that together covaried with the three memory conditions and which were functionally connected with activity in the right hippocampus to produce successful memory performance. Results indicate that activity in the right dorsolateral frontal cortex increases during conditions of DA at retrieval, and that successful memory performance in the DA-digit condition is associated with activation of the same network of brain regions functionally connected to the right hippocampus, as under FA, which increases with increasing memory performance. Finally, DA conditions that disrupt successful memory performance (DA-word) interfere with recruitment of both retrieval-effort and retrieval-success networks.

Conidiogenesis-related DNA photolyase gene in Beauveria bassiana.

Science.gov (United States)

Lee, Se Jin; Lee, Mi Rong; Kim, Sihyeon; Kim, Jong Cheol; Park, So Eun; Shin, Tae Young; Kim, Jae Su

2018-03-01

Beauveria bassiana is an entomopathogenic fungi used in environmentally mindful pest management. Its main active ingredient, conidia, is commercially available as a fungal biopesticide. Many studies of conidia production have focused on how to optimize culture conditions for maximum productivity and stability against unfavorable abiotic factors. However, understanding of how conidiogenesis-related genes provide improved conidial production remains unclear. In this study, we focus on identifying conidiogenesis-related genes in B. bassiana ERL1170 using a random mutagenesis technique. Transformation of ERL1170 using restriction enzyme-mediated integration generated one morphologically different transformant, ERL1170-pABeG #163. The transformant was confirmed to represent B. bassiana, and the binary vector was successfully integrated into the genome of ERL1170. Compared to the wild type, transformant #163 showed very slow hyphal growth and within 6 days only produced bassiana exhibits thread-like hyphae and conidiophore structures and circular conidia. To determine the location of the randomly inserted DNA, we conducted thermal asymmetric interlaced (TAIL) PCR and Escherichia coli cloning to clearly sequence the disrupted region. We identified one colony (colony No. 7) with an insertion site identified as DNA photolyase. This was confirmed through a gene knock-out study. It is possible the gene that encodes for DNA photolyase was disrupted during the insertion process and might be involved in fungal conidiogenesis. This work serves as a platform for exploring the function of a variety of B. bassiana genes involved in pest management and their downstream processing. Copyright © 2018 Elsevier Inc. All rights reserved.

GRtoGR: a system for mapping GO relations to gene relations.

Science.gov (United States)

Taha, Kamal

2013-12-01

We introduce in this paper a biological search engine called GRtoGR. Given a set of S genes, GRtoGR would determine from GO graph the most significant Lowest Common Ancestor (LCA) of the GO terms annotating the set S. This significant LCA annotates the genes that are the most semantically related to the set S. The framework of GRtoGR refines the concept of LCA by introducing the concepts of Relevant Lowest Common Ancestor (RLCA) and Semantically Relevant Lowest Common Ancestor (SRLCA). A SRLCA is the most significant LCA of the GO terms annotating the set S. We observe that the existence of the GO terms annotating the set S is dependent on the existence of this SRLCA in GO graph. That is, the terms annotating a given set of genes usually have existence dependency relationships with the SRLCA of these terms. We evaluated GRtoGR experimentally and compared it with nine other methods. Results showed marked improvement.

Interactive Information Retrieval: An Introduction

Directory of Open Access Journals (Sweden)

Borlund, Pia

2013-09-01

Full Text Available The paper introduces the research area of interactive information retrieval (IIR from a historical point of view. Further, the focus here is on evaluation, because much research in IR deals with IR evaluation methodology due to the core research interest in IR performance, system interaction and satisfaction with retrieved information. In order to position IIR evaluation, the Cranfield model and the series of tests that led to the Cranfield model are outlined. Three iconic user-oriented studies and projects that all have contributed to how IIR is perceived and understood today are presented: The MEDLARS test, the Book House fiction retrieval system, and the OKAPI project. On this basis the call for alternative IIR evaluation approaches motivated by the three revolutions (the cognitive, the relevance, and the interactive revolutions put forward by Robertson & Hancock-Beaulieu (1992 is presented. As a response to this call the 'IIR evaluation model' by Borlund (e.g., 2003a is introduced. The objective of the IIR evaluation model is to facilitate IIR evaluation as close as possible to actual information searching and IR processes, though still in a relatively controlled evaluation environment, in which the test instrument of a simulated work task situation plays a central part.

Sex-related differences in gene expression in human skeletal muscle.

Directory of Open Access Journals (Sweden)

Stephen Welle

2008-01-01

Full Text Available There is sexual dimorphism of skeletal muscle, the most obvious feature being the larger muscle mass of men. The molecular basis for this difference has not been clearly defined. To identify genes that might contribute to the relatively greater muscularity of men, we compared skeletal muscle gene expression profiles of 15 normal men and 15 normal women by using comprehensive oligonucleotide microarrays. Although there were sex-related differences in expression of several hundred genes, very few of the differentially expressed genes have functions that are obvious candidates for explaining the larger muscle mass of men. The men tended to have higher expression of genes encoding mitochondrial proteins, ribosomal proteins, and a few translation initiation factors. The women had >2-fold greater expression than the men (P<0.0001 of two genes that encode proteins in growth factor pathways known to be important in regulating muscle mass: growth factor receptor-bound 10 (GRB10 and activin A receptor IIB (ACVR2B. GRB10 encodes a protein that inhibits insulin-like growth factor-1 (IGF-1 signaling. ACVR2B encodes a myostatin receptor. Quantitative RT-PCR confirmed higher expression of GRB10 and ACVR2B genes in these women. In an independent microarray study of 10 men and 9 women with facioscapulohumeral dystrophy, women had higher expression of GRB10 (2.7-fold, P<0.001 and ACVR2B (1.7-fold, P<0.03. If these sex-related differences in mRNA expression lead to reduced IGF-1 activity and increased myostatin activity, they could contribute to the sex difference in muscle size.

The Retrieval Knowledge Center Evaluation Of Low Tank Level Mixing Technologies For DOE High Level Waste Tank Retrieval 10516

International Nuclear Information System (INIS)

Fellinger, A.

2009-01-01

The Department of Energy (DOE) Complex has over two-hundred underground storage tanks containing over 80-million gallons of legacy waste from the production of nuclear weapons. The majority of the waste is located at four major sites across the nation and is planned for treatment over a period of almost forty years. The DOE Office of Technology Innovation and Development within the Office of Environmental Management (DOE-EM) sponsors technology research and development programs to support processing advancements and technology maturation designed to improve the costs and schedule for disposal of the waste and closure of the tanks. Within the waste processing focus area are numerous technical initiatives which included the development of a suite of waste removal technologies to address the need for proven equipment and techniques to remove high level radioactive wastes from the waste tanks that are now over fifty years old. In an effort to enhance the efficiency of waste retrieval operations, the DOE-EM Office of Technology Innovation and Development funded an effort to improve communications and information sharing between the DOE's major waste tank locations as it relates to retrieval. The task, dubbed the Retrieval Knowledge Center (RKC) was co-lead by the Savannah River National Laboratory (SRNL) and the Pacific Northwest National Laboratory (PNNL) with core team members representing the Oak Ridge and Idaho sites, as well as, site contractors responsible for waste tank operations. One of the greatest challenges to the processing and closure of many of the tanks is complete removal of all tank contents. Sizeable challenges exist for retrieving waste from High Level Waste (HLW) tanks; with complications that are not normally found with tank retrieval in commercial applications. Technologies currently in use for waste retrieval are generally adequate for bulk removal; however, removal of tank heels, the materials settled in the bottom of the tank, using the same

The Wikipedia Image Retrieval Task

NARCIS (Netherlands)

T. Tsikrika (Theodora); J. Kludas

2010-01-01

htmlabstractThe wikipedia image retrieval task at ImageCLEF provides a testbed for the system-oriented evaluation of visual information retrieval from a collection of Wikipedia images. The aim is to investigate the effectiveness of retrieval approaches that exploit textual and visual evidence in the

DORS: DDC Online Retrieval System.

Science.gov (United States)

Liu, Songqiao; Svenonius, Elaine

1991-01-01

Describes the Dewey Online Retrieval System (DORS), which was developed at the University of California, Los Angeles (UCLA), to experiment with classification-based search strategies in online catalogs. Classification structures in automated information retrieval are discussed; and specifications for a classification retrieval interface are…

Medial temporal lobe contributions to cued retrieval of items and contexts.

Science.gov (United States)

Hannula, Deborah E; Libby, Laura A; Yonelinas, Andrew P; Ranganath, Charan

2013-10-01

Several models have proposed that different regions of the medial temporal lobes contribute to different aspects of episodic memory. For instance, according to one view, the perirhinal cortex represents specific items, parahippocampal cortex represents information regarding the context in which these items were encountered, and the hippocampus represents item-context bindings. Here, we used event-related functional magnetic resonance imaging (fMRI) to test a specific prediction of this model-namely, that successful retrieval of items from context cues will elicit perirhinal recruitment and that successful retrieval of contexts from item cues will elicit parahippocampal cortex recruitment. Retrieval of the bound representation in either case was expected to elicit hippocampal engagement. To test these predictions, we had participants study several item-context pairs (i.e., pictures of objects and scenes, respectively), and then had them attempt to recall items from associated context cues and contexts from associated item cues during a scanned retrieval session. Results based on both univariate and multivariate analyses confirmed a role for hippocampus in content-general relational memory retrieval, and a role for parahippocampal cortex in successful retrieval of contexts from item cues. However, we also found that activity differences in perirhinal cortex were correlated with successful cued recall for both items and contexts. These findings provide partial support for the above predictions and are discussed with respect to several models of medial temporal lobe function. Copyright © 2013 Elsevier Ltd. All rights reserved.

Medial Temporal Lobe Contributions to Cued Retrieval of Items and Contexts

Science.gov (United States)

Hannula, Deborah E.; Libby, Laura A.; Yonelinas, Andrew P.; Ranganath, Charan

2013-01-01

Several models have proposed that different regions of the medial temporal lobes contribute to different aspects of episodic memory. For instance, according to one view, the perirhinal cortex represents specific items, parahippocampal cortex represents information regarding the context in which these items were encountered, and the hippocampus represents item-context bindings. Here, we used event-related functional magnetic resonance imaging (fMRI) to test a specific prediction of this model – namely, that successful retrieval of items from context cues will elicit perirhinal recruitment and that successful retrieval of contexts from item cues will elicit parahippocampal cortex recruitment. Retrieval of the bound representation in either case was expected to elicit hippocampal engagement. To test these predictions, we had participants study several item-context pairs (i.e., pictures of objects and scenes, respectively), and then had them attempt to recall items from associated context cues and contexts from associated item cues during a scanned retrieval session. Results based on both univariate and multivariate analyses confirmed a role for hippocampus in content-general relational memory retrieval, and a role for parahippocampal cortex in successful retrieval of contexts from item cues. However, we also found that activity differences in perirhinal cortex were correlated with successful cued recall for both items and contexts. These findings provide partial support for the above predictions and are discussed with respect to several models of medial temporal lobe function. PMID:23466350

A hybrid network-based method for the detection of disease-related genes

Science.gov (United States)

Cui, Ying; Cai, Meng; Dai, Yang; Stanley, H. Eugene

2018-02-01

Detecting disease-related genes is crucial in disease diagnosis and drug design. The accepted view is that neighbors of a disease-causing gene in a molecular network tend to cause the same or similar diseases, and network-based methods have been recently developed to identify novel hereditary disease-genes in available biomedical networks. Despite the steady increase in the discovery of disease-associated genes, there is still a large fraction of disease genes that remains under the tip of the iceberg. In this paper we exploit the topological properties of the protein-protein interaction (PPI) network to detect disease-related genes. We compute, analyze, and compare the topological properties of disease genes with non-disease genes in PPI networks. We also design an improved random forest classifier based on these network topological features, and a cross-validation test confirms that our method performs better than previous similar studies.

A literature search tool for intelligent extraction of disease-associated genes.

Science.gov (United States)

Jung, Jae-Yoon; DeLuca, Todd F; Nelson, Tristan H; Wall, Dennis P

2014-01-01

To extract disorder-associated genes from the scientific literature in PubMed with greater sensitivity for literature-based support than existing methods. We developed a PubMed query to retrieve disorder-related, original research articles. Then we applied a rule-based text-mining algorithm with keyword matching to extract target disorders, genes with significant results, and the type of study described by the article. We compared our resulting candidate disorder genes and supporting references with existing databases. We demonstrated that our candidate gene set covers nearly all genes in manually curated databases, and that the references supporting the disorder-gene link are more extensive and accurate than other general purpose gene-to-disorder association databases. We implemented a novel publication search tool to find target articles, specifically focused on links between disorders and genotypes. Through comparison against gold-standard manually updated gene-disorder databases and comparison with automated databases of similar functionality we show that our tool can search through the entirety of PubMed to extract the main gene findings for human diseases rapidly and accurately.

Single-Shell Tank (SST) Retrieval Project Plan for Tank 241-C-104 Retrieval

International Nuclear Information System (INIS)

DEFIGH PRICE, C.

2000-01-01

In support of the SST Interim Closure Project, Project W-523 ''Tank 241-C-104 Waste Retrieval System'' will provide systems for retrieval and transfer of radioactive waste from tank 241-C-104 (C-104) to the DST staging tank 241-AY-101 (AY-101). At the conclusion of Project W-523, a retrieval system will have been designed and tested to meet the requirements for Acceptance of Beneficial Use and been turned over to operations. Completion of construction and operations of the C-104 retrieval system will meet the recently proposed near-term Tri-Party Agreement milestone, M-45-03F (Proposed Tri-Party Agreement change request M-45-00-01A, August, 30 2000) for demonstrating limits of retrieval technologies on sludge and hard heels in SSTs, reduce near-term storage risks associated with aging SSTs, and provide feed for the tank waste treatment plant. This Project Plan documents the methodology for managing Project W-523; formalizes responsibilities; identifies key interfaces required to complete the retrieval action; establishes the technical, cost, and schedule baselines; and identifies project organizational requirements pertaining to the engineering process such as environmental, safety, quality assurance, change control, design verification, testing, and operational turnover

NHR-23 dependent collagen and hedgehog-related genes required for molting

International Nuclear Information System (INIS)

Kouns, Nathaniel A.; Nakielna, Johana; Behensky, Frantisek; Krause, Michael W.; Kostrouch, Zdenek; Kostrouchova, Marta

2011-01-01

Highlights: → NHR-23 is a critical regulator of nematode development and molting. → The manuscript characterizes the loss-of-function phenotype of an nhr-23 mutant. → Whole genome expression analysis identifies new potential targets of NHR-23. → Hedgehog-related genes are identified as NHR-23 dependent genes. → New link between sterol mediated signaling and regulation by NHR-23 is found. -- Abstract: NHR-23, a conserved member of the nuclear receptor family of transcription factors, is required for normal development in Caenorhabditis elegans where it plays a critical role in growth and molting. In a search for NHR-23 dependent genes, we performed whole genome comparative expression microarrays on both control and nhr-23 inhibited synchronized larvae. Genes that decreased in response to nhr-23 RNAi included several collagen genes. Unexpectedly, several hedgehog-related genes were also down-regulated after nhr-23 RNAi. A homozygous nhr-23 deletion allele was used to confirm the RNAi knockdown phenotypes and the changes in gene expression. Our results indicate that NHR-23 is a critical co-regulator of functionally linked genes involved in growth and molting and reveal evolutionary parallels among the ecdysozoa.

NHR-23 dependent collagen and hedgehog-related genes required for molting

Energy Technology Data Exchange (ETDEWEB)

Kouns, Nathaniel A.; Nakielna, Johana; Behensky, Frantisek [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic); Krause, Michael W. [Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD (United States); Kostrouch, Zdenek [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic); Kostrouchova, Marta, E-mail: marta.kostrouchova@lf1.cuni.cz [Laboratory of Model Systems, Institute of Inherited Metabolic Disorders, First Faculty of Medicine, Charles University, Prague (Czech Republic)

2011-10-07

Highlights: {yields} NHR-23 is a critical regulator of nematode development and molting. {yields} The manuscript characterizes the loss-of-function phenotype of an nhr-23 mutant. {yields} Whole genome expression analysis identifies new potential targets of NHR-23. {yields} Hedgehog-related genes are identified as NHR-23 dependent genes. {yields} New link between sterol mediated signaling and regulation by NHR-23 is found. -- Abstract: NHR-23, a conserved member of the nuclear receptor family of transcription factors, is required for normal development in Caenorhabditis elegans where it plays a critical role in growth and molting. In a search for NHR-23 dependent genes, we performed whole genome comparative expression microarrays on both control and nhr-23 inhibited synchronized larvae. Genes that decreased in response to nhr-23 RNAi included several collagen genes. Unexpectedly, several hedgehog-related genes were also down-regulated after nhr-23 RNAi. A homozygous nhr-23 deletion allele was used to confirm the RNAi knockdown phenotypes and the changes in gene expression. Our results indicate that NHR-23 is a critical co-regulator of functionally linked genes involved in growth and molting and reveal evolutionary parallels among the ecdysozoa.

A pathway-based network analysis of hypertension-related genes

Science.gov (United States)

Wang, Huan; Hu, Jing-Bo; Xu, Chuan-Yun; Zhang, De-Hai; Yan, Qian; Xu, Ming; Cao, Ke-Fei; Zhang, Xu-Sheng

2016-02-01

Complex network approach has become an effective way to describe interrelationships among large amounts of biological data, which is especially useful in finding core functions and global behavior of biological systems. Hypertension is a complex disease caused by many reasons including genetic, physiological, psychological and even social factors. In this paper, based on the information of biological pathways, we construct a network model of hypertension-related genes of the salt-sensitive rat to explore the interrelationship between genes. Statistical and topological characteristics show that the network has the small-world but not scale-free property, and exhibits a modular structure, revealing compact and complex connections among these genes. By the threshold of integrated centrality larger than 0.71, seven key hub genes are found: Jun, Rps6kb1, Cycs, Creb312, Cdk4, Actg1 and RT1-Da. These genes should play an important role in hypertension, suggesting that the treatment of hypertension should focus on the combination of drugs on multiple genes.

Venous Thromboembolism After Removal of Retrievable Inferior Vena Cava Filters

International Nuclear Information System (INIS)

Yamagami, Takuji; Tanaka, Osamu; Yoshimatsu, Rika; Miura, Hiroshi; Nishimura, Tsunehiko

2010-01-01

The purpose of this study was to examine the incidence of new or recurrent venous thromboembolism (VTE) after retrieval of inferior vena cava (IVC) filters and risk factors associated with such recurrence. Between March 2001 and September 2008, at our institution, implanted retrievable vena cava filters were retrieved in 76 patients. The incidence of new or recurrent VTE after retrieval was reviewed and numerous variables were analyzed to assess risk factors for redevelopment of VTE after filter retrieval. In 5 (6.6%) of the 76 patients, redevelopment or worsening of VTE was seen after retrieval of the filter. Three patients (4.0%) had recurrent deep venous thrombosis (DVT) in the lower extremities and 2 (2.6%) had development of pulmonary embolism, resulting in death. Although there was no significant difference in the incidence of new or recurrent VTE related to any risk factor investigated, a tendency for development of VTE after filter retrieval was higher in patients in whom DVT in the lower extremities had been so severe during filter implantation that interventional radiological therapies in addition to traditional anticoagulation therapies were required (40% in patients with recurrent VTE vs. 23% in those without VTE; p = 0.5866 according to Fisher's exact probability test) and in patients in whom DVT remained at the time of filter retrieval (60% in patients with recurrent VTE vs. 37% in those without VTE; p = 0.3637). In conclusion, new or recurrent VTE was rare after retrieval of IVC filters but was most likely to occur in patients who had severe DVT during filter implantation and/or in patients with a DVT that remained at the time of filter retrieval. We must point out that the fatality rate from PE after filter removal was high (2.6%).

miRNA-mediated functional changes through co-regulating function related genes.

Directory of Open Access Journals (Sweden)

Jie He

Full Text Available BACKGROUND: MicroRNAs play important roles in various biological processes involving fairly complex mechanism. Analysis of genome-wide miRNA microarray demonstrate that a single miRNA can regulate hundreds of genes, but the regulative extent on most individual genes is surprisingly mild so that it is difficult to understand how a miRNA provokes detectable functional changes with such mild regulation. RESULTS: To explore the internal mechanism of miRNA-mediated regulation, we re-analyzed the data collected from genome-wide miRNA microarray with bioinformatics assay, and found that the transfection of miR-181b and miR-34a in Hela and HCT-116 tumor cells regulated large numbers of genes, among which, the genes related to cell growth and cell death demonstrated high Enrichment scores, suggesting that these miRNAs may be important in cell growth and cell death. MiR-181b induced changes in protein expression of most genes that were seemingly related to enhancing cell growth and decreasing cell death, while miR-34a mediated contrary changes of gene expression. Cell growth assays further confirmed this finding. In further study on miR-20b-mediated osteogenesis in hMSCs, miR-20b was found to enhance osteogenesis by activating BMPs/Runx2 signaling pathway in several stages by co-repressing of PPARγ, Bambi and Crim1. CONCLUSIONS: With its multi-target characteristics, miR-181b, miR-34a and miR-20b provoked detectable functional changes by co-regulating functionally-related gene groups or several genes in the same signaling pathway, and thus mild regulation from individual miRNA targeting genes could have contributed to an additive effect. This might also be one of the modes of miRNA-mediated gene regulation.

Phase 2, Solid waste retrieval strategy

International Nuclear Information System (INIS)

Johnson, D.M.

1994-01-01

Solid TRU retrieval, Phase 1 is scheduled to commence operation in 1998 at 218W-4C-T01 and complete recovery of the waste containers in 2001. Phase 2 Retrieval will recover the remaining buried TRU waste to be retrieved and provide the preliminary characterization by non-destructive means to allow interim storage until processing for disposal. This document reports on researching the characterization documents to determine the types of wastes to be retrieved and where located, waste configurations, conditions, and required methods for retrieval. Also included are discussions of wastes encompassed by Phase 2 for which there are valid reasons to not retrieve

Phase 2, Solid waste retrieval strategy

Energy Technology Data Exchange (ETDEWEB)

Johnson, D.M.

1994-09-29

Solid TRU retrieval, Phase 1 is scheduled to commence operation in 1998 at 218W-4C-T01 and complete recovery of the waste containers in 2001. Phase 2 Retrieval will recover the remaining buried TRU waste to be retrieved and provide the preliminary characterization by non-destructive means to allow interim storage until processing for disposal. This document reports on researching the characterization documents to determine the types of wastes to be retrieved and where located, waste configurations, conditions, and required methods for retrieval. Also included are discussions of wastes encompassed by Phase 2 for which there are valid reasons to not retrieve.

Vertical grid of retrieved atmospheric profiles

International Nuclear Information System (INIS)

Ceccherini, Simone; Carli, Bruno; Raspollini, Piera

2016-01-01

The choice of the vertical grid of atmospheric profiles retrieved from remote sensing observations is discussed considering the two cases of profiles used to represent the results of individual measurements and of profiles used for subsequent data fusion applications. An ozone measurement of the MIPAS instrument is used to assess, for different vertical grids, the quality of the retrieved profiles in terms of profile values, retrieval errors, vertical resolutions and number of degrees of freedom. In the case of individual retrievals no evident advantage is obtained with the use of a grid finer than the one with a reduced number of grid points, which are optimized according to the information content of the observations. Nevertheless, this instrument dependent vertical grid, which seems to extract all the available information, provides very poor results when used for data fusion applications. A loss of about a quarter of the degrees of freedom is observed when the data fusion is made using the instrument dependent vertical grid relative to the data fusion made using a vertical grid optimized for the data fusion product. This result is explained by the analysis of the eigenvalues of the Fisher information matrix and leads to the conclusion that different vertical grids must be adopted when data fusion is the expected application. - Highlights: • Data fusion application is taken into account for the choice of the vertical grid. • The study is performed using ozone profiles retrieved from MIPAS measurements. • A very fine vertical grid is not needed for the analysis of a single instrument. • The instrument dependent vertical grid is not the best choice for data fusion. • A data fusion dependent vertical grid must be used for profiles that will be fused.

Use of information-retrieval languages in automated retrieval of experimental data from long-term storage

Science.gov (United States)

Khovanskiy, Y. D.; Kremneva, N. I.

1975-01-01

Problems and methods are discussed of automating information retrieval operations in a data bank used for long term storage and retrieval of data from scientific experiments. Existing information retrieval languages are analyzed along with those being developed. The results of studies discussing the application of the descriptive 'Kristall' language used in the 'ASIOR' automated information retrieval system are presented. The development and use of a specialized language of the classification-descriptive type, using universal decimal classification indices as the main descriptors, is described.

Neural activations associated with feedback and retrieval success

Science.gov (United States)

Wiklund-Hörnqvist, Carola; Andersson, Micael; Jonsson, Bert; Nyberg, Lars

2017-11-01

There is substantial behavioral evidence for a phenomenon commonly called "the testing effect", i.e. superior memory performance after repeated testing compared to re-study of to-be-learned materials. However, considerably less is known about the underlying neuro-cognitive processes that are involved in the initial testing phase, and thus underlies the actual testing effect. Here, we investigated functional brain activity related to test-enhanced learning with feedback. Subjects learned foreign vocabulary across three consecutive tests with correct-answer feedback. Functional brain-activity responses were analyzed in relation to retrieval and feedback events, respectively. Results revealed up-regulated activity in fronto-striatal regions during the first successful retrieval, followed by a marked reduction in activity as a function of improved learning. Whereas feedback improved behavioral performance across consecutive tests, feedback had a negligable role after the first successful retrieval for functional brain-activity modulations. It is suggested that the beneficial effects of test-enhanced learning is regulated by feedback-induced updating of memory representations, mediated via the striatum, that might underlie the stabilization of memory commonly seen in behavioral studies of the testing effect.

Deep learning of mutation-gene-drug relations from the literature.

Science.gov (United States)

Lee, Kyubum; Kim, Byounggun; Choi, Yonghwa; Kim, Sunkyu; Shin, Wonho; Lee, Sunwon; Park, Sungjoon; Kim, Seongsoon; Tan, Aik Choon; Kang, Jaewoo

2018-01-25

Molecular biomarkers that can predict drug efficacy in cancer patients are crucial components for the advancement of precision medicine. However, identifying these molecular biomarkers remains a laborious and challenging task. Next-generation sequencing of patients and preclinical models have increasingly led to the identification of novel gene-mutation-drug relations, and these results have been reported and published in the scientific literature. Here, we present two new computational methods that utilize all the PubMed articles as domain specific background knowledge to assist in the extraction and curation of gene-mutation-drug relations from the literature. The first method uses the Biomedical Entity Search Tool (BEST) scoring results as some of the features to train the machine learning classifiers. The second method uses not only the BEST scoring results, but also word vectors in a deep convolutional neural network model that are constructed from and trained on numerous documents such as PubMed abstracts and Google News articles. Using the features obtained from both the BEST search engine scores and word vectors, we extract mutation-gene and mutation-drug relations from the literature using machine learning classifiers such as random forest and deep convolutional neural networks. Our methods achieved better results compared with the state-of-the-art methods. We used our proposed features in a simple machine learning model, and obtained F1-scores of 0.96 and 0.82 for mutation-gene and mutation-drug relation classification, respectively. We also developed a deep learning classification model using convolutional neural networks, BEST scores, and the word embeddings that are pre-trained on PubMed or Google News data. Using deep learning, the classification accuracy improved, and F1-scores of 0.96 and 0.86 were obtained for the mutation-gene and mutation-drug relations, respectively. We believe that our computational methods described in this research could be

BIOSPIDA: A Relational Database Translator for NCBI.

Science.gov (United States)

Hagen, Matthew S; Lee, Eva K

2010-11-13

As the volume and availability of biological databases continue widespread growth, it has become increasingly difficult for research scientists to identify all relevant information for biological entities of interest. Details of nucleotide sequences, gene expression, molecular interactions, and three-dimensional structures are maintained across many different databases. To retrieve all necessary information requires an integrated system that can query multiple databases with minimized overhead. This paper introduces a universal parser and relational schema translator that can be utilized for all NCBI databases in Abstract Syntax Notation (ASN.1). The data models for OMIM, Entrez-Gene, Pubmed, MMDB and GenBank have been successfully converted into relational databases and all are easily linkable helping to answer complex biological questions. These tools facilitate research scientists to locally integrate databases from NCBI without significant workload or development time.

Autobiographical memory in Parkinson's disease: a retrieval deficit.

Science.gov (United States)

Souchay, Celine; Smith, Sarah Jane

2013-09-01

This study examined the effects of providing cues to facilitate autobiographical memory retrieval in Parkinson's disease. Previous findings have shown that individuals with Parkinson's disease retrieve fewer specific autobiographical memories than older adult controls. These findings are clinically significant since the quality of autobiographical memory is linked to identity and sense of self. In the current study, 16 older adults with Parkinson's disease without dementia and 16 matched older adult controls were given 3 min in which to recall autobiographical memories associated with five different time periods and to give each memory a short title. Participants were later asked to retrieve the memories in three phases: firstly in a free recall phase; secondly in response to general cues (time periods) and finally in response to specific cues (the short titles previously given). The number of memories and the quality of the memory (general or specific) was recorded in each condition. Compared with matched older adult controls, the Parkinson's disease group was impaired in retrieving the memories that they had previously given in the free recall phase and in response to general cues. The performance of the group with Parkinson's disease was only equivalent to the older adults when they retrieved memories in response to self-generated cues. The findings are discussed in relation to theories of autobiographical memory and the neuropsychology of Parkinson's disease. © 2013 The British Psychological Society.

Demographic factors and retrieval of object and proper names after age 70.

Directory of Open Access Journals (Sweden)

Gitit Kavé

Full Text Available This research aimed to investigate whether demographic factors are similarly related to retrieval of object and proper names.The sample included 5,907 individuals above age 70 who participated in the Health and Retirement Study between 2004 and 2012. Participants were asked to name two objects as well as the US President and Vice President. Latent growth curve models examined the associations of age, education, and self-rated health with baseline levels and change trajectories in retrieval.Age and education were more strongly related to retrieval of proper names than to retrieval of object names, both for baseline scores and for change trajectory. Similar effects of self-rated health emerged for both types of stimuli.The results show that examining object names and proper names together as indication of cognitive status in the HRS might overlook important differences between the two types of stimuli, in both baseline performance and longitudinal change.

Episodic memory retrieval in adolescents with and without developmental language disorder (DLD).

Science.gov (United States)

Lee, Joanna C

2018-03-01

Two reasons may explain the discrepant findings regarding declarative memory in developmental language disorder (DLD) in the literature. First, standardized tests are one of the primary tools used to assess declarative memory in previous studies. It is possible they are not sensitive enough to subtle memory impairment. Second, the system underlying declarative memory is complex, and thus results may vary depending on the types of encoding and retrieval processes measured (e.g., item specific or relational) and/or task demands (e.g., recall or recognition during memory retrieval). To adopt an experimental paradigm to examine episodic memory functioning in adolescents with and without DLD, with the focus on memory recognition of item-specific and relational information. Two groups of adolescents, one with DLD (n = 23; mean age = 16.73 years) and the other without (n = 23; mean age = 16.75 years), participated in the study. The Relational and Item-Specific Encoding (RISE) paradigm was used to assess the effect of different encoding processes on episodic memory retrieval in DLD. The advantage of using the RISE task is that both item-specific and relational encoding/retrieval can be examined within the same learning paradigm. Adolescents with DLD and those with typical language development showed comparable engagement during the encoding phase. The DLD group showed significantly poorer item recognition than the comparison group. Associative recognition was not significantly different between the two groups; however, there was a non-significant trend for to be poorer in the DLD group than in the comparison group, suggesting a possible impairment in associative recognition in individuals with DLD, but to a lesser magnitude. These results indicate that adolescents with DLD have difficulty with episodic memory retrieval when stimuli are encoded and retrieved without support from contextual information. Associative recognition is relatively less affected than item

A Neuroanatomical Model of Prefrontal Inhibitory Modulation of Memory Retrieval

Science.gov (United States)

Depue, Brendan E.

2012-01-01

Memory of past experience is essential for guiding goal-related behavior. Being able to control accessibility of memory through modulation of retrieval enables humans to flexibly adapt to their environment. Understanding the specific neural pathways of how this control is achieved has largely eluded cognitive neuroscience. Accordingly, in the current paper I review literature that examines the overt control over retrieval in order to reduce accessibility. I first introduce three hypotheses of inhibition of retrieval. These hypotheses involve: i) attending to other stimuli as a form of diversionary attention, ii) inhibiting the specific individual neural representation of the memory, and iii) inhibiting the hippocampus and retrieval process more generally to prevent reactivation of the representation. I then analyze literature taken from the White Bear Suppression, Directed Forgetting and Think/No-Think tasks to provide evidence for these hypotheses. Finally, a neuroanatomical model is developed to indicate three pathways from PFC to the hippocampal complex that support inhibition of memory retrieval. Describing these neural pathways increases our understanding of control over memory in general. PMID:22374224

Resolving Interference between Body Movements: Retrieval-Induced Forgetting of Motor Sequences

Science.gov (United States)

Tempel, Tobias; Frings, Christian

2013-01-01

When body movements are stored in memory in an organized manner, linked to a common retrieval cue like the effector with which to execute the movement, interference may arise as soon as one initiates the execution of a specific body movement in the presence of the retrieval cue because related motor programs also are activated. We investigated the…

[Phylogenetic analysis of closely related Leuconostoc citreum species based on partial housekeeping genes].

Science.gov (United States)

Lv, Qiang; Chen, Ming; Xu, Haiyan; Song, Yuqin; Sun, Zhihong; Dan, Tong; Sun, Tiansong

2013-07-04

Using the 16S rRNA, dnaA, murC and pyrG gene sequences, we identified the phylogenetic relationship among closely related Leuconostoc citreum species. Seven Leu. citreum strains originally isolated from sourdough were characterized by PCR methods to amplify the dnaA, murC and pyrG gene sequences, which were determined to assess the suitability as phylogenetic markers. Then, we estimated the genetic distance and constructed the phylogenetic trees including 16S rRNA and above mentioned three housekeeping genes combining with published corresponding sequences. By comparing the phylogenetic trees, the topology of three housekeeping genes trees were consistent with that of 16S rRNA gene. The homology of closely related Leu. citreum species among dnaA, murC, pyrG and 16S rRNA gene sequences were different, ranged from75.5% to 97.2%, 50.2% to 99.7%, 65.0% to 99.8% and 98.5% 100%, respectively. The phylogenetic relationship of three housekeeping genes sequences were highly consistent with the results of 16S rRNA gene sequence, while the genetic distance of these housekeeping genes were extremely high than 16S rRNA gene. Consequently, the dnaA, murC and pyrG gene are suitable for classification and identification closely related Leu. citreum species.

A Systematic Investigation into Aging Related Genes in Brain and Their Relationship with Alzheimer's Disease.

Science.gov (United States)

Meng, Guofeng; Zhong, Xiaoyan; Mei, Hongkang

2016-01-01

Aging, as a complex biological process, is accompanied by the accumulation of functional loses at different levels, which makes age to be the biggest risk factor to many neurological diseases. Even following decades of investigation, the process of aging is still far from being fully understood, especially at a systematic level. In this study, we identified aging related genes in brain by collecting the ones with sustained and consistent gene expression or DNA methylation changes in the aging process. Functional analysis with Gene Ontology to these genes suggested transcriptional regulators to be the most affected genes in the aging process. Transcription regulation analysis found some transcription factors, especially Specificity Protein 1 (SP1), to play important roles in regulating aging related gene expression. Module-based functional analysis indicated these genes to be associated with many well-known aging related pathways, supporting the validity of our approach to select aging related genes. Finally, we investigated the roles of aging related genes on Alzheimer's Disease (AD). We found that aging and AD related genes both involved some common pathways, which provided a possible explanation why aging made the brain more vulnerable to Alzheimer's Disease.

Semantic-based surveillance video retrieval.

Science.gov (United States)

Hu, Weiming; Xie, Dan; Fu, Zhouyu; Zeng, Wenrong; Maybank, Steve

2007-04-01

Visual surveillance produces large amounts of video data. Effective indexing and retrieval from surveillance video databases are very important. Although there are many ways to represent the content of video clips in current video retrieval algorithms, there still exists a semantic gap between users and retrieval systems. Visual surveillance systems supply a platform for investigating semantic-based video retrieval. In this paper, a semantic-based video retrieval framework for visual surveillance is proposed. A cluster-based tracking algorithm is developed to acquire motion trajectories. The trajectories are then clustered hierarchically using the spatial and temporal information, to learn activity models. A hierarchical structure of semantic indexing and retrieval of object activities, where each individual activity automatically inherits all the semantic descriptions of the activity model to which it belongs, is proposed for accessing video clips and individual objects at the semantic level. The proposed retrieval framework supports various queries including queries by keywords, multiple object queries, and queries by sketch. For multiple object queries, succession and simultaneity restrictions, together with depth and breadth first orders, are considered. For sketch-based queries, a method for matching trajectories drawn by users to spatial trajectories is proposed. The effectiveness and efficiency of our framework are tested in a crowded traffic scene.

The medial prefrontal cortex is involved in spatial memory retrieval under partial-cue conditions.

Science.gov (United States)

Jo, Yong Sang; Park, Eun Hye; Kim, Il Hwan; Park, Soon Kwon; Kim, Hyun; Kim, Hyun Taek; Choi, June-Seek

2007-12-05

Brain circuits involved in pattern completion, or retrieval of memory from fragmented cues, were investigated. Using different versions of the Morris water maze, we explored the roles of the CA3 subregion of the hippocampus and the medial prefrontal cortex (mPFC) in spatial memory retrieval under various conditions. In a hidden platform task, both CA3 and mPFC lesions disrupted memory retrieval under partial-cue, but not under full-cue, conditions. For a delayed matching-to-place task, CA3 lesions produced a deficit in both forming and recalling spatial working memory regardless of extramaze cue conditions. In contrast, damage to mPFC impaired memory retrieval only when a fraction of cues was available. To corroborate the lesion study, we examined the expression of the immediate early gene c-fos in mPFC and the hippocampus. After training of spatial reference memory in full-cue conditions for 6 d, the same training procedure in the absence of all cues except one increased the number of Fos-immunoreactive cells in mPFC and CA3. Furthermore, mPFC inactivation with muscimol, a GABA agonist, blocked memory retrieval in the degraded-cue environment. However, mPFC-lesioned animals initially trained in a single-cue environment had no difficulty in retrieving spatial memory when the number of cues was increased, demonstrating that contextual change per se did not impair the behavioral performance of the mPFC-lesioned animals. Together, these findings strongly suggest that pattern completion requires interactions between mPFC and the hippocampus, in which mPFC plays significant roles in retrieving spatial information maintained in the hippocampus for efficient navigation.

The Development of Relevance in Information Retrieval

Directory of Open Access Journals (Sweden)

Mu-hsuan Huang

1997-12-01

Full Text Available This article attempts to investigate the notion of relevance in information retrieval. It discusses various definitions for relevance from historical viewpoints and the characteristics of relevance judgments. Also, it introduces empirical results of important related researches.[Article content in Chinese

EST sequencing and gene expression profiling of defence-related genes from Persea americana infected with Phytophthora cinnamomi

Directory of Open Access Journals (Sweden)

Mahomed Waheed

2011-11-01

Full Text Available Abstract Background Avocado (Persea americana belongs to the Lauraceae family and is an important commercial fruit crop in over 50 countries. The most serious pathogen affecting avocado production is Phytophthora cinnamomi which causes Phytophthora root rot (PRR. Root pathogens such as P. cinnamomi and their interactions with hosts are poorly understood and despite the importance of both the avocado crop and the effect Phytophthora has on its cultivation, there is a lack of molecular knowledge underpinning our understanding of defence strategies against the pathogen. In order to initiate a better understanding of host-specific defence we have generated EST data using 454 pyrosequencing and profiled nine defence-related genes from Pc-infected avocado roots. Results 2.0 Mb of data was generated consisting of ~10,000 reads on a single lane of the GS FLX platform. Using the Newbler assembler 371 contigs were assembled, of which 367 are novel for Persea americana. Genes were classified according to Gene Ontology terms. In addition to identifying root-specific ESTs we were also able to identify and quantify the expression of nine defence-related genes that were differentially regulated in response to P. cinnamomi. Genes such as metallothionein, thaumatin and the pathogenesis related PsemI, mlo and profilin were found to be differentially regulated. Conclusions This is the first study in elucidating the avocado root transcriptome as well as identifying defence responses of avocado roots to the root pathogen P. cinnamomi. Our data is currently the only EST data that has been generated for avocado rootstocks, and the ESTs identified in this study have already been useful in identifying defence-related genes as well as providing gene information for other studies looking at processes such as ROS regulation as well as hypoxia in avocado roots. Our EST data will aid in the elucidation of the avocado transcriptome and identification of markers for improved

Ocean Wave Parameters Retrieval from Sentinel-1 SAR Imagery

Directory of Open Access Journals (Sweden)

Weizeng Shao

2016-08-01

Full Text Available In this paper, a semi-empirical algorithm for significant wave height (Hs and mean wave period (Tmw retrieval from C-band VV-polarization Sentinel-1 synthetic aperture radar (SAR imagery is presented. We develop a semi-empirical function for Hs retrieval, which describes the relation between Hs and cutoff wavelength, radar incidence angle, and wave propagation direction relative to radar look direction. Additionally, Tmw can be also calculated through Hs and cutoff wavelength by using another empirical function. We collected 106 C-band stripmap mode Sentinel-1 SAR images in VV-polarization and wave measurements from in situ buoys. There are a total of 150 matchup points. We used 93 matchups to tune the coefficients of the semi-empirical algorithm and the rest 57 matchups for validation. The comparison shows a 0.69 m root mean square error (RMSE of Hs with a 18.6% of scatter index (SI and 1.98 s RMSE of Tmw with a 24.8% of SI. Results indicate that the algorithm is suitable for wave parameters retrieval from Sentinel-1 SAR data.

The GRAPE aerosol retrieval algorithm

Directory of Open Access Journals (Sweden)

G. E. Thomas

2009-11-01

Full Text Available The aerosol component of the Oxford-Rutherford Aerosol and Cloud (ORAC combined cloud and aerosol retrieval scheme is described and the theoretical performance of the algorithm is analysed. ORAC is an optimal estimation retrieval scheme for deriving cloud and aerosol properties from measurements made by imaging satellite radiometers and, when applied to cloud free radiances, provides estimates of aerosol optical depth at a wavelength of 550 nm, aerosol effective radius and surface reflectance at 550 nm. The aerosol retrieval component of ORAC has several incarnations – this paper addresses the version which operates in conjunction with the cloud retrieval component of ORAC (described by Watts et al., 1998, as applied in producing the Global Retrieval of ATSR Cloud Parameters and Evaluation (GRAPE data-set.

The algorithm is described in detail and its performance examined. This includes a discussion of errors resulting from the formulation of the forward model, sensitivity of the retrieval to the measurements and a priori constraints, and errors resulting from assumptions made about the atmospheric/surface state.

Dress like a Star: Retrieving Fashion Products from Videos

OpenAIRE

Garcia, Noa; Vogiatzis, George

2017-01-01

This work proposes a system for retrieving clothing and fashion products from video content. Although films and television are the perfect showcase for fashion brands to promote their products, spectators are not always aware of where to buy the latest trends they see on screen. Here, a framework for breaking the gap between fashion products shown on videos and users is presented. By relating clothing items and video frames in an indexed database and performing frame retrieval with temporal a...

Identification of immunity related genes to study the Physalis peruviana--Fusarium oxysporum pathosystem.

Science.gov (United States)

Enciso-Rodríguez, Felix E; González, Carolina; Rodríguez, Edwin A; López, Camilo E; Landsman, David; Barrero, Luz Stella; Mariño-Ramírez, Leonardo

2013-01-01

The Cape gooseberry (Physalisperuviana L) is an Andean exotic fruit with high nutritional value and appealing medicinal properties. However, its cultivation faces important phytosanitary problems mainly due to pathogens like Fusarium oxysporum, Cercosporaphysalidis and Alternaria spp. Here we used the Cape gooseberry foliar transcriptome to search for proteins that encode conserved domains related to plant immunity including: NBS (Nucleotide Binding Site), CC (Coiled-Coil), TIR (Toll/Interleukin-1 Receptor). We identified 74 immunity related gene candidates in P. peruviana which have the typical resistance gene (R-gene) architecture, 17 Receptor like kinase (RLKs) candidates related to PAMP-Triggered Immunity (PTI), eight (TIR-NBS-LRR, or TNL) and nine (CC-NBS-LRR, or CNL) candidates related to Effector-Triggered Immunity (ETI) genes among others. These candidate genes were categorized by molecular function (98%), biological process (85%) and cellular component (79%) using gene ontology. Some of the most interesting predicted roles were those associated with binding and transferase activity. We designed 94 primers pairs from the 74 immunity-related genes (IRGs) to amplify the corresponding genomic regions on six genotypes that included resistant and susceptible materials. From these, we selected 17 single band amplicons and sequenced them in 14 F. oxysporum resistant and susceptible genotypes. Sequence polymorphisms were analyzed through preliminary candidate gene association, which allowed the detection of one SNP at the PpIRG-63 marker revealing a nonsynonymous mutation in the predicted LRR domain suggesting functional roles for resistance.

Identification of immunity related genes to study the Physalis peruviana--Fusarium oxysporum pathosystem.

Directory of Open Access Journals (Sweden)

Felix E Enciso-Rodríguez

Full Text Available The Cape gooseberry (Physalisperuviana L is an Andean exotic fruit with high nutritional value and appealing medicinal properties. However, its cultivation faces important phytosanitary problems mainly due to pathogens like Fusarium oxysporum, Cercosporaphysalidis and Alternaria spp. Here we used the Cape gooseberry foliar transcriptome to search for proteins that encode conserved domains related to plant immunity including: NBS (Nucleotide Binding Site, CC (Coiled-Coil, TIR (Toll/Interleukin-1 Receptor. We identified 74 immunity related gene candidates in P. peruviana which have the typical resistance gene (R-gene architecture, 17 Receptor like kinase (RLKs candidates related to PAMP-Triggered Immunity (PTI, eight (TIR-NBS-LRR, or TNL and nine (CC-NBS-LRR, or CNL candidates related to Effector-Triggered Immunity (ETI genes among others. These candidate genes were categorized by molecular function (98%, biological process (85% and cellular component (79% using gene ontology. Some of the most interesting predicted roles were those associated with binding and transferase activity. We designed 94 primers pairs from the 74 immunity-related genes (IRGs to amplify the corresponding genomic regions on six genotypes that included resistant and susceptible materials. From these, we selected 17 single band amplicons and sequenced them in 14 F. oxysporum resistant and susceptible genotypes. Sequence polymorphisms were analyzed through preliminary candidate gene association, which allowed the detection of one SNP at the PpIRG-63 marker revealing a nonsynonymous mutation in the predicted LRR domain suggesting functional roles for resistance.

Impact of an inferior vena cava filter retrieval algorithm on filter retrieval rates in a cancer population.

Science.gov (United States)

Litwin, Robert J; Huang, Steven Y; Sabir, Sharjeel H; Hoang, Quoc B; Ahrar, Kamran; Ahrar, Judy; Tam, Alda L; Mahvash, Armeen; Ensor, Joe E; Kroll, Michael; Gupta, Sanjay

2017-09-01

Our primary purpose was to assess the impact of an inferior vena cava filter retrieval algorithm in a cancer population. Because cancer patients are at persistently elevated risk for development of venous thromboembolism (VTE), our secondary purpose was to assess the incidence of recurrent VTE in patients who underwent filter retrieval. Patients with malignant disease who had retrievable filters placed at a tertiary care cancer hospital from August 2010 to July 2014 were retrospectively studied. A filter retrieval algorithm was established in August 2012. Patients and referring physicians were contacted in the postintervention period when review of the medical record indicated that filter retrieval was clinically appropriate. Patients were classified into preintervention (August 2010-July 2012) and postintervention (August 2012-July 2014) study cohorts. Retrieval rates and clinical pathologic records were reviewed. Filter retrieval was attempted in 34 (17.4%) of 195 patients in the preintervention cohort and 66 (32.8%) of 201 patients in the postintervention cohort (P filter retrieval in the preintervention and postintervention cohorts was 60 days (range, 20-428 days) and 107 days (range, 9-600 days), respectively (P = .16). In the preintervention cohort, 49 of 195 (25.1%) patients were lost to follow-up compared with 24 of 201 (11.9%) patients in the postintervention cohort (P filter placement to death, when available. The overall survival for patients whose filters were retrieved was longer compared with the overall survival for patients whose filters were not retrieved (P filter retrieval, two patients (2.5%) suffered from recurrent VTE (n = 1 nonfatal pulmonary embolism; n = 1 deep venous thrombosis). Both patients were treated with anticoagulation without filter replacement. Inferior vena cava filter retrieval rates can be significantly increased in patients with malignant disease with a low rate (2.5%) of recurrent VTE after filter retrieval

Retrieval orientation and the control of recollection: an fMRI study

Science.gov (United States)

Morcom, Alexa M.; Rugg, Michael D.

2012-01-01

The present study used event-related fMRI to examine the impact of the adoption of different retrieval orientations on the neural correlates of recollection. In each of two study-test blocks, subjects encoded a mixed list of words and pictures, and then performed a recognition memory task with words as the test items. In one block, the requirement was to respond positively to test items corresponding to studied words, and to reject both new items and items corresponding to the studied pictures. In the other block, positive responses were made to test items corresponding to pictures, and items corresponding to words were classified along with the new items. Based on previous event-related potential (ERP) findings, we predicted that in the word task, recollection-related effects would be found for target information only. This prediction was fulfilled. In both tasks, targets elicited the characteristic pattern of recollection-related activity. By contrast, non-targets elicited this pattern in the picture task, but not in the word task. Importantly, the left angular gyrus was among the regions demonstrating this dissociation of non-target recollection effects according to retrieval orientation. The findings for the angular gyrus parallel prior findings for the `left-parietal' ERP old/new effect, and add to the evidence that the effect reflects recollection-related neural activity originating in left ventral parietal cortex. Thus, the results converge with the previous ERP findings to suggest that the processing of retrieval cues can be constrained to prevent the retrieval of goal-irrelevant information. PMID:23110678

Applying Semantic Web technologies to improve the retrieval, credibility and use of health-related web resources.

Science.gov (United States)

Mayer, Miguel A; Karampiperis, Pythagoras; Kukurikos, Antonis; Karkaletsis, Vangelis; Stamatakis, Kostas; Villarroel, Dagmar; Leis, Angela

2011-06-01

The number of health-related websites is increasing day-by-day; however, their quality is variable and difficult to assess. Various "trust marks" and filtering portals have been created in order to assist consumers in retrieving quality medical information. Consumers are using search engines as the main tool to get health information; however, the major problem is that the meaning of the web content is not machine-readable in the sense that computers cannot understand words and sentences as humans can. In addition, trust marks are invisible to search engines, thus limiting their usefulness in practice. During the last five years there have been different attempts to use Semantic Web tools to label health-related web resources to help internet users identify trustworthy resources. This paper discusses how Semantic Web technologies can be applied in practice to generate machine-readable labels and display their content, as well as to empower end-users by providing them with the infrastructure for expressing and sharing their opinions on the quality of health-related web resources.

Extinction learning, which consists of the inhibition of retrieval, can be learned without retrieval.

Science.gov (United States)

de Carvalho Myskiw, Jociane; Furini, Cristiane Regina Guerino; Schmidt, Bianca; Ferreira, Flávia; Izquierdo, Ivan

2015-01-13

In the present study we test the hypothesis that extinction is not a consequence of retrieval in unreinforced conditioned stimulus (CS) presentation but the mere perception of the CS in the absence of a conditioned response. Animals with cannulae implanted in the CA1 region of hippocampus were subjected to extinction of contextual fear conditioning. Muscimol infused intra-CA1 before an extinction training session of contextual fear conditioning (CFC) blocks retrieval but not consolidation of extinction measured 24 h later. Additionally, this inhibition of retrieval does not affect early persistence of extinction when tested 7 d later or its spontaneous recovery after 2 wk. Furthermore, both anisomycin, an inhibitor of ribosomal protein synthesis, and rapamycin, an inhibitor of extraribosomal protein synthesis, given into the CA1, impair extinction of CFC regardless of whether its retrieval was blocked by muscimol. Therefore, retrieval performance in the first unreinforced session is not necessary for the installation, maintenance, or spontaneous recovery of extinction of CFC.

Ocorrência do SNP c.767G>T no gene DNM1responsável pelo colapso induzido pelo exercício em cães da raça Labrador Retriever no Estado de São Paulo

Directory of Open Access Journals (Sweden)

Roberta M. Basso

2015-05-01

Full Text Available Resumo:O colapso induzido pelo exercício (EIC é considerado uma síndrome autossômica recessiva que afeta principalmente cães da raça Labrador Retriever. A doença é caracterizada por fraqueza muscular e colapso após exercício intenso. Usualmente, ocorre recuperação clínica após o episódio, mas alguns animais podem vir a óbito. Os sinais clínicos são decorrentes do polimorfismo de base única (SNP c.767G>T no gene Dynamin 1 (DNM1. O objetivo deste trabalho foi determinar a ocorrência deste SNP em 321 cães da raça Labrador Retriever do Estado de São Paulo. Primers específicos para a amplificação de todo o exon 6 do gene DNM1 foram usados nas PCRs utilizando DNA a partir de amostras de sangue ou swab bucal, a avaliação final foi realizada com sequenciamento direto dos produtos da PCR. Dentre os 321 animais estudados, 3,4 % (11/321 eram homozigotos para o SNP c.767G>T no gene DNM1 e 24,6% (79/321 eram heterozigotos. Somente um dos 11 animais homozigotos apresentavam sinais clínicos compatíveis com a EIC. Este é o primeiro estudo sobre a ocorrência deste SNP no Brasil e considerando que quase 25% dos animais estudados eram heterozigotos, a genotipagem dos animais para este SNP pode ser importante antes dos acasalamentos para cães desta raça. A EIC deve ser considerada nos diagnósticos diferenciais de enfermidades neuromusculares em cães da raça Labrador Retriever.

Task Oriented Tools for Information Retrieval

Science.gov (United States)

Yang, Peilin

2017-01-01

Information Retrieval (IR) is one of the most evolving research fields and has drawn extensive attention in recent years. Because of its empirical nature, the advance of the IR field is closely related to the development of various toolkits. While the traditional IR toolkit mainly provides a platform to evaluate the effectiveness of retrieval…

A stochastic cloud model for cloud and ozone retrievals from UV measurements

International Nuclear Information System (INIS)

Efremenko, Dmitry S.; Schüssler, Olena; Doicu, Adrian; Loyola, Diego

2016-01-01

The new generation of satellite instruments provides measurements in and around the Oxygen A-band on a global basis and with a relatively high spatial resolution. These data are commonly used for the determination of cloud properties. A stochastic model and radiative transfer model, previously developed by the authors, is used as the forward model component in retrievals of cloud parameters and ozone total and partial columns. The cloud retrieval algorithm combines local and global optimization routines, and yields a retrieval accuracy of about 1% and a fast computational time. Retrieved parameters are the cloud optical thickness and the cloud-top height. It was found that the use of the independent pixel approximation instead of the stochastic cloud model leads to large errors in the retrieved cloud parameters, as well as, in the retrieved ozone height resolved partial columns. The latter can be reduced by using the stochastic cloud model to compute the optimal value of the regularization parameter in the framework of Tikhonov regularization. - Highlights: • A stochastic radiative transfer model for retrieving clouds/ozone is designed. • Errors of independent pixel approximation (IPA) for O3 total column are small. • The error of IPA for ozone profile retrieval may become large. • The use of stochastic model reduces the error of ozone profile retrieval.

FRESCO+: an improved O2 A-band cloud retrieval algorithm for tropospheric trace gas retrievals

Directory of Open Access Journals (Sweden)

M. van Roozendael

2008-11-01

Full Text Available The FRESCO (Fast Retrieval Scheme for Clouds from the Oxygen A-band algorithm has been used to retrieve cloud information from measurements of the O2 A-band around 760 nm by GOME, SCIAMACHY and GOME-2. The cloud parameters retrieved by FRESCO are the effective cloud fraction and cloud pressure, which are used for cloud correction in the retrieval of trace gases like O3 and NO2. To improve the cloud pressure retrieval for partly cloudy scenes, single Rayleigh scattering has been included in an improved version of the algorithm, called FRESCO+. We compared FRESCO+ and FRESCO effective cloud fractions and cloud pressures using simulated spectra and one month of GOME measured spectra. As expected, FRESCO+ gives more reliable cloud pressures over partly cloudy pixels. Simulations and comparisons with ground-based radar/lidar measurements of clouds show that the FRESCO+ cloud pressure is about the optical midlevel of the cloud. Globally averaged, the FRESCO+ cloud pressure is about 50 hPa higher than the FRESCO cloud pressure, while the FRESCO+ effective cloud fraction is about 0.01 larger. The effect of FRESCO+ cloud parameters on O3 and NO2 vertical column density (VCD retrievals is studied using SCIAMACHY data and ground-based DOAS measurements. We find that the FRESCO+ algorithm has a significant effect on tropospheric NO2 retrievals but a minor effect on total O3 retrievals. The retrieved SCIAMACHY tropospheric NO2 VCDs using FRESCO+ cloud parameters (v1.1 are lower than the tropospheric NO2VCDs which used FRESCO cloud parameters (v1.04, in particular over heavily polluted areas with low clouds. The difference between SCIAMACHY tropospheric NO2 VCDs v1.1 and ground-based MAXDOAS measurements performed in Cabauw, The Netherlands, during the DANDELIONS campaign is about −2.12×1014molec cm−2.

Wellhead bowl protector and retrieving tool

International Nuclear Information System (INIS)

Young, J.A.

1991-01-01

This patent describes improvement in a wellhead protection system including a wear bushing and a retrieving tool. The improvement comprises a wear bushing supported within the wellhead, wherein the wear bushing includes an enlarged upper end having an external support shoulder for engagement with an internal support shoulder formed in the wellhead; wherein the wear bushing further includes an internal circumferential slot intersected by at least one vertically extending slot, the vertical slot extending from the circumferential slot to the upper end of the wear bushing; a retrieving tool having at least one outwardly biased, retractable lug member mounted thereon; and wherein the retrieving tool includes an enlarged portion adapted to be received within the enlarged upper end of the wear bushing. This patent also describes a method of retrieving a wear bushing from a wellhead comprising the steps of: lowering a retrieving tool into the wellhead for locking engagement with the wear bushing; aligning the retrieving tool with the wear bushing for automatically forcing lug members carried by the retrieving tool outwardly into locking engagement with the wear bushing; monitoring drill string weight for determining engagement of the retrieving tool with the wear bushing, wherein a substantial decrease in drill string weight is an indication that the retrieving tool is engaged with the wear bushing; and removing the wear bushing from the wellhead

Transcriptional regulation of genes related to progesterone production.

Science.gov (United States)

Mizutani, Tetsuya; Ishikane, Shin; Kawabe, Shinya; Umezawa, Akihiro; Miyamoto, Kaoru

2015-01-01

Steroid hormones are synthesized from cholesterol in various tissues, mainly in the adrenal glands and gonads. Because these lipid-soluble steroid hormones immediately diffuse through the cells in which they are produced, their secretion directly reflects the activity of the genes related to their production. Progesterone is important not only for luteinization and maintenance of pregnancy, but also as a substrate for most other steroids. Steroidogenic acute regulatory protein (STAR), cytochrome P450 cholesterol side-chain cleavage enzyme (P450scc), and 3β-hydroxysteroid dehydrogenase/Δ(5)-Δ(4) isomerase (3β-HSD) are well-known proteins essential for progesterone production. In addition to them, glutathione S-transferase A1-1 and A3-3 are shown to exert Δ(5)-Δ(4) isomerization activity to produce progesterone in a cooperative fashion with 3β-HSD. 5-Aminolevulinic acid synthase 1, ferredoxin 1, and ferredoxin reductase also play a role in steroidogenesis as accessory factors. Members of the nuclear receptor 5A (NR5A) family (steroidogenic factor 1 and liver receptor homolog 1) play a crucial role in the transcriptional regulation of these genes. The NR5A family activates these genes by binding to NR5A responsive elements present within their promoter regions, as well as to the elements far from their promoters. In addition, various NR5A-interacting proteins including peroxisome proliferator-activated receptor-γ coactivator-1α (PGC-1α), nuclear receptor subfamily 0, group B, member 1 (DAX-1), and CCAAT/enhancer-binding proteins (C/EBP) are involved in the transcription of NR5A target genes and regulate the transcription either positively or negatively under both basal and tropic hormone-stimulated conditions. In this review, we describe the transcriptional regulation of genes related to progesterone production.

Radiographic features of Golden Retriever muscular dystrophy.

Science.gov (United States)

Brumitt, Jason W; Essman, Stephanie C; Kornegay, Joe N; Graham, John P; Weber, William J; Berry, Clifford R

2006-01-01

Golden Retriever muscular dystrophy is an inherited, degenerative myopathy due to the absence of dystrophin and is used as a model of Duchenne muscular dystrophy of young boys. This report describes the radiographic abnormalities of Golden Retriever muscular dystrophy in 26 dogs. The thoracic abnormalities included diaphragmatic asymmetry (18/26), diaphragmatic undulation (18/26), and gastro-esophageal hiatal hernia (6/26). Pelvic abnormalities included narrowing of the body of the ilia (14/19), ventral deviation and curvature of the tuber ischii (14/19), elongation of the obturator foramen with a decrease in opacity of the surrounding bone (12/19), and lateral flaring of the wings of the ilia (12/19). Abdominal abnormalities consisted of hepatomegaly (14/22) and poor serosal detail (12/22). The unique thoracic abnormalities were a consistent finding in affected Golden Retriever muscular dystrophy dogs. The diagnosis of muscular dystrophy should be included in the differential list if the combination of diaphragm undulation and asymmetry, and gastro-esophageal hiatal hernia are identified. These diaphragmatic abnormalities are related to hypertrophy and hyperplasia of the diaphragm. Additionally, the skeletal changes of pelvic tilt, elongation of the pelvis, widening of the obturator foramina and thinning of the ischiatic tables appear to be specific to Golden Retriever muscular dystrophy in dogs. These pelvic abnormalities are most likely secondary to bone remodeling associated with the progressive skeletal myopathy and subsequent contracture/fibrosis.

Adaptive neuro-fuzzy inference system for temperature and humidity profile retrieval from microwave radiometer observations

Science.gov (United States)

Ramesh, K.; Kesarkar, A. P.; Bhate, J.; Venkat Ratnam, M.; Jayaraman, A.

2015-01-01

The retrieval of accurate profiles of temperature and water vapour is important for the study of atmospheric convection. Recent development in computational techniques motivated us to use adaptive techniques in the retrieval algorithms. In this work, we have used an adaptive neuro-fuzzy inference system (ANFIS) to retrieve profiles of temperature and humidity up to 10 km over the tropical station Gadanki (13.5° N, 79.2° E), India. ANFIS is trained by using observations of temperature and humidity measurements by co-located Meisei GPS radiosonde (henceforth referred to as radiosonde) and microwave brightness temperatures observed by radiometrics multichannel microwave radiometer MP3000 (MWR). ANFIS is trained by considering these observations during rainy and non-rainy days (ANFIS(RD + NRD)) and during non-rainy days only (ANFIS(NRD)). The comparison of ANFIS(RD + NRD) and ANFIS(NRD) profiles with independent radiosonde observations and profiles retrieved using multivariate linear regression (MVLR: RD + NRD and NRD) and artificial neural network (ANN) indicated that the errors in the ANFIS(RD + NRD) are less compared to other retrieval methods. The Pearson product movement correlation coefficient (r) between retrieved and observed profiles is more than 92% for temperature profiles for all techniques and more than 99% for the ANFIS(RD + NRD) technique Therefore this new techniques is relatively better for the retrieval of temperature profiles. The comparison of bias, mean absolute error (MAE), RMSE and symmetric mean absolute percentage error (SMAPE) of retrieved temperature and relative humidity (RH) profiles using ANN and ANFIS also indicated that profiles retrieved using ANFIS(RD + NRD) are significantly better compared to the ANN technique. The analysis of profiles concludes that retrieved profiles using ANFIS techniques have improved the temperature retrievals substantially; however, the retrieval of RH by all techniques considered in this paper (ANN, MVLR and

An improvement of the retrieval of temperature and relative humidity profiles from a combination of active and passive remote sensing

Science.gov (United States)

Che, Yunfei; Ma, Shuqing; Xing, Fenghua; Li, Siteng; Dai, Yaru

2018-03-01

This paper focuses on an improvement of the retrieval of atmospheric temperature and relative humidity profiles through combining active and passive remote sensing. Ground-based microwave radiometer and millimeter-wavelength cloud radar were used to acquire the observations. Cloud base height and cloud thickness determinations from cloud radar were added into the atmospheric profile retrieval process, and a back-propagation neural network method was used as the retrieval tool. Because a substantial amount of data are required to train a neural network, and as microwave radiometer data are insufficient for this purpose, 8 years of radiosonde data from Beijing were used as the database. The monochromatic radiative transfer model was used to calculate the brightness temperatures in the same channels as the microwave radiometer. Parts of the cloud base heights and cloud thicknesses in the training data set were also estimated using the radiosonde data. The accuracy of the results was analyzed through a comparison with L-band sounding radar data and quantified using the mean bias, root-mean-square error (RMSE), and correlation coefficient. The statistical results showed that an inversion with cloud information was the optimal method. Compared with the inversion profiles without cloud information, the RMSE values after adding cloud information reduced to varying degrees for the vast majority of height layers. These reductions were particularly clear in layers with clouds. The maximum reduction in the RMSE for the temperature profile was 2.2 K, while that for the humidity profile was 16%.

Protein expression and genetic variability of canine Can f 1 in golden and Labrador retriever service dogs.

Science.gov (United States)

Breitenbuecher, Christina; Belanger, Janelle M; Levy, Kerinne; Mundell, Paul; Fates, Valerie; Gershony, Liza; Famula, Thomas R; Oberbauer, Anita M

2016-01-01

Valued for trainability in diverse tasks, dogs are the primary service animal used to assist individuals with disabilities. Despite their utility, many people in need of service dogs are sensitive to the primary dog allergen, Can f 1, encoded by the Lipocalin 1 gene (LCN1). Several organizations specifically breed service dogs to meet special needs and would like to reduce allergenic potential if possible. In this study, we evaluated the expression of Can f 1 protein and the inherent variability of LCN1 in two breeds used extensively as service dogs. Saliva samples from equal numbers of male and female Labrador retrievers (n = 12), golden retrievers (n = 12), and Labrador-golden crosses (n = 12) were collected 1 h after the morning meal. Can f 1 protein concentrations in the saliva were measured by ELISA, and the LCN1 5' and 3' UTRs and exons sequenced. There was no sex effect (p > 0.2) nor time-of-day effect; however, Can f 1 protein levels varied by breed with Labrador retrievers being lower than golden retrievers (3.18 ± 0.51 and 5.35 ± 0.52 μg/ml, respectively, p < 0.0075), and the Labrador-golden crosses having intermediate levels (3.77 ± 0.48 μg/ml). Although several novel SNPs were identified in LCN1, there were no significant breed-specific sequence differences in the gene and no association of LCN1 genotypes with Can f 1 expression. As service dogs, Labrador retrievers likely have lower allergenic potential and, though there were no DNA sequence differences identified, classical genetic selection on the estimated breeding values associated with salivary Can f 1 expression may further reduce that potential.

Retrieval from semantic memory.

NARCIS (Netherlands)

Noordman-Vonk, Wietske

1977-01-01

The present study has been concerned with the retrieval of semantic information. Retrieving semantic information is a fundamental process in almost any kind of cognitive behavior. The introduction presented the main experimental paradigms and results found in the literature on semantic memory as

Statistical retrieval of thin liquid cloud microphysical properties using ground-based infrared and microwave observations

Science.gov (United States)

Marke, Tobias; Ebell, Kerstin; Löhnert, Ulrich; Turner, David D.

2016-12-01

In this article, liquid water cloud microphysical properties are retrieved by a combination of microwave and infrared ground-based observations. Clouds containing liquid water are frequently occurring in most climate regimes and play a significant role in terms of interaction with radiation. Small perturbations in the amount of liquid water contained in the cloud can cause large variations in the radiative fluxes. This effect is enhanced for thin clouds (liquid water path, LWP cloud properties crucial. Due to large relative errors in retrieving low LWP values from observations in the microwave domain and a high sensitivity for infrared methods when the LWP is low, a synergistic retrieval based on a neural network approach is built to estimate both LWP and cloud effective radius (reff). These statistical retrievals can be applied without high computational demand but imply constraints like prior information on cloud phase and cloud layering. The neural network retrievals are able to retrieve LWP and reff for thin clouds with a mean relative error of 9% and 17%, respectively. This is demonstrated using synthetic observations of a microwave radiometer (MWR) and a spectrally highly resolved infrared interferometer. The accuracy and robustness of the synergistic retrievals is confirmed by a low bias in a radiative closure study for the downwelling shortwave flux, even for marginally invalid scenes. Also, broadband infrared radiance observations, in combination with the MWR, have the potential to retrieve LWP with a higher accuracy than a MWR-only retrieval.

A Novel Relevance Feedback Approach Based on Similarity Measure Modification in an X-Ray Image Retrieval System Based on Fuzzy Representation Using Fuzzy Attributed Relational Graph

Directory of Open Access Journals (Sweden)

Hossien Pourghassem

2011-04-01

Full Text Available Relevance feedback approaches is used to improve the performance of content-based image retrieval systems. In this paper, a novel relevance feedback approach based on similarity measure modification in an X-ray image retrieval system based on fuzzy representation using fuzzy attributed relational graph (FARG is presented. In this approach, optimum weight of each feature in feature vector is calculated using similarity rate between query image and relevant and irrelevant images in user feedback. The calculated weight is used to tune fuzzy graph matching algorithm as a modifier parameter in similarity measure. The standard deviation of the retrieved image features is applied to calculate the optimum weight. The proposed image retrieval system uses a FARG for representation of images, a fuzzy matching graph algorithm as similarity measure and a semantic classifier based on merging scheme for determination of the search space in image database. To evaluate relevance feedback approach in the proposed system, a standard X-ray image database consisting of 10000 images in 57 classes is used. The improvement of the evaluation parameters shows proficiency and efficiency of the proposed system.

Expression and functional analysis of apoptosis-related gene ...

African Journals Online (AJOL)

Administrator

2011-10-19

Oct 19, 2011 ... conducted a molecular cloning and functional analysis to study a specific silkworm gene BmICAD related to apoptosis. .... blocking with 5% non-fat milk for 1 h at room temperature, the .... requirements for all next experiments.

Validating Satellite-Retrieved Cloud Properties for Weather and Climate Applications

Science.gov (United States)

Minnis, P.; Bedka, K. M.; Smith, W., Jr.; Yost, C. R.; Bedka, S. T.; Palikonda, R.; Spangenberg, D.; Sun-Mack, S.; Trepte, Q.; Dong, X.; Xi, B.

2014-12-01

Cloud properties determined from satellite imager radiances are increasingly used in weather and climate applications, particularly in nowcasting, model assimilation and validation, trend monitoring, and precipitation and radiation analyses. The value of using the satellite-derived cloud parameters is determined by the accuracy of the particular parameter for a given set of conditions, such as viewing and illumination angles, surface background, and cloud type and structure. Because of the great variety of those conditions and of the sensors used to monitor clouds, determining the accuracy or uncertainties in the retrieved cloud parameters is a daunting task. Sensitivity studies of the retrieved parameters to the various inputs for a particular cloud type are helpful for understanding the errors associated with the retrieval algorithm relative to the plane-parallel world assumed in most of the model clouds that serve as the basis for the retrievals. Real world clouds, however, rarely fit the plane-parallel mold and generate radiances that likely produce much greater errors in the retrieved parameter than can be inferred from sensitivity analyses. Thus, independent, empirical methods are used to provide a more reliable uncertainty analysis. At NASA Langley, cloud properties are being retrieved from both geostationary (GEO) and low-earth orbiting (LEO) satellite imagers for climate monitoring and model validation as part of the NASA CERES project since 2000 and from AVHRR data since 1978 as part of the NOAA CDR program. Cloud properties are also being retrieved in near-real time globally from both GEO and LEO satellites for weather model assimilation and nowcasting for hazards such as aircraft icing. This paper discusses the various independent datasets and approaches that are used to assessing the imager-based satellite cloud retrievals. These include, but are not limited to data from ARM sites, CloudSat, and CALIPSO. This paper discusses the use of the various

Discovering implicit entity relation with the gene-citation-gene network.

Directory of Open Access Journals (Sweden)

Min Song

Full Text Available In this paper, we apply the entitymetrics model to our constructed Gene-Citation-Gene (GCG network. Based on the premise there is a hidden, but plausible, relationship between an entity in one article and an entity in its citing article, we constructed a GCG network of gene pairs implicitly connected through citation. We compare the performance of this GCG network to a gene-gene (GG network constructed over the same corpus but which uses gene pairs explicitly connected through traditional co-occurrence. Using 331,411 MEDLINE abstracts collected from 18,323 seed articles and their references, we identify 25 gene pairs. A comparison of these pairs with interactions found in BioGRID reveal that 96% of the gene pairs in the GCG network have known interactions. We measure network performance using degree, weighted degree, closeness, betweenness centrality and PageRank. Combining all measures, we find the GCG network has more gene pairs, but a lower matching rate than the GG network. However, combining top ranked genes in both networks produces a matching rate of 35.53%. By visualizing both the GG and GCG networks, we find that cancer is the most dominant disease associated with the genes in both networks. Overall, the study indicates that the GCG network can be useful for detecting gene interaction in an implicit manner.

Construction, emplacement, and retrievability (preclosure)

International Nuclear Information System (INIS)

McClain, W.

1985-01-01

Each of the three preclosure subgroups of the Construction, Emplacement, and Retrievability Working Group adopted a six-step approach to identify and assess current needs in geotechnical modeling and characterization. This approach may be summarized as follows: identify phenomena related to emplacement of high-level nuclear wastes, identify types of models which are required to calculate the phenomena, establish the input data needs for the models, assess the current availability of the models, assess the current status of documentation, verification, and validation of the models, and determine the adequacy of instrumentation and measurement techniques to (a) validate the models, where necessary, and (b) obtain input data for design. Systematic application of these six steps leads to the establishment of the research requirements for geotechnical modeling and characterization. A summary of modeling techniques which apply to the three subsequent sections on construction, emplacement, and retrievability is presented. Research needs, which apply to all preclosure activities, are summarized

Identifying Novel Candidate Genes Related to Apoptosis from a Protein-Protein Interaction Network

Directory of Open Access Journals (Sweden)

Baoman Wang

2015-01-01

Full Text Available Apoptosis is the process of programmed cell death (PCD that occurs in multicellular organisms. This process of normal cell death is required to maintain the balance of homeostasis. In addition, some diseases, such as obesity, cancer, and neurodegenerative diseases, can be cured through apoptosis, which produces few side effects. An effective comprehension of the mechanisms underlying apoptosis will be helpful to prevent and treat some diseases. The identification of genes related to apoptosis is essential to uncover its underlying mechanisms. In this study, a computational method was proposed to identify novel candidate genes related to apoptosis. First, protein-protein interaction information was used to construct a weighted graph. Second, a shortest path algorithm was applied to the graph to search for new candidate genes. Finally, the obtained genes were filtered by a permutation test. As a result, 26 genes were obtained, and we discuss their likelihood of being novel apoptosis-related genes by collecting evidence from published literature.

TLR-related pathway analysis : novel gene-gene interactions in the development of asthma and atopy

NARCIS (Netherlands)

Reijmerink, N. E.; Bottema, R. W. B.; Kerkhof, M.; Gerritsen, J.; Stelma, F. F.; Thijs, C.; van Schayck, C. P.; Smit, H. A.; Brunekreef, B.; Koppelman, G. H.; Postma, D. S.

P>Background: The toll-like receptor (TLR)-related pathway is important in host defence and may be crucial in the development of asthma and atopy. Numerous studies have shown associations of TLR-related pathway genes with asthma and atopy phenotypes. So far it has not been investigated whether

Remembering episodic memories is not necessary for forgetting of negative words: Semantic retrieval can cause forgetting of negative words.

Science.gov (United States)

Kobayashi, Masanori; Tanno, Yoshihiko

2015-06-01

Retrieval of a memory can induce forgetting of other related memories, which is known as retrieval-induced forgetting. Although most studies have investigated retrieval-induced forgetting by remembering episodic memories, this also can occur by remembering semantic memories. The present study shows that retrieval of semantic memories can lead to forgetting of negative words. In two experiments, participants learned words and then engaged in retrieval practice where they were asked to recall words related to the learned words from semantic memory. Finally, participants completed a stem-cued recall test for the learned words. The results showed forgetting of neutral and negative words, which was characteristic of semantic retrieval-induced forgetting. A certain degree of overlapping features, except same learning episode, is sufficient to cause retrieval-induced forgetting of negative words. Given the present results, we conclude that retrieval-induced forgetting of negative words does not require recollection of episodic memories.

Retrieval of tropospheric NO2 using the MAX-DOAS method combined with relative intensity measurements for aerosol correction

Directory of Open Access Journals (Sweden)

P. F. Levelt

2010-10-01

Full Text Available Multi-Axis Differential Optical Absorption Spectroscopy (MAX-DOAS is a technique to measure trace gas amounts in the lower troposphere from ground-based scattered sunlight observations. MAX-DOAS observations are especially suitable for validation of tropospheric trace gas observations from satellite, since they have a representative range of several kilometers, both in the horizontal and in the vertical dimension. A two-step retrieval scheme is presented here, to derive aerosol corrected tropospheric NO2 columns from MAX-DOAS observations. In a first step, boundary layer aerosols, characterized in terms of aerosol optical thickness (AOT, are estimated from relative intensity observations, which are defined as the ratio of the sky radiance at elevation α and the sky radiance in the zenith. Relative intensity measurements have the advantage of a strong dependence on boundary layer AOT and almost no dependence on boundary layer height. In a second step, tropospheric NO2 columns are derived from differential slant columns, based on AOT-dependent air mass factors. This two-step retrieval scheme was applied to cloud free periods in a twelve month data set of observations in De Bilt, The Netherlands. In a comparison with AERONET (Cabauw site a mean difference in AOT (AERONET minus MAX-DOAS of −0.01±0.08 was found, and a correlation of 0.85. Tropospheric-NO2 columns were compared with OMI-satellite tropospheric NO2. For ground-based observations restricted to uncertainties below 10%, no significant difference was found, and a correlation of 0.88.

Utilizing Structural Knowledge for Information Retrieval in XML Databases

NARCIS (Netherlands)

Mihajlovic, V.; Hiemstra, Djoerd; Blok, H.E.; Apers, Peter M.G.

In this paper we address the problem of immediate translation of eXtensible Mark-up Language (XML) information retrieval (IR) queries to relational database expressions and stress the benefits of using an intermediate XML-specific algebra over relational algebra. We show how adding an XML-specific

The prediction of candidate genes for cervix related cancer through gene ontology and graph theoretical approach.

Science.gov (United States)

Hindumathi, V; Kranthi, T; Rao, S B; Manimaran, P

2014-06-01

With rapidly changing technology, prediction of candidate genes has become an indispensable task in recent years mainly in the field of biological research. The empirical methods for candidate gene prioritization that succors to explore the potential pathway between genetic determinants and complex diseases are highly cumbersome and labor intensive. In such a scenario predicting potential targets for a disease state through in silico approaches are of researcher's interest. The prodigious availability of protein interaction data coupled with gene annotation renders an ease in the accurate determination of disease specific candidate genes. In our work we have prioritized the cervix related cancer candidate genes by employing Csaba Ortutay and his co-workers approach of identifying the candidate genes through graph theoretical centrality measures and gene ontology. With the advantage of the human protein interaction data, cervical cancer gene sets and the ontological terms, we were able to predict 15 novel candidates for cervical carcinogenesis. The disease relevance of the anticipated candidate genes was corroborated through a literature survey. Also the presence of the drugs for these candidates was detected through Therapeutic Target Database (TTD) and DrugMap Central (DMC) which affirms that they may be endowed as potential drug targets for cervical cancer.

A Survey: Framework of an Information Retrieval for Malay Translated Hadith Document

Directory of Open Access Journals (Sweden)

Zulkefli Nurul Syeilla Syazhween

2017-01-01

Full Text Available This paper reviews and analyses the limitation of the existing method used in the IR process in retrieving Malay Translated Hadith documents related to the search request. Traditional Malay Translated Hadith retrieval system has not focused on semantic extraction from text. The bag-of-words representation ignores the conceptual similarity of information in the query text and documents, which produce unsatisfactory retrieval results. Therefore, a more efficient IR framework is needed. This paper claims that the significant information extraction and subject-related information are actually important because the clues from this information can be used to search and find the relevance document to a query. Also, unimportant information can be discarded to represent the document content. So, semantic understanding of query and document is necessary to improve the effectiveness and accuracy of retrieval results for this domain study. Therefore, advance research is needed and it will be experimented in the future work. It is hoped that it will help users to search and find information regarding to the Malay Translated Hadith document.

Impact of retrievability of repository design

International Nuclear Information System (INIS)

Heijdra, J.J.; Gaag, J. v.d.; Prij, J.

1995-01-01

In this paper the impact of the retrievability on the design of the repository will be handled. Retrievability of radioactive waste from a repository in geological formations has received increasing attention during recent years. It is obvious that this retrievability will have consequences in terms of mining engineering, safety and cost. The purpose of the present study is to evaluate cost consequences by comparing two extreme options for retrievable storage. (author). 6 refs., 3 figs

Response of the Ubiquitin-Proteasome System to Memory Retrieval After Extended-Access Cocaine or Saline Self-Administration.

Science.gov (United States)

Werner, Craig T; Milovanovic, Mike; Christian, Daniel T; Loweth, Jessica A; Wolf, Marina E

2015-12-01

The ubiquitin-proteasome system (UPS) has been implicated in the retrieval-induced destabilization of cocaine- and fear-related memories in Pavlovian paradigms. However, nothing is known about its role in memory retrieval after self-administration of cocaine, an operant paradigm, or how the length of withdrawal from cocaine may influence retrieval mechanisms. Here, we examined UPS activity after an extended-access cocaine self-administration regimen that leads to withdrawal-dependent incubation of cue-induced cocaine craving. Controls self-administered saline. In initial experiments, memory retrieval was elicited via a cue-induced seeking/retrieval test on withdrawal day (WD) 50-60, when craving has incubated. We found that retrieval of cocaine- and saline-associated memories produced similar increases in polyubiquitinated proteins in the nucleus accumbens (NAc), compared with rats that did not undergo a seeking/retrieval test. Measures of proteasome catalytic activity confirmed similar activation of the UPS after retrieval of saline and cocaine memories. However, in a subsequent experiment in which testing was conducted on WD1, proteasome activity in the NAc was greater after retrieval of cocaine memory than saline memory. Analysis of other brain regions confirmed that effects of cocaine memory retrieval on proteasome activity, relative to saline memory retrieval, depend on withdrawal time. These results, combined with prior studies, suggest that the relationship between UPS activity and memory retrieval depends on training paradigm, brain region, and time elapsed between training and retrieval. The observation that mechanisms underlying cocaine memory retrieval change depending on the age of the memory has implications for development of memory destabilization therapies for cue-induced relapse in cocaine addicts.

Interactive Information Retrieval

DEFF Research Database (Denmark)

Borlund, Pia

2013-01-01

The paper introduces the research area of interactive information retrieval (IIR) from a historical point of view. Further, the focus here is on evaluation, because much research in IR deals with IR evaluation methodology due to the core research interest in IR performance, system interaction...... and satisfaction with retrieved information. In order to position IIR evaluation, the Cranfield model and the series of tests that led to the Cranfield model are outlined. Three iconic user-oriented studies and projects that all have contributed to how IIR is perceived and understood today are presented......: The MEDLARS test, the Book House fiction retrieval system, and the OKAPI project. On this basis the call for alternative IIR evaluation approaches motivated by the three revolutions (the cognitive, the relevance, and the interactive revolutions) put forward by Robertson & Hancock-Beaulieu (1992) is presented...

Integrative analyses of leprosy susceptibility genes indicate a common autoimmune profile.

Science.gov (United States)

Zhang, Deng-Feng; Wang, Dong; Li, Yu-Ye; Yao, Yong-Gang

2016-04-01

Leprosy is an ancient chronic infection in the skin and peripheral nerves caused by Mycobacterium leprae. The development of leprosy depends on genetic background and the immune status of the host. However, there is no systematic view focusing on the biological pathways, interaction networks and overall expression pattern of leprosy-related immune and genetic factors. To identify the hub genes in the center of leprosy genetic network and to provide an insight into immune and genetic factors contributing to leprosy. We retrieved all reported leprosy-related genes and performed integrative analyses covering gene expression profiling, pathway analysis, protein-protein interaction network, and evolutionary analyses. A list of 123 differentially expressed leprosy related genes, which were enriched in activation and regulation of immune response, was obtained in our analyses. Cross-disorder analysis showed that the list of leprosy susceptibility genes was largely shared by typical autoimmune diseases such as lupus erythematosus and arthritis, suggesting that similar pathways might be affected in leprosy and autoimmune diseases. Protein-protein interaction (PPI) and positive selection analyses revealed a co-evolution network of leprosy risk genes. Our analyses showed that leprosy associated genes constituted a co-evolution network and might undergo positive selection driven by M. leprae. We suggested that leprosy may be a kind of autoimmune disease and the development of leprosy is a matter of defect or over-activation of body immunity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Emplacement and retrieval equipment design considerations for a repository in salt

International Nuclear Information System (INIS)

Nair, B.R.; Bahorich, R.J.

1987-01-01

The current design concept for the disposal of nuclear high level waste packages in a repository in salt is based on the emplacement of individual packages in vertical boreholes in the underground mine floor. A key requirement is that the waste packages be capable of being retrieved during the last 26 years of the 76-year repository operating period. The unique design considerations relating to the retrieval of waste packages emplaced in bedded salt are presented in this paper. The information is based on the experience developed during the design of vertical emplacement and retrieval equipment in support of the Sandia Defense High Level Waste experiments at the Waste Isolation Pilot Plant. Also included are the impact of retrievability on the design of the equipment, the special salt cutting technology that was developed for this application, and a description of the equipment

Potential for criticality in Hanford tanks resulting from retrieval of tank waste

International Nuclear Information System (INIS)

Whyatt, G.A.; Sterne, R.J.; Mattigod, S.V.

1996-09-01

This report assesses the potential during retrieval operations for segregation and concentration of fissile material to result in a criticality. The sluicing retrieval of C-106 sludge to AY-102 and the operation of mixer pumps in SY-102 are examined in some detail. These two tanks (C-106, SY-102) were selected because of the near term plans for retrieval of these tanks and their high plutonium inventories relative to other tanks. Although all underground storage tanks are subcritical by a wide margin if assumed to be uniform in composition, the possibility retrieval operations could preferentially segregate the plutonium and locally concentrate it sufficiently to result in criticality was a concern. This report examines the potential for this segregation to occur

Changes in the modulation of brain activity during context encoding vs. context retrieval across the adult lifespan.

Science.gov (United States)

Ankudowich, E; Pasvanis, S; Rajah, M N

2016-10-01

Age-related deficits in context memory may arise from neural changes underlying both encoding and retrieval of context information. Although age-related functional changes in the brain regions supporting context memory begin at midlife, little is known about the functional changes with age that support context memory encoding and retrieval across the adult lifespan. We investigated how age-related functional changes support context memory across the adult lifespan by assessing linear changes with age during successful context encoding and retrieval. Using functional magnetic resonance imaging (fMRI), we compared young, middle-aged and older adults during both encoding and retrieval of spatial and temporal details of faces. Multivariate behavioral partial least squares (B-PLS) analysis of fMRI data identified a pattern of whole-brain activity that correlated with a linear age term and a pattern of whole-brain activity that was associated with an age-by-memory phase (encoding vs. retrieval) interaction. Further investigation of this latter effect identified three main findings: 1) reduced phase-related modulation in bilateral fusiform gyrus, left superior/anterior frontal gyrus and right inferior frontal gyrus that started at midlife and continued to older age, 2) reduced phase-related modulation in bilateral inferior parietal lobule that occurred only in older age, and 3) changes in phase-related modulation in older but not younger adults in left middle frontal gyrus and bilateral parahippocampal gyrus that was indicative of age-related over-recruitment. We conclude that age-related reductions in context memory arise in midlife and are related to changes in perceptual recollection and changes in fronto-parietal retrieval monitoring. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

Dissociating the Electrophysiological correlates between Item Retrieval and Associative Retrieval in Associative Recognition: From the Perspective of Directed Forgetting

Directory of Open Access Journals (Sweden)

Yujuan Wang

2016-11-01

Full Text Available Although many behavioral studies have reported associative memory was different from item memory, evidence coming from ERP researches has been in debate. In addition, directed forgetting effect for items has been fully discussed, but whether association between items can be directed-forgotten was unclear. The directed forgetting effect was important for disassociating the item retrieval and associative retrieval because of the one-to-one mapping relationship both between item retrieval and familiarity and between associative retrieval and recollection Thus, the aim of this study was to investigate the dissociation between item retrieval and associative retrieval and test directed forgetting effect for associative information. Associative recognition paradigm combined with directed forgetting paradigm by ERP recording was employed. Old/rearranged effect in to-be-remembered condition, which was associated with associative memory, was significant at 500-800 ms (LPC but not at 300-500 ms interval (FN400, indicating that item information was retrieved prior to associative information. The ERP wave calculated by subtracting the to-be-forgotten old pairs with old response from those with rearranged response, which reflected associative retrieval in the to-be-forgotten condition, was negative from 500 to 800 ms (reversal old/new effect, indicating that association between items can be directed-forgotten. Similar evidence was obtained by contrasting rearranged responses aimed to the to-be-forgotten old pairs with those aimed to the to-be-remembered rearranged pairs, which actually represented the complete failure of associative retrieval. Therefore, item retrieval and associative retrieval were indexed by FN400 and LPC respectively, with associative retrieval more inhibited than item retrieval.

An improved ptychographical phase retrieval algorithm for diffractive imaging

International Nuclear Information System (INIS)

Maiden, Andrew M.; Rodenburg, John M.

2009-01-01

The ptychographical iterative engine (or PIE) is a recently developed phase retrieval algorithm that employs a series of diffraction patterns recorded as a known illumination function is translated to a set of overlapping positions relative to a target sample. The technique has been demonstrated successfully at optical and X-ray wavelengths and has been shown to be robust to detector noise and to converge considerably faster than support-based phase retrieval methods. In this paper, the PIE is extended so that the requirement for an accurate model of the illumination function is removed.

Addiction and Reward-related Genes Show Altered Expression in the Postpartum Nucleus Accumbens

Directory of Open Access Journals (Sweden)

Changjiu eZhao

2014-11-01

Full Text Available Motherhood involves a switch in natural rewards, whereby offspring become highly rewarding. Nucleus accumbens (NAC is a key CNS region for natural rewards and addictions, but to date no study has evaluated on a large scale the events in NAC that underlie the maternal change in natural rewards. In this study we utilized microarray and bioinformatics approaches to evaluate postpartum NAC gene expression changes in mice. Modular Single-set Enrichment Test (MSET indicated that postpartum (relative to virgin NAC gene expression profile was significantly enriched for genes related to addiction and reward in 5 of 5 independently curated databases (e.g., Malacards, Phenopedia. Over 100 addiction/reward related genes were identified and these included: Per1, Per2, Arc, Homer2, Creb1, Grm3, Fosb, Gabrb3, Adra2a, Ntrk2, Cry1, Penk, Cartpt, Adcy1, Npy1r, Htr1a, Drd1a, Gria1, and Pdyn. ToppCluster analysis found maternal NAC expression profile to be significantly enriched for genes related to the drug action of nicotine, ketamine, and dronabinol. Pathway analysis indicated postpartum NAC as enriched for RNA processing, CNS development/differentiation, and transcriptional regulation. Weighted Gene Coexpression Network Analysis identified possible networks for transcription factors, including Nr1d1, Per2, Fosb, Egr1, and Nr4a1. The postpartum state involves increased risk for mental health disorders and MSET analysis indicated postpartum NAC to be enriched for genes related to depression, bipolar disorder, and schizophrenia. Mental health related genes included: Fabp7, Grm3, Penk, and Nr1d1. We confirmed via quantitative PCR Nr1d1, Per2, Grm3, Penk, Drd1a, and Pdyn. This study indicates for the first time that postpartum NAC involves large scale gene expression alterations linked to addiction and reward. Because the postpartum state also involves decreased response to drugs, the findings could provide insights into how to mitigate addictions.

Mapping of genes for flower-related traits and QTLs for flowering ...

Indian Academy of Sciences (India)

Mapping of genes for flower-related traits and QTLs for flowering time ... which would greatly enhance the use of G. darwinii-specific desirable genes in ... used to determine all linkage groups, the order of groups on the same ... age groups.

Divided attention improves delayed, but not immediate retrieval of a consolidated memory.

Science.gov (United States)

Kessler, Yoav; Vandermorris, Susan; Gopie, Nigel; Daros, Alexander; Winocur, Gordon; Moscovitch, Morris

2014-01-01

A well-documented dissociation between memory encoding and retrieval concerns the role of attention in the two processes. The typical finding is that divided attention (DA) during encoding impairs future memory, but retrieval is relatively robust to attentional manipulations. However, memory research in the past 20 years had demonstrated that retrieval is a memory-changing process, in which the strength and availability of information are modified by various characteristics of the retrieval process. Based on this logic, several studies examined the effects of DA during retrieval (Test 1) on a future memory test (Test 2). These studies yielded inconsistent results. The present study examined the role of memory consolidation in accounting for the after-effect of DA during retrieval. Initial learning required a classification of visual stimuli, and hence involved incidental learning. Test 1 was administered 24 hours after initial learning, and therefore required retrieval of consolidated information. Test 2 was administered either immediately following Test 1 or after a 24-hour delay. Our results show that the effect of DA on Test 2 depended on this delay. DA during Test 1 did not affect performance on Test 2 when it was administered immediately, but improved performance when Test 2 was given 24-hours later. The results are consistent with other findings showing long-term benefits of retrieval difficulty. Implications for theories of reconsolidation in human episodic memory are discussed.

Application of discriminative models for interactive query refinement in video retrieval

Science.gov (United States)

Srivastava, Amit; Khanwalkar, Saurabh; Kumar, Anoop

2013-12-01

The ability to quickly search for large volumes of videos for specific actions or events can provide a dramatic new capability to intelligence agencies. Example-based queries from video are a form of content-based information retrieval (CBIR) where the objective is to retrieve clips from a video corpus, or stream, using a representative query sample to find more like this. Often, the accuracy of video retrieval is largely limited by the gap between the available video descriptors and the underlying query concept, and such exemplar queries return many irrelevant results with relevant ones. In this paper, we present an Interactive Query Refinement (IQR) system which acts as a powerful tool to leverage human feedback and allow intelligence analyst to iteratively refine search queries for improved precision in the retrieved results. In our approach to IQR, we leverage discriminative models that operate on high dimensional features derived from low-level video descriptors in an iterative framework. Our IQR model solicits relevance feedback on examples selected from the region of uncertainty and updates the discriminating boundary to produce a relevance ranked results list. We achieved 358% relative improvement in Mean Average Precision (MAP) over initial retrieval list at a rank cutoff of 100 over 4 iterations. We compare our discriminative IQR model approach to a naïve IQR and show our model-based approach yields 49% relative improvement over the no model naïve system.

Memory retrieval as a self-propagating process.

Science.gov (United States)

Bäuml, Karl-Heinz T; Schlichting, Andreas

2014-07-01

Retrieval of a subset of studied items and the presentation of those items as retrieval cues typically impair retrieval of the other items. Previous research on this self-limiting property of memory retrieval has relied heavily on short retention intervals and similar context between encoding and test. Here, we examined retrieval dynamics also after a prolonged retention interval with different spatial and social context between encoding and test, conditions that mimic people's remembering in many situations of daily life. For both unrelated word lists and more integrated prose material, we found retrieval and cuing to impair recall of other studied items after a short retention interval, but to improve recall in the prolonged retention interval condition. The results demonstrate that retrieval dynamics depend critically on situation, indicating that quite often in daily life, retrieval may be a self-propagating, rather than a self-limiting process. Copyright © 2014 Elsevier B.V. All rights reserved.

Elaboration over a discourse facilitates retrieval in sentence processing

Directory of Open Access Journals (Sweden)

Melissa eTroyer

2016-03-01

Full Text Available Language comprehension requires access to stored knowledge and the ability to combine knowledge in new, meaningful ways. Previous work has shown that processing linguistically more complex expressions (‘Texas cattle rancher’ vs. ‘rancher’ leads to slow-downs in reading during initial processing, possibly reflecting effort in combining information. Conversely, when this information must subsequently be retrieved (as in filler-gap constructions, processing is facilitated for more complex expressions, possibly because more semantic cues are available during retrieval. To follow up on this hypothesis, we tested whether information distributed across a short discourse can similarly provide effective cues for retrieval. Participants read texts introducing two referents (e.g., two senators, one of whom was described in greater detail than the other (e.g., ‘The Democrat had voted for one of the senators, and the Republican had voted for the other, a man from Ohio who was running for president’. The final sentence (e.g., ‘The senator who the {Republican / Democrat} had voted for…’ contained a relative clause picking out either the Many-Cue referent (with ‘Republican’ or the One-Cue referent (with ‘Democrat’. We predicted facilitated retrieval (faster reading times for the Many-Cue condition at the verb region (‘had voted for’, where readers could understand that ‘The senator’ is the object of the verb. As predicted, this pattern was observed at the retrieval region and continued throughout the rest of the sentence. Participants also completed the Author/Magazine Recognition Tests (ART/MRT; Stanovich & West, 1989, providing a proxy for world knowledge. Since higher ART/MRT scores may index (a greater experience accessing relevant knowledge and/or (b richer/more highly-structured representations in semantic memory, we predicted it would be positively associated with effects of elaboration on retrieval. We did not observe

Transcription profiling and identification of infection-related genes in Phytophthora cactorum.

Science.gov (United States)

Chen, Xiao-Ren; Huang, Shen-Xin; Zhang, Ye; Sheng, Gui-Lin; Zhang, Bo-Yue; Li, Qi-Yuan; Zhu, Feng; Xu, Jing-You

2018-04-01

Phytophthora cactorum, an oomycete pathogen, infects more than 200 plant species within several plant families. To gain insight into the repertoire of the infection-related genes of P. cactorum, Illumina RNA-Seq was used to perform a global transcriptome analysis of three life cycle stages of the pathogen, mycelia (MY), zoospores (ZO) and germinating cysts with germ tubes (GC). From over 9.8 million Illumina reads for each library, 18,402, 18,569 and 19,443 distinct genes were identified for MY, ZO and GC libraries, respectively. Furthermore, the transcriptome difference among MY, ZO and GC stages was investigated. Gene ontology (GO) and KEGG pathway enrichment analyses revealed diverse biological functions and processes. Comparative analysis identified a large number of genes that are associated with specific stages and pathogenicity, including 166 effector genes. Of them, most of RXLR and NLP genes showed induction while the majority of CRN genes were down-regulated in GC, the important pre-infection stage, compared to either MY or ZO. And 14 genes encoding small cysteine-rich (SCR) secretory proteins showed differential expression during the developmental stages and in planta. Ectopic expression in the Solanaceae indicated that SCR113 and one elicitin PcINF1 can trigger cell death on Nicotiana benthamiana, tobacco (N. tabacum) and tomato (Solanum lycopersicum) leaves. Neither conserved domain nor homologues of SCR113 in other organisms can be identified. Collectively, our study provides a comprehensive examination of gene expression across three P. cactorum developmental stages and describes pathogenicity-related genes, all of which will help elucidate the pathogenicity mechanism of this destructive pathogen.

Cytochrome cd1-containing nitrite reductase encoding gene nirS as a new functional biomarker for detection of anaerobic ammonium oxidizing (Anammox) bacteria.

Science.gov (United States)

Li, Meng; Ford, Tim; Li, Xiaoyan; Gu, Ji-Dong

2011-04-15

A newly designed primer set (AnnirS), together with a previously published primer set (ScnirS), was used to detect anammox bacterial nirS genes from sediments collected from three marine environments. Phylogenetic analysis demonstrated that all retrieved sequences were clearly different from typical denitrifiers' nirS, but do group together with the known anammox bacterial nirS. Sequences targeted by ScnirS are closely related to Scalindua nirS genes recovered from the Peruvian oxygen minimum zone (OMZ), whereas sequences targeted by AnnirS are more closely affiliated with the nirS of Candidatus 'Kuenenia stuttgartiensis' and even form a new phylogenetic nirS clade, which might be related to other genera of the anammox bacteria. Analysis demonstrated that retrieved sequences had higher sequence identities (>60%) with known anammox bacterial nirS genes than with denitrifiers' nirS, on both nucleotide and amino acid levels. Compared to the 16S rRNA and hydrazine oxidoreductase (hzo) genes, the anammox bacterial nirS not only showed consistent phylogenetic relationships but also demonstrated more reliable quantification of anammox bacteria because of the single copy of the nirS gene in the anammox bacterial genome and the specificity of PCR primers for different genera of anammox bacteria, thus providing a suitable functional biomarker for investigation of anammox bacteria.

Interactive information seeking, behaviour and retrieval

CERN Document Server

Ruthven, Ian

2011-01-01

Information retrieval (IR) is a complex human activity supported by sophisticated systems. This book covers the whole spectrum of information retrieval, including: history and background information; behaviour and seeking task-based information; searching and retrieval approaches to investigating information; and, evaluation interfaces for IR.

Credibility improves topical blog post retrieval

NARCIS (Netherlands)

Weerkamp, W.; de Rijke, M.

2008-01-01

Topical blog post retrieval is the task of ranking blog posts with respect to their relevance for a given topic. To improve topical blog post retrieval we incorporate textual credibility indicators in the retrieval process. We consider two groups of indicators: post level (determined using

Diminishing-cues retrieval practice: A memory-enhancing technique that works when regular testing doesn't.

Science.gov (United States)

Fiechter, Joshua L; Benjamin, Aaron S

2017-08-28

Retrieval practice has been shown to be a highly effective tool for enhancing memory, a fact that has led to major changes to educational practice and technology. However, when initial learning is poor, initial retrieval practice is unlikely to be successful and long-term benefits of retrieval practice are compromised or nonexistent. Here, we investigate the benefit of a scaffolded retrieval technique called diminishing-cues retrieval practice (Finley, Benjamin, Hays, Bjork, & Kornell, Journal of Memory and Language, 64, 289-298, 2011). Under learning conditions that favored a strong testing effect, diminishing cues and standard retrieval practice both enhanced memory performance relative to restudy. Critically, under learning conditions where standard retrieval practice was not helpful, diminishing cues enhanced memory performance substantially. These experiments demonstrate that diminishing-cues retrieval practice can widen the range of conditions under which testing can benefit memory, and so can serve as a model for the broader application of testing-based techniques for enhancing learning.

Role of G-protein-coupled receptor-related genes in insecticide resistance of the mosquito, Culex quinquefasciatus.

Science.gov (United States)

Li, Ting; Liu, Lena; Zhang, Lee; Liu, Nannan

2014-09-29

G-protein-coupled receptors regulate signal transduction pathways and play diverse and pivotal roles in the physiology of insects, however, the precise function of GPCRs in insecticide resistance remains unclear. Using quantitative RT-PCR and functional genomic methods, we, for the first time, explored the function of GPCRs and GPCR-related genes in insecticide resistance of mosquitoes, Culex quinquefasciatus. A comparison of the expression of 115 GPCR-related genes at a whole genome level between resistant and susceptible Culex mosquitoes identified one and three GPCR-related genes that were up-regulated in highly resistant Culex mosquito strains, HAmCq(G8) and MAmCq(G6), respectively. To characterize the function of these up-regulated GPCR-related genes in resistance, the up-regulated GPCR-related genes were knockdown in HAmCq(G8) and MAmCq(G6) using RNAi technique. Knockdown of these four GPCR-related genes not only decreased resistance of the mosquitoes to permethrin but also repressed the expression of four insecticide resistance-related P450 genes, suggesting the role of GPCR-related genes in resistance is involved in the regulation of resistance P450 gene expression. This results help in understanding of molecular regulation of resistance development in Cx. quinquefasciatus.

Electrophysiological evidence for flexible goal-directed cue processing during episodic retrieval.

Science.gov (United States)

Herron, Jane E; Evans, Lisa H; Wilding, Edward L

2016-05-15

A widely held assumption is that memory retrieval is aided by cognitive control processes that are engaged flexibly in service of memory retrieval and memory decisions. While there is some empirical support for this view, a notable exception is the absence of evidence for the flexible use of retrieval control in functional neuroimaging experiments requiring frequent switches between tasks with different cognitive demands. This absence is troublesome in so far as frequent switches between tasks mimic some of the challenges that are typically placed on memory outside the laboratory. In this experiment we instructed participants to alternate frequently between three episodic memory tasks requiring item recognition or retrieval of one of two different kinds of contextual information encoded in a prior study phase (screen location or encoding task). Event-related potentials (ERPs) elicited by unstudied items in the two tasks requiring retrieval of study context were reliably different, demonstrating for the first time that ERPs index task-specific processing of retrieval cues when retrieval goals change frequently. The inclusion of the item recognition task was a novel and important addition in this study, because only the ERPs elicited by unstudied items in one of the two context conditions diverged from those in the item recognition condition. This outcome constrains functional interpretations of the differences that emerged between the two context conditions and emphasises the utility of this baseline in functional imaging studies of retrieval processing operations. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Overexpression of erg1 gene in Trichoderma harzianum CECT 2413: effect on the induction of tomato defence-related genes.

Science.gov (United States)

Cardoza, R E; Malmierca, M G; Gutiérrez, S

2014-09-01

To investigate the effect of the overexpression of erg1 gene of Trichoderma harzianum CECT 2413 (T34) on the Trichoderma-plant interactions and in the biocontrol ability of this fungus. Transformants of T34 strain overexpressing erg1 gene did not show effect on the ergosterol level, although a drastic decrease in the squalene level was observed in the transformants at 96 h of growth. During interaction with plants, the erg1 overexpression resulted in a reduction of the priming ability of several tomato defence-related genes belonging to the salicylate pathway, and also of the TomLoxA gene, which is related to the jasmonate pathway. Interestingly, other jasmonate-related genes, such as PINI and PINII, were slightly induced. The erg1 overexpressed transformants also showed a reduced ability to colonize tomato roots. The ergosterol biosynthetic pathway might play an important role in regulating Trichoderma-plant interactions, although this role does not seem to be restricted to the final product; instead, other intermediates such as squalene, whose role in the Trichoderma-plant interaction has not been characterized, would also play an important role. The functional analysis of genes involved in the synthesis of ergosterol could provide additional strategies to improve the ability of biocontrol of the Trichoderma strains and their interaction with plants. © 2014 The Society for Applied Microbiology.

Does retrieval intentionality really matter? Similarities and differences between involuntary memories and directly and generatively retrieved voluntary memories

DEFF Research Database (Denmark)

Barzykowski, Krystian; Staugaard, Søren Risløv

2016-01-01

differences between the characteristics of involuntary and directly retrieved memories. The results imply that retrieval intention seems to differentiate how a memory appears in a person’s mind. Furthermore, we argue that these differences in part could result from differences in encoding and consolidation.......Theories of autobiographical memory distinguish between involuntary and voluntary retrieval as a consequence of conscious intention (i.e., wanting to remember). Another distinction can be made between direct and generative retrieval, which reflects the effort involved (i.e., trying to remember......). However, it is unclear how intention and effort interacts. For example, involuntary memories and directly retrieved memories have been used interchangeably in the literature to refer to the same phenomenon of effortless, nonstrategic retrieval. More recent theoretical advances suggest...

ColoLipidGene: signature of lipid metabolism-related genes to predict prognosis in stage-II colon cancer patients

Science.gov (United States)

Vargas, Teodoro; Moreno-Rubio, Juan; Herranz, Jesús; Cejas, Paloma; Molina, Susana; González-Vallinas, Margarita; Mendiola, Marta; Burgos, Emilio; Aguayo, Cristina; Custodio, Ana B.; Machado, Isidro; Ramos, David; Gironella, Meritxell; Espinosa-Salinas, Isabel; Ramos, Ricardo; Martín-Hernández, Roberto; Risueño, Alberto; De Las Rivas, Javier; Reglero, Guillermo; Yaya, Ricardo; Fernández-Martos, Carlos; Aparicio, Jorge; Maurel, Joan; Feliu, Jaime; de Molina, Ana Ramírez

2015-01-01

Lipid metabolism plays an essential role in carcinogenesis due to the requirements of tumoral cells to sustain increased structural, energetic and biosynthetic precursor demands for cell proliferation. We investigated the association between expression of lipid metabolism-related genes and clinical outcome in intermediate-stage colon cancer patients with the aim of identifying a metabolic profile associated with greater malignancy and increased risk of relapse. Expression profile of 70 lipid metabolism-related genes was determined in 77 patients with stage II colon cancer. Cox regression analyses using c-index methodology was applied to identify a metabolic-related signature associated to prognosis. The metabolic signature was further confirmed in two independent validation sets of 120 patients and additionally, in a group of 264 patients from a public database. The combined analysis of these 4 genes, ABCA1, ACSL1, AGPAT1 and SCD, constitutes a metabolic-signature (ColoLipidGene) able to accurately stratify stage II colon cancer patients with 5-fold higher risk of relapse with strong statistical power in the four independent groups of patients. The identification of a group of 4 genes that predict survival in intermediate-stage colon cancer patients allows delineation of a high-risk group that may benefit from adjuvant therapy, and avoids the toxic and unnecessary chemotherapy in patients classified as low-risk group. PMID:25749516

Elaborative Retrieval: Do Semantic Mediators Improve Memory?

Science.gov (United States)

Lehman, Melissa; Karpicke, Jeffrey D.

2016-01-01

The elaborative retrieval account of retrieval-based learning proposes that retrieval enhances retention because the retrieval process produces the generation of semantic mediators that link cues to target information. We tested 2 assumptions that form the basis of this account: that semantic mediators are more likely to be generated during…

Re-engaging with the past: recapitulation of encoding operations during retrieval

Directory of Open Access Journals (Sweden)

Alexa eMorcom

2014-05-01

Full Text Available Recollection of events is accompanied by selective reactivation of cortical regions which responded to specific sensory and cognitive dimensions of the original events. This reactivation is thought to reflect the reinstatement of stored memory representations and therefore to reflect memory content, but it may also reveal processes which support both encoding and retrieval. The present study used event-related functional magnetic resonance imaging (fMRI to investigate whether regions selectively engaged in encoding face and scene context with studied words are also re-engaged when the context is later retrieved. As predicted, encoding face and scene context with visually presented words elicited activity in distinct, context-selective regions. Retrieval of face and scene context also re-engaged some of the regions which had shown successful encoding effects. However, this recapitulation of encoding activity did not show the same context selectivity observed at encoding. Successful retrieval of both face and scene context re-engaged regions which had been associated with encoding of the other type of context, as well as those associated with encoding the same type of context. This recapitulation may reflect retrieval attempts which are not context-selective, but use shared retrieval cues to re-engage encoding operations in service of recollection.

The impact of intermediate-term alcohol abstinence on memory retrieval and suppression

Directory of Open Access Journals (Sweden)

Viola Luca Nemeth

2014-12-01

Full Text Available Background: The nature of episodic memory deficit in intermediate-term abstinence from alcohol in alcohol dependence (AD is not yet clarified. Deficits in inhibitory control are commonly reported in substance use disorders. However, much less is known about cognitive control suppressing interference from memory. The Think/No-think (TNT paradigm is a well established method to investigate inhibition of associative memory retrieval.Methods: Thirty-six unmedicated alcohol dependent (AD patients and 36 healthy controls (HC performed the TNT task. Thirty image-word pairs were trained up to a predefined accuracy level. Cued recall was examined in three conditions: Think (T for items instructed to-be-remembered, No-think (NT assessing the ability to suppress retrieval and Baseline (B for general relational memory. Premorbid IQ, clinical variables and impulsivity measures were quantified. Results: AD patients had a significantly increased demand for training. Baseline memory abilities and effect of practice on retrieval were not markedly different between the groups. We found a significant main effect of group (HC vs AD x condition (B, T and NT and a significant difference in mean NT-B scores for the two groups. Discussion: AD and HC groups did not differ essentially in their baseline memory abilities. Also, the instruction to focus on retrieval improved episodic memory performance in both groups. Crucially, control participants were able to suppress relational words in the NT condition supporting the critical effect of cognitive control processes over inhibition of retrieval. In contrast to this, the ability of AD patients to suppress retrieval was found to be impaired.

A passage retrieval method based on probabilistic information retrieval model and UMLS concepts in biomedical question answering.

Science.gov (United States)

Sarrouti, Mourad; Ouatik El Alaoui, Said

2017-04-01

Passage retrieval, the identification of top-ranked passages that may contain the answer for a given biomedical question, is a crucial component for any biomedical question answering (QA) system. Passage retrieval in open-domain QA is a longstanding challenge widely studied over the last decades. However, it still requires further efforts in biomedical QA. In this paper, we present a new biomedical passage retrieval method based on Stanford CoreNLP sentence/passage length, probabilistic information retrieval (IR) model and UMLS concepts. In the proposed method, we first use our document retrieval system based on PubMed search engine and UMLS similarity to retrieve relevant documents to a given biomedical question. We then take the abstracts from the retrieved documents and use Stanford CoreNLP for sentence splitter to make a set of sentences, i.e., candidate passages. Using stemmed words and UMLS concepts as features for the BM25 model, we finally compute the similarity scores between the biomedical question and each of the candidate passages and keep the N top-ranked ones. Experimental evaluations performed on large standard datasets, provided by the BioASQ challenge, show that the proposed method achieves good performances compared with the current state-of-the-art methods. The proposed method significantly outperforms the current state-of-the-art methods by an average of 6.84% in terms of mean average precision (MAP). We have proposed an efficient passage retrieval method which can be used to retrieve relevant passages in biomedical QA systems with high mean average precision. Copyright © 2017 Elsevier Inc. All rights reserved.

LGscore: A method to identify disease-related genes using biological literature and Google data.

Science.gov (United States)

Kim, Jeongwoo; Kim, Hyunjin; Yoon, Youngmi; Park, Sanghyun

2015-04-01

Since the genome project in 1990s, a number of studies associated with genes have been conducted and researchers have confirmed that genes are involved in disease. For this reason, the identification of the relationships between diseases and genes is important in biology. We propose a method called LGscore, which identifies disease-related genes using Google data and literature data. To implement this method, first, we construct a disease-related gene network using text-mining results. We then extract gene-gene interactions based on co-occurrences in abstract data obtained from PubMed, and calculate the weights of edges in the gene network by means of Z-scoring. The weights contain two values: the frequency and the Google search results. The frequency value is extracted from literature data, and the Google search result is obtained using Google. We assign a score to each gene through a network analysis. We assume that genes with a large number of links and numerous Google search results and frequency values are more likely to be involved in disease. For validation, we investigated the top 20 inferred genes for five different diseases using answer sets. The answer sets comprised six databases that contain information on disease-gene relationships. We identified a significant number of disease-related genes as well as candidate genes for Alzheimer's disease, diabetes, colon cancer, lung cancer, and prostate cancer. Our method was up to 40% more accurate than existing methods. Copyright © 2015 Elsevier Inc. All rights reserved.

Method of and System for Information Retrieval

DEFF Research Database (Denmark)

2015-01-01

This invention relates to a system for and a method (100) of searching a collection of digital information (150) comprising a number of digital documents (110), the method comprising receiving or obtaining (102) a search query, the query comprising a number of search terms, searching (103) an ind......, a method of and a system for information retrieval or searching is readily provided that enhances the searching quality (i.e. the number of relevant documents retrieved and such documents being ranked high) when (also) using queries containing many search terms.......This invention relates to a system for and a method (100) of searching a collection of digital information (150) comprising a number of digital documents (110), the method comprising receiving or obtaining (102) a search query, the query comprising a number of search terms, searching (103) an index...... (300) using the search terms thereby providing information (301) about which digital documents (110) of the collection of digital information (150) that contains a given search term and one or more search related metrics (302; 303; 304; 305; 306), ranking (105) at least a part of the search result...

Comparative sequence analysis of nitrogen fixation-related genes in six legumes

Directory of Open Access Journals (Sweden)

Dong Hyun eKim

2013-08-01

Full Text Available Legumes play an important role as food and forage crops in international agriculture especially in developing countries. Legumes have a unique biological process called nitrogen fixation (NF by which they convert atmospheric nitrogen to ammonia. Although legume genomes have undergone polyploidization, duplication and divergence, NF-related genes, because of their essential functional role for legumes, might have remained conserved. To understand the relationship of divergence and evolutionary processes in legumes, this study analyzes orthologs and paralogs for selected 20 NF-related genes by using comparative genomic approaches in six legumes i.e. Medicago truncatula (Mt, Cicer arietinum, Lotus japonicus, Cajanus cajan (Cc, Phaseolus vulgaris (Pv and Glycine max (Gm. Subsequently, sequence distances, numbers of synonymous substitutions per synonymous site (Ks and nonsynonymous substitutions per nonsynonymous site (Ka between orthologs and paralogs were calculated and compared across legumes. These analyses suggest the closest relationship between Gm and Cc and the farthest distance between Mt and Pv in 6 legumes. Ks proportional plots clearly showed ancient genome duplication in all legumes, whole genome duplication event in Gm and also speciation pattern in different legumes. This study also reported some interesting observations e.g. no peak at Ks 0.4 in Gm-Gm, location of two independent genes next to each other in Mt and low Ks values for outparalogs for three genes as compared to other 12 genes. In summary, this study underlines the importance of NF-related genes and provides important insights in genome organization and evolutionary aspects of six legume species analyzed.

Gathering International Competitive Intelligence via Online Data Retrieval in the International Marketing Class.

Science.gov (United States)

Miller, Fred

A unit on online data retrieval techniques designed for a college course in international marketing is described. The unit is intended to teach students how to compile information on overseas markets and competitors. Online retrieval is seen as a relatively inexpensive means of gathering important data from otherwise inaccessible international…

Practice patterns of retrievable inferior vena cava filters and predictors of filter retrieval in patients with pulmonary embolism.

Science.gov (United States)

Kang, Jieun; Ko, Heung-Kyu; Shin, Ji Hoon; Ko, Gi-Young; Jo, Kyung-Wook; Huh, Jin Won; Oh, Yeon-Mok; Lee, Sang-Do; Lee, Jae Seung

2017-12-01

Retrievable inferior vena cava (IVC) filters are increasingly used in patients with venous thromboembolism (VTE) who have contraindications to anticoagulant therapy. However, previous studies have shown that many retrievable filters are left permanently in patients. This study aimed to identify the common indications for IVC filter insertion, the filter retrieval rate, and the predictive factors for filter retrieval attempts. To this end, a retrospective cohort study was performed at a tertiary care center in South Korea between January 2010 and May 2016. Electronic medical charts were reviewed for patients with pulmonary embolism (PE) who underwent IVC filter insertion. A total of 439 cases were reviewed. The most common indication for filter insertion was a preoperative/procedural aim, followed by extensive iliofemoral deep vein thrombosis (DVT). Retrieval of the IVC filter was attempted in 44.9% of patients. The retrieval success rate was 93.9%. History of cerebral hemorrhage, malignancy, and admission to a nonsurgical department were the significant predictive factors of a lower retrieval attempt rate in multivariate analysis. With the increased use of IVC filters, more issues should be addressed before placing a filter and physicians should attempt to improve the filter retrieval rate.

BIR 2014 - Bibliometric-enhanced Information Retrieval

DEFF Research Database (Denmark)

This first “Bibliometric-enhanced Information Retrieval” (BIR 2014) workshop1 aims to engage with the IR community about possible links to bibliometrics and scholarly communication. Bibliometric techniques are not yet widely used to enhance retrieval processes in digital libraries, although...... analysis of co-authorship network, can improve retrieval services for specific communities, as well as for large, cross-domain collections. This workshop aims to raise awareness of the missing link between information retrieval (IR) and bibliometrics / scientometrics and to create a common ground...... for the incorporation of bibliometric-enhanced services into retrieval at the digital library interface. Our interests include information retrieval, information seeking, science modelling, network analysis, and digital libraries. The goal is to apply insights from bibliometrics, scientometrics, and informetrics...

Schizophrenia and vitamin D related genes could have been subject to latitude-driven adaptation.

Science.gov (United States)

Amato, Roberto; Pinelli, Michele; Monticelli, Antonella; Miele, Gennaro; Cocozza, Sergio

2010-11-11

Many natural phenomena are directly or indirectly related to latitude. Living at different latitudes, indeed, has its consequences with being exposed to different climates, diets, light/dark cycles, etc. In humans, one of the best known examples of genetic traits following a latitudinal gradient is skin pigmentation. Nevertheless, also several diseases show latitudinal clinals such as hypertension, cancer, dismetabolic conditions, schizophrenia, Parkinson's disease and many more. We investigated, for the first time on a wide genomic scale, the latitude-driven adaptation phenomena. In particular, we selected a set of genes showing signs of latitude-dependent population differentiation. The biological characterization of these genes showed enrichment for neural-related processes. In light of this, we investigated whether genes associated to neuropsychiatric diseases were enriched by Latitude-Related Genes (LRGs). We found a strong enrichment of LRGs in the set of genes associated to schizophrenia. In an attempt to try to explain this possible link between latitude and schizophrenia, we investigated their associations with vitamin D. We found in a set of vitamin D related genes a significant enrichment of both LRGs and of genes involved in schizophrenia. Our results suggest a latitude-driven adaptation for both schizophrenia and vitamin D related genes. In addition we confirm, at a molecular level, the link between schizophrenia and vitamin D. Finally, we discuss a model in which schizophrenia is, at least partly, a maladaptive by-product of latitude dependent adaptive changes in vitamin D metabolism.

Identification of Immunity Related Genes to Study the Physalis peruviana – Fusarium oxysporum Pathosystem

Science.gov (United States)

Enciso-Rodríguez, Felix E.; González, Carolina; Rodríguez, Edwin A.; López, Camilo E.; Landsman, David; Barrero, Luz Stella; Mariño-Ramírez, Leonardo

2013-01-01

The Cape gooseberry ( Physalis peruviana L) is an Andean exotic fruit with high nutritional value and appealing medicinal properties. However, its cultivation faces important phytosanitary problems mainly due to pathogens like Fusarium oxysporum, Cercosporaphysalidis and Alternaria spp. Here we used the Cape gooseberry foliar transcriptome to search for proteins that encode conserved domains related to plant immunity including: NBS (Nucleotide Binding Site), CC (Coiled-Coil), TIR (Toll/Interleukin-1 Receptor). We identified 74 immunity related gene candidates in P . peruviana which have the typical resistance gene (R-gene) architecture, 17 Receptor like kinase (RLKs) candidates related to PAMP-Triggered Immunity (PTI), eight (TIR-NBS-LRR, or TNL) and nine (CC–NBS-LRR, or CNL) candidates related to Effector-Triggered Immunity (ETI) genes among others. These candidate genes were categorized by molecular function (98%), biological process (85%) and cellular component (79%) using gene ontology. Some of the most interesting predicted roles were those associated with binding and transferase activity. We designed 94 primers pairs from the 74 immunity-related genes (IRGs) to amplify the corresponding genomic regions on six genotypes that included resistant and susceptible materials. From these, we selected 17 single band amplicons and sequenced them in 14 F. oxysporum resistant and susceptible genotypes. Sequence polymorphisms were analyzed through preliminary candidate gene association, which allowed the detection of one SNP at the PpIRG-63 marker revealing a nonsynonymous mutation in the predicted LRR domain suggesting functional roles for resistance. PMID:23844210

POST-RETRIEVAL EXTINCTION ATTENUATES ALCOHOL CUE REACTIVITY IN RATS

Science.gov (United States)

Cofresí, Roberto U.; Lewis, Suzanne M.; Chaudhri, Nadia; Lee, Hongjoo J.; Monfils, Marie-H.; Gonzales, Rueben A.

2017-01-01

BACKGROUND Conditioned responses to alcohol-associated cues can hinder recovery from alcohol use disorder (AUD). Cue exposure (extinction) therapy (CET) can reduce reactivity to alcohol cues, but its efficacy is limited by phenomena such as spontaneous recovery and reinstatement that can cause a return of conditioned responding after extinction. Using a preclinical model of alcohol cue reactivity in rats, we evaluated whether the efficacy of alcohol CET could be improved by conducting CET during the memory reconsolidation window after retrieval of a cue-alcohol association. METHODS Rats were provided with intermittent access to unsweetened alcohol. Rats were then trained to predict alcohol access based on a visual cue. Next, rats were treated with either standard extinction (n=14) or post-retrieval extinction (n=13). Rats were then tested for long-term memory of extinction and susceptibility to spontaneous recovery and reinstatement. RESULTS Despite equivalent extinction, rats treated with post-retrieval extinction exhibited reduced spontaneous recovery and reinstatement relative to rats treated with standard extinction. CONCLUSIONS Post-retrieval CET shows promise for persistently attenuating the risk to relapse posed by alcohol cues in individuals with AUD. PMID:28169439

Retrievability of high-level nuclear waste from geologic repositories - Regulatory and rock mechanics/design considerations

International Nuclear Information System (INIS)

Tanious, N.S.; Nataraja, M.S.; Daemen, J.J.K.

1987-01-01

Retrievability of nuclear waste from high-level geologic repositories is one of the performance objectives identified in 10CFR60 (Code of Federal Regulations, 1985). 10CFR60.111 states that the geologic repository operations area shall be designed to preserve the option of waste retrieval. In designing the repository operations area, rock mechanics considerations play a major role especially in evaluating the feasibility of retrieval operations. This paper discusses generic considerations affecting retrievability as they relate to repository design, construction, and operation, with emphasis on regulatory and rock mechanics aspects

Towards Augmented Human Memory: Retrieval-Induced Forgetting and Retrieval Practice in an Interactive, End-of-Day Review

Science.gov (United States)

2018-01-01

The authors report 6 experiments that examined the contention that an end-of-day review could lead to augmentation in human memory. In Experiment 1, participants in the study phase were presented with a campus tour of different to-be-remembered objects in different university locations. Each to-be-remembered object was presented with an associated specific comment. Participants were then shown the location name and photographs of half of the objects from half of the locations, and they were asked to try to name the object and recall the associated comment specific to each item. Following a filled delay, participants were presented with the name of each campus location and were asked to free recall the to-be-remembered objects. Relative to the recall from the unpracticed location categories, participants recalled the names of significantly more objects that they practiced (retrieval practice) and significantly fewer unpracticed objects from the practiced locations (retrieval-induced forgetting, RIF). These findings were replicated in Experiment 2 using a campus scavenger hunt in which participants selected their own stimuli from experimenter’s categories. Following an examination of factors that maximized the effects of RIF and retrieval practice in the laboratory (Experiment 3), the authors applied these findings to the campus scavenger hunt task to create different retrieval practice schedules to maximize and minimize recall of items based on experimenter-selected (Experiment 4) and participant-selected items using both category-cued free recall (Experiment 5) and item-specific cues (Experiment 6). Their findings support the claim that an interactive, end-of-day review could lead to augmentation in human memory. PMID:29745709