Gap analysis of marine ecosystem data for the Department of Interior, National Park Service Inventory & Monitoring Program

The Gap Analysis of Marine Ecosystem Data project is a review of available geospatial data which can assist in marine natural resource management for eight park units. The project includes the collection of geospatial information and its incorporation in a single consistent geodatabase format. The project also includes a mapping portal which can be seen at: http://ccma.nos.noaa.gov/explorer/gapanalysis/gap_analysis.html In addition to the collection of geospatial information and mapping portal we have conducted a gap analysis of a standard suite of available information for managing marine resources. Additional gap were identified by interviewing park service staff.

A GIS analysis of coastal development and trends in bottlenose dolphin strandings in Charleston, SC: implications for coastal marine spatial planning

Bottlenose dolphins (Tursiops truncatus) inhabit estuarine waters near Charleston, South Carolina (SC) feeding, nursing and socializing. While in these waters, dolphins are exposed to multiple direct and indirect threats such as anthropogenic impacts (egs. harassment with boat traffic and entanglements in fishing gear) and environmental degradation. Bottlenose dolphins are protected under the Marine Mammal Protection Act of 1972. Over the years, the percentage of strandings in the estuaries has increased in South Carolina and, specifically, recent stranding data shows an increase in strandings occurring in Charleston, SC near areas of residential development. During the same timeframe, Charleston experienced a shift in human population towards the coastline. These two trends, rise in estuarine dolphin strandings and shift in human population, have raised questions on whether the increase in strandings is a result of more detectable strandings being reported, or a true increase in stranding events. Using GIS, the trends in strandings were compared to residential growth, boat permits, fishing permits, and dock permits in Charleston County from 1994-2009. A simple linear regression analysis was performed to determine if there were any significant relationships between strandings, boat permits, commercial fishing permits, and crabpot permits. The results of this analysis show the stranding trend moves toward Charleston Harbor and adjacent rivers over time which suggests the increase in strandings is related to the strandings becoming more detectable. The statistical analysis shows that the factors that cause human interaction strandings such as boats, commercial fishing, and crabpot line entanglements are not significantly related to strandings further supporting the hypothesis that the increase in strandings are due to increased observations on the water as human coastal population increases and are not a natural phenomenon. This study has local and potentially regional marine spatial planning implications to protect coastal natural resources, such as the bottlenose dolphin, while balancing coastal development.

Microbial community analysis of Acropora palamata mucus swabs, water and sediment samples from Hawksnest Bay, St. John, U.S. Virgin Islands

Colonies of the scleractinian coral Acropora palmata, listed as threatened under the US Endangered Species Act in 2006, have been monitored in Hawksnest Bay, within Virgin Islands National Park, St. John, from 2004 through 2010 by scientists with the US Geological Survey, National Park Service, and the University of the Virgin Islands. The focus has been on documenting the prevalence of disease, including white band, white pox (also called patchy necrosis and white patches), and unidentified diseases (Rogers et al., 2008; Muller et al., 2008). In an effort to learn more about the pathologies that might be involved with the diseases that were observed, samples were collected from apparently healthy and diseased colonies in July 2009 for analysis. Two different microbial assays were performed on Epicentre Biotechnologies DNA swabs containing A. palmata coral mucus, and on water and sediment samples collected in Hawksnest Bay. Both assays are based on polymerase chain reaction (PCR) amplification of portions of the small rRNA gene (16S). The objectives were to determine 1) if known coral bacterial pathogens Serratia marcescens (Acroporid Serratiosis), Vibrio coralliilyticus (temperature-dependent bleaching, White Syndrome), Vibrio shiloi (bleaching, necrosis), and Aurantimonas coralicida (White Plague Type II) were present in any samples, and 2) if there were any differences in microbial community profiles of each healthy, unaffected or diseased coral mucus swab. In addition to coral mucus, water and sediment samples were included to show ambient microbial populations. In the first test, PCR was used to separately amplify the unique and diagnostic region of the 16S rRNA gene for each of the coral pathogens being screened. Each pathogen test was designed so that an amplified DNA fragment could be seen only if the specific pathogen was present in a sample. A positive result was indicated by bands of DNA of the appropriate size on an agarose gel, which separates DNA fragments based on the size of the molecule. DNA from pure cultures of each of the pathogens was used as a positive control for each assay.

Value chain analysis of the Egyptian aquaculture feed industry

The commercial aquaculture feed industry in Egypt is growing at a rapid rate. As a result, the number of fish feed mills has increased from just 5 mills producing about 20,000 t per year in 1999, to over 60 mills with a current production estimate of 800,000–1,000,000 t/year. The performance of the aquafeed industry in Egypt is not well understood, as the value chain structure has not yet been mapped. This study aims to assess the status of the fish feed sector in Egypt, with an emphasis on: mapping and understanding fish feed value chains, describing the main actors and stakeholders within the chain, assessing value chain performance, identifying major strengths and weakness of the sector, and suggesting appropriate actions, management and development strategies.

Exploratory analysis of resource demand and the environmental footprint of future aquaculture development using Life Cycle Assessment

Increases in fish demand in the coming decades are projected to be largely met by growth of aquaculture. However, increased aquaculture production is linked to higher demand for natural resources and energy as well as emissions to the environment. This paper explores the use of Life Cycle Assessment to improve knowledge of potential environmental impacts of future aquaculture growth. Different scenarios of future aquaculture development are taken into account in calculating the life cycle environmental impacts. The environmental impact assessments were built on Food and Agriculture Organization statistics in terms of production volume of different species, whereas the inputs and outputs associated with aquaculture production systems were sourced from the literature. The matrix of input-output databases was established through the Blue Frontiers study.

An analysis of records of gillnet fishing in Pilkington Bay, Lake Victoria

Among the commercially valuable species occurring in Lake Victoria the two endemic species of Tilapia, T. esculenta (Graham) and T. variabilis (Boulenger) still provide the basis for the fishery in many areas, though in some places the non-cichlid species are more important, for example in the Kagera river area where large numbers of Labeo victorianus and Schilbe mystus migrate seasonally into the river. Although certain species show these habitat preferences. Most of the coastline of Lake Victoria supports a wide variety of species, all of which contribute to the commercial fishery. Over the past ten years the East African Fisheries Research Organisation has fished experimentally a number of stations within a radius of fifty miles from Jinja. These stations have been selected so as to cover a variety of habitats which range from sheltered bays to exposed coastlines. The records discussed in this paper are the result of fishing operations carried out in Pilkington Bay over the period December 1954 to November 1956. This series of fishing operations was carried out in an attempt to assess the composition of the fish populations contained in this area. To this end a variety of nets of differing mesh sizes were used. Pilkington Bay is about ten square miles in extent and is an irregular and deep indentation on the north coast of Buvuma Island. It lies within the sleeping siclmess area where fishing by Africans is prohibited. When selecting an experimental fishing ground, it is important to have some idea of the amount of commercial fishing being carried out in the area. Throughout the period of this experiment a few African fishermen were seen operating illegally in the area, but it is unlikely that their efforts greatly affected the results obtained. Pilkington Bay was fished by E.A.F.R.O. in 1949 and 1950 (Lowe McConnell 1956) but since then till the present experiment, fishing in the area has been infrequent.

Identification of native American founder mtDNAs through the analysis of complete mtDNA sequences: Some caveats

In this study, a detailed analysis of both previously published and new data was performed to determine whether complete, or almost complete, mtDNA sequences can resolve the long-debated issue of which Asian mtDNAs were founder sequences for the Native American mtDNA pool. Unfortunately, we now know that coding region data and their analysis are not without problems. To obtain and report reasonably correct sequences does not seem to be a trivial task, and to discriminate between Asian-and Native American mtDNA ancestries may be more complex than previously believed. It is essential to take into account the effects of mutational hot spots in both the control and coding regions, so that the number of apparent Native American mtDNA founder sequences is not erroneously inflated. As we report here, a careful analysis of all available data indicates that there is very little evidence that more than five founder mtDNA sequences entered Beringia before the Last Glacial Maximum and left their traces in the current Native American mtDNA pool.

Lineshape Analysis of the Beat Signal Between Optical Carrier and Delayed Sidebands

This paper presents the lineshape analysis of the beat signal between the optical carrier and the shifted and delayed side-bands produced by sinusoidal amplitude modulation. It is shown that the beat signal has a typical lineshape with a very narrow delta-peak superposed on a quasi-Lorentzian profile. Theoretical explanation for the appearance of this peak has been given based on optical spectral structure constructed by a large number of optical wave trains. It is predicted that the delta-peak is originated from the beat between the wave trains in the carrier and those in the delayed sidebands when their average coherence length is longer than the delay line. Experiments carried out using different delay lines clearly show that the delta-peak is always located at the modulation frequency and decreases with the increasing delay line. Our analysis explicitly indicates that the linewidth is related to the observation time. It is also suggested that the disappearance of the delta-peak can be used as the criterion of coherence elimination.

Analysis of coupled microcircular resonators coupled to a bus waveguide with high output efficiency

Coupled microcircular resonators tangentially coupled to a bus waveguide, which is between the resonators, are numerically investigated by the finite-difference time-domain technique. For symmetrically coupled microcircular resonators with refractive index of 3.2, radius of 2 mu m, and width of the bus waveguide of 0.4 mu m, a mode Q factor of the order of 105 is obtained for a mode at the frequency of 243 THz. An output coupling efficiency of as high as 0.99 is calculated for a mode with a Q factor ranging from 10(3) to 10(4). The mode Q factor is 2 orders larger than that of the modes confined in a single circular resonator tangentially coupled to the same bus waveguide. Furthermore, the high Q traveling modes in the coupled microcircular resonators are suitable for optical single processing.

Microstructure and strain analysis of GaN epitaxial films using in-plane grazing incidence x-ray diffraction

This paper investigates the major structural parameters, such as crystal quality and strain state of (001)-oriented GaN thin films grown on sapphire substrates by metalorganic chemical vapour deposition, using an in-plane grazing incidence x-ray diffraction technique. The results are analysed and compared with a complementary out-of-plane x-ray diffraction technique. The twist of the GaN mosaic structure is determined through the direct grazing incidence measurement of (100) reflection which agrees well with the result obtained by extrapolation method. The method for directly determining the in-plane lattice parameters of the GaN layers is also presented. Combined with the biaxial strain model, it derives the lattice parameters corresponding to fully relaxed GaN films. The GaN epilayers show an increasing residual compressive stress with increasing layer thickness when the two dimensional growth stage is established, reaching to a maximum level of -0.89 GPa.

Analysis of lateral current spreading in solar cell devices by spatially-resolved electroluminescence

Spatially-resolved electroluminescence (EL) images from solar cells contain information of local current distribution. By theoretical analysis of the EL intensity distribution, the current density distribution under a certain current bias and the sheet resistance can be obtained quantitatively. Two-dimensional numerical simulation of the current density distribution is employed to a GaInP cell, which agrees very well with the experimental results. A reciprocity theorem for current spreading is found and used to interpret the EL images from the viewpoint of current extraction. The optimization of front electrodes is discussed based on the results. (C) 2010 American Institute of Physics. [doi:10.1063/1.3431390]

Analysis of output coupling efficiencies for directional emission triangle and square microlasers

Output coupling efficiencies are analyzed for triangular and square microlasers connected with an output waveguide by FDTD simulation. The results show that square resonator with an output waveguide connected to the midpoint of one side can have high output coupling efficiency and a good mode selection.

Measurement and analysis of microwave frequency response of semiconductor optical amplifiers - art. no. 682406

The measurement and analysis of the microwave frequency response of semiconductor optical amplifiers (SOAs) are proposed in this paper. The response is measured using a vector network analyzer. Then with the direct-subtracting method, which is based on the definition of scattering parameters of optoelectronic devices, the responses of both the optical signal source and the photodetector are eliminated, and the response of only the SOA is extracted. Some characteristics of the responses can be observed: the responses are quasi-highpass; the gain increases with the bias current; and the response becomes more gradient while the bias current is increasing. The multisectional model of an SOA is then used to analyze the response theoretically. By deducing from the carrier rate equation of one section under the steady state and the small-signal state, the expression of the frequency response is obtained. Then by iterating the expression, the response of the whole SOA is simulated. The simulated results are in good agreement with the measured on the three main characteristics, which are also explained by the deduced results. This proves the validity of the theoretical analysis.

Analysis of leakage current in GaAs micro-solar cell arrays

The output characteristics of micro-solar cell arrays are analyzed on the basis of a modified model in which the shunt resistance between cell lines results in current leakage. The modification mainly consists of adding a shunt resistor network to the traditional model. The obtained results agree well with the reported experimental results. The calculation results demonstrate that leakage current in substrate affects seriously the performance of GaAs micro- solar cell arrays. The performance of arrays can be improved by reducing the number of cells per line. In addition, at a certain level of integration, an appropriate space occupancy rate of the single cell is recommended for ensuring high open circuit voltages, and it is more appropriate to set the rates at 80%-90% through the calculation.

Characterization and analysis of two-dimensional GaAs-based photonic crystal nanocavities at room temperature

This paper describes the design and fabrication process of a two-dimensional GaAs-based photonic crystal nanocavity and analyzes the optical characterization of cavity modes at room temperature. Single InAs/InGaAs quantum dots (QDs) layer was embedded in a GaAs waveguide layer grown on an Al0.7Ga0.3As layer and GaAs substrate. The patterning of the structure and the membrane release were achieved by using electron-beam lithography, reaction ion etching, inductively coupled plasma etching and selective wet etching. The micro-luminescence spectrum is recorded from the fabricated nanocavities, and it is found that some high-order cavity modes are clearly observed besides the lowest-order resonant mode is exhibited in spite of much high rate of nonradiative recombination. The variance of resonant modes is also discussed as a function of r/a ratio and will be used in techniques aimed to improve the probability of achieving spectral coupling of a single QD to a cavity mode.