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PubMed2002

EXProt--a database for EXPerimentally verified Protein functions.

EXProt (database for EXPerimentally verified Protein functions) is a new non-redundant database containing protein sequences for which the function has been experimentally verified. It is a selection of 3976 entries from the Prokaryotes section of the EMBL Nucleotide Sequence Database, Release 66, and 375 entries from the Pseudomonas Community Annotation Project (PseudoCAP). The entries in EXProt all have a unique ID number and provide information about the organism, protein sequence, functional annotation, link to entry in original database, and if known, gene name and link to references in PubMed/Medline. The EXProt web page (http://www.cmbi.nl/EXProt) provides further details of the database and a link to a BLAST search (blastp & blastx) of the database. The EXProt entries are indexed in SRS (http://www.cmbi.nl/srs/) and can be searched by means of keywords. Authors can be reached by email (exprot(cmbi.kun.nl).

Amino Acid Sequence↗
PubMedDate not supplied

An on-line two-dimensional polyacrylamide gel electrophoresis protein database of adult Drosophila melanogaster.

An annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) protein database of adult Drosophila melanogaster has been constructed, based on the protein patterns of heads, thoraces and abdomens of adult male and female Drosophila melanogaster. About 1200 major protein spots are catalogued. Common proteins, found in all body parts, as well as bodypart- and sex-specifically expressed proteins are reported. Of the major proteins, 91, or 7.5%, are differentially expressed in the two sexes or in different body parts, at least in part reflecting specific functional requirements. At the present time 43 proteins, or about 3.5% of the detected proteins, have been identified. These data can be accessed interactively from our World Wide Web (WWW) server through clickable inline gel images and hypertext links. Identified protein spots are cross-referenced, through hypertext links, to the SWISS-PROT annotated database of protein primary sequences and the Fly-Base database of Drosophila genomic data. Our reference gels can be used to gain immediate access to protein spot identify and to the pattern of differentially expressed proteins in Drosophila melanogaster. The work presented in this article ties together information from protein 2-D PAGE, molecular biology and genetics and offers a uniform way to access this large volume of data.

Abdomen↗
PubMed2002

[Usefulness of some databases in medical practice].

The following publication include results of thinking the matter over usefulness some computer, medical databases as well as Internet drug information resources. Quantity of medical software and Internet portals is not equal to quality, so it is necessary to order and classify medical electronic tools. It was bring MICROMEDEX databases system to readers attention, as a model, reference tool helpful in computer aided medicine.

Databases, Factual↗
PubMed2002

Using Medline to achieve an evidence-based approach to diagnostic clinical biochemistry.

Medline is the US National Library of Medicine database that is used for searching the medical biochemistry literature. The database is structured using medical subject subheadings (MeSH terms) to classify the content of references; indexing is done manually using MeSH terms as key words. Searching the database effectively means finding the maximum number of relevant references together with the minimum number of irrelevant ones. This article is aimed at explaining the limitations of Medline and suggesting some solutions to key problems. The goal is that users can improve their literature search technique by employing a structured approach. As usual, asking relevant questions before starting a search is essential.

Biochemical Phenomena↗
PubMed2006

Meta-analysis of the complications of laparoscopic renal surgery: comparison of procedures and techniques.

PURPOSE: We performed a meta-analysis of the literature to define the current expectations of complications during laparoscopic renal surgery. MATERIALS AND METHODS: References were searched in the MEDLINE database from 1995 to 2004 using the terms complications and laparoscopic nephrectomy. Inclusion criteria were any series with greater than 20 cases, patient age older than 16 years and any complications listed for certain procedures, including laparoscopic radical nephrectomy, HA laparoscopic radical nephrectomy, LPN, HALPN, laparoscopic donor nephrectomy, HA laparoscopic donor nephrectomy, laparoscopic simple nephrectomy, laparoscopic nephroureterectomy and retroperitoneal laparoscopic nephrectomy. A data extraction form was created to categorize major or minor complications. A 5 member panel adhered to the strict criteria and extracted data from articles that met inclusion criteria. Data were entered into a spreadsheet and a meta-analysis was performed. RESULTS: Initial review identified 73 of 405 references that were acceptable for retrieval and data extraction, of which 56 met inclusion criteria. The overall major and minor complication rates of laparoscopic renal surgery were 9.5% and 1.9%, respectively. There was a significant difference between the major complication rates of LPN and HALPN (21.0% vs 3.3%, p <0.05). CONCLUSIONS: Our results show that patients who undergo laparoscopic renal surgery may have an overall major complication rate of 9.5%. The highest major complication rate is associated with technically challenging LPN (21%). There appears to be a significantly higher wound complication rate associated with HA surgery in comparison to that of standard laparoscopy (1.9% vs 0.2%, p <0.05).

Humans↗
PubMed2004

COACH: profile-profile alignment of protein families using hidden Markov models.

MOTIVATION: Alignments of two multiple-sequence alignments, or statistical models of such alignments (profiles), have important applications in computational biology. The increased amount of information in a profile versus a single sequence can lead to more accurate alignments and more sensitive homolog detection in database searches. Several profile-profile alignment methods have been proposed and have been shown to improve sensitivity and alignment quality compared with sequence-sequence methods (such as BLAST) and profile-sequence methods (e.g. PSI-BLAST). Here we present a new approach to profile-profile alignment we call Comparison of Alignments by Constructing Hidden Markov Models (HMMs) (COACH). COACH aligns two multiple sequence alignments by constructing a profile HMM from one alignment and aligning the other to that HMM. RESULTS: We compare the alignment accuracy of COACH with two recently published methods: Yona and Levitt's prof_sim and Sadreyev and Grishin's COMPASS. On two sets of reference alignments selected from the FSSP database, we find that COACH is able, on average, to produce alignments giving the best coverage or the fewest errors, depending on the chosen parameter settings. AVAILABILITY: COACH is freely available from www.drive5.com/lobster

Algorithms↗
PubMed1997

A support system for content-based medical image retrieval in object oriented databases.

This work describes both the concepts used in an Object Manager for storage of medical images as one more data type associated to objects, and a support system developed to offer this kind of tool to medical application developers. The purpose of this work is to support the retrieval of images through queries based on the graphical contents of the stored images. The usual approach uses icons and textual attributes stored with the images to specify the queries. This work uses a novel modeling technique to define the "image data type," by means of which it is possible to decide, before the query itself, the key data of each image that must be extracted from the image when it is stored in the database, so the search can be accelerated when queries are issued. This approach enables building of expansible systems, where new image processing algorithms can be added easily, using its syntactic representation stored through an Image Meta-schema into the application database schema. This work shows how such a system has been implemented, and also provides a query language used to refer and execute these algorithms from inside the database management system.

Algorithms↗
PubMed2025

eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA.

Extrachromosomal circular DNA (eccDNA) refers to small, circular DNA molecules that originate from chromosomal sequences and are prevalent across nearly all eukaryotic organisms. In humans, eccDNAs are widely distributed in normal tissues, cancerous tissues, and body fluids, where they play important roles in tumorigenesis and are often associated with poor clinical outcomes. Given their biological and clinical significance, a well-integrated and high-quality database is essential for advancing eccDNA-related research. To address this need, we developed eccDNABase, a comprehensive and curated resource for browsing, searching, and analyzing eccDNAs across multiple species. The database systematically catalogs eccDNA-disease associations from diverse tissues and organisms. Currently, eccDNABase contains 1,875,452 eccDNA-disease associations, encompassing 8,398 ecDNA entries across nine species, 63 diseases, and healthy individuals. Each entry provides detailed information, including eccDNA ID, type, chromosomal localization, species, tissue or cell line source, disease name and Disease Ontology ID, overlap length and percentage with genes, oncogene overlap, detection method, and links to literature and source databases. Given its extensive and curated datasets, eccDNABase serves as a valuable resource for both basic and translational research, offering deeper insights into the role of eccDNA in health and disease. The database is publicly accessible at http://cgga.org.cn/eccDNABase/.

Humans↗
PubMed2003

Avoiding surgery in patients with colorectal polyps.

PURPOSE: Colonic polyps are sometimes difficult to remove endoscopically and are referred for surgical resection. This study was performed to determine how many polyps referred for surgery could actually be managed endoscopically. METHODS: An endoscopic database with data entered prospectively and consecutively was used to identify patients referred for surgery for a colonic polyp. Rectal polyps were excluded. All patients underwent colonoscopy before surgery to see if the polyp could be managed endoscopically. Cases were reviewed to see the method and outcome of treatment. RESULTS: The study population consists of 58 patients referred for surgical resection of a colorectal polyp. Endoscopic polypectomy was initially successful in 48. Five of the 48 needed surgery later for a final success rate of 43/58 avoiding surgery. There were no deaths, four complications of endoscopic polypectomy (three bleeds, one post-polypectomy syndrome) and two patients had complications of surgery (one splenic injury, one ventral hernia). Polyps ranged in size from 1.5 cm to 8.0 cm. Seven polyps contained invasive cancer (three needing surgical resection), eight contained intramucosal cancer (one operated) and 11 had severe dysplasia (three operated). Rate of persistent polyp was 16/37 at first follow up, 7/23 at second, 1/14 at third and 0/8 at fourth. CONCLUSION: Most polyps referred for surgical resection were successfully managed endoscopically. Patients with colonic polyps that are difficult or potentially dangerous to remove endoscopically should be sent for a second opinion before surgery is performed.

Aged↗
PubMed1991

The gene-protein database of Escherichia coli: edition 4.

The gene-protein database of Escherichia coli has as its core an index that links each of the protein spots from a two-dimensional polyacrylamide gel to the gene that encodes the protein. Additional information about each protein and its gene is generated from two-dimensional gel analysis or collated from the literature to form the database. Earlier editions of the database have provided periodic updates of information. The current edition does this, but also introduces a new reference gel image produced by an electrophoresis system recently adopted in this laboratory. The new gel system was chosen because it offers an improved opportunity for other investigations to produce close replicas of the reference gel pattern, thereby allowing easier access to the information of the database and encouraging independent contribution to the database. The new gel format also is larger and hence more compatible with computer assisted image analysis, which has become essential for a project of this magnitude. This edition continues the use of the former reference gel images, but adds a reference image of an equilibrium gel of E. coli strain W3110 produced by the new standardized gel system. At this time, 55% of the protein spots annotated on the previous equilibrium reference gel for this organism have been located on the new reference image, and these identifications are included in the tables of the database.

Bacterial Proteins↗
PubMed2001

Clinical and exercise test predictors of all-cause mortality: results from > 6,000 consecutive referred male patients.

OBJECTIVE: To report the prevalence of abnormal treadmill test responses and their association with mortality in a large consecutive series of patients referred for standard exercise tests, with testing performed and reported in a standardized fashion. BACKGROUND: Exercise testing is widely performed, but few databases exist of large numbers of consecutive tests performed on patients referred for routine clinical purposes using standardized methods. Even fewer of the available databases have information regarding all-cause mortality as an outcome. METHODS: All patients referred for evaluation at two university-affiliated Veterans Affairs medical centers who underwent exercise treadmill testing for clinical indications between 1987 and 2000 were determined to be dead or alive using the Social Security death index after a mean 6.2 years (median, 7 years) of follow-up. Clinical and exercise test variables were collected prospectively according to standard definitions; testing and data management were performed in a standardized fashion using a computer-assisted protocol. All-cause mortality was utilized as the end point for follow-up. Standard survival analysis was performed, including Kaplan-Meier curves and a Cox hazard model. RESULTS: There were 6,213 male patients (mean +/- SD age, 59 +/- 11 years) who underwent standard exercise ECG treadmill testing over the study period with a mean follow-up duration of 6.2 +/- 3.7 years. There were no complications of testing in this clinically referred population, 78% of whom were referred for chest pain, or risk factors or signs or symptoms of ischemic heart disease. Overlapping thirds had typical angina or history of myocardial infarction (MI). Five hundred seventy-nine patients had prior coronary artery bypass surgery, and 522 patients had a history of congestive heart failure (CHF). Indications for testing were in accordance with published guidelines. Twenty percent died over the follow-up period, for an average annual mortality rate of 2.6%. Cox hazard function chose the following variables in rank order as independently and significantly associated with time to death: exercise capacity (metabolic equivalents < 5, age > 65 years, history of CHF, and history of MI. A score based on these variables (summing up the four variables [if yes = 1 point]) classified patients into low-risk, medium-risk, and high-risk groups. The high-risk group (score > or = 3) has a hazard ratio of 5.0 (95% confidence interval, 4.7 to 5.3) and a 5-year mortality rate of 31%. CONCLUSION: This comprehensive analysis provides rates of various abnormal responses that can be expected in patients referred for exercise testing at a typical medical center. Four simple variables combined as a score powerfully stratified patients according to prognosis.

Aged↗
PubMedDate not supplied

Medical subject headings used to search the biomedical literature.

The National Library of Medicine's MEDLINE (MEDLARS Online) database was the first database to be searched nationwide via value-added telecommunication networks. Now available on the World Wide Web free of charge from the National Library of Medicine and from many other sources, it is the world's most heavily used medical database. MEDLINE is unique in that each reference to the medical literature is indexed under a controlled vocabulary called Medical Subject Headings (MeSH). These headings are the keys that unlock the medical literature. MeSH multiplies the usefulness of the MEDLINE database and makes it possible to search the medical literature as we do today. This paper commemorates the 40th anniversary of the introduction of MeSH and salutes some of the farsighted persons who conceived and developed the MEDLINE database.

Abstracting and Indexing↗
PubMed2004

The inadequate smear: does it matter?

The objective of this study was to quantify the incidence of underlying cervical intraepithelial neoplasia (CIN) among women referred for colposcopy with three consecutive inadequate smears. The design was a retrospective cohort study analysing data from a regional colposcopy database at Cervical Screening Wales. Women who were referred to all the colposcopy clinics in Wales with three consecutive inadequate smears, the third inadequate smear being taken between 1 April 2001 and 31 March 2002 constituted the study population. The results of the fourth smear taken at the colposcopy clinic after three consecutive inadequate smears, the worst biopsy results from any of the subsequent colposcopies and the relationship between the result of the fourth smear taken at colposcopy clinic and any histology result were the main outcome measures. The accuracy of the colposcopic opinion was also examined. Of the 433 women identified as having been referred because of three consecutive inadequate smears, 302 were linked to either a subsequent smear and/or a biopsy result. An adequate smear result was available for 85% of these women when the smear was taken in the colposcopy clinic; 77% were reported as negative and 8% were abnormal. Of the 347 women seen in the colposcopy clinic, high-grade CIN was seen in 3% and low-grade lesion in 8%. The sensitivity and specificity of the fourth inadequate smear test in predicting underlying CIN were 15% and 84% respectively, with a positive predictive value of 8%. The sensitivity and specificity of colposcopy in predicting histological CIN among patients with three inadequate smears was 70% and 49%, respectively, and the positive predictive value was 44%. This study raises the question as to whether three consecutive inadequate smears should be considered as an indication for colposcopy, or merely for a further smear to be taken in circumstances where there is a greater likelihood getting an adequate result.

Adult↗
PubMed2006

Mapping the literature of transcultural nursing.

OVERVIEW: No bibliometric studies of the literature of the field of transcultural nursing have been published. This paper describes a citation analysis as part of the project undertaken by the Nursing and Allied Health Resources Section of the Medical Library Association to map the literature of nursing. OBJECTIVE: The purpose of this study was to identify the core literature and determine which databases provided the most complete access to the transcultural nursing literature. METHODS: Cited references from essential source journals were analyzed for a three-year period. Eight major databases were compared for indexing coverage of the identified core list of journals. RESULTS: This study identifies 138 core journals. Transcultural nursing relies on journal literature from associated health sciences fields in addition to nursing. Books provide an important format. Nearly all cited references were from the previous 18 years. In comparing indexing coverage among 8 major databases, 3 databases rose to the top. CONCLUSIONS: No single database can claim comprehensive indexing coverage for this broad field. It is essential to search multiple databases. Based on this study, PubMed/MEDLINE, Social Sciences Citation Index, and CINAHL provide the best coverage. Collections supporting transcultural nursing require robust access to literature beyond nursing publications.

Abstracting and Indexing↗
PubMed1989

Electrocardiographic quantitation of ventricular repolarization.

Quantification of the electrocardiographic ventricular repolarization involving the T-U wave complex is usually performed with reference to the axis of the T wave and the QT interval duration. A novel quantitative approach to improve the description of ventricular repolarization was applied to the digitized electrocardiograms of 423 normal subjects. Six electrocardiographic repolarization characteristics were identified: duration, rate, area, symmetry, late phenomena, and interlead heterogeneity. A computer algorithm was designed to automatically interpret the electrocardiographic repolarization segment and measure 11 variables that quantified these repolarization characteristics. The application of redundancy-reduction techniques selected a final set of seven variables that were used in the statistical analysis. The QT interval, which was included in the initial group of variables, was replaced by the time interval between S wave offset and T wave maximum. All selected electrocardiographic variables were independent of age (r2 less than 0.11) and body surface area (r2 less than 0.03); all except the early duration variable were heart rate- and QT interval-independent (r2 less than 0.2, r2 less than 0.13, respectively; and most were uncorrelated to each other. A comparison of repolarization characteristics by gender revealed that repolarization duration was significantly more prolonged (p less than 0.0001) in women than in men. This multidimensional quantitative approach conveys a new and more complete description of the repolarization process and provides an electrocardiographic repolarization database in normal subjects as a reference standard for identifying patients with disordered repolarization.

Adult↗
PubMed2002

Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA).

Comparative genomics promises to rapidly accelerate the identification and functional classification of biologically important human genes. We developed the TIGR Orthologous Gene Alignment (TOGA; ) database to provide a cross-reference between fully and partially sequenced eukaryotic transcribed sequences. Starting with the assembled expressed sequence tag (EST) and gene sequences that comprise the 28 TIGR Gene Indices, we used high-stringency pair-wise sequence searches and a reflexive, transitive closure process to associate sequence-specific best hits, generating 32,652 tentative ortholog groups (TOGs). This has allowed us to identify putative orthologs and paralogs for known genes, as well as those that exist only as uncharacterized ESTs and to provide links to additional information including genome sequence and mapping data. TOGA provides an important new resource for the analysis of gene function in eukaryotes. In addition, an analysis of the most widely represented sequences can begin to provide insight into eukaryotic biological processes.

Algorithms↗
PubMed2000

Peripheral retinal ablation for threshold retinopathy of prematurity in preterm infants.

BACKGROUND: This section is under preparation and will be included in the next issue. OBJECTIVES: In premature infants with threshold retinopathy of prematurity (ROP) does peripheral retinal ablation, by any means, reduce the incidence of adverse ophthalmic outcome? SEARCH STRATEGY: The standard search strategy of the Cochrane Neonatal Review Group was used. This included a search of the Cochrane Neonatal Group Register of Clinical Trials, MEDLINE, EMBASE, previous reviews including cross references, abstracts from pediatric and ophthalmologic meetings, letters and expert informants. Search terms included "Retinopathy of Prematurity" [MeSH Terms], "Retrolental Fibroplasia" [All Fields] and "Lightcoagulation" [All Fields] or "Cryosurgery" [All Fields]. In addition, a personal bibliographic database was used as a cross-reference. SELECTION CRITERIA: All trials in human premature infants with threshold ROP utilizing random or quasi random allocation to either peripheral retinal ablation of the avascular retina, by any means, or concurrent control group with independent outcome assessment were initially selected for review. Following methodologic review, only studies using random allocation were selected for data extraction. DATA COLLECTION AND ANALYSIS: Relevance and validity were assessed by the two authors and consensus reached. Each author extracted clinical outcomes from valid reports independently. Data analysis was conducted according to the standards of the Cochrane Neonatal Review Group. MAIN RESULTS: Two randomised trials were identified. Data from these studies show that peripheral retinal ablation reduces the risk of (1) early unfavorable retinal structure from 47. 9% to 28.1% (absolute risk reduction 19.8% [95% CI 27.9 - 11.8%]), (2) unfavorable retinal structure in early childhood from 44.3% to 26.3% (absolute risk reduction 18% [95% CI 27.0 - 9.1%]) and (3) unfavorable visual acuity in early childhood from 63% to 50.6% (absolute risk reduction 12.2% [95% CI 21.2 - 3.1]). In addition, visual fields in sighted eyes were slightly smaller in the treated (51.3 degrees +/- 11.8 degrees ) group as compared to the control (58.2 degrees +/- 14.5 degrees ) group. REVIEWER'S CONCLUSIONS: Peripheral retinal ablation reduces the incidence of adverse ophthalmic outcome in premature infants with threshold ROP. In sighted eyes, peripheral retinal ablation may reduce the size of the visual field. At this stage, long term outcomes remain unknown.

Cryosurgery↗
PubMed2004

A similarity learning approach to content-based image retrieval: application to digital mammography.

In this paper, we describe an approach to content-based retrieval of medical images from a database, and provide a preliminary demonstration of our approach as applied to retrieval of digital mammograms. Content-based image retrieval (CBIR) refers to the retrieval of images from a database using information derived from the images themselves, rather than solely from accompanying text indices. In the medical-imaging context, the ultimate aim of CBIR is to provide radiologists with a diagnostic aid in the form of a display of relevant past cases, along with proven pathology and other suitable information. CBIR may also be useful as a training tool for medical students and residents. The goal of information retrieval is to recall from a database information that is relevant to the user's query. The most challenging aspect of CBIR is the definition of relevance (similarity), which is used to guide the retrieval machine. In this paper, we pursue a new approach, in which similarity is learned from training examples provided by human observers. Specifically, we explore the use of neural networks and support vector machines to predict the user's notion of similarity. Within this framework we propose using a hierarchal learning approach, which consists of a cascade of a binary classifier and a regression module to optimize retrieval effectiveness and efficiency. We also explore how to incorporate online human interaction to achieve relevance feedback in this learning framework. Our experiments are based on a database consisting of 76 mammograms, all of which contain clustered microcalcifications (MCs). Our goal is to retrieve mammogram images containing similar MC clusters to that in a query. The performance of the retrieval system is evaluated using precision-recall curves computed using a cross-validation procedure. Our experimental results demonstrate that: 1) the learning framework can accurately predict the perceptual similarity reported by human observers, thereby serving as a basis for CBIR; 2) the learning-based framework can significantly outperform a simple distance-based similarity metric; 3) the use of the hierarchical two-stage network can improve retrieval performance; and 4) relevance feedback can be effectively incorporated into this learning framework to achieve improvement in retrieval precision based on online interaction with users; and 5) the retrieved images by the network can have predicting value for the disease condition of the query.

Algorithms↗