Detection of quantitative trait loci for androstenone, skatole and boar taint in a cross between Large White and Meishan pigs

'Boar taint' is a strong perspiration-like, urine-like unpleasant odour given off upon heating or cooking of meat from some intact (uncastrated) male pigs. Data from the F(2) generation of a Large White (LW) x Meishan (MS) crossbred population were analysed to detect quantitative trait loci (QTL) for traits associated with boar taint. Fat samples from 178 intact male pigs slaughtered at 85 +/- 5 kg were analysed for the major contributors to boar taint (androstenone, indole and skatole). Fat and lean samples from cooked meat were scored for boar, abnormal and pork flavour and odour by a trained sensory panel (SP). A scan with 117 markers covering the whole genome was performed in the F(2) individuals, together with their F(1) parents and purebred grandparents. At the 5% chromosomal significance threshold (approximately equal to the genome-wide suggestive significance threshold), QTL were detected for the laboratory estimate of androstenone on chromosomes 2, 4, 6, 7 and 9. However, only on chromosome 6 were there QTL for boar flavour (BF) traits in the same or adjacent marker intervals as a QTL for the laboratory estimate of androstenone. On chromosome 14, QTL were detected for the laboratory estimates of indole and skatole, the SP score for skatole and the scores for BF in lean and BF in fat. In all five cases, the MS allele generally increased the estimate or score, compared with the LW allele, but it appeared that desirable and undesirable alleles were present in both breeds. This locus on chromosome 14 has considerable potential for use to reduce the incidence of boar taint, especially if further research can identify the causative polymorphism or strongly associated markers.

The neoliberalisation of the Cathedral Quarter and its contestations

Over time Belfast has been well researched as a site of ethnosectarian conflict, segregation and fear see (Boal et al 1976) and (Gaffiken and Morrisey 2011). The study of socio-spatial patterns of ‘ethnocracy’ is useful, but this article will argue how it is equally important to understand local forms of urban restructuring in terms of global processes that are linked to neoliberalism. To better understand the neoliberal urbanisation of Belfast this article is organised into two parts. The first part will demonstrate how the Northern Ireland State has sought legitimacy in the free market as ‘therapy’ for the production of neutral socio-spatial formations such as the Cathedral Quarter. Secondly it will examine this performance of neoliberal urbanism, as it ‘actually exists’ and demonstrate how market-led renewal has been extended through the clustering and non-sectarian interests, ‘soft’ arrangements of urban governance, cultural re-branding strategies, economic development incentives, and the development of various flagship projects. Critically this place-based grounding of neoliberalism is useful, as it also allows for the contestations of neoliberal urbanism to become real rather than just theoretical. The second part of the article will draw attention to the responses of local, and sometimes marginal, interests that have looked to challenge, adapt and, at times, divert the extension of market-led renewal. To be clear, this article does not want to overstate the performance of such interests. Nor does it want to claim that they significantly impact or obstruct the wider neoliberal urbanisation of Belfast. Instead it is interested in their behaviours and their different methods of working to explore what may be constituted as ‘alternative’, at least in the locality of the Cathedral Quarter. By studying how and why these interests have responded to the extension of neoliberal urbanism over time, it may just be possible to provide a better platform to articulate what more progressive forms of urban resistance might look like.

Acid-labile protein-adducted heterocyclic aromatic amines in human blood are not viable biomarkers of dietary exposure: A systematic study.

Heterocyclic aromatic amines (HCA) are carcinogenic mutagens formed during cooking of protein-rich foods. HCA residues adducted to blood proteins have been postulated as biomarkers of HCA exposure. However, the viability of quantifying HCAs following hydrolytic release from adducts in vivo and correlation with dietary intake are unproven. To definitively assess the potential of labile HCA-protein adducts as biomarkers, a highly sensitive UPLC-MS/MS method was validated for four major HCAs: 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 2-amino-3,8-dimethylimidazo[4,5-f]quinoxaline (MeIQx), 2-amino-3,4,8-trimethylimidazo[4,5-f]quinoxaline (4,8-DiMeIQx) and 2-amino-3,7,8-trimethylimidazo[4,5-f]quinoxaline (7,8-DiMeIQx). Limits of detection were 1e5 pg/ml plasma and recoveries 91e115%. Efficacy of hydrolysis was demonstrated by HCA-protein adducts synthesised in vitro. Plasma and 7-day food diaries were collected from 122 fasting adults consuming their habitual diets. Estimated HCA intakes ranged from 0 to 2.5 mg/day. An extensive range of hydrolysis conditions was examined for release of adducted HCAs in plasma. HCA was detected in only one sample (PhIP, 9.7 pg/ml), demonstrating conclusively for the first time that acid-labile HCA adducts do not reflect dietary HCA intake and are present at such low concentrations that they are not feasible biomarkers of exposure. Identification of biomarkers remains important. The search should concentrate on stabilised HCA peptide markers and use of untargeted proteomic and metabolomic approaches.

Investigating the Implications of a Variable RBE on Proton Dose Fractionation Across a Clinical Pencil Beam Scanned Spread-Out Bragg Peak

Purpose: To investigate the clinical implications of a variable relative biological effectiveness (RBE) on proton dose fractionation. Using acute exposures, the current clinical adoption of a generic, constant cell killing RBE has been shown to underestimate the effect of the sharp increase in linear energy transfer (LET) in the distal regions of the spread-out Bragg peak (SOBP). However, experimental data for the impact of dose fractionation in such scenarios are still limited.

Methods and Materials: Human fibroblasts (AG01522) at 4 key depth positions on a clinical SOBP of maximum energy 219.65 MeV were subjected to various fractionation regimens with an interfraction period of 24 hours at Proton Therapy Center in Prague, Czech Republic. Cell killing RBE variations were measured using standard clonogenic assays and were further validated using Monte Carlo simulations and parameterized using a linear quadratic formalism.

Results: Significant variations in the cell killing RBE for fractionated exposures along the proton dose profile were observed. RBE increased sharply toward the distal position, corresponding to a reduction in cell sparing effectiveness of fractionated proton exposures at higher LET. The effect was more pronounced at smaller doses per fraction. Experimental survival fractions were adequately predicted using a linear quadratic formalism assuming full repair between fractions. Data were also used to validate a parameterized variable RBE model based on linear α parameter response with LET that showed considerable deviations from clinically predicted isoeffective fractionation regimens.

Conclusions: The RBE-weighted absorbed dose calculated using the clinically adopted generic RBE of 1.1 significantly underestimates the biological effective dose from variable RBE, particularly in fractionation regimens with low doses per fraction. Coupled with an increase in effective range in fractionated exposures, our study provides an RBE dataset that can be used by the modeling community for the optimization of fractionated proton therapy.

Multilinear and Integer Programming for Markov Decision Processes with Imprecise Probabilities

Markov Decision Processes (MDPs) are extensively used to encode sequences of decisions with probabilistic effects. Markov Decision Processes with Imprecise Probabilities (MDPIPs) encode sequences of decisions whose effects are modeled using sets of probability distributions. In this paper we examine the computation of Γ-maximin policies for MDPIPs using multilinear and integer programming. We discuss the application of our algorithms to “factored” models and to a recent proposal, Markov Decision Processes with Set-valued Transitions (MDPSTs), that unifies the fields of probabilistic and “nondeterministic” planning in artificial intelligence research. 

PageRank in Malware Categorization

In this paper, we propose a malware categorization method that models malware behavior in terms of instructions using PageRank. PageRank computes ranks of web pages based on structural information and can also compute ranks of instructions that represent the structural information of the instructions in malware analysis methods. Our malware categorization method uses the computed ranks as features in machine learning algorithms. In the evaluation, we compare the effectiveness of different PageRank algorithms and also investigate bagging and boosting algorithms to improve the categorization accuracy.

US Dollar Carry Trades in the Era of 'Cheap Money'

In this paper, we employ a unique dataset of actual US dollar (USD) forward positions against a number of currencies taken by so-called Commodity Trading Advisors (CTAs). We investigate to what extent these positions exhibit a pattern of USD carry trading or other patterns of currency trading over the recent period of the ultra-loose US monetary policy. Our analysis indeed shows that USD positions against emerging market currencies are characterised by a pattern of carry trading. That is, the USD, as the lower yielding currency, is associated with short positions. The payoff distributions of these positions, moreover, are found to have positive Sharpe ratios, negative skewness and high kurtosis. On the other hand, we find that USD positions against other advanced country currencies have a pattern completely opposite to carry trading which is in line with uncovered interest parity trading; that is, the lower (higher) yielding currency is associated with long (short) positions.