On the application and grid-size sensitivity of the urban dispersion model CAIRDIO v2.0 under real city weather conditions

There is a gap between the need for city-wide air-quality simulations considering the intra-urban variability and mircoscale dispersion features and the computational capacities that conventional urban microscale models require. This gap can be bridged by targeting model applications on the gray zone situated between the mesoscale and large-eddy scale. The urban dispersion model CAIRDIO is a new contribution to the class of computational-fluid dynamics models operating in this scale range. It uses a diffuse-obstacle boundary method to represent buildings as physical obstacles at gray-zone resolutions in the order of tens of meters. The main objective of this approach is to find an acceptable compromise between computationally inexpensive grid sizes for spatially comprehensive applications and the required accuracy in the description of building and boundary-layer effects. In this paper, CAIRDIO is applied on the simulation of black carbon and particulate matter dispersion for an entire mid-size city using a uniform horizontal grid spacing of 40gm. For model evaluation, measurements from five operational air monitoring stations representative for the urban background and high-traffic roads are used. The comparison also includes the mesoscale host simulation, which provides the boundary conditions. The measurements show a dominant influence of the mixing layer evolution at background sites, and therefore both the mesoscale and large-eddy simulation (LES) results are in good agreement with the observed air pollution levels. In contrast, at the high-traffic sites the proximity to emissions and the interactions with the building environment lead to a significantly amplified diurnal variability in pollutant concentrations. These urban road conditions can only be reasonably well represented by CAIRDIO while the meosocale simulation indiscriminately reproduces a typical urban-background profile, resulting in a large positive model bias. Remaining model discrepancies are further addressed by a grid-spacing sensitivity study using offline-nested refined domains. The results show that modeled peak concentrations within street canyons can be further improved by decreasing the horizontal grid spacing down to 10gm, but not beyond. Obviously, the default grid spacing of 40gm is too coarse to represent the specific environment within narrow street canyons. The accuracy gains from the grid refinements are still only modest compared to the remaining model error, which to a large extent can be attributed to uncertainties in the emissions. Finally, the study shows that the proposed gray-scale modeling is a promising downscaling approach for urban air-quality applications. The results, however, also show that aspects other than the actual resolution of flow patterns and numerical effects can determine the simulations at the urban microscale

Dust mobilization and aerosol transport from West Africa to Cape Verde - a meteorological overview of SAMUM-2

The second field campaign of the SAharan Mineral dUst experiMent (SAMUM-2) was performed between 15 January and 14 February 2008 at the airport of Praia, Cape Verde, and provided valuable information to study the westward transport of Saharan dust and the mixing with biomass-burning smoke and sea-salt aerosol. Here lidar, meteorological, and particle measurements at Praia, together with operational analyses, trajectories, and satellite and synoptic station data are used to give an overview of the meteorological conditions and to place other SAMUM-2 measurements into a large-scale context. It is demonstrated that wintertime dust conditions at Cape Verde are closely related to the movement and intensification of mid-latitude high-pressure systems and the associated pressure gradients at their southern flanks. These cause dust emission over Mauritania, Mali, and Niger, and subsequent westward transport to Cape Verde within about 1–5 d. Dust emissions often peak around midday, suggesting a relation to daytime mixing of momentum from nocturnal low-level jets to the surface. The dust layer over Cape Verde is usually restricted to the lowest 1.5 km of the atmosphere. During periods with near-surface wind speeds about 5.5 ms−1, a maritime aerosol layer develops which often mixes with dust from above. On most days, the middle levels up to about 5 km additionally contain smoke that can be traced back to sources in southernWest Africa. Above this layer, clean air masses are transported to Cape Verde with the westerly flow at the southern side of the subtropical jet. The penetration of extra-tropical disturbances to low latitudes can bring troposphere-deep westerly flow and unusually clean conditions to the region

Knowledge Transfer with Citizen Science: Luft-Leipzig Case Study

Community-based participatory research initiatives such as “hackAir”, “luftdaten.info”, “senseBox”, “CAPTOR”, “CurieuzeNeuzen Vlaanderen”, “communityAQ”, and “Healthy Air, Healthier Children” campaign among many others for mitigating short-lived climate pollutants (SLCPs) and improving air quality have reported progressive knowledge transfer results. These research initiatives provide the research community with the practical four-element state-of-the-art method for citizen science. For the preparation-, measurements-, data analysis-, and scientific support-elements that collectively present the novel knowledge transfer method, the Luft-Leipzig project results are presented. This research contributes to science by formulating a novel method for SLCP mitigation projects that employ citizen scientists. The Luft-Leipzig project results are presented to validate the four-element state-of-the-art method. The method is recommended for knowledge transfer purposes beyond the scope of mitigating short-lived climate pollutants (SLCPs) and improving air quality

Properties of dust aerosol particles transported to Portugal from the Sahara desert

Aerosol properties of mineral particles in the far field of an African desert dust outbreak were investigated that brought Saharan dust over the Mediterranean in different layers to Portugal. The measurements were performed inside the project Desert Aerosols over Portugal (DARPO) which was linked to the Saharan Mineral Dust Experiment (SAMUM). The maximum particle mass concentration was about 150μgm−3 and the corresponding scattering coefficient was 130Mm−1 which results in a mass scattering efficiency of 0.87m2 g−1. The aerosol optical depth reached values up to 0.53 and the lidar ratio was between 45 and 50 in the whole dust loaded column. A comparison between particle size distributions and refractive indices derived from different instruments and models showed a general good agreement but some minor differences could also be observed. Measurements as well as calculations with a particle transport model suggest that there is a relatively higher concentration of very large particles in the upper region of the dust layer than on the surface which is likely connected with meteorological conditions at the observational site ( Évora, Portugal)

Coupling aerosols to (cirrus) clouds in the global EMAC-MADE3 aerosol–climate model

A new cloud microphysical scheme including a detailed parameterization for aerosol-driven ice formation in cirrus clouds is implemented in the global ECHAM/MESSy Atmospheric Chemistry (EMAC) chemistry–climate model and coupled to the third generation of the Modal Aerosol Dynamics model for Europe adapted for global applications (MADE3) aerosol submodel. The new scheme is able to consistently simulate three regimes of stratiform clouds – liquid, mixed-, and ice-phase (cirrus) clouds – considering the activation of aerosol particles to form cloud droplets and the nucleation of ice crystals. In the cirrus regime, it allows for the competition between homogeneous and heterogeneous freezing for the available supersaturated water vapor, taking into account different types of ice-nucleating particles, whose specific ice-nucleating properties can be flexibly varied in the model setup. The new model configuration is tuned to find the optimal set of parameters that minimizes the model deviations with respect to observations. A detailed evaluation is also performed comparing the model results for standard cloud and radiation variables with a comprehensive set of observations from satellite retrievals and in situ measurements. The performance of EMAC-MADE3 in this new coupled configuration is in line with similar global coupled models and with other global aerosol models featuring ice cloud parameterizations. Some remaining discrepancies, namely a high positive bias in liquid water path in the Northern Hemisphere and overestimated (underestimated) cloud droplet number concentrations over the tropical oceans (in the extratropical regions), which are both a common problem in these kinds of models, need to be taken into account in future applications of the model. To further demonstrate the readiness of the new model system for application studies, an estimate of the anthropogenic aerosol effective radiative forcing (ERF) is provided, showing that EMAC-MADE3 simulates a relatively strong aerosol-induced cooling but within the range reported in the Intergovernmental Panel on Climate Change (IPCC) assessments

ACEseq – allele specific copy number estimation from whole genome sequencing

ACEseq is a computational tool for allele-specific copy number estimation in tumor genomes based on whole genome sequencing. In contrast to other tools it features GC-bias correction, unique replication timing-bias correction and integration of structural variant (SV) breakpoints for improved genome segmentation. ACEseq clearly outperforms widely used state-of-the art methods, provides a fully automated estimation of tumor cell content and ploidy, and additionally computes homologous recombination deficiency scores.</jats:p

Regional modelling of Saharan dust and biomass-burning smoke, Part I: Model description and evaluation

The spatio-temporal evolution of the Saharan dust and biomass-burning plume during the SAMUM-2 field campaign in January and February 2008 is simulated at 28 km horizontal resolution with the regional model-system COSMOMUSCAT. The model performance is thoroughly tested using routine ground-based and space-borne remote sensing and local field measurements. Good agreement with the observations is found in many cases regarding transport patterns, aerosol optical thicknesses and the ratio of dust to smoke aerosol. The model also captures major features of the complex aerosol layering. Nevertheless, discrepancies in the modelled aerosol distribution occur, which are analysed in detail. The dry synoptic dynamics controlling dust uplift and transport during the dry season are well described by the model, but surface wind peaks associated with the breakdown of nocturnal low-level jets are not always reproduced. Thus, a strong dust outbreak is underestimated. While dust emission modelling is a priori more challenging, since strength and placement of dust sources depend on on-line computed winds, considerable inaccuracies also arise in observation-based estimates of biomass-burning emissions. They are caused by cloud and spatial errors of satellite fire products and uncertainties in fire emission parameters, and can lead to unrealistic model results of smoke transport

The impact of mineral dust on cloud formation during the Saharan dust event in April 2014 over Europe

A regional modeling study on the impact of desert dust on cloud formation is presented for a major Saharan dust outbreak over Europe from 2 April to 5 April 2014. The dust event coincided with an extensive and dense cirrus cloud layer, suggesting an influence of dust on atmospheric ice nucleation. Using interactive simulation with the regional dust model COSMO-MUSCAT, we investigate cloud and precipitation representation in the model and test the sensitivity of cloud parameters to dust-cloud and dust-radiation interactions of the simulated dust plume. We evaluate model results with ground-based and space-borne remote sensings of aerosol and cloud properties, as well as the in situ measurements obtained during the ML-CIRRUS aircraft campaign

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.We thank the DKFZ Genomics and Proteomics Core Facility and the OICR Genome Technologies Platform for provision of sequencing services. Financial support was provided by the consortium projects READNA under grant agreement FP7 Health-F4-2008-201418, ESGI under grant agreement 262055, GEUVADIS under grant agreement 261123 of the European Commission Framework Programme 7, ICGC-CLL through the Spanish Ministry of Science and Innovation (MICINN), the Instituto de Salud Carlos III (ISCIII) and the Generalitat de Catalunya. Additional financial support was provided by the PedBrain Tumor Project contributing to the International Cancer Genome Consortium, funded by German Cancer Aid (109252) and by the German Federal Ministry of Education and Research (BMBF, grants #01KU1201A, MedSys #0315416C and NGFNplus #01GS0883; the Ontario Institute for Cancer Research to PCB and JDM through funding provided by the Government of Ontario, Ministry of Research and Innovation; Genome Canada; the Canada Foundation for Innovation and Prostate Cancer Canada with funding from the Movember Foundation (PCB). PCB was also supported by a Terry Fox Research Institute New Investigator Award, a CIHR New Investigator Award and a Genome Canada Large-Scale Applied Project Contract. The Synergie Lyon Cancer platform has received support from the French National Institute of Cancer (INCa) and from the ABS4NGS ANR project (ANR-11-BINF-0001-06). The ICGC RIKEN study was supported partially by RIKEN President’s Fund 2011, and the supercomputing resource for the RIKEN study was provided by the Human Genome Center, University of Tokyo. MDE, LB, AGL and CLA were supported by Cancer Research UK, the University of Cambridge and Hutchison-Whampoa Limited. SD is supported by the Torres Quevedo subprogram (MI CINN) under grant agreement PTQ-12-05391. EH is supported by the Research Council of Norway under grant agreements 221580 and 218241 and by the Norwegian Cancer Society under grant agreement 71220-PR-2006-0433. Very special thanks go to Jennifer Jennings for administrating the activity of the ICGC Verification Working Group and Anna Borrell for administrative support.This is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/ncomms1000