Quantification of the Heterogeneity of Prognostic Cellular Biomarkers in Ewing Sarcoma Using Automated Image and Random Survival Forest Analysis

Driven by genomic somatic variation, tumour tissues are typically heterogeneous, yet unbiased quantitative methods are rarely used to analyse heterogeneity at the protein level. Motivated by this problem, we developed automated image segmentation of images of multiple biomarkers in Ewing sarcoma to generate distributions of biomarkers between and within tumour cells. We further integrate high dimensional data with patient clinical outcomes utilising random survival forest (RSF) machine learning. Using material from cohorts of genetically diagnosed Ewing sarcoma with EWSR1 chromosomal translocations, confocal images of tissue microarrays were segmented with level sets and watershed algorithms. Each cell nucleus and cytoplasm were identified in relation to DAPI and CD99, respectively, and protein biomarkers (e.g. Ki67, pS6, Foxo3a, EGR1, MAPK) localised relative to nuclear and cytoplasmic regions of each cell in order to generate image feature distributions. The image distribution features were analysed with RSF in relation to known overall patient survival from three separate cohorts (185 informative cases). Variation in pre-analytical processing resulted in elimination of a high number of non-informative images that had poor DAPI localisation or biomarker preservation (67 cases, 36%). The distribution of image features for biomarkers in the remaining high quality material (118 cases, 104 features per case) were analysed by RSF with feature selection, and performance assessed using internal cross-validation, rather than a separate validation cohort. A prognostic classifier for Ewing sarcoma with low cross-validation error rates (0.36) was comprised of multiple features, including the Ki67 proliferative marker and a sub-population of cells with low cytoplasmic/nuclear ratio of CD99. Through elimination of bias, the evaluation of high-dimensionality biomarker distribution within cell populations of a tumour using random forest analysis in quality controlled tumour material could be achieved. Such an automated and integrated methodology has potential application in the identification of prognostic classifiers based on tumour cell heterogeneity

Comparison of surface seismic sources at the CO<inf>2</inf> SINK site, Ketzin, Germany

In 2004 three seismic surface sources (VIBSIST, accelerated weight drop and MiniVib) were tested in a pilot study at the Ketzin test site, Germany, a study site for geological storage of CO2 (EU project CO2 SINK). The main objectives of this pilot study were to 1) evaluate the response of the Ketzin site to reflection seismics, especially at the planned injection depth, 2) test different acquisition parameters and 3) use the results to guide the planning of the 3D survey. As part of these objectives, we emphasize the source performance comparison in this study. The sources were tested along two perpendicular lines of 2.4 km length each. Data were acquired by shooting at all stations (source and receiver spacing of 20 m) on both lines, allowing common-midpoint stacked sections to be produced. The sources' signal characteristics based on signal-to-noise ratio, signal penetration and frequency content of raw shot records were analysed and stacked sections were compared. The results show that all three surface sources are suitable for reflection seismic studies down to a depth of about 1 km and provide enough bandwidth for resolving the geological targets at the site, i.e., the Weser and Stuttgart Formations. Near surface conditions, especially a thick weathering layer present in this particular area, strongly influence the data quality, as indicated by the difference in reflectivity and signal-to-noise ratio of the two common-midpoint lines. The stacked sections of the MiniVib source show the highest frequency signals down to about 500 ms traveltime (approximately 500 m depth) but also the shallowest signal penetration depth. The VIBSIST source generates signals with the highest signal-to-noise ratio and greatest signal penetration depth of the tested sources. In particular, reflections below 900 ms (approximately 1 km depth) are best imaged by the VIBSIST source. The weight drop performance lies in between these two sources and might be recommended as an appropriate source for a 3D survey at this site because of the shorter production time compared to the VIBSIST and MiniVib sources. © 2009 European Association of Geoscientists & Engineers

Tai chi and yoga in residential aged care: Perspectives of participants: A qualitative study

© 2018 John Wiley & Sons Ltd Aims and objectives: This qualitative study examined the appropriateness and acceptability of 14-week modified tai chi and yoga programmes in an Australian residential aged care (RAC) setting by exploring experiences and perspectives of frail older residents and staff participants. Background: Older persons in RAC have limited opportunities for physical activity. Tai chi and yoga are mindfulness-based exercise interventions that have been used to promote physical and psychological health of older adults in community settings. While research on tai chi and yoga interventions in community settings is promising, there is limited research regarding the interventions’ appropriateness and acceptability for frail older residents in residential care settings in Australia. Design: Descriptive and qualitative component of a mixed-methods study. Methods: All residents who participated in the modified yoga and tai chi interventions and staff who supported them were invited. A total of 19 individuals comprising 16 residents and three staff members participated in three focus group interviews. The interviews were audio-recorded, transcribed and analysed thematically using a qualitative descriptive approach. Results: Nine themes that reflected the uniqueness of the programmes' mind–body approach are presented: (a) novel, new and exciting; (b) smoothness, rhythm and flow; (c) slow and mindful; (d) gentle but rewarding; (e) moving whole body; (f) perceived benefits; (g) worthwhile; (h) feeling alive; and (i) calming and relaxing. Conclusions: The modified programmes of tai chi and yoga was acceptable, appropriate, enjoyable and helpful. Both tai chi and yoga appear to provide appropriate physical exercise and opportunities for older persons to enhance their quality of life through interaction of physical, emotional and intellectual wellness domains. Relevance to clinical practice: The 14-week modified programmes of tai chi and yoga could be applied to frail older RAC population to promote health and active ageing

Outcomes from a mechanistic biomarker multi-arm and randomised study of liposomal MTP-PE (Mifamurtide) in metastatic and/or recurrent osteosarcoma (EuroSarc-Memos trial)

The phase III clinical study of adjuvant liposomal muramyl tripeptide (MTP-PE) in resected high-grade osteosarcoma (OS) documented positive results that have been translated into regulatory approval, supporting initial promise for innate immune therapies in OS. There remains, however, no new approved treatment such as MTP-PE for either metastatic or recurrent OS. Whilst the addition of different agents, including liposomal MTP-PE, to surgery for metastatic or recurrent high-grade osteosarcoma has tried to improve response rates, a mechanistic hiatus exists in terms of a detailed understanding the therapeutic strategies required in advanced disease. Here we report a Bayesian designed multi-arm, multi-centre, open-label phase II study with randomisation in patients with metastatic and/or recurrent OS, designed to investigate how patients with OS might respond to liposomal MTP-PE, either given alone or in combination with ifosfamide. Despite the trial closing because of poor recruitment within the allocated funding period, with no objective responses in eight patients, we report the design and feasibility outcomes for patients registered into the trial. We demonstrate the feasibility of the Bayesian design, European collaboration, tissue collection with genomic analysis and serum cytokine characterisation. Further mechanistic investigation of liposomal MTP-PE alone and in combination with other agents remains warranted in metastatic OS