Classification of Quantitative Light-Induced Fluorescence Images Using Convolutional Neural Network

Images are an important data source for diagnosis and treatment of oral diseases. The manual classification of images may lead to misdiagnosis or mistreatment due to subjective errors. In this paper an image classification model based on Convolutional Neural Network is applied to Quantitative Light-induced Fluorescence images. The deep neural network outperforms other state of the art shallow classification models in predicting labels derived from three different dental plaque assessment scores. The model directly benefits from multi-channel representation of the images resulting in improved performance when, besides the Red colour channel, additional Green and Blue colour channels are used.Comment: Full version of ICANN 2017 submissio

Effects of school quality, school citizenship policy, and student body composition on the acquisition of citizenship competences in the final year of primary education

This study examines the effects of general educational quality of schools, school citizenship policy, and ethnic homogeneity of the student body on the acquisition of citizenship competences in the final year of primary education. The theoretical framework is based on developmental, psychological, and sociological studies into effects of social context on educational outcomes and research into effective schools. The effects of school quality, school policy, and student population were analysed using 2-level (students, school) multilevel models. The results show that differences in citizenship competences between students and schools are mainly explained by factors at student level. Although the school also appeared to play a role, the school variables used in the analysis did not offer sufficient explanation for these differences. In order to further investigate the relationship between school factors and students’ citizenship, more insight is needed into characteristics of citizenship practices of schools

Why are plant–soil feedbacks so unpredictable, and what to do about it?

1.The study of feedbacks between plants and soils (plant‐soil feedbacks; PSFs) is receiving increased attention. However, PSFs have been mostly studied in isolation of abiotic and biotic drivers that could affect their strength and direction. This is problematic because it has led to limited predictive power of PSFs in ‘the real world’, leaving large knowledge gaps in our ability to predict how PSFs contribute to ecosystem processes and functions. 2.Here, we present a synthetic framework to elucidate how abiotic and biotic drivers affect PSFs. We focus on two key abiotic drivers (temperature and soil moisture) and two key biotic drivers (aboveground plant consumers and belowground top‐down control of pathogens and mutualists). We focus on these factors because they are known drivers of plants and soil organisms and the ecosystem processes they control, and hence would be expected to strongly influence PSFs. 3.Our framework describes the proposed mechanisms behind these drivers and explores their effects on PSFs. We demonstrate the impacts of these drivers using the fast‐ to slow‐growing plant economics spectrum. We use this well‐established paradigm because plants on opposite ends of this spectrum differ in their relationships with soil biota and have developed contrasting strategies to cope with abiotic and biotic environmental conditions. 4.Finally, we present suggestions for improved experimental designs and scientific inference that will capture and elucidate the influence of above‐ and belowground drivers on PSFs. By establishing the role of abiotic and biotic drivers of PSFs, we will be able to make more robust predictions of how PSFs impact on ecosystem function

Validation and verification of the GeneFinder (TM) COVID-19 Plus RealAmp kit on the ELITe InGenius (R) instrument

Background: Throughout the SARS-CoV-2 pandemic, a rapid identification of the virus was essential to quickly recognize positive cases and limit further spread by applying appropriate infection prevention. Many diagnostic laboratories use a multiplex Real-Time PCR assay, as they are not only highly sensitive but also specific. Currently, there are several assays and platforms in the market available which target different SARS-CoV-2 genes. The aim of this study was to validate and verify the GeneFinder (TM) COVID-19 PLUS RealAmp kit on the ELITe InGenius (R) instrument and compare to the national reference method. Methods: GeneFinder (TM) COVID-19 PLUS RealAmp kit was evaluated against the routine WHO in- house RealTime PCR assay, which is also the national reference method in the Netherlands and used in our laboratory. The sensitivity was tested using the analytical panel from Qnostics (Glasgow, United Kingdom) and the specificity was tested with patient material comprising of other seasonal respiratory viruses. In addition, 96 clinical samples initially analyzed by routine Real-Time PCR were tested using the GeneFinder (TM) COVID-19 PLUS RealAmp kit on the ELITe InGenius (R) instrument. Results: The GeneFinder (TM) COVID-19 PLUS RealAmp kit had a similar performance compared to routine in-house testing, with a limit of detection of 500 dC/mL for the RdRp-gene and E gene. Meanwhile, the N gene showed a limit of detection of 50 dC/mL. The SARS-CoV-2 test was highly specific and detected no other respiratory viruses. The results of the clinical samples were comparable between both assays with similar Ct values observed for the in-house Real-Time-PCR and the GeneFinder (TM) COVID-19 PLUS RealAmp kit for the N gene. Conclusion: The GeneFinder (TM) COVID-19 PLUS RealAmp kit on the ELITe InGenius (R) instrument had an appropriate sensitivity and specificity that could be used in small scale laboratories or during night shifts where accurate diagnostics are crucial

HST Snapshot Survey of Post-AGB Objects

The results from a Hubble Space Telescope (HST) snapshot survey of post-AGB objects are shown. The aim of the survey is to complement existing HST images of PPN and to connect various types of nebulosities with physical and chemical properties of their central stars. Nebulosities are detected in 15 of 33 sources. Images and photometric and geometric measurements are presented. For sources with nebulosities we see a morphological bifurcation into two groups, DUPLEX and SOLE, as previous studies have found. We find further support to the previous results suggesting that this dichotomy is caused by a difference in optical thickness of the dust shell. The remaining 18 sources are classified as stellar post-AGB objects, because our observations indicate a lack of nebulosity. We show that some stellar sources may in fact be DUPLEX or SOLE based on their infrared colors. The cause of the differences among the groups are investigated. We discuss some evidence suggesting that high progenitor-mass AGB stars tend to become DUPLEX post-AGB objects. Intermediate progenitor-mass AGB stars tend to be SOLE post-AGB objects. Most of the stellar sources probably have low mass progenitors and do not seem to develop nebulosities during the post-AGB phase and therefore do not become planetary nebulae.Comment: 21 pages, 11 figure

Investigation of the chemical vicinity of crystal defects in ion-irradiated Mg and AZ31 with coincident Doppler broadening spectroscopy

Crystal defects in magnesium and magnesium based alloys like AZ31 are of major importance for the understanding of their macroscopic properties. We have investigated defects and their chemical surrounding in Mg and AZ31 on an atomic scale with Doppler broadening spectroscopy of the positron annihilation radiation. In these Doppler spectra the chemical information and the defect contribution have to be thoroughly separated. For this reason samples of annealed Mg were irradiated with Mg-ions in order to create exclusively defects. In addition Al- and Zn-ion irradiation on Mg-samples was performed in order to create samples with defects and impurity atoms. The ion irradiated area on the samples was investigated with laterally and depth resolved positron Doppler broadening spectroscopy (DBS) and compared with preceding SRIM-simulations of the vacancy distribution, which are in excellent agreement. The investigation of the chemical vicinity of crystal defects in AZ31 was performed with coincident Doppler broadening spectroscopy (CDBS) by comparing Mg-ion irradiated AZ31 with Mg-ion irradiated Mg. No formation of solute-vacancy complexes was found due to the ion irradiation, despite the high defect mobility.Comment: Submitted to Physical Review B on March 20 20076. Revised version submitted on September 28 2007. Accepted on October 19 200

Proton Motive Force-Dependent Hoechst 33342 Transport by the ABC Transporter LmrA of Lactococcus lactis

The fluorescent compound Hoechst 33342 is a substrate for many multidrug resistance (MDR) transporters and is widely used to characterize their transport activity. We have constructed mutants of the adenosine triphosphate (ATP) binding cassette (ABC)-type MDR transporter LmrA of Lactococcus lactis that are defective in ATP hydrolysis. These mutants and wild-type LmrA exhibited an atypical behavior in the Hoechst 33342 transport assay. In membrane vesicles, Hoechst 33342 transport was shown to be independent of the ATPase activity of LmrA, and it was not inhibited by orthovanadate but sensitive to uncouplers that collapse the proton gradient and to N,N'-dicyclohexylcarbodiimide, an inhibitor of the F0F1-ATPase. In contrast, transport of Hoechst 33342 by the homologous, heterodimeric MDR transporter LmrCD showed a normal ATP dependence and was insensitive to uncouplers of the proton gradient. With intact cells, expression of LmrA resulted in an increased rate of Hoechst 33342 influx while LmrCD caused a decrease in the rate of Hoechst 33342 influx. Cellular toxicity assays using a triple knockout strain, i.e., L. lactis ΔlmrA ΔlmrCD, demonstrate that expression of LmrCD protects cells against the growth inhibitory effects of Hoechst 33342, while in the presence of LmrA, cells are more susceptible to Hoechst 33342. Our data demonstrate that the LmrA-mediated Hoechst 33342 transport in membrane vesicles is influenced by the transmembrane pH gradient due to a pH-dependent partitioning of Hoechst 33342 into the membrane.

Revealing the mid-infrared emission structure of IRAS 16594-4656 and IRAS 07027-7934

TIMMI2 diffraction-limited mid-infrared images of a multipolar proto-planetary nebula IRAS 16594-4656 and a young [WC] elliptical planetary nebula IRAS 07027-7934 are presented. Their dust shells are for the first time resolved (only marginally in the case of IRAS 07027-7934) by applying the Lucy-Richardson deconvolution algorithm to the data, taken under exceptionally good seeing conditions (<0.5"). IRAS 16594-4656 exhibits a two-peaked morphology at 8.6, 11.5 and 11.7 microns which is mainly attributed to emission from PAHs. Our observations suggest that the central star is surrounded by a toroidal structure observed edge-on with a radius of 0.4" (~640 AU at an assumed distance of 1.6 kpc) with its polar axis at P.A.~80 degrees, coincident with the orientation defined by only one of the bipolar outflows identified in the HST optical images. We suggest that the material expelled from the central source is currently being collimated in this direction and that the multiple outflow formation has not been coeval. IRAS 07027-7934 shows a bright, marginally extended emission (FWHM=0.3") in the mid-infrared with a slightly elongated shape along the N-S direction, consistent with the morphology detected by HST in the near-infrared. The mid-infrared emission is interpreted as the result of the combined contribution of small, highly ionized PAHs and relatively hot dust continuum. We propose that IRAS 07027-7934 may have recently experienced a thermal pulse (likely at the end of the AGB) which has produced a radical change in the chemistry of its central star.Comment: 35 pages, 8 figures (figures 1, 2, 4 and 6 are in low resolution) accepted for publication in Ap

The Role of Plant Litter in Driving Plant-Soil Feedbacks

Most studies focusing on plant-soil feedbacks (PSFs) have considered direct interactions between plants, abiotic conditions (e. g., soil nutrients) and rhizosphere communities (e.g., pathogens, mutualists). However, few studies have addressed the role of indirect interactions mediated by plant litter inputs. This is problematic because it has left a major gap in our understanding of PSFs in natural ecosystems, where plant litter is a key component of feedback effects. Here, we propose a new conceptual framework that integrates rhizosphere- and litter-mediated PSF effects. Our framework provides insights into the relative contribution of direct effects mediated by interactions between plants and soil rhizosphere organisms, and indirect effects between plants and decomposer organisms mediated by plant root and shoot litter. We distinguish between three pathways through which senesced root and shoot litter may influence PSFs. Specifically, we examine: (1) physical effects of litter (layer) traits on seed germination, soil structure, and plant growth; (2) chemical effects of litter on concentrations of soil nutrients and secondary metabolites (e.g., allelopathic chemicals); and (3) biotic effects of saprotrophic soil communities that can perform different functional roles in the soil food web, or that may have specialized interactions with litter types, thereby altering soil nutrient cycling. We assess the role of litter in PSF effects via physical, chemical and biotic pathways to address how litter-mediated feedbacks may play out relative to, and in interaction with, feedbacks mediated through the plant rhizosphere. We also present one of the first experimental studies to show the occurrence and species-specificity of litter-mediated feedbacks and we identify critical research gaps. By formally incorporating the plant-litter feedback pathway into PSF experiments, we will further our understanding of PSFs under natural conditions