An AUC-based Permutation Variable Importance Measure for Random Forests

The random forest (RF) method is a commonly used tool for classification with high dimensional data as well as for ranking candidate predictors based on the so-called random forest variable importance measures (VIMs). However the classification performance of RF is known to be suboptimal in case of strongly unbalanced data, i.e. data where response class sizes differ considerably. Suggestions were made to obtain better classification performance based either on sampling procedures or on cost sensitivity analyses. However to our knowledge the performance of the VIMs has not yet been examined in the case of unbalanced response classes. In this paper we explore the performance of the permutation VIM for unbalanced data settings and introduce an alternative permutation VIM based on the area under the curve (AUC) that is expected to be more robust towards class imbalance. We investigated the performance of the standard permutation VIM and of our novel AUC-based permutation VIM for different class imbalance levels using simulated data and real data. The results suggest that the standard permutation VIM loses its ability to discriminate between associated predictors and predictors not associated with the response for increasing class imbalance. It is outperformed by our new AUC-based permutation VIM for unbalanced data settings, while the performance of both VIMs is very similar in the case of balanced classes. The new AUC-based VIM is implemented in the R package party for the unbiased RF variant based on conditional inference trees. The codes implementing our study are available from the companion website: http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/070_drittmittel/janitza/index.html

Variational bound on energy dissipation in turbulent shear flow

We present numerical solutions to the extended Doering-Constantin variational principle for upper bounds on the energy dissipation rate in plane Couette flow, bridging the entire range from low to asymptotically high Reynolds numbers. Our variational bound exhibits structure, namely a pronounced minimum at intermediate Reynolds numbers, and recovers the Busse bound in the asymptotic regime. The most notable feature is a bifurcation of the minimizing wavenumbers, giving rise to simple scaling of the optimized variational parameters, and of the upper bound, with the Reynolds number.Comment: 4 pages, RevTeX, 5 postscript figures are available as one .tar.gz file from [email protected]

Variational bound on energy dissipation in plane Couette flow

We present numerical solutions to the extended Doering-Constantin variational principle for upper bounds on the energy dissipation rate in turbulent plane Couette flow. Using the compound matrix technique in order to reformulate this principle's spectral constraint, we derive a system of equations that is amenable to numerical treatment in the entire range from low to asymptotically high Reynolds numbers. Our variational bound exhibits a minimum at intermediate Reynolds numbers, and reproduces the Busse bound in the asymptotic regime. As a consequence of a bifurcation of the minimizing wavenumbers, there exist two length scales that determine the optimal upper bound: the effective width of the variational profile's boundary segments, and the extension of their flat interior part.Comment: 22 pages, RevTeX, 11 postscript figures are available as one uuencoded .tar.gz file from [email protected]

Zambian Peer Educators for HIV Self-Testing (ZEST) study: rationale and design of a cluster randomised trial of HIV self-testing among female sex workers in Zambia

BACKGROUND: HIV testing and knowledge of status are starting points for HIV treatment and prevention interventions. Among female sex workers (FSWs), HIV testing and status knowledge remain far from universal. HIV self-testing (HIVST) is an alternative to existing testing services for FSWs, but little evidence exists how it can be effectively and safely implemented. Here, we describe the rationale and design of a cluster randomised trial designed to inform implementation and scale-up of HIVST programmes for FSWs in Zambia. METHODS: The Zambian Peer Educators for HIV Self-Testing (ZEST) study is a 3-arm cluster randomised trial taking place in 3 towns in Zambia. Participants (N=900) are eligible if they are women who have exchanged sex for money or goods in the previous 1 month, are HIV negative or status unknown, have not tested for HIV in the previous 3 months, and are at least 18 years old. Participants are recruited by peer educators working in their communities. Participants are randomised to 1 of 3 arms: (1) direct distribution (in which they receive an HIVST from the peer educator directly); (2) fixed distribution (in which they receive a coupon with which to collect the HIVST from a drug store or health post) or (3) standard of care (referral to existing HIV testing services only, without any offer of HIVST). Participants are followed at 1 and 4 months following distribution of the first HIVST. The primary end point is HIV testing in the past month measured at the 1-month and 4-month visits. ETHICS AND DISSEMINATION: This study was approved by the Institutional Review Boards at the Harvard T.H. Chan School of Public Health in Boston, USA and ERES Converge in Lusaka, Zambia. The findings of this trial will be presented at local, regional and international meetings and submitted to peer-reviewed journals for publication. TRIAL REGISTRATION NUMBER: Pre-results; NCT02827240

In vitro analysis, an accurate tool to estimate dry matter digestibility in rabbits. Intra- and inter- laboratory variability

[EN] The aim of the present study was to determine the intra- and inter-laboratory variability of an enzymatic system of in vitro analysis for estimating dry matter (DM) digestibility in rabbits and validating the predicted nutritive value of 4 complete diets and 4 raw materials during three different periods of time. Chemical composition, DM digestibility and digestible energy (diets only) were known. In vitro DM digestibility (DMdinv) of all samples was determined by 4 laboratories (triplicate analysis) at different times with an interval of one month between analyses. DMdinv variability and chemical parameters were measured in terms of repeatability (SR: intra-series variability within each laboratory), reproducibility (SL: intra-series variability among laboratories) and reliability (SF: variability through time within each laboratory). Both the laboratory and sample affected DMdinv values (P<0.001). The period of time also had a significant effect (P=0.002) on mean DMdinv values (67.4, 66.8 and 67.0% for the 1st, 2nd and 3rd month, respectively). Significant laboratory x sample, time x laboratory and time x sample interaction effects were also observed. Repeatability, reproducibility and reliability values for the diets were better than those obtained for the raw materials (by 2.0, 1.9 and 2.4 times, respectively). Repeatability values were also better than the values obtained for reproducibility and reliability (by 2.2 and 3.6 times, respectively). Repeatability and reproducibility values were consistently worse for raw materials than for complete diets (by 1.5, 4, 2.9 and 1.3, 4.3, 2.8 times for SR and SL in period 1, period 2 and period 3, respectively), and were also worse in period 1 with respect to the other two periods (by 2.1 and 2.2 times for SR and SL, respectively). Finally, the in vitro method always showed better coefficients of variation of repeatability (CVR) and reproducibility (CVL) than those of the chemical parameters frequently used as predictors of dietary energy value (acid detergent fibre and crude fibre) (1.73 vs. 2.41 and 3.88 for CVR and 3.24 vs. 3.70 and 5.17 for CVL, respectively). In conclusion, the proposed in vitro methodology showed adequate repeatability and reproducibility, being suitable for predictive purposes.This research was supported by ERAFE project CE-FAIR (3-CT96-1651)Carabaño, R.; Nicodemus, N.; García, J.; Xiccato, G.; Trocino, A.; Pascual Amorós, JJ.; Falcão-E-Cunha, L.... (2008). In vitro analysis, an accurate tool to estimate dry matter digestibility in rabbits. Intra- and inter- laboratory variability. World Rabbit Science. 16(4). doi:10.4995/wrs.2008.614SWORD16

The Optical Design and Characterization of the Microwave Anisotropy Probe

The primary goal of the MAP satellite, now in orbit, is to make high fidelity polarization sensitive maps of the full sky in five frequency bands between 20 and 100 GHz. From these maps we will characterize the properties of the cosmic microwave background (CMB) anisotropy and Galactic and extragalactic emission on angular scales ranging from the effective beam size, <0.23 degree, to the full sky. MAP is a differential microwave radiometer. Two back-to-back shaped offset Gregorian telescopes feed two mirror symmetric arrays of ten corrugated feeds. We describe the prelaunch design and characterization of the optical system, compare the optical models to the measurements, and consider multiple possible sources of systematic error.Comment: ApJ in press; 22 pages with 11 low resolution figures; paper is available with higher quality figures at http://map.gsfc.nasa.gov/m_mm/tp_links.htm

Efecto del nivel de fibra soluble y de la suplementación con celobiosa sobre los rendimientos productivos en conejos en cebo

El objetivo de este trabajo fue estudiar el efecto de la fibra soluble y la suplementación de con celobiosa en agua sobre los rencimientos productivos del gazapo tras el destete. A los gazapos se les suministró dos piensos que difirieron en el nivel de fibra soluble (7,7 vs.15,2%, sobre MS) y tres concentraciones de celobiosa en agua (0,0,75 y 1,5 fl). Los piensos y la celobiosa se suministraron a gazapos desde el destete (34 d edad 781±88 g, 44 gazapos/pienso) hasta los 48 d edad

Wall roughness induces asymptotic ultimate turbulence

Turbulence is omnipresent in Nature and technology, governing the transport of heat, mass, and momentum on multiple scales. For real-world applications of wall-bounded turbulence, the underlying surfaces are virtually always rough; yet characterizing and understanding the effects of wall roughness for turbulence remains a challenge, especially for rotating and thermally driven turbulence. By combining extensive experiments and numerical simulations, here, taking as example the paradigmatic Taylor-Couette system (the closed flow between two independently rotating coaxial cylinders), we show how wall roughness greatly enhances the overall transport properties and the corresponding scaling exponents. If only one of the walls is rough, we reveal that the bulk velocity is slaved to the rough side, due to the much stronger coupling to that wall by the detaching flow structures. If both walls are rough, the viscosity dependence is thoroughly eliminated in the boundary layers and we thus achieve asymptotic ultimate turbulence, i.e. the upper limit of transport, whose existence had been predicted by Robert Kraichnan in 1962 (Phys. Fluids {\bf 5}, 1374 (1962)) and in which the scalings laws can be extrapolated to arbitrarily large Reynolds numbers

People of the British Isles: preliminary analysis of genotypes and surnames in a UK control population

There is a great deal of interest in fine scale population structure in the UK, both as a signature of historical immigration events and because of the effect population structure may have on disease association studies. Although population structure appears to have a minor impact on the current generation of genome-wide association studies, it is likely to play a significant part in the next generation of studies designed to search for rare variants. A powerful way of detecting such structure is to control and document carefully the provenance of the samples involved. Here we describe the collection of a cohort of rural UK samples (The People of the British Isles), aimed at providing a well-characterised UK control population that can be used as a resource by the research community as well as providing fine scale genetic information on the British population. So far, some 4,000 samples have been collected, the majority of which fit the criteria of coming from a rural area and having all four grandparents from approximately the same area. Analysis of the first 3,865 samples that have been geocoded indicates that 75% have a mean distance between grandparental places of birth of 37.3km, and that about 70% of grandparental places of birth can be classed as rural. Preliminary genotyping of 1,057 samples demonstrates the value of these samples for investigating fine scale population structure within the UK, and shows how this can be enhanced by the use of surnames

Epigenome-wide analysis links SMAD3 methylation at birth to asthma in children of asthmatic mothers

Background The timing and mechanisms of asthma inception remain imprecisely defined. Although epigenetic mechanisms likely contribute to asthma pathogenesis, little is known about their role in asthma inception. Objective We sought to assess whether the trajectory to asthma begins already at birth and whether epigenetic mechanisms, specifically DNA methylation, contribute to asthma inception. Methods We used the Methylated CpG Island Recovery Assay chip to survey DNA methylation in cord blood mononuclear cells from 36 children (18 nonasthmatic and 18 asthmatic subjects by age 9 years) from the Infant Immune Study (IIS), an unselected birth cohort closely monitored for asthma for a decade. SMAD3 methylation in IIS (n = 60) and in 2 replication cohorts (the Manchester Asthma and Allergy Study [n = 30] and the Childhood Origins of Asthma Study [n = 28]) was analyzed by using bisulfite sequencing or Illumina 450K arrays. Cord blood mononuclear cell–derived IL-1β levels were measured by means of ELISA. Results Neonatal immune cells harbored 589 differentially methylated regions that distinguished IIS children who did and did not have asthma by age 9 years. In all 3 cohorts methylation in SMAD3, the most connected node within the network of asthma-associated, differentially methylated regions, was selectively increased in asthmatic children of asthmatic mothers and was associated with childhood asthma risk. Moreover, SMAD3 methylation in IIS neonates with maternal asthma was strongly and positively associated with neonatal production of IL-1β, an innate inflammatory mediator. Conclusions The trajectory to childhood asthma begins at birth and involves epigenetic modifications in immunoregulatory and proinflammatory pathways. Maternal asthma influences epigenetic mechanisms that contribute to the inception of this trajectory