Estimating the population health impact of a multi-cancer early detection genomic blood test to complement existing screening in the US and UK

Background: Multi-cancer early detection (MCED) next-generation-sequencing blood tests represent a potential paradigm shift in screening. Methods: We estimated the impact of screening in the US and UK. We used country-specific parameters for uptake, and test-specific sensitivity and false-positive rates for current screening: breast, colorectal, cervical and lung (US only) cancers. For the MCED test, we used cancer-specific sensitivities by stage. Outcomes included the true-positive:false-positive (TP:FP) ratio; and the cost of diagnostic investigations among screen positives, per cancer detected (Diagcost). Outcomes were estimated for recommended screening only, and then when giving the MCED test to anyone without cancer detected by current screening plus similarly aged adults ineligible for recommended screening. Results: In the US, current screening detects an estimated 189,498 breast, cervical, colorectal and lung cancers. An MCED test with 25–100% uptake detects an additional 105,526–422,105 cancers (multiple types). The estimated TP:FP (Diagcost) was 1.43 ($89,042) with current screening but only 1:1.8 ($7060) using an MCED test. For the UK the corresponding estimates were 1:18 (£10,452) for current screening, and 1:1.6 (£2175) using an MCED test. Conclusions: Adding an MCED blood test to recommended screening can potentially be an efficient strategy. Ongoing randomised studies are required for full efficacy and cost-effectiveness evaluations

MFV Reductions of MSSM Parameter Space

The 100+ free parameters of the minimal supersymmetric standard model (MSSM) make it computationally difficult to compare systematically with data, motivating the study of specific parameter reductions such as the cMSSM and pMSSM. Here we instead study the reductions of parameter space implied by using minimal flavour violation (MFV) to organise the R-parity conserving MSSM, with a view towards systematically building in constraints on flavour-violating physics. Within this framework the space of parameters is reduced by expanding soft supersymmetry-breaking terms in powers of the Cabibbo angle, leading to a 24-, 30- or 42-parameter framework (which we call MSSM-24, MSSM-30, and MSSM-42 respectively), depending on the order kept in the expansion. We provide a Bayesian global fit to data of the MSSM-30 parameter set to show that this is manageable with current tools. We compare the MFV reductions to the 19-parameter pMSSM choice and show that the pMSSM is not contained as a subset. The MSSM-30 analysis favours a relatively lighter TeV-scale pseudoscalar Higgs boson and $\tan \beta \sim 10$ with multi-TeV sparticles.Comment: 2nd version, minor comments and references added, accepted for publication in JHE

Incremental dimension reduction of tensors with random index

We present an incremental, scalable and efficient dimension reduction technique for tensors that is based on sparse random linear coding. Data is stored in a compactified representation with fixed size, which makes memory requirements low and predictable. Component encoding and decoding are performed on-line without computationally expensive re-analysis of the data set. The range of tensor indices can be extended dynamically without modifying the component representation. This idea originates from a mathematical model of semantic memory and a method known as random indexing in natural language processing. We generalize the random-indexing algorithm to tensors and present signal-to-noise-ratio simulations for representations of vectors and matrices. We present also a mathematical analysis of the approximate orthogonality of high-dimensional ternary vectors, which is a property that underpins this and other similar random-coding approaches to dimension reduction. To further demonstrate the properties of random indexing we present results of a synonym identification task. The method presented here has some similarities with random projection and Tucker decomposition, but it performs well at high dimensionality only (n>10^3). Random indexing is useful for a range of complex practical problems, e.g., in natural language processing, data mining, pattern recognition, event detection, graph searching and search engines. Prototype software is provided. It supports encoding and decoding of tensors of order >= 1 in a unified framework, i.e., vectors, matrices and higher order tensors.Comment: 36 pages, 9 figure

Experimental validation of a new biphasic model of the contact mechanics of the porcine hip

Hip models that incorporate the biphasic behaviour of articular cartilage can improve understanding of the joint function, pathology of joint degeneration and effect of potential interventions. The aim of this study was to develop a specimen-specific biphasic finite element model of a porcine acetabulum incorporating a biphasic representation of the articular cartilage and to validate the model predictions against direct experimental measurements of the contact area in the same specimen. Additionally, the effect of using a different tension-compression behaviour for the solid phase of the articular cartilage was investigated. The model represented different radial clearances and load magnitudes. The comparison of the finite element predictions and the experimental measurement showed good agreement in the location, size and shape of the contact area, and a similar trend in the relationship between contact area and load was observed. There was, however, a deviation of over 30% in the magnitude of the contact area, which might be due to experimental limitations or to simplifications in the material constitutive relationships used. In comparison with the isotropic solid phase model, the tension-compression solid phase model had better agreement with the experimental observations. The findings provide some confidence that the new biphasic methodology for modelling the cartilage is able to predict the contact mechanics of the hip joint. The validation provides a foundation for future subject-specific studies of the human hip using a biphasic cartilage model

On correlation functions of operators dual to classical spinning string states

We explore how to compute, classically at strong coupling, correlation functions of local operators corresponding to classical spinning string states. The picture we obtain is of `fattened' Witten diagrams, the evaluation of which turns out to be surprisingly subtle and requires a modification of the naive classical action due to a necessary projection onto appropriate wave functions. We examine string solutions which compute the simplest case of a two-point function and reproduce the right scaling with the anomalous dimensions corresponding to the energies of the associated spinning string solutions. We also describe, under some simplifying assumptions, how the spacetime dependence of a conformal three-point correlation function arises in this setup.Comment: 27 pages, 3 figures; v2: references and comments added

The safety evaluation of food flavoring substances: the role of genotoxicity studies

The Flavor and Extract Manufacturers Association (FEMA) Expert Panel relies on the weight of evidence from all available data in the safety evaluation of flavoring substances. This process includes data from genotoxicity studies designed to assess the potential of a chemical agent to react with DNA or otherwise cause changes to DNA, either in vitro or in vivo. The Panel has reviewed a large number of in vitro and in vivo genotoxicity studies during the course of its ongoing safety evaluations of flavorings. The adherence of genotoxicity studies to standardized protocols and guidelines, the biological relevance of the results from those studies, and the human relevance of these studies are all important considerations in assessing whether the results raise specific concerns for genotoxic potential. The Panel evaluates genotoxicity studies not only for evidence of genotoxicity hazard, but also for the probability of risk to the consumer in the context of exposure from their use as flavoring substances. The majority of flavoring substances have given no indication of genotoxic potential in studies evaluated by the FEMA Expert Panel. Examples illustrating the assessment of genotoxicity data for flavoring substances and the consideration of the factors noted above are provided. The weight of evidence approach adopted by the FEMA Expert Panel leads to a rational assessment of risk associated with consumer intake of flavoring substances under the conditions of use

Necessary and sufficient conditions of solution uniqueness in ℓ1\ell_1 minimization

This paper shows that the solutions to various convex $\ell_1$ minimization problems are \emph{unique} if and only if a common set of conditions are satisfied. This result applies broadly to the basis pursuit model, basis pursuit denoising model, Lasso model, as well as other $\ell_1$ models that either minimize $f(Ax-b)$ or impose the constraint $f(Ax-b)\leq\sigma$, where $f$ is a strictly convex function. For these models, this paper proves that, given a solution $x^*$ and defining I=\supp(x^*) and s=\sign(x^*_I), $x^*$ is the unique solution if and only if $A_I$ has full column rank and there exists $y$ such that $A_I^Ty=s$ and $|a_i^Ty|_\infty<1$ for $i\not\in I$. This condition is previously known to be sufficient for the basis pursuit model to have a unique solution supported on $I$. Indeed, it is also necessary, and applies to a variety of other $\ell_1$ models. The paper also discusses ways to recognize unique solutions and verify the uniqueness conditions numerically.Comment: 6 pages; revised version; submitte

Safety evaluation of substituted thiophenes used as flavoring ingredients.

This publication is the second in a series by the Expert Panel of the Flavor and Extract Manufacturers Association summarizing the conclusions of its third systematic re-evaluation of the safety of flavorings previously considered to be generally recognized as safe (GRAS) under conditions of intended use. Re-evaluation of GRAS status for flavorings is based on updated considerations of exposure, structural analogy, metabolism, pharmacokinetics and toxicology and includes a comprehensive review of the scientific information on the flavorings and structurally related substances. Of the 12 substituted thiophenes reviewed here, 11 were reaffirmed as GRAS based on their rapid absorption, metabolism and excretion in humans and animals; the low estimated dietary exposure from flavor use; the wide margins of safety between the conservative estimates of intake and the no-observed-adverse effect levels; and the lack of significant genotoxic and mutagenic potential. For one of the substituted thiophenes, 3-acetyl-2,5-dimethylthiophene, it was concluded that more detailed exposure information, comparative metabolism studies and comprehensive toxicity data, including an in-depth evaluation of the mechanism of action for any adverse effects observed, are required for continuation of its FEMA GRAS™ status. In the absence of these data, the compound was removed from the FEMA GRAS list

Reliability of Eye Tracking and Pupillometry Measures in Individuals with Fragile X Syndrome

Recent insight into the underlying molecular and cellular mechanisms of fragile X syndrome (FXS) has led to the proposal and development of new pharmaceutical treatment strategies, and the initiation of clinical trials aimed at correcting core symptoms of the developmental disorder. Consequently, there is an urgent and critical need for outcome measures that are valid for quantifying specific symptoms of FXS and that are consistent across time. We used eye tracking to evaluate test–retest reliability of gaze and pupillometry measures in individuals with FXS and we demonstrate that these measures are viable options for assessing treatment-specific outcomes related to a core behavioral feature of the disorder