Optimal designs for rational function regression

We consider optimal non-sequential designs for a large class of (linear and nonlinear) regression models involving polynomials and rational functions with heteroscedastic noise also given by a polynomial or rational weight function. The proposed method treats D-, E-, A-, and $\Phi_p$-optimal designs in a unified manner, and generates a polynomial whose zeros are the support points of the optimal approximate design, generalizing a number of previously known results of the same flavor. The method is based on a mathematical optimization model that can incorporate various criteria of optimality and can be solved efficiently by well established numerical optimization methods. In contrast to previous optimization-based methods proposed for similar design problems, it also has theoretical guarantee of its algorithmic efficiency; in fact, the running times of all numerical examples considered in the paper are negligible. The stability of the method is demonstrated in an example involving high degree polynomials. After discussing linear models, applications for finding locally optimal designs for nonlinear regression models involving rational functions are presented, then extensions to robust regression designs, and trigonometric regression are shown. As a corollary, an upper bound on the size of the support set of the minimally-supported optimal designs is also found. The method is of considerable practical importance, with the potential for instance to impact design software development. Further study of the optimality conditions of the main optimization model might also yield new theoretical insights.Comment: 25 pages. Previous version updated with more details in the theory and additional example

Metagenomics-based proficiency test of smoked salmon spiked with a mock community

An inter-laboratory proficiency test was organized to assess the ability of participants to perform shotgun metagenomic sequencing of cold smoked salmon, experimentally spiked with a mock community composed of six bacteria, one parasite, one yeast, one DNA, and two RNA viruses. Each participant applied its in-house wet-lab workflow(s) to obtain the metagenomic dataset(s), which were then collected and analyzed using MG-RAST. A total of 27 datasets were analyzed. Sample pre-processing, DNA extraction protocol, library preparation kit, and sequencing platform, influenced the abundance of specific microorganisms of the mock community. Our results highlight that despite differences in wet-lab protocols, the reads corresponding to the mock community members spiked in the cold smoked salmon, were both detected and quantified in terms of relative abundance, in the metagenomic datasets, proving the suitability of shotgun metagenomic sequencing as a genomic tool to detect microorganisms belonging to different domains in the same food matrix. The implementation of standardized wet-lab protocols would highly facilitate the comparability of shotgun metagenomic sequencing dataset across laboratories and sectors. Moreover, there is a need for clearly defining a sequencing reads threshold, to consider pathogens as detected or undetected in a food sample

Disease knowledge after an educational program in patients with GERD – a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>Patient education has proved beneficial in several but not all chronic disease. Inconsistent findings may rely on varying educational effects of various programs and differential effects on subgroups of patients. Patients' increase in disease knowledge may serve as a feedback to the educator on how well the education program works – but may not be associated to relevant clinical outcomes like quality of life (QoL). This study aimed to investigate the effects of a group based education program for patients with gastroesophageal reflux disease (GERD) on disease knowledge and the association between knowledge and QoL.</p> <p>Methods</p> <p>Patients with GERD were randomly allocated to education (102 patients) or control (109 patients). The education program was designed as a structured dialogue conveying information about pathophysiology, pharmacological and non-pharmacological treatment of GERD, patients' rights and use of healthcare. Outcomes were a 24 item knowledge test on GERD (score 0 – 24) 2 and 12 months after the educational program and disease specific and general QoL (Digestive symptoms and disease impact, DSIQ, and General Health Questionnaire, GHQ).</p> <p>Results</p> <p>Patients allocated to education achieved higher knowledge test scores than controls at 2 months (17.0 vs. 13.1, p < 0.001) and at 12 months (17.1 vs. 14.0, p < 0.001) follow-up. Knowledge test score was positively associated with having completed advanced school and inversely related to psychiatric illness and poor QoL as perceived by the patients at the time of inclusion. Overall, changes in knowledge test score were not associated with change in QoL.</p> <p>Conclusion</p> <p>A group based education program for patients with GERD designed as a structured dialogue increased patients' disease knowledge, which was retained after 1 year. Changes in GERD-knowledge were not associated with change in QoL.</p> <p>Trial registration</p> <p>ClinicalTrials.gov: NCT0061850</p

The Arabidopsis RNA Polymerase II Carboxyl Terminal Domain (CTD) Phosphatase-Like1 (CPL1) is a biotic stress susceptibility gene

© 2018, The Author(s). Crop breeding for improved disease resistance may be achieved through the manipulation of host susceptibility genes. Previously we identified multiple Arabidopsis mutants known as enhanced stress response1 (esr1) that have defects in a KH-domain RNA-binding protein and conferred increased resistance to the root fungal pathogen Fusarium oxysporum. Here, screening the same mutagenized population we discovered two further enhanced stress response mutants that also conferred enhanced resistance to F. oxysporum. These mutants also have enhanced resistance to a leaf fungal pathogen (Alternaria brassicicola) and an aphid pest (Myzus persicae), but not to the bacterial leaf pathogen Pseudomonas syringae. The causal alleles in these mutants were found to have defects in the ESR1 interacting protein partner RNA Polymerase II Carboxyl Terminal Domain (CTD) Phosphatase-Like1 (CPL1) and subsequently given the allele symbols cpl1-7 and cpl1-8. These results define a new role for CPL1 as a pathogen and pest susceptibility gene. Global transcriptome analysis and oxidative stress assays showed these cpl1 mutants have increased tolerance to oxidative stress. In particular, components of biotic stress responsive pathways were enriched in cpl1 over wild-type up-regulated gene expression datasets including genes related to defence, heat shock proteins and oxidative stress/redox state processes

Search for Colour Reconnection Effects in e+e- -> W+W- -> hadrons through Particle-Flow Studies at LEP

A search for colour reconnection effects in hadronic decays of W pairs is performed with the L3 detector at centre-of-mass energies between 189 and 209 GeV. The analysis is based on the study of the particle flow between jets associated to the same W boson and between two different W bosons in qqqq events. The ratio of particle yields in the different interjet regions is found to be sensitive to colour reconnection effects implemented in some hadronisation models. The data are compared to different models with and without such effects. An extreme scenario of colour reconnection is ruled out

Event shapes in e+e- annihilation and deep inelastic scattering

This article reviews the status of event-shape studies in e+e- annihilation and DIS. It includes discussions of perturbative calculations, of various approaches to modelling hadronisation and of comparisons to data.Comment: Invited topical review for J.Phys.G; 40 pages; revised version corrects some nomenclatur

Inclusive Jet Production in Two-Photon Collisions at LEP

Inclusive jet production, e+e- -> e+e- \ee$ jet X, is studied using 560/pb of data collected at LEP with the L3 detector at centre-of-mass energies between 189 and 209 GeV. The inclusive differential cross section is measured using a k_t jet algorithm as a function of the jet transverse momentum, pt, in the range 3<pt<50 GeV for a pseudorapidity, eta, in the range -1<eta<1. This cross section is well represented by a power law. For high pt, the measured cross section is significantly higher than the NLO QCD predictions, as already observed for inclusive charged and neutral pion production

The Spider Effect: Morphological and Orienting Classification of Microglia in Response to Stimuli in Vivo

The different morphological stages of microglial activation have not yet been described in detail. We transected the olfactory bulb of rats and examined the activation of the microglial system histologically. Six stages of bidirectional microglial activation (A) and deactivation (R) were observed: from stage 1A to 6A, the cell body size increased, the cell process number decreased, and the cell processes retracted and thickened, orienting toward the direction of the injury site; until stage 6A, when all processes disappeared. In contrast, in deactivation stages 6R to 1R, the microglia returned to the original site exhibiting a stepwise retransformation to the original morphology. Thin highly branched processes re-formed in stage 1R, similar to those in stage 1A. This reverse transformation mirrored the forward transformation except in stages 6R to 1R: cells showed multiple nuclei which were slowly absorbed. Our findings support a morphologically defined stepwise activation and deactivation of microglia cells

Search for squarks and gluinos in events with isolated leptons, jets and missing transverse momentum at s√=8 TeV with the ATLAS detector

The results of a search for supersymmetry in final states containing at least one isolated lepton (electron or muon), jets and large missing transverse momentum with the ATLAS detector at the Large Hadron Collider are reported. The search is based on proton-proton collision data at a centre-of-mass energy s√=8 TeV collected in 2012, corresponding to an integrated luminosity of 20 fb−1. No significant excess above the Standard Model expectation is observed. Limits are set on supersymmetric particle masses for various supersymmetric models. Depending on the model, the search excludes gluino masses up to 1.32 TeV and squark masses up to 840 GeV. Limits are also set on the parameters of a minimal universal extra dimension model, excluding a compactification radius of 1/R c = 950 GeV for a cut-off scale times radius (ΛR c) of approximately 30