A new method to retrieve the real part of the equivalent refractive index of atmospheric aerosols

This document is the Accepted Manuscript version of the following article: S. Vratolis, et al, ‘A new method to retrieve the real part of the equivalent refractive index of atmospheric aerosols’, Journal of Aerosol Science, Vol. 117: 54-62, March 2018. Under embargo until 29 December 2019. The final, published version is available online at DOI: https://doi.org/10.1016/j.jaerosci.2017.12.013.In the context of the international experimental campaign Hygroscopic Aerosols to Cloud Droplets (HygrA-CD, 15 May to 22 June 2014), dry aerosol size distributions were measured at Demokritos station (DEM) using a Scanning Mobility Particle Sizer (SMPS) in the size range from 10 to 550 nm (electrical mobility diameter), and an Optical Particle Counter (OPC model Grimm 107 operating at the laser wavelength of 660 nm) to acquire the particle size distribution in the size range of 250 nm to 2.5 μm optical diameter. This work describes a method that was developed to align size distributions in the overlapping range of the SMPS and the OPC, thus allowing us to retrieve the real part of the aerosol equivalent refractive index (ERI). The objective is to show that size distribution data acquired at in situ measurement stations can provide an insight to the physical and chemical properties of aerosol particles, leading to better understanding of aerosol impact on human health and earth radiative balance. The resulting ERI could be used in radiative transfer models to assess aerosol forcing direct effect, as well as an index of aerosol chemical composition. To validate the method, a series of calibration experiments were performed using compounds with known refractive index (RI). This led to a corrected version of the ERI values, (ERICOR). The ERICOR values were subsequently compared to model estimates of RI values, based on measured PM2.5 chemical composition, and to aerosol RI retrieved values by inverted lidar measurements on selected days.Peer reviewe

Comparison and complementary use of in situ and remote sensing aerosol measurements in the Athens Metropolitan Area

© 2020 Elsevier Ltd. All rights reserved. This manuscript is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence http://creativecommons.org/licenses/by-nc-nd/4.0/.In the summer of 2014 in situ and remote sensing instruments were deployed in Athens, in order to study the concentration, physical properties, and chemical composition of aerosols. In this manuscript we aim to combine the measurements of collocated in situ and remote sensing instruments by comparison and complementary use, in order to increase the accuracy of predictions concerning climate change and human health. We also develop a new method in order to select days when a direct comparison on in situ and remote sensing instruments is possible. On selected days that displayed significant turbulence up to approximately 1000 m above ground level (agl), we acquired the aerosol extinction or scattering coefficient by in situ instruments using three approaches. In the first approach the aerosol extinction coefficient was acquired by adding a Nephelometer scattering coefficient in ambient conditions and an Aethalometer absorption coefficient. The correlation between the in situ and remote sensing instruments was good (coefficient of determination R2 equal to 0.69). In the second approach we acquired the aerosol refractive index by fitting dry Nephelometer and Aethalometer measurements with Mie algorithm calculations of the scattering and absorption coefficients for the size distribution up to a maximum diameter of 1000 nm obtained by in situ instruments. The correlation in this case was relatively good (R2 equal to 0.56). Our next step was to compare the extinction coefficient acquired by remote sensing instruments to the scattering coefficient calculated by Mie algorithm using the size distribution up to a maximum diameter of 1000 nm and the equivalent refractive index (ERICOR), which is acquired by the comparison of the size distributions obtained by a Scanning Mobility Particle Sizer (SMPS) and an Optical Particle Counter (OPC). The agreement between the in situ and remote sensing instruments in this case was not satisfactory (R2 equal to 0.35). The last comparison for the selected days was between the aerosol extinction Ångström exponent acquired by in situ and remote sensing instruments. The correlation was not satisfactory (R2 equal to 0.4), probably due to differences in the number size distributions present in the air volumes measured by in situ and remote sensing instruments. We also present a day that a Saharan dust event occurred in Athens in order to demonstrate the information we obtain through the synergy of in situ and remote sensing instruments on how regional aerosol is added to local aerosol, especially during pollution events due to long range transport.Peer reviewe

Possible Role of Meckel's Scan Fused with SPECT CT Imaging: Unraveling the Cause of Abdominal Pain and Obscure-Overt Gastrointestinal Bleeding

A 27-year-old male presented with recurrent abdominal pain and high volume hematochezia despite undergoing extensive testing and a right hemicolectomy 3 years prior for a linear bleeding ulceration in the ascending colon. Studies at the University of Michigan included esophagogastroduodenoscopy (EGD), colonoscopy and video capsule endoscopy (VCE), revealing an arteriovenous malformation (AVM) in the terminal ileum. He was hospitalized for recurrent symptoms. His presentation suggested a small bowel source of obscure-overt GI bleeding based on prior non-diagnostic colonoscopy and EGD and a bilious nasogastric lavage. Tagged red blood cell scan localized bleeding to the right lower quadrant. Colonoscopy showed fresh blood in the terminal ileum without a clear source. Angiography showed no evidence of bleeding or terminal ileal AVM. A novel Meckel's scan fused with SPECT imaging showed focal uptake in the terminal ileum. The patient underwent Meckel's diverticulectomy with sparing of adjacent bowel and has remained asymptomatic for 19 months. This case illustrates that patients with obscure-overt GI bleeding require a step-wise multi-modality diagnostic work-up. Because Meckel's scans are false-positive in 28% of adults, Meckel's scan fused with SPECT imaging may offer an approach to refine diagnostic accuracy of either scan alone, but requires further investigation. Exploratory laparotomy should be reserved as a last option and is best performed with intraoperative endoscopy

Screening of the DNA mismatch repair genes MLH1, MSH2 and MSH6 in a Greek cohort of Lynch syndrome suspected families

<p>Abstract</p> <p>Background</p> <p>Germline mutations in the DNA mismatch repair genes predispose to Lynch syndrome, thus conferring a high relative risk of colorectal and endometrial cancer. The <it>MLH1, MSH2 </it>and <it>MSH6 </it>mutational spectrum reported so far involves minor alterations scattered throughout their coding regions as well as large genomic rearrangements. Therefore, a combination of complete sequencing and a specialized technique for the detection of genomic rearrangements should be conducted during a proper DNA-testing procedure. Our main goal was to successfully identify Lynch syndrome families and determine the spectrum of <it>MLH1</it>, <it>MSH2 </it>and <it>MSH6 </it>mutations in Greek Lynch families in order to develop an efficient screening protocol for the Greek colorectal cancer patients' cohort.</p> <p>Methods</p> <p>Forty-two samples from twenty-four families, out of which twenty two of Greek, one of Cypriot and one of Serbian origin, were screened for the presence of germline mutations in the major mismatch repair genes through direct sequencing and MLPA. Families were selected upon Amsterdam criteria or revised Bethesda guidelines.</p> <p>Results</p> <p>Ten deleterious alterations were detected in twelve out of the twenty-four families subjected to genetic testing, thus our detection rate is 50%. Four of the pathogenic point mutations, namely two nonsense, one missense and one splice site change, are novel, whereas the detected genomic deletion encompassing exon 6 of the <it>MLH1 </it>gene has been described repeatedly in the LOVD database. The average age of onset for the development of both colorectal and endometrial cancer among mutation positive families is 43.2 years.</p> <p>Conclusion</p> <p>The mutational spectrum of the MMR genes investigated as it has been shaped by our analysis is quite heterogeneous without any strong indication for the presence of a founder effect.</p

EARLINET observations of Saharan dust intrusions over the northern Mediterranean region (2014--2017): properties and impact on radiative forcing

Remote sensing measurements of aerosols using depolarization Raman lidar systems from four EARLINET (European Aerosol Research Lidar Network) stations are used for a comprehensive analysis of Saharan dust events over the Mediterranean basin in the period 2014–2017. In this period, 51 dust events regarding the geometrical, optical and microphysical properties of dust were selected, classified and assessed according to their radiative forcing effect on the atmosphere. From west to east, the stations of Granada, Potenza, Athens and Limassol were selected as representative Mediterranean cities regularly affected by Saharan dust intrusions. Emphasis was given on lidar measurements in the visible (532 nm) and specifically on the consistency of the particle linear depolarization ratio (δp532), the extinction-to-backscatter lidar ratio (LR532) and the aerosol optical thickness (AOT532) within the observed dust layers. We found mean δp532 values of 0.24±0.05, 0.26±0.06, 0.28±0.05 and 0.28±0.04, mean LR532 values of 52±8, 51±9, 52±9 and 49±6 sr and mean AOT532 values of 0.40±0.31, 0.11±0.07, 0.12±0.10 and 0.32±0.17, for Granada, Potenza, Athens and Limassol, respectively. The mean layer thickness values were found to range from ∼ 1700 to ∼ 3400 m a.s.l. Additionally, based also on a previous aerosol type classification scheme provided by airborne High Spectral Resolution Lidar (HSRL) observations and on air mass backward trajectory analysis, a clustering analysis was performed in order to identify the mixing state of the dusty layers over the studied area. Furthermore, a synergy of lidar measurements and modeling was used to analyze the solar and thermal radiative forcing of airborne dust in detail. In total, a cooling behavior in the solar range and a significantly lower heating behavior in the thermal range was estimated. Depending on the dust optical and geometrical properties, the load intensity and the solar zenith angle (SZA), the estimated solar radiative forcing values range from −59 to −22 W m−2 at the surface and from −24 to −1 W m−2 at the top of the atmosphere (TOA). Similarly, in the thermal spectral range these values range from +2 to +4 W m−2 for the surface and from +1 to +3 W m−2 for the TOA. Finally, the radiative forcing seems to be inversely proportional to the dust mixing ratio, since higher absolute values are estimated for less mixed dust layers

A Role for the RNA Chaperone Hfq in Controlling Adherent-Invasive Escherichia coli Colonization and Virulence

Adherent-invasive Escherichia coli (AIEC) has been linked with the onset and perpetuation of inflammatory bowel diseases. The AIEC strain LF82 was originally isolated from an ileal biopsy from a patient with Crohn's disease. The pathogenesis of LF82 results from its abnormal adherence to and subsequent invasion of the intestinal epithelium coupled with its ability to survive phagocytosis by macrophages once it has crossed the intestinal barrier. To gain further insight into AIEC pathogenesis we employed the nematode Caenorhabditis elegans as an in vivo infection model. We demonstrate that AIEC strain LF82 forms a persistent infection in C. elegans, thereby reducing the host lifespan significantly. This host killing phenotype was associated with massive bacterial colonization of the nematode intestine and damage to the intestinal epithelial surface. C. elegans killing was independent of known LF82 virulence determinants but was abolished by deletion of the LF82 hfq gene, which encodes an RNA chaperone involved in mediating posttranscriptional gene regulation by small non-coding RNAs. This finding reveals that important aspects of LF82 pathogenesis are controlled at the posttranscriptional level by riboregulation. The role of Hfq in LF82 virulence was independent of its function in regulating RpoS and RpoE activity. Further, LF82Δhfq mutants were non-motile, impaired in cell invasion and highly sensitive to various chemical stress conditions, reinforcing the multifaceted function of Hfq in mediating bacterial adaptation. This study highlights the usefulness of simple non-mammalian infection systems for the identification and analysis of bacterial virulence factors

Tropospheric and stratospheric smoke over Europe as observed within EARLINET/ACTRIS in summer 2017

For several weeks in summer 2017, strong smoke layers were observed over Europe at numerous EARLINET stations. EARLINET is the European research lidar network and part of ACTRIS and comprises more than 30 ground-based lidars. The smoke layers were observed in the troposphere as well as in the stratosphere up to 25 km from Northern Scandinavia over whole western and central Europe to the Mediterranean regions. Backward trajectory analysis among other tools revealed that these smoke layers originated from strong wild fires in western Canada in combination with pyrocumulus convection. An extraordinary fire event in the mid of August caused intense smoke layers that were observed across Europe for several weeks starting on 18 August 2017. Maximum aerosol optical depths up to 1.0 at 532 nm were observed at Leipzig, Germany, on 22 August 2017 during the peak of this event. The stratospheric smoke layers reached extinction coefficient values of more than 600 Mm−1 at 532 nm, a factor of 10 higher than observed for volcanic ash after the Pinatubo eruption in the 1990s. First analyses of the intensive optical properties revealed low particle depolarization values at 532 nm for the tropospheric smoke (spherical particles) and rather high values (up to 20%) in the stratosphere. However, a strong wavelength dependence of the depolarization ratio was measured for the stratospheric smoke. This indicates irregularly shaped stratospheric smoke particles in the size range of the accumulation mode. This unique depolarization feature makes it possible to distinguish clearly smoke aerosol from cirrus clouds or other aerosol types by polarization lidar measurements. Particle extinction-to-backscatter ratios were rather low in the order of 40 to 50 sr at 355 nm, while values between 70-90 sr were measured at higher wavelengths. In the western and central Mediterranean, stratospheric smoke layers were most prominent in the end of August at heights between 16 and 20 km. In contrast, stratospheric smoke started to occur in the eastern Mediterranean (Cyprus and Israel) in the beginning of September between 18 and 23 km. Stratospheric smoke was still visible in the beginning of October at certain locations (e.g. Evora, Portugal), while tropospheric smoke was mainly observed until the end of August within Europe. An overview of the smoke layers measured at several EARLINET sites will be given. The temporal development of these layers as well as their geometrical and optical properties will be presented

Retrieval of optical and microphysical properties of transported Saharan dust over Athens and Granada based on multi-wavelength Raman lidar measurements: Study of the mixing processes

In this paper we extract the aerosol microphysical properties for a collection of mineral dust cases measured by multi-wavelength depolarization Raman lidar systems located at the National Technical University of Athens (NTUA, Athens, Greece) and the Andalusian Institute for Earth System Research (IISTA-CEAMA, Granada, Spain). The lidar-based retrievals were carried out with the Spheroidal Inversion eXperiments software tool (SphInX) developed at the University of Potsdam (Germany). The software uses regularized inversion of a two-dimensional enhancement of the Mie model based on the spheroid-particle approximation with the aspect ratio determining the particle shape. The selection of the cases was based on the transport time from the source regions to the measuring sites. The aerosol optical depth as measured by AERONET ranged from 0.27 to 0.54 (at 500 nm) depending on the intensity of each event. Our analysis showed the hourly mean particle linear depolarization ratio and particle lidar ratio values at 532 nm ranging from 11 to 34% and from 42 to 79 sr respectively, depending on the mixing status, the corresponding air mass pathways and their transport time. Cases with shorter transport time showed good agreement in terms of the optical and SphInX-retrieved microphysical properties between Athens and Granada providing a complex refractive index value equal to 1.4 + 0.004i. On the other hand, the results for cases with higher transport time deviated from the aforementioned ones as well as from each other, providing, in particular, an imaginary part of the refractive index ranging from 0.002 to 0.005. Reconstructions of two-dimensional shape-size distributions for each selected layer showed that the dominant effective particle shape was prolate with diverse spherical contributions. The retrieved volume concentrations reflect overall the intensity of the episodes.Spanish Ministry of Sciences, Innovation and Universities through project CGL2016-81092,Spanish Ministry of Education, Culture and Sports through grant FPU14/0368

Complete Genome Sequence of Crohn's Disease-Associated Adherent-Invasive E. coli Strain LF82

International audienceBACKGROUND: Ileal lesions of Crohn's disease (CD) patients are abnormally colonized by pathogenic adherent-invasive Escherichia coli (AIEC) able to invade and to replicate within intestinal epithelial cells and macrophages. PRINCIPAL FINDINGS: We report here the complete genome sequence of E. coli LF82, the reference strain of adherent-invasive E. coli associated with ileal Crohn's disease. The LF82 genome of 4,881,487 bp total size contains a circular chromosome with a size of 4,773,108 bp and a plasmid of 108,379 bp. The analysis of predicted coding sequences (CDSs) within the LF82 flexible genome indicated that this genome is close to the avian pathogenic strain APEC_01, meningitis-associated strain S88 and urinary-isolated strain UTI89 with regards to flexible genome and single nucleotide polymorphisms in various virulence factors. Interestingly, we observed that strains LF82 and UTI89 adhered at a similar level to Intestine-407 cells and that like LF82, APEC_01 and UTI89 were highly invasive. However, A1EC strain LF82 had an intermediate killer phenotype compared to APEC-01 and UTI89 and the LF82 genome does not harbour most of specific virulence genes from ExPEC. LF82 genome has evolved from those of ExPEC B2 strains by the acquisition of Salmonella and Yersinia isolated or clustered genes or CDSs located on pLF82 plasmid and at various loci on the chromosome. CONCLUSION: LF82 genome analysis indicated that a number of genes, gene clusters and pathoadaptative mutations which have been acquired may play a role in virulence of AIEC strain LF82