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PubMed2004

Quality-related variables at hepatological websites.

BACKGROUND: The amount of hepatology-related information available on the Internet has substantially increased, but little is known about the characteristics and quality of the websites. AIM: The aim of this study was to describe analytically and evaluate critically the information concerning three diseases of hepatological interest: chronic hepatitis, hemochromatosis and Caroli's disease. METHODS: In accordance with a validated method, the three search terms were entered into four English language search engines and the first five links of each were considered (a total of 60 sites). The characteristics of the websites were described and their quality was evaluated by three independent reviewers who assigned scores of 1-5 for accuracy, reliability and depth. The relationships between the site characteristics and quality scores were analysed by means of multiple logistic regression. RESULTS: The overall rating score was sufficient (>3) in 51% (95% confidence interval: 38-65%) of cases. The majority of the sites (73%) were aimed at patients rather than at physicians. Commercial sponsorship was significantly more frequent among the chronic hepatitis sites (45%) than among the hemochromatosis (15%) or Caroli's disease sites (0%) (P = 0.002); 61% of the commercial sites did not include a financial disclosure. The only variable that independently related to poor quality was the presence of commercial sponsorship (odds ratio 18.1; 95% confidence interval: 1.7-192.5). CONCLUSIONS: Hepatological websites are characterised by poor quality and are mainly aimed at patients. Quality is negatively affected by commercial interests, which are often undeclared. Guidelines for the certification and surveillance of websites relating to liver diseases are highly advisable.

Authorship↗

PubMed2005

Molecular prognostic markers in pancreatic cancer: a systematic review.

Pancreatic cancer is one of the most lethal tumours of the gastrointestinal tract. The ability to predict which patients would benefit most from surgical intervention and/or chemotherapy would be a great clinical asset. Considerable research has focused on identifying molecular events in pancreatic carcinogenesis, and their correlation with clinicopathological variables of pancreatic tumours and survival. This systematic review examined evidence from published manuscripts looking at molecular markers in pancreatic cancer and their correlation with tumour stage and grade, response to chemotherapy and long-term survival. A literature search was undertaken using PubMed and MEDLINE search engines, using the keywords p53, p21, p16, p27, SMAD4, K-ras, cyclin D1, Bax, Bcl-2, EGFR, EGF, c-erbB2, HB-EGF, TGFbeta, FGF, MMP, uPA, cathepsin, heparanase, E-cadherin, laminins, integrins, TMSF, CD44, cytokines, angiogenesis, VEGF, IL-8, beta-catenin, DNA microarray, and gene profiling. A bewildering number of biomarkers are currently under evaluation. For the most part, the evidence regarding their application as prognostic indicators is conflicting. The advent of gene microarray and mass spectrometric protein profiling offers the potential to examine many different biomarkers simultaneously. This 'protein/gene signature' could revolutionise work in this field and allow researchers to develop accurate and reproducible predictions of survival based on protein or gene profiles.

Apoptosis↗

PubMed2006

TuBaFrost 1: Uniting local frozen tumour banks into a European network: an overview.

TuBaFrost is the consortium responsible for the creation of a virtual European human frozen tumour tissue bank: a collection of high quality frozen residual, accurately classified tumour tissue samples, which are stored in European cancer centres and universities. This virtual tissue bank, searchable on the internet, has rules for access and use, and a code of conduct to comply with the various legal and ethical regulations in European countries. The easy accessibility and the European scale of the bank will result in the availability of a large number of samples even of rarer tumour types. Standardisation of collection, storage and quality control throughout the network is achieved minimising inter-institutional variability. A website providing access to upload, search and request samples is a key tool of the tissue bank. The search engine makes use of virtual microscopy. An overview of the development of the European virtual frozen tissue bank infrastructure is described in this paper. The various key aspects are described in more detail in a series of articles to appear in this Journal.

Biological Specimen Banks↗

PubMed2006

Effects of chronic ethanol administration on brain protein levels: a proteomic investigation using 2-D DIGE system.

The effects of chronic ethanol treatment on the brain proteome were investigated in the long-fin striped strain of zebrafish Danio rerio. Prolonged exposure to 0.5% (v/v) ethanol resulted in the development of tolerance to the ethanol-induced disruption of normal swimming behavior. This behavioral tolerance was manifested after two weeks of continuous treatment and was maintained for an additional three weeks. After four weeks of ethanol treatment, zebrafish brains were divided into 40,000 g supernatant and pellet fractions, and an Ettan 2-D fluorescence difference gel electrophoresis (DIGE) system was used to detect ethanol-induced alterations in the level of protein expression. Protein identification was carried out using matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and the Mascot and ProFound search engines. In the present study, we have identified some novel protein targets as well as substantiated some putative previous targets of chronic ethanol exposure.

Animals↗

PubMed2004

Non-traumatic lower limb vascular complications in endurance athletes. Review of literature.

OBJECTIVES: To review the importance, clinical features, investigations, management and prognosis of non-traumatic vascular injuries, affecting the lower limbs of endurance athletes. DESIGN: Review of literature. MATERIALS AND METHODS: A literature search was conducted from Medline, Pubmed, the National Electronic Library for Health, Google and Yahoo search engines for related articles and case reports regarding non-traumatic vascular complications involving the lower limb of endurance athletes. CONCLUSIONS: Non-traumatic vascular complications affecting the lower limbs include endofibrosis, stenosis/kinking of iliac arteries, dissection of external iliac artery, adductor canal syndrome, popliteal entrapment syndrome, chronic exertional compartment syndrome and effort-induced venous thrombosis. These are important as they affect athletes at the peak of their career and can be confusing to diagnose. The management is relatively well documented and produces good results in short term but the long term results are not known.

Humans↗

PubMed2005

Review of prevalence and outcome of vascular disease in patients with diabetes mellitus.

OBJECTIVES: Review the literature to determine the prevalence and outcome in patients with diabetes that undergo surgery to correct carotid artery stenosis, lower extremity arterial disease, and abdominal aortic aneurysm (AAA). DESIGN AND MATERIALS: Studies were obtained from searches over the past 15 years on the National Library of Medicine's online search engine. RESULTS: The review demonstrated an equivalent prevalence of carotid artery stenosis requiring surgery in patients with diabetes, it favored no increase risk of post-CEA stroke, and it was split on perioperative morbidity and mortality risk. There was an increase prevalence of lower extremity arterial disease requiring surgery in patients with diabetes, it favored equivalent patency and limb salvage rates, and it was split on the morbidity and mortality risk. The review demonstrated a decrease in AAA prevalence among patients with diabetes, it found an increase in the morbidity risk, and equivalent mortality risk. CONCLUSIONS: Stroke, graft patency, and limb salvage rates in patients with diabetes after surgery are similar to patients without diabetes; however, their risk of complications is increased after surgery and the mortality risk may be higher after CEA.

Aortic Aneurysm, Abdominal↗

PubMed2006

Determinants of seeking of primary care for lower urinary tract symptoms: the Krimpen study in community-dwelling men.

OBJECTIVES: To determine which factors predict seeking of primary care among men with lower urinary tract symptoms (LUTS). METHODS: A longitudinal, population-based study with a follow-up period of 6.5 yr was conducted among 1688 men aged 50-78 yr. The following data were collected: prostate volume (using transrectal ultrasonometry), urinary flow rate, ultrasound-estimated postvoid residual urine volume, generic and disease-specific quality of life (QOL), and symptom severity (International Prostate Symptom Score [IPSS]). Information on the seeking of primary care by all participants during 2 yr of follow-up was collected from the general practitioner's (GP) record using a computerised search engine and a manual check of electronically selected files. RESULTS: Prostate volume, postvoid residual volume, IPSS, and social generic QOL are important determinants of first GP consultation in men with LUTS. Measurements (physical urologic parameters) and self-reported items (symptom severity and QOL) contribute almost equally to GP consultation in these men. CONCLUSIONS: Both measurements of prostate volume and postvoid residual urine volume and self-reported information about symptoms or QOL can help to select those who will benefit from medical care and to reassure those men not likely to need help in the near future.

Aged↗

PubMed2005

List of lists-annotated (LOLA): a database for annotation and comparison of published microarray gene lists.

Microarray profiling of RNA expression is a powerful tool that generates large lists of transcripts that are potentially relevant to a disease or treatment. However, because the lists of changed transcripts are embedded in figures and tables, they are typically inaccessible for search engines. Due to differences in gene nomenclatures, the lists are difficult to compare between studies. LOLA (Lists of Lists Annotated) is an internet-based database for comparing gene lists from microarray studies or other genomic-scale methods. It serves as a common platform to compare and reannotate heterogeneous gene lists from different microarray platforms or different genomic methodologies such as serial analysis of gene expression (SAGE) or proteomics. LOLA () provides researchers with a means to store, annotate, and compare gene lists produced from different studies or different analyses of the same study. It is especially useful in identifying potentially "high interest" genes which are reported as significant across multiple studies and species. Its application to the fields of stem cell, cancer, and aging research is demonstrated by comparing published papers.

Animals↗

PubMed2006

Linkage of ciprofloxacin resistance with a single genotypic cluster of Klebsiella pneumoniae.

The objective of this study was to examine the epidemiology of ciprofloxacin-resistant, extended-spectrum beta-lactamase (ESBL)-producing Klebsiella pneumoniae strains. Sixty-nine unique patient isolates of K. pneumoniae isolated from a variety of clinical specimens submitted to the clinical bacteriology laboratories of The Royal Infirmary of Edinburgh and associated General Practices were identified and susceptibility testing was performed with the Vitek system. Strains flagged as ESBL-positive by the Vitek system were subjected to isoelectric focusing. The results suggested that all 69 isolates harboured at least one ESBL, which was later confirmed by polymerase chain reaction (PCR) with bla(TEM) and/or bla(SHV) primers. The purified PCR product was subjected to automated sequencing and the results were compared with the BLAST online search engine. Of the 69 isolates, 32 (46.4%) were found to be resistant to ciprofloxacin, 11 (15.9%) were intermediate and 26 (37.7%) were sensitive. To investigate the epidemiological relationship between the ciprofloxacin-resistant ESBL-positive strains, pulsed-field gel electrophoresis (PFGE) was performed. Rapidest software was used to calculate the genetic distance by the Nei distance method. PFGE analysis indicated that the clinical isolates belonged to four distinct genotype clusters (Groups A, B, C and D); each group or cluster was homogeneous or compact with respect to certain characteristics. Group A consisted of 25 isolates, group B of 3 isolates and Groups C and D of 2 isolates each. These results indicate that the spread of resistance is largely as a result of the dissemination of a single clonal strain. PCR was used to amplify the gyrA and parC genes from genomic DNA of the ciprofloxacin-resistant isolates. The amplified product was sent for analysis by automated DNA sequencing and the resulting DNA sequences were compared with the gyrA gene of K. pneumoniae. The sequencing results demonstrated that alteration of the GyrA subunit of DNA gyrase at amino acid 83 and/or amino acid 87 plays a central role in conferring high-level quinolone resistance in K. pneumoniae possessing ESBLs.

Anti-Infective Agents↗

PubMed2005

The JAVA-based DICOM query interface DicoSE.

DICOM 3 is a very elaborate standard for the communication between medical image devices. It is published in several parts by the National Electrical Manufacturers Association (NEMA). To adequately visualize the data structure defined in parts 3, 5 and 6 of the DICOM standard, we implemented the web based Dicom Search Engine (DicoSE). It allows for querying the DICOM standard data dictionary for defined data fields and visualizes the topology of the data which is inherently present in DICOM datasets. For the administration of the underlying data a web based administration interface is provided. The service is entirely based on freely available software.

Information Storage and Retrieval↗

PubMed2005

Managing educational resource in medicine: system design and integration.

The objective of this paper is to describe our experience in developing a tool based on web technologies, for storing, managing and providing medical courses written by professors in the medical university of Rennes. The increasing number of documents sent by professors leaded us to build a specific resource management system. We created a relational database, containing all meta information about each available document. Professors provide their courses in various formats. We use natural language parsing techniques to extract information from the text, and provide a proper semantic indexation which will be used by a medical-specific search engine. Then the content of our database is dynamically displayed on a web interface. A user's directory identifies teachers and students, controls the access, tracks the students' navigation and allows an on-line discussion forum. This portal contains 524 courses and we had more than 3,000,000 connections on it last year. We are now integrating its content using the semantic web approach in a larger project: the French Virtual Medical University.

Computer Security↗

PubMed2005

Instruments to assess the quality of health information on the World Wide Web: what can our patients actually use?

OBJECTIVE: To find and assess quality-rating instruments that can be used by health care consumers to assess websites displaying health information. DATA SOURCES: Searches of PubMed, the World Wide Web (using five different search engines), reference tracing from identified articles, and a review of the of the American Medical Informatics Association's annual symposium proceedings. REVIEW METHODS: Sources were examined for availability, number of elements, objectivity, and readability. RESULTS: A total of 273 distinct instruments were found and analyzed. Of these, 80 (29%) made evaluation criteria publicly available and 24 (8.7%) had 10 or fewer elements (items that a user has to assess to evaluate a website). Seven instruments consisted of elements that could all be evaluated objectively. Of these seven, one instrument consisted entirely of criteria with acceptable interobserver reliability (kappa> or =0.6); another instrument met readability standards. CONCLUSIONS: There are many quality-rating instruments, but few are likely to be practically usable by the intended audience.

Humans↗

PubMed2005

Future directions for depicting credibility in health care web sites.

OBJECTIVES: The purpose of the paper was to determine appropriate terminology, criteria, implementation, and develop a theoretical framework by which credibility in health care web sites can be depicted. Future research directions for evaluating credibility in health care web sites was also discussed. METHOD: A comprehensive literature review of published articles, policy papers, and grey literature using relevant search terms was conducted. Sources for articles reviewed included MEDLINE (from 1966 to present), PsycINFO (from 1840 to present), ERIC (from 1966 to present), and the Association for Computing Machinery (ACM) databases. The Web of Science citation service was continuously searched using a subscription service from 2002 to 2004. The search engine Google was also implemented. RESULTS: A common term, credibility, was purposed for use in this context. A comprehensive set of credibility criteria, presented within a theoretical framework was also developed. Implementation by means of a browser-based graphic icon was purposed. CONCLUSIONS: Relevancy and readiness of the purposed common terminology, criteria, and implementation within the theoretical framework must be further researched. More knowledge of consumers' behaviour regarding use of online health content and collaboration with others when implementing such information should be considered in future research.

Canada↗

PubMed2007

A web-based patient education system and self-help group in Persian language for inflammatory bowel disease patients.

BACKGROUND AND AIMS: To study the use patterns of a Persian web-based patient education system for inflammatory bowel disease (IBD) patients in Iran. METHODS: A web-based patient education system was developed with Persian content in three sections: general, ulcerative colitis (UC), and Crohn's disease (CD). The website included a forum for patients to communicate as a self-help group. A customized web tracking system recorded web use statistics. Polls at the bottom of each page collected the visitors' opinion on the extent of helpfulness and readability of page contents. Web use data were analyzed for an 18-month period from October 2004 to April 2006. RESULTS: Having excluded page visits from search engine robots, the website's homepage was visited 4452 times (mean of monthly visits: 234, range: 102-330). The web pages titled Anatomy of gastrointestinal system, Nutrition in IBD, Diagnostic tests, How to cope with IBD, and IBD in women were the most favorite in general section. The web page titled IBD treatment was the most visited in both CD and UC sections followed by the web pages on cause of disease, diagnostic procedures and complications in CD section; and those titled symptoms, cause of disease and risk factors in the UC section. Overall, the content evaluation polls received 294 hits (from 186 unique visitors) of which, 196 (67%) were from patients, 30 (10%) from patients' relatives/friends, 21 (7%) from doctors, and 47 (16%) from other groups. During the 18-month period, 47 patients registered in the self-help forum, 24 threads were opened, and 97 posts (33 in CD and 64 in UC section) were sent. CONCLUSIONS: Considering the increasing trend of Internet use in developing countries like Iran, and the consequent increase in the proportion of Internet-using patients, and finally the time constraints gastroenterologists face answering patients' questions; similar websites seem to be effective ways of patient education in close future.

Humans↗

PubMed2003

Peptide sequencing using a patchwork approach and surface-induced dissociation in sector-TOF and dual quadrupole mass spectrometers.

Surface-induced ion activation in combination with a database search strategy based on the Patchwork concept is applied to the determination of peptide sequences. Surface-induced dissociation (SID) is performed in a tandem quadrupole mass spectrometer and in a hybrid sector/time-of-flight mass spectrometer in order to evaluate the importance of accurate mass analysis of the SID fragment ions for peptide identification. The modified Patchwork approach is based on piecing together the peptide blocks in a bidirectional way, simultaneously using low-mass fragments originating from the C-terminus and N-terminus of the molecule, and relying on the measurement of the peptide's molecular weight with moderate mass accuracy. The results from this analysis are used as search filters in MASCOT's (http://www.matrixscience.com) Sequence Query search engine, with the simultaneous addition of the full MS/MS peak list. SID is performed with collision targets coated with pure and mixed composition self-assembled monolayers produced by fluorocarbon and hydrocarbon alkanethiolate solutions of varying chemical composition. The resulting MS/MS spectra produced on pure and mixed hydrocarbon SAMs are submitted to the modified version of Patchwork sequencing. It is found that hydrocarbon surfaces improve the relative abundance of larger fragments. Under the moderate mass accuracy conditions (+/-0.3 u) offered by our linear-TOF-SID instrument, it is found that increasing the abundance of larger fragments dramatically improves the sequencing scores.

Algorithms↗

PubMed2006

Carbohydrate-deficient transferrin (CDT) as a marker of alcohol abuse: a critical review of the literature 2001-2005.

The diagnosis of alcohol abuse based on objective data is a necessary requirement in both clinical and forensic environments. Among the different biomarkers of chronic alcohol abuse, carbohydrate-deficient transferrin (CDT) is world wide recognized as the most reliable indicator. However, several problems about the real meaning of CDT and the reliability of its use for the diagnosis of alcohol abuses are still open, as reported by numerous research articles and reviews. The present article presents a critical review of the literature on CDT appeared in the period from 2001 to 2005 (included). The article is organized in the following sections: (1) introduction, (2) definition and structure of human serum CDT, (3) pathomechanisms of the ethanol-induced CDT increase, (4) preanalysis, (5) analysis, (6) data interpretation, (7) review papers, (8) conclusions. As many as 127 papers appeared in the international literature and retrieved by the search engines PubMed and Scopus are quoted.

Alcoholism↗

PubMed2004

Duplicate publication in the Journal of Hand Surgery.

This study evaluates the extent of duplicate publication in the Hand Surgery literature. A retrospective review of original articles published in the American and the British & European editions of Journal of Hand Surgery during the years 1999 and 2000 was performed using MEDLINE (PUBMED) search engine. Index articles suspected of dual publication were identified by using key words in the title and the names of the first, second and last authors. The full initial text was carefully studied and suspected duplicate articles were classified as dual, potentially dual or fragmented. Six hundred articles were evaluated, of which 25 (4%) index articles were identified with 33 "suspects". Eleven "index" and 15 "suspected" articles were cleared on closer scrutiny. Thus 14 "index" articles (2%) were found to be associated with 18 duplicated articles. Of these, four were classified as dual, five as potentially dual and nine as fragmented. We conclude that although duplicate publication of articles in the Journals of Hand Surgery (American and British/European Volumes) does occur, the incidence in the sample studied is lower than some other surgical journals.

Duplicate Publications as Topic↗

PubMed2006

Evidence for the location of the allosteric activation switch in the multisubunit phosphorylase kinase complex from mass spectrometric identification of chemically crosslinked peptides.

Phosphorylase kinase (PhK), an (alphabetagammadelta)(4) complex, regulates glycogenolysis. Its activity, catalyzed by the gamma subunit, is tightly controlled by phosphorylation and activators acting through allosteric sites on its regulatory alpha, beta and delta subunits. Activation by phosphorylation is predominantly mediated by the regulatory beta subunit, which undergoes a conformational change that is structurally linked with the gamma subunit and that is characterized by the ability of a short chemical crosslinker to form beta-beta dimers. To determine potential regions of interaction of the beta and gamma subunits, we have used chemical crosslinking and two-hybrid screening. The beta and gamma subunits were crosslinked to each other in phosphorylated PhK, and crosslinked peptides from digests were identified by Fourier transform mass spectrometry, beginning with a search engine developed "in house" that generates a hypothetical list of crosslinked peptides. A conjugate between beta and gamma that was verified by MS/MS corresponded to crosslinking between K303 in the C-terminal regulatory domain of gamma (gammaCRD) and R18 in the N-terminal regulatory region of beta (beta1-31), which contains the phosphorylatable serines 11 and 26. A synthetic peptide corresponding to residues 1-22 of beta inhibited the crosslinking between beta and gamma, and was itself crosslinked to K303 of gamma. In two-hybrid screening, the beta1-31 region controlled beta subunit self-interactions, in that they were favored by truncation of this region or by mutation of the phosphorylatable serines 11 and 26, thus providing structural evidence for a phosphorylation-dependent subunit communication network in the PhK complex involving at least these two regulatory regions of the beta and gamma subunits. The sum of our results considered together with previous findings implicates the gammaCRD as being an allosteric activation switch in PhK that interacts with all three of the enzyme's regulatory subunits and is proximal to the active site cleft.

Allosteric Regulation↗