Converting systematic reviews to Cochrane format: a cross-sectional survey of Australian authors of systematic reviews

BACKGROUND: Despite the growing reputation and subject coverage of the Cochrane Database of Systematic Reviews, many systematic reviews continue to be published solely in paper-based health care journals. This study was designed to determine why authors choose to publish their systematic reviews outside of the Cochrane Collaboration and if they might be interested in converting their reviews to Cochrane format for publication in the Cochrane Database of Systematic Reviews. METHODS: Cross-sectional survey of Australian primary authors of systematic reviews not published on the Cochrane Database of Systematic Reviews identified from the Database of Abstracts of Reviews of Effectiveness. RESULTS: We identified 88 systematic reviews from the Database of Abstracts of Reviews of Effectiveness with an Australian as the primary author. We surveyed 52 authors for whom valid contact information was available. The response rate was 88 per cent (46/52). Ten authors replied without completing the survey, leaving 36 valid surveys for analysis. The most frequently cited reasons for not undertaking a Cochrane review were: lack of time (78%), the need to undergo specific Cochrane training (46%), unwillingness to update reviews (36%), difficulties with the Cochrane process (26%) and the review topic already registered with the Cochrane Collaboration (21%). (Percentages based on completed responses to individual questions.) Nearly half the respondents would consider converting their review to Cochrane format. Dedicated time emerged as the most important factor in facilitating the potential conversion process. Other factors included navigating the Cochrane system, assistance with updating and financial support. Eighty-six per cent were willing to have their review converted to Cochrane format by another author. CONCLUSION: Time required to complete a Cochrane review and the need for specific training are the primary reasons why some authors publish systematic reviews outside of the Cochrane Collaboration. Encouragingly, almost half of the authors would consider converting their review to Cochrane format. Based on the current number of reviews in the Database of Abstracts of Reviews of Effectiveness, this could result in more than 700 additional Cochrane reviews. Ways of supporting these authors and how to provide dedicated time to convert systematic reviews needs further consideration

Theoretical and Methodological Perspectives

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Methodological quality of systematic reviews of animal studies: a survey of reviews of basic research

BACKGROUND: Systematic reviews can serve as a tool in translation of basic life sciences research from laboratory to human research and healthcare. The extent to which reviews of animal research are systematic and unbiased is not known. METHODS: We searched, without language restrictions, Medline, Embase, bibliographies of known reviews (1996–2004) and contacted experts to identify citations of reviews of basic science literature which, as a minimum, performed search of a publicly available resource. From these we identified reviews of animal studies where laboratory variables were measured or where treatments were administered to live animals to examine their effects, and compared them with reviews of bench studies in which human or animal tissues, cell systems or organ preparations were examined in laboratories to better understand mechanisms of diseases. RESULTS: Systematic reviews of animal studies often lacked methodological features such as specification of a testable hypothesis (9/30, 30%); literature search without language restriction (8/30, 26.6%); assessment of publication bias (5/30, 16.6%), study validity (15/30, 50%) and heterogeneity (10/30, 33.3%); and meta-analysis for quantitative synthesis (12/30, 40%). Compared to reviews of bench studies, they were less prone to bias as they specified the question (96.6% vs. 80%, p = 0.04), searched multiple databases (60% vs. 26.6%, p = 0.01), assessed study quality (50% vs. 20%, p = 0.01), and explored heterogeneity (33.3% vs. 2.2%, p = 0.001) more often. CONCLUSION: There seems to be a gradient of frequency of methodological weaknesses among reviews: Attempted systematic reviews of whole animal research tend to be better than those of bench studies, though compared to systematic reviews of human clinical trials they are apparently poorer. There is a need for rigour when reviewing animal research

Verified and potential pathogens of predatory mites (Acari: Phytoseiidae)

Several species of phytoseiid mites (Acari: Phytoseiidae), including species of the genera Amblyseius, Galendromus, Metaseiulus, Neoseiulus, Phytoseiulus and Typhlodromus, are currently reared for biological control of various crop pests and/or as model organisms for the study of predator¿prey interactions. Pathogen-free phytoseiid mites are important to obtain high efficacy in biological pest control and to get reliable data in mite research, as pathogens may affect the performance of their host or alter their reproduction and behaviour. Potential and verified pathogens have been reported for phytoseiid mites during the past 25 years. The present review provides an overview, including potential pathogens with unknown host effects (17 reports), endosymbiotic Wolbachia (seven reports), other bacteria (including Cardinium and Spiroplasma) (four reports), cases of unidentified diseases (three reports) and cases of verified pathogens (six reports). From the latter group four reports refer to Microsporidia, one to a fungus and one to a bacterium. Only five entities have been studied in detail, including Wolbachia infecting seven predatory mite species, other endosymbiotic bacteria infecting Metaseiulus (Galendromus, Typhlodromus) occidentalis (Nesbitt), the bacterium Acaricomes phytoseiuli infecting Phytoseiulus persimilis Athias-Henriot, the microsporidium Microsporidium phytoseiuli infecting P. persimilis and the microsporidium Oligosproridium occidentalis infecting M. occidentalis. In four cases (Wolbachia, A. phytoseiuli, M. phytoseiuli and O. occidentalis) an infection may be connected with fitness costs of the host. Moreover, infection is not always readily visible as no obvious gross symptoms are present. Monitoring of these entities on a routine and continuous basis should therefore get more attention, especially in commercial mass-production. Special attention should be paid to field-collected mites before introduction into the laboratory or mass rearing, and to mites that are exchanged among rearing facilities. However, at present general pathogen monitoring is not yet practical as effects of many entities are unknown. More research effort is needed concerning verified and potential pathogens of commercially reared arthropods and those used as model organisms in research

Are smoking and chlamydial infection risk factors for CIN? Different results after adjustment for HPV DNA and antibodies

To identify the risk factors for cervical intraepithelial neoplasia (CIN), we reanalysed the data from our previous case-control study by adjusting for human papillomavirus (HPV) antibodies. Unlike our previous study based only on HPV DNA, smoking and Chlamydia trachomatis infection were revealed as significant risk factors for CIN after adjustment for HPV antibodies

Genetic support for a quantitative trait nucleotide in the ABCG2 gene affecting milk composition of dairy cattle

<p>Abstract</p> <p>Background</p> <p>Our group has previously identified a quantitative trait locus (QTL) affecting fat and protein percentages on bovine chromosome 6, and refined the QTL position to a 420-kb interval containing six genes. Studies performed in other cattle populations have proposed polymorphisms in two different genes (<it>ABCG2 </it>and <it>OPN</it>) as the underlying functional QTL nucleotide. Due to these conflicting results, we have included these QTNs, together with a large collection of new SNPs produced from PCR sequencing, in a dense marker map spanning the QTL region, and reanalyzed the data using a combined linkage and linkage disequilibrium approach.</p> <p>Results</p> <p>Our results clearly exclude the <it>OPN </it>SNP (<it>OPN_3907</it>) as causal site for the QTL. Among 91 SNPs included in the study, the <it>ABCG2 </it>SNP (<it>ABCG2_49</it>) is clearly the best QTN candidate. The analyses revealed the presence of only one QTL for the percentage traits in the tested region. This QTL was completely removed by correcting the analysis for <it>ABCG2_49</it>. Concordance between the sires' marker genotypes and segregation status for the QTL was found for <it>ABCG2_49 </it>only. The C allele of <it>ABCG2_49 </it>is found in a marker haplotype that has an extremely negative effect on fat and protein percentages and positive effect on milk yield. Of the 91 SNPs, <it>ABCG2_49 </it>was the only marker in perfect linkage disequilibrium with the QTL.</p> <p>Conclusion</p> <p>Based on our results, OPN_3907 can be excluded as the polymorphism underlying the QTL. The results of this and other papers strongly suggest the [A/C] mutation in <it>ABCG2_49 </it>as the causal mutation, although the possibility that <it>ABCG2_49 </it>is only a marker in perfect LD with the true mutation can not be completely ruled out.</p

Isoforms of U1-70k control subunit dynamics in the human spliceosomal U1 snRNP

Most human protein-encoding genes contain multiple exons that are spliced together, frequently in alternative arrangements, by the spliceosome. It is established that U1 snRNP is an essential component of the spliceosome, in human consisting of RNA and ten proteins, several of which are post- translationally modified and exist as multiple isoforms. Unresolved and challenging to investigate are the effects of these post translational modifications on the dynamics, interactions and stability of the particle. Using mass spectrometry we investigate the composition and dynamics of the native human U1 snRNP and compare native and recombinant complexes to isolate the effects of various subunits and isoforms on the overall stability. Our data reveal differential incorporation of four protein isoforms and dynamic interactions of subunits U1-A, U1-C and Sm-B/B’. Results also show that unstructured post- ranslationally modified C-terminal tails are responsible for the dynamics of Sm-B/B’ and U1-C and that their interactions with the Sm core are controlled by binding to different U1-70k isoforms and their phosphorylation status in vivo. These results therefore provide the important functional link between proteomics and structure as well as insight into the dynamic quaternary structure of the native U1 snRNP important for its function.This work was funded by: BBSRC (OVM), BBSRC and EPSRC (HH and NM), EU Prospects (HH), European Science Foundation (NM), the Royal Society (CVR), and fellowship from JSPS and HFSP (YM and DAPK respectively)

Genetic Diversity Enhances Restoration Success by Augmenting Ecosystem Services

Disturbance and habitat destruction due to human activities is a pervasive problem in near-shore marine ecosystems, and restoration is often used to mitigate losses. A common metric used to evaluate the success of restoration is the return of ecosystem services. Previous research has shown that biodiversity, including genetic diversity, is positively associated with the provision of ecosystem services. We conducted a restoration experiment using sources, techniques, and sites similar to actual large-scale seagrass restoration projects and demonstrated that a small increase in genetic diversity enhanced ecosystem services (invertebrate habitat, increased primary productivity, and nutrient retention). In our experiment, plots with elevated genetic diversity had plants that survived longer, increased in density more quickly, and provided more ecosystem services (invertebrate habitat, increased primary productivity, and nutrient retention). We used the number of alleles per locus as a measure of genetic diversity, which, unlike clonal diversity used in earlier research, can be applied to any organism. Additionally, unlike previous studies where positive impacts of diversity occurred only after a large disturbance, this study assessed the importance of diversity in response to potential environmental stresses (high temperature, low light) along a water–depth gradient. We found a positive impact of diversity along the entire depth gradient. Taken together, these results suggest that ecosystem restoration will significantly benefit from obtaining sources (transplants or seeds) with high genetic diversity and from restoration techniques that can maintain that genetic diversity

Total Catch of a Red-Listed Marine Species Is an Order of Magnitude Higher than Official Data

Accurate information on total catch and effort is essential for successful fisheries management. Officially reported landings, however, may be underestimates of total catch in many fisheries. We investigated the fishery for the nationally red-listed European lobster (Homarus gammarus) in south-eastern Norway. Probability-based strip transect surveys were used to count buoys in the study area in combination with catch per unit effort data obtained independently from volunteer catch diaries, phone interviews, and questionnaires. We estimate that recreational catch accounts for 65% of total catch in the study area. Moreover, our results indicate that only a small proportion (24%) of lobsters landed commercially were sold through the legal market and documented. Total estimated lobster catch was nearly 14 times higher than reported officially. Our study highlights the need for adequate catch monitoring and data collection efforts in coastal areas, presents a clear warning to resource managers that illegal, unreported and unregulated (IUU) fisheries in coastal areas should not be ignored, and shows the potential impact of recreational fisheries

Scalar and vector Slepian functions, spherical signal estimation and spectral analysis

It is a well-known fact that mathematical functions that are timelimited (or spacelimited) cannot be simultaneously bandlimited (in frequency). Yet the finite precision of measurement and computation unavoidably bandlimits our observation and modeling scientific data, and we often only have access to, or are only interested in, a study area that is temporally or spatially bounded. In the geosciences we may be interested in spectrally modeling a time series defined only on a certain interval, or we may want to characterize a specific geographical area observed using an effectively bandlimited measurement device. It is clear that analyzing and representing scientific data of this kind will be facilitated if a basis of functions can be found that are "spatiospectrally" concentrated, i.e. "localized" in both domains at the same time. Here, we give a theoretical overview of one particular approach to this "concentration" problem, as originally proposed for time series by Slepian and coworkers, in the 1960s. We show how this framework leads to practical algorithms and statistically performant methods for the analysis of signals and their power spectra in one and two dimensions, and, particularly for applications in the geosciences, for scalar and vectorial signals defined on the surface of a unit sphere.Comment: Submitted to the 2nd Edition of the Handbook of Geomathematics, edited by Willi Freeden, Zuhair M. Nashed and Thomas Sonar, and to be published by Springer Verlag. This is a slightly modified but expanded version of the paper arxiv:0909.5368 that appeared in the 1st Edition of the Handbook, when it was called: Slepian functions and their use in signal estimation and spectral analysi