Investigations of boundary layer structure, cloud characteristics and vertical mixing of aerosols at Barbados with large eddy simulations

Large eddy simulations (LESs) are performed for the area of the Caribbean island Barbados to investigate island effects on boundary layer modification, cloud generation and vertical mixing of aerosols. Due to the presence of a topographically structured island surface in the domain center, the model setup has to be designed with open lateral boundaries. In order to generate inflow turbulence consistent with the upstream marine boundary layer forcing, we use the cell perturbation method based on finite amplitude potential temperature perturbations. In this work, this method is for the first time tested and validated for moist boundary layer simulations with open lateral boundary conditions. Observational data obtained from the SALTRACE field campaign is used for both model initialization and a comparison with Doppler wind and Raman lidar data. Several numerical sensitivity tests are carried out to demonstrate the problems related to “gray zone modeling” when using coarser spatial grid spacings beyond the inertial subrange of three-dimensional turbulence or when the turbulent marine boundary layer flow is replaced by laminar winds. Especially cloud properties in the downwind area west of Barbados are markedly affected in these kinds of simulations. Results of an additional simulation with a strong trade-wind inversion reveal its effect on cloud layer depth and location. Saharan dust layers that reach Barbados via long-range transport over the North Atlantic are included as passive tracers in the model. Effects of layer thinning, subsidence and turbulent downward transport near the layer bottom at z ≈ 1800 m become apparent. The exact position of these layers and strength of downward mixing is found to be mainly controlled atmospheric stability (especially inversion strength) and wind shear. Comparisons of LES model output with wind lidar data show similarities in the downwind vertical wind structure. Additionally, the model results accurately reproduce the development of the daytime convective boundary layer measured by the Raman lidar

Airborne observations of newly formed boundary layer aerosol particles under cloudy conditions

This study describes the appearance of ultrafine boundary layer aerosol particles under classical "non-favourable" conditions at the research site of TROPOS (Leibniz Institute for Tropospheric Research). Airborne measurements of meteorological and aerosol properties of the atmospheric boundary layer (ABL) were repeatedly performed with the unmanned aerial system ALADINA (Application of Light-weight Aircraft for Detecting IN-situ Aerosol) during three seasons between October 2013 and July 2015. More than 100 measurement flights were conducted on 23 different days with a total flight duration of 53h. In 26% of the cases, maxima of ultrafine particles were observed close to the inversion layer at altitudes between 400 and 600m and the particles were rapidly mixed vertically and mainly transported downwards during short time intervals of cloud gaps. This study focuses on two measurement days affected by low-level stratocumulus clouds, but different wind directions (NE, SW) and minimal concentrations (<4.6µgm−3) of SO2, as a common indicator for precursor gases at ground. Taken from vertical profiles, the onset of clouds led to a non-linearity of humidity that resulted in an increased turbulence at the local-scale and caused fast nucleation e.g., but in relation to rapid dilution of surrounding air, seen in sporadic clusters of ground data, so that ultrafine particles disappeared in the verticality. The typical "banana shape" of new particle formation (NPF) and growth was not seen at ground and thus these days might not have been classified as NPF event days by pure surface studies

Multimodal X-ray imaging of nanocontainer-treated macrophages and calcium distribution in the perilacunar bone matrix

Studies of biological systems typically require the application of several complementary methods able to yield statistically-relevant results at a unique level of sensitivity. Combined X-ray fluorescence and ptychography offer excellent elemental and structural imaging contrasts at the nanoscale. They enable a robust correlation of elemental distributions with respect to the cellular morphology. Here we extend the applicability of the two modalities to higher X-ray excitation energies, permitting iron mapping. Using a long-range scanning setup, we applied the method to two vital biomedical cases. We quantified the iron distributions in a population of macrophages treated with Mycobacterium-tuberculosis-targeting iron-oxide nanocontainers. Our work allowed to visualize the internalization of the nanocontainer agglomerates in the cytosol. From the iron areal mass maps, we obtained a distribution of antibiotic load per agglomerate and an average areal concentration of nanocontainers in the agglomerates. In the second application we mapped the calcium content in a human bone matrix in close proximity to osteocyte lacunae (perilacunar matrix). A concurrently acquired ptychographic image was used to remove the mass-thickness effect from the raw calcium map. The resulting ptychography-enhanced calcium distribution allowed then to observe a locally lower degree of mineralization of the perilacunar matrix

The Dectin-2 family of C-type lectin-like receptors : an update

Peer reviewedPublisher PD

An Integrated Model for User Attribute Discovery: A Case Study on Political Affiliation Identification

Discovering user demographic attributes from social media is a problem of considerable interest. The problem setting can be generalized to include three components - users, topics and behaviors. In recent studies on this problem, however, the behavior between users and topics are not effectively incorporated. In our work, we proposed an integrated unsupervised model which takes into consideration all the three components integral to the task. Furthermore, our model incorporates collaborative filtering with probabilistic matrix factorization to solve the data sparsity problem, a computational challenge common to all such tasks. We evaluated our method on a case study of user political affiliation identification, and compared against state-of-the-art baselines. Our model achieved an accuracy of 70.1% for user party detection task. ? 2014 Springer International Publishing.EI

The Human Phenotype Ontology project:linking molecular biology and disease through phenotype data

The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have developed logical definitions for 46% of all HPO classes using terms from ontologies for anatomy, cell types, function, embryology, pathology and other domains. This allows interoperability with several resources, especially those containing phenotype information on model organisms such as mouse and zebrafish. Here we describe the updated HPO database, which provides annotations of 7,278 human hereditary syndromes listed in OMIM, Orphanet and DECIPHER to classes of the HPO. Various meta-attributes such as frequency, references and negations are associated with each annotation. Several large-scale projects worldwide utilize the HPO for describing phenotype information in their datasets. We have therefore generated equivalence mappings to other phenotype vocabularies such as LDDB, Orphanet, MedDRA, UMLS and phenoDB, allowing integration of existing datasets and interoperability with multiple biomedical resources. We have created various ways to access the HPO database content using flat files, a MySQL database, and Web-based tools. All data and documentation on the HPO project can be found online

The Human Phenotype Ontology in 2017.

Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology

Airborne observations of newly formed boundary layer aerosol particles under cloudy conditions

This study describes the appearance of ultrafine boundary layer aerosol particles under classical non-favourable conditions at the research site of TROPOS (Leibniz Institute for Tropospheric Research). Airborne measurements of meteorological and aerosol properties of the atmospheric boundary layer (ABL) were repeatedly performed with the unmanned aerial system ALADINA (Application of Light-weight Aircraft for Detecting IN-situ Aerosol) during three seasons between October 2013 and July 2015. More than 100 measurement flights were conducted on 23 different days with a total flight duration of 53 h. In 26 % of the cases, maxima of ultrafine particles were observed close to the inversion layer at altitudes between 400 and 600 m and the particles were rapidly mixed vertically and mainly transported downwards during short time intervals of cloud gaps. This study focuses on two measurement days affected by low-level stratocumulus clouds, but different wind directions (NE, SW) and minimal concentrations (&lt; 4.6 µg m−3) of SO2, as a common indicator for precursor gases at ground. Taken from vertical profiles, the onset of clouds led to a non-linearity of humidity that resulted in an increased turbulence at the local-scale and caused fast nucleation e.g., but in relation to rapid dilution of surrounding air, seen in sporadic clusters of ground data, so that ultrafine particles disappeared in the verticality. The typical banana shape of new particle formation (NPF) and growth was not seen at ground and thus these days might not have been classified as NPF event days by pure surface studies