A methodology for investigating dust model performance using synergistic EARLINET/AERONET dust concentration retrievals

Systematic measurements of dust concentration profiles at a continental scale were recently made possible by the development of synergistic retrieval algorithms using combined lidar and sun photometer data and the establishment of robust remote-sensing networks in the framework of Aerosols, Clouds, and Trace gases Research Infra-Structure Network (ACTRIS)/European Aerosol Research Lidar Network (EARLINET). We present a methodology for using these capabilities as a tool for examining the performance of dust transport models. The methodology includes considerations for the selection of a suitable data set and appropriate metrics for the exploration of the results. The approach is demonstrated for four regional dust transport models (BSC-DREAM8b v2, NMMB/BSC-DUST, DREAM-ABOL, DREAM8-NMME-MACC) using dust observations performed at 10 ACTRIS/EARLINET stations. The observations, which include coincident multi-wavelength lidar and sun photometer measurements, were processed with the Lidar-Radiometer Inversion Code (LIRIC) to retrieve aerosol concentration profiles. The methodology proposed here shows advantages when compared to traditional evaluation techniques that utilize separately the available measurements such as separating the contribution of dust from other aerosol types on the lidar profiles and avoiding model assumptions related to the conversion of concentration fields to aerosol extinction values. When compared to LIRIC retrievals, the simulated dust vertical structures were found to be in good agreement for all models with correlation values between 0.5 and 0.7 in the 1-6 km range, where most dust is typically observed. The absolute dust concentration was typically underestimated with mean bias values of -40 to -20 mu g m(-3) at 2 km, the altitude of maximum mean concentration. The reported differences among the models found in this comparison indicate the benefit of the systematic use of the proposed approach in future dust model evaluation studies

iGEMS : an integrated model for identification of alternative exon usage events

DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2.0 and performance was validated using RT-qPCR. First, AEU was studied in adipocytes treated with (n = 9) or without (n = 8) the anti-diabetes drug, rosiglitazone. iGEMS identified 555 genes with AEU, and robust verification by RT-qPCR (similar to 90%). Second, in a three-way human tissue comparison (muscle, adipose and blood, n = 41) iGEMS identified 4421 genes with at least one AEU event, with excellent RT-qPCR verification (95%, n = 22). Importantly, iGEMS identified a variety of AEU events, including 3'UTR extension, as well as exon inclusion/exclusion impacting on protein kinase and extracellular matrix domains. In conclusion, iGEMS is a robust method for identification of AEU while the variety of exon usage between human tissues is 5-10 times more prevalent than reported by the Genotype-Tissue Expression consortium using RNA sequencing.Peer reviewe

Metabolomic analyses of Leishmania reveal multiple species differences and large differences in amino acid metabolism

Comparative genomic analyses of Leishmania species have revealed relatively minor heterogeneity amongst recognised housekeeping genes and yet the species cause distinct infections and pathogenesis in their mammalian hosts. To gain greater information on the biochemical variation between species, and insights into possible metabolic mechanisms underpinning visceral and cutaneous leishmaniasis, we have undertaken in this study a comparative analysis of the metabolomes of promastigotes of L. donovani, L. major and L. mexicana. The analysis revealed 64 metabolites with confirmed identity differing 3-fold or more between the cell extracts of species, with 161 putatively identified metabolites differing similarly. Analysis of the media from cultures revealed an at least 3-fold difference in use or excretion of 43 metabolites of confirmed identity and 87 putatively identified metabolites that differed to a similar extent. Strikingly large differences were detected in their extent of amino acid use and metabolism, especially for tryptophan, aspartate, arginine and proline. Major pathways of tryptophan and arginine catabolism were shown to be to indole-3-lactate and arginic acid, respectively, which were excreted. The data presented provide clear evidence on the value of global metabolomic analyses in detecting species-specific metabolic features, thus application of this technology should be a major contributor to gaining greater understanding of how pathogens are adapted to infecting their hosts

Ekonomiczna wycena usług ekosystemowych świadczonych przez park w Wilanowie. Badanie metodą transferu korzyści

King Jan III Sobieski (1629–1696), known as an excellent military commander who defeated the Turkish army near Vienna in 1683, was a profound nature lover. Unhappy with living in a castle in the capital city, he bought Wilanów near Warsaw, where he established his suburban residence with a beautiful baroque palace and gardens. After the World War II, the estate was nationalised, restored and turned into a museum. There are probably no trees planted by king Jan III Sobieski himself, but the Park is remarkable. It comprises gardens in various styles (baroque, neo-Renaissance, English and English-Chinese) and a nature reserve Morysin with valuable habitats of meadows and forests. Woodlands, grasslands and ponds constitute three main ecosystems in the Park. Tourists and Warsaw inhabitants appreciate the nature of the gardens and of the Morysin reserve. In addition to their unquestioned historical and cultural value, the Park ecosystems provide multiple environmental benefits. In this paper, we estimate the economic value of these benefits.Rezydencja królewska w Wilanowie to unikalne połączenie zdumiewającej architektury, historii i przyrody. Park w Wilanowie dostarcza wielu korzyści zarówno odwiedzającym go turystom, jak i mieszkańcom Warszawy. W niniejszym badaniu podjęto się oszacowania wartości ekonomicznej tych z korzyści, które mają związek z przyrodą, to jest wartości usług ekosystemowych świadczonych przez park. W oparciu o metodę transferu korzyści wartość usług ekosystemowych dostarczanych przez park w Wilanowie oszacowano na 500 tys. euro rocznie. Choć liczba wydaje się duża, jest znacznie niższa niż wartość innych świadczeń dostarczanych przez zasoby rezydencji

Synthesis of acyl(chloro)phosphines enabled by phosphinidene transfer

Acyl(chloro)phosphines RC(O)P(Cl)(t-Bu) have been prepared by formal insertion of tert-butyl phosphinidene (t-Bu-P) from t-BuPA (A = C14H10 or anthracene) into the C-Cl bond of acyl chlorides. We show that the under-explored acyl(chloro)phosphine functional group provides an efficient method to prepare bis(acyl)phosphines, which are important precursors to compounds used industrially as radical polymerization initiators. Experimental and computational investigations into the mechanism of formation of acyl(chloro)phosphines by our synthetic method reveal a pathway in which chloride attacks a phosphonium intermediate and leads to the reductive loss of anthracene from the phosphorus center in a P(v) to P(iii) process. The synthetic applicability of the acyl(chloro)phosphine functional group has been demonstrated by reduction to an acylphosphide anion, which can in turn be treated with an acyl chloride to furnish dissymmetric bis(acyl)phosphines.National Science Foundation (CHE-1664799