Spatial Patterns of Marine Larvae as Indicators of Incipient Invasions in Great Bay

Understanding the dynamics of coastal marine communities represents a substantial challenge, and one that is actively pursued globally. Within the United States, several sites have been designated as National Estuarine Research Reserves (NERR) with the idea that concentrated research at these sites will lead to greater understanding of the ecosystem. The Great Bay Estuary of New Hampshire is one of these sites. A wide spectrum of research is conducted within the Great Bay, and substantial financial support is committed to that research on an annual basis. To facilitate the success of these research efforts, it is particularly important to develop a working understanding of the dynamics of marine communities within the Great Bay. Invertebrate communities within the Bay and at other coastal sites are largely composed of open populations whose growth and maintenance depend on settlement of new recruits that may arrive from distant source populations. Larval monitoring programs designed to survey these incoming recruits should therefore be an important component of the research program within the Great Bay and other NERR sites. By monitoring recruitment within the Great Bay, we may begin to determine larval spatial patterns within potential habitats. This will then allow for comparison of observed larval spatial patterns and observed adult population distributions. If the two are similar, this would indicate that future adult populations can be predicted by knowledge of larval settlement. If the two are dissimilar, this indicates a need to investigate causes of post-settlement mortality that lead to discrepancies in larval and adult abundances. For example, if there is a large discrepancy between larval and adult abundances, then the Great Bay may be acting as a sink for some species whose larvae are transported into the bay, but do not survive to establish adult populations. By monitoring invertebrate recruitment into the Great Bay, we begin to establish a baseline for biotic conditions within the Bay against which future conditions can be compared. This is a crucial step in determining the effects of anthropogenically induced environmental changes, such as the introduction of nonindigenous species. Furthermore, we predict that because a sufficient influx of larvae is needed to establish a viable adult population, larvae of exotic species not currently present in Great Bay will be first detectable in the plankton, perhaps for several years before they arrive in sufficient numbers for adults to establish. This may provide an advanced warning of incipient invasions and allow managers to develop plans for eradication or mitigation in advance of the exotic species’ establishment. Here we report on a study designed to collect the baseline data necessary to establish patterns and make comparisons to future conditions. We have collected larvae on artificial settlement substrates at six sites within the Great Bay Estuary and at an adjacent coastal site during ice-free months since July 2002. This report gives a brief description of the results of this monitoring program to determine the species composition, spatial patterns, and timing of invertebrate settlement within the Great Bay. This report specifically includes data from April 2005 to June 2006, the portion of the project funded by NHEP. Data from 2002-04 are also available, but are not included in this report

The Effects of Varying Cosmological Parameters on Halo Substructure

We investigate how different cosmological parameters, such as those delivered by the WMAP and Planck missions, affect the nature and evolution of dark matter halo substructure. We use a series of flat $\Lambda$ cold dark matter ($\Lambda$CDM) cosmological $N$-body simulations of structure formation, each with a different power spectrum but the same initial white noise field. Our fiducial simulation is based on parameters from the WMAP 7th year cosmology. We then systematically vary the spectral index, $n_s$, matter density, $\Omega_M$, and normalization of the power spectrum, $\sigma_8$, for 7 unique simulations. Across these, we study variations in the subhalo mass function, mass fraction, maximum circular velocity function, spatial distribution, concentration, formation times, accretion times, and peak mass. We eliminate dependence of subhalo properties on host halo mass and average over many hosts to reduce variance. While the "same" subhalos from identical initial overdensity peaks in higher $\sigma_8, n_s$, and $\Omega_m$ simulations accrete earlier and end up less massive and closer to the halo center at $z=0$, the process of continuous subhalo accretion and destruction leads to a steady state distribution of these properties across all subhalos in a given host. This steady state mechanism eliminates cosmological dependence on all properties listed above except subhalo concentration and $V_{max}$, which remain greater for higher $\sigma_8, n_s$ and $\Omega_m$ simulations, and subhalo formation time, which remains earlier. We also find that the numerical technique for computing scale radius and the halo finder used can significantly affect the concentration-mass relationship computed for a simulation.Comment: 15 pages, 15 figures, Accepted to ApJ on March 15, 201

Direction of Arrival and the Rank-Revealing URV Decomposition

In many practical direction-of-arrival (DOA) problems the number of sources and their directions from an antenna array do not remain stationary. Hence a practical DOA algorithm must be able to track changes with a minimal number of snapshots. In this paper we describe DOA algorithms, based on a new decomposition, that are not expensive to compute or difficult to update. The algorithms are compared with algorithms based on the singular value decomposition (SVD). (Also cross-referenced as UMIACS-TR-91-166

TaxMan : a server to trim rRNA reference databases and inspect taxonomic coverage

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418.Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.)

Benzoate dioxygenase from<em> Ralstonia eutropha</em> B9 – unusual regiochemistry of dihydroxylation permits rapid access to novel chirons

Oxidation of benzoic acid by a microorganism expressing benzoate dioxygenase leads to the formation of an unusualipso,orthoarenecis-diol in sufficient quantities to be useful for synthesis.</p

Ten years of major equestrian injury: are we addressing functional outcomes?

YesFunding provided by the Open Access Authors Fund

Tolerance, adherence, and acceptability of a ketogenic 2.5:1 ratio, nutritionally complete, medium chain triglyceride-containing liquid feed in children and adults with drug-resistant epilepsy following a ketogenic diet

Objective: To investigate incorporating a ready-to-use 2.5:1 ratio liquid feed into a ketogenic diet (KD) in children and adults with drug-resistant epilepsy. Methods: Following a three-day baseline, patients (n = 19; age: 19 years [SD 13], range: 8–46 years) followed a KD for 28 days (control period), then incorporated ≥200 mL/day of a ready-to-use liquid feed, made with a ratio of 2.5 g of fat to 1 g of protein plus carbohydrate and including medium chain triglycerides ([MCTs]; 25.6% of total fat/100 mL) for 28 days as part of their KD (intervention period). Outcome measures (control vs intervention period) included gastrointestinal (GI) tolerance, adherence to KD and intervention feed, dietary intake, blood ß-hydroxybutyrate (BHB) concentration, seizure outcomes, health-related quality of life (HRQoL), acceptability and safety. Results: Compared to the control period, during the intervention period, the percentage of patients reporting no GI symptoms increased (+5% [SD 5], p = 0.02); adherence to the KD prescription was similar (p = 0.92) but higher in patients (n = 5) with poor adherence (&lt;50%) to KD during the control period (+33% [SD 26], p = 0.049); total MCT intake increased (+12.1 g/day [SD 14.0], p = 0.002), driven by increases in octanoic (C8; +8.3 g/day [SD 6.4], p &lt; 0.001) and decanoic acid (C10; +5.4 g/day [SD 5.4], p &lt; 0.001); KD ratio decreased (p = 0.047), driven by a nonsignificant increase in protein intake (+11 g/day [SD 44], p = 0.29); seizure outcomes were similar (p ≥ 0.63) but improved in patients (n = 6) with the worst seizure outcomes during the control period (p = 0.04); and HRQoL outcomes were similar. The intervention feed was well adhered to (96% [SD 8]) and accepted (≥88% of patients confirmed). Significance: These findings provide an evidence-base to support the effective management of children and adults with drug-resistant epilepsy following a KD with the use of a ready-to-use, nutritionally complete, 2.5:1 ratio feed including MCTs. Plain language summary: This study examined the use of a ready-to-use, nutritionally complete, 2.5:1 ratio (2.5 g of fat to 1 g of protein plus carbohydrate) liquid feed, including medium chain triglycerides (MCTs), into a ketogenic diet (KD) in children and adults with drug-resistant epilepsy. The results show that the 2.5:1 ratio feed was well tolerated, adhered to, and accepted in these patients. Increases in MCT intake (particularly C8 and C10) and improvements in seizure outcomes (reduced seizure burden and intensity) and KD adherence also occurred with the 2.5:1 ratio feed in patients with the worst seizures and adherence, respectively.</p

Tolerance, adherence, and acceptability of a ketogenic 2.5:1 ratio, nutritionally complete, medium chain triglyceride-containing liquid feed in children and adults with drug-resistant epilepsy following a ketogenic diet

Objective: To investigate incorporating a ready-to-use 2.5:1 ratio liquid feed into a ketogenic diet (KD) in children and adults with drug-resistant epilepsy. Methods: Following a three-day baseline, patients (n = 19; age: 19 years [SD 13], range: 8–46 years) followed a KD for 28 days (control period), then incorporated ≥200 mL/day of a ready-to-use liquid feed, made with a ratio of 2.5 g of fat to 1 g of protein plus carbohydrate and including medium chain triglycerides ([MCTs]; 25.6% of total fat/100 mL) for 28 days as part of their KD (intervention period). Outcome measures (control vs intervention period) included gastrointestinal (GI) tolerance, adherence to KD and intervention feed, dietary intake, blood ß-hydroxybutyrate (BHB) concentration, seizure outcomes, health-related quality of life (HRQoL), acceptability and safety. Results: Compared to the control period, during the intervention period, the percentage of patients reporting no GI symptoms increased (+5% [SD 5], p = 0.02); adherence to the KD prescription was similar (p = 0.92) but higher in patients (n = 5) with poor adherence (&lt;50%) to KD during the control period (+33% [SD 26], p = 0.049); total MCT intake increased (+12.1 g/day [SD 14.0], p = 0.002), driven by increases in octanoic (C8; +8.3 g/day [SD 6.4], p &lt; 0.001) and decanoic acid (C10; +5.4 g/day [SD 5.4], p &lt; 0.001); KD ratio decreased (p = 0.047), driven by a nonsignificant increase in protein intake (+11 g/day [SD 44], p = 0.29); seizure outcomes were similar (p ≥ 0.63) but improved in patients (n = 6) with the worst seizure outcomes during the control period (p = 0.04); and HRQoL outcomes were similar. The intervention feed was well adhered to (96% [SD 8]) and accepted (≥88% of patients confirmed). Significance: These findings provide an evidence-base to support the effective management of children and adults with drug-resistant epilepsy following a KD with the use of a ready-to-use, nutritionally complete, 2.5:1 ratio feed including MCTs. Plain language summary: This study examined the use of a ready-to-use, nutritionally complete, 2.5:1 ratio (2.5 g of fat to 1 g of protein plus carbohydrate) liquid feed, including medium chain triglycerides (MCTs), into a ketogenic diet (KD) in children and adults with drug-resistant epilepsy. The results show that the 2.5:1 ratio feed was well tolerated, adhered to, and accepted in these patients. Increases in MCT intake (particularly C8 and C10) and improvements in seizure outcomes (reduced seizure burden and intensity) and KD adherence also occurred with the 2.5:1 ratio feed in patients with the worst seizures and adherence, respectively.</p