Combining techniques for screening and evaluating interaction terms on high-dimensional time-to-event data

BACKGROUND: Molecular data, e.g. arising from microarray technology, is often used for predicting survival probabilities of patients. For multivariate risk prediction models on such high-dimensional data, there are established techniques that combine parameter estimation and variable selection. One big challenge is to incorporate interactions into such prediction models. In this feasibility study, we present building blocks for evaluating and incorporating interactions terms in high-dimensional time-to-event settings, especially for settings in which it is computationally too expensive to check all possible interactions. RESULTS: We use a boosting technique for estimation of effects and the following building blocks for pre-selecting interactions: (1) resampling, (2) random forests and (3) orthogonalization as a data pre-processing step. In a simulation study, the strategy that uses all building blocks is able to detect true main effects and interactions with high sensitivity in different kinds of scenarios. The main challenge are interactions composed of variables that do not represent main effects, but our findings are also promising in this regard. Results on real world data illustrate that effect sizes of interactions frequently may not be large enough to improve prediction performance, even though the interactions are potentially of biological relevance. CONCLUSION: Screening interactions through random forests is feasible and useful, when one is interested in finding relevant two-way interactions. The other building blocks also contribute considerably to an enhanced pre-selection of interactions. We determined the limits of interaction detection in terms of necessary effect sizes. Our study emphasizes the importance of making full use of existing methods in addition to establishing new ones

Common insect pests and diseases on vegetables in the home garden

Home gardeners frequently see insect pests and diseases affecting their vegetables. Usually they would have seen them in previous seasons, and the symptoms look familiar. However, there are occasions, when an unusual pest (not native to Western Australia) can occur. Exotic pests are a concern for the farming community, as they could threaten the agricultural and horticultural industries and increase the price of production and cost to the consumer. This bulletin describes the most common insect pests and diseases in home vegetable gardens.https://researchlibrary.agric.wa.gov.au/bulletins/1194/thumbnail.jp

Evaluation of the hyplex® TBC PCR test for detection of Mycobacterium tuberculosis complex in clinical samples

<p>Abstract</p> <p>Background</p> <p>Tuberculosis (TB) is one of the major public health concerns worldwide. The detection of the pathogen <it>Mycobacterium tuberculosis </it>complex (MTBC) as early as possible has a great impact on the effective control of the spread of the disease. In our study, we evaluated the hyplex^®TBC PCR test (BAG Health Care GmbH), a novel assay using a nucleic acid amplification technique (NAAT) with reverse hybridisation and ELISA read out for the rapid detection of <it>M. tuberculosis </it>directly in clinical samples.</p> <p>Results</p> <p>A total of 581 respiratory and non-respiratory specimens from our pneumological hospital and the National TB Institute of Uzbekistan were used for the evaluation of the PCR assay. Of these, 292 were classified as TB samples and 289 as non-TB samples based on the results of the TB cultures as reference method. The PCR results were initially used to optimise the cut-off value of the hyplex^®TBC test system by means of a ROC analysis. The overall sensitivity of the assay was determined to be 83.1%. In smear-positive TB samples, the sensitivity of the hyplex^®TBC PCR test was estimated to 93.4% versus 45.1% in smear-negative samples. The specificity of the test was 99.25%. Of the two specimens (0.75%) with false-positive PCR results, one yielded a culture positive for non-tuberculous mycobacteria. Based on the assumption of a prevalence of 8% TB positives among the samples in our diagnostic TB laboratory, the positive and negative predictive values were estimated to 90.4% and 98.5%, respectively.</p> <p>Conclusions</p> <p>The hyplex^®TBC PCR test is an accurate NAAT assay for a rapid and reliable detection of <it>M. tuberculosis </it>in various respiratory and non-respiratory specimens. Compared to many other conventional NAAT assays, the hyplex^®TBC PCR test is in a low price segment which makes it an attractive option for developing and emerging countries with high TB burdens.</p

Soil organic carbon in the rocky desert of northern Negev (Israel)

Purpose: So far, the soil organic carbon (SOC) literature is dominated by studies in the humid environments with huge stocks of vulnerable carbon. Limited attention has been given to dryland ecosystems despite being often considered to be highly sensitive to environmental change. Thus, there is insufficient research about the spatial patterns of SOC stocks and the interaction between soil depth, ecohydrology, geomorphic processes, and SOC stocks. This study aimed at identifying the relationship between surface characteristics, vegetation coverage, SOC, and SOC stocks in the arid northern Negev in Israel. Materials and methods: The study site Sede Boker is ideally suited because of well-researched but variable ecohydrology. For this purpose, we sampled five slope sections with different ecohydrologic characteristics (e.g., soil and vegetation) and calculate SOC stocks. To identify controlling factors of SOC stocks on rocky desert slopes, we compared soil properties, vegetation coverage, SOC concentration, and stocks between the five ecohydrologic units. Results and discussion: The results show that in Sede Boker, rocky desert slopes represent a significant SOC pool with a mean SOC stock of 0.58kgCm−2 averaged over the entire study area. The spatial variability of the soil coverage represents a strong control on SOC stocks, which varies between zero in uncovered areas and 1.54kgCm−2 on average in the soil-covered areas. Aspect-driven changes of solar radiation and thus of water availability are the dominant control of vegetation coverage and SOC stock in the study area. Conclusions: The data indicate that dryland soils contain a significant amount of SOC. The SOC varies between the ecohydrologic units, which reflect (1) aspect-driven differences, (2) microscale topography, (3) soil formation, and (4) vegetation coverage, which are of greatest importance for estimating SOC stocks in dryland

Common insect pests and diseases on fruit trees in the home garden

Home gardeners frequently see insect pests and diseases affecting their fruit trees. Usually they would have seen them in previous seasons, so the pests or diseases look familiar. However, there are occasions, when an unusual pest (not native to Western Australia) can occur. These exotic pests are a concern for the farming community, as they could threaten the agricultural and horticultural industries and increase the price of production and the cost to the consumer. This bulletin describes the most common insect pests and diseases on fruit trees in home gardens.https://researchlibrary.agric.wa.gov.au/bulletins/1193/thumbnail.jp

H2020 CABRISS Public Business Plan

The CABRISS project’s Public Business Plan gives an overview of the CABRISS circular PV value chain and connected economic aspects. CABRISS strives to implement a full cradle-to-cradle PV circular economy, to exploit the challenge and opportunity of PV wastes in Europe and globally by developing eco-efficient technologies for recycling and reuse. To date, CABRISS has led to a number of novel concepts for resource recycling and reuse as well as advantages in terms of improved energy payback time and lower carbon footprint. www.spire2030.eu/cabris

Situativity – Textuality – Virtuality

Electronic virtuality is a component of a new level in the evolution of mankind. Who knows the past will form a different future. Therefore it is useful to look at the patterns of development, applying different evaluation criteria. This text focuses on situativity, textuality and virtuality

Limb observations of the Martian atmosphere with Mars Express’ High Resolution Stereo Camera

Introduction: Good knowledge about the aerosol distribution and compositions is essential for the understanding of thermodynamic processes in the Martian atmosphere, which in turn is important for the understanding of the Martian climate and the altitude of the upper boundary of the atmosphere. The last point is of special interest for spacecraft aerobreaking manoeuvres. The Martian atmosphere often shows horizontal layers of haze up to altitudes of about 80 km. These have been described and analysed e.g. by Jaquin et al., 1986, usingViking Orbiter images and by Montmessin et al., 2006, who used SPICAM stellar occultation data. Both showed seasonal and latitudinal changes in the vertical structure of the aerosol distribution and composition. Apart from SPICAM, the High Resolution Stereo Camera (HRSC) is also on board ESA’s robotic spacecraft Mars Express. HRSC was build and is operated by the German Aerospace Center (Neukum et al. 2004; Jaumann et al. 2007). Mars Express is orbiting Mars in an elliptical orbit, with HRSC scanning the surface of Mars, primarily for geological research. In addition to that, HRSC has been used to sample the planetary limb. We examine the HRSC planetary limb data and analyse the seasonal and latitudinal variations of the maximum altitude of the haze layer and of the occurrence of high altitude detached hazes. We make some comparisons with earlier work. In contrast to the SPICAM instrument, HRSC observes the atmosphere during daytime, which makes it possible to compare night and daytime observations. The HRSC Limb Data: HRSC is a push broom scanner with nine line sensors pointing in different directions to facilitate stereoscopic imaging. Four of the sensors have colour filters at 440 nm, 530 nm, 750 nm and 970 nm, respectively. The five other sensors all have filters centred at 650 nm. These panchromatic filters have a much wider bandpass than the four colour filters. The surface observations which are HRSC’s main purpose, are usually take while the spacecraft is nadirtracking near pericentre. Limb observations, however, are mostly made with a pointing of the spacecraft being inertially fixxed in celestial space. This leaves only a small time window to make observations of the limb during descent or ascent. Therefore, usually only a few of the nine sensors can be used for the limb observation. Due to the motion of the spacecraft, the individual image lines are taken at different geographical locations and altitudes. The position of each image pixel above the limb has to be calculated from the spacecraft positioning information (Scholten, pers. comm.). The typical difference in altitude between two neighbouring pixels is between a couple of dozen metres and 150 m. HRSC has been observing the limb occasionally throughout the mission since 2004. So far the northern hemisphere and especially the north polar region, were particularly well covered (Figure 1 and 2). In Figure 2, we give an overview of the available data, sorted by season (LS) and latitude. The channel in which the observations have been made is colourcoded. Most observations were made with the panchromatic channels. There are also many observations with the blue and green sensors and only a few were made in the red and infra red channels. We find the best data coverage in northern spring in the northern most latitudes. For obvious reasons, we do not have any data during polar nights. For most of our actual analysis we sample the five central pixels of the sensor lines. This allows for minimal horizontal averaging. Analysis: As an example, Fig. 3 shows images and profiles for the blue, nadir, and green channels from orbit 6104. Al three images show a continuously bright limb haze until an altitude of about 20 km. At higher altitudes the limb haze becomes darker and stratified consistent with the limb profiles described by Jacquin et al., 1986. As Mars Express progresses along its orbit, the limb observations are made at different locations above the surface. The locations of the three profiles in Fig. 3 are still in close proximity of each other, in fact they overlap, but none the less they show different vertical aerosol distributions. Beginning above the North Polar cap and going southward, we observe less reflectivity above 20 km and more reflectivity below 20 km, hinting at different compositions or amounts of aerosols. It is not possible to obtain and compare profiles at the same location and at the same time with different sensors, but still, averages of profiles over place and season can provide us with information about typical atmospheric conditions. In Fig. 4 we show spectra from the average profiles at three different latitudinal bands between 70�N–90�N, 30�S–30�N, and 90�S– 70�S, on the left, centre, and right, respectively. The different symbols and colours represent the different altitudes at which the spectra were sampled. The size of the symbol increases with the number of averaged profiles. There are very few observations above the South Polar region (compare Fig. 1). In the North (and South) Polar region there is almost no signal above 30 km altitude, while around the equator the limb haze remains bright until altitudes of about 60 km. At the poles, the spectrum at 10 km is reddish. At higher altitudes the spectrum gets whiter, indicating smaller particles or higher ice content. At the low latitudes the spectra are reddish up to 40 km. At 60 km we see a more or less white spectrum. Figure 5 shows the maximum altitude of the aerosols as seen by HRSC, depending on season. During aphelion (LS � 70�) the maximum altitude of the aerosols that are visible with HRSC is around 40 km. During perihelion (LS � 250�) the maximum altitude is around 70 km. Discussion: Figure 1 and 2 show that there are plenty of visual and near infra red HRSC observations of the Martian limb available. These show aerosol distributions that change with season and latitude (Fig. 3 and 4). The plots in Fig. 4 show the spectra of the average limb profiles at several altitudes for three latitudinal bands. Two important distinctions can be made between the equatorial and the polar regions. First, the altitude at which aerosol occur is higher in the equatorial region and second, the composition of the aerosols at different altitudes is different. While the spectrum is white around 20 km altitude above the north pole, it is red at the low latitudes. The seasonal variations of maximum altitude of the aerosols is in good agreement with Jaquin et al. (1986) and with Montmessin et al. (2006). The similarity between Montmessin’s results and ours is likely to be due to the large annual variation of atmospheric dust load compared to the diurnal cycle. A much closer look at the data, is forseen to analyse the daily variation of aerosols in the Martian atmosphere. The CO2 and waterice aerosols are more likely to change their vertical distribution (above the planetary boundary layer) between day and night than the mineral (dust) aerosols. Spectral information would help to discriminate between these components. HRSC can not provide it, because the observation for the different filters take place at different locations and times (see Fig. 3). An alternative is to fit aerosol models to the inverted profiles. Currently, we are preparing this work. Mars Express’ HRSC limb data present a valuable opportunity to analyse Mars daytime atmospheric dust at a high vertical resolution. This work gives a short overview of the available data and analyses some seasonal and latitudinal properties

Neural correlates of the perception of dynamic versus static facial expressions of emotion

Aim: This study investigated brain areas involved in the perception of dynamic facial expressions of emotion