First results from the Very Small Array -- I. Observational methods

The Very Small Array (VSA) is a synthesis telescope designed to image faint structures in the cosmic microwave background on degree and sub-degree angular scales. The VSA has key differences from other CMB interferometers with the result that different systematic errors are expected. We have tested the operation of the VSA with a variety of blank-field and calibrator observations and cross-checked its calibration scale against independent measurements. We find that systematic effects can be suppressed below the thermal noise level in long observations; the overall calibration accuracy of the flux density scale is 3.5 percent and is limited by the external absolute calibration scale.Comment: 9 pages, 10 figures, MNRAS in press (Minor revisions

Multilevel Parallelization of AutoDock 4.2

<p>Abstract</p> <p>Background</p> <p>Virtual (computational) screening is an increasingly important tool for drug discovery. AutoDock is a popular open-source application for performing molecular docking, the prediction of ligand-receptor interactions. AutoDock is a serial application, though several previous efforts have parallelized various aspects of the program. In this paper, we report on a multi-level parallelization of AutoDock 4.2 (mpAD4).</p> <p>Results</p> <p>Using MPI and OpenMP, AutoDock 4.2 was parallelized for use on MPI-enabled systems and to multithread the execution of individual docking jobs. In addition, code was implemented to reduce input/output (I/O) traffic by reusing grid maps at each node from docking to docking. Performance of mpAD4 was examined on two multiprocessor computers.</p> <p>Conclusions</p> <p>Using MPI with OpenMP multithreading, mpAD4 scales with near linearity on the multiprocessor systems tested. In situations where I/O is limiting, reuse of grid maps reduces both system I/O and overall screening time. Multithreading of AutoDock's Lamarkian Genetic Algorithm with OpenMP increases the speed of execution of individual docking jobs, and when combined with MPI parallelization can significantly reduce the execution time of virtual screens. This work is significant in that mpAD4 speeds the execution of certain molecular docking workloads and allows the user to optimize the degree of system-level (MPI) and node-level (OpenMP) parallelization to best fit both workloads and computational resources.</p

WHF IASC Roadmap on Chagas Disease

Background: Chagas Disease is a neglected tropical disease caused by the protozoan Trypanosoma cruzi, with some of the most serious manifestations affecting the cardiovascular system. It is a chronic, stigmatizing condition, closely associated with poverty and affecting close to 6 million people globally. Although historically the disease was limited to endemic areas of Latin America recent years have seen an increasing global spread. In addition to the morbidity and mortality associated with the disease, the social and economic burdens on individuals and society are substantial. Often called the ‘silent killer’, Chagas disease is characterized by a long, asymptomatic phase in affected individuals. Approximately 30% then go on develop chronic Chagas cardiomyopathy and other serious cardiac complications such as stroke, rhythm disturbances and severe heart failure. Methods: In a collaboration of the World Hearth Federation (WHF) and the Inter-American Society of Cardiology (IASC) a writing group consisting of 20 diverse experts on Chagas disease (CD) was convened. The group provided up to date expert knowledge based on their area of expertise. An extensive review of the literature describing obstacles to diagnosis and treatment of CD along with proposed solutions was conducted. A survey was sent to all WHF Members and, using snowball sampling to widen the consultation, to a variety of health care professionals working in the CD global health community. The results were analyzed, open comments were reviewed and consolidated, and the findings were incorporated into this document, thus ensuring a consensus representation. Results: The WHF IASC Roadmap on Chagas Disease offers a comprehensive summary of current knowledge on prevention, diagnosis and management of the disease. In providing an analysis of ‘roadblocks’ in access to comprehensive care for Chagas disease patients, the document serves as a framework from which strategies for implementation such as national plans can be formulated. Several dimensions are considered in the analysis: healthcare system capabilities, governance, financing, community awareness and advocacy. Conclusion: The WHF IASC Roadmap proposes strategies and evidence-based solutions for healthcare professionals, health authorities and governments to help overcome the barriers to comprehensive care for Chagas disease patients. This roadmap describes an ideal patient care pathway, and explores the roadblocks along the way, offering potential solutions based on available research and examples in practice. It represents a call to action to decision-makers and health care professionals to step up efforts to eradicate Chagas disease

Assessing sea grass meadows condition at “El Río” Special Area of Conservation off “La Graciosa e Islotes del Norte de Lanzarote” Marine Reserve

Cymodosea nodosa meadows, known as ‘sebadales’ or ‘manchones’ at Canary Islands, represent EUNIS habitat type code A5.5311, called Macaronesian Cymodocea beds. As it’s described at European Union Habitats Directive (92/43/CEE) Annex 1, sea grass meadows belong to 1110 Sandbanks which are slightly covered by seawater all the time, within Natura 2000 Network. Several ‘sebadales’ throughout the archipelago are included in this Network as Special Areas of Conservation. Cymodosea nodosa is regionally included within the Canary Islands Protected Species List (Ley 4/2010), as a species ‘of interest to ecosystems of Canary Islands”, is usually found at a narrow depth range (10 to 20 m of depth) and, on the whole, best structured meadows are settled at sheltered bays, away from wave and current beating, flimsier at exposed areas. Deeper meadows are also sparser, being C. nodosa replaced by green algae Caulerpa prolifera and Caulerpa racemosa, although mixed algae-sea grass meadows are often found at different depths. The project Assessment of marine flora (‘sebadal’, ma¨erl, ‘mujo’) of ‘La Graciosa e Islotes del Norte de Lanzarote’ Marine Reserve, funded by ‘Viceconsejer´ıa de Pesca y Aguas de la Consejer´ıa de Agricultura, Ganader´ıa, Pesca y Aguas’, Canary Islands Government, has had the aim of assessing sea grass meadows condition and distribution at ‘El R´ıo’ Natura 2000 Network Special Area of Conservation, the channel between La Graciosa and Lanzarote. ‘LA GRACIOSA 1311’ cruise was performed within the framework of the project. First of all previous information on sea grass shallow distribution (up to a depth of 20 m) in the study area was reviewed. Afterwards, a tugged underwater video camera was used onboard of the Marine Reserve Surveillance Vessel to update cartographic info performing a grid of sampling stations, covering previously known distribution limits and verifying current presence/absence data and density. Furthermore, population parameters were obtained in order to assess ‘sebadal’ condition. Fixed stations were selected in regards to this process, and methodology applied on them was as follows: five radial arranged transects were performed, identifying fragmentation (it estimates meadow continuity regarding observed cover), density (mean value of several shoots number counts with 20 x 20 cm grids placed every 2 m), height (mean value in cm of 10 independent samples by transect) and fish and macroinvertebrate species richness for each transect. Graphic picture of sea grass density was made depending on two levels: low density level transects ( 10 shoots/grid ( 50 shoots/m2) and medium density level transects ( 10 shoots/grid ( 50 shoots/m2). Main study result is an estimate for the study region (‘El R´ıo’) and time of year of Cymodocea nodosa population total distribution cover which comes to 1.640.076 m2, including a higher density ‘sebadal’ of 178.256 m2

Peptide Models - XXIV: An ab Initio Study on N-formyl-l-prolinamide With Trans Peptide Bond. The Existence or Non-existence of Alpha(l) And Epsilon(l) Conformations

N-formyl-L-prolinamide was subjected to geometry optimization at three levels of theory: HF/3-21G, HF/6-31G (d) and B3LYP/6-31G (d). At all three levels of computation the global minimum was gamma(L) (inverse gamma-Turn) backbone conformation with two ring-puckered forms "UP" and "DOWN". At HF/3-21G level of theory three backbone conformations were found gamma(L), epsilon(L), and alpha(L). At higher levels of theory the epsilon(L), and alpha(L) conformations disappeared. The ''UP'' and ''DOWN'' ring-puckered forms, in the gamma(L) backbone conformation, led to practically identical vibrational spectra at the B3LYP/6-31G (d) level of theory

Searching for non-Gaussianity in the VSA data

We have tested Very Small Array (VSA) observations of three regions of sky for the presence of non-Gaussianity, using high-order cumulants, Minkowski functionals, a wavelet-based test and a Bayesian joint power spectrum/non-Gaussianity analysis. We find the data from two regions to be consistent with Gaussianity. In the third region, we obtain a 96.7% detection of non-Gaussianity using the wavelet test. We perform simulations to characterise the tests, and conclude that this is consistent with expected residual point source contamination. There is therefore no evidence that this detection is of cosmological origin. Our simulations show that the tests would be sensitive to any residual point sources above the data's source subtraction level of 20 mJy. The tests are also sensitive to cosmic string networks at an rms fluctuation level of $105 \mu K$ (i.e. equivalent to the best-fit observed value). They are not sensitive to string-induced fluctuations if an equal rms of Gaussian CDM fluctuations is added, thereby reducing the fluctuations due to the strings network to $74 \mu K$ rms . We especially highlight the usefulness of non-Gaussianity testing in eliminating systematic effects from our data.Comment: Minor corrections; accepted for publication to MNRA

Estimating the bispectrum of the Very Small Array data

We estimate the bispectrum of the Very Small Array data from the compact and extended configuration observations released in December 2002, and compare our results to those obtained from Gaussian simulations. There is a slight excess of large bispectrum values for two individual fields, but this does not appear when the fields are combined. Given our expected level of residual point sources, we do not expect these to be the source of the discrepancy. Using the compact configuration data, we put an upper limit of 5400 on the value of f_NL, the non-linear coupling parameter, at 95 per cent confidence. We test our bispectrum estimator using non-Gaussian simulations with a known bispectrum, and recover the input values.Comment: 17 pages, 16 figures, replaced with version accepted by MNRAS. Primordial bispectrum recalculated and figure 11 change

Effects of the anthropogenics pressures (marine litter) on the coastal ecosystems of the Marine Reserve “Isla de La Graciosa e islotes del norte de Lanzarote”

The European Marine Strategy Framework Directive (2008/56/EC) considers marine litter as one of its environmental descriptors, requiring the development and standardization of criteria and methodologies for its use to test the good environmental status of marine conditions. The assessment of the impact caused by litter accumulation in the shoreline lacked specific monitoring planning and had not been systematically performed to date in Canary Islands. During the project ”Evaluation of the effect of the anthropogenic pressures (marine litter in beaches and alteration of shallow seabed by boats anchoring) on the coastal ecosystems of the “Marine Reserve of Isla de La Graciosa e islotes del norte de Lanzarote (MRLG)” developed with the financial help of the Canary Islands Government (Council of Agriculture, Ranching, Fishing and Waters), two surveys were carried out, ”LA GRACIOSA 1310” and “LA GRACIOSA 1311”, both developed at MRLG and its vicinities. The aim has been to depict MRLG shoreline and to locate marine litter accumulation points the most, contributing with some tools to assess and manage the coastal ecosystems of the marine reserve. Total shoreline sampled at both surveys together was 38326 m, 1834 m at Alegranza, 1366 m at Monta˜na Clara, 24656 m at La Graciosa Island, and the rest, 10470 m, at the Lanzarote’s shoreline portion bathed by MRLG waters. Shoreline sampling was made qualitatively sorting the sampling stations, according to litter presence and distribution, by means of a upward numerical coding related to the type of waste or garbage found. Moreover, each station was additionally depicted according to the type of substrate as well as to the prevailing type of waste, defining what we named “transects”. To validate methodology to European standards, a more exhaustive experimental sampling was made in four transects identified as high density or high concentration of marine litter, following guidelines of a method developed for OSPAR maritime area during the first half of 2000 decade (OSPAR, 2007). It involves evaluating the possibilities and needs of adjustment of this methodology to the particular conditions of our region (Gonz´alez, et al., 2013 a and b). As preliminary results, the spatial distribution of garbage coastal accumulation will be shown in a cartographic base, expressed as relative abundance by island, according to a 4 degrees scale (no litter, low, medium and high litter presence) and according to the dominant kind of garbage in each transect. An example with one of the most densely occupied with trash transects is shown to illustrate a sampling method without the requirement of trash collection. This method uses a sampling unit of 1x1 m grid, divided in 10x10 cm subgrids. This grid is set parallel to sampling direction repeatedly. Distance between grids is determined by a randomizing software. Sampling direction zigzags from sea border to beach back shore, making 45° degrees angles. Subgrids occupied by trash are counted once the grid is set. Waste is depict and identified following a guide developed for this purpose by OSPAR in 2010

Cosmological parameter estimation using Very Small Array data out to l=1500

We estimate cosmological parameters using data obtained by the Very Small Array (VSA) in its extended configuration, in conjunction with a variety of other CMB data and external priors. Within the flat $\Lambda$CDM model, we find that the inclusion of high resolution data from the VSA modifies the limits on the cosmological parameters as compared to those suggested by WMAP alone, while still remaining compatible with their estimates. We find that $\Omega_{\rm b}h^2=0.0234^{+0.0012}_{-0.0014}$, $\Omega_{\rm dm}h^2=0.111^{+0.014}_{-0.016}$, $h=0.73^{+0.09}_{-0.05}$, $n_{\rm S}=0.97^{+0.06}_{-0.03}$, $10^{10}A_{\rm S}=23^{+7}_{-3}$ and $\tau=0.14^{+0.14}_{-0.07}$ for WMAP and VSA when no external prior is included.On extending the model to include a running spectral index of density fluctuations, we find that the inclusion of VSA data leads to a negative running at a level of more than 95% confidence ($n_{\rm run}=-0.069\pm 0.032$), something which is not significantly changed by the inclusion of a stringent prior on the Hubble constant. Inclusion of prior information from the 2dF galaxy redshift survey reduces the significance of the result by constraining the value of $\Omega_{\rm m}$. We discuss the veracity of this result in the context of various systematic effects and also a broken spectral index model. We also constrain the fraction of neutrinos and find that $f_{\nu}< 0.087$ at 95% confidence which corresponds to $m_\nu<0.32{\rm eV}$ when all neutrino masses are the equal. Finally, we consider the global best fit within a general cosmological model with 12 parameters and find consistency with other analyses available in the literature. The evidence for $n_{\rm run}<0$ is only marginal within this model