CDASH: a cloud-enabled program for structure solution from powder diffraction data

The simulated annealing approach to crystal structure determination from powder diffraction data, as implemented in the DASH program, is readily amenable to parallelization at the individual run level. Very large scale increases in speed of execution can be achieved by distributing individual DASH runs over a network of computers. The CDASH program delivers this by using scalable on-demand computing clusters built on the Amazon Elastic Compute Cloud service. By way of example, a 360 vCPU cluster returned the crystal structure of racemic ornidazole (Z0 = 3, 30 degrees of freedom) ca 40 times faster than a typical modern quad-core desktop CPU. Whilst used here specifically for DASH, this approach is of general applicability to other packages that are amenable to coarse-grained parallelism strategies.

Using data insertion with the NAME model to simulate the 8 May 2010 Eyjafjallajökull volcanic ash cloud

A data insertion method, where a dispersion model is initialized from ash properties derived from a series of satellite observations, is used to model the 8 May 2010 Eyjafjallajökull volcanic ash cloud which extended from Iceland to northern Spain. We also briefly discuss the application of this method to the April 2010 phase of the Eyjafjallajökull eruption and the May 2011 Grímsvötn eruption. An advantage of this method is that very little knowledge about the eruption itself is required because some of the usual eruption source parameters are not used. The method may therefore be useful for remote volcanoes where good satellite observations of the erupted material are available, but little is known about the properties of the actual eruption. It does, however, have a number of limitations related to the quality and availability of the observations. We demonstrate that, using certain configurations, the data insertion method is able to capture the structure of a thin filament of ash extending over northern Spain that is not fully captured by other modeling methods. It also verifies well against the satellite observations according to the quantitative object-based quality metric, SAL—structure, amplitude, location, and the spatial coverage metric, Figure of Merit in Space.

Inferences about pressures and vertical extension of cloud layers from POLDER3/PARASOL measurements in the oxygen A-band

We present new inferences about cloud vertical structures from multidirectionnal measurements in the oxygen A-band. The analysis of collocated data provided by instruments onboard satellite platforms within the A-Train, as well as simulations have shown that for monolayered clouds, the cloud oxygen pressure PO2PO2 derived from the POLDER3 instrument was sensitive to the cloud vertical structure in two ways: First, PO2PO2 is actually close to the pressure of the geometrical middle of cloud and we propose a method to correct it to get the cloud top pressure (CTP), and then to obtain the cloud geometrical extent. Second, for the liquid water clouds, the angular standard deviation σPO2σPO2 of PO2PO2 is correlated with the geometrical extent of cloud layers, which makes possible a second estimation of the cloud geometrical thickness. The determination of the vertical location of cloud layers from passive measurements, eventually completed from other observations, would be useful in many applications for which cloud macrophysical properties are needed

Cloud information content analysis of multi-angular measurements in the oxygen A-band: application to 3MI and MSPI

The vertical distribution of cloud cover has a significant impact on a large number of meteorological and climatic processes. Cloud top altitude and cloud geometrical thickness are then essential. Previous studies established the possibility of retrieving those parameters from multi-angular oxygen A-band measurements. Here we perform a study and comparison of the performances of future instruments. The 3MI (Multi-angle, Multi-channel and Multi-polarization Imager) instrument developed by EUMETSAT, which is an extension of the POLDER/PARASOL instrument, and MSPI (Multi-angles Spectro-Polarimetric Imager) develoloped by NASA's Jet Propulsion Laboratory will measure total and polarized light reflected by the Earth's atmosphere–surface system in several spectral bands (from UV to SWIR) and several viewing geometries. Those instruments should provide opportunities to observe the links between the cloud structures and the anisotropy of the reflected solar radiation into space. Specific algorithms will need be developed in order to take advantage of the new capabilities of this instrument. However, prior to this effort, we need to understand, through a theoretical Shannon information content analysis, the limits and advantages of these new instruments for retrieving liquid and ice cloud properties, and especially, in this study, the amount of information coming from the A-Band channel on the cloud top altitude (CTOP) and geometrical thickness (CGT). We compare the information content of 3MI A-Band in two configurations and that of MSPI. Quantitative information content estimates show that the retrieval of CTOP with a high accuracy is possible in almost all cases investigated. The retrieval of CGT seems less easy but possible for optically thick clouds above a black surface, at least when CGT > 1–2 km.

Constraining the aerosol influence on cloud fraction

Aerosol-cloud interactions have the potential to modify many different cloud properties. There is significant uncertainty in the strength of these aerosol-cloud interactions in analyses of observational data, partly due to the difficulty in separating aerosol effects on clouds from correlations generated by local meteorology. The relationship between aerosol and cloud fraction (CF) is particularly important to determine, due to the strong correlation of CF to other cloud properties and its large impact on radiation. It has also been one of the hardest to quantify from satellites due to the strong meteorological covariations involved. This work presents a new method to analyze the relationship between aerosol optical depth (AOD) and CF. By including information about the cloud droplet number concentration (CDNC), the impact of the meteorological covariations is significantly reduced. This method shows that much of the AOD-CF correlation is explained by relationships other than that mediated by CDNC. By accounting for these, the strength of the global mean AOD-CF relationship is reduced by around 80%. This suggests that the majority of the AOD-CF relationship is due to meteorological covariations, especially in the shallow cumulus regime. Requiring CDNC to mediate the AOD-CF relationship implies an effective anthropogenic radiative forcing from an aerosol influence on liquid CF of −0.48 W m−2 (−0.1 to −0.64 W m−2), although some uncertainty remains due to possible biases in the CDNC retrievals in broken cloud scenes.

Observational evidence for a negative shortwave cloud feedback in middle to high latitudes

Exploiting the observed robust relationships between temperature and optical depth in extratropical clouds, we calculate the shortwave cloud feedback from historical data, by regressing observed and modeled cloud property histograms onto local temperature in middle to high southern latitudes. In this region, all CMIP5 models and observational data sets predict a negative cloud feedback, mainly driven by optical thickening. Between 45° and 60°S, the mean observed shortwave feedback (−0.91 ± 0.82 W m−2 K−1, relative to local rather than global mean warming) is very close to the multimodel mean feedback in RCP8.5 (−0.98 W m−2 K−1), despite differences in the meridional structure. In models, historical temperature-cloud property relationships reliably predict the forced RCP8.5 response. Because simple theory predicts this optical thickening with warming, and cloud amount changes are relatively small, we conclude that the shortwave cloud feedback is very likely negative in the real world at middle to high latitudes.

What controls the vertical distribution of aerosol? Relationships between process sensitivity in HadGEM3–UKCA and inter-model variation from AeroCom Phase II

The vertical profile of aerosol is important for its radiative effects, but weakly constrained by observations on the global scale, and highly variable among different models. To investigate the controlling factors in one particular model, we investigate the effects of individual processes in HadGEM3–UKCA and compare the resulting diversity of aerosol vertical profiles with the inter-model diversity from the AeroCom Phase II control experiment. In this way we show that (in this model at least) the vertical profile is controlled by a relatively small number of processes, although these vary among aerosol components and particle sizes. We also show that sufficiently coarse variations in these processes can produce a similar diversity to that among different models in terms of the global-mean profile and, to a lesser extent, the zonal-mean vertical position. However, there are features of certain models' profiles that cannot be reproduced, suggesting the influence of further structural differences between models. In HadGEM3–UKCA, convective transport is found to be very important in controlling the vertical profile of all aerosol components by mass. In-cloud scavenging is very important for all except mineral dust. Growth by condensation is important for sulfate and carbonaceous aerosol (along with aqueous oxidation for the former and ageing by soluble material for the latter). The vertical extent of biomass-burning emissions into the free troposphere is also important for the profile of carbonaceous aerosol. Boundary-layer mixing plays a dominant role for sea salt and mineral dust, which are emitted only from the surface. Dry deposition and below-cloud scavenging are important for the profile of mineral dust only. In this model, the microphysical processes of nucleation, condensation and coagulation dominate the vertical profile of the smallest particles by number (e.g. total CN  >  3 nm), while the profiles of larger particles (e.g. CN  >  100 nm) are controlled by the same processes as the component mass profiles, plus the size distribution of primary emissions. We also show that the processes that affect the AOD-normalised radiative forcing in the model are predominantly those that affect the vertical mass distribution, in particular convective transport, in-cloud scavenging, aqueous oxidation, ageing and the vertical extent of biomass-burning emissions.

Cloud streets and land-water interactions in the Amazon

Cloud streets are common feature in the Amazon Basin. They form from the combination of the vertical trade wind stress and moist convection. Here, satellite imagery, data collected during the COBRA-PARA (Caxiuan Observations in the Biosphere, River and Atmosphere of Para) field campaign, and high resolution modeling are used to understand the streets` formation and behavior. The observations show that the streets have an aspect ratio of about 3.5 and they reach their maximum activity around 15:00 UTC when the wind shear is weaker, and the convective boundary layer reaches its maximum height. The simulations reveal that the cloud streets onset is caused by the local circulations and convection produced at the interfaces between forest and rivers of the Amazon. The satellite data and modeling show that the large rivers anchor the cloud streets producing a quasi-stationary horizontal pattern. The streets are associated with horizontal roll vortices parallel to the mean flow that organizes the turbulence causing advection of latent heat flux towards the upward branches. The streets have multiple warm plumes that promote a connection between the rolls. These spatial patterns allow fundamental insights on the interpretation of the Amazon exchanges between surface and atmosphere with important consequences for the climate change understanding.

The RAINY3D Code: The Treatment of Condensation in Nova Remnants during Nebular Phase

Classical nova remnants are important scenarios for improving the photoionization modeling. This work describes the pseudo-three-dimensional code RAINY3D, which drives the photoionization code Cloudy as a subroutine. Photoionization simulations of old nova remnants are also presented and discussed. In these simulations we analyze the effect of condensation in the remnant spectra. The condensed mass fraction affects the Balmer lines by a factor of greater than 4 when compared with homogeneous models, and this directly impacts the shell mass determination. The He II 4686/H beta ratio decreases by a factor of 10 in clumpy shells. These lines are also affected by the clump size and density distributions. The behavior of the strongest nebular line observed in nova remnants is also analyzed for heterogeneous shells. The gas diagnoses in novae ejecta are thought to be more accurate during the nebular phase, but we have determined that at this phase the matter distribution can strongly affect the derived shell physical properties and chemical abundances.

Gas streaming motions towards the nucleus of M81

We present two-dimensional stellar and gaseous kinematics of the inner 120 x 250 pc2 of the LINER/Seyfert 1 galaxy M81, from optical spectra obtained with the Gemini Multi-Object Spectrograph (GMOS) integral field spectrograph on the Gemini-North telescope at a spatial resolution of approximate to 10 pc. The stellar velocity field shows circular rotation and, overall, is very similar to the published large-scale velocity field, but deviations are observed close to the minor axis which can be attributed to stellar motions possibly associated with a nuclear bar. The stellar velocity dispersion of the bulge is 162 +/- 15 km s-1, in good agreement with previous measurements and leading to a black hole mass of M(BH) = 5.5+3.6(-2.0) x 107 M(circle dot) based on the M(BH)-Sigma relationship. The gas kinematics is dominated by non-circular motions and the subtraction of the stellar velocity field reveals blueshifts of approximate to-100 km s-1 on the far side of the galaxy and a few redshifts on the near side. These characteristics can be interpreted in terms of streaming towards the centre if the gas is in the plane. On the basis of the observed velocities and geometry of the flow, we estimate a mass inflow rate in ionized gas of approximate to 4.0 x 10-3 M(circle dot) yr-1, which is of the order of the accretion rate necessary to power the LINER nucleus of M81. We have also applied the technique of principal component analysis (PCA) to our data, which reveals the presence of a rotating nuclear gas disc within approximate to 50 pc from the nucleus and a compact outflow, approximately perpendicular to the disc. The PCA combined with the observed gas velocity field shows that the nuclear disc is being fed by gas circulating in the galaxy plane. The presence of the outflow is supported by a compact jet seen in radio observations at a similar orientation, as well as by an enhancement of the [O i]/H alpha line ratio, probably resulting from shock excitation of the circumnuclear gas by the radio jet. With these observations we are thus resolving both the feeding - via the nuclear disc and observed gas inflow, and the feedback - via the outflow, around the low-luminosity active nucleus of M81.

THE COMPTON-THICK SEYFERT 2 NUCLEUS OF NGC 3281: TORUS CONSTRAINTS FROM THE 9.7 mu m SILICATE ABSORPTION

We present mid-infrared (mid-IR) spectra of the Compton-thick Seyfert 2 galaxy NGC 3281, obtained with the Thermal-Region Camera Spectrograph at the Gemini-South telescope. The spectra present a very deep silicate absorption at 9.7 mu m, and [S IV] 10.5 mu m and [Ne II] 12.7 mu m ionic lines, but no evidence of polycyclic aromatic hydrocarbon emission. We find that the nuclear optical extinction is in the range 24 mag <= A(V) <= 83 mag. A temperature T = 300 K was found for the blackbody dust continuum component of the unresolved 65 pc nucleus and the region at 130 pc SE, while the region at 130 pc NW reveals a colder temperature (200 K). We describe the nuclear spectrum of NGC 3281 using a clumpy torus model that suggests that the nucleus of this galaxy hosts a dusty toroidal structure. According to this model, the ratio between the inner and outer radius of the torus in NGC 3281 is R(0)/R(d) = 20, with 14 clouds in the equatorial radius with optical depth of tau(V) = 40 mag. We would be looking in the direction of the torus equatorial radius (i = 60 degrees), which has outer radius of R(0) similar to 11 pc. The column density is N(H) approximate to 1.2 x 10(24) cm(-2) and the iron K alpha equivalent width (approximate to 0.5-1.2 keV) is used to check the torus geometry. Our findings indicate that the X-ray absorbing column density, which classifies NGC 3281 as a Compton-thick source, may also be responsible for the absorption at 9.7 mu m providing strong evidence that the silicate dust responsible for this absorption can be located in the active galactic nucleus torus.

Probing the Large Magellanic Cloud age gap at intermediate cluster masses

The Large Magellanic Cloud (LMC) has a rich star cluster system spanning a wide range of ages and masses. One striking feature of the LMC cluster system is the existence of an age gap between 3 and 10 Gyr. But this feature is not clearly seen among field stars. Three LMC fields containing relatively poor and sparse clusters whose integrated colours are consistent with those of intermediate-age simple stellar populations have been imaged in BVI with the Optical Imager (SOI) at the Southern Telescope for Astrophysical Research (SOAR). A total of six clusters, five of them with estimated initial masses M < 104 M(circle dot), were studied in these fields. Photometry was performed and colour-magnitude diagrams (CMDs) were built using standard point spread function fitting methods. The faintest stars measured reach V similar to 23. The CMD was cleaned from field contamination by making use of the three-dimensional colour and magnitude space available in order to select stars in excess relative to the field. A statistical CMD comparison method was developed for this purpose. The subtraction method has proven to be successful, yielding cleaned CMDs consistent with a simple stellar population. The intermediate-age candidates were found to be the oldest in our sample, with ages between 1 and 2 Gyr. The remaining clusters found in the SOAR/SOI have ages ranging from 100 to 200 Myr. Our analysis has conclusively shown that none of the relatively low-mass clusters studied by us belongs to the LMC age gap.

Contextual, but not auditory, fear conditioning is disrupted by neurotoxic selective lesion of the basal nucleus of amygdala in rats

The basolateral amygdala complex (BLA) is involved in acquisition of contextual and auditory fear conditioning. However, the BLA is not a single structure but comprises a group of nuclei, including the lateral (LA), basal (BA) and accessory basal (AB) nuclei. While it is consensual that the LA is critical for auditory fear conditioning, there is controversy on the participation of the BA in fear conditioning. Hodological and neurophysiological findings suggest that each of these nuclei processes distinct information in parallel; the BA would deal with polymodal or contextual representations, and the LA would process unimodal or elemental representations. Thus, it seems plausible to hypothesize that the BA is required for contextual, but not auditory, fear conditioning. This hypothesis was evaluated in Wistar rats submitted to multiple-site ibotenate-induced damage restricted to the BA and then exposed to a concurrent contextual and auditory fear conditioning training followed by separated contextual and auditory conditioning testing. Differing from electrolytic lesion and lidocaine inactivation, this surgical approach does not disturb fibers of passage originating in other brain areas, restricting damage to the aimed nucleus. Relative to the sham-operated controls, rats with selective damage to the BA exhibited disruption of performance in the contextual, but not the auditory, component of the task. Thus, while the BA seems required for contextual fear conditioning, it is not critical for both an auditory-US association, nor for the expression of the freezing response. (C) 2009 Elsevier Inc. All rights reserved.

Age-dependent changes in adenosine A(1) receptor distribution and density within the nucleus tractus solitarii of normotensive and hypertensive rats

This study shows the distribution and density of adenosine A1 receptor (A(1)R) within the nucleus tractus solitarii (NTS) of Wistar Kyoto (WKY) and spontaneously hypertensive rats (SHR) from birth to adulthood (1, 15, 30 and 90 days old). The NTS shows heterogeneous distribution of A(1)R in dorsomedial/dorsolateral, subpostremal and medial/intermediate subnuclei. A(1)R decrease from rostral to caudal within dorsomedial/dorsolateral subnucleus in 15-, 30- and 90-day-old WKY and SHR. A(1)R increase from rostral to caudal subpostremal subnucleus in 30- and 90-day-old WKY, and in 15-, 30- and 90-day-old SHR. Furthermore, A(1)Rs are increased in SHR as compared with WKY within dorsomedial/dorsolateral in 30- and 90-day-old and within subpostremal of 15-, 30- and 90-day-old rats. Finally, A(1)Rs increase from 1- to 30-day-old rats. Medial/intermediate did not show any changes in A(1)R from rostral to caudal levels, age or strain. In summary, our result highlights the importance of A1 adenosine system regarding the neural control of blood pressure and the development of hypertension.

On spermiogenesis, sperm cell morphology and accompanying secretions of Copidognathus (Acari: Halacaridae)

The genus Copidognathus includes one-third of the species of Halacaridae described to date. This article describes spermiogenesis, sperm cell morphology and accompanying secretions from three species of Copidognathus. Initial spermatids have electron-dense cytoplasm with scattered mitochondria, a well-developed Golgi body, and nuclei with patches of heterochromatin. The cytoplasm and nuclei of these cells undergo intense swelling. The second spermatids are large electron-translucent cells, with small mitochondria in row along the remains of the endoplasmatic reticulum. In the succeeding stage, most of the cytoplasmatic structures and mitochondria have disappeared or have undergone profound transformations. Nuclei and cells elongate and chromatin begins to condense near the nuclear envelope. An acrosomal complex appears at the tip of the nucleus. The acrosomal filament is thick and runs the entire length of the nucleus. Plasmalemmal invaginations at the cell surface give rise to tubules filled with an electron-dense material. Sperm cell maturation is completed in the ventral portion of the germinal part, near the testicular lumen. As a final step in spermiogenesis, cytoplasm of the last spermatid undergoes a moderate condensation and the cariotheca disappears. Mature sperm cells were found in a matrix of ""simple"" and ""complex"" corpuscles, the latter consisting of flattened, spindle-shaped secreted bodies. Rather than in individual sperm aggregates, spermatozoa were contained in a single droplet inside the vas deferens, on a large secretion mass, structured as rows of platelets sunk in a fine grained matrix. Each mature sperm cell is covered by a thick secreted coat. In contrast to the genera Rhombognathus and other Actinotrichida, Copidognathus displays a set of features that must be regarded as apomorphic. The absence of usual mitochondria, the presence of electro-dense tubules and secretions similar to those present in Thalassarachna and Halacarellus, and the pattern of nuclear condensation are possibly shared apomorphies with these latter genera. (C) 2010 Elsevier GmbH. All rights reserved.