High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs

<p>Abstract</p> <p>Background</p> <p>Three-dimensional (3D) reconstruction in electron tomography (ET) has emerged as a leading technique to elucidate the molecular structures of complex biological specimens. Blob-based iterative methods are advantageous reconstruction methods for 3D reconstruction in ET, but demand huge computational costs. Multiple graphic processing units (multi-GPUs) offer an affordable platform to meet these demands. However, a synchronous communication scheme between multi-GPUs leads to idle GPU time, and a weighted matrix involved in iterative methods cannot be loaded into GPUs especially for large images due to the limited available memory of GPUs.</p> <p>Results</p> <p>In this paper we propose a multilevel parallel strategy combined with an asynchronous communication scheme and a blob-ELLR data structure to efficiently perform blob-based iterative reconstructions on multi-GPUs. The asynchronous communication scheme is used to minimize the idle GPU time so as to asynchronously overlap communications with computations. The blob-ELLR data structure only needs nearly 1/16 of the storage space in comparison with ELLPACK-R (ELLR) data structure and yields significant acceleration.</p> <p>Conclusions</p> <p>Experimental results indicate that the multilevel parallel scheme combined with the asynchronous communication scheme and the blob-ELLR data structure allows efficient implementations of 3D reconstruction in ET on multi-GPUs.</p

(Z)-4-[4-(Dimethyl­amino)benzyl­idene]-3-methyl­isoxazol-5(4H)-one

The title compound, C13H14N2O2, an isoxazol-5-one derivative, was synthesized by a one-pot, three-component condensation reaction of methyl acetoacetate, hydroxy­lamine hydro­chloride and 4-(dimethyl­amino)benzaldehyde. All the non-H atoms are co-planar [r.m.s deviation = 0.0039 Å], with a Z configuration about the C=C bond. The dihedral angle between the phenyl ring and the isoxazole ring is 2.58 (19)°

Research on the Movement Law of Gravel under Water Based on the Principle of Audio Analysis

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchive

Size-dependent melting: Numerical calculations of the phonon spectrum

In order to clarify the relationship between the phonon spectra of nanoparticles and their melting temperature, we studied in detail the size-dependent low energy vibration modes. A minimum model with atoms on a lattice and harmonic potentials for neighboring atoms is used to reveal a general behavior. By calculating the phonon spectra for a series of nanoparticles of two lattice types in different sizes, we found that density of low energy modes increases as the size of nanoparticles decreases, and this density increasing causes decreasing of melting temperature. Size-dependent behavior of the phonon spectra accounts for typical properties of surface-premelting and irregular melting temperature on fine scales. These results show that our minimum model captures main physics of nanoparticles. Therefore, more physical characteristics for nanoparticles of certain types can be given by phonons and microscopic potential models.Comment: 5 pages, 5 figure

Turbulent Characteristics and Structures Influenced by Backwater in Non-uniform Open-channel Flows

Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchive

Transcriptome Analysis of Metapenaeus affinis Reveals Genes Involved in Gonadal Development

Metapenaeus affinis is a crustacean with important commercial value in the fishery of the South China Sea. Overfishing has resulted in the decline of the wild population and germplasm degradation. However, there is little background knowledge about its gonadal development, and there is a lack of research on the development of this species. To better understand the molecular regulatory mechanisms during gonadal development, here, we performed RNA-Seq on immature and mature ovaries and compared their transcriptomic signatures. 126,930,488 and 122,677,356 clean sequencing reads were obtained from the Illumina sequencing platform, respectively. 394 differentially expressed genes (DEGs) were identified, of which 136 were up-regulated, and 258 were down-regulated. Further analysis revealed rich transcriptional sequences, which have homology with genes related to reproduction and development. Expression patterns of COX, GPX, E3s, PCNA, STPK, and other genes were changed during ovarian development. Validation by qRT-PCR demonstrated the reliability of RNA-Seq. This study has made a significant contribution to the currently available sequence data of M. affinis and provided reference data for the development of genetic and breeding work

Effect of non-phytate phosphorus levels and phytase sources on the growth performance, serum biochemical and tibial parameters of broiler chickens

A 3×3 fattorial arrangement with dietary non-phytate phosphorus (NPP) levels and phytase sources (3- and 6-phytase) was conducted to evaluate the effects of NPP levels, phytase sources and their possible interactions on growth performance, serum biochemical and tibia parameters of broiler chickens from hatch to 42 days of age. A total of 540 1-day-old Arbor Acres male broiler chicks were randomly allocated into nine dietary treatments, each containing 5 replicates pens with 12 birds per pen. Interaction was statistically significant in the performance till day 21 of trial, supplementation of low NPP diet decreased body weight (BW) (P<0.001), depressed average daily gain (ADG) (P<0.001) and deteriorated average daily feed intake (ADFI) (P<0.001) over day 42. During the 8-to-21-day period, even if interaction between NPP levels and phytase sources was significant (P<0.01), BW, ADG and ADFI always increased due to dietary supplementation of phytase, with source not differing. Dietary high NPP enhanced serum calcium and P concentrations on day 21 and 42 (linear contrast, P<0.01), while decreased alkaline phosphatase (AKP) activity on day 42 (linear contrast, P<0.001), and interaction was not significant. Both dietary sources of phytase decreased serum AKP activities on day 42 (P<0.001), and urea nitrogen content on day 21 (P<0.01) and 42 (P<0.001). Both phytase improved ash percentage on day 21 and P content in tibia at 21 and 42 days of age (P<0.001). The results confirmed that dietary supplementation of phytase may enhance P availability during the 8-to-21-day period. Nevertheless, no difference between the two phytase sources was observed