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.

Measurement of the Electrogenicity of Bile Salt/H+ Antiport in Escherichia coli

The transmembrane proton gradient (ΔpH) is the primary source of energy exploited by secondary active substrate/H+ antiporters to drive the electroneutral transport of substrates across the Escherichia coli (E. coli) inner membrane. Such electroneutral transport results in no net movement of charges across the membrane. The charge on the transported substrate and the stoichiometry of the exchange reaction, however, can result in an electrogenic reaction which is driven by both the ΔpH and the electrical (∆Ψ) components of the proton electrochemical gradient, resulting in a net movement of electrical charges across the membrane. We have shown that the major facilitator superfamily transporter MdtM - a multidrug efflux protein from E. coli that functions physiologically in protection of bacterial cells against bile salts - imparts bile salt resistance to the bacterial cell by coupling the exchange of external protons (H+) to the efflux of bile salts from the cell interior via an electrogenic antiport reaction (Paul et al., 2014). This protocol describes, using fluorometry, how to detect electrogenic antiport activity of MdtM in inverted membrane vesicles of an antiporter-deficient strain of E. coli TO114 cells by measuring transmembrane ∆Ψ. The method exploits changes that occur in the intensity of the fluorescence signal (quenching and dequenching) of the probe Oxonol V in response to changes in membrane potential due to the MdtM-catalysed sodium cholate/H+ exchange reaction. The protocol can be adapted to detect activity of any secondary active antiporter that couples the electrogenic translocation of H+ across a biological membrane to that of its counter-substrate, and may be used to unmask otherwise camouflaged transport activities and physiological roles.

On the alignment of debris discs and their host stars' rotation axis - implications for spin-orbit misalignment in exoplanetary systems

It has been widely thought that measuring the misalignment angle between the orbital plane of a transiting exoplanet and the spin of its host star was a good discriminator between different migration processes for hot-Jupiters. Specifically, well-aligned hot-Jupiter systems (as measured by the Rossiter-McLaughlin effect) were thought to have formed via migration through interaction with a viscous disc, while misaligned systems were thought to have undergone a more violent dynamical history. These conclusions were based on the assumption that the planet-forming disc was well-aligned with the host star. Recent work by a number of authors has challenged this assumption by proposing mechanisms that act to drive the star-disc interaction out of alignment during the pre-main-sequence phase. We have estimated the stellar rotation axis of a sample of stars which host spatially resolved debris discs. Comparison of our derived stellar rotation axis inclination angles with the geometrically measured debris-disc inclinations shows no evidence for a misalignment between the two.

Slopes of Avian Species-Area Relationships, Human Population Density, and Environmental Factors

There is increasing interest in how humans influence spatial patterns in biodiversity. One of the most frequently noted and marked of these patterns is the increase in species richness with area, the species-area relationship (SAR). SARs are used for a number of conservation purposes, including predicting extinction rates, setting conservation targets, and identifying biodiversity hotspots. Such applications can be improved by a detailed understanding of the factors promoting spatial variation in the slope of SARs, which is currently the subject of a vigorous debate. Moreover, very few studies have considered the anthropogenic influences on the slopes of SARs; this is particularly surprising given that in much of the world areas with high human population density are typically those with a high number of species, which generates conservation conflicts. Here we determine correlates of spatial variation in the slopes of species-area relationships, using the British avifauna as a case study. Whilst we focus on human population density, a widely used index of human activities, we also take into account (1) the rate of increase in habitat heterogeneity with increasing area, which is frequently proposed to drive SARs, (2) environmental energy availability, which may influence SARs by affecting species occupancy patterns, and (3) species richness. We consider environmental variables measured at both local (10 km x 10 km) and regional (290 km x 290 km) spatial grains, but find that the former consistently provides a better fit to the data. In our case study, the effect of species richness on the slope SARs appears to be scale dependent, being negative at local scales but positive at regional scales. In univariate tests, the slope of the SAR correlates negatively with human population density and environmental energy availability, and positively with the rate of increase in habitat heterogeneity. We conducted two sets of multiple regression analyses, with and without species richness as a predictor. When species richness is included it exerts a dominant effect, but when it is excluded temperature has the dominant effect on the slope of the SAR, and the effects of other predictors are marginal.

Tumorigenesis and peritoneal colonization from fallopian tube epithelium

Ovarian cancer is the most lethal gynecological malignancy, primarily because its origin and initiation factors are unknown. A secretory murine oviductal epithelial (MOE) model was generated to address the hypothesis that the fallopian tube is an origin for high-grade serous cancer. MOE cells were stably altered to express mutation in p53, silence PTEN, activate AKT, and amplify KRAS alone and in combination, to define if this cell type gives rise to tumors and what genetic alterations are required to drive malignancy. Cell lines were characterized in vitro and allografted into mice. Silencing PTEN formed high-grade carcinoma with wide spread tumor explants including metastasis into the ovary. Addition of p53 mutation to PTEN silencing did not enhance this phenotype, whereas addition of KRAS mutation reduced survival. Interestingly, PTEN silencing and KRAS mutation originating from ovarian surface epithelium generated endometrioid carcinoma, suggesting that different cellular origins with identical genetic manipulations can give rise to distinct cancer histotypes. Defining the roles of specific signaling modifications in tumorigenesis from the fallopian tube/oviduct is essential for early detection and development of targeted therapeutics. Further, syngeneic MOE allografts provide an ideal model for pre-clinical testing in an in vivo environment with an intact immune system.

Effects of scalding and dehairing of pig carcasses at abattoirs on the visibility of welfare-related lesions

There is increasing interest in developing abattoir-based welfare measures for pigs.The primary aim of this study was to determine the most appropriate place on theslaughter line to conduct assessments of welfare-related lesions, namely apparentaggression-related skin lesions (hereafter referred to as 'skin lesions'), loin bruising andapparent tail biting damage. The study also lent itself to an assessment of theprevalence of these lesions, and the extent to which they were linked with productionparameters. Finishing pigs processed at two abattoirs on the Island of Ireland (n =1950 in abattoir A, and n = 1939 in abattoir B) were used. Data were collected over 6days in each abattoir in July 2014. Lesion scoring took place at two points on theslaughter line: (1) at exsanguination (Slaughter Stage 1 [SS1]), and (2) followingscalding and dehairing of carcasses (Slaughter Stage 2 [SS2]). At both points, eachcarcass was assigned a skin and tail lesion score ranging from 0 (lesion absent) to 3 or4 (severe lesions), respectively. Loin bruising was recorded as present or absent.Differences in the percentage of pigs with observable lesions of each type werecompared between SS1 and SS2 using McNemar/McNemar-Bowker tests. Theassociations between each lesion type, and both cold carcass weight andcondemnations, were examined at batch level using Pearson's correlations. Batch wasdefined as the group of animals with a particular farm identification code on a givenday. The overall percentage of pigs with a visible skin lesion (i.e. score > 0) decreasedbetween SS1 and SS2 (P<0.001). However, the percentage of pigs with a severe skinlesion increased numerically from SS1 to SS2. The percentage of pigs with a visible taillesion and with loin bruising also increased between SS1 and SS2 (P<0.001). Therewas a positive correlation between the percentage of carcasses that were partiallycondemned, and the percentage of pigs with skin lesions, tail lesions and loin bruising(P<0.05). Additionally, as the batch-level frequency of each lesion type increased,average cold carcass weight decreased (P<0.001). These findings suggest that severeskin lesions, tail lesions and loin bruising are more visible on pig carcasses after theyhave been scalded and dehaired, and that this is when abattoir-based lesion scoringshould take place. The high prevalence of all three lesion types, and the links witheconomically important production parameters, suggests more research into identifying key risk factors is warranted.

Pro-neural transcription factors as cancer markers

BACKGROUND: The aberrant transcription in cancer of genes normally associated with embryonic tissue differentiation at various organ sites may be a hallmark of tumour progression. For example, neuroendocrine differentiation is found more commonly in cancers destined to progress, including prostate and lung. We sought to identify proteins which are involved in neuroendocrine differentiation and differentially expressed in aggressive/metastatic tumours.

RESULTS: Expression arrays were used to identify up-regulated transcripts in a neuroendocrine (NE) transgenic mouse model of prostate cancer. Amongst these were several genes normally expressed in neural tissues, including the pro-neural transcription factors Ascl1 and Hes6. Using quantitative RT-PCR and immuno-histochemistry we showed that these same genes were highly expressed in castrate resistant, metastatic LNCaP cell-lines. Finally we performed a meta-analysis on expression array datasets from human clinical material. The expression of these pro-neural transcripts effectively segregates metastatic from localised prostate cancer and benign tissue as well as sub-clustering a variety of other human cancers.

CONCLUSION: By focussing on transcription factors known to drive normal tissue development and comparing expression signatures for normal and malignant mouse tissues we have identified two transcription factors, Ascl1 and Hes6, which appear effective markers for an aggressive phenotype in all prostate models and tissues examined. We suggest that the aberrant initiation of differentiation programs may confer a selective advantage on cells in all contexts and this approach to identify biomarkers therefore has the potential to uncover proteins equally applicable to pre-clinical and clinical cancer biology.

Resilience

Over the past decade the concept of ‘resilience’ has been mobilised across an increasingly wide range of policy arenas. For example, it has featured prominently within recent discussions on the nature of warfare, the purpose of urban and regional planning, the effectiveness of development policies, the intent of welfare reform and the stability of the international financial system. The term’s origins can be traced back to the work of the ecologist Crawford S. Holling and his formulation of a science of complexity. This paper reflects on the origins of these ideas and their travels from the field of natural resource management, which it now dominates, to contemporary social practices and policy arenas. It reflects on the ways in which a lexicon of complex adaptive systems, grounded in an epistemology of limited knowledge and uncertain futures, seeks to displace ongoing ‘dependence’ on professionals by valorising self-reliance and responsibility as techniques to be applied by subjects in the making of the resilient self. In so doing, resilience is being mobilised to govern a wide range of threats and sources of uncertainty, from climate change, financial crises and terrorism, to the sustainability of development, the financing of welfare and providing for an aging population. As such, ‘resilience’ risks becoming a measure of its subjects’ ‘fitness’ to survive in what are pre-figured as natural, turbulent orders of things.

Heller's myotomy and pneumatic dilatation in the treatment of achalasia: a population-based case–control study assessing long-term quality of life

Long-term health-related quality-of-life (HRQL) outcomes have not been widely reported in the
treatment of achalasia. The aims of this study were to examine long-term disease-specific and general HRQL in
achalasia patients using a population-based case–control method, and to assess HRQL between treatment interventions.
Manometrically diagnosed achalasia cases (n = 120) were identified and matched with controls (n = 115)
using a population-based approach. Participants completed general (SF-12) and disease-specific (Achalasia Severity
Questionnaire [ASQ]) HRQL questionnaires, as appropriate, in a structured interview. Mean composite scores
for SF-12 (Mental Component Summary score [MCS-12] and Physical Component Summary score [PCS-12]) and
ASQ were compared between cases and controls, or between intervention groups, using an independent t-test.
Adjusted mean differences in HRQL scores were evaluated using a linear regression model. Achalasia cases were
treated with a Heller’s myotomy (n = 43), pneumatic dilatation (n = 44), or both modalities (n = 33). The median
time from last treatment to HRQL assessment was 5.7 years (interquartile range 2.4–11.5). Comparing achalasia
patients with controls, PCS-12 was significantly worse (40.9 vs. 44.2, P = 0.01), but MCS-12 was similar. However,
both PCS-12 (39.9 vs. 44.2, P = 0.03) and MCS-12 (46.7 vs. 53.5, P = 0.004) were significantly impaired in those
requiring dual treatment compared with controls. Overall however, there was no difference in adjusted HRQL
between patients treated with Heller’s myotomy, pneumatic dilatation or both treatment modalities. In summary,
despite treatment achalasia patients have significantly worse long-term physical HRQL compared with population
controls. No HRQL differences were observed between the treatment modalities to suggest a benefit of one
treatment over another.

Undergraduate Student perceptions of a Restorative Dentistry OSCE

Objectives: The Objective Structured Clinical Exam (OSCE) is a widely accepted assessment method in undergraduate dental education. It aims to test higher order skills, attitudes and aspects of professionalism which other summative assessments such as MCQs and other written examinations are less able to do. The aim of this study was to evaluate the perceptions of 4th year undergraduate dental students of an OSCE undertaken in the Conservation Department.
Methods: On completion of the OSCE examination 51 fourth year undergraduate students were asked to complete an anonymised questionnaire. The questionnaire was made 22 questions, and requiring the students to provide both open and closed responses.
Results: A lot of positive aspects to the OSCE were observed in responses, students felt that the OSCE was a meaningful way for assessing their clinical skills (85%), it reflected real life conditions (79%) and that it was a fair method of assessment (75%).
A number of negative aspects were also noted. Most students felt the OSCE was stressful (72%) and they felt nervous during the examination (77%). Of the undergraduates asked 42% did not feel confident doing the OSCE.
A number of students felt it would be helpful to have additional information given to them on the OSCE prior to the assessment process.
Conclusion: In general the students found the OSCE a fair, meaningful form of assessment which reflected real life clinical situations, providing them with an opportunity to show their clinical knowledge and practical skills. A number study cohort did not feel confident during the OSCE and felt nervous and stressed by the experience. The information gained from the reflective nature of the feedback questionnaire has proved invaluable in the design of subsequent diets of the OSCE examination. 

Magnetospheric Structure and Atmospheric Joule Heating of Habitable Planets Orbiting M-dwarf Stars

We study the magnetospheric structure and the ionospheric Joule Heating of planets orbiting M-dwarf stars in the habitable zone using a set of magnetohydrodynamic models. The stellar wind solution is used to drive a model for the planetary magnetosphere, which is coupled with a model for the planetary ionosphere. Our simulations reveal that the space environment around close-in habitable planets is extreme, and the stellar wind plasma conditions change from sub- to super-Alfvénic along the planetary orbit. As a result, the magnetospheric structure changes dramatically with a bow shock forming in the super-Alfvénic sectors, while no bow shock forms in the sub-Alfvénic sectors. The planets reside most of the time in the sub-Alfvénic sectors with poor atmospheric protection. A significant amount of Joule Heating is provided at the top of the atmosphere as a result of the intense stellar wind. For the steady-state solution, the heating is about 0.1%-3% of the total incoming stellar irradiation, and it is enhanced by 50% for the time-dependent case. The significant Joule Heating obtained here should be considered in models for the atmospheres of habitable planets in terms of the thickness of the atmosphere, the top-side temperature and density, the boundary conditions for the atmospheric pressure, and particle radiation and transport. Here we assume constant ionospheric Pedersen conductance similar to that of the Earth. The conductance could be greater due to the intense EUV radiation leading to smaller heating rates. We plan to quantify the ionospheric conductance in future study.

Preparing assessments and examinations. Common errors and good practice.

Assessment forms an important part of the student learning experience and students place a high value on the quality of feedback that they receive from academic staff on where they might improve on their examinations or assignments. However while feedback is important the quality of the actual assessment itself before students undertake an examination or commence writing an assignment is also important. It is imperative that students are clear in their understanding of what is expected of them in order to achieve a particular grade and that there is lack of ambiguity in examinations or assignments. Biggs (2003) highlighted the importance of clarity in what students are expected to be able to do at the end of a unit of study, and that intended learning outcomes should be clearly aligned to the assessment and communicated to students so that they can structure their learning activities to optimize their assessment performance. However as Rust (2002) highlighted there are often inconsistencies in assessment practices ranging from a mis-match of assessment and learning outcomes to the inclusion of additional learning criteria and lack of clarity in the instructions. Such inconsistencies and unacceptable errors in examination papers can undermine student confidence in the assessment process
In order to try and minimise such inconsistencies an internal assessment group was set up October 2013 within the School of Nursing and Midwifery at Queens University Belfast, consisting of representative academic staff from across the range of undergraduate and post graduate courses in nursing and midwifery. The assessment group was to be a point of reference for all school examinations with a particular remit to develop an assessment strategy for all nursing and midwifery programmes and to ensure that all assessments comply with current best practice and with Nursing and Midwifery Council (NMC) requirements.
Aim
This paper aims to highlight some examples of good practice and common errors that were found in assignments and examinations that were submitted to the assessment group for review.
References

Biggs. J. (2003) Teaching for Quality Learning at University – What the Student Does 2nd Edition SRHE / Open University Press, Buckingham.
Rust, C.( 2002) The impact of assessment on student learning, Active Learning in Higher education Vol3(2):145-158

Petals of Resonance: A performance system for the transformation of small body sounds

A system of software and hardware that combines signal processing and contact microphones using normally inaudible body sounds, including heartbeat/pulse, respiration and internal sounds from the vocal tract that can be heard internally by the performer but not externally by others, to drive resonant filters. Performance at SARC Sonic Lab, Belfast, 19 Feb 2015 in collaboration with Birgit Ulher.

Personalised and Precision Medicine in Cancer Clinical Trials: Panacea for Progress or Pandora's Box?

Cancer clinical trials have been one of the key foundations for significant advances in oncology. However, there is a clear recognition within the academic, care delivery and pharmaceutical/biotech communities that our current model of clinical trial discovery and development is no longer fit for purpose. Delivering transformative cancer care should increasingly be our mantra, rather than maintaining the status quo of, at best, the often miniscule incremental benefits that are observed with many current clinical trials. As we enter the era of precision medicine for personalised cancer care (precision and personalised medicine), it is important that we capture and utilise our greater understanding of the biology of disease to drive innovative approaches in clinical trial design and implementation that can lead to a step change in cancer care delivery. A number of advances have been practice changing (e.g. imatinib mesylate in chronic myeloid leukaemia, Herceptin in erb-B2-positive breast cancer), and increasingly we are seeing the promise of a number of newer approaches, particularly in diseases like lung cancer and melanoma. Targeting immune checkpoints has recently yielded some highly promising results. New algorithms that maximise the effectiveness of clinical trials, through for example a multi-stage, multi-arm type design are increasingly gaining traction. However, our enthusiasm for the undoubted advances that have been achieved are being tempered by a realisation that these new approaches may have significant cost implications. This article will address these competing issues, mainly from a European perspective, highlight the problems and challenges to healthcare systems and suggest potential solutions that will ensure that the cost/value rubicon is addressed in a way that allows stakeholders to work together to deliver optimal cost-effective cancer care, the benefits of which can be transferred directly to our patients.

Sustainable non-automotive vehicles: The simulation challenges

Simulation is a well-established and effective approach to the development of fuel-efficient and low-emissions vehicles in both on-highway and off-highway applications.

The simulation of on-highway automotive vehicles is widely reported in literature, whereas research relating to non-automotive and off-highway vehicles is relatively sparse. This review paper focuses on the challenges of simulating such vehicles and discusses the differences in the approach to drive cycle testing and experimental validation of vehicle simulations. In particular, an inner-city diesel-electric hybrid bus and an ICE (Internal Combustion Engine) powered forklift truck will be used as case studies.

Computer prediction of fuel consumption and emissions of automotive vehicles on standardised drive cycles is well-established and commercial software packages such as AVL CRUISE have been specifically developed for this purpose. The vehicles considered in this review paper present new challenges from both the simulation and drive-cycle testing perspectives. For example, in the case of the forklift truck, the drive cycles involve reversing elements, variable mass, lifting operations, and do not specify a precise velocity-time profile. In particular, the difficulties associated with the prediction of productivity, i.e. the maximum rate of completing a series of defined operations, are discussed. In the case of the hybrid bus, the standardised drive cycles are unrepresentative of real-life use and alternative approaches are required in the development of efficient and low-emission vehicles.

Two simulation approaches are reviewed: the adaptation of a standard automotive vehicle simulation package, and the development of bespoke models using packages such as MATLAB/Simulink.