Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

BACKGROUND: Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome.

METHODS: In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone.

FINDINGS: We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions.

INTERPRETATION: For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.

CSFinder: A Cold-Start Friend Finder in Large-Scale Social Networks

Recommending users for a new social network user to follow is a topic of interest at present. The existing approaches rely on using various types of information about the new user to determine recommended users who have similar interests to the new user. However, this presents a problem when a new user joins a social network, who is yet to have any interaction on the social network. In this paper we present a particular type of conversational recommendation approach, critiquing-based recommendation, to solve the cold start problem. We present a critiquing-based recommendation system, called CSFinder, to recommend users for a new user to follow. A traditional critiquing-based recommendation system allows a user to critique a feature of a recommended item at a time and gradually leads the user to the target recommendation. However this may require a lengthy recommendation session. CSFinder aims to reduce the session length by taking a case-based reasoning approach. It selects relevant recommendation sessions of past users that match the recommendation session of the current user to shortcut the current recommendation session. It selects relevant recommendation sessions from a case base that contains the successful recommendation sessions of past users. A past recommendation session can be selected if it contains recommended items and critiques that sufficiently overlap with the ones in the current session. Our experimental results show that CSFinder has significantly shorter sessions than the ones of an Incremental Critiquing system, which is a baseline critiquing-based recommendation system.

Finite-element investigation of cold-formed steel portal frames in fire

This paper presents the results of a full-scale site fire test performed on a cold-formed steel portal frame building with semi-rigid joints. The purpose of the study is to establish a performance-based approach for the design of such structures in fire boundary conditions. In the full-scale site fire test, the building collapsed asymmetrically at a temperature of 714°C. A non-linear elasto-plastic finite-element shell model is described and is validated against the results of the full-scale test. A parametric study is presented that highlights the importance of in-plane restraint from the side rails in preventing an outwards sway failure for both a single portal and full building geometry model. The study also demonstrates that the semi-rigidity of the joints should be taken into account in the design. The single portal and full building geometry models display a close match to site test results with failure at 682°C and 704°C, respectively. A design case is described in accordance with Steel Construction Institute design recommendations. The validated single portal model is tested with pinned bases, columns protected, realistic loading and rafters subject to symmetric uniform heating in accordance with the ISO 834 standard fire curve; failure occurs at 703°C.

Atmospheric cold plasma process for vegetable leaf decontamination: A feasibility study on radicchio (red chicory, Cichorium intybus L.)

Cold plasma is an emerging non-thermal processing technology that could be used for large scale leaf decontamination as an alternative to chlorine washing. In this study the effect of an atmospheric cold plasma apparatus (air DBD, 15 kV) on the safety, antioxidant activity and quality of radicchio (red chicory, Cichorium intybus L.) was investigated after 15 and 30 min of treatment (in afterglow at 70 mm from the discharge, at 22 °C and 60% of RH) and during storage. Escherichia coli O157:H7 inoculated on radicchio leaves was significantly reduced after 15 min cold plasma treatment (-1.35 log MPN/cm²). However, a 30 min plasma treatment was necessary to achieve a significant reduction of Listeria monocytogenes counts (-2.2 log CFU/cm²). Immediately after cold plasma treatment, no significant effects emerged in terms of antioxidant activity assessed by the ABTS and ORAC assay and external appearance of the radicchio leaves. Significant changes between treated and untreated radicchio leaves are quality defects based on the cold plasma treatment. Atmospheric cold plasma appears to be a promising processing technology for the decontamination of leafy vegetables although some criticalities, that emerged during storage, need to be considered in future studies.

Finite element modelling of cyclic behaviour of cold-formed steel bolted moment-resisting connections

This paper investigates the accuracy of new finite element modelling approaches to predict the behaviour of bolted moment-connections between cold-formed steel members, formed by using brackets bolted to the webs of the section, under low cycle fatigue. ABAQUS software is used as a modelling platform. Such joints are used for portal frames and potentially have good seismic resisting capabilities, which is important for construction in developing countries. The modelling implications of a two-dimensional beam element model, a three-dimensional shell element model and a three-dimensional solid element model are reported. Quantitative and qualitative results indicate that the three-dimensional quadratic S8R shell element model most accurately predicts the hysteretic behaviour and energy dissipation capacity of the connection when compared to the test results.

Early Implementation of BIM into a Cold-Formed Steel Design/ Fabricator and an Architectural/Planning Consultancy

There is a broad consensus surrounding the ability of building information modelling (BIM) to positively impact a project by enabling greater collaboration. This paper aims to examine the development of BIM and how it can contribute to the evermore present and growing cold-formed steel (CFS) industry. This is achieved thorough a comprehensive literature review and four exploratory interviews with industry experts. Work has been carried out, for the first time, alongside one of the UK’s largest CFS Designer/Fabricators in conjunction with Northern Ireland’s leading Architectural and Town Planning Consultants in the identification and dissemination of information. The capabilities of BIM have been investigated through modeling of simple CFS structures n consultation with the project partners. By scrutinising the literature and associated interviews, the primary opportunities, as well as barriers, of BIM implementation have been investigated in the context of these companies. It is essential to develop greater understanding of the flexibility, adaptability and interoperability of BIM software as the UK construction industry faces a daunting challenge; fully collaborative 3D BIM as required by the UK Government under the “Government Construction Strategy” by 2016 in all public sector projects. This paper, and the wider study that it stems from, approaches the problem from a new angle, from sections of the construction industry that have not yet fully embedded BIM.

Challenging the cancer molecular stratification dogma: Intratumoral heterogeneity undermines consensus molecular subtypes and potential diagnostic value in colorectal cancer

Purpose:
A number of independent gene expression profiling studies have identified transcriptional subtypes in colorectal cancer (CRC) with potential diagnostic utility, culminating in publication of a CRC Consensus Molecular Subtype classification. The worst prognostic subtype has been defined by genes associated with stem-like biology. Recently, it has been shown that the majority of genes associated with this poor prognostic group are stromal-derived. We investigated the potential for tumor misclassification into multiple diagnostic subgroups based on tumoral region sampled.

Experimental Design:
We performed multi-region tissue RNA extraction/transcriptomic analysis using Colorectal Specific Arrays on invasive front, central tumor and lymph node regions selected from tissue samples from 25 CRC patients.

Results:
We identified a consensus 30 gene list which represents the intratumoral heterogeneity within a cohort of primary CRC tumors. Using a series of online datasets, we showed that this gene list displays prognostic potential (HR=2.914 (CI 0.9286-9.162) in stage II/III CRC patients, but in addition we demonstrated that these genes are stromal derived, challenging the assumption that poor prognosis tumors with stem-like biology have undergone a widespread Epithelial Mesenchymal Transition (EMT). Most importantly, we showed that patients can be simultaneously classified into multiple diagnostically relevant subgroups based purely on the tumoral region analysed.

Conclusions:
Gene expression profiles derived from the non-malignant stromal region can influence assignment of CRC transcriptional subtypes, questioning the current molecular classification dogma and highlighting the need to consider pathology sampling region and degree of stromal infiltration when employing transcription-based classifiers to underpin clinical decision-making in CRC.