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PubMedDate not supplied

Retrieval feedback in MEDLINE.

OBJECTIVE: To investigate a new approach for query expansion based on retrieval feedback. The first objective in this study was to examine alternative query-expansion methods within the same retrieval-feedback framework. The three alternatives proposed are: expansion on the MeSH query field alone, expansion on the free-text field alone, and expansion on both the MeSH and the free-text fields. The second objective was to gain further understanding of retrieval feedback by examining possible dependencies on relevant documents during the feedback cycle. DESIGN: Comparative study of retrieval effectiveness using the original unexpanded and the alternative expanded user queries on a MEDLINE test collection of 75 queries and 2,334 MEDLINE citations. MEASUREMENTS: Retrieval effectivenesses of the original unexpanded and the alternative expanded queries were compared using 11-point-average precision scores (11-AvgP). These are averages of precision scores obtained at 11 standard recall points. RESULTS: All three expansion strategies significantly improved the original queries in terms of retrieval effectiveness. Expansion on MeSH alone was equivalent to expansion on both MeSH and the free-text fields. Expansion on the free-text field alone improved the queries significantly less than did the other two strategies. The second part of the study indicated that retrieval-feedback-based expansion yields significant performance improvements independent of the availability of relevant documents for feedback information. CONCLUSIONS: Retrieval feedback offers a robust procedure for query expansion that is most effective for MEDLINE when applied to the MeSH field.

Feedback↗

PubMed2007

Utility of fiberoptic bronchoscopy for retrieval of aspirated headscarf pins.

BACKGROUND: Headscarf pin aspiration is a common and unique form of foreign body aspiration among young Moslem women. Rigid bronchoscopy (RB) is considered the standard procedure for retrieval. There are little data on the role of flexible fiberoptic bronchoscopy (FOB) in the retrieval of aspirated headscarf pins. OBJECTIVES: The aim of this study is to prospectively evaluate the utility of FOB for the retrieval of aspirated headscarf pins. METHODS: Patients with the diagnosis of headscarf pin aspiration admitted to King Abdullah University Hospital from December 2002 to December 2005 were included in the study. Standard FOB procedure under local anesthesia and conscious sedation was performed as the primary tool for retrieval. RESULTS: A total of 16 cases was admitted during the study period. The mean age was 19 years. The aspirated pin was successfully retrieved in 9/16 cases (56%) during the first attempt of FOB. In another 3 cases, although the pin was successfully retrieved from the bronchial tree, it was lost in the throat and swallowed, and then recovered by esophagogastroduodenoscopy. However, FOB was not successful in 4/16 cases. In 3 cases, the aspirated pins were successfully retrieved by RB under general anesthesia and the fourth case required thoracotomy. CONCLUSIONS: Headscarf pin aspiration is a relatively common form of foreign body aspiration among young Moslem Jordanian women. FOB under local anesthesia can be a useful first-step tool in retrieval, provided facilities for esophagogastroduodenoscopy and RB are readily available.

Adolescent↗

PubMed2001

Direct-Sun column ozone retrieval by the ultraviolet multifilter rotating shadow-band radiometer and comparison with those from Brewer and Dobson spectrophotometers.

A methodology for direct-Sun ozone retrieval using the ultraviolet multifilter rotating shadow-band radiometer (UV-MFRSR) is presented. Total vertical column ozone was retrieved in three stations: Mauna Loa, Hawaii, in the U.S., and Regina, Saskatchewan, and Toronto, Ontario, in Canada, from direct solar irradiances of the UV-MFRSR at 325-, 305-, 332-, and 311-nm channels (2-nm FWHM). The total uncertainty of ozone retrievals in this study is +/-2.0%. For Mauna Loa the mean ratios of the UV-MFRSR column ozone retrievals to the collocated Dobson and Brewer were 0.998 and 0.986 between May and September of 1999. The mean ratio of UV-MFRSR retrievals to the collocated Brewer retrievals was 1.012 in Toronto between April and August of 1999, and the mean ratio of retrievals of the UV-MFRSR to the collocated Brewer was 0.988 in Regina between June and September of 1999. Total vertical column ozone values for solar zenith angles of >70 degrees were not considered, because of the signal-to-noise ratio and the angular response of the instruments, and were not used in the evaluation. The advantages of total vertical column ozone retrieval using UV-MFRSR include relatively low cost, computer-controlled operation, automated calibration stability checks, and minimal maintenance. It allows for the real-time measurement of total vertical column ozone. The UV-MFRSR is being used at 28 sites across the United States and 2 sites in Canada that form the U.S. Department of Agriculture UV-B Radiation Monitoring and Research Program. This constitutes a unique network of total vertical colunm ozone measurement.

Journal Article↗

PubMed2005

Distinct contributions of hippocampal NMDA and AMPA receptors to encoding and retrieval of one-trial place memory.

Allocentric place memory may serve to specify the context of events stored in human episodic memory. Recently, our laboratory demonstrated that, analogous to event-place associations in episodic memory, rats could associate, within one trial, a specific food flavor with an allocentrically defined place in an open arena. Encoding, but not retrieval, of such flavor-place associations required hippocampal NMDA receptors; retrieval depended on hippocampal AMPA receptors. This might have partly reflected the contributions of these receptors to encoding and retrieval of one-trial place, rather than flavor-place, memory. Therefore, the present study developed a food-reinforced arena paradigm to study encoding and retrieval of one-trial allocentric place memory in rats; memory relied on visuospatial information and declined with increasing retention delay, still being significant after 6 h, the longest delay tested (experiments 1 and 2). Hippocampal infusion of the NMDA receptor antagonist d-AP-5 blocked encoding without affecting retrieval; hippocampal infusion of the AMPA receptor antagonist CNQX impaired retrieval (experiment 3). Finally, we confirmed that the d-AP-5 infusions selectively blocked induction of long-term potentiation, a form of synaptic plasticity, whereas CNQX impaired fast excitatory transmission, at perforant-path dentate gyrus synapses in the dorsal hippocampus in vivo (experiment 4). Our results support that encoding, but not retrieval, of one-trial allocentric place memory requires the NMDA receptor-dependent induction of hippocampal synaptic plasticity, whereas retrieval depends on AMPA receptor-mediated fast excitatory hippocampal transmission. The contributions of hippocampal NMDA and AMPA receptors to one-trial allocentric place memory may be central to episodic memory and related episodic-like forms of memory in rats.

2-Amino-5-phosphonovalerate↗

PubMedDate not supplied

Physiologic responses in healthy Labrador Retrievers during field trial training and competition.

Ten healthy Labrador Retrievers (4 females and 6 males aged 3-6.5 years [mean, 4.5 years]) training with a professional trainer were studied. The dogs were in training during the entire study. Dogs were monitored within 5 minutes after retrieving birds on land and in water on 2 consecutive days during training and on 2 consecutive days at the Atlanta Retriever Club Fall Field Trial. Baseline samples were taken in the morning on a separate day before the dogs were loaded onto a truck. Venous samples were analyzed with a portable blood analyzer. Measurements included hematocrit, sodium, potassium, chloride, blood urea nitrogen (BUN), glucose, lactate, blood pH, Pco2, Po2, HCO3, and TCO2 plus rectal temperature, pulse rate, and respiratory rate. Ambient temperatures were recorded. Distances and times were estimated. Compared to baseline, significant increases occurred in rectal temperature, pulse rate, respiratory rate, chloride, lactate, and pH postexercise (P < .05): sodium, potassium, BUN, Pco2, and TCO2 were significantly decreased postexercise. Blood pH was markedly higher after retrieves on land than after retrieves in water. Estimated mean speeds were 11.4 mph (18.3 km/h) during a triple retrieve on land and 5.6 mph (9.0 km/h) during a retrieve in water. Maximal ambient temperatures were 84-86 degrees F (29-30 degrees C). In summary, Labrador Retrievers training with a professional trainer had evidence of hyperthermia, respiratory alkalosis, hypocapnia, and mild metabolic acidosis monitored within 5 minutes postexercise during training and field trial competition when maximal ambient temperatures were 85 degrees F (29 degrees C). The results provide a baseline against which physiologic responses of dogs with poor performance can be compared.

Animals↗

PubMed2006

Involuntary awareness and implicit priming: role of retrieval context.

This study examined the role of retrieval context in implicit priming by manipulating percentage of word-stem index as shallow and deep processing while performing a word-stem completion task. 80 subjects were randomly divided into four groups each of 20 subjects: shallow processing or deep processing with few retrieval indices, and shallow processing or deep processing with many retrieval indices. Analysis indicated that proportion of word-stem completion was significantly higher for studied words than for nonstudied words in all four groups and that the subjects in the groups with many retrieval indices had a significantly increased proportion of word-stem completion between studied and nonstudied words than those in the groups with few retrieval indices. Postquestionnaire analysis indicated that more previously studied items were retrieved if many studied items were available during implicit word-stem completion and that only a small proportion of word-stem completion was finished with studied words by the subjects who were aware of the prior studied and test word relations in all four groups. It was concluded that having more studied words retrievable contributed to more being retrieved and that involuntary awareness had very limited influence on the priming in the implicit word-stem completion.

Adolescent↗

PubMed2003

Investigation of breeding strategies to increase the probability that German shepherd dog and Labrador retriever dog guides would attain optimum size.

An optimum-sized dog guide weighs 18 to 32 kg and measures 53 to 64 cm in height at the withers when mature body size is attained. Effects of selection index with and without restrictions, independent trait selection, directional selection, stabilizing selection, and negative assortative mating were modeled using data from German shepherd dogs and Labrador retrievers raised by the Seeing Eye, Inc., Morristown, NJ from 1979 to 1997. The selection goals were to decrease mature weight and mature height in German shepherd dogs and to decrease mature weight and increase mature height in Labrador retrievers. Mature weights were recorded for 1,333 German shepherd dog offspring and their 69 dams and 17 sires, and 1,081 Labrador retriever offspring and their 51 dams and 13 sires. Mature heights also were recorded for offspring and parents, including 871 German shepherd dogs from 70 dams and 15 sires, and 793 Labrador retrievers from 40 dams and 13 sires. Selecting on mature weight alone produced the highest aggregate genetic-economic gain for German shepherd dogs compared with the selection indices with and without restrictions, generating a 2.10-kg decrease in mature weight and a correlated 0.36-cm decrease in mature height. In Labrador retrievers, selecting for mature height alone produced the highest aggregate genetic-economic gain but caused an increase in mature weight. Weighting the two traits equally but in the opposite direction without restrictions was the only index that produced the desired effect of decreasing mature weight and increasing mature height in Labrador retrievers. Response to selection for one generation of directional selection for a single trait included a 0.50-kg decrease in mature weight for German shepherd dogs, a 0.59-kg decrease in mature weight for Labrador retrievers, a 0.18-cm decrease in mature height for German shepherd dogs, and a 0.91-cm increase in mature height for Labrador retrievers. Increasing the percentage of dogs attaining optimum size may decrease the cost of production for the Seeing Eye, Inc., because fewer dogs would need to be raised and trained to provide assistance to the same number of blind individuals.

Animals↗

PubMed2005

Retrieval-induced forgetting in implicit memory tests: the role of test awareness.

Retrieval practice with particular items in memory may result in decreased recall of different, semantically related, items. This retrieval-induced forgetting effect has been demonstrated in studies using explicit memory tests. Anderson and Spellman (1995) have attributed retrieval-induced forgetting to inhibitory mechanisms. This hypothesis predicts similar effects in implicit memory tasks. In our first experiment, using Anderson and Spellman's original paradigm, retrieval-induced forgetting was found using an explicit memory test with independent extralist retrieval cues. In our second experiment, using the same materials, retrieval-induced forgetting was also found using an implicit memory test with independent extralist retrieval cues, but only for participants who were aware of the relationship between the study and practice phase on the one hand, and the test phase of the experiment on the other. Thus, test awareness seems to mediate retrieval-induced forgetting in implicit memory tasks.

Awareness↗

PubMed2004

Retrieval-induced forgetting occurs in tests of item recognition.

Using the retrieval-practice paradigm (Anderson, R. A. Bjork, & E. L. Bjork, 1994), we tested whether or not retrieval-induced forgetting could be found in item recognition tests. In Experiment 1, retrieval practice on items from semantic categories depressed recognition of nonpracticed items from the same categories. Similar results were found in Experiment 2 in a more stringent source test for practiced, nonpracticed, and new items. These results conceptually replicate those of previous retrieval-induced forgetting studies done with cued recall (e.g., Anderson et al., 1994). Our findings are inconsistent with the hypothesis that item-specific cues during retrieval will eliminate retrieval interference in the retrieval-practice paradigm (Butler, Williams, Zacks, & Maki, 2001). We discuss our results in relation to other retrieval interference and inhibition effects in recall and recognition.

Cues↗

PubMed1999

Testicular sperm extraction with intracytoplasmic sperm injection for nonobstructive azoospermia: testicular histology can predict success of sperm retrieval.

PURPOSE: We present treatment results of testicular sperm extraction with intracytoplasmic sperm injection for men with nonobstructive azoospermia and reevaluate the role of testicular histology on open diagnostic testicular biopsy as a predictor of sperm retrieval success. MATERIALS AND METHODS: We evaluated 75 men diagnosed with nonobstructive azoospermia. Cases were categorized into 3 groups of hypospermatogenesis, maturation arrest or Sertoli-cell-only based on the most advanced pattern of spermatogenesis seen on histology. A total of 81 testicular sperm extractions with intracytoplasmic sperm injection were performed for these 75 men. The main outcome measures reviewed included sperm retrieval, fertilization and pregnancy rates with intracytoplasmic sperm injection. Sperm retrieval success rates for men in the 3 histological categories were compared. RESULTS: Spermatozoa were successfully retrieved during 47 of 81 (58%) testicular sperm extraction attempts, with subsequent fertilization of 268 of 439 (61%) injected metaphase II oocytes using intracytoplasmic sperm injection. Clinical pregnancies were obtained in 26 of 47 (55%) cycles when sperm were retrieved, with ongoing pregnancies or live deliveries for 20 of 47 (43%). Of 39 men with hypospermatogenesis on diagnostic biopsy 31 (79%) had successful sperm retrieval, compared to 9 of 19 (47%) with maturation arrest and 5 of 21 (24%) with a pure Sertolicell-only pattern. CONCLUSIONS: Critical examination of the most advanced pattern of spermatogenesis from open diagnostic testis biopsy allows prediction of sperm retrieval success with testicular sperm extraction. In this study population spermatozoa were retrieved in 58% of attempts. When this testicular sperm was used with intracytoplasmic sperm injection, clinical pregnancy rate was 55% for men with nonobstructive azoospermia.

Adult↗

PubMedDate not supplied

Heart retrieval for cardiac homograft.

BACKGROUND: The use of homograft tissue instead of various artificial materials in contemporary cardiovascular surgery, although limited by the constant shortage of donor organs, has become the clinically preferable procedure. The proper technique of heart retrieval, with strict donor qualification criteria and sterility procedures, is one of the key points in the successful preparation of allografts to be used later in a selected group of patients undergoing cardiac surgery, especially in the repair of pediatric congenital heart defects. MATERIAL AND METHODS: The article presents the most popular surgical technique to use for retrieving a heart for cardiac homograft in multiorgan procurement and routine autopsy, including the immediate preliminary preparation and transport, as recommended by the majority of tissue bank institutions. The qualification criteria for tissue donation, delicate preparation techniques, and sterility protocols are also important issues for successful cardiac homograft retrieval. Recently a tendency towards a growing number of pediatric donors can be observed. The techniques presented in this article should also be applied in cases of homograft retrieval from pediatric donors. RESULTS: This article analyzes our seven-year-long experience, involving a total number of 608 hearts retrieved for cardiac homografts, with special attention to the main reasons for disqualification of the organs delivered to the tissue bank. CONCLUSIONS: 1. The procedures for the sterility of tissue retrieval, especially in autopsies with heart retrieval, although they may sometimes be difficult for the surgeon or pathologist, are necessary to provide maximum benefit from harvested tissues. 2. The proper technique for pediatric homograft retrieval is twice as important in tissue delivery protocols.

Autopsy↗

PubMed2002

[Clinical experience with retrievable vena cava filters for prevention of pulmonary thromboembolism].

OBJECTIVES: To evaluate the feasibility, effectiveness and complications of the retrievable vena cava filter [Güther tulip vena cava filter(GTF)] for the prevention of pulmonary thromboembolism in patients with deep vein thrombosis. METHODS: Seventeen patients, 3 males and 14 females, aged 21 to 82 years (mean age 59 +/- 19 years), underwent implantation of GTFs between December 2000 and February 2002 at Mie University Hospital. All patients were treated under diagnoses of deep vein thrombosis with or without pulmonary thromboembolism based on venous ultrasonography, venography or computed tomography. Eleven patients were treated with thrombolysis. RESULTS: Significant thromboembolus was trapped within the filter in 3 of 12 patients. No acute pulmonary thromboembolism occurred during implantation or at retrieval of the GTF. Retrieval of the GTF was attempted in 9 patients, and 8 GTFs were retrieved successfully. Mean interval of the filter implantation was 13.4 +/- 6.3 days and the mean retrieval time was 4.8 +/- 3.2 min. No complications occurred except for one case of minor hemorrhage at the puncture site. CONCLUSIONS: The placement and retrieval of the retrievable vena cava filter was feasible and safe. This filter was also effective for the prevention of pulmonary thromboembolism. This retrievable vena cava filter may be a good first-choice filter for both permanent and temporary use.

Adult↗

PubMed2004

Validation of MODIS aerosol retrievals and evaluation of potential cloud contamination in East Asia.

MODIS aerosol retrievals onboard Terra/Aqua and ground truth data obtained from AERONET (Aerosol Robtic Network) solar direct radiance measurements are collocated to evaluate the quality of the former in East Asia. AERONET stations in East Asia are separated into two groups according to their locations and the preliminary validation results for each station. The validation results showed that the accuracy of MODIS aerosol retrievals in East Asia is a little worse than that obtained in other regions such as Eastern U.S., Western Europe, Brazil and so on. The primary reason is due to the improper aerosol model used in MODIS aerosol retrieval algorithm, so it is of significance to characterize aerosol properties properly according to long-term ground-based remote sensing or other relevant in situ observations in order to improve MODIS retrievals in East Asia. Cloud contamination is proved to be one of large errors, which is demonstrated by the significant relation between MODIS aerosol retrievals versus cloud fraction, as well as notable improvement of linear relation between satellite and ground aerosol data after potential cloud contamination screened. Hence, it is suggested that more stringent clear sky condition be set in use of MODIS aerosol data. It should be pointed out that the improvement might be offset by other error sources in some cases because of complex relation between different errors. Large seasonal variation of surface reflection and uncertainties associated with it result in large intercepts and random error in MODIS aerosol retrievals in northern inland of East Asia. It remains to be a big problem to retrieve aerosols accurately in inland characterized by relatively larger surface reflection than the requirement in MODIS aerosol retrieval algorithm.

Aerosols↗

PubMed1984

Unconstrained retrieval from semantic memory.

The present study was designed to examine developmental change in the processes used to retrieve lexical information from semantic memory. We asked 8-, 12-, and 21-year-olds to name as many animals and pieces of furniture as they could, in separate 7-min intervals. The principal results were the following: (1) the number of items retrieved increased with age, but at all ages retrieval declined hyperbolically over the 7-min interval; (2) analysis of the time between retrieval of successive items indicated that older individuals retrieved larger clusters of items, but that the number of clusters retrieved did not vary with age; and (3) at all ages prototypic category members were retrieved first, followed by typical (but not prototypic) and atypical category members. The results are explained in terms of a model in which the information in semantic memory changes with age, but the processes used to retrieve that information do not.

Adult↗

PubMed1996

[Antigen retrieval: its significance and drawbacks in immunohistochemistry].

One of the biggest problems in immunohistochemistry has been how to maintain both good morphology and the immunoreactivity of antigens in tissue sections. Various techniques to retrieve the immunoreactivities of antigens (unmasking) after routine tissue preparations, such as fixation, dehydration and embedding, have been devised and are now finding their way into use for immunostainings in not only cytohistological investigations but also pathoclinical diagnoses. In this report, first, the mechanisms and significance of both fixation and antigen retrieval were surveyed from the viewpoint of protein inactivation. Second, some practical problems and notes in two of the most popular unmasking techniques, enzyme digestion and heat-induced epitope retrieval (HIER), were reviewed in order to adapt the techniques precisely in immunohistochemistry. The major artifact induced by fixation is the masking of tissue antigens due to cross-linking among the amino-acid residues of proteins. It is important to choose a proper fixing condition for each antigen considering its biochemical nature and resistance to the fixation. (Table 2), and to keep the fixing conditions to a minimum so that the immunoreactivity of the antigen can be readily retrieved by various unmasking techniques (Table 3, Fig. 1). Antigen retrieval per se is the process causing protein denaturation in tissues, just like many other protein inactivation processes (Table 1). Enzyme digestion may etch the masking parts of proteins around an antigen to expose its epitope. Although enzyme digestion is relatively simple and its treatment condition easy to control, the results are not necessarily dramatic and consistent depending on the types or lots of enzymes. Thus, one must find his/her own digestion manual to achieve the best staining result for each antigen (e.g., Table 4). For example, pepsin digestion gave the best results in the immunostaining of bromo-deoxyuridine (BrdU) and proliferating cell nuclear antigen (PCNA), whereas other enzymes had little effect (Table 5). Heating may also cleave the polypeptide backbone and disrupt the cross-links produced by fixation. The heating effect on antigen retrieval is temperature-dependent and seems to be proportional to the product of temperature and time. In the case of PCNA immunostaining on paraformaldehyde-fixed paraffin-embedded sections, heating at 90 degrees C for at least 3 min was required, however, as the heating condition became more severe, non-specific background stains also increased (Table 6), which is one of the most serious problems in antigen retrieval (Fig. 2a, c). One possible choice for avoiding such undesirable results is the combination of suboptimal heating (at 80 degrees C for 10-15 min) and pepsin digestion (Fig. 2b, d). An important theoretical consideration for employing such a dramatic method of denaturation is whether the masked antigen epitopes can be adequately exposed without giving rise to false-positive (or false-negative) results with previously trusted antibodies. It seems that each antigen requires a "tailor-made" tissue preparation for optimal preservation of its antigenicity and precise localization. In accordance with the development of immunology, molecular biology, genetics or embryology, the need for multiple immunostaining in combination with other technologies like in situ hybridization should increase in order to analyze the spatial and functional relationships among various molecules in situ. Antigen retrieval would then become a powerful strategy.

Animals↗

PubMed2004

A reference data set for the evaluation of medical image retrieval systems.

Content-based image retrieval is starting to become an increasingly important factor in medical imaging research and image management systems. Several retrieval systems and methodologies exist and are used in a large variety of applications from automatic labelling of images to diagnostic aid and image classification. Still, it is very hard to compare the performance of these systems as the used databases often contain copyrighted or private images and are thus not interchangeable between research groups, also for patient privacy. Most of the currently used databases for evaluating systems are also fairly small which is partly due to the high cost in obtaining a gold standard or ground truth that is necessary for evaluation. Several large image databases, though without a gold standard, start to be available publicly, for example by the NIH (National Institutes for Health). This article describes the creation of a large medical image database that is used in a teaching file containing more than 8,700 varied medical images. The images are anonymised and can be exchanged free of charge and copyright. Ground truth (a gold standard) has been obtained for a set of 26 images being selected as query topics for content-based query by image example. To reduce the time for the generation of ground truth, pooling methods well known from the text or information retrieval field have been used. Such a database is a good starting point for comparing the current image retrieval systems and to measure the retrieval quality, especially within the context of teaching files, image case databases and the support of teaching. For a comparison of retrieval systems for diagnostic aid, specialised image databases, including the diagnosis and a case description will need to be made available, as well, including gold standards for a proper system evaluation. A first evaluation event for image retrieval is foreseen at the 2004 CLEF conference (Cross Language Evaluation Forum) to compare text-and content-based access mechanism to images.

Databases, Factual↗

PubMed2005

CLUE: cluster-based retrieval of images by unsupervised learning.

In a typical content-based image retrieval (CBIR) system, target images (images in the database) are sorted by feature similarities with respect to the query. Similarities among target images are usually ignored. This paper introduces a new technique, cluster-based retrieval of images by unsupervised learning (CLUE), for improving user interaction with image retrieval systems by fully exploiting the similarity information. CLUE retrieves image clusters by applying a graph-theoretic clustering algorithm to a collection of images in the vicinity of the query. Clustering in CLUE is dynamic. In particular, clusters formed depend on which images are retrieved in response to the query. CLUE can be combined with any real-valued symmetric similarity measure (metric or nonmetric). Thus, it may be embedded in many current CBIR systems, including relevance feedback systems. The performance of an experimental image retrieval system using CLUE is evaluated on a database of around 60,000 images from COREL. Empirical results demonstrate improved performance compared with a CBIR system using the same image similarity measure. In addition, results on images returned by Google's Image Search reveal the potential of applying CLUE to real-world image data and integrating CLUE as a part of the interface for keyword-based image retrieval systems.

Algorithms↗

PubMed2006

Retrieval with gene queries.

BACKGROUND: Accuracy of document retrieval from MEDLINE for gene queries is crucially important for many applications in bioinformatics. We explore five information retrieval-based methods to rank documents retrieved by PubMed gene queries for the human genome. The aim is to rank relevant documents higher in the retrieved list. We address the special challenges faced due to ambiguity in gene nomenclature: gene terms that refer to multiple genes, gene terms that are also English words, and gene terms that have other biological meanings. RESULTS: Our two baseline ranking strategies are quite similar in performance. Two of our three LocusLink-based strategies offer significant improvements. These methods work very well even when there is ambiguity in the gene terms. Our best ranking strategy offers significant improvements on three different kinds of ambiguities over our two baseline strategies (improvements range from 15.9% to 17.7% and 11.7% to 13.3% depending on the baseline). For most genes the best ranking query is one that is built from the LocusLink (now Entrez Gene) summary and product information along with the gene names and aliases. For others, the gene names and aliases suffice. We also present an approach that successfully predicts, for a given gene, which of these two ranking queries is more appropriate. CONCLUSION: We explore the effect of different post-retrieval strategies on the ranking of documents returned by PubMed for human gene queries. We have successfully applied some of these strategies to improve the ranking of relevant documents in the retrieved sets. This holds true even when various kinds of ambiguity are encountered. We feel that it would be very useful to apply strategies like ours on PubMed search results as these are not ordered by relevance in any way. This is especially so for queries that retrieve a large number of documents.

Abstracting and Indexing↗