North American monsoon and convectively coupled equatorial waves simulated by IPCC AR4 coupled GCMs

This study evaluates the fidelity of North American monsoon and associated intraseasonal variability in the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4) coupled general circulation models (CGCMs). Twenty years of monthly precipitation data from each of the 22 models' twentieth-century climate simulations, together with the available daily precipitation data from 12 of them, are analyzed and compared with Global Precipitation Climatology Project (GPCP) monthly and daily precipitation. The authors focus on the seasonal cycle and horizontal pattern of monsoon precipitation in conjunction with the two dominant convectively coupled equatorial wave modes: the eastward-propagating Madden-Julian oscillation (MJO) and the westward-propagating easterly waves. The results show that the IPCC AR4 CGCMs have significant problems and display a wide range of skill in simulating the North American monsoon and associated intraseasonal variability. Most of the models reproduce the monsoon rainbelt, extending from southeast to northwest, and its gradual northward shift in early summer, but overestimate the precipitation over the core monsoon region throughout the seasonal cycle and fail to reproduce the monsoon retreat in the fall. Additionally, most models simulate good westward propagation of the easterly waves, but relatively poor eastward propagation of the MJO and overly weak variances for both the easterly waves and the MJO. There is a tendency for models without undiluted updrafts in their deep convection scheme to produce better MJO propagation.open221

The correlation of RNase A enzymatic activity with the changes in the distance between Nepsilon2-His12 and N delta1-His119 upon addition of stabilizing and destabilizing salts.

The effect of stabilizing and destabilizing salts on the catalytic behavior of ribonuclease A (RNase A) was investigated at pH 7.5 and 25 degrees C, using spectrophotometric, viscometric and molecular dynamic methods. The changes in the distance between N(epsilon2) of His(12) and N(delta1) of His(119) at the catalytic center of RNase A upon the addition of sodium sulfate, sodium hydrogen sulfate and sodium thiocyanate were evaluated by molecular dynamic methods. The compactness and expansion in terms of Stokes radius of RNase A upon the addition of sulfate ions as kosmotropic salts, and thiocyanate ion as a chaotropic salt, were estimated by viscometric measurements. Enzyme activity was measured using cytidine 2', 3'-cyclic monophosphate as a substrate. The results from the measurements of distances between N(epsilon2) of His(12) and N(delta1) of His(119) and Stokes radius suggest (i) that the presence of sulfate ions decreases the distance between the catalytic His residues and increases the globular compactness, and (ii) that there is an expansion of the enzyme surface as well as elongation of the catalytic center in the presence of thiocyanate ion. These findings are in agreement with activity measurements

Tropical intraseasonal variability in 14 IPCC AR4 climate models. Part I: Convective signals

This study evaluates the tropical intraseasonal variability, especially the fidelity of The results show that current state-of-the-art GCMs still have significant problems and display a wide range of skill in simulating the tropical intraseasonal variability. The total intraseasonal (2-128 day) variance of precipitation is too weak in most of the models. About half of the models have signals of convectively coupled equatorial waves, with Kelvin and MRG-EIG waves especially prominent. However, the variances are generally too weak for all wave modes except the EIG wave, and the phase speeds are generally too fast, being scaled to excessively deep equivalent depths. An interesting result is that this scaling is consistent within a given model across modes, in that both the symmetric and antisymmetric modes scale similarly to a certain equivalent depth. Excessively deep equivalent depths suggest that these models may not have a large enough reduction in their "effective static stability" due to diabatic heating. 3 The MJO variance approaches the observed value in only two of the 14 models, but is less than half of the observed value in the other 12 models. The ratio between the eastward MJO variance and the variance of its westward counterpart is too small in most of the models, which is consistent with the lack of highly coherent eastward propagation of the MJO in many models. Moreover, the MJO variance in 13 of the 14 models does not come from a pronounced spectral peak, but usually is associated with an overreddened spectrum, which in turn is associated with a too strong persistence of equatorial precipitation. The two models that arguably do best at simulating the MJO are the only ones having convective closures/triggers linked in some way to moisture convergence

Evaluation of single and multiple Doppler lidar techniques to measure complex flow during the XPIA field campaign

Accurate three-dimensional information of wind flow fields can be an important tool in not only visualizing complex flow but also understanding the underlying physical processes and improving flow modeling. However, a thorough analysis of the measurement uncertainties is required to properly interpret results. The XPIA (eXperimental Planetary boundary layer Instrumentation Assessment) field campaign conducted at the Boulder Atmospheric Observatory (BAO) in Erie, CO, from 2 March to 31 May 2015 brought together a large suite of in situ and remote sensing measurement platforms to evaluate complex flow measurement strategies. In this paper, measurement uncertainties for different single and multi-Doppler strategies using simple scan geometries (conical, vertical plane and staring) are investigated. The tradeoffs (such as time–space resolution vs. spatial coverage) among the different measurement techniques are evaluated using co-located measurements made near the BAO tower. Sensitivity of the single-/multi-Doppler measurement uncertainties to averaging period are investigated using the sonic anemometers installed on the BAO tower as the standard reference. Finally, the radiometer measurements are used to partition the measurement periods as a function of atmospheric stability to determine their effect on measurement uncertainty. It was found that with an increase in spatial coverage and measurement complexity, the uncertainty in the wind measurement also increased. For multi-Doppler techniques, the increase in uncertainty for temporally uncoordinated measurements is possibly due to requiring additional assumptions of stationarity along with horizontal homogeneity and less representative line-of-sight velocity statistics. It was also found that wind speed measurement uncertainty was lower during stable conditions compared to unstable conditions

Application of MJO Simulation Diagnostics to Climate Models

The ability of eight climate models to simulate the Madden-Julian oscillation (MJO) is examined using diagnostics developed by the U.S. Climate Variability and Predictability (CLIVAR) MJO Working Group. Although the MJO signal has been extracted throughout the annual cycle, this study focuses on the boreal winter (November-April) behavior. Initially, maps of the mean state and variance and equatorial space-time spectra of 850-hPa zonal wind and precipitation are compared with observations. Models best represent the intraseasonal space-time spectral peak in the zonal wind compared to that of precipitation. Using the phase-space representation of the multivariate principal components (PCs), the life cycle properties of the simulated MJOs are extracted, including the ability to represent how the MJO evolves from a given subphase and the associated decay time scales. On average, the MJO decay (e-folding) time scale for all models is shorter (~20- 29 days) than observations (~31 days). All models are able to produce a leading pair of multivariate principal components that represents eastward propagation of intraseasonal wind and precipitation anomalies, although the fraction of the variance is smaller than observed for all models. In some cases, the dominant time scale of these PCs is outside of the 30-80-day band. Several key variables associated with the model's MJO are investigated, including the surface latent heat flux, boundary layer (925 hPa) moisture convergence, and the vertical structure of moisture. Low-level moisture convergence ahead (east) of convection is associated with eastward propagation in most of the models. A few models are also able to simulate the gradual moistening of the lower troposphere that precedes observed MJO convection, as well as the observed geographical difference in the vertical structure of moisture associated with the MJO. The dependence of rainfall on lower tropospheric relative humidity and the fraction of rainfall that is stratiform are also discussed, including implications these diagnostics have for MJO simulation. Based on having the most realistic intraseasonal multivariate empirical orthogonal functions, principal component power spectra, equatorial eastward propagating outgoing longwave radiation (OLR), latent heat flux, low-level moisture convergence signals, and vertical structure of moisture over the Eastern Hemisphere, the superparameterized Community Atmosphere Model (SPCAM) and the ECHAM4/Ocean Isopycnal Model (OPYC) show the best skill at representing the MJO.open1149

Overview of the 2010 Carbonaceous Aerosols and Radiative Effects Study (CARES)

Substantial uncertainties still exist in the scientific understanding of the possible interactions between urban and natural (biogenic) emissions in the production and transformation of atmospheric aerosol and the resulting impact on climate change. The US Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) program's Carbonaceous Aerosol and Radiative Effects Study (CARES) carried out in June 2010 in Central Valley, California, was a comprehensive effort designed to improve this understanding. The primary objective of the field study was to investigate the evolution of secondary organic and black carbon aerosols and their climate-related properties in the Sacramento urban plume as it was routinely transported into the forested Sierra Nevada foothills area. Urban aerosols and trace gases experienced significant physical and chemical transformations as they mixed with the reactive biogenic hydrocarbons emitted from the forest. Two heavily-instrumented ground sites – one within the Sacramento urban area and another about 40 km to the northeast in the foothills area – were set up to characterize the evolution of meteorological variables, trace gases, aerosol precursors, aerosol size, composition, and climate-related properties in freshly polluted and "aged" urban air. On selected days, the DOE G-1 aircraft was deployed to make similar measurements upwind and across the evolving Sacramento plume in the morning and again in the afternoon. The NASA B-200 aircraft, carrying remote sensing instruments, was also deployed to characterize the vertical and horizontal distribution of aerosols and aerosol optical properties within and around the plume. This overview provides: (a) the scientific background and motivation for the study, (b) the operational and logistical information pertinent to the execution of the study, (c) an overview of key observations and initial findings from the aircraft and ground-based sampling platforms, and (d) a roadmap of planned data analyses and focused modeling efforts that will facilitate the integration of new knowledge into improved representations of key aerosol processes and properties in climate models.United States. Dept. of Energy. Atmospheric System Research Program (Contract DE-AC06-76RLO 1830)United States. National Oceanic and Atmospheric AdministrationUnited States. National Aeronautics and Space Administration. HQ Science Mission Directorate Radiation Sciences ProgramUnited States. National Aeronautics and Space Administration. CALIPSO ProgramUnited States. Dept. of Energy. Atmospheric Radiation Measurement Program (Interagency Agreement No. DE-AI02-05ER63985

Correlation of SHOX2 Gene Amplification and DNA Methylation in Lung Cancer Tumors

<p>Abstract</p> <p>Background</p> <p>DNA methylation in the <it>SHOX2 </it>locus was previously used to reliably detect lung cancer in a group of critical controls, including 'cytologically negative' samples with no visible tumor cell content, at a high specificity based on the analysis of bronchial lavage samples. This study aimed to investigate, if the methylation correlates with <it>SHOX2 </it>gene expression and/or copy number alterations. An amplification of the <it>SHOX2 </it>gene locus together with the observed tumor-specific hypermethylation might explain the good performance of this marker in bronchial lavage samples.</p> <p>Methods</p> <p><it>SHOX2 </it>expression, gene copy number and DNA methylation were determined in lung tumor tissues and matched morphologically normal adjacent tissues (NAT) from 55 lung cancer patients. Quantitative HeavyMethyl (HM) real-time PCR was used to detect <it>SHOX2 </it>DNA methylation levels. <it>SHOX2 </it>expression was assayed with quantitative real-time PCR, and copy numbers alterations were measured with conventional real-time PCR and array CGH.</p> <p>Results</p> <p>A hypermethylation of the <it>SHOX2 </it>locus in tumor tissue as compared to the matched NAT from the same patient was detected in 96% of tumors from a group of 55 lung cancer patients. This correlated highly significantly with the frequent occurrence of copy number amplification (p < 0.0001), while the expression of the <it>SHOX2 </it>gene showed no difference.</p> <p>Conclusions</p> <p>Frequent gene amplification correlated with hypermethylation of the <it>SHOX2 </it>gene locus. This concerted effect qualifies <it>SHOX2 </it>DNA methylation as a biomarker for lung cancer diagnosis, especially when sensitive detection is needed, i.e. in bronchial lavage or blood samples.</p

North American monsoon and convectively coupled equatorial waves simulated by IPCC AR4 coupled GCMs

This study evaluates the fidelity of North American monsoon and associated intraseasonal variability in the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4) coupled general circulation models (CGCMs). Twenty years of monthly precipitation data from each of the 22 models' twentieth-century climate simulations, together with the available daily precipitation data from 12 of them, are analyzed and compared with Global Precipitation Climatology Project (GPCP) monthly and daily precipitation. The authors focus on the seasonal cycle and horizontal pattern of monsoon precipitation in conjunction with the two dominant convectively coupled equatorial wave modes: the eastward-propagating Madden-Julian oscillation (MJO) and the westward-propagating easterly waves. The results show that the IPCC AR4 CGCMs have significant problems and display a wide range of skill in simulating the North American monsoon and associated intraseasonal variability. Most of the models reproduce the monsoon rainbelt, extending from southeast to northwest, and its gradual northward shift in early summer, but overestimate the precipitation over the core monsoon region throughout the seasonal cycle and fail to reproduce the monsoon retreat in the fall. Additionally, most models simulate good westward propagation of the easterly waves, but relatively poor eastward propagation of the MJO and overly weak variances for both the easterly waves and the MJO. There is a tendency for models without undiluted updrafts in their deep convection scheme to produce better MJO propagation.open221

SHOX2 DNA Methylation is a Biomarker for the diagnosis of lung cancer based on bronchial aspirates

<p>Abstract</p> <p>Background</p> <p>This study aimed to show that SHOX2 DNA methylation is a tumor marker in patients with suspected lung cancer by using bronchial fluid aspirated during bronchoscopy. Such a biomarker would be clinically valuable, especially when, following the first bronchoscopy, a final diagnosis cannot be established by histology or cytology. A test with a low false positive rate can reduce the need for further invasive and costly procedures and ensure early treatment.</p> <p>Methods</p> <p>Marker discovery was carried out by differential methylation hybridization (DMH) and real-time PCR. The real-time PCR based HeavyMethyl technology was used for quantitative analysis of DNA methylation of SHOX2 using bronchial aspirates from two clinical centres in a case-control study. Fresh-frozen and Saccomanno-fixed samples were used to show the tumor marker performance in different sample types of clinical relevance.</p> <p>Results</p> <p>Valid measurements were obtained from a total of 523 patient samples (242 controls, 281 cases). DNA methylation of SHOX2 allowed to distinguish between malignant and benign lung disease, i.e. abscesses, infections, obstructive lung diseases, sarcoidosis, scleroderma, stenoses, at high specificity (68% sensitivity [95% CI 62-73%], 95% specificity [95% CI 91-97%]).</p> <p>Conclusions</p> <p>Hypermethylation of SHOX2 in bronchial aspirates appears to be a clinically useful tumor marker for identifying subjects with lung carcinoma, especially if histological and cytological findings after bronchoscopy are ambiguous.</p