Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

Deep sequencing has enabled the investigation of a wide range of environmental microbial ecosystems, but the high memory requirements for {\em de novo} assembly of short-read shotgun sequencing data from these complex populations are an increasingly large practical barrier. Here we introduce a memory-efficient graph representation with which we can analyze the k-mer connectivity of metagenomic samples. The graph representation is based on a probabilistic data structure, a Bloom filter, that allows us to efficiently store assembly graphs in as little as 4 bits per k-mer, albeit inexactly. We show that this data structure accurately represents DNA assembly graphs in low memory. We apply this data structure to the problem of partitioning assembly graphs into components as a prelude to assembly, and show that this reduces the overall memory requirements for {\em de novo} assembly of metagenomes. On one soil metagenome assembly, this approach achieves a nearly 40-fold decrease in the maximum memory requirements for assembly. This probabilistic graph representation is a significant theoretical advance in storing assembly graphs and also yields immediate leverage on metagenomic assembly

Study of Sabatier Catalyst Performance for a Mars ISRU Propellant Production Plant

NASA is currently developing technologies for use in the field of in-situ resource utilization (ISRU). One of the technologies being advanced is the Sabatier, or methanation, reactor which converts carbon dioxide and hydrogen into methane gas and water at high temperatures. This paper discusses the catalyst life and performance issues for these reactors that would be expected on Mars and describes the test methods employed and observed results. The various catalysts were tested in their capacity for the continuous production of methane gas via the Sabatier reaction and the possible effects of launch vibration loads, exposure to liquid water, particulate contamination, and chemical contamination to the overall observed reaction efficacy of the catalysts evaluated

High Temperature Microwave Dielectric Properties of JSC-1AC Lunar Simulant

Microwave heating has many potential lunar applications including sintering regolith for lunar surface stabilization and heating regolith for various oxygen production reactors. The microwave properties of lunar simulants must be understood so this technology can be applied to lunar operations. Dielectric properties at microwave frequencies for a common lunar simulant, JSC-1AC, were measured up to 1100 C, which is approximately the melting point. The experimentally determined dielectric properties included real and imaginary permittivity (epsilon', epsilon"), loss tangent (tan delta), and half-power depth, the di stance at which a material absorbs 50% of incident microwave energy. Measurements at 2.45 GHz revealed tan delta of JSC-1A increases from 0.02 at 25 C to 0.31 at 110 C. The corresponding half-power depth decreases from a peak of 286 mm at 110 C, to 13 mm at 1100 C. These data indicate that JSC-1AC becomes more absorbing, and thus a better microwave heater as temperature increases. A half-power depth maximum at 100-200 C presents a barrier to direct microwave heating at low temperatures. Microwave heating experiments confirm the sluggish heating effect of weak absorption below 200 C, and increasingly strong absorption above 200 C, leading to rapid heating and melting of JSC-1AC

The Prediction of Long-Term Coating Performance from Short-Term Electrochemical Data

The pace of coatings development is limited by the time required to assess their corrosion protection properties. This study takes a step f orward from Part I in that it correlates the corrosion performance of organic coatings assessed by a series of short-term electrochemical measurement with 18-month beachside exposure results of duplicate pan els. A series of 19 coating systems on A36 steel substrates were test ed in a completely blind study using the damage tolerance test (DTT). In the DTT, a through-film pinhole defect is created, and the electro chemical characteristics of the defect are then monitored over the ne xt 4 to 7 days while immersed in 0.SM NaCl. The open circuit potentia l, anodic potentiostatic polarization tests and electrochemical imped ance spectroscopy were used to study the corrosion behavior of the co ating systems. The beachside exposure tests were conducted at the Ken nedy Space Center according to ASTM D610-01. It was found that for 79 % of the coatings systems examined, the 18 month beachside exposure r esults could be predicted by two independent laboratory tests obtained within 7 days

Ba3Ga3N5 - A Novel Host Lattice for Eu2+ - Doped Luminescent Materials with Unexpected Nitridogallate Substructure

The alkaline earth nitridogallate Ba3Ga3N5 was synthesized from the elements in a sodium flux at 760°C utilizing weld shut tantalum ampules. The crystal structure was solved and refined on the basis of single-crystal X-ray diffraction data. Ba3Ga3N5 (space group C2/c (No. 15), a = 16.801(3), b = 8.3301(2), c = 11.623(2) Å, β = 109.92 (3)°, Z = 8) contains a hitherto unknown structural motif in nitridogallates, namely, infinite strands made up of GaN4 tetrahedra, each sharing two edges and at least one corner with neighboring GaN4 units. There are three Ba2+ sites with coordination numbers six or eight, respectively, and one Ba2+ position exhibiting a low coordination number 4 corresponding to a distorted tetrahedron. Eu2+ - doped samples show red luminescence when excited by UV irradiation at room temperature. Luminescence investigations revealed a maximum emission intensity at 638 nm (FWHM =2123 cm−1). Ba3Ga3N5 is the first nitridogallate for which parity allowed broadband emission due to Eu2+ - doping has been found. The electronic structure of both Ba3Ga3N5 as well as isoelectronic but not isostructural Sr3Ga3N5 was investigated by DFT methods. The calculations revealed a band gap of 1.53 eV for Sr3Ga3N5 and 1.46 eV for Ba3Ga3N5

An in vitro comparison between two methods of electrical resistance measurement for occlusal caries detection

Because of different measurement techniques and the easier design of the CRM prototype, this in vitro study aimed to compare the diagnostic performance and reproducibility of two electrical methods (Electronic Caries Monitor III, ECM and Cariometer 800, CRM) for occlusal caries detection, and to evaluate the effect of staining/ discoloration of fissures on diagnostic performance. Hundred and seventeen third molars with no apparent occlusal cavitation were selected. Six examiners inspected all specimens independently, using the CRM, and a subgroup of 4 using the ECM. Histological validation using a stereomicroscope was performed after hemisectioning. Intra- and interexaminer reproducibility was assessed by Lin's concordance correlation coefficient (CCC) and Bland and Altman analysis. Diagnostic performance parameters included sensitivity (SE), specificity (SP) and area under the ROC curve (A(z)). The CCC yielded an intra- and interexaminer reproducibility of 0.69/0.62 (ECM) and of 0.79/0.74 (CRM). The mean intra- and interexaminer 95% range of measurements (range between Bland and Altman limits of agreement) given in percentages of the instrument reading were 67%/65% for the ECM and 28%/33% for the CRM. A(z) at the D3-4 level was 0.74 (ECM) and 0.78 (CRM). The CRM showed at least equivalent diagnostic performance to the ECM. However, improvement is still desirable. Diagnostic performance appeared to be enhanced in discolored lesions; however, this may be related to sample lesion distribution characteristics. Copyright (C) 2006 S. Karger AG, Basel

Degradation of Organics in a Glow Discharge Under Martian Conditions

The primary objective of this project is to understand the consequences of glow electrical discharges on the chemistry and biology of Mars. The possibility was raised some time ago that the absence of organic material and carbonaceous matter in the Martian soil samples studied by the VikinG Landers might be due in part to an intrinsic atmospheric mechanism such as glow discharge. The high probability for dust interactions during Martian dust storms and dust devils, combined with the cold, dry climate of Mars most likely results in airborne dust that is highly charged. Such high electrostatic potentials generated during dust storms on Earth are not permitted in the low-pressure CO2 environment on Mars; therefore electrostatic energy released in the form of glow discharges is a highly likely phenomenon. Since glow discharge methods are used for cleaning and sterilizing surfaces throughout industry, the idea that dust in the Martian atmosphere undergoes a cleaning action many times over geologic time scales appears to be a plausible one