Middle Atlantic Outer Continental Shelf Environmental Studies Volume II-B: Chemical and Biological Benchmark Studies

The Middle Atlantic Outer Continental Shelf Environmental Studies is comprised of three volumes. Volume I. Executive Summary. Volume IIA, IIB, IIC and IID. Chemical and Biological Benchmark Studies. Volume III. Geologic Studies. This is the second of four sections of the Chemical and Biological Benchmark Studies CHAPTER 5. BOTTOM SEDIMENTS AND SEDIMENTARY FRAMEWORK by Donald .F. Boesch CHAPTER 6. BENTHIC ECOLOGICAL STUDIES: MACROBENTHOS by Donald F. Boesch CHAPTER 7. BENTHIC ECOLOGICAL STUDIES: MEIOBENTHOS by D.J. Hartzband and Donald F. Boesch CHAPTER 8. BENTHIC ECOLOGICAL STUDIES: FORAMINIFERA by Robert L. Ellison Chapters of this report contain the Institutes\u27 Special Reports in Applied Marine Science and Ocean Engineering No.193,194,195,196

The Bacterial Chemotactic Response Reflects a Compromise Between Transient and Steady State Behavior

Swimming bacteria detect chemical gradients by performing temporal comparisons of recent measurements of chemical concentration. These comparisons are described quantitatively by the chemotactic response function, which we expect to optimize chemotactic behavioral performance. We identify two independent chemotactic performance criteria: in the short run, a favorable response function should move bacteria up chemoattractant gradients, while in the long run, bacteria should aggregate at peaks of chemoattractant concentration. Surprisingly, these two criteria conflict, so that when one performance criterion is most favorable, the other is unfavorable. Since both types of behavior are biologically relevant, we include both behaviors in a composite optimization that yields a response function that closely resembles experimental measurements. Our work suggests that the bacterial chemotactic response function can be derived from simple behavioral considerations, and sheds light on how the response function contributes to chemotactic performance.Comment: 19 pages, 5 figure

Retrieval of XCO2 from simulated Orbiting Carbon Observatory measurements using the fast linearized R-2OS radiative transfer model

In a recent paper, we introduced a novel technique to compute the polarization in a vertically inhomogeneous, scattering-absorbing medium using a two orders of scattering (2OS) radiative transfer (RT) model. The 2OS computation is an order of magnitude faster than a full multiple scattering scalar calculation and can be implemented as an auxiliary code to compute polarization in operational retrieval algorithms. In this paper, we employ the 2OS model for polarization in conjunction with a scalar RT model (Radiant) to simulate backscatter measurements in near infrared (NIR) spectral regions by space-based instruments such as the Orbiting Carbon Observatory (OCO). Computations are performed for six different sites and two seasons, representing a variety of viewing geometries, surface and aerosol types. The aerosol extinction (at 13000 cm^−1) was varied from 0 to 0.3. The radiance errors using the Radiant/2OS (R-2OS) RT model are an order of magnitude (or more) smaller than errors arising from the use of the scalar model alone. In addition, we perform a linear error analysis study to show that the errors in the retrieved column-averaged dry air mole fraction of CO2 (XCO2) using the R-2OS model are much lower than the “measurement” noise and smoothing errors appearing in the inverse model. On the other hand, we show that use of the scalar model alone induces X CO2 errors that could dominate the retrieval error budget

The Price of Play: Self-Organized Infant Mortality Cycles in Chimpanzees

Chimpanzees have been used extensively as a model system for laboratory research on infectious diseases. Ironically, we know next to nothing about disease dynamics in wild chimpanzee populations. Here, we analyze long-term demographic and behavioral data from two habituated chimpanzee communities in Taï National Park, Côte d'Ivoire, where previous work has shown respiratory pathogens to be an important source of infant mortality. In this paper we trace the effect of social connectivity on infant mortality dynamics. We focus on social play which, as the primary context of contact between young chimpanzees, may serve as a key venue for pathogen transmission. Infant abundance and mortality rates at Taï cycled regularly and in a way that was not well explained in terms of environmental forcing. Rather, infant mortality cycles appeared to self-organize in response to the ontogeny of social play. Each cycle started when the death of multiple infants in an outbreak synchronized the reproductive cycles of their mothers. A pulse of births predictably arrived about twelve months later, with social connectivity increasing over the following two years as the large birth cohort approached the peak of social play. The high social connectivity at this play peak then appeared to facilitate further outbreaks. Our results provide the first evidence that social play has a strong role in determining chimpanzee disease transmission risk and the first record of chimpanzee disease cycles similar to those seen in human children. They also lend more support to the view that infectious diseases are a major threat to the survival of remaining chimpanzee populations

Bubble propagation in a helicoidal molecular chain

We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between complementary bases are disrupted, allowing access to the genetic code. We propose these kind of excitations in alternative to kinks and breathers. The model has been introduced by Barbi et al. [Phys. Lett. A 253, 358 (1999)], and up to now it has been used to study on the one hand low amplitude breather solutions, and on the other hand the DNA melting transition. We extend the model to include the case of heterogeneous chains, in order to get closer to a description of real DNA; in fact, the Morse potential representing the interaction between complementary bases has two possible depths, one for A-T and one for G-C base pairs. We first compute the equilibrium configurations of a chain with a degree of uncoiling, and we find that a static bubble is among them; then we show, by molecular dynamics simulations, that these bubbles, once generated, can move along the chain. We find that also in the most unfavourable case, that of a heterogeneous DNA in the presence of thermal noise, the excitation can travel for well more 1000 base pairs.Comment: 25 pages, 7 figures. Submitted to Phys. Rev.

Impact of a single oral dose of 100,000 IU vitamin D3 on profiles of serum 25(OH)D3 and its metabolites 24,25(OH)2D3, 3-epi-25(OH)D3, and 1,25(OH)2D3 in adults with vitamin D insufficiency

We investigate the effect of a high dose of vitamin D3 on circulating concentrations of 25(OH)D3 and its metabolites 24,25(OH)2D3, 3-epi-25(OH)D3, and 1,25(OH)2D3 in healthy individuals with self-perceived fatigue and vitamin D insufficiency (25(OH)D3 75 nmol/L. Among individuals who receivedvitamin D3, there were significant increases in serum concentrations of25(OH)D3 and its metabolites 24,25(OH)2D3, 3-epi-25(OH)D3, and1,25(OH)2D3 at 4 weeks; however, inter-individual variability inthese changes was substantial. Positive correlations between serum 25(OH)D3 and24,25(OH)2D3 and 3-epi-25(OH)D3, and a significant negativecorrelation between serum 1,25(OH)2D3 and 3-epi-25(OH)D3, were found4 weeks after supplementation. The 24,25(OH)2D3/25(OH)D3 and24,25(OH)2D3/1,25(OH)2D3 ratios were significantly increased,compared with baseline, in participants receiving vitamin D3. Baseline 25(OH)D3concentration was the only factor predictive of the change in 25(OH)D3 aftersupplementation.  Conclusions: Administration of a singlehigh dose of vitamin D3 leads to a significant increase in concentrations of25(OH)D3, 24,25(OH)2D3, 3-epi-25(OH)D3 and 1,25(OH)2D3;induction of the catabolic pathway predominates over the production of 1,25(OH)2D3.Due to the high inter-individual variation in the 25(OH)D3 response to supplementation,any given dose of vitamin D is unlikely to achieve optimal vitamin D status inall treated individual

Hypoxia in the northern Gulf of Mexico: Does the science support the Plan to Reduce, Mitigate, and Control Hypoxia?

We update and reevaluate the scientific information on the distribution, history, and causes of continental shelf hypoxia that supports the 2001 Action Plan for Reducing, Mitigating, and Controlling Hypoxia in the Northern Gulf of Mexico (Mississippi River/Gulf of Mexico Watershed Nutrient Task Force 2001), incorporating data, publications, and research results produced since the 1999 integrated assessment. The metric of mid-summer hypoxic area on the Louisiana-Texas shelf is an adequate and suitable measure for continued efforts to reduce nutrients loads from the Mississippi River and hypoxia in the northern Gulf of Mexico as outlined in the Action Plan. More frequent measurements of simple metrics (e.g., area and volume) from late spring through late summer would ensure that the metric is representative of the system in any given year and useful in a public discourse of conditions and causes. The long-term data on hypoxia, sources of nutrients, associated biological parameters, and paleoindicators continue to verify and strengthen the relationship between the nitrate-nitrogen load of the Mississippi River, the extent of hypoxia, and changes in the coastal ecosystem (eutrophication and worsening hypoxia). Multiple lines of evidence, some of them representing independent data sources, are consistent with the big picture pattern of increased eutrophication as a result of long-term nutrient increases that result in excess carbon production and accumulation and, ultimately, bottom water hypoxia. The additional findings arising since 1999 strengthen the science supporting the Action Plan that focuses on reducing nutrient loads, primarily nitrogen, through multiple actions to reduce the size of the hypoxic zone in the northern Gulf of Mexico

The Greenhouse Gas Climate Change Initiative (GHG-CCI): comparative validation of GHG-CCI SCIAMACHY/ENVISAT and TANSO-FTS/GOSAT CO₂ and CH₄ retrieval algorithm products with measurements from the TCCON

Column-averaged dry-air mole fractions of carbon dioxide and methane have been retrieved from spectra acquired by the TANSO-FTS (Thermal And Near-infrared Sensor for carbon Observations-Fourier Transform Spectrometer) and SCIAMACHY (Scanning Imaging Absorption Spectrometer for Atmospheric Cartography) instruments on board GOSAT (Greenhouse gases Observing SATellite) and ENVISAT (ENVIronmental SATellite), respectively, using a range of European retrieval algorithms. These retrievals have been compared with data from ground-based high-resolution Fourier transform spectrometers (FTSs) from the Total Carbon Column Observing Network (TCCON). The participating algorithms are the weighting function modified differential optical absorption spectroscopy (DOAS) algorithm (WFMD, University of Bremen), the Bremen optimal estimation DOAS algorithm (BESD, University of Bremen), the iterative maximum a posteriori DOAS (IMAP, Jet Propulsion Laboratory (JPL) and Netherlands Institute for Space Research algorithm (SRON)), the proxy and full-physics versions of SRON's RemoTeC algorithm (SRPR and SRFP, respectively) and the proxy and full-physics versions of the University of Leicester's adaptation of the OCO (Orbiting Carbon Observatory) algorithm (OCPR and OCFP, respectively). The goal of this algorithm inter-comparison was to identify strengths and weaknesses of the various so-called round- robin data sets generated with the various algorithms so as to determine which of the competing algorithms would proceed to the next round of the European Space Agency's (ESA) Greenhouse Gas Climate Change Initiative (GHG-CCI) project, which is the generation of the so-called Climate Research Data Package (CRDP), which is the first version of the Essential Climate Variable (ECV) "greenhouse gases" (GHGs). For XCO₂, all algorithms reach the precision requirements for inverse modelling (< 8 ppm), with only WFMD having a lower precision (4.7 ppm) than the other algorithm products (2.4–2.5 ppm). When looking at the seasonal relative accuracy (SRA, variability of the bias in space and time), none of the algorithms have reached the demanding < 0.5 ppm threshold. For XCH₄, the precision for both SCIAMACHY products (50.2 ppb for IMAP and 76.4 ppb for WFMD) fails to meet the < 34 ppb threshold for inverse modelling, but note that this work focusses on the period after the 2005 SCIAMACHY detector degradation. The GOSAT XCH₄ precision ranges between 18.1 and 14.0 ppb. Looking at the SRA, all GOSAT algorithm products reach the < 10 ppm threshold (values ranging between 5.4 and 6.2 ppb). For SCIAMACHY, IMAP and WFMD have a SRA of 17.2 and 10.5 ppb, respectively

Wild Chimpanzees Exchange Meat for Sex on a Long-Term Basis

Humans and chimpanzees are unusual among primates in that they frequently perform group hunts of mammalian prey and share meat with conspecifics. Especially interesting are cases in which males give meat to unrelated females. The meat-for-sex hypothesis aims at explaining these cases by proposing that males and females exchange meat for sex, which would result in males increasing their mating success and females increasing their caloric intake without suffering the energetic costs and potential risk of injury related to hunting. Although chimpanzees have been shown to share meat extensively with females, there has not been much direct evidence in this species to support the meat-for-sex hypothesis. Here we show that female wild chimpanzees copulate more frequently with those males who, over a period of 22 months, share meat with them. We excluded other alternative hypotheses to exchanging meat for sex, by statistically controlling for rank of the male, age, rank and gregariousness of the female, association patterns of each male-female dyad and meat begging frequency of each female. Although males were more likely to share meat with estrous than anestrous females given their proportional representation in hunting parties, the relationship between mating success and sharing meat remained significant after excluding from the analysis sharing episodes with estrous females. These results strongly suggest that wild chimpanzees exchange meat for sex, and do so on a long-term basis. Similar studies on humans will determine if the direct nutritional benefits that women receive from hunters in foraging societies could also be driving the relationship between reproductive success and good hunting skills