Space-time analysis of the Air Quality Model Evaluation International Initiative (AQMEII) Phase 1 air quality simulations.

UNLABELLED: This study presents an evaluation of summertime ozone concentrations over North America (NA) and Europe (EU) using the database generated from Phase 1 of the Air Quality Model Evaluation International Initiative (AQMEII). The analysis focuses on identifying temporal and spatial features that can be used to stratify operational model evaluation metrics and to test the extent to which the various modeling systems can replicate the features seen in the observations. Using a synoptic map typing approach, it is demonstrated that model performance varies with meteorological conditions associated with specific synoptic-scale flow patterns over both eastern NA and EU. For example, the root mean square error of simulated daily maximum 8-hr ozone was twice as high when cloud fractions were high compared with when cloud fractions were low over eastern NA. Furthermore, results show that over both NA and EU the regional models participating in AQMEII were able to better reproduce the observed variance in ambient ozone levels than the global model used to specify chemical boundary conditions, although the variance simulated by almost all regional models is still less that the observed variance on all spatiotemporal scales. In addition, all modeling systems showed poor correlations with observed fluctuations on the intraday time scale over both NA and EU. Furthermore, a methodology is introduced to distinguish between locally influenced and regionally representative sites for the purpose of model evaluation. Results reveal that all models have worse model performance at locally influenced sites. Overall, the analyses presented in this paper show how observed temporal and spatial information can be used to stratify operational model performance statistics and to test the modeling systems' ability to replicate observed temporal and spatial features, especially at scales the modeling systems are designed to capture. IMPLICATIONS: The analyses presented in this paper demonstrate how observed temporal and spatial information can be used to stratify operational model performance and to test the modeling systems' ability to replicate observed temporal and spatial features. Decisions for the improvement of regional air quality models should be based on the information derived from only regionally representative sites.

Assessment of geochemical processes occurring in groundwaters in the coastal alluvial aquifer.

Groundwater samples are collected from 30 observation wells in the study area to analyze the hydrochemical quality for determining the seawater encroachment in the part of Central Godavari Delta, Bay of Bengal, India. In order to establish the baseline hydrochemical conditions and processes determining the groundwater quality, an integrated investigation coupled with multivariate statistical analysis and hydrochemical methods are used to identify and interpret the groundwater chemistry of the aquifer system. The major land use is irrigated agriculture and aquaculture in the study area. The ground waters affected by the seawater intrusion featured high levels of sodium (Na(+)), chloride (Ca(+)), and TDS, which are the simplest common indicators for seawater influence. The elevated levels of NO3-N at some monitoring wells indicate nitrate pollution of groundwater due to anthropogenic origin such as septic effluents or chemical fertilizers. Besides the major chemical compositions, it was also demonstrated that ionic ratios would be useful to delineate seawater intrusion and they include Na(+)/Ca(2+), Mg(2+)/Ca(2+), SO4 (2-)/Ca(2+), Na(+)/(Na(+) + Cl(-)), and Ca(-)/sum of anions. This paper demonstrates the variations in hydrochemical quality of groundwater and its evolution processes in two different seasons in the coastal aquifer alluvial settings.

Molecular conformation of dihydrouridine: puckered base nucleoside of transfer RNA.

The crystal structure of dihydrouridine hemihydrate has been determined by x-ray diffraction. Crystals of dihydrouridine contain two independent molecules in the asymmetric unit and a molecule of water. The x-ray structure determination has shown that the conformations of both molecules differ in important respects in the saturated base and the ribose. The molecular conformation of dihydrouridine has, for the first time, provided structural evidence that the rare nucleoside can proinote "loop" formation in the sugar-phosphate chain.

X-ray diffraction patterns of transfer RNA consistent with the presence of short parallel helices in the molecule.

X-ray diffraction data of yeast formylmethionine transfer RNA, Escherichia coli phenylalanine transfer RNA, and Escherichia coli arginine transfer RNA single crystals are compared with the Fourier transform of a helix. The results are consistent with the presence of short parallel double helical segments in the transfer RNA molecules.

Molecular structure of troponin C from chicken skeletal muscle at 3-angstrom resolution.

The x-ray structure of chicken skeletal muscle troponin C (TnC), the Ca2+-binding subunit of the troponin complex, shows that the protein is about 70 angstroms long with an unusual dumbbell shape. The carboxyl and amino domains are separated by a single long alpha helix of about nine turns. Only the two high-affinity Ca2+-Mg2+ sites of the COOH-domain are occupied by metal ions resulting in conformational differences between the COOH- and NH2-domains. These differences are probably important in the triggering of muscle contraction by TnC. Also the structure of TnC is relevant in understanding the function of other calcium-regulated proteins, in particular that of calmodulin because of its strong similarity in amino acid sequence.

Recurrent alpha-fetoprotein secreting Sertoli-Leydig cell tumor of ovary with an unusual presentation.

Alpha-fetoprotein secreting (AFP) Sertoli-Leydig cell tumors of ovary (SLCT) are now identified as a distinct entity among the uncommon group of sex cord tumors of ovary. We report an unusual case of recurrent AFP secreting ovarian tumors and as ileocecal mesenteric cyst in a 25-year-old patient resulting in difficulty in initial diagnosis of AFP producing SLCT. Although six recurrent cases were described out of the 25 reported cases of AFP secreting SLCTs, this patient with an unusual presentation of recurrence is the second case in the literature to the best of our knowledge.

A Reduced Form Model for Ozone Based on Two Decades of CMAQ Simulations for the Continental United States.

A Reduced Form Model (RFM) is a mathematical relationship between the inputs and outputs of an air quality model, permitting estimation of additional modeling without costly new regional-scale simulations. A 21-year Community Multiscale Air Quality (CMAQ) simulation for the continental United States provided the basis for the RFM developed in this study. Predictors included the principal component scores (PCS) of emissions and meteorological variables, while the predictand was the monthly mean of daily maximum 8-hour CMAQ ozone for the ozone season at each model grid. The PCS form an orthogonal basis for RFM inputs. A few PCS incorporate most of the variability of emissions and meteorology, thereby reducing the dimensionality of the source-receptor problem. Stochastic kriging was used to estimate the model. The RFM was used to separate the effects of emissions and meteorology on ozone concentrations. by running the RFM with emissions constant (ozone dependent on meteorology), or constant meteorology (ozone dependent on emissions). Years with ozone-conducive meteorology were identified, and meteorological variables best explaining meteorology-dependent ozone were identified. Meteorology accounted for 19% to 55% of ozone variability in the eastern US, and 39% to 92% in the western US. Temporal trends estimated for original CMAQ ozone data and emission-dependent ozone were mostly negative, but the confidence intervals for emission-dependent ozone are much narrower. Emission-driven changes in monthly mean ozone levels for the period 2000-2010 ranged from 6.4 to 10.9 ppb for the eastern US and from 1.4 to 2.5 ppb for the western US.

Anaplastic lymphoma kinase status in lung cancers: An immunohistochemistry and fluorescence in situ hybridization study from a tertiary cancer center in India.

BACKGROUND AND OBJECTIVES: Fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) have shown good concordance for the detection of echinoderm microtubule-associated protein-like 4 and anaplastic lymphoma kinase (ALK) rearrangement. Since studies reporting FISH/IHC concordance, clinicopathological features, and clinical outcomes of ALK-positive patients from India are lacking, this study was undertaken. MATERIALS AND METHODS: This is a retrospective, observational study of patients with adenocarcinoma of the lung on whom ALK test was performed between March 2013 and December 2015. ALK status was assessed in 341 patients by FISH using Vysis ALK Dual Color Break Apart Rearrangement Probe and IHC using ALK D5F3 clone. Clinicopathological features were noted. Patients were managed as per the standard guidelines. Clinical outcomes - response rate (RR) and progression-free survival (PFS) - were measured. RESULTS: ALK rearrangement was positive in 37 patients (10.9%). ALK positivity was observed more commonly in younger patients with no predilection for any gender or any specific histological subtype. ALK by IHC was highly sensitive (100%), compared to FISH with concordance rate of 94.4%. Thirty one of thirty seven (31 of 37) patients received therapy of which 3 patients received palliative chemotherapy and 28 patients received tyrosine kinase inhibitors (crizotinib/ceritinib). Overall RR observed was 77.4%, and median PFS had not been reached at a median follow-up of 12.5 months. INTERPRETATION AND CONCLUSIONS: We report higher frequency of ALK positivity (10.9%) in patients with adenocarcinoma of the lung. ALK by IHC is more sensitive than FISH for ALK detection with high concordance. These patients had good clinical outcome with TKIs targeting ALK fusion protein.

Structure of Paramecium tetraurelia calmodulin at 1.8 A resolution.

The crystal structure of calmodulin (CaM; M(r) 16,700, 148 residues) from the ciliated protozoan Paramecium tetraurelia (PCaM) has been determined and refined using 1.8 A resolution area detector data. The crystals are triclinic, space group P1, a = 29.66, b = 53.79, c = 25.49 A, alpha = 92.84, beta = 97.02, and gamma = 88.54 degrees with one molecule in the unit cell. Crystals of the mammalian CaM (MCaM; Babu et al., 1988) and Drosophila CaM (DCaM; Taylor et al., 1991) also belong to the same space group with very similar cell dimensions. All three CaMs have 148 residues, but there are 17 sequence changes between PCaM and MCaM and 16 changes between PCaM and DCaM. The initial difference in the molecular orientation between the PCaM and MCaM crystals was approximately 7 degrees as determined by the rotation function. The reoriented Paramecium model was extensively refitted using omit maps and refined using XPLOR. The R-value for 11,458 reflections with F > 3 sigma is 0.21, and the model consists of protein atoms for residues 4-147, 4 calcium ions, and 71 solvent molecules. The root mean square (rms) deviations in the bond lengths and bond angles in the model from ideal values are 0.016 A and 3 degrees, respectively. The molecular orientation of the final PCaM model differs from MCaM by only 1.7 degrees. The overall Paramecium CaM structure is very similar to the other calmodulin structures with a seven-turn long central helix connecting the two terminal domains, each containing two Ca-binding EF-hand motifs. The rms deviation in the backbone N, Ca, C, and O atoms between PCaM and MCaM is 0.52 A and between PCaM and DCaM is 0.85 A. The long central helix regions differ, where the B-factors are also high, particularly in PCaM and MCaM. Unlike the MCaM structure, with one kink at D80 in the middle of the linker region, and the DCaM structure, with two kinks at K75 and I85, in our PCaM structure there are no kinks in the helix; the distortion appears to be more gradually distributed over the entire helical region, which is bent with an apparent radius of curvature of 74.5(2) A. The different distortions in the central helical region probably arise from its inherent mobility.

Structure of the oxidized long-chain flavodoxin from Anabaena 7120 at 2 A resolution.

The structure of the long-chain flavodoxin from the photosynthetic cyanobacterium Anabaena 7120 has been determined at 2 A resolution by the molecular replacement method using the atomic coordinates of the long-chain flavodoxin from Anacystis nidulans. The structure of a third long-chain flavodoxin from Chondrus crispus has recently been reported. Crystals of oxidized A. 7120 flavodoxin belong to the monoclinic space group P2(1) with a = 48.0, b = 32.0, c = 51.6 A, and beta = 92 degrees, and one molecule in the asymmetric unit. The 2 A intensity data were collected with oscillation films at the CHESS synchrotron source and processed to yield 9,795 independent intensities with Rmerg of 0.07. Of these, 8,493 reflections had I > 2 sigma and were used in the analysis. The model obtained by molecular replacement was initially refined by simulated annealing using the XPLOR program. Repeated refitting into omit maps and several rounds of conjugate gradient refinement led to an R-value of 0.185 for a model containing atoms for protein residues 2-169, flavin mononucleotide (FMN), and 104 solvent molecules. The FMN shows many interactions with the protein with the isoalloxazine ring, ribityl sugar, and the 5'-phosphate. The flavin ring has its pyrimidine end buried into the protein, and the functional dimethyl benzene edge is accessible to solvent. The FMN interactions in all three long-chain structures are similar except for the O4' of the ribityl chain, which interacts with the hydroxyl group of Thr 88 side chain in A. 7120, while with a water molecule in the other two. The phosphate group interacts with the atoms of the 9-15 loop as well as with NE1 of Trp 57. The N5 atom of flavin interacts with the amide NH of Ile 59 in A. 7120, whereas in A. nidulans it interacts with the amide NH of Val 59 in a similar manner. In C. crispus flavodoxin, N5 forms a hydrogen bond with the side chain hydroxyl group of the equivalent Thr 58. The hydrogen bond distances to the backbone NH groups in the first two flavodoxins are 3.6 A and 3.5 A, respectively, whereas in the third flavodoxin the distance is 3.1 A, close to the normal value. Even though the hydrogen bond distances are long in the first two cases, still they might have significant energy because their microenvironment in the protein is not accessible to solvent.(ABSTRACT TRUNCATED AT 400 WORDS)

Estimation of hookworm intensity by anthelmintic expulsion in primary schoolchildren in south India.

A study was carried out between March 1990 and February 1991 to determine the prevalence and intensity of hookworm infection in 151 primary schoolchildren, aged 6-12 years, in Jalaripet, a slum area in South India predominantly inhabited by fishermen. Pre-treatment stool samples were processed by a modified formalin-ethyl acetate sedimentation technique to determine ova counts. All children were treated with pyrantel pamoate and post-chemotherapy stools were collected over 48 h to recover expelled worms. The overall prevalence of hookworm infection was 45% and the mean egg count was 192 eggs/g. The mean worm burden was 1.25 worms/child. The influence of host factors such as age and sex, environmental factors and behavioural factors on the intensity of egg output and worm burden was investigated.

Spatial and temporal variations in the trace elemental data over the northeastern United States.

Time series of trace elemental concentrations (14 species) of atmospheric fine particles measured in the northeastern United States between 1988 and 1998 are analyzed for spatial and temporal variations. The influence of synoptic-scale systems to the transport and accumulation of pollutants can be investigated successfully if the short-term fluctuations (i.e. weather-induced variations) embedded in the time series of pollutant concentrations are separated from the original time series. The spatial short-term correlation coefficients for Al, Br, Fe, Se, and Zn permit good predictions of pollutant concentrations up to distances of about 350 km from a given monitor. The species correlation matrices for individual sites reveal that As, Br, Se, and Zn are highly correlated in New York State, while Fe, Mn, and V show also strong correlations, suggesting the commonality of source regions for these industrial and urban pollutants impacting New York.

Assessing the effects of transboundary ozone pollution between Ontario, Canada and New York, USA.

We investigated the effects of transboundary pollution between Ontario and New York using both observations and modeling results. Analysis of the spatial scales associated with ozone pollution revealed the regional and international character of this pollutant. A back-trajectory-clustering methodology was used to evaluate the potential for transboundary pollution trading and to identify potential pollution source regions for two sites: CN tower in Toronto and the World Trade Center in New York City. Transboundary pollution transport was evident at both locations. The major pollution source areas for the period examined were the Ohio River Valley and Midwest. Finally, we examined the transboundary impact of emission reductions through photochemical models. We found that emissions from both New York and Ontario were transported across the border and that reductions in predicted O3 levels can be substantial when emissions on both sides of the border are reduced.

Demonstrating attainment of the air quality standards: integration of observations and model predictions into the probabilistic framework.

This paper introduces an integrated observational-modeling approach to transform the deterministic nature of attainment demonstrations of the National Ambient Air Quality Standard (NAAQS) into the probabilistic framework. While the methods presented here can be used to address any air quality standard that is based on extreme values, this paper focuses on the application to the 1-hr and 8-hr NAAQS for ozone. Extreme value statistics and resampling techniques are applied to estimate the probability of exceeding the NAAQS for both 1-hr and 8-hr ozone concentrations. Within the integrated observation-modeling analysis approach, we show that the model-to-model differences in the predicted responses to emission reductions are smaller than the model-to-model differences in predicted absolute ozone concentrations. We illustrate that the emission reductions stemming from a real-world emission control strategy would substantially reduce the probability of exceeding the NAAQS over a large portion of the eastern United States, especially for the 8-hr average ozone concentrations.

Determining temporal and spatial variations in ozone air quality.

Unless the change in emissions is substantial, the resulting improvement in ozone air quality can be easily masked by the meteorological variability. Therefore, the meteorological and chemical signals must be separated in examining ozone trends. In this paper, we discuss the use of the Kolmogorov-Zurbenko filter in evaluating the temporal and spatial variations in ozone air quality utilizing ozone concentration data from several monitoring locations in the northeastern United States. The results indicate a downward trend in the ozone concentrations during the period 1983-1992 at most locations in the northeastern United States. The results also reveal that ozone is a regional-scale problem in the Northeast.

An evaluation of the UAM-V predicted concentrations of carbon monoxide and reactive nitrogen compounds over the eastern United States during summer 1995.

While there is a clear need to evaluate a photochemical model's ability in predicting not only the concentrations of O3, but also precursors and other trace species, many previous studies have focused only on the assessment of During the 1995 summer season, in addition to the routine monitoring of criteria pollutants, several research-oriented monitoring campaigns were conducted over the eastern United States, providing an extensive database of reactive nitrogen compounds, CO, and speciated hydrocarbon data. In this study, we examine the ability of a photochemical modeling system, RAMS/ UAM-V, to reproduce the measured concentrations of CO, NO2, and NOy over the region during the summer of 1995. The results demonstrate that there is agreement between modeled and measured seasonal average concentrations of NO2, both at the routine and research monitors. The same is true for NOy, but to a lesser degree. However, the model is found to significantly underpredict CO for the routine monitors in comparison to the research monitors.

A comparison of measured and simulated ozone concentrations in the rural areas of the eastern United States during summer 1995.

The recent regulatory actions toward a longer-term (i.e., 8-hr) average ozone standard have brought forth the potential for many rural areas in the eastern United States to be in noncompliance. However, since a majority of these rural areas have generally few sources of anthropogenic emissions, the measured ozone levels primarily reflect the effects of the transport of ozone and its precursor pollutants and natural emissions. While photochemical grid models have been applied to urban areas to develop ozone mitigation measures, these efforts have been limited to high ozone episode events only and do not adequately cover rural regions. In this study, we applied a photochemical modeling system, RAMS/UAM-V, to the eastern United States from June 1-August 31, 1995. The purpose of the study is to examine the predictive ability of the modeling system at rural monitoring stations that are part of the Clean Air Status Trends Network (CASTNet) and the Gaseous Pollutant Monitoring Program (GPMP). The results show that the measured daily 1-hr ozone maxima and the seasonal average of the daily 1-hr ozone maxima are in better agreement with the predictions of the modeling system than those for the daily 8-hr ozone maxima. Also, the response of the modeling system in reproducing the measured range of ozone levels over the diurnal cycle is poor, suggesting the need for improvement in the treatment of the physical and chemical processes of the modeling system during the nighttime and morning hours if it is to be used to address the 8-hr ozone standard.

Ozone air quality over North America: part I--a review of reported trends.

Ozone and precursor trends can be used to measure the effectiveness of regulatory programs that have been implemented. In this paper, we review trends in the concentrations of O3 NOx, and HCs over North America that have been reported in the literature. Although most existing trend studies are confounded by meteorological variability, both the raw data trends and the trends adjusted for meteorology collectively indicate a general decreasing trend in O3 concentrations in most areas of the United States during 1985-1996. In Canada, mean daily maximum 1-hr O3 concentrations at urban sites show mixed trends with a majority of sites showing an increase from 1980 to 1993. Mean daily maximum 1-hr O3 at most regionally representative Canadian sites appears to decrease from 1985 to 1993 or shows no significant change. There are far fewer data and analyses of NOx and HC trends. Available studies covering various ranges of years indicate decreases in ambient NO and HC concentrations in Los Angeles, CA, decreases in HC concentrations in northeastern U.S. cities, and decreases in NOx concentrations in Canadian cities. Two key needs are long-term HC and NOx measurements, particularly at rural sites, and a systematic comparison of trend detection techniques on a reference data set.

Ozone air quality over north america: part II--an analysis of trend detection and attribution techniques.

Assessment of regulatory programs aimed at improving ambient O3 air quality is of considerable interest to the scientific community and to policymakers. Trend detection, the identification of statistically significant long-term changes, and attribution, linking change to specific climatological and anthropogenic forcings, are instrumental to this assessment. Detection and attribution are difficult because changes in pollutant concentrations of interest to policymakers may be much smaller than natural variations due to weather and climate. In addition, there are considerable differences in reported trends seemingly based on similar statistical methods and databases. Differences arise from the variety of techniques used to reduce nontrend variation in time series, including mitigating the effects of meteorology and the variety of metrics used to track changes. In this paper, we review the trend assessment techniques being used in the air pollution field and discuss their strengths and limitations in discerning and attributing changes in O3 to emission control policies.

Do we understand trends in atmospheric sulfur species?

Anomalies appear to exist in our understanding of atmospheric sulfur compounds, specifically as evidenced in the time trends of the different chemical forms of these compounds. Trends determined at a number of locations by several different groups seem to indicate that, responding to emission reductions across North America, the concentration of SO2 in the atmosphere is declining more rapidly than that of aerosol SO4(2-). A number of possible reasons for this discrepancy are examined, but it is not possible to provide a definitive answer at this stage. The intent is to stimulate debate, because shortcomings in our understanding of the processes involved could have profound implications for the credibility of abatement strategies and policies for both acid deposition and fine particulate matter (PM).