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PubMed2006

Enteroaggregative Escherichia coli is a cause of acute diarrheal illness: a meta-analysis.

BACKGROUND: Conflicting studies exist regarding the role of enteroaggregative Escherichia coli (EAEC) as a cause of acute diarrheal illness. The objective of this meta-analysis was to determine whether identification of EAEC in stool samples is associated with acute diarrheal illness among different subpopulations, by geographic area. METHODS: A comprehensive search of electronic bibliographic databases (Medline and PubMed) from August 1985 to January 2006, as well as a search of conference proceedings, references of articles, and contacts with investigators of EAEC, yielded 354 studies. RESULTS: Forty-one studies (12%) that met the selection criteria (i.e., that examined the association between acute diarrheal illness and the excretion of EAEC among different subpopulations) were included. In this meta-analysis, presence of EAEC identified with the HEp-2 cell adherence assay was found to be significantly associated with acute diarrheal illness among children residing in developing regions (odds ratio [OR], 1.58; 95% confidence interval [CI], 1.36-1.83) and industrialized regions (OR, 1.23; 95% CI, 1.03-1.48), adults with human immunodeficiency virus infection residing in developing regions (OR, 6.43; 95% CI, 2.91-14.16), adults residing in developing regions (OR, 7.15; 95% CI, 1.96-26.04), and international travelers to developing regions (OR, 6.72; 95% CI, 2.62-17.20). A limited number of studies were available that examined the role of EAEC identified by its virulence genes by a DNA probe. CONCLUSIONS: On the basis of this meta-analysis, we conclude that EAEC is a cause of acute diarrheal illness among many different subpopulations in both developing and industrialized regions, that EAEC strains are very heterogeneous and that additional studies that examine the role of EAEC in acute diarrheal illness are needed.

Escherichia coli Infections↗

PubMed1999

Therapeutic benefits of qigong exercises in combination with drugs.

This article reviews clinical studies from the Qigong Bibliographic Database, developed by the Qigong Institute, a nonprofit organization. This database was started in 1994 and holds approximately 1300 references going back to 1986, covering medical applications, scientific, and experimental studies on qigong from China, the United States, and Europe. Records in English have been compiled from International Qigong conferences and seminars, scientific journals, magazines, dissertations, MEDLINE, and other databases. The therapeutic role of qigong exercises combined with drugs is reported for three medical conditions that require drug therapy for health maintenance: hypertension, respiratory disease, and cancer. In these studies, drugs were administered to all patients who were divided into two groups, a group that practiced qigong exercises and a control group that did not. Taken together, these studies suggest that practicing qigong exercises may favorably affect many functions of the body, permit reduction of the dosage of drugs required for health maintenance, and provide greater health benefits than the use of drug therapy alone. For hypertensive patients, combining qigong practice with drug therapy for hypertensive patients resulted in reduced incidence of stroke and mortality and reduced dosage of drugs required for blood pressure maintenance. For asthma patients, the combination therapy permitted reduction in drug dosage, the need for sick leave, duration of hospitalization, and costs of therapy. For cancer patients, the combination therapy reduced the side effects of cancer therapy. Also reported is a study showing that the practice of qigong helps to rehabilitate drug addicts. The reported studies do not necessarily measure up to the strict protocols required for randomized controlled clinical trials.

Breathing Exercises↗

PubMed1995

Beyond the information maze.

The exponentially increasing volume of scientific information is threatening to overwhelm the budgets and storage capacities of the world's academic libraries. At the same time, new information technologies are poised to revolutionize the publication infrastructure of science. In evaluating these new technologies we must pay attention to their scalability properties: how well will they perform as the amount of information they are handling increases by orders of magnitude? This article identifies some scalability criteria and evaluates some of the current information technologies with respect to them. It ends by suggesting future directions for these technologies.

Biotechnology↗

PubMed2006

Does back pain prevalence really decrease with increasing age? A systematic review.

BACKGROUND: It is believed that the prevalence of back pain decreases around the middle of the sixth decade. However, back pain is still among the most commonly reported symptoms in the elderly and osteoarthritis, disc degeneration, osteoporosis and spinal stenosis all increase with age. In light of this, it is difficult to understand why the prevalence of back pain would decrease with increasing age. OBJECTIVE: This study aimed at summarising the scientific evidence on the trends of back pain prevalence with age. METHODS: Population-based studies reporting the prevalence of back pain, including people aged 65 years and over, were systematically retrieved from several bibliographic databases. These were read and assessed by two reviewers, and papers retained ('good quality studies') were aggregated according to specific criteria. RESULTS: Good quality studies showed a large heterogeneity as to their methods and prevalence figures. No specific patterns were detected by country nor outcome measure. However, most studies that considered severe forms of back pain found an increase of prevalence with increasing age. The curvilinear association between age and back pain prevalence that is widely mentioned in the literature was found only for benign and mixed problems. CONCLUSIONS: The evidence concerning the association of back pain prevalence with age is more sparse than currently believed and this association seems to be modified by the severity of the problem. This knowledge could have important public health implications, as the proportion of older people will increase considerably in the coming years in most industrialised societies.

Age Distribution↗

PubMed1999

Publication trends of vegetarian nutrition articles in biomedical literature, 1966-1995.

We documented publication trends of vegetarian nutrition articles in biomedical literature between 1966 and 1995 using the National Institutes of Health MEDLINE bibliographic database. The publication rate of vegetarian articles increased steadily during the 3 decades, from an average of <10/y in the late 1960s to 76/y in the early 1990s. After adjusting for the total number of articles indexed in MEDLINE annually, we found that publication of vegetarian nutrition articles increased dramatically, by 4-fold, during the 1970s and reached an oscillating plateau during the 1980s. In the early 1990s, the proportion of vegetarian nutrition articles 8 articles per 1000 vegetarian nutrition articles and approximately 20 per 100000 articles indexed by MEDLINE. Non-nutrition journals have progressively published a larger share of all vegetarian articles in the biomedical literature during the period studied. The nature and study design of published vegetarian research has changed over the years as well. The proportion of original research and review articles increased whereas case series and letters to the editor decreased. Reports of epidemiologic studies of vegetarians with longitudinal designs have superseded cross-sectional designs in number and proportion. In 40% of all publications, preventive and therapeutic applications of vegetarian diets constituted the major themes of vegetarian articles in the decade of 1986-1995. However, 20 y earlier the main focus was on the nutritional adequacy of vegetarian diets. The progressive change in the themes of vegetarian nutrition publications is interpreted as a shift in the role of vegetarian diets in human nutrition.

Bibliometrics↗

PubMed2005

Breastfeeding in infancy and blood pressure in later life: systematic review and meta-analysis.

The influence of breastfeeding on blood pressure in later life is uncertain. The authors conducted a systematic review of published studies from which estimates of a mean difference (standard error) in blood pressure between breastfed and bottle-fed subjects could be derived. They searched MEDLINE and Excerpta Medica (EMBASE) bibliographic databases, which was supplemented by manual searches of reference lists. Fifteen studies (17 observations) including 17,503 subjects were summarized. Systolic blood pressure was lower in breastfed compared with bottle-fed infants (pooled difference: -1.4 mmHg, 95% confidence interval (CI): -2.2, -0.6), but evidence of heterogeneity between study estimates was evident (chi(2)(16) = 42.0, p < 0.001). A lesser effect of breastfeeding on systolic blood pressure was observed in larger (n > or = 1,000) studies (-0.6 mmHg, 95% CI: -1.2, 0.02) compared with smaller (n < 1,000) studies (-2.3 mmHg, 95% CI: -3.7, -0.9) (p for difference in pooled estimates = 0.02). A small reduction in diastolic blood pressure was associated with breastfeeding (pooled difference: -0.5 mmHg, 95% CI: -0.9, -0.04), which was independent of study size. If causal, the small reduction in blood pressure associated with breastfeeding could confer important benefits on cardiovascular health at a population level. Understanding the mechanism underlying this association may provide insights into pathways linking early life exposures with health in adulthood.

Adolescent↗

PubMed2002

An intelligent biological information management system.

MOTIVATION: As biomedical researchers are amassing a plethora of information in a variety of forms resulting from the advancements in biomedical research, there is a critical need for innovative information management and knowledge discovery tools to sift through these vast volumes of heterogeneous data and analysis tools. In this paper we present a general model for an information management system that is adaptable and scalable, followed by a detailed design and implementation of one component of the model. The prototype, called BioSifter, was applied to problems in the bioinformatics area. RESULTS: BioSifter was tested using 500 documents obtained from PubMed database on two biological problems related to genetic polymorphism and extracorporal shockwave lithotripsy. The results indicate that BioSifter is a powerful tool for biological researchers to automatically retrieve relevant text documents from biological literature based on their interest profile. The results also indicate that the first stage of information management process, i.e. data to information transformation, significantly reduces the size of the information space. The filtered data obtained through BioSifter is relevant as well as much smaller in dimension compared to all the retrieved data. This would in turn significantly reduce the complexity associated with the next level transformation, i.e. information to knowledge.

Abstracting and Indexing↗

PubMed2003

Protein structures and information extraction from biological texts: the PASTA system.

MOTIVATION: The rapid increase in volume of protein structure literature means useful information may be hidden or lost in the published literature and the process of finding relevant material, sometimes the rate-determining factor in new research, may be arduous and slow. RESULTS: We describe the Protein Active Site Template Acquisition (PASTA) system, which addresses these problems by performing automatic extraction of information relating to the roles of specific amino acid residues in protein molecules from online scientific articles and abstracts. Both the terminology recognition and extraction capabilities of the system have been extensively evaluated against manually annotated data and the results compare favourably with state-of-the-art results obtained in less challenging domains. PASTA is the first information extraction (IE) system developed for the protein structure domain and one of the most thoroughly evaluated IE system operating on biological scientific text to date. AVAILABILITY: PASTA makes its extraction results available via a browser-based front end: http://www.dcs.shef.ac.uk/nlp/pasta/. The evaluation resources (manually annotated corpora) are also available through the website: http://www.dcs.shef.ac.uk/nlp/pasta/results.html.

Abstracting and Indexing↗

PubMed1992

A profile for molecular biology databases and information resources.

This paper examines the requirements for building database management systems and multi-database information resources to support molecular biology research. The paper profiles the most important features of 16 integrated resources and 102 databases related to molecular biology research. The aspects surveyed in this paper include the nature of information in these databases, their sizes, update properties, cross-references, database management system heterogeneity, geographical distribution, data quality, use of temporal information and level of interpretation. The paper also comments on the access patterns to these databases. Since not all these aspects were available for all databases, specific comparisons sometimes compare fewer than the full 102 databases. Consequently, the same set of databases is not necessarily always being compared with respect to every aspect. The paper is organized primarily according to these comparison aspects and ends with some concluding remarks.

Databases, Bibliographic↗

PubMed2003

DigiNorthern, digital expression analysis of query genes based on ESTs.

DigiNorthern (DN) is a web-based tool for virtually displaying expression profiles of query genes based on EST sequences. Two utilities are available: DN1 takes one query gene and quantitatively display its expression levels in tissues/organs that express the gene with comparison between normal and neoplastic status of each tissue; DN2 takes two sequences as query genes and compares their expression profiles side by side.

DNA, Neoplasm↗

PubMed2003

Interpreting peptide mass spectra by VEMS.

Most existing Mass Spectra (MS) analysis programs are automatic and provide limited opportunity for editing during the interpretation. Furthermore, they rely entirely on publicly available databases for interpretation. VEMS (Virtual Expert Mass Spectrometrist) is a program for interactive analysis of peptide MS/MS spectra imported in text file format. Peaks are annotated, the monoisotopic peaks retained, and the b-and y-ion series identified in an interactive manner. The called peptide sequence is searched against a local protein database for sequence identity and peptide mass. The report compares the calculated and the experimental mass spectrum of the called peptide. The program package includes four accessory programs. VEMStrans creates protein databases in FASTA format from EST or cDNA sequence files. VEMSdata creates a virtual peptide database from FASTA files. VEMSdist displays the distribution of masses up to 5000 Da. VEMSmaldi searches singly charged peptide masses against the local database.

Databases, Bibliographic↗

PubMed2003

The discovery net system for high throughput bioinformatics.

MOTIVATION: Bioinformatics requires Grid technologies and protocols to build high performance applications without focusing on the low level detail of how the individual Grid components operate. RESULTS: The Discovery Net system is a middleware that allows service developers to integrate tools based on existing and emerging Grid standards such as web services. Once integrated, these tools can be used to compose reusable workflows using these services that can later be deployed as new services for others to use. Using the Discovery Net system and a range of different bioinformatics tools, we built a Grid based application for Genome Annotation. This includes workflows for automatic nucleotide annotation, annotation of predicted proteins and text analysis based on metabolic profiles and text analysis.

Algorithms↗

PubMed2003

NCL: a C++ class library for interpreting data files in NEXUS format.

UNLABELLED: The NEXUS Class Library (NCL) is a collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses. The NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored therein. Because users are not required to reformat the data file for each program, use of the NEXUS format prevents cut-and-paste errors as well as the proliferation of copies of the original data file. The purpose of making the NCL available is to encourage the use of the NEXUS format by making it relatively easy for programmers to add the ability to interpret NEXUS files in newly developed software. AVAILABILITY: The NCL is freely available under the GNU General Public License from http://hydrodictyon.eeb.uconn.edu/ncl/ SUPPLEMENTARY INFORMATION: Documentation for the NCL (general information and source code documentation) is available in HTML format at http://hydrodictyon.eeb.uconn.edu/ncl/

Databases, Bibliographic↗

PubMed2004

MedBlast: searching articles related to a biological sequence.

UNLABELLED: In the genomic era, researchers often want to know more information about a biological sequence by retrieving its related articles. However, there is no available tool yet to achieve conveniently this goal. Here we developed a new literature-mining tool MedBlast, which uses natural language processing techniques, to retrieve the related articles of a given sequence. An online server of this program is also provided. AVAILABILITY: Both online server and the program are available freely at http://medblast.sibsnet.org

Algorithms↗

PubMed2004

affy--analysis of Affymetrix GeneChip data at the probe level.

MOTIVATION: The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used. RESULTS: The affy package is an R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. The package is currently in its second release, affy provides the user with extreme flexibility when carrying out an analysis and make it possible to access and manipulate probe intensity data. In this paper, we present the main classes and functions in the package and demonstrate how they can be used to process probe-level data. We also demonstrate the importance of probe-level analysis when using the Affymetrix GeneChip platform.

Algorithms↗

PubMed2004

SaRAD: a Simple and Robust Abbreviation Dictionary.

MOTIVATION: Due to recent interest in the use of textual material to augment traditional experiments it has become necessary to automatically cluster, classify and filter natural language information. RESULTS: The Simple and Robust Abbreviation Dictionary (SaRAD) provides an easy to implement, high performance tool for the construction of a biomedical symbol dictionary. The algorithms, applied to the MEDLINE document set, result in a high quality dictionary and toolset to disambiguate abbreviation symbols automatically.

Abbreviations as Topic↗

PubMed2004

Automated extraction of mutation data from the literature: application of MuteXt to G protein-coupled receptors and nuclear hormone receptors.

MOTIVATION: The amount of genomic and proteomic data that is published daily in the scientific literature is outstripping the ability of experimental scientists to stay current. Reviews, the traditional medium for collating published observations, are also unable to keep pace. For some specific classes of information (e.g. sequences and protein structures), obligatory data deposition policies have helped. However, a great deal of other valuable information is spread throughout the literature hindering coherent access. We are involved in the Molecular Class-Specific Information System (MCSIS) project, a collaborative effort to design and automate the maintenance of protein family databases. The first two databases, the GPCRDB and NucleaRDB, are focused on G protein-coupled receptors (GPCRs) and nuclear hormone receptors (NRs), respectively. The main aim of the MCSIS project is to gather heterogeneous data from across a variety of electronic and literature sources in order to draw new inferences about the target protein families. RESULTS: We present a computational method that identifies and extracts mutation data from the scientific literature. We focused on the extraction of single point mutations for the GPCR and NR superfamilies. After validation by plausibility filters, the mutation data is integrated into the corresponding MCSIS where it is combined with structural and sequence information already stored in these databases. We extracted and validated 2736 true point mutations from 914 articles on GPCRs and 785 true point mutations from 1094 articles on NRs. The current version of our automated extraction algorithm identifies 49.3% of the GPCR point mutations with a specificity of 87.9%, and 64.5% of the NR point mutations with a specificity of 85.8%. MuteXt routinely analyzes 100 electronic articles in approximately 1 h.

Algorithms↗

PubMed2004

Probabilistic inference of molecular networks from noisy data sources.

Information on molecular networks, such as networks of interacting proteins, comes from diverse sources that contain remarkable differences in distribution and quantity of errors. Here, we introduce a probabilistic model useful for predicting protein interactions from heterogeneous data sources. The model describes stochastic generation of protein-protein interaction networks with real-world properties, as well as generation of two heterogeneous sources of protein-interaction information: research results automatically extracted from the literature and yeast two-hybrid experiments. Based on the domain composition of proteins, we use the model to predict protein interactions for pairs of proteins for which no experimental data are available. We further explore the prediction limits, given experimental data that cover only part of the underlying protein networks. This approach can be extended naturally to include other types of biological data sources.

Algorithms↗