Accelerating exhaustive pairwise metagenomic comparisons

In this manuscript, we present an optimized and parallel version of our previous work IMSAME, an exhaustive gapped aligner for the pairwise and accurate comparison of metagenomes. Parallelization strategies are applied to take advantage of modern multiprocessor architectures. In addition, sequential optimizations in CPU time and memory consumption are provided. These algorithmic and computational enhancements enable IMSAME to calculate near optimal alignments which are used to directly assess similarity between metagenomes without requiring reference databases. We show that the overall efficiency of the parallel implementation is superior to 80% while retaining scalability as the number of parallel cores used increases. Moreover, we also show thats equential optimizations yield up to 8x speedup for scenarios with larger data.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tec

Localization Effects on the Dissipation of Gravity Wave Packets in the Upper Mesophere and Lower Thermosphere

Gravity waves not subject to breaking or filtering will dissipate due to viscosity and thermal conduction in the thermosphere. However, the evolutions of wave packets, and the altitudes they reach, are highly dependent upon the spectral content. In this paper, a 2‐D numerical model is used to investigate the effect of spatial localization (and thus spectral content) of a wave packet on its dissipation, dispersion, and spectral evolution. It is found that most wave packets launched below the thermosphere evolve to smaller central vertical wavelengths as the faster, longer vertical wavelength components reach the dissipative thermosphere and are removed first, leaving the shorter, slower components to become dominant at later times. This effect is greater for more spatially localized packets (spectrally broadband) as rapid dispersion leads to the rapid spreading of the wave over large altitude regions that could be interpreted as different waves (i.e., from different sources) by instruments observing different altitudes. Dispersion can also be accelerated by the refractive effects of the thermospheric temperature gradient. Initially, Gaussian broadband packets can evolve into asymmetric distributions which are not well described by standard assumptions (e.g., Gaussian packets), requiring instead numerical simulation to properly describe them. In the case that the vertical scale is smaller than the scale height, and dissipation acts immediately on the packet (i.e., it is generated in situ in the dissipative thermosphere), then the scale‐dependent nature of dissipation removes the shorter wavelengths components first, leading to the spectrum evolving toward larger vertical wavelengths

Observations of the Breakdown of Mountain Waves Over the Andes Lidar Observatory at Cerro Pachon on 8/9 July 2012

Although mountain waves (MWs) are thought to be a ubiquitous feature of the wintertime southern Andes stratosphere, it was not known whether these waves propagated up to the mesopause region until Smith et al. (2009) confirmed their presence via airglow observations. The new Andes Lidar Observatory at Cerro Pachon in Chile provided the opportunity for a further study of these waves. Since MWs have near-zero phase speed, and zero wind lines often occur in the winter upper mesosphere (80 to 100 km altitude) region due to the reversal of the zonal mean and tidal wind, MW breakdown may routinely occur at these altitudes. Here we report on very high spatial/temporal resolution observations of the initiation of MW breakdown in the mesopause region. Because the waves are nearly stationary, the breakdown process was observed over several hours; a much longer interval than has previously been observed for any gravity wave breakdown. During the breakdown process observations were made of initial horseshoe-shaped vortices, leading to successive vortex rings, as is also commonly seen in Direct Numerical Simulations (DNS) of idealized and multiscale gravity wave breaking. Kelvin-Helmholtz instability (KHI) structures were also observed to form. Comparing the structure of observed KHI with the results of existing DNS allowed an estimate of the turbulent kinematic viscosity. This viscosity was found to be around 25 m2/s, a value larger than the nominal viscosity that is used in models

Seasonal Propagation Characteristics of MSTIDs Observed at High Latitudes Over Central Alaska Using the Poker Flat Incoherent Scatter Radar

Near‐continuous electron density measurements obtained over a ∼3 year period, 2010–2013, using the Poker Flat Incoherent Scatter Radar (PFISR) in central Alaska (69°N, 147°W) have been analyzed to quantify the properties of over 650 high‐latitude medium‐scale traveling ionospheric disturbances (MSTIDs). Our analysis focused on the altitude range 100–300 km encompassing the lower ionosphere/thermosphere and yielded first full seasonal day/night distributions of MSTIDs at high northern latitudes with mean values: horizontal wavelength 446 km, horizontal phase speed 187 m/s, and period 41 min. These year‐round measurements fill an important summertime gap in existing MSTID measurements revealing predominantly eastward wave propagation during the summer, while continued winter season observations agree well with previous reports of near southward propagating MSTIDs. Our 3 years of results suggest a cyclic change in the seasonal horizontal propagation directions that was found to be quantitatively consistent with critical level wind and dissipative filtering. Concurrent measurements of the vertical wavelength spectrum as a function of altitude also compared favorably in shape with that calculated using a theoretical dispersion relation (Vadas & Fritts, 2005, https://doi.org/10.1029/2004JD005574) for the thermosphere, but with a higher mean value. Evidence supporting the systematic broadening and shrinking in the azimuthal distributions of the MSTIDs during the course of the year was also found, as well as an unexpected correlation between the MSTID propagation directions and the AE index, both of which are under further investigation

Hardware aspects of algorithm generation

Bezier splines can be used to define the outlines of attractive fonts for high resolution laser printers. Pratt (1985) has shown how Pitteway’s conic drawing algorithm can be constrained to work with integers only, with the control of start and end points necessary to avoid bleeding from the seedfill of the outlines. Modern display devices cannot match the resolution of the printers, but many offer a grey-scale capability which can be used to improve the appearance of the edges bewteen lit and unlit regions. The conic drawing algorithm can be adapted for this purpose, while retaining integer control

High-resolution vector velocity determinations from the dynasonde

Line-of-sight Doppler velocity V∗ and three-dimensional apparent echolocation (XL, YL, ZL), are among the principal parameters available for each ionospheric echo from most observing modes of the dynasonde. An ensemble of three or more echoes containing diverse XL, YL, ZL is sufficient to determine the full vector velocity VX, VY, VZ common to the ensemble. We present a procedure based on weighted least-squares, which may be applied to an entire recording or to suitably selected parts of it, to yield ‘best’ estimates of VX, VY, VZ and their confidence limits. Each observation is weighted according to an r.m.s. phase error incurred in the estimation of XL, YL, ZL and V∗. A measure of the fraction of observed Doppler variance expressed by the analysis is useful to decide if spatial or temporal variabilities are significant within the ensemble. Often at Tromsø the results are directly applicable to the estimation of prevailing electric fields with high (⪢10 s) time resolution

The Ellipse and the Five-centred Arch

this paper we look at the next step in improving accuracy: insertion of an additional arc between each of the previous arcs to form the five-centred arch. Figure 1a shows the basic geometry. The ellipse has semi-major and semi-minor axes of length a and b respectively. The three approximating arcs are drawn in one of the quadrants, and have parameters arc A 1 : centre (0, -k), radius r 1 arc A 2 : centre (x 2 , y 2 ), radius r 2 arc A 3 : centre (h, 0), radius r

Toward an optimum receiving array and pulse set for the Dynasonde

The accuracy and efficiency with which radio echo parameters may be estimated by a programmable ionosonde of high resolution depend upon software-designed strategies of pulse set design and receiving antenna layout. All of the echo parameters, except amplitude and time of arrival (thus three components of echolocation, Doppler, polarization rotation, and an average phase angle) are determined by phase angle differences. The solution is conveniently expressed as a least squares estimation, provided that more than six independent phase measurements are available. Since the observed phases are necessarily obtained modulo 360°, from 12-bit complex amplitude data, each parameter is subject to aliasing ambiguities which must be anticipated in each strategy, and minimized