The Reframing of Methodology: Revisiting a PhD Study

The paper draws on a PhD study to explore some methodological dilemmas associated with the execution of qualitative research when framed within positivist study design. The PhD was linked to an externally funded research project which evaluated the implementation of a custody-based intervention in the secure estate. While the PhD was conceived as a qualitative study, informed by interpretivist methodology and associated epistemology, the wider funded study was informed by positivist tradition and used a quantitative method. This led to dilemmas of both practical and methodological nature. The author revisits her study's methodological position to review issues raised by the research design and suggests an alternative proposal informed methodologically by critical realism which may better serve the study's interests. In doing so, the paper suggests how revisiting previous research may assist us in gaining methodological understanding and allow us to reframe our future endeavours to more useful end

Numerical simulation of liquid-layer breakup on a moving wall due to an impinging jet

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Coding external causes of injuries: problems and solutions

Complete and accurate information about hospitalised injuries is essential for injury risk and outcome research, though the accuracy and reliability\ud of hospital data for injury surveillance are often questioned. To ascertain clinical coders' views of the reasons for a lack of specificity in external\ud cause code usage and ways to improve external cause coding, a nationwide survey of coders was conducted in Australia in 2006. Four hundred\ud and two coders participated in the questionnaire. The results of this study show that discharge summaries and doctors’ notes were the poorest\ud source of information regarding external causes, place of injury occurrence, and activity at the time of injury. Coders viewed missing external cause\ud information and missing documentation as having the greatest impact on the quality of external cause coding. A large majority of coders suggested\ud that improving clinical documentation in the emergency department and introducing a centralised structured form for external cause information\ud would improve the quality of external cause coding. Clinical coders are a valuable source of information regarding problems with, and solutions to\ud the collection of high quality data and this research has highlighted several areas where improvements can be made and further research is needed

Effect of periodontal treatment on the serum antibody levels to heat shock proteins

We have shown previously that both humoral and cellular immune responses to heat shock protein 60 (HSP60) are elevated in chronic periodontitis patients compared with non-diseased subjects. The aim of the present study was to determine whether periodontal treatment could influence the level of serum antibodies to human HSP60 and Porphyromonas gingivalis GroEL, a bacterial homologue of human HSP60. Sera were obtained from 21 patients with moderate to advanced chronic periodontitis at the baseline examination and again after completion of treatment. Antibody levels were determined using an enzyme-linked immunosorbent assay. The mean anti-P. gingivalis GroEL antibody levels were down-regulated significantly by periodontal treatment when recombinant P. gingivalis GroEL was used as an antigen, whereas antibody levels to P. gingivalis GroEL-specific peptide were significantly elevated following successful periodontal therapy. The mean level of anti-human HSP60 antibody remained unchanged although individual levels of antibody either increased or decreased after periodontal treatment, suggesting that synthesis of these antibodies might be regulated independently during the course of periodontal infection. Although their regulatory mechanisms in chronic infection are not understood, further study would provide insight not only into the role of these antibodies in the pathogenesis of periodontitis but also into the possible link between periodontitis and systemic diseases such as coronary heart disease

Abstract 639: Rapidly evaluating cancer dependencies by label-free imaging of zero-passage primary cells

Abstract Successful mapping of cancer dependencies requires conducting genetic and pharmacological screens in a diversity of cell models. However, existing model development approaches require long periods of culture time during which evolutionary pressures reduce heterogeneity. It also remains difficult to create long-term models of many cancers, greatly limiting the share of patient samples that can be studied. These limitations make it challenging to create large and diverse datasets for the discovery and validation of biomarker-vulnerability relationships. To enable high-throughput genetic and pharmacological screens in primary, including nondividing, cells without an intermediate model generation step, we are developing a label-free imaging-based platform of early living tissue perturbation. Here, we describe our efforts to establish an ex vivo cell-preservation and imaging system for malignant ascites from patients with advanced gastroesophageal (GE) cancer, whose prognosis remains poor and there is an urgent need for rapid evidence-based therapeutic discovery. First, we optimized a workflow to acquire and perturb cells within 24 hours of sample collection. We observed that incorporating microenvironmental factors by mixing ascites fluid with organoid media extends the preservation of cellular composition and viability. We next hypothesized that label-free microscopy can be a substitute for fluorescence-based labels which fade over time in live-cell imaging. To test this, we created a dataset consisting of over 1.0M cells from 14 samples (10 unique patients). Before seeding, we added fluorescence labels to annotate cell type and viability during imaging. We then trained predictive models to infer cell annotations based on brightfield morphological features only and observed an overall accuracy of 92% and 82% for cell identity and viability, respectively. Prediction of tumor cell fraction from label-free images alone showed strong correlation with tumor fractions estimated by flow cytometry. We also integrated single-cell RNA sequencing data to generate a candidate panel of 28 compounds which are predicted to exhibit antitumor activity via different mechanisms that are of relevance to our study cohort. We observe that label-free inference of compound activity showed strong correlation (R2 &amp;gt; 0.8) with fluorescent-based methods. We are now expanding the scale of our rapid screens and utilizing transcriptomics to link the molecular profile with response. Since our approach couples the timing of drug or genetic perturbation with the preservation of subcellular heterogeneity, it will serve as a strong foundation for preclinical studies. Importantly, our method substantially expands the fraction of samples that can be interrogated and will have application in other areas of need where material is limited or long-term model generation remains unsuccessful as is the case in many rare diseases. Citation Format: Mushriq Al-Jazrawe, Csaba Molnar, Niklas Rindtorff, Steven Blum, William Colgan, Maria Alimova, Sean Misek, Carmen Rios, Moony Tseng, James M. McFarland, Aviv Regev, Beth A. Cimini, Anne E. Carpenter, Adam Bass, Samuel J. Klempner, Jesse Boehm. Rapidly evaluating cancer dependencies by label-free imaging of zero-passage primary cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 639.</jats:p