FOCUS4 biomarker laboratories: from the benefits to the practical and logistical issues faced during 6 years of centralised testing.

AIMS: FOCUS4 was a phase II/III umbrella trial, recruiting patients with advanced or metastatic colorectal cancer, between 2014 and 2020. Molecular profiling of patients' formalin-fixed, paraffin-embedded tumour blocks was undertaken at two centralised biomarker laboratories (Leeds and Cardiff), and the results fed directly to the Medical Research Council Clinical Trials Unit, and used for subsequent randomisation. Here the laboratories discuss their experiences. METHODS: Following successful tumour content assessment, blocks were sectioned for DNA extraction and immunohistochemistry (IHC). Pyrosequencing was initially used to determine tumour mutation status (KRAS, NRAS, BRAF and PIK3CA), then from 2018 onwards, next-generation sequencing was employed to allow the inclusion of TP53. Protein expression of MLH1, MSH2, MSH6, PMS2 and pTEN was determined by IHC. An interlaboratory comparison programme was initiated, allowing sample exchanges, to ensure continued assay robustness. RESULTS: 1291 tumour samples were successfully analysed. Assay failure rates were very low; 1.9%-3.3% for DNA sequencing and 0.9%-1.3% for IHC. Concordance rates of >98% were seen for the interlaboratory comparisons, where a result was obtained by both laboratories. CONCLUSIONS: Practical and logistical problems were identified, including poor sample quality and difficulties with sample anonymisation. The often last-minute receipt of a sample for testing and a lack of integration with National Health Service mutation analysis services were challenging. The laboratories benefitted from both pretrial validations and interlaboratory comparisons, resulting in robust assay development and provided confidence during the implementation of new sequencing technologies. We conclude that our centralised approach to biomarker testing in FOCUS4 was effective and successful.

The effectiveness and safety of proton beam radiation therapy in children with malignant central nervous system (CNS) tumours: protocol for a systematic review.

BACKGROUND: The aim of this study is to use a systematic review framework to identify and synthesise the evidence on the use of proton beam therapy (PBT) for the treatment of children with CNS tumours and where possible compare this to the use of photon radiotherapy (RT). METHODS: Standard systematic review methods aimed at minimising bias will be employed for study identification, selection and data extraction. Twelve electronic databases have been searched, and further citation, hand searching and reference checking will be employed. Studies assessing the effects of PBT used either alone or as part of a multimodality treatment regimen in children with CNS tumours will be included. Relevant economic evaluations will also be identified. The outcomes are survival (overall, progression-free, event-free, disease-free), local and regional control rates, short- and long-term adverse events, functional status measures and quality of survival. Two reviewers will independently screen and select studies for inclusion in the review. All interventional study designs will be eligible for inclusion in the review. However, initial scoping searches indicate the evidence base is likely to be limited to case series studies, with no studies of a higher quality being identified. Quality assessment will be undertaken using pre-specified criteria and tailored to study design if applicable. Studies will be combined using a narrative synthesis, with differences in results between studies highlighted and discussed in relation to the patient population, intervention and study quality. Where appropriate, if no studies of a comparative design are identified, outcomes will be compared against a range of estimates from the literature for similar populations and treatment regimens from the best available evidence from studies that include the use of advanced conventional photon therapy. DISCUSSION: The evidence base for the use of PBT in children with CNS tumours is likely to be relatively sparse, highly heterogeneous and potentially of a low quality with small sample sizes. Furthermore, selection and publication biases may limit the internal and external validity of studies. However, any tentative results from the review on potential treatment effects can be used to plan better quality research studies that are of a design appropriate for outcome comparison with conventional therapy. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42015029583.

An Improved Binary Vector and Escherichia coli Strain for Agrobacterium tumefaciens-Mediated Plant Transformation.

The plasmid vector pGreenII is widely used to produce plant transformants via a process that involves propagation in Escherichia coli However, we show here that pGreenII-based constructs can be unstable in E. coli as a consequence of them hampering cell division and promoting cell death. In addition, we describe a new version of pGreenII that does not cause these effects, thereby removing the selective pressure for mutation, and a new strain of E. coli that better tolerates existing pGreenII-based constructs without reducing plasmid yield. The adoption of the new derivative of pGreenII and the E. coli strain, which we have named pViridis and MW906, respectively, should help to ensure the integrity of genes destined for study in plants while they are propagated and manipulated in E. coli The mechanism by which pGreenII perturbs E. coli growth appears to be dysregulation within the ColE1 origin of replication.

Making sense scientific claims in advertising. A study of scientifically aware consumers.

Evidence that science is becoming increasingly embedded in culture comes from the proliferation of discourses of ethical consumption, sustainability, and environmental awareness. Al Gore's recent award, along with UN's Inter-governmental Panel on Climate Change (IPCC) of the Nobel peace prize-- provided a recent high profile linking of consumption and science. It is not clear to what extent the public at large engages in evaluating the scientific merits of the arguments about the link between human consumption and global environmental catastrophes. But on a local scale, we are routinely required to evaluate, scientific and pseudoscientific claims in advertising. Since advertising is used to sell products, the discourse of scientifically framed claims is being used to persuade consumers of the benefits of these products. In the case of functional foods and cosmetics, such statements are deployed to promote the health benefits and effectiveness of their products. This exploratory study examines the views of British consumers about the scientific and pseudoscientific claims made in advertisements for foods, with particular reference to functional foods, and cosmetics. The participants in the study all worked in scientific environments, though they were not all scientists. The study found that scientific arguments that were congruent with existing health knowledge tended to be accepted while pseudoscientific knowledge was regarded skeptically and concerns were raised over the accuracy and believability of the pseudoscientific claims. It appears that scientific awareness may play a part in consumers' ability to critically examine scientifically and pseudoscientifically based advertising claims.

Test-retest reliability of the commercial volumeter.

OBJECTIVE: The purpose of this study was to improve the standardization of the current protocol for measuring hand volume with the commercial volumeter. METHOD: A repeated-measures design was used to determine test-retest reliability of the new protocol of measuring hand volume with the commercial volumeter. The new protocol used a height-adjustable table and external trunk support of the participant in order to maintain consistency of web-space pressure between the first and second measurement. A 1 ml micropipette was used to obtain a more accurate volume reading. An intraclass correlation (2,1), repeated measures ANOVA, and standard error of measurement were used to determine the results of this study. RESULTS: This study confirmed the test-retest reliability of the commercial volumeter and decreased the standard error of measurement to 3~ml as opposed to the current standard of 10 ml. CONCLUSION: Clinically, this study is significant in that occupational and physical therapists can detect more subtle change in hand volume.