Repeat-pass synthetic aperture sonar micro-navigation using redundant phase center arrays

In this paper, a new algorithm is introduced for high-precision underwater navigation using the coherent echo signals collected during repeat-pass synthetic aperture sonar (SAS) surveys. The algorithm is a generalization of redundant phase center (RPC) micronavigation, expanded to RPCs formed between overlapping pings in repeated passes. For each set of overlapping ping pairs (two intrapass and three interpass), five different RPC arrays can be formed to provide estimates of the vehicle's surge, sway, and yaw. These estimates are used to find a weighted least squares solution for the trajectories of the repeated passes. The algorithm can estimate the relative trajectories to subwavelength precision (on order of millimeters to hundreds of micrometers at typical SAS operating frequencies of hundreds of kilohertz) in a common coordinate frame. This will lead to improved focusing and coregistration for repeat-pass SAS interferometry and is an important step toward repeat-pass bathymetric mapping. The repeat-pass RPC micronavigation algorithm is demonstrated using data collected by the 300-kHz SAS of the NATO Center for Maritime Research and Experimentation (CMRE) Minehunting Unmanned underwater vehicle for Shallow water Covert Littoral Expeditions (MUSCLE)

454-Pyrosequencing: A Molecular Battiscope for Freshwater Viral Ecology

Viruses, the most abundant biological entities on the planet, are capable of infecting organisms from all three branches of life, although the majority infect bacteria where the greatest degree of cellular diversity lies. However, the characterization and assessment of viral diversity in natural environments is only beginning to become a possibility. Through the development of a novel technique for the harvest of viral DNA and the application of 454 pyrosequencing, a snapshot of the diversity of the DNA viruses harvested from a standing pond on a cattle farm has been obtained. A high abundance of viral genotypes (785) were present within the virome. The absolute numbers of lambdoid and Shiga toxin (Stx) encoding phages detected suggested that the depth of sequencing had enabled recovery of only ca. 8% of the total virus population, numbers that agreed within less than an order of magnitude with predictions made by rarefaction analysis. The most abundant viral genotypes in the pond were bacteriophages (93.7%). The predominant viral genotypes infecting higher life forms found in association with the farm were pathogens that cause disease in cattle and humans, e.g. members of the Herpesviridae. The techniques and analysis described here provide a fresh approach to the monitoring of viral populations in the aquatic environment, with the potential to become integral to the development of risk analysis tools for monitoring the dissemination of viral agents of animal, plant and human diseases

Statistics of an autoregressive correlated random walk along a return path

A closed-form analytical solution is derived for the statistical outcome of a random walk along a return path. The random walk is generated from the cumulative sum of correlated samples in a Gaussian-distributed autoregressive sequence. The outcome exhibits a smaller variance compared with a one-way path of equivalent length due to cancellation of correlated steps along the return leg. Furthermore, the variance decreases towards zero as the correlation coefficient approaches unity. An example application for this general result is the modelling of cumulative errors in dead-reckoning navigation systems, e.g. Doppler velocity log-aided inertial navigation systems used commonly on underwater vehicles. In this particular application, it can be used to express and quantify the natural cancellation of correlated error components between subsequent opposing legs in a typical ‘lawnmower’ survey pattern.<br/

Augustus Hamilton’s fossil collection at the Museum of New Zealand Te Papa Tongarewa

Augustus Hamilton (1853–1913) was a New Zealand ethnologist and naturalist who amassed a significant collection of fossils, mostly of birds, during his career. Today, those fossils are housed in the Museum of New Zealand Te Papa Tongarewa (NMNZ). While some fossils have been catalogued and integrated into the collection of the NMNZ, a large part remained unsorted and uncatalogued. The present study brings an integrated view of Hamilton’s collection at the NMNZ, highlighting the most significant fossils. In total, there are 3692 specimen lots collected by Hamilton in the NMNZ representing a large sample of taxa and a wide range of locations around Aotearoa New Zealand. Most fossils are of Holocene age and belong to birds. The collection includes type specimens, circa 250 specimen lots belonging to extinct species, and specimens belonging to otherwise poorly represented species in natural history collections. We hope that our study makes Hamilton’s fossils visible and more readily available for future research

Structural consequences of nucleophosmin mutations in acute myeloid leukemia.

Mutations affecting NPM1 (nucleophosmin) are the most common genetic lesions found in acute myeloid leukemia (AML). NPM1 is one of the most abundant proteins found in the nucleolus and has links to the MDM2/p53 tumor suppressor pathway. A distinctive feature of NPM1 mutants in AML is their aberrant localization to the cytoplasm of leukemic cells. This mutant phenotype is the result of the substitution of several C-terminal residues, including one or two conserved tryptophan residues, with a leucine-rich nuclear export signal. The exact molecular mechanism underlying the loss of nucleolar retention, and the role of the tryptophans, remains unknown. In this study we have determined the structure of an independently folded globular domain in the C terminus of NPM1 using NMR spectroscopy, and we report that the conserved tryptophans are critical for structure. This domain is necessary for the nucleolar targeting of NPM1 and is disrupted by mutations in AML with cytoplasmic NPM1. Furthermore, we identify conserved surface-exposed lysine residues that are functionally rather than structurally important for nucleolar localization. This study provides new focus for efforts to understand the pathogenesis of AML with cytoplasmic NPM1 and may be used to aid the design of small molecules that target the C-terminal domain of NPM1 to act as novel anti-proliferative and anti-leukemia therapeutics

High thymidylate synthase gene expression predicts poor outcome after resection of hepatocellular carcinoma.

IntroductionPrognosis after resection of hepatocellular carcinoma (HCC) is highly variable. Compared to clinicopathologic factors, the use of molecular markers to predict outcome has not been well studied. We investigated the prognostic importance of thymidylate synthase (TS) gene expression and polymorphisms in patients after resection of HCC.MethodsPatients who underwent complete resection of HCC for whom tissue was available were identified. TS gene expression level and polymorphisms were determined in HCC specimens. Prognostic factors were evaluated using Kaplan-Meier curves and Cox proportional hazard models.ResultsThe study included 67 patients. In univariate analysis, variables that negatively influenced survival included TNM stage, microvascular invasion, and high TS expression. For the high TS expression group, median survival was 54 months and 5-year actuarial survival was 47%. For the low TS expression group, median survival was not reached and the 5-year actuarial survival was 91%. In multivariate analysis, only high TS expression remained an independent predictor of poor survival (HR = 10.77, 95% CI 1.36-84.91; P = 0.02). TS gene polymorphisms were not associated with TS expression or overall survival.ConclusionsHigh TS expression predicts poor outcome after resection of HCC. Molecular markers might be robust predictors of patient outcome after resection of HCC

X-Ray and UV Orbital Phase Dependence in LMC X-3

The black-hole binary LMC X-3 is known to be variable on time scales of days to years. We investigate X-ray and ultraviolet variability in the system as a function of the 1.7 day binary phase using a 6.4 day observation with the Rossi X-ray Timing Explorer (RXTE) from December 1998. An abrupt 14% flux decrease, lasting nearly an entire orbit, is followed by a return to previous flux levels. This behavior occurs twice, at nearly the same binary phase, but it is not present in consecutive orbits. When the X-ray flux is at lower intensity, a periodic amplitude modulation of 7% is evident in data folded modulo the orbital period. The higher intensity data show weaker correlation with phase. This is the first report of X-ray variability at the orbital period of LMC X-3. Archival RXTE observations of LMC X--3 during a high flux state in December 1996 show similar phase dependence. An ultraviolet light curve obtained with the High Speed Photometer aboard the Hubble Space Telescope shows orbital modulation consistent with that in the optical, caused by the ellipsoidal variation of the spatially deformed companion. The X-ray spectrum of LMC X-3 can be acceptably represented by a phenomenological disk-black-body plus a power law. Changes in the spectrum of LMC X-3 during our observations are compatible with earlier observations during which variations in the 2-10 keV flux are tracked closely by the disk geometry spectral model parameter.Comment: 11 pages, 7 figures, ApJ in pres

An operational concept for correcting navigation drift during sonar surveys of the seafloor

The accumulation of navigation errors (drift) is a problem in many applications of autonomous underwater vehicles (AUVs), particularly during long-duration underwater surveys. Traditional methods for correcting drift require either surfacing of the vehicle for a global navigation satellite systemupdate or use of an independent acoustic positioning system. These methods may not be desirable or possible due to mission constraints. We propose a solution to this problem completely underwater and without the aid of external navigation systems. The approach is based on an operational concept that uses a modified paired-track survey pattern combined with through-the-sensor navigation corrections from a seafloor imaging sonar. We describe the operational concept, derive a model for its performance limits, validate this model, and demonstrate the concept with real experiments at sea. Using this approach, we provide an opportunity to use either coherent or incoherent through-the-sensor positioning corrections for a mission length increase of only the product of the intratrack spacing and the number of track pairs. We show results from a proof-of-principle experiment using data collected by the 300-kHz synthetic aperture sonar of the NATO Centre for Maritime Research and Experimentation’s Minehunting Unmanned underwater vehicle for Shallow water Covert Littoral Expeditions