Waves of intermediate length through an array of vertical cylinders

We report a semi-analytical theory of wave propagation through a vegetated water. Our aim is to construct a mathematical model for waves propagating through a lattice-like array of vertical cylinders, where the macro-scale variation of waves is derived from the dynamics in the micro-scale cells. Assuming infinitesimal waves, periodic lattice configuration, and strong contrast between the lattice spacing and the typical wavelength, the perturbation theory of homogenization (multiple scales) is used to derive the effective equations governing the macro-scale wave dynamics. The constitutive coefficients are computed from the solution of micro-scale boundary-value problem for a finite number of unit cells. Eddy viscosity in a unit cell is determined by balancing the time-averaged rate of dissipation and the rate of work done by wave force on the forest at a finite number of macro stations. While the spirit is similar to RANS scheme, less computational effort is needed. Using one fitting parameter, the theory is used to simulate three existing experiments with encouraging results. Limitations of the present theory are also pointed out.Cornell University (Mary Upson visiting professorship

Taxonomic placement of Paphiopedilum rungsuriyanum (Cypripedioideae; Orchidaceae) based on morphological, cytological and molecular analyses

Additional file 9: Table S4. The comparison of main significant traits between subgenera and sections of Paphiopedilum by Gorniak et al. (2014) and the present study

Japanese encephalitis virus induces matrix metalloproteinase-9 expression via a ROS/c-Src/PDGFR/PI3K/Akt/MAPKs-dependent AP-1 pathway in rat brain astrocytes

<p>Abstract</p> <p>Background</p> <p>Japanese encephalitis virus (JEV) infection is a major cause of acute encephalopathy in children, which destroys central nervous system (CNS) cells, including astrocytes and neurons. Matrix metalloproteinase (MMP)-9 has been shown to degrade components of the basal lamina, leading to disruption of the blood-brain barrier (BBB) and to contribute to neuroinflammatory responses in many neurological diseases. However, the detailed mechanisms of JEV-induced MMP-9 expression in rat brain astrocytes (RBA-1 cells) are largely unclear.</p> <p>Methods</p> <p>In this study, the effect of JEV on expression of MMP-9 was determined by gelatin zymography, western blot analysis, RT-PCR, and promoter assay. The involvement of AP-1 (c-Jun and c-Fos), c-Src, PDGFR, PI3K/Akt, and MAPKs in these responses were investigated by using the selective pharmacological inhibitors and transfection with siRNAs.</p> <p>Results</p> <p>Here, we demonstrate that JEV induces expression of pro-form MMP-9 via ROS/c-Src/PDGFR/PI3K/Akt/MAPKs-dependent, AP-1 activation in RBA-1 cells. JEV-induced MMP-9 expression and promoter activity were inhibited by pretreatment with inhibitors of AP-1 (tanshinone), c-Src (PP1), PDGFR (AG1296), and PI3K (LY294002), and by transfection with siRNAs of c-Jun, c-Fos, PDGFR, and Akt. Moreover, JEV-stimulated AP-1 activation was inhibited by pretreatment with the inhibitors of c-Src, PDGFR, PI3K, and MAPKs.</p> <p>Conclusion</p> <p>From these results, we conclude that JEV activates the ROS/c-Src/PDGFR/PI3K/Akt/MAPKs pathway, which in turn triggers AP-1 activation and ultimately induces MMP-9 expression in RBA-1 cells. These findings concerning JEV-induced MMP-9 expression in RBA-1 cells imply that JEV might play an important role in CNS inflammation and diseases.</p

Diffuse far-infrared and ultraviolet emission in the NGC4435/4438 system: tidal stream or Galactic cirrus?

We report the discovery of diffuse far-infrared and far-ultraviolet emission projected near the interacting pair NGC4435/4438, in the Virgo cluster. This feature spatially coincides with a well known low surface-brightness optical plume, usually interpreted as tidal debris. If extragalactic, this stream would represent not only one of the clearest examples of intracluster dust, but also a rare case of intracluster molecular hydrogen and large-scale intracluster star formation. However, the ultraviolet, far-infrared, HI and CO emission as well as the dynamics of this feature are extremely unusual for tidal streams but are typical of Galactic cirrus clouds. In support to the cirrus scenario, we show that a strong spatial correlation between far-infrared and far-ultraviolet cirrus emission is observed across the center of the Virgo cluster, over a scale of several degrees. This study demonstrates how dramatic Galactic cirrus contamination can be, even at optical and ultraviolet wavelengths and at high galactic latitudes. If ignored, the presence of diffuse light scattered by Galactic dust clouds could significantly bias our interpretation of low surface-brightness features and diffuse light observed around galaxies and in clusters of galaxies.Comment: 6 pages, 4 figures. Accepted for publication in MNRAS Letter

CODAG: Characterizing and Optimizing Decompression Algorithms for GPUs

Data compression and decompression have become vital components of big-data applications to manage the exponential growth in the amount of data collected and stored. Furthermore, big-data applications have increasingly adopted GPUs due to their high compute throughput and memory bandwidth. Prior works presume that decompression is memory-bound and have dedicated most of the GPU's threads to data movement and adopted complex software techniques to hide memory latency for reading compressed data and writing uncompressed data. This paper shows that these techniques lead to poor GPU resource utilization as most threads end up waiting for the few decoding threads, exposing compute and synchronization latencies. Based on this observation, we propose CODAG, a novel and simple kernel architecture for high throughput decompression on GPUs. CODAG eliminates the use of specialized groups of threads, frees up compute resources to increase the number of parallel decompression streams, and leverages the ample compute activities and the GPU's hardware scheduler to tolerate synchronization, compute, and memory latencies. Furthermore, CODAG provides a framework for users to easily incorporate new decompression algorithms without being burdened with implementing complex optimizations to hide memory latency. We validate our proposed architecture with three different encoding techniques, RLE v1, RLE v2, and Deflate, and a wide range of large datasets from different domains. We show that CODAG provides 13.46x, 5.69x, and 1.18x speed up for RLE v1, RLE v2, and Deflate, respectively, when compared to the state-of-the-art decompressors from NVIDIA RAPIDS

The Herschel Virgo Cluster Survey: IV. Resolved dust analysis of spiral galaxies

We present a resolved dust analysis of three of the largest angular size spiral galaxies, NGC 4501 and NGC 4567/8, in the Herschel Virgo Cluster Survey (HeViCS) Science Demonstration field. Herschel has unprecedented spatial resolution at far-infrared wavelengths and with the PACS and SPIRE instruments samples both sides of the peak in the far infrared spectral energy distribution (SED).We present maps of dust temperature, dust mass, and gas-to-dust ratio, produced by fitting modified black bodies to the SED for each pixel. We find that the distribution of dust temperature in both systems is in the range ~19 - 22 K and peaks away from the centres of the galaxies. The distribution of dust mass in both systems is symmetrical and exhibits a single peak coincident with the galaxy centres. This Letter provides a first insight into the future analysis possible with a large sample of resolved galaxies to be observed by Herschel.Comment: Letter accepted for publication in A&A (Herschel special issue