RevManHAL: towards automatic text generation in systematic reviews

Background: Systematic reviews are a key part of healthcare evaluation. They involve important painstaking but repetitive work. A major producer of systematic reviews, the Cochrane Collaboration, employs Review Manager (RevMan) programme—a software which assists reviewers and produces XML-structured files. This paper describes an add-on programme (RevManHAL) which helps auto-generate the abstract, results and discussion sections of RevMan-generated reviews in multiple languages. The paper also describes future developments for RevManHAL. Methods: RevManHAL was created in Java using NetBeans by a programmer working full time for 2 months. Results: The resulting open-source programme uses editable phrase banks to envelop text/numbers from within the prepared RevMan file in formatted readable text of a chosen language. In this way, considerable parts of the review’s ‘abstract’, ‘results’ and ‘discussion’ sections are created and a phrase added to ‘acknowledgements’. Conclusion: RevManHAL’s output needs to be checked by reviewers, but already, from our experience within the Cochrane Schizophrenia Group (200 maintained reviews, 900 reviewers), RevManHAL has saved much time which is better employed thinking about the meaning of the data rather than restating them. Many more functions will become possible as review writing becomes increasingly automated

The prevalence of and factors associated with inclusion of non-English language studies in Campbell systematic reviews:a survey and meta-epidemiological study

BACKGROUND: Studies published in languages other than English are often neglected when research teams conduct systematic reviews. Literature on how to deal with non-English studies when conducting reviews have focused on the importance of including such studies, while less attention has been paid to the practical challenges of locating and assessing relevant non-English studies. We investigated the factors which might predict the inclusion of non-English studies in systematic reviews in the social sciences, to better understand how, when and why these are included/excluded.METHODS: We appraised all Campbell Collaboration systematic reviews (n = 123) published to July 2016, categorising each by its language inclusiveness. We sought additional information from review authors via a questionnaire and received responses concerning 47 reviews. Data were obtained for 17 factors and we explored correlations with the number of non-English studies in the reviews via statistical regression models. Additionally, we asked authors to identify factors that support or hinder the inclusion of non-English studies.RESULTS: Of 123 reviews, 108 did not explicitly exclude, and of these, 17 included non-English language studies. One factor correlated with the number of included non-English studies across all models: the number of countries in which the members of the review team work (B-value = 0.56; SE B = 0.24; 95% CI = 0.07-1.03; p = 0.02). This indicates that reviews which included non-English studies were more likely to be produced by international review teams. Our survey showed a dominance of researchers from English-speaking countries (52.9%) and review teams consisting only of team members from these countries (65.9%). The most frequently mentioned challenge to including non-English studies was a lack of resources (funding and time) followed by a lack of language resources (e.g. professional translators).CONCLUSION: Our findings may indicate a connection between the limited inclusion of non-English studies and a lack of resources, which forces review teams to rely on their limited language skills rather than the support of professional translators. If unaddressed, review teams risk ignoring key data and introduce bias in otherwise high-quality reviews. However, the validity and interpretation of our findings should be further assessed if we are to tackle the challenges of dealing with non-English studies.</p

A novel BRCA-1 mutation in Arab kindred from east Jerusalem with breast and ovarian cancer

BACKGROUND: The incidence of breast cancer (BC) in Arab women is lower compared to the incidence in the Jewish population in Israel; still, it is the most common malignancy among Arab women. There is a steep rise in breast cancer incidence in the Arab population in Israel over the last 10 years that can be attributed to life style changes. But, the younger age of BC onset in Arab women compared with that of the Jewish population is suggestive of a genetic component in BC occurrence in that population. METHODS: We studied the family history of 31 women of Palestinian Arab (PA) origin affected with breast (n = 28), ovarian (n = 3) cancer. We used denaturing high performance liquid chromatography (DHPLC) to screen for mutations of BRCA1/2 in 4 women with a personal and family history highly suggestive of genetic predisposition. RESULTS: A novel BRCA1 mutation, E1373X in exon 12, was found in a patient affected with ovarian cancer. Four of her family members, 3 BC patients and a healthy individual were consequently also found to carry this mutation. Of the other 27 patients, which were screened for this specific mutation none was found to carry it. CONCLUSION: We found a novel BRCA1 mutation in a family of PA origin with a history highly compatible with BRCA1 phenotype. This mutation was not found in additional 30 PA women affected with BC or OC. Therefore full BRCA1/2 screening should be offered to patients with characteristic family history. The significance of the novel BRCA1 mutation we identified should be studied in larger population. However, it is likely that the E1373X mutation is not a founder frequent mutation in the PA population

Balance algorithm for cluster randomized trials

<p>Abstract</p> <p>Background</p> <p>Within cluster randomized trials no algorithms exist to generate a full enumeration of a block randomization, balancing for covariates across treatment arms. Furthermore, often for practical reasons multiple blocks are required to fully randomize a study, which may not have been well balanced within blocks.</p> <p>Results</p> <p>We present a convenient and easy to use randomization tool to undertake allocation concealed block randomization. Our algorithm highlights allocations that minimize imbalance between treatment groups across multiple baseline covariates.</p> <p>We demonstrate the algorithm using a cluster randomized trial in primary care (the PRE-EMPT Study) and show that the software incorporates a trade off between independent random allocations that were likely to be imbalanced, and predictable deterministic approaches that would minimise imbalance. We extend the methodology of single block randomization to allocate to multiple blocks conditioning on previous allocations.</p> <p>Conclusion</p> <p>The algorithm is included as Additional file <supplr sid="S1">1</supplr> and we advocate its use for robust randomization within cluster randomized trials.</p> <suppl id="S1"> <title> <p>Additional File 1</p> </title> <text> <p><b>Cluster randomization allocation algorithm version 1.</b> Algorithms scripted in R to provide robust cluster randomization.</p> </text> <file name="1471-2288-8-65-S1.zip"> <p>Click here for file</p> </file> </suppl

A randomized controlled trial reporting functional outcomes of cognitive-behavioural therapy in medication‑treated adults with ADHD and comorbid psychopathology

Studies assessing psychological treatment of attention deficit hyperactivity disorder (ADHD) in adults are increasingly reported. However, functional outcomes are often neglected in favour of symptom outcomes. We investigated functional outcomes in 95 adults with ADHD who were already treated with medication and randomized to receive treatment as usual (TAU/MED) or psychological treatment (CBT/MED) using a cognitive–behavioural programme, R&R2ADHD, which employs both group and individual modalities. RATE-S functional outcomes associated with ADHD symptoms, social functioning, emotional control and antisocial behaviour were given at baseline, end of treatment and three-month follow-up. The Total composite score of these scales is associated with life satisfaction. In addition, independent evaluator ratings of clinicians who were blind to treatment arm were obtained on the Clinical Global Impression scale at each time point. CBT/MED showed overall (combined outcome at end of treatment and 3-month follow-up) significantly greater functional improvement on all scales. Post-group treatment effects were maintained at follow-up with the exception of emotional control and the Total composite scales, which continued to improve. The largest treatment effect was for the RATE-S Total composite scale, associated with life satisfaction. CGI significantly correlated with all outcomes except for social functioning scale at follow-up. The study provides further evidence for the effectiveness of R&R2ADHD and demonstrates the importance of measuring functional outcomes. The key mechanism associated with improved functional outcomes is likely to be behavioural control

Ultrasound imaging versus morphopathology in cardiovascular diseases. Coronary collateral circulation and atherosclerotic plaque

This review article is aimed at comparing the results of histopathological and clinical imaging studies to assess coronary collateral circulation in humans. The role of collaterals, as emerging from morphological studies in both normal and atherosclerotic coronary vessels, is described; in addition, present role and future perpectives of echocardiographic techniques in assessing collateral circulation are briefly summarized

PRISMA for abstracts: best practice for reporting abstracts of systematic reviews in Endodontology

An abstract is a brief overview of a scientific, clinical or review manuscript as well as a stand‐alone summary of a conference abstract. Scientists, clinician–scientists and clinicians rely on the summary information provided in the abstracts of systematic reviews to assist in subsequent clinical decision‐making. The Preferred Reporting Items for Systematic Reviews and Meta‐Analyses (PRISMA) for Abstracts checklist was developed to improve the quality, accuracy and completeness of abstracts associated with systematic reviews and meta‐analyses. The PRISMA for Abstracts checklist provides a framework for authors to follow, which helps them provide in the abstract the key information from the systematic review that is required by stakeholders. The PRISMA for Abstracts checklist contains 12 items (title, objectives, eligibility criteria, information sources, risk of bias, included studies, synthesis of results, description of the effect, strength and limitations, interpretation, funding and systematic review registration) under six sections (title, background, methods, results, discussion, other). The current article highlights the relevance and importance of the items in the PRISMA for Abstracts checklist to the specialty of Endodontology, while offering explanations and specific examples to assist authors when writing abstracts for systematic reviews when reported in manuscripts or submitted to conferences. Strict adherence to the PRISMA for Abstracts checklist by authors, reviewers and journal editors will result in the consistent publication of high‐quality abstracts within Endodontology

Influence of Uranium on Bacterial Communities: A Comparison of Natural Uranium-Rich Soils with Controls

This study investigated the influence of uranium on the indigenous bacterial community structure in natural soils with high uranium content. Radioactive soil samples exhibiting 0.26% - 25.5% U in mass were analyzed and compared with nearby control soils containing trace uranium. EXAFS and XRD analyses of soils revealed the presence of U(VI) and uranium-phosphate mineral phases, identified as sabugalite and meta-autunite. A comparative analysis of bacterial community fingerprints using denaturing gradient gel electrophoresis (DGGE) revealed the presence of a complex population in both control and uranium-rich samples. However, bacterial communities inhabiting uraniferous soils exhibited specific fingerprints that were remarkably stable over time, in contrast to populations from nearby control samples. Representatives of Acidobacteria, Proteobacteria, and seven others phyla were detected in DGGE bands specific to uraniferous samples. In particular, sequences related to iron-reducing bacteria such as Geobacter and Geothrix were identified concomitantly with iron-oxidizing species such as Gallionella and Sideroxydans. All together, our results demonstrate that uranium exerts a permanent high pressure on soil bacterial communities and suggest the existence of a uranium redox cycle mediated by bacteria in the soil

A population-based lifestyle intervention to promote healthy weight and physical activity in people with cardiac disease: The PANACHE (Physical Activity, Nutrition And Cardiac HEalth) study protocol

<p>Abstract</p> <p>Background</p> <p>Maintaining a healthy weight and undertaking regular physical activity are important for the secondary prevention of cardiovascular disease (CVD). However, many people with CVD are overweight and insufficiently active. In addition, in Australia only 20-30% of people requiring cardiac rehabilitation (CR) for CVD actually attend. To improve outcomes of and access to CR the efficacy, effectiveness and cost-effectiveness of alternative approaches to CR need to be established.</p> <p>This research will determine the efficacy of a telephone-delivered lifestyle intervention, promoting healthy weight and physical activity, in people with CVD in urban and rural settings. The control group will also act as a replication study of a previously proven physical activity intervention, to establish whether those findings can be repeated in different urban and rural locations. The cost-effectiveness and acceptability of the intervention to CR staff and participants will also be determined.</p> <p>Methods/Design</p> <p>This study is a randomised controlled trial. People referred for CR at two urban and two rural Australian hospitals will be invited to participate. The intervention (healthy weight) group will participate in four telephone delivered behavioural coaching and goal setting sessions over eight weeks. The coaching sessions will be on weight, nutrition and physical activity and will be supported by written materials, a pedometer and two follow-up booster telephone calls. The control (physical activity) group will participate in a six week intervention previously shown to increase physical activity, consisting of two telephone delivered behavioural coaching and goal setting sessions on physical activity, supported by written materials, a pedometer and two booster phone calls. Data will be collected at baseline, eight weeks and eight months for the intervention group (baseline, six weeks and six months for the control group). The primary outcome is weight change. Secondary outcomes include physical activity, sedentary time and nutrition habits. Costs will be compared with outcomes to determine the relative cost-effectiveness of the healthy weight and physical activity interventions.</p> <p>Discussion</p> <p>This study addresses a significant gap in public health practice by providing evidence for the efficacy and cost-effectiveness of a low cost, low contact, high reach intervention promoting healthy weight and physical activity among people with CVD in rural and urban areas in Australia. The replication arm of the study, undertaken by the control group, will demonstrate whether the findings of the previously proven physical activity intervention can be generalised to new settings. This population-based approach could potentially improve access to and outcomes of secondary prevention programs, particularly for rural or disadvantaged communities.</p> <p>Trial Registration</p> <p>ACTRN12610000102077</p

Phagocytosis is the main CR3-mediated function affected by the lupus-associated variant of CD11b in human myeloid cells.

The CD11b/CD18 integrin (complement receptor 3, CR3) is a surface receptor on monocytes, neutrophils, macrophages and dendritic cells that plays a crucial role in several immunological processes including leukocyte extravasation and phagocytosis. The minor allele of a non-synonymous CR3 polymorphism (rs1143679, conversation of arginine to histidine at position 77: R77H) represents one of the strongest genetic risk factor in human systemic lupus erythematosus, with heterozygosity (77R/H) being the most common disease associated genotype. Homozygosity for the 77H allele has been reported to reduce adhesion and phagocytosis in human monocytes and monocyte-derived macrophages, respectively, without affecting surface expression of CD11b. Herein we comprehensively assessed the influence of R77H on different CR3-mediated activities in monocytes, neutrophils, macrophages and dendritic cells. R77H did not alter surface expression of CD11b including its active form in any of these cell types. Using two different iC3b-coated targets we found that the uptake by heterozygous 77R/H macrophages, monocytes and neutrophils was significantly reduced compared to 77R/R cells. Allele-specific transduced immortalized macrophage cell lines demonstrated that the minor allele, 77H, was responsible for the impaired phagocytosis. R77H did not affect neutrophil adhesion, neutrophil transmigration in vivo or Toll-like receptor 7/8-mediated cytokine release by monocytes or dendritic cells with or without CR3 pre-engagement by iC3b-coated targets. Our findings demonstrate that the reduction in CR3-mediated phagocytosis associated with the 77H CD11b variant is not macrophage-restricted but demonstrable in other CR3-expressing professional phagocytic cells. The association between 77H and susceptibility to systemic lupus erythematosus most likely relates to impaired waste disposal, a key component of lupus pathogenesis