Corrigendum "Portal protein diversity and phage ecology"

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Environmental Microbiology 13 (2011): 2832, doi:10.1111/j.1462-2920.2011.02616.x

The Richardson's Law in Large-Eddy Simulations of Boundary Layer flows

Relative dispersion in a neutrally stratified planetary boundary layer (PBL) is investigated by means of Large-Eddy Simulations (LES). Despite the small extension of the inertial range of scales in the simulated PBL, our Lagrangian statistics turns out to be compatible with the Richardson $t^3$ law for the average of square particle separation. This emerges from the application of nonstandard methods of analysis through which a precise measure of the Richardson constant was also possible. Its values is estimated as $C_2\sim 0.5$ in close agreement with recent experiments and three-dimensional direct numerical simulations.Comment: 15 LaTex pages, 4 PS figure

Photosynthetic and Growth Response of Sugar Maple (Acer saccharum Marsh.) Mature Trees and Seedlings to Calcium, Magnesium, and Nitrogen Additions in the Catskill Mountains, NY, USA

Funding for Open Access provided by the UMD Libraries Open Access Publishing Fund.Decline of sugar maple in North American forests has been attributed to changes in soil calcium (Ca) and nitrogen (N) by acidic precipitation. Although N is an essential and usually a limiting factor in forests, atmospheric N deposition may cause N-saturation leading to loss of soil Ca. Such changes can affect carbon gain and growth of sugar maple trees and seedlings. We applied a 2^2 factorial arrangement of N and dolomitic limestone containing Ca and Magnesium (Mg) to 12 forest plots in the Catskill Mountain region of NY, USA. To quantify the short-term effects, we measured photosynthetic-light responses of sugar maple mature trees and seedlings two or three times during two summers. We estimated maximum net photosynthesis (An-max) and its related light intensity (PAR at An-max), apparent quantum efficiency (Aqe), and light compensation point (LCP). To quantify the long-term effects, we measured basal area of living mature trees before and 4 and 8 years after treatment applications. Soil and foliar chemistry variables were also measured. Dolomitic limestone increased Ca, Mg, and pH in the soil Oe horizon. Mg was increased in the B horizon when comparing the plots receiving N with those receiving CaMg. In mature trees, foliar Ca and Mg concentrations were higher in the CaMg and N+CaMg plots than in the reference or N plots; foliar Ca concentration was higher in the N+CaMg plots compared with the CaMg plots, foliar Mg was higher in the CaMg plots than the N+CaMg plots; An-max was maximized due to N+CaMg treatment; Aqe decreased by N addition; and PAR at An-max increased by N or CaMg treatments alone, but the increase was maximized by their combination. No treatment effect was detected on basal areas of living mature trees four or eight years after treatment applications. In seedlings, An-max was increased by N+CaMg addition. The reference plots had an open herbaceous layer, but the plots receiving N had a dense monoculture of common woodfern in the forest floor, which can impede seedling survival

Deactivation of metastable single-crystal silicon hyperdoped with sulfur

Silicon supersaturated with sulfur by ion implantation and pulsed laser melting exhibits broadband optical absorption of photons with energies less than silicon's band gap. However, this metastable, hyperdoped material loses its ability to absorb sub-band gap light after subsequent thermal treatment. We explore this deactivation process through optical absorption and electronic transport measurements of sulfur-hyperdoped silicon subject to anneals at a range of durations and temperatures. The deactivation process is well described by the Johnson-Mehl-Avrami-Kolmogorov framework for the diffusion-mediated transformation of a metastable supersaturated solid solution, and we find that this transformation is characterized by an apparent activation energy of E[subscript A] = 1.7 ± 0.1  eV. Using this activation energy, the evolution of the optical and electronic properties for all anneal duration-temperature combinations collapse onto distinct curves as a function of the extent of reaction. We provide a mechanistic interpretation of this deactivation based on short-range thermally activated atomic movements of the dopants to form sulfur complexes.Center for Clean Water and Clean Energy at MIT and KFUPMNational Science Foundation (U.S.) (Energy, Power, and Adaptive Systems Grant Contract ECCS-1102050)National Science Foundation (U.S.) (United States. Dept. of Energy Contract EEC-1041895

Portal protein diversity and phage ecology

© 2008 The Authors. This article is distributed under the terms of the Creative Commons License, Attribution 2.5. The definitive version was published in Environmental Microbiology 10 (2008): 2810-2823, doi:10.1111/j.1462-2920.2008.01702.x.Oceanic phages are critical components of the global ecosystem, where they play a role in microbial mortality and evolution. Our understanding of phage diversity is greatly limited by the lack of useful genetic diversity measures. Previous studies, focusing on myophages that infect the marine cyanobacterium Synechococcus, have used the coliphage T4 portal-protein-encoding homologue, gene 20 (g20), as a diversity marker. These studies revealed 10 sequence clusters, 9 oceanic and 1 freshwater, where only 3 contained cultured representatives. We sequenced g20 from 38 marine myophages isolated using a diversity of Synechococcus and Prochlorococcus hosts to see if any would fall into the clusters that lacked cultured representatives. On the contrary, all fell into the three clusters that already contained sequences from cultured phages. Further, there was no obvious relationship between host of isolation, or host range, and g20 sequence similarity. We next expanded our analyses to all available g20 sequences (769 sequences), which include PCR amplicons from wild uncultured phages, non-PCR amplified sequences identified in the Global Ocean Survey (GOS) metagenomic database, as well as sequences from cultured phages, to evaluate the relationship between g20 sequence clusters and habitat features from which the phage sequences were isolated. Even in this meta-data set, very few sequences fell into the sequence clusters without cultured representatives, suggesting that the latter are very rare, or sequencing artefacts. In contrast, sequences most similar to the culture-containing clusters, the freshwater cluster and two novel clusters, were more highly represented, with one particular culture-containing cluster representing the dominant g20 genotype in the unamplified GOS sequence data. Finally, while some g20 sequences were non-randomly distributed with respect to habitat, there were always numerous exceptions to general patterns, indicating that phage portal proteins are not good predictors of a phage's host or the habitat in which a particular phage may thrive.This research was supported in part by funding from NSF (CMORE contribution #87), DOE, The Seaver Foundation and the Gordon and Betty Moore Foundation Marine Microbiology Program to S.W.C.; an NIH Bioinformatics Training Grant supported M.B.S.; MIT Undergraduate Research Opportunities Program supported V.Q., J.A.L., G.T., R.F. and J.E.R.; Howard Hughes Medical Institute funded MIT Biology Department Undergraduate Research Opportunities Program supported A.S.D.; NSERC (Canada) Discovery Grant (DG 298394) and a Grant from the Canadian Foundation for Innovation (NOF10394) to J.P.B.; NSF Graduate Fellowship funding supported M.L.C

Weight Loss Can Lead to Resolution of Gastroesophageal Reflux Disease Symptoms: A Prospective Intervention Trial

This is the peer reviewed version of the following article: Singh, M., Lee, J., Gupta, N., Gaddam, S., Smith, B. K., Wani, S. B., Sullivan, D. K., Rastogi, A., Bansal, A., Donnelly, J. E. and Sharma, P. (2013), Weight loss can lead to resolution of gastroesophageal reflux disease symptoms: A prospective intervention trial. Obesity, 21: 284–290. doi:10.1002/oby.20279, which has been published in final form at http://doi.org/10.1002/oby.20279. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.OBJECTIVE Weight gain is an important risk factor for gastroesophageal reflux disease (GERD); however, whether weight loss can lead to resolution of GERD symptoms is not clear. Our aim was to measure the impact of weight loss on GERD symptoms. DESIGN AND METHODS In a prospective cohort study at a tertiary referral center, overweight/obese subjects (BMI 25-39.9 kg/m2) were enrolled in a structured weight loss program. Weight loss strategies included dietary modifications, increased physical activity and behavioral changes. At baseline and at 6 months, BMI and waist circumference were measured and all participants completed a validated reflux disease questionnaire. RESULTS A total of 332 adult subjects, mean age 46 years and 66% women were prospectively enrolled. At baseline, the mean body weight, BMI, and waist circumference were 101 (±18) kg, 35 (±5) kg/m2 and 103 (±13) cm. At 6 months, majority of the subjects (97%) lost weight (average weight loss: 13 ± 7.7 kg) and as compared with baseline, there was a significant decrease in the overall prevalence of GERD (15 vs. 37%; P < 0.01) and the mean GERD symptom score (1.8 vs. 5.5; P < 0.01). Overall, 81% of the subjects had reduction in GERD symptom scores; 65% had complete resolution and 15% had partial resolution of reflux symptoms. There was a significant correlation between % body weight loss and reduction in GERD symptom scores (r = 0.17, P < 0.05). CONCLUSIONS In conclusion, the overall prevalence of GERD symptoms is high (37%) in overweight and obese subjects. A structured weight loss program can lead to complete resolution of GERD symptoms in the majority of these subjects

JWST mirror and actuator performance at cryo-vacuum

The James Webb Space Telescope (JWST) telescope’s Secondary Mirror Assembly (SMA) and eighteen Primary Mirror Segment Assemblies (PMSAs) are each actively controlled in rigid body position via six hexapod actuators. Each of the PMSAs additionally has a radius of curvature actuator. The mirrors are stowed to the mirror support structure to survive the launch environment and then must be deployed 12.5 mm to reach the nominally deployed position before the Wavefront Sensing & Control (WFSC) alignment and phasing process begins. JWST requires testing of the full optical system in a Cryogenic Vacuum (CV) environment before launch. The cryo vacuum test campaign was executed in Chamber A at the Johnson Space Center (JSC) in Houston Texas. The test campaign consisted of an ambient vacuum test, a cooldown test, a cryo stable test at 65 Kelvin, a warmup test, and finally a second ambient vacuum test. Part of that test campaign was the functional and performance testing of the hexapod actuators on the flight mirrors. This paper will describe the testing that was performed on all 132 hexapod and radius of curvature actuators. The test campaign first tests actuators individually then tested how the actuators perform in the hexapod system. Telemetry from flight sensors on the actuators and measurements from external metrology devices such as interferometers, photogrammetry systems and image analysis was used to demonstrate the performance of the JWST actuators. The mirror move commanding process was exercised extensively during the JSC CV test and many examples of accurately commanded moves occurred. The PMSA and SMA actuators performed extremely well during the JSC CV test, and we have demonstrated that the actuators are fully functional both at ambient and cryo temperatures and that the mirrors will go to their commanded positions with the accuracy needed to phase and align the telescope

Atrioventricular conduction in children of women with systemic lupus erythematosus

The neonatal lupus syndrome consists of transient cutaneous lupus lesions or permanent congenital complete heart block (or hepatic fibrosis), or both, in infants born to mothers with systemic lupus erythematosus (SLE). The frequency of conduction abnormalities was examined in 86 offspring of 53 women affected by SLE. Electrocardiograms from the offspring demonstrated normal sinus rhythm in 84 of 86 offspring. The PR interval was normal for age (95th percentile (i.e., first-degree heart block) for both age and heart rate. The PR interval of the other 6 subjects with first-degree heart block for age or heart rate (&gt;=95th percentile) was &lt;=0.18 second. In contrast, using a rank assignment of PR intervals in relation to heart rate and age derived from published standards, grouped data indicated that heart rate adjusted for age was greater and PR interval adjusted for heart rate longer in offspring of mothers who had the onset of SLE before or during pregnancy than in the normal population; this observation did not hold for offspring whose mothers developed SLE after the pregnancy. These findings indicate that offspring of mothers with SLE, even in the absence of an abnormal electrocardiogram, may have experienced a maternal internal environment that produces subclinical changes in atrioventricular conduction. However, newborns with a normal pulse rate are unlikely to have significant abnormalities in atrioventricular conduction and do not need screening electrocardiograms at birth.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/31047/1/0000724.pd