DiBELLA: Distributed long read to long read alignment

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers [29]. While long sequences of DNA offer enormous advantages for biological analysis and insight, current long read sequencing instruments have high error rates and therefore require different approaches to analysis than their short read counterparts. Our work focuses on an efficient distributed-memory parallelization of an accurate single-node algorithm for overlapping and aligning long reads. We achieve scalability of this irregular algorithm by addressing the competing issues of increasing parallelism, minimizing communication, constraining the memory footprint, and ensuring good load balance. The resulting application, diBELLA, is the first distributed memory overlapper and aligner specifically designed for long reads and parallel scalability. We describe and present analyses for high level design trade-offs and conduct an extensive empirical analysis that compares performance characteristics across state-of-the-art HPC systems as well as a commercial cloud architectures, highlighting the advantages of state-of-the-art network technologies

Effect of Mn substitution by Ga on the optical properties of a metallic manganite

In a metallic manganite like La(2/3)Sr(1/3)MnO(3), the substitution of Mn(+3) by Ga(+3) dilutes the ferromagnetic order and locally cancels the Jahn-Teller distortion, without heavily affecting the crystal structure. One can thus follow the changes in the charge dynamics induced by Ga, until the ferro-metallic manganite is turned into an insulator. Here this phenomenon is studied in detail through the infrared reflectivity of five samples of La(2/3)Sr(1/3)Mn(1-x)Ga(x)O(3), with x increasing from 0 to 0.30 and for 50 < T < 320 K. A simple model which links the measured optical parameters to the magnetization M(x, T) well describes the behavior of the plasma frequency, the scattering rate, and the mid-infrared absorption along the metal-to-insulator transition.Comment: 8 pages including 7 figure

3D Visualization of Cultural Heritage Artefacts with Virtual Reality devices

Although 3D models are useful to preserve the information about historical artefacts, the potential of these digital contents are not fully accomplished until they are not used to interactively communicate their significance to non-specialists. Starting from this consideration, a new way to provide museum visitors with more information was investigated. The research is aimed at valorising and making more accessible the Egyptian funeral objects exhibited in the Sforza Castle in Milan. The results of the research will be used for the renewal of the current exhibition, at the Archaeological Museum in Milan, by making it more attractive. A 3D virtual interactive scenario regarding the "path of the dead", an important ritual in ancient Egypt, was realized to augment the experience and the comprehension of the public through interactivity. Four important artefacts were considered for this scope: two ushabty, a wooden sarcophagus and a heart scarab. The scenario was realized by integrating low-cost Virtual Reality technologies, as the Oculus Rift DK2 and the Leap Motion controller, and implementing a specific software by using Unity. The 3D models were implemented by adding responsive points of interest in relation to important symbols or features of the artefact. This allows highlighting single parts of the artefact in order to better identify the hieroglyphs and provide their translation. The paper describes the process for optimizing the 3D models, the implementation of the interactive scenario and the results of some test that have been carried out in the lab

Contrasting distribution of aggregates >100 µm in the upper kilometre of the South-Eastern Pacific

International audienceLarge sinking particles transport organic and inorganic matter into the deeper layers of the oceans. From 70 to 90% of the superficial particulate material is disaggregated within the upper 1000 m. This decrease with depth indicates that remineralization processes are intense during sedimentation. Generally, the estimates of vertical flux rely on the sediment trap data but difficulties inherent in their design, limit the reliability of this information. During the BIOSOPE study in the southeastern Pacific, 76 vertical casts using the Underwater Video Profiler (UVP) and deployments of a limited number of drifting sediment traps provided an opportunity to fit the UVP data to sediment trap flux measurements. We applied than the calculated UVP flux in the upper 1000 m to the whole 8000 km BIOSOPE transect. Comparison between the large particulate material (LPM) abundance and the estimated fluxes from both UVP and sediment traps showed different patterns in different regions. On the western end of the BIOSOPE section the standing stock of particles in the superficial layer was high but the export between 150 and 250 m was low. Below this layer the flux values increased. High values of about 30% of the calculated UVP maximum superficial flux were observed below 900 m at the HNLC station. The South Pacific Gyre exported about 2 mg m-2 d-1. While off Chilean coast 95% of the superficial matter was remineralized or advected in the upper kilometer, 20% of the superficial flux was observed below 900 m near the Chilean coast. These results suggest that the export to deep waters is spatially heterogeneous and related to the different biotic and abiotic factors

Italian Science Case for ALMA Band 2+3

The Premiale Project "Science and Technology in Italy for the upgraded ALMA Observatory - iALMA" has the goal of strengthening the scientific, technological and industrial Italian contribution to the Atacama Large Millimeter/submillimeter Array (ALMA), the largest ground based international infrastructure for the study of the Universe in the microwave. One of the main objectives of the Science Working Group (SWG) inside iALMA, the Work Package 1, is to develop the Italian contribution to the Science Case for the ALMA Band 2 or Band 2+3 receiver. ALMA Band 2 receiver spans from ~67 GHz (bounded by an opaque line complex of ozone lines) up to 90 GHz which overlaps with the lower frequency end of ALMA Band 3. Receiver technology has advanced since the original definition of the ALMA frequency bands. It is now feasible to produce a single receiver which could cover the whole frequency range from 67 GHz to 116 GHz, encompassing Band 2 and Band 3 in a single receiver cartridge, a so called Band 2+3 system. In addition, upgrades of the ALMA system are now foreseen that should double the bandwidth to 16 GHz. The science drivers discussed below therefore also discuss the advantages of these two enhancements over the originally foreseen Band 2 system.Comment: 43 pages, 21 figure