Digital pathology and image analysis in tissue biomarker research

Digital pathology and the adoption of image analysis have grown rapidly in the last few years. This is largely due to the implementation of whole slide scanning, advances in software and computer processing capacity and the increasing importance of tissue-based research for biomarker discovery and stratified medicine. This review sets out the key application areas for digital pathology and image analysis, with a particular focus on research and biomarker discovery. A variety of image analysis applications are reviewed including nuclear morphometry and tissue architecture analysis, but with emphasis on immunohistochemistry and fluorescence analysis of tissue biomarkers. Digital pathology and image analysis have important roles across the drug/companion diagnostic development pipeline including biobanking, molecular pathology, tissue microarray analysis, molecular profiling of tissue and these important developments are reviewed. Underpinning all of these important developments is the need for high quality tissue samples and the impact of pre-analytical variables on tissue research is discussed. This requirement is combined with practical advice on setting up and running a digital pathology laboratory. Finally, we discuss the need to integrate digital image analysis data with epidemiological, clinical and genomic data in order to fully understand the relationship between genotype and phenotype and to drive discovery and the delivery of personalized medicine.

Haptic Aurality: Listening in a Digital World

I will question modes of listening in network music performance environments, drawing on my experience as a performer listening in these scenarios. I will situate network listening, which I have previously examined as ‘haptic aurality’ (Schroeder, 2009, 2012, 2013) within the context of current music making, and will refer to changes in compositional practices that draw specific attention to listening. I will show that some of these compositional developments play a determining role in articulating a new discourse of listening. French composer Eric Satie’s concept of Furniture Music (in Duckworth, 2005), Pierre Schaeffer’s ideas on reduced listening (1966), Pauline Oliveros’ deep listening practices (2005) as well as digital music platforms all serve to show a development towards a proliferation in listening experiences. I expand this narrative to listening practices in network performance environments, and identify a specific bodily fragility in listening in and to the network. This fragile state of listening and de-centered kind of performative being allow me to draw parallels to the Japanese art form Butoh (Kasai, 1999, 2000; Kasai and Parsons, 2003) and Elaine Scarry’s metaphor of beauty (Scarry, 2001). My own performance experiences, set within the context of several critical texts, allow me to understand network[ed] listening as an ideal corporeal state, which offers a rethinking of linear conceptions of the other and a subject’s own relation with her world. Ultimately, network[ed] listening posits listening as a corporeal and multi-dimensional experience that is continuously being re-shaped by technological, socio-political and cultural concerns.

Haptic Aurality – performing in a digital world

Paper accepted at 2015 ISIS in Utrecht. This presentation will examine the performative body from the viewpoint of the listening body in digital media platforms, and thus investigates the proposed conference issues which are at the intersections of ‘play’, ‘perform’ and ‘participate’.

Experiment of Digital Directional Modulation Transmitters

A digital directional modulation (DM) transmitter structure is proposed from a practical implementation point of view in this paper. This digital DM architecture is built with the help of several off-the-shelf physical layer wireless experiment platform hardware boards. When compared with previous analogue DM transmitter architectures, the digital means offers more precise and fast control on the updates of the array excitations. More importantly, it is an ideal physical arrangement to implement the most universal DM synthesis algorithm, i.e., the orthogonal vector approach. The practical issues in digital DM system calibrations are described and solved. The bit error rates (BERs) are measured via real-time data transmissions to illustrate the DM advantages, in terms of secrecy performance, over conventional non-DM beam-steering transmitters.

Practical Lattice-Based Digital Signature Schemes

Digital signatures are an important primitive for building secure systems and are used in most real-world security protocols. However, almost all popular signature schemes are either based on the factoring assumption (RSA) or the hardness of the discrete logarithm problem (DSA/ECDSA). In the case of classical cryptanalytic advances or progress on the development of quantum computers, the hardness of these closely related problems might be seriously weakened. A potential alternative approach is the construction of signature schemes based on the hardness of certain lattice problems that are assumed to be intractable by quantum computers. Due to significant research advancements in recent years, lattice-based schemes have now become practical and appear to be a very viable alternative to number-theoretic cryptography. In this article, we focus on recent developments and the current state of the art in lattice-based digital signatures and provide a comprehensive survey discussing signature schemes with respect to practicality. Additionally, we discuss future research areas that are essential for the continued development of lattice-based cryptography.

Digital slide viewing for primary reporting in gastrointestinal pathology: a validation study

Despite the increasing availability of digital slide viewing, and numerous advantages associated with its application, a lack of quality validation studies is amongst the reasons for poor uptake in routine practice. This study evaluated primary digital pathology reporting in the setting of routine subspecialist gastrointestinal pathology, commonplace in most tissue pathology laboratories and representing one of the highest volume specialties in most laboratories. Individual digital and glass slide diagnoses were compared amongst three pathologists reporting in a gastrointestinal subspecialty team, in a prospective series of 100 consecutive diagnostic cases from routine practice in a large teaching hospital laboratory. The study included a washout period of at least 6 months. Discordant diagnoses were classified, and the study evaluated against recent College of American Pathologists (CAP) recommendations for evaluating digital pathology systems for diagnostic use. The study design met all 12 of the CAP recommendations. The 100 study cases generated 300 pairs of diagnoses, comprising 100 glass slide diagnoses and 100 digital diagnoses from each of the three study pathologists. 286 of 300 pairs of diagnoses were concordant, representing intraobserver concordance of 95.3 %, broadly comparable to rates previously published in this field. In ten of the 14 discordant pairs, the glass slide diagnosis was favoured; in four cases, the digital diagnosis was favoured, but importantly, the 14 discordant intraobserver diagnoses were considered to be of minor clinical significance. Interobserver, or viewing modality independent, concordance was found in 94 of the total of 100 study cases, providing a comparable baseline discordance rate expected in any second viewing of pathology material. These overall results support the safe use of digital pathology in primary diagnostic reporting in this setting

A high performance IIR digital filter chip

The design of a high-performance IIR (infinite impulse response) digital filter is described. The chip architecture operates on 11-b parallel, two's complement input data with a 12-b parallel two's complement coefficient to produce a 14-b two's complement output. The chip is implemented in 1.5-µm, double-layer-metal CMOS technology, consumes 0.5 W, and can operate up to 15 Msample/s. The main component of the system is a fine-grained systolic array that internally is based on a signed binary number representation (SBNR). Issues addressed include testing, clock distribution, and circuitry for conversion between two's complement and SBNR.

A low-cost digital image correlation technique for characterising the shear deformation of fabrics for draping studies

A novel digital image correlation (DIC) technique has been developed to track changes in textile yarn orientations during shear characterisation experiments, requiring only low-cost digital imaging equipment. Fabric shear angles and effective yarn strains are calculated and visualised using this new DIC technique for bias extension testing of an aerospace grade, carbon-fibre reinforcement material with a plain weave architecture. The DIC results are validated by direct measurement, and the use of a wide bias extension sample is evaluated against a more commonly used narrow sample. Wide samples exhibit a shear angle range 25% greater than narrow samples and peak loads which are 10 times higher. This is primarily due to excessive yarn slippage in the narrow samples; hence, the wide sample configuration is recommended for characterisation of shear properties which are required for accurate modelling of textile draping.

Digital Dermatitis in Dairy Cows: A Review of Risk Factors and Potential Sources of Between-Animal Variation in Susceptibility

Digital dermatitis (DD) is a bacterial disease that primarily affects the skin on the heels of cattle. It is a major cause of lameness in dairy cows and a significant problem for the dairy industry in many countries, causing reduced animal welfare and economic loss. A wide range of infection levels has been found on infected farms, prompting investigations into both farm level and animal level risk factors for DD occurrence. There also appears to be individual variation between animals in susceptibility to the disease. The identification of factors affecting individual variation in susceptibility to DD might allow changes in breeding policies or herd management which could be used to reduce DD prevalence. Factors mentioned in the literature as possibly influencing individual variation in susceptibility to DD include physical factors such as hoof conformation and properties of the skin, physiological factors such as the efficacy of the immune response, and behavioural factors such as standing half in cubicles. Further work is required to determine the influence of these factors, identify the genetic basis of variation, clarify the level of heritability of DD susceptibility and to determine how this is correlated with production and health traits currently used in breeding programmes.

The Application of Digital Photogrammetric Techniques and Aerial Photography to the Preservation of Archaeological Detail. Case Study: The Copney Stone Circle Complex, Co. Tyrone, N. Ireland

The Copney Stone Circle Complex, Co. Tyrone, N. Ireland, is an important Bronze Age site forming part of the Mid-Ulster Stone Circle Complex. The Environment Service: Historic Monuments and Buildings (ESHMB) initiated a program of bog-clearance in August 1994 to excavate the stone circles. This work was completed by October 1994 and the excavated site was surveyed in August 1995. Almost immediately, the rate at which the stones forming the circles were breaking down was noted and a program of study initiated to make recommendations upon the conservation of this important site. Digital photogrammetric techniques were applied to aerial images of the stone circles and digital terrain models created from the images at a range of scales. These provide base data sets for comparison with identical surveys to be completed in successive years and will allow the rate of deterioration, and the areas most affected, of the circles to be determined. In addition, a 2D analysis of the stones provides an accurate analysis of the absolute 2D dimensions of the stones for rapid desktop computer analysis by researchers remote from the digital photogrammetric workstation used in the survey.

The products of this work are readily incorporated into web sites, educational packages and databases. The technique provides a rapid and user friendly method of presentation of a large body of information and measurements, and a reliable method of storage of the information from Copney should it become necessary to re-cover the site.