uFLIP: Understanding Flash IO Patterns

Does the advent of flash devices constitute a radical change for secondary storage? How should database systems adapt to this new form of secondary storage? Before we can answer these questions, we need to fully understand the performance characteristics of flash devices. More specifically, we want to establish what kind of IOs should be favored (or avoided) when designing algorithms and architectures for flash-based systems. In this paper, we focus on flash IO patterns, that capture relevant distribution of IOs in time and space, and our goal is to quantify their performance. We define uFLIP, a benchmark for measuring the response time of flash IO patterns. We also present a benchmarking methodology which takes into account the particular characteristics of flash devices. Finally, we present the results obtained by measuring eleven flash devices, and derive a set of design hints that should drive the development of flash-based systems on current devices.Comment: CIDR 200

Ground deformation and source geometry of the 30 October 2016 Mw 6.5 Norcia earthquake (Central Italy) investigated through seismological data, DInSAR measurements, and numerical modelling

We investigate the Mw 6.5 Norcia (Central Italy) earthquake by exploiting seismological data, DInSAR measurements, and a numerical modelling approach. In particular, we first retrieve the vertical component (uplift and subsidence) of the displacements affecting the hangingwall and the footwall blocks of the seismogenic faults identified, at depth, through the hypocenters distribution analysis. To do this, we combine the DInSAR measurements obtained from coseismic SAR data pairs collected by the ALOS-2 sensor from ascending and descending orbits. The achieved vertical deformation map displays three main deformation patterns: (i) a major subsidence that reaches the maximum value of about 98 cm near the epicentral zones nearby the town of Norcia; (ii) two smaller uplift lobes that affect both the hangingwall (reaching maximum values of about 14 cm) and the footwall blocks (reaching maximum values of about 10 cm). Starting from this evidence, we compute the rock volumes affected by uplift and subsidence phenomena, highlighting that those involved by the retrieved subsidence are characterized by significantly higher deformation values than those affected by uplift (about 14 times). In order to provide a possible interpretation of this volumetric asymmetry, we extend our analysis by applying a 2D numerical modelling approach based on the finite element method, implemented in a structural-mechanic framework, and exploiting the available geological and seismological data, and the ground deformation measurements retrieved from the multi-orbit ALOS-2 DInSAR analysis. In this case, we consider two different scenarios: the first one based on a single SW-dipping fault, the latter on a main SW-dipping fault and an antithetic zone. In this context, the model characterized by the occurrence of an antithetic zone presents the retrieved best fit coseismic surface deformation pattern. This result allows us to interpret the subsidence and uplift phenomena caused by the Mw 6.5 Norcia earthquake as the result of the gravitational sliding of the hangingwall along the main fault plane and the frictional force acting in the opposite direction, consistently with the double couple fault plane mechanism

The magnetic field in the NGC 2024 FIR 5 dense core

We used the Submillimeter Array (SMA) to observe the thermal polarized dust emission from the protostellar source NGC 2024 FIR 5. The polarized emission outlines a partial hourglass morphology for the plane-of-sky component of the core magnetic field. Our data are consistent with previous BIMA maps, and the overall magnetic field geometries obtained with both instruments are similar. We resolve the main core into two components, FIR 5A and FIR 5B. A possible explanation for the asymmetrical field lies in depolarization effects due to the lack of internal heating from FIR 5B source, which may be in a prestellar evolutionary state. The field strength was estimated to be 2.2 mG, in agreement with previous BIMA data. We discuss the influence of a nearby H{\sc ii} region over the field lines at scales of $\sim 0.01$ pc. Although the hot component is probably compressing the molecular gas where the dust core is embedded, it is unlikely that the radiation pressure exceeds the magnetic tension. Finally, a complex outflow morphology is observed in CO (3 $\rightarrow$ 2) maps. Unlike previous maps, several features associated with dust condensations other than FIR 5 are detected.Comment: 48 pages, 12 figures, accepted for publication in The Astrophysical Journa

Hexapod Design For All-Sky Sidereal Tracking

In this paper we describe a hexapod-based telescope mount system intended to provide sidereal tracking for the Fly's Eye Camera project -- an upcoming moderate, 21"/pixel resolution all-sky survey. By exploiting such a kind of meter-sized telescope mount, we get a device which is both capable of compensating for the apparent rotation of the celestial sphere and the same design can be used independently from the actual geographical location. Our construction is the sole currently operating hexapod telescope mount performing dedicated optical imaging survey with a sub-arcsecond tracking precision.Comment: Accepted for publication in PASP, 10 page

SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60 percent. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.Comment: 21 pages, 6 figures, submitted to PLoS ONE, additional files available at "https://www.dropbox.com/sh/bhclhxpoiubh371/O5CO_CkXQE". Comments most welcom

Present-day stress orientations and tectonic provinces of the NW Borneo collisional margin

Extent: 15p.Borehole failure observed on image and dipmeter logs from 55 petroleum wells across the NW Borneo collisional margin were used to determine maximum horizontal stress (σH) orientations; combined with seismic and outcrop data, they define seven tectonic provinces. The Baram Delta–Deepwater Fold-Thrust Belt exhibits three tectonic provinces: its inner shelf inverted province (σH is NW-SE, margin-normal), its outer shelf extension province (σH is NE-SW, margin-parallel), and its slope to basin floor compression province (σH is NW-SE, margin-normal). In the inverted province, σH reflects inversion of deltaic normal faults. The σH orientations in the extension and compression provinces reflect deltaic gravitational tectonics. The shale and minibasin provinces have been recognized in offshore Sabah. In the shale province, σH is N010°E, which aligns around the boundary of a massif of mobile shale. Currently, no data are available to determine σH in the minibasin province. In the Balingian province, σH is ESE-WNW, reflecting ESE absolute Sunda plate motions due to the absence of a thick detachment seen elsewhere in NW Borneo. The Central Luconia province demonstrates poorly constrained and variable σH orientations. These seven provinces result from the heterogeneous structural and stratigraphic development of the NW Borneo margin and formed due to complex collisional tectonics and the varied distribution and thicknesses of stratigraphic packages.Rosalind C. King, Mark R. P. Tingay, Richard R. Hillis, Christopher K. Morley, and James Clar

PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets

As 16S rRNA gene targeted massively parallel sequencing has become a common tool for microbial diversity investigations, numerous advances have been made to minimize the influence of sequencing and chimeric PCR artifacts through rigorous quality control measures. However, there has been little effort towards understanding the effect of multi-template PCR biases on microbial community structure. In this study, we used three bacterial and three archaeal mock communities consisting of, respectively, 33 bacterial and 24 archaeal 16S rRNA gene sequences combined in different proportions to compare the influences of (1) sequencing depth, (2) sequencing artifacts (sequencing errors and chimeric PCR artifacts), and (3) biases in multi-template PCR, towards the interpretation of community structure in pyrosequencing datasets. We also assessed the influence of each of these three variables on α- and β-diversity metrics that rely on the number of OTUs alone (richness) and those that include both membership and the relative abundance of detected OTUs (diversity). As part of this study, we redesigned bacterial and archaeal primer sets that target the V3–V5 region of the 16S rRNA gene, along with multiplexing barcodes, to permit simultaneous sequencing of PCR products from the two domains. We conclude that the benefits of deeper sequencing efforts extend beyond greater OTU detection and result in higher precision in β-diversity analyses by reducing the variability between replicate libraries, despite the presence of more sequencing artifacts. Additionally, spurious OTUs resulting from sequencing errors have a significant impact on richness or shared-richness based α- and β-diversity metrics, whereas metrics that utilize community structure (including both richness and relative abundance of OTUs) are minimally affected by spurious OTUs. However, the greatest obstacle towards accurately evaluating community structure are the errors in estimated mean relative abundance of each detected OTU due to biases associated with multi-template PCR reactions