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.

The Oswestry Disability Index

STUDY DESIGN

The Oswestry Disability Index (ODI) has become one of the principal condition-specific outcome measures used in the management of spinal disorders. This review is based on publications using the ODI identified from the authors' personal databases, the Science Citation Index, and hand searches of Spine and current textbooks of spinal disorders.

OBJECTIVES

To review the versions of this instrument, document methods by which it has been validated, collate data from scores found in normal and back pain populations, provide curves for power calculations in studies using the ODI, and maintain the ODI as a gold standard outcome measure.

SUMMARY OF BACKGROUND DATA

It has now been 20 years since its original publication. More than 200 citations exist in the Science Citation Index. The authors have a large correspondence file relating to the ODI, that is cited in most of the large textbooks related to spinal disorders.

METHODS

All the published versions of the questionnaire were identified. A systematic review of this literature was made. The various reports of validation were collated and related to a version.

RESULTS

Four versions of the ODI are available in English and nine in other languages. Some published versions contain misprints, and many omit the scoring system. At least 114 studies contain usable data. These data provide both validation and standards for other users and indicate the power of the instrument for detecting change in sample populations.

CONCLUSIONS

The ODI remains a valid and vigorous measure and has been a worthwhile outcome measure. The process of using the ODI is reviewed and should be the subject of further research. The receiver operating characteristics should be explored in a population with higher self-report disabilities. The behavior of the instrument is incompletely understood, particularly in sensitivity to real change.

The prevalence of comorbid depression in adults with diabetes: a meta-analysis

OBJECTIVE

To estimate the odds and prevalence of clinically relevant depression in adults with type 1 or type 2 diabetes. Depression is associated with hyperglycemia and an increased risk for diabetic complications; relief of depression is associated with improved glycemic control. A more accurate estimate of depression prevalence than what is currently available is needed to gauge the potential impact of depression management in diabetes.

RESEARCH DESIGN AND METHODS

MEDLINE and PsycINFO databases and published references were used to identify studies that reported the prevalence of depression in diabetes. Prevalence was calculated as an aggregate mean weighted by the combined number of subjects in the included studies. We used chi(2) statistics and odds ratios (ORs) to assess the rate and likelihood of depression as a function of type of diabetes, sex, subject source, depression assessment method, and study design.

RESULTS

A total of 42 eligible studies were identified; 20 (48%) included a nondiabetic comparison group. In the controlled studies, the odds of depression in the diabetic group were twice that of the nondiabetic comparison group (OR = 2.0, 95% CI 1.8-2.2) and did not differ by sex, type of diabetes, subject source, or assessment method. The prevalence of comorbid depression was significantly higher in diabetic women (28%) than in diabetic men (18%), in uncontrolled (30%) than in controlled studies (21%), in clinical (32%) than in community (20%) samples, and when assessed by self-report questionnaires (31%) than by standardized diagnostic interviews (11%).

CONCLUSIONS

The presence of diabetes doubles the odds of comorbid depression. Prevalence estimates are affected by several clinical and methodological variables that do not affect the stability of the ORs.

Java Treeview--extensible visualization of microarray data

Open source software encourages innovation by allowing users to extend the functionality of existing applications. Treeview is a popular application for the visualization of microarray data, but is closed-source and platform-specific, which limits both its current utility and suitability as a platform for further development. Java Treeview is an open-source, cross-platform rewrite that handles very large datasets well, and supports extensions to the file format that allow the results of additional analysis to be visualized and compared. The combination of a general file format and open source makes Java Treeview an attractive choice for solving a class of visualization problems. An applet version is also available that can be used on any website with no special server-side setup.

Effectiveness of self-management training in type 2 diabetes: a systematic review of randomized controlled trials

OBJECTIVE

To systematically review the effectiveness of self-management training in type 2 diabetes.

RESEARCH DESIGN AND METHODS

MEDLINE, Educational Resources Information Center (ERIC), and Nursing and Allied Health databases were searched for English-language articles published between 1980 and 1999. Studies were original articles reporting the results of randomized controlled trials of the effectiveness of self-management training in people with type 2 diabetes. Relevant data on study design, population demographics, interventions, outcomes, methodological quality, and external validity were tabulated. Interventions were categorized based on educational focus (information, lifestyle behaviors, mechanical skills, and coping skills), and outcomes were classified as knowledge, attitudes, and self-care skills; lifestyle behaviors, psychological outcomes, and quality of life; glycemic control; cardiovascular disease risk factors; and economic measures and health service utilization.

RESULTS

A total of 72 studies described in 84 articles were identified for this review. Positive effects of self-management training on knowledge, frequency and accuracy of self-monitoring of blood glucose, self-reported dietary habits, and glycemic control were demonstrated in studies with short follow-up (<6 months). Effects of interventions on lipids, physical activity, weight, and blood pressure were variable. With longer follow-up, interventions that used regular reinforcement throughout follow-up were sometimes effective in improving glycemic control. Educational interventions that involved patient collaboration may be more effective than didactic interventions in improving glycemic control, weight, and lipid profiles. No studies demonstrated the effectiveness of self-management training on cardiovascular disease-related events or mortality; no economic analyses included indirect costs; few studies examined health-care utilization. Performance, selection, attrition, and detection bias were common in studies reviewed, and external generalizability was often limited.

CONCLUSIONS

Evidence supports the effectiveness of self-management training in type 2 diabetes, particularly in the short term. Further research is needed to assess the effectiveness of self-management interventions on sustained glycemic control, cardiovascular disease risk factors, and ultimately, microvascular and cardiovascular disease and quality of life.

Stereochemical quality of protein structure coordinates

Methods have been developed to assess the stereochemical quality of any protein structure both globally and locally using various criteria. Several parameters can be derived from the coordinates of a given structure. Global parameters include the distribution of phi, psi and chi 1 torsion angles, and hydrogen bond energies. There are clear correlations between these parameters and resolution; as the resolution improves, the distribution of the parameters becomes more clustered. These features show a broad distribution about ideal values derived from high-resolution structures. Some structures have tightly clustered distributions even at relatively low resolutions, while others show abnormal scatter though the data go to high resolution. Additional indicators of local irregularity include proline phi angles, peptide bond planarities, disulfide bond lengths, and their chi 3 torsion angles. These stereochemical parameters have been used to generate measures of stereochemical quality which provide a simple guide as to the reliability of a structure, in addition to the most important measures, resolution and R-factor. The parameters used in this evaluation are not novel, and are easily calculated from structure coordinates. A program suite is currently being developed which will quickly check a given structure, highlighting unusual stereochemistry and possible errors.

The structure of scientific collaboration networks

The structure of scientific collaboration networks is investigated. Two scientists are considered connected if they have authored a paper together and explicit networks of such connections are constructed by using data drawn from a number of databases, including MEDLINE (biomedical research), the Los Alamos e-Print Archive (physics), and NCSTRL (computer science). I show that these collaboration networks form "small worlds," in which randomly chosen pairs of scientists are typically separated by only a short path of intermediate acquaintances. I further give results for mean and distribution of numbers of collaborators of authors, demonstrate the presence of clustering in the networks, and highlight a number of apparent differences in the patterns of collaboration between the fields studied.

NCBI Resource Coordinators AgarwalaRichaBarrettTanyaBeckJeffBensonDennis ABollinColleenBoltonEvanBourexisDevonBristerJ RodneyBryantStephen HCaneseKathiCavanaughMarkCharowhasChadClarkKarenDondoshanskyIlyaFeoloMichaelFitzpatrickLawrenceFunkKathrynGeerLewis YGorelenkovViatcheslavGraeffAlanHlavinaWratkoHolmesBradJohnsonMarkKattmanBrandiKhotomlianskiViatcheslavKimchiAviKimelmanMichaelKimuraMasatoKittsPaulKlimkeWilliamKotliarovAlexKrasnovSergeyKuznetsovAnatoliyLandrumMelissa JLandsmanDavidLathropStacyLeeJennifer MLeubsdorfCarlLuZhiyongMaddenThomas LMarchler-BauerAronMalheiroAdrianaMericPeterKarsch-MizrachiIleneMnevAnatolyMurphyTerenceOrrisRebeccaOstellJamesO'SullivanChristopherPalanigobuVasukiPanchenkoAnna RPhanLonPierovBorysPruittKim DRodarmerKurtSayersEric WSchneiderValerieSchochConrad LSchulerGregory DSherryStephen TSiyanKaranjitSobolevaAlexandraSoussovVladimirStarchenkoGrigoryTatusovaTatiana AThibaud-NissenFrancoiseTodorovKamenTrawickBart WVakatovDenisWardMinghongYaschenkoEugeneZasypkinAleksandrZbiczKerry. Database resources of the National Center for Biotechnology Information

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank^® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 39 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include PubMed Data Management, RefSeq Functional Elements, genome data download, variation services API, Magic-BLAST, QuickBLASTp, and Identical Protein Groups. Resources that were updated in the past year include the genome data viewer, a human genome resources page, Gene, virus variation, OSIRIS, and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

Collaborative care for depression: a cumulative meta-analysis and review of longer-term outcomes

BACKGROUND

Depression is common in primary care but is suboptimally managed. Collaborative care, that is, structured care involving a greater role of nonmedical specialists to augment primary care, has emerged as a potentially effective candidate intervention to improve quality of primary care and patient outcomes.

METHODS

To quantify the short-term and longer-term effectiveness of collaborative care compared with standard care and to understand mechanisms of action by exploring between-study heterogeneity, we conducted a systematic review of randomized controlled trials that compared collaborative care with usual primary care in patients with depression. We searched MEDLINE (from the beginning of 1966), EMBASE (from the beginning of 1980), CINAHL (from the beginning of 1980), PsycINFO (from the beginning of 1980), the Cochrane Library (from the beginning of 1966), and DARE (Database of Abstracts of Reviews of Effectiveness) (from the beginning of 1985) databases from study inception to February 6, 2006.

RESULTS

We found 37 randomized studies including 12 355 patients with depression receiving primary care. Random effects meta-analysis showed that depression outcomes were improved at 6 months (standardized mean difference, 0.25; 95% confidence interval, 0.18-0.32), and evidence of longer-term benefit was found for up to 5 years (standardized mean difference, 0.15; 95% confidence interval, 0.001-0.31). When exploring determinants of effectiveness, effect size was directly related to medication compliance and to the professional background and method of supervision of case managers. The addition of brief psychotherapy did not substantially improve outcome, nor did increased numbers of sessions. Cumulative meta-analysis showed that sufficient evidence had emerged by 2000 to demonstrate the statistically significant benefit of collaborative care.

CONCLUSIONS

Collaborative care is more effective than standard care in improving depression outcomes in the short and longer terms. Future research needs to address the implementation of collaborative care, particularly in settings other than the United States.

The Role of Google Scholar in Evidence Reviews and Its Applicability to Grey Literature Searching

Google Scholar (GS), a commonly used web-based academic search engine, catalogues between 2 and 100 million records of both academic and grey literature (articles not formally published by commercial academic publishers). Google Scholar collates results from across the internet and is free to use. As a result it has received considerable attention as a method for searching for literature, particularly in searches for grey literature, as required by systematic reviews. The reliance on GS as a standalone resource has been greatly debated, however, and its efficacy in grey literature searching has not yet been investigated. Using systematic review case studies from environmental science, we investigated the utility of GS in systematic reviews and in searches for grey literature. Our findings show that GS results contain moderate amounts of grey literature, with the majority found on average at page 80. We also found that, when searched for specifically, the majority of literature identified using Web of Science was also found using GS. However, our findings showed moderate/poor overlap in results when similar search strings were used in Web of Science and GS (10–67%), and that GS missed some important literature in five of six case studies. Furthermore, a general GS search failed to find any grey literature from a case study that involved manual searching of organisations’ websites. If used in systematic reviews for grey literature, we recommend that searches of article titles focus on the first 200 to 300 results. We conclude that whilst Google Scholar can find much grey literature and specific, known studies, it should not be used alone for systematic review searches. Rather, it forms a powerful addition to other traditional search methods. In addition, we advocate the use of tools to transparently document and catalogue GS search results to maintain high levels of transparency and the ability to be updated, critical to systematic reviews.

The appropriateness of asymmetry tests for publication bias in meta-analyses: a large survey

BACKGROUND

Statistical tests for funnel-plot asymmetry are common in meta-analyses. Inappropriate application can generate misleading inferences about publication bias. We aimed to measure, in a survey of meta-analyses, how frequently the application of these tests would be not meaningful or inappropriate.

METHODS

We evaluated all meta-analyses of binary outcomes with é 3 studies in the Cochrane Database of Systematic Reviews (2003, issue 2). A separate, restricted analysis was confined to the largest meta-analysis in each of the review articles. In each meta-analysis, we assessed whether criteria to apply asymmetry tests were met: no significant heterogeneity, I2 < 50%, é 10 studies (with statistically significant results in at least 1) and ratio of the maximal to minimal variance across studies > 4. We performed a correlation and 2 regression asymmetry tests and evaluated their concordance. Finally, we sampled 60 meta-analyses from print journals in 2005 that cited use of the standard regression test.

RESULTS

A total of 366 of 6873 (5%) and 98 of 846 meta-analyses (12%) in the wider and restricted Cochrane data set, respectively, would have qualified for use of asymmetry tests. Asymmetry test results were significant in 7%-18% of the meta-analyses. Concordance between the 3 tests was modest (estimated k 0.33-0.66). Of the 60 journal meta-analyses, 7 (12%) would qualify for asymmetry tests; all 11 claims for identification of publication bias were made in the face of large and significant heterogeneity.

INTERPRETATION

Statistical conditions for employing asymmetry tests for publication bias are absent from most meta-analyses; yet, in medical journals these tests are performed often and interpreted erroneously.

An official American Thoracic Society/European Respiratory Society statement: update on limb muscle dysfunction in chronic obstructive pulmonary disease

BACKGROUND

Limb muscle dysfunction is prevalent in chronic obstructive pulmonary disease (COPD) and it has important clinical implications, such as reduced exercise tolerance, quality of life, and even survival. Since the previous American Thoracic Society/European Respiratory Society (ATS/ERS) statement on limb muscle dysfunction, important progress has been made on the characterization of this problem and on our understanding of its pathophysiology and clinical implications.

PURPOSE

The purpose of this document is to update the 1999 ATS/ERS statement on limb muscle dysfunction in COPD.

METHODS

An interdisciplinary committee of experts from the ATS and ERS Pulmonary Rehabilitation and Clinical Problems assemblies determined that the scope of this document should be limited to limb muscles. Committee members conducted focused reviews of the literature on several topics. A librarian also performed a literature search. An ATS methodologist provided advice to the committee, ensuring that the methodological approach was consistent with ATS standards.

RESULTS

We identified important advances in our understanding of the extent and nature of the structural alterations in limb muscles in patients with COPD. Since the last update, landmark studies were published on the mechanisms of development of limb muscle dysfunction in COPD and on the treatment of this condition. We now have a better understanding of the clinical implications of limb muscle dysfunction. Although exercise training is the most potent intervention to address this condition, other therapies, such as neuromuscular electrical stimulation, are emerging. Assessment of limb muscle function can identify patients who are at increased risk of poor clinical outcomes, such as exercise intolerance and premature mortality.

CONCLUSIONS

Limb muscle dysfunction is a key systemic consequence of COPD. However, there are still important gaps in our knowledge about the mechanisms of development of this problem. Strategies for early detection and specific treatments for this condition are also needed.

The prevalence of neck pain in the world population: a systematic critical review of the literature

The objective of this study was to determine the prevalence of neck pain (NP) in the world population and to identify areas of methodological variation between studies. A systematic search was conducted in five databases (MEDLINE, EMBASE, CINAHL, OSH-ROM, and PsycINFO), followed by a screening of reference lists of relevant papers. Included papers were extracted for information and each paper was given a quality score. Mean prevalence estimates were calculated for six prevalence periods (point, week, month, 6 months, year, and lifetime), and considered separately for age, gender, quality score, response rate, sample size, anatomical definition, geography, and publication year. Fifty-six papers were included. The six most commonly reported types of prevalence were point, week, month, 6 months, year, and lifetime. Except for lifetime prevalence, women reported more NP than men. For 1-year prevalence, Scandinavian countries reported more NP than the rest of Europe and Asia. Prevalence estimates were not affected by age, quality score, sample size, response rate, and different anatomical definitions of NP. NP is a common symptom in the population. As expected, the prevalence increases with longer prevalence periods and generally women have more NP than men. At least for 1-year prevalence Scandinavian countries report higher mean estimates than the rest of Europe and Asia. The quality of studies varies greatly but is not correlated with the prevalence estimates. Design varies considerably and standardisation is needed in future studies.

SGD: Saccharomyces Genome Database

The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic sequence, its genes and their products, the phenotypes of its mutants, and the literature supporting these data. The amount of information and the number of features provided by SGD have increased greatly following the release of the S.cerevisiae genomic sequence, which is currently the only complete sequence of a eukaryotic genome. SGD aids researchers by providing not only basic information, but also tools such as sequence similarity searching that lead to detailed information about features of the genome and relationships between genes. SGD presents information using a variety of user-friendly, dynamically created graphical displays illustrating physical, genetic and sequence feature maps. SGD can be accessed via the World Wide Web at http://genome-www.stanford.edu/Saccharomyces/

Multimorbidity and quality of life in primary care: a systematic review

Background

Many patients with several concurrent medical conditions (multimorbidity) are seen in the primary care setting. A thorough understanding of outcomes associated with multimorbidity would benefit primary care workers of all disciplines. The purpose of this systematic review was to clarify the relationship between the presence of multimorbidity and the quality of life (QOL) or health-related quality of life (HRQOL) of patients seen, or likely to be seen, in the primary care setting.

Methods

Medline and Embase electronic databases were screened using the following search terms for the reference period 1990 to 2003: multimorbidity, comorbidity, chronic disease, and their spelling variations, along with quality of life and health-related quality of life. Only descriptive studies relevant to primary care were selected.

Results

Of 753 articles screened, 108 were critically assessed for compliance with study inclusion and exclusion criteria. Thirty of these studies were ultimately selected for this review, including 7 in which the relationship between multimorbidity or comorbidity and QOL or HRQOL was the main outcome measure. Major limitations of these studies include the lack of a uniform definition for multimorbidity or comorbidity and the absence of assessment of disease severity. The use of self-reported diagnoses may also be a weakness. The frequent exclusion of psychiatric diagnoses and presence of potential confounding variables are other limitations. Nonetheless, we did find an inverse relationship between the number of medical conditions and QOL related to physical domains. For social and psychological dimensions of QOL, some studies reveal a similar inverse relationship in patients with 4 or more diagnoses.

Conclusions

Our findings confirm the existence of an inverse relationship between multimorbidity or comorbidy and QOL. However, additional studies are needed to clarify this relationship, including the various dimensions of QOL affected. Those studies must employ a clear definition of multimorbidity or comorbidity and valid ways to measure these concepts in a primary care setting. Pursuit of this research will help to better understand the impact of chronic diseases on patients.

The human plasma proteome: a nonredundant list developed by combination of four separate sources

We have merged four different views of the human plasma proteome, based on different methodologies, into a single nonredundant list of 1175 distinct gene products. The methodologies used were 1) literature search for proteins reported to occur in plasma or serum; 2) multidimensional chromatography of proteins followed by two-dimensional electrophoresis and mass spectroscopy (MS) identification of resolved proteins; 3) tryptic digestion and multidimensional chromatography of peptides followed by MS identification; and 4) tryptic digestion and multidimensional chromatography of peptides from low-molecular-mass plasma components followed by MS identification. Of 1,175 nonredundant gene products, 195 were included in more than one of the four input datasets. Only 46 appeared in all four. Predictions of signal sequence and transmembrane domain occurrence, as well as Genome Ontology annotation assignments, allowed characterization of the nonredundant list and comparison of the data sources. The "nonproteomic" literature (468 input proteins) is strongly biased toward signal sequence-containing extracellular proteins, while the three proteomics methods showed a much higher representation of cellular proteins, including nuclear, cytoplasmic, and kinesin complex proteins. Cytokines and protein hormones were almost completely absent from the proteomics data (presumably due to low abundance), while categories like DNA-binding proteins were almost entirely absent from the literature data (perhaps unexpected and therefore not sought). Most major categories of proteins in the human proteome are represented in plasma, with the distribution at successively deeper layers shifting from mostly extracellular to a distribution more like the whole (primarily cellular) proteome. The resulting nonredundant list confirms the presence of a number of interesting candidate marker proteins in plasma and serum.

Complications following autologous bone graft harvesting from the iliac crest and using the RIA: a systematic review

Bone grafting is a commonly performed surgical procedure to augment bone regeneration in a variety of cases in orthopaedic and maxillofacial surgery. Autologous bone graft remains to be the 'gold standard' and the iliac crest to be the most common harvesting site. The intramedullary canal of long bones represents another potential site for large volume of autologous bone graft harvesting and is recently being used as an alternative donor site. However, harvesting of autologous bone graft is associated with morbidity and a number of complications. The aim of this systematic review was to collect and summarise the existing data on reported complications after harvesting autologous bone from the iliac crest (anterior and posterior) and the long bone intramedullary canal using the RIA device. We searched the PubMed Medline and Ovid Medline databases, from January 1990 to October 2010, to retrieve all relevant articles. A total of 92 articles (6682 patients) were included in the analysis. Overall, the complication rate following RIA was 6% (14 complications in 233 patients) and 19.37% after iliac crest bone graft harvesting (1249 complications in 6449 patients). The rate of each of the reported complications was assessed and, when the donor site was properly documented, comparison within the anterior and posterior iliac crest donor sites was performed. Although the difference of the overall morbidity rates between the two harvesting sites was not statistically significant (p=0.71); the rates of certain complications were found to significantly differ when anterior or posterior iliac crest was used. The rates of infection (p=0.016), haematoma formation (p=0.002), fracture (p=0.017), and hyperthrophic scar (p=0.017) were significantly higher when the donor site was the anterior iliac crest compared to the posterior iliac crest; whereas the rates of chronic donor site pain (p=0.004) and sensory disturbances (p=0.003) were significantly lower. The incidence of bone graft harvesting related complications can be reduced further if certain principles are followed depending on the performed harvesting methods; but overall the use of RIA device as harvesting method seems a promising alternative with a low complication rate.

Evidence based medicine: an approach to clinical problem-solving

Doctors within the NHS are confronting major changes at work. While we endeavour to improve the quality of health care, junior doctors' hours have been reduced and the emphasis on continuing medical education has increased. We are confronted by a growing body of information, much of it invalid or irrelevant to clinical practice. This article discusses evidence based medicine, a process of turning clinical problems into questions and then systematically locating, appraising, and using contemporaneous research findings as the basis for clinical decisions. The computerisation of bibliographies and the development of software that permits the rapid location of relevant evidence have made it easier for busy clinicians to make best use of the published literature. Critical appraisal can be used to determine the validity and applicability of the evidence, which is then used to inform clinical decisions. Evidence based medicine can be taught to, and practised by, clinicians at all levels of seniority and can be used to close the gulf between good clinical research and clinical practice. In addition it can help to promote self directed learning and teamwork and produce faster and better doctors.

Conservative treatment of acute and chronic nonspecific low back pain. A systematic review of randomized controlled trials of the most common interventions

STUDY DESIGN

A systematic review of randomized controlled trials.

OBJECTIVES

To assess the effectiveness of the most common conservative types of treatment for patients with acute and chronic nonspecific low back pain.

SUMMARY OF BACKGROUND DATA

Many treatment options for acute and chronic low back pain are available, but little is known about the optimal treatment strategy.

METHODS

A rating system was used to assess the strength of the evidence, based on the methodologic quality of the randomized controlled trials, the relevance of the outcome measures, and the consistency of the results.

RESULTS

The number of randomized controlled trials identified varied widely with regard to the interventions involved. The scores ranged from 20 to 79 points for acute low back pain and from 19 to 79 points for chronic low back pain on a 100-point scale, indicating the overall poor quality of the trials. Overall, only 28 (35%) randomized controlled trials on acute low back pain and 20 (25%) on chronic low back pain had a methodologic score of 50 or more points, and were considered to be of high quality. Various methodologic flaws were identified. Strong evidence was found for the effectiveness of muscle relaxants and nonsteroidal anti-inflammatory drugs and the ineffectiveness of exercise therapy for acute low back pain; strong evidence also was found for the effectiveness of manipulation, back schools, and exercise therapy for chronic low back pain, especially for short-term effects.

CONCLUSIONS

The quality of the design, execution, and reporting of randomized controlled trials should be improved, to establish strong evidence for the effectiveness of the various therapeutic interventions for acute and chronic low back pain.

Sequence identification of 2,375 human brain genes

We recently described a new approach for the rapid characterization of expressed genes by partial DNA sequencing to generate 'expressed sequence tags'. From a set of 600 human brain complementary DNA clones, 348 were informative nuclear-encoded messenger RNAs. We have now partially sequenced 2,672 new, independent cDNA clones isolated from four human brain cDNA libraries to generate 2,375 expressed sequence tags to nuclear-encoded genes. These sequences, together with 348 brain expressed sequence tags from our previous study, comprise more than 2,500 new human genes and 870,769 base pairs of DNA sequence. These data represent an approximate doubling of the number of human genes identified by DNA sequencing and may represent as many as 5% of the genes in the human genome.

OARSI recommendations for the management of hip and knee osteoarthritis, part I: critical appraisal of existing treatment guidelines and systematic review of current research evidence

PURPOSE

As a prelude to developing updated, evidence-based, international consensus recommendations for the management of hip and knee osteoarthritis (OA), the Osteoarthritis Research Society International (OARSI) Treatment Guidelines Committee undertook a critical appraisal of published guidelines and a systematic review (SR) of more recent evidence for relevant therapies.

METHODS

Sixteen experts from four medical disciplines (primary care two, rheumatology 11, orthopaedics one and evidence-based medicine two), two continents and six countries (USA, UK, France, Netherlands, Sweden and Canada) formed the guidelines development team. Three additional experts were invited to take part in the critical appraisal of existing guidelines in languages other than English. MEDLINE, EMBASE, Science Citation Index, CINAHL, AMED, Cochrane Library, seven Guidelines Websites and Google were searched systematically to identify guidelines for the management of hip and/or knee OA. Guidelines which met the inclusion/exclusion criteria were assigned to four groups of four appraisers. The quality of the guidelines was assessed using the AGREE (Appraisal of Guidelines for Research and Evaluation) instrument and standardised percent scores (0-100%) for scope, stakeholder involvement, rigour, clarity, applicability and editorial independence, as well as overall quality, were calculated. Treatment modalities addressed and recommended by the guidelines were summarised. Agreement (%) was estimated and the best level of evidence to support each recommendation was extracted. Evidence for each treatment modality was updated from the date of the last SR in January 2002 to January 2006. The quality of evidence was evaluated using the Oxman and Guyatt, and Jadad scales for SRs and randomised controlled trials (RCTs), respectively. Where possible, effect size (ES), number needed to treat, relative risk (RR) or odds ratio and cost per quality-adjusted life year gained (QALY) were estimated.

RESULTS

Twenty-three of 1462 guidelines or consensus statements retrieved from the literature search met the inclusion/exclusion criteria. Six were predominantly based on expert opinion, five were primarily evidence based and 12 were based on both. Overall quality scores were 28%, 41% and 51% for opinion-based, evidence-based and hybrid guidelines, respectively (P=0.001). Scores for aspects of quality varied from 18% for applicability to 67% for scope. Thirteen guidelines had been developed for specific care settings including five for primary care (e.g., Prodigy Guidance), three for rheumatology (e.g., European League against Rheumatism recommendations), three for physiotherapy (e.g., Dutch clinical practice guidelines for physical therapy) and two for orthopaedics (e.g., National Institutes of Health consensus guidelines), whereas 10 did not specify the target users (e.g., Ontario guidelines for optimal therapy). Whilst 14 guidelines did not separate hip and knee, eight were specific for knee but only one for hip. Fifty-one different treatment modalities were addressed by these guidelines, but only 20 were universally recommended. Evidence to support these modalities ranged from Ia (meta-analysis/SR of RCTs) to IV (expert opinion). The efficacy of some modalities of therapy was confirmed by the results of RCTs published between January 2002 and 2006. These included exercise (strengthening ES 0.32, 95% confidence interval (CI) 0.23, 0.42, aerobic ES 0.52, 95% CI 0.34, 0.70 and water-based ES 0.25, 95% CI 0.02, 0.47) and nonsteroidal anti-inflammatory drugs (NSAIDs) (ES 0.32, 95% CI 0.24, 0.39). Examples of other treatment modalities where recent trials failed to confirm efficacy included ultrasound (ES 0.06, 95% CI -0.39, 0.52), massage (ES 0.10, 95% CI -0.23, 0.43) and heat/ice therapy (ES 0.69, 95% CI -0.07, 1.45). The updated evidence on adverse effects also varied from treatment to treatment. For example, while the evidence for gastrointestinal (GI) toxicity of non-selective NSAIDs (RR=5.36, 95% CI 1.79, 16.10) and for increased risk of myocardial infarction associated with rofecoxib (RR=2.24, 95% CI 1.24, 4.02) were reinforced, evidence for other potential drug related adverse events such as GI toxicity with acetaminophen or myocardial infarction with celecoxib remained inconclusive.

CONCLUSION

Twenty-three guidelines have been developed for the treatment of hip and/or knee OA, based on opinion alone, research evidence or both. Twenty of 51 modalities of therapy are universally recommended by these guidelines. Although this suggests that a core set of recommendations for treatment exists, critical appraisal shows that the overall quality of existing guidelines is sub-optimal, and consensus recommendations are not always supported by the best available evidence. Guidelines of optimal quality are most likely to be achieved by combining research evidence with expert consensus and by paying due attention to issues such as editorial independence, stakeholder involvement and applicability. This review of existing guidelines provides support for the development of new guidelines cognisant of the limitations in existing guidelines. Recommendations should be revised regularly following SR of new research evidence as this becomes available.

The effectiveness of interventions for reducing stigma related to substance use disorders: a systematic review

AIMS

This study provides a systematic review of existing research that has empirically evaluated interventions designed to reduce stigma related to substance use disorders.

METHODS

A comprehensive review of electronic databases was conducted to identify evaluations of substance use disorder related stigma interventions. Studies that met inclusion criteria were synthesized and assessed using systematic review methods.

RESULTS

Thirteen studies met the inclusion criteria. The methodological quality of the studies was moderately strong. Interventions of three studies (23%) focused on people with substance use disorders (self-stigma), three studies (23%) targeted the general public (social stigma) and seven studies (54%) focused on medical students and other professional groups (structural stigma). Nine interventions (69%) used approaches that included education and/or direct contact with people who have substance use disorders. All but one study indicated their interventions produced positive effects on at least one stigma outcome measure. None of the interventions have been evaluated across different settings or populations.

CONCLUSIONS

A range of interventions demonstrate promise for achieving meaningful improvements in stigma related to substance use disorders. The limited evidence indicates that self-stigma can be reduced through therapeutic interventions such as group-based acceptance and commitment therapy. Effective strategies for addressing social stigma include motivational interviewing and communicating positive stories of people with substance use disorders. For changing stigma at a structural level, contact-based training and education programs targeting medical students and professionals (e.g. police, counsellors) are effective.

A review of the application of propensity score methods yielded increasing use, advantages in specific settings, but not substantially different estimates compared with conventional multivariable methods

OBJECTIVE

Propensity score (PS) analyses attempt to control for confounding in nonexperimental studies by adjusting for the likelihood that a given patient is exposed. Such analyses have been proposed to address confounding by indication, but there is little empirical evidence that they achieve better control than conventional multivariate outcome modeling.

STUDY DESIGN AND METHODS

Using PubMed and Science Citation Index, we assessed the use of propensity scores over time and critically evaluated studies published through 2003.

RESULTS

Use of propensity scores increased from a total of 8 reports before 1998 to 71 in 2003. Most of the 177 published studies abstracted assessed medications (N=60) or surgical interventions (N=51), mainly in cardiology and cardiac surgery (N=90). Whether PS methods or conventional outcome models were used to control for confounding had little effect on results in those studies in which such comparison was possible. Only 9 of 69 studies (13%) had an effect estimate that differed by more than 20% from that obtained with a conventional outcome model in all PS analyses presented.

CONCLUSIONS

Publication of results based on propensity score methods has increased dramatically, but there is little evidence that these methods yield substantially different estimates compared with conventional multivariable methods.

El Cuestionario de Salud SF-36 español: una década de experiencia y nuevos desarrollos

OBJECTIVE

The Short Form-36 Health Survey (SF-36) is one of the most widely used and evaluated generic health-related quality of life (HRQL) questionnaires. After almost a decade of use in Spain, the present article critically reviews the content and metric properties of the Spanish version, as well as its new developments.

METHODS

A review of indexed articles that used the Spanish version of the SF-36 was performed in Medline (PubMed), the Spanish bibliographic databases IBECS and IME. Articles that provided information on the measurement model, reliability, validity, and responsiveness to change of the instrument were selected.

RESULTS

Seventy-nine articles were found, of which 17 evaluated the metric characteristics of the questionnaire. The reliability of the SF-36 scales was higher than the suggested standard (Cronbach's alpha) of 0.7 in 96% of the evaluations. Grouped evaluations obtained by meta-analysis were higher than 0.7 in all cases. The SF-36 showed good discrimination among severity groups, moderate correlations with clinical indicators, and high correlations with other HRQL instruments. Moreover, questionnaire scores predicted mortality and were able to detect improvement due to therapeutic interventions such as coronary angioplasty, benign prostatic hyperplasia surgery, and non-invasive positive pressure home ventilation. The new developments (norm-based scoring, version 2, the SF-12 and SF-8) improved both the metric properties and interpretation of the questionnaire.

CONCLUSIONS

The Spanish version of the SF-36 and its recently developed versions is a suitable instrument for use in medical research, as well as in clinical practice.