Automated tumour annotation and analysis for molecular pathology using TissueMark (R)

Objective: Molecular pathology relies on identifying anomalies using PCR or analysis of DNA/RNA. This is important in solid tumours where molecular stratification of patients define targeted treatment. These molecular biomarkers rely on examination of tumour, annotation for possible macro dissection/tumour cell enrichment and the estimation of % tumour. Manually marking up tumour is error prone. Method: We have developed a method for automated tumour mark-up and % cell calculations using image analysis called TissueMark® based on texture analysis for lung, colorectal and breast (cases=245, 100, 100 respectively). Pathologists marked slides for tumour and reviewed the automated analysis. A subset of slides was manually counted for tumour cells to provide a benchmark for automated image analysis. Results: There was a strong concordance between pathological and automated mark-up (100 % acceptance rate for macro-dissection). We also showed a strong concordance between manually/automatic drawn boundaries (median exclusion/inclusion error of 91.70 %/89 %). EGFR mutation analysis was precisely the same for manual and automated annotation-based macrodissection. The annotation accuracy rates in breast and colorectal cancer were 83 and 80 % respectively. Finally, region-based estimations of tumour percentage using image analysis showed significant correlation with actual cell counts. Conclusion: Image analysis can be used for macro-dissection to (i) annotate tissue for tumour and (ii) estimate the % tumour cells and represents an approach to standardising/improving molecular diagnostics.

Prognostic Impact of Monocyte Count at Presentation in Mantle Cell Lymphoma

Increased number of circulating monocytes at presentation has been recently associated with shorter survival in Hodgkin lymphoma, follicular lymphoma and diffuse large B cell lymphoma. This study aimed to assess the prognostic impact of the absolute monocyte count (AMC) at diagnosis in mantle cell lymphoma (MCL). From the series of MCL cases recorded on the databases of the Oncology Institute of Southern Switzerland in Bellinzona (Switzerland) and the Division of Haematology of the Amedeo Avogadro University of Eastern Piedmont in Novara (Italy), the AMC at diagnosis was available in 97 cases. Cox regression was used for both univariate and multivariate analysis. With a median follow up of 7 years, the 5-year overall survival (OS) was 29% for patients with AMC >500/ul and 62% for patients with AMC

Ecological dynamics of extinct species in empty habitat networks. 2. The role of host plant dynamics

This paper explores the relative effects of host plant dynamics and butterfly-related parameters on butterfly persistence. It considers an empty habitat network where a rare butterfly (Cupido minimus) became extinct in 1939 in part of its historical range in north Wales, UK. Surviving populations of the butterfly in southern Britain were visited to assess use of its host plant (Anthyllis vulneraria) in order to calibrate habitat suitability and carrying capacity in the empty network in north Wales. These data were used to deduce that only a portion ( similar to 19%) of the host plant network from north Wales was likely to be highly suitable for oviposition. Nonetheless, roughly 65,460 eggs (3273 adult equivalents) could be expected to be laid in north Wales, were the empty network to be populated at the same levels as observed on comparable plants in surviving populations elsewhere. Simulated metapopulations of C. minimus in the empty network revealed that time to extinction and patch occupancy were significantly influenced by carrying capacity, butterfly mean dispersal distance and environmental stochasticity, although for most reasonable parameter values, the model system persisted. Simulation outputs differed greatly when host plant dynamics was incorporated into the modelled butterfly dynamics. Cupido minimus usually went extinct when host plant were at low densities. In these simulations host plant dynamics appeared to be the most important determinant of the butterfly's regional extirpation. Modelling the outcome of a reintroduction programme to C. minimus variation at high quality locations, revealed that 65% of systems survived at least 100 years. Given the current amount of resources of the north Wales landscape, the persistence of C. minimus under a realistic reintroduction programme has a good chance of being successful, if carried out in conjunction with a host plant management programme.

Accurate image capturing control of bottle caps based on iterative learning control and Kalman filtering

This paper investigates camera control for capturing bottle cap target images in the fault-detection system of an industrial production line. The main purpose is to identify the targeted bottle caps accurately in real time from the images. This is achieved by combining iterative learning control and Kalman filtering to reduce the effect of various disturbances introduced into the detection system. A mathematical model, together with a physical simulation platform is established based on the actual production requirements, and the convergence properties of the model are analyzed. It is shown that the proposed method enables accurate real-time control of the camera, and further, the gain range of the learning rule is also obtained. The numerical simulation and experimental results confirm that the proposed method can not only reduce the effect of repeatable disturbances but also non-repeatable ones.

M-L band x-rays (3-3.5 KeV) from palladium coated targets for isochoric radiative heating of thin foil samples

We describe experiments designed to produce a bright M-L band x-ray source in the 3-3.5 keV region. Palladium targets irradiated with a 10(15) W cm(-2) laser pulse have previously been shown to convert up to similar to 2% of the laser energy into M-L band x-rays with similar pulse duration to that of the incident laser. This x-ray emission is further characterized here, including pulse duration and source size measurements, and a higher conversion efficiency than previously achieved is demonstrated (similar to 4%) using more energetic and longer duration laser pulses (200 ps). The emission near the aluminium K-edge (1.465-1.550 keV) is also reported for similar conditions, along with the successful suppression of such lower band x-rays using a CH coating on the rear side of the target. The possibility of using the source to radiatively heat a thin aluminium foil sample to uniform warm dense matter conditions is discussed.

Modelling Duqu 2.0 Malware using Attack Trees with Sequential Conjunction

In this paper we identify requirements for choosing a threat modelling formalisation for modelling sophisticated malware such as Duqu 2.0. We discuss the gaps in current formalisations and propose the use of Attack Trees with Sequential Conjunction when it comes to analysing complex attacks. The paper models Duqu 2.0 based on the latest information sourced from formal and informal sources. This paper provides a well structured model which can be used for future analysis of Duqu 2.0 and related attacks.

Associations between intensive diabetes therapy and NMR-determined lipoprotein subclass profiles in Type 1 diabetes

Our objective is to define differences in circulating lipoprotein subclasses between intensive vs. conventional management of Type 1 diabetes during the randomization phase of the Diabetes Control and Complications Trial (DCCT). Nuclear magnetic resonance-determined lipoprotein subclass profiles (NMR-LSP), which estimate molar subclass concentrations and mean particle diameters, were determined in 1,294 DCCT subjects after a median of five (interquartile range: four, six) years following randomization to intensive or conventional diabetes management. In cross-sectional analyses, we compared standard lipids and NMR-LSP between treatment groups. Standard total-, LDL- and HDL-cholesterol levels were similar between randomization groups, while triglyceride levels were lower in the intensively treated group. NMR-LSP showed that intensive therapy was associated with larger LDL diameter (20.7 vs. 20.6 nm, p=0.01) and lower levels of small LDL (median: 465 vs. 552 nmol/l, p=0.007), total IDL/LDL (mean: 1000 vs. 1053 nmol/l, p=0.01), and small HDL (mean: 17.3 vs. 18.6 μmol/l, p<0.0001), the latter accounting for reduced total HDL (mean: 33.8 vs. 34.8 μmol/l, p=0.01). In conclusion, intensive diabetes therapy was associated with potentially favorable changes in LDL and HDL subclasses in sera. Further research will determine whether these changes contribute to the beneficial effects of intensive diabetes management on vascular complications.

Ultra-High-Resolution Observations of MHD Waves in Photospheric Magnetic Structures

This chapter reviews the recent observations of waves and oscillations manifesting in fine-scale magnetic structures in the solar photosphere, which are often interpreted as the "building blocks' of the magnetic Sun. The authors found, through phase relationships between the various waveforms, that small-scale magnetic bright points (MBPs) in the photosphere demonstrated signatures of specific magnetoacoustic waves, in particular the sausage and kink modes. Modern magnetohydrodynamic (MHD) simulations of the lower solar atmosphere clearly show how torsional motions can easily be induced in magnetic elements in the photosphere through the processes of vortical motions and/or buffeting by neighboring granules. The authors detected significant power associated with high-frequency horizontal motions, and suggested that these cases may be especially important in the creation of a turbulent environment that efficiently promotes Alfvén wave dissipation.