Maximum size binary matroids with no AG(3,2)-minor are graphic

We prove that the maximum size of a simple binary matroid of rank $r \geq 5$ with no AG(3,2)-minor is $\binom{r+1}{2}$ and characterise those matroids achieving this bound. When $r \geq 6$, the graphic matroid $M(K_{r+1})$ is the unique matroid meeting the bound, but there are a handful of smaller examples. In addition, we determine the size function for non-regular simple binary matroids with no AG(3,2)-minor and characterise the matroids of maximum size for each rank

Systematic review of the clinical effectiveness and cost-effectiveness, and economic evaluation, of denosumab for the treatment of bone metastases from solid tumours

Peer reviewedPublisher PD

Large-scale variation in density of an aquatic ecosystem indicator species

Funding: This work was supported by the New York State Department of Environmental Conservation and the Hudson River Natural Resource Trustees.Monitoring indicator species is a pragmatic approach to natural resource assessments, especially when the link between the indicator species and ecosystem state is well justified. However, conducting ecosystem assessments over representative spatial scales that are insensitive to local heterogeneity is challenging. We examine the link between polychlorinated biphenyl (PCB) contamination and population density of an aquatic habitat specialist over a large spatial scale using non-invasive genetic spatial capture-recapture. Using American mink (Neovison vison), a predatory mammal and an indicator of aquatic ecosystems, we compared estimates of density in two major river systems, one with extremely high levels of PCB contamination (Hudson River), and a hydrologically independent river with lower PCB levels (Mohawk River). Our work supports the hypothesis that mink densities are substantially (1.64-1.67 times) lower in the contaminated river system. We demonstrate the value of coupling the indicator species concept with well-conceived and spatially representative monitoring protocols. PCBs have demonstrable detrimental effects on aquatic ecosystems, including mink, and these effects are likely to be profound and long-lasting, manifesting as population-level impacts. Through integrating non-invasive data collection, genetic analysis, and spatial capture-recapture methods, we present a monitoring framework for generating robust density estimates across large spatial scales.Publisher PDFPeer reviewe

Tournaments and Even Graphs are Equinumerous

A graph is called \emph{odd} if there is an orientation of its edges and an automorphism that reverses the sense of an odd number of its edges, and \emph{even} otherwise. Pontus von Br\"omssen (n\'e Andersson) showed that the existence of such an automorphism is independent of the orientation, and considered the question of counting pairwise non-isomorphic even graphs. Based on computational evidence, he made the rather surprising conjecture that the number of pairwise non-isomorphic \emph{even graphs} on $n$ vertices is equal to the number of pairwise non-isomorphic \emph{tournaments} on $n$ vertices. We prove this conjecture using a counting argument with several applications of the Cauchy-Frobenius Theorem

Paratexts seeking understanding: manuscripts and aesthetic cognitivism

This article explores the relationship between manuscripts of ancient religious literature and aesthetic cognitivism, a normative theory of the value of art. Arguing that manuscripts both contain and constitute works of art, we explore paratextuality as a phenomenon that connects manuscript studies to both qualitative and quantitative sides of aesthetic cognitivism. Focusing on our work with a single unpublished gospel manuscript (Dublin, CBL W 139) in the context of a larger project called Paratextual Understanding, we make that case that paratexts have aesthetic functions that allow them to contribute to the knowledge yielded by the larger literary work of which they are a part. We suggest a number of avenues for further research that engages with material culture, non-typography, paratexts, and the arts

A systematic review of biomarkers for disease progression in Parkinson's disease

This article presents independent research funded by the National Institute for Health Research (NIHR) under its Programme Grants for Applied Research Programme (Grant Reference Number RP-PG-0707-10124).BACKGROUND: Using surrogate biomarkers for disease progression as endpoints in neuroprotective clinical trials may help differentiate symptomatic effects of potential neuroprotective agents from true disease-modifying effects. A systematic review was undertaken to determine what biomarkers for disease progression in Parkinson's disease (PD) exist. METHODS: MEDLINE and EMBASE (1950-2010) were searched using five search strategies. Abstracts were assessed to identify papers meriting review in full. Studies of participants with idiopathic PD diagnosed by formal criteria or clearly described clinical means were included. We made no restriction on age, disease duration, drug treatment, or study design. We included studies which attempted to draw associations between any tests used to investigate disease progression and any clinical measures of disease progression. The electronic search was validated by hand-searching the two journals from which most included articles came. RESULTS: 183 studies were included: 163 (89%) cross-sectional, 20 (11%) longitudinal. The electronic search strategy had a sensitivity of 71.4% (95% CI 51.1-86.0) and a specificity of 97.1% (95% CI 96.5-97.7). In longitudinal studies median follow-up was 2.0 years (IQR 1.1-3.5). Included studies were generally poor quality--cross-sectional with small numbers of participants, applying excessive inclusion/exclusion criteria, with flawed methodologies and simplistic statistical analyses. CONCLUSION: We found insufficient evidence to recommend the use of any biomarker for disease progression in PD clinical trials, which may simply reflect the poor quality of research in this area. We therefore present a provisional 'roadmap' for conducting future disease progression biomarker studies, and recommend new quality criteria by which future studies may be judged.Publisher PDFPeer reviewe

Semantic distillation: a method for clustering objects by their contextual specificity

Techniques for data-mining, latent semantic analysis, contextual search of databases, etc. have long ago been developed by computer scientists working on information retrieval (IR). Experimental scientists, from all disciplines, having to analyse large collections of raw experimental data (astronomical, physical, biological, etc.) have developed powerful methods for their statistical analysis and for clustering, categorising, and classifying objects. Finally, physicists have developed a theory of quantum measurement, unifying the logical, algebraic, and probabilistic aspects of queries into a single formalism. The purpose of this paper is twofold: first to show that when formulated at an abstract level, problems from IR, from statistical data analysis, and from physical measurement theories are very similar and hence can profitably be cross-fertilised, and, secondly, to propose a novel method of fuzzy hierarchical clustering, termed \textit{semantic distillation} -- strongly inspired from the theory of quantum measurement --, we developed to analyse raw data coming from various types of experiments on DNA arrays. We illustrate the method by analysing DNA arrays experiments and clustering the genes of the array according to their specificity.Comment: Accepted for publication in Studies in Computational Intelligence, Springer-Verla

Endomembranes promote chromosome missegregation by ensheathing misaligned chromosomes

Errors in mitosis that cause chromosome missegregation lead to aneuploidy and micronucleus formation, which are associated with cancer. Accurate segregation requires the alignment of all chromosomes by the mitotic spindle at the metaphase plate, and any misalignment must be corrected before anaphase is triggered. The spindle is situated in a membrane-free “exclusion zone”; beyond this zone, endomembranes (mainly endoplasmic reticulum) are densely packed. We investigated what happens to misaligned chromosomes localized beyond the exclusion zone. Here we show that such chromosomes become ensheathed in multiple layers of endomembranes. Chromosome ensheathing delays mitosis and increases the frequency of chromosome missegregation and micronucleus formation. We use an induced organelle relocalization strategy in live cells to show that clearance of endomembranes allows for the rescue of chromosomes that were destined for missegregation. Our findings indicate that endomembranes promote the missegregation of misaligned chromosomes that are outside the exclusion zone and therefore constitute a risk factor for aneuploidy

Optimized I-values for the use with the Bragg additivity rule and their impact on proton stopping power and range uncertainty

Purpose: Novel imaging modalities estimate patient elemental compositions for particle treatment planning. The mean excitation energy (I-value) is a main contributor to the proton range uncertainty. To minimize their impact on beam range errors and quantify their uncertainties, the currently used I-values proposed in 1982 are revisited. The study aims at proposing a new set of optimized elemental I-values for use with the Bragg additivity rule (BAR) and establishing uncertainties on optimized I-values and the BAR. // Methods: We optimize elemental I-values for the use in compounds based on measured material I-values. We gain a new set of elemental I-values and corresponding uncertainties, based on the experimental uncertainties and our uncertainty model. We evaluate uncertainties on I-values and relative stopping powers (RSP) of 70 human tissues, taking into account statistical correlations between tissues and water. The effect of new I-values on proton beam ranges is quantified using Monte Carlo simulations. // Results: Our elemental I-values describe measured material I-values with higher accuracy than ICRU-recommended I-values (RMSE: 6.17% (ICRU), 5.19% (this work)). Our uncertainty model estimates an uncertainty component from the BAR to 4.42%. Using our elemental I-values, we calculate the I-value of water as 78.73+/-2.89 eV, being consistent with ICRU 90 (78+/-2 eV). We observe uncertainties on tissue I-values between 1.82-3.38 eV, and RSP uncertainties between 0.002%-0.44%. With transport simulations of a proton beam in human tissues, we observe range uncertainties between 0.31% and 0.47%, as compared to current estimates of 1.5%. // Conclusion: We propose a set of elemental I-values well suited for human tissues in combination with the BAR. Our model establishes uncertainties on elemental I-values and the BAR, enabling to quantify uncertainties on tissue I-values, RSP as well as particle range. This work is particularly relevant for Monte Carlo simulations where the interaction probabilities are reconstructed from elemental compositions