A TMA De-Arraying Method for High Throughput Biomarker Discovery in Tissue Research

Background: Tissue MicroArrays (TMAs) represent a potential high-throughput platform for the analysis and discovery of tissue biomarkers. As TMA slides are produced manually and subject to processing and sectioning artefacts, the layout of TMA cores on the final slide and subsequent digital scan (TMA digital slide) is often disturbed making it difficult to associate cores with their original position in the planned TMA map. Additionally, the individual cores can be greatly altered and contain numerous irregularities such as missing cores, grid rotation and stretching. These factors demand the development of a robust method for de-arraying TMAs which identifies each TMA core, and assigns them to their appropriate coordinates on the constructed TMA slide.

Methodology: This study presents a robust TMA de-arraying method consisting of three functional phases: TMA core segmentation, gridding and mapping. The segmentation of TMA cores uses a set of morphological operations to identify each TMA core. Gridding then utilises a Delaunay Triangulation based method to find the row and column indices of each TMA core. Finally, mapping correlates each TMA core from a high resolution TMA whole slide image with its name within a TMAMap.

Conclusion: This study describes a genuine robust TMA de-arraying algorithm for the rapid identification of TMA cores from digital slides. The result of this de-arraying algorithm allows the easy partition of each TMA core for further processing. Based on a test group of 19 TMA slides (3129 cores), 99.84% of cores were segmented successfully, 99.81% of cores were gridded correctly and 99.96% of cores were mapped with their correct names via TMAMaps. The gridding of TMA cores were also extensively tested using a set of 113 pseudo slide (13,536 cores) with a variety of irregular grid layouts including missing cores, rotation and stretching. 100% of the cores were gridded correctly.

Scientific revolutions, progess and accounting research

Thomas Kuhn’s concept of a normal science paradigm has been utilised and criticised across a range of social science fields. However, Kuhn’s aim was to argue that science progresses not in an incremental manner but through a series of paradigms that need a revolution in thought to shift from one to the next. This paper addresses Kuhn’s work focusing on the totality of his model, but recognising the ambiguities concerning paradigm shifts that have led to charges of relativism. To address this weakness an argument is advanced for a political economy analysis of the publication process and the development of critical accounting research centred on human emancipation. The paper concludes with some suggested research agendas particularly relevant to the Irish context.

Implications for practice of recent effectiveness research

This article results from an analysis of 95 studies of the effectiveness of social work. The good news from this research, which features a wide range of demanding social problems, is that 75 per cent of results are positive. In this article the authors present their findings and consider their implications for practice.

FACTORIAL EXPERIMENTAL-DESIGN FOR CONCRETE DURABILITY RESEARCH

It is widely accepted that concrete designed to perform satisfactorily in adverse environmental conditions must have a high cement content and a low water-cement ratio. In addition, in order to enhance its durability, many types of additive and admixture such as super-plasticizers, fly ash, silica fume, ggbfs, etc., have been used in the past. However, a close study of the published literature indicates that the effect of mix variables on the durability and the interaction between the various ingredients are not fully understood. Some of these apparent contradictions are due to the limitations in the design of the experimental programme. For instance, it is evident that relatively higher concentrations of aggregates increase the tortuosity of the flow path and hence reduce the permeability, which results in an improvement in the durability. Therefore, an increase in cement content without a proportional decrease in water-cement ratio may reduce the durability. In such cases, the interactive effects of factors can be established by resorting to a properly designed experimental programme, such as the factorial experimental design.

Bracketing: practical considerations in Husserlian phenomenological research

Nursing research leans heavily towards naturalism, with phenomenology commonly adopted. The three main schools of phenomenology used are Husserl's descriptive approach, Heidegger's interpretive hermeneutic approach and the Dutch Utrecht School of phenomenology which combines characteristics of both. Husserl's approach--the description of ordinary human experiences as perceived by each individual--involves four main steps: bracketing, intuiting, analysing and describing. Many phenomenological nurse researchers consciously decide to adopt a Heideggerian approach because of the perceived difficulties in achieving bracketing. This paper examines the concept of bracketing (epoché) and outlines some of the practical considerations when attempting to achieve it.