Phenocopy – A Strategy to Qualify Chemical Compounds during Hit-to-Lead and/or Lead Optimization

A phenocopy is defined as an environmentally induced phenotype of one individual which is identical to the genotype-determined phenotype of another individual. The phenocopy phenomenon has been translated to the drug discovery process as phenotypes produced by the treatment of biological systems with new chemical entities (NCE) may resemble environmentally induced phenotypic modifications. Various new chemical entities exerting inhibition of the kinase activity of Transforming Growth Factor β Receptor I (TGF-βR1) were qualified by high-throughput RNA expression profiling. This chemical genomics approach resulted in a precise time-dependent insight to the TGF-β biology and allowed furthermore a comprehensive analysis of each NCE's off-target effects. The evaluation of off-target effects by the phenocopy approach allows a more accurate and integrated view on optimized compounds, supplementing classical biological evaluation parameters such as potency and selectivity. It has therefore the potential to become a novel method for ranking compounds during various drug discovery phases

Stratospheric aerosol radiative forcing simulated by the chemistry climate model EMAC using Aerosol CCI satellite data

This paper presents decadal simulations of stratospheric and tropospheric aerosol and its radiative effects by the chemistry general circulation model EMAC constrained with satellite observations in the framework of the ESA Aerosol CCI project such as GOMOS (Global Ozone Monitoring by Occultation of Stars) and (A)ATSR ((Advanced) Along Track Scanning Radiometer) on the ENVISAT (European Environmental Satellite), IASI (Infrared Atmospheric Sounding Interferometer) on MetOp (Meteorological Operational Satellite), and, additionally, OSIRIS (Optical Spectrograph and InfraRed Imaging System). In contrast to most other studies, the extinctions and optical depths from the model are compared to the observations at the original wavelengths of the satellite instruments covering the range from the UV (ultraviolet) to terrestrial IR (infrared). This avoids conversion artifacts and provides additional constraints for model aerosol and interpretation of the observations. MIPAS (Michelson Interferometer for Passive Atmospheric Sounding) SO2 limb measurements are used to identify plumes of more than 200 volcanic eruptions. These three-dimensional SO2 plumes are added to the model SO2 at the eruption times. The interannual variability in aerosol extinction in the lower stratosphere, and of stratospheric aerosol radiative forcing at the tropopause, is dominated by the volcanoes. To explain the seasonal cycle of the GOMOS and OSIRIS observations, desert dust simulated by a new approach and transported to the lowermost stratosphere by the Asian summer monsoon and tropical convection turns out to be essential. This also applies to the radiative heating by aerosol in the lowermost stratosphere. The existence of wet dust aerosol in the lowermost stratosphere is indicated by the patterns of the wavelength dependence of extinction in observations and simulations. Additional comparison with (A)ATSR total aerosol optical depth at different wavelengths and IASI dust optical depth demonstrates that the model is able to represent stratospheric as well as tropospheric aerosol consistently.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Merging regional and global aerosol optical depth records from major available satellite products

Satellite instruments provide a vantage point for studying aerosol loading consistently over different regions of the world. However, the typical lifetime of a single satellite platform is on the order of 5-15 years; thus, for climate studies, the use of multiple satellite sensors should be considered. Discrepancies exist between aerosol optical depth (AOD) products due to differences in their information content, spatial and temporal sampling, calibration, cloud masking, and algorithmic assumptions. Users of satellite-based AOD time-series are confronted with the challenge of choosing an appropriate dataset for the intended application. In this study, 16 monthly AOD products obtained from different satellite sensors and with different algorithms were inter-compared and evaluated against Aerosol Robotic Network (AERONET) monthly AOD. Global and regional analyses indicate that products tend to agree qualitatively on the annual, seasonal and monthly timescales but may be offset in magnitude. Several approaches were then investigated to merge the AOD records from different satellites and create an optimised AOD dataset. With few exceptions, all merging approaches lead to similar results, indicating the robustness and stability of the merged AOD products. We introduce a gridded monthly AOD merged product for the period 1995-2017. We show that the quality of the merged product is as least as good as that of individual products. Optimal agreement of the AOD merged product with AERONET further demonstrates the advantage of merging multiple products. This merged dataset provides a long-term perspective on AOD changes over different regions of the world, and users are encouraged to use this dataset

Evaluation of seven European aerosol optical depth retrieval algorithms for climate analysis

Satellite data are increasingly used to provide observation-based estimates of the effects of aerosols on climate. The Aerosol-cci project, part of the European Space Agency's Climate Change Initiative (CCI), was designed to provide essential climate variables for aerosols from satellite data. Eight algorithms, developed for the retrieval of aerosol properties using data from AATSR (4), MERIS (3) and POLDER, were evaluated to determine their suitability for climate studies. The primary result from each of these algorithms is the aerosol optical depth (AOD) at several wavelengths, together with the Ångström exponent (AE) which describes the spectral variation of the AOD for a given wavelength pair. Other aerosol parameters which are possibly retrieved from satellite observations are not considered in this paper. The AOD and AE (AE only for Level 2) were evaluated against independent collocated observations from the ground-based AERONET sun photometer network and against “reference” satellite data provided by MODIS and MISR. Tools used for the evaluation were developed for daily products as produced by the retrieval with a spatial resolution of 10 × 10 km2 (Level 2) and daily or monthly aggregates (Level 3). These tools include statistics for L2 and L3 products compared with AERONET, as well as scoring based on spatial and temporal correlations. In this paper we describe their use in a round robin (RR) evaluation of four months of data, one month for each season in 2008. The amount of data was restricted to only four months because of the large effort made to improve the algorithms, and to evaluate the improvement and current status, before larger data sets will be processed. Evaluation criteria are discussed. Results presented show the current status of the European aerosol algorithms in comparison to both AERONET and MODIS and MISR data. The comparison leads to a preliminary conclusion that the scores are similar, including those for the references, but the coverage of AATSR needs to be enhanced and further improvements are possible for most algorithms. None of the algorithms, including the references, outperforms all others everywhere. AATSR data can be used for the retrieval of AOD and AE over land and ocean. PARASOL and one of the MERIS algorithms have been evaluated over ocean only and both algorithms provide good results

AeroCom phase III multi-model evaluation of the aerosol life cycle and optical properties using ground- and space-based remote sensing as well as surface in situ observations

Within the framework of the AeroCom (Aerosol Comparisons between Observations and Models) initiative, the state-of-the-art modelling of aerosol optical properties is assessed from 14 global models participating in the phase III control experiment (AP3). The models are similar to CMIP6/AerChemMIP Earth System Models (ESMs) and provide a robust multi-model ensemble. Inter-model spread of aerosol species lifetimes and emissions appears to be similar to that of mass extinction coefficients (MECs), suggesting that aerosol optical depth (AOD) uncertainties are associated with a broad spectrum of parameterised aerosol processes. Total AOD is approximately the same as in AeroCom phase I (AP1) simulations. However, we find a 50% decrease in the optical depth (OD) of black carbon (BC), attributable to a combination of decreased emissions and lifetimes. Relative contributions from sea salt (SS) and dust (DU) have shifted from being approximately equal in AP1 to SS contributing about 2/3 of the natural AOD in AP3. This shift is linked with a decrease in DU mass burden, a lower DU MEC, and a slight decrease in DU lifetime, suggesting coarser DU particle sizes in AP3 compared to AP1. Relative to observations, the AP3 ensemble median and most of the participating models underestimate all aerosol optical properties investigated, that is, total AOD as well as fine and coarse AOD (AOD(f), AOD(c)), Angstrom exponent (AE), dry surface scattering (SCdry), and absorption (AC(dry)) coefficients. Compared to AERONET, the models underestimate total AOD by ca. 21% +/- 20% (as inferred from the ensemble median and interquartile range). Against satellite data, the ensemble AOD biases range from -37% (MODIS-Terra) to -16% (MERGED-FMI, a multi-satellite AOD product), which we explain by differences between individual satellites and AERONET measurements themselves. Correlation coefficients (R) between model and observation AOD records are generally high (R > 0.75), suggesting that the models are capable of capturing spatiotemporal variations in AOD. We find a much larger underestimate in coarse AOD(c) (similar to-45% +/- 25 %) than in fine AOD(f) (similar to-15% +/- 25 %) with slightly increased inter-model spread compared to total AOD. These results indicate problems in the modelling of DU and SS. The AOD(c) bias is likely due to missing DU over continental land masses (particularly over the United States, SE Asia, and S. America), while marine AERONET sites and the AATSR SU satellite data suggest more moderate oceanic biases in AOD(c). Column AEs are underestimated by about 10% +/- 16 %. For situations in which measurements show AE > 2, models underestimate AERONET AE by ca. 35 %. In contrast, all models (but one) exhibit large overestimates in AE when coarse aerosol dominates (bias ca. +140% if observed AE < 0.5). Simulated AE does not span the observed AE variability. These results indicate that models overestimate particle size (or underestimate the fine-mode fraction) for fine-dominated aerosol and underestimate size (or overestimate the fine-mode fraction) for coarse-dominated aerosol. This must have implications for lifetime, water uptake, scattering enhancement, and the aerosol radiative effect, which we can not quantify at this moment. Comparison against Global Atmosphere Watch (GAW) in situ data results in mean bias and inter-model variations of -35% +/- 25% and -20% +/- 18% for SCdry and AC(dry), respectively. The larger underestimate of SCdry than AC(dry) suggests the models will simulate an aerosol single scattering albedo that is too low. The larger underestimate of SCdry than ambient air AOD is consistent with recent findings that models overestimate scattering enhancement due to hygroscopic growth. The broadly consistent negative bias in AOD and surface scattering suggests an underestimate of aerosol radiative effects in current global aerosol models. Considerable inter-model diversity in the simulated optical properties is often found in regions that are, unfortunately, not or only sparsely covered by ground-based observations. This includes, for instance, the Sahara, Amazonia, central Australia, and the South Pacific. This highlights the need for a better site coverage in the observations, which would enable us to better assess the models, but also the performance of satellite products in these regions. Using fine-mode AOD as a proxy for present-day aerosol forcing estimates, our results suggest that models underestimate aerosol forcing by ca. -15 %, however, with a considerably large interquartile range, suggesting a spread between -35% and +10 %.Peer reviewe

Endogenous egg immune defenses in the yellow mealworm beetle (Tenebrio molitor)

In order to survive microbe encounters, insects rely on both physical barriers as well as local and systemic immune responses. Most research focusses on adult or larval defenses however, whereas insect eggs are also in need of protection. Lately, the defense of eggs against microbes has received an increasing amount of attention, be it through endogenous egg defenses, trans-generational immune priming (TGIP) or parental investment. Here we studied the endogenous immune response in eggs and adults of Tenebrio molitor. We show that many immune genes are induced in both adults and eggs. Furthermore, we show that eggs reach comparable levels of immune gene expression as adults. These findings show that the eggs of Tenebrio are capable of an impressive endogenous immune response, and indicate that such inducible egg defenses are likely common in insects

Development, Production and Evaluation of Aerosol Climate Data Records from European Satellite Observations (Aerosol_cci)

Producing a global and comprehensive description of atmospheric aerosols requires integration of ground-based, airborne, satellite and model datasets. Due to its complexity, aerosol monitoring requires the use of several data records with complementary information content. This paper describes the lessons learned while developing and qualifying algorithms to generate aerosol Climate Data Records (CDR) within the European Space Agency (ESA) Aerosol_cci project. An iterative algorithm development and evaluation cycle involving core users is applied. It begins with the application-specific refinement of user requirements, leading to algorithm development, dataset processing and independent validation followed by user evaluation. This cycle is demonstrated for a CDR of total Aerosol Optical Depth (AOD) from two subsequent dual-view radiometers. Specific aspects of its applicability to other aerosol algorithms are illustrated with four complementary aerosol datasets. An important element in the development of aerosol CDRs is the inclusion of several algorithms evaluating the same data to benefit from various solutions to the ill-determined retrieval problem. The iterative approach has produced a 17-year AOD CDR, a 10-year stratospheric extinction profile CDR and a 35-year Absorbing Aerosol Index record. Further evolution cycles have been initiated for complementary datasets to provide insight into aerosol properties (i.e., dust aerosol, aerosol absorption).Peer reviewe

Azimuthal anisotropy of charged jet production in root s(NN)=2.76 TeV Pb-Pb collisions

We present measurements of the azimuthal dependence of charged jet production in central and semi-central root s(NN) = 2.76 TeV Pb-Pb collisions with respect to the second harmonic event plane, quantified as nu(ch)(2) (jet). Jet finding is performed employing the anti-k(T) algorithm with a resolution parameter R = 0.2 using charged tracks from the ALICE tracking system. The contribution of the azimuthal anisotropy of the underlying event is taken into account event-by-event. The remaining (statistical) region-to-region fluctuations are removed on an ensemble basis by unfolding the jet spectra for different event plane orientations independently. Significant non-zero nu(ch)(2) (jet) is observed in semi-central collisions (30-50% centrality) for 20 <p(T)(ch) (jet) <90 GeV/c. The azimuthal dependence of the charged jet production is similar to the dependence observed for jets comprising both charged and neutral fragments, and compatible with measurements of the nu(2) of single charged particles at high p(T). Good agreement between the data and predictions from JEWEL, an event generator simulating parton shower evolution in the presence of a dense QCD medium, is found in semi-central collisions. (C) 2015 CERN for the benefit of the ALICE Collaboration. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Peer reviewe

Production of He-4 and (4) in Pb-Pb collisions at root(NN)-N-S=2.76 TeV at the LHC

Results on the production of He-4 and (4) nuclei in Pb-Pb collisions at root(NN)-N-S = 2.76 TeV in the rapidity range vertical bar y vertical bar <1, using the ALICE detector, are presented in this paper. The rapidity densities corresponding to 0-10% central events are found to be dN/dy4(He) = (0.8 +/- 0.4 (stat) +/- 0.3 (syst)) x 10(-6) and dN/dy4 = (1.1 +/- 0.4 (stat) +/- 0.2 (syst)) x 10(-6), respectively. This is in agreement with the statistical thermal model expectation assuming the same chemical freeze-out temperature (T-chem = 156 MeV) as for light hadrons. The measured ratio of (4)/He-4 is 1.4 +/- 0.8 (stat) +/- 0.5 (syst). (C) 2018 Published by Elsevier B.V.Peer reviewe