Lidar observations and modeling of cold air outbreaks during MASEX and GALE

As part of MASEX and GALE a number of research flights were carried out over the Marine Boundary Layer (MBL) during periods when extremely cold and dry continental air was flowing out over the warm coastal waters at the east coast of the U.S. Such periods, which are named cold air outbreaks are characterized by massive warming and moistening of the MBL resulting in rapid entrainment conditions. As the MBL deepens as a function of fetch over the ocean, clouds develop. The line of cloud formation typically follows the coast line closely as has been observed many times from satellite imagery. The backscatter data from the NASA Goddard airborne lidar, which was used to measure the depth of the MBL in great detail, is ideally suited to verify parametrized models of boundary layer growth rate. The data indicates that the deepening MBL gradually develops clouds at its top. Those clouds form an integral part of the MBL and exercise an important influence on the energy cycle within the MBL. It is suggested that the rapid entrainment observed during overcast conditions represent an increase in efficiency of conversion of available turbulence kinetic energy into entrainment energy

Convective structure of the planetary boundary layer of the ocean during gale

The structure of the Planetary Boundary Layer (PBL) was measured, using an airborne lidar, over the Atlantic Ocean during several intensive observation periods of the Genesis of Atlantic Lows Experiment (GALE). Primary emphasis is on the understanding of the convective structure within the PBL during cold air outbreaks. Cold outbreaks generally occur in between the development of coastal storms; and behind a cold front sweeping down from Canada out across the Atlantic. As the cold dry air moves over the relatively warm ocean, it is heated and moistened. The transfer of latent and sensible heat during these events accounts for most of the heat transfer between the ocean and atmosphere during winter. Moistening of the PBL during these eventsis believed to be an important factor in determining the strength of development of the storm system which follows. In general, the more PBL moisture available as latent heat the higher the probability the storm will intensify. The major mechanism for vertical mixing of heat and mositure within the PBL is cellular convection. Knowlede of the organization and structure of the convection is important for understanding the process

Haze in the Klang Valley of Malaysia

Continuous measurements of dry aerosol light scattering (Bsp) were made at two sites in the Klang Valley of Malaysia between December 1998 and December 2000. In addition 24-h PM2.5 samples were collected on a one-day-in-six cycle and the chemical composition of the aerosol was determined. Periods of excessive haze were defined as 24-h average Bsp values greater than 150 Mm-1 and these occurred on a number of occasions, between May and September 1999, during May 2000, and between July and September 2000. The evidence for smoke being a significant contributor to aerosol during periods of excessive haze is discussed and includes features of the aerosol chemistry, the diurnal cycle of Bsp, and the coincidence of forest fires on Sumatra during the southwest (SW) monsoon period, as well as transport modelling for one week of the southwest Monsoon of 2000. The study highlights that whilst transboundary smoke is a major contributor to poor visibility in the Klang Valley, smoke from fires on Peninsular Malaysia is also a contributor, and at all times, the domestic source of secondary particle production is present

Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures

16S rRNA gene profiling has revolutionized the field of microbial ecology. Many researchers in various fields have embraced this technology to investigate bacterial compositions of samples derived from many different ecosystems. However, it is important to acknowledge the current limitations and drawbacks of 16S rRNA gene profiling. Although sample handling, DNA extraction methods and the choice of universal 16S rRNA gene PCR primers are well known factors that could seriously affect the final results of microbiota profiling studies, inevitable amplification artifacts, such as chimera formation and PCR competition, are seldom appreciated. Here we report on a novel micelle based amplification strategy, which overcomes these limitations via the clonal amplification of targeted DNA molecules. Our results show that micelle PCR drastically reduces chimera formation by a factor of 38 (1.5% vs. 56.9%) compared with traditional PCR, resulting in improved microbial diversity estimates. In addition, compartmentalization during micelle PCR prevents PCR competition due to unequal amplification rates of different 16S template molecules, generating robust and accurate 16S microbiota profiles required for comparative studies (e.g. longitudinal surveys)

Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling

In the last decade, many researchers have embraced 16S rRNA gene sequencing techniques, which has led to a wealth of publications and documented differences in the composition of microbial communities derived from many different ecosystems. However, comparison between different microbiota studies is currently very difficult due to the lack of a standardized 16S rRNA gene sequencing protocol. Here we report on a novel approach employing micelle PCR (micPCR) in combination with an internal calibrator that allows for standardization of microbiota profiles via their absolute abundances. The addition of an internal calibrator allows the researcher to express the resulting operational taxonomic units (OTUs) as a measure of 16S rRNA gene copies by correcting the number of sequences of each individual OTU in a sample for efficiency differences in the NGS process. Additionally, accurate quantification of OTUs obtained from negative extraction control samples allows for the subtraction of contaminating bacterial DNA derived from the laboratory environment or chemicals/reagents used. Using equimolar synthetic microbial community samples and low biomass clinical samples, we demonstrate that the calibrated micPCR/NGS methodology possess a much higher precision and a lower limit of detection compared with traditional PCR/NGS, resulting in more accurate microbiota profiles suitable for multi-study comparison

Outcome measures in rheumatoid arthritis randomised trials over the last 50 years

BACKGROUND: The development and application of standardised sets of outcomes to be measured and reported in clinical trials have the potential to increase the efficiency and value of research. One of the most notable of the current outcome sets began nearly 20 years ago: the World Health Organization and International League of Associations for Rheumatology core set of outcomes for rheumatoid arthritis clinical trials, originating from the OMERACT (Outcome Measures in Rheumatology) Initiative. This study assesses the use of this core outcome set by randomised trials in rheumatology. METHODS: An observational review was carried out of 350 randomised trials for the treatment of rheumatoid arthritis identified through The Cochrane Library (up to and including September 2012 issue). Reports of these trials were evaluated to determine whether or not there were trends in the proportion of trials reporting on the full set of core outcomes over time. Researchers who conducted trials after the publication of the core set were contacted to assess their awareness of it and to collect reasons for non-inclusion of the full core set of outcomes in the study. RESULTS: Since the introduction of the core set of outcomes for rheumatoid arthritis, the consistency of measurement of the core set of outcomes has improved, although variation in the choice of measurement instrument remains. The majority of trialists who responded said that they would consider using the core outcome set in the design of a new trial. CONCLUSIONS: This observational review suggests that a higher percentage of trialists conducting trials in rheumatoid arthritis are now measuring the rheumatoid arthritis core outcome set. Core outcome sets have the potential to improve the evidence base for health care, but consideration must be given to the methods for disseminating their availability amongst the relevant communities

Large aperture scanning airborne lidar

A large aperture scanning airborne lidar facility is being developed to provide important new capabilities for airborne lidar sensor systems. The proposed scanning mechanism allows for a large aperture telescope (25 in. diameter) in front of an elliptical flat (25 x 36 in.) turning mirror positioned at a 45 degree angle with respect to the telescope optical axis. The lidar scanning capability will provide opportunities for acquiring new data sets for atmospheric, earth resources, and oceans communities. This completed facility will also make available the opportunity to acquire simulated EOS lidar data on a near global basis. The design and construction of this unique scanning mechanism presents exciting technological challenges of maintaining the turning mirror optical flatness during scanning while exposed to extreme temperatures, ambient pressures, aircraft vibrations, etc