NDSF technical operations via telecommunications

In 2015, the Woods Hole Oceanographic Institution (WHOI) commissioned an external study concerning the use of modern telecommunications and telepresence technologies in the potential reduction of manpower in National Deep Submergence Operations. That study has been completed, and the final report is attached as Appendix A.Funding was provided by the Nereus Legacy Fund at the Woods Hole Oceanographic Institutio

Methods for Collecting and Using Backscatter Field Calibration Information for the Reson 7000 Series Multibeams

In support of Integrated Ocean and Coastal Mapping, the National Oceanic and Atmospheric Administration’s (NOAA) Office of Coast Survey collects meaningful acoustic backscatter as a ancillary product of its navigational charting mission. Many of NOAA’s field units have Reson 7000 series multibeam echosounders which have been shown to have decidedly non-linear response characteristics under certain high signal conditions. This non-linear behavior significantly increases the complexity of the radiometric corrections required to make use of backscatter under a variety of processing paradigms. Avoiding operating these systems in the non-linear operational domain is a simpler approach. However, the onset of non-linear behavior is not a simple function of the output signal level but instead depends on a number of tunable settings. Here we present a method for both determining the onset of non-linear behavior in any installed Reson 7000 series sonar and monitoring the system during real-time acquisition to ensure the system is operating in a linear fashion. In general this information improves the operator’s understanding of the system status and can lead to additional post processing advantages

Improved Fast Randomized Iteration Approach to Full Configuration Interaction

We present three modifications to our recently introduced fast randomized iteration method for full configuration interaction (FCI-FRI) and investigate their effects on the method's performance for Ne, H$_2$O, and N$_2$. The initiator approximation, originally developed for full configuration interaction quantum Monte Carlo, significantly reduces statistical error in FCI-FRI when few samples are used in compression operations, enabling its application to larger chemical systems. The semi-stochastic extension, which involves exactly preserving a fixed subset of elements in each compression, improves statistical efficiency in some cases but reduces it in others. We also developed a new approach to sampling excitations that yields consistent improvements in statistical efficiency and reductions in computational cost. We discuss possible strategies based on our findings for improving the performance of stochastic quantum chemistry methods more generally.Comment: 13 pages, 5 figure

Approximating matrix eigenvalues by subspace iteration with repeated random sparsification

Traditional numerical methods for calculating matrix eigenvalues are prohibitively expensive for high-dimensional problems. Iterative random sparsification methods allow for the estimation of a single dominant eigenvalue at reduced cost by leveraging repeated random sampling and averaging. We present a general approach to extending such methods for the estimation of multiple eigenvalues and demonstrate its performance for several benchmark problems in quantum chemistry.Comment: 31 pages, 7 figure

ALMA Observations of Asymmetric Molecular Gas Emission from a Protoplanetary Disk in the Orion Nebula

We present Atacama Large Millimeter/submillimeter Array (ALMA) observations of molecular line emission from d216-0939, one of the largest and most massive protoplanetary disks in the Orion Nebula Cluster (ONC). We model the spectrally resolved HCO$^+$ (4--3), CO (3--2), and HCN (4--3) lines observed at 0\farcs5 resolution to fit the temperature and density structure of the disk. We also weakly detect and spectrally resolve the CS (7--6) line but do not model it. The abundances we derive for CO and HCO$^+$ are generally consistent with expected values from chemical modeling of protoplanetary disks, while the HCN abundance is higher than expected. We dynamically measure the mass of the central star to be $2.17\pm0.07\,M_\odot$ which is inconsistent with the previously determined spectral type of K5. We also report the detection of a spatially unresolved high-velocity blue-shifted excess emission feature with a measurable positional offset from the central star, consistent with a Keplerian orbit at $60\pm20\,\mathrm{au}$. Using the integrated flux of the feature in HCO$^+$ (4--3), we estimate the total H$_2$ gas mass of this feature to be at least $1.8-8\,M_\mathrm{Jupiter}$, depending on the assumed temperature. The feature is due to a local temperature and/or density enhancement consistent with either a hydrodynamic vortex or the expected signature of the envelope of a forming protoplanet within the disk.Comment: 19 pages, 12 figures, accepted for publication in A

Beyond Walkers in Stochastic Quantum Chemistry: Reducing Error using Fast Randomized Iteration

We introduce a family of methods for the full configuration interaction problem in quantum chemistry, based on the fast randomized iteration (FRI) framework [L.-H. Lim and J. Weare, SIAM Rev. 59, 547 (2017)]. These methods, which we term "FCI-FRI," stochastically impose sparsity during iterations of the power method and can be viewed as a generalization of full configuration interaction quantum Monte Carlo (FCIQMC) without walkers. In addition to the multinomial scheme commonly used to sample excitations in FCIQMC, we present a systematic scheme where excitations are not sampled independently. Performing ground-state calculations on five small molecules at fixed cost, we find that the systematic FCI-FRI scheme is 11 to 45 times more statistically efficient than the multinomial FCI-FRI scheme, which is in turn 1.4 to 178 times more statistically efficient than the original FCIQMC algorithm.Comment: 19 pages, 7 figure

Crystal structure of Mycobacterium tuberculosis FadB2 implicated in mycobacterial β-oxidation

The intracellular pathogen Mycobacterium tuberculosis is the causative agent of tuberculosis, which is a leading cause of mortality worldwide. The survival of M. tuberculosis in host macrophages through long-lasting periods of persistence depends, in part, on breaking down host cell lipids as a carbon source. The critical role of fatty-acid catabolism in this organism is underscored by the extensive redundancy of the genes implicated in β-oxidation (∼100 genes). In a previous study, the enzymology of the M. tuberculosisl-3-hydroxyacyl-CoA dehydrogenase FadB2 was characterized. Here, the crystal structure of this enzyme in a ligand-free form is reported at 2.1 Å resolution. FadB2 crystallized as a dimer with three unique dimer copies per asymmetric unit. The structure of the monomer reveals a dual Rossmann-fold motif in the N-terminal domain, while the helical C-terminal domain mediates dimer formation. Comparison with the CoA- and NAD + -bound human orthologue mitochondrial hydroxyacyl-CoA dehydrogenase shows extensive conservation of the residues that mediate substrate and cofactor binding. Superposition with the multi-catalytic homologue M. tuberculosis FadB, which forms a trifunctional complex with the thiolase FadA, indicates that FadB has developed structural features that prevent its self-association as a dimer. Conversely, FadB2 is unable to substitute for FadB in the tetrameric FadA–FadB complex as it lacks the N-terminal hydratase domain of FadB. Instead, FadB2 may functionally (or physically) associate with the enoyl-CoA hydratase EchA8 and the thiolases FadA2, FadA3, FadA4 or FadA6 as suggested by interrogation of the STRING protein-network database

Infancy and childhood growth and physical activity in adolescence: prospective birth cohort study from Brazil.

BACKGROUND: The Developmental Origins of Health and Disease hypothesis suggests that intrauterine, infancy and early childhood variables play a key role at programming later health. However, little is known on the programming of behavioral variables, because most studies so far focused on chronic disease-related and human capital outcomes. The aim of the present study was to evaluate the effects of prenatal, infancy and childhood weight and length/height gains on objectively-measured physical activity (PA) in adolescence. METHODS: This is a prospective birth cohort study in Pelotas, Brazil, including 457 adolescents (mean age: 13.3 years) with weight and length/height data at birth, one, three and six months, one and four years of age. PA was measured using a GT1M Actigraph accelerometer, and expressed as (a) minutes per day spent on sedentary, light, moderate, vigorous and very-vigorous activities; (b) total counts per day. RESULTS: 61.3% of the adolescents accumulated 60+ minutes of moderate-to-vigorous PA per day. Weight and length/height trajectories in infancy and childhood were similar between those classified as active or inactive at 13.3 years. However, those classified as inactive were heavier and taller at all ages; differences were statistically significant only in terms of length at three, six and 12 months. CONCLUSIONS: Weight gain in infancy and childhood did not predict variability in adolescent PA, but those active in adolescence showed somewhat smaller average gains in length in infancy. These findings suggest that PA may partially be sensitive to early hormonal programming, or that genetic factors may affect both early growth and later metabolism or predisposition for PA.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

A Malvaceae mystery: A mallow maelstrom of genome multiplications and maybe misleading methods?

Previous research suggests that Gossypium has undergone a 5- to 6-fold multiplication following its divergence from Theobroma. However, the number of events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data from representatives of eight of the nine Malvaceae subfamilies. Phylogenetic analysis of nuclear data placed Dombeya (Dombeyoideae) as sister to the rest of Malvadendrina clade, but the plastid DNA tree strongly supported Durio (Helicteroideae) in this position. Intraspecific Ks plots indicated that all sampled taxa, except Theobroma (Byttnerioideae), Corchorus (Grewioideae), and Dombeya (Dombeyoideae), have experienced whole genome multiplications (WGMs). Quartet analysis suggested WGMs were shared by Malvoideae-Bombacoideae and Sterculioideae-Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae (Durio). Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They differ in that one entails an allopolyploid origin for the Durio lineage, whereas the other invokes an allopolyploid origin for Malvoideae-Bombacoideae. We highlight the need for more genomic information in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of gene and genome evolution

An Observational Study of the Etiology, clinical presentation and outcomes associated with peritonitis in Lilongwe, Malawi

<p>Abstract</p> <p>Introduction</p> <p>Peritonitis is a life-threatening condition with a multitude of etiologies that can vary with geographic location. The aims of this study were to elucidate the etiology, clinical presentation and outcomes associated with peritonitis in Lilongwe, Malawi.</p> <p>Methods</p> <p>All patients admitted to Kamuzu Central Hospital (KCH) who underwent an operation for treatment of peritonitis during the calendar year 2008 were eligible. Peritonitis was defined as abdominal rigidity, rebound tenderness, and/or guarding in one or more abdominal quadrants. Subjects were identified from a review of the medical records for all patients admitted to the adult general surgical ward and the operative log book. Those who met the definition of peritonitis and underwent celiotomy were included.</p> <p>Results</p> <p>190 subjects were identified. The most common etiologies were appendicitis (22%), intestinal volvulus (17%), perforated peptic ulcer (11%) and small bowel perforation (11%). The overall mortality rate associated with peritonitis was 15%, with the highest mortality rates observed in solid organ rupture (35%), perforated peptic ulcer (33%), primary/idiopathic peritonitis (27%), tubo-ovarian abscess (20%) and small bowel perforation (15%). Factors associated with death included abdominal rigidity, generalized (versus localized) peritonitis, hypotension, tachycardia and anemia (p < 0.05). Age, gender, symptoms (obstipation, vomiting) and symptom duration, tachypnea, abnormal temperature, leukocytosis, hemoconcentration, thrombocytopenia and thrombocytosis were not associated with mortality (p = NS).</p> <p>Conclusions</p> <p>There are several signs and laboratory findings predictive of poor outcome in Malawian patients with peritonitis. Tachycardia, hypotension, anemia, abdominal rigidity and generalized peritonitis are the most predictive of death (P < 0.05 for each). Similar to studies from other African countries, in our population the most common cause of peritonitis was appendicitis, and the overall mortality rate among all patients with peritonitis was 15%. Identified geographical differences included intestinal volvulus, rare in the US but the 2^ndmost common cause of peritonitis in Malawi and gallbladder disease, common in Ethiopia but not observed in Malawi. Future research should investigate whether correction of factors associated with mortality might improve outcomes.</p